@article {pmid33864868,
year = {2021},
author = {Tang, D and Li, H and Wu, C and Jia, T and He, H and Yao, S and Yu, Y and Chen, Q},
title = {A distinct structure of Cas1-Cas2 complex provides insights into the mechanism for the longer spacer acquisition in Pyrococcus furiosus.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2021.04.074},
pmid = {33864868},
issn = {1879-0003},
abstract = {In the adaptation stage of CRISPR-Cas systems, the Cas1-Cas2 integrase captures and integrates new invader-derived spacers into the CRISPR locus, serving as a molecular memory of prior infection. As of yet, the structural information of Cas1-Cas2 complex is available only for two species. Here we present the crystal structure of Cas1-Cas2 complex of Pyrococcus furiosus, which showed a distinct architecture from the known Cas1-Cas2 complexes. The shorter C-terminal tail of Pfu Cas2 directs the Cas1 dimers go in the opposite direction, resulting in a different prespacer binding mode. Based on our structural and mutagenesis results, we modeled a prespacer with a shorter duplex and longer 3' overhangs to bind Pfu Cas1-Cas2 complex. The prespacer preference was confirmed by EMSA, fluorescence polarization, and in vitro integration assays. This model provides a potential explanation for the longer spacer acquisition observed in P. furiosus when deleting both cas4 genes. Our study highlights the diversity of the CRISPR adaptation module.},
}

@article {pmid33862567,
year = {2021},
author = {Wang, M and Han, D and Zhang, J and Zhang, R and Li, J},
title = {High-fidelity detection of DNA combining the CRISPR/Cas9 system and hairpin probe.},
journal = {Biosensors & bioelectronics},
volume = {184},
number = {},
pages = {113212},
doi = {10.1016/j.bios.2021.113212},
pmid = {33862567},
issn = {1873-4235},
abstract = {Methods that enable specific and sensitive detection of DNA are greatly required for high-fidelity sequence measurement and single-nucleotide variations (SNVs) genotyping. The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas systems have provided revolutionary tools for detecting nucleic acids. However, most of the current CRISPR/Cas-based DNA biosensing platforms suffer from inherent off-target effects of Cas proteins and require pre-amplification processes, which compromise the analytical fidelity. In this work, a CRISPR/Cas9-triggered hairpin probe-mediated biosensing method (namely CHP) was used to directly read the original DNA sequences, while effectively neutralizing the off-target effect and achieving high sensitivity. This technique can quantify DNA targets with a limit of detection (LOD) at the attomole level and identify SNVs with allelic fractions as low as 0.01%~0.1%. Moreover, we show that the CHP system is applicable in detecting mutations in serum samples without DNA isolation steps. Collectively, the CHP system is a sensitive and high-fidelity platform, which promises a great potential for providing robust tool for DNA sequence analysis and SNVs genotyping.},
}

@article {pmid33862076,
year = {2021},
author = {Prakash, A and Kumar, M},
title = {Characterizing the transcripts of Leptospira CRISPR I-B array and its processing with endoribonuclease LinCas6.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2021.04.066},
pmid = {33862076},
issn = {1879-0003},
abstract = {In Leptospira interrogans serovar Copenhageni, the CRISPR-Cas IB locus possesses a CRISPR array between the two independent cas-operons. Using the reverse transcription-PCR and the in vitro endoribonuclease assay with Cas6 of Leptospira (LinCas6), we account that the CRISPR is transcriptionally active and is conventionally processed. The LinCas6 specifically excises at one site within the synthetic cognate repeat RNA or the repeats of precursor-CRISPR RNA (pre-crRNA) in the sense direction. In contrast, the antisense repeat RNA is cleaved at multiple sites. LinCas6 functions as a single turnover endoribonuclease on its repeat RNA substrate, where substitution of one of predicted active site residues (His38) resulted in reduced activity. This study highlights the comprehensive understanding of the Leptospira CRISPR array transcription and its processing by LinCas6 that is central to RNA mediated CRISPR-Cas IB adaptive immunity.},
}

@article {pmid33861513,
year = {2021},
author = {Verhage, L},
title = {Twelve genes at one blow: multiplex genome editing with CRISPR/Cas.},
journal = {The Plant journal : for cell and molecular biology},
volume = {106},
number = {1},
pages = {6-7},
doi = {10.1111/tpj.15228},
pmid = {33861513},
issn = {1365-313X},
}

@article {pmid33720132,
year = {2021},
author = {Ma, J and van der Zon, G and Sanchez-Duffhues, G and Ten Dijke, P},
title = {TGF-β-mediated Endothelial to Mesenchymal Transition (EndMT) and the Functional Assessment of EndMT Effectors using CRISPR/Cas9 Gene Editing.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {168},
pages = {},
doi = {10.3791/62198},
pmid = {33720132},
issn = {1940-087X},
mesh = {Animals ; CRISPR-Associated Protein 9/*metabolism ; CRISPR-Cas Systems/*genetics ; Cell Line ; Endothelial Cells/*metabolism ; Endothelial Growth Factors/genetics/metabolism ; Fluorescent Antibody Technique ; *Gene Editing ; Mesoderm/*metabolism ; Mice ; Snail Family Transcription Factors/metabolism ; Transforming Growth Factor beta/genetics/*metabolism ; },
abstract = {In response to specific external cues and the activation of certain transcription factors, endothelial cells can differentiate into a mesenchymal-like phenotype, a process that is termed endothelial to mesenchymal transition (EndMT). Emerging results have suggested that EndMT is causally linked to multiple human diseases, such as fibrosis and cancer. In addition, endothelial-derived mesenchymal cells may be applied in tissue regeneration procedures, as they can be further differentiated into various cell types (e.g., osteoblasts and chondrocytes). Thus, the selective manipulation of EndMT may have clinical potential. Like epithelial-mesenchymal transition (EMT), EndMT can be strongly induced by the secreted cytokine transforming growth factor-beta (TGF-β), which stimulates the expression of so-called EndMT transcription factors (EndMT-TFs), including Snail and Slug. These EndMT-TFs then up- and downregulate the levels of mesenchymal and endothelial proteins, respectively. Here, we describe methods to investigate TGF-β-induced EndMT in vitro, including a protocol to study the role of particular TFs in TGF-β-induced EndMT. Using these techniques, we provide evidence that TGF-β2 stimulates EndMT in murine pancreatic microvascular endothelial cells (MS-1 cells), and that the genetic depletion of Snail using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing, abrogates this phenomenon. This approach may serve as a model to interrogate potential modulators of endothelial biology, and can be used to perform genetic or pharmacological screens in order to identify novel regulators of EndMT, with potential application in human disease.},
}

Animals
CRISPR-Associated Protein 9/*metabolism
CRISPR-Cas Systems/*genetics
Cell Line
Endothelial Cells/*metabolism
Endothelial Growth Factors/genetics/metabolism
Fluorescent Antibody Technique
*Gene Editing
Mesoderm/*metabolism
Mice
Snail Family Transcription Factors/metabolism
Transforming Growth Factor beta/genetics/*metabolism

@article {pmid33593219,
year = {2021},
author = {El Jaddaoui, I and Allali, M and Raoui, S and Sehli, S and Habib, N and Chaouni, B and Al Idrissi, N and Benslima, N and Maher, W and Benrahma, H and Hamamouch, N and El Bissati, K and El Kasmi, S and Hamdi, S and Bakri, Y and Nejjari, C and Amzazi, S and Ghazal, H},
title = {A review on current diagnostic techniques for COVID-19.},
journal = {Expert review of molecular diagnostics},
volume = {21},
number = {2},
pages = {141-160},
doi = {10.1080/14737159.2021.1886927},
pmid = {33593219},
issn = {1744-8352},
mesh = {Antibodies, Viral/immunology ; Biosensing Techniques ; COVID-19/*diagnosis ; COVID-19 Nucleic Acid Testing/*methods/*trends ; COVID-19 Serological Testing/*methods/*trends ; CRISPR-Cas Systems ; Clinical Laboratory Techniques ; Humans ; Immunoassay ; Immunoglobulin G/immunology ; Immunoglobulin M/immunology ; Laboratories ; Radiography, Thoracic ; Reagent Kits, Diagnostic ; Reverse Transcriptase Polymerase Chain Reaction ; Tomography, X-Ray Computed ; },
abstract = {INTRODUCTION: SARS-Cov-2 first appeared in Wuhan, China, in December 2019 and spread all over the world soon after that. Given the infectious nature ofSARS-CoV-2, fast and accurate diagnosis tools are important to detect the virus. In this review, we discuss the different diagnostic tests that are currently being implemented in laboratories and provide a description of various COVID-19 kits.

AREAS COVERED: We summarize molecular techniques that target the viral load, serological methods used for SARS-CoV-2 specific antibodies detection as well as newly developed faster assays for the detection of SARS-COV 2 in various biological samples.

EXPERT OPINION: In the light of the widespread pandemic, the massive diagnosis of COVID-19, using various detection techniques, appears to be the most effective strategy for monitoring and containing its propagation.},
}

Antibodies, Viral/immunology
Biosensing Techniques
COVID-19/*diagnosis
COVID-19 Nucleic Acid Testing/*methods/*trends
COVID-19 Serological Testing/*methods/*trends
CRISPR-Cas Systems
Clinical Laboratory Techniques
Humans
Immunoassay
Immunoglobulin G/immunology
Immunoglobulin M/immunology
Laboratories
Radiography, Thoracic
Reagent Kits, Diagnostic
Reverse Transcriptase Polymerase Chain Reaction
Tomography, X-Ray Computed

@article {pmid33434526,
year = {2021},
author = {Wu, H and Voeltz, GK},
title = {Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites.},
journal = {Developmental cell},
volume = {56},
number = {1},
pages = {52-66.e7},
pmid = {33434526},
issn = {1878-1551},
support = {R01 GM120998/GM/NIGMS NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Autophagosomes/genetics/metabolism ; CRISPR-Cas Systems ; Carrier Proteins/genetics/*metabolism ; Cell Line, Tumor ; Endoplasmic Reticulum/genetics/*metabolism ; Endosomes/genetics/*metabolism ; Gene Knockdown Techniques ; Gene Knockout Techniques ; Humans ; Lysosomes/genetics/metabolism ; Membrane Proteins/genetics/*metabolism ; Microtubules/metabolism ; Nerve Tissue Proteins/genetics/*metabolism ; Nogo Proteins/genetics/metabolism ; Protein Transport/*genetics ; RNA, Small Interfering ; rab GTP-Binding Proteins/genetics/metabolism ; },
abstract = {ER tubules form and maintain membrane contact sites (MCSs) with endosomes. How and why these ER-endosome MCSs persist as endosomes traffic and mature is poorly understood. Here we find that a member of the reticulon protein family, Reticulon-3L (Rtn3L), enriches at ER-endosome MCSs as endosomes mature. We show that this localization is due to the long divergent N-terminal cytoplasmic domain of Rtn3L. We found that Rtn3L is recruited to ER-endosome MCSs by endosomal protein Rab9a, which marks a transition stage between early and late endosomes. Rab9a utilizes an FSV region to recruit Rtn3L via its six LC3-interacting region motifs. Consistent with our localization results, depletion or deletion of RTN3 from cells results in endosome maturation and cargo sorting defects, similar to RAB9A depletion. Together our data identify a tubular ER protein that promotes endosome maturation at ER MCSs.},
}

Amino Acid Motifs
Autophagosomes/genetics/metabolism
CRISPR-Cas Systems
Carrier Proteins/genetics/*metabolism
Cell Line, Tumor
Endoplasmic Reticulum/genetics/*metabolism
Endosomes/genetics/*metabolism
Gene Knockdown Techniques
Gene Knockout Techniques
Humans
Lysosomes/genetics/metabolism
Membrane Proteins/genetics/*metabolism
Microtubules/metabolism
Nerve Tissue Proteins/genetics/*metabolism
Nogo Proteins/genetics/metabolism
Protein Transport/*genetics
RNA, Small Interfering
rab GTP-Binding Proteins/genetics/metabolism

@article {pmid33110234,
year = {2021},
author = {Li, H and Zhao, L and Lau, YS and Zhang, C and Han, R},
title = {Genome-wide CRISPR screen identifies LGALS2 as an oxidative stress-responsive gene with an inhibitory function on colon tumor growth.},
journal = {Oncogene},
volume = {40},
number = {1},
pages = {177-188},
pmid = {33110234},
issn = {1476-5594},
support = {R01 HL116546/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Azoxymethane/*adverse effects ; CRISPR-Cas Systems ; Cell Survival/drug effects ; Colitis/chemically induced/complications/*genetics/metabolism ; Colorectal Neoplasms/chemically induced/*genetics/metabolism ; Dextran Sulfate/*adverse effects ; Disease Models, Animal ; Female ; Galectin 2/*genetics ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen Peroxide/adverse effects ; Male ; Mice ; Oxidative Stress ; Phosphorylation ; Reactive Oxygen Species/metabolism ; STAT3 Transcription Factor/metabolism ; Whole Genome Sequencing/*methods ; },
abstract = {Colorectal cancer is the third leading cause of cancer-related deaths in the United States and the third most common cancer in men and women. Around 20% colon cancer cases are closely linked with colitis. Both environmental and genetic factors are thought to contribute to colon inflammation and tumor development. However, the genetic factors regulating colitis and colon tumorigenesis remain elusive. Since reactive oxygen species (ROS) is vitally involved in tissue inflammation and tumorigenesis, here we employed a genome-wide CRISPR knockout screening approach to systemically identify the genetic factors involved in the regulation of oxidative stress. Next generation sequencing (NGS) showed that over 600 gRNAs including the ones targeting LGALS2 were highly enriched in cells survived after sublethal H2O2 challenge. LGALS2 encodes the glycan-binding protein Galectin 2 (Gal2), which is predominantly expressed in the gastrointestinal tract and downregulated in human colon tumors. To examine the role of Gal2 in colitis, we employed the dextran sodium sulfate (DSS)-induced acute colitis model in mice with (WT) or without Lgals2 (Gal2-KO) and showed that Gal2 deficiency ameliorated DSS-induced colitis. We further demonstrated that Gal2-KO mice developed significantly larger tumors than WT mice using Azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colorectal cancer model. We found that STAT3 phosphorylation was significantly increased in Gal2-deficient tumors as compared to those in WT mice. Gal2 overexpression decreased the proliferation of human colon tumor epithelial cells and blunted H2O2-induced STAT3 phosphorylation. Overall, our results demonstrate that Gal2 plays a suppressive role in colon tumor growth and highlights the therapeutic potential of Gal2 in colon cancer.},
}

Animals
Azoxymethane/*adverse effects
CRISPR-Cas Systems
Cell Survival/drug effects
Colitis/chemically induced/complications/*genetics/metabolism
Colorectal Neoplasms/chemically induced/*genetics/metabolism
Dextran Sulfate/*adverse effects
Disease Models, Animal
Female
Galectin 2/*genetics
HEK293 Cells
High-Throughput Nucleotide Sequencing
Humans
Hydrogen Peroxide/adverse effects
Male
Mice
Oxidative Stress
Phosphorylation
Reactive Oxygen Species/metabolism
STAT3 Transcription Factor/metabolism
Whole Genome Sequencing/*methods

@article {pmid32820039,
year = {2020},
author = {Yang, B and Schwartz, M and McJunkin, K},
title = {In vivo CRISPR screening for phenotypic targets of the mir-35-42 family in C. elegans.},
journal = {Genes & development},
volume = {34},
number = {17-18},
pages = {1227-1238},
pmid = {32820039},
issn = {1549-5477},
support = {P40 OD010440/OD/NIH HHS/United States ; ZIA DK075147/ImNIH/Intramural NIH HHS/United States ; },
mesh = {3' Untranslated Regions/genetics ; Alleles ; Animals ; Binding Sites/genetics ; CRISPR-Cas Systems ; Caenorhabditis elegans/*genetics ; Gene Editing ; Genetic Testing ; MicroRNAs/genetics/*metabolism ; Mutation ; Phenotype ; },
abstract = {Identifying miRNA target genes is difficult, and delineating which targets are the most biologically important is even more difficult. We devised a novel strategy to test the phenotypic impact of individual microRNA-target interactions by disrupting each predicted miRNA-binding site by CRISPR-Cas9 genome editing in C. elegans We developed a multiplexed negative selection screening approach in which edited loci are deep sequenced, and candidate sites are prioritized based on apparent selection pressure against mutations that disrupt miRNA binding. Importantly, our screen was conducted in vivo on mutant animals, allowing us to interrogate organism-level phenotypes. We used this approach to screen for phenotypic targets of the essential mir-35-42 family. By generating 1130 novel 3'UTR alleles across all predicted targets, we identified egl-1 as a phenotypic target whose derepression partially phenocopies the mir-35-42 mutant phenotype by inducing embryonic lethality and low fecundity. These phenotypes can be rescued by compensatory CRISPR mutations that retarget mir-35 to the mutant egl-1 3'UTR. This study demonstrates that the application of in vivo whole organismal CRISPR screening has great potential to accelerate the discovery of phenotypic negative regulatory elements in the noncoding genome.},
}

3' Untranslated Regions/genetics
Alleles
Animals
Binding Sites/genetics
CRISPR-Cas Systems
Caenorhabditis elegans/*genetics
Gene Editing
Genetic Testing
MicroRNAs/genetics/*metabolism
Mutation
Phenotype

@article {pmid32592028,
year = {2020},
author = {Varela, C and Bartel, C and Onetto, C and Borneman, A},
title = {Targeted gene deletion in Brettanomyces bruxellensis with an expression-free CRISPR-Cas9 system.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {16},
pages = {7105-7115},
doi = {10.1007/s00253-020-10750-5},
pmid = {32592028},
issn = {1432-0614},
mesh = {Alleles ; Biotechnology/*methods ; Brettanomyces/drug effects/*genetics/metabolism ; *CRISPR-Cas Systems ; *Gene Deletion ; *Genome, Fungal ; Sulfites/pharmacology ; Transformation, Genetic ; },
abstract = {The ability to genetically manipulate microorganisms has been essential for understanding their biology and metabolism. Targeted genome editing relies on highly efficient homologous recombination, and while this is readily observed in the yeast Saccharomyces cerevisiae, most non-conventional yeast species do not display this trait and remain recalcitrant to targeted editing methods. CRISPR-based editing can bypass the requirement for high levels of native homologous recombination, enabling targeted modification to be more broadly implemented. While genetic transformation has been reported previously in Brettanomyces bruxellensis, a yeast with broad biotechnological potential and responsible for significant economic losses during the production of fermented beverages, targeted editing approaches have not been reported. Here, we describe the use of an expression-free CRISPR-Cas9 system, in combination with gene transformation cassettes tailored for B. bruxellensis, to provide the means for targeted gene deletion in this species. Deletion efficiency was shown to be dependent on homologous flanking DNA length, with higher targeting efficiencies observed with cassettes containing longer flanking regions. In a diploid strain, it was not possible to delete multiple alleles in one step, with heterozygous deletants only obtained when using DNA cassettes with long flanking regions. However, stepwise transformations (using two different marker genes) were successfully used to delete both wild-type alleles. Thus, the approach reported here will be crucial to understand the complex physiology of B. bruxellensis. Key points • The use of CRISPR-Cas9 enables targeted gene deletion in Brettanomyces bruxellensis. • Homozygous diploid deletions are possible with step-wise transformations. • Deletion of SSU1 confirmed the role of this gene in sulphite tolerance.},
}

Alleles
Biotechnology/*methods
Brettanomyces/drug effects/*genetics/metabolism
*CRISPR-Cas Systems
*Gene Deletion
*Genome, Fungal
Sulfites/pharmacology
Transformation, Genetic

@article {pmid32330446,
year = {2020},
author = {Kwon, JB and Vankara, A and Ettyreddy, AR and Bohning, JD and Gersbach, CA},
title = {Myogenic Progenitor Cell Lineage Specification by CRISPR/Cas9-Based Transcriptional Activators.},
journal = {Stem cell reports},
volume = {14},
number = {5},
pages = {755-769},
pmid = {32330446},
issn = {2213-6711},
support = {UH3 TR002142/TR/NCATS NIH HHS/United States ; T32 HD040372/HD/NICHD NIH HHS/United States ; R21 NS103007/NS/NINDS NIH HHS/United States ; R21 AR072265/AR/NIAMS NIH HHS/United States ; U01 HL156348/HL/NHLBI NIH HHS/United States ; R01 AR069085/AR/NIAMS NIH HHS/United States ; U01 EB028901/EB/NIBIB NIH HHS/United States ; UG3 AR075336/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; CRISPR-Cas Systems ; Cell Differentiation ; *Cell Lineage ; Cells, Cultured ; Cellular Reprogramming Techniques/*methods ; Dystrophin/genetics/metabolism ; Epigenesis, Genetic ; Female ; Gene Editing/methods ; HEK293 Cells ; Humans ; Induced Pluripotent Stem Cells/cytology/*metabolism ; Infant, Newborn ; Male ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Muscle Development ; Myoblasts/cytology/*metabolism ; PAX7 Transcription Factor/genetics/*metabolism ; },
abstract = {Engineered CRISPR/Cas9-based transcriptional activators can potently and specifically activate endogenous fate-determining genes to direct differentiation of pluripotent stem cells. Here, we demonstrate that endogenous activation of the PAX7 transcription factor results in stable epigenetic remodeling and differentiates human pluripotent stem cells into skeletal myogenic progenitor cells. Compared with exogenous overexpression of PAX7 cDNA, we find that endogenous activation results in the generation of more proliferative myogenic progenitors that can maintain PAX7 expression over multiple passages in serum-free conditions while preserving the capacity for terminal myogenic differentiation. Transplantation of human myogenic progenitors derived from endogenous activation of PAX7 into immunodeficient mice resulted in a greater number of human dystrophin+ myofibers compared with exogenous PAX7 overexpression. RNA-sequencing analysis also revealed transcriptome-wide differences between myogenic progenitors generated via CRISPR-based endogenous activation of PAX7 and exogenous PAX7 cDNA overexpression. These studies demonstrate the utility of CRISPR/Cas9-based transcriptional activators for controlling cell-fate decisions.},
}

Animals
CRISPR-Cas Systems
Cell Differentiation
*Cell Lineage
Cells, Cultured
Cellular Reprogramming Techniques/*methods
Dystrophin/genetics/metabolism
Epigenesis, Genetic
Female
Gene Editing/methods
HEK293 Cells
Humans
Induced Pluripotent Stem Cells/cytology/*metabolism
Infant, Newborn
Male
Mice
Mice, Inbred NOD
Mice, SCID
Muscle Development
Myoblasts/cytology/*metabolism
PAX7 Transcription Factor/genetics/*metabolism

@article {pmid33854845,
year = {2021},
author = {Oliveira de Almeida, M and Carvalho, R and Figueira Aburjaile, F and Malcher Miranda, F and Canário Cerqueira, J and Brenig, B and Ghosh, P and Ramos, R and Kato, RB and de Castro Soares, S and Silva, A and Azevedo, V and Canário Viana, MV},
title = {Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11079},
doi = {10.7717/peerj.11079},
pmid = {33854845},
issn = {2167-8359},
abstract = {Background: Lactobacillus crispatus is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of L. crispatus involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. To further investigate these mechanisms, we sequenced and characterized the first four L. crispatus genomes from vaginal samples from Brazilian women and used genome-wide association study (GWAS) and comparative analyses to identify genetic mechanisms involved in healthy or BV conditions and selective pressures acting in the vaginal microbiome.

Methods: The four genomes were sequenced, assembled using ten different strategies and automatically annotated. The functional characterization was performed by bioinformatics tools comparing with known probiotic strains. Moreover, it was selected one representative strain (L. crispatus CRI4) for in vitro detection of phages by electron microscopy. Evolutionary analysis, including phylogeny, GWAS and positive selection were performed using 46 public genomes strains representing health and BV conditions.

Results: Genes involved in probiotic effects such as lactic acid production, hydrogen peroxide, bacteriocins, and adhesin were identified. Three hemolysins and putrescine production were predicted, although these features are also present in other probiotic strains. The four genomes presented no plasmids, but 14 known families insertion sequences and several prophages were detected. However, none of the mobile genetic elements contained antimicrobial resistance genes. The genomes harbor a CRISPR-Cas subtype II-A system that is probably inactivated due to fragmentation of the genes csn2 and cas9. No genomic feature was associated with a health condition, perhaps due to its multifactorial characteristic. Five genes were identified as under positive selection, but the selective pressure remains to be discovered. In conclusion, the Brazilian strains investigated in this study present potential protective properties, although in vitro and in vivo studies are required to confirm their efficacy and safety to be considered for human use.},
}

@article {pmid33854491,
year = {2021},
author = {Medina-Aparicio, L and Rodriguez-Gutierrez, S and Rebollar-Flores, JE and Martínez-Batallar, ÁG and Mendoza-Mejía, BD and Aguirre-Partida, ED and Vázquez, A and Encarnación, S and Calva, E and Hernández-Lucas, I},
title = {The CRISPR-Cas System Is Involved in OmpR Genetic Regulation for Outer Membrane Protein Synthesis in Salmonella Typhi.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {657404},
doi = {10.3389/fmicb.2021.657404},
pmid = {33854491},
issn = {1664-302X},
abstract = {The CRISPR-Cas cluster is found in many prokaryotic genomes including those of the Enterobacteriaceae family. Salmonella enterica serovar Typhi (S. Typhi) harbors a Type I-E CRISPR-Cas locus composed of cas3, cse1, cse2, cas7, cas5, cas6e, cas1, cas2, and a CRISPR1 array. In this work, it was determined that, in the absence of cas5 or cas2, the amount of the OmpC porin decreased substantially, whereas in individual cse2, cas6e, cas1, or cas3 null mutants, the OmpF porin was not observed in an electrophoretic profile of outer membrane proteins. Furthermore, the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin, in individual S. Typhi cse2, cas5, cas6e, cas1, cas2, and cas3 mutants. Remarkably, the expression of the master porin regulator OmpR was dependent on the Cse2, Cas5, Cas6e, Cas1, Cas2, and Cas3 proteins. Therefore, the data suggest that the CRISPR-Cas system acts hierarchically on OmpR to control the synthesis of outer membrane proteins in S. Typhi.},
}

@article {pmid33847177,
year = {2021},
author = {Hart-Johnson, S and Mankelow, K},
title = {Archiving genetically altered animals: a review of cryopreservation and recovery methods for genome edited animals.},
journal = {Laboratory animals},
volume = {},
number = {},
pages = {236772211007306},
doi = {10.1177/00236772211007306},
pmid = {33847177},
issn = {1758-1117},
abstract = {With the ever-expanding numbers of genetically altered (GA) animals created in this new age of CRISPR/Cas, tools for helping the management of this vast and valuable resource are essential. Cryopreservation of embryos and germplasm of GA animals has been a widely used tool for many years now, allowing for the archiving, distribution and colony management of stock. However, each year brings an array of advances, improving survival rates of embryos, success rates of in-vitro fertilisation and the ability to better share lines and refine the methods to preserve them. This article will focus on the mouse field, referencing the latest developments and assessing their efficacy and ease of implementation, with a brief note on other common genetically altered species (rat, zebrafish, Xenopus, avian species and non-human Primates).},
}

@article {pmid33846956,
year = {2021},
author = {Schaart, JG and van de Wiel, CCM and Smulders, MJM},
title = {Genome editing of polyploid crops: prospects, achievements and bottlenecks.},
journal = {Transgenic research},
volume = {},
number = {},
pages = {},
pmid = {33846956},
issn = {1573-9368},
abstract = {Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.},
}

@article {pmid33846767,
year = {2021},
author = {Falzone, L and Gattuso, G and Tsatsakis, A and Spandidos, DA and Libra, M},
title = {Current and innovative methods for the diagnosis of COVID‑19 infection (Review).},
journal = {International journal of molecular medicine},
volume = {47},
number = {6},
pages = {},
doi = {10.3892/ijmm.2021.4933},
pmid = {33846767},
issn = {1791-244X},
abstract = {The Coronavirus Disease 2019 (COVID‑19) pandemic has forced the scientific community to rapidly develop highly reliable diagnostic methods in order to effectively and accurately diagnose this pathology, thus limiting the spread of infection. Although the structural and molecular characteristics of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) were initially unknown, various diagnostic strategies useful for making a correct diagnosis of COVID‑19 have been rapidly developed by private research laboratories and biomedical companies. At present, rapid antigen or antibody tests, immunoenzymatic serological tests and molecular tests based on RT‑PCR are the most widely used and validated techniques worldwide. Apart from these conventional methods, other techniques, including isothermal nucleic acid amplification techniques, clusters of regularly interspaced short palindromic repeats/Cas (CRISPR/Cas)‑based approaches or digital PCR methods are currently used in research contexts or are awaiting approval for diagnostic use by competent authorities. In order to provide guidance for the correct use of COVID‑19 diagnostic tests, the present review describes the diagnostic strategies available which may be used for the diagnosis of COVID‑19 infection in both clinical and research settings. In particular, the technical and instrumental characteristics of the diagnostic methods used are described herein. In addition, updated and detailed information about the type of sample, the modality and the timing of use of specific tests are also discussed.},
}

@article {pmid33846535,
year = {2021},
author = {Young, AN and Perlas, E and Ruiz-Blanes, N and Hierholzer, A and Pomella, N and Martin-Martin, B and Liverziani, A and Jachowicz, JW and Giannakouros, T and Cerase, A},
title = {Deletion of LBR N-terminal domains recapitulates Pelger-Huet anomaly phenotypes in mouse without disrupting X chromosome inactivation.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {478},
pmid = {33846535},
issn = {2399-3642},
abstract = {Mutations in the gene encoding Lamin B receptor (LBR), a nuclear-membrane protein with sterol reductase activity, have been linked to rare human disorders. Phenotypes range from a benign blood disorder, such as Pelger-Huet anomaly (PHA), affecting the morphology and chromatin organization of white blood cells, to embryonic lethality as for Greenberg dysplasia (GRBGD). Existing PHA mouse models do not fully recapitulate the human phenotypes, hindering efforts to understand the molecular etiology of this disorder. Here we show, using CRISPR/Cas-9 gene editing technology, that a 236bp N-terminal deletion in the mouse Lbr gene, generating a protein missing the N-terminal domains of LBR, presents a superior model of human PHA. Further, we address recent reports of a link between Lbr and defects in X chromosome inactivation (XCI) and show that our mouse mutant displays minor X chromosome inactivation defects that do not lead to any overt phenotypes in vivo. We suggest that our N-terminal deletion model provides a valuable pre-clinical tool to the research community and will aid in further understanding the etiology of PHA and the diverse functions of LBR.},
}

@article {pmid33846411,
year = {2021},
author = {Pastor-Arroyo, EM and Rodriguez, JMM and Pellegrini, G and Bettoni, C and Levi, M and Hernando, N and Wagner, CA},
title = {Constitutive depletion of Slc34a2/NaPi-IIb in rats causes perinatal mortality.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7943},
pmid = {33846411},
issn = {2045-2322},
support = {176125/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Absorption of dietary phosphate (Pi) across intestinal epithelia is a regulated process mediated by transcellular and paracellular pathways. Although hyperphosphatemia is a risk factor for the development of cardiovascular disease, the amount of ingested Pi in a typical Western diet is above physiological needs. While blocking intestinal absorption has been suggested as a therapeutic approach to prevent hyperphosphatemia, a complete picture regarding the identity and regulation of the mechanism(s) responsible for intestinal absorption of Pi is missing. The Na+/Pi cotransporter NaPi-IIb is a secondary active transporter encoded by the Slc34a2 gene. This transporter has a wide tissue distribution and within the intestinal tract is located at the apical membrane of epithelial cells. Based on mouse models deficient in NaPi-IIb, this cotransporter is assumed to mediate the bulk of active intestinal absorption of Pi. However, whether or not this is also applicable to humans is unknown, since human patients with inactivating mutations in SLC34A2 have not been reported to suffer from Pi depletion. Thus, mice may not be the most appropriate experimental model for the translation of intestinal Pi handling to humans. Here, we describe the generation of a rat model with Crispr/Cas-driven constitutive depletion of Slc34a2. Slc34a2 heterozygous rats were indistinguishable from wild type animals under standard dietary conditions as well as upon 3 days feeding on low Pi. However, unlike in humans, homozygosity resulted in perinatal lethality.},
}

@article {pmid33842501,
year = {2021},
author = {Yeh, KB and Scullion, M and Michelotti, JM and Olinger, G},
title = {First Movers in Molecular Detection: Case Comparison on Harnessing Research and Development, Industry, and Entrepreneurship.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {639440},
pmid = {33842501},
issn = {2296-858X},
abstract = {The current unprecedented COVID-19 pandemic underscores the importance of diagnostic assays in health security preparedness and readiness. Advancing new technologies for rapid molecular detection of high consequence infectious pathogens is an ongoing challenge that requires ingenuity and vision. Sustainment of a robust supply chain for materials and the logistics of timely product delivery further challenge diagnostic kit and device manufacturers. Business economists often characterize technology companies that discover unique breakthroughs in their field and are first to bring related products to market as first movers. From a market perspective, three first mover characteristics include: having the knowledge and capability to address a unique breakthrough, excellent technological leadership, and the ability to capitalize on the opportunity. Current mainstays for molecular detection include using Taq DNA Polymerase enzyme and fluorescent chemistry for quantitative PCR (qPCR). A newer and promising technology uses CRISPR-Cas proteins for nucleic acid detection. Our panel discussion from the 2020 ASM Biothreats conference, which included members from two prototypical first mover companies, explored their respective corporate experiences. Both companies were selected for the discussion based on their revolutionary innovations and similarities in their research and development, corporate culture and trajectory. One company, established over 20 years ago, became a market leader in the biothreat detection market by advancing air thermocycling qPCR across multiple product families. The second company is a rapidly growing start-up and a scientific pioneer in establishing next generation CRISPR technologies. Here we discuss their technology development, product deployment, and customer markets to draw lessons learned for researchers, end users, and funders.},
}

@article {pmid33842017,
year = {2021},
author = {Zhang, D and Zhang, Z and Unver, T and Zhang, B},
title = {CRISPR/Cas: A powerful tool for gene function study and crop improvement.},
journal = {Journal of advanced research},
volume = {29},
number = {},
pages = {207-221},
pmid = {33842017},
issn = {2090-1224},
abstract = {Background: It is a long-standing goal of scientists and breeders to precisely control a gene for studying its function as well as improving crop yield, quality, and tolerance to various environmental stresses. The discovery and modification of CRISPR/Cas system, a nature-occurred gene editing tool, opens an era for studying gene function and precision crop breeding.

Aim of Review: In this review, we first introduce the brief history of CRISPR/Cas discovery followed the mechanism and application of CRISPR/Cas system on gene function study and crop improvement. Currently, CRISPR/Cas genome editing has been becoming a mature cutting-edge biotechnological tool for crop improvement that already used in many different traits in crops, including pathogen resistance, abiotic tolerance, plant development and morphology and even secondary metabolism and fiber development. Finally, we point out the major issues associating with CRISPR/Cas system and the future research directions.Key Scientific Concepts of Review: CRISPR/Cas9 system is a robust and powerful biotechnological tool for targeting an individual DNA and RNA sequence in the genome. It can be used to target a sequence for gene knockin, knockout and replacement as well as monitoring and regulating gene expression at the genome and epigenome levels by binding a specific sequence. Agrobacterium-mediated method is still the major and efficient method for delivering CRISPR/Cas regents into targeted plant cells. However, other delivery methods, such as virus-mediated method, have been developed and enhanced the application potentials of CRISPR/Cas9-based crop improvement. PAM requirement offers the CRISPR/Cas9-targted genetic loci and also limits the application of CRISPR/Cas9. Discovering new Cas proteins and modifying current Cas enzymes play an important role in CRISPR/Cas9-based genome editing. Developing a better CRISPR/Cas9 system, including the delivery system and the methods eliminating off-target effects, and finding key/master genes for controlling crop growth and development is two major directions for CRISPR/Cas9-based crop improvement.},
}

@article {pmid33841487,
year = {2021},
author = {Kumar, S and Rymarquis, LA and Ezura, H and Nekrasov, V},
title = {Editorial: CRISPR-Cas in Agriculture: Opportunities and Challenges.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {672329},
pmid = {33841487},
issn = {1664-462X},
}

@article {pmid33840678,
year = {2021},
author = {Tanihara, F and Hirata, M and Otoi, T},
title = {Current status of the application of gene editing in pigs.},
journal = {The Journal of reproduction and development},
volume = {},
number = {},
pages = {},
doi = {10.1262/jrd.2021-025},
pmid = {33840678},
issn = {1348-4400},
abstract = {Genetically modified animals, especially rodents, are widely used in biomedical research. However, non-rodent models are required for efficient translational medicine and preclinical studies. Owing to the similarity in the physiological traits of pigs and humans, genetically modified pigs may be a valuable resource for biomedical research. Somatic cell nuclear transfer (SCNT) using genetically modified somatic cells has been the primary method for the generation of genetically modified pigs. However, site-specific gene modification in porcine cells is inefficient and requires laborious and time-consuming processes. Recent improvements in gene-editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system, represent major advances. The efficient introduction of site-specific modifications into cells via gene editors dramatically reduces the effort and time required to generate genetically modified pigs. Furthermore, gene editors enable direct gene modification during embryogenesis, bypassing the SCNT procedure. The application of gene editors has progressively expanded, and a range of strategies is now available for porcine gene engineering. This review provides an overview of approaches for the generation of genetically modified pigs using gene editors, and highlights the current trends, as well as the limitations, of gene editing in pigs.},
}

@article {pmid33839534,
year = {2021},
author = {Niu, C and Wang, C and Li, F and Zheng, X and Xing, X and Zhang, C},
title = {Aptamer assisted CRISPR-Cas12a strategy for small molecule diagnostics.},
journal = {Biosensors & bioelectronics},
volume = {183},
number = {},
pages = {113196},
doi = {10.1016/j.bios.2021.113196},
pmid = {33839534},
issn = {1873-4235},
abstract = {Molecular diagnostics are vital for the identification, prevention, and treatment of numerous diseases and are of particular demand in point-of-care (POC) settings. Nevertheless, most reported biosensors based on the CRISPR-Cas system have focused on nucleic-acid targets. Here, we report a versatile diagnostic strategy for small molecules called Molecular Radar (Random Molecular Aptamer-Dependent CRISPR-Assist Reporter), The workflow is simple, convenient, and rapid (conducted at 37 °C in under 25 min), indicating the substantial potential of the proposed assay could be adapted into a biosensor for POC settings and on-site molecular diagnostics. This strategy is based on the CRISPR Cas12a-assisted fluorescence reporter system that consists of Cas12a, CRISPR RNA (crRNA), a single-stranded DNA (ssDNA) probe labeled with a fluorophore at the 5' end and a quencher at the 3' end (F-Q probe), and a single-stranded DNA aptamer for the target molecule. In the presence of a target molecule, the aptamer binds to this small molecule with high specificity and affinity, resulting in a decrease of aptamer hybridized to the crRNA-Cas12a duplex. This decrease in activated Cas12a leads to a significant reduction in fluorescence signal. In this study, adenosine-5'-triphosphate (ATP) was selected as model target molecule and an ATP detect method was developed with high specificity and sensitivity with a linear range from 25 to 500 μM and a detection limit of 104 nM. Moreover, the particular characteristics of CRISPR-Cas12a that we report here for the first time have enriched our understanding of Cas12a and provided guidance for further research on CRISPR-Cas12a-based biosensors.},
}

@article {pmid33839288,
year = {2021},
author = {Kostyusheva, A and Brezgin, S and Babin, Y and Vasilyeva, I and Glebe, D and Kostyushev, D and Chulanov, V},
title = {CRISPR-Cas systems for diagnosing infectious diseases.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2021.04.007},
pmid = {33839288},
issn = {1095-9130},
abstract = {Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas3, Cas9, Cas12, Cas13, Cas14 etc.) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, lateral flow assay detection and other. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, CARMEN or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing COVID-19) and outbreaks of zoonotic viruses (African Swine Fever Virus etc.) urgently need the developing and distribution of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.},
}

@article {pmid33838632,
year = {2021},
author = {Isaev, AB and Musharova, OS and Severinov, KV},
title = {Microbial Arsenal of Antiviral Defenses - Part I.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {3},
pages = {319-337},
doi = {10.1134/S0006297921030081},
pmid = {33838632},
issn = {1608-3040},
abstract = {Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.},
}

@article {pmid33837536,
year = {2021},
author = {Jain, M and Garg, R},
title = {Enhancers as potential targets for engineering salinity stress tolerance in crop plants.},
journal = {Physiologia plantarum},
volume = {},
number = {},
pages = {},
doi = {10.1111/ppl.13421},
pmid = {33837536},
issn = {1399-3054},
abstract = {Enhancers represent non-coding regulatory regions of the genome located distantly from their target genes. They regulate gene expression programs in a context-specific manner via interacting with promoters of one or more target genes and are generally associated with transcription factor binding sites and epi(genomic)/chromatin features, such as regions of chromatin accessibility and histone modifications. The enhancers are difficult to identify due to the modularity of their associated features. Although enhancers have been studied extensively in human and animals, only a handful of them has been identified in few plant species till date due to non-availability of plant-specific experimental and computational approaches for enhancer identification. Being an important regulatory component of the genome, enhancers represent potential targets for engineering agronomic traits, including salinity stress tolerance in plants. Here, we provide a review of the available experimental and computational approaches along with the associated sequence and chromatin/epigenetic features for the discovery of enhancers in plants. In addition, we provide insights into the challenges and future prospects of enhancer research in plant biology with emphasis on potential applications in engineering salinity stress tolerance in crop plants.},
}

@article {pmid33837440,
year = {2021},
author = {Ou, L and Long, J and Teng, Y and Yang, H and Xi, Y and Duan, G and Chen, S},
title = {Diversity of the type I-U CRISPR-Cas system in Bifidobacterium.},
journal = {Archives of microbiology},
volume = {},
number = {},
pages = {},
pmid = {33837440},
issn = {1432-072X},
support = {2018ZX10301407//National Science and Technology Specific Projects/ ; Grant No. 81573205//National Natural Science Foundation of China/ ; Grant No. 20A330004//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; },
abstract = {The CRISPR-Cas system is widely distributed in prokaryotes and plays an important role in the adaptive immunity of bacteria and archaea. Bifidobacterium is an important component of the intestinal flora of humans and animals, and some species of this bacterium can be employed as food additives. However, the Bifidobacterium CRISPR-Cas system has not been fully elucidated to date. In this study, the genomes of 110 strains of Bifidobacterium were employed to research the diversity of the type I-U system. The 110 strains were divided into five groups according to the genes adjacent to the CRISPR locus, including group A, B, C, D and E. Strains in the intergroup had unique species classifications and MLST types. An evolutionary tree was constructed based on the conserved cas4/cas1 fusion gene. The results showed that group A had a different evolutionary branch compared with the other groups and had a relatively low spacer number. Notably, group B, C and E had exhibited ABC transporter regulators in the genes adjacent to the CRISPR locus. ABC transporters play important roles in the exocytosis of many antibiotics and are involved in horizontal gene transfer. This mechanism may have promoted the evolution of Bifidobacterium and the horizontal gene transfer of the type I-U system, which may have promoted the generation of system diversity. In summary, our results help to elucidate the role of the type I-U system in the evolution of Bifidobacterium.},
}

@article {pmid33836052,
year = {2021},
author = {Sizova, I and Kelterborn, S and Verbenko, V and Kateriya, S and Hegemann, P},
title = {Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkab114},
pmid = {33836052},
issn = {2160-1836},
abstract = {The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent non-homologous end-joining and polymerase theta (POLQ)-mediated end-joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect homology-directed repair of the inactivated paromomycin resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate homology-directed repair/gene inactivation. Our data suggests that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced homology-directed repair and random integration of transgenes, while KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in Chlamydomonas reinhardtii and can be used for future development of algal biotechnology.},
}

@article {pmid33835761,
year = {2021},
author = {Li, C and Brant, E and Budak, H and Zhang, B},
title = {CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement.},
journal = {Journal of Zhejiang University. Science. B},
volume = {22},
number = {4},
pages = {253-284},
doi = {10.1631/jzus.B2100009},
pmid = {33835761},
issn = {1862-1783},
mesh = {*CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Crops, Agricultural/genetics ; Gene Editing/*methods ; *Genetic Therapy ; Humans ; Nobel Prize ; *Plant Breeding ; },
abstract = {Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.},
}

*CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Crops, Agricultural/genetics
Gene Editing/*methods
*Genetic Therapy
Humans
Nobel Prize
*Plant Breeding

@article {pmid33834450,
year = {2021},
author = {Kim, GN and Sung, YH},
title = {The Genetic Basis of Reporter Mouse Strains.},
journal = {Advances in experimental medicine and biology},
volume = {1310},
number = {},
pages = {551-564},
pmid = {33834450},
issn = {0065-2598},
mesh = {Animals ; CRISPR-Cas Systems/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Endonucleases/genetics ; Gene Editing ; Gene Targeting ; Genetic Engineering ; Mice ; Transcription Activator-Like Effector Nucleases/genetics ; Zygote ; },
abstract = {Genetically engineered mouse (GEM) models have been revolutionizing the biomedical studies on deciphering the physiological roles of genes in vivo. In addition to deactivating a gene in mice, diverse strategies have been created to monitor gene expressions and molecular dynamics of specific proteins in vivo. Although gene targeting in mouse embryonic stem (ES) cells was essential for the precise engineering of the mouse genome over almost three decades, this process is a time-consuming, expensive, and laborious one. These days, new technologies that directly apply engineered endonucleases, such as zinc-finger nucleases (ZFNs), Transcription Activator-Like Effector (TALE) Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, into the mouse zygotes are enabling us to rapidly replace conventional gene targeting in mouse ES cells. In this chapter, we will describe the principles of reporter mouse strains and the recent advances in generating them using engineered endonucleases.},
}

Animals
CRISPR-Cas Systems/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
*Endonucleases/genetics
Gene Editing
Gene Targeting
Genetic Engineering
Mice
Transcription Activator-Like Effector Nucleases/genetics
Zygote

@article {pmid33833286,
year = {2021},
author = {Wong, TH and Khater, IM and Joshi, B and Shahsavari, M and Hamarneh, G and Nabi, IR},
title = {Single molecule network analysis identifies structural changes to caveolae and scaffolds due to mutation of the caveolin-1 scaffolding domain.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7810},
pmid = {33833286},
issn = {2045-2322},
support = {PJT-159845/CAPMC/CIHR/Canada ; PJT-159845/CAPMC/CIHR/Canada ; },
abstract = {Caveolin-1 (CAV1), the caveolae coat protein, also associates with non-caveolar scaffold domains. Single molecule localization microscopy (SMLM) network analysis distinguishes caveolae and three scaffold domains, hemispherical S2 scaffolds and smaller S1B and S1A scaffolds. The caveolin scaffolding domain (CSD) is a highly conserved hydrophobic region that mediates interaction of CAV1 with multiple effector molecules. F92A/V94A mutation disrupts CSD function, however the structural impact of CSD mutation on caveolae or scaffolds remains unknown. Here, SMLM network analysis quantitatively shows that expression of the CAV1 CSD F92A/V94A mutant in CRISPR/Cas CAV1 knockout MDA-MB-231 breast cancer cells reduces the size and volume and enhances the elongation of caveolae and scaffold domains, with more pronounced effects on S2 and S1B scaffolds. Convex hull analysis of the outer surface of the CAV1 point clouds confirms the size reduction of CSD mutant CAV1 blobs and shows that CSD mutation reduces volume variation amongst S2 and S1B CAV1 blobs at increasing shrink values, that may reflect retraction of the CAV1 N-terminus towards the membrane, potentially preventing accessibility of the CSD. Detection of point mutation-induced changes to CAV1 domains highlights the utility of SMLM network analysis for mesoscale structural analysis of oligomers in their native environment.},
}

@article {pmid33833247,
year = {2021},
author = {Miller, K and Eggenberger, AL and Lee, K and Liu, F and Kang, M and Drent, M and Ruba, A and Kirscht, T and Wang, K and Jiang, S},
title = {An improved biolistic delivery and analysis method for evaluation of DNA and CRISPR-Cas delivery efficacy in plant tissue.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7695},
pmid = {33833247},
issn = {2045-2322},
support = {2019-67013-29016//U.S. Department of Agriculture/ ; IOW04714//U.S. Department of Agriculture/ ; 60264-DNI7//American Chemical Society Petroleum Research Fund/ ; },
abstract = {Biolistic delivery is widely used for genetic transformation but inconsistency between bombardment samples for transient gene expression analysis often hinders quantitative analyses. We developed a methodology to improve the consistency of biolistic delivery results by using a double-barrel device and a cell counting software. The double-barrel device enables a strategy of incorporating an internal control into each sample, which significantly decreases variance of the results. The cell counting software further reduces errors and increases throughput. The utility of this new platform is demonstrated by optimizing conditions for delivering DNA using the commercial transfection reagent TransIT-2020. In addition, the same approach is applied to test the efficacy of multiple gRNAs for CRISPR-Cas9-mediated gene editing. The novel combination of the bombardment device and analysis method allows simultaneous comparison and optimization of parameters in the biolistic delivery. The platform developed here can be broadly applied to any target samples using biolistics, including animal cells and tissues.},
}

@article {pmid32789192,
year = {2020},
author = {Sankaranarayanan, G and Coghlan, A and Driguez, P and Lotkowska, ME and Sanders, M and Holroyd, N and Tracey, A and Berriman, M and Rinaldi, G},
title = {Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni.},
journal = {Wellcome open research},
volume = {5},
number = {},
pages = {178},
pmid = {32789192},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Background. At least 250 million people worldwide suffer from schistosomiasis, caused by Schistosoma worms. Genome sequences for several Schistosoma species are available, including a high-quality annotated reference for Schistosoma mansoni. There is a pressing need to develop a reliable functional toolkit to translate these data into new biological insights and targets for intervention. CRISPR-Cas9 was recently demonstrated for the first time in S. mansoni, to produce somatic mutations in the omega-1 (ω1) gene. Methods. We employed CRISPR-Cas9 to introduce somatic mutations in a second gene, SULT-OR, a sulfotransferase expressed in the parasitic stages of S. mansoni, in which mutations confer resistance to the drug oxamniquine. A 262-bp PCR product spanning the region targeted by the gRNA against SULT-OR was amplified, and mutations identified in it by high-throughput sequencing. Results. We found that 0.3-2.0% of aligned reads from CRISPR-Cas9-treated adult worms showed deletions spanning the predicted Cas9 cut site, compared to 0.1-0.2% for sporocysts, while deletions were extremely rare in eggs. The most common deletion observed in adults and sporocysts was a 34 bp-deletion directly upstream of the predicted cut site, but rarer deletions reaching as far as 102 bp upstream of the cut site were also detected. The CRISPR-Cas9-induced deletions, if homozygous, are predicted to cause resistance to oxamniquine by producing frameshifts, ablating SULT-OR transcription, or leading to mRNA degradation via the nonsense-mediated mRNA decay pathway. However, no SULT-OR knock down at the mRNA level was observed, presumably because the cells in which CRISPR-Cas9 did induce mutations represented a small fraction of all cells expressing SULT-OR. Conclusions. Further optimisation of CRISPR-Cas protocols for different developmental stages and particular cell types, including germline cells, will contribute to the generation of a homozygous knock-out in any gene of interest, and in particular the SULT-OR gene to derive an oxamniquine-resistant stable transgenic line.},
}

@article {pmid33830423,
year = {2021},
author = {Ghorbani, A and Hadifar, S and Salari, R and Izadpanah, K and Burmistrz, M and Afsharifar, A and Eskandari, MH and Niazi, A and Denes, CE and Neely, GG},
title = {A short overview of CRISPR-Cas technology and its application in viral disease control.},
journal = {Transgenic research},
volume = {},
number = {},
pages = {},
pmid = {33830423},
issn = {1573-9368},
abstract = {Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) together with CRISPR-associated (Cas) proteins have catalysed a revolution in genetic engineering. Native CRISPR-Cas systems exist in many bacteria and archaea where they provide an adaptive immune response through sequence-specific degradation of an invading pathogen's genome. This system has been reconfigured for use in genome editing, drug development, gene expression regulation, diagnostics, the prevention and treatment of cancers, and the treatment of genetic and infectious diseases. In recent years, CRISPR-Cas systems have been used in the diagnosis and control of viral diseases, for example, CRISPR-Cas12/13 coupled with new amplification techniques to improve the specificity of sequence-specific fluorescent probe detection. Importantly, CRISPR applications are both sensitive and specific and usually only require commonly available lab equipment. Unlike the canonical Cas9 which is guided to double-stranded DNA sites of interest, Cas13 systems target RNA sequences and thus can be employed in strategies directed against RNA viruses or for transcriptional silencing. Many challenges remain for these approach, including issues with specificity and the requirement for better mammalian delivery systems. In this review, we summarize the applications of CRISPR-Cas systems in controlling mammalian viral infections. Following necessary improvements, it is expected that CRISPR-Cas systems will be used effectively for such applications in the future.},
}

@article {pmid33828299,
year = {2021},
author = {Mo, CY and Mathai, J and Rostøl, JT and Varble, A and Banh, DV and Marraffini, LA},
title = {Type III-A CRISPR immunity promotes mutagenesis of staphylococci.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {33828299},
issn = {1476-4687},
abstract = {Horizontal gene transfer and mutation are the two major drivers of microbial evolution that enable bacteria to adapt to fluctuating environmental stressors1. Clustered, regularly interspaced, short palindromic repeats (CRISPR) systems use RNA-guided nucleases to direct sequence-specific destruction of the genomes of mobile genetic elements that mediate horizontal gene transfer, such as conjugative plasmids2 and bacteriophages3, thus limiting the extent to which bacteria can evolve by this mechanism. A subset of CRISPR systems also exhibit non-specific degradation of DNA4,5; however, whether and how this feature affects the host has not yet been examined. Here we show that the non-specific DNase activity of the staphylococcal type III-A CRISPR-Cas system increases mutations in the host and accelerates the generation of antibiotic resistance in Staphylococcus aureus and Staphylococcus epidermidis. These mutations require the induction of the SOS response to DNA damage and display a distinct pattern. Our results demonstrate that by differentially affecting both mechanisms that generate genetic diversity, type III-A CRISPR systems can modulate the evolution of the bacterial host.},
}

@article {pmid33827404,
year = {2021},
author = {Rozhkova, AM and Kislitsin, VY},
title = {CRISPR/Cas Genome Editing in Filamentous Fungi.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {Suppl 1},
pages = {S120-S139},
doi = {10.1134/S0006297921140091},
pmid = {33827404},
issn = {1608-3040},
abstract = {The review describes the CRISPR/CAS system and its adaptation for the genome editing in filamentous fungi commonly used for production of enzyme complexes, enzymes, secondary metabolites, and other compounds used in industrial biotechnology and agriculture. In the second part of this review, examples of the CRISPR/CAS technology application for improving properties of the industrial strains of fungi from the Trichoderma, Aspergillus, Penicillium, and other genera are presented. Particular attention is given to the efficiency of genome editing, as well as system optimization for specific industrial producers.},
}

@article {pmid33825100,
year = {2021},
author = {Ramirez-Torres, F and Ghogare, R and Stowe, E and Cerdá-Bennasser, P and Lobato-Gómez, M and Williamson-Benavides, BA and Giron-Calva, PS and Hewitt, S and Christou, P and Dhingra, A},
title = {Genome editing in fruit, ornamental, and industrial crops.},
journal = {Transgenic research},
volume = {},
number = {},
pages = {},
pmid = {33825100},
issn = {1573-9368},
support = {WNP00011//National Institute of Food and Agriculture/ ; PGC2018-097655-B-I00//MINECO, Spain/ ; 2017 SGR 828//Generalitat de Catalunya/ ; },
abstract = {The advent of genome editing has opened new avenues for targeted trait enhancement in fruit, ornamental, industrial, and all specialty crops. In particular, CRISPR-based editing systems, derived from bacterial immune systems, have quickly become routinely used tools for research groups across the world seeking to edit plant genomes with a greater level of precision, higher efficiency, reduced off-target effects, and overall ease-of-use compared to ZFNs and TALENs. CRISPR systems have been applied successfully to a number of horticultural and industrial crops to enhance fruit ripening, increase stress tolerance, modify plant architecture, control the timing of flower development, and enhance the accumulation of desired metabolites, among other commercially-important traits. As editing technologies continue to advance, so too does the ability to generate improved crop varieties with non-transgenic modifications; in some crops, direct transgene-free edits have already been achieved, while in others, T-DNAs have successfully been segregated out through crossing. In addition to the potential to produce non-transgenic edited crops, and thereby circumvent regulatory impediments to the release of new, improved crop varieties, targeted gene editing can speed up trait improvement in crops with long juvenile phases, reducing inputs resulting in faster market introduction to the market. While many challenges remain regarding optimization of genome editing in ornamental, fruit, and industrial crops, the ongoing discovery of novel nucleases with niche specialties for engineering applications may form the basis for additional and potentially crop-specific editing strategies.},
}

@article {pmid33823546,
year = {2021},
author = {Villegas Kcam, MC and Tsong, AJ and Chappell, J},
title = {Rational engineering of a modular bacterial CRISPR-Cas activation platform with expanded target range.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkab211},
pmid = {33823546},
issn = {1362-4962},
abstract = {CRISPR-Cas activator (CRISPRa) systems that selectively turn on transcription of a target gene are a potentially transformative technology for programming cellular function. While in eukaryotes versatile CRISPRa systems exist, in bacteria these systems suffer from a limited ability to activate different genes due to strict distance-dependent requirements of functional target binding sites, and require greater customization to optimize performance in different genetic and cellular contexts. To address this, we apply a rational protein engineering approach to create a new CRISPRa platform that is highly modular to allow for easy customization and has increased targeting flexibility through harnessing engineered Cas proteins. We first demonstrate that transcription activation domains can be recruited by CRISPR-Cas through noncovalent protein-protein interactions, which allows each component to be encoded on separate and easily interchangeable plasmid elements. We then exploit this modularity to rapidly screen a library of different activation domains, creating new systems with distinct regulatory properties. Furthermore, we demonstrate that by harnessing a library of circularly permuted Cas proteins, we can create CRISPRa systems that have different target binding site requirements, which together, allow for expanded target range.},
}

@article {pmid33823301,
year = {2021},
author = {Choi, E and Koo, T},
title = {CRISPR Technologies for the Treatment of Duchenne Muscular Dystrophy.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2021.04.002},
pmid = {33823301},
issn = {1525-0024},
abstract = {The emerging clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing technologies have progressed remarkably in recent years, opening up the potential of precise genome editing as a therapeutic approach to treat various diseases. The CRISPR/CRISPR associated (Cas) system is an attractive platform for the treatment of Duchenne muscular dystrophy (DMD), which is a neuromuscular disease caused by mutations in the DMD gene. CRISPR/Cas can be used to permanently repair the mutated DMD gene, leading to expression of the encoded protein, dystrophin, in systems ranging from cells derived from DMD patients to animal models of DMD. However, the development of more efficient therapeutic approaches and delivery methods remains a great challenge for DMD. Herein, we review various therapeutic strategies that use CRISPR/Cas to correct or bypass DMD mutations and discuss their therapeutic potential, as well as obstacles that lie ahead.},
}

@article {pmid33823021,
year = {2021},
author = {Gaillochet, C and Develtere, W and Jacobs, TB},
title = {CRISPR Screens in Plants: Approaches, Guidelines, and Future Prospects.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koab099},
pmid = {33823021},
issn = {1532-298X},
abstract = {CRISPR-Cas systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in the development of powerful new screens to test gene functions at the genomic scale. While there is tremendous potential to map and interrogate gene regulatory networks at unprecedented speed and scale using CRISPR screens, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools, and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports describing the use of this strategy to generate mutant knockout collections or to diversify DNA sequences. In addition, we provide insight into how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene function in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the numerous genomic profiles that have been generated over the past two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will lead to great advances in functional and synthetic biology.},
}

@article {pmid33817273,
year = {2020},
author = {Schenke, D},
title = {CRISPR/Cas9 or prime editing? - It depends on….},
journal = {Open life sciences},
volume = {15},
number = {1},
pages = {868-870},
pmid = {33817273},
issn = {2391-5412},
}

@article {pmid33816560,
year = {2021},
author = {Zhuang, C and Zhuang, C and Zhou, Q and Huang, X and Gui, Y and Lai, Y and Yang, S},
title = {Engineered CRISPR/Cas13d Sensing hTERT Selectively Inhibits the Progression of Bladder Cancer In Vitro.},
journal = {Frontiers in molecular biosciences},
volume = {8},
number = {},
pages = {646412},
pmid = {33816560},
issn = {2296-889X},
abstract = {Aptazyme and CRISPR/Cas gene editing system were widely used for regulating gene expression in various diseases, including cancer. This work aimed to reconstruct CRISPR/Cas13d tool for sensing hTERT exclusively based on the new device OFF-switch hTERT aptazyme that was inserted into the 3' UTR of the Cas13d. In bladder cancer cells, hTERT ligand bound to aptamer in OFF-switch hTERT aptazyme to inhibit the degradation of Cas13d. Results showed that engineered CRISPR/Cas13d sensing hTERT suppressed cell proliferation, migration, invasion and induced cell apoptosis in bladder cancer 5637 and T24 cells without affecting normal HFF cells. In short, we constructed engineered CRISPR/Cas13d sensing hTERT selectively inhibited the progression of bladder cancer cells significantly. It may serve as a promising specifically effective therapy for bladder cancer cells.},
}

@article {pmid33813884,
year = {2021},
author = {Potts, RWA and Gutierrez, AP and Penaloza, CS and Regan, T and Bean, TP and Houston, RD},
title = {Potential of genomic technologies to improve disease resistance in molluscan aquaculture.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1825},
pages = {20200168},
doi = {10.1098/rstb.2020.0168},
pmid = {33813884},
issn = {1471-2970},
abstract = {Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially the development of cost-efficient genomic selection, have the potential to accelerate genetic improvement. However, tailored approaches are required owing to the distinctive reproductive and life cycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole-organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools and genome editing approaches to understand and improve host resistance to infectious disease in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.},
}

@article {pmid33813641,
year = {2021},
author = {Baliga, P and Shekar, M and Kallappa, GS},
title = {Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
pmid = {33813641},
issn = {1432-0991},
support = {BT/BI/04/049/99//Department of Biotechnology , Ministry of Science and Technology/ ; },
abstract = {Klebsiella pneumoniae, an opportunistic pathogen found in the environment and human mucosal surfaces, is a leading cause of nosocomial infections. K. pneumoniae is now considered a global threat owing to the emergence of multidrug-resistant strains making its infections untreatable. In this study, 254 strains of K. pneumoniae were screened for the presence of prophages using the PHASTER tool. Very few strains lacked prophages (3.1%), while the remaining harboured both intact (811) and defective prophages (709). A subset of 42 unique strains of K. pneumoniae was chosen for further analysis. Our analysis revealed the presence of 110 complete prophages which were further classified as belonging to Myoviridae (67.3%), Siphoviridae (28.2%) and Podoviridae family (4.5%). An alignment of the 110 complete, prophage genome sequences clustered the prophages into 16 groups and 3 singletons. While none of the prophages encoded for virulence factors, 2 (1.8%) prophages were seen to encode for the antibiotic resistance-related genes. The CRISPR-Cas system was prevalent in 10 (23.8%) out of the 42 strains. Further analysis of the CRISPR spacers revealed 11.42% of the total spacers integrated in K. pneumoniae chromosome to match prophage protein sequences.},
}

@article {pmid33812397,
year = {2021},
author = {Wang, LY and Lin, RZ and Jiang, PF and Zhang, Y and Li, JZ and Chen, YW and Hu, JD},
title = {[Identify Myeloid Differentiation-Related MiRNAs Response to ATRA Induction by RNA Sequencing and CRISPR/Cas9 Gene Editing].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {29},
number = {2},
pages = {339-347},
doi = {10.19746/j.cnki.issn.1009-2137.2021.02.006},
pmid = {33812397},
issn = {1009-2137},
mesh = {CRISPR-Cas Systems ; Cell Differentiation ; *Gene Editing ; *MicroRNAs/genetics ; Sequence Analysis, RNA ; Tretinoin ; },
abstract = {OBJECTIVE: To identify differentiation related miRNA and evaluate roles of miRNA during ATRA induced myeloid differentiation.

METHODS: The small RNA sequencing was used to analyze differential expressed miRNAs in ATRA induced NB4 cells. Then the several up or down-regulated miRNA were selected as the research candidates. SgRNAs targeting the genome of each miRNA were designed and NB4 cells with inducible expression of Cas9 protein were generated. After transduced sgRNA into NB4/Cas9 cells, the mutation level by PCR and surveyor assay were evaluated. The cell differentiation level was investigated by surface CD11b expression via flow cytometry.

RESULTS: A total of 410 mature miRNAs which expressed in NB4 cells were detected out after treated by ATRA, 74 miRNAs were up-regulated and 55 were down-regulated miRNAs with DNA cleavage generated by CRISPR/Cas9 was assayed directly by PCR or surveyor assay, quantitative PCR showed that the expression of miRNA was downregulated, which evaluated that gene edition successfully inhibitied the expression of mature miRNA. MiR-223 knockout showed the myeloid differentation of NB4 significantly inhibitied, while miRNA-155 knockout showed the myeloid differentation of NB4 cells significantly increased.

CONCLUSION: CRISPR/Cas9 is a powerful tool for gene editing and can lead to miRNA knockout. Knockouts of miR-223 and miR-155 have shown a differentiation-related phenotype, and the potential mechanism is the integrative regulation of target genes.},
}

CRISPR-Cas Systems
Cell Differentiation
*Gene Editing
*MicroRNAs/genetics
Sequence Analysis, RNA
Tretinoin

@article {pmid33809410,
year = {2021},
author = {Adiguzel, MC and Goulart, DB and Wu, Z and Pang, J and Cengiz, S and Zhang, Q and Sahin, O},
title = {Distribution of CRISPR Types in Fluoroquinolone-Resistant Campylobacter jejuni Isolates.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {33809410},
issn = {2076-0817},
abstract = {To aid development of phage therapy against Campylobacter, we investigated the distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) systems in fluoroquinolone (FQ)-resistant Campylobacter jejuni. A total of 100 FQ-resistant C. jejuni strains from different sources were analyzed by PCR and DNA sequencing to determine resistance-conferring mutation in the gyrA gene and the presence of various CRISPR systems. All but one isolate harbored 1-5 point mutations in gyrA, and the most common mutation was the Thr86Ile change. Ninety-five isolates were positive with the CRISPR PCR, and spacer sequences were found in 86 of them. Among the 292 spacer sequences identified in this study, 204 shared 93-100% nucleotide homology to Campylobacter phage D10, 44 showed 100% homology to Campylobacter phage CP39, and 3 had 100% homology with Campylobacter phage CJIE4-5. The remaining 41 spacer sequences did not match with any phages in the database. Based on the results, it was inferred that the FQ-resistant C. jejuni isolates analyzed in this study were potentially resistant to Campylobacter phages D10, CP39, and CJIE4-5 as well as some unidentified phages. These phages should be excluded from cocktails of phages that may be utilized to treat FQ-resistant Campylobacter.},
}

@article {pmid33807610,
year = {2021},
author = {Diakatou, M and Dubois, G and Erkilic, N and Sanjurjo-Soriano, C and Meunier, I and Kalatzis, V},
title = {Allele-Specific Knockout by CRISPR/Cas to Treat Autosomal Dominant Retinitis Pigmentosa Caused by the G56R Mutation in NR2E3.},
journal = {International journal of molecular sciences},
volume = {22},
number = {5},
pages = {},
pmid = {33807610},
issn = {1422-0067},
support = {ANR-10-LABX-12-01//Laboratoire d'Excellence EpiGenMed/ ; },
abstract = {Retinitis pigmentosa (RP) is an inherited retinal dystrophy that causes progressive vision loss. The G56R mutation in NR2E3 is the second most common mutation causing autosomal dominant (ad) RP, a transcription factor that is essential for photoreceptor development and maintenance. The G56R variant is exclusively responsible for all cases of NR2E3-associated adRP. Currently, there is no treatment for NR2E3-related or, other, adRP, but genome editing holds promise. A pertinent approach would be to specifically knockout the dominant mutant allele, so that the wild type allele can perform unhindered. In this study, we developed a CRISPR/Cas strategy to specifically knockout the mutant G56R allele of NR2E3 and performed a proof-of-concept study in induced pluripotent stem cells (iPSCs) of an adRP patient. We demonstrate allele-specific knockout of the mutant G56R allele in the absence of off-target events. Furthermore, we validated this knockout strategy in an exogenous overexpression system. Accordingly, the mutant G56R-CRISPR protein was truncated and mis-localized to the cytosol in contrast to the (peri)nuclear localizations of wild type or G56R NR2E3 proteins. Finally, we show, for the first time, that G56R iPSCs, as well as G56R-CRISPR iPSCs, can differentiate into NR2E3-expressing retinal organoids. Overall, we demonstrate that G56R allele-specific knockout by CRISPR/Cas could be a clinically relevant approach to treat NR2E3-associated adRP.},
}

@article {pmid33806233,
year = {2021},
author = {Numan, M and Khan, AL and Asaf, S and Salehin, M and Beyene, G and Tadele, Z and Ligaba-Osena, A},
title = {From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [Eragrostis tef (Zucc.) Trotter].},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {4},
pages = {},
doi = {10.3390/plants10040628},
pmid = {33806233},
issn = {2223-7747},
support = {133504//University of North Carolina at Greensboro/ ; },
abstract = {Tef (Eragrostis tef (Zucc.) Trotter) is a staple food crop for 70% of the Ethiopian population and is currently cultivated in several countries for grain and forage production. It is one of the most nutritious grains, and is also more resilient to marginal soil and climate conditions than major cereals such as maize, wheat and rice. However, tef is an extremely low-yielding crop, mainly due to lodging, which is when stalks fall on the ground irreversibly, and prolonged drought during the growing season. Climate change is triggering several biotic and abiotic stresses which are expected to cause severe food shortages in the foreseeable future. This has necessitated an alternative and robust approach in order to improve resilience to diverse types of stresses and increase crop yields. Traditional breeding has been extensively implemented to develop crop varieties with traits of interest, although the technique has several limitations. Currently, genome editing technologies are receiving increased interest among plant biologists as a means of improving key agronomic traits. In this review, the potential application of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) technology in improving stress resilience in tef is discussed. Several putative abiotic stress-resilient genes of the related monocot plant species have been discussed and proposed as target genes for editing in tef through the CRISPR-Cas system. This is expected to improve stress resilience and boost productivity, thereby ensuring food and nutrition security in the region where it is needed the most.},
}

@article {pmid33806186,
year = {2021},
author = {Gu, D and Xue, H and Yuan, X and Yu, J and Xu, X and Huang, Y and Li, M and Zhai, X and Pan, Z and Zhang, Y and Jiao, X},
title = {Genome-Wide Identification of Genes Involved in Acid Stress Resistance of Salmonella Derby.},
journal = {Genes},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/genes12040476},
pmid = {33806186},
issn = {2073-4425},
support = {BK20180911//National Natural Science Foundation of Jiangsu Province/ ; },
abstract = {Resistance to and survival under acidic conditions are critical for Salmonella to infect the host. As one of the most prevalent serotypes identified in pigs and humans, how S. Derby overcomes acid stress remains unclear. Here, we de novo sequenced the genome of a representative S. Derby strain 14T from our S. Derby strain stock and identified its acid resistance-associated genes using Tn-seq analysis. A total of 35 genes, including those belonging to two-component systems (TCS) (cpxAR), the CRISPR-Cas system (casCE), and other systems, were identified as essential for 14T to survive under acid stress. The results demonstrated that the growth curve and survival ability of ΔcpxA and ΔcpxR were decreased under acid stress, and the adhesion and invasion abilities to the mouse colon cancer epithelial cells (MC38) of ΔcpxR were also decreased compared with the wild type strain, suggesting that the TCS CpxAR plays an essential role in the acid resistance and virulence of S. Derby. Also, CasC and CasE were found to be responsible for acid resistance in S. Derby. Our results indicate that acid stress induces multiple genes' expression to mediate the acid resistance of S. Derby and enhance its pathogenesis during an infection.},
}

@article {pmid33805897,
year = {2021},
author = {Sansbury, BM and Kmiec, EB},
title = {On the Origins of Homology Directed Repair in Mammalian Cells.},
journal = {International journal of molecular sciences},
volume = {22},
number = {7},
pages = {},
pmid = {33805897},
issn = {1422-0067},
abstract = {Over the course of the last five years, expectations surrounding our capacity to selectively modify the human genome have never been higher. The reduction to practice site-specific nucleases designed to cleave at a unique site within the DNA is now centerstage in the development of effective molecular therapies. Once viewed as being impossible, this technology now has great potential and, while cellular and molecular barriers persist to clinical implementations, there is little doubt that these barriers will be crossed, and human beings will soon be treated with gene editing tools. The most ambitious of these desires is the correction of genetic mutations resident within the human genome that are responsible for oncogenesis and a wide range of inherited diseases. The process by which gene editing activity could act to reverse these mutations to wild-type and restore normal protein function has been generally categorized as homology directed repair. This is a catch-all basket term that includes the insertion of short fragments of DNA, the replacement of long fragments of DNA, and the surgical exchange of single bases in the correction of point mutations. The foundation of homology directed repair lies in pioneering work that unravel the mystery surrounding genetic exchange using single-stranded DNA oligonucleotides as the sole gene editing agent. Single agent gene editing has provided guidance on how to build combinatorial approaches to human gene editing using the remarkable programmable nuclease complexes known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their closely associated (Cas) nucleases. In this manuscript, we outline the historical pathway that has helped evolve the current molecular toolbox being utilized for the genetic re-engineering of the human genome.},
}

@article {pmid33805879,
year = {2021},
author = {Chen, M and Zhu, X and Liu, X and Wu, C and Yu, C and Hu, G and Chen, L and Chen, R and Bouzayen, M and Zouine, M and Hao, Y},
title = {Knockout of Auxin Response Factor SlARF4 Improves Tomato Resistance to Water Deficit.},
journal = {International journal of molecular sciences},
volume = {22},
number = {7},
pages = {},
pmid = {33805879},
issn = {1422-0067},
support = {31870286//National Natural Science Foundation of China/ ; 31902013//National Natural Science Foundation of China/ ; 2017A030313114//Natural Science Foundation of Guangdong Province/ ; 2018A030310205//Natural Science Foundation of Guangdong Province/ ; 201804010031//General Project of Guangzhou city/ ; 2019SCAUGH05//International Science and Technology Cooperation Major Project Cultivation Special Fund of SCAU/ ; },
abstract = {Auxin response factors (ARFs) play important roles in various plant physiological processes; however, knowledge of the exact role of ARFs in plant responses to water deficit is limited. In this study, SlARF4, a member of the ARF family, was functionally characterized under water deficit. Real-time fluorescence quantitative polymerase chain reaction (PCR) and β-glucuronidase (GUS) staining showed that water deficit and abscisic acid (ABA) treatment reduced the expression of SlARF4. SlARF4 was expressed in the vascular bundles and guard cells of tomato stomata. Loss of function of SlARF4 (arf4) by using Clustered Regularly Interspaced Short Palindromic Repeats/Cas 9 (CRISPR/Cas 9) technology enhanced plant resistance to water stress and rehydration ability. The arf4 mutant plants exhibited curly leaves and a thick stem. Malondialdehyde content was significantly lower in arf4 mutants than in wildtype plants under water stress; furthermore, arf4 mutants showed higher content of antioxidant substances, superoxide dismutase, actual photochemical efficiency of photosystem II (PSII), and catalase activities. Stomatal and vascular bundle morphology was changed in arf4 mutants. We identified 628 differentially expressed genes specifically expressed under water deficit in arf4 mutants; six of these genes, including ABA signaling pathway-related genes, were differentially expressed between the wildtype and arf4 mutants under water deficit and unlimited water supply. Auxin responsive element (AuxRE) elements were found in these genes' promoters indicating that SlARF4 participates in ABA signaling pathways by regulating the expression of SlABI5/ABF and SCL3, thereby influencing stomatal morphology and vascular bundle development and ultimately improving plant resistance to water deficit.},
}

@article {pmid33805113,
year = {2021},
author = {Nidhi, S and Anand, U and Oleksak, P and Tripathi, P and Lal, JA and Thomas, G and Kuca, K and Tripathi, V},
title = {Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives.},
journal = {International journal of molecular sciences},
volume = {22},
number = {7},
pages = {},
pmid = {33805113},
issn = {1422-0067},
support = {VT2019-2021//UHK/ ; },
abstract = {According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.},
}

@article {pmid33804420,
year = {2021},
author = {Achigar, R and Scarrone, M and Rousseau, GM and Philippe, C and Machado, F and Duvós, V and Campot, MP and Dion, MB and Shao, Y and Pianzzola, MJ and Moineau, S},
title = {Ectopic Spacer Acquisition in Streptococcus thermophilus CRISPR3 Array.},
journal = {Microorganisms},
volume = {9},
number = {3},
pages = {},
pmid = {33804420},
issn = {2076-2607},
support = {N/A//Uruguayan National Research and Innovation Agency (ANII)/ ; N/A//Department of Foreign Affairs and International Trade of Canada/ ; Discovery Program//Natural Sciences and Engineering Research Council of Canada/ ; Canada Research Chair in Bacteriophages//Canada Research Chairs/ ; },
abstract = {Streptococcus thermophilus relies heavily on two type II-A CRISPR-Cas systems, CRISPR1 and CRISPR3, to resist siphophage infections. One hallmark of these systems is the integration of a new spacer at the 5' end of the CRISPR arrays following phage infection. However, we have previously shown that ectopic acquisition of spacers can occur within the CRISPR1 array. Here, we present evidence of the acquisition of new spacers within the array of CRISPR3 of S. thermophilus. The analysis of randomly selected bacteriophage-insensitive mutants of the strain Uy01 obtained after phage infection, as well as the comparison with other S. thermophilus strains with similar CRISPR3 content, showed that a specific spacer within the array could be responsible for misguiding the adaptation complex. These results also indicate that while the vast majority of new spacers are added at the 5' end of the CRISPR array, ectopic spacer acquisition is a common feature of both CRISPR1 and CRISPR3 systems in S. thermophilus, and it can still provide phage resistance. Ectopic spacer acquisition also appears to have occurred naturally in some strains of Streptococcus pyogenes, suggesting that it is a general phenomenon, at least in type II-A systems.},
}

@article {pmid33802904,
year = {2021},
author = {Parsons, C and Brown, P and Kathariou, S},
title = {Use of Bacteriophage Amended with CRISPR-Cas Systems to Combat Antimicrobial Resistance in the Bacterial Foodborne Pathogen Listeria monocytogenes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {33802904},
issn = {2079-6382},
support = {2019-67017-29581//National Institute of Food and Agriculture/ ; },
abstract = {Listeria monocytogenes is a bacterial foodborne pathogen and the causative agent of the disease listeriosis, which though uncommon can result in severe symptoms such as meningitis, septicemia, stillbirths, and abortions and has a high case fatality rate. This pathogen can infect humans and other animals, resulting in massive health and economic impacts in the United States and globally. Listeriosis is treated with antimicrobials, typically a combination of a beta-lactam and an aminoglycoside, and L. monocytogenes has remained largely susceptible to the drugs of choice. However, there are several reports of antimicrobial resistance (AMR) in both L. monocytogenes and other Listeria species. Given the dire health outcomes associated with listeriosis, the prospect of antimicrobial-resistant L. monocytogenes is highly problematic for human and animal health. Developing effective tools for the control and elimination of L. monocytogenes, including strains with antimicrobial resistance, is of the utmost importance to prevent further dissemination of AMR in this pathogen. One tool that has shown great promise in combating antibiotic-resistant pathogens is the use of bacteriophages (phages), which are natural bacterial predators and horizontal gene transfer agents. Although native phages can be effective at killing antibiotic-resistant pathogens, limited host ranges and evolved resistance to phages can compromise their use in the efforts to mitigate the global AMR challenge. However, recent advances can allow the use of CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) to selectively target pathogens and their AMR determinants. Employment of CRISPR-Cas systems for phage amendment can overcome previous limitations in using phages as biocontrol and allow for the effective control of L. monocytogenes and its AMR determinants.},
}

@article {pmid33802772,
year = {2021},
author = {Ge, H and Marchisio, MA},
title = {Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {33802772},
issn = {2075-1729},
support = {31571373//National Natural Science Foundation of China/ ; },
abstract = {Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.},
}

@article {pmid33801686,
year = {2021},
author = {Salanga, CM and Salanga, MC},
title = {Genotype to Phenotype: CRISPR Gene Editing Reveals Genetic Compensation as a Mechanism for Phenotypic Disjunction of Morphants and Mutants.},
journal = {International journal of molecular sciences},
volume = {22},
number = {7},
pages = {},
pmid = {33801686},
issn = {1422-0067},
abstract = {Forward genetic screens have shown the consequences of deleterious mutations; however, they are best suited for model organisms with fast reproductive rates and large broods. Furthermore, investigators must faithfully identify changes in phenotype, even if subtle, to realize the full benefit of the screen. Reverse genetic approaches also probe genotype to phenotype relationships, except that the genetic targets are predefined. Until recently, reverse genetic approaches relied on non-genomic gene silencing or the relatively inefficient, homology-dependent gene targeting for loss-of-function generation. Fortunately, the flexibility and simplicity of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system has revolutionized reverse genetics, allowing for the precise mutagenesis of virtually any gene in any organism at will. The successful integration of insertions/deletions (INDELs) and nonsense mutations that would, at face value, produce the expected loss-of-function phenotype, have been shown to have little to no effect, even if other methods of gene silencing demonstrate robust loss-of-function consequences. The disjunction between outcomes has raised important questions about our understanding of genotype to phenotype and highlights the capacity for compensation in the central dogma. This review describes recent studies in which genomic compensation appears to be at play, discusses the possible compensation mechanisms, and considers elements important for robust gene loss-of-function studies.},
}

@article {pmid33801499,
year = {2021},
author = {Bæksted Holme, I and Dionisio, G and Brinch-Pedersen, H},
title = {A Roadmap to Modulated Anthocyanin Compositions in Carrots.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {33801499},
issn = {2223-7747},
support = {9067-00006B//Innovation Fund Denmark/ ; },
abstract = {Anthocyanins extracted from black carrots have received increased interest as natural colorants in recent years. The reason is mainly their high content of acylated anthocyanins that stabilizes the color and thereby increases the shelf-life of products colored with black carrot anthocyanins. Still, the main type of anthocyanins synthesized in all black carrot cultivars is cyanidin limiting their use as colorants due to the narrow color variation. Additionally, in order to be competitive against synthetic colors, a higher percentage of acylated anthocyanins and an increased anthocyanin content in black carrots are needed. However, along with the increased interest in black carrots there has also been an interest in identifying the structural and regulatory genes associated with anthocyanin biosynthesis in black carrots. Thus, huge progress in the identification of genes involved in anthocyanin biosynthesis has recently been achieved. Given this information it is now possible to attempt to modulate anthocyanin compositions in black carrots through genetic modifications. In this review we look into genetic modification opportunities for generating taproots of black carrots with extended color palettes, with a higher percentage of acylated anthocyanins or a higher total content of anthocyanins.},
}

@article {pmid33801123,
year = {2021},
author = {Ryczek, N and Hryhorowicz, M and Zeyland, J and Lipiński, D and Słomski, R},
title = {CRISPR/Cas Technology in Pig-to-Human Xenotransplantation Research.},
journal = {International journal of molecular sciences},
volume = {22},
number = {6},
pages = {},
pmid = {33801123},
issn = {1422-0067},
support = {INNOMED/I/17/NCBR/2014//Narodowe Centrum Badań i Rozwoju/ ; },
abstract = {CRISPR/Cas (clustered regularly interspaced short palindromic repeats linked to Cas nuclease) technology has revolutionized many aspects of genetic engineering research. Thanks to it, it became possible to study the functions and mechanisms of biology with greater precision, as well as to obtain genetically modified organisms, both prokaryotic and eukaryotic. The changes introduced by the CRISPR/Cas system are based on the repair paths of the single or double strand DNA breaks that cause insertions, deletions, or precise integrations of donor DNA. These changes are crucial for many fields of science, one of which is the use of animals (pigs) as a reservoir of tissues and organs for xenotransplantation into humans. Non-genetically modified animals cannot be used to save human life and health due to acute immunological reactions resulting from the phylogenetic distance of these two species. This review is intended to collect and summarize the advantages as well as achievements of the CRISPR/Cas system in pig-to-human xenotransplantation research. In addition, it demonstrates barriers and limitations that require careful evaluation before attempting to experiment with this technology.},
}

@article {pmid33799666,
year = {2021},
author = {Stamereilers, C and Wong, S and Tsourkas, PK},
title = {Characterization of CRISPR Spacer and Protospacer Sequences in Paenibacillus larvae and Its Bacteriophages.},
journal = {Viruses},
volume = {13},
number = {3},
pages = {},
pmid = {33799666},
issn = {1999-4915},
abstract = {The bacterium Paenibacillus larvae is the causative agent of American foulbrood, the most devastating bacterial disease of honeybees. Because P. larvae is antibiotic resistant, phages that infect it are currently used as alternative treatments. However, the acquisition by P. larvae of CRISPR spacer sequences from the phages could be an obstacle to treatment efforts. We searched nine complete genomes of P. larvae strains and identified 714 CRISPR spacer sequences, of which 384 are unique. Of the four epidemiologically important P. larvae strains, three of these have fewer than 20 spacers, while one strain has over 150 spacers. Of the 384 unique spacers, 18 are found as protospacers in the genomes of 49 currently sequenced P. larvae phages. One P. larvae strain does not have any protospacers found in phages, while another has eight. Protospacer distribution in the phages is uneven, with two phages having up to four protospacers, while a third of phages have none. Some phages lack protospacers found in closely related phages due to point mutations, indicating a possible escape mechanism. This study serve a point of reference for future studies on the CRISPR-Cas system in P. larvae as well as for comparative studies of other phage-host systems.},
}

@article {pmid33798831,
year = {2021},
author = {Ezawa, M and Kouno, F and Kubo, H and Sakuma, T and Yamamoto, T and Kinoshita, T},
title = {Pou5f3.3 is involved in establishment and maintenance of hematopoietic cells during Xenopus development.},
journal = {Tissue & cell},
volume = {72},
number = {},
pages = {101531},
doi = {10.1016/j.tice.2021.101531},
pmid = {33798831},
issn = {1532-3072},
abstract = {Three POU family class V gene homologues are expressed in the development of Xenopus. In contrast to the expression of Pou5f3.1 and Pou5f3.2 in organogenesis, Pou5f3.3 is expressed during oogenesis in ovary. We investigated the expression and function of Pou5f3.3 in organogenesis of Xenopus laevis. RT-PCR and immunohistochemical analysis indicated that Pou5f3.3 was expressed in a small number of adult liver cells and blood cells. Immunocytochemical investigation proved that Bmi1, a marker for hematopoietic progenitor cells, was co-expressed in Pou5f3.3-expressing small spherical cells in the peripheral blood. In anemic induction by intraperitoneal injection of phenyl hydrazine, the number of Pou5f3.3-expressing cells significantly increased within 3 days after phenyl hydrazine injection. In CRISPR/Cas mutagenesis of Pou5f3.3, Bmi1-positive hematopoietic progenitor cell count decreased in the hematopoietic dorsal-lateral plate (DLP) region, resulting in a considerable reduction in peripheral blood cells. CRISPR/Cas-induced hematopoietic deficiency was completely rescued by Pou5f3.3 supplementation, but not by Pou5f3.1 or Pou5f3.2. Transplantation experiments using the H2B-GFP transgenic line demonstrated that DLP-derived Pou5f3.3-positive and Bmi1-positive cells were translocated into the liver and bone through the bloodstream. These results suggest that Pou5f3.3 plays an essential role in the establishment and maintenance of hematopoietic progenitor cells during Xenopus development.},
}

@article {pmid33797713,
year = {2021},
author = {Carrijo, J and Illa-Berenguer, E and LaFayette, P and Torres, N and Aragão, FJL and Parrott, W and Vianna, GR},
title = {Two efficient CRISPR/Cas9 systems for gene editing in soybean.},
journal = {Transgenic research},
volume = {},
number = {},
pages = {},
pmid = {33797713},
issn = {1573-9368},
abstract = {Genome editing using CRISPR/Cas9 has been highlighted as a powerful tool for crop improvement. Nevertheless, its efficiency can be improved, especially for crops with a complex genome, such as soybean. In this work, using the CRISPR/Cas9 technology we evaluated two CRISPR systems, a one-component vs. a two-component strategy. In a simplified system, the single transcriptional unit (STU), SpCas9 and sgRNA are driven by only one promoter, and in the conventional system, the two-component transcriptional unit (TCTU), SpCas9, is under the control of a pol II promoter and the sgRNAs are under the control of a pol III promoter. A multiplex system with three targets was designed targeting two different genes, GmIPK1 and GmIPK2, coding for enzymes from the phytic acid synthesis pathway. Both systems were tested using the hairy root soybean methodology. Results showed gene-specific edition. For the GmIPK1 gene, edition was observed in both configurations, with a deletion of 1 to 749 base pairs; however, the TCTU showed higher indel frequencies. For GmIPK2 major exclusions were observed in both systems, but the editing efficiency was low for STU. Both systems (STU or TCTU) have been shown to be capable of promoting effective gene editing in soybean. The TCTU configuration proved to be preferable, since it was more efficient. The STU system was less efficient, but the size of the CRISPR/Cas cassette was smaller.},
}

@article {pmid33797415,
year = {2021},
author = {Mckay, A and Burgio, G},
title = {Harnessing CRISPR-Cas system diversity for gene editing technologies.},
journal = {Journal of biomedical research},
volume = {35},
number = {2},
pages = {91-106},
doi = {10.7555/JBR.35.20200184},
pmid = {33797415},
issn = {1674-8301},
abstract = {The discovery and utilization of RNA-guided surveillance complexes, such as CRISPR-Cas9, for sequence-specific DNA or RNA cleavage, has revolutionised the process of gene modification or knockdown. To optimise the use of this technology, an exploratory race has ensued to discover or develop new RNA-guided endonucleases with the most flexible sequence targeting requirements, coupled with high cleavage efficacy and specificity. Here we review the constraints of existing gene editing and assess the merits of exploiting the diversity of CRISPR-Cas effectors as a methodology for surmounting these limitations.},
}

@article {pmid33795753,
year = {2021},
author = {Nguyen, ND and Matsuura, T and Kato, Y and Watanabe, H},
title = {DNMT3.1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7326},
pmid = {33795753},
issn = {2045-2322},
support = {18H04884//Japan Society for the Promotion of Science/ ; 17H01880//Japan Society for the Promotion of Science/ ; },
abstract = {The cladoceran crustacean Daphnia has long been a model of energy allocation studies due to its important position in the trophic cascade of freshwater ecosystems. However, the loci for controlling energy allocation between life history traits still remain unknown. Here, we report CRISPR/Cas-mediated target mutagenesis of DNA methyltransferase 3.1 (DNMT3.1) that is upregulated in response to caloric restriction in Daphnia magna. The resulting biallelic mutant is viable and did not show any change in growth rate, reproduction, and longevity under nutrient rich conditions. In contrast, under starved conditions, the growth rate of this DNMT3.1 mutant was increased but its reproduction was reciprocally reduced compared to the wild type when the growth and reproduction activities competed during a period from instar 4 to 8. The life span of this mutant was significantly shorter than that of the wild type. We also compared transcriptomes between DNMT3.1 mutant and wild type under nutrient-rich and starved conditions. Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to changes in the transcriptomes of the mutant including differential expression of vitellogenin genes. In addition, we found upregulation of the I am not dead yet (INDY) ortholog, which has been known to shorten the life span in Drosophila, explaining the shorter life span of the DNMT3.1 mutant. These results establish DNMT3.1 as a key regulator for life span and energy allocation between growth and reproduction during caloric restriction. Our findings reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog that is widely distributed among animals. We also infer a previously unidentified adaptation of Daphnia that invests more energy for reproduction than growth under starved conditions.},
}

@article {pmid33793824,
year = {2020},
author = {Riediger, M and Spät, P and Bilger, R and Voigt, K and Maček, B and Hess, WR},
title = {Analysis of a Photosynthetic Cyanobacterium Rich in Internal Membrane Systems via Gradient Profiling by Sequencing (Grad-seq).},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaa017},
pmid = {33793824},
issn = {1532-298X},
abstract = {Although regulatory small RNAs have been reported in photosynthetic cyanobacteria, the lack of clear RNA chaperones involved in their regulation poses a conundrum. Here, we analyzed the full complement of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished, supporting the high quality of this approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include a YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.},
}

@article {pmid33791736,
year = {2021},
author = {Liu, TY and Knott, GJ and Smock, DCJ and Desmarais, JJ and Son, S and Bhuiya, A and Jakhanwal, S and Prywes, N and Agrawal, S and de León Derby, MD and Switz, NA and Armstrong, M and Harris, AR and Charles, EJ and Thornton, BW and Fozouni, P and Shu, J and Stephens, SI and Kumar, GR and Zhao, C and Mok, A and Iavarone, AT and Escajeda, AM and McIntosh, R and Kim, SE and Dugan, EJ and , and Pollard, KS and Tan, MX and Ott, M and Fletcher, DA and Lareau, LF and Hsu, PD and Savage, DF and Doudna, JA},
title = {Accelerated RNA detection using tandem CRISPR nucleases.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {33791736},
support = {F30 AI143401/AI/NIAID NIH HHS/United States ; R01 GM131073/GM/NIGMS NIH HHS/United States ; DP5 OD021369/OD/NIH HHS/United States ; R61 AI140465/AI/NIAID NIH HHS/United States ; R01 GM127463/GM/NIGMS NIH HHS/United States ; S10 OD020062/OD/NIH HHS/United States ; },
abstract = {Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule 1,2 , but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ∼30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.},
}

@article {pmid33791325,
year = {2021},
author = {Silveira, MC and Rocha-de-Souza, CM and de Oliveira Santos, IC and Pontes, LDS and Oliveira, TRTE and Tavares-Teixeira, CB and Cossatis, NA and Pereira, NF and da Conceição-Neto, OC and da Costa, BS and Rodrigues, DCS and Albano, RM and da Silva, FAB and Marques, EA and Leão, RS and Carvalho-Assef, APD},
title = {Genetic Basis of Antimicrobial Resistant Gram-Negative Bacteria Isolated From Bloodstream in Brazil.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {635206},
pmid = {33791325},
issn = {2296-858X},
abstract = {Multidrug-resistant microorganisms are a well-known global problem, and gram-negative bacilli are top-ranking. When these pathogens are associated with bloodstream infections (BSI), outcomes become even worse. Here we applied whole-genome sequencing to access information about clonal distribution, resistance mechanism diversity and other molecular aspects of gram-negative bacilli (GNB) isolated from bloodstream infections in Brazil. It was possible to highlight international high-risk clones circulating in the Brazilian territory, such as CC258 for Klebsiella pneumoniae, ST79 for Acinetobacter baumannii and ST233 for Pseudomonas aeruginosa. Important associations can be made such as a negative correlation between CRISPR-Cas and K. pneumoniae CC258, while the genes blaTEM, blaKPC and blaCTX-M are highly associated with this clone. Specific relationships between A. baumannii clones and blaOXA-51 variants were also observed. All P. aeruginosa ST233 isolates showed the genes blaVIM and blaOXA486. In addition, some trends could be identified, where a new P. aeruginosa MDR clone (ST3079), a novel A. baumannii clonal profile circulating in Brazil (ST848), and important resistance associations in the form of blaVIM-2 and blaIMP-56 being found together in one ST233 strain, stand out. Such findings may help to develop approaches to deal with BSI and even other nosocomial infections caused by these important GNB.},
}

@article {pmid33788831,
year = {2021},
author = {Biayna, J and Garcia-Cao, I and Álvarez, MM and Salvadores, M and Espinosa-Carrasco, J and McCullough, M and Supek, F and Stracker, TH},
title = {Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.},
journal = {PLoS biology},
volume = {19},
number = {3},
pages = {e3001176},
doi = {10.1371/journal.pbio.3001176},
pmid = {33788831},
issn = {1545-7885},
abstract = {Analysis of cancer mutagenic signatures provides information about the origin of mutations and can inform the use of clinical therapies, including immunotherapy. In particular, APOBEC3A (A3A) has emerged as a major driver of mutagenesis in cancer cells, and its expression results in DNA damage and susceptibility to treatment with inhibitors of the ATR and CHK1 checkpoint kinases. Here, we report the implementation of CRISPR/Cas-9 genetic screening to identify susceptibilities of multiple A3A-expressing lung adenocarcinoma (LUAD) cell lines. We identify HMCES, a protein recently linked to the protection of abasic sites, as a central protein for the tolerance of A3A expression. HMCES depletion results in synthetic lethality with A3A expression preferentially in a TP53-mutant background. Analysis of previous screening data reveals a strong association between A3A mutational signatures and sensitivity to HMCES loss and indicates that HMCES is specialized in protecting against a narrow spectrum of DNA damaging agents in addition to A3A. We experimentally show that both HMCES disruption and A3A expression increase susceptibility of cancer cells to ionizing radiation (IR), oxidative stress, and ATR inhibition, strategies that are often applied in tumor therapies. Overall, our results suggest that HMCES is an attractive target for selective treatment of A3A-expressing tumors.},
}

@article {pmid33785958,
year = {2021},
author = {Miranda, AV and Wiyono, L and Nurachman, LA},
title = {Clustered regularly interspaced palindromic repeats-cas9-based strategies towards HIV eradication: A literature review.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {71(Suppl 2)},
number = {2},
pages = {S134-S139},
pmid = {33785958},
issn = {0030-9982},
abstract = {OBJECTIVE: Despite Human Immunodeficiency Virus (HIV) being a major global health burden, no currently available therapy can eliminate it. One of the major challenges in developing treatment is the presence of latent HIV reservoirs. On the other hand, development of Clustered Regularly Interspaced Palindromic Repeats-Cas9 (CRISPR-Cas9) has made genome editing possible and thus can be used to address HIV latency and successfully treat HIV. This literature review aims to identify and appraise existing CRISPR-Cas9 strategies that address HIV treatment, particularly during latency.

Methods: The PubMed Database was used to retrieve relevant articles. This review included articles that mentioned the use of CRISPR-Cas9 as a treatment for HIV and are written in English and/or Indonesian language.

RESULTS: The included studies (n = 17) showed that the CRISPR-Cas9 system can be utilized to disrupt the HIV-1 genome to inhibit viral reproduction and virulence. This system can be further optimized by combining several CRISPR-Cas9 systems. However, the use of CRISPR-Cas9 may cause HIV resistance, particularly to its guide RNA. This technique has also never been applied in vivo, thus more research is needed before wider implementation. A limitation of this review is the lack of data regarding CRISPR-Cas9 systems quality in some studies, thus limiting appraisal.

CONCLUSIONS: While the use of CRISPR-Cas9 to cure HIV seems promising, further studies regarding CRISPR-Cas9 quality, potential for development of gRNA-resistant HIV-1 strains and in vivo demonstration of the techniques are needed to progress this concept toward HIV eradication.},
}

@article {pmid33785624,
year = {2021},
author = {Hoikkala, V and Ravantti, J and Díez-Villaseñor, C and Tiirola, M and Conrad, RA and McBride, MJ and Moineau, S and Sundberg, LR},
title = {Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System.},
journal = {mBio},
volume = {12},
number = {2},
pages = {},
pmid = {33785624},
issn = {2150-7511},
abstract = {CRISPR-Cas immune systems adapt to new threats by acquiring new spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition despite variation in spacer content between microbial strains. It has been suggested that such loci may use acquisition machinery from cooccurring CRISPR-Cas systems within the same strain. Here, following infection by a virulent phage with a double-stranded DNA (dsDNA) genome, we observed spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient CRISPR-Cas subtype VI-B system and a complete subtype II-C system. We show that the VI-B locus acquires spacers from both the bacterial and phage genomes, while the newly acquired II-C spacers mainly target the viral genome. Both loci preferably target the terminal end of the phage genome, with priming-like patterns around a preexisting II-C protospacer. Through gene deletion, we show that the RNA-cleaving VI-B system acquires spacers in trans using acquisition machinery from the DNA-cleaving II-C system. Our observations support the concept of cross talk between CRISPR-Cas systems and raise further questions regarding the plasticity of adaptation modules.IMPORTANCE CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader's genome. These fragments, called spacers, are integrated into a memory bank on the bacterial genome called the CRISPR array. The spacers allow for the recognition of the same invader upon subsequent infection. Most CRISPR-Cas systems target DNA, but recently, systems that exclusively target RNA have been discovered. RNA-targeting CRISPR-Cas systems often lack genes necessary for spacer acquisition, and it is thus unknown how new spacers are acquired and if they can be acquired from DNA phages. Here, we show that an RNA-targeting system "borrows" acquisition machinery from another CRISPR-Cas locus in the genome. Most new spacers in this locus are unable to target phage mRNA and are therefore likely redundant. Our results reveal collaboration between distinct CRISPR-Cas types and raise further questions on how other CRISPR-Cas loci may cooperate.},
}

@article {pmid33785178,
year = {2021},
author = {Jothi, R and Karthika, C and Kamaladevi, A and Satish, L and Pandian, SK and Gowrishankar, S},
title = {CRISPR based bacterial genome editing and removal of pathogens.},
journal = {Progress in molecular biology and translational science},
volume = {179},
number = {},
pages = {77-92},
doi = {10.1016/bs.pmbts.2020.12.013},
pmid = {33785178},
issn = {1878-0814},
abstract = {Engineering nucleases to achieve targeted genome editing has turned out to be a revolutionary means for manipulating the genetic content in diversified living organisms. For targeted genome editing, till to date, only three engineered nucleases exist viz. zinc finger nucleases, transcription activator-like effector nucleases and RNA-mediated nucleases (RGNs) (Cas nucleases) from the clustered regularly interspaced short palindromic repeat (CRISPR). Among, Cas9 nuclease has been considered as a simplest tool for efficient modification of endogenous genes in an extensive stretch of organisms, owing to its amenability to design guide RNA compatible to the sequence of new targets. Moreover, CRISPR/Cas system delivers a multipurpose RNA-guided DNA-targeting platform called as CRISPR interference (CRISPRi), as well as epigenetic modifications and high throughput screening in diverse organism including bacteria, all in a sequence explicit way. With these entire advancements, the present chapter illustrates the deployment of CRISPR/Cas9 in bacterial genome editing and removal of pathogens.},
}

@article {pmid33785176,
year = {2021},
author = {Arazoe, T},
title = {CRISPR-based pathogenic fungal genome editing for control of infection and disease.},
journal = {Progress in molecular biology and translational science},
volume = {179},
number = {},
pages = {161-196},
doi = {10.1016/bs.pmbts.2020.12.016},
pmid = {33785176},
issn = {1878-0814},
abstract = {Fungi play important roles in many aspects of human life, such as in various food, beverage, agricultural, chemical, and pharmaceutical industries. Meanwhile, some fungal species cause several severe diseases in plants, humans and animals. Fungal and fungal-like diseases pose a severe threat to human health, food security, and ecosystem health worldwide. This chapter introduces CRISPR-based genome editing technologies for pathogenic fungi and their application in controlling fungal diseases.},
}

@article {pmid33785175,
year = {2021},
author = {Satish, L and Lavanya, G and Kasthuri, T and Kalaivaani, A and Shamili, S and Muthuramalingam, P and Gowrishankar, S and Pandian, SK and Singh, V and Sitrit, Y and Kushmaro, A},
title = {CRISPR based development of RNA editing and the diagnostic platform.},
journal = {Progress in molecular biology and translational science},
volume = {179},
number = {},
pages = {117-159},
doi = {10.1016/bs.pmbts.2020.12.015},
pmid = {33785175},
issn = {1878-0814},
abstract = {Clustered Regularly Interspersed Short Palindromic Repeat-CRISPR-Associated (CRISPR-Cas) system has improved the ability to edit and control gene expression as desired. Genome editing approaches are currently leading the biomedical research with improved focus on direct nuclease dependent editing. So far, the research was predominantly intended on genome editing over the DNA level, recent adapted techniques are initiating to secure momentum through their proficiency to provoke modifications in RNA sequence. Integration of this system besides to lateral flow method allows reliable, quick, sensitive, precise and inexpensive diagnostic. These interesting methods illustrate only a small proportion of what is technically possible for this novel technology, but several technological obstacles need to be overcome prior to the CRISPR-Cas genome editing system can meet its full ability. This chapter covers the particulars on recent advances in CRISPR-Cas9 genome editing technology including diagnosis and technical advancements, followed by molecular mechanism of CRISPR-based RNA editing and diagnostic tools and types, and CRISPR-Cas-based biosensors.},
}

@article {pmid33785174,
year = {2021},
author = {Agarwal, N and Gupta, R},
title = {History, evolution and classification of CRISPR-Cas associated systems.},
journal = {Progress in molecular biology and translational science},
volume = {179},
number = {},
pages = {11-76},
doi = {10.1016/bs.pmbts.2020.12.012},
pmid = {33785174},
issn = {1878-0814},
abstract = {This chapter provides a detailed description of the history of CRISPR-Cas and its evolution into one of the most efficient genome-editing strategies. The chapter begins by providing information on early findings that were critical in deciphering the role of CRISPR-Cas associated systems in prokaryotes. It then describes how CRISPR-Cas had been evolved into an efficient genome-editing strategy. In the subsequent section, latest developments in the genome-editing approaches based on CRISPR-Cas are discussed. The chapter ends with the recent classification and possible evolution of CRISPR-Cas systems.},
}

@article {pmid33785173,
year = {2021},
author = {Singh, V},
title = {An introduction and use of the CRISPR-Cas systems.},
journal = {Progress in molecular biology and translational science},
volume = {179},
number = {},
pages = {1-10},
doi = {10.1016/bs.pmbts.2020.12.011},
pmid = {33785173},
issn = {1878-0814},
abstract = {Clusters of regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins (Cas) system (CRISPR-Cas) is a rapidly evolving field of targeted genome engineering. The type II CRISPR-Cas9 is used for genome editing of many organisms. Single guide RNA (sgRNA) can bind to Cas9 protein that can target desired sequences in presence of protospacer adjacent motif (PAM) sequences. This complex binds and generate a DSB that is repaired by NHEJ or HDR pathways, subsequently gene insertion/deletion (Indels) is generated that leads to change in the organism's genotype followed by its phenotype. In this chapter, CRISPR-mediated targeted genome editing in different lower organisms has been highlighted to promote its basic understanding to be applied for biotechnological, biomedical and therapeutic applications.},
}

@article {pmid33784525,
year = {2021},
author = {Griesbeck, O},
title = {CRISPR/Cas9-based directed evolution in mammalian cells.},
journal = {Current opinion in structural biology},
volume = {69},
number = {},
pages = {35-40},
doi = {10.1016/j.sbi.2021.02.005},
pmid = {33784525},
issn = {1879-033X},
abstract = {An increasingly powerful set of new CRISPR/Cas-based methods is becoming available for directed evolution of proteins in mammalian cells. Although in vitro techniques or microbial expression systems have been dominating directed evolution, there are now promising approaches to diversify proteins in mammalian cells in situ. This can be achieved by simple indel mutagenesis or more sophisticated homology repair mechanisms for cassette mutagenesis of coding sequences. Cas9 variant fusions to base editors and other effectors pose another promising way to introduce diversity into proteins. CRISPR/Cas9-based directed evolution in mammalian cells opens a new exciting era of discovery for the many classes of proteins for which a mammalian cellular context is preferable.},
}

@article {pmid33783162,
year = {2021},
author = {Zheng, X and Zheng, P and Sun, J},
title = {[CRISPR/Cas-based genome editing in Aspergillus niger].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {3},
pages = {980-990},
doi = {10.13345/j.cjb.200613},
pmid = {33783162},
issn = {1872-2075},
mesh = {Aspergillus niger/genetics ; CRISPR-Cas Systems/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Gene Editing ; Genome ; },
abstract = {Aspergillus niger is a vital industrial workhouse widely used for the production of organic acids and industrial enzymes. This fungus is a crucial cell factory due to its innate tolerance to a diverse range of abiotic conditions, high production titres, robust growth during industrial scale fermentation, and status as a generally recognized as safe (GRAS) organism. Rapid development of synthetic biology and systems biology not only offer powerful approaches to unveil the molecular mechanisms of A. niger productivity, but also provide more new strategies to construct and optimize the A. niger cell factory. As a new generation of genome editing technology, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated (Cas) system brings a revolutionary breakthrough in targeted genome modification for A. niger. In this review, we focus on current advances to the CRISPR/Cas genome editing toolbox, its application on gene modification and gene expression regulation in this fungal. Moreover, the future directions of CRISPR/Cas genome editing in A. niger are highlighted.},
}

Aspergillus niger/genetics
CRISPR-Cas Systems/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
*Gene Editing
Genome

@article {pmid33783160,
year = {2021},
author = {Li, H and Liang, X and Zhou, J},
title = {[Progress in gene editing technologies for Saccharomyces cerevisiae].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {3},
pages = {950-965},
doi = {10.13345/j.cjb.200542},
pmid = {33783160},
issn = {1872-2075},
mesh = {CRISPR-Cas Systems/genetics ; Endonucleases/genetics ; *Gene Editing ; *Saccharomyces cerevisiae/genetics ; Technology ; },
abstract = {Saccharomyces cerevisiae is one of the most important hosts in metabolic engineering. Advanced gene editing technology has been widely used in the design and construction of S. cerevisiae cell factories. With the rapid development of gene editing technology, early gene editing technologies based on recombinase and homologous recombination have been gradually replaced by new editing systems. In this review, the principle and application of gene editing technology in S. cerevisiae are summarized. Here, we first briefly describe the classical gene editing techniques of S. cerevisiae. Then elaborate the genome editing system of MegNs, ZFNs and TALENs based on endonuclease. The latest research progress is especially introduced and discussed, including the CRISPR/Cas system, multi-copy integration of heterologous metabolic pathways, and genome-scale gene editing. Finally, we envisage the application prospects and development directions of Saccharomyces cerevisiae gene editing technology.},
}

CRISPR-Cas Systems/genetics
Endonucleases/genetics
*Gene Editing
*Saccharomyces cerevisiae/genetics
Technology

@article {pmid33782402,
year = {2021},
author = {Zhang, Y and Ren, Q and Tang, X and Liu, S and Malzahn, AA and Zhou, J and Wang, J and Yin, D and Pan, C and Yuan, M and Huang, L and Yang, H and Zhao, Y and Fang, Q and Zheng, X and Tian, L and Cheng, Y and Le, Y and McCoy, B and Franklin, L and Selengut, JD and Mount, SM and Que, Q and Zhang, Y and Qi, Y},
title = {Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1944},
pmid = {33782402},
issn = {2041-1723},
mesh = {Agrobacterium tumefaciens ; Alleles ; Arabidopsis/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; CRISPR-Associated Protein 9/genetics/metabolism ; CRISPR-Associated Proteins/*genetics/metabolism ; *CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Crops, Agricultural ; Endodeoxyribonucleases/*genetics/metabolism ; Gene Editing/*methods ; Genetic Engineering/*methods ; *Genome, Plant ; Humans ; Isoenzymes/genetics/metabolism ; Oryza/*genetics/metabolism ; Plants, Genetically Modified ; RNA, Guide/genetics/metabolism ; Sequence Alignment ; },
abstract = {CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expand the targeting scope of Cas12a, we screen nine Cas12a orthologs that have not been demonstrated in plants, and identify six, ErCas12a, Lb5Cas12a, BsCas12a, Mb2Cas12a, TsCas12a and MbCas12a, that possess high editing activity in rice. Among them, Mb2Cas12a stands out with high editing efficiency and tolerance to low temperature. An engineered Mb2Cas12a-RVRR variant enables editing with more relaxed PAM requirements in rice, yielding two times higher genome coverage than the wild type SpCas9. To enable large-scale genome engineering, we compare 12 multiplexed Cas12a systems and identify a potent system that exhibits nearly 100% biallelic editing efficiency with the ability to target as many as 16 sites in rice. This is the highest level of multiplex edits in plants to date using Cas12a. Two compact single transcript unit CRISPR-Cas12a interference systems are also developed for multi-gene repression in rice and Arabidopsis. This study greatly expands the targeting scope of Cas12a for crop genome engineering.},
}

Agrobacterium tumefaciens
Alleles
Arabidopsis/*genetics/metabolism
Bacterial Proteins/*genetics/metabolism
Base Sequence
CRISPR-Associated Protein 9/genetics/metabolism
CRISPR-Associated Proteins/*genetics/metabolism
*CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Crops, Agricultural
Endodeoxyribonucleases/*genetics/metabolism
Gene Editing/*methods
Genetic Engineering/*methods
*Genome, Plant
Humans
Isoenzymes/genetics/metabolism
Oryza/*genetics/metabolism
Plants, Genetically Modified
RNA, Guide/genetics/metabolism
Sequence Alignment

@article {pmid33782125,
year = {2021},
author = {France, MG and Enderle, J and Röhrig, S and Puchta, H and Franklin, FCH and Higgins, JD},
title = {ZYP1 is required for obligate cross-over formation and cross-over interference in Arabidopsis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {14},
pages = {},
doi = {10.1073/pnas.2021671118},
pmid = {33782125},
issn = {1091-6490},
abstract = {The synaptonemal complex is a tripartite proteinaceous ultrastructure that forms between homologous chromosomes during prophase I of meiosis in the majority of eukaryotes. It is characterized by the coordinated installation of transverse filament proteins between two lateral elements and is required for wild-type levels of crossing over and meiotic progression. We have generated null mutants of the duplicated Arabidopsis transverse filament genes zyp1a and zyp1b using a combination of T-DNA insertional mutants and targeted CRISPR/Cas mutagenesis. Cytological and genetic analysis of the zyp1 null mutants reveals loss of the obligate chiasma, an increase in recombination map length by 1.3- to 1.7-fold and a virtual absence of cross-over (CO) interference, determined by a significant increase in the number of double COs. At diplotene, the numbers of HEI10 foci, a marker for Class I interference-sensitive COs, are twofold greater in the zyp1 mutant compared to wild type. The increase in recombination in zyp1 does not appear to be due to the Class II interference-insensitive COs as chiasmata were reduced by ∼52% in msh5/zyp1 compared to msh5 These data suggest that ZYP1 limits the formation of closely spaced Class I COs in Arabidopsis Our data indicate that installation of ZYP1 occurs at ASY1-labeled axial bridges and that loss of the protein disrupts progressive coalignment of the chromosome axes.},
}

@article {pmid33782110,
year = {2021},
author = {Liu, J and Cvirkaite-Krupovic, V and Baquero, DP and Yang, Y and Zhang, Q and Shen, Y and Krupovic, M},
title = {Virus-induced cell gigantism and asymmetric cell division in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {15},
pages = {},
doi = {10.1073/pnas.2022578118},
pmid = {33782110},
issn = {1091-6490},
abstract = {Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.},
}

@article {pmid33779839,
year = {2021},
author = {Bouchaut, B and Asveld, L},
title = {Responsible Learning About Risks Arising from Emerging Biotechnologies.},
journal = {Science and engineering ethics},
volume = {27},
number = {2},
pages = {22},
pmid = {33779839},
issn = {1471-5546},
support = {15809//Stichting voor de Technische Wetenschappen/ ; },
abstract = {Genetic engineering techniques (e.g., CRISPR-Cas) have led to an increase in biotechnological developments, possibly leading to uncertain risks. The European Union aims to anticipate these by embedding the Precautionary Principle in its regulation for risk management. This principle revolves around taking preventive action in the face of uncertainty and provides guidelines to take precautionary measures when dealing with important values such as health or environmental safety. However, when dealing with 'new' technologies, it can be hard for risk managers to estimate the societal or environmental consequences of a biotechnology that might arise once introduced or embedded in society due to that these sometimes do not comply with the established norms within risk assessment. When there is insufficient knowledge, stakeholders active in early developmental stages (e.g., researchers) could provide necessary knowledge by conducting research specifically devoted to what these unknown risks could entail. In theory, the Safe-by-Design (SbD) approach could enable such a controlled learning environment to gradually identify what these uncertain risks are, to which we refer as responsible learning. In this paper, we argue that three conditions need to be present to enable such an environment: (1) regulatory flexibility, (2) co-responsibility between researchers and regulators, and (3) openness towards all stakeholders. If one of these conditions would not be present, the SbD approach cannot be implemented to its fullest potential, thereby limiting an environment for responsible learning and possibly leaving current policy behind to anticipate uncertain risks.},
}

@article {pmid33774733,
year = {2021},
author = {Singh, R and Chandel, S and Ghosh, A and Dey, D and Chakravarti, R and Roy, S and Ravichandiran, V and Ghosh, D},
title = {Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33774733},
issn = {1559-0305},
support = {BT/PR26301/GET/119/258/2017//DBT, Govt. of India/ ; BT/P/Budget/RD-74/2017//WBDBT/ ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas protein technology area is rapidly growing technique for genome editing and modulation of transcription of several microbes. Successful engineering in microbes requires an emphasis on the aspect of efficiency and targeted aiming, which can be employed using CRISPR/Cas system. Hence, this type of system is used to modify the genome of several microbes such as yeast and bacteria. In recent years, CRISPR/Cas systems have been chosen for metabolic engineering in microbes due to their specificity, orthogonality, and efficacy. Therefore, we need to review the scheme which was acquired for the execution of the CRISPR/Cas system for the modification and metabolic engineering in yeast and bacteria. In this review, we highlighted the application of the CRISPR/Cas system which has been used for the production of small molecules in the microbial system that is chemically and biologically important.},
}

@article {pmid33774312,
year = {2021},
author = {El Ouar, I and Djekoun, A},
title = {Therapeutic and diagnostic relevance of Crispr technology.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {138},
number = {},
pages = {111487},
doi = {10.1016/j.biopha.2021.111487},
pmid = {33774312},
issn = {1950-6007},
abstract = {CRISPR is a family of DNA repeats providing immunity against viral and plasmid invading DNA in bacteria and archaea. The system consist of an endonuclease Cas, guided by a RNA sequence, able to cleave the DNA double strand at a specific site. The discovery of Crispr function in 2007 has revolutionized genetic engineering by giving to the world the most powerful and precise tool for targeted genome editing. The aim of this review is to synthesize the current knowledge on Crispr/cas system and its application in biomedical field. In particular, we focus on the relevance of this new tool in progressing our comprehension for biological mechanisms and improving our ability to treat and prevent genetic diseases, to control microbial virulence and to generate animal models for basic and clinical research. We discuss also the ethical issues that may prevent the application of Crispr technology in living beings.},
}

@article {pmid33774158,
year = {2021},
author = {Hao, L and Pu, X and Song, J},
title = {Introduction of mutations in plants with prime editing.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2021.03.014},
pmid = {33774158},
issn = {1095-9130},
abstract = {The emergence of a clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas) system has had a revolutionary impact on plant biology. However, this system and further developed base editing are limited by their inherent imperfection. Prime editing, a just arrival technology based on CRISPR/Cas, can directly and precisely edit a specified DNA site without double strand breaks and donor DNA by integrating an engineered reverse transcriptase (RT) with a catalytically impaired Cas9 endonuclease and introducing genetic information into prime editing guide RNA (pegRNA). In addition, it has a wider range of editing types than base editing and can install all types of editing theoretically. Prime editing was originally developed in mammalian cells and has recently been applied to plants. Here, we describe the origin of prime editing and compare it with traditional CRISPR/Cas9 and base editing; then, we exemplify it in plants, including strategies and methods. Accordingly, we generate the overall procedures of prime editing to provide instructions for its application. Furthermore, we summarize its improvements in the approach, such as optimizing the length of a primer binding site and RT template, as well as pursuing an optimal nicking site in the unedited sequence. Finally, we discuss the potential impact on domestication and improvement of agricultural crops, sustainable utilization of medicinal plants, cultivation of varieties of horticultural plants, and revelation of the genetic code, in order to offer a reference for the further study and development of prime editing.},
}

@article {pmid33774156,
year = {2021},
author = {Yang, L and Tang, J and Ma, X and Lin, Y and Ma, G and Shan, M and Wang, L and Yang, Y},
title = {Progression and application of CRISPR-Cas genomic editors.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2021.03.013},
pmid = {33774156},
issn = {1095-9130},
abstract = {Base editing technology is an efficient tool for genome editing, particularly in the correction of base mutations. Diverse base editing systems were developed according to the dCas9 or nCas9 linked with different deaminase or reverse transcriptase in the editors, including ABEs, CBEs, PEs and dual-functional of base editor (such as CGBE1, A&C-BEmax, ACBE, etc.). Currently, Base editing technology has been widely applied to various fields such as microorganisms, plants, animals and medicine for basic research and therapeutics. Here, we reviewed the advancement of base editing technology. We also discussed the application of base editors in different areas in the future.},
}

@article {pmid33771254,
year = {2021},
author = {Shi, L and Li, W and Dong, Y and Shi, Y and Zhou, Y and Liao, X},
title = {NADPH-cytochrome P450 reductase potentially involved in indoxacarb resistance in Spodoptera litura.},
journal = {Pesticide biochemistry and physiology},
volume = {173},
number = {},
pages = {104775},
doi = {10.1016/j.pestbp.2021.104775},
pmid = {33771254},
issn = {1095-9939},
mesh = {Animals ; *Insecticide Resistance/genetics ; *NADPH-Ferrihemoprotein Reductase/genetics ; Oxazines ; Spodoptera/genetics ; },
abstract = {NADPH-cytochrome P450 reductase (CPR) plays a central role in the metabolism of insecticides. Numerous studies have shown that CPR is associated with insecticide resistance in insect. In this study, two transcripts of Spodoptera litura CPR (SlCPR-X1 and SlCPR-X2) were identified and cloned, and the deduced protein of SlCPR-X1 contains all the conserved CPR structural features (N-terminal membrane anchor, FMN, FAD and NADP binding domains, FAD binding motif, and catalytic residues). However, no N-terminal member anchor and a shorter FMN binding region have been identified in the deduced protein of SlCPR-X2. The specific expression patterns showed that SlCPR-X1 and SlCPR-X2 were detected in all tested developmental stages and tissues, but highly expressed in third-, fourth-, and fifth-instar larvae, and in midgut and fat body. In addition, compared with the susceptible strain, SlCPR-X1 and SlCPR-X2 were up-regulated and more inducible when treated with indoxacarb in the indoxacarb-resistant strain. However, the relative expression, up-regulation and induction of SlCPR-X1 were all higher than those of SlCPR-X2 in the indoxacarb-resistant strain. Furthermore, RNA interference and baculovirus expression system combined with MTT cytotoxicity assay demonstrated that only SlCPR-X1 with the N-terminal membrane anchor as the major CPR potentially involved in S. litura indoxacarb resistance. The outcome of this study further expands our understanding of the important role of insect CPR in xenobiotics detoxification and resistance development, and CPR could be a potential target for insecticide resistance management mediated by RNAi or CRISPR/Cas.},
}

Animals
*Insecticide Resistance/genetics
*NADPH-Ferrihemoprotein Reductase/genetics
Oxazines
Spodoptera/genetics

@article {pmid33770071,
year = {2021},
author = {Pavlova, YS and Paez-Espino, D and Morozov, AY and Belalov, IS},
title = {Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.},
journal = {PLoS computational biology},
volume = {17},
number = {3},
pages = {e1008841},
doi = {10.1371/journal.pcbi.1008841},
pmid = {33770071},
issn = {1553-7358},
abstract = {Understanding CRISPR-Cas systems-the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks-is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical 'rich-get-richer' mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.},
}

@article {pmid33767677,
year = {2021},
author = {Wang, Y and Ji, Q and Li, S and Liu, M},
title = {Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {620482},
pmid = {33767677},
issn = {1664-302X},
abstract = {Listeria monocytogenes is a ubiquitous bacteria and causative agent of zoonotic listeriosis with high mortality. The consumption of contaminated animal-derived foods has been linked with both epidemic and sporadic listeriosis. In this work, a total of 64 L. monocytogenes isolates from 259 pork samples sold in 11 supermarket chains were identified and characterized by comparative whole-genome analysis. All isolates were delineated into eight clonal complexes (CCs), namely CC2, CC8, CC9, CC11, CC155, CC121, CC204, and CC619, spanning two lineages (I and II) and carrying 3-5 antibiotic-resistant genes (fosX, lnu, mprF, tetM, and dhfR). It is noted that Listeria pathogenicity island (LIPI)-1, LIPI-3, and LIPI-4 were distributed in all ST619 isolates from two supermarket chains that were closely related with clinical isolates (<40 SNP). Some of the isolates from different supermarket chains with 0 SNP difference indicated a common pork supply source. Notably, 57.81% of the strains carried types IB, IIA, or IIIB CRISPR-Cas system, CC121 isolates carried both types IB and IIA CRISPR-Cas systems, Cas proteins of CC155 isolates located between two CRISPR loci, each CC has unique organization of Cas proteins as well as CRISPR loci. CRISPR-Cas system-based subtyping improved discrimination of pork-derived L. monocytogenes isolates. Comparisons at the genome level contributed to understand the genetic diversities and variations among the isolates and provided insights into the genetic makeup and relatedness of these pathogens.},
}

@article {pmid33766108,
year = {2021},
author = {Keller-Costa, T and Lago-Lestón, A and Saraiva, JP and Toscan, R and Silva, SG and Gonçalves, J and Cox, CJ and Kyrpides, N and Nunes da Rocha, U and Costa, R},
title = {Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {72},
pmid = {33766108},
issn = {2049-2618},
abstract = {BACKGROUND: In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella.

RESULTS: Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system.

CONCLUSIONS: This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.},
}

@article {pmid33765408,
year = {2021},
author = {Chakraborty, D and Agrawal, A and Maiti, S},
title = {Rapid identification and tracking of SARS-CoV-2 variants of concern.},
journal = {Lancet (London, England)},
volume = {397},
number = {10282},
pages = {1346-1347},
doi = {10.1016/S0140-6736(21)00470-0},
pmid = {33765408},
issn = {1474-547X},
}

@article {pmid33764459,
year = {2021},
author = {Meng, F and Zhao, H and Zhu, B and Zhang, T and Yang, M and Li, Y and Han, Y and Jiang, J},
title = {Genomic Editing of Intronic Enhancers Unveils Their Role in Fine-Tuning Tissue-Specific Gene Expression in Arabidopsis thaliana.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koab093},
pmid = {33764459},
issn = {1532-298X},
abstract = {Enhancers located in introns are abundant and play a major role in the regulation of gene expression in mammalian species. By contrast, the functions of intronic enhancers in plants have largely been unexplored and only a handful of plant intronic enhancers have been reported and characterized. We performed a genome-wide prediction of intronic enhancers in Arabidopsis thaliana using open chromatin signatures based on DNase I sequencing. We identified 941 candidate intronic enhancers associated with 806 genes in seedling tissue and 1,271 intronic enhancers associated with 1,069 genes in floral tissue. We validated the function of 15 of 21 (71%) of the predicted intronic enhancers in transgenic assays using a reporter gene. We also created deletion lines of three intronic enhancers associated with two different genes using CRISPR/Cas. Deletion of these enhancers, which span key transcription factor binding sites, did not abolish gene expression but caused varying levels of transcriptional repression of their cognate genes. Remarkably, the transcriptional repression of the deletion lines occurred at specific developmental stages and resulted in distinct phenotypic effects on plant morphology and development. Clearly, these three intronic enhancers are important in fine-tuning tissue- and development-specific expression of their cognate genes.},
}

@article {pmid33764415,
year = {2021},
author = {Xiao, R and Li, Z and Wang, S and Han, R and Chang, L},
title = {Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR-Cas12f nuclease.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkab179},
pmid = {33764415},
issn = {1362-4962},
abstract = {Cas12f, also known as Cas14, is an exceptionally small type V-F CRISPR-Cas nuclease that is roughly half the size of comparable nucleases of this type. To reveal the mechanisms underlying substrate recognition and cleavage, we determined the cryo-EM structures of the Cas12f-sgRNA-target DNA and Cas12f-sgRNA complexes at 3.1 and 3.9 Å, respectively. An asymmetric Cas12f dimer is bound to one sgRNA for recognition and cleavage of dsDNA substrate with a T-rich PAM sequence. Despite its dimerization, Cas12f adopts a conserved activation mechanism among the type V nucleases which requires coordinated conformational changes induced by the formation of the crRNA-target DNA heteroduplex, including the close-to-open transition in the lid motif of the RuvC domain. Only one RuvC domain in the Cas12f dimer is activated by substrate recognition, and the substrate bound to the activated RuvC domain is captured in the structure. Structure-assisted truncated sgRNA, which is less than half the length of the original sgRNA, is still active for target DNA cleavage. Our results expand our understanding of the diverse type V CRISPR-Cas nucleases and facilitate potential genome editing applications using the miniature Cas12f.},
}

@article {pmid33762831,
year = {2021},
author = {Oishee, MJ and Ali, T and Jahan, N and Khandker, SS and Haq, MA and Khondoker, MU and Sil, BK and Lugova, H and Krishnapillai, A and Abubakar, AR and Kumar, S and Haque, M and Jamiruddin, MR and Adnan, N},
title = {COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools.},
journal = {Infection and drug resistance},
volume = {14},
number = {},
pages = {1049-1082},
pmid = {33762831},
issn = {1178-6973},
abstract = {Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.},
}

@article {pmid33760341,
year = {2021},
author = {Jungblut, AD and Raymond, F and Dion, MB and Moineau, S and Mohit, V and Nguyen, GQH and Deraspe, M and Francovic-Fontaine, E and Lovejoy, C and Culley, AI and Corbeil, J and Vincent, WF},
title = {Genomic diversity and CRISPR-Cas systems in the cyanobacterium Nostoc in the High Arctic.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15481},
pmid = {33760341},
issn = {1462-2920},
abstract = {Nostoc (Nostocales, Cyanobacteria) has a global distribution in the Polar Regions. However, the genomic diversity of Nostoc is little known and there are no genomes available for polar Nostoc. Here we carried out the first genomic analysis of the N. commune morphotype with a recent sample from the High Arctic and a herbarium specimen collected during the British Arctic Expedition (1875-76). Comparisons of the polar genomes with 26 present-day non-polar members of the Nostocales family highlighted that there are pronounced genetic variations among Nostoc strains and species. Osmoprotection and other stress genes were found in all Nostoc strains, but the two Arctic strains had markedly higher numbers of biosynthetic gene clusters for uncharacterised nonribosomal peptide synthetases, suggesting a high diversity of secondary metabolites. Since viral-host interactions contribute to microbial diversity, we analysed the CRISPR-Cas systems in the Arctic and two temperate Nostoc species. There were a large number of unique repeat-spacer arrays in each genome, indicating diverse histories of viral attack. All Nostoc strains had a subtype I-D system, but the polar specimens also showed evidence of a subtype I-B system that has not been previously reported in cyanobacteria, suggesting diverse cyanobacteria-virus interactions in the Arctic. This article is protected by copyright. All rights reserved.},
}

@article {pmid33756158,
year = {2021},
author = {Zhou, W and Wang, X},
title = {Human gene therapy: A scientometric analysis.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {138},
number = {},
pages = {111510},
doi = {10.1016/j.biopha.2021.111510},
pmid = {33756158},
issn = {1950-6007},
abstract = {To provide a clear landscape, trends, and research frontiers of gene therapy, we systematically retrieved a total of 62,961 peer-viewed studies published between 1996 and 2020 from the Scopus, Web of Science, and 42,120 Inpadoc patent families from Derwent Innovation databases. Multiple bibliometric approaches suggest that gene therapy began to recover in 2013 after a period of significant decline. However, metrics in terms of authors and scholarly output growth, FWCI, annual citations, percentage of high-impact journal literature, and patent-citations per scholarly output are still weak at this stage, indicating a lack of research momentum. We also visualized gene therapy's knowledge structure by employing citation analysis, co-citation analysis, and co-word analysis, revealing its research hotspots and trends by text mining with Natural Language Processing. For the current predicament, we propose that the future success of gene therapy may depend on breakthroughs in more advanced and exhilarating technologies such as the CRISPR-Cas system, CAR-T cell therapies, and gene delivery vector technology. The results show that evidence-based bibliometrics allows the dissection of gene therapy to inform scientific planning and decision-making.},
}

@article {pmid33754804,
year = {2021},
author = {Dailey, KM and Allgood, JE and Johnson, PR and Ostlie, MA and Schaner, KC and Brooks, BD and Brooks, AE},
title = {The next frontier of oncotherapy: accomplishing clinical translation of oncolytic bacteria through genetic engineering.},
journal = {Future microbiology},
volume = {16},
number = {},
pages = {341-368},
doi = {10.2217/fmb-2020-0245},
pmid = {33754804},
issn = {1746-0921},
support = {1P20 GM109024//NIH COBRE Pilot Award/ ; },
abstract = {The development of a 'smart' drug capable of distinguishing tumor from host cells has been sought for centuries, but the microenvironment of solid tumors continues to confound therapeutics. Solid tumors present several challenges for current oncotherapeutics, including aberrant vascularization, hypoxia, necrosis, abnormally high pH and local immune suppression. While traditional chemotherapeutics are limited by such an environment, oncolytic microbes are drawn to it - having an innate ability to selectively infect, colonize and eradicate solid tumors. Development of an oncolytic species would represent a shift in the cancer therapeutic paradigm, with ramifications reaching from the medical into the socio-economic. Modern genetic engineering techniques could be implemented to customize 'Frankenstein' bacteria with advantageous characteristics from several species.},
}

@article {pmid33754170,
year = {2021},
author = {Meliawati, M and Schilling, C and Schmid, J},
title = {Recent advances of Cas12a applications in bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33754170},
issn = {1432-0614},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome engineering and related technologies have revolutionized biotechnology over the last decade by enhancing the efficiency of sophisticated biological systems. Cas12a (Cpf1) is an RNA-guided endonuclease associated to the CRISPR adaptive immune system found in many prokaryotes. Contrary to its more prominent counterpart Cas9, Cas12a recognizes A/T rich DNA sequences and is able to process its corresponding guide RNA directly, rendering it a versatile tool for multiplex genome editing efforts and other applications in biotechnology. While Cas12a has been extensively used in eukaryotic cell systems, microbial applications are still limited. In this review, we highlight the mechanistic and functional differences between Cas12a and Cas9 and focus on recent advances of applications using Cas12a in bacterial hosts. Furthermore, we discuss advantages as well as current challenges and give a future outlook for this promising alternative CRISPR-Cas system for bacterial genome editing and beyond. KEY POINTS: • Cas12a is a powerful tool for genome engineering and transcriptional perturbation • Cas12a causes less toxic side effects in bacteria than Cas9 • Self-processing of crRNA arrays facilitates multiplexing approaches.},
}

@article {pmid33753124,
year = {2021},
author = {Waldt, N and Kesseler, C and Fala, P and John, P and Kirches, E and Angenstein, F and Mawrin, C},
title = {Crispr/Cas-based modeling of NF2 loss in meningioma cells.},
journal = {Journal of neuroscience methods},
volume = {356},
number = {},
pages = {109141},
doi = {10.1016/j.jneumeth.2021.109141},
pmid = {33753124},
issn = {1872-678X},
abstract = {BACKGROUND: Alterations of the neurofibromatosis type 2 gene (NF2) occur in more than fifty percent of sporadic meningiomas. Meningiomas develop frequently in the setting of the hereditary tumor syndrome NF2. Investigation of potential drug-based treatment options has been limited by the lack of appropriate in vitro and in vivo models.

NEW METHODS: Using Crispr/Cas gene editing, of the malignant meningioma cell line IOMM-Lee, we generated a pair of cell clones characterized by either stable knockout of NF2 and loss of the protein product merlin or retained merlin protein (transfected control without gRNA).

RESULTS: IOMM-Lee cells lacking NF2 showed reduced apoptosis and formed bigger colonies compared to control IOMM-Lee cells. Treatment of non-transfected IOMM-Lee cells with the focal adhesion kinase (FAK) inhibitor GSK2256098 resulted in reduced colony sizes. Orthotopic mouse xenografts showed the formation of convexity tumors typical for meningiomas with NF2-depleted and control cells.

No orthotopic meningioma models with genetically-engineered cell pairs are available so far.

CONCLUSION: Our model based on Crispr/Cas-based gene editing provides paired meningioma cells suitable to study functional consequences and therapeutic accessibility of NF2/merlin loss.},
}

@article {pmid33751147,
year = {2021},
author = {de Oliveira Luz, AC and da Silva Junior, WJ and do Nascimento Junior, JB and da Silva, JMA and de Queiroz Balbino, V and Leal-Balbino, TC},
title = {Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems.},
journal = {Current genetics},
volume = {},
number = {},
pages = {},
pmid = {33751147},
issn = {1432-0983},
support = {404016/2016-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-0836-2.02/16//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; VPPCB-007-FIO-18-2-99//Fundação Oswaldo Cruz/ ; },
abstract = {The CRISPR-Cas are adaptive immune systems found in archaea and bacteria, responsible for providing sequence-specific resistance against foreign DNA. Strains of Pseudomonas aeruginosa may carry CRISPR/Cas system types I-F, I-E and/or I-C; however, several aspects related to the epidemiology and functionality of these systems have not yet been revealed. Here, we report 13 genomes of clinical strains of P. aeruginosa from Brazil that were positive for CRISPR/Cas system types I-F and I-E, a rare feature in this species. The phylogenetic tree, which was constructed with 161 other publicly available genomes, suggested no direct relationship between positive strains, and the various types of CRISPR/Cas systems were spread throughout the tree. Comparative analysis of the genetic locations of type I-F and a specific orphan CRISPR array (without cas genes), named the LES locus, showed sequence similarities between this orphan locus and type I-F, but these LES loci were inserted in a different genomic location. We also report the presence of prophages, the presence of anti-CRISPR genes, and possibly the presence of self-targeting spacers. Here, we conclude that CRISPR/Cas is highly associated with certain lineages and is spread throughout the phylogenetic tree, showing no clear pattern of evolutionary distribution. Moreover, the LES locus might be a CRISPR1 locus related to type I-F that may have been misplaced and maintained over time. Furthermore, strains carrying I-F and I-E are rare, and not all of them are closely related. Further functional work is needed to better comprehend if aspects reported in this study are functional, including the LES locus, self-targeting spacers, anti-CRISPR protection, and I-F/I-E-carrying lineages.},
}

@article {pmid33750221,
year = {2021},
author = {Dasgupta, I and Flotte, TR and Keeler, AM},
title = {CRISPR/Cas-Dependent and Nuclease-Free In Vivo Therapeutic Gene Editing.},
journal = {Human gene therapy},
volume = {32},
number = {5-6},
pages = {275-293},
pmid = {33750221},
issn = {1557-7422},
abstract = {Precise gene manipulation by gene editing approaches facilitates the potential to cure several debilitating genetic disorders. Gene modification stimulated by engineered nucleases induces a double-stranded break (DSB) in the target genomic locus, thereby activating DNA repair mechanisms. DSBs triggered by nucleases are repaired either by the nonhomologous end-joining or the homology-directed repair pathway, enabling efficient gene editing. While there are several ongoing ex vivo genome editing clinical trials, current research underscores the therapeutic potential of CRISPR/Cas-based (clustered regularly interspaced short palindrome repeats-associated Cas nuclease) in vivo gene editing. In this review, we provide an overview of the CRISPR/Cas-mediated in vivo genome therapy applications and explore their prospective clinical translatability to treat human monogenic disorders. In addition, we discuss the various challenges associated with in vivo genome editing technologies and strategies used to circumvent them. Despite the robust and precise nuclease-mediated gene editing, a promoterless, nuclease-independent gene targeting strategy has been utilized to evade the drawbacks of the nuclease-dependent system, such as off-target effects, immunogenicity, and cytotoxicity. Thus, the rapidly evolving paradigm of gene editing technologies will continue to foster the progress of gene therapy applications.},
}