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Bibliography on: History of Genetics

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ESP: PubMed Auto Bibliography 18 Apr 2021 at 01:37 Created: 

History of Genetics

Created with PubMed® Query: "Genetics/*history"[MESH] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-04-16
CmpDate: 2021-04-16

Weake VM (2021)

Gcn5: The quintessential histone acetyltransferase.

Biochimica et biophysica acta. Gene regulatory mechanisms, 1864(2):194658.

RevDate: 2021-04-01
CmpDate: 2021-04-01

Bruckner-Tuderman L (2020)

ESDR around the Millennium Change.

The Journal of investigative dermatology, 140(9S):S158-S159.

RevDate: 2021-04-01
CmpDate: 2021-04-01

Cramer P (2020)

Rosalind Franklin and the Advent of Molecular Biology.

Cell, 182(4):787-789.

Rosalind Franklin provided the key data for deriving the double helix structure of DNA. The English chemist also pioneered structural studies of colloids, viruses, and RNA. To celebrate the 100th anniversary of Franklin's birth, I summarize her work, which shaped the emerging discipline of molecular biology.

RevDate: 2021-04-01
CmpDate: 2021-04-01

Tomáška Ľ, Cesare AJ, AlTurki TM, et al (2020)

Twenty years of t-loops: A case study for the importance of collaboration in molecular biology.

DNA repair, 94:102901.

Collaborative studies open doors to breakthroughs otherwise unattainable by any one laboratory alone. Here we describe the initial collaboration between the Griffith and de Lange laboratories that led to thinking about the telomere as a DNA template for homologous recombination, the proposal of telomere looping, and the first electron micrographs of t-loops. This was followed by collaborations that revealed t-loops across eukaryotic phyla. The Griffith and Tomáška/Nosek collaboration revealed circular telomeric DNA (t-circles) derived from the linear mitochondrial chromosomes of nonconventional yeast, which spurred discovery of t-circles in ALT-positive human cells. Collaborative work between the Griffith and McEachern labs demonstrated t-loops and t-circles in a series of yeast species. The de Lange and Zhuang laboratories then applied super-resolution light microscopy to demonstrate a genetic role for TRF2 in loop formation. Recent work from the Griffith laboratory linked telomere transcription with t-loop formation, providing a new model of the t-loop junction. A recent collaboration between the Cesare and Gaus laboratories utilized super-resolution light microscopy to provide details about t-loops as protective elements, followed by the Boulton and Cesare laboratories showing how cell cycle regulation of TRF2 and RTEL enables t-loop opening and reformation to promote telomere replication. Twenty years after the discovery of t-loops, we reflect on the collective history of their research as a case study in collaborative molecular biology.

RevDate: 2021-03-31
CmpDate: 2021-03-31

Anonymous (2021)

The next 20 years of human genomics must be more equitable and more open.

Nature, 590(7845):183-184.

RevDate: 2021-03-24
CmpDate: 2021-03-24

Eichler EE (2021)

2020 William Allan Award introduction: Mary-Claire King.

American journal of human genetics, 108(3):383-385.

This article is based on the address given by the author at the 2020 virtual meeting of the American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website. Photo credit: Clare McLean.

RevDate: 2021-03-24
CmpDate: 2021-03-24

Van Houten B (2020)

Graphical snapshot of Samuel H. Wilson.

DNA repair, 93:102934.

RevDate: 2021-03-24
CmpDate: 2021-03-24

Hanawalt PC (2020)

Tribute to Sam Wilson: Shining a light on base excision DNA repair.

DNA repair, 93:102933.

RevDate: 2021-03-09
CmpDate: 2021-03-09

Powell K (2021)

The broken promise that undermines human genome research.

Nature, 590(7845):198-201.

RevDate: 2021-03-09
CmpDate: 2021-03-09

Gates AJ, Gysi DM, Kellis M, et al (2021)

A wealth of discovery built on the Human Genome Project - by the numbers.

Nature, 590(7845):212-215.

RevDate: 2021-03-09
CmpDate: 2021-03-09

Rotimi CN, AA Adeyemo (2021)

From one human genome to a complex tapestry of ancestry.

Nature, 590(7845):220-221.

RevDate: 2021-03-09
CmpDate: 2021-03-09

Miga KH (2021)

Breaking through the unknowns of the human reference genome.

Nature, 590(7845):217-218.

RevDate: 2021-03-02
CmpDate: 2021-03-02

Letarov AV (2020)

History of Early Bacteriophage Research and Emergence of Key Concepts in Virology.

Biochemistry. Biokhimiia, 85(9):1093-1010.

The viruses of bacteria - bacteriophages - were discovered 20 years after the discovery of viruses. However, this was mainly the bacteriophage research that, after the first 40 years, yielded the modern concept of the virus and to large extent formed the grounds of the emerging molecular genetics and molecular biology. Many specific aspects of the bacteriophage research history have been addressed in the existing publications. The integral outline of the events that led to the formation of the key concepts of modern virology is presented in this review. This includes the opposition of F. d'Herelle and J. Bordet viewpoints over the nature of the bacteriophage, the history of lysogeny discovery and of determination of the mechanisms of underlying this phenomenon, the work of the Phage group led by M. Delbruck in USA, the development of the genetic analysis of bacteriophages and other research that eventually led to emergence of the concept of the virus (bacteriophage) as a transmissive genetic program. The review also covers a brief history of early applications of the bacteriophages such as phage therapy and phage typing.

RevDate: 2021-02-25
CmpDate: 2021-02-25

Peixoto P, Cartron PF, Serandour AA, et al (2020)

From 1957 to Nowadays: A Brief History of Epigenetics.

International journal of molecular sciences, 21(20):.

Due to the spectacular number of studies focusing on epigenetics in the last few decades, and particularly for the last few years, the availability of a chronology of epigenetics appears essential. Indeed, our review places epigenetic events and the identification of the main epigenetic writers, readers and erasers on a historic scale. This review helps to understand the increasing knowledge in molecular and cellular biology, the development of new biochemical techniques and advances in epigenetics and, more importantly, the roles played by epigenetics in many physiological and pathological situations.

RevDate: 2021-02-23
CmpDate: 2021-02-23

Fraser CM (2021)

A genome to celebrate.

Science (New York, N.Y.), 371(6529):545.

RevDate: 2021-02-23
CmpDate: 2021-02-23

Nekrutenko A, MC Schatz (2020)

In memory of James Taylor: the birth of Galaxy.

Genome biology, 21(1):105.

RevDate: 2021-02-22
CmpDate: 2021-02-22

Guffroy A, Martin T, V Gies (2020)


La Revue de medecine interne, 41(10):649-652.

RevDate: 2021-02-16
CmpDate: 2021-02-16

Grote M, Onaga L, Creager ANH, et al (2021)

The molecular vista: current perspectives on molecules and life in the twentieth century.

History and philosophy of the life sciences, 43(1):16.

This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries to biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science.

RevDate: 2021-02-15
CmpDate: 2021-02-15

Keyser C, Zvénigorosky V, Gonzalez A, et al (2021)

Genetic evidence suggests a sense of family, parity and conquest in the Xiongnu Iron Age nomads of Mongolia.

Human genetics, 140(2):349-359.

In an effort to characterize the people who composed the groups known as the Xiongnu, nuclear and whole mitochondrial DNA data were generated from the skeletal remains of 52 individuals excavated from the Tamir Ulaan Khoshuu (TUK) cemetery in Central Mongolia. This burial site, attributed to the Xiongnu period, was used from the first century BC to the first century AD. Kinship analyses were conducted using autosomal and Y-chromosomal DNA markers along with complete sequences of the mitochondrial genome. These analyses suggested close kin relationships between many individuals. Nineteen such individuals composed a large family spanning five generations. Within this family, we determined that a woman was of especially high status; this is a novel insight into the structure and hierarchy of societies from the Xiongnu period. Moreover, our findings confirmed that the Xiongnu had a strongly admixed mitochondrial and Y-chromosome gene pools and revealed a significant western component in the Xiongnu group studied. Using a fine-scale approach (haplotype instead of haplogroup-level information), we propose Scytho-Siberians as ancestors of the Xiongnu and Huns as their descendants.

RevDate: 2021-02-08
CmpDate: 2021-02-08

Azar B (2020)

Profile of Haig H. Kazazian Jr.

Proceedings of the National Academy of Sciences of the United States of America, 117(51):32185-32188.

RevDate: 2021-02-08
CmpDate: 2021-02-08

Anonymous (2020)

Frans H. J. Claas, PhD, Eurotransplant Reference Laboratory, Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands.

Transplantation, 104(12):2461-2463.

RevDate: 2021-02-08
CmpDate: 2021-02-08

Turda M (2020)

Subversive affinities: Embracing soviet science in late 1940s Romania.

Studies in history and philosophy of biological and biomedical sciences, 83:101131.

This article discusses the appropriation of Soviet science in Romania during the late 1940s. To achieve this, I discuss various publications on biology, anthropology, heredity and genetics. In a climate of major political change, following the end of the Second World War, all scientific fields in Romania were gradually subjected to political pressures to adapt and change according to a new ideological context. Yet the adoption of Soviet science during the late 1940s was not a straightforward process of scientific acculturation. Whilst the deference to Soviet authors remained consistent through most of Romanian scientific literature at the time, what is perhaps less visible is the attempt to refashion Romanian science itself in order to serve the country's new political imaginary and social transformation. Some Romanian biologists and physicians embraced Soviet scientific theories as a demonstration of their loyalty to the newly established regime. Others, however, were remained committed to local and Western scientific traditions they deemed essential to the survival of their discipline. A critical reassessment of the late 1940s is essential to an understanding of these dissensions as well as of the overall political and institutional constraints shaping the development of a new politics of science in communist Romania.

RevDate: 2021-02-03
CmpDate: 2021-02-03

Rustgi S, B Skadhauge (2020)

Diter von Wettstein, Professor of Genetics and Master of Translating Science into Applications.

Methods in molecular biology (Clifton, N.J.), 2124:3-18.

The present and subsequent chapters in this volume are dedicated to the life and research of Professor Diter von Wettstein who contributed immensely to the development of science and education. His contributions spanned various fields of science such as genetics, physiology, ultrastructural analysis, molecular biology, genomics, and biotechnology including genome editing. He performed and promoted pioneering research in the fields of epigenetics, directed evolution of enzymes, synthetic biology (promoter and gene optimizations), and genomics (genome sequencing of baker's yeast). Glimpses of his time at the Carlsberg Laboratory and Washington State University, with examples from the research performed at these institutions, are included in this chapter. His life is an inspiration to the next generation of biologists. Despite difficult situations, his persistent efforts and keen desire to learn enabled him to overcome obstacles. He always tried to attain the best, excelling in translating fundamental knowledge into applications.

RevDate: 2021-02-02
CmpDate: 2021-02-02

Li Wan Po A (2020)

Genomic research delivering on promises: From rejuvenation to vaccines and pharmacogenetics.

Journal of clinical pharmacy and therapeutics, 45(3):585-589.

WHAT IS KNOWN AND OBJECTIVE: There has been astounding progress made in the treatment of disease over recent years. This progress is particularly marked in cell therapy and in the personalization of therapy based on genetic insight, an approach known as genomic medicine. Our objective is to comment on the progress made in cell and genomic medicine against an historical backcloth of the search for rejuvenation.

COMMENT: In 1741, close to seven decades after Antoine van Leeuwenhoek first saw his microscopic animalcules, Abraham Trembley, a tutor in Leiden, reported on an organism that could regenerate itself. The strange organism was thought to hold the secret of life. If it does, we have yet to prise the secret out. However, the ensuing study of cell programming and induced stem cells has shed considerable light on cellular development and provided new insights on the rejuvenative capacity of organisms. Inventive scientists have provided a deeper understanding of cell replication and, from this, developed new medicines for an increasing range of diseases. Targeted therapies, oligonucleotide therapy, therapeutic monoclonal antibodies and pharmacogenetics are all new therapeutic areas originating from the improved insights. More will surely follow.

WHAT IS NEW AND CONCLUSION: Immortality is for the gods, but man's search for its elusive secrets, perhaps as old as man himself, will continue. Huge leaps have been made, and effective medicines have been developed from our improved insights into the mechanism of life. However, only the foolish will predict how far this new knowledge will lead us, and more particularly, at what speed new therapies will follow.

RevDate: 2021-02-01
CmpDate: 2021-02-01

Lee SH, Kim DH, Kuzmanov U, et al (2021)

Membrane proteomic profiling of the heart: past, present, and future.

American journal of physiology. Heart and circulatory physiology, 320(1):H417-H423.

Cardiovascular diseases remain the most rapidly rising contributing factor of all-cause mortality and the leading cause of inpatient hospitalization worldwide, with costs exceeding $30 billion annually in North America. Cell surface and membrane-associated proteins play an important role in cardiomyocyte biology and are involved in the pathogenesis of many human heart diseases. In cardiomyocytes, membrane proteins serve as critical signaling receptors, Ca2+ cycling regulators, and electrical propagation regulators, all functioning in concert to maintain spontaneous and synchronous contractions of cardiomyocytes. Membrane proteins are excellent pharmaceutical targets due to their uniquely exposed position within the cell. Perturbations in cardiac membrane protein localization and function have been implicated in the progression and pathogenesis of many heart diseases. However, previous attempts at profiling the cardiac membrane proteome have yielded limited results due to poor technological developments for isolating hydrophobic, low-abundance membrane proteins. Comprehensive mapping and characterization of the cardiac membrane proteome thereby remains incomplete. This review will focus on recent advances in mapping the cardiac membrane proteome and the role of novel cardiac membrane proteins in the healthy and the diseased heart.

RevDate: 2021-01-21
CmpDate: 2021-01-21

Collins FS, Doudna JA, Lander ES, et al (2021)

Human Molecular Genetics and Genomics - Important Advances and Exciting Possibilities.

The New England journal of medicine, 384(1):1-4.

RevDate: 2021-01-21
CmpDate: 2021-01-21

Ravindran S (2020)

Profile of Se-Jin Lee.

Proceedings of the National Academy of Sciences of the United States of America, 117(49):30870-30872.

RevDate: 2021-01-15
CmpDate: 2021-01-15

Viegas J (2020)

Profile of Masayori Inouye.

Proceedings of the National Academy of Sciences of the United States of America, 117(46):28543-28545.

RevDate: 2021-01-04
CmpDate: 2021-01-04

Anava S, Neuhof M, Gingold H, et al (2020)

Illuminating Genetic Mysteries of the Dead Sea Scrolls.

Cell, 181(6):1218-1231.e27.

The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together" scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint" pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.

RevDate: 2020-12-30
CmpDate: 2020-12-30

Morris CB, Poland JC, May JC, et al (2020)

Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules.

Methods in molecular biology (Clifton, N.J.), 2084:1-31.

Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.

RevDate: 2020-12-21
CmpDate: 2020-12-21

Verdin E (2020)

Paolo Sassone-Corsi (1956-2020).

Science (New York, N.Y.), 370(6516):532.

RevDate: 2020-12-16
CmpDate: 2020-12-16

Anonymous (2020)

Education, Experience, and Action: An Interview with Dr. Trevor K. Archer.

Molecular cell, 80(5):749-751.

We asked Dr. Archer about his experiences in academia, struggles he has faced, and thoughts on addressing racial bias. We hope that this series sparks a larger discussion of issues faced by underrepresented scientists and ways the scientific community can foster diversity and better support underrepresented scientists. The opinions expressed here are those of Dr. Archer and not the NIH/NIEHS or the US government.

RevDate: 2020-12-14
CmpDate: 2020-12-14

Anonymous (2020)

Marking a milestone.

Nature reviews. Genetics, 21(10):573.

RevDate: 2020-12-14
CmpDate: 2020-12-10

Lodish HF (2020)

Over 60 Years of Experimental Hematology (without a License).

Experimental hematology, 89:1-12.

I am deeply honored to receive the International Society for Experimental Hematology (ISEH) 2020 Donald Metcalf Lecture Award. Although I am not a physician and have had no formal training in hematology, I have had the privilege of working with some of the top hematologists in the world, beginning in 1970 when Dr. David Nathan was a sabbatical visitor in my laboratory and introduced me to hematological diseases. And I take this award to be given not just to me but to an exceptional group of MD and PhD trainees and visitors in my laboratory who have cloned and characterized many proteins and RNAs important for red cell development and function. Many of these projects involved taking exceptionally large risks in developing and employing novel experimental technologies. Unsurprisingly, all of these trainees have gone on to become leaders in hematology and, more broadly, in molecular cell biology and molecular medicine. To illustrate some of the challenges we have faced and the technologies we had to develop, I have chosen several of our multiyear projects to describe in some detail: elucidating the regulation of translation of α- and β-globin mRNAs and the defect in beta thalassemia in the 1970s; cloning the Epo receptor and several red cell membrane proteins in the 1980s and 1990s; and more recently, determining the function of many microRNAs and long noncoding RNAs in red cell development. I summarize how we are currently utilizing single-cell transcriptomics (scRNAseq) to understand how dividing transit-amplifying burst-forming unit erythroid progenitors balance the need for more progenitor cells with the need for terminally differentiated erythroid cells, and to identify drugs potentially useful in treating Epo-resistant anemias such as Diamond Blackfan anemia. I hope that the lessons I learned in managing these diverse fellows and projects, initially without having grants to support them, will be helpful to others who would like to undertake ambitious and important lines of research in hematology.

RevDate: 2020-12-14
CmpDate: 2020-12-08

Yunusbaev U, Ionusbaev A, Han G, et al (2020)

Recent effective population size in Eastern European plain Russians correlates with the key historical events.

Scientific reports, 10(1):9729 pii:10.1038/s41598-020-66734-y.

Effective population size reflects the history of population growth, contraction, and structuring. When the effect of structuring is negligible, the inferred trajectory of the effective population size can be informative about the key events in the history of a population. We used the IBDNe and DoRIS approaches, which exploit the data on IBD sharing between genomes, to reconstruct the recent effective population size in two population datasets of Russians from Eastern European plain: (1) ethnic Russians sampled from the westernmost part of Russia; (2) ethnic Russians, Bashkirs, and Tatars sampled from the Volga-Ural region. In this way, we examined changes in effective population size among ethnic Russians that reside in their historical area at the West of the plain, and that expanded eastward to come into contact with the indigenous peoples at the East of the plain. We compared the inferred demographic trajectories of each ethnic group to written historical data related to demographic events such as migration, war, colonization, famine, establishment, and collapse of empires. According to IBDNe estimations, 200 generations (~6000 years) ago, the effective size of the ancestral populations of Russians, Bashkirs, and Tatars hovered around 3,000, 30,000, and 8,000 respectively. Then, the ethnic Russians exponentially grew with increasing rates for the last 115 generations and become the largest ethnic group of the plain. Russians do not show any drop in effective population size after the key historical conflicts, including the Mongol invasion. The only exception is a moderate drop in the 17th century, which is well known in Russian history as The Smuta. Our analyses suggest a more eventful recent population history for the two small ethnic groups that came into contact with ethnic Russians in the Volga-Ural region. We found that the effective population size of Bashkirs and Tatars started to decrease during the time of the Mongol invasion. Interestingly, there is an even stronger drop in the effective population size that coincides with the expansion of Russians to the East. Thus, 15-20 generations ago, i.e. in the 16-18th centuries in the trajectories of Bashkirs and Tatars, we observe the bottlenecks of four and twenty thousand, respectively. Our results on the recent effective population size correlate with the key events in the history of populations of the Eastern European plain and have importance for designing biomedical studies in the region.

RevDate: 2020-11-30
CmpDate: 2020-11-30

Ragsdale AP, Nelson D, Gravel S, et al (2020)

Lessons Learned from Bugs in Models of Human History.

American journal of human genetics, 107(4):583-588.

Simulation plays a central role in population genomics studies. Recent years have seen rapid improvements in software efficiency that make it possible to simulate large genomic regions for many individuals sampled from large numbers of populations. As the complexity of the demographic models we study grows, however, there is an ever-increasing opportunity to introduce bugs in their implementation. Here, we describe two errors made in defining population genetic models using the msprime coalescent simulator that have found their way into the published record. We discuss how these errors have affected downstream analyses and give recommendations for software developers and users to reduce the risk of such errors.

RevDate: 2020-11-06
CmpDate: 2020-11-06

Josephy D (2020)

A tribute to Prof. Bruce Ames.

Mutation research, 856-857:503221.

RevDate: 2020-11-02
CmpDate: 2020-11-02

Moreau-Gachelin F, Camonis J, de Gunzburg J, et al (2020)

[Armand Tavitian (1931-2020): from oncogenes to the Ras superfamily].

Medecine sciences : M/S, 36(8-9):810-812.

RevDate: 2020-12-01
CmpDate: 2020-12-01

Rahman AH, D Homann (2020)

Mass cytometry and type 1 diabetes research in the age of single-cell data science.

Current opinion in endocrinology, diabetes, and obesity, 27(4):231-239.

PURPOSE OF REVIEW: New single-cell tec. hnologies developed over the past decade have considerably reshaped the biomedical research landscape, and more recently have found their way into studies probing the pathogenesis of type 1 diabetes (T1D). In this context, the emergence of mass cytometry in 2009 revolutionized immunological research in two fundamental ways that also affect the T1D world: first, its ready embrace by the community and rapid dissemination across academic and private science centers alike established a new standard of analytical complexity for the high-dimensional proteomic stratification of single-cell populations; and second, the somewhat unexpected arrival of mass cytometry awoke the flow cytometry field from its seeming sleeping beauty stupor and precipitated substantial technological advances that by now approach a degree of analytical dimensionality comparable to mass cytometry.

RECENT FINDINGS: Here, we summarize in detail how mass cytometry has thus far been harnessed for the pursuit of discovery studies in T1D science; we provide a succinct overview of other single-cell analysis platforms that already have been or soon will be integrated into various T1D investigations; and we briefly consider how effective adoption of these technologies requires an adjusted model for expense allocation, prioritization of experimental questions, division of labor, and recognition of scientific contributions.

SUMMARY: The introduction of contemporary single-cell technologies in general, and of mass cytometry, in particular, provides important new opportunities for current and future T1D research; the necessary reconfiguration of research strategies to accommodate implementation of these technologies, however, may both broaden research endeavors by fostering genuine team science, and constrain their actual practice because of the need for considerable investments into infrastructure and technical expertise.

RevDate: 2020-10-09
CmpDate: 2020-10-09

Jordan B (2020)

[Junk DNA is out of fashion].

Medecine sciences : M/S, 36(6-7):675-677.

A systematic search for non-conventional open reading frames in human DNA reveals a large number of small ORFs encoding peptides generally smaller than 100 amino-acids. These ORFs are transcribed and translated into small proteins, which are demonstrated to have functional significance by bulk CRISPR inactivation. Evidence is also found for bicistronic mRNAs including such a small ORF upstream of a canonical coding sequence. These findings add a new facet to our understanding of biological processes.

RevDate: 2020-10-16
CmpDate: 2020-10-14

Immunological Genome Project (2020)

ImmGen at 15.

Nature immunology, 21(7):700-703.

RevDate: 2020-09-09
CmpDate: 2020-09-09

Konashev M (2020)

Soviet genetics and the communist party: was it all bad and wrong, or none at all?.

History and philosophy of the life sciences, 42(2):27 pii:10.1007/s40656-020-00323-0.

The history of genetics and the evolutionary theory in the USSR is multidimensional. Only in the 1920s after the October Revolution, and due in large part to that Revolution, the science of genetics arose in Soviet Russia. Genetics was limited, but not obliterated in the second half of the 1950s, and was restored in the late 1960s, after the resignation of Nikita S. Khrushchev. In the subsequent period, Soviet genetics experienced a resurgence, though one not as successful as geneticists would have liked. The Communist party bodies interfered constantly, but with different consequences for the development of genetics than when the earlier periods. The main troubles for Soviet genetics occurred during the unique, well-known, most contradictory, and tragic Stalinist period. The start date for the defeat of genetics is also known-August, 1948. In the social history of science and especially in the history of evolutionary biology (including genetics) it is natural, necessary, and even expected to adopt an evolutionary approach. In particular, historians of science need to consider and explain the evolution and dependence of Soviet science in regards to the evolution of Soviet society, the Soviet state, and the Communist party. This evolutionary perspective reflects the standards of evolutionary biology, evolutionary macrosociology, and also the history of science.

RevDate: 2020-09-07
CmpDate: 2020-09-07

Pederson T (2020)

The 50th anniversary of reverse transcriptase-and its ironic legacy in the time of coronavirus.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 34(6):7219-7221.

RevDate: 2020-08-28
CmpDate: 2020-08-28

Ravindran S (2020)

Profile of Christopher A. Walsh.

Proceedings of the National Academy of Sciences of the United States of America, 117(25):13861-13863.

RevDate: 2020-11-23
CmpDate: 2020-11-23

Veigl SJ, Harman O, E Lamm (2020)

Friedrich Miescher's Discovery in the Historiography of Genetics: From Contamination to Confusion, from Nuclein to DNA.

Journal of the history of biology, 53(3):451-484.

In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher's name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher's reception in the historiography of genetics. To his critics, Miescher was a "contaminator," whose preparations were impure. Modern historians portrayed him as a "confuser," whose misunderstandings delayed the development of molecular biology. Each of these portrayals reflects the disciplinary context in which Miescher's work was evaluated. Using archival sources to unearth Miescher's unpublished speculations-including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation-this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago.

RevDate: 2020-10-13
CmpDate: 2020-10-13

Haber M, Nassar J, Almarri MA, et al (2020)

A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years.

American journal of human genetics, 107(1):149-157.

The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world's great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

RevDate: 2020-08-24
CmpDate: 2020-08-24

Hermes TR, Frachetti MD, Voyakin D, et al (2020)

High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor.

PloS one, 15(5):e0233333.

Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats (Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region.

RevDate: 2020-09-16
CmpDate: 2020-08-04

Furtwängler A, Rohrlach AB, Lamnidis TC, et al (2020)

Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland.

Nature communications, 11(1):1915 pii:10.1038/s41467-020-15560-x.

Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860-2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region.

RevDate: 2020-10-19
CmpDate: 2020-10-19

Frantz LAF, Bradley DG, Larson G, et al (2020)

Animal domestication in the era of ancient genomics.

Nature reviews. Genetics, 21(8):449-460.

The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.

RevDate: 2020-09-23
CmpDate: 2020-07-14

Davis TH (2020)

QnAs with Jens Nielsen.

Proceedings of the National Academy of Sciences of the United States of America, 117(14):7548-7549.

RevDate: 2020-03-31
CmpDate: 2020-03-31

Kirby T (2020)

Barbara Franke-unravelling ADHD's biology.

The lancet. Psychiatry, 7(4):310.

RevDate: 2020-04-02
CmpDate: 2020-04-02

Miranda C M, MF Alamos (2019)

[The influence of medicine in Emile Zola's "Fortune of the Rougon-Macquart"].

Revista medica de Chile, 147(10):1329-1334.

Emile Zola is one of the greatest writers in universal literature. In his important series of novels called "The Fortune of the Rougon-Macquart", Zola shows a surprising medical knowledge even though he did not have a formal medical education. We highlight not only his outstanding literary talent, but also the scientific relevance of the tremendous contribution to the medical field that can be extracted from his work. In this series, which describe the history of five generations within a large family suffering from neuropsychiatric and general pathologies, Zola emphasizes the hereditary component of several diseases. These observations probably place him as the first novelist who made an explicit emphasis on the power of inheritance in human behavior. He also mentions for the first time several medical aspects that were seldom addressed in the scientific literature of the time, demonstrating the genius of the writer, his outstanding power of observation and the rigorous preparation with which he wrote his work.

RevDate: 2020-10-28
CmpDate: 2020-10-28

Eve A (2020)

An interview with Eric Olson.

Development (Cambridge, England), 147(6): pii:147/6/dev188854.

Eric Olson is Professor and Chair of Molecular Biology at the University of Texas Southwestern Medical Center, USA, where he holds the Robert A. Welch Distinguished Chair in Science, the Annie and Willie Nelson Professorship in Stem Cell Research and the Pogue Distinguished Chair in Research in Cardiac Birth Defects. In 1999, he was elected to the US National Academy of Sciences and, in 2001, to the Institute of Medicine of the National Academy. He has received several awards, including the American Heart Association Research Achievement Award in 2008 and the Eugene Braunwald Academic Mentorship award in 2016. He has a lifelong interest in muscle development and disease, with a particular interest in Duchenne muscular dystrophy. In this interview, conducted at the Society for Developmental Biology's 2019 meeting in Boston, Massachusetts, USA, he discusses his experiences in academia and industry, as well as reflecting on the people and opportunities that contributed to his career.

RevDate: 2020-10-05
CmpDate: 2020-10-05

Hall K (2019)

"In Praise of Wool": The development of partition chromatography and its under-appreciated impact on molecular biology.

Endeavour, 43(4):100708.

The invention of partition chromatography by the biochemists Archer Martin and Richard Synge in 1941 offered crucial insights into the structure and function of DNA, insights at least as important as those from X-ray crystallography. Even so, the role that partition chromatography played in molecular biological studies is far less well known. Using new archival material, this article describes the origins of Martin and Synge's work, arguing that their achievement was far more than a new technical innovation; it went on to have a profound impact on the development of molecular biology to an extent that scholars have insufficiently appreciated.

RevDate: 2020-05-05
CmpDate: 2020-05-05

Marcus JH, Posth C, Ringbauer H, et al (2020)

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.

Nature communications, 11(1):939.

The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

RevDate: 2020-09-28
CmpDate: 2020-09-28

Pederson T (2020)

The double helix: "Photo 51" revisited.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 34(2):1923-1927.

RevDate: 2020-03-12
CmpDate: 2020-03-12

Hunter DJ (2019)

Adventures in the environment and genes.

European journal of epidemiology, 34(12):1111-1117.

RevDate: 2020-11-04
CmpDate: 2020-11-04

Butel-Simoes GI, Macrae F, AD Spigelman (2020)

Celebrating the career and contributions of Dr Henry T. Lynch (1928-2019).

Internal medicine journal, 50(1):108-109.

This article celebrates the career of Dr Henry Lynch and his contributions to cancer genetics through his extensive research, clinical practice and his passion for personalising care by using a patient's genetic profile to determine management and treatment. Dr Lynch's contributions were momentous and continue to have relevance to medical practice, in particular in the fields of clinical genetics, medical oncology and gastroenterology.

RevDate: 2020-11-16
CmpDate: 2020-11-16

Peifer M (2020)

The Eighth Day of Creation: looking back across 40 years to the birth of molecular biology and the roots of modern cell biology.

Molecular biology of the cell, 31(2):81-86.

Forty years ago, Horace Judson's The Eighth Day of Creation was published, a book vividly recounting the foundations of modern biology, the molecular biology revolution. This book inspired many in my generation. The anniversary provides a chance for a new generation to take a look back, to see how science has and hasn't changed. Many central players in the book, including Sydney Brenner, Seymour Benzer, and François Jacob, would go on to be among the founders of modern cell biology, developmental biology, and neurobiology. These players come alive via their own words, as complex individuals, both heroes and anti-heroes. The technologies and experimental approaches they pioneered, ranging from cell fractionation to immunoprecipitation to structural biology, and the multidisciplinary approaches they took continue to power and inspire our work today. In the process, Judson brings out of the shadows the central roles played by women in many of the era's discoveries. He provides us with a vision of how science and scientists have changed, of how many things about our endeavor never change, and of how some new ideas are perhaps not as new as we would like to think.

RevDate: 2020-10-13
CmpDate: 2020-10-13

Bensch S (2020)

Scott V. Edwards-Recipient of the 2019 Molecular Ecology Prize.

Molecular ecology, 29(1):20-22.

RevDate: 2020-06-23
CmpDate: 2020-05-11

Suran M (2020)

Finding the tail end: The discovery of RNA splicing.

Proceedings of the National Academy of Sciences of the United States of America, 117(4):1829-1832.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Anonymous (2019)

13th East-West Immunogenetics Conference, 14-16 March 2019, Zagreb, Croatia.

HLA, 94 Suppl 2:3-76.

RevDate: 2020-10-19
CmpDate: 2020-10-19

Meli AC, CE Seidman (2020)

Scientists on the Spot: Putting a halt to hypertrophic cardiomyopathy.

Cardiovascular research, 116(3):e42-e43.

RevDate: 2020-04-24
CmpDate: 2020-04-24

Schüpbach T (2019)

Genetic Screens to Analyze Pattern Formation of Egg and Embryo in Drosophila: A Personal History.

Annual review of genetics, 53:1-18.

In Drosophila development, the axes of the egg and future embryo are established during oogenesis. To learn about the underlying genetic and molecular pathways that lead to axis formation, I conducted a large-scale genetic screen at the beginning of my independent career. This led to the eventual understanding that both anterior-posterior and dorsal-ventral pattern information is transmitted from the oocyte to the surrounding follicle cells and in turn from the follicle cells back to the oocyte. How I came to conduct this screen and what further insights were gained by studying the mutants isolated in the screen are the topics of this autobiographical article.

RevDate: 2020-09-29
CmpDate: 2020-09-29

Hewitt JK (2020)

Celebrating the 50th Anniversary of the Journal, Behavior Genetics.

Behavior genetics, 50(1):1-2.

RevDate: 2020-04-16
CmpDate: 2020-04-16

Genetic Selection Evolution’s Editorial Board (2019)

GSE's 50th anniversary: where do we go from now?.

Genetics, selection, evolution : GSE, 51(1):66 pii:10.1186/s12711-019-0504-4.

RevDate: 2020-04-13
CmpDate: 2020-04-13

Berthel E, Ferlazzo ML, Devic C, et al (2019)

What Does the History of Research on the Repair of DNA Double-Strand Breaks Tell Us?-A Comprehensive Review of Human Radiosensitivity.

International journal of molecular sciences, 20(21):.

Our understanding of the molecular and cellular response to ionizing radiation (IR) has progressed considerably. This is notably the case for the repair and signaling of DNA double-strand breaks (DSB) that, if unrepaired, can result in cell lethality, or if misrepaired, can cause cancer. However, through the different protocols, techniques, and cellular models used during the last four decades, the DSB repair kinetics and the relationship between cellular radiosensitivity and unrepaired DSB has varied drastically, moving from all-or-none phenomena to very complex mechanistic models. To date, personalized medicine has required a reliable evaluation of the IR-induced risks that have become a medical, scientific, and societal issue. However, the molecular bases of the individual response to IR are still unclear: there is a gap between the moderate radiosensitivity frequently observed in clinic but poorly investigated in the publications and the hyper-radiosensitivity of rare but well-characterized genetic diseases frequently cited in the mechanistic models. This paper makes a comprehensive review of semantic issues, correlations between cellular radiosensitivity and unrepaired DSB, shapes of DSB repair curves, and DSB repair biomarkers in order to propose a new vision of the individual response to IR that would be more coherent with clinical reality.

RevDate: 2020-07-13
CmpDate: 2020-07-13

Rawson RV, RA Scolyer (2020)

From Breslow to BRAF and immunotherapy: evolving concepts in melanoma pathogenesis and disease progression and their implications for changing management over the last 50 years.

Human pathology, 95:149-160.

Since it was first recognized as a disease entity more than two centuries ago, advanced melanoma has, until recently, followed a very aggressive and almost universally fatal clinical course. However, over the past 50 years crucial ground breaking research has greatly enhanced our understanding of the etiology, risk factors, genomic pathogenesis, immunological interactions, prognostic features and management of melanoma. It is this combined body of work which has culminated in the exciting improvements in patient outcomes for those with advanced melanoma over the last ten years. In this the 50th anniversary of Human Pathology, we highlight the key developments in melanoma over this period.

RevDate: 2020-01-30
CmpDate: 2020-01-30

Meunier R (2019)

Project knowledge and its resituation in the design of research projects: Seymour Benzer's behavioral genetics, 1965-1974.

Studies in history and philosophy of science, 77:39-53.

The article introduces a framework for analyzing the knowledge that researchers draw upon when designing a research project by distinguishing four types of "project knowledge": goal knowledge, which concerns possible outcomes, and three forms of implementation knowledge that concern the realization of the project: 1) methodological knowledge that specifies possible experimental and non-experimental strategies to achieve the chosen goal; 2) representational knowledge that suggests ways to represent data, hypotheses, or outcomes; and 3) organizational knowledge that helps to build or navigate the material and social structures that enable a project. In the design of research projects such knowledge will be transferred from other successful projects and these processes will be analyzed in terms of modes of resituating knowledge. The account is developed by analyzing a case from the history of biology. In a reciprocal manner, it enables a better understanding of the historical episode in question: around 1970, several researchers who had made successful careers in the emerging field of molecular biology, working with bacterial model systems, attempted to create a molecular biology of the physiological processes in multicellular organisms. One of them was Seymour Benzer, who designed a research project addressing the physiological processes underlying behavior in Drosophila.

RevDate: 2020-09-30
CmpDate: 2020-05-18

Wolinsky H (2019)

Ancient DNA and contemporary politics: The analysis of ancient DNA challenges long-held beliefs about identity and history with potential for political abuse.

EMBO reports, 20(12):e49507.

The sequencing and analysis of ancient human DNA has helped to rewrite human history. But it is also tempting politicians, nationalists and supremacists to abuse this research for their agendas.

RevDate: 2020-01-08
CmpDate: 2019-11-18

Anonymous (2019)

Nature at 150: evidence in pursuit of truth.

Nature, 575(7781):7-8.

RevDate: 2020-07-13
CmpDate: 2020-07-13

Solanki M, D Visscher (2020)

Pathology of breast cancer in the last half century.

Human pathology, 95:137-148.

The past 50 years has been an era of technological innovation converging with the now dominant culture of testing hypotheses using clinical trials and case cohort methodology with rigorous statistical analysis. Great advances have been made in early diagnosis and, especially, less toxic and disfiguring primary therapy. Many of the advances in pathology have been in conjunction with efforts to support clinical initiatives, improve diagnostic reliability and translate basic science discoveries into tests that stratify patient management. Pathologists, with the support of epidemiologists, have lead significant advancements in the description and clinical significance of benign breast disease. Despite considerable efforts, the cure for breast cancer awaits better understanding of the pathophysiology of metastasis. We stand now at the brink a new era of technology, in which powerful genomic assays may be put to use in uncovering targets of therapy and defining mechanisms of disease progression. Pathologists must be active in ensuring that discoveries in this realm are optimized by assuring association with appropriate histological correlation and valid clinical endpoints.

RevDate: 2020-11-27
CmpDate: 2020-11-27

Cavaillon JM (2020)

André Boivin: A pioneer in endotoxin research and an amazing visionary during the birth of molecular biology.

Innate immunity, 26(3):165-171.

RevDate: 2020-07-13
CmpDate: 2020-07-13

Folpe AL (2020)

"Hey! Whatever happened to hemangiopericytoma and fibrosarcoma?" An update on selected conceptual advances in soft tissue pathology which have occurred over the past 50 years.

Human pathology, 95:113-136.

Hemangiopericytoma and fibrosarcoma represented at one time two of the most common diagnoses in soft tissue pathology. Both terms are now largely extinct. This article will review the clinicopathologic, immunohistochemical and molecular genetic advances that have led to these changes, and review the pathologic features of a select group of soft tissue tumors previously classified as hemangiopericytoma or fibrosarcoma.

RevDate: 2020-01-29
CmpDate: 2020-01-29

Lowe JWE, A Bruce (2019)

Genetics without genes? The centrality of genetic markers in livestock genetics and genomics.

History and philosophy of the life sciences, 41(4):50 pii:10.1007/s40656-019-0290-x.

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a (usually material) element existing in different forms in the genome, that can be identified and mapped using a variety (and often combination) of quantitative, classical and molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align (but never fully integrate) in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden.

RevDate: 2020-07-13
CmpDate: 2020-07-13

MacLennan GT, L Cheng (2020)

Five decades of urologic pathology: the accelerating expansion of knowledge in renal cell neoplasia.

Human pathology, 95:24-45.

Those who are knowledgeable in cosmology inform us that the expansion of the universe is such that the velocity at which a distant galaxy is receding from the observer is continually increasing with time. We humbly paraphrase that as "The bigger the universe gets, the faster it gets bigger." This is an interesting analogy for the expansion of knowledge in the field of renal tumor pathology over the past 30 to 50 years. It is clear that a multitude of dedicated investigators have devoted incalculable amounts of time and effort to the pursuit of knowledge about renal epithelial neoplasms. As a consequence of the contributions of numerous investigators over many decades, the most recent World Health Organization classification of renal neoplasms includes about 50 well defined and distinctive renal tumors, as well as various miscellaneous and metastatic tumors. In addition, a number of emerging or provisional new entities are under active investigation and may be included in future classifications. In this review, we will focus on a number of these tumors, tracing as accurately as we can the origins of their discovery, relating relevant additions to the overall knowledge base surrounding them, and in some instances addressing changes in nomenclature.

RevDate: 2020-07-13
CmpDate: 2020-07-13

Baloch Z, VA LiVolsi (2020)

Fifty years of thyroid pathology: concepts and developments.

Human pathology, 95:46-54.

The past half century has seen a number of advances in pathology of thyroid diseases, especially neoplastic lesions. These include the description of new entities, the definition of prognostically important lesions, the incorporation of fine needle aspiration biopsy and its functional risk stratification of diagnoses into the clinical evaluation and therapeutic recommendations of the patient with thyroid nodules and the understanding of thyroid neoplastic development, diagnostic and prognostic parameters by use of molecular analysis so that such techniques are becoming standard of care for patients with thyroid tumors. The histopathologist and cytopathologist have been and continue to be at the forefront in the definition and understanding of these areas of thyroid disease. This review describes many of the most important advances in this area in an attempt bring the practicing pathologist up to date in these developments.

RevDate: 2020-08-07
CmpDate: 2020-08-07

de Wit E (2020)

TADs as the Caller Calls Them.

Journal of molecular biology, 432(3):638-642.

Developments in proximity ligation methods and sequencing technologies have provided high-resolution views of the organization of the genome inside the nucleus. A prominent feature of Hi-C maps is regions of increased self-interaction called topologically associating domains (TADs). Despite the strong evolutionary conservation and clear link with gene expression, the exact role of TADs and even their definition remains debatable. Here, I review the discovery of TADs, how they are commonly identified, and the mechanisms that lead to their formation. Furthermore, I discuss recent results that have created a more nuanced view of the role of TADs in the regulation of genes. In light of this, I propose that when we define TADs, we also consider the mechanisms that shape them.

RevDate: 2020-04-23
CmpDate: 2020-04-23

Veuille M (2019)

Chance, Variation and Shared Ancestry: Population Genetics After the Synthesis.

Journal of the history of biology, 52(4):537-567.

Chance has been a focus of attention ever since the beginning of population genetics, but neutrality has not, as natural selection once appeared to be the only worthwhile issue. Neutral change became a major source of interest during the neutralist-selectionist debate, 1970-1980. It retained interest beyond this period for two reasons that contributed to its becoming foundational for evolutionary reasoning. On the one hand, neutral evolution was the first mathematical prediction to emerge from Mendelian inheritance: until then evolution by natural selection was considered the alternative to the fixity of species; now it appears to be the alternative to continuous change. Second, neutral change generated a set of clear predictions on standing variation. These could be used as a reference for detecting more elusive alternative mechanisms of evolution including natural selection. In the wake of the transition from Mendelism to genomics, the combination of coalescent theory, DNA sequence variation, and numerical analysis made it possible to integrate contingent aspects of the history of species into a new null model, thus opening a new dimension in the concept of population that the Modern Synthesis formerly considered as a mere gene pool.

RevDate: 2020-11-23
CmpDate: 2020-11-23

Roy S, Liu W, Nandety RS, et al (2020)

Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation.

The Plant cell, 32(1):15-41.

Since 1999, various forward- and reverse-genetic approaches have uncovered nearly 200 genes required for symbiotic nitrogen fixation (SNF) in legumes. These discoveries advanced our understanding of the evolution of SNF in plants and its relationship to other beneficial endosymbioses, signaling between plants and microbes, the control of microbial infection of plant cells, the control of plant cell division leading to nodule development, autoregulation of nodulation, intracellular accommodation of bacteria, nodule oxygen homeostasis, the control of bacteroid differentiation, metabolism and transport supporting symbiosis, and the control of nodule senescence. This review catalogs and contextualizes all of the plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean). We also briefly consider the future of SNF genetics in the era of pan-genomics and genome editing.

RevDate: 2020-07-20
CmpDate: 2020-07-20

Benson DL (2020)

Of Molecules and Mechanisms.

The Journal of neuroscience : the official journal of the Society for Neuroscience, 40(1):81-88.

Without question, molecular biology drives modern neuroscience. The past 50 years has been nothing short of revolutionary as key findings have moved the field from correlation toward causation. Most obvious are the discoveries and strategies that have been used to build tools for visualizing circuits, measuring activity, and regulating behavior. Less flashy, but arguably as important are the myriad investigations uncovering the actions of single molecules, macromolecular structures, and integrated machines that serve as the basis for constructing cellular and signaling pathways identified in wide-scale gene or RNA studies and for feeding data into informational networks used in systems biology. This review follows the pathways that were opened in neuroscience by major discoveries and set the stage for the next 50 years.

RevDate: 2020-07-06
CmpDate: 2020-07-06

Salomé PA (2019)

Sabeeha Merchant.

The Plant cell, 31(12):2814-2816.

RevDate: 2020-02-13
CmpDate: 2020-02-13

Sakaki Y (2019)

A Japanese history of the Human Genome Project.

Proceedings of the Japan Academy. Series B, Physical and biological sciences, 95(8):441-458.

The Human Genome Project (HGP) is one of the most important international achievements in life sciences, to which Japanese scientists made remarkable contributions. In the early 1980s, Akiyoshi Wada pioneered the first project for the automation of DNA sequencing technology. Ken-ichi Matsubara exhibited exceptional leadership to launch the comprehensive human genome program in Japan. Hideki Kambara made a major contribution by developing a key device for high-speed DNA sequencers, which enabled scientists to construct human genome draft sequences. The RIKEN team led by Yoshiyuki Sakaki (the author) played remarkable roles in the draft sequencing and completion of chromosomes 21, 18, and 11. Additionally, the Keio University team led by Nobuyoshi Shimizu made noteworthy contributions to the completion of chromosomes 22, 21, and 8. In April 2003, the Japanese team joined the international consortium in declaring the completion of the human genome sequence. Consistent with the HGP mandate, Japan has successfully developed a wide range of ambitious genomic sciences.

RevDate: 2020-03-31
CmpDate: 2020-03-31

Cox SL, Ruff CB, Maier RM, et al (2019)

Genetic contributions to variation in human stature in prehistoric Europe.

Proceedings of the National Academy of Sciences of the United States of America, 116(43):21484-21492.

The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height-consistent with genetic predictions-although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.

RevDate: 2020-10-01
CmpDate: 2020-03-10

Marnett LJ (2019)

Adventures with Bruce Ames and the Ames test.

Mutation research, 846:403070.

Bruce Ames has had an enormous impact on human health by developing facile methods for the identification of mutagens. This research also provided important insights into the relationship between mutagenesis and carcinogenesis. Bruce is a highly innovative and creative individual who has followed his interests across disciplines into diverse fields of inquiry. The present author had the pleasure of spending a sabbatical in the Ames lab and utilized the Ames test in multiple aspects of his research. He describes both in this honorific to Bruce on the occasion of his 90th birthday.

RevDate: 2020-04-23
CmpDate: 2020-04-23

Beatty J (2019)

The Creativity of Natural Selection? Part II: The Synthesis and Since.

Journal of the history of biology, 52(4):705-731.

This is the second of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. In the first part, I focussed on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled "mutationists." The second part focuses on the evolutionary synthesis and some of its critics, especially the "neutralists" and "neo-mutationists." Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as "Darwinism." I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection directing evolutionary change, for example by creating the variation that it subsequently acts upon. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.

RevDate: 2020-09-01
CmpDate: 2020-09-01

Wilson K, Narasimhan V, Pham T, et al (2019)

Precision medicine in colorectal surgery: coming to a hospital near you.

ANZ journal of surgery, 89(9):995-996.

RevDate: 2020-07-13
CmpDate: 2020-07-13

Hruban RH, Klimstra DS, Zamboni G, et al (2020)

A semicentennial of pancreatic pathology: the genetic revolution is here, but don't throw the baby out with the bath water!.

Human pathology, 95:99-112.

The last 50 years have witnessed an explosion in our understanding of the pathology of pancreatic diseases. Entities known to exist 50 years ago have been defined more precisely and are now better classified. New entities, previously not recognized, have been discovered and can now be treated. Importantly, new tools have been developed that have unraveled the fundamental biological drivers of a number of pancreatic diseases. Many of these same tools have also been applied clinically, supplementing the tried and true hematoxylin and eosin stained slide with a plethora of new, highly sensitive and specific tests that improve diagnostic accuracy and delineate best treatments. As exciting as these many advances are, our knowledge of pancreatic pathology remains incomplete, and there is much to be learned.

RevDate: 2019-11-12
CmpDate: 2019-11-12

Nik-Zainal S (2019)

A path inspired by people.

Nature medicine, 25(9):1329.

RevDate: 2020-06-29
CmpDate: 2020-06-29

Hyun J (2019)

Doctors Discussing "the Root of Koreans": Medical Genetics and the Korean Origin, 1975-1987.

Ui sahak, 28(2):551-590.

Anthropological genetics emerged as a new discipline to investigate the origin of human species in the second half of the twentieth century. Using the genetic database of blood groups and other protein polymorphisms, anthropological geneticists started redrawing the ancient migratory history of human populations. A peculiarity of the Korean experience is that clinical physicians were the first experts using genetic data to theorize the historical origin of the respective population. This paper examines how South Korean physicians produced the genetic knowledge and discourse of the Korean origin in the 1970s and 1980s. It argues that transnational scientific exchange led clinical researchers to engage in global anthropological studies. The paper focuses on two scientific cooperative cases in medical genetics at the time: the West German-South Korean pharmacogenetic research on the Korean population and the Asia-Oceania Histocompatibility Workshop. At the outset, physicians introduced medical genetics into their laboratory for clinical applications. Involved in cooperative projects on investigating anthropological implications of their clinical work, medical researchers came to use their genetic data for studying the Korean origin. In the process, physicians simply followed a nationalist narrative of the Korean origin rather than criticizing it. This was partially due to their lack of serious interest in anthropological work. Their explanations about the Korean origin would be considered "scientific" while hiding their embracing of the nationalist narrative.

RevDate: 2020-09-02
CmpDate: 2020-02-11

Heitman J (2019)

E Pluribus Unum: The Fungal Kingdom as a Rosetta Stone for Biology and Medicine.

Genetics, 213(1):1-7.

THE Genetics Society of America's (GSA's) Edward Novitski Prize recognizes a single experimental accomplishment or a body of work in which an exceptional level of creativity, and intellectual ingenuity, has been used to design and execute scientific experiments to solve a difficult problem in genetics. The 2019 recipient is Joseph Heitman, who is recognized for his work on fungal pathogens of humans and for ingenious experiments using yeast to identify the molecular targets of widely used immunosuppressive drugs. The latter work, part of Heitman's postdoctoral research, proved to be a seminal contribution to the discovery of the conserved Target of Rapamycin (TOR) pathway. In his own research group, a recurring theme has been the linking of fundamental insights in fungal biology to medically important problems. His studies have included defining fungal mating-type loci, including their evolution and links to virulence, and illustrating convergent transitions from outcrossing to inbreeding in fungal pathogens of plants and animals. He has led efforts to establish new genetic and genomic methods for studying pathogenesis in Cryptococcus species. Heitman's group also discovered unisexual reproduction, a novel mode of fungal reproduction with implications for pathogen evolution and the origins of sexual reproduction.

RevDate: 2020-08-20
CmpDate: 2020-08-20

Gazzaniga MS (2019)

Following Schrödinger's Code: A Personal Journey.

Journal of cognitive neuroscience, 31(12):1777-1781.

On a wintery afternoon over 60 years ago, I was browsing the Baker Library stacks at Dartmouth College and stumbled across a small book with an arresting title: What Is Life? [Schrödinger, E. What is Life? The physical aspect of the living cell and mind. Cambridge: Cambridge University Press, 1944]. This small volume contained numerous concepts that would transform the future of the biological sciences, giving rise to new fields, dogmas, approaches, and debates. Here, I present the core concepts of Schrödinger's book, the influence they have had on biology, and the influence they may continue to have on the cognitive neurosciences.

RevDate: 2020-02-12
CmpDate: 2020-02-12

Anonymous (2019)

Five decades of eukaryotic transcription.

Nature structural & molecular biology, 26(9):757.

RevDate: 2020-08-31
CmpDate: 2020-08-31

Ramamoorthy A, Karnes JH, Finkel R, et al (2019)

Evolution of Next Generation Therapeutics: Past, Present, and Future of Precision Medicines.

Clinical and translational science, 12(6):560-563.

RevDate: 2020-09-04
CmpDate: 2020-02-12

Lis JT (2019)

A 50 year history of technologies that drove discovery in eukaryotic transcription regulation.

Nature structural & molecular biology, 26(9):777-782.

Transcription regulation is critical to organism development and homeostasis. Control of expression of the 20,000 genes in human cells requires many hundreds of proteins acting through sophisticated multistep mechanisms. In this Historical Perspective, I highlight the progress that has been made in elucidating eukaryotic transcriptional mechanisms through an array of disciplines and approaches, and how this concerted effort has been driven by the development of new technologies.

RevDate: 2020-09-04
CmpDate: 2020-02-12

Roeder RG (2019)

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms.

Nature structural & molecular biology, 26(9):783-791.

The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.

RevDate: 2020-08-18
CmpDate: 2020-02-12

Conaway RC, JW Conaway (2019)

The hunt for RNA polymerase II elongation factors: a historical perspective.

Nature structural & molecular biology, 26(9):771-776.

The discovery of the three eukaryotic nuclear RNA polymerases paved the way for serious biochemical investigations of eukaryotic transcription and the identification of eukaryotic transcription factors. Here we describe this adventure from our vantage point, with a focus on the hunt for factors that regulate elongation by RNA polymerase II.

RevDate: 2020-09-04
CmpDate: 2020-02-12

Kadonaga JT (2019)

The transformation of the DNA template in RNA polymerase II transcription: a historical perspective.

Nature structural & molecular biology, 26(9):766-770.

The discovery of RNA polymerases I, II, and III opened up a new era in gene expression. Here I provide a personal retrospective account of the transformation of the DNA template, as it evolved from naked DNA to chromatin, in the biochemical analysis of transcription by RNA polymerase II. These studies have revealed new insights into the mechanisms by which transcription factors function with chromatin to regulate gene expression.

RevDate: 2020-05-29
CmpDate: 2020-05-29

Fernández-Irigoyen J, Corrales F, E Santamaría (2019)

The Human Brain Proteome Project: Biological and Technological Challenges.

Methods in molecular biology (Clifton, N.J.), 2044:3-23.

Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.

RevDate: 2020-08-02
CmpDate: 2020-01-08

Weir BS (2019)

The Summer Institute in Statistical Genetics.

Genetics, 212(4):955-957.

The Elizabeth W. Jones Award for Excellence in Education recognizes an individual or group that has had significant, sustained impact on genetics education at any level, from K-12 through graduate school and beyond. Bruce Weir (University of Washington) is the 2019 recipient in recognition of his work training thousands of researchers in the rigorous use of statistical analysis methods for genetic and genomic data. His contributions fall into three categories: the acclaimed Summer Institute in Statistical Genetics, which has been held continuously for 23 years and has trained > 10,000 researchers worldwide; the popular graduate-level textbook Genetic Data Analysis; and the training of a growing number of forensic geneticists during the rise of DNA evidence in courts around the world.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )