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Bibliography on: History of Genetics

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ESP: PubMed Auto Bibliography 24 Jan 2022 at 01:34 Created: 

History of Genetics

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

Citations The Papers (from PubMed®)

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RevDate: 2022-01-20
CmpDate: 2022-01-20

D'Cunha Burkardt D, Sanchez-Lara PA, Girisha KM, et al (2021)

A celebration in honor of John M. Graham, Jr, MD, ScD.

American journal of medical genetics. Part A, 185(9):2617-2619.

RevDate: 2022-01-20
CmpDate: 2022-01-20

Miller M (2021)

The Dysmorphology Unit from 1976 to 1980: Fleeting fellow, deformations, and John Graham.

American journal of medical genetics. Part A, 185(9):2622-2626.

RevDate: 2022-01-20
CmpDate: 2022-01-20

Graham JM (Jr) (2021)

Reflections on a career in dysmorphology, teratology, and clinical genetics.

American journal of medical genetics. Part A, 185(9):2620-2621.

RevDate: 2022-01-14
CmpDate: 2022-01-14

Melero-Martin JM, Dudley AC, AW Griffioen (2021)

Adieu to parting Editor in Chief and pioneering scientist Dr. Joyce Bischoff.

Angiogenesis, 24(2):191-193.

RevDate: 2022-01-12
CmpDate: 2022-01-12

Abbasi J (2021)

After 12 Years, NIH Director Francis S. Collins Seeks His Next Chapter.

JAMA, 326(23):2349-2352.

RevDate: 2022-01-04
CmpDate: 2022-01-04

Almarri MA, Haber M, Lootah RA, et al (2021)

The genomic history of the Middle East.

Cell, 184(18):4612-4625.e14.

The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15-20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.

RevDate: 2021-12-29
CmpDate: 2021-12-29

Allen KN, CP Whitman (2021)

The Birth of Genomic Enzymology: Discovery of the Mechanistically Diverse Enolase Superfamily.

Biochemistry, 60(46):3515-3528.

Enzymes are categorized into superfamilies by sequence, structural, and mechanistic similarities. The evolutionary implications can be profound. Until the mid-1990s, the approach was fragmented largely due to limited sequence and structural data. However, in 1996, Babbitt et al. published a paper in Biochemistry that demonstrated the potential power of mechanistically diverse superfamilies to identify common ancestry, predict function, and, in some cases, predict specificity. This Perspective describes the findings of the original work and reviews the current understanding of structure and mechanism in the founding family members. The outcomes of the genomic enzymology approach have reached far beyond the functional assignment of members of the enolase superfamily, inspiring the study of superfamilies and the adoption of sequence similarity networks and genome context and yielding fundamental insights into enzyme evolution.

RevDate: 2021-12-28
CmpDate: 2021-12-28

Byeon YJJ, Islamaj R, Yeganova L, et al (2021)

Evolving use of ancestry, ethnicity, and race in genetics research-A survey spanning seven decades.

American journal of human genetics, 108(12):2215-2223.

To inform continuous and rigorous reflection about the description of human populations in genomics research, this study investigates the historical and contemporary use of the terms "ancestry," "ethnicity," "race," and other population labels in The American Journal of Human Genetics from 1949 to 2018. We characterize these terms' frequency of use and assess their odds of co-occurrence with a set of social and genetic topical terms. Throughout The Journal's 70-year history, "ancestry" and "ethnicity" have increased in use, appearing in 33% and 26% of articles in 2009-2018, while the use of "race" has decreased, occurring in 4% of articles in 2009-2018. Although its overall use has declined, the odds of "race" appearing in the presence of "ethnicity" has increased relative to the odds of occurring in its absence. Forms of population descriptors "Caucasian" and "Negro" have largely disappeared from The Journal (<1% of articles in 2009-2018). Conversely, the continental labels "African," "Asian," and "European" have increased in use and appear in 18%, 14%, and 42% of articles from 2009-2018, respectively. Decreasing uses of the terms "race," "Caucasian," and "Negro" are indicative of a transition away from the field's history of explicitly biological race science; at the same time, the increasing use of "ancestry," "ethnicity," and continental labels should serve to motivate ongoing reflection as the terminology used to describe genetic variation continues to evolve.

RevDate: 2021-12-20
CmpDate: 2021-12-20

Pederson T (2021)

Francis S. Collins: Transformer and translator for NIH.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 35(12):e22022.

RevDate: 2021-12-17
CmpDate: 2021-12-17

Burgess RR (2021)

What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase.

The Journal of biological chemistry, 297(5):101310.

This Reflections article is focused on the 5 years while I was a graduate student (1964-1969). During this period, I made some of the most significant discoveries of my career. I have written this article primarily for a protein biochemistry audience, my colleagues who shared this exciting time in science, and the many scientists over the last 50 years who have contributed to our knowledge of transcriptional machinery and their regulation. It is also written for today's graduate students, postdocs, and scientists who may not know much about the discoveries and technical advances that are now taken for granted, to show that even with methods primitive by today's standards, we were still able to make foundational advances. I also hope to provide a glimpse into how fortunate I was to be a graduate student over 50 years ago in the golden age of molecular biology.

RevDate: 2021-12-14
CmpDate: 2021-12-06

Ravindran S (2021)

Profile of Patrick Cramer.

Proceedings of the National Academy of Sciences of the United States of America, 118(30):.

RevDate: 2021-12-14
CmpDate: 2021-12-03

Viegas J (2021)

Profile of Claude Desplan.

Proceedings of the National Academy of Sciences of the United States of America, 118(28):.

RevDate: 2021-12-14
CmpDate: 2021-12-03

Davis TH (2021)

Profile of Scott Edwards.

Proceedings of the National Academy of Sciences of the United States of America, 118(21):.

RevDate: 2021-12-14
CmpDate: 2021-12-06

Pehlivanoglu B, Aysal A, Kececi SD, et al (2021)

A Nobel-Winning Scientist: Aziz Sancar and the Impact of his Work on the Molecular Pathology of Neoplastic Diseases.

Turk patoloji dergisi, 37(2):93-105.

Aziz Sancar, Nobel Prize winning Turkish scientist, made several discoveries which had a major impact on molecular sciences, particularly disciplines that focus on carcinogenesis and cancer treatment, including molecular pathology. Cloning the photolyase gene, which was the initial step of his work on DNA repair mechanisms, discovery of the "Maxicell" method, explanation of the mechanism of nucleotide excision repair and transcription-coupled repair, discovery of "molecular matchmakers", and mapping human excision repair genes at single nucleotide resolution constitute his major research topics. Moreover, Sancar discovered the cryptochromes, the clock genes in humans, in 1998, and this discovery led to substantial progress in the understanding of the circadian clock and the introduction of the concept of "chrono-chemoterapy" for more effective therapy in cancer patients. This review focuses on Aziz Sancar's scientific studies and their reflections on molecular pathology of neoplastic diseases. While providing a new perspective for researchers working in the field of pathology and molecular pathology, this review is also an evidence of how basic sciences and clinical sciences complete each other.

RevDate: 2021-12-14
CmpDate: 2021-12-13

Cabrera VM (2021)

Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes.

Scientific reports, 11(1):5036.

Human evolutionary genetics gives a chronological framework to interpret the human history. It is based on the molecular clock hypothesis that suppose a straightforward relationship between the mutation rate and the substitution rate with independence of other factors as demography dynamics. Analyzing ancient and modern human complete mitochondrial genomes we show here that, along the time, the substitution rate can be significantly slower or faster than the average germline mutation rate confirming a time dependence effect mainly attributable to changes in the effective population size of the human populations, with an exponential growth in recent times. We also detect that transient polymorphisms play a slowdown role in the evolutionary rate deduced from haplogroup intraspecific trees. Finally, we propose the use of the most divergent lineages within haplogroups as a practical approach to correct these molecular clock mismatches.

RevDate: 2021-12-14
CmpDate: 2021-12-13

Tsagakis I, Vertessy B, D Wright (2021)

An open chat with…Beáta Vertessy.

FEBS open bio, 11(2):338-339.

RevDate: 2021-11-29
CmpDate: 2021-11-29

Eve A (2021)

Transitions in development - an interview with Tom Nowakowski.

Development (Cambridge, England), 148(19):.

Tom Nowakowski is an Assistant Professor at University of California San Francisco (UCSF), where he uses single-cell sequencing technologies to study neurodevelopment. He is also a Chan Zuckerberg Biohub Investigator and a Next Generation Leader at the Allen Institute for Brain Science. We met with Tom over Zoom to hear more about his career, his transition to becoming a group leader and his plans for the future.

RevDate: 2021-11-29
CmpDate: 2021-11-29

Ahmed F (2021)

Profile of Howard Y. Chang.

Proceedings of the National Academy of Sciences of the United States of America, 118(15):.

RevDate: 2021-11-29
CmpDate: 2021-11-29

Borovik A (2021)

A mathematician's view of the unreasonable ineffectiveness of mathematics in biology.

Bio Systems, 205:104410.

This paper discusses, from a mathematician's point of view, the thesis formulated by Israel Gelfand, one of the greatest mathematicians of the 20th century, and one of the pioneers of mathematical biology, about the unreasonable ineffectiveness of mathematics in biology as compared with the obvious success of mathematics in physics. The author discusses the limitations of the mainstream mathematics of today when it is used in biology. He suggests that some emerging directions in mathematics have potential to enhance the role of mathematics in biology.

RevDate: 2021-11-29
CmpDate: 2021-11-29

de la Vega CG, Gómez R, Page J, et al (2021)

Julio S. Rufas: A true chromosome lover.

Chromosoma, 130(1):1-2.

RevDate: 2021-11-29
CmpDate: 2021-11-29

Valdebenito J, F Medina (2019)

Machine learning approaches to study glioblastoma: A review of the last decade of applications.

Cancer reports (Hoboken, N.J.), 2(6):e1226.

BACKGROUND: Glioblastoma (GB, formally glioblastoma multiforme) is a malignant type of brain cancer that currently has no cure and is characterized by being highly heterogeneous with high rates of re-incidence and therapy resistance. Thus, it is urgent to characterize the mechanisms of GB pathogenesis to help researchers identify novel therapeutic targets to cure this devastating disease. Recently, a promising approach to identifying novel therapeutic targets is the integration of tumor omics data with clinical information using machine learning (ML) techniques.

RECENT FINDINGS: ML has become a valuable addition to the researcher's toolbox, thanks to its flexibility, multidimensional approach, and a growing community of users. The goal of this review is to introduce basic concepts and applications of ML for studying GB to clinicians and practitioners who are new to data science. ML applications include exploring large data sets, finding new relevant patterns, predicting outcomes, or merely understanding associations of the complex molecular networks presented within the tumor. Here, we review ML applications published between 2008 and 2018 and discuss ML strategies intending to identify new potential therapeutic targets to improve the management and treatment of GB.

CONCLUSIONS: ML applications to study GB vary in purpose and complexity, with positive results. In GB studies, ML is often used to analyze high-dimensional datasets with prediction or classification as a primary goal. Despite the strengths of ML techniques, they are not fail-safe and methodological issues can occur in GB studies that use them. This is why researchers need to be aware of these issues when planning and appraising studies that apply ML to the study of GB.

RevDate: 2021-11-22
CmpDate: 2021-11-22

Ikle JM, AL Gloyn (2021)

100 YEARS OF INSULIN: A brief history of diabetes genetics: insights for pancreatic beta-cell development and function.

The Journal of endocrinology, 250(3):R23-R35 pii:JOE-21-0067.

Since the discovery of insulin 100 years ago, our knowledge and understanding of diabetes have grown exponentially. Specifically, with regards to the genetics underlying diabetes risk, our discoveries have paralleled developments in our understanding of the human genome and our ability to study genomics at scale; these advancements in genetics have both accompanied and led to those in diabetes treatment. This review will explore the timeline and history of gene discovery and how this has coincided with progress in the fields of genomics. Examples of genetic causes of monogenic diabetes are presented and the continuing expansion of allelic series in these genes and the challenges these now cause for diagnostic interpretation along with opportunities for patient stratification are discussed.

RevDate: 2021-11-16
CmpDate: 2021-11-16

Monckton DG (2021)

The Contribution of Somatic Expansion of the CAG Repeat to Symptomatic Development in Huntington's Disease: A Historical Perspective.

Journal of Huntington's disease, 10(1):7-33.

The discovery in the early 1990s of the expansion of unstable simple sequence repeats as the causative mutation for a number of inherited human disorders, including Huntington's disease (HD), opened up a new era of human genetics and provided explanations for some old problems. In particular, an inverse association between the number of repeats inherited and age at onset, and unprecedented levels of germline instability, biased toward further expansion, provided an explanation for the wide symptomatic variability and anticipation observed in HD and many of these disorders. The repeats were also revealed to be somatically unstable in a process that is expansion-biased, age-dependent and tissue-specific, features that are now increasingly recognised as contributory to the age-dependence, progressive nature and tissue specificity of the symptoms of HD, and at least some related disorders. With much of the data deriving from affected individuals, and model systems, somatic expansions have been revealed to arise in a cell division-independent manner in critical target tissues via a mechanism involving key components of the DNA mismatch repair pathway. These insights have opened new approaches to thinking about how the disease could be treated by suppressing somatic expansion and revealed novel protein targets for intervention. Exciting times lie ahead in turning these insights into novel therapies for HD and related disorders.

RevDate: 2021-11-02
CmpDate: 2021-11-02

Anonymous (2020)

Society for Glycobiology Awards-2020.

Glycobiology, 30(12):936-940.

RevDate: 2021-10-27
CmpDate: 2021-10-27

Jordan B (2021)

[CRISPR Nobel, at last…].

Medecine sciences : M/S, 37(1):77-80.

The 2020 Nobel Prize in chemistry rewards two brilliant scientists who have followed quite different career paths but have collaborated very successfully. Of course, the history of the CRISPR system is complex and involves many other individuals, but their contribution has been essential. It is difficult to overstate the importance of this system for the functional interpretation of massive genome data as well as for (sometimes problematic) clinical applications.

RevDate: 2021-10-26
CmpDate: 2021-10-26

Loison L (2021)

Epigenetic inheritance and evolution: a historian's perspective.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 376(1826):20200120.

The aim of this article is to put the growing interest in epigenetics in the field of evolutionary theory into a historical context. First, I assess the view that epigenetic inheritance could be seen as vindicating a revival of (neo)Lamarckism. Drawing on Jablonka's and Lamb's considerable output, I identify several differences between modern epigenetics and what Lamarckism was in the history of science. Even if Lamarckism is not back, epigenetic inheritance might be appealing for evolutionary biologists because it could potentiate two neglected mechanisms: the Baldwin effect and genetic assimilation. Second, I go back to the first ideas about the Baldwin effect developed in the late nineteenth century to show that the efficiency of this mechanism was already linked with a form of non-genetic inheritance. The opposition to all forms of non-genetic inheritance that prevailed at the time of the rise of the Modern Synthesis helps to explain why the Baldwin effect was understood as an insignificant mechanism during the second half of the twentieth century. Based on this historical reconstruction, in §4, I examine what modern epigenetics can bring to the picture and under what conditions epigenetic inheritance might be seen as strengthening the causal relationship between adaptability and adaptation. Throughout I support the view that the Baldwin effect and genetic assimilation, even if they are quite close, should not be conflated, and that drawing a line between these concepts is helpful in order to better understand where epigenetic inheritance might endorse a new causal role. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

RevDate: 2021-10-22
CmpDate: 2021-10-22

Batista FD (2021)

In conversation with the Chief Editor.

The EMBO journal, 40(8):e108116.

An interview with Facundo D Batista, The EMBO Journal new Editor-in-Chief.

RevDate: 2021-10-20
CmpDate: 2021-10-20

Cooper KL (2021)

In the Spotlight-Early Career Researcher.

Journal of experimental zoology. Part B, Molecular and developmental evolution, 336(5):391-392.

RevDate: 2021-10-20
CmpDate: 2021-10-20

Mendenhall AR, Lithgow GJ, Kim S, et al (2021)

Career Retrospective: Tom Johnson-Genetics, Genomics, Stress, Stochastic Variation, and Aging.

The journals of gerontology. Series A, Biological sciences and medical sciences, 76(7):e85-e91.

RevDate: 2021-10-12
CmpDate: 2021-10-12

Hanawalt PC, Samson LD, B Van Houten (2021)

The life and legacy of Sam Wilson (1939-2021).

DNA repair, 104:103138.

RevDate: 2021-10-04
CmpDate: 2021-10-04

Sollid LM, Lundin KEA, Leivestad T, et al (2021)

Erik Thorsby (1938-2021).

Immunogenetics, 73(3):203-205.

RevDate: 2021-10-04
CmpDate: 2021-10-04

Wynshaw-Boris A (2021)

EDITORIAL: 'An Improbable Fifteen Years as Executive Editor'.

Human molecular genetics, 30(1):1-2.

RevDate: 2021-09-30
CmpDate: 2021-09-30

Jackson L, Tsosie KS, K Fox (2021)

Changing the wrapping won't fix genetic-racism package.

Nature, 597(7877):475.

RevDate: 2021-09-30
CmpDate: 2021-09-30

Aneli S, Caldon M, Saupe T, et al (2021)

Through 40,000 years of human presence in Southern Europe: the Italian case study.

Human genetics, 140(10):1417-1431.

The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.

RevDate: 2021-09-28
CmpDate: 2021-09-28

FEBS Journal Editorial Team, A Heck (2021)

Editor Profile: Albert Heck.

The FEBS journal, 288(18):5228-5230.

In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research and perspectives on the journal and more. Albert Heck is Professor of Chemistry and Pharmaceutical Sciences at Utrecht University, Scientific Director of the Netherlands Proteomics Center, and Head of the Biomolecular Mass Spectrometry and Proteomics group in Utrecht University since September 1998. He has served as Editorial Board Member of The FEBS Journal since 2020.

RevDate: 2021-09-23
CmpDate: 2021-09-23

Dorado G, Gálvez S, Rosales TE, et al (2021)

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review.

Biomolecules, 11(8):.

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

RevDate: 2021-09-01
CmpDate: 2021-09-01

Anonymous (2021)

Meet the authors: Michael Ranes and Sebastian Guettler.

Molecular cell, 81(16):3237-3240.

We talk to first and last authors Michael Ranes and Sebastian Guettler about their paper, "Reconstitution of the destruction complex defines roles of AXIN polymers and APC in β-catenin capture, phosphorylation, and ubiquitylation," how questions at conferences drove the work, the research in the Guettler lab, and Michael's experience as a Black scientist and his hopes for the future.

RevDate: 2021-09-01
CmpDate: 2021-09-01

Anonymous (2021)

The power of perpetual collaboration: An interview with Elçin Ünal and Gloria Brar.

Molecular cell, 81(16):3229-3236.

Here, Elçin Ünal and Gloria Brar tell us how the Br-Ün Lab came to be, the cons, but mostly the pros, of running a joint lab and things to consider, as well as their philosophies in research and mentoring a diverse group of scientists.

RevDate: 2021-08-26
CmpDate: 2021-08-26

FEBS Journal Editorial Team, B Derry (2021)

Editor Profile: Brent Derry.

The FEBS journal, 288(15):4435-4438.

In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research focus and perspectives on the journal and future directions in their field. Brent Derry is Professor at the Department of Molecular Genetics of University of Toronto and Senior Scientist of the Developmental & Stem Cell Biology Program at The Hospital for Sick Children (Toronto, Canada). He has served as an editorial board member of The FEBS Journal since 2017.

RevDate: 2021-08-26
CmpDate: 2021-08-26

The Febs Journal Editorial Team , H Lee (2021)

Editor Profile: Hyunsook Lee.

The FEBS journal, 288(15):4439-4441.

In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research focus, perspectives on the journal and future directions in their field. Hyunsook Lee is Professor at the Laboratory of Cancer Cell Biology at Seoul National University in Korea. She has served as an editorial board member of The FEBS Journal since 2018.

RevDate: 2021-08-03
CmpDate: 2021-08-03

Minor W, Jaskolski M, Martin SJ, et al (2021)

Dr. Alexander Wlodawer-celebrating five decades of service to the structural biology community.

The FEBS journal, 288(14):4160-4164.

This 75th birthday tribute to our Editorial Board member Alexander Wlodawer recounts his decades-long service to the community of structural biology researchers. His former and current colleagues tell the story of his upbringing and education, followed by an account of his dedication to quality and rigor in crystallography and structural science. The FEBS Journal Editor-in-Chief Seamus Martin further highlights Alex's outstanding contributions to the journal's success over many years.

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

Breslauer KJ (2021)

The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication.

The Journal of biological chemistry, 296:100522.

My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial "late bloomer." Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a "molecular linguist." For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.

RevDate: 2021-08-23
CmpDate: 2021-08-23

Fernández-Medarde A, De Las Rivas J, E Santos (2021)

40 Years of RAS-A Historic Overview.

Genes, 12(5):.

It has been over forty years since the isolation of the first human oncogene (HRAS), a crucial milestone in cancer research made possible through the combined efforts of a few selected research groups at the beginning of the 1980s. Those initial discoveries led to a quantitative leap in our understanding of cancer biology and set up the onset of the field of molecular oncology. The following four decades of RAS research have produced a huge pool of new knowledge about the RAS family of small GTPases, including how they regulate signaling pathways controlling many cellular physiological processes, or how oncogenic mutations trigger pathological conditions, including developmental syndromes or many cancer types. However, despite the extensive body of available basic knowledge, specific effective treatments for RAS-driven cancers are still lacking. Hopefully, recent advances involving the discovery of novel pockets on the RAS surface as well as highly specific small-molecule inhibitors able to block its interaction with effectors and/or activators may lead to the development of new, effective treatments for cancer. This review intends to provide a quick, summarized historical overview of the main milestones in RAS research spanning from the initial discovery of the viral RAS oncogenes in rodent tumors to the latest attempts at targeting RAS oncogenes in various human cancers.

RevDate: 2021-07-23
CmpDate: 2021-06-25

Yu X, H Li (2021)

Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome.

Molecular genetics and genomics : MGG, 296(4):783-797.

East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north-south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans.

RevDate: 2021-06-16
CmpDate: 2021-06-16

Anonymous (2021)

Meet the author: Amy Tresenrider.

Molecular cell, 81(10):2055-2056.

Amy Tresenrider is the first author of "Integrated genomic analysis reveals key features of long undecoded transcript isoform (LUTI)-based gene repression." She shares with us insights behind the paper along with her perspectives on the importance of individualized mentorship and collaborations near and far.

RevDate: 2021-08-19
CmpDate: 2021-08-19

McGovern MF (2021)

Genes go digital: Mendelian Inheritance in Man and the genealogy of electronic publishing in biomedicine.

British journal for the history of science, 54(2):213-231.

Mendelian Inheritance in Man (MIM), a computerized catalogue of human genetic disorders authored and maintained by cardiologist and medical genetics pioneer Victor A. McKusick, played a major part in demarcating between a novel biomedical science and the eugenic projects of racial betterment which existed prior to its emergence. Nonetheless, it built upon prior efforts to systematize genetic knowledge tied to individuals and institutions invested in eugenics. By unpacking the process of digitizing a homespun cataloguing project and charting its development into an online database, this article aims to illuminate how the institution-building efforts of one individual created an 'information order' for accessing genetic information that tacitly shaped the norms and priorities of the field toward the pursuit of specific genes associated with discernible genetic disorders. This was not by design, but rather arose through negotiation with the catalogue's users; it accommodated further changes as biomedical research displaced the Mendelian paradigm. While great effort was expended toward making sequence data available to investigators during the Human Genome Project, MIM was largely taken for granted as a 'legacy system', McKusick's own labour of love. Drawing on recent histories of biomedical data, the article suggests that the bibliographical work of curation and translation is a central feature of value production in the life sciences meriting attention in its own right.

RevDate: 2021-09-18
CmpDate: 2021-06-30

Byers PH (2021)

2020 McKusick Award address.

American journal of human genetics, 108(5):761-763.

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.

RevDate: 2021-06-14
CmpDate: 2021-06-14

Anonymous (2021)

Meet the authors: Ewelina M. Małecka and Sarah A. Woodson.

Molecular cell, 81(9):1857-1858.

We talk to Ewelina Małecka and Sarah Woodson about their paper, "Stepwise sRNA targeting of structured bacterial mRNAs leads to abortive annealing," who inspired them along their scientific paths, the research in Sarah's lab and the environment she looks to create, as well as Ewelina's advice for aspiring scientists.

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

Richardson JS, Richardson DC, DS Goodsell (2021)

Seeing the PDB.

The Journal of biological chemistry, 296:100742.

Ever since the first structures of proteins were determined in the 1960s, structural biologists have required methods to visualize biomolecular structures, both as an essential tool for their research and also to promote 3D comprehension of structural results by a wide audience of researchers, students, and the general public. In this review to celebrate the 50th anniversary of the Protein Data Bank, we present our own experiences in developing and applying methods of visualization and analysis to the ever-expanding archive of protein and nucleic acid structures in the worldwide Protein Data Bank. Across that timespan, Jane and David Richardson have concentrated on the organization inside and between the macromolecules, with ribbons to show the overall backbone "fold" and contact dots to show how the all-atom details fit together locally. David Goodsell has explored surface-based representations to present and explore biological subjects that range from molecules to cells. This review concludes with some ideas about the current challenges being addressed by the field of biomolecular visualization.

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

Wolberger C (2021)

How structural biology transformed studies of transcription regulation.

The Journal of biological chemistry, 296:100741.

The past 4 decades have seen remarkable advances in our understanding of the structural basis of gene regulation. Technological advances in protein expression, nucleic acid synthesis, and structural biology made it possible to study the proteins that regulate transcription in the context of ever larger complexes containing proteins bound to DNA. This review, written on the occasion of the 50th anniversary of the founding of the Protein Data Bank focuses on the insights gained from structural studies of protein-DNA complexes and the role the PDB has played in driving this research. I cover highlights in the field, beginning with X-ray crystal structures of the first DNA-binding domains to be studied, through recent cryo-EM structures of transcription factor binding to nucleosomal DNA.

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

Sali A (2021)

From integrative structural biology to cell biology.

The Journal of biological chemistry, 296:100743.

Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, and dynamic systems, such as the ∼52-MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, and completeness. Key challenges in improving integrative modeling include expanding model representations, increasing the variety of input data and prior information, quantifying a match between input information and a model in a Bayesian fashion, inventing more efficient structural sampling, as well as developing better model validation, analysis, and visualization. In addition, two community-level challenges in integrative modeling are being addressed under the auspices of the Worldwide Protein Data Bank (wwPDB). First, the impact of integrative structures is maximized by PDB-Development, a prototype wwPDB repository for archiving, validating, visualizing, and disseminating integrative structures. Second, the scope of structural biology is expanded by linking the wwPDB resource for integrative structures with archives of data that have not been generally used for structure determination but are increasingly important for computing integrative structures, such as data from various types of mass spectrometry, spectroscopy, optical microscopy, proteomics, and genetics. To address the largest of modeling problems, a type of integrative modeling called metamodeling is being developed; metamodeling combines different types of input models as opposed to different types of data to compute an output model. Collectively, these developments will facilitate the structural biology mindset in cell biology and underpin spatiotemporal mapping of the entire cell.

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

Michalska K, A Joachimiak (2021)

Structural genomics and the Protein Data Bank.

The Journal of biological chemistry, 296:100747.

The field of Structural Genomics arose over the last 3 decades to address a large and rapidly growing divergence between microbial genomic, functional, and structural data. Several international programs took advantage of the vast genomic sequence information and evaluated the feasibility of structure determination for expanded and newly discovered protein families. As a consequence, structural genomics has developed structure-determination pipelines and applied them to a wide range of novel, uncharacterized proteins, often from "microbial dark matter," and later to proteins from human pathogens. Advances were especially needed in protein production and rapid de novo structure solution. The experimental three-dimensional models were promptly made public, facilitating structure determination of other members of the family and helping to understand their molecular and biochemical functions. Improvements in experimental methods and databases resulted in fast progress in molecular and structural biology. The Protein Data Bank structure repository played a central role in the coordination of structural genomics efforts and the structural biology community as a whole. It facilitated development of standards and validation tools essential for maintaining high quality of deposited structural data.

RevDate: 2021-08-11
CmpDate: 2021-08-11

Zebell SG (2021)

A broad view: Dick Flavell.

Plant physiology, 185(3):727-730.

RevDate: 2021-09-01
CmpDate: 2021-09-01

Lipshitz HD (2021)

The Descent of Databases.

Genetics, 217(3):.

RevDate: 2021-08-18
CmpDate: 2021-08-18

Limon J, K Mrózek (2021)

Albert de la Chapelle-pro memoriam.

Journal of applied genetics, 62(3):455-458.

In this brief article, we celebrate the life and numerous scientific achievements of Dr. Albert de la Chapelle, a pioneer in the fields of human genetics and cytogenetics.

RevDate: 2021-08-12
CmpDate: 2021-08-12

Lipshitz HD (2021)

The Origin of GENETICS.

Genetics, 217(1):1-2.

RevDate: 2021-09-05
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: 2021-08-20
CmpDate: 2021-08-02

Viegas J (2021)

Profile of Mark Stoneking.

Proceedings of the National Academy of Sciences of the United States of America, 118(8):.

RevDate: 2021-04-30
CmpDate: 2021-04-30

Portera M, M Mandrioli (2021)

Who's afraid of epigenetics? Habits, instincts, and Charles Darwin's evolutionary theory.

History and philosophy of the life sciences, 43(1):20.

Our paper aims at bringing to the fore the crucial role that habits play in Charles Darwin's theory of evolution by means of natural selection. We have organized the paper in two steps: first, we analyse value and functions of the concept of habit in Darwin's early works, notably in his Notebooks, and compare these views to his mature understanding of the concept in the Origin of Species and later works; second, we discuss Darwin's ideas on habits in the light of today's theories of epigenetic inheritance, which describe the way in which the functioning and expression of genes is modified by the environment, and how these modifications are transmitted over generations. We argue that Darwin's lasting and multifaceted interest in the notion of habit, throughout his intellectual life, is both conceptually and methodologically relevant. From a conceptual point of view, intriguing similarities can be found between Darwin's (early) conception of habit and contemporary views on epigenetic inheritance. From a methodological point of view, we suggest that Darwin's plastic approach to habits, from his early writings up to the mature works, can provide today's evolutionary scientists with a viable methodological model to address the challenging task of extending and expanding evolutionary theory, with particular reference to the integration of epigenetic mechanisms into existing models of evolutionary change. Over his entire life Darwin has modified and reassessed his views on habits as many times as required by evidence: his work on this notion may represent the paradigm of a habit of good scientific research methodology.

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: 2021-03-31
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: 2021-03-09
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: 2021-08-03
CmpDate: 2021-03-09

Miga KH (2021)

Breaking through the unknowns of the human reference genome.

Nature, 590(7845):217-218.

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

Fraser CM (2021)

A genome to celebrate.

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

RevDate: 2021-03-26
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: 2021-07-27
CmpDate: 2021-07-27

Stretton AOW (2020)

My life with Sydney, 1961-1971.

Journal of neurogenetics, 34(3-4):225-237.

During the 1961-1971 decade, Sydney Brenner made several significant contributions to molecular biology-showing that the genetic code is a triplet code; discovery of messenger RNA; colinearity of gene and protein; decoding of chain terminating codons; and then an important transition: the development of the nematode Caenorhabditis elegans into the model eucaryote genetic system that has permeated the whole of recent biology.

RevDate: 2021-07-27
CmpDate: 2021-07-27

Waterston RH, DG Moerman (2020)

John Sulston (1942-2018): a personal perspective.

Journal of neurogenetics, 34(3-4):238-246.

John Sulston changed the way we do science, not once, but three times - initially with the complete cell lineage of the nematode Caenorhabditis elegans, next with completion of the genome sequences of the worm and human genomes and finally with his strong and active advocacy for open data sharing. His contributions were widely recognized and in 2002 he received the Nobel Prize in Physiology and Medicine.

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: 2021-08-11
CmpDate: 2021-08-11

Rushton AR (2021)

Counting human chromosomes before 1960: preconceptions, perceptions and predilections.

Annals of science, 78(1):92-116.

In 1956 the biomedical world was surprised to hear a report that human cells each contained forty six chromosomes, rather than the forty eight count that had been documented since the 1920s. Application of available techniques to culture human cells in vitro, halt their division at metaphase, and disperse chromosomes in an optical plane permitted perception of visual images not seen before. Researchers continued to obtain the preconceived forty eight counts until reeducation with these novel epistemic 'chromosomes' convinced them that they could confidently report forty six chromosomes per cell. Within only a few years, and virtually without dissent, the social community of human cytogeneticists agreed upon a shared visual culture of human chromosome count and morphology. The initial forty six count proved not to be an anomaly. A new comparison of historical and ethnomethodological studies has suggested a better understanding of how applied technologies coupled with altered human perceptions established a new science. Human cytogenetics then collaborated with medical genetics to correlate changes in the new human karyotype with disorders of clinical significance.

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: 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: 2021-07-14
CmpDate: 2021-07-14

Reha-Krantz LJ, MF Goodman (2020)

John W. (Jan) Drake: A Biochemical View of a Geneticist Par Excellence.

Genetics, 216(4):827-836.

John W. Drake died 02-02-2020, a mathematical palindrome, which he would have enjoyed, given his love of "word play and logic," as stated in his obituary and echoed by his family, friends, students, and colleagues. Many aspects of Jan's career have been reviewed previously, including his early years as a Caltech graduate student, and when he was editor-in-chief, with the devoted assistance of his wife Pam, of this journal for 15 impactful years. During his editorship, he raised the profile of GENETICS as the flagship journal of the Genetics Society of America and inspired and contributed to the creation of the Perspectives column, coedited by Jim Crow and William Dove. At the same time, Jan was building from scratch the Laboratory of Molecular Genetics on the newly established Research Triangle Park campus of the National Institute of Environmental Health Science, which he headed for 30 years. This commentary offers a unique perspective on Jan's legacy; we showcase Jan's 1969 benchmark discovery of antimutagenic T4 DNA polymerases and the research by three generations (and counting) of scientists whose research stems from that groundbreaking discovery. This is followed by a brief discussion of Jan's passion: his overriding interest in analyzing mutation rates across species. Several anecdotal stories are included to bring alive one of Jan's favorite phrases, "to think like a geneticist." We feature Jan's genetical approach to mutation studies, along with the biochemistry of DNA polymerase function, our area of expertise. But in the end, we acknowledge, as Jan did, that genetics, also known as in vivo biochemistry, prevails.

RevDate: 2021-05-31
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: 2021-04-16
CmpDate: 2021-04-16

Weake VM (2021)

Gcn5: The quintessential histone acetyltransferase.

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

RevDate: 2021-07-07
CmpDate: 2021-07-07

Pierpont EI, Berry SA, Lin AE, et al (2021)

Mary Ella Mascia Pierpont: Geneticist, scientist, mentor, friend (1945-2020).

American journal of medical genetics. Part A, 185(2):319-323.

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: 2021-07-29
CmpDate: 2021-07-29

Roca-Rada X, Souilmi Y, Teixeira JC, et al (2020)

Ancient DNA Studies in Pre-Columbian Mesoamerica.

Genes, 11(11):.

Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.

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: 2021-05-09
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: 2021-07-30
CmpDate: 2021-07-30

Ortiz R (2020)

Göte Turesson's research legacy to Hereditas: from the ecotype concept in plants to the analysis of landraces' diversity in crops.

Hereditas, 157(1):44.

Hereditas began with articles on plants since its first issue in May 1920 (six out of eight) and continued with more original articles (43% of the total of this journal) on plants (of which 72% of those in plants were on crops) until today. In December 1922, the 140-page article The Genotypical Response of the Plant Species to the Habitat by evolutionary botanist Göte Turesson (Institute of Genetics, Lund University, Åkarp, Sweden) became available. This publication shows that plant phenology has a genetic basis and may ensue from local adaptation. As a result of this research involving various plant species, Turesson elaborated further in this article his term ecotype "as an ecological sub-unit to cover the product arising as a result of the genotypical response of an ecospecies to a particular habitat." Although plant articles included in Hereditas involved from its beginning, trait inheritance, mutants, linkage analysis, cytology or cytogenetics, and more recently gene mapping and analysis of quantitative trait loci with the aid of DNA markers, among others, since the mid-1980s several publications refer to the population biology of plant landraces, which are locally grown cultivars that evolved over time by adapting to their natural and cultural environment (i.e., agriculture), and that may become isolated from other populations of the same crop. This article provides a briefing about research on plant science in the journal with emphasis on crops, summarizes the legacy to genetics of Göte Turesson, and highlights some landrace diversity research results and their potential for plant breeding.

RevDate: 2021-07-14
CmpDate: 2021-07-14

Bender WW (2020)

Molecular Lessons from the Drosophila Bithorax Complex.

Genetics, 216(3):613-617.

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 2020 recipient is Welcome W. Bender of Harvard Medical School, recognizing his creativity and ingenuity in revealing the molecular nature and regulation of the bithorax gene complex.

RevDate: 2021-07-14
CmpDate: 2021-07-14

Fink GR (2020)

A Morgan Legacy.

Genetics, 216(3):611-612.

The Thomas Hunt Morgan Medal recognizes lifetime contributions to the field of genetics. The 2020 recipient is Gerald R. Fink of Massachusetts Institute of Technology and the Whitehead Institute for Biomedical Research, recognizing the discovery of principles central to genome organization and regulation in eukaryotic cells.

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: 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: 2021-06-28
CmpDate: 2021-06-28

Zvénigorosky V, Duchesne S, Romanova L, et al (2020)

The genetic legacy of legendary and historical Siberian chieftains.

Communications biology, 3(1):581.

Seventeen years of archaeological and anthropological expeditions in North-Eastern Siberia (in the Sakha Republic, Yakutia) have permitted the genetic analysis of 150 ancient (15th-19th century) and 510 modern individuals. Almost all males were successfully analysed (Y-STR) and this allowed us to identify paternal lineages and their geographical expansion through time. This genetic data was confronted with mythological, historical and material evidence to establish the sequence of events that built the modern Yakut genetic diversity. We show that the ancient Yakuts recovered from this large collection of graves are not representative of an ancient population. Uncommonly, we were also able to demonstrate that the funerary preference observed here involved three specific male lineages, especially in the 18th century. Moreover, this dominance was likely caused by the Russian conquest of Siberia which allowed some male clans to rise to new levels of power. Finally, we give indications that some mythical and historical figures might have been the actors of those genetic changes. These results help us reconsider the genetic dynamics of colonization in some regions, question the distinction between fact and myth in national histories and provide a rare insight into a funerary ensemble by revealing the biased process of its composition.

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: 2021-07-26
CmpDate: 2021-07-26

Kendler KS (2021)

The Prehistory of Psychiatric Genetics: 1780-1910.

The American journal of psychiatry, 178(6):490-508.

While psychiatric genetics has emerged as one of our most dynamic research fields, the historical context in which we view these developments is limited. To provide such a perspective, the author reviews 48 representative texts, published from 1780 to 1910, examining the inheritance of insanity. Six main conclusions emerge. First, most authors viewed heredity as among the strongest risk factors for insanity. Second, most writers concluded that a predisposition to illness rather than the illness itself was transmitted in families. Third, the probabilistic nature of the transmission was noted, as insanity often skipped generations or affected only a few of many siblings. Fourth, authors discussed the homogeneity versus heterogeneity of familial transmission of the various forms of insanities. Heterogeneous transmission was usually seen as the rule-with relatives of insane patients affected with a wide variety of psychiatric, and sometimes neurological, illnesses. Homogeneous transmission ("like begets like") was the exception. Fifth, writers noted that odd and eccentric personality features were common in the relatives of their insane patients. Finally, inheritance was commonly understood to include prior environmental parental experiences, and some authors noted that parent-offspring transmission of insanity could arise from psychological or intrauterine effects. Many of these conclusions, arising solely from clinical experience and without an understanding of biological mechanisms, statistical analyses, or necessary controls, are supported by later, more rigorous methods. Rather than entirely rejecting its value, we might view this literature as a complementary resource, likely more biased, but suffused with the extensive clinical knowledge of our forebears.

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: 2021-07-14
CmpDate: 2021-07-14

Botstein D (2020)

Perspective: Linkage Maps, Communities of Geneticists, and Genome Databases.

Genetics, 216(2):261-262.

The Thomas Hunt Morgan Medal recognizes lifetime contributions to the field of genetics. The 2020 recipient is David Botstein of Calico Labs and Princeton University, recognizing his multiple contributions to genetics, including the collaborative development of methods for defining genetic pathways, mapping genomes, and analyzing gene expression.

RevDate: 2021-06-03
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: 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: 2021-02-16
CmpDate: 2020-12-14

Anonymous (2020)

Marking a milestone.

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

RevDate: 2021-09-20
CmpDate: 2020-11-06

Josephy D (2020)

A tribute to Prof. Bruce Ames.

Mutation research. Genetic toxicology and environmental mutagenesis, 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: 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: 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: 2021-02-22
CmpDate: 2021-02-22

Guffroy A, Martin T, V Gies (2020)

.

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

RevDate: 2021-08-02
CmpDate: 2021-07-02

Mathieson I (2020)

Human adaptation over the past 40,000 years.

Current opinion in genetics & development, 62:97-104.

Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.

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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 @ gmail.com

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).

Timelines

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

Biographies

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 )