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18 Aug 2019 at 01:33
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Bibliography on: History of Genetics


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RJR: Recommended Bibliography 18 Aug 2019 at 01:33 Created: 

History of Genetics

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

Citations The Papers (from PubMed®)

RevDate: 2019-08-16
CmpDate: 2019-08-16

La Gruta NL, Gras S, Daley SR, et al (2018)

Understanding the drivers of MHC restriction of T cell receptors.

Nature reviews. Immunology, 18(7):467-478.

T cell discrimination of self and non-self is predicated on αβ T cell receptor (TCR) co-recognition of peptides presented by MHC molecules. Over the past 20 years, structurally focused investigations into this MHC-restricted response have provided profound insights into T cell function. Simultaneously, two models of TCR recognition have emerged, centred on whether the TCR has, through evolution, acquired an intrinsic germline-encoded capacity for MHC recognition or whether MHC reactivity is conferred by developmental selection of TCRs. Here, we review the structural and functional data that pertain to these theories of TCR recognition, which indicate that it will be necessary to assimilate features of both models to fully account for the molecular drivers of this evolutionarily ancient interaction between the TCR and MHC molecules.

RevDate: 2019-08-13
CmpDate: 2019-08-13

Henn BM, L Quintana-Murci (2018)

Editorial overview: The history, geography and adaptation of human genes: A tribute to L. Luca Cavalli-Sforza.

Current opinion in genetics & development, 53:iii-v.

RevDate: 2019-08-12
CmpDate: 2019-08-12

Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, et al (2018)

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

Nucleic acids research, 46(W1):W209-W214.

RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes from all kingdoms. Six novel or refactored programs have been added since the 2015 NAR Web Software Issue, including updated programs to analyse regulatory variants (retrieve-variation-seq, variation-scan, convert-variations), along with tools to extract sequences from a list of coordinates (retrieve-seq-bed), to select motifs from motif collections (retrieve-matrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara). Three use cases illustrate the integration of new and refactored tools to the suite. This Anniversary update gives a 20-year perspective on the software suite. RSAT is well-documented and available through Web sites, SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

RevDate: 2019-08-13
CmpDate: 2019-08-13

Pluta D, Tokarski M, Karpiewska A, et al (2017)

15th Anniversary of the Molecular Techniques Unit at the Department of Forensic Medicine at Wroclaw Medical University.

Archiwum medycyny sadowej i kryminologii, 67(2):142-149.

Molecular Techniques Unit at the Department of Forensic Medicine, Wroclaw Medical University has been operating since December 2003. Soon it will be 15 years since its establishment. This anniversary become an inspiration to write down the story of this institution whose origins illustrate the immense changes that have taken place in forensic genetics. The aim of our work was also to consolidate the professional achievements of Professor Tadeusz Dobosz, chief of the Unit, one of the pioneers of introducing DNA testing technology into Polish forensic medicine. The most important achievements of the Unit include participation in two EU research projects, the development of a non-destructive method of extraction of genetic material, research in field of gene therapy and certification of the Laboratory of the Molecular Techniques Unit by the Polish Accreditation Center (PCA) confirming compliance with the requirements of the PN-EN ISO/IEC 17025:2005 standard.

RevDate: 2019-08-09
CmpDate: 2019-08-09

Kasahara M, Flajnik MF, Y Takahama (2019)

Biology, evolution, and history of antigen processing and presentation: Immunogenetics special issue 2019.

Immunogenetics, 71(3):137-139.

RevDate: 2019-08-09
CmpDate: 2019-08-09

Sadayappan S (2018)

My Life, My Heart, and My(osin) Binding Protein-C.

Circulation research, 122(7):918-920.

RevDate: 2019-07-30
CmpDate: 2019-07-30

Schmidt C, T Hubbard (2018)

Scientists on the Spot: Sequencing the human genome to influence patient healthcare.

Cardiovascular research, 114(9):e66-e67.

RevDate: 2019-07-30
CmpDate: 2019-07-30

Schunkert H, NJ Samani (2018)

Into the great wide open: 10 years of genome-wide association studies.

Cardiovascular research, 114(9):1189-1191.

RevDate: 2019-07-24
CmpDate: 2019-07-24

Cameron RA (2019)

A personal history of the echinoderm genome sequencing.

Methods in cell biology, 151:55-61.

At the most fundamental level, the genome is the basis for questions about the mechanisms of development: how it works. This perspective provides a brief historical review of the sequencing of the echinoderm genome and the progress in answering this complex question, which depends on technological advances as well as intellectual ones.

RevDate: 2019-07-24
CmpDate: 2019-07-24

Shay JW, WE Wright (2019)

Telomeres and telomerase: three decades of progress.

Nature reviews. Genetics, 20(5):299-309.

Many recent advances have emerged in the telomere and telomerase fields. This Timeline article highlights the key advances that have expanded our views on the mechanistic underpinnings of telomeres and telomerase and their roles in ageing and disease. Three decades ago, the classic view was that telomeres protected the natural ends of linear chromosomes and that telomerase was a specific telomere-terminal transferase necessary for the replication of chromosome ends in single-celled organisms. While this concept is still correct, many diverse fields associated with telomeres and telomerase have substantially matured. These areas include the discovery of most of the key molecular components of telomerase, implications for limits to cellular replication, identification and characterization of human genetic disorders that result in premature telomere shortening, the concept that inhibiting telomerase might be a successful therapeutic strategy and roles for telomeres in regulating gene expression. We discuss progress in these areas and conclude with challenges and unanswered questions in the field.

RevDate: 2019-07-08
CmpDate: 2019-07-08

Pejchinovski M, H Mischak (2017)

Clinical Proteomics in Kidney Disease: From Discovery to Clinical Application.

Prilozi (Makedonska akademija na naukite i umetnostite. Oddelenie za medicinski nauki), 38(3):39-54.

Proteome analysis has been applied in multiple studies in the context of chronic kidney disease, aiming at improving our knowledge on the molecular pathophysiology of the disease. The approach is generally based on the hypothesis that proteins are key in maintaining kidney function, and disease is a clinical consequence of a significant change of the protein level. Knowledge on critical proteins and their alteration in disease should in turn enable identification of ideal biomarkers that could guide patient management. In addition, all drugs currently employed target proteins. Hence, proteome analysis also promises to enable identifying the best suited therapeutic target, and, in combination with biomarkers, could be used as the rationale basis for personalized intervention. To assess the current status of proteome analysis in the context of CKD, we present the results of a systematic review, of up-to-date scientific research, and give an outlook on the developments that can be expected in near future. Based on the current literature, proteome analysis has already seen implementation in the management of CKD patients, and it is expected that this approach, also supported by the positive results generated to date, will see advanced high-throughput application.

RevDate: 2019-07-05
CmpDate: 2019-07-05

Brownlee GG (2018)

The Legacy of Fred Sanger-100 Years on from 1918.

Journal of molecular biology, 430(17):2661-2669.

RevDate: 2019-06-28
CmpDate: 2019-06-28

Salter B, C Salter (2017)

Controlling new knowledge: Genomic science, governance and the politics of bioinformatics.

Social studies of science, 47(2):263-287.

The rise of bioinformatics is a direct response to the political difficulties faced by genomics in its quest to be a new biomedical innovation, and the value of bioinformatics lies in its role as the bridge between the promise of genomics and its realization in the form of health benefits. Western scientific elites are able to use their close relationship with the state to control and facilitate the emergence of new domains compatible with the existing distribution of epistemic power - all within the embrace of public trust. The incorporation of bioinformatics as the saviour of genomics had to be integrated with the operation of two key aspects of governance in this field: the definition and ownership of the new knowledge. This was achieved mainly by the development of common standards and by the promotion of the values of communality, open access and the public ownership of data to legitimize and maintain the governance power of publicly funded genomic science. Opposition from industry advocating the private ownership of knowledge has been largely neutered through the institutions supporting the science-state concordat. However, in order for translation into health benefits to occur and public trust to be assured, genomic and clinical data have to be integrated and knowledge ownership agreed upon across the separate and distinct governance territories of scientist, clinical medicine and society. Tensions abound as science seeks ways of maintaining its control of knowledge production through the negotiation of new forms of governance with the institutions and values of clinicians and patients.

RevDate: 2019-06-24
CmpDate: 2019-06-24

Barciszewski J, Szymański M, Malesa A, et al (2018)

[Origins of molecular life sciences. Polish context].

Postepy biochemii, 64(1):55-66.

Different scientific disciplines such as physics, genetics or biochemistry crossed over into molecular biology in the last century. The Polish state didn't existed at the beginning of XX century, but the territory for a large number of scientists was not a limitation in delineating new routes, making fundamental discoveries or training the new generation of distinguished people of sciences. We want to tell the story of roots of molecular biology from the Polish perspective and outline its importance, by bringing closer the most essential discoveries of elite scientists in different fields of life science, associated with Poland and its territory.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Bonneuil C (2019)

Seeing nature as a 'universal store of genes': How biological diversity became 'genetic resources', 1890-1940.

Studies in history and philosophy of biological and biomedical sciences, 75:1-14.

Till late in the 20th century, biological diversity has been understood and addressed in terms of "genetic resources". This paper proposes a history of this "genetic resources" concept and the biopolitical practices it was related to. A semantic history of the 'resource' idiom first sheds light on how, in the age of empires and fossil industrialism, the Earth came to be considered as a stock of static mineral and living reserves. Then we follow how the gene became the unit of this "resourcist" view of biological diversity as static stocks of entities open to prospection, harnessing and "conservation". Erwin Baur, Nikolai I. Vavilov, Aleksandr S. Serebrovsky and Hermann J. Muller were key biologists who introduced a spatial turn to the gene concept. Beyond the space-time of Neo-mendelian and Morganian laboratory genetics, genes became understood though a geographical gaze at a planetary scale. The world became a "universal store of genes" (Vavilov, 1929). From 1926 to World War 2, this advent of genes as new global epistemic objects went hand in hand with genes' new modes of existence as geopolitical objects. The article documents Interwar years' scramble for genes as well as first collaborative international efforts to conserve and exchange genetic material (which prefigured post WW2 initiatives), and situates the rise of the 'genetic resources' category within mid 20th century's imperialism, high-modernism, agricultural modernization and biopolitics.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Folle GA (2018)

Chromosomes forever Prof. Máximo Eduardo Drets (1930-2017).

Mutation research. Genetic toxicology and environmental mutagenesis, 836(Pt B):2-3.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Maxson Jones K, Ankeny RA, R Cook-Deegan (2018)

The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project.

Journal of the history of biology, 51(4):693-805.

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the "community" of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner's proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Green ED, CR Donohue (2018)

Special Issue Editors' Introduction: "Genomics and the Human Genome Project".

Journal of the history of biology, 51(4):625-629.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Nicoglou A (2018)

Waddington's epigenetics or the pictorial meetings of development and genetics.

History and philosophy of the life sciences, 40(4):61 pii:10.1007/s40656-018-0228-8.

In 1956, in his Principles of Embryology, Conrad Hal Waddington explained that the word "epigenetics" should be used to translate and update Wilhelm Roux' German notion of "Entwicklungsmechanik" (1890) to qualify the studies focusing on the mechanisms of development. When Waddington mentioned it in 1956, the notion of epigenetics was not yet popular, as it would become from the 1980s. However, Waddington referred first to the notion in the late 1930s. While his late allusion clearly reveals that Waddington readily associated the notion of epigenetics with the developmental process, in the contemporary uses of the notion this developmental connotation seems to have disappeared. The advent and success of molecular biology have probably contributed to focusing biologists' attention on the "genetic" or the "non-genetic" over the "developmental". In the present paper, I first examine the links that exist, in Waddington's work, between the classical notion of epigenesis in embryology and those of epigenetics that Waddington proposed to connect, and even synthesize, data both from embryology and genetics. Second, I show that Waddington's own view of epigenetics has changed over time and I analyze how these changes appear through his many representations (both schematic or metaphorical images) of the relationships between genetic signals and developmental processes.

RevDate: 2019-06-13
CmpDate: 2019-06-11

November J (2018)

More than Moore's Mores: Computers, Genomics, and the Embrace of Innovation.

Journal of the history of biology, 51(4):807-840.

The genomics community has frequently compared advances in sequencing to advances in microelectronics. Lately there have been many claims, including by the National Human Genome Research Institute (NHGRI), that genomics is outpacing developments in computing as measured by Moore's law - the notion that computers double in processing capability per dollar spent every 18-24 months. Celebrations of the "$1000 genome" and other speed-related sequencing milestones might be dismissed as a distraction from genomics' slowness in delivering clinical breakthroughs, but the fact that such celebrations have been persistently encouraged by the NHGRI reveals a great deal about the priorities and expectations of the American general public, the intended audience of the genomics-computing comparison. By delving into the history of speculative thinking about sequencing and computing, this article demonstrates just how much more receptive to high-risk/high-payoff ventures the NIH and the general public have become. The article also provides access to some of the roots and consequences of the association of "innovation talk" with genomics, and the means to look past that association to the less glamorous (but arguably much more important) contributions of the NHGRI to building the field of genomics.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Kornfeld S (2018)

A Lifetime of Adventures in Glycobiology.

Annual review of biochemistry, 87:1-21.

My initial research experience involved studying how bacteria synthesize nucleotide sugars, the donors for the formation of cell wall polysaccharides. During this time, I became aware that mammalian cells also have a surface coat of sugars and was intrigued as to whether these sugars might be arranged in specific sequences that function as information molecules in biologic processes. Thus began a long journey that has taken me from glycan structural analysis and determination of plant lectin-binding preferences to the biosynthesis of Asn-linked oligosaccharides and the mannose 6-phosphate (Man-6-P) lysosomal enzyme targeting pathway. The Man-6-P system represents an early example of a glycan serving as an information molecule in a fundamental cellular function. The remarkable advances in the field of glycobiology since I entered have uncovered scores of additional examples of oligosaccharide-lectin interactions mediating critical biologic processes. It has been a rewarding experience to participate in the efforts that have established a central role for glycans in biology.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Frezza G, M Capocci (2018)

Thomas Hunt Morgan and the invisible gene: the right tool for the job.

History and philosophy of the life sciences, 40(2):31 pii:10.1007/s40656-018-0196-z.

The paper analyzes the early theory building process of Thomas Hunt Morgan (1866-1945) from the 1910s to the 1930s and the introduction of the invisible gene as a main explanatory unit of heredity. Morgan's work marks the transition between two different styles of thought. In the early 1900s, he shifted from an embryological study of the development of the organism to a study of the mechanism of genetic inheritance and gene action. According to his contemporaries as well as to historiography, Morgan separated genetics from embryology, and the gene from the whole organism. Other scholars identified an underlying embryological focus in Morgan's work throughout his career. Our paper aims to clarify the debate by concentrating on Morgan's theory building-characterized by his confidence in the power of experimental methods, and carefully avoiding any ontological commitment towards the gene-and on the continuity of the questions to be addressed by both embryology and genetics.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Button C (2018)

James Cossar Ewart and the Origins of the Animal Breeding Research Department in Edinburgh, 1895-1920.

Journal of the history of biology, 51(3):445-477.

In 1919 the Animal Breeding Research Department was established in Edinburgh. This Department, later renamed the Institute of Animal Genetics, forged an international reputation, eventually becoming the centrepiece of a cluster of new genetics research units and institutions in Edinburgh after the Second World War. Yet despite its significance for institutionalising animal genetics research in the UK, the origins and development of the Department have not received as much scholarly attention as its importance warrants. This paper sheds new light on Edinburgh's place in early British genetics by drawing upon recently catalogued archival sources including the papers of James Cossar Ewart, Regius Professor of Natural History at the University of Edinburgh between 1882 and 1927. Although presently a marginal figure in genetics historiography, Ewart established two sites for experimental animal breeding work between 1895 and 1911 and played a central role in the founding of Britain's first genetics lectureship, also in 1911. These early efforts helped to secure government funding in 1913. However, a combination of the First World War, bureaucratic problems and Ewart's personal ambitions delayed the creation of the Department and the appointment of its director by another six years. This paper charts the institutionalisation of animal breeding and genetics research in Edinburgh within the wider contexts of British genetics and agriculture in the early twentieth century.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Deichmann U (2017)

Hierarchy, determinism, and specificity in theories of development and evolution.

History and philosophy of the life sciences, 39(4):33 pii:10.1007/s40656-017-0160-3.

The concepts of hierarchical organization, genetic determinism and biological specificity (for example of species, biologically relevant macromolecules, or genes) have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information (specificity) and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled "reductionist". However, the concepts have been marginalized or rejected in some of the research that in the late 1960s began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that 'molecular reductionism' has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular 'reductionism', in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Morange M (2017)

Homage to Eric Davidson.

History and philosophy of the life sciences, 39(4):30 pii:10.1007/s40656-017-0157-y.

The Britten-Davidson model of genetic regulation was well received by American molecular biologists and embryologists, but not by the members of the French School of molecular biology. In particular, François Jacob considered it too abstract and too removed from experiments. I re-examine the contrast between the Britten-Davidson model and the operon model by Jacob and Monod, the different scientific contexts in which they were produced and the different roles they played. I also describe my recent encounters with Eric Davidson, and how I discovered the extraordinary continuity of his work on the development of the sea urchin, as well as his rich personality.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Deichmann U (2017)

Eric Davidson, his philosophy, and the history of science.

History and philosophy of the life sciences, 39(4):31 pii:10.1007/s40656-017-0158-x.

Eric Davidson, a passionate molecular developmental biologist and intellectual, believed that conceptual advances in the sciences should be based on knowledge of conceptual history. Convinced of the superiority of a causal-analytical approach over other methods, he succeeded in successfully applying this approach to the complex feature of organismal development by introducing the far-reaching concept of developmental Gene Regulatory Networks. This essay reviews Davidson's philosophy, his support for the history of science, and some aspects of his scientific personality.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Morange M, U Deichmann (2017)

Introduction: Eric Davidson and the molecular biology of evolution and development.

History and philosophy of the life sciences, 39(4):28 pii:10.1007/s40656-017-0155-0.

Between November 30th and December 2nd, 2015, the Jacques Loeb Centre for the History and Philosophy of the Life Sciences at Ben-Gurion University of the Negev in Beer Sheva (Israel) held its Eighth International Workshop under the title "From Genome to Gene: Causality, Synthesis and Evolution". Eric Davidson, the founder of the concept of developmental Gene Regulatory Networks, had regularly attended the previous meetings, and his participation in this one was expected, but he suddenly passed away 3 months before. In this paper, we provide an introduction and overview on five papers that were presented at the workshop and examine the importance of genomes and gene regulatory networks in extant biology, developmental biology, evolutionary biology and medicine, as well as a collection of remembrances of Eric Davidson, of his personality as well as of his scientific contributions. Historical perspectives are provided, and the ethical issues raised by the new tools developed to modify the genome are also discussed.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Stevens H (2018)

Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration.

Journal of the history of biology, 51(4):657-691.

Genomics is increasingly considered a global enterprise - the fact that biological information can flow rapidly around the planet is taken to be important to what genomics is and what it can achieve. However, the large-scale international circulation of nucleotide sequence information did not begin with the Human Genome Project. Efforts to formalize and institutionalize the circulation of sequence information emerged concurrently with the development of centralized facilities for collecting that information. That is, the very first databases build for collecting and sharing DNA sequence information were, from their outset, international collaborative enterprises. This paper describes the origins of the International Nucleotide Sequence Database Collaboration between GenBank in the United States, the European Molecular Biology Laboratory Databank, and the DNA Database of Japan. The technical and social groundwork for the international exchange of nucleotide sequences created the conditions of possibility for imagining nucleotide sequences (and subsequently genomes) as a "global" objects. The "transnationalism" of nucleotide sequence was critical to their ontology - what DNA sequences came to be during the Human Genome Project was deeply influenced by international exchange.

RevDate: 2019-06-13
CmpDate: 2019-06-11

O'Malley MA (2018)

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

Journal of the history of biology, 51(2):319-354.

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Peterson EL (2017)

'So far like the present period': a reply to 'C.H. Waddington's differences with the creators of the Modern Evolutionary Synthesis: a Tale of Two Genes'.

History and philosophy of the life sciences, 39(3):19 pii:10.1007/s40656-017-0145-2.

RevDate: 2019-06-13
CmpDate: 2019-06-10

Bard JBL (2017)

C.H. Waddington's differences with the creators of the modern evolutionary synthesis: a tale of two genes.

History and philosophy of the life sciences, 39(3):18.

In 2011, Peterson suggested that the main reason why C.H. Waddington was essentially ignored by the framers of the modern evolutionary synthesis in the 1950s was because they were Cartesian reductionists and mathematical population geneticists while he was a Whiteheadian organicist and experimental geneticist who worked with Drosophila. This paper suggests a further reason that can only be seen now. The former defined genes and their alleles by their selectable phenotypes, essentially the Mendelian view, while Waddington defined a gene through its functional role as determined by genetic analysis, a view that foresaw the modern view that a gene is a DNA sequence with some function. The former were interested in selection, while Waddington focused on variation. The differences between the two views of a gene are briefly considered in the context of systems biology.

RevDate: 2019-06-13
CmpDate: 2019-06-11

de Chadarevian S (2018)

Whose Turn? Chromosome Research and the Study of the Human Genome.

Journal of the history of biology, 51(4):631-655.

A common account sees the human genome sequencing project of the 1990s as a "natural outgrowth" of the deciphering of the double helical structure of DNA in the 1950s. The essay aims to complicate this neat narrative by putting the spotlight on the field of human chromosome research that flourished at the same time as molecular biology. It suggests that we need to consider both endeavors - the human cytogeneticists who collected samples and looked down the microscope and the molecular biologists who probed the molecular mechanisms of gene function - to understand the rise of the human genome sequencing project and the current genomic practices. In particular, it proposes that what has often been described as the "molecularization" of cytogenetics could equally well be viewed as the turn of molecular biologists to human and medical genetics - a field long occupied by cytogeneticists. These considerations also have implications for the archives that are constructed for future historians and policy makers.

RevDate: 2019-05-22
CmpDate: 2019-05-22

O'Mahony S (2019)

After the golden age: what is medicine for?.

Lancet (London, England), 393(10183):1798-1799.

RevDate: 2019-05-20
CmpDate: 2019-05-20

Visscher PM, ME Goddard (2019)

From R.A. Fisher's 1918 Paper to GWAS a Century Later.

Genetics, 211(4):1125-1130.

The genetics and evolution of complex traits, including quantitative traits and disease, have been hotly debated ever since Darwin. A century ago, a paper from R.A. Fisher reconciled Mendelian and biometrical genetics in a landmark contribution that is now accepted as the main foundation stone of the field of quantitative genetics. Here, we give our perspective on Fisher's 1918 paper in the context of how and why it is relevant in today's genome era. We mostly focus on human trait variation, in part because Fisher did so too, but the conclusions are general and extend to other natural populations, and to populations undergoing artificial selection.

RevDate: 2019-05-16
CmpDate: 2019-05-16

Azar B (2019)

Profile of Daniel A. Haber.

Proceedings of the National Academy of Sciences of the United States of America, 116(13):5840-5842.

RevDate: 2019-03-29
CmpDate: 2019-03-28

Strauss BS (2019)

Martynas Yčas: The "Archivist" of the RNA Tie Club.

Genetics, 211(3):789-795.

Between about 1951 and the early 1960s, the basic structure of molecular biology was revealed. Central to our understanding was the unraveling of the various roles of RNA, culminating in the identification of messenger RNA (mRNA) and the deciphering of the genetic code. We know a great deal about the role of Brenner, Crick, Jacob, and Nirenberg in these discoveries, but many others played important supporting parts. One of these is a little-known scientist, Martynas Yčas, who appears in histories, generally without explanation, as the "archivist of the RNA Tie Club." Yčas was born in Lithuania. His father helped write the Lithuanian Constitution in 1919. He studied Roman Law and served in the Lithuanian army before escaping from the Russians in 1940. The records of correspondence of Yčas with the physicist George Gamow and with Francis Crick throw some light on the genesis of our understanding of the role of mRNA. The story of the "RNA Tie Club" illustrates the difficulty in assigning credit for important discoveries and underscores the importance of a free exchange of information, even (or especially) among competitors.

RevDate: 2019-04-29
CmpDate: 2019-04-29

Frixione E, L Ruiz-Zamarripa (2019)

The "scientific catastrophe" in nucleic acids research that boosted molecular biology.

The Journal of biological chemistry, 294(7):2249-2255.

RevDate: 2019-03-28
CmpDate: 2019-03-28

Dung SK, López A, Barragan EL, et al (2019)

Illuminating Women's Hidden Contribution to Historical Theoretical Population Genetics.

Genetics, 211(2):363-366.

While productivity in academia is measured through authorship, not all scientific contributors have been recognized as authors. We consider nonauthor "acknowledged programmers" (APs), who developed, ran, and sometimes analyzed the results of computer programs. We identified APs in Theoretical Population Biology articles published between 1970 and 1990, finding that APs were disproportionately women (P = 4.0 × 10-10). We note recurrent APs who contributed to several highly-cited manuscripts. The occurrence of APs decreased over time, corresponding to the masculinization of computer programming and the shift of programming responsibilities to individuals credited as authors. We conclude that, while previously overlooked, historically, women have made substantial contributions to computational biology. For a video of this abstract, see: https://vimeo.com/313424402.

RevDate: 2019-05-20
CmpDate: 2019-05-20

Moniz MBJ, FG Hutton (2019)

Genetics Research turns a new [open access] leaf….

Genetics research, 101:e1 pii:S0016672318000071.

RevDate: 2019-02-19
CmpDate: 2019-02-18

Morganti S, Tarantino P, Ferraro E, et al (2019)

Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life.

Critical reviews in oncology/hematology, 133:171-182.

The finalization of the Human Genome Project in 2003 paved the way for a deeper understanding of cancer, favouring a faster progression towards "personalized" medicine. Research in oncology has progressively focused on the sequencing of cancer genomes, to better understand the genetic basis of tumorigenesis and identify actionable alterations to guide cancer therapy. Thanks to the development of next-generation-sequencing (NGS) techniques, sequencing of tumoral DNA is today technically easier, faster and cheaper. Commercially available NGS panels enable the detection of single or global genomic alterations, namely gene mutation and mutagenic burden, both on germline and somatic DNA, potentially predicting the response or resistance to cancer treatments. Profiling of tumor DNA is nowadays a standard in cancer research and treatment. In this review we discuss the history, techniques and applications of NGS in cancer care, under a "personalized tailored therapy" perspective.

RevDate: 2019-03-05
CmpDate: 2019-03-05

Livi GP (2019)

Halcyon days of TOR: Reflections on the multiple independent discovery of the yeast and mammalian TOR proteins.

Gene, 692:145-155.

The quest to elucidate the molecular mechanism of action of rapamycin in the early 1990s led to the discovery of the novel TOR (target of rapamycin) proteins in yeast and mammalian cells. This was a major breakthrough that resulted in the development of new rapamycin analogs as anti-cancer agents, and launched new research that revealed the pre-eminent biological role of mTOR (mammalian or mechanistic TOR). Beyond mediating rapamycin sensitivity, the TOR proteins are nutrient sensing protein kinases, conserved from yeast to man, with a core function in regulating cell growth, metabolism and overall cell survival. There have been many insightful historical accounts of the origins of TOR; however, the complete TOR dossier would benefit from a chapter on the untold story of the simultaneous co-discovery of the yeast TOR proteins by two independent laboratories, one that is inclusive of the discoveries made at the former SmithKline Beecham (legacy GlaxoSmithKline). Accordingly, this comprehensive retrospective retraces the provenance of yeast TOR (circa 1990-1996) and highlights the early groundbreaking publications that revealed the identity of the TOR genes and proteins. It also commemorates key companion papers which helped to clarify yeast TOR gene nomenclature, identified structural motifs in the predicted TOR protein sequences, demonstrated interactions between yeast FKBP12-rapamycin and TOR, characterized mutations responsible for drug resistance, and began to decipher TOR protein function; some of these crucial early studies appeared in this journal (e.g., Koser et al., 1993. Gene 129, 159-165; Cafferkey et al., 1994. Gene 141, 133-136; Freeman and Livi, 1996. Gene 172, 143-147). A period of intensive investigation, events are portrayed chronologically and juxtaposed alongside the independent parallel efforts to identify and purify mTOR. Finally, in a broader historical context, TOR and mTOR are examined a posteriori as paragons of multiple discovery, illustrating how this common phenomenon (also known as simultaneous invention) can greatly accelerate problem solving and advance human knowledge in a fast-breaking area of scientific research.

RevDate: 2019-03-12
CmpDate: 2019-03-12

Haloupek N (2019)

Barbara J. Meyer: 2018 Thomas Hunt Morgan Medal.

Genetics, 211(1):1-3.

The Genetics Society of America's (GSA) Thomas Hunt Morgan Medal honors researchers for lifetime achievement in genetics. The recipient of the 2018 Morgan Medal, Barbara J. Meyer of the Howard Hughes Medical Institute and the University of California, Berkeley, is recognized for her career-long, groundbreaking investigations of how chromosome behaviors are controlled. Meyer's work has revealed mechanisms of sex determination and dosage compensation in Caenorhabditis elegans that continue to serve as the foundation of diverse areas of study on chromosome structure and function today, nearly 40 years after she began her work on the topic.

RevDate: 2019-04-08
CmpDate: 2019-04-08

Jager MJ, Brand A, FHJ Claas (2019)

Jon van Rood: The pioneer and his personal view on the early developments of HLA and immunogenetics.

Transplant immunology, 52:1-26.

A single observation in a patient with an unusual transfusion reaction led to a life-long fascination with immunogenetics, and a strong wish to improve the care for patients needing a transplantation. In 2017, Jon van Rood, one of the pioneers in the field of HLA and immunogenetics of transplantation, passed away. Several obituaries have appeared describing some of the highlights of his career. However, the details of the early developments leading among others to the routine use of HLA as an important parameter for donor selection in organ- and hematopoietic stem cell transplantation are largely unknown to the community. After his retirement as Chair of the Department of Immunohaematology and Blood Transfusion (IHB) in 1991, Jon van Rood wrote regularly in the "Crosstalk", the departmental journal, and gave his personal view on the history of the discovery and implications of HLA. These autobiographic descriptions were originally written in Dutch and have been translated, while texts from other sources and the relevant references have been added to illustrate the historical perspective. This special issue of Transplant Immunology combines the autobiographic part, Jon's own version of the history, with other facts of his scientific life and the impact of his findings on the field of clinical transplantation. Hopefully, this knowledge of the history will be of benefit for future developments in transplantation immunology.

RevDate: 2019-05-30
CmpDate: 2019-05-30

Krumlauf R (2018)

Hox genes, clusters and collinearity.

The International journal of developmental biology, 62(11-12):659-663.

This year marks the 40th anniversary of the discovery by Ed Lewis of the property of collinearity in the bithorax gene complex in Drosophila. This landmark work illustrated the need to understand regulatory mechanisms that coordinate expression of homeotic gene clusters. Through the efforts of many groups, investigation of the Hox gene family has generated many fundamental findings on the roles and regulation of this conserved gene family in development, disease and evolution. This has led to a number of important conceptual advances in gene regulation and evolutionary biology. This article presents some of the history and advances made through studies on Hox gene clusters.

RevDate: 2019-05-01
CmpDate: 2019-05-01

Anonymous (2018)

GGS Prize 2018.

Genes & genetic systems, 93(5):169.

RevDate: 2019-04-15
CmpDate: 2019-04-15

Heithaus JL (2019)

50 Years Ago in The Journal Of Pediatrics: Cytogenetics in Mentally Defective Children with Anomalies: A Controlled Study.

The Journal of pediatrics, 204:161.

RevDate: 2019-03-29
CmpDate: 2019-03-26

Hoßfeld U, Levit GS, E Watts (2019)

100 Years of phenogenetics: Valentin Haecker and his examination of the phenotype.

Molecular genetics and genomics : MGG, 294(2):445-456.

Following the 'rediscovery' of Mendel's work around 1900 the study of genetics grew rapidly and multiple new inheritance theories quickly emerged such as Hugo de Vries' "Mutation Theory" (1901) and the "Boveri-Sutton Chromosome Theory" (1902). Mendel's work also caught the attention of the German geneticist Valentin Haecker, yet he was generally dissatisfied the simplicity of Mendelian genetics as he believed that inheritance and the expression of various characteristics appeared to be much more complex than the proposed "on-off hypotheses". Haecker's primary objection was that Mendelian-based theories still failed to bridge the gap between hereditary units and phenotypic traits. Haecker thus set out to bridge this gap in his research program, which he called Phänogenetik ("phenogenetics"). He outlined his work in a special study "Entwicklungsgeschichtliche Eigenschaftsanalyse (Phänogenetik)" in 1918. 2018 thus marks the 100th anniversary of Haecker's seminal publication, which was devoted to the analysis of the phenotype and highlighted the true complexity of heredity. This article takes a specific look at Haecker and his work, while also illustrating how this often forgotten scientist influenced the field of genetics and other scientists.

RevDate: 2019-02-26
CmpDate: 2019-02-26

Charlesworth D (2018)

Mogens Westergaard's Contributions to Understanding Sex Chromosomes.

Genetics, 210(4):1143-1149.

A long-standing question in biology concerns the genetic mechanisms by which two sexes can evolve (botanists call this the dioecious condition and zoologists call it gonochory) from a functionally ancestral hermaphroditic state (without separate sexes). In 1932, H. J. Muller, one of the great 20th century geneticists but also a fine evolutionary biologist, pointed out that two mutations were necessary. It was therefore puzzling that sex determination often involves a single genetic locus. Muller believed that the evolution of a single-gene system was possible, because maize geneticists had synthesized a single-gene system with separate sexes. However, this system is highly artificial, requiring geneticists to actively eliminate the wild-type allele at one of the two genes involved. This genetic system cannot therefore explain the natural evolution of dioecy. In 1958, Westergaard reviewed studies from a diversity of flowering plants, and showed that the genetics of natural sex determination in plants does not support the maize system. Instead, the genetic results pointed to a model involving two separate factors, with close linkage creating a single genetic locus. Moreover, Westergaard also pointed out that a two-gene model offers a natural explanation for the evolution of suppressed recombination between sex chromosome pairs. Studying plants allowed genetic analyses of the early steps in the evolution of dioecy, using dioecious species that evolved recently from species without separate sexes, whereas Muller failed to fully understand such evolutionary changes because he focused on animals, where later changes have often happened and obscured the early stages.

RevDate: 2019-02-26
CmpDate: 2019-02-26

Haloupek N (2018)

Mariana Wolfner: 2018 Genetics Society of America Medal.

Genetics, 210(4):1139-1141.

The Genetics Society of America (GSA) Medal recognizes researchers who have made outstanding contributions to the field of genetics in the past 15 years. The 2018 GSA Medal has been awarded to Mariana Wolfner of Cornell University for her work on reproductive processes that occur around the time of fertilization. This includes characterization of seminal proteins in Drosophila melanogaster, which has uncovered a wealth of information about sexual conflict in evolution.

RevDate: 2019-04-17
CmpDate: 2019-04-17

Russell DW (2018)

Lucky, times ten: A career in Texas science.

The Journal of biological chemistry, 293(49):18804-18827.

On January 21, 2017, I received an E-mail from Herb Tabor that I had been simultaneously hoping for and dreading for several years: an invitation to write a "Reflections" article for the Journal of Biological Chemistry On the one hand, I was honored to receive an invitation from Herb, a man I have admired for over 40 years, known for 24 years, and worked with as a member of the Editorial Board and Associate Editor of the Journal of Biological Chemistry for 17 years. On the other hand, the invitation marked the waning of my career as an academic scientist. With these conflicting emotions, I wrote this article with the goals of recording my career history and recognizing the many mentors, trainees, and colleagues who have contributed to it and, perhaps with pretension, with the desire that students who are beginning a career in research will find inspiration in the path I have taken and appreciate the importance of luck.

RevDate: 2019-05-21
CmpDate: 2019-05-21

Arnone MI, Oliveri P, P Martinez (2019)

A conceptual history of the "regulatory genome": From Theodor Boveri to Eric Davidson.

Marine genomics, 44:24-31.

The formalization of the idea of "Regulatory Genome" is a recent one. However, it stems from a long tradition in the study of how the genetic information is transferred between generations. Theodore Boveri suggested for the first time that the whole genome participates in the shaping of individuals. Through a long lineage of researchers, we have learned how this whole-genome activity is regulated, in space and time. It is, however, due to the insights and experimental approaches taken by different researchers, among them Eric Davidson and associates, that we understand the mechanistic basis of this regulation. Whole batteries of regulatory genes interact through their cis-regulatory modules, generating a precise pattern of cross-controlled gene activity (Gene Regulatory Networks). How these genes are deployed in development and evolution has become an area of vibrant research. Here we revisit the history of this intellectual endeavour, taking as key defining points along this historical trajectory the contributions of Theodor Boveri and Eric Davidson.

RevDate: 2019-06-05
CmpDate: 2019-06-05

Datta MS, R Kishony (2018)

A spotlight on bacterial mutations for 75 years.

Nature, 563(7733):633-644.

RevDate: 2019-04-08
CmpDate: 2019-04-08

Ramakrishnan V, R Henderson (2018)

Thomas A. Steitz (1940-2018).

Science (New York, N.Y.), 362(6417):897.

RevDate: 2019-02-25
CmpDate: 2019-02-25

Ma Q, Adua E, Boyce MC, et al (2018)

IMass Time: The Future, in Future!.

Omics : a journal of integrative biology, 22(11):679-695.

Joseph John Thomson discovered and proved the existence of electrons through a series of experiments. His work earned him a Nobel Prize in 1906 and initiated the era of mass spectrometry (MS). In the intervening time, other researchers have also been awarded the Nobel Prize for significant advances in MS technology. The development of soft ionization techniques was central to the application of MS to large biological molecules and led to an unprecedented interest in the study of biomolecules such as proteins (proteomics), metabolites (metabolomics), carbohydrates (glycomics), and lipids (lipidomics), allowing a better understanding of the molecular underpinnings of health and disease. The interest in large molecules drove improvements in MS resolution and now the challenge is in data deconvolution, intelligent exploitation of heterogeneous data, and interpretation, all of which can be ameliorated with a proposed IMass technology. We define IMass as a combination of MS and artificial intelligence, with each performing a specific role. IMass will offer advantages such as improving speed, sensitivity, and analyses of large data that are presently not possible with MS alone. In this study, we present an overview of the MS considering historical perspectives and applications, challenges, as well as insightful highlights of IMass.

RevDate: 2019-03-20
CmpDate: 2019-03-20

Uhlenbeck OC (2019)

Thomas A. Steitz (1940-2018).

RNA (New York, N.Y.), 25(2):169-172.

RevDate: 2019-02-15
CmpDate: 2019-02-12

Haloupek N (2018)

Job Dekker: 2018 Edward Novitski Prize.

Genetics, 210(3):745-746.

The Genetics Society of America's (GSA) Edward Novitski Prize is awarded to researchers who have solved challenging problems in genetics through experiments that demonstrate exceptional creativity and ingenuity. Job Dekker of the University of Massachusetts Medical School has been selected for the 2018 award in recognition of his innovative approach to understanding chromosome interactions and nuclear organization. Among Dekker's contributions are the development of the now-ubiquitous approach of chromosome conformation capture and the discovery of topologically associating domains.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Tan SY, JK Furubayashi (2018)

Jacques Lucien Monod (1910-1976): Co-discoverer of the operon system.

Singapore medical journal, 59(10):555-556.

RevDate: 2019-05-03
CmpDate: 2019-05-03

Hanage WP (2018)

From bacterial genomics to clinical epidemiology: an interview with Bill Hanage.

BMC biology, 16(1):122.

Bill Hanage is an Associate Professor of Epidemiology at Harvard School of Public Health, where he studies fundamental and applied epidemiology using genomic and evolutionary methods. Bill spoke to us about the different types of selection that determine pathogen populations, asking reviewers to highlight positives of papers, and whether we're closer to a causal framework for studying the microbiome.

RevDate: 2019-03-28
CmpDate: 2019-03-28

Chen F, Lu DR, Zhang FX, et al (2018)

[The development of genetics teaching in China in the last four decades and its future prospect].

Yi chuan = Hereditas, 40(10):916-923.

Chinese genetics educators have carried out a comprehensive and systematic exploration and reform since 1978. With the guidance and help of the Genetics Society of China, they have made significant strides in the fields of genetics teaching system, publication of genetics textbooks, content of genetics teaching, workshop on genetics teaching, experimental teaching, application of advanced techniques, etc. These efforts have made remarkable achievements and promoted the vitality of genetics. The comprehensive development of education and teaching has trained a large number of excellent genetic talents for the development of China's economy and society. Here, we sum up the overall achievements of the teaching reform and propose some suggestions on the future development of genetics teaching in China, hoping that the quality of genetics teaching in China will take a new step in the new era.

RevDate: 2019-03-28
CmpDate: 2019-03-28

Sun LY, Xing QH, L He (2018)

[Retrospect and prospect of the genetic research on birth defects in China].

Yi chuan = Hereditas, 40(10):800-813.

An important part of China's "Healthy China 2030" planning is to lower the rate of birth defects. Because genetic factors contribute solely or collaboratively to about 80% of the occurrence of birth defects, genetic studies on birth defects can provide precise molecular targets for clinical screening, diagnosis and treatment. Genetic research on birth defects in China has developed by leaps and bounds since 1960s. At the same time, as related research achievements keep accumulating, translation of these scientific discoveries to clinical applications, with genetic counseling and testing as the core practices, has been developed and optimized. A close collaboration between genetic researches and clinical applications would provide reliable technical support for giving birth to more "healthy children" in China. This article firstly reviews China's history of genetic research on birth defects, then introduces current situation and hot topics of the research area at home and abroad and finally discusses about future trend and related clinical applications. In summary, an overall view is provided here for the readers to understand the development route of genetic research on birth defects in China.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Lowe JWE (2018)

Sequencing through thick and thin: Historiographical and philosophical implications.

Studies in history and philosophy of biological and biomedical sciences, 72:10-27.

DNA sequencing has been characterised by scholars and life scientists as an example of 'big', 'fast' and 'automated' science in biology. This paper argues, however, that these characterisations are a product of a particular interpretation of what sequencing is, what I call 'thin sequencing'. The 'thin sequencing' perspective focuses on the determination of the order of bases in a particular stretch of DNA. Based upon my research on the pig genome mapping and sequencing projects, I provide an alternative 'thick sequencing' perspective, which also includes a number of practices that enable the sequence to travel across and be used in wider communities. If we take sequencing in the thin manner to be an event demarcated by the determination of sequences in automated sequencing machines and computers, this has consequences for the historical analysis of sequencing projects, as it focuses attention on those parts of the work of sequencing that are more centralised, fast (and accelerating) and automated. I argue instead that sequencing can be interpreted as a more open-ended process including activities such as the generation of a minimum tile path or annotation, and detail the historiographical and philosophical consequences of this move.

RevDate: 2019-02-28
CmpDate: 2019-02-28

Anonymous (2018)

Society for Glycobiology Awards - 2018.

Glycobiology, 28(12):906-909.

RevDate: 2018-12-21
CmpDate: 2018-12-21

van Dijk PJ, Weissing FJ, THN Ellis (2018)

How Mendel's Interest in Inheritance Grew out of Plant Improvement.

Genetics, 210(2):347-355.

Despite the fact that Gregor Mendel is generally respected as the founder of genetics, little is known about the origin of and motivation for his revolutionary work. No primary sources are known that discuss his work during the period of his pea crossing experiments. Here, we report on two previously unknown interconnected local newspaper articles about Mendel's work that predate his famous Pisum lectures by 4 years. These articles describe Mendel as a plant breeder and a horticulturist. We argue that Mendel's initial interests concerned crop improvement, but that with time he became more interested in fundamental questions about inheritance, fertilization, and natural hybridization.

RevDate: 2018-12-21
CmpDate: 2018-12-21

Haloupek N (2018)

Philip Hieter: 2018 George W. Beadle Award.

Genetics, 210(2):345-346.

The Genetics Society of America's (GSA) George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers and who exemplify the qualities of its namesake. For his work fostering communication and collaboration among members of the many subfields of genetics, Philip Hieter of the University of British Columbia has been named 2018's recipient of the award. Among his contributions are many initiatives that aim to better link human and model organism geneticists, including the Canadian Rare Diseases Models and Mechanisms Network-a consortium that connects investigators who identify rare disease genes in humans to basic scientists who can study the genes in model organisms.

RevDate: 2019-02-15
CmpDate: 2019-02-04

Jonna S, Giaccone G, DS Subramaniam (2018)

Understanding molecular diagnostic technology in oncology through the lens of lung cancer.

Discovery medicine, 26(141):21-29.

Historically, advanced lung cancer conferred a poor prognosis, and chemotherapy only improved outcomes in patients with good performance status. The identification of certain molecular subtypes of non-small cell lung cancer changed the treatment paradigm by incorporating tumor genomic information into clinical decision-making. To meet the demands of this emerging approach, genomic technology rapidly expanded in an effort to detect specific driver mutations. While polymerase-chain reaction testing, immunohistochemistry, and fluorescent-in-situ hybridization have been standard-of-care, next-generation sequencing is increasingly replacing older technologies. Plasma-based testing is also gaining use given its convenience. Advances in molecular technology in this new era of precision medicine have led to the parallel development of companion diagnostics and novel tyrosine kinase inhibitors.

RevDate: 2018-12-12
CmpDate: 2018-12-12

Leeming W, A Barahona (2018)

Synthesis, convergence, and differences in the entangled histories of cytogenetics in medicine: A comparative study of Canada and Mexico.

Studies in history and philosophy of biological and biomedical sciences, 71:8-16.

Most historians of science and medicine agree that medical interest in genetics intensified after 1930, and interest in the relationship of radiation damage and genetics continued and expanded after World War II. Moreover, they maintain that the synthesis and convergence of human genetics and cytological techniques in European centers resulted in their dissemination to centers in the United States, resulting in a new field of expertise focused on medicine and clinical research, known as cytogenetics. In this article, we broaden the scope of the inquiry by showing how the early histories of cytogenetics in Canada and Mexico unfolded against strikingly different backgrounds in clinical research and the delivery of health care. We thus argue that the field of cytogenetics did not emerge in a straightforward manner and develop in the same way in all countries. The article provides a brief background to the history of human cytogenetics, and then outlines key developments related to the early adoption of cytogenetics in Canada and Mexico. Conclusions are then drawn using comparisons of the different ways in which local determinants affected adoption. We then propose directions for future study focused on the ways in which circuits of practices, collaborative research, and transfers of knowledge have shaped how cytogenetics has come to be organised in medicine around the world.

RevDate: 2019-02-25
CmpDate: 2019-02-25

Wilson JM (2018)

University Flunk-Out to Genomics Pioneer: An Interview with George Church, PhD.

Human gene therapy. Clinical development, 29(3):118-120.

RevDate: 2018-10-11
CmpDate: 2018-10-11

Lieberman J (2018)

Unveiling the RNA World.

The New England journal of medicine, 379(13):1278-1280.

RevDate: 2019-05-06
CmpDate: 2019-05-06

Balzi E, WS Moye-Rowley (2019)

Unveiling the transcriptional control of pleiotropic drug resistance in Saccharomyces cerevisiae: Contributions of André Goffeau and his group.

Yeast (Chichester, England), 36(4):195-200.

Studies in the yeast Saccharomyces cerevisiae have provided much of the basic detail underlying the organization and regulation of multiple or pleiotropic drug resistance gene network in eukaryotic microbes. As with many aspects of yeast biology, the initial observations that drove the eventual molecular characterization of multidrug resistance gene were provided by genetics. This review focuses on contributions from the laboratory of Dr. André Goffeau that uncovered key aspects of the transcriptional regulation of these multidrug resistance genes. André's group made many seminal discoveries that helped lead to the current picture we have of how eukaryotic microbes respond to and deal with a variety of antifungal agents. The importance of the transcriptional contribution to antifungal drugs is illustrated by the large number of drug resistant mutants found in several yeast species that lead to increased activity of transcriptional regulators. The characterization of the Saccharomyces cerevisiae PDR1 gene by the Goffeau group provided the first molecular basis explaining the link between this hyperactive transcription factor and drug resistance.

RevDate: 2019-03-07
CmpDate: 2019-03-07

Harding SE, Channell G, MK Phillips-Jones (2018)

The discovery of hydrogen bonds in DNA and a re-evaluation of the 1948 Creeth two-chain model for its structure.

Biochemical Society transactions, 46(5):1171-1182.

We recall the experimental approaches involved in the discovery of hydrogen bonds in deoxyribonucleic acid (DNA) made 70 years ago by a team of scientists at University College Nottingham led by J.M. Gulland, and in relation to previous studies. This discovery proved an important step in the elucidation of the correct structure for DNA made by J.D. Watson and F.H.C. Crick, as acknowledged in 'The Double Helix'. At that time of the discovery, however, it was impossible to delineate between inter- and intra-chain hydrogen bonds. We also consider in the light of more recent hydrodynamic theory a tentative model for DNA proposed by Gulland's and D.O. Jordan's PhD student J.M. Creeth in his PhD thesis of 1948, with the correct prediction of two chains with a sugar-phosphate backbone on the exterior and hydrogen-bonded bases between the nucleotide bases of opposite chains in the interior. Our analysis shows that his incorporation of alternating breaks in the two-chain structure was not necessary to explain the viscosity data on scission of hydrogen bonds after titrating to high or low pH. Although Creeth's model is a depiction of DNA structure alone, he could not know whether the hydrogen bonding was intermolecular, although this was subsequently proved correct by others. The mechanisms by which replicative processes occurred were of course unknown at that time, and so, he could not have realised how closely his tentative model resembled steps in some viral replicative mechanisms involving the molecule of life that he was working on.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Schaeffer SW (2018)

Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics.

Genetics, 210(1):3-13.

The concept of synteny, or conservation of genes on the same chromosome, traces its origins to the early days of Drosophila genetics. This discovery emerged from comparisons of linkage maps from different species of Drosophila with the goal of understanding the process of speciation. H. J. Muller published a landmark article entitled Bearings of the "Drosophila" work on systematics, where he synthesized genetic and physical map data and proposed a model of speciation and chromosomal gene content conservation. These models have withstood the test of time with the advent of molecular genetic analysis from protein to genome level variation. Muller's ideas provide a framework to begin to answer questions about the evolutionary forces that shape the structure of the genome.

RevDate: 2019-05-07
CmpDate: 2019-05-07

Zatz M (2018)

Helping our country as women scientists.

Nature cell biology, 20(9):1012.

RevDate: 2019-05-15
CmpDate: 2019-05-07

Schuh M (2018)

Taking a confident leap into uncertainty.

Nature cell biology, 20(9):1007.

RevDate: 2019-05-07
CmpDate: 2019-05-07

Nik-Zainal S (2018)

The duty to speak up.

Nature cell biology, 20(9):1006.

RevDate: 2019-05-07
CmpDate: 2019-05-07

Akhtar A (2018)

Finding your way through the science maze.

Nature cell biology, 20(9):1000.

RevDate: 2019-02-15
CmpDate: 2019-02-12

Mezquita-Pla J (2018)

Gordon H. Dixon's trace in my personal career and the quantic jump experienced in regulatory information.

Systems biology in reproductive medicine, 64(6):448-468.

Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field. Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5'-UTR: 5'-untranslated sequences; 3'-UTR: 3'-untranslated sequences.

RevDate: 2019-02-15
CmpDate: 2019-02-13

Lombardo PA (2018)

The power of heredity and the relevance of eugenic history.

Genetics in medicine : official journal of the American College of Medical Genetics, 20(11):1305-1311.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Godde K (2018)

A new analysis interpreting Nilotic relationships and peopling of the Nile Valley.

Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen, 69(4):147-157.

The process of the peopling of the Nile Valley likely shaped the population structure and early biological similarity of Egyptians and Nubians. As others have noted, affinity among Nilotic populations was due to an aggregation of events, including environmental, linguistic, and sociopolitical changes over a great deal of time. This study seeks to evaluate the relationships of Nubian and Egyptian groups in the context of the original peopling event. Cranial nonmetric traits from 18 Nubian and Egyptian samples, spanning Lower Egypt to Lower Nubia and approximately 7400 years, were analyzed using Mahalanobis D2 as a measure of biological distance. A principal coordinates analysis and spatial-temporal model were applied to these data. The results reveal temporal and spatial patterning consistent with documented events in Egyptian and Nubian population history. Moreover, the Mesolithic Nubian sample clustered with later Nubian and Egyptian samples, indicating that events prior to the Mesolithic were important in shaping the later genetic patterning of the Nubian population. Later contact through the establishment of the Egyptian fort at Buhen, Kerma's position as a strategic trade center along the Nile, and Egyptian colonization at Tombos maintained genetic similarity among the populations.

RevDate: 2018-12-20
CmpDate: 2018-12-20

Segal NL (2018)

Symposium in Honor of Irving I. Gottesman (December 29, 1930-June 29, 2016).

Twin research and human genetics : the official journal of the International Society for Twin Studies, 21(4):281-284.

The June 2016 death of our esteemed colleague, Dr Irving I. Gottesman, was felt as an extreme loss at so many levels by colleagues, students, friends, and family across the globe. Irv's stellar contributions to the field of twin research will continue to be remembered and cited for many years to come. In commemoration of his life and work, I organized a symposium at the 16th meeting of the International Society for Twin Studies, held in Madrid, Spain, November 16-18, 2017. The panelists included mostly former students, as well as colleagues, who presented their scientific research and personal remarks reflecting Irv's profound influence in shaping their lives and careers. A chronology of Irv's academic positions and honors is included in the introduction to this special issue of Twin Research and Human Genetics, followed by brief sketches of the panel participants; their scholarly papers and personal reflections follow.

RevDate: 2019-02-15
CmpDate: 2019-02-08

Tavaré S, EO Buzbas (2018)

Introduction to the Paul Joyce special issue.

Theoretical population biology, 122:1-2.

RevDate: 2018-11-14
CmpDate: 2018-07-05

Weinberg SM, Cornell R, EJ Leslie (2018)

Craniofacial genetics: Where have we been and where are we going?.

PLoS genetics, 14(6):e1007438.

RevDate: 2018-12-21
CmpDate: 2018-12-21

Morrison PJ (2018)

Medical Myths and Legends: Presidential Address to the Ulster Medical Society. 6th October 2016.

The Ulster medical journal, 87(2):102-108.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Anonymous (2018)

James Watson at 90.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 32(6):2901-2902.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Kropinski AM (2018)

Bacteriophage research - What we have learnt and what still needs to be addressed.

Research in microbiology, 169(9):481-487.

Research on bacteriophages has significantly enhanced our understanding of molecular biology, the genomes of prokaryotic cells, and viral ecology. Phages and lysins offer a viable alternative to the declining utility of antibiotics in this post-antibiotic era. They also provide ideal teaching tools for genomics and bioinformatics. This article touches on the first 100 years of phage research with the author commenting on what he thinks are the highlights, and what needs to be addressed.

RevDate: 2019-02-19
CmpDate: 2019-02-18

Karlin-Neumann G, F Bizouarn (2018)

Entering the Pantheon of 21st Century Molecular Biology Tools: A Perspective on Digital PCR.

Methods in molecular biology (Clifton, N.J.), 1768:3-10.

After several decades of relatively modest use, in the last several years digital PCR (dPCR) has grown to become the new gold standard for nucleic acid quantification. This coincides with the commercial availability of scalable, affordable, and reproducible droplet-based dPCR platforms in the past five years and has led to its rapid dissemination into diverse research fields and testing applications. Among these, it has been adopted most vigorously into clinical oncology where it is beginning to be used for plasma genotyping in cancer patients undergoing treatment. Additionally, innovation across the scientific community has extended the benefits of reaction partitioning beyond DNA and RNA quantification alone, and demonstrated its usefulness in evaluating DNA size and integrity, the physical linkage of colocalized markers, levels of enzyme activity and specific cation concentrations in a sample, and more. As dPCR technology gains in popularity and breadth, its power and simplicity can often be taken for granted; thus, the reader is reminded that due diligence must be exercised in order to make claims not only of precision but also of accuracy in their measurements.

RevDate: 2019-05-21
CmpDate: 2019-05-21

Opitz JM (2018)

Arno G. Motulsky, 1923-2018, Luck and Service.

American journal of medical genetics. Part A, 176(6):1285-1288.

RevDate: 2018-11-14
CmpDate: 2018-09-26

Jarvik GP (2018)

Arno G. Motulsky, MD (1923-2018): Holocaust survivor who cofounded the field of medical genetics.

Genetics in medicine : official journal of the American College of Medical Genetics, 20(5):477-479.

RevDate: 2018-11-14
CmpDate: 2018-08-15

Doctrow B (2018)

QnAs with Howard Y. Chang.

Proceedings of the National Academy of Sciences of the United States of America, 115(19):4805-4806.

RevDate: 2019-04-11
CmpDate: 2019-04-11

Ganesan A (2018)

Epigenetics: the first 25 centuries.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 373(1748):.

Epigenetics is a natural progression of genetics as it aims to understand how genes and other heritable elements are regulated in eukaryotic organisms. The history of epigenetics is briefly reviewed, together with the key issues in the field today. This themed issue brings together a diverse collection of interdisciplinary reviews and research articles that showcase the tremendous recent advances in epigenetic chemical biology and translational research into epigenetic drug discovery.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.

RevDate: 2018-11-14
CmpDate: 2018-09-24

Elloumi-Zghal H, H Chaabouni Bouhamed (2018)

Genetics and genomic medicine in Tunisia.

Molecular genetics & genomic medicine, 6(2):134-159.

RevDate: 2018-11-14
CmpDate: 2018-09-24

Leppig KA (2018)

Collaborations in medical genetics: 10-Year history of an ongoing Vietnamese-North American Collaboration.

Molecular genetics & genomic medicine, 6(2):129-133.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Romero R (2018)

A Profile of Dennis Lo, DM, DPhil, FRCP, FRCPath, FRS.

American journal of obstetrics and gynecology, 218(4):371-378.

RevDate: 2018-08-29
CmpDate: 2018-08-29

Hill WG (2018)

Contributions to quantitative genetic models by Yule and by Weinberg prior to Fisher 1918.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie, 135(2):93-94.

RevDate: 2018-12-02
CmpDate: 2018-04-02

Ferguson-Smith AC, MS Bartolomei (2018)

Obituary: Denise Barlow (1950-2017).

Development (Cambridge, England), 145(5): pii:145/5/dev164616.

Anne Ferguson-Smith and Marisa Bartolomei look back at the life and science of Denise Barlow, a pioneer in genomic imprinting and epigenetics.

RevDate: 2018-11-14
CmpDate: 2018-06-25

Rusu I, Modi A, Vai S, et al (2018)

Maternal DNA lineages at the gate of Europe in the 10th century AD.

PloS one, 13(3):e0193578.

Given the paucity of archaeogenetic data available for medieval European populations in comparison to other historical periods, the genetic landscape of this age appears as a puzzle of dispersed, small, known pieces. In particular, Southeastern Europe has been scarcely investigated to date. In this paper, we report the study of mitochondrial DNA in 10th century AD human samples from Capidava necropolis, located in Dobruja (Southeastern Romania, Southeastern Europe). This geographical region is particularly interesting because of the extensive population flux following diverse migration routes, and the complex interactions between distinct population groups during the medieval period. We successfully amplified and typed the mitochondrial control region of 10 individuals. For five of them, we also reconstructed the complete mitochondrial genomes using hybridization-based DNA capture combined with Next Generation Sequencing. We have portrayed the genetic structure of the Capidava medieval population, represented by 10 individuals displaying 8 haplotypes (U5a1c2a, V1a, R0a2'3, H1, U3a, N9a9, H5e1a1, and H13a1a3). Remarkable for this site is the presence of both Central Asiatic (N9a) and common European mtDNA haplotypes, establishing Capidava as a point of convergence between East and West. The distribution of mtDNA lineages in the necropolis highlighted the existence of two groups of two individuals with close maternal relationships as they share the same haplotypes. We also sketch, using comparative statistical and population genetic analyses, the genetic relationships between the investigated dataset and other medieval and modern Eurasian populations.

RevDate: 2019-04-01
CmpDate: 2019-02-06

Charney AW (2018)

Pamela Sklar.

Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology, 43(5):1191-1192.

RevDate: 2018-10-16
CmpDate: 2018-10-16

Jones ED (2018)

Ancient DNA: a history of the science before Jurassic Park.

Studies in history and philosophy of biological and biomedical sciences, 68-69:1-14.

RevDate: 2019-01-07
CmpDate: 2019-01-07

von Heijne G (2018)

Membrane protein serendipity.

The Journal of biological chemistry, 293(10):3470-3476.

My scientific career has taken me from chemistry, via theoretical physics and bioinformatics, to molecular biology and even structural biology. Along the way, serendipity led me to work on problems such as the identification of signal peptides that direct protein trafficking, membrane protein biogenesis, and cotranslational protein folding. I've had some great collaborations that came about because of a stray conversation or from following up on an interesting paper. And I've had the good fortune to be asked to sit on the Nobel Committee for Chemistry, where I am constantly reminded of the amazing pace and often intricate history of scientific discovery. Could I have planned this? No way! I just went with the flow ….

RevDate: 2018-12-11
CmpDate: 2018-12-11

Brunner HG (2018)

2017 Curt Stern Award Introduction: Nico Katsanis.

American journal of human genetics, 102(3):354.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Cox NJ (2018)

2017 Presidential Address: Checking, Balancing, and Celebrating Diversity: Celebrating Some of the Women Who Paved the Way.

American journal of human genetics, 102(3):342-349.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

963 Red Tail Lane
Bellingham, WA 98226


E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )