Molecular, developmental, and evolutionary genetic studies highlight rapid evolution of genes and genetic systems

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 848-852
Author(s):  
Jianping Xu
Keyword(s):  
Large Scale ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Annual Conference ◽  
Genetic Studies ◽  
The Us ◽  
Evolutionary Genetic ◽  
Genetic Systems ◽  
Oral Presentations ◽  
The Impact

The 53rd annual conference of the Genetics Society of Canada was held at McMaster University in Hamilton, Ontario, from 17 to 20 June 2010. About 100 geneticists from across Canada and the US attended the meeting, with a total of 27 posters and 55 oral presentations. The presentations highlighted the power of genetics for understanding a variety of biological issues from sex and recombination to alcoholism and cancer, from DNA replication to antimicrobial resistance, horizontal gene transfer, foraging, and courtship. Large-scale genomic and transcriptomic comparisons were included in many presentations to demonstrate the impact of genomics in biomedical research. The combined molecular, developmental, and evolutionary genetic investigations presented at the meeting, especially those on model organisms, highlighted that genes and genetic systems can evolve very rapidly.

scholarly journals The daunting polygenicity of mental illness: making a new map

2018 ◽  
Vol 373 (1742) ◽  
pp. 20170031 ◽  
Author(s):  
Steven E. Hyman
Keyword(s):  
Mental Health ◽  
Large Scale ◽  
Computational Models ◽  
Model Organisms ◽  
Human Biology ◽  
Genetic Studies ◽  
Computational Tools ◽  
Experimental Systems ◽  
Terra Incognita ◽  
Phenotypic Complexity

An epochal opportunity to elucidate the pathogenic mechanisms of psychiatric disorders has emerged from advances in genomic technology, new computational tools and the growth of international consortia committed to data sharing. The resulting large-scale, unbiased genetic studies have begun to yield new biological insights and with them the hope that a half century of stasis in psychiatric therapeutics will come to an end. Yet a sobering picture is coming into view; it reveals daunting genetic and phenotypic complexity portending enormous challenges for neurobiology. Successful exploitation of results from genetics will require eschewal of long-successful reductionist approaches to investigation of gene function, a commitment to supplanting much research now conducted in model organisms with human biology, and development of new experimental systems and computational models to analyse polygenic causal influences. In short, psychiatric neuroscience must develop a new scientific map to guide investigation through a polygenic terra incognita . This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.

Cigarette and cigar sales in Hawaii before and after implementation of a Tobacco 21 Law

2020 ◽  
Vol 30 (1) ◽  
pp. 98-102 ◽  
Author(s):  
Rebecca Glover-Kudon ◽  
Doris G Gammon ◽  
Todd Rogers ◽  
Ellen M Coats ◽  
Brett Loomis ◽  
...  
Keyword(s):  
Large Scale ◽  
Geographical Area ◽  
Upward Trend ◽  
Food Stores ◽  
The Us ◽  
Before And After ◽  
Youth And Young Adults ◽  
The Usa ◽  
Product Sales ◽  
The Impact

IntroductionOn 1 January 2016, Hawaii raised the minimum legal age for tobacco access from 18 to 21 years (‘Tobacco 21 (T21)’) statewide, with no special population exemptions. We assessed the impact of Hawaii’s T21 policy on sales of cigarettes and large cigars/cigarillos in civilian food stores, including menthol/flavoured product sales share.MethodsCigarette and large cigar/cigarillo sales and menthol/flavoured sales share were assessed in Hawaii, California (implemented T21 in June 2016 with a military exemption), and the US mainland using the only Nielsen data consistently available for each geographical area. Approximate monthly sales data from large-scale food stores with sales greater than US$2 million/year covered June 2012 to February 2017. Segmented regression analyses estimated changes in sales from prepolicy to postpolicy implementation periods.ResultsFollowing T21 in Hawaii, average monthly cigarette unit sales dropped significantly (−4.4%, p<0.01) coupled with a significant decrease in menthol market share (−0.8, p<0.01). This combination of effects was not observed in comparison areas. Unit sales of large cigars/cigarillos decreased significantly in each region following T21 implementation. T21 policies in Hawaii and California showed no association with flavoured/menthol cigar sales share, but there was a significant increase in flavoured/menthol cigar sales share in the USA (7.1%, p<0.01) relative to Hawaii’s implementation date, suggesting T21 may have attenuated an otherwise upward trend.ConclusionsAs part of a comprehensive approach to prevent or delay tobacco use initiation, T21 laws may help to reduce sales of cigarette and large cigar products most preferred by US youth and young adults.

The impact of “omics” technologies for grapevine (Vitis vinifera) research

2020 ◽  
pp. 1-15
Author(s):  
Nicolas Fischer ◽  
Thomas Efferth
Keyword(s):  
Vitis Vinifera ◽  
Large Scale ◽  
Abiotic Factors ◽  
Rapid Evolution ◽  
Vitis Vinifera L ◽  
Wine Quality ◽  
Omics Technologies ◽  
Biological Studies ◽  
Holistic Understanding ◽  
The Impact

BACKGROUND: Grapevine (Vitis vinifera L.) as basis for winemaking is one of the most economically important plants in modern agriculture. As requirements in viticulture are increasing due to changing environments, terroir and pests, classical agriculture techniques reach their limits. OBJECTIVE: We summarize the impact of modern “omics” technologies on modern grapevine breeding and cultivation, as well as for dealing with challenges in viniculture caused by environmental or terroir changes and pests and diseases. In this review, we give an overview on current research on the influence of “omics” technologies on modern viticulture. RESULTS: Considerable advances in bioinformatics and analytical techniques such as next generation sequencing or mass spectrometry fueled new molecular biological studies. Modern “omics” technologies such as “genomics”, “transcriptomics”, “proteomics” and “metabolomics” allow the investigation on a large-scale data basis and the identification of key markers. Holistic understanding of genes, proteins and metabolites in combination with external biotic and abiotic factors improves vine and wine quality. CONCLUSION: The rapid evolution in wine quality was only enabled by the progress of modern biotechnological methods developing enology from a handcraft to science.

A look back on 30 years of the Gordon Bell Prize

2017 ◽  
Vol 31 (6) ◽  
pp. 469-484 ◽  
Author(s):  
Gordon Bell ◽  
David H Bailey ◽  
Jack Dongarra ◽  
Alan H Karp ◽  
Kevin Walsh
Keyword(s):  
Parallel Computing ◽  
High Performance ◽  
Large Scale ◽  
Peak Performance ◽  
Outstanding Achievement ◽  
Computing Machinery ◽  
Large Scale Data ◽  
The Us ◽  
The Impact ◽  
Performance Computing

The Gordon Bell Prize is awarded each year by the Association for Computing Machinery to recognize outstanding achievement in high-performance computing (HPC). The purpose of the award is to track the progress of parallel computing with particular emphasis on rewarding innovation in applying HPC to applications in science, engineering, and large-scale data analytics. Prizes may be awarded for peak performance or special achievements in scalability and time-to-solution on important science and engineering problems. Financial support for the US$10,000 award is provided through an endowment by Gordon Bell, a pioneer in high-performance and parallel computing. This article examines the evolution of the Gordon Bell Prize and the impact it has had on the field.

scholarly journals Rapid evolution by spontaneous mutation increases genetic diversity facilitating plant population survival

2018 ◽  
Author(s):  
Henning Nottebrock ◽  
Mao-Lun Weng ◽  
Matthew T Rutter ◽  
Charles B. Fenster
Keyword(s):  
Large Scale ◽  
Community Dynamics ◽  
Spontaneous Mutation ◽  
Rapid Evolution ◽  
Potential Effect ◽  
Small Scale ◽  
Negative Effects ◽  
Population Survival ◽  
Population And Community Dynamics ◽  
The Impact

Using a mechanistic eco-evolutionary trait-based neighborhood-model, we quantify the impact of mutations on spatial interactions to better understand the potential effect of niche evolution through mutations on the population dynamics of Arabidopsis thaliana. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000 individuals), including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale, survival is enhanced but reproduction is decreased when a genotype is surrounded by different genotypes. At large-scale, seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. Mutations may provide a mechanism for plants to quickly evolve niches and may drive competition, facilitation and selection with profound consequences for future population and community dynamics.

THE CAAV 2017 Immersive Scholar Presentation: Visualizing Digital Scholarship Across Institutions

2018 ◽  
Author(s):  
Shelby Hallman ◽  
Mike Nutt
Keyword(s):  
Community Of Practice ◽  
Large Scale ◽  
Annual Conference ◽  
State University ◽  
Scholarly Work ◽  
University Libraries ◽  
Learning Spaces ◽  
Immersive Environments ◽  
Digital Scholarship ◽  
The Impact

NC State University Libraries has been awarded a three-year, $414,000 grant from the Andrew W. Mellon Foundation to develop extensible models and programs for the creation and sharing of digital scholarship in large-scale and immersive environments. Entitled “Visualizing Digital Scholarship in Libraries and Learning Spaces,” or Immersive Scholar for short, the grant aims to 1) build a community of practice of scholars and librarians to help visually immersive scholarly work enter the research lifecycle; and 2) overcome technical and resource barriers that limit the number of scholars and libraries who use visualization environments and the impact of generated knowledge. This presentation introduced the grant and it's components to The Higher Education Campus Alliance of Advanced Visualization (THE CAAV) at THE CAAV's 2017 annual conference.

Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis

2016 ◽  
Author(s):  
Alan Medlar ◽  
Laura Laakso ◽  
Andreia Miraldo ◽  
Ari Löytynoja
Keyword(s):  
Comparative Analysis ◽  
Large Scale ◽  
De Novo ◽  
Sequence Data ◽  
Model Organism ◽  
Model Organisms ◽  
Rna Seq ◽  
Reference Species ◽  
Wide Range ◽  
The Impact

AbstractHigh-throughput RNA-seq data has become ubiquitous in the study of non-model organisms, but its use in comparative analysis remains a challenge. Without a reference genome for mapping, sequence data has to be de novo assembled, producing large numbers of short, highly redundant contigs. Preparing these assemblies for comparative analyses requires the removal of redundant isoforms, assignment of orthologs and converting fragmented transcripts into gene alignments. In this article we present Glutton, a novel tool to process transcriptome assemblies for downstream evolutionary analyses. Glutton takes as input a set of fragmented, possibly erroneous transcriptome assemblies. Utilising phylogeny-aware alignment and reference data from a closely related species, it reconstructs one transcript per gene, finds orthologous sequences and produces accurate multiple alignments of coding sequences. We present a comprehensive analysis of Glutton’s performance across a wide range of divergence times between study and reference species. We demonstrate the impact choice of assembler has on both the number of alignments and the correctness of ortholog assignment and show substantial improvements over heuristic methods, without sacrificing correctness. Finally, using inference of Darwinian selection as an example of downstream analysis, we show that Glutton-processed RNA-seq data give results comparable to those obtained from full length gene sequences even with distantly related reference species. Glutton is available from http://wasabiapp.org/software/glutton/ and is licensed under the GPLv3.

scholarly journals BSPAR ANNUAL CONFERENCE ABSTRACTS * Oral presentations * O1. The impact of modern management on outcomes of JIA compared with healthy controls

Rheumatology ◽  
2012 ◽  
Vol 51 (suppl 8) ◽  
pp. viii2-viii14 ◽  
Author(s):  
D. Lim ◽  
M. Todd ◽  
N. Kourtoglou ◽  
K. Gerasimidis ◽  
J. Gardner-Medwin ◽  
...  
Keyword(s):  
Annual Conference ◽  
Healthy Controls ◽  
Modern Management ◽  
Oral Presentations ◽  
The Impact

scholarly journals Genetic epidemiology approach to estimating birth incidence and current disease prevalence for rhizomelic chondrodysplasia punctata

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Tarik Luisman ◽  
Tara Smith ◽  
Shawn Ritchie ◽  
Karen E. Malone
Keyword(s):  
Genetic Epidemiology ◽  
Large Scale ◽  
Disease Incidence ◽  
Disease Prevalence ◽  
Chondrodysplasia Punctata ◽  
Rhizomelic Chondrodysplasia Punctata ◽  
Specific Patient ◽  
Medical Need ◽  
The Us ◽  
The Impact

Abstract Background Rhizomelic chondrodysplasia punctata (RCDP) is an inherited ultra-rare disease which results in severely impaired physical and mental development. Mutations in one of five genes involved in plasmalogen biosynthesis have been reported to drive disease pathology. Estimates of disease incidence have been extremely challenging due to the rarity of the disorder, preventing an understanding of the unmet medical need. To address this, we have prepared a disease incidence and prevalence model based on genetic epidemiology approaches to estimate the total number of RCDP patients affected, and their demographic characteristics. Results Extraction of allelic frequencies for known and predicted pathogenic variants in PEX7, GNPAT, AGPS, FAR1, PEX5 (limited to the PTS2 domain encoding region) genes, from large-scale human genetic diversity datasets (TopMed and gnomAD) revealed the mutational landscape contributing to the RCDP patient population in the US and Europe. We computed genetic prevalence to derive birth incidence for RCDP and modeled the impact to life expectancy to obtain high confidence estimates of disease prevalence. Our population genetics-based model indicates PEX7 variants are expected to contribute to the majority of RCDP cases in both the US and Europe; closely aligning with clinical reports. Furthermore, this model provides estimates for RCDP subtypes due to mutations in other genes, including exceedingly rare subtypes. Conclusion In total, the estimated number of RCDP patients in the US and the five largest European countries (UK, Germany, France, Italy and Spain) is between 516 and 847 patients, all under the age of 35 years old. This model provides a quantitative framework for better understanding the unmet medical need in RCDP, to help guide disease awareness and diagnosis efforts for this specific patient group.

scholarly journals Cranial shape diversification in horses: variation and covariation patterns under the impact of artificial selection

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pauline Hanot ◽  
Jamsranjav Bayarsaikhan ◽  
Claude Guintard ◽  
Ashleigh Haruda ◽  
Enkhbayar Mijiddorj ◽  
...  
Keyword(s):  
Artificial Selection ◽  
Large Scale ◽  
Phenotypic Diversity ◽  
Morphological Changes ◽  
Rapid Evolution ◽  
Time Interval ◽  
Short Time Interval ◽  
Skull Morphology ◽  
Domestic Species ◽  
The Impact

AbstractThe potential of artificial selection to dramatically impact phenotypic diversity is well known. Large-scale morphological changes in domestic species, emerging over short timescales, offer an accelerated perspective on evolutionary processes. The domestic horse (Equus caballus) provides a striking example of rapid evolution, with major changes in morphology and size likely stemming from artificial selection. However, the microevolutionary mechanisms allowing to generate this variation in a short time interval remain little known. Here, we use 3D geometric morphometrics to quantify skull morphological diversity in the horse, and investigate modularity and integration patterns to understand how morphological associations contribute to cranial evolvability in this taxon. We find that changes in the magnitude of cranial integration contribute to the diversification of the skull morphology in horse breeds. Our results demonstrate that a conserved pattern of modularity does not constrain large-scale morphological variations in horses and that artificial selection has impacted mechanisms underlying phenotypic diversity to facilitate rapid shape changes. More broadly, this study demonstrates that studying microevolutionary processes in domestic species produces important insights into extant phenotypic diversity.

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