scholarly journals Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Malte Petersen ◽  
Sven Winter ◽  
Raphael Coimbra ◽  
Menno J. de Jong ◽  
Vladimir V. Kapitonov ◽  
...  
Keyword(s):  
Large Scale ◽  
Population Analysis ◽  
Model Organism ◽  
Population Level ◽  
Data Sets ◽  
Ltr Retrotransposons ◽  
Scale Population ◽  
Mammalian Genomes ◽  
Genome Assemblies ◽  
First Time

Abstract Background The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.

scholarly journals Large-scale population analysis of SARS-CoV-2 whole genome sequences reveals host-mediated viral evolution with emergence of mutations in the viral Spike protein associated with elevated mortality rates

2020 ◽  
Author(s):  
Carlos Farkas ◽  
Andy Mella ◽  
Jody J. Haigh
Keyword(s):  
Large Scale ◽  
Population Analysis ◽  
Viral Evolution ◽  
Population Level ◽  
Spike Protein ◽  
Host Immune System ◽  
Sequencing Data ◽  
Scale Population ◽  
Significant Public Health ◽  
Viral Sequences

AbstractBackgroundWe aimed to further characterize and analyze in depth intra-host variation and founder variants of SARS-CoV-2 worldwide up until August 2020, by examining in excess of 94,000 SARS-CoV-2 viral sequences in order to understand SARS-CoV-2 variant evolution, how these variants arose and identify any increased mortality associated with these variants.Methods and FindingsWe combined worldwide sequencing data from GISAID and Sequence Read Archive (SRA) repositories and discovered SARS-CoV-2 hypermutation occurring in less than 2% of COVID19 patients, likely caused by host mechanisms involved APOBEC3G complexes and intra-host microdiversity. Most of this intra-host variation occurring in SARS-CoV-2 are predicted to change viral proteins with defined variant signatures, demonstrating that SARS-CoV-2 can be actively shaped by the host immune system to varying degrees. At the global population level, several SARS-CoV-2 proteins such as Nsp2, 3C-like proteinase, ORF3a and ORF8 are under active evolution, as evidenced by their increased πN/πS ratios per geographical region. Importantly, two emergent variants: V1176F in co-occurrence with D614G mutation in the viral Spike protein, and S477N, located in the Receptor Binding Domain (RBD) of the Spike protein, are associated with high fatality rates and are increasingly spreading throughout the world. The S477N variant arose quickly in Australia and experimental data support that this variant increases Spike protein fitness and its binding to ACE2.ConclusionsSARS-CoV-2 is evolving non-randomly, and human hosts shape emergent variants with positive fitness that can easily spread into the population. We propose that V1776F and S477N variants occurring in the Spike protein are two novel mutations occurring in SARS-CoV-2 and may pose significant public health concerns in the future.

scholarly journals An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Genome Project ◽  
Personal Genome ◽  
Personal Genomic ◽  
Personal Reference ◽  
Scale Population ◽  
Genome Assemblies

Abstract Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals Ethnically relevant consensus Korean reference genome towards personal reference genomes

2016 ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Personal Genomic ◽  
Personal Reference ◽  
Human Genomes ◽  
Scale Population ◽  
Genome Assemblies ◽  
Universal Reference

AbstractHuman genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals Reliability of the NIH toolbox cognitive battery in children and adolescents: a 3-year longitudinal examination

2020 ◽  
pp. 1-10
Author(s):  
Brittany K. Taylor ◽  
Michaela R. Frenzel ◽  
Jacob A. Eastman ◽  
Alex I. Wiesman ◽  
Yu-Ping Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Intraclass Correlation ◽  
Temporal Stability ◽  
Correlation Coefficients ◽  
Population Level ◽  
Clinical Applications ◽  
Intraclass Correlation Coefficients ◽  
Scale Population ◽  
Longitudinal Examination

Abstract Background The Cognitive Battery of the National Institutes of Health Toolbox (NIH-TB) is a collection of assessments that have been adapted and normed for administration across the lifespan and is increasingly used in large-scale population-level research. However, despite increasing adoption in longitudinal investigations of neurocognitive development, and growing recommendations that the Toolbox be used in clinical applications, little is known about the long-term temporal stability of the NIH-TB, particularly in youth. Methods The present study examined the long-term temporal reliability of the NIH-TB in a large cohort of youth (9–15 years-old) recruited across two data collection sites. Participants were invited to complete testing annually for 3 years. Results Reliability was generally low-to-moderate, with intraclass correlation coefficients ranging between 0.31 and 0.76 for the full sample. There were multiple significant differences between sites, with one site generally exhibiting stronger temporal stability than the other. Conclusions Reliability of the NIH-TB Cognitive Battery was lower than expected given early work examining shorter test-retest intervals. Moreover, there were very few instances of tests meeting stability requirements for use in research; none of the tests exhibited adequate reliability for use in clinical applications. Reliability is paramount to establishing the validity of the tool, thus the constructs assessed by the NIH-TB may vary over time in youth. We recommend further refinement of the NIH-TB Cognitive Battery and its norming procedures for children before further adoption as a neuropsychological assessment. We also urge researchers who have already employed the NIH-TB in their studies to interpret their results with caution.

Learnings from Large-Scale, Population-Level Implementation of Parenting Support

2017 ◽  
pp. 419-421
Author(s):  
Trevor G. Mazzucchelli
Keyword(s):  
Large Scale ◽  
Best Practice ◽  
Systems Approach ◽  
Positive Impact ◽  
Population Level ◽  
The United States ◽  
Parenting Support ◽  
Scale Population ◽  
The Many ◽  
Learning Principles

There is considerable evidence supporting the efficacy and effectiveness of parenting interventions based on social learning principles for a range of social, emotional, and health problems, involving different types of families and through a variety of delivery systems. The challenge now is “going to scale” in order to have a positive impact at a population level. This chapter introduces three best practice exemplars that have taken place in the United States, Ireland, and Australia, where a full multilevel systems approach to parenting support has been applied and evaluated. These applications provide important lessons regarding the barriers and facilitators that can influence an initiative’s success and degree of impact. By illustrating how these approaches have involved different populations, behavioral targets, evaluation designs, and means of assessing outcome, they also hint at the many possibilities that are available in future dissemination efforts.

Regimes and stock-recruitment relationships in Japanese sardine (Sardinops melanostictus), 1951-1995

1998 ◽  
Vol 55 (11) ◽  
pp. 2455-2463 ◽  
Author(s):  
Tokio Wada ◽  
Larry D Jacobson
Keyword(s):  
Reproductive Success ◽  
Large Scale ◽  
Environmental Changes ◽  
Environmental Variability ◽  
Population Analysis ◽  
Search Time ◽  
Data Sets ◽  
Japanese Sardine ◽  
Density Dependent ◽  
Peak Abundance

We used reproductive success, rather than abundance or catch, to identify regimes because reproductive success responds faster to environmental changes. Peak abundance of Japanese sardine during 1951-1995 was about 1000 times higher than minimum abundance. A regime shift occurred in the early 1970s when carrying capacity (measured using spawner-recruit models) increased by about 75 times. We hypothesize that this was due to large-scale changes in the Kuroshio and Oyashio Current systems. Long-term environmental variation (regimes), interannual variability in recruitment success, and density-dependent recruitment and growth rates affected dynamics of Japanese sardine. We hypothesize that density-dependent effects on recruitment of Sardinops spp. are common but usually obscured in short data sets by environmental variability and measurement error. Virtual population analysis and forward-simulation modeling approaches gave similar biomass and recruitment estimates. The relationship between sardine biomass and catch per unit search time was nonlinear. Mass-at-age and biomass were correlated, and it may be possible to use mass-at-age as an abundance index. Current abundance is low, and we believe that the environment has shifted to a regime that is unfavorable for Japanese sardine.

scholarly journals Screening for multi-drug-resistant Gram-negative bacteria: what is effective and justifiable?

2020 ◽  
Vol 38 (S1) ◽  
pp. 72-90 ◽  
Author(s):  
Niels Nijsingh ◽  
Christian Munthe ◽  
Anna Lindblom ◽  
Christina Åhrén
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Large Scale ◽  
Population Level ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Gram Negative ◽  
Screening Programs ◽  
Scale Population ◽  
Current Screening

AbstractEffectiveness is a key criterion in assessing the justification of antibiotic resistance interventions. Depending on an intervention’s effectiveness, burdens and costs will be more or less justified, which is especially important for large scale population-level interventions with high running costs and pronounced risks to individuals in terms of wellbeing, integrity and autonomy. In this paper, we assess the case of routine hospital screening for multi-drug-resistant Gram-negative bacteria (MDRGN) from this perspective. Utilizing a comparison to screening programs for Methicillin-Resistant Staphylococcus aureus (MRSA) we argue that current screening programmes for MDRGN in low endemic settings should be reconsidered, as its effectiveness is in doubt, while general downsides to screening programs remain. To accomplish justifiable antibiotic stewardship, MDRGN screening should not be viewed as a separate measure, but rather as part of a comprehensive approach. The program should be redesigned to focus on those at risk of developing symptomatic infections with MDRGN rather than merely detecting those colonised.

scholarly journals Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0249254
Author(s):  
Barbara Schrörs ◽  
Pablo Riesgo-Ferreiro ◽  
Patrick Sorn ◽  
Ranganath Gudimella ◽  
Thomas Bukur ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Large Scale ◽  
Median Number ◽  
Spike Protein ◽  
Human Populations ◽  
Data Sets ◽  
Spike Glycoprotein ◽  
Synonymous Mutations ◽  
Different Strains ◽  
Genome Assemblies

Due to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it. We analyzed 1,036,030 SARS-CoV-2 genome assemblies and 30,806 NGS datasets from GISAID and European Nucleotide Archive (ENA) focusing on non-synonymous mutations in the spike protein. Only around 2.5% of the samples contained the wild-type spike protein with no variation from the reference. Among the spike protein mutants, we confirmed a low mutation rate exhibiting less than 10 non-synonymous mutations in 99.6% of the analyzed sequences, but the mean and median number of spike protein mutations per sample increased over time. 5,472 distinct variants were found in total. The majority of the observed variants were recurrent, but only 21 and 14 recurrent variants were found in at least 1% of the mutant genome assemblies and NGS samples, respectively. Further, we found high-confidence subclonal variants in about 2.6% of the NGS data sets with mutant spike protein, which might indicate co-infection with various SARS-CoV-2 strains and/or intra-host evolution. Lastly, some variants might have an effect on antibody binding or T-cell recognition. These findings demonstrate the continuous importance of monitoring SARS-CoV-2 sequences for an early detection of variants that require adaptations in preventive and therapeutic strategies.

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