scholarly journals Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?

2019 ◽  
Vol 76 (11) ◽  
pp. 2080-2088 ◽  
Author(s):  
Suzanne J. Kelson ◽  
Michael R. Miller ◽  
Tasha Q. Thompson ◽  
Sean M. O’Rourke ◽  
Stephanie M. Carlson
Keyword(s):  
Life History ◽  
Oncorhynchus Mykiss ◽  
Genomic Region ◽  
Strongly Correlated ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Individual Level ◽  
Highly Correlated ◽  
The Individual ◽  
Specific Genomic Region

Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.

scholarly journals Major Evolutionary Transitions in Social Insects, the Importance of Worker Sterility and Life History Trade-Offs

2021 ◽  
Vol 9 ◽  
Author(s):  
Abel Bernadou ◽  
Boris H. Kramer ◽  
Judith Korb
Keyword(s):  
Life History ◽  
Social Insects ◽  
Division Of Labour ◽  
Evolutionary Transitions ◽  
Individual Level ◽  
Individual Fitness ◽  
Trade Offs ◽  
Group Members ◽  
The Individual ◽  
Worker Sterility

The evolution of eusociality in social insects, such as termites, ants, and some bees and wasps, has been regarded as a major evolutionary transition (MET). Yet, there is some debate whether all species qualify. Here, we argue that worker sterility is a decisive criterion to determine whether species have passed a MET (= superorganisms), or not. When workers are sterile, reproductive interests align among group members as individual fitness is transferred to the colony level. Division of labour among cooperating units is a major driver that favours the evolution of METs across all biological scales. Many METs are characterised by a differentiation into reproductive versus maintenance functions. In social insects, the queen specialises on reproduction while workers take over maintenance functions such as food provisioning. Such division of labour allows specialisation and it reshapes life history trade-offs among cooperating units. For instance, individuals within colonies of social insects can overcome the omnipresent fecundity/longevity trade-off, which limits reproductive success in organisms, when increased fecundity shortens lifespan. Social insect queens (particularly in superorganismal species) can reach adult lifespans of several decades and are among the most fecund terrestrial animals. The resulting enormous reproductive output may contribute to explain why some genera of social insects became so successful. Indeed, superorganismal ant lineages have more species than those that have not passed a MET. We conclude that the release from life history constraints at the individual level is a important, yet understudied, factor across METs to explain their evolutionary success.

Can an automated sleep detection algorithm for waist-worn accelerometry replace sleep logs?

2018 ◽  
Vol 43 (10) ◽  
pp. 1027-1032
Author(s):  
Tiago V. Barreira ◽  
Jessica G. Redmond ◽  
Tom D. Brutsaert ◽  
John M. Schuna ◽  
Emily F. Mire ◽  
...  
Keyword(s):  
Detection Algorithm ◽  
Good Evidence ◽  
Mean Difference ◽  
Absolute Difference ◽  
Individual Level ◽  
Wake Time ◽  
Highly Correlated ◽  
Mean Differences ◽  
Dependent Sample ◽  
The Individual

The purpose of this study was to test whether estimates of bedtime, wake time, and sleep period time (SPT) were comparable between an automated algorithm (ALG) applied to waist-worn accelerometry data and a sleep log (LOG) in an adult sample. A total of 104 participants were asked to log evening bedtime and morning wake time and wear an ActiGraph wGT3X-BT accelerometer at their waist for 24 h/day for 7 consecutive days. Mean difference and mean absolute difference (MAD) were computed. Pearson correlations and dependent-sample t tests were used to compare LOG-based and ALG-based sleep variables. Effect sizes were calculated for variables with significant mean differences. A total of 84 participants provided 2+ days of valid accelerometer and LOG data for a total of 368 days. There was no mean difference (p = 0.47) between LOG 472 ± 59 min and ALG SPT 475 ± 66 min (MAD = 31 ± 23 min, r = 0.81). There was no significant mean difference between bedtime (2348 h and 2353 h for LOG and ALG, respectively; p = 0.14, MAD = 25 ± 21 min, r = 0.92). However, there was a significant mean difference between LOG (0741 h) and ALG (0749 h) wake times (p = 0.01, d = 0.11, MAD = 24 ± 21 min, r = 0.92). The LOG and ALG data were highly correlated and relatively small differences were present. The significant mean difference in wake time might not be practically meaningful (Cohen’s d = 0.11), making the ALG useful for sample estimates. MAD, which gives a better estimate of the expected differences at the individual level, also demonstrated good evidence supporting ALG individual estimates.

EPCO-02. GERMLINE SINGLE NUCLEOTIDE POLYMORPHISM rs55705857 AT 8q24 INTERACTS WITH SOMATIC IDH1 MUTATION TO ENHANCE HUMAN GLIOMA FORMATION

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi1-vi1
Author(s):  
Kristen Drucker ◽  
Connor Yanchus ◽  
Thomas Kollmeyer ◽  
Asma Ali ◽  
Decker Paul ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Dna Interaction ◽  
Genomic Region ◽  
Idh1 Mutation ◽  
Normal Brain ◽  
Nucleotide Polymorphisms ◽  
Human Glioma ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Chromatin Immunoprecipitation Sequencing

Abstract BACKGROUND Determination of the causation of germline single nucleotide polymorphisms (SNPs) located in non-coding regions of the genome is challenging. The genomic region of 8q24 has been identified as important in many kinds of cancer, linked to a topologically associated domain (TAD) encompassing MYC; this TAD contains a GWAS SNP (rs55705857) associated with IDH-mutant glioma. METHODS Germline genotyping data from 622 IDH-mutant glioma and 668 controls were used to fine map the rs55705857 locus by detailed haplotype analysis. Chromatin immunoprecipitation sequencing (ChIP-seq) of histone markers H3K4me1, H3K4me3, H3K27ac and H3K36me3 was performed on normal brain samples (n=8) and human glioma samples (n=11 IDH-wt and 52 IDH-mut). RNAseq from 9 normal and 83 brain tumors (n=26 IDH-wt and 55 IDH-mut) were used to assess differential gene expression. RESULTS Fine-mapping identified rs55705857 SNP as the most likely causative allele (OR=8.69; p<0.001) within 8q24 for the development of IDH-mutant glioma. At rs55705857, both H3K27ac and H3K4me1 in IDH-mutant vs IDH-wt tumors were increased 3.05- and 1.58-fold, respectively (DiffBind; p=5.81×10-7 and p=2.31×10-3). ChromHMM analysis of the marks indicated that promoter and enhancer functions were significantly increased, and the activity broadened at rs55705857 in IDH-mut gliomas compared to IDH-wt tumors and normal brain samples. This enhancement correlated with significant increased MYC expression in IDH-mut gliomas (p=3.1×10-13), as well as alterations of Myc signaling targets. Publicly available ATACseq, ChIPseq and long-range DNA interaction data demonstrated that the rs55705857 locus is open and interacts with the MYC promoter. CONCLUSIONS Fine-mapping of the 8q24 locus provided strong evidence that rs55705857 is the causative 8q24 locus associated with IDH-mut glioma. Functional experiments suggest that IDH mutation facilitates rs55705857 interaction with MYC to alter downstream MYC targets.

scholarly journals Validation of a digitally displayed photographic food portion-size estimation aid among women in urban and rural Malawi

2019 ◽  
Vol 22 (17) ◽  
pp. 3140-3150 ◽  
Author(s):  
Valerie L Flax ◽  
Chrissie Thakwalakwa ◽  
Courtney H Schnefke ◽  
Heather Stobaugh ◽  
John C Phuka ◽  
...  
Keyword(s):  
Rural Communities ◽  
Low Income ◽  
Portion Size ◽  
Size Estimation ◽  
Individual Level ◽  
Low Income Country ◽  
Urban Rural ◽  
Highly Correlated ◽  
The Individual ◽  
Portion Size Estimation

AbstractObjective:To validate digitally displayed photographic portion-size estimation aids (PSEA) against a weighed meal record and compare findings with an atlas of printed photographic PSEA and actual prepared-food PSEA in a low-income country.Design:Participants served themselves water and five prepared foods, which were weighed separately before the meal and again after the meal to measure any leftovers. Participants returned the following day and completed a meal recall. They estimated the quantities of foods consumed three times using the different PSEA in a randomized order.Setting:Two urban and two rural communities in southern Malawi.Participants:Women (n 300) aged 18–45 years, equally divided by urban/rural residence and years of education (≤4 years and ≥5 years).Results:Responses for digital and printed PSEA were highly correlated (>91 % agreement for all foods, Cohen’s κw = 0·78–0·93). Overall, at the individual level, digital and actual-food PSEA had a similar level of agreement with the weighed meal record. At the group level, the proportion of participants who estimated within 20 % of the weighed grams of food consumed ranged by type of food from 30 to 45 % for digital PSEA and 40–56 % for actual-food PSEA. Digital PSEA consistently underestimated grams and nutrients across foods, whereas actual-food PSEA provided a mix of under- and overestimates that balanced each other to produce accurate mean energy and nutrient intake estimates. Results did not differ by urban and rural location or participant education level.Conclusions:Digital PSEA require further testing in low-income settings to improve accuracy of estimations.

scholarly journals Seasonal Temperature Fluctuations Differently Affect the Immune and Biochemical Parameters of Diploid and Triploid Oncorhynchus mykiss Cage-Cultured in Temperate Latitudes

2020 ◽  
Vol 12 (21) ◽  
pp. 8785 ◽  
Author(s):  
Andreia C. M. Rodrigues ◽  
Carlos Gravato ◽  
Carlos J. M. Silva ◽  
Sílvia F. S. Pires ◽  
Ana P. L. Costa ◽  
...  
Keyword(s):  
Oncorhynchus Mykiss ◽  
Energy Production ◽  
Antioxidant Defenses ◽  
Seasonal Temperature ◽  
Glutathione S Transferase ◽  
Blood Leukocytes ◽  
Individual Level ◽  
Trade Offs ◽  
Resistant Strains ◽  
The Individual

In the coming decades, and despite advances in the selection of resistant strains and the production of triploid organisms, the temperature could seriously affect salmonid aquaculture. Lower environmental tolerance has been hinted at for triploids, but the physiological mechanisms leading to such differences, and whether they are translated to the individual level, are poorly understood. This study aimed to evaluate the effects of seasonal variations on the humoral and immune status in the blood (peripheral blood leukocytes) and plasma (antiprotease, lysozyme and peroxidase activities), the oxidative stress (catalase, glutathione-S-transferase, total glutathione and lipid peroxidation) balance in the liver, and the energy budget (sugars, lipids, proteins and energy production) in the liver and muscle of diploid and triploid Oncorhynchus mykiss. Leukocytes’ numbers changed with the water temperature and differed between fish ploidies. Peroxidase activity was increased in the summer, but lysozyme and antiprotease activities were increased in the winter. Concomitantly, antioxidant defenses were significantly altered seasonally, increasing oxidative damage at higher temperatures. Moreover, warmer waters induced a reduction in the energy production measured in the liver. Differences in feed efficiency, which have been previously reported, were confirmed by the low lipid and protein contents of the muscle of the triploids. In sum, the inherent trade-offs to deal with the seasonal changes culminated in the higher growth observed for diploid fish.

scholarly journals Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 743
Author(s):  
Caiyong Yin ◽  
Kaiyuan Su ◽  
Ziwei He ◽  
Dian Zhai ◽  
Kejian Guo ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Forensic Analysis ◽  
Copy Number Variations ◽  
Null Alleles ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Pathway ◽  
Individual Level ◽  
Population Comparisons ◽  
Heated Debate ◽  
The Individual

Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

scholarly journals In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex

2019 ◽  
Vol 9 (10) ◽  
pp. 3249-3262 ◽  
Author(s):  
R. Rebecca Love ◽  
Seth N. Redmond ◽  
Marco Pombi ◽  
Beniamino Caputo ◽  
Vincenzo Petrarca ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
In Silico ◽  
Mosquito Species ◽  
Chromosomal Rearrangements ◽  
Small Subset ◽  
Anopheles Coluzzii ◽  
Strongly Correlated ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Malaria Mosquitoes

Chromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in the Anopheles gambiae complex that are significant vectors of human malaria, paracentric inversion polymorphisms are abundant and are associated with ecologically and epidemiologically important phenotypes. Improved understanding of these traits relies on determining mosquito karyotype, which currently depends upon laborious cytogenetic methods whose application is limited both by the requirement for specialized expertise and for properly preserved adult females at specific gonotrophic stages. To overcome this limitation, we developed sets of tag single nucleotide polymorphisms (SNPs) inside inversions whose biallelic genotype is strongly correlated with inversion genotype. We leveraged 1,347 fully sequenced An. gambiae and Anopheles coluzzii genomes in the Ag1000G database of natural variation. Beginning with principal components analysis (PCA) of population samples, applied to windows of the genome containing individual chromosomal rearrangements, we classified samples into three inversion genotypes, distinguishing homozygous inverted and homozygous uninverted groups by inclusion of the small subset of specimens in Ag1000G that are associated with cytogenetic metadata. We then assessed the correlation between candidate tag SNP genotypes and PCA-based inversion genotypes in our training sets, selecting those candidates with >80% agreement. Our initial tests both in held-back validation samples from Ag1000G and in data independent of Ag1000G suggest that when used for in silico inversion genotyping of sequenced mosquitoes, these tags perform better than traditional cytogenetics, even for specimens where only a small subset of the tag SNPs can be successfully ascertained.

scholarly journals The role of genetic polymorphism in the formation of atherosclerosis in the vessels of lower extremities

2012 ◽  
Vol 93 (3) ◽  
pp. 513-516
Author(s):  
M N Katina ◽  
R F Gayfullina ◽  
V V Valiullin ◽  
A A Rizvanov ◽  
R F Khamitov ◽  
...  
Keyword(s):  
Human Genome ◽  
Literature Search ◽  
Lower Extremities ◽  
Disease Course ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Genes ◽  
Genomics And Proteomics ◽  
The Individual

Personalized medicine involves the use of methods of genomics and proteomics by physicians for early diagnosis, prediction of the nature of the disease course and the choice of medicines and their doses based on personalized characteristics of the individual patient. Advances in the study of the human genome make it possible to reveal the interrelation between the individual mutations in the human genes (polymorphisms) and predisposition to certain diseases. Currently there are more than 10 million single-nucleotide polymorphisms in the human genome, however their biological role remains poorly understood. On the basis of a literature search of electronic full-text and abstract-only versions of articles, which was conducted in the PUBMED, OMIM and GENE databases, collected was the information on genetic predisposition to systemic atherosclerosis. The review is dedicated to polymorphisms of the major genes that play a role in the pathophysiology of atherosclerosis of the lower extremities.

scholarly journals BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs

2020 ◽  
Author(s):  
Nina Luhmann ◽  
Guillaume Holley ◽  
Mark Achtman
Keyword(s):  
Data Structure ◽  
Fluoroquinolone Resistance ◽  
Nucleotide Polymorphisms ◽  
Bacterial Genomes ◽  
Single Nucleotide ◽  
De Bruijn Graphs ◽  
Practical Applications ◽  
The Individual ◽  
Dynamic Data Structure ◽  
Genome Assemblies

AbstractBlastFrost is a highly efficient method for querying 100,000s of genome assemblies. It builds on Bifrost, a recently developed dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants. Here we describe the algorithms and implementation of BlastFrost. We also present two exemplar practical applications. In the first, we determined the presence of the individual genes within the SPI-2 Salmonella pathogenicity island within a collection of 926 representative genomes in minutes. In the second application, we determined the existence of known single nucleotide polymorphisms associated with fluoroquinolone resistance in the genes gyrA, gyrB and parE among 190, 209 Salmonella genomes. BlastFrost is available for download at https://github.com/nluhmann/BlastFrost.

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