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 A Linear Algebra Approach to Fast DNA Mixture Analysis Using GPUs

2017 ◽  
Author(s):  
Siddharth Samsi ◽  
Brian Helfer ◽  
Jeremy Kepner ◽  
Albert Reuther ◽  
Darrell O. Ricke
Keyword(s):  
Linear Algebra ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Matrix Multiplication ◽  
Forensic Analysis ◽  
Dense Matrix ◽  
Nucleotide Polymorphisms ◽  
Base Pairs ◽  
Algebra Approach ◽  
Speed Up

AbstractAnalysis of DNA samples is an important tool in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base pairs. Current forensics approaches use 20 STR loci for analysis. The use of single nucleotide polymorphisms (SNPs) has utility for analysis of complex DNA mixtures. The use of tens of thousands of SNPs loci for analysis poses significant computational challenges because the forensic analysis scales by the product of the loci count and number of DNA samples to be analyzed. In this paper, we discuss the implementation of a DNA sequence comparison algorithm by re-casting the algorithm in terms of linear algebra primitives. By developing an overloaded matrix multiplication approach to DNA comparisons, we can leverage advances in GPU hardware and algoithms for dense matrix multiplication (DGEMM) to speed up DNA sample comparisons. We show that it is possible to compare 2048 unknown DNA samples with 20 million known samples in under 6 seconds using a NVIDIA K80 GPU.

scholarly journals A computational analysis of the genetic and transcript diversity at the kallikrein locus

2016 ◽  
Vol 397 (12) ◽  
pp. 1307-1313 ◽  
Author(s):  
John Lai ◽  
Jiyuan An ◽  
Srilakshmi Srinivasan ◽  
Judith A. Clements ◽  
Jyotsna Batra
Keyword(s):  
Genetic Variants ◽  
Tandem Repeats ◽  
Copy Number Variations ◽  
Genome Project ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Fusion Transcripts ◽  
Wide Range ◽  
Transcript Diversity

Abstract The kallikrein related peptidase gene family (KLKs) comprises 15 genes located between 19q13.3-13.4. KLKs have chymotrypsin and/or trypsin like activity, but the tissue/organ expression profile of each KLK varies considerably. Thus, the role of KLKs in human biology is also very diverse, and the deregulation of their function results in a wide-range of diseases. Here, we have cataloged the transcript (variants and fusions) and genetic (single nucleotide polymorphisms, small insertions/deletions, copy number variations (CNVs), and short tandem repeats) diversity at the KLK locus, providing a data set for researchers to explore the mechanisms through which KLK function may be deregulated. We reveal that the KLK locus hosts 85 fusion transcripts, and 80 variant transcripts. Interestingly, some fusion transcripts comprise up to 6 KLK genes. Our analysis of genetic variations of 2504 individuals from the 1000 Genome Project indicated that the KLK locus is rich in genetic diversity, with some fusion transcripts harboring over 1000 single nucleotide variations. We also found evidence from the literature linking 2387 KLK genetic variants with many types of diseases. Finally, genotyping data from the 131 KLK genetic variants in the NCI-60 cancer cell lines is provided as a resource for the cancer and KLK field.

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 Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”

2019 ◽  
Vol 20 (9) ◽  
pp. 2196 ◽  
Author(s):  
Hyun Oh Lee ◽  
Ho Jun Joh ◽  
Kyunghee Kim ◽  
Sang-Choon Lee ◽  
Nam-Hoon Kim ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
Tandem Repeats ◽  
Herbal Medicines ◽  
Copy Number Variations ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Glehnia Littoralis ◽  
History Of ◽  
Cp Genome

Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name “Bang-poong”. We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of G. littoralis, L. seseloides, and P. japonicum were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the P. japonicum cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the P. japonicum cp genome, phylogenetic analysis revealed that G. littoralis diverged 5–6 million years ago (Mya), while P. japonicum diverged from L. seseloides only 2–3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for L. seseloides and G. littoralis. We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between L. seseloides, P. japonicum, and G. littoralis; provides a method of species identification; and sheds light on the evolutionary history of these three species.

Differential Effects of Competence and Morality on Self-Esteem at the Individual and the Collective Level

2020 ◽  
Vol 51 (3) ◽  
pp. 183-198
Author(s):  
Wiktor Soral ◽  
Mirosław Kofta
Keyword(s):  
Self Esteem ◽  
Differential Effects ◽  
Individual Level ◽  
The Subject ◽  
The Individual

Abstract. The importance of various trait dimensions explaining positive global self-esteem has been the subject of numerous studies. While some have provided support for the importance of agency, others have highlighted the importance of communion. This discrepancy can be explained, if one takes into account that people define and value their self both in individual and in collective terms. Two studies ( N = 367 and N = 263) examined the extent to which competence (an aspect of agency), morality, and sociability (the aspects of communion) promote high self-esteem at the individual and the collective level. In both studies, competence was the strongest predictor of self-esteem at the individual level, whereas morality was the strongest predictor of self-esteem at the collective level.

Metonymy in Dance: Ballet Bunheads Take a Cognitive Turn

2019 ◽  
Vol 37 (1) ◽  
pp. 18-34
Author(s):  
Edward C. Warburton
Keyword(s):  
Identity Formation ◽  
Cognitive Science ◽  
Artistic Development ◽  
Individual Level ◽  
Figures Of Speech ◽  
Self Image ◽  
Level I ◽  
Dance Educators ◽  
The Individual ◽  
Metaphor And Metonymy

This essay considers metonymy in dance from the perspective of cognitive science. My goal is to unpack the roles of metaphor and metonymy in dance thought and action: how do they arise, how are they understood, how are they to be explained, and in what ways do they determine a person's doing of dance? The premise of this essay is that language matters at the cultural level and can be determinative at the individual level. I contend that some figures of speech, especially metonymic labels like ‘bunhead’, can not only discourage but dehumanize young dancers, treating them not as subjects who dance but as objects to be danced. The use of metonymy to sort young dancers may undermine the development of healthy self-image, impede strong identity formation, and retard creative-artistic development. The paper concludes with a discussion of the influence of metonymy in dance and implications for dance educators.

Exploring the effect of weight loss on food reward at the individual level

2019 ◽  
Author(s):  
Pauline Oustric ◽  
Kristine Beaulieu ◽  
Nuno Casanova ◽  
Francois Husson ◽  
Catherine Gibbons ◽  
...  
Keyword(s):  
Weight Loss ◽  
Food Reward ◽  
Individual Level ◽  
The Individual

Personality change and environmental concerns

2020 ◽  
Author(s):  
Christopher James Hopwood ◽  
Ted Schwaba ◽  
Wiebke Bleidorn
Keyword(s):  
Personality Traits ◽  
Personality Change ◽  
Environmental Concerns ◽  
Big Five Personality ◽  
German Population ◽  
Individual Level ◽  
Sustainable Behavior ◽  
Nationally Representative ◽  
The Individual ◽  
Over Time

Personal concerns about climate change and the environment are a powerful motivator of sustainable behavior. People’s level of concern varies as a function of a variety of social and individual factors. Using data from 58,748 participants from a nationally representative German sample, we tested preregistered hypotheses about factors that impact concerns about the environment over time. We found that environmental concerns increased modestly from 2009-2017 in the German population. However, individuals in middle adulthood tended to be more concerned and showed more consistent increases in concern over time than younger or older people. Consistent with previous research, Big Five personality traits were correlated with environmental concerns. We present novel evidence that increases in concern were related to increases in the personality traits neuroticism and openness to experience. Indeed, changes in openness explained roughly 50% of the variance in changes in environmental concerns. These findings highlight the importance of understanding the individual level factors associated with changes in environmental concerns over time, towards the promotion of more sustainable behavior at the individual level.

Reply to Connor and Evers (2020): Critique of the Bias of Crowds Model Simply Restates the Model

2020 ◽  
Author(s):  
Keith Payne ◽  
Heidi A. Vuletich ◽  
Kristjen B. Lundberg
Keyword(s):  
Implicit Bias ◽  
Group Level ◽  
Systemic Racism ◽  
Individual Level ◽  
The Core ◽  
Psychological Science ◽  
Implicit Biases ◽  
The Individual

The Bias of Crowds model (Payne, Vuletich, & Lundberg, 2017) argues that implicit bias varies across individuals and across contexts. It is unreliable and weakly associated with behavior at the individual level. But when aggregated to measure context-level effects, the scores become stable and predictive of group-level outcomes. We concluded that the statistical benefits of aggregation are so powerful that researchers should reconceptualize implicit bias as a feature of contexts, and ask new questions about how implicit biases relate to systemic racism. Connor and Evers (2020) critiqued the model, but their critique simply restates the core claims of the model. They agreed that implicit bias varies across individuals and across contexts; that it is unreliable and weakly associated with behavior at the individual level; and that aggregating scores to measure context-level effects makes them more stable and predictive of group-level outcomes. Connor and Evers concluded that implicit bias should be considered to really be noisily measured individual construct because the effects of aggregation are merely statistical. We respond to their specific arguments and then discuss what it means to really be a feature of persons versus situations, and multilevel measurement and theory in psychological science more broadly.

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