Biology subjects

Luo, R.

Publications and source records attributed to Luo, R..

9 recordsLinked to original sources

bioRxiv2018

Oxytocin amplifies sex differences in human mate choice

Infidelity is the major cause of breakups and individuals with a history of infidelity are more likely to repeat it, but may also present a greater opportunity for short-term sexual relationships. Here in a pre-registered, double-blind study involving 160 subjects we report that while both sexes valued faithful individuals most for long-term relationships, both single men and those in a relationship were more interested in having short-term relationships with previously unfaithful individuals than women. Oxytocin administration resulted in men rating the faces of unfaithful women as more attractive but in women rating those of unfaithful men as less attractive and also finding them less memorable. Oxytocin also increased mens interest in having short-term relationships with previously unfaithful women whereas it increased womens interest in having long-term relationships with faithful men. Thus, oxytocin release during courtship may first act to amplify sex-dependent priorities in attraction and mate choice before subsequently promoting romantic bonds.

neuroscience↗

bioRxiv2018

Oxytocin promotes lying for personal gain in a genotype-dependent manner

Society values honesty, since it fosters trust in others. Although we have a strong moral aversion to lying, particularly when it is self-serving, we nevertheless lie quite frequently and the biological basis for this is poorly understood. The hypothalamic neuropeptide oxytocin has been implicated in a number of anti-social as well as pro-social behaviours, including lying to benefit in-group members or in competitive situations. The aim of the present study was to investigate the effects of oxytocin administration on self-serving lying behaviour and possible moderating effects of genetic underpinnings of the oxytocin receptor. A total of 161 adult men participated in a randomized double-blind placebo-controlled between-subject intranasal oxytocin administration (24 International Units) study where self-serving lying was assessed using the die-in-a-cup paradigm. Additionally, contributions of polymorphisms in the oxytocin receptor gene were investigated using a haplotype approach. Results showed that while placebo-treated subjects behaved honestly across three successive rounds, oxytocin administration promoted self-serving lying, particularly in the third / last round and only to a certain degree (not to the maximum). Moreover, this effect of oxytocin was strongest in carriers of the GCG individual haplotype (rs237887-rs2268491-rs2254298) and non-carriers of the GT individual haplotype (rs53576-rs2268498) on the oxytocin receptor gene. Overall our findings demonstrate that oxytocin administration can promote self-serving lying when subjects are given repeated opportunities to lie and that these effects are moderated by genetic underpinnings of the oxytocin receptor.

genetics↗

bioRxiv2018

First report and multilocus genotyping of Enterocytozoon bieneusi from Tibetan pigs in southwestern China

Enterocytozoon bieneusi is a common intestinal pathogen and a major cause of diarrhea and enteric diseases in a variety of animals. While the E. bieneusi genotype has become better-known, there are few reports on its prevalence in the Tibetan pig. This study investigated the prevalence, genetic diversity, and zoonotic potential of E. bieneusi in the Tibetan pig in southwestern China. Tibetan pig feces (266 samples) were collected from three sites in the southwest of China. Feces were subjected to PCR amplification of the internal transcribed spacer (ITS) region. E. bieneusi was detected in 83 (31.2%) of Tibetan pigs from the three different sites, with 25.4% in Kangding, 56% in Yaan and 26.7% in Qionglai. Age group demonstrated the prevalence of E. bieneusi range from 24.4%(aged 0 to 1 years) to 44.4%(aged 1 to 2 years). Four genotypes of E. bieneusi were identified: two known genotypes EbpC (n=58), Henan-IV (n=24) and two novel genotypes, SCT01 and SCT02 (one of each). Phylogenetic analysis showed these four genotypes clustered to group 1 with zoonotic potential. Multilocus sequence typing (MLST) analysis three microsatellites (MS1, MS3, MS7) and one minisatellite (MS4) revealed 47, 48, 23 and 47 positive specimens were successfully sequenced, and identified ten, ten, five and five genotypes at four loci, respectively. This study indicates the potential danger of E. bieneusi to Tibetan pigs in southwestern China, and offers basic data for preventing and controlling infections.

genetics↗

bioRxiv2018

Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants

MotivationMany rare diseases and cancers are fundamentally diseases of the genome. In the past several years, genome sequencing has become one of the most important tools in clinical practice for rare disease diagnosis and targeted cancer therapy. However, variant interpretation remains the bottleneck as is not yet automated and may take a specialist several hours of work per patient. On average, one-fifth of this time is spent on visually confirming the authenticity of the candidate variants. ResultsWe developed Skyhawk, an artificial neural network-based discriminator that mimics the process of expert review on clinically significant genomics variants. Skyhawk runs in less than one minute to review ten thousand variants, and about 30 minutes to review all variants in a typical whole-genome sequencing sample. Among the false positive singletons identified by GATK HaplotypeCaller, UnifiedGenotyper and 16GT in the HG005 GIAB sample, 79.7% were rejected by Skyhawk. Worked on the Variants with Unknown Significance (VUS), Skyhawk marked most of the false positive variants for manual review and most of the true positive variants no need for review. AvailabilitySkyhawk is easy to use and freely available at https://github.com/aquaskyline/Skyhawk

bioinformatics↗

bioRxiv2018

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5%-15%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieved 99.73%, 97.68% and 95.36% precision on known variants, and 98.65%, 92.57%, 87.26% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than two hours on a standard server. Furthermore, we identified 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source (https://github.com/aquaskyline/Clairvoyante), with modules to train, utilize and visualize the model.

bioinformatics↗

bioRxiv2018

Sex- and Context-dependent Effects of Oxytocin on Social Reward Processing

We interact socially and form bonds with others because such experiences are rewarding. However, an insecure attachment style or social anxiety can reduce these rewarding effects. The neuropeptide oxytocin (OXT) may facilitate social interactions either by increasing their rewarding experience or by attenuating anxiety, although effects can be sex- and attachment-style dependent. In this study, 64 pairs of same-sex friends completed a social sharing paradigm in a double-blind, placebo-controlled, between-subject design with one friend inside an MRI scanner and the other in a remote behavioral testing room. In this way we could examine whether intranasal-OXT differentially modulated the emotional impact of social sharing and associated neural processing. Additionally, we investigated if OXT effects were modulated by sex and attachment style. Results showed that in women, but not men, OXT increased ratings for sharing stimuli with their friend but not with a stranger, particularly in the friend in the scanner. Corresponding neuroimaging results showed that OXT decreased both amygdala and insula activity as well as their functional connectivity in women when they shared with friends but had the opposite effect in men. On the other hand, OXT did not enhance responses in brain reward circuitry. In the PLC treated group amygdala responses in women when they shared pictures with their friend were positively associated with attachment anxiety and OXT uncoupled this. Our findings demonstrate that OXT facilitates the impact of sharing positive experiences with others in women, but not men, and that this is associated with differential effects on the amygdala and insula and their functional connections. Furthermore, OXT particularly reduced increased amygdala responses during sharing in individuals with higher attachment anxiety. Thus, OXT effects in this context may be due more to reduced anxiety when sharing with a friend than to enhanced social reward.

neuroscience↗

bioRxiv2017

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)

Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,630,066 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8,656 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.

microbiology↗

bioRxiv2017

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

Summary16GT is a variant caller for Illumina WGS and WES germline data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT ran faster and demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy in calling indels as compared to the GATK HaplotypeCaller.\n\nAvailability and implementationhttps://github.com/aquaskyline/16GT\n\nContactrluo5@jhu.edu\n\nSupplementary informationSupplementary tables and notes are available at Bioinformatics online.

bioinformatics↗

bioRxiv2017

LRSim: a Linked Reads Simulator generating insights for better genome partitioning

MotivationLinked reads are a form of DNA sequencing commercialized by 10X Genomics that uses highly multiplexed barcoding within microdroplets to tag short reads to progenitor molecules. The linked reads, spanning tens to hundreds of kilobases, offer an alternative to long-read sequencing for de novo assembly, haplotype phasing and other applications. However, there is no available simulator, making it difficult to measure their capability or develop new informatics tools.\n\nResultsOur analysis of 13 real linked read datasets revealed their characteristics of barcodes, molecules and partitions. Based on this, we introduce LRSim that simulates linked reads by emulating the library preparation and sequencing process with fine control of 1) the number of simulated variants; 2) the linked-read characteristics; and 3) the Illumina reads profile. We conclude from the phasing and genome assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing human and non-human genome.\n\nAvailabilityLRSIM is under MIT license and is freely available at https://github.com/aquaskyline/LRSIM\n\nContactrluo5@jhu.edu

bioinformatics↗