ALBERT

Description: Background: The theoretical basis of genome-wide association studies (GWAS) is statistical inference of linkage disequilibrium (LD) between any polymorphic marker and a putative disease locus. Most methods widely implemented for such analyses are vulnerable to several key demographic factors and deliver a poor statistical power for detecting genuine associations and also a high false positive rate. Here, we present a likelihood-based statistical approach that accounts properly for non-random nature of case--control samples in regard of genotypic distribution at the loci in populations under study and confers flexibility to test for genetic association in presence of different confounding factors such as population structure, non-randomness of samples etc. Results: We implemented this novel method together with several popular methods in the literature of GWAS, to re-analyze recently published Parkinson's disease (PD) case--control samples. The real data analysis and computer simulation show that the new method confers not only significantly improved statistical power for detecting the associations but also robustness to the difficulties stemmed from non-randomly sampling and genetic structures when compared to its rivals. In particular, the new method detected 44 significant SNPs within 25 chromosomal regions of size 〈 1 Mb but only 6 SNPs in two of these regions were previously detected by the trend test based methods. It discovered two SNPs located 1.18 Mb and 0.18 Mb from the PD candidates, FGF20 and PARK8, without invoking false positive risk. Conclusions: We developed a novel likelihood-based method which provides adequate estimation of LD and other population model parameters by using case and control samples, the ease in integration of these samples from multiple genetically divergent populations and thus confers statistically robust and powerful analyses of GWAS. On basis of simulation studies and analysis of real datasets, we demonstrated significant improvement of the new method over the non-parametric trend test, which is the most popularly implemented in the literature of GWAS.

Description: Background: As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. However, limited information is available for underlying genetic architecture of longitudinal trend in EW. Herein, we measured EWs at nine time points from onset of laying to 60 week of age, and conducted comprehensive genome-wide association studies (GWAS) in 1,534 F 2 hens derived from reciprocal crosses between White Leghorn and Dongxiang chickens. Results: Egg weights at all ages except the first egg weight (FEW) exhibited high SNP-based heritability estimates (0.47 ~ 0.60). Strong pair-wise genetic correlations (0.77 ~ 1.00) were found among all EWs. Nine separate univariate genome-wide screens suggested 73 signals showing significant associations with longitudinal EWs. After multivariate and conditional analyses, four variants on three chromosomes remained independent contributions. The minor alleles at two loci exerted consistent and positive substitution effects on EWs, and other two were negative. The four loci together accounted for 3.84 % of the phenotypic variance for FEW and 7.29 ~ 11.06 % for EWs from 32 to 60 week of age. We obtained five candidate genes, of which NCAPG harbors a non-synonymous SNP (rs14491030) causing a valine-to-alanine amino-acid substitution. Genome partitioning analysis indicated a strong linear correlation between the variance explained by each chromosome and its length, which provided evidence that EW follows a highly polygenic nature of inheritance. Conclusions: Identification of significant genetic causes that together implicate EWs at different ages will greatly advance our understanding of the genetic basis behind longitudinal EWs, and would be helpful to illuminate the future breeding direction on how to select desired egg size.

Description: Background: Adaption to cold temperatures, especially those below freezing, is essential for animal survival in cold environments. Freezing is also used for many medical, scientific, and industrial purposes. Natural freezing survival in animals has been extensively studied. However, the underlying mechanisms remain unclear. Previous studies demonstrated that animals survive in extremely cold weather by avoiding freezing or controlling the rate of ice-crystal formation in their bodies, which indicates that freezing survival is a passive thermodynamic process. Results: Here, we showed that genetic programming actively promotes freezing survival in Caenorhabditis elegans. We found that daf-2, an insulin/IGF-1 receptor homologue, and loss-of-function enhanced survival during freeze–thaw stress, which required the transcription factor daf-16/FOXO and age-independent target genes. In particular, the freeze–thaw resistance of daf-2(rf) is highly allele-specific and has no correlation with lifespan, dauer formation, or hypoxia stress resistance. Conclusions: Our results reveal a new function for daf-2 signaling, and, most importantly, demonstrate that genetic programming contributes to freezing survival.

Description: Background: N-3 PUFAs have been demonstrated in vitro it could prevent the intestinal tight junctions (TJs) from the ischemia/re-perfusion injury and the inflammatory reaction injury. The purpose of this study was to evaluate the protection of n-3 PUFAs on the intestinal TJs in the rat model of hemorrhagic shock followed by resuscitation. Methods: Male SD rats (n = 72; 250 ~ 300 g) were randomly divided into 6 groups: SHAM, hemorrhagic shock (HS), hemorrhagic shock/resuscitation (HS/R), omega-6 group, omega-3 group and omega-3 treatment group. Shock was induced, and a mean arterial pressure was maintained at 35 to 40 mmHg for 60 minutes. Resuscitation was carried out by returning half of the shed blood and Ringer's lactate solution. In omega-6 and omega-3 group, Intralipid or fish oil (0.2 g/Kg), respectively, was infused 30 minutes after shock. And fish oil was infused with resuscitation in omega-3 treatment group. Half of each group was killed at 30 minutes and 4 hours after resuscitation, respectively. The serum samples and the intestinal sample was collected for further examination.Result: There is no difference between omega-3, omega-3 treatment and sham group in Chiu's score, but the other three groups have higher scores than they did. Compared with HS, HSR and omega-6 group, omega-3 and omega-3 treatment group showed most intact in intestinal mucoscal villi and TJs through HE, SEM and LSCM. The levels of IL-6 and TNF-alpha of bowel tissue in omega-3 and omega-3 treatment group were significantly lower than HS and HSR groups'. At the time point of 30 min, the levels of serum endotoxin were dramatically higher in HS[ideographic comma]HSR and omega-6 groups when compared with omega-3, omega-3 treatment and sham group. However, it in omega-3 group was greater than sham and HS group until 4 hours. Conclusion: Fish oil pretreatment before resuscitation showed a beneficial effect to the intestinal TJs and atteunated inflammation after H/R in HS/R rat model and is better than omega-6 PUFAs did.

Description: Background: Vision-based surveillance and monitoring is a potential alternative for early detection of respiratorydisease outbreaks in urban areas complementing molecular diagnostics and hospital and doctor visitbasedalert systems. Visible actions representing typical flu-like symptoms include sneeze and coughthat are associated with changing patterns of hand to head distances, among others. The technicaldifficulties lie in the high complexity and large variation of those actions as well as numerous similarbackground actions such as scratching head, cell phone use, eating, drinking and so on. Results: In this paper, we make a first attempt at the challenging problem of recognizing flu-like symptomsfrom videos. Since there was no related dataset available, we created a new public health dataset foraction recognition that includes two major flu-like symptom related actions (sneeze and cough) and a number of background actions. We also developed a suitable novel algorithm by introducing two typesof Action Matching Kernels, where both types aim to integrate two aspects of local features, namelythe space-time layout and the Bag-of-Words representations. In particular, we show that the PyramidMatch Kernel and Spatial Pyramid Matching are both special cases of our proposed kernels. Besidesexperimenting on standard testbed, the proposed algorithm is evaluated also on the new sneeze andcough set. Empirically, we observe that our approach achieves competitive performance compared tothe state-of-the-arts, while recognition on the new public health dataset is shown to be a non-trivialtask even with simple single person unobstructed view. Conclusions: Our sneeze and cough video dataset and newly developed action recognition algorithm is the first ofits kind and aims to kick-start the field of action recognition of flu-like symptoms from videos. It willbe challenging but necessary in future developments to consider more complex real-life scenario ofdetecting these actions simultaneously from multiple persons in possibly crowded environments.

Description: Background: The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. Results: GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Conclusions: Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

Description: Background: Eggshell is subject to quality loss with aging process of laying hens, and damaged eggshells result in economic losses of eggs. However, the genetic architecture underlying the dynamic eggshell quality remains elusive. Here, we measured eggshell quality traits, including eggshell weight (ESW), eggshell thickness (EST) and eggshell strength (ESS) at 11 time points from onset of laying to 72 weeks of age and conducted comprehensive genome-wide association studies (GWAS) in 1534 F 2 hens derived from reciprocal crosses between White Leghorn (WL) and Dongxiang chickens (DX). Results: ESWs at all ages exhibited moderate SNP-based heritability estimates (0.30 ~ 0.46), while the estimates for EST (0.21 ~ 0.31) and ESS (0.20 ~ 0.27) were relatively low. Eleven independent univariate genome-wide screens for each trait totally identified 1059, 1026 and 1356 significant associations with ESW, EST and ESS, respectively. Most significant loci were in a region spanning from 57.3 to 71.4 Mb of chromosome 1 (GGA1), which together account for 8.4 ~ 16.5 % of the phenotypic variance for ESW from 32 to 72 weeks of age, 4.1 ~ 6.9 % and 2.95 ~ 16.1 % for EST and ESS from 40 to 72 weeks of age. According to linkage disequilibrium (LD) and conditional analysis, the significant SNPs in this region were in extremely strong linkage disequilibrium status. Ultimately, two missense SNPs in GGA1 and one in GGA4 were considered as promising loci on three independent genes including ITPR2, PIK3C2G, and NCAPG. The homozygotes of advantageously effective alleles on PIK3C2G and ITPR2 possessed the best eggshell quality and could partly counteract the negative effect of aging process. NCAPG had certain effect on eggshell quality for young hens. Conclusions: Identification of the promising region as well as potential candidate genes will greatly advance our understanding of the genetic basis underlying dynamic eggshell quality and has the practical significance in breeding program for the improvement of eggshell quality, especially at the later part of laying cycle.

Description: Background In the past several millenniums, we have domesticated several crop species that are crucial for human civilization, which is a symbol of significant human influence on plant evolution. A pressing question to address is if plant diversity will increase or decrease in this warming world since contradictory pieces of evidence exit of accelerating plant speciation and plant extinction in the Anthropocene. Results Comparison may be made of the Anthropocene with the past geological times characterised by a warming climate, e.g., the Palaeocene-Eocene Thermal Maximum (PETM) 55.8 million years ago (Mya)—a period of “crocodiles in the Arctic”, during which plants saw accelerated speciation through autopolyploid speciation. Three accelerators of plant speciation were reasonably identified in the Anthropocene, including cities, polar regions and botanical gardens where new plant species might be accelerating formed through autopolyploid speciation and hybridization. Conclusions However, this kind of positive effect of climate warming on new plant species formation would be thoroughly offset by direct and indirect intensive human exploitation and human disturbances that cause habitat loss, deforestation, land use change, climate change, and pollution, thus leading to higher extinction risk than speciation in the Anthropocene. At last, four research directions are proposed to deepen our understanding of how plant traits affect speciation and extinction, why we need to make good use of polar regions to study the mechanisms of dispersion and invasion, how to maximize the conservation of plant genetics, species, and diverse landscapes and ecosystems and a holistic perspective on plant speciation and extinction is needed to integrate spatiotemporally.