Inference of Gene Flow between Species under Misspecified Models

Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models. Here we use mathematical analysis and computer simulation to examine estimation bias and issues of interpretation when the model of gene flow is misspecified in analysis of genomic datasets, for example, if introgression is assigned to the wrong lineages. In the case of two species, we establish a correspondence between the migration rate in the continuous migration model and the introgression probability in the introgression model. When gene flow occurs continuously through time but in the analysis is assumed to occur at a fixed time point, common evolutionary parameters such as species divergence times are surprisingly well estimated. However, the time of introgression tends to be estimated towards the recent end of the period of continuous gene flow. When introgression events are assigned incorrectly to the parental or daughter lineages, introgression times tend to collapse onto species divergence times, with introgression probabilities underestimated. Overall, our analyses suggest that the simple introgression model is useful for extracting information concerning between-specific gene flow and divergence even when the model may be misspecified. However, for reliable inference of gene flow it is important to include multiple samples per species, in particular, from hybridizing species.     

AnnexinA7 promotes epithelial–mesenchymal transition by interacting with Sorcin and contributes to aggressiveness in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and metastasis is the major cause of the high mortality of HCC. In this study, we identified that AnnexinA7 (ANXA7) and Sorcin (SRI) are overexpressed and interacting proteins in HCC tissues and cells. In vitro functional investigations revealed that the interaction between ANXA7 and SRI regulated epithelial–mesenchymal transition (EMT), and then affected migration, invasion, and proliferation in HCC cells. Furthermore overexpression/knockdown of ANXA7 was remarkably effective in promoting/inhibiting tumorigenicity and EMT in vivo. Altogether, our study unveiled a mechanism that ANXA7 promotes EMT by interacting with SRI and further contributes to the aggressiveness in HCC, which provides a novel potential therapeutic target for preventing recurrence and metastasis in HCC.Subject terms: Medical research, Genetics research     

Complete Genome Sequence of Human Respiratory Syncytial Virus Genotype A with a 72-Nucleotide Duplication in the Attachment Protein G Gene

The complete genome sequence of human respiratory syncytial virus genotype A (HRSV-A) with a 72-nucleotide duplication in the C-terminal part of the attachment protein G gene was determined and analyzed. The genome was 15,277 bp in length, and 0.46 to 6.03% variations were identified at the nucleotide level compared with the previously reported complete genome of HRSV-A. Characterization of the genome will improve understanding of the diversity of the HRSV-A major antigens and enable an in-depth analysis of its genetics.     

Associations between the FAS ?670?A/G and ?1,377?G/A polymorphisms and susceptibility to autoimmune rheumatic diseases: a meta-analysis

The aim of this study was to explore whether FAS ?670?A/G and ?1,377?G/A polymorphisms confer susceptibility to autoimmune rheumatic diseases. A meta-analysis was conducted on the associations between the FAS ?670?A/G and ?1,377?G/A polymorphisms and autoimmune rheumatic diseases using allele contrast, a recessive model, a dominant model, and an additive model. Thirteen articles with 21 comparison studies (16 on FAS ?670?A/G and 5 on ?1,377?G/A polymorphisms) including systemic lupus erythematosus (SLE), four systemic sclerosis, four Sjogren’s syndrome, three rheumatoid arthritis (RA), one juvenile idiopathic arthritis, and one spondyloarthropathy were available for the meta-analysis. Meta-analysis revealed an association between rheumatic diseases and the FAS ?670?A/G polymorphism in the dominant model (odds ratio [OR]?=?0.761, 95?% confidence interval [CI]?=?0.621–0.932, p?=?0.008]. Stratification by ethnicity indicated an association between the FAS ?670?G allele carrier and rheumatic diseases in Asian (OR?=?0.569, 95?% CI?=?0.409–0.791, p?=?0.001). Furthermore, stratification by disease indicated an association between the FAS ?670?G allele carrier and SLE and RA (OR?=?0.578, 95?% CI?=?0.358–0.934, p?=?0.025; OR?=?0.609, 95?% CI?=?0.398–0.934, p?=?0.023, respectively). The FAS ?670?G allele was negatively associated with SLE susceptibility. Meta-analysis of the FAS ?1,377?G/A polymorphism stratified by disease showed an association between the FAS ?1,377 A allele and SLE (OR?=?0.783, 95?% CI?=?0.613–0.997, p?=?0.047). Meta-analyses using the dominant model also showed a significant association in SLE (OR?=?0.712, 95?% CI?=?0.528–0.961, p?=?0.027). This meta-analysis demonstrates that the FAS ?670?A/G polymorphism confers susceptibility to rheumatic diseases in Asians and SLE and RA, and the FAS ?1,377?G/A polymorphism is associated with SLE susceptibility.     

Preliminary studies on leaf beetle, Galeruca daurica on grassland

沙葱萤叶甲Galeruca daurica Joannis是近年来严重危害葱属(AUium)植物建群草场的重要食叶害虫.该虫在内蒙古地区一年发生1代,以卵越冬.本文介绍了该虫生活史、生活习性、发生范围、发生面积、危害症状、生境特征、危害损失,并提出了防治策略.     

Hyphal heterogeneity in Aspergillus oryzae is the result of dynamic closure of septa by Woronin bodies

Hyphae of higher fungi are compartmentalized by septa. These septa contain a central pore that allows for inter‐compartmental and inter‐hyphal cytoplasmic streaming. The cytoplasm within the mycelium is therefore considered to be a continuous system. In this study, however, we demonstrate by laser dissection that 40% of the apical septa of exploring hyphae of Aspergillus oryzae are closed. Closure of septa correlated with the presence of a peroxisome‐derived organelle, known as Woronin body, near the septal pore. The location of Woronin bodies in the hyphae was dynamic and, as a result, plugging of the septal pore was reversible. Septal plugging was abolished in a ΔAohex1 strain that cannot form Woronin bodies. Notably, hyphal heterogeneity was also affected in the ΔAohex1 strain. Wild‐type strains of A. oryzae showed heterogeneous distribution of GFP between neighbouring hyphae at the outer part of the colony when the reporter was expressed from the promoter of the glucoamylase gene glaA or the α‐glucuronidase gene aguA. In contrast, GFP fluorescence showed a normal distribution in the case of the ΔAohex1 strain. Taken together, it is concluded that Woronin bodies maintain hyphal heterogeneity in a fungal mycelium by impeding cytoplasmic continuity.     

The antioxidative property of green tea against iron-induced oxidative stress in rat brain

The antioxidative property of green tea against iron-induced oxidative stress was investigated in the rat brain both in vivo and in vivo. Incubation of brain homogenates at 37 degrees C for 4 hours in vitro increased the formation of Schiff base fluorescent products of malonaldehyde, an indicator of lipid peroxidation. Auto-oxidation (without exogenous iron) of brain homogenates was inhibited by green tea extract in a concentration-dependent manner. Moreover, incubation with iron (1 microM) elevated lipid peroxidation of brain homogenates after 4-hour incubation at 37 degrees C. Co-incubation with green tea extract dose-dependently inhibited the iron-induced elevation in lipid peroxidation. For the in vivo studies: ferrous citrate (iron, 4.2 nmoles) was infused intranigrally and induced degeneration of the nigrostriatal dopaminergic system of rat brain. An increase in lipid peroxidation in substantia nigra as well as a decrease in dopamine content in striatum was observed seven days after the iron infusion. Intranigral infusion of green tea extract alone did not increase, and in some cases, even decreased lipid peroxidation in substantia nigra. Co-infusion of green tea extract prevented oxidative injury induced by iron. Both iron-induced elevation in lipid peroxidation in substantia nigra and iron-induced decrease in dopamine content in striatum were suppressed. Oral administration of green tea extract for two weeks did not prevent the iron-induced oxidative injury in nigrostriatal dopaminergic system. Our results suggest that intranigral infusion of green tea extract appears to be nontoxic to the nigrostriatal dopaminergic system. Furthermore, the potent antioxidative action of green tea extract protects the nigrostriatal dopaminergic system from the iron-induced oxidative injury.     

哑蟋属两新种及峨眉哑蟋雌虫的发现(直翅目：蟋蟀科)

哑蟋属两新种及峨眉哑蟋雌虫的发现（直翅目：蟋蟀科）陈军,郑哲民（陕西师范大学动物研究所西安７１００６２）１９９３年在整理陕西师范大学动物研究所蝗虫标本室的蟋蟀标本以及作者于１９９２年夏季在四川采集的蟋蟀标本时,发现有哑蟋属ＧｏｎｉｏｇｒｙｌｌｕｓＣｈ...     

Lipid production by microalgae <Emphasis Type="Italic">Chlorella protothecoides</Emphasis> with volatile fatty acids (VFAs) as carbon sources in heterotrophic cultivation and its economic assessment

Volatile fatty acids (VFAs) that can be derived from food wastes were used for microbial lipid production by Chlorella protothecoides in heterotrophic cultures. The usage of VFAs as carbon sources for lipid accumulation was investigated in batch cultures. Culture medium, culture temperature, and nitrogen sources were explored for lipid production in the heterotrophic cultivation. The concentration and the ratio of VFAs exhibited significant influence on cell growth and lipid accumulation. The highest lipid yield coefficient and lipid content of C. protothecoides grown on VFAs were 0.187 g/g and 48.7 %, respectively. The lipid content and fatty acids produced using VFAs as carbon sources were similar to those seen on growth and production using glucose. The techno-economic analysis indicates that the biodiesel derived from the lipids produced by heterotrophic C. protothecoides with VFAs as carbon sources is very promising and competitive with other biofuels and fossil fuels.