An effective strategy for assembling the sex-limited chromosome.

BACKGROUND: Most currently available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which results in incomplete assemblies that hinder further research on sex chromosomes. Recent advancements in long-read sequencing and population sequencing have provided the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts. FINDINGS: We introduce the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieves improved assembly results compared to flow sorting. Specifically, SRY outperforms in the heterochromatic region and demonstrates comparable performance in other regions. Furthermore, SRY enhances the capabilities of the hybrid assembly software, resulting in improved continuity and accuracy. CONCLUSIONS: Our method enables true complete genome assembly and facilitates downstream research of sex-limited chromosomes.

Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study.

Cattle and water buffalo belong to the same subfamily Bovinae and share chromosome banding and gene order homology. In this study, we used genome-wide Illumina BovineSNP50 BeadChip to analyze 91 DNA samples from three breeds of water buffalo (Nili-Ravi, Murrah and their crossbred with local GuangXi buffalos in China), to demonstrate the genetic divergence between cattle and water buffalo through a large single nucleotide polymorphism (SNP) transferability study at the whole genome level, and performed association analysis of functional traits in water buffalo as well. A total of 40,766 (75.5 %) bovine SNPs were found in the water buffalo genome, but 49,936 (92.5 %) were with only one allele, and finally 935 were identified to be polymorphic and useful for association analysis in water buffalo. Therefore, the genome sequences of water buffalo and cattle shared a high level of homology but the polymorphic status of the bovine SNPs varied between these two species. The different patterns of mutations between species may associate with their phenotypic divergence due to genome evolution. Among 935 bovine SNPs, we identified a total of 9 and 7 SNPs significantly associated to fertility and milk production traits in water buffalo, respectively. However, more works in larger sample size are needed in future to verify these candidate SNPs for water buffalo.

Comparative analysis of ESTs in response to drought stress in chickpea (C. arietinum L.).

Chickpea (Cicer arietinum L.) is an important pulse crop grown mainly in the arid and semi-arid regions. To identify the water-stress-induced genes, two non-normalized cDNA libraries were constructed from the seedling leaves of a drought-tolerant chickpea cultivar under PEG-treated and -nontreated conditions. About 2500 clones from each library were selected randomly for sequencing analysis. Based on IDEG6 online software analysis, 92 genes were differentially expressed, and these genes were involved in diverse biological progresses, such as metabolism, transcription, signal transduction, protein synthesis and others. Most of the up-regulated genes were related to drought tolerance, and the down-regulated genes were mainly involved in photosynthesis. The differential expression patterns of five functional unigenes were confirmed by quantitative real-time PCR (qPCR). The results will help in understanding the molecular basis of drought tolerance in chickpea.

Comparison of chemical, electrical, and combined activation methods for in vitro matured porcine oocytes.

Factors influencing porcine oocyte activation were systematically studied. This study included (1) the effect of ionomycin plus various chemical agents on activation, (2) comparison of different electrical activation parameters, (3) optimization of combined activation, and (4) evaluation of the optimized protocols. The results showed that (1) blastocyst rates of ionomycin (Ion) + 6-dimethylaminopurine (6-DMAP) (29.7 ± 1.1%), Ion + cytochalasin B (CB) + cycloheximide (CHX) (29.8 ± 1.2%), Ion + CB + 6-DMAP (30.4 ± 1.6%), and Ion + CB + CHX + 6-DMAP (30.2 ± 2.7%) were significantly higher than Ion + CHX (15.8 ± 1.5%, p < 0.05); (2) the parthenogenetic blastocyst formation of electrical activation was optimal when oocytes were activated by three direct current (DC) pulses of 1.00 kV cm(-1) for 80 µs (39.5 ± 1.1%); (3) blastocyst rates of DC + CB + CHX (55.4 ± 1.2%) and DC + CB + 6-DMAP (50.4 ± 2.9%) were significantly higher than DC + 6-DMAP, DC + CB + CHX + 6-DMAP, electrical activation, and chemical activation alone (p < 0.05); and (4) approximately 84% of parthenogenetic blastocysts yielded by the optimized protocol were diploid, which was significantly higher than that of electrical activation blastocysts (40%). Using the optimized electrical and combined activation protocol, high blastocyst rates were generated by intracytoplasmic sperm injection (ICSI) (34.6 ± 1.1%), cytoplasmic microinjection (CI) (52.3 ± 2.2%), and handmade cloning (HMC) (31.2 ± 1.0%), respectively. This study concludes that the optimal activation protocol of in vitro matured porcine oocytes was combined activation with parameter as three DC pulses of 1.00 kV cm(-1) for 80 µs plus CB and CHX treatment.

Association between social health status and depressive symptoms among community-dwelling elderly adults in Zhejiang Province, China / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

OBJECTIVE@#Mental disorders of the elderly population in China deserve attention. Social health is significantly associated with depression. This study aimed to evaluate the rate of depressive symptoms and to test the relationships between social health and depressive symptoms among a large sample of community-dwelling elderly adults.@*METHODS@#We conducted a cross-sectional study among community-dwelling adults aged 60 years or above in Zhejiang Province, China. Face-to-face interviews were used to complete a structured questionnaire for all participants. We used the Social Health Scale for the Elderly (SHSE) to evaluate social health status and used the short form of the Geriatric Depression Scale to evaluate depressive symptoms. Multivariate logistic regression was used to evaluate the association between social health status and depressive symptoms.@*RESULTS@#Of the total of 3757 participants included, 1887 (50.23%) were female, and the mean±standard deviation (SD) age was (70.0±8.3) years. The rate of depressive symptoms was 25.92%. The social health score was higher in non-depressed participants than in depressed participants (raw score 50.7 vs. 48.3, P<0.001). Participants with "moderate" or "good" social health had a significantly lower risk of depressive symptoms than those with "poor" social health (odds ratio (OR)=0.55, 95% confidence interval (CI): 0.46-0.66 for moderate social health; OR=0.45, 95% CI: 0.35-0.60 for good social health). The association between social health and depressive symptoms was consistent across several subgroups.@*CONCLUSIONS@#Social health is significantly inversely associated with depressive symptoms. The SHSE may serve as an efficient screener to identify those elderly adults with social health deficits, but systematic assessment to guide intervention merits further investigation.

Comparative characterization of microRNAs from the liver flukes Fasciola gigantica and F. hepatica.

MicroRNAs (miRNAs) are key regulators of gene expression at the post-transcription level. The present study specifically explored and compared the miRNA expression profiles of F. gigantica and F. hepatica using an integrated sequencing and bioinformatics platform and quantitative real-time PCR. Nineteen and 16 miRNA candidates were identified from F. gigantica and F. hepatica, respectively. The two parasites shared 11 miRNAs, with 8 also showing similarity to miRNAs of Schistosoma japonicum. Another 8 miRNAs were identified as F. gigantica-specific and 5 as F. hepatica-specific, most of which were novel. Predicted target analysis with 11465 mRNA and EST sequences of F. hepatica and F. gigantica revealed that all of the miRNAs had more than one target, ranging from 2 to 398 with an average of 51 targets. Some functions of the predicted targets were only found in F. gigantica, such as "transcription regulator", while some others were only found in F. hepatica, such as "reproduction" and "response to stimulus", indicating the different metabolism and gene regulation patterns of the two parasites. The present study represents the first global comparative characterization of miRNA expression profiles of F. gigantica and F. hepatica, which has provided novel valuable resources for a better understanding of the two zoonotic trematodes.