A semi-parametric statistical model for integrating gene expression profiles across different platforms

Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the two technologies. Integration data across these two platforms has the potential to improve the power and reliability of DEG detection. We propose a rank-based semi-parametric model to determine DEGs using information across different sources and apply it to the integration of RNA-seq and microarray data. By incorporating both the significance of differential expression and the consistency across platforms, our method effectively detects DEGs with moderate but consistent signals. We demonstrate the effectiveness of our method using simulation studies, MAQC/SEQC data and a synthetic microRNA dataset. Our integration method is not only robust to noise and heterogeneity in the data, but also adaptive to the structure of data. In our simulations and real data studies, our approach shows a higher discriminate power and identifies more biologically relevant DEGs than eBayes, DEseq and some commonly used meta-analysis methods.     

Decreases in Both the Seroprevalence of Serum Antibodies and Seroprotection against Japanese Encephalitis Virus among Vaccinated Children

The incidence of Japanese encephalitis(JE) has significantly decreased in China due to JE vaccines. In this study, we investigated the post-JE vaccination seroprevalence and protection provided by vaccinated sera against Japanese encephalitis virus(JEV) to elucidate the persistence and waning of antibodies to JEV among JE-SA14-14-2-vaccinated children. A total of 300 serum samples were collected from vaccinated children aged 3–10 years in Zhaotong, Yunnan,China. The seroprevalence of anti-JEV antibodies was determined by enzyme-linked immune sorbent assay and plaque reduction neutralization test. The highest seropositivity of 82% was observed in vaccinated children during the first0.5–1.5 years after booster vaccination. Then, the seropositivity began to decline and remained lower than the original level observed in the 0.5–1.5-year group. An association was found between the waning of seroprevalence and elapsed time of the post-booster vaccination. Similarly, the neutralizing antibody(nAb) titres gradually decreased over time, and the levels showed a positive correlation with the protective efficacy in mice. This finding suggests that nAbs play an important role in the antiviral process and that the nAb titre is an adequately credible parameter for evaluating the protective efficacy induced by the JE vaccine. Our results provide data that clarify the persistence and waning of antibodies to JEV, which may help elucidate the pathogenesis of JE.     

Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population

Plants are considered an important food and nutrition source for humans. Despite advances in plant seed metabolomics, knowledge about the genetic and molecular bases of rice seed metabolomes at different developmental stages is still limited. Here, using Zhenshan 97 (ZS97) and Minghui 63 (MH63), we performed a widely targeted metabolic profiling in seeds during grain filling, mature seeds and germinating seeds. The diversity between MH63 and ZS97 was characterized in terms of the content of metabolites and the metabolic shifting across developmental stages. Taking advantage of the ultra‐high‐density genetic map of a population of 210 recombinant inbred lines (RILs) derived from a cross between ZS97 and MH63, we identified 4681 putative metabolic quantitative trait loci (mQTLs) in seeds across the three stages. Further analysis of the mQTLs for the codetected metabolites across the three stages revealed that the genetic regulation of metabolite accumulation was closely related to developmental stage. Using in silico analyses, we characterized 35 candidate genes responsible for 30 structurally identified or annotated compounds, among which LOC_Os07g04970 and LOC_Os06g03990 were identified to be responsible for feruloylserotonin and l ‐asparagine content variation across populations, respectively. Metabolite?agronomic trait association and colocation between mQTLs and phenotypic quantitative trait loci (pQTLs) revealed the complexity of the metabolite?agronomic trait relationship and the corresponding genetic basis.     

Morphogenesis and Molecular Phylogeny of the Soil Ciliate Holostichides chardezi (Ciliophora,Hypotrichia, Bakuellidae), with Redefinition of Holostichides Foissner, 1987 and Establishment of a New Genus Anteholostichides

Morphogenesis of the soil hypotrich ciliate, Holostichides chardezi Foissner, 1987, collected from southeastern China, was investigated using the protargol staining method. The main morphogenetic events follow a similar process with that of its congeners. Phylogenetic analyses based on the SSU rDNA sequence data indicate that Holostichides is nonmonophyletic; H. chardezi, the type species of Holostichides, clusters with H. heterotypicus, while H. terrae is distinctly separate from these species. H. terrae can be distinguished from H. chardezi (type species of Holostichides) and H. heterotypicus by undulating membranes relatively long and distinctly curved (vs. relatively short and straight), pharynx with (vs. without) rod‐shaped structure, and two (vs. more than two) frontoterminal cirri. Therefore, a new genus, Anteholostichides nov. gen., has been proposed for H. terrae. Further, the diagnosis of the genus Holostichides is improved.     

Effects of biodiversity,stand factors and functional identity on biomass and productivity during the restoration of subtropical forests in Central China

恢复梯度上华中亚热带森林生物多样性、林分因子及功能特性对生物量、生产力的影响 草地群落上进行的控制实验大都发现生物多样性对生态系统功能有显著促进作用。然而,在天然林中,多样性与林分因子、群落功能特性的相对作用大小仍存在争议。本文在森林恢复梯度上,研究这3类因素对生物量和生产力的相对影响。我们在湖北神农架设置了处于不同恢复阶段的24块(600 m²)亚热 带森林样地,计算了林分生物量和生产力。选择5个关键的植物功能性状,并计算了群落的功能多样性(功能丰富度、功能均匀度和功能离散度)和性状的加权平均值(CWM)。使用一般线性模型(GLMs)、变异分离等方法探究林分因子(密度、林龄、群落最大树高等)、功能特性、物种和功能多样性对生物量和生产力的相对重要性。研究结果表明,随着森林恢复,林分生物量和生产力显著增加,群落物种丰富度显著增加,而功能离散度显著降低。变异分离结果表明,多样性对生物量和生产力的单独效应不显著,但可能通过与林分因子和功能特性的协同效应来影响生物量和生产力。总体而言,我们发现林分因子对亚热带森林生物量和生产力的影响最大,功能特性显著影响生产力,但不影响生物量。这些结果说明,在森林经营中,调整林分结构和群落物种特性是提高森林碳储量和固碳潜力的有效途径。     

Biosynthesis and biotechnological production of salidroside from Rhodiola genus plants

Phytochemistry Reviews - Salidroside is a precious phenylethanoid glycoside derived from Rhodiola genus plants, which possesses a broad spectrum of biological properties for application in the...     

A prostate cancer tissue specific spectral library for targeted proteomic analysis

Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens.     

云南省爬行动物名录和地理区划更新

云南省作为中国生物多样性最高的省份, 其详实的物种本底资料对我国生物多样性研究和保护具有重要意义。本文在前期研究的基础上, 结合实体标本, 汇总编制了云南省现生、原生爬行动物更新名录。截至2021年12月31日, 云南省记录爬行动物25科82属235种, 其中龟鳖目4科12属16种, 有鳞目蜥蜴亚目6科20属72种, 蛇亚目15科50属147种。较《云南两栖爬行动物》确认新增82种, 存疑收录21种, 移除23种。基于先前云南省爬行动物区划和更新后的物种分布信息, 将云南省爬行动物地理分为6个动物地理区, 即滇西北横断山区、滇西山地区、滇南山地区、滇东南山地区、滇中高原区以及滇东北山地区; 其中滇西北横断山区、滇西山地区、滇中高原区和滇东南山地区的范围与先前研究相比有所调整。结合调整后的爬行动物地理区划, 对物种分布、物种特有性、受威胁状况等给出了统计结果。云南省爬行动物特有物种、国内仅见于云南的非特有物种数量较多, 受威胁等级高。建议今后继续加大分类学研究投入, 对滇西北、滇中特有爬行动物分布集中的区域积极开展栖息地保护工作, 同时在最新调整的《国家重点保护野生动物名录》基础上, 定期组织专家研讨, 对《云南省省级重点保护动物名录》提出更新建议。