Rosetta error model for gene expression analysis

MOTIVATION: In microarray gene expression studies, the number of replicated microarrays is usually small because of cost and sample availability, resulting in unreliable variance estimation and thus unreliable statistical hypothesis tests. The unreliable variance estimation is further complicated by the fact that the technology-specific variance is intrinsically intensity-dependent. RESULTS: The Rosetta error model captures the variance-intensity relationship for various types of microarray technologies, such as single-color arrays and two-color arrays. This error model conservatively estimates intensity error and uses this value to stabilize the variance estimation. We present two commonly used error models: the intensity error-model for single-color microarrays and the ratio error model for two-color microarrays or ratios built from two single-color arrays. We present examples to demonstrate the strength of our error models in improving statistical power of microarray data analysis, particularly, in increasing expression detection sensitivity and specificity when the number of replicates is limited.     

生物合成聚3-羟基丙酸酯的研究进展

聚3-羟基丙酸酯(P3HP)作为聚羟基脂肪酸酯家族(PHAs)中的新型热塑性塑料,具有生物降解性和生物相容性等优点。目前,未见野生微生物可以合成P3HP的报道,生产途径主要为化学法和生物法。其中,通过化学法或添加3-HP单体及其结构类似物作为前体的P3HP合成效率低、成本高且不具环保性;而通过构建和改造工程菌的生物代谢途径,能够利用廉价、可再生的碳源,已经逐渐成为研究热点。文中综述了国内外P3HP生物合成研究进展,并对甘油途径、丙二酸单酰辅酶A(Malonyl-Co A)途径和β-丙氨酸途径等合成方法进行了优缺点分析,为生物合成P3HP的深入研究奠定理论基础。     

PSW1, an LRR receptor kinase,regulates pod size in peanut

Pod size is a key agronomic trait that greatly determines peanut yield, the regulatory genes and molecular mechanisms that controlling peanut pod size are still unclear. Here, we used quantitative trait locus analysis to identify a peanut pod size regulator, P OD S IZE/W EIGHT1 (PSW1), and characterized the associated gene and protein. PSW1 encoded leucine-rich repeat receptor-like kinase (LRR–RLK) and positively regulated pod stemness. Mechanistically, this allele harbouring a 12-bp insertion in the promoter and a point mutation in the coding region of PSW1 causing a serine-to-isoleucine (S618I) substitution substantially increased mRNA abundance and the binding affinity of PSW1 for BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1). Notably, PSW1^HapII (super-large pod allele of PSW1) expression led to up-regulation of a positive regulator of pod stemness PLETHORA 1 (PLT1), thereby resulting in larger pod size. Moreover, overexpression of PSW1^HapII increased seed/fruit size in multiple plant species. Our work thus discovers a conserved function of PSW1 that controls pod size and provides a valuable genetic resource for breeding high-yield crops.     

Immunosuppressive Bibenzyl-phenylpropane Hybrids from Dendrobium devonianum

Two new bibenzyl-phenylpropane hybrids, dendrophenols A and B ( 1 and 2 ), along with nine known bibenzyls, were isolated from the aerial part of Dendrobium devonianum Paxt. Their structures were determined by extensive spectroscopic methods and methylation. Bioassays revealed that compounds 1–9 were specifically immunosuppressive to T lymphocytes with IC₅₀ values ranging from 0.41 to 9.4 μM, of which compounds 1 (IC₅₀=1.62 μM) and 2 (IC₅₀=0.41 μM) were promising immunosuppressive agents for T lymphocytes with the selectivity indices of 19.9 and 79.5, respectively.     

Horsfielenigans A and B,Two Rearranged Lignans with Anti-Inflammatory Effects from Horsfieldia kingii

Seven lignans were isolated from 70 % aqueous acetone extracts of the twigs and leaves of Horsfieldia kingii. Among these, new compounds 1 – 3 were identified by spectroscopic techniques, with horsfielenigans A and B ( 1 and 2 ) being particularly noteworthy for their rare β-benzylnaphthalene skeleton, where compound 1 contains an oxabicyclo[3,2,1]octane moiety. In vitro evaluation of bioactivity against nitric oxide (NO) production in LPS-activated RAW264.7 macrophages revealed inhibitory effects by 1 (IC₅₀=7.3 μM) and 2 (IC₅₀=9.7 μM).     

Identification of soybean drought-tolerant genotypes and loci correlated with agronomic traits contributes new candidate genes for breeding

Plant Molecular Biology - Drought tolerance level of 136 soybean genotypes, the correlations among traits were evaluated, and several important drought-tolerant genotypes, traits, SNPs and genes...     

MiR‐671‐5p plays a promising role in restraining osteosarcoma cell characteristics through targeting TUFT1

The aim of our study was to explore the roles of miR‐671‐5p in mediating biological processes of osteosarcoma (OS) cells and clinical implications. On the basis of the OS samples acquired from the GEO database, the expression difference and overall survival analyses of miR‐671‐5p and TUFT1 were determined. The expression of MiR‐671‐5p was verified using OS cell lines. 3‐(4,5‐Dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide, wound‐healing, and Transwell assays were respectively carried out to probe whether miR‐671‐5p regulated OS cell vitality, migration, and invasion. The expression of miR‐671‐5p was downregulated in OS tissues and cell lines. High expression of MiR‐671‐5p blocked OS cell growth, migration, and invasion. TUFT1 was predicted and validated as the target of miR‐671‐5p in OS cells using in silico analysis and luciferase reporter assays. Forced expression of TUFT1 reversed the suppressive influence of miR‐671‐5p on cell viability, migration, and invasion of OS cells. Moreover, the low expression of miR‐671‐5p and the high expression of TUFT1 led to poor prognosis. Taken together, targeting miR‐671‐5p/TUFT1 may be a promising strategy for treating OS.     

Design,Synthesis and Interaction of BRCA1 Peptide Fragments with RAD51(181–200)

International Journal of Peptide Research and Therapeutics - Six breast cancer susceptibility gene 1 (BRCA1) peptide fragments were designed by removing N-terminal amino acid residues of...