Using weighted permutation scores to detect differential gene expression with microarray data

A class of nonparametric statistical methods, including a nonparametric empirical Bayes (EB) method, the Significance Analysis of Microarrays (SAM) and the mixture model method (MMM) have been proposed to detect differential gene expression for replicated microarray experiments. They all depend on constructing a test statistic, for example, a t-statistic, and then using permutation to draw inferences. However, due to special features of microarray data, using standard permutation scores may not estimate the null distribution of the test statistic well, leading to possibly too conservative inferences. We propose a new method of constructing weighted permutation scores to overcome the problem: posterior probabilities of having no differential expression from the EB method are used as weights for genes to better estimate the null distribution of the test statistic. We also propose a weighted method to estimate the false discovery rate (FDR) using the posterior probabilities. Using simulated data and real data for time-course microarray experiments, we show the improved performance of the proposed methods when implemented in MMM, EB and SAM.     

CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible

The structure of the free form HIV gp120, critical for therapeutic agent development, is unavailable due to its high flexibility. Previous thermodynamic data, structural analysis and simulation results have suggested a large conformational change in the core domain upon CD4 binding. The bridging sheet, which consists of four beta-strands with beta20/21 nestling against the inner/outer domains and beta2/3 facing outward, more exposed to the solvent, was proposed to be unfolded in the native state. In order to test this proposition and to characterize the native conformations, we performed potential mean force (PMF) molecular dynamics (MD) simulations on the CD4-bound crystal structure. We pushed the bridging sheet away from the inner and outer domain to explore the accessible conformational space for the bridging sheet. In addition, we performed conventional MD simulations on structures with the bridging sheet partially unfolded to investigate the stability of the association between the inner and outer domains. Based on the free energy profiles, we find that the whole bridging sheet is unlikely to unfold without other concurrent conformational changes. On the other hand, the partial bridging sheet, beta strands 2/3, can switch its conformation from the folded to the unfolded state. Furthermore, relaxation of conformation with partially unfolded bridging sheet through MD simulations leads to a conformation with beta strands 20/21 quickly re-anchoring against the inner and outer domains. Such a conformation, although lacking some of the hydrophobic interactions present in the CD4-bound structure, displayed high stability as further indicated by other restrained MD simulations. The relevance of this conformation to the free form structure and the pathway for conformational change from the free form to the CD4-bound structure is discussed in detail in light of the available unliganded SIV gp120 crystal structure.     

Interactions between rho and gamma2 subunits of the GABA receptor

The gamma-aminobutyric acid type C (GABA(C)) receptor is a ligand-gated chloride channel with distinct physiological and pharmacological properties. Although the exact subunit composition of native GABA(C) receptors has yet to be firmly established, there is general agreement that GABA rho subunits participate in their formation. Recent studies on white perch suggest that certain GABA rho subunits can co-assemble with the GABA(A) receptor gamma2 subunit to form a heteromeric receptor with electrophysiological properties that correspond more closely to the native GABA(C) receptor on retinal neurons than any of the homomeric rho receptors. In the present study we examined the interactions among various perch GABA rho and gamma2 subunits. When co-expressed in Xenopus oocytes, the gamma2 subunit co-immunoprecipitated with Flag-tagged perch rho1A, rho1B, and rho2B subunits, but not with the Flag-tagged perch rho2A subunit. Immunocytochemical studies indicated that the membrane surface expression of the gamma2 subunit was detected only when it was co-expressed with perch rho1A, rho1B, or rho2B subunit, but not with the perch rho2A subunit or when expressed alone. In addition, co-immunoprecipitation of perch rho1B and gamma2 subunits was also detected in protein samples of the teleost retina. Taken together, these findings suggest that a heteromeric rho(gamma2) receptor could represent one form of GABA(C) receptor on retinal neurons.     

Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes

The parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, is one of the extremely AT-rich genomes sequenced so far and known to possess many atypical characteristics. Using multivariate statistical approaches, the present study analyzes the amino acid usage pattern in 5038 annotated protein-coding sequences in P. falciparum clone 3D7. The amino acid composition of individual proteins, though dominated by the directional mutational pressure, exhibits wide variation across the proteome. The Asn content, expression level, mean molecular weight, hydropathy, and aromaticity are found to be the major sources of variation in amino acid usage. At all stages of development, frequencies of residues encoded by GC-rich codons such as Gly, Ala, Arg, and Pro increase significantly in the products of the highly expressed genes. Investigation of nucleotide substitution patterns in P. falciparum and other Plasmodium species reveals that the nonsynonymous sites of highly expressed genes are more conserved than those of the lowly expressed ones, though for synonymous sites, the reverse is true. The highly expressed genes are, therefore, expected to be closer to their putative ancestral state in amino acid composition, and a plausible reason for their sequences being GC-rich at nonsynonymous codon positions could be that their ancestral state was less AT-biased. Negative correlation of the expression level of proteins with respective molecular weights supports the notion that P. falciparum, in spite of its intracellular parasitic lifestyle, follows the principle of cost minimization. [Reviewing Editor : Dr. Richard Kliman]     

Embryonic gene expression and pro-protein processing of proSAAS during rodent development

In vitro assays have demonstrated that peptides derived from the recently-identified proSAAS precursor inhibit prohormone convertase 1 (PC1) suggesting that this novel peptide may function as an endogenous inhibitor of PC1. To further understand the role of proSAAS in vivo, we have investigated the expression of proSAAS mRNA and processing of proSAAS during pre- and early postnatal rodent development. In situ hybridization showed that, by embryonic day 12.5 (e12.5) in the rat, proSAAS mRNA was present in essentially all differentiating neurons in the mantle layer of the myelencephalon, metencephalon, diencephalon, spinal cord and several sympathetic ganglia. During later stages of prenatal development, widespread proSAAS expression continues in post-mitotic neurons of both the CNS and PNS and begins in endocrine cells of the anterior and intermediate pituitary. Although proSAAS expression overlaps with PC1 in several regions, its overall expression pattern is significantly more extensive, suggesting that proSAAS may be multifunctional during development. Processed forms of proSAAS are present by at least mid-gestation with marked accumulation of two C-terminal forms, comprising the PC1 inhibitory fragment of proSAAS.     

Apelin及其生物学效应

Apelin是Tatemoto等利用反向药理学方法从牛胃分泌物中提取并纯化出的孤儿G蛋白偶联受体——血管紧张素受体AT1相关的受体蛋白(putativereceptorproteinrelatedtotheangiotensinreceptorAT1,APJ)的天然配体。Apelin及其受体APJ在体内分布广泛,以内分泌、旁/自分泌的方式调节心血管系统稳态、水盐平衡等,是一种重要的生理调节肽。有意义的是,Apelin还是一种免疫调节肽,可通过与其受体APJ结合抵抗病毒的入侵,抑制淋巴细胞胆碱能活性,参与免疫缺陷疾病和获得性免疫缺陷综合征(acquiredimmunedeficiencysyndrome,AIDS)免疫反应,调节免疫炎症因子生成,在调节免疫反应中起一定作用。作为心血管活性肽Apelin具有扩张血管、降低血压和增强心肌收缩力的效应;心血管疾病中,Apelin及其受体APJ均有不同程度的变化,在心力衰竭及心肌重塑中具有重要调节意义。     

Isolation, purification and structural investigation of a water-soluble polysaccharide from Solanum lyratum Thunb

Polysaccharides, extracted from the herbs of Chinese natural Solanum lyratum Thunb (SLT), which is a traditional Chinese medicine with hot water and 0.04 M sodium hydroxide successively, were fractionated and purified by ion-exchange and gel-filtration chromatography. According to methylation, periodate oxidation, NMR spectroscopy, partial and graded acid and enzymic hydrolysis analysis, the results indicated the D-glucan to be linear and to contain both (1-->3)- and (1-->4)-linkages. The anomeric NMR and IR spectra measurements confirmed that the sugar residues were beta-glycosidically linked.