Biomarker discovery for arsenic exposure using functional data. Analysis and feature learning of mass spectrometry proteomic data

Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case study for measuring arsenic concentrations in a population residing in an As-endemic region of Bangladesh using plasma protein expressions measured by SELDI-TOF mass spectrometry. We analyze the data using a unified statistical method based on functional learning to preprocess mass spectra and extract mass spectrometry (MS) features and to associate the selected MS features with arsenic exposure measurements. The task is challenging due to several factors, the high dimensionality of mass spectrometry data, complicated error structures, and a multiple comparison problem. We use nonparametric functional regression techniques for MS modeling, peak detection based on the significant zero-downcrossing method, and peak alignment using a warping algorithm. Our results show significant associations of arsenic exposure to either under- or overexpressions of 20 proteins.     

PLOD3基因3’调控区的人类特异突变改变miR-124a对PLOD3的调控

microRNAs(miRNAs)是一类在转录后水平调控基因表达的不编码蛋白质的小RNA(长度20-24个碱基).其中,miR-124a是一个在哺乳动物中枢神经系统高度表达的miRNA,在神经前体细胞向神经元分化的过程中起着举足轻重的作用.由于miRNAs特异性地识别靶基因的3'端调控区(3'UTR)的靶序列,因此,在人类起源过程中基因3'UTR的单核苷酸序列变异有可能导致miRNA调控的改变.通过靶基因预测和3'UTR区在哺乳动物代表物种间的同源序列比较,我们发现miR-124a的靶基冈中有一个基因(PLOD3)3UTR的靶位点中存在人类特异突变位点.利用体外报告基因系统,发现PLOD3基因3'UTR靶位点中所含的一个人类特异的突变导致miR-124a对PLOD3的调控效率降低.研究表明,miRNAs靶基因3'UTR的序列变异具有功能效应,它有可能足人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一.     

The Toxoplasma gondii type-II NADH dehydrogenase TgNDH2-I is inhibited by 1-hydroxy-2-alkyl-4(1H)quinolones

The apicomplexan parasite Toxoplasma gondii does not possess complex I of the mitochondrial respiratory chain, but has two genes encoding rotenone-insensitive, non-proton pumping type-II NADH dehydrogenases (NDH2s). The absence of such "alternative" NADH dehydrogenases in the human host defines these enzymes as potential drug targets. TgNDH2-I and TgNDH2-II are constitutively expressed in tachyzoites and bradyzoites and are localized to the mitochondrion as shown by epitope tagging. Functional expression of TgNDH2-I in the yeast Yarrowia lipolytica as an internal enzyme, with the active site facing the mitochondrial matrix, permitted growth in the presence of the complex I inhibitor DQA. Bisubstrate kinetics of TgNDH2-I measured within Y. lipolytica mitochondrial membrane preparations were in accordance with a ping-pong mechanism. Using inhibition kinetics we demonstrate here that 1-hydroxy-2-alkyl-4(1)quinolones with long alkyl chains of C(12) (HDQ) and C(14) are high affinity inhibitors for TgNDH2-I, while compounds with shorter side chains (C(5) and C(6)) displayed significantly higher IC(50) values. The efficiency of the various quinolone derivatives to inhibit TgNDH2-I enzyme activity mirrors their inhibitory potency in vivo, suggesting that a long acyl site chain is critical for the inhibitory potential of these compounds.     

An internal signal sequence directs intramembrane proteolysis of a cellular immunoglobulin domain protein

Precursor proteolysis is a crucial mechanism for regulating protein structure and function. Signal peptidase (SP) is an enzyme with a well defined role in cleaving N-terminal signal sequences but no demonstrated function in the proteolysis of cellular precursor proteins. We provide evidence that SP mediates intraprotein cleavage of IgSF1, a large cellular Ig domain protein that is processed into two separate Ig domain proteins. In addition, our results suggest the involvement of signal peptide peptidase (SPP), an intramembrane protease, which acts on substrates that have been previously cleaved by SP. We show that IgSF1 is processed through sequential proteolysis by SP and SPP. Cleavage is directed by an internal signal sequence and generates two separate Ig domain proteins from a polytopic precursor. Our findings suggest that SP and SPP function are not restricted to N-terminal signal sequence cleavage but also contribute to the processing of cellular transmembrane proteins.     

Isolation and characterization of polymorphic microsatellite loci from RAPD product in half-smooth tongue sole (Cynoglossus semilaevis) and a test of cross-species amplification

Eleven polymorphic microsatellite loci have been isolated and characterized from random amplified polymorphic DNA product in half-smooth tongue sole, Cynoglossus semilaevis. Twenty-one microsatellites were selected for designing microsatellite primers, of which 11 gave working primer pairs. They had between three and 12 alleles. Observed and expected heterozygosities varied from 0.53 to 0.93, and from 0.52 to 0.80, respectively. Five additional fish species assessed for cross-species amplification revealed between one and three positive amplifications and between zero and three polymorphic loci per species.     

A powerful and flexible multilocus association test for quantitative traits

Association mapping of complex traits typically employs tagSNP genotype data to identify a trait locus within a region of interest. However, considerable debate exists regarding the most powerful strategy for utilizing such tagSNP data for inference. A popular approach tests each tagSNP within the region individually, but such tests could lose power as a result of incomplete linkage disequilibrium between the genotyped tagSNP and the trait locus. Alternatively, one can jointly test all tagSNPs simultaneously within the region (by using genotypes or haplotypes), but such multivariate tests have large degrees of freedom that can also compromise power. Here, we consider a semiparametric model for quantitative-trait mapping that uses genetic information from multiple tagSNPs simultaneously in analysis but produces a test statistic with reduced degrees of freedom compared to existing multivariate approaches. We fit this model by using a dimension-reducing technique called least-squares kernel machines, which we show is identical to analysis using a specific linear mixed model (which we can fit by using standard software packages like SAS and R). Using simulated SNP data based on real data from the International HapMap Project, we demonstrate that our approach often has superior performance for association mapping of quantitative traits compared to the popular approach of single-tagSNP testing. Our approach is also flexible, because it allows easy modeling of covariates and, if interest exists, high-dimensional interactions among tagSNPs and environmental predictors.     

Protective effect of a RSV subunit vaccine candidate G1F/M2 was enhanced by a HSP70-Like protein in mice

Respiratory syncytial virus (RSV) is a major respiratory pathogen in newborns. Neonate vaccine should induce strong protective immunity. We have engineered a subunit vaccine candidate G1F/M2. A major problem in developing subunit vaccines is their limited immunogenicity. Aluminium adjuvants with a long history of use with routine childhood vaccines have some limitations, especially inability to elicit CTL response. There is a need for alternative adjuvants. Heat shock proteins (HSPs) are characterized as potent immunoadjuvants. In this study, HSP70-like protein 1 (HSP70L1) gene was cloned. The recombinant protein HSP70L1 was expressed in E. coli, purified and renaturated. We evaluated the potential of HSP70L1 used as the adjuvant of G1F/M2. G1F/M2 was chemically cross-linked with HSP70L1 (HSP-G1F/M2). HSP70L1 enhanced significantly the immunogenicity and protective effect of G1F/M2. HSP-G1F/M2 induced significant higher levels of antibodies, neutralizing antibodies and CTL activity than unadjuvanted G1F/M2. The antibody titers induced by HSP-G1F/M2 were similar to that by G1F/M2 + Alum. RSV-specific CTL activity induced by HSP-G1F/M2 was stronger than that by G1F/M2 + Alum. Interestingly, the protective effect of HSP-G1F/M2 against RSV was significantly stronger than that of G1F/M2 + Alum. The results suggest that HSP70L1 is a potent adjuvant of G1F/M2.     

ISSR analysis of genetic diversity in sacred lotus cultivars

In this study, inter-simple sequence repeats (ISSR) markers were applied to assess genetic diversity and genetic relationships of 92 cultivars of sacred lotus (Nelumbo nucifera Gaertn.), one of the most famous flowers in China. Our results showed that sacred lotus exhibited a low level of genetic diversity (percentage of polymorphic bands, PPB = 55.8%), which may result from its asexual mode of reproduction and long-term artificial selection. Clustering analyses indicated that these cultivars could be divided into two clades. Most cultivars of Chinese lotus species origin were included in one clade, and one cultivar of American lotus species origin was nested in the other clade. The hybrid cultivars from hybridization between the two subspecies were interspersed in these two clades. Seven cultivars native to Thailand formed a distinct subclade among the cultivars of Chinese lotus species origin. Genetic differentiation between two subspecies, and between cultivars from Thailand and other cultivars could be attributed to geographic isolation. The monophyly of three cultivars of Sanshui Winter Lotus and their closest relationships to Chinese lotus species origin suggests that they might have a common origin and may consist completely or mainly of genetic material from N. nucifera subsp. nucifera.