Mutation identification of the DSPP in a Chinese family with DGI-II and an up-to-date bioinformatic analysis

In this study, through linkage analysis of a four-generation Chinese family with multiple members afflicted with DGI (type II), we identified a novel missense mutation in DSPP. The mutation was located in exon 2 at the second nucleotide position of the last codon and resulted in a substitution of a proline with a leucine residue (c.50C>T, p.P17L, g.50C>T). To assess the potential effects of this novel mutation, we utilized various bioinformatics analysis programs. The results indicate that the mutation likely affects protein cleavage/trafficking. We also analyzed previously reported mutations of DSPP. In summary, our finding supports that the genomic sequence that corresponds to the P17 residue of DSPP is a mutational hotspot and P17 may be critical for the function of DSPP.     

Comprehensive gene and microRNA expression profiling reveals the crucial role of hsa-let-7i and its target genes in colorectal cancer metastasis

Accumulating evidence has demonstrated that miRNAs play important roles in the occurrence and development of colorectal cancer (CRC). However, whether miRNAs are associated with the metastasis of CRC remains largely unexplored. The aim of the current study is to profile miRNAs in different CRC metastatic cell lines to identify the biomarkers in CRC metastasis. Gene and miRNA expression profiling was performed to analyze the global expression of mRNAs and miRNAs in the four human CRC cell lines (LoVo, SW480, HT29 and Caco-2) with different potential of metastasis. Expression patterns of mRNAs and miRNAs were altered in different CRC cell lines. By developing an integrated bioinformatics analysis of gene and miRNA expression patterns, hsa-let-7i was identified to show the highest degree in the microRNA-GO-network and microRNA-Gene-network. The expression level of hsa-let-7i was further validated by qRT-PCR in CRC cells. In addition, the targets of hsa-let-7i were predicted by two programs TargetScan and PicTar, and target genes were validated by expression profiling in the most epresentative LoVo and Caco-2 cell lines. Eight genes including TRIM41, SOX13, SLC25A4, SEMA4F, RPUSD2, PLEKHG6, CCND2, and BTBD3 were identified as hsa-let-7i targets. Our data showed the power of comprehensive gene and miRNA expression profiling and the application of bioinformatics tools in the identification of novel biomarkers in CRC metastasis.     

Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution

MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ～50% of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms.     

Structure-based phylogeny of polyene macrolide antibiotic glycosyltransferases

Antibiotic glycosyltransferases (AGts) attach unusual deoxy-sugars to aglycons so antibiotics can exert function. It has been reported that polyene macrolide (PEM) AGts have different evolutionary origin when compared with other polyketide AGts, and our previous analysis have suggested that they could be results of horizontal gene transfer (HGT) from eukaryotes. In this paper, we compared the structures of PEM AGts with structures of eukaryotes and other AGts, and then built models of the representative PEM AGts and GT-1 glycosyltransferases. We also constructed the Neighbor-Joining (NJ) trees based on the normalized Root Mean Square (RMS) distance, the Bayesian tree guided by structural alignments, and carried out analysis on several key conserved residues in PEM AGts. The NJ tree showed a close relationship between PEM AGts and eukaryotic glycosyltransferases, and Bayesian tree further supported their affinity with UDP-glucuronosyltransferases (UGTs). Analysis on key conserved residues showed that PEM AGts may have similar interaction mechanism such as in the formation of hydrogen bonds as eukaryotic glycosyltransferases. Using structure-based phylogenetic approaches, this study further supported that PEM AGts were the result of HGT between prokaryotes and eukaryotes.     

Mycobacterium tuberculosis ESAT-6 Exhibits a Unique Membrane-interacting Activity That Is Not Found in Its Ortholog from Non-pathogenic Mycobacterium smegmatis

Mycobacterium tuberculosis ESAT-6 (MtbESAT-6) reportedly shows membrane/cell-lysis activity, and recently its biological roles in pathogenesis have been implicated in rupture of the phagosomes for bacterial cytosolic translocation. However, molecular mechanism of MtbESAT-6-mediated membrane interaction, particularly in relation with its biological functions in pathogenesis, is poorly understood. In this study, we investigated the pH-dependent membrane interaction of MtbESAT-6, MtbCFP-10, and the MtbESAT-6/CFP-10 heterodimer, by using liposomal model membranes that mimic phagosomal compartments. MtbESAT-6, but neither MtbCFP-10 nor the heterodimer, interacted with the liposomal membranes at acidic conditions, which was evidenced by release of K⁺ ions from the liposomes. Most importantly, the orthologous ESAT-6 from non-pathogenic Mycobacterium smegmatis (MsESAT-6) was essentially inactive in release of K⁺. The differential membrane interactions between MtbESAT-6 and MsESAT-6 were further confirmed in an independent membrane leakage assay using the dye/quencher pair, 8-aminonapthalene-1,3,6 trisulfonic acid (ANTS)/p-xylene-bis-pyridinium bromide (DPX). Finally, using intrinsic and extrinsic fluorescence approaches, we probed the pH-dependent conformational changes of MtbESAT-6 and MsESAT-6. At acidic pH conditions, MtbESAT-6 underwent a significant conformational change, which was featured by an increased solvent-exposed hydrophobicity, while MsESAT-6 showed little conformational change in response to acidification. In conclusion, we have demonstrated that MtbESAT-6 possesses a unique membrane-interacting activity that is not found in MsESAT-6 and established the utility of rigorous biochemical approaches in dissecting the virulence of M. tuberculosis.     

A nitrogen budget of mainland China with spatial and temporal variation

The present study evaluated nitrogen (N) input and output in mainland China using updated data of temporally and spatially-based land use maps and statistical data at national and provincial scales. The total N inputs increased from 3,081 kg km^?2 in 1985 to 5,426 kg km^?2 in 2007. Chemical fertilizer dominated the N input and showed an increasing trend. Biological N fixation was the second important N input till 1990 and atmospheric deposition became the second most important source after that, accounting for 24.0% in 2007. There was no net N input through food/feed import in 1985, but it accounted for 3.5% of the total N input in 2007. According to a mass balance model, we assumed total N input equal to output. The results showed that more than half of the total N was denitrified or stored in the system. Ammonia volatilization accounted for 18.9–22.9% of the total N input, and N export to water bodies accounted for 17.9–20.7%. About 5.1–7.7% of the N input was emitted to the atmosphere through biomass burning. When calculated per unit area, total N input, N export to water bodies, denitrification and storage could be very well explained by human population density. Nitrogen input and major outputs were also positively related to per capita gross domestic product and the percentage of total land area used as cropland. The N budget is compared to that of some other countries and the environmental impacts of the N cycle is discussed.     

Model-based approaches for the determination of lipid bilayer structure from small-angle neutron and X-ray scattering data

Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Ku?erka et al. (Biophys J 95:2356–2367, 2008; J Phys Chem B 116:232–239, 2012). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent to these models. In particular, it is recognized that standalone data do not contain enough information to fully resolve the structure of naturally disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structure parameters, including the much-sought-after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data, as well as the implementation of local volume conservation within the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.     

鳄蜥对熟悉和陌生个体气味的辨别

个体辨别对于减少同种争斗以及配偶选择具有重要意义。我们用棉棒粘取鳄蜥(Shinisaurus crocodilurus)尿液作为气味源,以香水作为对照,测定鳄蜥对熟悉个体气味、陌生个体气味以及香水的舔舌次数和舔舌潜伏期,来探讨鳄蜥通过化学信息辨别熟悉和陌生个体的能力。结果显示,不论是雌性还是雄性,对不同个体尿液的舔舌次数均显著高于对香水的,舔舌潜伏期显著短于香水的;尽管雄性对陌生同性个体气味与熟悉同性个体气味的舔舌次数无显著差异,但对前者的舔舌潜伏期显著短于后者;雄性对陌生雌性气味的舔舌次数显著多于熟悉雌性气味的,对前者的舔舌潜伏期显著短于后者;雌性对陌生雄性气味的舔舌潜伏期显著短于对熟悉雄性气味的;雄鳄蜥对陌生雌性气味的舔舌次数显著多于雌鳄蜥对陌生雄性的。结果表明,鳄蜥能辨别同种个体的化学信息,并能通过化学信息来辨别熟悉和陌生个体,推测鳄蜥的这种辨别能力对其领域分配以及繁殖交配有重要作用。     

气调包装生鲜冷却牛肉贮藏的微生物种类变化

在冷却牛肉的贮藏过程中,微生物的生长繁殖是导致其腐败变质的主要原因。在低温冷藏条件下,大多数微生物的生长受到抑制,但仍有一些嗜冷菌可以生长繁殖,从而对冷却肉的品质及人类健康安全造成威胁。因此,研究和分析生鲜冷却牛肉中菌群构成及其演替规律,不但具有重要的