Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Integrated computational approaches to screen gene expression data to determine key genes and therapeutic targets for type-2 diabetes mellitus

There is a rapid rise in cases of Type-2-diabetes mellitus (T2DM) globally, irrespective of the geography, ethnicity or any other variable factors. The molecular mechanisms that could cause the condition of T2DM need to be more thoroughly analysed to understand the clinical manifestations and to derive better therapeutic regimes. Tools in bioinformatics are used to trace out key gene elements and to identify the key causative gene elements and their possible therapeutic agents. Microarray datasets were retrieved from the Gene expression omnibus database and studied using R to derive different expressed gene (DEG) elements. With the comparison of the expressed genes with disease specific genes in DisGeNET, the final annotated genes were taken for analysis. Gene Ontology studies, Protein–protein interaction (PPI), Co-expression analysis, Gene-drug interactions were performed to scale down the hub genes and to identify the novelty across the genes analysed so far. In vivo and invitro analysis of key genes and the trace of interaction pathway is crucial to better understand the unique outcomes from the novel genes, forming the basis to understand the pathway that ends up causing T2DM. Afterwards, docking was executed enabling recognition of interacting residues involved in inhibition. The complex CCL5-265 and CD8A-40585 thus docked showed best results as is evident from its PCA analysis and MMGBSA calculation. There is now scope for deriving candidate drugs that could possibly detect personalized therapies for T2DM.     

植物KCO基因密码子使用特性

以植物钾离子外排通道（K’channeloutward．rectifier,KCO）基因为研究对象,运用CodonW软件分析了75个植物KCO基因密码子的使用模式,探讨密码子的使用模式和影响密码子使用的各种可能因素。结果表明：碱基组成差异（r=0．961,P〈0．01）和自然选择（r=0．568,P〈0．01）是影响密码子使用的主要因素,并且高表达的基因强烈偏爱使用以G或C结尾的密码子。确定了UUC、CUC等26个均以G／C结尾的密码子为植物KcD基因的高表达优越密码子。     

Callus,shoot and hairy root formation in vitro as affected by the sensitivity to auxin and ethylene in tomato mutants

We analyzed the impact of ethylene and auxin disturbances on callus, shoots and Agrobacterium rhizogenes-induced hairy root formation in tomato (Solanum lycopersicum L.). The auxin low-sensitivity dgt mutation showed little hairy root initiation, whereas the ethylene low-sensitivity Nr mutation did not differ from the control Micro-Tom cultivar. Micro-Tom and dgt hairy roots containing auxin sensitivity/biosynthesis rol and aux genes formed prominent callus onto media supplemented with cytokinin. Under the same conditions, Nr hairy roots did not form callus. Double mutants combining Rg1, a mutation conferring elevated shoot formation capacity, with either dgt or Nr produced explants that formed shoots with little callus proliferation. The presence of rol + aux genes in Rg1 hairy roots prevented shoot formation. Taken together, the results suggest that although ethylene does not affect hairy root induction, as auxin does, it may be necessary for auxin-induced callus formation in tomato. Moreover, excess auxin prevents shoot formation in Rg1.     

Colours of domestication

During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat‐colour‐associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat‐colour variants. Recent studies demonstrate that this selection for coat‐colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat‐colour‐associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat‐colour‐associated genes act.     

Are Circadian Rhythms the Code of Hypothalamic-Immune Communication? Insights from Natural Killer Cells

Circadian rhythms in physiology and behavior are ultimately regulated at the hypothalamic level by the suprachiasmatic nuclei (SCN). This central oscillator transduces photic information to the cellular clocks in the periphery through the autonomic nervous system and the neuroendocrine system. The fact that these two systems have been shown to modulate leukocyte physiology supports the concept that the circadian component is an important aspect of hypothalamic-immune communication. Circadian disruption has been linked to immune dysregulation, and recent reports suggest that several circadian clock genes, in addition to their time-keeping role, are involved in the immune response. In this overview, we summarize the findings demonstrating that Natural Killer (NK) cell function is under circadian control. Special issue article in honor of George Fink.     

The phylogenetic position of taxaceae based on 18S rRNA sequences

The evolutionary position of the yew family, Taxaceae, has been very controversial. Some plant taxonomists strongly advocate excluding Taxaceae from the conifer order and raising its taxonomic status to a new order or even class because of its absence of seed cones, contrary to the case in the majority of conifers. However, other authors believe that the Taxaceae are not fundamentally different from the rest of the conifers except in that they possess the most reduced solitary-ovule cones. To resolve the controversy, we have sequenced the 18S rRNA genes from representative gymnosperms: Taxus mairei (Taxaceae), Podocarpus nakaii (Podocarpaceae), Pinus luchuensis (Pinaceae), and Ginkgo biloba (Ginkgoales). Our phylogenetic analysis of the new sequence data with the published 18S rRNA sequence of Zamia pumila (a cycad) as an outgroup strongly indicates that Taxus, Pinus, and Podocarpus form a monophyletic group with the exclusion of Ginkgo and that Taxus is more closely related to Pinus than to Podocarpus. Therefore, Taxaceae should be classified as a family of Coniferales. Our finding that Taxaceae, Pinaceae, and Podocarpaceae form a clade contradicts both the view that the uniovulate seed of Taxaceae is a primitive character and the view that the Taxaceae are descendants of the Podocarpaceae. Rather, the uniovulate seed of Taxaceae and that of some species of Podocarpus appear to have different origins, probably all reduced from multiovulate cones. Correspondence to: W.-H. Li     

Making heads from tails: Development of a reversed anterior-posterior axis during budding in an acoel

The anterior-posterior axis is a key feature of the bilaterian body plan. Although axis specification during embryogenesis has been studied extensively, virtually nothing is known about how this axis can be established post-embryonically, as occurs in budding animals. We investigated bud formation in the acoel Convolutriloba retrogemma, which reproduces by a remarkable process involving the formation of animals with linked but completely opposite body axes. Reverse axes are established anew during each round of budding and manifestations of the bud's new axis develop gradually, with regionalization of axial patterning genes (Hox and otx) and the establishment of organized musculature occurring secondarily, after bud initiation. A swath of tissue at the parent-bud boundary has no regenerative potential and appears devoid of inherent axial polarity. GSK-3 inhibitor trials suggest that Wnt/β-catenin or Hedgehog signalling may mediate the establishment of this unpolarized zone. Formation of unpolarized tissue may provide a buffer between opposing polarity cues and be a general mechanism by which budding animals establish and maintain linked body axes. In addition to elucidating the developmental basis of budding in a bilaterian, this study provides insight into convergence in animal budding mechanisms, redeployment of embryonic gene expression during budding, and Hox gene evolution.     

循环包装回收技术在筛选肝癌细胞相关耐药基因中的应用

肝癌先天性多表达多药耐药基因,严重影响肝癌的化疗效果,筛选肝癌细胞中的耐药基因,研究其耐药机制有助于提高肝癌化疗效果,提高肝癌的治愈率。首先构建肝癌细胞逆转录病毒的cDNA文库,感染成纤维细胞,使得逆转录病毒基因整合进细胞,加药筛选,存活细胞中的基因再次包装成病毒,用于下一轮筛选。采用循环包装回收(Cyclical packaging rescue,CPR)技术进行肝癌细胞耐药基因的筛选即是通过病毒包装将基因从细胞中钓取出来,相比于常规筛选方法,仅通过一轮筛选可能会出现很多假阳性基因,采用CPR技术则是通过多轮筛选,很大程度减少了假阳性细胞的出现。通过该方法经过四轮筛选获得核糖体蛋白S11(RPS11)、核糖体蛋白L6(RPL6)、核糖体蛋白L11(RPL11)、核糖体蛋白L24(RPL24)等几种基因,经初步检测,增加了细胞的耐药性。