IdentiCS – Identification of coding sequence and <Emphasis Type="Italic">in silico</Emphasis> reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence

Background  

A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. The available methods are mainly based on the annotation of genome sequences including two successive steps, the prediction of coding sequences (CDS) and their function assignment. The annotation process takes time. The available methods often encounter difficulties when dealing with unfinished error-containing genomic sequence.     

Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways

Background  

Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. Recently, it has been proposed that autoinducer-2 (AI-2), a furanosyl borate diester derived from the recycling of S-adenosyl-homocysteine (SAH) to homocysteine, serves as a universal signal for interspecies communication.     

Cryopreserved human hepatocytes as alternative in vitro model for cytochrome P450 induction studies

Induction of cytochrome P450 (CYP) by drugs is one of major concerns for drug-drug interactions. Thus, the assessment of CYP induction by novel compounds is a vital component in the drug discovery and development processes. Primary human hepatocytes are the preferred in vitro model for predicting CYP induction in vivo. However, their use is hampered by the erratic supply of human tissue and donor-to-donor variability. Although cryopreserved hepatocytes have been recommended for short-term applications in suspension, their use in studies on induction of enzyme activity has been limited because of poor attachment and response to enzyme inducers. In this study, we report culture conditions that allowed the attachment of cryopreserved human hepatocytes and responsiveness to CYP inducers. We evaluated the inducibility of CYP1A1/2 and CYP3A4 enzymes in cryopreserved hepatocytes from three human donors. Cryopreserved human hepatocytes were cultured in serum-free medium for 4 d. They exhibited normal morphology and measurable viability as evaluated by the reduction of tetrazolium salts (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt) by cellular dehydrogenases. Treatment with beta-naphthoflavone (10 microM) for 3 d increased ethoxyresorufin-O-deethylase activity (CYP1A1/2) by 6- to 11-fold over untreated cultures and increased CYP1A2 messenger ribonucleic acid (mRNA) expression by three- to eightfold. Similarly, treatment of cryopreserved human hepatocytes with rifampicin (25 microM) for 3 d increased testosterone 6 beta-hydroxylase activity (CYP3A4) by five- to eightfold over untreated cultures and increased CYP3A4 mRNA expression by four- to eightfold. The results suggest that cryopreserved human hepatocytes can be a suitable in vitro model for evaluating xenobiotics as inducers of CYP1A1/2 and CYP3A4 enzymes.     

Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data

Probiotic Escherichia coli strain Nissle 1917 (O6:K5:H1) is a commensal E. coli isolate that has a long tradition in medicine for the treatment of various intestinal disorders in humans. To elucidate the molecular basis of its probiotic nature, we started sequencing the genome of this organism with a whole-genome shotgun approach. A 7.8-fold coverage of the genomic sequence has been generated and is now in the finishing stage. To exploit the genome data as early as possible and to generate hypotheses for functional studies, the unfinished sequencing data were analyzed in this work using a new method [Sun, J., Zeng, A.P., 2004. IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics 5, 112] which is particularly suitable for the prediction of coding sequences (CDSs) from unannotated genome sequence. The CDSs predicted for E. coli Nissle 1917 were compared with those of all five other sequenced E. coli strains (E. coli K-12 MG1655, E. coli K-12 W3110, E. coli CFT073, EHEC O157:H7 EDL933 and EHEC O157:H7 Sakai) published to date. Five thousand one hundred and ninety-two CDSs were predicted for E. coli Nissle 1917, of which 1065 were assigned with enzyme EC numbers. The comparison of all predicted CDSs of E. coli Nissle 1917 to the other E. coli strains revealed 108 CDSs specific for this isolate. They are organized as four big genome islands and many other smaller gene clusters. Based on CDSs with EC numbers for enzymes, the potential metabolic network of Nissle 1917 was reconstructed and compared to those of the other five E. coli strains. Overall, the comparative genomic analysis sheds light on the genomic peculiarity of the probiotic E. coli strain Nissle 1917 and is helpful for designing further functional studies long before the sequencing project is completely finished.     

Higher Caffeinated Coffee Intake Is Associated with Reduced Malignant Melanoma Risk: A Meta-Analysis Study

Background

Several epidemiological studies have determined the associations between coffee intake level and skin cancer risk; however, the results were not yet conclusive. Herein, we conducted a systematic review and meta-analysis of the cohort and case-control studies for the association between coffee intake level and malignant melanoma (MM) risk.

Methods

Studies were identified through searching the PubMed and MEDLINE databases (to November, 2015). Study-specific risk estimates were pooled under the random-effects model.

Results

Two case-control studies (846 MM patients and 843 controls) and five cohort studies (including 844,246 participants and 5,737 MM cases) were identified. For caffeinated coffee, the pooled relative risk (RR) of MM was 0.81 [95% confidential interval (95% CI) = 0.68–0.97; P-value for Q-test = 0.003; I² = 63.5%] for those with highest versus lowest quantity of intake. In the dose-response analysis, the RR of MM was 0.955 (95% CI = 0.912–0.999) for per 1 cup/day increment of caffeinated coffee consumption and linearity dose-response association was found (P-value for nonlinearity = 0.326). Strikingly, no significant association was found between the decaffeinated coffee intake level and MM risk (pooled RR = 0.92, 95% CI = 0.81–1.05; P-value for Q-test = 0.967; I² = 0%; highest versus lowest quantity of intake).

Conclusions

This meta-analysis suggested that caffeinated coffee might have chemo-preventive effects against MM but not decaffeinated coffee. However, larger prospective studies and the intervention studies are warranted to confirm these findings.     

柴达木盆地尕斯库勒盐湖区邻近水体对湖泊微生物群落的贡献

【目的】探究尕斯库勒盐湖生态系统中邻近水体对湖泊微生物的贡献。【方法】采集尕斯库勒盐湖区湖水、沉积物以及邻近的泉水、河水和盐田的水样,对其进行地球化学分析;通过16S rRNA基因的Illumina MiSeq高通量测序分析样品的微生物群落组成。【结果】尕斯库勒盐湖区水体和沉积物中的优势门是变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteria)和广古菌门(Euryarchaeota)。盐度和pH是影响尕斯库勒盐湖区群落组成的最主要环境因素。邻近水体对湖泊水体和沉积物的贡献分别为12.94%和7.53%。【结论】邻近水体对尕斯库勒盐湖微生物群落的贡献有限。     

Improvement in bioconversion efficiency and reduction of ammonia emission by introduction of fruit fermentation broth in a black soldier fly larvae and kitchen waste conversion system

The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is an insect commonly used for the bioconversion of various organic wastes. Not only can the BSF convert organic waste into macromolecular organic substances, such as insect proteins, but it can also lessen the pollution associated with these waste products by reducing ammonia emissions, for example. In this study, we measured the effects of adding fruit fermentation broth (Fer) and commercial lactic acid bacteria fermentation broth (Em) to kitchen waste (KW), as deodorizing auxiliary substances, on the growth performance of black soldier fly larvae (BSFL), the intestinal flora structure of BSFL, the ammonia emission from the KW substrate, and the microbial community structure of the KW substrate. We found that the addition of Fer or Em increased the body weight of BSFL after 6 d of culture, increasing the growth rate by 9.96% and 7.96%, respectively. The addition of Fer not only reduced the pH of the KW substrate but also increased the relative abundance of probiotics, such as Lactobacillus, Lysinibacillus, and Vagococcus, which inhibited the growth of ammonifiers such as Bacillus, Oligella, Paenalcaligenes, Paenibacillus, Pseudogracilibacillus, and Pseudomonas, resulting in the reduction of ammonia emission in the KW substrate. Moreover, the addition of Fer or Em significantly increased the relative abundances of Bacteroides, Campylobacter, Dysgonomonas, Enterococcus, and Ignatzschineria in the gut of BSFL and increased the species diversity and richness in the KW substrate. Our findings provide a novel way to improve the conversion rate of organic waste and reduce the environmental pollution caused by BSF.     

Comprehensive optimization of the metabolomic methodology for metabolite profiling of Corynebacterium glutamicum

Applied Microbiology and Biotechnology - Metabolomics has been a potential tool for strain improvement through analyzing metabolite changes in the context of different conditions. However, the...     

神经外科临床决策支持系统设计研究

临床决策支持系统(Clinical decision support system,CDSS)是利用决策支持系统相关理论和技术,为临床医师在诊疗过程中提供诊疗决策的支持系统。本文根据临床神经外科疾病特点,提出基于KD、DB、和MD的框架系统结构,并构建临床疾病知识库、病人信息数据库和决策模型库,为下一步实现NCDSS功能提供理论基础和方法指导。