拟南芥过氧化物酶序列与功能的生物信息学分析

植物过氧化物酶(POD)属于多基因家族,不仅是植物体内清除活性氧自由基的重要酶类之一,而且参与多种生理生化过程,在维系植物生长发育过程中发挥重要的作用。采用生物信息学方法对拟南芥过氧化物酶家族的73个基因编码的蛋白质序列的结构和功能进行了分析,其中包含氨基酸的数量、等电点、跨膜结构域、信号肽、二级结构组成及磷酸化位点等,并用Mega4.0软件构建了去除信号肽前后的系统进化树,旨在了解其结构特征。对已经进行功能研究的成员进行结构分析,以此来揭示结构与功能之间的联系,为植物抵御氧化胁迫方面研究提供理论基础。     

Development of a colorimetric assay for rapid quantitative measurement of clavulanic acid in microbial samples

We developed a colorimetric assay to quantify clavulanic acid (CA) in culture broth of Streptomyces clavuligerus, to facilitate screening of a large number of S. clavuligerus mutants. The assay is based on a β-lactamase-catalyzed reaction, in which the yellow substrate nitrocefin (λ _max=390 nm) is converted to a red product (λ _max=486 nm). Since CA can irreversibly inhibit β-lactamase activity, the level of CA in a sample can be measured as a function of the A ₃₉₀/A ₄₈₆ ratio in the assay mixture. The sensitivity and detection window of the assay were determined to be 50 μg L⁻¹ and 50 μg L⁻¹ to 10 mg L⁻¹, respectively. The reliability of the assay was confirmed by comparing assay results with those obtained by HPLC. The assay was used to screen a pool of 65 S. clavuligerus mutants and was reliable for identifying CA over-producing mutants. Therefore, the assay saves time and labor in large-scale mutant screening and evaluation tasks. The detection window and the reliability of this assay are markedly better than those of previously reported CA assays. This assay method is suitable for high throughput screening of microbial samples and allows direct visual observation of CA levels on agar plates.     

Biomechanism of adhesion in gecko setae

The study of the adhesion of millions of setae on the toes of geckos has been advanced in recent years with the emergence of new technology and measurement methods. The theory of the mechanism of adhesion by van der Waals forces is now accepted and broadly understood. However, this paper presents limitations of this theory and gives a new hypothesis of the biomechanism of gecko adhesion. The findings are obtained through measurements of the magnitude of the adhesion of setae under three different conditions, to show the close relationship between adhesion and status of the setae. They are reinforced by demonstrating two setal structures, follicle cells and hair, the former making the setae capable of producing bioelectrical charges, which play an important role in attachment and detachment processes. It is shown that the abundant muscular tissues at the base of the setae cells, which are controlled by peripheral nerves, are instrumental in producing the foot movement involved in attachment and detachment. Our study will further uncover the adhesion mechanism of geckos, and provide new ideas for designing and fabricating synthetic setae.     

Genetic diversity and phylogeny of rhizobia isolated from Caragana microphylla growing in desert soil in Ningxia, China

Rhizobia are soil bacteria with the capacity to induce nitrogen-fixing nodules on the roots or stems of legume plants. A total of 40 bacterial isolates from the root nodules of Caragana microphylla growing in desert soil in Ningxia, China, were analyzed for genetic diversity and phylogenetic position. These isolates were classified into 7 types of 16S ribosomal DNA (rDNA) using polymerase chain reaction-restriction fragment length polymorphism analysis. They were grouped into 4 clades, Rhizobium-Agrobacterium, Sinorhizobium, Phyllobacterium, and Bradyrhizobium, when the phylogenies of 16S rDNA, recA, and atpD genes were applied. Phylogenetic analysis showed that the tree generated from the 16S rDNA sequencing agreed with that produced from the recA and atpD genes. By analyzing phylogenetic relationship using the 3 loci, the isolates in the branches of Phyllobacterium and Sinorhizobium could be identified as P. brassicacearum and S. meliloti. The isolates in the branch of Rhizobium-Agrobacterium were the most abundant microsymbiont of C. microphylla and were designated R. leguminosarum, R. galegae, R. alamii, and A. tumefaciens. Two isolates with low sequence similarity to the known species of Bradyrhizobium might be novel species in this genus.     

A graphene oxide-peptide fluorescence sensor for proteolytically active prostate-specific antigen

This paper presents a novel sensor to detect proteolytically active prostate-specific antigen (PSA) by assembling a purpose-designed FITC-labeled peptide with graphene oxide (GO). The fluorescence of the dye-labeled peptide was quenched in the presence of GO. Reaction of the sensor with PSA cleaves the peptide, leading to the release of the dye moiety and a great increase in fluorescence intensity in a dose- and time-dependent manner, and PSA can be quantified accordingly. This approach is simple compared to existing methods since the GO-peptide-based sensor is easily assembled and detection can be achieved without the involvement of complicated procedures. Moreover, the applicability of the method has been demonstrated by detecting PSA in spiked urine samples.     

Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

Common inflammatome gene signatures as well as disease‐specific signatures were identified by analyzing 12 expression profiling data sets derived from 9 different tissues isolated from 11 rodent inflammatory disease models. The inflammatome signature significantly overlaps with known drug targets and co‐expressed gene modules linked to metabolic disorders and cancer. A large proportion of genes in this signature are tightly connected in tissue‐specific Bayesian networks (BNs) built from multiple independent mouse and human cohorts. Both the inflammatome signature and the corresponding consensus BNs are highly enriched for immune response‐related genes supported as causal for adiposity, adipokine, diabetes, aortic lesion, bone, muscle, and cholesterol traits, suggesting the causal nature of the inflammatome for a variety of diseases. Integration of this inflammatome signature with the BNs uncovered 151 key drivers that appeared to be more biologically important than the non‐drivers in terms of their impact on disease phenotypes. The identification of this inflammatome signature, its network architecture, and key drivers not only highlights the shared etiology but also pinpoints potential targets for intervention of various common diseases.     

A transient parabiosis skin transplantation model in mice

Parabiosis-conjoined surgery to provide a shared circulation between two mice-has been previously developed to study the hematopoietic system. This protocol describes the use of parabiosis for efficient transplantation of skin from a transgenic to a wild-type mouse. It can be used to study the role of stromal cells in a spontaneous model of distant cancer dissemination (metastasis). We have recently shown that primary tumor-derived stromal cells may facilitate metastasis by providing a provisional stroma at the secondary site. Studying the role of primary tumor-derived stroma cells requires methods for distinguishing and targeting stromal cells originating from the primary tumor versus their counterparts in the metastatic site. Parabiosis may also be used, taking advantage of the shared circulation between the parabiosed mice, to study tumor metastasis from one parabiont to another, or to investigate the role of circulating inflammatory cells or stem cells. Studying the role of stromal cells in metastasis using this model typically takes up to 11 weeks.     

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

Despite a long-suspected role in the development of human colorectal cancer (CRC), the composition of gut microbiota in CRC patients has not been adequately described. In this study, fecal bacterial diversity in CRC patients (n=46) and healthy volunteers (n=56) were profiled by 454 pyrosequencing of the V3 region of the 16S ribosomal RNA gene. Both principal component analysis and UniFrac analysis showed structural segregation between the two populations. Forty-eight operational taxonomic units (OTUs) were identified by redundancy analysis as key variables significantly associated with the structural difference. One OTU closely related to Bacteroides fragilis was enriched in the gut microbiota of CRC patients, whereas three OTUs related to Bacteroides vulgatus and Bacteroides uniformis were enriched in that of healthy volunteers. A total of 11 OTUs belonging to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus and Peptostreptococcus were significantly more abundant in the gut microbiota of CRC patients, and 5 OTUs belonging to the genus Roseburia and other butyrate-producing bacteria of the family Lachnospiraceae were less abundant. Real-time quantitative PCR further validated the significant reduction of butyrate-producing bacteria in the gut microbiota of CRC patients by measuring the copy numbers of butyryl-coenzyme A CoA transferase genes (Mann–Whitney test, P<0.01). Reduction of butyrate producers and increase of opportunistic pathogens may constitute a major structural imbalance of gut microbiota in CRC patients.     

Host tree-recurrence of wood-decaying Dacrymycetes

Host-recurrence of wood-decaying polypores has been substantiated and some species of the class Dacrymycetes, consisting of wood-decaying jelly fungi, occur recurrently on coniferous and broad-leaved tree wood. However, there has been no quantitative analysis for Dacrymycetes. To evaluate their host-recurrence, the fruit body occurrence of Dacrymycetes was investigated at 60 sites, including 13 core sampling sites. A total of 577 samples of 28 species were collected. Principal component analysis revealed characteristic communities on conifers and broad-leaved trees. Binomial tests showed that 12 and four Dacrymycetes species occurred significantly more frequently on conifers and broad-leaved trees, respectively. Of these host-recurrent species, eight and two species exclusively occurred on conifers and broad-leaved trees, respectively, suggesting that some Dacrymycetes species have a strict host-recurrence on these tree groups.     

DNA barcoding analysis of Coleoidea (Mollusca: Cephalopoda) from Chinese waters

Coleoids are part of the Cephalopoda class, which occupy an important position in most oceans both at an ecological level and at a commercial level. Nevertheless, some coleoid species are difficult to distinguish with traditional morphological identification in cases when specimens are heavily damaged during collection or when closely related taxa are existent. As a useful tool for rapid species assignment, DNA barcoding may offer significant potential for coleoid identification. Here, we used two mitochondrial fragments, cytochrome c oxidase I and the large ribosomal subunit (16S rRNA), to assess whether 34 coleoids accounting for about one-third of the Chinese coleoid fauna could be identified by DNA barcoding technique. The pairwise intra- and interspecific distances were assessed, and relationships among species were estimated by NJ and bayesian analyses. High levels of genetic differentiation within Loliolus beka led to an overlap between intra- and interspecific distances. All remaining species forming well-differentiated clades in the NJ and bayesian trees were identical for both fragments. Loliolus beka possessed two mitochondrial lineages with high levels of intraspecific distances, suggesting the occurrence of cryptic species. This study confirms the efficacy of DNA barcoding for identifying species as well as discovering cryptic diversity of Chinese coleoids. It also lays a foundation for other ecological and biological studies of Coleoidea.