The proteome and secretome of human arterial smooth muscle cells

Smooth muscle cells (SMCs) play a crucial role in cardiovascular disorders. A differential proteomic approach should help to elucidate SMC dysfunctions involved in these diseases. With this goal in mind, we plotted the first 2-dimensional (2-D) maps of the proteome and secretome of human arterial smooth muscle cell (ASMC). Intracellular and secreted proteins were extracted from a primary culture of SMCs obtained from patients undergoing coronary artery bypass surgery (n = 11) and separated by 2-dimensional gel electrophoresis. Silver-stained gels were analyzed using Progenesis software. A high level of between-gel reproducibility was obtained, allowing us to generate two protein patterns specific to the ASMC proteome and secretome, respectively. A total of 121 and 40 distinct intracellular and secreted polypeptide spots, corresponding to 83 and 18 different proteins, respectively, were identified by matrix-assisted laser desorption/ionization mass spectrometry. The 2-D reference maps and database resulting from this study confirm that SMCs are involved in a wide range of biological functions. They could constitute a useful tool for a wide range of investigators involved in vascular biology, allowing them to investigate SMC protein changes associated with cardiovascular disorders or environmental stimuli.     

On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing

The control of bacterial pathogens requires the development of tools allowing the precise identification of strains at the subspecies level. It is now widely accepted that these tools will need to be DNA-based assays (in contrast to identification at the species level, where biochemical based assays are still widely used, even though very powerful 16S DNA sequence databases exist). Typing assays need to be cheap and amenable to the designing of international databases. The success of such subspecies typing tools will eventually be measured by the size of the associated reference databases accessible over the internet. Three methods have shown some potential in this direction, the so-called spoligotyping assay (Mycobacterium tuberculosis, 40,000 entries database), Multiple Loci Sequence Typing (MLST; up to a few thousands entries for the more than 20 bacterial species), and more recently Multiple Loci VNTR Analysis (MLVA; up to a few hundred entries, assays available for more than 20 pathogens). In the present report we will review the current status of the tools and resources we have developed along the past seven years to help in the setting-up or the use of MLVA assays or lately for analysing Clustered Regularly Interspaced Short Palindromic Repeats called CRISPRs which are the basis for spoligotyping assays.     

A web platform for the network analysis of high-throughput data in melanoma and its use to investigate mechanisms of resistance to anti-PD1 immunotherapy

Cellular phenotypes are established and controlled by complex and precisely orchestrated molecular networks. In cancer, mutations and dysregulations of multiple molecular factors perturb the regulation of these networks and lead to malignant transformation. High-throughput technologies are a valuable source of information to establish the complex molecular relationships behind the emergence of malignancy, but full exploitation of this massive amount of data requires bioinformatics tools that rely on network-based analyses.In this report we present the Virtual Melanoma Cell, an online tool developed to facilitate the mining and interpretation of high-throughput data on melanoma by biomedical researches. The platform is based on a comprehensive, manually generated and expert-validated regulatory map composed of signaling pathways important in malignant melanoma. The Virtual Melanoma Cell is a tool designed to accept, visualize and analyze user-generated datasets. It is available at: https://www.vcells.net/melanoma. To illustrate the utilization of the web platform and the regulatory map, we have analyzed a large publicly available dataset accounting for anti-PD1 immunotherapy treatment of malignant melanoma patients.     

Extending biochemical databases by metabolomic surveys

Metabolomics can map the large metabolic diversity in species, organs, or cell types. In addition to gains in enzyme specificity, many enzymes have retained substrate and reaction promiscuity. Enzyme promiscuity and the large number of enzymes with unknown enzyme function may explain the presence of a plethora of unidentified compounds in metabolomic studies. Cataloguing the identity and differential abundance of all detectable metabolites in metabolomic repositories may detail which compounds and pathways contribute to vital biological functions. The current status in metabolic databases is reviewed concomitant with tools to map and visualize the metabolome.     

生物信息学在蛋白质组学研究中的应用进展

生物信息学是运用数学和信息学方法阐明和解释海量生物学数据所蕴含的生物学意义的重要手段和工具.随着蛋白质组学研究的不断发展和深入,大量的蛋白序列、结构、功能以及互作数据不断产生.面对海量蛋白质组数据的获取、处理、存储以及蛋白质组数据信息的挖掘,生物信息学已成为蛋白组学研究中不可或缺的组成部分.本文结合蛋白质组学的发展历程...     

Benchmarking of 16S rRNA gene databases using known strain sequences

16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at various taxonomic levels using various methods and databases.     

Classification of habitats highlights priorities for conservation policies: The case of Spanish Mediterranean tall humid herb grasslands

The Mediterranean grasslands of Molinio-Holoschoenion are one of the lesser known natural habitat types of interest for conservation in the European Community. A study on their content with regard to their plant-communities and interest for plant conservation is conducted on a regional scale for the first time. A new comprehensive classification is proposed for this habitat type in Spain (Iberian Peninsula and Balearic and Canary Islands) where they have their highest European diversity. Twenty-five plant-community types are floristically identified by k-means clustering. Cluster analysis reveals a major hierarchical aggregation in two vegetation groups: (i) rush meadows of Scirpoides holoschoenus (L.) Soják; and (ii) communities of herbs and forbs dominated by Molinia caerulea (L.) Moench subsp. arundinacea (Schrank) H. Paul and/or Schoenus nigricans L. These groups are associated with different positions along a soil moisture gradient where rush formations occupy the positions farthest from the water table. Cluster Analysis also shows an uneven distribution of species with conservation interest. The highest content in endangered species is found in halophilous rushes. Grasslands on mineralised soils host the highest number of vulnerable species. Spanish Molinio-Holoschoenion plant communities were ranked using three criteria (regional responsibility, local rarity and habitat vulnerability) in order to set conservation priorities. The highest conservation values were achieved by coastal rush communities developing on dune slacks, and by forbs and rushes in the Baetic System growing on banks of streams with oligotrophic waters.     

DNA banking for plant breeding,biotechnology and biodiversity evaluation

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.