A new species of Tigriopus (Copepoda, Harpacticoida, Harpacticidae) from Thailand with the description of its naupliar development

Both genders of Tigriopus thailandensis sp. nov. are described from a laboratory stock raised from individuals collected from the seaweed Enteromorpha clathrata in Thailand (Bangsaen Beach, Chonburi Province). Tigriopus thailandensis sp. nov. shares with its closest relative T. japonicus Mori, 1932 two setae on the third exopodal segment of leg 4 while other congeners bear 3 inner setae. However, allobasis and exopod of antenna in both genders are much more slender and elongate than in T. japonicus. All six naupliar stages of T. thailandensis are described from the offspring of isolated females. In comparison with nauplii of T. japonicus, T. thailandensis nauplii are characterized by the following: a smaller body size throughout the naupliar phase; first antennular segment without seta, second antennular segment with only one small seta plus two longer setae; third antennular segment with additional spinules from naupliar stage II onwards; antenna bears three small spinules on the terminal exopodal segment; one additional seta on the anterior surface of the antennary basis, tubular endopod of antenna with one tiny seta midlength at naupliar stage III that increases in size; mandibular basis with several spinules on anterior surface; mandibular coxa with one spinulose seta that is smooth in T. japonicus.     

Potential natural product discovery from microbes through a diversity-guided computational framework

As the occurrence of natural compounds is related to the spatial distribution and evolution of microorganisms for biological and ecological relevance, the data integration of chemistry, geography, and phylogeny within an analytical framework is needed to make better decisions on sourcing the microbes for drug discovery. Such a framework should help researcher to decide on (a) which microorganisms are capable to produce the structurally diverse-bioactive compounds and (b) where those microbes could be found. Here, we present GIST (Geospatial Integrated Species, sites and bioactive compound relationships Tracking tool), a computational framework that could describe and compare how the chemical and genetic diversity varied among microbes in different areas. GIST mainly exploits the measures of bioactive diversity (BD) and phylogenetic diversity (PD), derived from the branch length of bioactive dendrogram and phylogenetic tree, respectively. Based on BD and PD, our framework could provide guidance and tools for measuring, monitoring, and evaluating of patterns and changes in biodiversity of microorganisms to improve the success rate of drug discovery. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hydrogen production and anaerobic decolorization of wastewater containing Reactive Blue 4 by a bacterial consortium of Salmonella subterranea and Paenibacillus polymyxa

Anaerobic biodegradability of wastewater (3,000 mg CODcr/l) containing 300 mg/l Reactive Blue 4, with different co-substrates, glucose, butyrate and propionate by a bacterial consortium of Salmonella subterranea and Paenibacillus polymyxa, concomitantly with hydrogen production was investigated at 35°C. The accumulative hydrogen production at 3,067 mg CODcr/l was obtained after 7 days of incubation with glucose, sludge, the bacterial consortium. The volatile fatty acids, residual glucose and the total organic carbon were correlated to hydrogen obtained. Interestingly, the bacterial consortium possess decolorization ability showing approximately 24% dye removal after 24 h incubation using glucose as a co-substrate, which was about two and eight times those of butyrate (10%), propionate (12%) and control (3%), respectively. RB4 decolorization occurred through acidogenesis, as high volatile fatty acids but low methane was detected. The bacterial consortium will be the bacterial strains of interest for further decolorization and hydrogen production of industrial waste water.     

Enhanced detectability in proteome studies

The discovery of candidate biomarkers from biological materials coupled with the development of detection methods holds both incredible clinical potential as well as significant challenges. However, the proteomic techniques still provide the low dynamic range of protein detection at lower abundances. This review describes the current development of potential methods to enhance the detection and quantification in proteome studies. It also includes the bioinformatics tools that are helpfully used for data mining of protein ontology. Therefore, we believe that this review provided many proteomic approaches, which would be very potent and useful for proteome studies and for further diagnostic and therapeutic applications.     

sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets

sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create personal databases by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools from Weka and R packages to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data and (4) building the classification model of biological activity. AVAILABILITY: sMOL Explorer is an Open Source project and is freely available to all interested users at http://www.biotec.or.th/ISL/SMOL/.     

Review of naupliar development among Miraciidae (Copepoda,Harpacticoida) with a naupliar description of <Emphasis Type="Italic">Paramphiascella</Emphasis><Emphasis Type="Italic">choi</Emphasis> sp. nov. from Thailand

Both genders of Paramphiascella choi sp. nov. were collected from the green alga Enteromorpha clathrata in Rayong province, Thailand. P. choi shares with other species of the genus: cylindrical body shape, rostrum not bifid, eight-segmented antennules, three-segmented exopodal antenna, and female P5 exopod with five setae. The new species distinguished from other conspecific species by: three-segmented exopodal antenna, inner edge of basis of male P1 and P2 bear a bare ovate-knob each. Enp-1 very elongate, Enp-2 of male P2 transformed into a large, strong, slightly curved and tapering attenuation with two central chitinous ridges, and bearing one medially directed knob close to enp-1. At the base of this knob arise three plumose setae of unequal length. These characters are suggested to be autapomorphies of the new species. Six naupliar stages are obtained and described a key for the identification of stages is provided. Nauplius I has one pair of caudal setae; three-segmented antennules; antenna consists of a coxa, basis, endopod and exopod; mandible has a coxa, basis, endopod and exopod; hindbody bears two caudal setae. Nauplius II develops one aesthetasc on the antennule; antenna has added an arthrite arising from the coxa; mandible has a row of tiny spinulose setae. Nauplius III has added two pairs of caudal setae. Nauplius IV bears bilobed bud of the maxillule armed with two setae and four pairs of caudal setae. Nauplius V bears a multilobed bud of the maxillule with three setae and five pairs of caudal setae. At Nauplius VI, the buds of swimming legs 1 and 2 are added.     

Autophagy in the thymic epithelium is dispensable for the development of self-tolerance in a novel mouse model

The thymic epithelium plays critical roles in the positive and negative selection of T cells. Recently, it was proposed that autophagy in thymic epithelial cells is essential for the induction of T cell tolerance to self antigens and thus for the prevention of autoimmune diseases. Here we have tested this hypothesis using mouse models in which autophagy was blocked specifically in epithelial cells expressing keratin 14 (K14), including the precursor of thymic epithelial cells. While the thymic epithelial cells of mice carrying the floxed Atg7 gene (ATG7 f/f) showed a high level of autophagy, as determined by LC3 Western blot analysis and fluorescence detection of the recombinant green fluorescent protein (GFP)-LC3 reporter protein on autophagosomes, autophagy in the thymic epithelium was efficiently suppressed by deletion of the Atg7 gene using the Cre-loxP system (ATG7 f/f K14-Cre). Suppression of autophagy led to the massive accumulation of p62/sequestosome 1 (SQSTM1) in thymic epithelial cells. However, the structure of the thymic epithelium as well as the organization and the size of the thymus were not altered in mutant mice. The ratio of CD4 to CD8-positive T cells, as well as the frequency of activated (CD69+) CD4 T cells in lymphoid organs, did not differ between mice with autophagy-competent and autophagy-deficient thymic epithelium. Inflammatory infiltrating cells, potentially indicative of autoimmune reactions, were present in the liver, lung, and colon of a similar fraction of ATG7 f/f and ATG7 f/f K14-Cre mice. In contrast to previously reported mice, that had received an autophagy-deficient thymus transplant, ATG7 f/f K14-Cre mice did not suffer from autoimmunity-induced weight loss. In summary, the results of this study suggest that autophagy in the thymic epithelium is dispensable for negative selection of autoreactive T cells.     

Sixteen EST-linked microsatellite markers in Günther's walking catfish, Clarias macrocephalus

Twenty-seven new microsatellite sequences were identified by screening 2029 expressed sequence tags from Günther's walking catfish, Clarias macrocephalus. Sixteen loci were polymorphic with the number of alleles ranging from two to 16 per locus and the observed and expected heterozygosities ranging from 0.4667 to 0.9333 and from 0.427 to 0.8819 per locus, respectively. Cross-species amplifications of all 16 primer pairs were tested in four other species of catfish including Clarias gariepinus, Pangasius hypophthalmus, Pangasius larnaudii and Pangasianodon gigas. Eleven loci were found to amplify in other species, with the number of polymorphic loci ranging from one in P. larnaudii to nine in C. gariepinus.