The phylogenetic status of arthropods, as inferred from 18S rRNA sequences

Partial 18S rRNA sequences of five chelicerate arthropods plus a crustacean, myriapod, insect, chordate, echinoderm, annelid, and platyhelminth were compared. The sequence data were used to infer phylogeny by using a maximum-parsimony method, an evolutionary-distance method, and the evolutionary-parsimony method. The phylogenetic inferences generated by maximum-parsimony and distance methods support both monophyly of the Arthropoda and monophyly of the Chelicerata within the Arthropoda. These results are congruent with phylogenies based on rigorous cladistic analyses of morphological characters. Results support the inclusion of the Arthropoda within a spiralian or protostome coelomate clade that is the sister group of a deuterostome clade, refuting the hypothesis that the arthropods represent the "primitive" sister group of a protostome coelomate clade. Bootstrap analyses and consideration of all trees within 1% of the length of the most parsimonious tree suggest that relationships between the nonchelicerate arthropods and relationships within the chelicerate clade cannot be reliably inferred with the partial 18S rRNA sequence data. With the evolutionary-parsimony method, support for monophyly of the Arthropoda is found in the majority of the combinations analyzed if the coelomates are used as "outgroups." Monophyly of the Chelicerata is supported in most combinations assessed. Our analyses also indicate that the evolutionary-parsimony method, like distance and parsimony, may be biased by taxa with long branches. We suggest that a previous study's inference of the Arthropoda as paraphyletic may be the result of (a) having two few arthropod taxa available for analysis and (b) including long-branched taxa.      

Scalable purification of Bacillus anthracis protective antigen from Escherichia coli

The anthrax toxin consists of three proteins, protective antigen (PA), lethal factor, and edema factor that are produced by the Gram-positive bacterium, Bacillus anthracis. Current vaccines against anthrax use PA as their primary component. In this study, we developed a scalable process to produce and purify multi-gram quantities of highly pure, recombinant PA (rPA) from Escherichia coli. The rPA protein was produced in a 50-L fermentor and purified to >99% purity using anion-exchange, hydrophobic interaction, and hydroxyapatite chromatography. The final yield of purified rPA from medium cell density fermentations resulted in approximately 2.7 g of rPA per kg of cell paste (approximately 270 mg/L) of highly pure, biologically active rPA protein. The results presented here exhibit the ability to generate multi-gram quantities of rPA from E. coli that may be used for the development of new anthrax vaccines and anthrax therapeutics.     

Hypoxia in the thymus: role of oxygen tension in thymocyte survival

Our previous studies using oxygen microelectrodes showed that the thymus is grossly hypoxic under normal physiological conditions. We now have investigated how oxygen tension affects the thymus at the cellular and molecular level. Adducts of the hypoxia marker drug pimonidazole accumulated in foci within the cortex and medulla and at the corticomedullary junction, consistent with the presence of widespread cellular hypoxia in the normal thymus. Hypoxia-associated pimonidazole accumulation was decreased but not abrogated by oxygen administration. Genes previously reported to be induced by hypoxia were expressed at baseline levels in the normal thymus, indicating that physiological adaptation to hypoxia occurred. Despite changes in thymus size and cellularity, thymic PO(2) did not change with age. Combined assays for hypoxia and cell death showed that hypoxia achieved using either hypoxic gas mixtures or high-density culture in normoxia decreased spontaneous thymocyte apoptosis in vitro. Taken together, these data suggest that regulatory mechanisms exist to maintain thymic cellular hypoxia in vivo and that oxygen tension may regulate thymocyte survival both in vitro and in vivo.     

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.     

静磁场对单株人体体表正常菌生长影响的研究

本文通过40mT和120mT两种静磁场作用下表皮葡萄球菌生长过程的研究,发现试验所选强度静磁场加速了表皮葡萄球菌在对数生长期的生长速率,而在进入稳定生长期后其生长速率反而低于对照组,但就整个生长周期而言,静磁场作用下表皮葡萄球菌的总量大于对照组,表明了试验所选静磁场对表皮葡萄球菌生长有一定促进作用.     

Modelling the longitudinal distribution,abundance, and habitat use of the giant freshwater shrimp (Macrobrachium spinipes) in a large intermittent,tropical Australian river to inform water resource policy

1. Water development threatens rivers and their biodiversity. Amphidromous shrimp are particularly vulnerable as they require migration between freshwater and estuaries to complete their life cycle. The Fitzroy River is a large tropical intermittent river undergoing water development that is home to the amphidromous shrimp Macrobrachium spinipes (cherabin), yet little is known about its habitat use and flow-ecology making it difficult to inform sustainable water-take.
2. We investigated habitat associations, distributional patterns suggestive of amphidromy, and the influence of water availability by sampling main channel and floodplain pools along a 350-km river length during 2 contrasting flow years. Applying a size-specific abundance model, we estimated abundance per size class, site, and year. We then predicted abundance at the landscape scale with remotely sensed water to reveal the impact of water availability on the meta-population.
3. Our model revealed that juveniles were in greatest abundance in downstream main channel pools, whereas adults were in greatest abundance in upstream floodplain pools. Abundance varied by year with lower numbers predicted in the low-flow year. Longitudinal and habitat patterns remained when our pool-level results were scaled to the landscape, and the positive relationship of abundance to wet-season flow was strengthened. The predominance of smaller cherabin in the lower reaches of the river provides indirect support for an estuarine nursery and amphidromous life history; however, small individuals observed in landlocked pools, during late dry season suggests possible within-river recruitment.
4. The importance of water development policies that protect wet-season flow and passage along the Fitzroy River is supported by this work. These types of policies are likely to be important for this and other amphidromous shrimp species across Australia, Southeast Asia and further afield. Further research detailing the species life history and describing flow–recruitment relationships will be important contributions to understanding this important taxonomic group and refining policies for current and future water resource development.

     

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

Background  

Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies.     

Human formyl peptide receptor function role of conserved and nonconserved charged residues.

In this study, we investigated the role of charged residues in ligand binding interactions of f-Met-Leu-Phe receptors (FPR). Charged residues of FPR, both conserved and nonconserved, which are located close to the membrane interface were mutated to alanine to determine their role in ligand binding. The mutated residues belonged to specific domains of FPR which have previously been implicated in FPR ligand binding interactions. We demonstrate that nonconserved charged residues such as Arg84, Lys85, Arg205 and Asp284 and conserved charge residue Arg163 seem to play a role in ligand binding. However, alteration of nonconserved charged residue Asp106 did not have any effect. In conclusion, specific charged residues of FPR, both conserved nonconserved, may contribute to FPR function either directly or indirectly.