Metagenomic analyses of an uncultured viral community from human feces

Here we present the first metagenomic analyses of an uncultured viral community from human feces, using partial shotgun sequencing. Most of the sequences were unrelated to anything previously reported. The recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes.     

PHACCS,an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

Background  

Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.     

Correction to: Mephisto albomaculosus,a new spikefish (Actinopterygii: Tetraodontiformes: Triacanthodidae) collected off Myanmar,Indian Ocean

Ichthyological Research - The spelling of the third author name was incorrectly published.     

Human herpesvirus 7 open reading frame U12 encodes a functional beta-chemokine receptor

Human herpesvirus 7 (HHV-7), which belongs to the betaherpesvirus subfamily, infects mainly CD4+ T cells in vitro and infects children during infancy. After the primary infection, HHV-7 becomes latent. HHV-7 contains two genes (U12 and U51) that encode putative homologs of cellular G-protein-coupled receptors. To analyze the biological function of the U12 gene, we cloned the gene and expressed the U12 protein in cells. The U12 gene encoded a calcium-mobilizing receptor for the EBI1 ligand chemokine-macrophage inflammatory protein 3beta (ELC/MIP-3beta) but not for other chemokines, suggesting that the chemokine selectivity of the U12 gene product is distinct from that of the known mammalian chemokine receptors. These studies revealed that U12 activates distinct transmembrane signaling pathways that may mediate biological functions by binding with a beta-chemokine, ELC/MIP-3beta.     

Regulation of sperm motility by PIP2(4,5) and actin polymerization

Actin polymerization and development of hyperactivated (HA) motility are two processes that take place during sperm capacitation. In previous studies, we demonstrated that the increase in F-actin during capacitation depends upon inactivation of the actin severing protein, gelsolin, by its binding to phosphatydilinositol-4, 5-bisphosphate (PIP₂). Here, we showed for the first time the involvement of PIP₂/gelsolin in human sperm motility before and during capacitation. Activation of gelsolin by causing its release from PIP₂ inhibited sperm motility, which could be restored by adding PIP₂ to the cells. Reduction of PIP₂ synthesis inhibited actin polymerization and motility, and increasing PIP₂ synthesis enhanced these activities. Furthermore, sperm demonstrating low motility contained low levels of PIP₂ and F-actin. During capacitation there was an increase in PIP₂ and F-actin levels in the sperm head and a decrease in the tail. In sperm with high motility, gelsolin was mainly localized to the sperm head before capacitation, whereas in low motility sperm, most of the gelsolin was localized to the tail before capacitation and translocated to the head during capacitation. We also showed that phosphorylation of gelsolin on tyrosine-438 depends on its binding to PIP₂. Activation of phospholipase C by Ca²⁺-ionophore or by activating the epidermal-growth-factor-receptor inhibits tyrosine phosphorylation of gelsolin. In conclusion, the data indicate that the increase of PIP₂ and/or F-actin in the head during capacitation enhances gelsolin translocation to the head. As a result the decrease of gelsolin in the tail allows keeping high level of F-actin in the tail, which is essential for the development of HA motility.     

Role and regulation of sperm gelsolin prior to fertilization

To acquire fertilization competence, spermatozoa should undergo several biochemical changes in the female reproductive tract, known as capacitation. The capacitated spermatozoon can interact with the egg zona pellucida resulting in the occurrence of the acrosome reaction, a process that allowed its penetration into the egg and fertilization. Sperm capacitation requires actin polymerization, whereas F-actin must disperse prior to the acrosome reaction. Here, we suggest that the actin-severing protein, gelsolin, is inactive during capacitation and is activated prior to the acrosome reaction. The release of bound gelsolin from phosphatidylinositol 4,5-bisphosphate (PIP(2)) by PBP10, a peptide containing the PIP(2)-binding domain of gelsolin, or by activation of phospholipase C, which hydrolyzes PIP(2), caused rapid Ca(2+)-dependent F-actin depolymerization as well as enhanced acrosome reaction. Using immunoprecipitation assays, we showed that the tyrosine kinase SRC and gelsolin coimmunoprecipitate, and activating SRC by adding 8-bromo-cAMP (8-Br-cAMP) enhanced the amount of gelsolin in this precipitate. Moreover, 8-Br-cAMP enhanced tyrosine phosphorylation of gelsolin and its binding to PIP(2(4,5)), both of which inactivated gelsolin, allowing actin polymerization during capacitation. This actin polymerization was blocked by inhibiting the Src family kinases, suggesting that gelsolin is activated under these conditions. These results are further supported by our finding that PBP10 was unable to cause complete F-actin breakdown in the presence of 8-Br-cAMP or vanadate. In conclusion, inactivation of gelsolin during capacitation occurs by its binding to PIP(2) and tyrosine phosphorylation by SRC. The release of gelsolin from PIP(2) together with its dephosphorylation enables gelsolin activation, resulting in the acrosome reaction.     

Developmentally induced, muscle-specific trans factors control the differential splicing of alternative and constitutive troponin T exons

Alternative RNA splicing is a ubiquitous process permitting single genes to encode multiple protein isoforms. Here we report experiments in which a gene construct, containing combinatorial Troponin T (TnT) exons that manifest an exceptional diversity of alternative splicing in vivo, has been transfected into muscle and nonmuscle cells. Analyses of the spliced RNAs show that the alternative TnT exons retain their capacity for differential splicing in the modified minigene context when introduced into a variety of nonmuscle and muscle cells. The patterns of alternative splicing differ depending on cell type. Only in differentiated myotubes are the alternative exons normally incorporated during splicing, reproducing their behavior in the native gene; they are excluded in nonmuscle cells and myoblasts that do not express the endogenous TnT. These results provide proof that trans factors required for correct alternative splicing are induced during myogenesis. Surprisingly, such factors are also required for the correct splicing of constitutive TnT exons.     

Stimulation of Ca2+ uptake into epididymal bull spermatozoa by analogues of amiloride

Certain amiloride analogues 3',4'-dichlorobenzamil 2',4'-dimethylbenzamil and alpha',2'-benzobenzamil hydrochloride (ATBB) stimulate calcium accumulation and motility by epididymal bovine spermatozoa. This stimulation can be seen at a range of 0.1-0.4 mM, while at higher concentration there is inhibition of calcium uptake by these amiloride analogues. The amiloride derivative 5-(4-chlorobenzyl)-2',4'-dimethylbenzamil (CBDMB), which bears a 4-chlorobenzyl substituent on the 5-amino nitrogen atom, did not stimulate calcium uptake. The amiloride analogue 3',4'-dichlorobenzamil inhibits the Na+/Ca2(+)-exchange activity in isolated plasma membrane vesicles, and the stimulatory effect of 3',4'-dichlorobenzamil on calcium uptake into epididymal sperm could be seen in Na(+)-free medium. Thus, the stimulation of Ca2+ accumulation in the cells caused by 3',4'-dichlorobenzamil is not a result of inhibiting the Na(+)-dependent Ca2+ clearance. There is no stimulation of Ca2+ uptake into ejaculated cells by adding 3',4'-dichlorobenzamil, which is not due to the presence of the calcium-transport inhibitor (caltrin) in these cells [Rufo, G.A., Schoff, P.K. & Lardy, H.A. (1984) J. Biol. Chem. 259, 2547-2552]. The stimulatory effect of 3',4'-dichlorobenzamil on Ca2+ uptake is inhibited by the voltage-dependent Ca2(+)-channel blockers nifedipin and diltiazem. This indicates that the stimulation of Ca2+ uptake by the amiloride analogues is due to the activation of a voltage-dependent Ca2+ channel of the plasma membrane.     

Estimating predation pressure in ecological studies: controlling bias imposed by using sentinel plasticine prey

Sentinel plasticine prey has been increasingly used to estimate predation pressure. The use of plasticine prey may, however, bias the results, as this method was originally designed to account for predation by organisms that can visually recognize the shapes and colors of their prey. To evaluate the limitations of using sentinel plasticine prey, we compared predator attack rates between real prey – dead and live mealworms, Tenebrio molitor L. (Coleoptera: Tenebrionidae) – and plasticine models in a monsoonal tropical rainforest of southeastern China. The attack rates by invertebrates were highest on dead prey followed by live prey and plasticine models, whereas the attack rates by vertebrates were lowest on dead prey, and did not differ between live prey and plasticine models. These results confirm that bias imposed by using the plasticine models is affected by the type of predators. In addition, we tested the validity and generality of the premise that predators can distinguish the shapes of plasticine model prey and preferentially attack a caterpillar-like shape over other shapes. To test this hypothesis, we conducted three independent experiments in China, Papua New Guinea, and Finland. In the two latter localities, predation rates on plasticine caterpillars were higher than on models of other shapes, whereas in China, these differences were not significant. Taken together, our study suggests that plasticine models may underestimate the predation by invertebrates to a greater extent than predation by vertebrates, and the preference of model shape by predators may be locality-specific, presumably due to differences in the composition of the predator community. We propose that predation be estimated on both live and plasticine prey in future studies to measure the potential bias imposed by using plasticine models and its variation among various habitats and predator groups.