Diversity and population structure of a near-shore marine-sediment viral community

Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near-shore marine-sediment viral community. Three-quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double-stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under-represented or absent. This 'marineness' suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10(4) viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine-sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.     

Involvement of MEK-mitogen-activated protein kinase pathway in follicle-stimulating hormone-induced but not spontaneous meiotic resumption of mouse oocytes

Mitogen-activated protein (MAP) kinase has been reported to be activated during oocyte meiotic maturation in a variety of mammalian species. However, the mechanism(s) responsible for MAP kinase activation and the consequence of its premature activation during gonadotropin-induced oocyte meiotic resumption have not been examined. The present experiments were conducted to investigate the possible role of MAP kinase in FSH-induced and spontaneous oocyte meiotic resumption in the mouse. MAP kinase kinase (MAPKK, MEK) inhibitor, PD98059 or U0126, produced a dose-dependent inhibitory effect on both FSH-induced oocyte meiotic resumption and MAP kinase activation in the oocytes. However, the same inhibitor did not block spontaneous meiotic resumption of either denuded or cumulus cell-enclosed mouse oocytes, despite the activity of MAP kinase being totally inhibited. Immunoblotting the oocytes and the cumulus cells with the anti-active MAP kinase antibody showed that MAP kinase activity in the oocytes was detected at 8 h of FSH treatment, prior to germinal vesicle breakdown and increased as maturation progressed in the following culture period. In the cumulus cells, MAP kinase was activated even faster, its activity was detected at 1 h of FSH stimulation and increased gradually until 8 h of FSH treatment, then decreased and diminished after 12 h of FSH action. These data demonstrated that the MEK-MAP kinase pathway is implicated in FSH-induced but not spontaneous oocyte meiotic resumption.     

Role of PI3-kinase and PI4-kinase in actin polymerization during bovine sperm capacitation

We have recently demonstrated the involvement of phospholipase D (PLD) in actin polymerization during mammalian sperm capacitation. In the present study, we investigated the involvement of phosphatidylinositol 3- and 4-kinases (PI3K and PI4K) in actin polymerization, as well as the production of PIP(2(4,5)), which is a known cofactor for PLD activation, during bovine sperm capacitation. PIK3R1 (p85 alpha regulatory subunit of PI3K) and PIKCB (PI4K beta) in bovine sperm were detected by Western blotting and immunocytochemistry. Wortmannin (WT) inhibited PI3K and PI4K type III at concentrations of 10 nM and 10 microM, respectively. PI4K activity and PIP(2(4,5)) production were blocked by 10 microM WT but not by 10 nM WT, whereas PI3K activity and PIP(3(3,4,5)) production were blocked by 10 nM WT. Moreover, spermine, which is a known PI4K activator and a component of semen, activated sperm PI4K, resulting in increased cellular PIP(2(4,5)) and F-actin formation. The increases in PIP(2(4,5)) and F-actin intracellular levels during sperm capacitation were mediated by PI4K but not by PI3K activity. Activation of protein kinase A (PKA) by dibutyryl cAMP enhanced PIP(2(4,5)), PIP(3(3,4,5)), and F-actin formation, and these effects were mediated through PI3K. On the other hand, activation of PKC by phorbol myristate acetate enhanced PIP(2(4,5)) and F-actin formation mediated by PI4K activity, while the PI3K activity and intracellular PIP(3(3,4,5)) levels were reduced. These results suggest that two alternative pathways lead to PI4K activation: indirect activation by PKA, which is mediated by PI3K; and activation by PKC, which is independent of PI3K activity. Our results also suggest that spermine, which is present in the ejaculate, regulates PI4K activity during the capacitation process in vivo.     

Power law rank-abundance models for marine phage communities

Metagenomic analyses suggest that the rank-abundance curve for marine phage communities follows a power law distribution. A new type of power law dependence based on a simple model in which a modified version of Lotka-Volterra predator-prey dynamics is sampled uniformly in time is presented. Biologically, the model embodies a kill the winner hypothesis and a neutral evolution hypothesis. The model can match observed power law distributions and uses very few parameters that are readily identifiable and characterize phage ecosystems. The model makes new untested predictions: (1) it is unlikely that the most abundant phage genotype will be the same at different time points and (2) the long-term decay of isolated phage populations follows a power law.     

Blocking the apolipoprotein E/Amyloid β interaction in triple transgenic mice ameliorates Alzheimer's disease related amyloid β and tau pathology

Inheritance of the apolipoprotein E4 (apoE4) genotype has been identified as the major genetic risk factor for late‐onset Alzheimer's disease (AD). Studies have shown that the binding between apoE and amyloid‐β (Aβ) peptides occurs at residues 244–272 of apoE and residues 12–28 of Aβ. ApoE4 has been implicated in promoting Aβ deposition and impairing clearance of Aβ. We hypothesized that blocking the apoE/Aβ interaction would serve as an effective new approach to AD therapy. We have previously shown that treatment with Aβ12‐28P can reduce amyloid plaques in APP/PS1 transgenic (Tg) mice and vascular amyloid in TgSwDI mice with congophilic amyloid angiopathy. In the present study, we investigated whether the Aβ12‐28P elicits a therapeutic effect on tau‐related pathology in addition to amyloid pathology using old triple transgenic AD mice (3xTg, with PS1_M146V, APP_Swe and tau_P30IL transgenes) with established pathology from the ages of 21 to 26 months. We show that treatment with Aβ12‐28P substantially reduces tau pathology both immunohistochemically and biochemically, as well as reducing the amyloid burden and suppressing the activation of astrocytes and microglia. These affects correlate with a behavioral amelioration in the treated Tg mice.

     

Elephant calling patterns as indicators of group size and composition: the basis for an acoustic monitoring system

The paper gives evidence that the vocal activity of elephants varies with group size, composition and reproductive status, and that elephants' calling patterns could therefore provide the basis for a remote monitoring system. We examined a 3‐week set of array‐based audio recordings of savanna elephants (Loxodonta africana), searching for diagnostic acoustic parameters. An acoustic array made it possible to locate recorded sounds and attribute the calls to particular elephants or elephant groups. Simultaneous video recordings made it possible to document visible behaviour and roughly correlate it with vocalizations. We compared several measures of call density in elephant groups containing up to 59 individuals, and found that rates of calling increased with increasing numbers of elephants. We divided all call events into three structural types (single‐voice low‐frequency calls, multiple‐voice clustered low‐frequency calls, and single‐voice high frequency calls), and found that the incidence of these varies predictably with group composition. These results suggest the value of a network of listening systems in remote areas for the collection of information on elephant abundance and population structure.     

FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries

Background  

High-throughput sequencing makes it possible to rapidly obtain thousands of 16S rDNA sequences from environmental samples. Bioinformatic tools for the analyses of large 16S rDNA sequence databases are needed to comprehensively describe and compare these datasets.     

Changes in energy charge and block of protein synthesis in rabbit reticulocytes under the action of valinomycin

Valinomycin blocks protein synthesis at the elongation stage in intact reticulocyte while being without action on a cell free system. We demonstrate here that this membrane mediated inhibition is accompanied by a change of the energy charge (ATP/ADP/AMP ratio) of the cells. There seems to be an accumulation of AMP without a proportional gain in ADP. The change in energy charge in itself can be the cause of the inhibition of protein synthesis. We show also that valinomycin can cause a decrease of the energy charge at concentrations where its action as an ionophore is not seen and independent of a possible activation of the Na-K dependent ATPase.Present address: Meir Hospital, Kfar Saba, Israel     

Adaptation of the polony technique to quantify Gokushovirinae,a diverse group of single-stranded DNA phage

Advances in metagenomics have revealed the ubiquity of single-stranded DNA (ssDNA) phage belonging to the subfamily Gokushovirinae in the oceans; however, the abundance and ecological roles of this group are unknown. Here, we quantify gokushoviruses through adaptation of the polony method, in which viral template DNA is immobilized in a gel, amplified by PCR, and subsequently detected by hybridization. Primers and probes for this assay were designed based on PCR amplicon diversity of gokushovirus major capsid protein gene sequences from a depth profile in the Gulf of Aqaba, Red Sea sampled in September 2015. At ≥95% identity, these 87 gokushovirus sequences formed 14 discrete clusters with the largest clades showing distinct depth distributions. The application of the polony method enabled the first quantification of gokushoviruses in any environment. The gokushoviruses were most abundant in the upper 40 m of the stratified water column, with a subsurface peak in abundance of 1.26 × 10⁵ viruses ml⁻¹. These findings suggest that discrete gokushovirus genotypes infect bacterial hosts that differentially partition in the water column. Since the designed primers and probe are conserved across marine ecosystems, this polony method can be applied broadly for the quantification of gokushoviruses throughout the global oceans.