Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

Despite recent advances in metagenomic and single-cell genomic sequencing to investigate uncultivated microbial diversity and metabolic potential, fundamental questions related to population structure, interactions, and biogeochemical roles of candidate divisions remain. Numerous molecular surveys suggest that stratified ecosystems manifesting anoxic, sulfidic, and/or methane-rich conditions are enriched in these enigmatic microbes. Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution. Operational taxonomic units (OTUs) were affiliated with 64 phyla, including more than 25 candidate divisions. Pronounced trends in community structure were observed for all three domains with eukaryotic sequences vanishing almost completely below the mixolimnion, followed by a rapid and sustained increase in methanogen-affiliated (∼10%) and unassigned (∼60%) archaeal sequences as well as bacterial OTUs affiliated with Chloroflexi (∼22%) and candidate divisions (∼28%). Network analysis revealed highly correlated, depth-dependent cooccurrence patterns between Chloroflexi, candidate divisions WWE1, OP9/JS1, OP8, and OD1, methanogens, and unassigned archaeal OTUs indicating niche partitioning and putative syntrophic growth modes. Indeed, pathway reconstruction using recently published Sakinaw Lake single-cell genomes affiliated with OP9/JS1 and OP8 revealed complete coverage of the Wood-Ljungdahl pathway with potential to drive syntrophic acetate oxidation to hydrogen and carbon dioxide under methanogenic conditions. Taken together, these observations point to previously unrecognized syntrophic networks in meromictic lake ecosystems with the potential to inform design and operation of anaerobic methanogenic bioreactors.     

Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity

Bacteriophages are the most abundant biological entities in the biosphere, and this dynamic and old population is, not surprisingly, highly diverse genetically. Relative to bacterial genomics, phage genomics has advanced slowly, and a higher-resolution picture of the phagosphere is only just emerging. This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history.     

Effect of Changing the Light/Dark Schedule, the Time of Onset of the Light or Dark Period, or the Daylength, on Rhythms of Epidermal Cell Proliferation

Rhythms of labeling and mitotic indices were studied in the hindlimb epidermis of the anuran tadpole Rana pipiens under different light/dark (LD) cycles and daylengths in order to examine the role of the various parameters of the lighting regimen in setting the periods of the rhythms and the timing of the cell proliferation peaks. Altering the time of, or inverting, the 12 h light period on a 24 h day resulted in phase shifting of basically bimodal circadian rhythms with peaks in the light and dark. Thus the cell proliferation rhythms were entrained to the LD cycle. These rhythms also entrained to noncircadian schedules since they lengthened on a 15L : 15D cycle and shortened on a 9L : 9D cycle, although the bimodal characteristic of a peak in the light and a peak in the dark remained. Studies of 18L: 6D and 6L : 18D cycles in which either the time of onset of light or dark was changed relative to the 12L: 12D control indicated that the onset of dark may regulate the timing of the labeling index peaks while the onset of light may determine the time of occurrence of mitotic index peaks. Control of the timing of labeling and mitotic index peaks by different parameters of the LD cycle suggests a mechanism for cell cycle regulation by the environmental lighting schedule. Analysis of the rhythms on all the cycles studied suggested that labeling index rhythms equal the length of, or twice the length of, the dark period. Mitotic index rhythms equal the daylfength or a multiple of the length of the dark period.     

Aerobic Denitrification of Pseudomonas stutzeri yjy-10 and Genomic Analisis of This Process

Applied Biochemistry and Microbiology - In this study, Pseudomonas stutzeri yjy-10, an aerobic denitrifier identified by the morphological tests and 16S rDNA analysis was isolated from activated...     

Functionality of Dengue Virus Specific Memory T Cell Responses in Individuals Who Were Hospitalized or Who Had Mild or Subclinical Dengue Infection

Background

Although antibody responses to dengue virus (DENV) in naturally infected individuals have been extensively studied, the functionality of DENV specific memory T cell responses in relation to clinical disease severity is incompletely understood.

Methodology/Principal findings

Using ex vivo IFNγ ELISpot assays, and by determining cytokines produced in ELISpot supernatants, we investigated the functionality of DENV-specific memory T cell responses in a large cohort of individuals from Sri Lanka (n=338), who were naturally infected and were either hospitalized due to dengue or had mild or sub clinical dengue infection. We found that T cells of individuals with both past mild or sub clinical dengue infection and who were hospitalized produced multiple cytokines when stimulated with DENV-NS3 peptides. However, while DENV-NS3 specific T cells of those with mild/sub clinical dengue infection were more likely to produce only granzyme B (p=0.02), those who were hospitalized were more likely to produce both TNFα and IFNγ (p=0.03) or TNFα alone.We have also investigated the usefulness of a novel T cell based assay, which can be used to determine the past infecting DENV serotype. 92.4% of DENV seropositive individuals responded to at least one DENV serotype of this assay and none of the seronegatives responded. Individuals who were seronegative, but had received the Japanese encephalitis vaccine too made no responses, suggesting that the peptides used in this assay did not cross react with the Japanese encephalitis virus.

Conclusions/significance

The types of cytokines produced by DENV-specific memory T cells appear to influence the outcome of clinical disease severity. The novel T cell based assay, is likely to be useful in determining the past infecting DENV serotype in immune-epidemiological studies and also in dengue vaccine trials.     

Who dares, wins

Heroism is apparently nonadaptive in Darwinian terms, so why does it exist at all? Risk-taking and heroic behavior are predominantly male tendencies, and literature and legend reflect this. This study explores the possibility that heroism persists in many human cultures owing to a female preference for risk-prone rather than risk-averse males as sexual partners, and it suggests that such a preference may be exploited as a male mating strategy. It also attempts to quantify the relative influences of altruism and bravery in the evolution of heroism. Our study found that females do prefer risk-prone brave males to risk-averse non-brave males, and that men are aware of this preference. Bravery in a male was shown to be the stronger factor influencing female choice of short-term partners, long-term partners, and male friends, with altruism playing a lesser part in their choice. Altruism was deemed important in long-term relationships and friendships, but for short-term liaisons, non-altruists were preferred to altruists. Heroism may therefore have evolved owing to a female preference for brave, risk-prone males because risk-taking acts as an honest cue for good genes. Altruism was judged to be a less influential factor in the evolution of heroism than bravery and a demonstrated willingness to take risks.     

高温、颗粒物污染环境与运动促进健康

特殊环境对人体健康形成了挑战,如何在特殊环境保证人体健康具有较为重要的意义。本文针对高温和颗粒物污染两种特殊环境,对其与运动促进健康的国内外研究动态进行综述。运动和高温是胰岛素抵抗非药物干预治疗的主流,PGC-1α是机体通过运动、高温获得诸多益处的关键调控因子,新型激素Irisin可能是运动和高温改善胰岛素抵抗内在机理的重要环节。颗粒物暴露对运动机体运动能力和呼吸系统有一定的负面影响,但系统运动可以抵抗颗粒物染污负面作用,自由基和炎症途径关系系统运动阻碍颗粒物染污的可能机制。     

Phase Shifts of Potassium Uptake Rhythm in Lemna gibba G3 Due to Light, Dark or Temperature Pulses

Phase shifts in potassium uptake rhythm during continuous lightin flow medium (FMC) and static (STC) culture of Lemna gibbaG3, produced by various light and temperature pulses were examined.The phase responses were very similar to those known for a varietyof circadian rhythms: A pulse of high temperature (39°C)shifted the phase in the same way as a light pulse insertedduring darkness. A pulse of darkness, or of low temperature(5 or 10°C), however, caused a phase shift that was theinverse of that caused by a light pulse. A temperature pulseof definite timing erased the rhythm. Although the rhythms inthe STC and FMC had essentially the same phase response, a highintensitylight pulse was more effective in FMC and dark and temperaturepulses in STC. (Received December 18, 1982; Accepted March 8, 1983)     

Resolving Nonstop Translation Complexes Is a Matter of Life or Death

Problems during gene expression can result in a ribosome that has translated to the 3′ end of an mRNA without terminating at a stop codon, forming a nonstop translation complex. The nonstop translation complex contains a ribosome with the mRNA and peptidyl-tRNA engaged, but because there is no codon in the A site, the ribosome cannot elongate or terminate the nascent chain. Recent work has illuminated the importance of resolving these nonstop complexes in bacteria. Transfer-messenger RNA (tmRNA)-SmpB specifically recognizes and resolves nonstop translation complexes in a reaction known as trans-translation. trans-Translation releases the ribosome and promotes degradation of the incomplete nascent polypeptide and problematic mRNA. tmRNA and SmpB have been found in all bacteria and are essential in some species. However, other bacteria can live without trans-translation because they have one of the alternative release factors, ArfA or ArfB. ArfA recruits RF2 to nonstop translation complexes to promote hydrolysis of the peptidyl-tRNAs. ArfB recognizes nonstop translation complexes in a manner similar to tmRNA-SmpB recognition and directly hydrolyzes the peptidyl-tRNAs to release the stalled ribosomes. Genetic studies indicate that most or all species require at least one mechanism to resolve nonstop translation complexes. Consistent with such a requirement, small molecules that inhibit resolution of nonstop translation complexes have broad-spectrum antibacterial activity. These results suggest that resolving nonstop translation complexes is a matter of life or death for bacteria.     

Genomic Uracil Homeostasis during Normal B Cell Maturation and Loss of This Balance during B Cell Cancer Development

Activation-induced deaminase (AID) converts DNA cytosines to uracils in immunoglobulin genes, creating antibody diversification. It also causes mutations and translocations that promote cancer. We examined the interplay between uracil creation by AID and its removal by UNG2 glycosylase in splenocytes undergoing maturation and in B cell cancers. The genomic uracil levels remain unchanged in normal stimulated B cells, demonstrating a balance between uracil generation and removal. In stimulated UNG^−/− cells, uracil levels increase by 11- to 60-fold during the first 3 days. In wild-type B cells, UNG2 gene expression and enzymatic activity rise and fall with AID levels, suggesting that UNG2 expression is coordinated with uracil creation by AID. Remarkably, a murine lymphoma cell line, several human B cell cancer lines, and human B cell tumors expressing AID at high levels have genomic uracils comparable to those seen with stimulated UNG^−/−splenocytes. However, cancer cells express UNG2 gene at levels similar to or higher than those seen with peripheral B cells and have nuclear uracil excision activity comparable to that seen with stimulated wild-type B cells. We propose that more uracils are created during B cell cancer development than are removed from the genome but that the uracil creation/excision balance is restored during establishment of cell lines, fixing the genomic uracil load at high levels.