Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

Permafrost contains an estimated 1672?Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5?°C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.     

Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type

Methylmalonic aciduria and homocystinuria, cblC type (OMIM 277400), is the most common inborn error of vitamin B(12) (cobalamin) metabolism, with about 250 known cases. Affected individuals have developmental, hematological, neurological, metabolic, ophthalmologic and dermatologic clinical findings. Although considered a disease of infancy or childhood, some individuals develop symptoms in adulthood. The cblC locus was mapped to chromosome region 1p by linkage analysis. We refined the chromosomal interval using homozygosity mapping and haplotype analyses and identified the MMACHC gene. In 204 individuals, 42 different mutations were identified, many consistent with a loss of function of the protein product. One mutation, 271dupA, accounted for 40% of all disease alleles. Transduction of wild-type MMACHC into immortalized cblC fibroblast cell lines corrected the cellular phenotype. Molecular modeling predicts that the C-terminal region of the gene product folds similarly to TonB, a bacterial protein involved in energy transduction for cobalamin uptake.     

Domination of heliosheath pressure by shock-accelerated pickup ions from observations of neutral atoms

The solar wind blows an immense magnetic bubble, the heliosphere, in the local interstellar medium (mostly neutral gas) flowing by the Sun. Recent measurements by Voyager 2 across the termination shock, where the solar wind is slowed to subsonic speeds before entering the heliosheath, found that the shocked solar wind plasma contains only approximately 20 per cent of the energy released by the termination shock, whereas energetic particles above approximately 28 keV contain only approximately 10 per cent; approximately 70 per cent of the energy is unaccounted for, leading to speculation that the unmeasured pickup ions or energetic particles below 28 keV contain the missing energy. Here we report the detection and mapping of heliosheath energetic ( approximately 4-20 keV) neutral atoms produced by charge exchange of suprathermal ions with interstellar neutral atoms. The energetic neutral atoms come from a source approximately 60 degrees wide in longitude straddling the direction of the local interstellar medium. Their energy spectra resemble those of solar wind pickup ions, but with a knee at approximately 11 keV instead of approximately 4 keV, indicating that their parent ions are pickup ions energized by the termination shock. These termination-shock-energized pickup ions contain the missing approximately 70 per cent of the energy dissipated in the termination shock, and they dominate the pressure in the heliosheath.     

Biodiversity and biogeography of phages in modern stromatolites and thrombolites

Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.     

Prostitution and Human Rights in Indonesia: A Critical Systemic Review of Policy Discourses and Scenarios

This article considers policy making in practice focussing on case studies drawn from ethnographic research on prostitution in Indonesia carried out between 2012 and 2013 (this article is based on field research undertaken in Java, Indonesia, between November 2012 and 28 February 2013). Its theoretical underpinnings is that of ‘critical systemic heuristics’ which contends that policy making with respect to prostitution needs to take into account a range of factors and diverse views based on a process of ‘unfolding values’ and ‘sweeping in’ many variables before a decision is made. Applying ‘critical systemic approach’ or ‘critical heuristics’provides a means to test out the policy making ideas, as opposed to merely implementing the ideas of the powerful. The paper applies critical heuristic thinking to argue that the policy response ought to take into account the voices of those with a lived experience of poverty and prostitution, in order to protect their rights when making policy decisions.     

Timing is everything: the regulation of type III secretion

Type Three Secretion Systems (T3SSs) are essential virulence determinants of many Gram-negative bacteria. The T3SS is an injection device that can transfer bacterial virulence proteins directly into host cells. The apparatus is made up of a basal body that spans both bacterial membranes and an extracellular needle that possesses a channel that is thought to act as a conduit for protein secretion. Contact with a host-cell membrane triggers the insertion of a pore into the target membrane, and effectors are translocated through this pore into the host cell. To assemble a functional T3SS, specific substrates must be targeted to the apparatus in the correct order. Recently, there have been many developments in our structural and functional understanding of the proteins involved in the regulation of secretion. Here we review the current understanding of protein components of the system thought to be involved in switching between different stages of secretion.     

How Lemmings on Wheels Can Make a U-Turn Through Social Inclusion and Democracy

The challenge is (a) to balance both centralised control to preserve the global commons and (b) to involve people in policy making so that they feel culturally engaged and committed to the policy. Dictatorships and forms of World government from above to support the global commons are no more of an answer than forms of liberal democracy that do not engage people in between national elections. Passive voting does not help people in diverse democracies to engage in thinking through ‘if then scenarios’ about their social, economic and environmental future.