Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge

A novel anaerobic, thermophilic, carbon monoxide-utilizing bacterium, strain E3-O, was isolated from anaerobic sludge of a municipal solid waste digester. Cells were straight rods, 0.6 to 1μm in diameter and 2 to 3 μm in length, growing as single cells or in pairs. Cells formed round terminal endospores. The temperature range for growth was 50 to 70°C, with an optimum at 65°C. The pH range for growth was 5.7 to 8.0, with an optimum at 7.5. Strain E3-O had the capability to ferment various sugars, such as fructose, galactose, glucose, mannose, raffinose, ribose, sucrose and xylose, producing mainly H2 and acetate. In addition, the isolate was able to grow with CO as the sole carbon and energy source. CO oxidation was coupled to H2 and CO2 formation. The G+C content of the genomic DNA was 54.6 mol %. Based on 16S rRNA gene sequence analysis, this bacterium is most closely related to Moorella glycerini (97% sequence identity). Based on the physiological features and phylogenetic analysis, it is proposed that strain E3-O should be classified in the genus Moorella as a new species, Moorella stamsii. The type strain of Moorella stamsii is E3-OT (=DMS 26271T=CGMCC 1.5181T).This work was possible through the financial support provided by the Portuguese Science Foundation (FCT) and the European Social Fund (POPH-QREN) through a PhD grant SFRH/BD/48965/2008 to J.I.A

CCPG1 Is a Non-canonical Autophagy Cargo Receptor Essential for ER-Phagy and Pancreatic ER Proteostasis

Mechanisms of selective autophagy of the ER, known as ER-phagy, require molecular delineation, particularly in vivo. It is unclear how these events control ER proteostasis and cellular health. Here, we identify cell-cycle progression gene 1 (CCPG1), an ER-resident protein with no known physiological role, as a non-canonical cargo receptor that directly binds to core autophagy proteins via an LIR motif to mammalian ATG8 proteins and, independently and via a discrete motif, to FIP200. These interactions facilitate ER-phagy. The CCPG1 gene is inducible by the unfolded protein response and thus directly links ER stress to ER-phagy. In vivo, CCPG1 protects against ER luminal protein aggregation and consequent unfolded protein response hyperactivation and tissue injury of the exocrine pancreas. Thus, via identification of this autophagy protein, we describe an unexpected molecular mechanism of ER-phagy and provide evidence that this may be physiologically relevant in ER luminal proteostasis

Host-pathogen interactions and subversion of autophagy

Macroautophagy (“autophagy”), is the process by which cells can form a double membraned vesicle that encapsulates material to be degraded by the lysosome. This can include complex structures such as damaged mitochondria, peroxisomes, protein aggregates and large swathes of cytoplasm that could not be processed efficiently by other means of degradation. Recycling of amino acids and lipids through autophagy, allows the cell to form intracellular pools that aids survival during periods of stress, including growth factor deprivation, amino acid starvation or a depleted oxygen supply. One of the major functions of autophagy that has emerged over the last decade is its importance as a safeguard against infection. The ability of autophagy to selectively target intracellular pathogens for destruction is now regarded as a key aspect of the innate immune response. However, pathogens have evolved mechanisms to either evade or reconfigure the autophagy pathway for their own survival. Understanding how pathogens interact with and manipulate the host autophagy pathway will hopefully provide a basis for combating infection and increase our understanding of the role and regulation of autophagy. Herein, we will discuss how the host cell can identify and target invading pathogens and how pathogens have adapted in order to evade destruction by the host cell. In particular, we will focus on interactions between the mammalian ATG8 proteins and the host and pathogen effector proteins

Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia

Bathyarchaeia are widespread in various anoxic ecosystems and are considered one of the most abundant microbial groups on the earth. There are only a few reports of laboratory cultivation of Bathyarchaeia, and none of the representatives of this class has been isolated in pure culture. Here, we report a sustainable cultivation of the Bathyarchaeia archaeon (strain M17CTs) enriched from anaerobic sediment of a coastal lake. The cells of strain M17CTs were small non-motile cocci, 0.4–0.7 μm in diameter. The cytoplasmic membrane was surrounded by an S-layer and covered with an outermost electron-dense sheath. Strain M17CTs is strictly anaerobic mesophile. It grows at 10–45°C (optimum 37°C), at pH 6.0–10.0 (optimum 8.0), and at NaCl concentrations of 0–60 g l−1 (optimum 20 g l−1). Growth occurred in the presence of methoxylated aromatic compounds (3,4-dimethoxybenzoate and vanillate) together with complex proteinaceous substrates. Dimethyl sulfoxide and nitrate stimulated growth. The phylogenomic analysis placed strain M17CTs to BIN-L-1 genus-level lineage from the BA1 family-level lineage and B26-1 order-level lineage (former subgroup-8) within the class Bathyarchaeia. The complete genome of strain M17CTs had a size of 2.15 Mb with a DNA G + C content of 38.1%. Based on phylogenomic position and phenotypic and genomic properties, we propose to assign strain M17CTs to a new species of a novel genus Bathyarchaeum tardum gen. nov., sp. nov. within the class Bathyarchaeia. This is the first sustainably cultivated representative of Bathyarchaeia. We propose under SeqCode the complete genome sequence of strain M17CTs (CP122380) as a nomenclatural type of Bathyarchaeum tardum, which should be considered as a type for the genus Bathyarchaeum, which is proposed as a type for the family Bathyarchaeaceae, order Bathyarchaeales, and of the class Bathyarchaeia

Survivability Is More Fundamental Than Evolvability

For a lineage to survive over long time periods, it must sometimes change. This has given rise to the term evolvability, meaning the tendency to produce adaptive variation. One lineage may be superior to another in terms of its current standing variation, or it may tend to produce more adaptive variation. However, evolutionary outcomes depend on more than standing variation and produced adaptive variation: deleterious variation also matters. Evolvability, as most commonly interpreted, is not predictive of evolutionary outcomes. Here, we define a predictive measure of the evolutionary success of a lineage that we call the k-survivability, defined as the probability that the lineage avoids extinction for k generations. We estimate the k-survivability using multiple experimental replicates. Because we measure evolutionary outcomes, the initial standing variation, the full spectrum of generated variation, and the heritability of that variation are all incorporated. Survivability also accounts for the decreased joint likelihood of extinction of sub-lineages when they 1) disperse in space, or 2) diversify in lifestyle. We illustrate measurement of survivability with in silico models, and suggest that it may also be measured in vivo using multiple longitudinal replicates. The k-survivability is a metric that enables the quantitative study of, for example, the evolution of 1) mutation rates, 2) dispersal mechanisms, 3) the genotype-phenotype map, and 4) sexual reproduction, in temporally and spatially fluctuating environments. Although these disparate phenomena evolve by well-understood microevolutionary rules, they are also subject to the macroevolutionary constraint of long-term survivability

Discussions and Reviews : Toward an ethology of human conflict: a review

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67149/2/10.1177_002200276701100310.pd

The role of supportive supervision on immunization program outcome - a randomized field trial from Georgia

<p>Abstract</p> <p>Background</p> <p>One of the most common barriers to improving immunization coverage rates is human resources and its management. In the Republic of Georgia, a country where widespread health care reforms have taken place over the last decade, an intervention was recently implemented to strengthen performance of immunization programs. A range of measures were taken to ensure that immunization managers carry out their activities effectively through direct, personal contact on a regular basis to guide, support and assist designated health care facility staff to become more competent in their immunization work. The aim of this study was to document the effects of "supportive" supervision on the performance of the immunization program at the district(s) level in Georgia.</p> <p>Methods</p> <p>A pre-post experimental research design is used for the quantitative evaluation. Data come from baseline and follow-up surveys of health care providers and immunization managers in 15 intervention and 15 control districts. These data were supplemented by focus group discussions amongst Centre of Public Health and health facility staff.</p> <p>Results</p> <p>The results of the study suggest that the intervention package resulted in a number of expected improvements. Among immunization managers, the intervention independently contributed to improved knowledge of supportive supervision, and helped remove self-perceived barriers to supportive supervision such as availability of resources to supervisors, lack of a clear format for providing supportive supervision, and lack of recognition among providers of the importance of supportive supervision. The intervention independently contributed to relative improvements in district-level service delivery outcomes such as vaccine wastage factors and the DPT-3 immunization coverage rate. The clear positive improvement in all service delivery outcomes across both the intervention and control districts can be attributed to an overall improvement in the Georgian population's access to health care.</p> <p>Conclusion</p> <p>Provider-based interventions such as supportive supervision can have independent positive effects on immunization program indicators. Thus, it is recommended to implement supportive supervision within the framework of national immunization programs in Georgia and other countries in transition with similar institutional arrangements for health services organization.</p> <p>Abstract in Russian</p> <p>See the full article online for a translation of this abstract in Russian.</p

The adaptive significance of cultural behavior: Comments and reply

Fundamentally, theoretically, there is only one process underlying genetic and cultural evolution: natural selection. Organism fitness-enhancement (“adaptive significance”) is one of its practical mechanisms; group formation and maintenance is another, often but not always through fitness-enhancement; and need-fulfillment is still another. If Durham can accept that formulation, and switch from “organism-thinking” to “instruction-thinking” (Cloak, 1975: 178), he will free himself from two handicaps: First, he can forget his worries about “reductionism” and “determinism” (1976a: 100, 101). Under this general theory of natural selection, cultural evolution is biological evolution, continued by “other” (nongenetic) means. Second, he will spare himself the appearance of anthropomorphism, mentalism, and wishy-washiness attendant on his discussion of kinds of “significance,” other than adaptive “significance,” of cultural behaviors (1976a: 102–106, 115).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44494/1/10745_2005_Article_BF01880258.pd

Warming and Resource Availability Shift Food Web Structure and Metabolism

Experimental warming of a marine food web suggests that ocean warming can lead to greater consumer abundance but reduced overall biomass, providing a potentially species-independent response to environmental warming