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Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Archaea (5):
Recent article
Archaea
Abstract
We provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. Three major types of CRISPR-Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the ex...
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PMID: 21552286
PDF is available here.
PDF is available here.
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ISME Journal (5)6 2011
Abstract
We describe the sediment metagenome from the oligotrophic Brazos-Trinity Basin (Site 1320) and show similarities and differences with the dataset from the Pacific Peru Margin (Site 1229) and other pyrosequenced datasets. The microbial community found at Integrated Ocean Drilling Program Site 1320 li...
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PMID: 21209666
PDF is available here.
PDF is available here.
Abstract
We studied how nucleotides bind to PAN. Although PAN has six identical subunits, it binds ATPs in pairs, and its subunits exhibit three conformational states with high, low, or no affinity for ATP. When PAN binds two ATPγS molecules or two ATPγS plus two ADP molecules, it is maximally active in bi...
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PMID: 21335235
PDF is available here.
PDF is available here.
ISME Journal (5)2 2011
Abstract
We examined the influence of precisely controlled diets in 14 overweight men. Volunteers were provided successively with a control diet, diets high in resistant starch (RS) or non-starch polysaccharides (NSPs) and a reduced carbohydrate weight loss (WL) diet, over 10 weeks. Analysis of 16S rRNA sequ...
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PMID: 20686513
PDF is available here.
PDF is available here.
ISME Journal (5)2 2011
Abstract
We produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencin...
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PMID: 20668488
PDF is available here.
PDF is available here.
Research in Microbiology (162)1 2011
Abstract
Abstract
We think that the test of Theobald is not sufficient enough to reject the alternative hypothesis of the separate origins of life, despite the Akaike information criterion (AIC) of model selection giving a clear distinction between the competing hypotheses....
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PMID: 21164432
PDF is available here.
PDF is available here.
Abstract
Viral and prokaryotic abundance, production and diversity were determined throughout the water column of the subtropical Atlantic Ocean to assess potential variations in the relation between viruses and prokaryotes. Prokaryotic abundance and heterotrophic activity decreased by one and three orders o...
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PMID: 20485386
PDF is available here.
PDF is available here.
Abstract
The aim of this study was to compare the effect of industrial discharges on the anaerobic treatment of domestic wastewater in both laboratory and pilot-plant scales at mesophilic conditions. The laboratory experiment results have shown the low process efficiency of anaerobic treatment of DW by the u...
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PMID: 21121456
PDF is available here.
PDF is available here.
Waste Management (30)11 2010
Abstract
This study investigates changes in waste microbial community composition and biomass during in situ aeration in laboratory-scale columns over 32 weeks. Microbial profiles were assessed in solid and leachate samples in relation to physical-chemical parameters using phospholipid ester linked fatty aci...
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PMID: 20483579
PDF is available here.
PDF is available here.
Abstract
V-Xtractor (http://www.cmde.science.ubc.ca/mohn/software.html) uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. With a detection efficiency of 99.6% and low susceptibility to fa...
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PMID: 20804791
PDF is available here.
PDF is available here.
Abstract
We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed dive...
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PMID: 20457585
PDF is available here.
PDF is available here.
Microbial Ecology (60)3 2010
Abstract
Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed space...
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PMID: 20449582
PDF is available here.
PDF is available here.
ISME Journal (4)9 2010
Abstract
Trends in Microbiology (18)9 2010
Abstract
We review the diversity, metabolic characteristics, geomicrobiology and biogeochemistry of the deep-sea piezophiles.
Copyright 2010 Elsevier Ltd. All rights reserved....
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PMID: 20663673
PDF is available here.
PDF is available here.
Journal of Biotechnology (149)3 2010
Abstract
We will outline some ongoing work towards the foundations of this new approach.
Copyright 2009 Elsevier B.V. All rights reserved....
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PMID: 20036699
PDF is available here.
PDF is available here.
Theory in Biosciences (129)2-3 2010
Abstract
Symbiosis has long been associated with saltational evolutionary change in contradistinction to gradual Darwinian evolution based on gene mutations and recombination between individuals of a species, as well as with super-organismal views of the individual in contrast to the classical one-genome: on...
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PMID: 20535601
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)8 2010
Abstract
The discovery of two nonstandard amino acids, selenocysteine and pyrrolysine, in the genetic code is discussed. These findings have expanded our understanding of the genetic code, since the repertoire of amino acids in the genetic code was supplemented by two novel ones, in addition of the standard...
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PMID: 20873198
PDF is available here.
PDF is available here.
Bioresource Technology (101)15 2010
Abstract
The rhizosphere and phyllosphere of the halophyte Halonemum strobilaceum naturally inhabiting hypersaline coastal areas of the Arabian Gulf harbor up to 8.1 x 10(4)g(-1) and 3 x 10(2)g(-1), respectively, of extremely halophilic oil-utilizing microorganisms. Such organisms were 14- to 38-fold more fr...
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PMID: 20303746
PDF is available here.
PDF is available here.
Abstract
Abstract
We discuss the ecological coherence of high bacterial taxa in the light of genome analyses and present examples of niche differentiation between deeply diverging groups in terrestrial and aquatic systems. The ecological relevance of high bacterial taxa has implications for bacterial taxonomy, evolut...
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PMID: 20531276
PDF is available here.
PDF is available here.
Abstract
Biochimica et Biophysica Acta (1804)7 2010
Abstract
We have cloned, expressed and characterised a cysteine desulphurase (SufS) from Haloferax volcanii and demonstrated that this protein is able to reconstitute the [Fe-S] cluster of halophilic ferredoxin.
Copyright (c) 2010 Elsevier B.V. All rights reserved....
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PMID: 20226884
PDF is available here.
PDF is available here.
FEBS Letters (584)13 2010
Abstract
We studied the cellular localization of the archaeal exosome, an RNA-processing protein complex containing orthologs of the eukaryotic proteins Rrp41, Rrp42, Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. Fractionation of cell-free extracts of Sulfolobus solfataricus in sucrose de...
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PMID: 20488181
PDF is available here.
PDF is available here.
Abstract
The monomolecular organisation of the natural asymmetric and symmetric bolaamphiphilic (archaebacterial tetraether lipids) was studied using a combination of Langmuir film balance, ellipsometry, and atomic force microscopy (AFM). Monolayer films were transferred onto silicon wafer substrates. After...
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PMID: 20399080
PDF is available here.
PDF is available here.
Abstract
We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic anal...
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PMID: 20455933
PDF is available here.
PDF is available here.
Abstract
The relationship between biogeochemical process rates and microbial functional activity was investigated by analysis of the transcriptional dynamics of the key functional genes for methanogenesis (methyl coenzyme M reductase; mcrA) and methane oxidation (particulate methane monooxygenase; pmoA) and...
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PMID: 20455935
PDF is available here.
PDF is available here.
Abstract
The 4th European Congress of Virology, hosted by the Italian Society for Virology, attracted approximately 1300 scientists from 46 countries worldwide. It also represented the first conference of the European Society for Virology, which was established in Campidoglio, Rome, Italy in 2009. The main g...
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PMID: 20624042
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)14 2010
Abstract
We developed a methodology for assessments of intragenomic heterogeneity of these periodic patterns and applied it in analysis of 1,025 prokaryotic chromosomes. This technique allows more detailed analysis of sequence periodicity than previous methods where sequence periodicity was assessed in an in...
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PMID: 20494989
PDF is available here.
PDF is available here.
Characteristic of biodiversity of thermophilic microbial community by parallel pyrosequencing method
Abstract
Abstract
Ethanol-based fuels are becoming more heavily used, increasing the likelihood of ethanol-based fuel spills during transportation and storage. Although ethanol is well-known to be readily biodegradable, very little is known about the effects that such a spill might have on an indigenous microbial com...
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PMID: 20481624
PDF is available here.
PDF is available here.
Journal of Hazardous Materials (178)1-3 2010
Abstract
The native microbial community of a contaminated sediment from Brentella Canal (Venice Lagoon, Italy) was enriched in slurry microcosms consisting of sterile sediment suspended in sterile site water in the presence of 3,3',4,4'-tetrachlorobiphenyl, 3,3',4,4',5- and 2,3',4,4',5-pentachlorobiphenyls,...
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PMID: 20153926
PDF is available here.
PDF is available here.
Abstract
We found that the AOA population size increased significantly and AOA community changed greatly in the urea only treatment. However, HA could inhibit the increase of AOA population, moreover, HA could buffer the change in AOA community showed by canonical correspondence analysis (CCA) result. On the...
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PMID: 20687344
PDF is available here.
PDF is available here.
ISME Journal (4)6 2010
Abstract
These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-...
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PMID: 20147985
PDF is available here.
PDF is available here.
Abstract
Our data describe variability in the rate of mutation and likelihoods for phylogenetic trees based on protein sequence data and endorse the extension of substitution models by incorporating data on conservation and distance to C/ACs rather than only using cumulative levels. The data support the view...
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PMID: 20069373
PDF is available here.
PDF is available here.
ISME Journal (4)5 2010
Abstract
We review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex sy...
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PMID: 20164865
PDF is available here.
PDF is available here.
Abstract
1) The positive relationship previously found between the percentage of homoplasy and genome size is a direct consequence of the number of observed bands and the GC content. For the same number of observed bands, the percentage of homoplasy is independent of the genome size of the species. 2) The di...
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PMID: 20056690
PDF is available here.
PDF is available here.
Abstract
The archaeal community in the fermentative compartment and faeces of the cow and the rabbit were compared by analysis capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. Ruminal and faecal contents were sampled in five cows for th...
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PMID: 20417714
PDF is available here.
PDF is available here.
Abstract
We summarized the discovery, progress and prospect of archaeal ammonia oxidation. Of great interest in the future would be to elucidate the metabolisms of ammonia-oxidizing archaeon in natural environment and the underlying mechanism that leads to the physiological divergence of ammonia oxidizers....
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PMID: 20560343
PDF is available here.
PDF is available here.
Abstract
We propose a new and precise chronoamperometric method for studying the anaerobic inactivation mechanism of hydrogenase, which we apply to the oxygen-tolerant NiFe enzyme from Aquifex aeolicus . We demonstrate that the voltammetric data cannot be used for measuring the reduction potential of the so-...
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PMID: 20230028
PDF is available here.
PDF is available here.
Environmental Entomology (39)2 2010
Abstract
The symbiotic relationship of termites and their eukaryotic and prokaryotic gut microbiota is a focal point of research because of the important roles symbionts play in termite nutrition. The use of molecular methods has recently provided valuable insights into the species diversity and the roles of...
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PMID: 20388266
PDF is available here.
PDF is available here.
Abstract
During signal transduction by two-component regulatory systems, sensor kinases detect and encode input information while response regulators (RRs) control output. Most receiver domains function as phosphorylation-mediated switches within RRs, but some transfer phosphoryl groups in multistep phosphor...
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PMID: 20211578
PDF is available here.
PDF is available here.
Abstract
Response regulators (RRs) within two-component signal transduction systems control a variety of cellular processes. Most RRs contain DNA-binding output domains and serve as transcriptional regulators. Other RR types contain RNA-binding, ligand-binding, protein-binding or transporter output domains a...
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PMID: 20226724
PDF is available here.
PDF is available here.
Abstract
Abstract
Protein histidine kinases (PHKs) function in Two Component Signaling pathways utilized extensively by bacteria and archaea. Many PHKs participate in three distinct, but interrelated signaling reactions: autophoshorylation, phosphotransfer (to a partner Response Regulator (RR) protein), and dephospho...
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PMID: 20117042
PDF is available here.
PDF is available here.
Abstract
We review reports establishing the origins of two-component systems and documenting their occurrence in major lineages of Life.
Copyright 2010 Elsevier Ltd. All rights reserved....
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PMID: 20133179
PDF is available here.
PDF is available here.
Abstract
The deep phreatic thermal explorer (DEPTHX) is an autonomous underwater vehicle designed to navigate an unexplored environment, generate high-resolution three-dimensional (3-D) maps, collect biological samples based on an autonomous sampling decision, and return to its origin. In the spring of 2007,...
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PMID: 20298146
PDF is available here.
PDF is available here.
Abstract
We propose a new way forward by investigating the second derivative, deconvolution, and chemometrics of the carbon first-order spectra to build a database of structural parameters that may yield distinguishable characteristics between biogenic and abiogenic carbonaceous material. To place Raman spec...
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PMID: 20402584
PDF is available here.
PDF is available here.
Abstract
The activated structure of RNase P RNA (PhopRNA) in Pyrococcus horikoshii OT3 was characterized by circular dichroism (CD) and ultraviolet (UV) absorbance spectra. The results suggested that interaction of four RNase P proteins (PhoPop5, PhoRpp21, PhoRpp29, and PhoRpp30) with PhopRNA results in dest...
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PMID: 20139624
PDF is available here.
PDF is available here.
Abstract
A variety of archaeal lineages have been identified using culture-independent molecular phylogenetic surveys of microbial habitats occurring in deep-sea hydrothermal environments such as chimney structures, sediments, vent emissions, and chemosynthetic macrofauna. With the exception of a few taxa, m...
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PMID: 20023079
PDF is available here.
PDF is available here.
Abstract
We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, a...
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PMID: 19948847
PDF is available here.
PDF is available here.
Abstract
Abundance of ammonia-oxidizing Archaea (AOA) was found to be always greater than that of ammonia-oxidizing Bacteria along an estuarine salinity gradient, and AOA abundance was highest at intermediate salinity. However, AOA abundance did not correlate with potential nitrification rates. This lack of...
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PMID: 20038706
PDF is available here.
PDF is available here.
Abstract
Keratinases are exciting proteolytic enzymes that display the capability to degrade the insoluble protein keratin. These enzymes are produced by diverse microorganisms belonging to the Eucarya, Bacteria, and Archea domains. Keratinases display a great diversity in their biochemical a...
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PMID: 20039036
PDF is available here.
PDF is available here.
Molecular Cell (37)1 2010
Abstract
We review the inner workings of this adaptable and heritable immune system and draw comparisons to small RNA-guided defense mechanisms in eukaryotic cells.
Copyright 2010 Elsevier Inc. All rights reserved....
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PMID: 20129051
PDF is available here.
PDF is available here.
Abstract
Abstract
Phylogenetic analysis of 16S rRNA was used to investigate for the first time the structure of the microbial community that inhabits salt crystals retrieved from the bottom of a solar saltern, located in the coastal area of the Mediterranean Sea (Sfax, Tunisia). This community lives in an extremely s...
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PMID: 20130693
PDF is available here.
PDF is available here.
Abstract
Total biomass in the collected hot spring samples was 10(8) - 10(9) cells/g, among which ammonia-oxidizing archaea (AOA) occupied 0.02%-1.32%, whereas no ammonia-oxidizing bacteria were detected. Statistical analysis indicated that AOA abundance was significantly (P < 0.05) correlated with concentra...
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PMID: 20344952
PDF is available here.
PDF is available here.
Abstract
We found that these growth-related traits in 214 species of bacteria and archaea are highly correlated, suggesting they all result from growth optimization. While modeling their association with maximal growth rates in view of synthetic biology applications, we observed that codon usage biases are b...
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PMID: 20090831
PDF is available here.
PDF is available here.
Journal of Environmental Science and Health, Part A: Toxic/Hazardous Substances & Environmental Engineering (45)7 2010
Abstract
This work presents the effect of ammonia nitrogen concentration and zeolite addition on the specific methanogenic activity (SMA) of different anaerobic sludges with various physical structures (granular and flocculent), operating in batch conditions. Piggery, malting production and urban sludges der...
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PMID: 20419585
PDF is available here.
PDF is available here.