Draft genome sequences of two strains isolated from I plumes at the Hanford Site.

strains DVZ6 and DVZ24 were isolated from a sediment trap incubated in an I plume at the Hanford Site (Washington State, USA). Whole-genome sequencing of the strains revealed that both genomes are 5.77 Mb in size, with a G + C content of 64.

Draft genome sequence of DVZ29, an iodide-oxidizing bacterium isolated from the Hanford site.

DVZ29 was isolated from a sediment trap incubated in an I plume at the Hanford Site (Washington State, USA). A whole genome sequencing of the strain resulted in 32 contigs and revealed that the genome is 4.90 Mb, with a G + C content of 55.

Complete genome sequence of sp., strain ES6, a chromate-reducing bacterium isolated from chromium-contaminated subsurface sediment.

sp. strain ES6 is a chromate-reducing bacterium isolated from chromium contaminated subsurface sediment. Illumina MiSeq and Oxford Nanopore sequencing were used to assemble the genome sequence which consisted of a single circular chromosome of 4.

Iodate Reduction by Requires Genes Encoding an Extracellular Dimethylsulfoxide Reductase.

Microbial iodate (IO ) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO to iodide (I) and microbial methylation of I to volatile gases. The metal reduction pathway is required for anaerobic IO respiration by the gammaproteobacterium .

Biotic dissolution of autunite under anaerobic conditions: effect of bicarbonates and Shewanella oneidensis MR1 microbial activity.

Uranium is a contaminant of major concern across the US Department of Energy complex that served a leading role in nuclear weapon fabrication for half a century. In an effort to decrease the concentration of soluble uranium, tripolyphosphate injections were identified as a feasible remediation strategy for sequestering uranium in situ in contaminated groundwater at the Hanford Site. The introduction of sodium tripolyphosphate into uranium-bearing porous media results in the formation of uranyl phosphate minerals (autunite) of general formula {X[(UO)(PO)]·nHO}, where X is a monovalent or divalent cation.

Metal Reduction and Protein Secretion Genes Required for Iodate Reduction by Shewanella oneidensis.

The metal-reducing gammaproteobacterium reduces iodate (IO) as an anaerobic terminal electron acceptor. Microbial IO electron transport pathways are postulated to terminate with nitrate (NO) reductase, which reduces IO as an alternative electron acceptor. Recent studies with , however, have demonstrated that NO reductase is not involved in IO reduction.

Bead-linked transposomes enable a normalization-free workflow for NGS library preparation.

Background: Transposome-based technologies have enabled the streamlined production of sequencer-ready DNA libraries; however, current methods are highly sensitive to the amount and quality of input nucleic acid.

Results: We describe a new library preparation technology (Nextera DNA Flex) that utilizes a known concentration of transposomes conjugated directly to beads to bind a fixed amount of DNA, and enables direct input of blood and saliva using an integrated extraction protocol. We further report results from libraries generated outside the standard parameters of the workflow, highlighting novel applications for Nextera DNA Flex, including human genome builds and variant calling from below 1 ng DNA input, customization of insert size, and preparation of libraries from short fragments and severely degraded FFPE samples.

Glycoside hydrolase gene transcription by during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism.

Background: Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the Type Strain ATCC27009/DSM 446 genome.

Iodate and nitrate transformation by Agrobacterium/Rhizobium related strain DVZ35 isolated from contaminated Hanford groundwater.

Nitrate and radioiodine (I) contamination is widespread in groundwater underneath the Central Plateau of the Hanford Site. I, a byproduct of nuclear fission, is of concern due to a 15.7 million year half-life, and toxicity.

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism.

Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution.

Identification of genome-wide targets of Olig2 in the adult mouse spinal cord using ChIP-Seq.

In jawed vertebrates, oligodendrocytes (OLs) are the myelin-producing glial cells responsible for ensheathment of axons within the central nervous system and are also crucial for remyelination following injury or disease. Olig2 is a crucial factor in the specification and differentiation of oligodendrocyte precursor cells (OPCs) that give rise to mature, myelin-producing OLs in the developing and postnatal CNS; however, its role in adulthood is less well understood. To investigate the role Olig2 plays in regulating gene expression in the adult OL lineage in a physiologically-relevant context, we performed chromatin immunoprecipitation followed by next generation sequencing analysis (ChIP-Seq) using whole spinal cord tissue harvested from adult mice.

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius.

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A.

Degradation of phenolic compounds by the lignocellulose deconstructing thermoacidophilic bacterium Alicyclobacillus Acidocaldarius.

Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium, has a repertoire of thermo- and acid-stable enzymes that deconstruct lignocellulosic compounds. The work presented here describes the ability of A. acidocaldarius to reduce the concentration of the phenolic compounds: phenol, ferulic acid, ρ-coumaric acid and sinapinic acid during growth conditions.

The effect of uranium on bacterial viability and cell surface morphology using atomic force microscopy in the presence of bicarbonate ions.

Past disposal practices at nuclear production facilities have led to the release of liquid waste into the environment creating multiple radionuclide plumes. Microorganisms are known for the ability to interact with radionuclides and impact their mobility in soils and sediments. Gram-positive Arthrobacter sp.

Extinction risks and the conservation of Madagascar's reptiles.

Background: An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises.

Methodology/principal Findings: Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species.

3 mm can save your case: Making beauty function.

Understanding esthetic design is not enough if restorations are to withstand the forces of function. Dentists also must understand the relationships of incisal tables, the interincisal angle, disclusion forces, and the implications of changing those parameters when restoring the anterior dentition. While canine-protected occlusion is often a goal, it may not always be appropriate or attainable.

Uranium exerts acute toxicity by binding to pyrroloquinoline quinone cofactor.

Uranium as an environmental contaminant has been shown to be toxic to eukaryotes and prokaryotes; however, no specific mechanisms of uranium toxicity have been proposed so far. Here a combination of in vivo, in vitro, and in silico studies are presented describing direct inhibition of pyrroloquinoline quinone (PQQ)-dependent growth and metabolism by uranyl cations. Electrospray-ionization mass spectroscopy, UV-vis optical spectroscopy, competitive Ca(2+)/uranyl binding studies, relevant crystal structures, and molecular modeling unequivocally indicate the preferred binding of uranyl simultaneously to the carboxyl oxygen, pyridine nitrogen, and quinone oxygen of the PQQ molecule.

Effects of ferrous sulfate, inoculum history, and anionic form on lead, zinc, and copper toxicity to Acidithiobacillus caldus strain BC13.

The current study reports the single and combined toxicities of Pb, Zn, and Cu to Acidithiobacillus caldus strain BC13. The observed half-maximal inhibitory concentrations (IC50), ± 95% confidence intervals, for Pb, Zn, and Cu were 0.9 ± 0.

Effects of cell condition, pH, and temperature on lead, zinc, and copper sorption to Acidithiobacillus caldus strain BC13.

This study describes the effects of cell condition, pH, and temperature on lead, zinc, and copper sorption to Acidithiobacillus caldus strain BC13 with a Langmuir model. Copper exhibited the highest loading capacity, 4.76 ± 0.

UO(2) 2+ speciation determines uranium toxicity and bioaccumulation in an environmental Pseudomonas sp. isolate.

In the present study, experiments were performed to investigate how representative cellulosic breakdown products, when serving as growth substrates under aerobic conditions, affect hexavalent uranyl cation (UO(2) (2+)) toxicity and bioaccumulation within a Pseudomonas sp. isolate (designated isolate A). Isolate A taken from the Cold Test Pit South (CTPS) region of the Idaho National Laboratory (INL), Idaho Falls, ID, USA.