During the isolation of bacteria from the Agave L. rhizosphere in northeast Mexico, four strains with similar BOX-PCR patterns were collected. The 16S rRNA gene sequences of all four strains were very similar to each other and that of the type strains of
Cupriavidus metallidurans
CH34T (98.49 % sequence similarity) and
Cupriavidus necator
N-1T (98.35 %). The genome of strain ASC-9842T was sequenced and compared to those of other
Cupriavidus
species. ANIb and ANIm values with the most closely related species were lower than 95%, while the in silico DNA–DNA hybridization values were also much lower than 70 %, consistent with the proposal that they represent a novel species. This conclusion was supported by additional phenotypic and chemotaxonomic analyses. Therefore, the name Cupriavidus agavae sp. nov. is proposed with the type strain ASC-9842T (=LMG 26414T=CIP 110327T).
Phosphate metabolism was studied to determine whether polyphosphate (polyP) pools play a role in the enhanced resistance against Cd2+ and metal-removal capacity of Cd2+-preadapted (CdPA) Methanosarcina acetivorans. Polyphosphate kinase (PPK), exopolyphosphatase (PPX) and phosphate transporter transcript levels and their activities increased in CdPA cells compared to control (Cnt) cells. K+ inhibited recombinant Ma-PPK and activated Ma-PPX, whereas divalent cations activated both enzymes. Metal-binding polyP and thiol-containing molecule contents, Cd2+-removal, and biofilm synthesis were significantly higher in CdPA cells >Cnt cells plus a single addition of Cd2+>Cnt cells. Also, CdPA cells showed a higher number of cadmium, sulfur, and phosphorus enriched-acidocalcisomes than control cells. Biochemical and physiological phenotype exhibited by CdPA cells returned to that of Cnt cells when cultured without Cd2+. Furthermore, no differences in the sequenced genomes upstream and downstream of the genes involved in Cd2+ resistance were found between CdPA and Cnt cells, suggesting phenotype loss rather than genome mutations induced by chronic Cd2+-exposure. Instead, a metabolic adaptation induced by Cd2+ stress was apparent. The dynamic ability of M. acetivorans to change its metabolism, depending on the environmental conditions, may be advantageous to remove cadmium in nature and biodigesters.
Helicobacter pylori strains are the major risk factor for gastric cancer. Strains vary in their content of disease-associated genes, so genome-wide analysis of cancer-isolated strains will help elucidate their pathogenesis and genetic diversity. We present the draft genome sequence of H. pylori isolated from a Mexican patient with intestinal gastric cancer.
The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence,
including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases
that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential
hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off
value, it is considered as a site of high probability of hybridization. The Universal Fingerprinting Chip Applications Server contains
the software for visualizing predicted hybridization patterns, which yields a simulated hybridization fingerprint that can be
compared with experimentally derived fingerprints or with a virtual fingerprint arising from a different sample.Availability
http://bioinformatica.homelinux.org/UFCVH/
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