Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY

Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY.Microorganisms from diverse anoxic environments are capable of nitrate-dependent Fe(II) oxidation at circumneutral pH (4, 11, 17, 18, 20, 21). Despite their geochemical importance (22), little is known of the underlying biochemical and genetic mechanisms. Genome sequencing of several nitrate-dependent Fe(II) oxidizers will provide insight into this process. By comparing Fe(II) oxidation mechanisms in various organisms, we hope to identify both the conserved and disparate aspects of the metabolism. The genome of Acidovorax ebreus strain TPSY is the first of these to be sequenced.Strain TPSY is a motile, Gram-negative facultative anaerobe isolated from groundwater collected from the U.S. Department of Energy Integrated Field Research Challenge site at Oak Ridge, TN. Growth experiments performed as previously described (21) revealed TPSY''s incapacity for lithoautotrophic growth, which was supported by a lack of genes in the genome encoding any known CO₂ fixation pathways. TPSY did grow mixotrophically with Fe(II) as the electron donor and a 0.1 mM acetate carbon source. 16S rRNA gene sequence analysis placed TPSY in the class Betaproteobacteria with 99.8% similarity to Acidovorax sp. strain JS42 in the family Comamonadaceae.The completed genome consisted of a single circular chromosome of 3,796,573 bp with an average 66.8% G+C content. A total of 3,479 protein-encoding genes were predicted, and 34 (0.98%) had no similarity to public database sequences. Sequencing performed at the Department of Energy Joint Genome Institute (JGI) used Sanger sequencing and 454 pyrosequencing to a depth of 20× coverage. All JGI library construction and sequencing techniques can be found at http://www.jgi.doe.gov/. Sequence assembly, quality assessment, and annotation were performed using the software Phred/Phrap/Consed (www.phrap.com) (6-8), Dupfinisher (10), CRITICA (2), GLIMMER, and GENERATION (5) and the JGI Integrated Microbial Genomes site (12). The completed genome sequence contained 33,341 reads and had an average of ninefold coverage per base and an error rate of <1 in 100,000.TPSY was named in part for its meandering motility, and its genome confirmed the twitching phenotype with the presence of pilT, pilU, and a complete set of flagellar and chemotaxis genes. The ability of TPSY to oxidize simple alcohols and acids with oxygen or nitrate respiration was confirmed by the genome. In addition, biosynthetic pathways for all amino acids except tyrosine and phenylalanine were present. No homologues of chorismate mutase (EC 5.4.99.5), an enzyme required for tyrosine and phenylalanine anabolism, were identified. The genome contained both intact Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in addition to a pentose phosphate pathway and a trichloroacetic acid cycle.In support of its facultative anaerobicity, a complete set of genes for denitrification and three different terminal oxidases (cytochrome aa₃, cbb₃, and cytochrome d quinol oxidase) were present. The cbb₃ and cytochrome d oxidases, with their high oxygen affinity, putatively enable survival in microaerobic environments (14).TPSY had sequences encoding 30 transposases, 11 integrases, and 11 phage/prophage-related genes. A region of particular interest putatively conferred resistance to lead, arsenate, and mercury: pbrRATARTBC, arsRDAB, and merRPCADE. Evidence suggests horizontal transfer and insertion of this region, as it was flanked on the 5′ end by λ prophage-related genes and the 3′ end encoded a putative Tn21 transposase. Phenotypic studies by the method of Wang et al. (19) revealed MICs of 16 μM phenylmercuric acetate and 250 μM MgCl₂. TPSY was also capable of growth in the presence of arsenate (10 mM) but did not use it as an electron acceptor.Related to phage infection, one CRISPR (clustered, regularly interspaced, short palindromic repeats) region (3, 16) was predicted. The core proteins, the cas1 and cas2 genes, and a csn1 gene formed the CRISPR subtype Nmeni, which is associated with vertebrate pathogens and commensals (9). However, the lack of typical pathogenic type I or III secretion systems such as the hec cluster of Dickeya chrysanthemi (15) or the inv/spa system of Salmonella enterica serovar Typhimurium (13) indicated that TPSY would probably not exhibit a pathogenic lifestyle.     

Expression of a novel tropomyosin isoform in axolotl heart and skeletal muscle

TPM1κ is an alternatively spliced isoform of the TPM1 gene whose specific role in cardiac development and disease is yet to be elucidated. Although mRNA studies have shown TPM1κ expression in axolotl heart and skeletal muscle, it has not been quantified. Also the presence of TPM1κ protein in axolotl heart and skeletal muscle has not been demonstrated. In this study, we quantified TPM1κ mRNA expression in axolotl heart and skeletal muscle. Using a newly developed TPM1κ specific antibody, we demonstrated the expression and incorporation of TPM1κ protein in myofibrils of axolotl heart and skeletal muscle. The results support the potential role of TPM1κ in myofibrillogenesis and sarcomeric function. J. Cell. Biochem. 110: 875–881, 2010. © 2010 Wiley‐Liss, Inc.     

Comments on the rarity of tinea capitis in india

Summary Cause of the rarity oftinea capitis in India was surmised byAjello to be due to the use of vegetable hair-oils as hair-dressings by Indians. In this paper, experimental evidence has been brought forward to show that one of the hair-fungi,Microsporon gypseum, never penetrates into the human hairs smeared with mustard oil though hyphal filaments ofM. gypseum copiously encircled only the outer surfaces of hairs experimented upon. Clinically also, not a single instance oftinea capitis at our Outdoor Hospital has been noted during the last five years. Completely defatted hairs show three kinds of hair-digestion.The slide-culture technique ofLü (1962) was adopted for the experiments. This technique allowed continuous microscopic examination of hairs throughout. This reveals the first attack of the fungus and progress of the invasion.The first entry of a dermatophyte into the keratin of the hair has been discussed. The properties and nature of keratinolytic enzymes remain, however, undiscovered.     

A Rapid Method for Isolating Mutants of Bacillus subtilis Producing Increased or Decreased Amounts of the Antibiotic, Mycobacillin

S ummary : A simple, rapid and efficient technique is described for the isolation of mutants of Bacillus subtilis in which the synthesis of mycobacillin, an antifungal antibiotic, is blocked. Suspensions of a chosen culture were subjected to ultraviolet radiation and then plated; colonies failing to produce antibiotic were located by flooding the incubated plates with agar seeded with sensitive fungi such as Candida albicans and Aspergillus niger . The method is also applicable for the isolation of high potency strains.     

Fungi Growing on Jute Fabrics Deteriorating under Weather Exposure and in Storage

Special media suitable for the isolation of fungi growing on jute were developed. Species that would better resist sunlight, such as organisms with dark hyphae and spores or closed fruit bodies, predominated on weather-exposed fabrics. Several strongly cellulolytic organisms not previously implicated in fiber decomposition were isolated from this source. On the other hand, the fungi obtained from jute materials damaged in storage were mostly of the familiar types. Most of the newly isolated fungi are generally missed on ordinary media, but they probably play an important role in the natural decomposition of jute materials.