Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.

Rhizobium leguminosarum bv. trifolii SRDI943 (strain syn. V2-2) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Trifolium michelianum Savi cv. Paradana that had been grown in soil collected from a mixed pasture in Victoria, Australia. This isolate was found to have a broad clover host range but was sub-optimal for nitrogen fixation with T. subterraneum (fixing 20-54% of reference inoculant strain WSM1325) and was found to be totally ineffective with the clover species T. polymorphum and T. pratense. Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943, together with genome sequence information and annotation. The 7,412,387 bp high-quality-draft genome is arranged into 5 scaffolds of 5 contigs, contains 7,317 protein-coding genes and 89 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.     

Biosystematics of Draba cuneifolia and D. platycarpa (cruciferae) with emphasis on volatile and flavonoid constituents

Brittonia - Droba platycarpa Torrey & Gray has been frequently treated as a variety ofD. cuneijolia Nutt. ex Torrey & Gray, but our data indicate that it is sufficiently distinct...     

In vitro propagation and assessment of genetic uniformity along with chemical characterization in Hildegardia populifolia (Roxb.) Schott & Endl.: a critically endangered medicinal tree

In Vitro Cellular & Developmental Biology - Plant - Hildegardia populifolia (Roxb.) Schott & Endl. is a critically endangered medicinal tree species which also provide high-quality...     

Sexual isolation between Drosophila simulans and D. mauritiana: D. simulans females do not discriminate against intact-wing D. mauritiana males

Journal of Ethology - Female mate choice plays an important role in sexual isolation. The present study examined sexual isolation using D. simulans and D. mauritiana in conditions...     

Amyloid β-peptide (1-42)-induced Oxidative Stress and Neurotoxicity: Implications for Neurodegeneration in Alzheimer's Disease Brain. A Review

Oxidative stress, manifested by protein oxidation, lipid peroxidation, DNA oxidation and 3-nitrotyrosine formation, among other indices, is observed in Alzheimer's disease (AD) brain. Amyloid &#103 -peptide (1-42) [A &#103 (1-42)] may be central to the pathogenesis of AD. Our laboratory and others have implicated A &#103 (1-42)-induced free radical oxidative stress in the neurodegeneration observed in AD brain. This paper reviews some of these studies from our laboratory. Recently, we showed both in-vitro and in-vivo that methionine residue 35 (Met-35) of A &#103 (1-42) was critical to its oxidative stress and neurotoxic properties. Because the C-terminal region of A &#103 (1-42) is helical, and invoking the i +4 rule of helices, we hypothesized that the carboxyl oxygen of lle-31, known to be within a van der Waals distance of the S atom of Met-35, would interact with the latter. This interaction could alter the susceptibility for oxidation of Met-35, i.e. free radical formation. Consistent with this hypothesis, substitution of lle-31 by the helix-breaking amino acid, proline, completely abrogated the oxidative stress and neurotoxic properties of A &#103 (1-42). Removal of the Met-35 residue from the lipid bilayer by substitution of the negatively charged Asp for Gly-37 abrogated oxidative stress and neurotoxic properties of A &#103 (1-42). The free radical scavenger vitamin E prevented A &#103 (1-42)-induced ROS formation, protein oxidation, lipid peroxidation, and neurotoxicity in hippocampal neurons, consistent with our model for A &#103 -associated free radical oxidative stress induced neurodegeneration in AD. ApoE, allele 4, is a risk factor for AD. Synaptosomes from apoE knock-out mice are more vulnerable to A &#103 -induced oxidative stress (protein oxidation, lipid peroxidation, and ROS generation) than are those from wild-type mice. We also studied synaptosomes from allele-specific human apoE knock-in mice. Brain membranes from human apoE4 mice have greater vulnerability to A &#103 (1-42)-induced oxidative stress than brain membranes from apoE2 or E3, assessed by the same indices, consistent with the notion of a coupling of the oxidative environment in AD brain and increased risk of developing this disorder. Using immunoprecipitation of proteins from AD and control brain obtained no longer than 4 h PMI, selective oxidized proteins were identified in the AD brain. Creatine kinase (CK) and &#103 -actin have increased carbonyl groups, an index of protein oxidation, and Glt-1, the principal glutamate transporter, has increased binding of the lipid peroxidation product, 4-hydroxy-2-nonenal (HNE). A &#103 inhibits CK and causes lipid peroxidation, leading to HNE formation. Implications of these findings relate to decreased energy utilization, altered assembly of cytoskeletal proteins, and increased excitotoxicity to neurons by glutamate, all reported for AD. Other oxidatively modified proteins have been identified in AD brain by proteomics analysis, and these oxidatively-modified proteins may be related to increased excitotoxicity (glutamine synthetase), aberrant proteasomal degradation of damaged or aggregated proteins (ubiquitin C-terminal hydrolase L-1), altered energy production ( &#102 -enolase), and diminished growth cone elongation and directionality (dihydropyrimindase-related protein 2). Taken together, these studies outlined above suggest that Met-35 is key to the oxidative stress and neurotoxic properties of A &#103 (1-42) and may help explain the apoE allele dependence on risk for AD, some of the functional and structural alterations in AD brain, and strongly support a causative role of A &#103 (1-42)-induced oxidative stress and neurodegeneration in AD.     

Identification of Hybrids between the Far Eastern Redfins Tribolodon hakonensis and T. brandtii Based on the Cephalic Lateral-Line System and Four Molecular Genetic Markers

Journal of Ichthyology - Three species of the genus Tribolodon (T. hakonensis, T. brandtii, and T. sachalinensis) and hybrids between T. hakonensis and...     

Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying,hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment

Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis within Epsilonproteobacteria, which is involved in marine sedimentary sulfur oxidation and denitrification. Strain AST-10^T (= DSM 22096^T = JCM 18418^T) was isolated from the coastal sediment at the Kai Tak Approach Channel connected to Victoria Harbour in Hong Kong. It grew chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole electron donor and nitrate as the electron acceptor under anoxic conditions. It was rod-shaped and grew at 15-35°C (optimum at 30°C), pH 6.5-8.5 (optimum at 7.0-7.5), and 10-60 g L^-1 NaCl (optimum at 30 g L^-1). Genome sequencing and annotation of strain AST-10^T showed a 2,302,023 bp genome size, with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3 rRNA genes.     

Review of records of hymenolepidids (Eucestoda: Hymenolepididae) from dormice (Rodentia: Gliridae) in Europe,with a redescription of Armadolepis spasskyi Tenora & Baruš, 1958 and the description of A. genovi n. sp.

Systematic Parasitology - Armadolepis (Armadolepis) spasskyi Tenora & Baru?, 1958 is redescribed on the basis of the type-series consisting of the holotype from the garden dormouse...     

In vitro propagation of Farsetia macrantha Blatt. & Hallb.: an endemic and threatened plant of Indian Thar Desert

Plant Cell, Tissue and Organ Culture (PCTOC) - Farsetia macrantha Blatt. & Hallb. is an endemic and critically endangered plant species of Indian Thar desert. Being an endemic and...     

Characterization of aneuploidy in interspecific hybrid between Urochloa ruziziensis (R. Germ. & Evrard) Crins and Urochloa decumbens (Stapf) R. D. Webster

Molecular Biology Reports - The aim of the study was to characterize the type of aneuploidy present in the hybrid Urochloa ruziziensis × Urochloa decumbens and to confirm the...     

In vitro shoot regeneration from cotyledons of immature ovules ofImpatiens platypetala Lindl.

Summary An efficient and reproducible protocol has been developed for in vitro shoot regeneration from cotyledonary explants derived by germinating immature ovules ofImpatiens platypetala Lindl. ‘TR6-27-2’. Cotyledonary explants were cultured on a modified Murashige and Skoog (MS) agar-solidified medium containing 7.5g · liter^−1 sucrose, 22.2µ M N⁶-benzyladenine (BA), and 0.54µM α-naphthaleneacetic acid (NAA). The induction of organogenic tissues occurred after 6 to 8 wk in culture. Exogenous auxin and cytokinin were essential for the induction of organogenic tissues and survival of explants, and BA was most effective for the induction of organogenic tissues, compared with other cytokinins tested. The addition of glutamine (500 mg · liter^−1) was also important for growth of organogenic tissues after induction and for reducing explant death during culture. The induction of organogenic tissue was also influenced by the type of cotyledon cultured and the age of the donor seedlings. On average, eight shoots per explant were induced from organogenic tissues larger than 0.5 cm in diameter 6 to 8 wk after transfer to a modified MS agar-solidified medium without NAA and BA reduced to 4.44µM. Shoots longer than 0.5 cm in length were successfully rooted 2 to 4 wk after transfer to a basal MS medium containing 30g · liter^−1 sucrose.     

An updated and comprehensive review on the ethnomedicinal uses,phytochemistry, pharmacological activity and toxicological profile of Tinospora crispa (L.) Hook. f. & Thomson

Phytochemistry Reviews - Tinospora crispa (L.) Hook. f. & Thomson (Menispermaceae) is a plant indigenous to Africa and South-East Asia. It is widely used in ethnomedicine to alleviate...     

Genome sequence and description of Corynebacterium ihumii sp. nov.

Corynebacterium ihumii strain GD7^T sp. nov. is proposed as the type strain of a new species, which belongs to the family Corynebacteriaceae of the class Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old male patient, as a part of the culturomics study. Corynebacterium ihumii is a Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe the features of this organism, together with the high quality draft genome sequence, annotation and the comparison with other member of the genus Corynebacteria. C. ihumii genome is 2,232,265 bp long (one chromosome but no plasmid) containing 2,125 protein-coding and 53 RNA genes, including 4 rRNA genes. The whole-genome shotgun sequence of Corynebacterium ihumii strain GD7^T sp. nov has been deposited in EMBL under accession number GCA_000403725.     

Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov.

Holdemania massiliensis strain AP2^T sp. nov. is the type strain of H. massiliensis sp. nov., a new species within the genus Holdemania. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA genes.     

Eutetrarhynchus pacificus n. sp. (Cestoda: Trypanorhyncha) from Raja inornata Jordan & Gilbert (Batoidea: Rajiformes) off the coast of California with comments on congeners

Systematic Parasitology - Eutetrarhynchus pacificus n. sp. is described from the spiral valve of Raja inornata Jordan & Gilbert off the coast of California, USA. The new species is...     

In vitro propagation and establishment of adventitious root cultures of Rheum emodi Wall. ex Meisn for quantification of emodin production

In Vitro Cellular & Developmental Biology - Plant - Rheum emodi Wall. ex Meisn is an important medicinal herb used in treating type II diabetes mellitus, arthritis, inflammation, and...     

Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.

Oceanobacillus massiliensis strain N’Diop^T sp. nov. is the type strain of O. massiliensis sp. nov., a new species within the genus Oceanobacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. O. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes, including between 6 and 8 rRNA operons.     

Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov.

Enorma timonensis strain GD5^T sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes.