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231.
Iain Anderson Luke E. Ulrich Boguslaw Lupa Dwi Susanti Iris Porat Sean D. Hooper Athanasios Lykidis Magdalena Sieprawska-Lupa Lakshmi Dharmarajan Eugene Goltsman Alla Lapidus Elizabeth Saunders Cliff Han Miriam Land Susan Lucas Biswarup Mukhopadhyay William B. Whitman Carl Woese James Bristow Nikos Kyrpides 《PloS one》2009,4(6)
Background
Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens.Methodology/Principal Findings
In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales.Conclusions/Significance
Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III). 相似文献232.
Fiber mats with average fiber diameter ranging between 80 and 250 nm of polyvinyl alcohol (PVA)/water solution having a concentration of 4 wt.% have been prepared by electrospinning method. The influence of applied voltage, flow rate, and needle-to-collector distance on the fiber morphology and diameters has been studied. Scanning electron microscopy and atomic force microscopy are used to characterize the fibers. It has been observed that bead-free fibers of 4 wt.% PVA can be obtained at lower voltages (9 kV). Also, density and the deposition area of the fiber mats showed a clear dependence on the applied voltage, flow rate, and collector distance. 相似文献
233.
Annedi SC Biabani F Poduch E Mannargudi BM Majumder K Wei L Khayat R Tong L Kotra LP 《Bioorganic & medicinal chemistry》2006,14(1):214-236
The mechanism of proteolysis by serine proteases is a reasonably well-understood process. Typically, a histidine residue acting as a general base deprotonates the catalytic serine residue and the hydrolytic water molecule. We disclose here, the use of an unnatural d-amino acid as a strategic residue in P1 position, designed de novo based on the architecture of the protease catalytic site to impede the catalytic histidine residue at the stage of acyl-enzyme intermediate. Several probe molecules containing d-homoserine or its derivatives at P1 position are evaluated. Compounds 1, 6, and 8-10 produced up to 57% loss of activity against chymotrypsin. More potent and specific inhibitors could be designed with structure optimization as this strategy is completely general and can be used to design inhibitors against any serine or cysteine protease. 相似文献
234.
Neelakandan Vidhya Lakshmi Prakasam Thirumurugan K.M. Noorulla Paramasivan.T. Perumal 《Bioorganic & medicinal chemistry letters》2010,20(17):5054-5061
A simple and convenient method for the one-pot three-component synthesis of 3-pyranyl indoles has been accomplished by tandem Knoevenagel–Michael reaction of 3-cyanoacetyl indole, various aromatic aldehydes and malononitrile catalyzed by InCl3 in ethanol under reflux conditions. The newly synthesized 3-pyranyl indoles were evaluated for anti-microbial, antioxidant, and anticancer activities. Some of the compounds showed good anticancer activity against MCF-7 breast cancer cell lines on comparison with of standard drug. 相似文献
235.
Muriel Mari Janice Griffith Ester Rieter Lakshmi Krishnappa Daniel J. Klionsky Fulvio Reggiori 《The Journal of cell biology》2010,190(6):1005-1022
Eukaryotes use the process of autophagy, in which structures targeted for lysosomal/vacuolar degradation are sequestered into double-membrane autophagosomes, in numerous physiological and pathological situations. The key questions in the field relate to the origin of the membranes as well as the precise nature of the rearrangements that lead to the formation of autophagosomes. We found that yeast Atg9 concentrates in a novel compartment comprising clusters of vesicles and tubules, which are derived from the secretory pathway and are often adjacent to mitochondria. We show that these clusters translocate en bloc next to the vacuole to form the phagophore assembly site (PAS), where they become the autophagosome precursor, the phagophore. In addition, genetic analyses indicate that Atg1, Atg13, and phosphatidylinositol-3-phosphate are involved in the further rearrangement of these initial membranes. Thus, our data reveal that the Atg9-positive compartments are important for the de novo formation of the PAS and the sequestering vesicle that are the hallmarks of autophagy. 相似文献
236.
Kannanganat S Nigam P Velu V Earl PL Lai L Chennareddi L Lawson B Wilson RL Montefiori DC Kozlowski PA Moss B Robinson HL Amara RR 《Journal of immunology (Baltimore, Md. : 1950)》2010,185(12):7262-7273
The influence of preexisting immunity to viral vectors is a major issue for the development of viral-vectored vaccines. In this study, we investigate the effect of preexisting vaccinia virus immunity on the immunogenicity and efficacy of a DNA/modified vaccinia Ankara (MVA) SIV vaccine in rhesus macaques using a pathogenic intrarectal SIV251 challenge. Preexisting immunity decreased SIV-specific CD8 and CD4 T cell responses but preserved the SIV-specific humoral immunity. In addition, preexisting immunity did not diminish the control of an SIV challenge mediated by the DNA/MVA vaccine. The peak and set point viremia was 150- and 17-fold lower, respectively, in preimmune animals compared with those of control animals. The peak and set point viremia correlated directly with colorectal virus at 2 wk postchallenge suggesting that early control of virus replication at the site of viral challenge was critical for viral control. Factors that correlated with early colorectal viral control included 1) the presence of anti-SIV IgA in rectal secretions, 2) high-avidity binding Ab for the native form of Env, and 3) low magnitude of vaccine-elicited SIV-specific CD4 T cells displaying the CCR5 viral coreceptor. The frequency of SIV-specific CD8 T cells in blood and colorectal tissue at 2 wk postchallenge did not correlate with early colorectal viral control. These results suggest that preexisting vaccinia virus immunity may not limit the potential of recombinant MVA vaccines to elicit humoral immunity and highlight the importance of immunodeficiency virus vaccines achieving early control at the mucosal sites of challenge. 相似文献
237.
238.
239.
Lakshmi K Matukumalli John J Grefenstette David L Hyten Ik-Young Choi Perry B Cregan Curtis P Van Tassell 《BMC bioinformatics》2006,7(1):468-7
Background
Single nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs or microsatellite) markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in a relational database to facilitate interrogation through queries or to generate data for further analyses such as determination of linkage disequilibrium and identification of common haplotypes. Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable. 相似文献240.
George?E?LiuEmail author Lakshmi?K?Matukumalli Tad?S?Sonstegard Larry?L?Shade Curtis?P?Van Tassell 《BMC genomics》2006,7(1):140