Genetic analysis of housekeeping genes of members of the genus Acholeplasma: phylogeny and complementary molecular markers to the 16S rRNA gene

The partial nucleotide sequences of the rpoB and gyrB genes as well as the complete sequence of the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known Acholeplasma species. The same genes of Mesoplasma and Entomoplasma species were also sequenced and used to infer phylogenetic relationships among the species within the orders Entomoplasmatales and Acholeplasmatales. The comparison of the ITS, rpoB, and gyrB phylogenetic trees with the 16S rRNA phylogenetic tree revealed a similar branch topology suggesting that the ITS, rpoB, and gyrB could be useful complementary phylogenetic markers for investigation of evolutionary relationships among Acholeplasma species. Thus, the multilocus phylogenetic analysis of Acholeplasma multilocale sequence data (ATCC 49900 (T) = PN525 (NCTC 11723)) strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family Entomoplasmataceae) and form the branch with Mesoplasma seiffertii, Mesoplasma syrphidae, and Mesoplasma photuris. The closest genetic relatedness of this species to the order Entomoplasmatales was additionally supported by the finding that A. multilocale uses UGA as the tryptophan codon in its gyrB and gyrA sequences. Use of the UGA codon for encoding tryptophan was previously reported as a unique genetic feature of Entomoplasmatales and Mycoplasmatales but not of Acholeplasmatales. These data, as well as previously published data on metabolic features of A. multilocale, leads to the proposal to reclassify A. multilocale as a member of the family Entomoplasmataceae.     

AMPA receptor-dependent clustering of synaptic NMDA receptors is mediated by Stargazin and NR2A/B in spinal neurons and hippocampal interneurons

Under standard conditions, cultured ventral spinal neurons cluster AMPA- but not NMDA-type glutamate receptors at excitatory synapses on their dendritic shafts in spite of abundant expression of the ubiquitous NMDA receptor subunit NR1. We demonstrate here that the NMDA receptor subunits NR2A and NR2B are not routinely expressed in cultured spinal neurons and that transfection with NR2A or NR2B reconstitutes the synaptic targeting of NMDA receptors and confers on exogenous application of the immediate early gene product Narp the ability to cluster both AMPA and NMDA receptors. The use of dominant-negative mutants of GluR2 further showed that the synaptic targeting of NMDA receptors is dependent on the presence of synaptic AMPA receptors and that synaptic AMPA and NMDA receptors are linked by Stargazin and a MAGUK protein. This system of AMPA receptor-dependent synaptic NMDA receptor localization was preserved in hippocampal interneurons but reversed in hippocampal pyramidal neurons.     

Discovery of novel conformationally restricted diazocan peptidomimetics as inhibitors of interleukin-1beta synthesis

A novel diazocan containing dipeptide mimetic was synthesized via reductive N-N bond cleavage of a pyrazolidino-pyrazolidine using Raney-Ni and evaluated as an ICE inhibitor. This versatile 8-membered ring containing scaffold possesses an N-5 ring nitrogen that was used to explore structure-activity relationships in a cell-based assay measuring inhibition of interleukin-1beta.     

Chemical composition of the cell walls of Lolium multiflorum endosperm

Cell walls isolated from Lolium multiflorum endosperm grown in liquid suspension culture contain 90% carbohydrate (as anhydro-glucose), 0·3 nitrogen, 1·9% lipid and 4·3% ash. The relative proportions of neutral sugars present in hydrolysates of the wall polysaccharides are glucose, 50%; arabinose, 19%; xylose, 26% and galactose, 5%. Extraction of the wall with 7 M urea solubilizes a polysaccharide representing 19% of the wall and composed of glucose and minor amounts of pentoses. This fraction has been examined by acid and enzymic hydrolysis and by periodate oxidation, and was shown to be a β-1,3; 1,4-glucan with approx. 79% 1,4-linkages. A specific β-glucan hydrolase has been used to determine the content of this mixed-linked glucan in isolated endosperm cell walls.     

Symbiosome-like intracellular colonization of cereals and other crop plants by nitrogen-fixing bacteria for reduced inputs of synthetic nitrogen fertilizers

It has been forecast that the challenge of meeting increased food demand and protecting environmental quality will be won or lost in maize, rice and wheat cropping systems, and that the problem of environmental nitrogen enrichment is most likely to be solved by substituting synthetic nitrogen fertilizers by the creation of cereal crops that are able to fix nitrogen symbiotically as legumes do. In legumes, rhizobia present intracellularly in membrane-bound vesicular compartments in the cytoplasm of nodule cells fix nitrogen endosymbiotically. Within these symbiosomes, membrane-bound vesicular compartments, rhizobia are supplied with energy derived from plant photosynthates and in return supply the plant with biologically fixed nitrogen, usually as ammonia. This minimizes or eliminates the need for inputs of synthetic nitrogen fertilizers. Recently we have demonstrated, using novel inoculation conditions with very low numbers of bacteria, that cells of root meristems of maize, rice, wheat and other major non-legume crops, such as oilseed rape and tomato, can be intracellularly colonized by the non-rhizobial, non-nodulating, nitrogen fixing bacterium,Gluconacetobacter diazotrophicus that naturally occurs in sugarcane.G. diazotrophicus expressing nitrogen fixing (nifH) genes is present in symbiosome-like compartments in the cytoplasm of cells of the root meristems of the target cereals and non-legume crop species, somewhat similar to the intracellular symbiosome colonization of legume nodule cells by rhizobia. To obtain an indication of the likelihood of adequate growth and yield, of maize for example, with reduced inputs of synthetic nitrogen fertilizers, we are currently determining the extent to which nitrogen fixation, as assessed using various methods, is correlated with the extent of systemic intracellular colonization byG. diazotrophicus, with minimal or zero inputs.     

Evolutionary relationships among Ascochyta species infecting wild and cultivated hosts in the legume tribes Cicereae and Vicieae

Evolutionary relationships were inferred among a worldwide sample of Ascochyta fungi from wild and cultivated legume hosts based on phylogenetic analyses of DNA sequences from the ribosomal internal transcribed spacer regions (ITS), as well as portions of three protein-coding genes: glyceraldehyde-3-phosphate-dehydrogenase (G3PD), translation elongation factor 1-alpha (EF) and chitin synthase 1 (CHS). All legume-associated Ascochyta species had nearly identical ITS sequences and clustered with other Ascochyta, Phoma and Didymella species from legume and nonlegume hosts. Ascochyta pinodes (teleomorph: Mycosphaerella pinodes [Berk. & Blox.] Vestergen) clustered with Didymella species and not with well characterized Mycosphaerella species from other hosts and we propose that the name Didymella pinodes (Berk. & Blox.) Petrak (anamorph: Ascochyta pinodes L.K. Jones) be used to describe this fungus. Analysis of G3PD revealed two major clades among legume-associated Ascochyta fungi with members of both clades infecting pea ("Ascochyta complex"). Analysis of the combined CHS, EF and G3PD datasets revealed that isolates from cultivated pea (P. sativum), lentil (Lens culinaris), faba bean (Vicia faba) and chickpea (Cicer arietinum) from diverse geographic locations each had identical or similar sequences at all loci. Isolates from these hosts clustered in well supported clades specific for each host, suggesting a co-evolutionary history between pathogen and cultivated host. A. pisi, A. lentis, A. fabae and A. rabiei represent phylogenetic species infecting pea, lentil, faba bean and chickpea, respectively. Ascochyta spp. from wild relatives of pea and chickpea clustered with isolates from related cultivated hosts. Isolates sampled from big-flower vetch (Vicia grandiflora) were polyphyletic suggesting that either this host is colonized by phylogenetically distinct lineages of Ascochyta or that the hosts are polyphyletic and infected by distinct evolutionary lineages of the pathogen. Phylogenetic species identified among legume-associated Ascochyta spp. were fully concordant with previously described morphological and biological species.     

Aerobic and anaerobic correlates of multiple sprint cycling performance

The aims of this study were to examine (a) the relationship between maximal oxygen uptake (VO(2)max) and several performance indices of multiple sprint cycling; (b) the relationship between maximal accumulated oxygen deficit (MAOD) and those same performance indices; and (c) the influence of recovery duration on the magnitude of those relationships. Twenty-five physically active men completed a VO(2)max test, a MAOD test, and 2 maximal intermittent (20 x 5 seconds) sprint cycling tests with contrasting recovery periods (10 seconds or 30 seconds). Mean +/- SD for age, height, and body mass were 20.6 +/- 1.5 years, 177.2 +/- 5.4 cm, and 78.2 +/- 8.2 kg, respectively. All tests were conducted on a friction-braked cycle ergometer with subsequent data normalized for body mass. Moderate (0.3 < or = r < 0.5) positive correlations were observed between power output data and MAOD (range, 0.31-0.46; 95% confidence limits, -0.10 to 0.72). Moderate to large positive correlations also were observed between power output data and VO(2)max, the magnitude of which increased as values were averaged across all sprints (range, 0.45-0.67; 95% confidence limits 0.07-0.84). Correlations between fatigue and VO(2)max were greater in the intermittent protocol with 30-second recovery periods (r = -0.34; 95% confidence limits, 0.06 to -0.65). The results of this study reflect the complex energetics associated with multiple sprint work. Though the findings add support to the idea that multiple sprint sports demand a combination of speed and endurance, further longitudinal research is required to confirm the relative importance of these parameters.     

YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.