Analysis and visualization of H7 influenza using genomic,evolutionary and geographic information in a modular web service

We have reported previously on use of a web‐based application, Supramap ( http://supramap.org ) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug‐resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY ( http://poyws.org ) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes ( http://geogenes.org ). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012.     

The chain length of the glycans in bacterial cell walls (Short Communication)

The glycan chain length of peptidoglycan was measured by reduction with NaB³H₄ and isolation of the resulting muramitol, indicative of the length of the chains as biosynthesized, and glucosaminol, which measured the length of the chains after rupture by endo-β-N-acetylglucosaminidases. Measurement of the non-reducing terminal N-acetylglucosamine by Smith degradation confirmed the result.     

Xanthine dehydrogenase and aldehyde oxidase in chicken liver: Molecular identity?

Evidence is presented to suggest that in chick liver, xanthine dehydrogenase and aldehyde oxidase activities are associated with only one protein species. The results of SDS electrophoresis of the purified material indicate a subunit MW of 120 000.     

Comparative analyses of RFLP diversity in landraces of Triticum aestivum and collections of T. tauschii from China and Southwest Asia

 Chinese accessions of Triticum tauschii and T. aestivum L. from the Sichuan white (SW), Yunnan hulled (YH), Tibetan weedrace (TW), and Xinjiang rice (XR) wheat groups were subjected to RFLP analysis. T. tauschii and landraces of T. aestivum from countries in Southwest Asia were also evaluated. For T. tauschii, a west to east gradient was apparent where the Chinese accessions exhibited less diversity than those from Southwest Asia. Compared to the Southwest Asian gene pool, the Chinese T. tauschii was highly homogeneous giving a low frequency of polymorphic bands (16%) and banding patterns (1.33 per probe) with 75 RFLP probe-HindIII combinations. Accessions of T. tauschii from Afghanistan and Pakistan were genetically more similar to the Chinese T. tauschii than those from Iran. Of 368 bands found for 39 Chinese hexaploid wheat accessions with 63 RFLP probe-HindIII combinations, 28.3% were polymorphic with an average of 2.6 banding patterns per probe and 5.0 bands per genotype. The individual Chinese landrace wheat groups revealed less variation than those from Afghanistan, Iran, and Turkey. When classified into country based groups, however, the diversity level over all Chinese landraces was greater than that of some Southwest Asian landraces, especially those from Afghanistan and Iran . The XR wheat group was genetically distinct from the other three Chinese landrace groups and was more related to the Southwest Asian landraces. The TW group was genetically similar to, but more diverse than, the SW and YH groups. The Chinese landraces had a higher degree of genetic relatedness to the Southwest Asian T. tauschii, particularly to accessions from Iran, rather than to the Chinese T. tauschii. ‘Chinese Spring’ was most related to ‘Chengdu-guang-tou’, a cultivar from the SW wheat group. Received: 13 May 1997 / Accepted: 19 September 1997     

Distribution of interstitial cells of Cajal in tunica muscularis of the canine rectoanal region

Electrical and mechanical activity of the circular muscle layer in the rectoanal region of the gastrointestinal tract undergoes considerable changes in the site of dominant pacemaking activity, frequency, and waveform shape. The present study was performed to determine whether changes in the structural organization of the circular layer or in the density, distribution, and ultrastructure of interstitial cells of Cajal (ICC) could account for this heterogeneity in electrical and mechanical activities. Light microscopy revealed that the structural organization of the circular muscle layer underwent dramatic morphological changes, from a tightly packed layer with poorly defined septa in the proximal rectum to one of discrete muscle bundles separated by large septae in the internal anal sphincter. Kit immunohistochemistry revealed a dense network of ICC along the submucosal and myenteric borders in the rectum, whereas in the internal anal sphincter, ICC were located along the periphery of muscle bundles within the circular layer. Changes in electrical activity within the circular muscle layer can be partially explained by changes in the structure of the muscle layer and changes in the distribution of ICC in the rectoanal region of the gastrointestinal tract.     

The UL20 gene of herpes simplex virus 1 encodes a function necessary for viral egress.

A recombinant virus from which the start codon and 53% of the UL20 open reading frame had been deleted was constructed and characterized. We report the following: (i) The UL20- mutant formed small plaques in 143 tk- cells but failed to form plaques in Vero cells. Virus yields were approximately 10- to 100-fold lower than those of wild-type virus in all cell lines tested. (ii) Electron microscopic examination of Vero cells infected with the UL20- mutant revealed that enveloped and unenveloped capsids accumulated in the cytoplasm, possibly in the space between the inner and outer lamellae of the nuclear membrane, and that virtually no virus was present in the extracellular space. (iii) Glycoproteins B, C, D, E, H, and I recovered from lysates of cells infected with the UL20- mutant could not be differentiated from those present in lysates of cells infected with the wild-type parent virus with respect to the electrophoretic mobility of mature and precursor forms. (iv) Repair of the deleted sequences restored the wild-type phenotype. (v) The gene product of the UL20 gene was shown to be associated with cellular membranes and to possess characteristics of integral membrane proteins. We conclude that the UL20 gene encodes an integral membrane protein with a hitherto unrecognized function in that it enables the transit of virions to the extracellular space. The function of the UL20 gene product is complemented by some cell lines but not by Vero cells. The vesicles which serve to transport virions may have an origin different from those associated with transport of normal cellular proteins.     

Carbon-starvation induction of the ugp operon, encoding the binding protein-dependent sn-glycerol-3-phosphate transport system in Escherichia coli.

Summary The gene products of the ugp operon of Escherichia coli are responsible for the uptake of sn-glycerol-3-phosphate and certain glycerophosphodiesters. The regulation of ugp is mainly phoBR-dependent. Significant expression, however, can be observed even in the presence of high concentrations of phosphate, a condition which normally completely represses pho expression. Pho-independent ugp expression was found to be derepressed during the late logarithmic growth phase due to carbon starvation. Among different carbon sources tested, glucose caused the most complete repression. Addition of cAMP prevented glucose repression, indicating that a cAMP-CRP control mechanism may be directly or indirectly involved in the carbon-starvation response. This conclusion is supported by the fact that pho-independent ugp expression correlated with the presence of the cya and crp gene products.     

Characterization of the protein fraction of the temporary adhesive secreted by the tube feet of the sea star Asterias rubens

Sea stars are able to make firm but temporary attachments to various substrata by secretions released by their tube feet. After tube foot detachment, the adhesive secretions remain on the substratum as a footprint. Proteins presumably play a key role in sea star adhesion, as evidenced by the removal of footprints from surfaces after a treatment with trypsin. However, until now, characterisation was hampered by their high insolubility. In this study, a non-hydrolytic method was used to render most of the proteins constituting the adhesive footprints soluble. After analysis by SDS-PAGE, the proteins separated into about 25 bands, which ranged from 25 to 450 kDa in apparent molecular weight. Using mass spectrometry and a homology-database search, it was shown that several of the proteins are known intracellular proteins, presumably resulting from contamination of footprint material with tube foot epidermal cells. However, 11 protein bands, comprising the most abundant proteins, were not identified and might correspond to novel adhesive proteins. They were named ‘Sea star footprint proteins’ (Sfps). Tandem mass spectrometry analysis of the protein bands yielded 43 de novo-generated peptide sequences. Most of them were shared by several, if not all, Sfps. Polyclonal antibodies were raised against one of the peptides (HEASGEYYR from Sfp-115) and were used in immunoblotting. They specifically labelled Sfp-115 and other bands with lower apparent molecular weights. The different results suggest that all Sfps might belong to a single family of related proteins sharing similar motifs or, alternatively, they are the products of polymerization and/or degradation processes.     

Investigation of the biodegradation of pentachlorophenol by the predominant bacterial strains in a mixed culture

A pentachlorophenol (PCP) degrading mixed culture contained three predominant strains identified as Flavobacterium gleum, Agrobacterium radiobacter and Pseudomonas sp. The relative abilities of the three strains to degrade PCP were tested individually and in combination. Rates of PCP degradation by individual isolates were lower than that observed for the three isolates combined. Of the individual strains, Flavobacterium gleum manifested highest PCP degradation ability. A biodegradation medium inoculated with a combination of the three isolates exhibited PCP degradation patterns similar to the original mixed culture. Varying low amounts of tetrachlorophenol were found in degradation medium inoculated with individual isolates, but this intermediate was absent from media inoculated with the mixed culture.