NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the “concatesome,” as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.     

Purification, characterization and immunological properties of the serotype-specific capsular polysaccharide of Pasteurella haemolytica serotype A7 organisms

The serotype-specific capsular polysaccharide from two strains of Pasteurella haemolytica serotype A7 organisms was purified and characterized by chemical analysis and by 1H and 13C NMR spectroscopy using one- and two-dimensional methods. The polymer has the repeating unit----3)-beta-2-acetamido-2-deoxygalactopyranose-(1----3)-alpha- 2-acetamido- 2-deoxy-6-O-acetyl-glucopyranose-(1-phosphate----. It was immunogenic (capable of eliciting antibodies) for sheep. Chemical removal of O-acetyl groups destroyed both the ability of the polymer to adhere to sheep erythrocytes at neutral pH and the ability to form immune precipitates with specific antisera. Studies using the protein A-gold technique in the electron microscope showed the polysaccharide to be peripherally localized on the bacterial surface.     

Characterization of envelope proteins from Pasteurella haemolytica and Pasteurella multocida

A method was devised for the reproducible isolation of envelopes from Pasteurella haemolytica serotype A2. It was also possible to prepare envelopes from other serotypes of P. haemolytica and Pasteurella multocida using this methodology. Examination of these preparations by SDS-PAGE showed major differences between strains of P. haemolytica and strains of P. multocida which allowed the clear distinction of isolates of these species. Amongst the P. haemolytica serotypes it was possible to distinguish envelope preparations made from A biotype and T biotype organisms easily, but it was not possible to identify individual serotypes from each other. Envelope profiles were sufficiently different between the individual P. multocida serotypes examined to allow each to be identified by its polypeptide profile. Experiments using radiolabelling, antibody absorption, and susceptibility to protease digestion, together with heat modifiability and detergent solubility characteristics indicated that 13 of the envelope proteins were probably surface-located. A high molecular mass immunogenic envelope protein was shown, by immunoblotting, to be present in all strains of P. haemolytica and P. multocida examined.     

Effect of neurotensin on pancreatic function in man

The effect of neurotensin on submaximally-stimulated hepatobiliary and pancreatic secretion was studied in 6 healthy subjects. An intravenous infusion of neurotensin 1.4 ± 0.3 pmol/kg/min, designed to reproduce plasma neurotensin immunoreactivity levels within the physiological range, produced a significant increase in pancreatic bicarbonate output. Plasma concentrations of pancreatic polypeptide rose by 83 ± 16 pmol/l and were associated with a small reduction in trypsin, but no significant change in bilirubin outputs.     

β-Diketones in Rhododendron waxes

Chromatographic, mass spectrometric and spectroscopic evidence has been obtained for four β-diketones occurring in the leaf waxes of some members of     

Do positive interactions between marine invaders increase likelihood of invasion into natural and artificial habitats?

Positive species interactions such as facilitation are important for enabling species to persist, especially in stressful conditions, and the nature and strength of facilitation varies along physical and biological gradients. Expansion of coastal infrastructure is creating hotspots of invasive species which can spillover into natural habitats, but the role of positive species interactions associated with biological invasions remains understudied. Theory suggests that stronger biotic pressure in natural habitats inhibits invasion success. In space-limited marine systems, sessile organisms can overcome this limiting resource by settling as an epibiont on a substrate organism – basibiont. Using a series of spatially extensive surveys, we explored the role of invasive and native basibionts in providing habitat for other invasive and native epibionts, and tested whether environmental context (i.e. if the receiving habitat was natural or artificial), altered ecological outcomes. Overall, provision of space by basibionts was more important for invasive epibionts than for native epibionts but was dependent on the environmental context. Invasive basibionts facilitated invasive epibionts in natural habitats, and appeared to be more important for native epibionts in artificial habitats respectively. Native basibionts facilitated invasive, but not native epibionts in both natural and artificial habitats. These results advance our understanding of facilitation and highlight the idiosyncratic nature of biofouling and epibiosis, and the potentially important influence of environmental context. The degree to which native habitat-forming species versus invasive habitat-forming species either do or do not facilitate other native or non-native species is a rich area for investigation. Experimental work is required to disentangle the processes underpinning these patterns.