Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

BACKGROUND: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. RESULTS: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. CONCLUSIONS: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-356) contains supplementary material, which is available to authorized users

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis

The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment

Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316T is a Gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

The DBA/2J strain and prepulse inhibition of startle: a model system to test antipsychotics?

Rationale: Prepulse inhibition (PPI) of the startle response in mice is increasingly used as a paradigm of sensory gating with potential predictive and construct validity towards schizophrenia. \ud \ud Objectives: Establishment of a mouse PPI paradigm in which typical and atypical antipsychotic drugs directly improve a low performance PPI. \ud \ud Methods: Three strains of mice – C57Bl/6J, 129S6/SvEvTac and DBA/2J – were tested in a startle paradigm with three prepulse intensities, 2, 4 and 8 dB above background. \ud \ud Results: Under these conditions, risperidone (0, 0.25, 0.5 and 1 mg/kg i.p.) and clozapine (0, 1, 3 and 9 mg/kg i.p.) improved PPI in all three strains, with order of effect in DBA/2J > 129S6SvEvTac > C57Bl/6J. The DBA/2J strain showed larger PPI-enhancing effects, without disturbing the basal startle response. Two α7 nicotinic receptor agonists, GTS-21 (1–10 mg/kg i.p.) and AR-R17779 (1–10 mg/kg i.p.) were inactive in the PPI procedure in DBA/2J mice. \ud \ud Conclusions: DBA/2J mice were very sensitive to the antipsychotic-like effects of atypical (clozapine) and typical (risperidone) antipsychotics, and this strain is proposed as a model to directly measure sensory gating properties of drugs. α7 Nicotinergic receptor agonists were ineffective in this PPI paradigm

Older adults experience of transition to the community from the emergency department: a qualitative evidence synthesis

Abstract Aim Older adults comprise a growing proportion of Emergency Department (ED) attendees and are vulnerable to adverse outcomes following an ED visit including ED reattendance within 30 days. Interventions to reduce older adults’ risk of adverse outcomes following an ED attendance are proliferating and often focus on improving the transition from the ED to the community. To optimise the effectiveness of interventions it is important to determine how older adults experience the transition from the ED to the community. This study aims to systematically review and synthesise qualitative studies reporting older adults’ experiences of transition to the community from the ED. Methods Six databases (Academic Search Complete, CINAHL, MEDLINE, PsycARTICLES, PsycINFO, and Social Science Full Text) were searched in March 2022 and 2023. A seven-step approach to meta-ethnography, as described by Noblit and Hare, was used to synthesise findings across included studies. The methodological quality of the included studies was appraised using the 10-item Critical Appraisal Skills Programme (CASP) checklist for qualitative research. A study protocol was registered on PROSPERO (Registration: CRD42022287990). Findings Ten studies were included, and synthesis led to the development of five themes. Unresolved symptoms reported by older adults on discharge impact their ability to manage at home (theme 1). Limited community services and unresolved symptoms drive early ED reattendance for some older adults (theme 2). Although older adults value practical support and assistance transporting home from the ED this is infrequently provided (theme 3). Accessible health information and interactions are important for understanding and self-managing health conditions on discharge from the ED (theme 4). Fragmented Care between ED and community is common, stressful and impacts on older adult’s ability to manage health conditions (theme 5). A line of argument synthesis integrated these themes into one overarching concept; after an ED visit older adults often struggle to manage changed, complex, health and care needs at home, in the absence of comprehensive support and guidance. Discussion/ conclusion Key areas for consideration in future service and intervention development are identified in this study; ED healthcare providers should adapt their communication to the needs of older adults, provide accessible information and explicitly address expectations about symptom resolution during discharge planning. Concurrently, community health services need to be responsive to older adults’ changed health and care needs after an ED visit to achieve care integration. Those developing transitional care interventions should consider older adults needs for integration of care, symptom management, clear communication and information from providers and desire to return to daily life

Anaerobically Grown <i>Escherichia coli</i> Has an Enhanced Mutation Rate and Distinct Mutational Spectra

<div><p>Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in <i>Escherichia coli</i> populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements. The anaerobically grown populations displayed a mutation rate nearly twice that of the aerobic populations, showed distinct asymmetric mutational strand biases, and greater insertion element activity. Consistent with mutation rate and spectra observations, genes for transposition and recombination repair associated with SVs were up-regulated during anaerobic growth. Together, these results define differences in mutational spectra affecting the evolution of facultative anaerobes.</p></div