Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota

Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity—including of low-abundance taxa—with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease

Programming gene expression with combinatorial promoters

Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple −10 and −35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters

Vitamin B12 Deficiency Alters the Gut Microbiota in a Murine Model of Colitis

Purpose: Inflammatory bowel disease (IBD) refers to a spectrum of autoimmune diseases, which result in chronic intestinal inflammation. Previous findings suggest a role for diet, nutrition and dysbiosis of the gut microbiota in both the development and progression of the condition. Vitamin B12 is a key cofactor of methionine synthase and is produced solely by microbes. Previous work links increased levels of homocysteine, a substrate of methionine synthase, MetH, to IBD indicating a potential role for vitamin B12 deficiency in intestinal injury and inflammation. This study assessed the role of vitamin B12 in shaping the gut microbiota and determining responses to intestinal injury using a reproducible murine model of colitis. Methods: The effects of vitamin B12 supplementation and deficiency were assessed in vivo; 3-week-old post-weanling C57Bl/6 mice were divided into three dietary treatment groups: (1) sufficient vitamin B12 (50 mg/Kg), (2) deficient vitamin B12 (0 mg/Kg) and (3) supplemented vitamin B12 (200 mg/Kg) for a period of 4 weeks. Intestinal injury was induced with 2% dextran sodium sulphate (DSS) via drinking water for 5 days. The impact of varying levels of dietary vitamin B12 on gut microbiota composition was assessed using 16S rRNA gene sequencing from fecal samples collected at day 0 and day 28 of the dietary intervention, and 7 days following induction of colitis on day 38, when blood and colonic tissues were also collected. Results: No significant alterations were found in the gut microbiota composition of disease-free animals in response to dietary interventions. By contrast, after DSS-induced colitis, >30 genera were significantly altered in vitamin B12 deficient mice. Altered B12 levels produced no significant effect on composite disease-activity scores; however, administration of a B12 deficient diet resulted in reduced DSS-induced epithelial tissue damage. Conclusions: Vitamin B12 supplementation does not alter the gut microbiota composition under healthy conditions, but does contribute to differential microbial responses and intestinal dysbiosis following the induction of experimental colitis

Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis

Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age-and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients. Both clinical groups displayed 1,200-1,400 bacterial genomes/cm(3) and low bacterial rRNA: rDNA ratios in WM. RNAseq analyses showed a predominance of Proteobacteria in progressive MS patients' WM, associated with increased inflammatory gene expression, relative to a broader range of bacterial phyla in relapsing-remitting MS patients' WM. Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Principal component analysis revealed that demyelination, PGN and inflammatory gene expression accounted for 86% of the observed variance. Thus, inflammatory demyelination is linked to an organ-specific dysbiosis in MS that could contribute to underlying disease mechanisms

Effect of diets enriched in Delta 6 desaturated fatty acids (18:3n-6 and 18:4n-3), on growth, fatty acid composition and highly unsaturated fatty acid synthesis in two populations of Arctic charr (Salvelinus alpinus L.)

This study aimed to test the hypothesis that diets containing relatively high amounts of the Δ6 desaturated fatty acids stearidonic acid (STA, 18:4n-3) and γ-linolenic acid (GLA, 18:3n-6), may be beneficial in salmonid culture. The rationale being that STA and GLA would be better substrates for highly unsaturated fatty acid (HUFA) synthesis as their conversion does not require the activity of the reputed rate-limiting enzyme, fatty acid Δ6 desaturase. Duplicate groups of two Arctic charr (Salvelinus alpinus L.) populations with different feeding habits, that had been reported previously to show differences in HUFA biosynthetic capacity, were fed for 16 weeks on two fish meal based diets containing 47% protein and 21% lipid differing only in the added lipid component, which was either fish oil (FO) or echium oil (EO). Dietary EO had no detrimental effect on growth performance and feed efficiency, mortalities, or liver and flesh lipid contents in either population. The proportions of 18:2n-6, 18:3n-3, 18:3n-6, 18:4n-3, 20:3n-6 and 20:4n-3 in total lipid in both liver and flesh were increased by dietary EO in both populations. However, the percentages of 20:5n-3 and 22:6n-3 were reduced by EO in both liver and flesh in both strains, whereas 20:4n-6 was only significantly reduced in flesh. In fish fed FO, HUFA synthesis from both [1-14C]18:3n-3 and [1-14C]20:5n-3 was significantly higher in the planktonivorous Coulin charr compared to the demersal, piscivorous Rannoch charr morph. However, HUFA synthesis was increased by EO in Rannoch charr, but not in Coulin charr. In conclusion, dietary EO had differential effects in the two populations of charr, with HUFA synthesis only stimulated by EO in the piscivorous Rannoch morph, which showed lower activities in fish fed FO. However, the hypothesis was not proved as, irrespective of the activity of the HUFA synthesis pathway in either population, feeding EO resulted in decreased tissue levels of n-3HUFA and 20:4n-6. This has been observed previously in salmonids fed vegetable oils, and thus the increased levels of Δ6 desaturated fatty acids in EO did not effectively compensate for the lack of dietary HUFA

Identification of a Key Amino Acid of LuxS Involved in AI-2 Production in Campylobacter jejuni

Autoinducer-2 (AI-2) mediated quorum sensing has been associated with the expression of virulence factors in a number of pathogenic organisms and has been demonstrated to play a role in motility and cytolethal distending toxin (cdt) production in Campylobacter jejuni. We have initiated the work to determine the molecular basis of AI-2 synthesis and the biological functions of quorum sensing in C. jejuni. In this work, two naturally occurring variants of C. jejuni 81116 were identified, one producing high-levels of AI-2 while the other is defective in AI-2 synthesis. Sequence analysis revealed a G92D mutation in the luxS gene of the defective variant. Complementation of the AI-2− variant with a plasmid encoded copy of the wild-type luxS gene or reversion of the G92D mutation by site-directed mutagenesis fully restored AI-2 production by the variant. These results indicate that the G92D mutation alone is responsible for the loss of AI-2 activity in C. jejuni. Kinetic analyses showed that the G92D LuxS has a ∼100-fold reduced catalytic activity relative to the wild-type enzyme. Findings from this study identify a previously undescribed amino acid that is essential for AI-2 production by LuxS and provide a unique isogenic pair of naturally occurring variants for us to dissect the functions of AI-2 mediated quorum sensing in Campylobacter

On Early Applications of Psychology in Music Education

Granville Stanley Hall, founder of the American Psychological Association and president of Clark University, was the first American psychologist to speak and write about music's place in the educational curriculum. An examination of his published writings reveals Hall based his theory of music education on principles of Social Darwinism and Child Study perspectives on education. Hall's theories are referenced and paraphrased in several song series textbooks and music appreciation texts published by music educators during his professional career. These sources indicate that Hall influenced the thinking of certain music educators and was important to music education, in general, in developing a receptivity toward psychological processes in music education practice.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Experiments at the margins: Ethics and transgression in cinema science

Science is a discipline defined by empiricism and reliable methodologies that result in predictable outcomes. Yet, cutting-edge experiments inevitably involve an element of the unknown, an aspect which science-fiction exploits for dramatic effect. Furthermore, fictional science is freed from the ethical constraints that regulate real-world experimentation and therefore often trangressive. Even as films capitalise on unethical practices and cutting edge scenarios for dramatic and commercial reasons, the origin of the filmmaker and/or place of production may affect a film’s content. A film is also obviously subject to legal constraints, according to the country of origin, and classification codes in its place of exhibition. Thus, while the very nature of science fiction may cause it to appear morally unbridled, there are nonetheless multiple inhibitions entrenched in such depictions. By drawing on relevant cinematic examples, including Prometheus, The Hunger Games and District 9, and scientific scenarios on which these films are based, this essay explores how the unpredictable nature of advances in science, in combination with a lack of ethics, foregrounds the dangerous dimensions of science-fiction

Activation of tissue plasminogen activator by metastasis-inducing S100P protein

S100P protein in human breast cancer cells is associated with reduced patient survival and, in a model system of metastasis, it confers a metastatic phenotype upon benign mammary tumour cells. S100P protein possesses a C-terminal lysine residue. Using a multiwell in vitro assay, S100P is now shown for the first time to exhibit a strong, C-terminal lysine-dependent activation of tissue plasminogen activator (tPA), but not of urokinase-catalysed plasminogen activation. The presence of 10 μM calcium ions stimulates tPA activation of plasminogen 2-fold in an S100P-dependent manner. S100P physically interacts with both plasminogen and tPA in vitro, but not with urokinase. Cells constitutively expressing S100P exhibit detectable S100P protein on the cell surface, and S100P-containing cells show enhanced activation of plasminogen compared with S100P-negative control cells. S100P shows C-terminal lysine-dependent enhancement of cell invasion. An S100P antibody, when added to the culture medium, reduced the rate of invasion of wild-type S100P-expressing cells, but not of cells expressing mutant S100P proteins lacking the C-terminal lysine, suggesting that S100P functions outside the cell. The protease inhibitors, aprotinin or α-2-antiplasmin, reduced the invasion of S100P-expressing cells, but not of S100P-negative control cells, nor cells expressing S100P protein lacking the C-terminal lysine. It is proposed that activation of tPA via the C-terminal lysine of S100P contributes to the enhancement of cell invasion by S100P and thus potentially to its metastasis-promoting activity