In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

peer-reviewedBackground The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated. Results We identified 74 clusters of note from 59 unique members of the Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Synergistetes. The most commonly identified class of bacteriocin was the >10 kDa class, formerly known as bacteriolysins, followed by lantibiotics and sactipeptides. Conclusions Multiple bacteriocin gene clusters were identified in a dataset representative of the human gut microbiota. Interestingly, many of these were associated with species and genera which are not typically associated with bacteriocin production.CJW, CMG and PDC are supported by a SFI PI award to PDC “Obesibiotics” (11/PI/1137)

Cell fate patterning during C. elegans vulval development

Precursor cells of the vulva of the C. elegans hermaphrodite choose between two vulval cell fates (1° and 2°) and a non-vulval epidermal fate (3°) in response to three intercellular signals. An inductive signal produced by the anchor cell induces the vulval precursors to assume the 1° and 2° vulval fates. This inductive signal is an EGF-like growth factor encoded by the gene lin-3. An inhibitory signal mediated by lin-15, and which may originate from the surrounding epidermis, prevents the vulval precursors from assuming vulval fates in the absence of the inductive signal. A short range lateral signal, which acts through the gene lin-12, regulates the pattern of 1° and 2° fates assumed by the induced vulval precursors. The combined action of the three signals precisely directs the six vulval precursors to adopt a 3° 3° 2° 1° 2 ° 3° pattern of fates. The amount of inductive signal produced by the anchor cell appears to determine the number or vulval precursors that assume vulval fates. The three induced vulval precursors most proximal to the anchor cell are proposed to adopt the 2° 1° 2° pattern of fates in response to a gradient of the inductive signal and also in response to lateral signalling that inhibits adjacent vulval precursor cells from both assuming the 1° fate

Responding to the Needs of Geographically Dispersed Military Youth

When the U.S. military reshaped its deployment methods in response to conflicts in Iraq and Afghanistan, the number of deployed Reserve and National Guard soldiers increased to nearly half of all deployed servicemen. Unfortunately, support to reduce the stresses of deployment is not readily available to these families because they live in geographically dispersed civilian communities. In 2011, Utah 4-H responded as the key partner and ideal organization to align resources and work with community partners to provide a variety of summer camps designed to support military families during the Post-Deployment stage of the Deployment Cycle

Ground Water Monitoring Project for Arkansas, Phase III

This report is composed of two parts. The first part is an interpretation of the pesticide and nitrate data collected in Woodruff County based on samples collected during 1994. Because there is an indication that there were hydrological differences between 1994 and 1995, and because most of the pesticide data is from 1994, this interpretive portion is restricted to 1994 data. Six wells initially sampled in 1994 that contained pesticides had continuing contamination in re-sampling in 1994 and 1995. Part II lists a seventh well in Woodruff County that contained pesticides in February and May of 199

Next-generation probiotics: the spectrum from probiotics to live biotherapeutics

The leading probiotics currently available to consumers are generally drawn from a narrow range of organisms. Knowledge of the gut microbiota and its constituent actors is changing this paradigm, particularly given the phylogenetic range and relatively unknown characteristics of the organisms under investigation as novel therapeutics. For this reason, and because their development is likely to be more amenable to a pharmaceutical than a food delivery route, these organisms are often operationally referred to as next-generation probiotics, a concept that overlaps with the emerging concept of live biotherapeutic products. The latter is a class of organisms developed exclusively for pharmaceutical application. In this Perspective, we discuss what lessons have been learned from working with traditional probiotics, explore the kinds of organisms that are likely to be used as novel microbial therapeutics, discuss the regulatory framework required, and propose how scientists may meet this challenge

Identification and predictability of soil quality indicators from conventional soil and vegetation classifications

The physical, chemical and biological attributes of a soil combined with abiotic factors (e.g. climate and topography) drive pedogenesis and some of these attributes have been used as proxies to soil quality. Thus, we investigated: (1) whether appropriate soil quality indicators (SQIs) could be identified in soils of Great Britain, (2) whether conventional soil classification or aggregate vegetation classes (AVCs) could predict SQIs and (3) to what extent do soil types and/ or AVCs act as major regulators of SQIs. Factor analysis was used to group 20 soil attributes into six SQI which were named as; soil organic matter (SOM), dissolved organic matter (DOM), soluble N, reduced N, microbial biomass, DOM humification (DOMH). SOM was identified as the most important SQI in the discrimination of both soil types and AVCs. Soil attributes constituting highly to the SOM factor were, microbial quotient and bulk density. The SOM indicator discriminated three soil type groupings and four aggregate vegetation class groupings. Among the soil types, only the peat soils were discriminated from other groups while among the AVCs only the heath and bog classes were isolated from others. However, the peat soil and heath and bog AVC were the only groups that were distinctly discriminated from other groups. All other groups heavily overlapped with one another, making it practically impossible to define reference values for each soil type or AVC. The two-way ANOVA showed that the AVCs were a better regulator of the SQIs than the soil types. We conclude that conventionally classified soil types cannot predict the SQIs defined from large areas with differing climatic and edaphic factors. Localised areas with similar climatic and topoedaphic factors may hold promise for the definition of SQI that may predict the soil types or AVCs

4-H and the Maker Movement

The Maker Movement is thriving, and 4-H programs have the opportunity to get involved and keep 4-H relevant. Making is gaining traction as a strategy to engage young people in building their science abilities. Collectively joining the Maker Movement would accelerate 4-H\u27s national STEM goals and initiatives while enhancing the abilities of youth as they make innovative breakthroughs