Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics

BACKGROUND: The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere. RESULTS: Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere. CONCLUSIONS: Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants

Genomic Diversity of Pigeon Pea (Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants

Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of “elite” inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India

Farmers’ market use is associated with fruit and vegetable consumption in diverse southern rural communities

Background While farmers’ markets are a potential strategy to increase access to fruits and vegetables in rural areas, more information is needed regarding use of farmers’ markets among rural residents. Thus, this study’s purpose was to examine (1) socio-demographic characteristics of participants; (2) barriers and facilitators to farmers’ market shopping in southern rural communities; and (3) associations between farmers’ market use with fruit and vegetable consumption and body mass index (BMI). Methods Cross-sectional surveys were conducted with a purposive sample of farmers’ market customers and a representative sample of primary household food shoppers in eastern North Carolina (NC) and the Appalachian region of Kentucky (KY). Customers were interviewed using an intercept survey instrument at farmers’ markets. Representative samples of primary food shoppers were identified via random digit dial (RDD) cellular phone and landline methods in counties that had at least one farmers’ market. All questionnaires assessed socio-demographic characteristics, food shopping patterns, barriers to and facilitators of farmers’ market shopping, fruit and vegetable consumption and self-reported height and weight. The main outcome measures were fruit and vegetable consumption and BMI. Descriptive statistics were used to examine socio-demographic characteristics, food shopping patterns, and barriers and facilitators to farmers’ market shopping. Linear regression analyses were used to examine associations between farmers’ market use with fruit and vegetable consumption and BMI, controlling for age, race, education, and gender. Results Among farmers’ market customers, 44% and 55% (NC and KY customers, respectively) reported shopping at a farmers’ market at least weekly, compared to 16% and 18% of NC and KY RDD respondents. Frequently reported barriers to farmers’ market shopping were market days and hours, “only come when I need something�, extreme weather, and market location. Among the KY farmers’ market customers and NC and KY RDD respondents, fruit and vegetable consumption was positively associated with use of farmers’ markets. There were no associations between use of farmers’ markets and BMI. Conclusions Fruit and vegetable consumption was associated with farmers’ market shopping. Thus, farmers’ markets may be a viable method to increase population-level produce consumption

Mitsui-7, heat-treated, and nitrogen-doped multi-walled carbon nanotubes elicit genotoxicity in human lung epithelial cells

Background: The unique physicochemical properties of multi-walled carbon nanotubes (MWCNT) have led to many industrial applications. Due to their low density and small size, MWCNT are easily aerosolized in the workplace making respiratory exposures likely in workers. The International Agency for Research on Cancer designated the pristine Mitsui-7 MWCNT (MWCNT-7) as a Group 2B carcinogen, but there was insufficient data to classify all other MWCNT. Previously, MWCNT exposed to high temperature (MWCNT-HT) or synthesized with nitrogen (MWCNT-ND) have been found to elicit attenuated toxicity; however, their genotoxic and carcinogenic potential are not known. Our aim was to measure the genotoxicity of MWCNT-7 compared to these two physicochemically-altered MWCNTs in human lung epithelial cells (BEAS-2B & SAEC). Results: Dose-dependent partitioning of individual nanotubes in the cell nuclei was observed for each MWCNT material and was greatest for MWCNT-7. Exposure to each MWCNT led to significantly increased mitotic aberrations with multi- and monopolar spindle morphologies and fragmented centrosomes. Quantitative analysis of the spindle pole demonstrated significantly increased centrosome fragmentation from 0.024–2.4 μg/mL of each MWCNT. Significant aneuploidy was measured in a dose-response from each MWCNT-7, HT, and ND; the highest dose of 24 μg/mL produced 67, 61, and 55%, respectively. Chromosome analysis demonstrated significantly increased centromere fragmentation and translocations from each MWCNT at each dose. Following 24 h of exposure to MWCNT-7, ND and/or HT in BEAS-2B a significant arrest in the G1/S phase in the cell cycle occurred, whereas the MWCNT-ND also induced a G2 arrest. Primary SAEC exposed for 24 h to each MWCNT elicited a significantly greater arrest in the G1 and G2 phases. However, SAEC arrested in the G1/S phase after 72 h of exposure. Lastly, a significant increase in clonal growth was observed one month after exposure to 0.024 μg/mL MWCNT-HT & ND. Conclusions: Although MWCNT-HT & ND cause a lower incidence of genotoxicity, all three MWCNTs cause the same type of mitotic and chromosomal disruptions. Chromosomal fragmentation and translocations have not been observed with other nanomaterials. Because in vitro genotoxicity is correlated with in vivo genotoxic response, these studies in primary human lung cells may predict the genotoxic potency in exposed human populations

NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.

Genetic defects that affect intestinal epithelial barrier function can present with very early-onset inflammatory bowel disease (VEOIBD). Using whole-genome sequencing, a novel hemizygous defect in NOX1 encoding NAPDH oxidase 1 was identified in a patient with ulcerative colitis-like VEOIBD. Exome screening of 1,878 pediatric patients identified further seven male inflammatory bowel disease (IBD) patients with rare NOX1 mutations. Loss-of-function was validated in p.N122H and p.T497A, and to a lesser degree in p.Y470H, p.R287Q, p.I67M, p.Q293R as well as the previously described p.P330S, and the common NOX1 SNP p.D360N (rs34688635) variant. The missense mutation p.N122H abrogated reactive oxygen species (ROS) production in cell lines, ex vivo colonic explants, and patient-derived colonic organoid cultures. Within colonic crypts, NOX1 constitutively generates a high level of ROS in the crypt lumen. Analysis of 9,513 controls and 11,140 IBD patients of non-Jewish European ancestry did not reveal an association between p.D360N and IBD. Our data suggest that loss-of-function variants in NOX1 do not cause a Mendelian disorder of high penetrance but are a context-specific modifier. Our results implicate that variants in NOX1 change brush border ROS within colonic crypts at the interface between the epithelium and luminal microbes

Enhanced invitation methods to increase uptake of NHS health checks: study protocol for a randomized controlled trial

Background: NHS Health Checks is a new program for primary prevention of heart disease, stroke, diabetes, chronic kidney disease, and vascular dementia in adults aged 40 to 74 years in England. Individuals without existing cardiovascular disease or diabetes are invited for a Health Check every 5 years. Uptake among those invited is lower than anticipated. Method: The project is a three-arm randomized controlled trial to test the hypothesis that enhanced invitation methods, using the Question-Behaviour Effect (QBE), will increase uptake of NHS Health Checks compared with a standard invitation. Participants comprise individuals eligible for an NHS Health Check registered in two London boroughs. Participants are randomized into one of three arms. Group A receives the standard NHS Health Check invitation letter, information sheet, and reminder letter at 12 weeks for nonattenders. Group B receives a QBE questionnaire 1 week before receiving the standard invitation, information sheet, and reminder letter where appropriate. Group C is the same as Group B, but participants are offered a £5 retail voucher if they return the questionnaire. Participants are randomized in equal proportions, stratified by general practice. The primary outcome is uptake of NHS Health Checks 6 months after invitation from electronic health records. We will estimate the incremental health service cost per additional completed Health Check for trial groups B and C versus trial arm A, as well as evaluating the impact of the QBE questionnaire, and questionnaire plus voucher, on the socioeconomic inequality in uptake of Health Checks. The trial includes a nested comparison of two methods for implementing allocation, one implemented manually at general practices and the other implemented automatically through the information systems used to generate invitations for the Health Check. Discussion: The research will provide evidence on whether asking individuals to complete a preliminary questionnaire, by using the QBE, is effective in increasing uptake of Health Checks and whether an incentive alters questionnaire return rates as well as uptake of Health Checks. The trial interventions can be readily translated into routine service delivery if they are shown to be cost-effective

Origins Space Telescope: baseline mission concept

The Origins Space Telescope will trace the history of our origins from the time dust and heavy elements permanently altered the cosmic landscape to present-day life. How did galaxies evolve from the earliest galactic systems to those found in the Universe today? How do habitable planets form? How common are life-bearing worlds? To answer these alluring questions, Origins will operate at mid- and far-infrared (IR) wavelengths and offer powerful spectroscopic instruments and sensitivity three orders of magnitude better than that of the Herschel Space Observatory, the largest telescope flown in space to date. We describe the baseline concept for Origins recommended to the 2020 US Decadal Survey in Astronomy and Astrophysics. The baseline design includes a 5.9-m diameter telescope cryocooled to 4.5 K and equipped with three scientific instruments. A mid-infrared instrument (Mid-Infrared Spectrometer and Camera Transit spectrometer) will measure the spectra of transiting exoplanets in the 2.8 to 20  μm wavelength range and offer unprecedented spectrophotometric precision, enabling definitive exoplanet biosignature detections. The far-IR imager polarimeter will be able to survey thousands of square degrees with broadband imaging at 50 and 250  μm. The Origins Survey Spectrometer will cover wavelengths from 25 to 588  μm, making wide-area and deep spectroscopic surveys with spectral resolving power R  ∼  300, and pointed observations at R  ∼  40,000 and 300,000 with selectable instrument modes. Origins was designed to minimize complexity. The architecture is similar to that of the Spitzer Space Telescope and requires very few deployments after launch, while the cryothermal system design leverages James Webb Space Telescope technology and experience. A combination of current-state-of-the-art cryocoolers and next-generation detector technology will enable Origins’ natural background-limited sensitivity

Factors Influencing Brand Loyalty to Craft Breweries in North Carolina

In 2005 North Carolina passed a law allowing breweries to give product samples to employees and guests. The law also changed the definition of a malt beverage and increased the amount of alcohol by volume (ABV) from 6%ABV to 15%ABV allowing brewers to legally make and distribute high gravity craft brews. Since that law has passed 23 more breweries have opened in North Carolina (North Carolina Alcoholic Beverage Control 2010 Annual Report). The purpose of this study is to gain a clearer understanding of what factors influence brand loyalty to microbreweries. The study looks at why visitors to Mother Earth Brewery in Kinston North Carolina and Aviator Brewery in Fuquay-Varina North Carolina chose to visit and purchase from that microbrewery instead of other breweries by examining concepts used in brand loyalty access environmental consumption connection with the community quality and satisfaction desire for unique consumer products and involvement in the industry. Results show that while access connection with the community and satisfaction are important to respondents connection with the community satisfaction and uniqueness are the three factors that most align themselves with brand loyalty. Connection with the community was the most important factor in influencing brand loyalty especially among residents and those born in the study region.

Mining the <em>Sinorhizobium meliloti</em> Transportome to Develop FRET Biosensors for Sugars, Dicarboxylates and Cyclic Polyols

<div><h3>Background</h3><p>Förster resonance energy transfer (FRET) biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens). To expand the number of available FRET biosensors we used the induction profile of the <em>Sinorhizobium meliloti</em> transportome to systematically screen for new FRET biosensors.</p> <h3>Methodology/Principal Findings</h3><p>Two new vectors were developed for cloning genes for solute-binding proteins (SBPs) between those encoding FRET partner fluorescent proteins. In addition to a vector with the widely used cyan and yellow fluorescent protein FRET partners, we developed a vector using orange (mOrange2) and red fluorescent protein (mKate2) FRET partners. From the sixty-nine SBPs tested, seven gave a detectable FRET signal change on binding substrate, resulting in biosensors for D-quinic acid, <em>myo-</em>inositol, L-rhamnose, L-fucose, <b>β</b>-diglucosides (cellobiose and gentiobiose), D-galactose and C4-dicarboxylates (malate, succinate, oxaloacetate and fumarate). To our knowledge, we describe the first two FRET biosensor constructs based on SBPs from Tripartite ATP-independent periplasmic (TRAP) transport systems.</p> <h3>Conclusions/Significance</h3><p>FRET based on orange (mOrange2) and red fluorescent protein (mKate2) partners allows the use of longer wavelength light, enabling deeper penetration of samples at lower energy and increased resolution with reduced back-ground auto-fluorescence. The FRET biosensors described in this paper for four new classes of compounds; (i) cyclic polyols, (ii) L-deoxy sugars, (iii) β-linked disaccharides and (iv) C4-dicarboxylates could be developed to study metabolism <em>in vivo</em>.</p> </div