Potential use of rhizobium for vegetable crops growth promotion

The system of vegetable crops production required large amounts of mineral fertilizers. One of the possible alternatives to assure the economic and environmental sustainability of this production system would be the use of promoting growth plant rhizobacteria (PGPR). However, care is needed to select a microorganism to be used in crops that are usually consumed raw, so human health is not at risk. It was important to search for PGPR, as rhizobium, that already were broadly used as inoculants for leguminous plants for several decades, without risks to human health. PGPR can promote growth and development of plants through direct and indirect mechanisms, by production and secretion of chemical substances in the rhizosphere. The direct mechanisms were involved with the uptake of nutrients by the plants (nitrogen, phosphorus and essential minerals) through phosphate solubilization, production of siderophores and growth regulators. The indirect mechanisms were involved with the decrease of inhibitory effects from various pathogenic agents related with biological pest control, thereby favoring plant growth. Nevertheless, due to its ability to promote beneficial effects to plants, effective bacterial colonization was extremely important. Some bacteria that colonized the rhizoplane may penetrate the plant roots and some strains may move to the aerial part, with decreased bacterial density, compared with colonizing populations in the rhizosphere or roots. It can be concluded that Rhizobia promotes plant growth using different mechanisms as biological nitrogen fixation and production of different plant growth regulators (e.g. auxins). Therefore, new studies with Rhizobia characterization and observation about its different mechanisms of promoting plant growth should be performed. Such information would be useful for the identification of plants with potential to increase agricultural production due to the benefits of using plant growth promoter’s rhizobia

Inoculação e coinoculação de rizobactérias promotoras de crescimento em plantas de arroz irrigado

Aiming at obtaining high productivity and reduction of production costs, new techniques have been studied in rice crops, such as the use of plant growth promoting rhizobacteria (PGPR). The objective of this study was to evaluate the efficiency of inoculation and co-inoculation of rhizobia and Azospirillum brasilense in promoting the growth of irrigated rice plants cultivated in the field. Two experiments were conducted in the field, in the 2014/15 and 2015/16 crops, at the Rio Grande do Sul Rice Experiment Station. The experiment was composed of seven treatments, with two control treatments, without inoculation (81 kg ha-1 N and 135 kg ha-1 N, equivalent to 60% and 100%, respectively, of the recommended nitrogen dose). The other five treatments received only 60% of the N dose and were inoculated with the UFRGS Vp16 (Burkholderia sp.) and UFRGS Lc348 (Mesorhizobium sp.) Rhizobia, and with the commercial product containing the A. brasilense AbV5 and AbV6 strains. Inoculation and co-inoculation with PGPR may represent a viable alternative to reduce the amount of nitrogen fertilizers in rice crops.Visando a obtenção de altas produtividades e redução dos custos de produção, novas técnicas vêm sendo estudadas nas lavouras de arroz, como a utilização de rizobactérias promotoras de crescimento de plantas (RPCPs). O objetivo do trabalho foi avaliar a eficiência da inoculação e coinoculação de rizóbios e Azospirillum brasilense na promoção de crescimento de plantas de arroz irrigado cultivadas a campo. Foram conduzidos dois experimentos a campo, nas safras 2014/15 e 2015/16, na Estação Experimental do Instituto Rio Grandense do Arroz. O experimento foi composto por sete tratamentos, sendo dois tratamentos controle, sem inoculação (81 kg ha-1 de N e 135 kg ha-1 N, equivalente a 60% e 100%, respectivamente, da dose de nitrogênio recomendada). Os outros cinco tratamentos receberam apenas 60% da dose de N e foram inoculados com os rizóbios UFRGS Vp16 (Burkholderia sp.) e UFRGS Lc348 (Mesorhizobium sp.), e com o produto comercial contendo as estirpes de A. brasilense AbV5 e AbV6. A inoculação e coinoculação com RPCPs podem representar uma alternativa viável para reduzir a quantidade de adubos nitrogenados nas lavouras de arroz

Does dietary calcium interact with dietary fiber against colorectal cancer? : a case-control study in Central Europe

BACKGROUND: An unfavorable trend of increasing rates of colorectal cancer has been observed across modern societies. In general, dietary factors are understood to be responsible for up to 70% of the disease’s incidence, though there are still many inconsistencies regarding the impact of specific dietary items. Among the dietary minerals, calcium intake may play a crucial role in the prevention. The purpose of this study was to assess the effect of intake of higher levels of dietary calcium on the risk of developing of colorectal cancer, and to evaluate dose dependent effect and to investigate possible effect modification. METHODS: A hospital based case–control study of 1556 patients (703 histologically confirmed colon and rectal incident cases and 853 hospital-based controls) was performed between 2000–2012 in Krakow, Poland. The 148-item semi-quantitative Food Frequency Questionnaire to assess dietary habits and level of nutrients intake was used. Data regarding possible covariates was also collected. RESULTS: After adjustment for age, gender, education, consumption of fruits, raw and cooked vegetables, fish, and alcohol, as well as for intake of fiber, vitamin C, dietary iron, lifetime recreational physical activity, BMI, smoking status, and taking mineral supplements, an increase in the consumption of calcium was associated with the decrease of colon cancer risk (OR = 0.93, 95% CI: 0.89-0.98 for every 100 mg Ca/day increase). Subjects consumed >1000 mg/day showed 46% decrease of colon cancer risk (OR = 0.54, 95% CI: 0.35-0.83). The effect of dietary calcium was modified by dietary fiber (p for interaction =0.015). Finally, consistent decrease of colon cancer risk was observed across increasing levels of dietary calcium and fiber intake. These relationships were not proved for rectal cancer. CONCLUSIONS: The study confirmed the effect of high doses of dietary calcium against the risk of colon cancer development. This relationship was observed across different levels of dietary fiber, and the beneficial effect of dietary calcium depended on the level of dietary fiber suggesting modification effect of calcium and fiber. Further efforts are needed to confirm this association, and also across higher levels of dietary fiber intake

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills

Sediment geochemistry of streams draining abandoned lead / zinc mines in central Wales: the Afon Twymyn

Purpose Despite the decline of metal mining in the UK during the early 20th century, a substantial legacy of heavy metal contamination persists in river channel and floodplain sediments. Poor sediment quality is likely to impede the achievement of ’good’ chemical and ecological status for surface waters under the European Union Water Framework Directive. This paper examines the environmental legacy of the Dylife lead/zinc mine in the central Wales mining district. Leachable heavy metal concentrations in the bed sediments of the Afon Twymyn are established and the geochemical partitioning, potential mobility and bioavailability of sediment-associated heavy metals are established. Materials and methods Sediment samples were collected from the river bed and dry-sieved into two size fractions (<63 μm and 64–2,000 μm). The fractionated samples were then subjected to a sequential extraction procedure to isolate heavy metals (Pb, Zn, Cu, Cd, Fe, Mn) in three different geochemical phases. Sediment samples were then analysed for heavy metals using ICP-AES. Results and discussion The bed sediment of the Afon Twymyn is grossly polluted with heavy metals. Within the vicinity of the former mine, Pb concentrations are up to 100 times greater than levels reported to have deleterious impacts on aquatic ecology. Most heavy metals exist in the most mobile easily exchangeable and carbonate-bound geochemical phases, potentially posing serious threats to ecological integrity and constituting a significant, secondary, diffuse source of pollution. Metal concentrations decrease sharply downstream of the former mine, although there is a gradual increase in the proportion of readily extractable Zn and Cd. Conclusions Implementation of sediment quality guidelines is important in order to achieve the aims of the Water Framework Directive. Assessments of sediment quality should include measurements of background metal concentrations, river water physico-chemistry and, most importantly, metal mobility and potential bioavailability. Uniformity of sediment guidelines throughout Europe and flexibility of targets with regard to the most heavily contaminated mine sites are recommended

The Gene Ontology resource: enriching a GOld mine

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations

Gene Ontology Consortium: going forward

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology