Manary legume intervention
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB24771 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2278930.fastq.gz | Fastqsanger.gz | |||
| ERR2278940.fastq.gz | Fastqsanger.gz | |||
| ERR2278950.fastq.gz | Fastqsanger.gz | |||
| ERR2278960.fastq.gz | Fastqsanger.gz | |||
| ERR2278970.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 3903 |
Similar Datasets
Project description:This study, sponsored by the National Cancer Institute and Penn State University, will examine how a diet high in legumes (dried beans) influences risk factors for colon cancer and polyps. Many scientists believe that colon and rectal cancers develop from polyps (tumors of the lining of the large bowel). This study will test whether a high-legume diet can reduce levels of certain factors (blood insulin, blood glucose, and markers of inflammation such as C-reactive protein) that at elevated levels are known to increase the risk of colorectal polyps and colon cancer.
Healthy men between 35 and 75 years of age may be eligible for this study, conducted at Penn State University in University Park, Pennsylvania. Candidates are screened with blood tests and measurements of height, weight, and blood pressure. All candidates must have had a colonoscopy within 2 years of entering the study. They may or may not have had adenomas and may or may not be insulin-resistant. Candidates must not have cancer, heart disease, kidney disease, diabetes, or other serious medical condition, and they must have no history of colorectal cancer, polyp removal, bowel surgery, polyposis syndrome, or inflammatory bowel disease. Participants undergo the following tests and procedures:
* Caloric requirement testing: The subject’s resting metabolic rate is measured while fasting and in the early morning at rest to determine daily calorie requirement before beginning the study diet. A special clear plastic hood is placed over the subject’s head while his breathing is measured. He can communicate with the technician at all times during the 30-minute test.
* Study diet: Subjects follow two required 4-week diets with a 3-week break in between, followed by an optional third 4-week diet. Subjects eat a healthy American diet for both of the required 4-week diet periods; about 1-1/2 cups of cooked legumes, such as pinto, baked, and navy beans are added to one of the two required diets. For the third (optional) diet period, subjects are given the same 1-1/2 cups of legumes, but are allowed to lose weight. Participants are given packages with all of the food they are to consume during the three diet periods. They may add up to five caffeine-containing beverages per day and up to two alcoholic drinks per week. They must eat all of the food they are given and only the food they are given. Subjects are expected to maintain a constant body weight during the two 4-week required diets, and their caloric intake may be increased or decreased as needed to maintain their screening weight.
* Weight measurements: Subjects are weighed regularly at the clinic.
* Blood samples: Subjects have blood samples drawn at the mid-point of each of the two required 4-week diets and at the beginning and end of each of the three 4-week diets.
* Urine and stool samples: Urine and stool samples are collected at the beginning and end of the two required 4-week diets.
| 2029934 | ecrin-mdr-crc
Project description:Photoperiod regulated flowering is a well understood developmental pathway in the intensively studied Brassicaceae species Arabidopsis thaliana and in the monocot rice, but less so in other angiosperm groups. One such group, the temperate legumes in the Fabaceae family which are important both agriculturally and ecologically, accelerate their flowering in response to long-day photoperiods (LD), but lack functional homologues of key regulatory genes present in A. thaliana such as CO. Curiously previous work in the reference legume Medicago truncatula has shown that floral activator MtFTa1, which is upregulated by LD and vernalisation, does not exhibit a peak in expression at dusk like its homologue in A. thaliana FLOWERING LOCUS T, instead MtFTa1 maintains a near constant pattern of expression. In addition legumes possess for other FT-like genes such as the MtFTb genes expressed in LD which may also act in the regulation of flowering time. This study utilises RNA-Seq to identify genes which may regulate or be co-expressed with these FT-like genes in Medicago truncatula. Following a shift from short-day photoperiods to inductive long-days genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). Specifically this study focuses on the first few hours of the day in the young leaves which coincides with the first diurnal peak of the FTb genes. It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering. In the process this study identifies a number of potential candidate genes for future studies to consider.
2018-08-23 | GSE118893 | GEO
Project description:Certain alpha- and beta-proteobacteria, the rhizobia, are able to infect legume roots, elicit root nodules, and live therein as endosymbiotic, nitrogen-fixing bacteroids. Host recognition and specificity are the results of consecutive programming events in bacteria and host plants in which important signaling molecules, e.g. plant flavonoids and rhizobial lipooligosaccharides, play key roles. Here, we introduce a new aspect of this symbiosis: the adaptive response to hosts. In contrast to host specificity, which determines early steps in bacteria-plant interaction, the adaptation to hosts refers to late events in mature bacteroids where specific genes are transcribed and translated that help the endosymbionts to meet the disparate environmental requirements imposed by the hosts in which they live. This concept was elaborated with Bradyrhizobium japonicum and three different legumes (soybean, cowpea, siratro). We systematically analyzed and compared the transcriptomes as well as the proteomes in bacteroids from root nodules of the three hosts. Transcripts and proteins were thus identified which are induced in only one of the three hosts. We then focused on those determinants that were congruent in the two data sets of host-specific transcripts and proteins, and arrived at 20 for soybean, 7 for siratro, and 4 for cowpea. One conspicuous gene cluster for a predicted ABC-type transporter, differentially expressed in siratro, was deleted. The corresponding mutant had a symbiotic defect on siratro rather than on soybean or cowpea. This result demonstrates the value of the applied approach and corroborates the host-specific adaptation concept. B. japonicum transcriptome was determined for the three different host plants
2010-05-06 | E-GEOD-18884 | biostudies-arrayexpress
Project description:Certain alpha- and beta-proteobacteria, the rhizobia, are able to infect legume roots, elicit root nodules, and live therein as endosymbiotic, nitrogen-fixing bacteroids. Host recognition and specificity are the results of consecutive programming events in bacteria and host plants in which important signaling molecules, e.g. plant flavonoids and rhizobial lipooligosaccharides, play key roles. Here, we introduce a new aspect of this symbiosis: the adaptive response to hosts. In contrast to host specificity, which determines early steps in bacteria-plant interaction, the adaptation to hosts refers to late events in mature bacteroids where specific genes are transcribed and translated that help the endosymbionts to meet the disparate environmental requirements imposed by the hosts in which they live. This concept was elaborated with Bradyrhizobium japonicum and three different legumes (soybean, cowpea, siratro). We systematically analyzed and compared the transcriptomes as well as the proteomes in bacteroids from root nodules of the three hosts. Transcripts and proteins were thus identified which are induced in only one of the three hosts. We then focused on those determinants that were congruent in the two data sets of host-specific transcripts and proteins, and arrived at 20 for soybean, 7 for siratro, and 4 for cowpea. One conspicuous gene cluster for a predicted ABC-type transporter, differentially expressed in siratro, was deleted. The corresponding mutant had a symbiotic defect on siratro rather than on soybean or cowpea. This result demonstrates the value of the applied approach and corroborates the host-specific adaptation concept.
2010-03-07 | GSE18884 | GEO
Project description:Legumes establish nitrogen-fixing symbiosis with beneficial rhizobia. On the other hand, they might be attacked concomitantly by pathogens raising the question of potential trade-off between mutualism and immunity. Here, using a tripartite system involving the model legume Lotus japonicus, its rhizobial symbiont Mesorhizobium loti and the soil-borne pathogen Ralstonia solanacearum we investigated such trade-offs. We found that interaction with M. loti increases plant resistance against the pathogen without impairing mutualism. Genetic and proteomics characterisation indicate that Lotus resistance is mediated by Effector Triggered Immunity and is associated with distinct proteome modifications in roots and nodules. The inoculation of rhizobia, even if they are not mutualist, increases plant resistance. Our results question the concept of interference between efficient defense reactions and mutualistic interactions and is of great interest for agricultural purposes as it not only restricts pathogen colonisation but would also preserve nitrogen fixation and yield.
2024-01-30 | PXD048803 | Pride
Project description:Abiotic stresses disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. In particular, the effect of extracellular acidity on rhizobia has been taken as a model example for analysis because of the economic impact and worldwide distribution of these symbionts in agricultural countries. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0â??6.1. Under such a limiting acid stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a remarkably higher aerobic-respiration rate in acid-stressed rhizobia. Changes in the transcripts encoding enzymes for lipid biosynthesis were also observed, consistent with previous data on rhizobial pH-dependent membrane remodelling. Together with increased energy demands under acidity, proteomic and transcriptomic data revealed that while at pH 7.0 the transport and biosynthesis of cellular compounds were quite active processes, under acid stress most overexpressed markers were associated with protein biosynthesis, macromolecular degradation and/or recycling, and energy metabolism. Within this context, the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Moreover, multivariate analysis of global metabolome data (more than 60 compounds) served to unequivocally correlate the specific-metabolite profiles with the extracellular pH for growth, with strikingly sensitive variations being observed in the rhizobial metabolomes upon extracellular-pH changes of less than 0.5 units. Except for a ca. 120-kb DNA stretch within the pSymA no specific genomic regions were associated with the observed acid-stress responses. Further practical analyses should be focussed on the phenotypic impact and time course of the observed changes during the acid-stress perception and on the search for common responses during the previously described sublethal acid-adaptive processes in rhizobia pH 6.1 vs pH 7
2015-10-29 | E-GEOD-74449 | biostudies-arrayexpress
Project description:<p>Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.</p>
2024-03-19 | MTBLS6537 | MetaboLights
Project description:There is a growing interest in assessing dietary intake more accurately across different population groups, and biomarkers have emerged as a complementary tool to replace traditional dietary assessment methods. The purpose of this study was to conduct a systematic review of the literature available and evaluate the applicability and validity of biomarkers of legume intake reported across various observational and intervention studies. A systematic search in PubMed, Scopus, and ISI Web of Knowledge identified 44 studies which met the inclusion criteria for the review. Results from observational studies focused on soy or soy-based foods and demonstrated positive correlations between soy intake and urinary, plasma or serum isoflavonoid levels in different population groups. Similarly, intervention studies demonstrated increased genistein and daidzein levels in urine and plasma following soy intake. Both genistein and daidzein exhibited dose-response relationships. Other isoflavonoid levels such as O-desmethylangolensin (O-DMA) and equol were also reported to increase following soy consumption. Using a developed scoring system, genistein and daidzein can be considered as promising candidate markers for soy consumption. Furthermore, genistein and daidzein also served as good estimates of soy intake as evidenced from long-term exposure studies marking their status as validated biomarkers. On the contrary, only few studies indicated proposed biomarkers for pulses intake, with pipecolic acid and S-methylcysteine reported as markers reflecting dry bean consumption, unsaturated aliphatic, hydroxyl-dicarboxylic acid related to green beans intake and trigonelline reported as marker of peas consumption. However, data regarding criteria such as specificity, dose-response and time-response relationship, reliability, and feasibility to evaluate the validity of these markers is lacking. In conclusion, despite many studies suggesting proposed biomarkers for soy, there is a lack of information on markers of other different subtypes of legumes. Further discovery and validation studies are needed in order to identify reliable biomarkers of legume intake.
| S-EPMC6131749 | biostudies-other
Project description:Abiotic stresses disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. In particular, the effect of extracellular acidity on rhizobia has been taken as a model example for analysis because of the economic impact and worldwide distribution of these symbionts in agricultural countries. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0–6.1. Under such a limiting acid stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a remarkably higher aerobic-respiration rate in acid-stressed rhizobia. Changes in the transcripts encoding enzymes for lipid biosynthesis were also observed, consistent with previous data on rhizobial pH-dependent membrane remodelling. Together with increased energy demands under acidity, proteomic and transcriptomic data revealed that while at pH 7.0 the transport and biosynthesis of cellular compounds were quite active processes, under acid stress most overexpressed markers were associated with protein biosynthesis, macromolecular degradation and/or recycling, and energy metabolism. Within this context, the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Moreover, multivariate analysis of global metabolome data (more than 60 compounds) served to unequivocally correlate the specific-metabolite profiles with the extracellular pH for growth, with strikingly sensitive variations being observed in the rhizobial metabolomes upon extracellular-pH changes of less than 0.5 units. Except for a ca. 120-kb DNA stretch within the pSymA no specific genomic regions were associated with the observed acid-stress responses. Further practical analyses should be focussed on the phenotypic impact and time course of the observed changes during the acid-stress perception and on the search for common responses during the previously described sublethal acid-adaptive processes in rhizobia
2015-10-29 | GSE74449 | GEO
Project description:Legumes establish symbiosis with soil rhizobia forming root nodules that fix atmospheric nitrogen. The central role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in nodule biology has been clearly established. Recently, hydrogen sulfide (H2S) and other reactive sulfur species (RSS) have emerged as novel signaling molecules in animals and plants. A major mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification of proteins. To identify possible functions of H2S in nodule development and senescence, we used the tag-switch method to analyze quantitative changes in the persulfidation profile of common bean (Phaseolus vulgaris) nodules at different developmental stages. The proteomic analysis suggests that persulfidation plays a major regulatory role in plant and bacteroid metabolism and senescence. In addition, the effect of a H2S donor on several proteins involved in ROS and RNS homeostasis was investigated. The results obtained using nodule extracts and recombinant proteins suggest a crosstalk between H2S, ROS, and RNS, and a protective function of persulfidation on redox-sensitive enzymes from oxidative modifications that may cause enzyme inactivation. It is concluded that the general decrease of persulfidation levels observed in plant proteins of aging nodules is one of the mechanisms that cause the disruption of redox homeostasis leading to senescence.
2024-06-16 | PXD039852 | Pride