Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1012483 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25892600_1.fastq.gz | Fastqsanger.gz | |||
| SRR25892600_2.fastq.gz | Fastqsanger.gz | |||
| SRR25892601_1.fastq.gz | Fastqsanger.gz | |||
| SRR25892601_2.fastq.gz | Fastqsanger.gz | |||
| SRR25892602_1.fastq.gz | Fastqsanger.gz |
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Project description:Cassava’s storage roots represent one of the most important sources of nutritional carbohydrates worldwide. Particularly, smallholder farmers in Sub-Saharan Africa depend on this crop plant, where resilient and yield-improved varieties are of vital importance to support steadily increasing populations. Aided by a growing understanding of the plant’s metabolism and physiology, targeted improvement concepts already led to visible gains in recent years. To expand our knowledge and to contribute to these successes, we investigated storage roots of eight cassava genotypes with differential dry matter content from three successive field trials for their proteomic and metabolic profiles. At large, the metabolic focus in storage roots transitioned from cellular growth processes towards carbohydrate and nitrogen storage with increasing dry matter content. This is reflected in higher abundance of proteins related to nucleotide synthesis, protein turnover and vacuolar energization in low starch genotypes, while proteins involved in sugar conversion and glycolysis were more prevalent in high dry matter genotypes. This shift in metabolic orientation was underlined by a clear transition from oxidative- to substrate-level phosphorylation in high dry matter genotypes. Our analyses highlight metabolic patterns that are consistently and quantitatively associated with high dry matter accumulation in cassava storage roots, providing fundamental understandings of cassava’s metabolism as well as a data resource for targeted genetic improvement.
2023-06-21 | PXD038813 | Pride
Project description:Dairy ruminants are often fed high grain diets to meet the energy demand for high milk production. As a result, body metabolism occurs change and milk quality was suppression. As the vital organ that controls metabolism, the liver contributes to the input of substrate precursors to the mammary gland. To further investigate the role of genes in feeding high concentrate diet metabolic characters, a comparison of mRNA expression profiles in liver of feeding high-concentrate diet (60% concentrate of dry matter, HC) and low-concentrate diet (40% concentrate of dry matter, LC) was carried out.When compaired with LC goats, 43 genes were significantly down-regulated and 112 genes were significantly up-regulated (fold change >2 and p value < 0.01) in the liver of HC among the 115 probes. Through Co-expression network analysis to find K-core regulatory factors (genes). These genes were mainly involved in immune and inflammatory responses (n = 8), lipid metabolism (n = 5), protein metabolism (n = 26), carbohydrate metabolism (n = 7). These results were further described in the unpublished paper
2014-08-29 | GSE50448 | GEO
Project description:Cows were selected from two groups of 12 cows enrolled in a large experiment to assess the effects of ad libitum or restricted intake of moderate-energy diets during the entire dry period on pre-partum metabolism and post-partum metabolism and performance. A corn silage-based diet (26% of diet dry matter) providing 1.59 Mcal/kg during the far-off dry period (first 5 wk of an 8-wk dry period) or providing 1.61 Mcal/kg during the close-up dry period (last 3 wk of the dry period) was fed for ad libitum or restricted intake. Four multiparous Holstein cows were randomly selected from the ad libitum and restricted intake groups. Keywords: time course, ad libitum or restricted feeding prepartum
2006-05-23 | GSE3331 | GEO
Project description:Inflammatory Bowel Disease (IBD) is a term describing a collection of conditions characterised by chronic inflammatory disorder of the gastrointestinal tract involving an inappropriate immune response to commensal microorganisms in a genetically susceptible host. Four kiwifruit extracts, aqueous and ethyl acetate extracts of gold kiwifruit (Actinidia chinensis) or green kiwifruit (A. deliciosa), have previously demonstrated anti-inflammatory activity using in vitro models of IBD. This study examined whether these kiwifruit extracts had immune modulating effects in vivo against inflammatory processes known to be increased in patients with IBD. KFEs were used as a dietary intervention in Il10-/- mice (an in vivo model of IBD) and the C57BL/6J background strain in a 3 x 2 factorial design. While all Il10-/- mice developed significant colonic inflammation compared to the C57BL/6J mice, this was not affected by the inclusion of KFE in the diet. Whole genome gene and protein expression level profiling indicated that KFEs influenced immune signalling pathways and metabolic processes within the colonic tissue; however, the effects were subtle. In particular, adaptive immune pathways were reduced by three out of four kiwifruit extracts, with greater reduction seen in the C57BL/6J mice. This suggests that while immune-modulating activity was present in vivo, KFEs did not reduce inflammatory processes relevant to IBD. Experimental design. Two experiments were conducted, one using extracts from gold kiwifruit and one using extracts from green kiwifruit. Within each experiment, both Il10-/- and C57 mice were randomly divided into three diet treatment groups, to ive the following 12 treatments: 1) Gold Kiwifruit Experiment, C57BL/6J mice, Control diet (AIN-76A), 2) Gold Kiwifruit Experiment, C57BL/6J mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 3) Gold Kiwifruit Experiment, C57BL/6J mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) 4) Gold Kiwifruit Experiment, Il10-/- mice, Control diet (AIN-76A), 5) Gold Kiwifruit Experiment, Il10-/- mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 6) Gold Kiwifruit Experiment, Il10-/- mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) 7) Green Kiwifruit Experiment, C57BL/6J mice, Control diet (AIN-76A), 8) Green Kiwifruit Experiment, C57BL/6J mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 9) Green Kiwifruit Experiment, C57BL/6J mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) 10) Green Kiwifruit Experiment, Il10-/- mice, Control diet (AIN-76A), 11) Green Kiwifruit Experiment, Il10-/- mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 12) Green Kiwifruit Experiment, Il10-/- mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) Six biological replicates were analysed from each treatment group, except for groups 3 and 7 where five replicates were analysed due to array quality issues with the sixth replicate. Each replicate contained mRNA from one mouse. A reference design was used, where each slide was hybridised with mRNA from one sample (green channel) and mRNA from a common reference pool (red channel).
2011-03-05 | E-GEOD-27684 | biostudies-arrayexpress
Project description:Dairy ruminants are often fed high grain diets to meet the energy demand for high milk production. As a result, body metabolism occurs change and milk quality was suppression. As the vital organ that controls metabolism, the liver contributes to the input of substrate precursors to the mammary gland. To further investigate the role of genes in feeding high concentrate diet metabolic characters, a comparison of mRNA expression profiles in liver of feeding high-concentrate diet (60% concentrate of dry matter, HC) and low-concentrate diet (40% concentrate of dry matter, LC) was carried out.When compaired with LC goats, 43 genes were significantly down-regulated and 112 genes were significantly up-regulated (fold change >2 and p value < 0.01) in the liver of HC among the 115 probes. Through Co-expression network analysis to find K-core regulatory factors (genes). These genes were mainly involved in immune and inflammatory responses (n = 8), lipid metabolism (n = 5), protein metabolism (n = 26), carbohydrate metabolism (n = 7). These results were further described in the unpublished paper Eight mid-lactating goats (LC, n=3;HC, n=5). Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 M-BM-0C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturerM-bM-^@M-^Ys instructions. samples were named as LC1-3 and HC1-3, representing 3 respective liver RNA samples each from LC and HC goats. Microarray experiment was performed by a service provider
2014-08-29 | E-GEOD-50448 | biostudies-arrayexpress
Project description:A large-scale excavation of soil microbial dark matter
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Project description:Unravelling large-scale patterns and drivers of biodiversity in dry rivers
| PRJEB66196 | ENA
Project description:Pseudomonas syringae pv. actinidiae (Psa) is responsible for causing kiwifruit canker disease, which severely impacts on the global kiwifruit industry, leading to substantial economic losses. Cooler environmental temperatures (below 20℃) are known to favor the outbreak of this bacterial disease in the field. However, the specific mechanisms that enable Psa to adapt and thrive in such conditions have remained elusive. In this study, we discovered that the gene RS16350, encoding a heat shock protein, positively regulates pathogenicity in kiwifruit leaves at low temperature (16℃), but not at room temperature (28℃). Delving into the mechanics, we found that RS16350 directly interacts with HrpL, an RpoN-dependent RNA polymerase sigma factor that serves as a master regulator of the type III secretion system (T3SS) in Psa. This RS16350-HrpL interaction enhances HrpL’s binding affinity to hrp-box, which in turn elevates the expression of downstream T3SS genes, thereby boosting virulence. Consequently, we have designated RS16350 as TspR (temperature sensitive and pathogenic regulator). Our findings shed light on how a kiwi pathogen enhances its virulence in response to low temperatures, paving the way for the development of innovative strategies to combat kiwifruit canker disease.
2025-06-16 | GSE283068 | GEO
Project description:High-Fidelity, Large-Scale Targeted Profiling of Microsatellites
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Project description:High-Fidelity, Large-Scale Targeted Profiling of Microsatellites
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