Soil substrates display higher impact on maize rhizosphere microbiome and soil enzyme activities than depth and plant genotypes
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PROVIDER: PRJEB49274 | ENA |
REPOSITORIES: ENA
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Project description:Lysosomes are acidic cytoplasmic organelles that are present in all nucleated mammalian cells and are involved in a variety of cellular processes including repair of the plasma membrane, defense against pathogens, cholesterol homeostasis, bone remodeling, metabolism, apoptosis and cell signaling. Defects in lysosomal enzyme activity have been associated with a variety of neurological diseases including Parkinson's Disease, Lysosomal Storage Diseases, Alzheimer's disease and Huntington's disease. Fluorogenic lysosomal staining probes were synthesized for labeling lysosomes and other acidic organelles in a live-cell format and were shown to be capable of monitoring lysosomal metabolic activity. The new targeted substrates were prepared from fluorescent dyes having a low pKa value for optimum fluorescence at the lower physiological pH found in lysosomes. They were modified to contain targeting groups to direct their accumulation in lysosomes as well as enzyme-cleavable functions for monitoring specific enzyme activities using a live-cell staining format. Application to the staining of cells derived from blood and skin samples of patients with Metachromatic Leukodystrophy, Krabbe and Gaucher Diseases as well as healthy human fibroblast and leukocyte control cells exhibited localization to the lysosome when compared with known lysosomal stain LysoTracker® Red DND-99 as well as with anti-LAMP1 Antibody staining. When cell metabolism was inhibited with chloroquine, staining with an esterase substrate was reduced, demonstrating that the substrates can be used to measure cell metabolism. When applied to diseased cells, the intensity of staining was reflective of lysosomal enzyme levels found in diseased cells. Substrates specific to the enzyme deficiencies in Gaucher or Krabbe disease patient cell lines exhibited reduced staining compared to that in non-diseased cells. The new lysosome-targeted fluorogenic substrates should be useful for research, diagnostics and monitoring the effect of secondary therapeutic agents on lysosomal enzyme activity in drug development for the lysosomal storage disorders and allied diseases.
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Project description:The analysis of capped RNAs by massively parallel sequencing has identified a large number of previously unknown transcripts, some of which are small RNAs and others are 5’ truncated forms of RefSeq genes. The latter may be generated by endonuclease cleavage or by stalling of Xrn1 at defined sites. With the exception of promoter-proximal transcripts the caps on all of these are added post-transcriptionally by a cytoplasmic capping enzyme complex that includes capping enzyme and a kinase that converts 5’-monophosphate ends to a diphosphate capping substrate. We previously described a modified form of capping enzyme with dominant negative activity against cytoplasmic capping (DN-cCE). A tet-inducible form of this was used to identify substrates for cytoplasmic capping by treating cytoplasmic RNA from control and induced cells with and without Xrn1. Surviving RNA was analyzed on Affymetrix Human Exon 1.0 arrays and scored for changes in probe intensity as a function of its position on each RefSeq gene to derive a factor (alpha) that could be compared between sets. Notably, transcriptome-wide changes were not evident unless RNA was treated with Xrn1. This analysis identified 2,666 uncapped mRNAs in uninduced cells, 672 mRNAs that appeared in the uncapped pool in cells expressing DN-cCE, and 835 mRNAs that were in both populations. Changes in cap status of 10 re-capping targets and 5 controls were assessed by 3 independent measures; susceptibility to Xrn1, recovery with a biotin-tagged DNA primer after ligating a complementary RNA oligonucleotide to uncapped 5’ ends, and binding or exclusion from a high affinity cap-binding matrix comprised of immobilized eIF4E and the corresponding binding domain of eIF4G.
2012-12-20 | GSE36729 | GEO
Project description:The analysis of capped RNAs by massively parallel sequencing has identified a large number of previously unknown transcripts, some of which are small RNAs and others are 5M-bM-^@M-^Y truncated forms of RefSeq genes. The latter may be generated by endonuclease cleavage or by stalling of Xrn1 at defined sites. With the exception of promoter-proximal transcripts the caps on all of these are added post-transcriptionally by a cytoplasmic capping enzyme complex that includes capping enzyme and a kinase that converts 5M-bM-^@M-^Y-monophosphate ends to a diphosphate capping substrate. We previously described a modified form of capping enzyme with dominant negative activity against cytoplasmic capping (DN-cCE). A tet-inducible form of this was used to identify substrates for cytoplasmic capping by treating cytoplasmic RNA from control and induced cells with and without Xrn1. Surviving RNA was analyzed on Affymetrix Human Exon 1.0 arrays and scored for changes in probe intensity as a function of its position on each RefSeq gene to derive a factor (alpha) that could be compared between sets. Notably, transcriptome-wide changes were not evident unless RNA was treated with Xrn1. This analysis identified 2,666 uncapped mRNAs in uninduced cells, 672 mRNAs that appeared in the uncapped pool in cells expressing DN-cCE, and 835 mRNAs that were in both populations. Changes in cap status of 10 re-capping targets and 5 controls were assessed by 3 independent measures; susceptibility to Xrn1, recovery with a biotin-tagged DNA primer after ligating a complementary RNA oligonucleotide to uncapped 5M-bM-^@M-^Y ends, and binding or exclusion from a high affinity cap-binding matrix comprised of immobilized eIF4E and the corresponding binding domain of eIF4G. 3 biological replicates of 4 different samples comparing XRN1 treatment/non-treatment and Dox induction/non-induction of K294A
2012-12-20 | E-GEOD-36729 | biostudies-arrayexpress
Project description:Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality. We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance.
2010-12-01 | GSE22479 | GEO
Project description:Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality. We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance.
2010-09-20 | GSE21070 | GEO
Project description:This dataset accompanies the meta-analysis entitled "Intercropping increases soil extracellular enzyme activity: A meta-analysis" Curtright and Tiemann (2021). Sustainable agriculture practices often aim to increase plant diversity. One means of doing this is through intercropping, where two or more plants are grown in the same field at the same time. Aboveground plant diversity may result in changes to the functioning of belowground microbial communities. Soil enzyme activities are frequently used as indicators of soil health and descriptors of soil nutrient cycling. While some studies have described the effect of intercropping on soil enzyme activities, results vary widely. To assess the overall effect that intercropping has on soil enzyme activities and describe the largest sources of variation, we performed a global meta-analysis of all studies found in the literature reporting enzyme activities in an intercropping system. Data were collected using exhaustive keyword searches on studies published through January 2021. We provide here a dataset of 969 observations across 100 studies. In addition to average enzyme activities in intercropping, metadata on environmental, edaphic, and agronomic properties were also collected.
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Project description:The goal of the present work was to evaluate the additive effects of biochar and chicken manure on maize growth in Pb-contaminated soils. In this study, we conducted a pot experiment to investigate how biochar in soil (20, 40 g·kg-1), chicken manure in soil (20, 40 g·kg-1), or a combination of biochar and chicken manure in soil (each at 20 g·kg-1) effect maize growth, Pb uptake, leaves' antioxidant enzymatic activities, and soil enzyme activities under artificial conditions to simulate moderate soil pollution (800 Pb mg·kg-1). The results showed that all biochar and/or chicken manure treatments significantly (P < 0.05) increased maize plant height, biomass, and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activity but decreased the malondialdehyde (MDA) content. These results indicated that amending the soil with biochar and/or chicken manure could alleviate Pb's phytotoxicity. The biochar and/or chicken manure treatments remarkably decreased the Pb concentration in maize roots, stems, leaves, bioconcentration factor (BCF), translocation factor (TF), and available Pb concentration in the soil. Amending the soil with chicken manure alone was more effective at increasing maize growth and antioxidant enzymatic activity; the biochar treatment alone was more effective at inducing soil alkalinization and contributing to Pb immobilization. The combined use of biochar and chicken manure had an additive effect and produced the largest increases in maize growth, leaves' antioxidant enzymatic activity, and soil enzyme activity. Their combined use also led to the most significant decreases in maize tissues Pb and soil available Pb. These results suggest that a combination of biochar and chicken manure was more effective at reducing soil Pb bioavailability and uptake by maize tissues, and increasing maize growth. This combination increased plant height by 43.23% and dry weight by 69.63% compared to the control.
| S-EPMC8280880 | biostudies-literature
Project description:Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality. We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance. Leaves from Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) maize genotypes were harvested after growing on acid or control soil for 3 days. Total RNA was extracted and hybridized to Affymetrix GeneChip Maize Genome Array. Three biological replicates were used for each sample.
2010-12-01 | E-GEOD-22479 | biostudies-arrayexpress
Project description:Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality. We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance. Root tips from Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) maize genotypes were harvested after growing on acid or control soil for 1 or 3 days. Total RNA was extracted and hybridized to Affymetrix GeneChip Maize Genome Array. Three biological replicates were used for each sample.
2010-09-20 | E-GEOD-21070 | biostudies-arrayexpress
Project description:Filamentous fungi produce a great variety of enzymes, and research on their biotechnological potential has recently intensified. The objective of this work was to identify, at the species level, using DNA barcoding, 46 fungal isolates obtained from maize grains with rot symptoms. We also analyzed the production of extracellular amylases, cellulases, proteases and lipases of 33 of those fungal isolates. The enzymatic activities were evaluated by the formation of a clear halo or a white precipitate around the colonies in defined substrate media. The found fungi belong to the genera Talaromyces, Stenocarpella, Penicillium, Phlebiopsis, Cladosporium, Hyphopichia, Epicoccum, Trichoderma, Aspergillus, Irpex, Fusarium, Microdochium, Mucor and Sarocladium. In the genus Fusarium, the species Fusarium verticillioides was predominant and this genus presented the highest diversity, followed by the genera Aspergillus. The best genera for lipase production were Cladosporium and Penicillium; while Cladosporium, Aspergillus and Penicillium were best for cellulase activity; Hyphopichia, Aspergillus and Irpex for amylase activity; and Cladosporium and Sarocladium for proteases activity. In conclusion, a collection of fungi from maize seeds presenting rotten symptoms were obtained, among which exist important producers of hydrolases.
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