Photosynthetic microorganisms ribosomal amplicons from rain water
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ABSTRACT:
PROVIDER: PRJEB35600 | ENA |
REPOSITORIES: ENA
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Project description:Acid rain, as a worldwide environmental issue, can cause serious damage to plants. In this study, we provided the first case study on the systematic responses of arabidopsis (Arabidopsis thaliana (L.) Heynh.) to simulated acid rain (SiAR) by transcriptome approach. In this dataset, we include the expression data obtained from Arabidopsis with simulated acid rain treatments for 68 hr, and contrasting with control group in the same time. Totally, 439 differetal expression genes were obtained in our stduy. Form them, 13 genes which dramatically changed their expression were found related to S metabolism.
2013-11-20 | GSE52487 | GEO
Project description:Acid rain, as a worldwide environmental issue, can cause serious damage to plants. In this study, we provided the first case study on the systematic responses of arabidopsis (Arabidopsis thaliana (L.) Heynh.) to simulated acid rain (SiAR) by transcriptome approach. In this dataset, we include the expression data obtained from Arabidopsis with simulated acid rain treatments for 68 hr, and contrasting with control group in the same time. Totally, 439 differetal expression genes were obtained in our stduy. Form them, 13 genes which dramatically changed their expression were found related to S metabolism. 6 Total samples were analyzed. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). Preparation of labeled target cRNA was carried out following the technical manual of Arabidopsis Genome GeneChip array (Affymetrix). Double-stranded cDNA was synthesized from 5 M-NM-<g of template total RNA using the One-Cycle cDNA Synthesis kit (Affymetrix), and biotin labeled cRNA was synthesized using the IVT Labeling kit (Affymetrix). The labeled cRNA was purified with GeneChip Sample Cleanup Module (Affymetrix). The quality and quantity of the cRNA was checked by conducting gel electrophoresis. Twenty micrograms of the purified cRNA of each sample was fragmented and hybridized to arrays for 16 h at 45M-BM-0C. All arrays were washed and stained automatically by using a fluidics Station 450 (Affymetrix) and scanned by GeneChipM-BM-. scanner 3000 (Affymetrix). All procedures were performed according to the manufacturerM-bM-^@M-^Ys protocols (Affymetrix). Normalization and expression estimate computation were calculated from the .CEL output files from the Affymetrix GCOS 1.1 software using RMA implemented in R language using standard settings. Statistical testing for differential expression was performed with logic-t analysis. Functional categories were assigned to genes using the AGI number to search the MIPS database (http://mips.gsf.de/cgi-bin/proj/thal/) and the Arabidopsis Information Resource website, TAIR (http://www.arabidopsis.org/).
2013-11-20 | E-GEOD-52487 | biostudies-arrayexpress
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2024-09-13 | E-MTAB-13776 | biostudies-arrayexpress
Project description:The aim of this experiment was to identify the RUNX2- and RAIN-dependent transcriptional program in thyroid cancer. TPC1 and MDA-T41 cell line were infected with dCas9-KRAB and sgRNA targeting the gene of interest (RAIN or RUNX2 respectively) or a non-targeting (NT) sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by total RNA-seq.
2024-09-12 | E-MTAB-13777 | biostudies-arrayexpress
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Project description:Bacterial diversity in clouds versus precipitation at puy de Dome, France
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2019-01-25 | PXD006472 | Pride
Project description:Megapolis such as Mexico City, have atmospheric pollutants that interact with the humidity and solar radiation. The topography of this city promotes air stagnation, generating atmospheric pollutants and episodes of acid rain, a phenomenon well recorded since the end of the 1980s. However, little we know about how urban trees respond to acid rain in the city. Here we present how simulated acid rain causes anatomical and changes in photosynthetic pigments in two of the most abundant urban trees in Mexico City: Liquidambar styraciflua L. and Fraxinus uhdei (Wenz.) Lingelsh. We first described the leaf anatomy of both species. Then, we used one-year-old trees sprayed with sulfuric acid solutions at pH 2.5 and 3.8, and evaluated visible leaf damage, anatomical alterations, and chlorophyll contents. In both species, the pH 2.5 caused cuticle alterations and areas of total tissue destruction. L. styraciflua showed greater sensitivity, but we discuss some of the tolerance mechanisms. Finally, acid rain also reduced the chlorophyll contents. These results contribute toward a catalogue of urban tree species to describe pollution-induced damages, and the identification of tolerant species useful for short- and mid-term detection of environmental crisis, in cities with similar environmental conditions and urban tree composition.
| S-EPMC7411892 | biostudies-literature
Project description:Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.
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Project description:Persistently cold environments constitute one of our world's largest ecosystems, and microorganisms dominate the biomass and metabolic activity in these extreme environments. The stress of low temperatures on life is exacerbated in organisms that rely on photoautrophic production of organic carbon and energy sources. Phototrophic organisms must coordinate temperature-independent reactions of light absorption and photochemistry with temperature-dependent processes of electron transport and utilization of energy sources through growth and metabolism. Despite this conundrum, phototrophic microorganisms thrive in all cold ecosystems described and (together with chemoautrophs) provide the base of autotrophic production in low-temperature food webs. Psychrophilic (organisms with a requirement for low growth temperatures) and psychrotolerant (organisms tolerant of low growth temperatures) photoautotrophs rely on low-temperature acclimative and adaptive strategies that have been described for other low-temperature-adapted heterotrophic organisms, such as cold-active proteins and maintenance of membrane fluidity. In addition, photoautrophic organisms possess other strategies to balance the absorption of light and the transduction of light energy to stored chemical energy products (NADPH and ATP) with downstream consumption of photosynthetically derived energy products at low temperatures. Lastly, differential adaptive and acclimative mechanisms exist in phototrophic microorganisms residing in low-temperature environments that are exposed to constant low-light environments versus high-light- and high-UV-exposed phototrophic assemblages.
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