scholarly journals Transcriptional and post-transcriptional regulation and transcriptional memory of chromatin regulators in response to low temperature

2019 ◽  
Author(s):  
K. Vyse ◽  
L. Faivre ◽  
M. Romich ◽  
M. Pagter ◽  
D. Schubert ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Low Temperature ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Transcriptional Profiling ◽  
Large Fraction ◽  
Histone Variants ◽  
Transcriptional Level ◽  
Large Set ◽  
Dynamic Regulation

AbstractChromatin regulation ensures stable repression of stress-inducible genes under non-stress conditions and transcriptional activation and memory of such an activation of those genes when plants are exposed to stress. However, there is only limited knowledge on how chromatin genes are regulated at the transcriptional and post-transcriptional level upon stress exposure and relief from stress. We have therefore set-up a RT-qPCR-based platform for high-throughput transcriptional profiling of a large set of chromatin genes. We find that the expression of a large fraction of these genes is regulated by cold. In addition, we reveal an induction of several DNA and histone demethylase genes and certain histone variants after plants have been shifted back to ambient temperature (deacclimation), suggesting a role in the memory of cold acclimation. We also re-analyse large scale transcriptomic datasets for transcriptional regulation and alternative splicing (AS) of chromatin genes, uncovering an unexpected level of regulation of these genes, particularly at the splicing level. This includes several vernalization regulating genes whose AS results in cold-regulated protein diversity. Overall, we provide a profiling platform for the analysis of chromatin regulatory genes and integrative analyses of their regulation, suggesting a dynamic regulation of key chromatin genes in response to low temperature stress.

Adsorption Isotherm Predictions for Multiple Molecules in MOFs Using the Same Deep Learning Model

2019 ◽  
Author(s):  
Ryther Anderson ◽  
Achay Biong ◽  
Diego Gómez-Gualdrón
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Molecular Simulation ◽  
Large Scale ◽  
Learning Model ◽  
Operating Conditions ◽  
Small Subset ◽  
Screening Methods ◽  
Large Set ◽  
Metal Organic

<div>Tailoring the structure and chemistry of metal-organic frameworks (MOFs) enables the manipulation of their adsorption properties to suit specific energy and environmental applications. As there are millions of possible MOFs (with tens of thousands already synthesized), molecular simulation, such as grand canonical Monte Carlo (GCMC), has frequently been used to rapidly evaluate the adsorption performance of a large set of MOFs. This allows subsequent experiments to focus only on a small subset of the most promising MOFs. In many instances, however, even molecular simulation becomes prohibitively time consuming, underscoring the need for alternative screening methods, such as machine learning, to precede molecular simulation efforts. In this study, as a proof of concept, we trained a neural network as the first example of a machine learning model capable of predicting full adsorption isotherms of different molecules not included in the training of the model. To achieve this, we trained our neural network only on alchemical species, represented only by their geometry and force field parameters, and used this neural network to predict the loadings of real adsorbates. We focused on predicting room temperature adsorption of small (one- and two-atom) molecules relevant to chemical separations. Namely, argon, krypton, xenon, methane, ethane, and nitrogen. However, we also observed surprisingly promising predictions for more complex molecules, whose properties are outside the range spanned by the alchemical adsorbates. Prediction accuracies suitable for large-scale screening were achieved using simple MOF (e.g. geometric properties and chemical moieties), and adsorbate (e.g. forcefield parameters and geometry) descriptors. Our results illustrate a new philosophy of training that opens the path towards development of machine learning models that can predict the adsorption loading of any new adsorbate at any new operating conditions in any new MOF.</div>

scholarly journals Sustainable Large-Scale Aquaculture of the Northern Hemisphere Sea Lettuce, Ulva fenestrata, in an Off-Shore Seafarm

2021 ◽  
Vol 9 (6) ◽  
pp. 615
Author(s):  
Sophie Steinhagen ◽  
Swantje Enge ◽  
Karin Larsson ◽  
Joakim Olsson ◽  
Göran M. Nylund ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Low Temperature ◽  
Northern Hemisphere ◽  
Biochemical Composition ◽  
Large Scale ◽  
Biomass Yield ◽  
Phenolic Content ◽  
Seedling Density ◽  
Ulva Fenestrata ◽  
High Nutrient

The growing world population demands an increase in sustainable resources for biorefining. The opening of new farm grounds and the cultivation of extractive species, such as marine seaweeds, increases worldwide, aiming to provide renewable biomass for food and non-food applications. The potential for European large-scale open ocean farming of the commercial green seaweed crop Ulva is not yet fully realized. Here we conducted manipulative cultivation experiments in order to investigate the effects of hatchery temperature (10 and 15 °C), nutrient addition (PES and 3xPES) and swarmer density (500 and 10,000 swarmers ml−1) on the biomass yield and biochemical composition (fatty acid, protein, carbohydrate, pigment and phenolic content) of off-shore cultivated Ulva fenestrata in a Swedish seafarm. High seedling densities were optimal for the growth of this northern hemisphere crop strain and significantly increased the mean biomass yield by ~84% compared to low seedling densities. Variations of nutrients or changes in temperature levels during the hatchery phase were not necessary to increase the subsequent growth in an open-water seafarm, however effects of the factors on the thallus habitus (thallus length/width) were observed. We found no significant effect of the environmental factors applied in the hatchery on the total fatty acid or crude protein content in the off-shore cultivated Ulva. However, low seedling density and low temperature increased the total carbohydrate content and furthermore, high temperature in combination with high nutrient levels decreased the pigment content (chlorophyll a, b, carotenoids). Low temperature in combination with high nutrient levels increased the phenolic content. Our study confirms the successful and sustainable potential for large-scale off-shore cultivation of the Scandinavian crop U. fenestrata. We conclude that high seedling density in the hatchery is most important for increasing the total biomass yield of sea-farmed U. fenestrata, and that changing temperature or addition of nutrients overall does not have a large effect on the biochemical composition. To summarize, our study contributes novel insights into the large-scale off-shore cultivation potential of northern hemisphere U. fenestrata and underpins suitable pre-treatments during the hatchery phase of seedlings to facilitate a successful and cost-efficient large-scale rope cultivation.

scholarly journals Elevated Expression of Toxin TisB Protects Persister Cells against Ciprofloxacin but Enhances Susceptibility to Mitomycin C

2021 ◽  
Vol 9 (5) ◽  
pp. 943
Author(s):  
Daniel Edelmann ◽  
Florian H. Leinberger ◽  
Nicole E. Schmid ◽  
Markus Oberpaul ◽  
Till F. Schäberle ◽  
...  
Keyword(s):  
Dna Damage ◽  
Mitomycin C ◽  
Transcriptional Activation ◽  
Structural Features ◽  
Atp Depletion ◽  
Transcriptional Level ◽  
Persister Cells ◽  
Sos Induction ◽  
Bacterial Chromosomes ◽  
Elevated Expression

Bacterial chromosomes harbor toxin-antitoxin (TA) systems, some of which are implicated in the formation of multidrug-tolerant persister cells. In Escherichia coli, toxin TisB from the tisB/istR-1 TA system depolarizes the inner membrane and causes ATP depletion, which presumably favors persister formation. Transcription of tisB is induced upon DNA damage due to activation of the SOS response by LexA degradation. Transcriptional activation of tisB is counteracted on the post-transcriptional level by structural features of tisB mRNA and RNA antitoxin IstR-1. Deletion of the regulatory RNA elements (mutant Δ1-41 ΔistR) uncouples TisB expression from LexA-dependent SOS induction and causes a ‘high persistence’ (hip) phenotype upon treatment with different antibiotics. Here, we demonstrate by the use of fluorescent reporters that TisB overexpression in mutant Δ1-41 ΔistR inhibits cellular processes, including the expression of SOS genes. The failure in SOS gene expression does not affect the hip phenotype upon treatment with the fluoroquinolone ciprofloxacin, likely because ATP depletion avoids strong DNA damage. By contrast, Δ1-41 ΔistR cells are highly susceptible to the DNA cross-linker mitomycin C, likely because the expression of SOS-dependent repair systems is impeded. Hence, the hip phenotype of the mutant is conditional and strongly depends on the DNA-damaging agent.

Low Temperature Large Scale CVD Synthesis of Nano Onion-Like Fullerenes

2012 ◽  
Vol 490-495 ◽  
pp. 3211-3214 ◽  
Author(s):  
Lei Shan Chen ◽  
Cun Jing Wang
Keyword(s):  
Electron Microscopy ◽  
Low Temperature ◽  
Aluminum Hydroxide ◽  
Large Scale ◽  
Iron Catalyst ◽  
Chemical Vapor ◽  
X Ray Diffraction ◽  
Transmission Electron ◽  
Naoh Solution ◽  
Synthesis Reactions

Synthesis reactions were carried out by chemical vapor deposition using iron catalyst supported on aluminum hydroxide at 400 °C and 420 °C, in the presence of argon as carrier gas and acetylene as carbon source. The aluminum hydroxide support was separated by refluxing the samples in 40% NaOH solution for 2 h and 36% HCl solution for 24 h, respectively. The samples were characterized by field-emission scanning electron microscopy, energy dispersive spectroscopy, high-resolution transmission electron microscopy and X-ray diffraction. The results show that carbon nanotubes were the main products at 420 °C, while large scale high purity nano onion-like fullerenes encapsulating Fe3C, with almost uniform sizes ranging from 10-50 nm, were obtained at the low temperature of 400 °C.

Transcriptional regulation of Pseudomonas aeruginosa rhlR, encoding a quorum-sensing regulatory protein

Microbiology ◽  
2003 ◽  
Vol 149 (11) ◽  
pp. 3073-3081 ◽  
Author(s):  
Gerardo Medina ◽  
Katy Juárez ◽  
Rafael Díaz ◽  
Gloria Soberón-Chávez
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Transcriptional Regulation ◽  
Quorum Sensing ◽  
Regulatory Protein ◽  
Culture Conditions ◽  
Transcriptional Level ◽  
Coding Region ◽  
Upstream Gene ◽  
Transcription Start Sites ◽  
Response Systems

The Pseudomonas aeruginosa rhlR gene encodes the transcriptional regulator RhlR which has a central role in the quorum-sensing response. Different gene products involved in bacterial pathogenesis are regulated at the transcriptional level by two quorum-sensing response systems, Las and Rhl. The expression of rhlR has been reported to be under the control of the Las system, but its transcriptional regulation has not been studied in detail. Here, the rhlR promoter region has been characterized and shown to present four different transcription start sites, two of which are included in the upstream gene (rhlB) coding region. It was found that rhlR expression is not only dependent on LasR but also on different regulatory proteins such as Vfr and RhlR itself, and also on the alternative sigma factor σ 54. It is reported that rhlR expression is partially LasR-independent under certain culture conditions and is strongly influenced by environmental factors.

The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs

2018 ◽  
Vol 16 (01) ◽  
pp. 1750029 ◽  
Author(s):  
Vladimir Y. Ovchinnikov ◽  
Denis V. Antonets ◽  
Lyudmila F. Gulyaeva
Keyword(s):  
Transcriptional Activation ◽  
Binding Sites ◽  
In Silico ◽  
Target Genes ◽  
Nuclear Translocation ◽  
Regulation Of Gene Expression ◽  
Experimental Studies ◽  
Transcriptional Level ◽  
Aryl Hydrocarbon ◽  
Exogenous Compounds

MicroRNAs (miRNAs) play important roles in the regulation of gene expression at the post-transcriptional level. Many exogenous compounds or xenobiotics may affect microRNA expression. It is a well-established fact that xenobiotics with planar structure like TCDD, benzo(a)pyrene (BP) can bind aryl hydrocarbon receptor (AhR) followed by its nuclear translocation and transcriptional activation of target genes. Another chemically diverse group of xenobiotics including phenobarbital, DDT, can activate the nuclear receptor CAR and in some cases estrogen receptors ESR1 and ESR2. We hypothesized that such chemicals can affect miRNA expression through the activation of AHR, CAR, and ESRs. To prove this statement, we used in silico methods to find DRE, PBEM, ERE potential binding sites for these receptors, respectively. We have predicted AhR, CAR, and ESRs binding sites in 224 rat, 201 mouse, and 232 human promoters of miRNA-coding genes. In addition, we have identified a number of miRNAs with predicted AhR, CAR, and ESRs binding sites that are known as oncogenes and as tumor suppressors. Our results, obtained in silico, open a new strategy for ongoing experimental studies and will contribute to further investigation of epigenetic mechanisms of carcinogenesis.

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