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12,683 results for “tolerability”
Simulations For: Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa
<p>Coordinate, simulation input and simulation output files for atomistic molecular dynamics simulations in Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa. </p><p> </p>
Drought tolerant grassland species are generally more resistant to competition
<ol> <li>Plant populations are limited by resource availability and exhibit physiological trade-offs in resource acquisition strategies. These trade-offs may constrain the ability of populations to exhibit fast growth rates under water limitation and high cover of neighbors. However, traits that confer drought tolerance may also confer resistance to competition. It remains unclear how fitness responses to these abiotic conditions and biotic interactions combine to structure grassland communities and how this relationship may change along a gradient of water availability.</li> <li>To address these knowledge gaps, we estimated the low-density growth rates of populations in drought conditions with low neighbor cover and in ambient conditions with average neighbor cover for 82 species in six grassland communities across the Central Plains and Southwestern United States. We assessed the relationship between population tolerance to drought and resistance to competition and determined if this relationship was consistent across a precipitation gradient. We also tested whether population growth rates could be predicted using plant functional traits.</li> <li>Across six sites, we observed a positive correlation between low-density population growth rates in drought and in the presence of interspecific neighbors. This positive relationship was particularly strong in grasslands of the northern Great Plains but weak in the most xeric grasslands. High leaf dry matter content and low (more negative) leaf turgor loss point were associated with high population growth rates in drought and with neighbors in most grassland communities.</li> <li> <em>Synthesis</em>: A better understanding of how both biotic and abiotic factors impact population fitness provides valuable insights into how grasslands will respond to extreme drought. Our results advance plant strategy theory by suggesting that drought tolerance increases population resistance to interspecific competition in grassland communities. However, this relationship is not evident in the driest grasslands where aboveground competition is likely less important. Leaf dry matter content and turgor loss point may help predict which populations will establish and persist based on local water availability and neighbor cover, and these predictions can be used to guide the conservation and restoration of biodiversity in grasslands.</li> </ol>
Convergent evolution of desiccation tolerance in grasses
<p>Desiccation tolerance has evolved repeatedly in plants as an adaptation to survive extreme environments. Plants use similar biophysical and cellular mechanisms to survive life without water, but convergence at the molecular, gene, and regulatory levels remains to be tested. Here, we explore the evolutionary mechanisms underlying the recurrent evolution of desiccation tolerance across grasses. We present genomes of three resurrection grasses native Sub-Saharan Africa. We leveraged comparative genomic and transcriptomic approaches to identify patterns of convergence and divergence across these species. <strong></strong>We observed substantial overlap in gene duplication and expression associated with desiccation, and syntenic genes of shared origin are activated across species, indicative of parallel evolution. In other cases, similar metabolic pathways are induced, but using different gene sets, pointing towards phenotypic convergence. Species-specific mechanisms supplement these shared core mechanisms, underlining the complexity and diversity of evolutionary adaptations. Our findings provide insight into the evolutionary processes driving desiccation tolerance and highlight the roles of parallel mutation and complementary pathway adaptation in response to environmental challenges.</p>
Data - Krieg et al. Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum)
<p>Data used in analyses and code to produce figures.</p>
Divergence in cold tolerance promotes niche differentiation between diploid and polyploid kiwifruits along an altitudinal gradient in Southwest China
<p>Polyploidization is hypothesized to improve the freezing resistance of plants in cold regions. However, adaptive strategies and key physiological mechanisms involved in the freezing resistant ability of polyploids remain unclear. In <em>Actinidia chinensis</em> (kiwifruits), the tetraploids and hexaploids occupy higher altitude habitats with colder climates than the diploids, providing a study system to investigate mechanisms responsible for differentiation in freezing resistance between cytotypes. We characterized environmental conditions of their natural distribution areas, and measured leaf-level traits of cold damages and water relations at typical sites of each cytotype along an altitudinal gradient. Polyploids showed lower semi-lethal temperature (LT<sub>50</sub>) than ice nucleation temperature (INT), reflecting a tolerance strategy to cope with freezing events in the plateau regions. More negative turgor loss points and larger cell elastic modulus of polyploids could help to alleviate damages from freezing-induced cell dehydration, thus strengthening their tolerance to lower subzero temperatures (lower LT<sub>50</sub>). The increased supercooling capacity of polyploids (lower INT) might correlate with less extracellular ice formation due to lower osmotic potential at full turgor, apoplastic water fraction and tissue capacitance. Our study uncovers a greater cold tolerance in polyploid kiwifruits than diploids, and suggests the potential linkage between freezing tolerance and water relations. Taken together, such a divergence in stress resistance may underlie the niche shift of polyploid plants towards harsh environments.</p>
Defect tolerance of lead-halide perovskite (100) surface relative to bulk: band bending, surface states, and characteristics of vacancies (dataset)
<p>This repository contains an input data set as well as the output data that were used in a study of surface and bulk defects in cubic CsPbI<sub>3</sub>. using a Vienna ab initio simulation package (VASP) and PyDEF 2 package for processing of defect calculations. More details about organization of the dataset can be found within REDME.txt files</p>
Data from: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria
<p>Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an <em>in vitro</em> experimental evolution approach to investigate if the phytopathogenic <em>Ralstonia solanacearum </em>bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by <em>Pseudomonas</em> bacteria. We further asked if tolerance was specific to pairs of <em>R. solanacearum</em> and <em>Pseudomonas</em> strain and certain antimicrobial compounds produced by <em>Pseudomonas</em>. We found that while all <em>R. solanacearum</em> strains could initially be inhibited by <em>Pseudomonas</em> strains, this inhibition decreased following successive subculturing with or without <em>Pseudomonas</em> supernatants. Using separate tolerance assays, we show that the majority of <em>R. solanacearum </em>strains evolved increased tolerance to multiple <em>Pseudomonas</em> strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by <em>Pseudomonas</em> strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.</p>
Addressing the Challenge of Wildlife Conservation in Urban Landscapes by Increasing Human Tolerance for Wildlife
<p>Data that supports the journal manuscript: Puri, M., Johannsen, K.L., Goode, K.O., & Pienaar, E.F. (2024) Addressing the challenge of wildlife conservation in urban landscapes by increasing human tolerance for wildlife. <em>People and Nature.</em></p>
Flying, nectar-loaded honey bees conserve water and improve heat tolerance by reducing wingbeat frequency and metabolic heat production
<p><span>Heat waves are becoming increasingly common due to climate change, making it crucial to identify and understand the capacities for insect pollinators, such as honey bees, to avoid overheating. We examined the effects of hot, dry air temperatures on the physiological and behavioral mechanisms that honey bees use to fly when carrying nectar loads, to assess how foraging is limited by overheating or desiccation. We found that flight muscle temperatures increased linearly with load mass at air temperatures of 20</span><span> or 30°C, but, remarkably, there was no change with increasing nectar loads at an air temperature of 40°C. Flying, nectar-loaded bees were able to avoid overheating at 40°C by reducing their flight metabolic rates and increasing evaporative cooling. At high body temperatures, bees apparently increase flight efficiency by lowering their wingbeat frequency and increasing stroke amplitude to compensate, reducing the need for evaporative cooling. However, even with reductions in metabolic heat production, desiccation likely limits foraging at temperatures well below bees' critical thermal maxima in hot, dry conditions.</span></p>
Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters
<p>Freshwater salinisation is an important threat to biodiversity, ecosystem functioning, and the provision of ecosystem services. Therefore, understanding the capacity of species to adapt to salinity gradients is crucial. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinisation. We studied local genetic adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes - a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. The population-level salinity tolerance range was reduced in more saline bomb crater ponds through an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show genetic adaptation to salinity gradients at different spatial scales and fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.</p>
Recent tree diversity increase in NE Iberian forests following intense management release: a task for animal-dispersed and drought tolerant species
<ol> <li>Under increasing human-related threats to forests, many studies suggest that increasing tree species diversity may boost forest resilience by enhancing the range of species' responses to disturbances. However, it remains unclear whether passive or active forest management strategies should be applied to increase tree diversity. This issue would benefit from investigating which management and environmental factors, together with species' functional traits influence temporal changes in tree species diversity.</li> <li>We explored the influence of the bioclimatic region, land-use history, forest cover, protection, management, forest structure and changes in temperature and precipitation, to explain tree species diversity changes in NE Iberian forests, by comparing 3141 plots from the Spanish National Forest Inventory sampled between 1989 and 2016. Moreover, we assessed which species' functional traits (dispersal habit, drought and shade tolerance) were most relevant for diversity changes.</li> <li>After 27 years, tree species richness and diversity moderately increased in the tree and regeneration layers. This trend occurred mostly in long-established, non-recently managed forests and in those with a lower initial basal area. Increasing temperature had negative effects for diversity increase in the tree layer but positive for the regeneration compartment, while decreasing precipitation showed the opposite effects.</li> <li>Tree species with higher drought tolerance, and especially those animal-dispersed ones arriving from the regional pool, mostly contributed to the local diversity increase. This pattern occurred in all forest types, although the taxonomic array of species varied.</li> <li> <em>Synthesis and applications.</em> The main drivers influencing the passive increase in tree species diversity suggest a primary role of diminishing forest exploitation in this recovery process, fine-tuned by climatic changes. This ecological scenario has particularly favored animal-dispersed tree species with higher drought tolerance, which mostly led the diversity increase. A higher presence of such highly mobile and drought-tolerant species can be crucial to increase functional diversity and, ultimately, increase forest resilience under future scenarios of greater aridity. In light of these results, management strategies should continue fostering the restoration of diversity in once intensively exploited forests while ensuring the maintenance of the already gained tree species diversity.</li> </ol>
Data for: Evolution of avian heat tolerance: The role of atmospheric humidity
<p>The role of atmospheric humidity in the evolution of endotherms' thermoregulatory performance remains largely unexplored, despite elevated atmospheric humidity being known to impede evaporative cooling capacity. Using a phylogenetically informed comparative framework, we tested the hypothesis that pronounced hyperthermia tolerance among birds occupying humid lowlands evolved to reduce the impact of humidity-impeded scope for evaporative heat dissipation by comparing heat tolerance limits (HTL; maximum tolerable air temperature), maximum body temperatures (<em>T</em><sub>b</sub><em>max</em>) and associated thermoregulatory variables in humid (19.2 g H<sub>2</sub>O m<sup>− 3</sup>) <em>versus</em> dry (1.1 g H<sub>2</sub>O m<sup>− 3</sup>) air among 30 species from three climatically distinct sites (arid, mesic montane and humid lowland). Humidity-associated decreases in evaporative water loss and resting metabolic rate were 27 - 38% and 21 - 27%, respectively, and did not differ significantly between climatic sites. Decreases in heat tolerance limits were significantly larger among arid-zone (mean ± SD = 3.13 ± 1.12 °C) and montane species (2.44 ± 1.0 °C) compared to lowland species (1.23 ± 1.34 °C), with more pronounced hyperthermia among lowland (<em>T</em><sub>b</sub><em>max</em> = 46.26 ± 0.48°C) and montane birds (<em>T</em><sub>b</sub><em>max</em> = 46.19 ± 0.92°C) compared to arid-zone species (45.23 ± 0.24°C). Our findings reveal a functional link between facultative hyperthermia and humidity-related constraints on evaporative cooling, providing novel insights into how hygric and thermal environments interact to constrain avian performance during hot weather. Moreover, the macrophysiological patterns we report provide further support for the concept of a continuum from thermal specialization to thermal generalization among endotherms, with adaptive variation in body temperature correlated with prevailing climatic conditions.</p>
Beyond a single temperature threshold: applying a cumulative thermal stress framework to plant heat tolerance
<p>Most plant thermal tolerance studies focus on single critical thresholds, which limit the capacity to generalise across studies and predict heat stress under natural conditions. In animals and microbes, thermal tolerance landscapes describe the more realistic, cumulative effects of temperature. We tested this in plants by measuring the decline in leaf photosynthetic efficiency (F<sub>V</sub>/F<sub>M</sub>) following a combination of temperatures and exposure times, then modelled these physiological indices alongside recorded environmental temperatures. We demonstrate that a general relationship between stressful temperatures and exposure durations can be effectively employed to quantify and compare heat tolerance within and across plant species and over time. Importantly, we show how F<sub>V</sub>/F<sub>M</sub> curves translate to plants under natural conditions, suggesting that environmental temperatures often impair photosynthetic function. Our findings provide more robust descriptors of heat tolerance in plants and suggest that heat tolerance in disparate groups of organisms can be studied with a single predictive framework.</p>
Safety and tolerability of a low glycemic load dietary intervention in adults with cystic fibrosis: A pilot study
<p><strong>Context</strong>: To achieve and maintain adequate weight, people with cystic fibrosis (CF) may often consume energy-dense, nutrient-poor foods high in added sugars and refined carbohydrates; however, little is known about the glycemic and metabolic effects of dietary composition in this patient population.</p> <p><strong>Objective</strong>: To investigate the safety and tolerability of a low glycemic load (LGL) diet in adults with CF and abnormal glucose tolerance (AGT).</p> <p><strong>Design</strong>: Prospective, open-label pilot study.</p> <p><strong>Intervention</strong>: Each participant followed his/her typical diet for eight weeks, then transitioned to an LGL diet via meal delivery service for eight weeks.</p> <p><strong>Participants</strong>: Ten adults with CF and AGT completed the trial. Mean age was 27.0±2.1 years, 64% were female, and all had pancreatic insufficiency.</p> <p><strong>Outcome Measures</strong>: The primary outcome was a change in weight from baseline to study completion, with safety established if no significant decline was noted. Other key safety outcomes included change in hypoglycemia measured by patient reports and continuous glucose monitoring (CGM). Exploratory outcomes included changes in other CGM measures, body composition by dual-energy X-ray absorptiometry (DXA), and patient-reported outcomes.</p> <p><strong>Results</strong>:<strong> </strong>There were no significant changes in weight or in subjectively-reported or objectively-measured hypoglycemia. Favorable non-significant trends were noted in CGM measures of hyperglycemia and glycemic variability, DXA measures of fat mass, and gastrointestinal symptom surveys. </p> <p><strong>Conclusions</strong>:<strong> </strong>An LGL dietary intervention was safe and well tolerated in adults with CF and AGT. These results lay the groundwork for future trials investigating the impact of low-glycemic dietary interventions on metabolic outcomes in the CF population.</p>
Reducing the runtime of fault-tolerant quantum simulations in chemistry through symmetry-compressed double factorization
<p>Data repository for "Reducing the runtime of fault-tolerant quantum simulations in chemistry through symmetry-compressed double factorization" <a href="https://arxiv.org/abs/2403.03502" target="_blank" rel="noopener">arXiv:2403.03502</a>.</p>
Data from: Contrasting heat tolerance of evergreen and deciduous urban woody species during heat waves
<p>The increasing frequency and intensity of heat waves caused significant damages to urban woody species, and the different leaf structures between evergreen and deciduous species may be closely related to leaf heat tolerance. However, whether the different leaf structural traits of evergreen and deciduous plants contribute to their different responses under heat waves is still unclear.</p> <p>During the record-breaking and long-lasting 2022 summer heat waves in China, we investigated the relationships between leaf thermal indices and leaf structural traits of 36 urban woody species in four cities along the Yangtze River.</p> <p>We found that all the four thermal indices were significantly but weakly related with leaf damage status. The critical temperature that causes the initial 15% damage to photosystem II (Tcrit) may serve as a sensitive measure of heat tolerance. Evergreen species suffered less leaf damage during the heat waves and exhibited higher leaf heat tolerance, thicker leaves than deciduous species. Tcrit was significantly correlated with leaf mass per area, leaf thickness and thickness of spongy tissue.</p> <p><em>Synthesis</em>:<em> </em>Urban woody species with high Tcrit, leaf mass per area, and leaf thickness tend to be more tolerant to heat stress. This study provides insights for predicting leaf heat tolerance of urban woody plants in subtropical China and their physiological and ecological responses to severe heat waves.</p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS livers injected or not with heme
<p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of livers <span>(indicated foie)</span> from HbSS mice injected or not with heme are presented here. </p> <p>The results of livers <span>(indicated foie)</span> from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10963640. </p> <p>Thirty μm-thick frozen tissue sections of livers were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p> <p> </p>
Monosaccharide transporter OsMST6 is activated by transcription factor OsERF120 to enhance chilling tolerance in rice seedlings
<p>Chilling stress caused by extreme weather is threatening global rice (<em>Oryza sativa</em> L.) production. Identifying components of the signal transduction pathways underlying chilling tolerance in rice would advance molecular breeding. Here, we report that <em>OsMST6</em>, which<em> </em>encodes<em> </em>a monosaccharide transporter, positively regulates the chilling tolerance of rice seedlings. The <em>mst6</em> mutants showed hypersensitivity to chilling, while the <em>OsMST6</em> overexpression lines were tolerant. During chilling stress, OsMST6 transported more glucose into cells to modulate sugar and ABA signal pathways. We showed that the transcription factor OsERF120 could bind to the DRE/CRT element of the <em>OsMST6</em> promoter and activate the expression of <em>OsMST6</em> to positively regulate chilling tolerance. Genetically, OsERF120 was functionally dependent on OsMST6 when promoting chilling tolerance. In summary, OsERF120 and OsMST6 form a new downstream chilling regulatory pathway in rice in response to chilling stress, providing valuable findings for molecular breeding aimed at achieving global food security.</p> <p><span>The stored data is the analysis results of transcriptome data from ZH11 and <em>mst6-1</em> after 0 hours and 4 hours of chilling treatment. These data form the basis for the transcriptome data visualization in the article.</span></p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA heart injected or not with heme
<p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of heart (indicated coeur) from HbAA mice injected or not with heme are presented here . </p> <p>The results of heart (indicated coeur) from HbSS mice injected or not with heme can be found at number 10.5281/zenodo.10964159</p> <p>Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS kidneys injected or not with heme
<p>The objective of this experiment was to explore the <span>transcriptome</span> of the <span>HbSS Townes</span> <span>mouse model</span> of <span>sickle cell disease</span>.Townes model mice carry several human hemoglobin <span>knock-in</span> genes replacing the endogenous mouse genes and may be useful in studying <span>sickle cell disease</span>.All mice were <span>genotyped</span>, age- and sex-matched littermates. All <span>HbAA</span> (control, normal human hemoglobin) vs HbSS (<span>sickle cell disease</span>, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group <span>heterogeneity</span>. <span>Hemin</span> (<span>Ferriprotoporphyrin IX</span>) was purchased from <span>Frontiers Scientific</span> and injected <span>intravenously</span> (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received <span>PBS</span> instead. Mice were anesthetized with <span>isoflurane</span> 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of kidney (indicated rein) from HbSS mice injected or not with <span>heme</span> are presented here . </p> <p>The results of kidney (indicated rein) from HbAA mice injected or not with <span>heme</span> can be found at number 10.5281/zenodo.10963926.</p> <p>Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit <span>Promega</span> AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all <span>Agilent Technologies</span>, <span>Palo Alto, CA</span>, <span>USA</span>). RNA Integrity Numbers superior to 7 were eligible for subsequent <span>reverse transcription</span> into <span>cDNA</span>. <span>RNAseq</span> was performed at the GenomIC plateform <span>Cochin Institute INSERM U1016</span>. After <span>RNA extraction</span>, RNA quality (<span>RNA integrity number</span>) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (<span>Illumina</span>) according to manufacturer instructions. Briefly, purified <span>poly-A</span> containing mRNA molecules were fragmented and <span>reverse-transcribed</span> using random <span>primers</span>. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the <span>cDNA</span> was followed by <span>ligation</span> of <span>Illumina</span> adapters.<br>Libraries were quantified by <span>qPCR</span> using <span>KAPA Library Quantification</span> Kits for <span>Illumina</span> Libraries (KapaBiosystems, <span>Wilmington</span>, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an <span>Agilent</span> Bioanalyzer. Libraries were sequenced on an <span>Illumina</span> Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a <span>paired-end</span> mode. After sequencing, primary analysis based on AOZAN software (ENS, <span>Paris</span>), was applied to <span>demultiplex</span> and control the quality of the <span>raw data</span> (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA <span>PBS</span>, HbAA <span>heme</span>, HbSS <span>PBS</span>, <span>HbSS</span> <span>heme</span>. </p>
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