The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance

Like many cereal crops, barley is also negatively affected by drought stress. However, due to its simple genome as well as enhanced stress resilient nature compared to rice and wheat, barley has been considered as a model to decipher drought tolerance in cereals. In the present study, transcriptomic and hormonal profiles along with several biochemical features were compared between drought-tolerant (Otis) and drought-sensitive (Baronesse) barley genotypes subjected to drought to identify molecular and biochemical differences between the genotypes. The drought-induced decrease in the leaf relative water content, net photosynthesis, and biomass accumulation was relatively low in Otis compared to Baronesse. The hormonal profiles did not reveal significant differences for majority of the compounds other than the GA20 and the cis-zeatin-o-glucoside (c-ZOG), whose levels were greatly increased in Otis compared to Baronesse under drought. The major differences that emerged from the transcriptome analysis are; (1), the overall number of differentially expressed genes was relatively low in drought-tolerant Otis compared to drought-sensitive Baronesse; (2), a wax biosynthesis gene (CER1), and NAC transcription factors were specifically induced in Otis but not in Baronesse; (3), the degree of upregulation of betaine aldehyde dehydrogenase and a homeobox transcription factor (genes with proven roles in imparting drought tolerance), was greater in Otis compared to Baronesse; (4) the extent of downregulation of gene expression profiles for proteins of the reaction center photosystem II (PSII) (D1 and D2) was low in Otis compared to Baronesse; and, (5), alternative splicing (AS) was also found to differ between the genotypes under drought. Taken together, the overall transcriptional responses were low in drought-tolerant Otis but the genes that could confer drought tolerance were either specifically induced or greatly upregulated in the tolerant genotype and these differences could be important for drought tolerance in barley.

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Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley

International Journal of Molecular Sciences ◽

10.3390/ijms21082795 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2795

Author(s):

Cheng-Wei Qiu ◽

Li Liu ◽

Xue Feng ◽

Peng-Fei Hao ◽

Xiaoyan He ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Target Genes ◽

Wild Barley ◽

Expression Profiles ◽

Tibetan Wild Barley ◽

Drought Tolerant ◽

Genome Wide ◽

Barley Genotypes

Drought stress is a major obstacle to agricultural production. Tibetan wild barley with rich genetic diversity is useful for drought-tolerant improvement of cereals. MicroRNAs (miRNAs) play critical roles in controlling gene expression in response to various environment perturbations in plants. However, the genome-wide expression profiles of miRNAs and their targets in response to drought stress are largely unknown in wild barley. In this study, a polyethylene glycol (PEG) induced drought stress hydroponic experiment was performed, and the expression profiles of miRNAs from the roots of two contrasting Tibetan wild barley genotypes XZ5 (drought-tolerant) and XZ54 (drought-sensitive), and one cultivated barley Tadmor (drought-tolerant) generated by high-throughput sequencing were compared. There were 69 conserved miRNAs and 1574 novel miRNAs in the dataset of three genotypes under control and drought conditions. Among them, seven conserved miRNAs and 36 novel miRNAs showed significantly genotype-specific expression patterns in response to drought stress. And 12 miRNAs were further regarded as drought tolerant associated miRNAs in XZ5, which mostly participate in gene expression, metabolism, signaling and transportation, suggesting that they and their target genes play important roles in plant drought tolerance. This is the first comparation study on the miRNA transcriptome in the roots of two Tibetan wild barley genotypes differing in drought tolerance and one drought tolerant cultivar in response to PEG treatment. Further results revealed the candidate drought tolerant miRNAs and target genes in the miRNA regulation mechanism in wild barley under drought stress. Our findings provide valuable understandings for the functional characterization of miRNAs in drought tolerance.

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FC1000: normalized gene expression changes of systematically perturbed human cells

Statistical Applications in Genetics and Molecular Biology ◽

10.1515/sagmb-2016-0072 ◽

2017 ◽

Vol 16 (4) ◽

Cited By ~ 1

Author(s):

Ingrid M. Lönnstedt ◽

Sven Nelander

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Estimation Procedure ◽

Human Cells ◽

Biomedical Data ◽

Transcriptional Responses ◽

Statistical Framework ◽

Statistical Measures ◽

Change Response

AbstractThe systematic study of transcriptional responses to genetic and chemical perturbations in human cells is still in its early stages. The largest available dataset to date is the newly released L1000 compendium. With its 1.3 million gene expression profiles of treated human cells it offers many opportunities for biomedical data mining, but also data normalization challenges of new dimensions. We developed a novel and practical approach to obtain accurate estimates of fold change response profiles from L1000, based on the RUV (Remove Unwanted Variation) statistical framework. Extending RUV to a big data setting, we propose an estimation procedure, in which an underlying RUV model is tuned by feedback through dataset specific statistical measures, reflecting

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Agronomic Performance and Flowering Behavior in Response to Photoperiod and Vernalization in Barley (Hordeum vulgare L.) Genotypes with Contrasting Drought Tolerance Behavior

10.21203/rs.3.rs-289948/v1 ◽

2021 ◽

Author(s):

Jamal Abu-Elenein ◽

Rabea Al-Sayaydeh ◽

Zahera Akkeh ◽

Zakaria Al-Ajlouni ◽

AbdRaheem A. Al-Bawalize ◽

...

Keyword(s):

Drought Tolerance ◽

Shoot Apical Meristem ◽

Apical Meristem ◽

Agronomic Performance ◽

Short Day ◽

Drought Tolerant ◽

Long Day ◽

Meristem Development ◽

Rainfed Conditions ◽

Barley Genotypes

Abstract Background In barley, flowering behavior is a highly regulated and complex process where the appropriate matching of reproductive development with seasonal variation in water availability confer barley adaptation to different environments. In this study, the role of variation in flowering time and drought tolerance in four selected barley genotypes was studied under field and controlled conditions. For this purpose, field trials were conducted for two consecutive seasons at three diverse environments where the studied genotypes were subjected to either rainfed conditions or rainfed plus supplementary irrigation under two different sowing dates. Furthermore, reproductive meristem development in two selected barley genotypes, Rum (drought tolerant) and Steptoe (drought-sensitive) was also assessed in response to both vernalization and water stress under two different photoperiod conditions.Results Variation in the number of days to heading was more pronounced under rainfed conditions than under well water conditions. For agronomic performance, Rum was superior under all tested environments, which assure its general adaptability to multiple environments, while Steptoe was the poorest. The transition to reproductive meristem was faster under vernalized long-day conditions as compared to vernalized short-day conditions. The progress of shoot apical meristem development and heading under long-day conditions was significantly faster in Rum than that of Steptoe. A clear effect of drought stress was observed on shoot apical meristem development in Steptoe. Under short-day conditions, vernalized Rum plants subjected to water deficit showed an advanced meristem development stage a significant earlier HD when compared with non-stressed plants. This early flowering behavior in stressed Rum plants under short-day conditions was accompanied by higher gene expression of the Vrn-H1 gene. Conclusion In conclusion, the integration of vernalization and photoperiod signals in drought-tolerant barley genotypes is associated with early flowering behavior and higher productivity in dry environments.

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Sex differences in viral entry protein expression and host transcript responses to SARS-CoV-2

10.21203/rs.3.rs-100914/v2 ◽

2020 ◽

Author(s):

Mengying Sun ◽

Rama Shankar ◽

Meehyun Ko ◽

Christopher Daniel Chang ◽

Shan-Ju Yeh ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Viral Entry ◽

Large Scale ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Scale Analysis ◽

Transcriptional Responses ◽

Deconvolution Analysis ◽

Large Scale Analysis

Abstract Epidemiological studies suggest that men exhibit a higher mortality rate to COVID-19 than women, yet the underlying biology is largely unknown. Here, we seek to delineate sex differences in the gene expression of viral entry proteins ACE2 and TMPRSS2, and host transcriptional responses to SARS-CoV-2 through large-scale analysis of genomic and clinical data. We first compiled 220,000 human gene expression profiles from three databases and completed the meta-information through machine learning and manual annotation. Large scale analysis of these profiles indicated that male samples show higher expression levels of ACE2 and TMPRSS2 than female samples, especially in the older group (>60 years) and in the kidney. Subsequent analysis of 6,031 COVID-19 patients at Mount Sinai Health System revealed that men have significantly higher creatinine levels, an indicator of impaired kidney function. Further analysis of 782 COVID-19 patient gene expression profiles taken from upper airway and blood suggested men and women present distinct expression changes. Computational deconvolution analysis of these profiles revealed male COVID-19 patients have enriched kidney-specific mesangial cells in blood compared to healthy patients. Together, this study suggests biological differences in the kidney between sexes may contribute to sex disparity in COVID-19.

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Transcriptional responses to water stress and recovery in a drought-tolerant fescue wild grass (Festuca ovina; Poaceae)

Genome ◽

10.1139/gen-2020-0055 ◽

2021 ◽

Vol 64 (1) ◽

pp. 15-27

Author(s):

Fan Qiu ◽

Seton Bachle ◽

Ryan Estes ◽

Melvin R. Duvall ◽

Jesse B. Nippert ◽

...

Keyword(s):

Water Stress ◽

Drought Tolerance ◽

Molecular Mechanisms ◽

Model Species ◽

Transcriptional Responses ◽

Festuca Ovina ◽

Drought Tolerant ◽

Plant Genes ◽

Initial Recovery ◽

Transcriptomic Changes

Water stress associated with drought-like conditions is a major factor limiting plant growth and impacts productivity of natural plant communities and agricultural crops. Molecular responses of plants to water stress have been studied most extensively in model species and crops, few of which have evolved natural drought tolerance. In the current study, we examined physiological and transcriptomic responses at multiple timepoints during increasing water stress and following initial recovery from stress in a drought-tolerant C3 species, Festuca ovina. Results demonstrated non-linear transcriptomic changes during increasing stress, but largely linear declines in physiological measurements during this same period. Transcription factors represented approximately 12.7% of all differentially expressed genes. In total, 117 F. ovina homologs of previously identified and molecularly characterized drought-responsive plant genes were identified. This information will be valuable for further investigations of the molecular mechanisms involved in drought tolerance in C3 plants.

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Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton (Gossypium spp.) Species Under Drought Stress

International Journal of Molecular Sciences ◽

10.3390/ijms20092076 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2076 ◽

Cited By ~ 3

Author(s):

Md Mosfeq-Ul Hasan ◽

Fanglu Ma ◽

Faisal Islam ◽

Muhammad Sajid ◽

Zakaria H. Prodhan ◽

...

Keyword(s):

Drought Stress ◽

Heat Shock ◽

Drought Tolerance ◽

Heat Shock Protein ◽

Molecular Mechanisms ◽

Biological Process ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Small Heat Shock Protein ◽

Cotton Species

Drought is one of the most important abiotic stresses that seriously affects cotton growth, development, and production worldwide. However, the molecular mechanism, key pathway, and responsible genes for drought tolerance incotton have not been stated clearly. In this research, high-throughput next generation sequencing technique was utilized to investigate gene expression profiles of three cotton species (Gossypium hirsutum, Gossypium arboreum, and Gossypium barbadense L.) under drought stress. A total of 6968 differentially expressed genes (DEGs) were identified, where 2053, 742, and 4173 genes were tested as statistically significant; 648, 320, and 1998 genes were up-regulated, and 1405, 422, and 2175 were down-regulated in TM-1, Zhongmian-16, and Pima4-S, respectively. Total DEGs were annotated and classified into functional groups under gene ontology analysis. The biological process was present only in tolerant species(TM-1), indicating drought tolerance condition. The Kyoto encyclopedia of genes and genomes showed the involvement of plant hormone signal transduction and metabolic pathways enrichment under drought stress. Several transcription factors associated with ethylene-responsive genes (ICE1, MYB44, FAMA, etc.) were identified as playing key roles in acclimatizing to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to abscisic acid (ABA) responses (NCED, PYL, PP2C, and SRK2E), reactive oxygen species (ROS) related in small heat shock protein and 18.1 kDa I heat shock protein, YLS3, and ODORANT1 genes. These results will provide deeper insights into the molecular mechanisms of drought stress adaptation in cotton.

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Effect of Water Deficit on Morphoagronomic and Physiological Traits of Common Bean Genotypes with Contrasting Drought Tolerance

Water ◽

10.3390/w12010217 ◽

2020 ◽

Vol 12 (1) ◽

pp. 217

Author(s):

Leonardo Godoy Androcioli ◽

Douglas Mariani Zeffa ◽

Daniel Soares Alves ◽

Juarez Pires Tomaz ◽

Vânia Moda-Cirino

Keyword(s):

Drought Tolerance ◽

Common Bean ◽

Water Deficit ◽

Net Photosynthesis ◽

Physiological Traits ◽

Limiting Factors ◽

Direct Result ◽

Drought Tolerant ◽

Intrinsic Water Use Efficiency ◽

Influence Of Water

Water deficit is considered one of the most limiting factors of the common bean. Understanding the adaptation mechanisms of the crop to this stress is fundamental for the development of drought-tolerant cultivars. In this sense, the objective of this study was to analyze the influence of water deficit on physiological and morphoagronomic traits of common bean genotypes with contrasting drought tolerance, aiming to identify mechanisms associated with tolerance to water deficit. The experiment was carried out in a greenhouse, arranged in a randomized complete block 4 × 2 factorial design, consisting of four common bean genotypes under two water regimes (with and without water stress), with six replications. The morphoagronomic and physiological traits of four cultivars, two drought-tolerant (IAPAR 81 and BAT 477) and two drought-sensitive (IAC Tybatã and BRS Pontal), were measured for 0, 4, 8, and 12 days, under water deficit, initiated in the phenological stage R5. Water-deficit induced physiological changes in the plants, altering the evaluated morphoagronomic traits. The drought tolerance of cultivar BAT 477 is not only a direct result of the low influence of water deficit on its yield components, but also a consequence of the participation of multiple adaptive physiological mechanisms, such as higher intrinsic water use efficiency, net photosynthesis rate, transpiration, carboxylation efficiency, stomatal conductance, and intracellular concentration of CO2 under water deficit conditions. On the other hand, cultivar IAPAR 81 can be considered drought-tolerant for short water-deficit periods only, since after the eighth day of water deficit, the physiological activities decline drastically.

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Kinetics of Gene Expression Changes in Equine Fetal Interzone and Anlagen Cells Over 14 Days of Induced Chondrogenesis

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.722324 ◽

2021 ◽

Vol 8 ◽

Author(s):

Chan Hee Mok ◽

James N. MacLeod

Keyword(s):

Gene Expression ◽

Articular Cartilage ◽

Cell Biology ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cartilage Regeneration ◽

Transcriptional Responses ◽

Functional Annotations ◽

Kinetics Of ◽

Tgf Β1

Within developing synovial joints, interzone and anlagen cells progress through divergent chondrogenic pathways to generate stable articular cartilage and transient hypertrophic anlagen cartilage, respectively. Understanding the comparative cell biology between interzone and anlagen cells may provide novel insights into emergent cell-based therapies to support articular cartilage regeneration. The aim of this study was to assess the kinetics of gene expression profiles in these skeletal cell lines after inducing chondrogenesis in culture. Interzone and anlagen cells from seven equine fetuses were isolated and grown in a TGF-β1 chondrogenic inductive medium. Total RNA was isolated at ten time points (0, 1.5, 3, 6, 12, 24, 48, 96, 168, and 336 h), and gene expression for 93 targeted gene loci was measured in a microfluidic RT-qPCR system. Differential transcriptional responses were observed as early as 1.5 h after the initiation of chondrogenesis. Genes with functional annotations that include transcription regulation responded to the chondrogenic stimulation earlier (1.5–96 h) than genes involved in signal transduction (1.5–336 h) and the extracellular matrix biology (3–336 h). Between interzone and anlagen cell cultures, expression levels of 73 out of the 93 targeted genes were not initially different at 0 h, but 47 out of the 73 genes became differentially expressed under the chondrogenic stimulation. While interzone and anlagen cells are both chondrogenic, they display clear differences in response to the same TGF-β1 chondrogenic stimulation. This study provides new molecular insight into a timed sequence of the divergent developmental fates of interzone and anlagen cells in culture over 14 days.

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Systemic Transcriptional Responses to Hemarthrosis and FVIII Replacement in FVIII-Deficient Mice

Blood ◽

10.1182/blood-2018-99-120092 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 381-381

Author(s):

Esther J Cooke ◽

Srila Gopal ◽

John Shimashita ◽

Chanond A Nasamran ◽

Kathleen M Fisch ◽

...

Keyword(s):

Gene Expression ◽

T Cell ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cell Receptor ◽

Post Injury ◽

Transcriptional Responses ◽

T Cell Receptor Signaling ◽

Deficient Mice ◽

Cell Receptor Signaling

Abstract Introduction Hemarthrosis in patients with hemophilia (PWH) leads to local inflammation and vascular changes in the joint, but little is known about the extent and nature of systemic responses to joint bleeding. Since the spleen is a major systemic immune-modulatory organ, we quantified changes in splenic gene expression profiles in FVIII-deficient mice at baseline and after induced hemarthrosis, and in the presence and absence of FVIII replacement therapy. Methods Hemarthrosis was induced in FVIII-deficient mice by sub-patellar needle puncture +/- 100 IU/kg recombinant human FVIII (rhFVIII) intravenously 2 hours before and 6 hours after injury. Spleens were harvested on day 3 or 2 weeks post-injury (n=3-5). Spleens from uninjured mice +/- rhFVIII treatment served as controls. RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illumina NextSeq500 platform (single-end; 75bp reads). The limma-voom method (R Bioconductor) was used for differential expression analyses. The criteria for differential expression were: i) a log fold-change (logFC) >1 or <-1, and ii) an adjusted p value <0.05. Functional enrichment was performed using Signaling Pathway Impact Analysis and the STRING database of protein-protein interactions. Results Knee injury in FVIII-deficient mice caused gross hemarthrosis that was largely prevented with rhFVIII prophylaxis (day 2 hematocrit: 26.4% and 46.3%). Pronounced alterations in splenic gene expression profiles occurred in vehicle-treated mice on day 3 post-injury, with 4227 differentially expressed genes (DEG) and 41 perturbed pathways. This response was markedly improved with rhFVIII treatment (386 DEG; 5 pathways), and almost entirely corrected by 2 weeks. Multiple pathways relating to immune processes, inflammation, and cell survival were highly perturbed on day 3 post-injury, including cytokine-cytokine receptor interactions (pNDE=1.4x10-6) and cell cycle (pNDE=5.3x10-5). The cell cycle pathway remained significantly altered despite rhFVIII treatment (pNDE=3.5x10-6), while other pathways were comparable to uninjured mice. Analysis of the top 50 DEG that are mutual to both treatment groups revealed a striking difference in directionality, with up-regulation in the vehicle group, and down-regulation in the rhFVIII group. Together, these findings demonstrate a significant effect of rhFVIII treatment on systemic transcriptional responses to joint bleeding. Treatment with rhFVIII in the absence of hemarthrosis resulted in only 97 DEG on day 3 by the same criteria, and 233 DEG after lowering the logFC threshold from (-)1 to (-)0.5. Of these 233 genes, STRING analysis revealed perturbation of the platelet activation pathway (FDR: 7.7x10-10) for up-regulated genes (93 DEG) and the T cell receptor signaling pathway (FDR: 1.3x10-8) for down-regulated genes (140 DEG), which may corroborate a role of T cell responses to rhFVIII treatment in the development of inhibitors. These responses to rhFVIII were unique to uninjured mice and did not occur in mice with induced hemarthrosis and rhFVIII treatment. Conclusions Joint bleeding in hemophilic mice leads to acute, profound changes in multiple systemic pathways, including immune and inflammatory processes, as shown by gene expression profiling. Prophylactic treatment with rhFVIII largely corrects this response to hemarthrosis. Interestingly, in the absence of hemarthrosis, rhFVIII treatment affects platelet activation and T cell receptor signaling, whereby further analyses are required to determine if these effects stimulate or dampen immune responses. This approach can be used to explore the systemic mechanisms contributing to progressive hemophilic arthropathy in PWH, elucidate immune responses that may facilitate inhibitor formation, and lead to development of novel therapeutic strategies. Disclosures von Drygalski: UniQure BV, Bayer, Bioverativ/Sanofi, Pfizer, Novo Nordisk, Biomarin, Shire, CSL Behring: Consultancy.

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Interspecies bacterial interactions stabilize transcriptional responses of ancestral wild types and biofilm-optimised variants

10.5194/biofilms9-78 ◽

2020 ◽

Author(s):

Mette Burmølle ◽

Nanna Mee Coops Olsen ◽

Samuel Jacquiod ◽

Henriette Lyng Røder

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Niche Partitioning ◽

Gene Expression Profiles ◽

Biotic Interactions ◽

Culture Conditions ◽

Differentially Expressed ◽

Natural Environments ◽

Transcriptional Responses ◽

The Impact

Most bacteria in natural environments live in multispecies biofilms, featuring high diversity and chemical heterogeneity. The cell-to-cell proximity found in these biofilms results in biotic interactions and niche-partitioning, facilitating co-existence of species that may otherwise out-compete each other. Additionally, due to the fast generation time of microbes and ceaseless biotic interactions, biofilms accelerate adaptation through the emergence of more fit genetic variants, most probably in response to niche-partitioning and local constraints. We have previously isolated and characterized biofilm-optimised (wrinkled) variants of Xanthomonas retroflexus. These variants emerged in biofilm co-cultures with Paenibacillus amylolyticus and reinforced the original interspecific mutualistic interaction, due to altered c-di-GMP regulation and spatial organisation. The aim of the present study was to examine the impact on gene expression profiles of either co-cultivation of the wild type (WT) or the wrinkled variant X. retroflexus with P. amylolyticus or its supernatant. We hypothesised that the gene expression of the two X. retroflexus strains would differ significantly and that these differences would be even more pronounced when co-cultured with P. amylolyticus or its supernatant. Mono- and dual species biofilms were grown in 24-well plates for 24 h. The liquid culture was removed, and the remaining biofilm from the sides of the wells and the air-liquid interface was sampled and processed for mRNA sequencing. After sequencing, X. retroflexus&#160;reads were mapped against its concatenated genome and genes of which expression differed by fold changes of log2 <-1 and >1 were considered differentially expressed. Unexpectedly, most marked differences in gene expression were observed when comparing mono-cultures of the WT and the wrinkled X. retroflexus, as approximately 500 genes were differentially expressed in these biofilms. Of these, 30 genes were predicted to encode biofilm-associated functions. When exposed to either live P. amylolyticus or its supernatant, expression profiles of the WT and the wrinkled variant were more similar, with the living partner P. amylolyticus being the key factor of this stabilization. Specifically, the stabilisation was caused by opposite regulation of specific genes in the wrinkled X. retroflexus&#160;variant compared to the WT in mono- vs. co-culture conditions. In conclusion, our data indicates that differences in gene expression of X. retroflexus WT and the biofilm-optimised variant were neutralised by co-cultivation with P. amylolyticus. To our knowledge, such comparative analyses of ancestral and biofilm-optimised variants have not previously been presented, despite being instrumental in elucidating evolutionary trajectories of such variants in complex environments.

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