scholarly journals Drought stress-induced irregularities in male organ development cause stage-specific morpho-physiological and transcriptome changes in tomato

2021 ◽  
Author(s):  
Anthony Tumbeh Lamin-Samu ◽  
Mohamed Farghal ◽  
Muhammad Ali ◽  
Gang Lu
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
Fruit Set ◽  
Floral Development ◽  
Soluble Sugars ◽  
Rna Seq ◽  
Drought Effect ◽  
Sugar Utilization ◽  
Male Organ ◽  
Insight Into

Drought limits the growth and productivity of plants. Reproductive development is sensitive to drought but the underlying physiological and molecular mechanisms remain unclear in tomato. Here, we investigated drought effect on tomato floral development using morpho-physiological and transcriptome analyses. Drought induced bud and flower abortions, and reduced fruit set/yield, triggered by male sterility due to abnormal anther and pollen development. Under drought stress (DS), anthers at pollen mother cell to meiotic (PMC-MEI) stage survived while anthers at tetrad to uninucleate microspore (TED-VUM) stage aborted. PMC-MEI stage had lower ABA increase, reduced IAA and higher sugar contents under DS relative to well-watered. However, TED-VUM stage had higher ABA increase, higher IAA level and no accumulation of soluble sugars, indicating abnormal carbohydrate and hormone metabolisms. Moreover, RNA-Seq analysis identified altogether ˃15,000 differentially expressed genes that were assigned to multiple pathways, suggesting tomato anthers utilize complicated mechanisms to cope with drought. Major genes involved in tapetum/microspore development and ABA homeostasis were drought-induced while those involved in sugar utilization and IAA metabolism were repressed at PMC-MEI stage. Our results suggest crosstalks between phytohormones and carbohydrate metabolism at different anther stages under DS and provide novel insight into molecular mechanisms of drought tolerance in tomato.

scholarly journals Morpho-Physiological and Transcriptome Changes in Tomato Anthers of Different Developmental Stages under Drought Stress

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1809
Author(s):  
Anthony Tumbeh Lamin-Samu ◽  
Mohamed Farghal ◽  
Muhammad Ali ◽  
Gang Lu
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Soluble Sugars ◽  
Anther Development ◽  
Starch Accumulation ◽  
Pollen Abortion ◽  
Metabolic Genes ◽  
Floral Bud

Drought limits the growth and productivity of plants. Reproductive development is sensitive to drought but the underlying physiological and molecular mechanisms remain unclear in tomatoes. Here, we investigated the effect of drought on tomato floral development using morpho-physiological and transcriptome analyses. Drought-induced male sterility through abnormal anther development includes pollen abortion, inadequate pollen starch accumulation and anther indehiscence which caused floral bud and opened flower abortions and reduced fruit set/yield. Under drought stress (DS), pollen mother cell to meiotic (PMC-MEI) anthers survived whereas tetrad to vacuolated uninucleate microspore (TED-VUM) anthers aborted. PMC-MEI anthers had lower ABA increase, reduced IAA and elevated sugar contents under DS relative to well-watered tomato plants. However, TED-VUM anthers had higher ABA increase and IAA levels, and lower accumulation of soluble sugars, indicating abnormal carbohydrate and hormone metabolisms when exposed to drought-stress conditions. Moreover, RNA-Seq analysis identified altogether >15,000 differentially expressed genes that were assigned to multiple pathways, suggesting that tomato anthers utilize complicated mechanisms to cope with drought. In particular, we found that tapetum development and ABA homeostasis genes were drought-induced while sugar utilization and IAA metabolic genes were drought-repressed in PMC-MEI anthers. Our results suggest an important role of phytohormones metabolisms in anther development under DS and provide novel insight into the molecular mechanism underlying drought resistance in tomatoes.

scholarly journals De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

2018 ◽  
Author(s):  
Federico Vita ◽  
Amedeo Alpi ◽  
Edoardo Bertolini
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Genetic Studies ◽  
Protein Coding ◽  
Important Species ◽  
White Truffle ◽  
Tuber Magnatum ◽  
Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

scholarly journals Single Cell Transcriptome-Based Dissection of Lineage Fate Decisions in Myelopoiesis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1395-1395
Author(s):  
Andre Olsson ◽  
H. Leighton Grimes ◽  
Virendra K Chaudhri ◽  
Philip Dexheimer ◽  
Bruce J Aronow ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Expression Patterns ◽  
Rna Seq ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Cell Data ◽  
Insight Into

Abstract In spite of tremendous advances in the analysis of hematopoietic progenitors and transcription factors that give rise to different lineages, molecular insight into the mechanisms that underlie cell fate choice at the level of individual cells is lacking. We utilized single-cell RNA sequencing of murine granulocyte-monocyte progenitors (GMPs) to analyze the molecular basis of cell fate choice. Over 200 libraries were generated with average read depths of 4 million per library and an expressed gene call of over 3,800 genes with FPKM >3. Our data reveal a varied but coherent spectrum of gene expression patterns in individual murine GMPs. The majority of cells could be clustered into ones expressing either granulocytic or monocytic genes, suggesting that they were primed for lineage determination. A minority of GMPs expressed a mixed-lineage pattern of genes. The single-cell data suggested an antagonistic transcription factor circuit involving Gfi1 and IRF8 that was validated with both loss- and gain-of-function experiments in GMPs. Our data highlight the utility of single cell RNA-Seq analysis to reveal molecular mechanisms controlling lineage fate decisions in hematopoiesis. Disclosures No relevant conflicts of interest to declare.

Distinctive Potassium-Accumulation Capability of Alligatorweed (Alternanthera philoxeroides) Links to High-Affinity Potassium Transport Facilitated by K+-Uptake Systems

Weed Science ◽  
2013 ◽  
Vol 61 (1) ◽  
pp. 77-84 ◽  
Author(s):  
Zhi-zhong Song ◽  
Yan-hua Su
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
Growth Conditions ◽  
Alternanthera Philoxeroides ◽  
Potassium Accumulation ◽  
High Affinity ◽  
Entire Plant ◽  
Consistent Increase ◽  
Rapid Amplification ◽  
Insight Into

Alligatorweed is well known for its potassium (K+)-accumulating capabilities and its strong resistance to undesired growth conditions. The results of this study revealed properties of K+ accumulation and its contribution to drought stress in alligatorweed. In addition, we attempted to characterize the molecular mechanisms of K+ accumulation in this plant. Alligatorweed plants showed a consistent increase in biomass in response to external K+ concentrations, ranging from micromolar levels up to 50 mmol L−1; K+ was also accumulated accordingly in the plants. The stem was the most K+-accumulating organ, accumulating up to 13% of the K+. Moreover, this K+ superaccumulation caused improved resistance to drought stress. The apparent K+ uptake by the roots showed a typical high-affinity property, and the Michaelis constant increased at higher rates of plant K+ in the starting materials. Furthermore, three putative, K+-uptake transporter complementary DNAs (cDNAs) were isolated from alligatorweed (ApKUP1, ApKUP2, and ApKUP3, respectively) using degenerated primers and rapid amplification of cDNA end techniques. The expression of ApKUP1 and ApKUP3 was predominately localized to the leaves, whereas ApKUP2 was expressed throughout the entire plant. The expression of ApKUP1 and ApKUP3 was stimulated in the stems and roots when K+ was depleted from the external medium. Moreover, ApKUP3 expression was enhanced in the stem in response to abscisic acid treatment and drought stress. In conclusion, our findings provide further insight into the mechanisms of K+ accumulation linked to K+ uptake in alligatorweed.

scholarly journals Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ling Xu ◽  
Zhaobin Dong ◽  
Dawn Chiniquy ◽  
Grady Pierroz ◽  
Siwen Deng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Iron Metabolism ◽  
Iron Transport ◽  
Iron Homeostasis ◽  
Molecular Mechanisms ◽  
Microbial Community Composition ◽  
Rna Seq ◽  
Highly Correlated ◽  
Root Microbiome

AbstractRecent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome’s response to drought and may inform efforts to improve plant drought tolerance to increase food security.

scholarly journals Transcriptome Analysis of Tolerant and Susceptible Maize Genotypes Reveals Novel Insights about the Molecular Mechanisms Underlying Drought Responses in Leaves

2021 ◽  
Vol 22 (13) ◽  
pp. 6980
Author(s):  
Joram Kiriga Waititu ◽  
Xingen Zhang ◽  
Tianci Chen ◽  
Chunyi Zhang ◽  
Yang Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Seedling Stage ◽  
Molecular Networks ◽  
Rna Seq ◽  
Drought Treatment ◽  
Cell Wall Modification ◽  
Susceptible Line ◽  
Tolerant Line

Maize (Zea mays L.) is the most essential food crop in the world. However, maize is highly susceptible to drought stress, especially at the seedling stage, and the molecular mechanisms underlying drought tolerance remain elusive. In this study, we conducted comparative transcriptome and physiological analyses of drought-tolerant (CML69) and susceptible (LX9801) inbred lines subjected to drought treatment at the seedling stage for three and five days. The tolerant line had significantly higher relative water content in the leaves, as well as lower electrolyte leakage and malondialdehyde levels, than the susceptible line. Using an RNA-seq-based approach, we identified 10,084 differentially expressed genes (DEGs) with 6906 and 3178 DEGs been annotated and unannotated, respectively. Two critical sets of drought-responsive DEGs, including 4687 genotype-specific and 2219 common drought-responsive genes, were mined out of the annotated DEGs. The tolerant-line DEGs were predominantly associated with the cytoskeleton, cell wall modification, glycolysis/gluconeogenesis, transport, osmotic regulation, drought avoidance, ROS scavengers, defense, and transcriptional factors. For the susceptible line, the DEGs were highly enriched in the photosynthesis, histone, and carbon fixation pathways. The unannotated DEGs were implicated in lncRNAs, including 428 previously reported and 22% putative TE-lncRNAs. There was consensus on both the physiological response and RNA-seq outcomes. Collectively, our findings will provide a comprehensive basis of the molecular networks mediating drought stress tolerance of maize at the seedling stage.

scholarly journals TIGER: The gene expression regulatory variation landscape of human pancreatic islets

2021 ◽  
Author(s):  
Lorena Alonso ◽  
Anthony Piron ◽  
Ignasi Moran ◽  
Marta Guindo-Martinez ◽  
Silvia Bonas-Guarch ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Low Frequency ◽  
Tissue Expression ◽  
Human Islet ◽  
Rna Seq ◽  
Specific Expression ◽  
Data Resource ◽  
Allele Specific ◽  
Insight Into

GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.

scholarly journals Clinical Candidates Targeting the ATR–CHK1–WEE1 Axis in Cancer

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 795
Author(s):  
Lukas Gorecki ◽  
Martin Andrs ◽  
Jan Korabecny
Keyword(s):  
Cell Cycle ◽  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Patient Survival ◽  
Current Status ◽  
Future Perspectives ◽  
Phase Ii Trials ◽  
Anticancer Treatment ◽  
Positive Outlook ◽  
Insight Into

Selective killing of cancer cells while sparing healthy ones is the principle of the perfect cancer treatment and the primary aim of many oncologists, molecular biologists, and medicinal chemists. To achieve this goal, it is crucial to understand the molecular mechanisms that distinguish cancer cells from healthy ones. Accordingly, several clinical candidates that use particular mutations in cell-cycle progressions have been developed to kill cancer cells. As the majority of cancer cells have defects in G1 control, targeting the subsequent intra‑S or G2/M checkpoints has also been extensively pursued. This review focuses on clinical candidates that target the kinases involved in intra‑S and G2/M checkpoints, namely, ATR, CHK1, and WEE1 inhibitors. It provides insight into their current status and future perspectives for anticancer treatment. Overall, even though CHK1 inhibitors are still far from clinical establishment, promising accomplishments with ATR and WEE1 inhibitors in phase II trials present a positive outlook for patient survival.

scholarly journals Phloem-Feeding Herbivores Affect Floral Development and Reproduction in the Etruscan Honeysuckle (Lonicera etrusca Santi)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 815
Author(s):  
Sandra V. Rojas-Nossa ◽  
José María Sánchez ◽  
Luis Navarro
Keyword(s):  
Fruit Set ◽  
Floral Development ◽  
Seed Set ◽  
Wild Populations ◽  
Ecological Processes ◽  
Trade Offs ◽  
Complex Landscape ◽  
Fruit And Seed Set ◽  
Phloem Feeding ◽  
Growth And Reproduction

Floral development depends on multifactor processes related to genetic, physiological, and ecological pathways. Plants respond to herbivores by activating mechanisms aimed at tolerating, compensating, or avoiding loss of biomass and nutrients, and thereby survive in a complex landscape of interactions. Thus, plants need to overcome trade-offs between development, growth, and reproduction vs. the initiation of anti-herbivore defences. This study aims to assess the frequency of phloem-feeding herbivores in wild populations of the Etruscan honeysuckle (Lonicera etrusca Santi) and study their effects on floral development and reproduction. The incidence of herbivory by the honeysuckle aphid (Hyadaphis passerinii del Guercio) was assessed in three wild populations of the Iberian Peninsula. The effect of herbivory on floral morphology, micromorphology of stigmas and pollen, floral rewards, pollination, and fruit and seed set were studied. The herbivory by aphids reduces the size of flowers and pollen. Additionally, it stops nectar synthesis and causes malformation in pollen and microstructures of stigmas, affecting pollination. As a consequence, fruit set and seed weight are reduced. This work provides evidence of the changes induced by phloem-feeding herbivores in floral development and functioning that affect the ecological processes necessary to maintain the reproductive success of plants.

scholarly journals Molecular Pathways Involved in the Development of Congenital Erythrocytosis

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1150
Author(s):  
Jana Tomc ◽  
Nataša Debeljak
Keyword(s):  
Signal Transduction ◽  
Iron Homeostasis ◽  
Molecular Mechanisms ◽  
Oxygen Affinity ◽  
Molecular Pathways ◽  
Disease Development ◽  
Post Translational Modifications ◽  
Hemoglobin Oxygen Affinity ◽  
Insight Into ◽  
Idiopathic Erythrocytosis

Patients with idiopathic erythrocytosis are directed to targeted genetic testing including nine genes involved in oxygen sensing pathway in kidneys, erythropoietin signal transduction in pre-erythrocytes and hemoglobin-oxygen affinity regulation in mature erythrocytes. However, in more than 60% of cases the genetic cause remains undiagnosed, suggesting that other genes and mechanisms must be involved in the disease development. This review aims to explore additional molecular mechanisms in recognized erythrocytosis pathways and propose new pathways associated with this rare hematological disorder. For this purpose, a comprehensive review of the literature was performed and different in silico tools were used. We identified genes involved in several mechanisms and molecular pathways, including mRNA transcriptional regulation, post-translational modifications, membrane transport, regulation of signal transduction, glucose metabolism and iron homeostasis, which have the potential to influence the main erythrocytosis-associated pathways. We provide valuable theoretical information for deeper insight into possible mechanisms of disease development. This information can be also helpful to improve the current diagnostic solutions for patients with idiopathic erythrocytosis.

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