Differentially Expressed miRNAs Potentially Involved in the Regulation of Defense Mechanism to Drought Stress in Maize Seedlings

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identiﬁed. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

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Insight of Transcriptional Regulators reveals the Tolerance Mechanism of Carpet-grass (Axonopus compressus) Against Drought

10.21203/rs.3.rs-41830/v1 ◽

2020 ◽

Author(s):

Mohsin Nawaz ◽

Liao Li ◽

Farrukh Azeem ◽

Samina Shabbir ◽

Ali Zohaib ◽

...

Keyword(s):

Drought Stress ◽

Defense Mechanism ◽

Perennial Grass ◽

Warm Season ◽

Transcriptional Response ◽

Data Bank ◽

Differentially Expressed ◽

Severe Drought ◽

Public Data ◽

Validation Experiment

Abstract Highlights:1. Axonopus compressus can stand severe drought stress by activating the potential defense mechanism.2. We investigated the differential transcriptome of drought stressed and normal Axonopus compressus plants3. New comers have been identified that involved in the drought response4. Identified drought responsive genes which never known for other stresses.5. The identified genes also respond to stress in Arabidopsis thaliana in different manners.Background: Carpet grass [Axonopus compressus (L.)] is an important warm season perennial grass around the world and is renowned for its adaptability to varied environmental conditions. However, Carpet grass lacks enough data in public data bank, which confined our comprehension of the mechanism of environmental adaptations, gene discovery and development of molecular marker. Methods: In current study, the DEGs (differentially expressed genes) in Axonopus compressus under drought stress (DS) were identified and compared with CK (control) by RNA-Seq. Results: the 263,835 of total unigenes were identified in Axonopus compressus, and 201,303 (also add the numbers of remaining2 data bases) a sequence of unigenes significantly matched in at least one of the seven databases. A total of 153697 (58.25%) unigenes can be classified to 144 KEGG pathways, and 7,444 unigenes were expressed differentially between DS and CK, of which 4,249 were up-regulated and 3,195 were down-regulated unigenes. Of the 50 significantly enriched GO terms, 18, 6 and 14 items were related to BP, CC and MF, respectively. Analysis of KEGG enrichment showed 2569 DEGs involved in 143 different pathways, under drought stress 2,747 DEGs were up-regulated and 2,502 DEGs were down-regulated. Moreover, we identified 352 transcriptor factors (TFs) in Axonopus compressus, of which 270 were differentially expressed between CK and DS. The qRT-PCR validation experiment also support the transcriptional response of Axonopus compressus against drought. Conclusions: The current findings provide the first framework for further investigation for the particular roles of these unigenes in Axonopus compressus in response to droughts.

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Differentially expressed miRNAs in spindle cell oncocytoma of the pituitary gland

Endocrine Abstracts ◽

10.1530/endoabs.63.p1057 ◽

2019 ◽

Author(s):

Lilla Krokker ◽

Gabor Nyirő ◽

Lilla Reininger ◽

Otto Darvasi ◽

Nikolette Szucs ◽

...

Keyword(s):

Pituitary Gland ◽

Spindle Cell ◽

Differentially Expressed ◽

Differentially Expressed Mirnas ◽

Spindle Cell Oncocytoma

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Role of Suillus placidus in Improving the Drought Tolerance of Masson Pine (Pinus massoniana Lamb.) Seedlings

Forests ◽

10.3390/f12030332 ◽

2021 ◽

Vol 12 (3) ◽

pp. 332

Author(s):

Min Li ◽

Haoyun Wang ◽

Xizhou Zhao ◽

Zhongke Lu ◽

Xueguang Sun ◽

...

Keyword(s):

Drought Stress ◽

Defense Mechanism ◽

Southern China ◽

Dry Weight ◽

Pinus Massoniana ◽

Photosynthetic Performance ◽

Ectomycorrhizal Fungus ◽

Severe Drought ◽

Masson Pine ◽

Pine Seedlings

Masson pine is an important afforestation species in southern China, where seasonal drought is common. The present study focused on the effects of Suillus placidus, an ectomycorrhizal fungus, inoculation on the growth and physiological and biochemical performance of masson pine seedlings under four different watering treatments (well-watered, mild drought, moderate drought, and severe drought) to evaluate the symbiotic relationship between S. placidus and masson pine seedlings. Ectomycorrhizal-inoculated (ECM) and non-inoculated (NM) seedlings were grown in pots and maintained for 60 days using the weighing method. Results showed that seedlings’ growth, dry weight, RWC, chlorophyll content, PSII efficiency, and photosynthesis decreased as drought stress intensified in both ECM and NM plants. This suggests that drought stress significantly limits the growth and photosynthetic performance of masson pine seedlings. Nevertheless, increased An/gs and proline contents in both NM and ECM prevented oxidative damage caused by drought stress. In addition, increased peroxidase (POD) activity is an essential defense mechanism of ECM seedling under drought stress. Compared with NM, ECM seedlings showed faster growth, higher RWC, and photosynthetic performance, and lower lipid peroxidation in cell membranes under drought stress, as indicated by higher POD activity and lower proline and malondialdehyde (MDA). Our experiment found that S. placidus inoculation can enhance the drought resistance of masson pine seedlings by increasing antioxidant enzyme activity, water use efficiency, and proline content, thereby enhancing growth under water-deficiency conditions. S. placidus can be used to cultivate high-quality seedlings and improve their survival in regions that experience seasonal droughts.

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Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

BMC Plant Biology ◽

10.1186/s12870-020-02818-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Z. Y. Su ◽

J. J. Powell ◽

S. Gao ◽

M. Zhou ◽

C. Liu

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Crown Rot ◽

Differentially Expressed ◽

Transcriptional Responses ◽

Drought Treatment ◽

Crop Species ◽

Fusarium Crown Rot ◽

Important Relationship ◽

The Impact

Abstract Background Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops. Results In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection. Conclusions Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

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miRNA Expression Characterizes Histological Subtypes and Metastasis in Penile Squamous Cell Carcinoma

Cancers ◽

10.3390/cancers13061480 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1480

Author(s):

Hiresh Ayoubian ◽

Joana Heinzelmann ◽

Sebastian Hölters ◽

Oybek Khalmurzaev ◽

Alexey Pryalukhin ◽

...

Keyword(s):

Microarray Data ◽

Expression Patterns ◽

Hpv Infection ◽

Differentially Expressed ◽

Histological Subtypes ◽

Specific Expression ◽

Tissue Samples ◽

Qrt Pcr ◽

Differentially Expressed Mirnas ◽

The Impact

Although microRNAs are described as promising biomarkers in many tumor types, little is known about their role in PSCC. Thus, we attempted to identify miRNAs involved in tumor development and metastasis in distinct histological subtypes considering the impact of HPV infection. In a first step, microarray analyses were performed on RNA from formalin-fixed, paraffin-embedded tumor (22), and normal (8) tissue samples. Microarray data were validated for selected miRNAs by qRT-PCR on an enlarged cohort, including 27 tumor and 18 normal tissues. We found 876 significantly differentially expressed miRNAs (p ≤ 0.01) between HPV-positive and HPV-negative tumor samples by microarray analysis. Although no significant differences were detected between normal and tumor tissue in the whole cohort, specific expression patterns occurred in distinct histological subtypes, such as HPV-negative usual PSCC (95 differentially expressed miRNAs, p ≤ 0.05) and HPV-positive basaloid/warty subtypes (247 differentially expressed miRNAs, p ≤ 0.05). Selected miRNAs were confirmed by qRT-PCR. Furthermore, microarray data revealed 118 miRNAs (p ≤ 0.01) that were significantly differentially expressed in metastatic versus non-metastatic usual PSCC. The lower expression levels for miR-137 and miR-328-3p in metastatic usual PSCC were validated by qRT-PCR. The results of this study confirmed that specific miRNAs could serve as potential diagnostic and prognostic markers in single PSCC subtypes and are associated with HPV-dependent pathways.

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Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species

Biotechnology for Biofuels ◽

10.1186/s13068-021-01915-z ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Jose J. De Vega ◽

Abel Teshome ◽

Manfred Klaas ◽

Jim Grant ◽

John Finnan ◽

...

Keyword(s):

Drought Stress ◽

Water Supply ◽

Biomass Yield ◽

Transcriptional Response ◽

Biomass Productivity ◽

Differentially Expressed ◽

Model Organisms ◽

Drought Conditions ◽

Multiple Copies ◽

Response To Water

Abstract Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. Results A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. Conclusions Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.

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MicroRNA expression profile in bovine mammary gland parenchyma infected by coagulase-positive or coagulase-negative staphylococci

Veterinary Research ◽

10.1186/s13567-021-00912-2 ◽

2021 ◽

Vol 52 (1) ◽

Author(s):

Emilia Bagnicka ◽

Ewelina Kawecka-Grochocka ◽

Klaudia Pawlina-Tyszko ◽

Magdalena Zalewska ◽

Aleksandra Kapusta ◽

...

Keyword(s):

Mammary Gland ◽

Immune System ◽

Differentially Expressed ◽

Bacterial Invasion ◽

Coagulase Negative Staphylococci ◽

Cellular Processes ◽

Differentially Expressed Mirnas ◽

Non Coding Rnas ◽

Coagulase Positive Staphylococci ◽

Generation Sequencing

AbstractMicroRNAs (miRNAs) are short, non-coding RNAs, 21–23 nucleotides in length which are known to regulate biological processes that greatly impact immune system activity. The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphylococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing. The miRNA profile of the parenchyma was found to change during mastitis, with its profile depending on the type of pathogen. Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identified, including 32 that were differentially expressed (p ≤ 0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identified: 10 were upregulated (p ≤ 0.05), and 2 downregulated (p ≤ 0.05). In addition, comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identified; in both comparisons, differentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identified in each comparison, with 2 being common to both immune system processes and signal transduction. Our results indicate that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).

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