Physiological and Comparative Transcriptomic Analysis Provide Insight Into Cotton (Gossypium hirsutum L.) Root Senescence in Response

Nitrogen (N) deficiency is one of the pivotal environmental factors that induce leaf senescence. However, little is known regarding the impact of low N on root senescence in cotton. Thus, the objective of this study was to investigate the effect of low nitrogen on root senescence. In this study, the molecular mechanism of cotton root senescence in response to nitrogen deficiency was investigated by combing physiological and transcriptomic analysis when no nitrogen and normal nitrogen (138mg N·kg−1 soil). The results showed that: (1) nitrogen starvation induced the premature senescence of leaf, while delaying root senescence. (2) The increase in catalase (CAT) activity at 60, 80, and 100days after emergence (DAE), combined with decrease of malonaldehyde content at 60, 80, and 100 DAE, and the content of abscisic acid (ABA), all of these contributed to the delay of root senescence by low nitrogen treatment. (3) To study the molecular mechanisms underlying root senescence, the gene expression profiling between low nitrogen and normal nitrogen treatments were compared pairwise at 20, 40, 60, 80, and 100 DAE. A total of 14,607 genes were identified to be differentially expressed at these five points. (5) Most genes involved in glutathione (GSH) and ascorbate peroxidase (APX) synthesis were upregulated, while ABA, apoptosis, caspase, and cell cycle-related differentially expressed genes (DEGs) were downregulated. Coupled with the physiology data, these results provide new insights into the effect of nitrogen starvation on root senescence.

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QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice

Frontiers in Genetics ◽

10.3389/fgene.2021.616428 ◽

2021 ◽

Vol 12 ◽

Author(s):

Congcong Shen ◽

Kai Chen ◽

Yanru Cui ◽

Jiantao Chen ◽

Xuefei Mi ◽

...

Keyword(s):

Grain Yield ◽

Nitrogen Deficiency ◽

Breeding Population ◽

Recurrent Parent ◽

Chromosome 2 ◽

Favorable Alleles ◽

Growing Seasons ◽

Nitrogen Treatments ◽

Normal Nitrogen ◽

Low Nitrogen

Nitrogen is one of the most important nutrients for rice growth and development. Breeding of nitrogen deficiency tolerance (NDT) variety is considered to be the most economic measure to solve the constrain of low nitrogen stress on grain yield in rice. An interconnected breeding (IB) population of 497 lines developed using Huanghuazhan (HHZ) as the recurrent parent and eight elite lines as the donor parents were tested for five traits including grain yield, biomass, harvest index, thousand grain weight, and spikelet fertility under two nitrogen treatments in three growing seasons. Association analysis using 7,388 bins generated by sequencing identified a total of 14, 14, and 12 QTLs for the five traits under low nitrogen (LN), normal nitrogen (NN), and LN/NN conditions, respectively, across three seasons. Favorable alleles were dissected for the 40 QTLs at the 10 NDT regions, and OM1723 was considered as the most important parent with the highest frequency of favorable alleles contributing to NDT-related traits. Six superior lines all showed significantly higher GY in LN environments and similar GY under NN environments except for H10. Substitution mapping using near-isogenic introgression lines delimited the qTGW2-1, which was identified on chromosome 2 under LN, NN, and LN/NN conditions into two QTLs, which were located in the two regions of about 200 and 350 kb with different favorable alleles. The bins 16, 1301, 1465, 1486, 3464, and 6249 harbored the QTLs for NDT detected in this study, and the QTLs/genes previously identified for NDT or nitrogen use efficiency (NUE) could be used for enhancing NDT and NUE by marker-assisted selection (MAS).

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Proteomic Insights into Starvation of Nitrogen-Replete Cells of Nostoc sp. PCC 7120 under β-N-Methylamino-L-Alanine (BMAA) Treatment

Toxins ◽

10.3390/toxins12060372 ◽

2020 ◽

Vol 12 (6) ◽

pp. 372

Author(s):

Olga A. Koksharova ◽

Ivan O. Butenko ◽

Olga V. Pobeguts ◽

Nina A. Safronova ◽

Vadim M. Govorun

Keyword(s):

Molecular Mechanisms ◽

Nitrogen Starvation ◽

Regulatory Protein ◽

Nitrogen Deficiency ◽

Regulatory Proteins ◽

Pii Protein ◽

Significant Difference ◽

Pcc 7120 ◽

Nitrogen Excess ◽

Starvation Conditions

All cyanobacteria produce a neurotoxic non-protein amino acid β-N-methylamino-L-alanine (BMAA). However, the biological function of BMAA in the regulation of cyanobacteria metabolism still remains undetermined. It is known that BMAA suppresses the formation of heterocysts in diazotrophic cyanobacteria under nitrogen starvation conditions, and BMAA induces the formation of heterocyst-like cells under nitrogen excess conditions, by causing the expression of heterocyst-specific genes that are usually “silent” under nitrogen-replete conditions, as if these bacteria receive a nitrogen deficiency intracellular molecular signal. In order to find out the molecular mechanisms underlying this unexpected BMAA effect, we studied the proteome of cyanobacterium Nostoc sp. PCC 7120 grown under BMAA treatment in nitrogen-replete medium. Experiments were performed in two experimental settings: (1) in control samples consisted of cells grown without the BMAA treatment and (2) the treated samples consisted of cells grown with addition of an aqueous solution of BMAA (20 µM). In total, 1567 different proteins of Nostoc sp. PCC 7120 were identified by LC-MS/MS spectrometry. Among them, 80 proteins belonging to different functional categories were chosen for further functional analysis and interpretation of obtained proteomic data. Here, we provide the evidence that a pleiotropic regulatory effect of BMAA on the proteome of cyanobacterium was largely different under conditions of nitrogen-excess compared to its effect under nitrogen starvation conditions (that was studied in our previous work). The most significant difference in proteome expression between the BMAA-treated and untreated samples under different growth conditions was detected in key regulatory protein PII (GlnB). BMAA downregulates protein PII in nitrogen-starved cells and upregulates this protein in nitrogen-replete conditions. PII protein is a key signal transduction protein and the change in its regulation leads to the change of many other regulatory proteins, including different transcriptional factors, enzymes and transporters. Complex changes in key metabolic and regulatory proteins (RbcL, RbcS, Rca, CmpA, GltS, NodM, thioredoxin 1, RpbD, ClpP, MinD, RecA, etc.), detected in this experimental study, could be a reason for the appearance of the “starvation” state in nitrogen-replete conditions in the presence of BMAA. In addition, 15 proteins identified in this study are encoded by genes, which are under the control of NtcA—a global transcriptional regulator—one of the main protein partners and transcriptional regulators of PII protein. Thereby, this proteomic study gives a possible explanation of cyanobacterium starvation under nitrogen-replete conditions and BMAA treatment. It allows to take a closer look at the regulation of cyanobacteria metabolism affected by this cyanotoxin.

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DOP22 Integrative -omic analysis reveals microbiota mediated molecular mechanisms influencing host mucosal gene expression in Crohn’s Disease

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab073.061 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S061-S062

Author(s):

P Sudhakar ◽

T Andrighetti ◽

S Verstockt ◽

C Caenepeel ◽

M Ferrante ◽

...

Keyword(s):

Gene Expression ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Molecular Mechanisms ◽

Bacterial Species ◽

Differentially Expressed ◽

Mucosal Barrier ◽

Bacterial Proteins ◽

The Impact ◽

Hub Proteins

Abstract Background Mechanistic evidence linking gut microbial changes and host mucosal barrier responses in patients with Crohn’s disease (CD) is lacking. In this study, we used a computational approach to integrate gut microbial and intestinal gene expression in CD patients. Methods Bacterial species, bacterial genes/transcripts with enhanced abundances/transcriptional activity in CD (t-statistic of > 2 and Q-value < 0.05), as well as mucosal (ileum/rectum) differentially expressed genes (DEGs) between CD (n =43) and non-IBD (n=22) subjects were retrieved from the Inflammatory Bowel Disease Meta -Omics Database (IBDMDB). The impact of bacterial proteins on host gene expression was inferred using MicrobioLink, a computational tool for inferring microbe-host interactions. Drug target information was retrieved from OpenTargets. Paired 16S read-outs from stool samples and gene expression data from ileal biopsies in CD patients (n=20) and non-IBD controls (n=15), cross-sectionally collected at our IBD referral center, were used for independent validation. Results Across the 8 identified bacterial species enriched in CD, 3.7% (n= 743) of the orthologous groups were identified as being able to bind to human proteins. Network diffusion analysis uncovered bacterial proteins which could cumulatively modulate the expression of 42% of the genes differentially expressed in the ileum of CD patients. Topological and pathway analysis of the inferred signaling network modulated by the microbiota revealed several key hub proteins and immune-related pathways associated with IL-4, IL-2 and IL-13 signaling, receptor tyrosine-kinases, NFkB, and toll-like receptors including TLR4. Seventy-eight percent of the DEGs in our discovery cohort were also differentially expressed in the validation cohort (R2 = 0.907). Bacterial proteins post-translationally modifying host receptors resulted in the up-regulation of several pro-inflammatory cytokines via critical hub proteins such as NFkB (Figure 1). We observed different levels of locational specificity (from 35 to 61%) for the top regulators such as SPI1, STAT1 and NFKB1in terms of genes regulated by them in ileum and rectum. 24 proteins including ITGA4 and JAK1 from the ileal and rectal signaling networks are existing targets of CD drugs such as vedolizumab and tofacitinib, filgotinib and upadacitinib respectively. Conclusion Our findings outline the potential mechanisms of microbiome-induced host responses and provide insights into designing microbiome-mediated therapies to prevent and/or treat CD.

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Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing

PeerJ ◽

10.7717/peerj.9737 ◽

2020 ◽

Vol 8 ◽

pp. e9737

Author(s):

Zhongwu Su ◽

Hao Xiong ◽

Yi Liu ◽

Jiaqi Pang ◽

Hanqing Lin ◽

...

Keyword(s):

Hearing Loss ◽

Next Generation Sequencing ◽

Molecular Mechanisms ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Next Generation ◽

Age Related ◽

Cochlear Inflammation ◽

Age Related Hearing Loss ◽

Generation Sequencing

Background In our aging society, age-related hearing loss (AHL) is the most common sensory disorder in old people. Much progress has been made in understanding the pathological process of AHL over the past few decades. However, the mechanism of cochlear degeneration during aging is still not fully understood. Methods Next generation sequencing technique was used to sequence the whole transcriptome of the cochlea of C57BL/6 mice, a mouse model of AHL. Differentially expressed genes (DEGs) were identified using the Cuffdiff software. GO and KEGG pathway enrichment analyses of the DEGs were implemented by using the GOseq R package and KOBAS software, respectively. Results A total of 731 genes (379 up- and 352 down-regulated) were revealed to be differentially expressed in the cochlea of aged mice compared to the young. Many genes associated with aging, apoptosis, necroptosis and particularly, inflammation were identified as being significantly modulated in the aged cochlea. GO and KEGG analyses of the upregulated DEGs revealed that the most enriched terms were associated with immune responses and inflammatory pathways, whereas many of the downregulated genes are involved in ion channel function and neuronal signaling. Real-time qPCR showed that H2O2 treatment significantly induced the expression of multiple inflammation and necroptosis-related genes in HEI-OC1 cells. Conclusion Using next generation sequencing, our transcriptomic analysis revealed the differences of gene expression pattern with age in the cochlea of C57BL/6 mice. Our study also revealed multiple immune and inflammatory transcriptomic changes during cochlear aging and provides new insights into the molecular mechanisms underlying cochlear inflammation in AHL.

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Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals ◽

10.3390/ani9060387 ◽

2019 ◽

Vol 9 (6) ◽

pp. 387 ◽

Cited By ~ 6

Author(s):

Zengkui Lu ◽

Mingxing Chu ◽

Qing Li ◽

Meilin Jin ◽

Xiaojuan Fei ◽

...

Keyword(s):

Heat Stress ◽

Differentially Expressed Genes ◽

Stress Responses ◽

Large Scale ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

P Value ◽

Comprehensive Overview

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

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Transcriptomic Analysis Reveals the Contribution of QMrl-7B to Wheat Root Growth and Development

10.21203/rs.3.rs-124839/v1 ◽

2020 ◽

Author(s):

Jiajia Liu ◽

Hanwen Li ◽

Na Zhang ◽

Deyuan Meng ◽

Liya Zhi ◽

...

Keyword(s):

Root Growth ◽

Root System ◽

Root Traits ◽

Wheat Root ◽

Root System Architecture ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Yield Potential ◽

Trait Locus ◽

Normal Nitrogen

Abstract Backgound: Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for increasing yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), strongly contributes to an improved root system in wheat. Results: To further analyse the biological functions of QMrl-7B in root development, two types of Triticum aestivum near isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411), were subjected to transcriptomic analysis. Among all the mapped genes analysed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that include mainly NO3- transporters, phytohormone signalling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this assay, 4308 were specifically expressed in the A-NIL which brings superior alleles, and 2463 were expressed specifically in the B-NIL which brings inferior alleles. These DEGs reflect different responses of the two types of NILs to varying N supplies, which likely involve LN-induced root growth. Conclusions: These results explain the better-developed root system and increased root vitality provided by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.

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Congenital cystic adenomatoid malformations of the lung: an epithelial transcriptomic approach

Respiratory Research ◽

10.1186/s12931-020-1306-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Guillaume Lezmi ◽

Shamila Vibhushan ◽

Claudia Bevilaqua ◽

Nicolas Crapart ◽

Nicolas Cagnard ◽

...

Keyword(s):

Molecular Mechanisms ◽

Branching Morphogenesis ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Protein Levels ◽

Redundant Genes ◽

And Control ◽

Laser Capture ◽

Congenital Cystic Adenomatoid Malformations

Abstract Background The pathophysiology of congenital cystic adenomatoid malformations (CCAM) of the lung remains poorly understood. Aim This study aimed to identify more precisely the molecular mechanisms limited to a compartment of lung tissue, through a transcriptomic analysis of the epithelium of macrocystic forms. Methods Tissue fragments displaying CCAM were obtained during planned surgical resections. Epithelial mRNA was obtained from cystic and normal areas after laser capture microdissection (LCM). Transcriptomic analyses were performed and the results were confirmed by RT-PCR and immunohistochemistry in independent samples. Results After controlling for RNA quality, we analysed the transcriptomes of six cystic areas and five control areas. In total, 393 transcripts were differentially expressed in the epithelium, between CCAM and control areas. The most highly redundant genes involved in biological functions and signalling pathways differentially expressed between CCAM and control epithelium included TGFB2, TGFBR1, and MAP 2 K1. These genes were considered particularly relevant as they have been implicated in branching morphogenesis. RT-qPCR analysis confirmed in independent samples that TGFBR1 was more strongly expressed in CCAM than in control tissues (p < 0.03). Immunohistochemistry analysis showed TGFBR1 (p = 0.0007) and TGFB2 (p < 0.02) levels to be significantly higher in the epithelium of CCAM than in that of control tissues. Conclusions This compartmentalised transcriptomic analysis of the epithelium of macrocystic lung malformations identified a dysregulation of TGFB signalling at the mRNA and protein levels, suggesting a possible role of this pathway in CCAM pathogenesis. Trial registration ClinicalTrials.gov Identifier: NCT01732185.

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Transcriptomic Analysis of Methyl Jasmonate Treatment Reveals Gene Networks Involved in Drought Tolerance at the Early Developmental Stage in Pearl Millet (Pennisetum Glaucum L. Br)

10.21203/rs.3.rs-1125460/v1 ◽

2021 ◽

Author(s):

Adama Ndiaye ◽

Amadou Oury Diallo ◽

Ndèye Coura Fall ◽

Rose Diambogne Diouf ◽

Diaga Diouf ◽

...

Keyword(s):

Drought Tolerance ◽

Methyl Jasmonate ◽

Pearl Millet ◽

Molecular Mechanisms ◽

Early Stage ◽

Reduction Process ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Stage Of Development ◽

Oxidation Reduction

Abstract Water deficit stress at the early stage of development is one of the main factors limiting pearl millet production. A practice to cope with would be to apply hormones to stimulate plant growth and development. Exogenous methyl jasmonate (MeJA) can improve drought tolerance by modulating key pathways, therefore, we assumed that can occur in pearl millet during the early stage of development. To decipher the molecular mechanisms controlling these pathways, RNAseq was conducted in two pearl millet genotypes, drought-sensitive SosatC88 and drought-tolerant Souna3, in response to 200 µM of MeJA. Transcriptomic analysis between the MeJA-treated and non-treated plants revealed 3270 differentially expressed genes (DEGs) in SosatC88 and 127 DEGs in Souna3. Gene ontology (GO) classification assigned most regulated DEGs in SosatC88 to heme binding, oxidation-reduction process, response to oxidative stress and membrane, and in Souna3 to terpene synthase activity, lyase activity, magnesium ion binding, and thylakoid. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis reveals that DEGs in SosatC88 are related to the oxidation-reduction process, the biosynthesis of other secondary metabolites, the signal transduction, and the metabolism of terpenoids, while in Souna3, DEGs are related to the metabolism of terpenoids and the energy metabolism. Two genes encoding a diterpenoid biosynthesis-related and a Glutathione S transferase T3 were contra-regulated between SosatC88 and Souna3. Additionally, five random genes differentially expressed by RNAseq were validated using qPCR. These insights into the molecular mechanisms of pearl millet genotype tolerance at the early stage of development contribute to the understanding of the role of hormones in adaptation to drought-prone environments.

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Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

10.1101/245670 ◽

2018 ◽

Cited By ~ 1

Author(s):

Roberta Davoli ◽

Enrico Gaffo ◽

Martina Zappaterra ◽

Stefania Bortoluzzi ◽

Paolo Zambonelli

Keyword(s):

Mirna Expression ◽

Small Rnas ◽

Genetic Improvement ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Fat Deposition ◽

Differentially Expressed ◽

Large White ◽

The Impact

SummaryThe identification of the molecular mechanisms regulating pathways associated to the potential of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. MicroRNAs (miRNAs) interactions with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is well far from saturation and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations are still fragmentary. We characterized by RNAseq the small RNAs (sRNAs) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs, 14 up-regulated (including ssc-miR-132, ssc-miR-146b, sscmiR-221–5p, ssc-miR-365–5p, and the moRNA ssc-moR-21–5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p, and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network resulted to be expressed from backfat related pig QTLs. These results are informative on the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs, and facilitate the perspective implementation of innovative strategies of pig genetic improvement based on genomic markers.

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The Impact of Ultraviolet Radiation on Barrier Function in Human Skin: Molecular Mechanisms and Topical Therapeutics

Current Medicinal Chemistry ◽

10.2174/0929867324666171106164916 ◽

2019 ◽

Vol 25 (40) ◽

pp. 5503-5511 ◽

Cited By ~ 5

Author(s):

Abdulaziz Alhasaniah ◽

Michael J. Sherratt ◽

Catherine A. O'Neill

Keyword(s):

Ultraviolet Radiation ◽

Barrier Function ◽

Molecular Mechanisms ◽

Transepidermal Water Loss ◽

Protective Effects ◽

Barrier Dysfunction ◽

Epidermal Barrier ◽

Positive Effects ◽

Terrestrial Mammals ◽

The Impact

A competent epidermal barrier is crucial for terrestrial mammals. This barrier must keep in water and prevent entry of noxious stimuli. Most importantly, the epidermis must also be a barrier to ultraviolet radiation (UVR) from the sunlight. Currently, the effects of ultraviolet radiation on epidermal barrier function are poorly understood. However, studies in mice and more limited work in humans suggest that the epidermal barrier becomes more permeable, as measured by increased transepidermal water loss, in response UVR, at doses sufficiently high to induce erythema. The mechanisms may include disturbance in the organisation of lipids in the stratum corneum (the outermost layer of the epidermis) and reduction in tight junction function in the granular layer (the first living layer of the skin). By contrast, suberythemal doses of UVR appear to have positive effects on epidermal barrier function. Topical sunscreens have direct and indirect protective effects on the barrier through their ability to block UV and also due to their moisturising or occlusive effects, which trap water in the skin, respectively. Some topical agents such as specific botanical extracts have been shown to prevent the loss of water associated with high doses of UVR. In this review, we discuss the current literature and suggest that the biology of UVR-induced barrier dysfunction, and the use of topical products to protect the barrier, are areas worthy of further investigation.

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