scholarly journals Gene Expression and Proteomics Studies Suggest an Involvement of Multiple Pathways Under Day and Day–Night Combined Heat Stresses During Grain Filling in Wheat

2021 ◽  
Vol 12 ◽  
Author(s):  
Venkatesh Chunduri ◽  
Amandeep Kaur ◽  
Shubhpreet Kaur ◽  
Aman Kumar ◽  
Saloni Sharma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Weight ◽  
Heat Stress ◽  
Developmental Stages ◽  
Storage Proteins ◽  
Polyacrylamide Gel Electrophoresis ◽  
Grain Filling ◽  
Early Gene ◽  
Real Time Quantitative Pcr ◽  
Expression Of Genes

Recent weather fluctuations imposing heat stress at the time of wheat grain filling cause frequent losses in grain yield and quality. Field-based studies for understanding the effect of terminal heat stress on wheat are complicated by the effect of multiple confounding variables. In the present study, the effect of day and day–night combined heat stresses during the grain-filling stage was studied using gene expression and proteomics approaches. The gene expression analysis was performed by using real-time quantitative PCR (RT-qPCR). The expression of genes related to the starch biosynthetic pathway, starch transporters, transcription factors, and stress-responsive and storage proteins, at four different grain developmental stages, indicated the involvement of multiple pathways. Under the controlled conditions, their expression was observed until 28 days after anthesis (DAA). However, under the day stress and day–night stress, the expression of genes was initiated earlier and was observed until 14 DAA and 7 DAA, respectively. The protein profiles generated using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF MS/MS) showed a differential expression of the proteins belonging to multiple pathways that included the upregulation of proteins related to the translation, gliadins, and low-molecular-weight (LMW) glutenins and the downregulation of proteins related to the glycolysis, photosynthesis, defense, and high-molecular-weight (HMW) glutenins. Overall, the defense response to the day heat stress caused early gene expression and day–night heat stress caused suppression of gene expression by activating multiple pathways, which ultimately led to the reduction in grain-filling duration, grain weight, yield, and processing quality.

scholarly journals Evaluation of putative reference genes for quantitative real-time PCR normalization inLilium regaleduring development and under stress

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1837 ◽  
Author(s):  
Qiang Liu ◽  
Chi Wei ◽  
Ming-Fang Zhang ◽  
Gui-Xia Jia
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Real Time ◽  
Quantitative Pcr ◽  
Biotic Stress ◽  
Reference Genes ◽  
Developmental Stages ◽  
Real Time Quantitative Pcr ◽  
The Stability ◽  
Experimental Treatments

Normalization to reference genes is the most common method to avoid bias in real-time quantitative PCR (qPCR), which has been widely used for quantification of gene expression. Despite several studies on gene expression,Lilium, and particularlyL. regale, has not been fully investigated regarding the evaluation of reference genes suitable for normalization. In this study, nine putative reference genes, namely18S rRNA,ACT,BHLH,CLA,CYP,EF1,GAPDH,SANDandTIP41, were analyzed for accurate quantitative PCR normalization at different developmental stages and under different stress conditions, including biotic (Botrytis elliptica), drought, salinity, cold and heat stress. All these genes showed a wide variation in their Cq (quantification Cycle) values, and their stabilities were calculated by geNorm, NormFinder and BestKeeper. In a combination of the results from the three algorithms,BHLHwas superior to the other candidates when all the experimental treatments were analyzed together;CLAandEF1were also recommended by two of the three algorithms. As for specific conditions,EF1under various developmental stages,SANDunder biotic stress,CYP/GAPDHunder drought stress, andTIP41under salinity stress were generally considered suitable. All the algorithms agreed on the stability ofSANDandGAPDHunder cold stress, while onlyCYPwas selected under heat stress by all of them. Additionally, the selection of optimal reference genes under biotic stress was further verified by analyzing the expression level ofLrLOXin leaves inoculated withB. elliptica. Our study would be beneficial for future studies on gene expression and molecular breeding ofLilium.

scholarly journals Wheat (Triticum aestivum L.) TaHMW1D Transcript Variants Are Highly Expressed in Response to Heat Stress and in Grains Located in Distal Part of the Spike

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 687
Author(s):  
Chan Seop Ko ◽  
Jin-Baek Kim ◽  
Min Jeong Hong ◽  
Yong Weon Seo
Keyword(s):  
Heat Stress ◽  
High Temperature ◽  
Temperature Stress ◽  
Storage Proteins ◽  
Seed Storage ◽  
Seed Storage Proteins ◽  
Grain Filling ◽  
High Temperature Stress ◽  
Two Dimensional Gel Electrophoresis ◽  
Transcript Variants

High-temperature stress during the grain filling stage has a deleterious effect on grain yield and end-use quality. Plants undergo various transcriptional events of protein complexity as defensive responses to various stressors. The “Keumgang” wheat cultivar was subjected to high-temperature stress for 6 and 10 days beginning 9 days after anthesis, then two-dimensional gel electrophoresis (2DE) and peptide analyses were performed. Spots showing decreased contents in stressed plants were shown to have strong similarities with a high-molecular glutenin gene, TraesCS1D02G317301 (TaHMW1D). QRT-PCR results confirmed that TaHMW1D was expressed in its full form and in the form of four different transcript variants. These events always occurred between repetitive regions at specific deletion sites (5′-CAA (Glutamine) GG/TG (Glycine) or (Valine)-3′, 5′-GGG (Glycine) CAA (Glutamine) -3′) in an exonic region. Heat stress led to a significant increase in the expression of the transcript variants. This was most evident in the distal parts of the spike. Considering the importance of high-molecular weight glutenin subunits of seed storage proteins, stressed plants might choose shorter polypeptides while retaining glutenin function, thus maintaining the expression of glutenin motifs and conserved sites.

scholarly journals DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Wang ◽  
Quanwei Lu ◽  
Hui Song ◽  
Nan Hu ◽  
Yangyang Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Potential Function ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Dynamic Change ◽  
Foxtail Millet ◽  
Grain Filling ◽  
Sequencing Analysis ◽  
Grain Development

Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.

scholarly journals Evidence of positive regulation of mycobacteriophage D29 early gene expression obtained from an investigation using a temperature-sensitive mutant of the phage

2020 ◽  
Vol 367 (21) ◽  
Author(s):  
Shrestha Ghosh ◽  
Rahul Shaw ◽  
Apurba Sarkar ◽  
Sujoy K Das Gupta
Keyword(s):  
Gene Expression ◽  
Proteome Analysis ◽  
Early Gene ◽  
Specific Factor ◽  
Temperature Sensitive ◽  
Expression Of Genes ◽  
Infected Cells ◽  
Ts Mutant ◽  
The Right ◽  
High Level

ABSTRACT Mycobacteriophages are phages that infect and kill Mycobacteria, several of which, Mycobacterium tuberculosis (Mtb), for example, cause the disease tuberculosis. Although genomes of many such phages have been sequenced, we have very little insight into how they express their genes in a controlled manner. To address this issue, we have raised a temperature-sensitive (ts) mutant of phage D29 that can grow at 37°C but not at 42°C and used it to perform differential gene expression and proteome analysis studies. Our analysis results indicate that expression of genes located in the right arm, considered to be early expressed, was lowered as the temperature was shifted from 37°C to 42°C. In contrast, expression of those on the left, the late genes were only marginally affected. Thus, we conclude that transcription of genes from the two arms takes place independently of each other and that a specific factor must be controlling the expression of the right arm genes. We also observe that within the right arm itself; there exists a mechanism to ensure high-level synthesis of Gp48, a thymidylate synthase X. Enhanced presence of this protein in infected cells results in delayed lysis and higher phage yields.

scholarly journals Diurnal Changes in Water Soluble Carbohydrate Components in Leaves and Sucrose Associated TaSUT1 Gene Expression during Grain Development in Wheat

2020 ◽  
Vol 21 (21) ◽  
pp. 8276
Author(s):  
Sarah Al-Sheikh Ahmed ◽  
Jingjuan Zhang ◽  
Hussein Farhan ◽  
Yingquan Zhang ◽  
Zitong Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Grain Filling ◽  
Water Soluble ◽  
Soluble Carbohydrate ◽  
Diurnal Changes ◽  
Flag Leaves ◽  
Diurnal Patterns ◽  
Carbohydrate Components ◽  
Water Soluble Carbohydrate

In plant tissues, sugar levels are determined by the balance between sugar import, export, and sugar synthesis. So far, water soluble carbohydrate (WSC) dynamics have not been investigated in a diurnal context in wheat stems as compared to the dynamics in flag leaves during the terminal phases of grain filling. Here, we filled this research gap and tested the hypothesis that WSC dynamics interlink with gene expression of TaSUT1. The main stems and flag leaves of two genotypes, Westonia and Kauz, were sampled at four hourly intervals over a 24 h period at six developmental stages from heading to 28 DAA (days after anthesis). The total levels of WSC and WSC components were measured, and TaSUT1 gene expression was quantified at 21 DAA. On average, the total WSC and fructan levels in the stems were double those in the flag leaves. In both cultivars, diurnal patterns in the total WSC and sucrose were detected in leaves across all developmental stages, but not for the fructans 6-kestose and bifurcose. However, in stems, diurnal patterns of the total WSC and fructan were only found at anthesis in Kauz. The different levels of WSC and WSC components between Westonia and Kauz are likely associated with leaf chlorophyll levels and fructan degradation, especially 6-kestose degradation. High correlation between levels of TaSUT1 expression and sucrose in leaves indicated that TaSUT1 expression is likely to be influenced by the level of sucrose in leaves, and the combination of high levels of TaSUT1 expression and sucrose in Kauz may contribute to its high grain yield under well-watered conditions.

The high-molecular-weight glutenin subunit composition of Japanese hexaploid wheat landraces

2000 ◽  
Vol 51 (6) ◽  
pp. 673 ◽  
Author(s):  
H. Nakamura
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Hexaploid Wheat ◽  
Storage Proteins ◽  
Allelic Variation ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Glutenin Subunit ◽  
Subunit Composition ◽  
Wheat Landraces

The endosperm storage proteins of 174 Japanese wheat (Triticum aestivum) landraces were fractionated by sodium dodecyl sulfate polyacrylamide gel electrophoresis to determine their high-molecular-weight (HMW) glutenin subunit composition. These are alleles for complex gene loci, Glu-A1, Glu-B1, and Glu-D1, that are present in Japanese hexaploid wheat landraces. These were identified by comparison with the subunit mobility previously found in hexaploid wheat. Twenty-four different, major glutenin HMW subunits were identified. Each landrace contained 3–5 subunits, and 17 different glutenin subunit patterns were observed for 13 alleles in Japanese landraces. Japanese landraces showed specific allelic variation in glutenin HMW subunits, different from those in non-Japanese hexaploid wheats.

scholarly journals Dynamic Clustering of Gene Expression

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lingling An ◽  
R. W. Doerge
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Optimal Number ◽  
Sequential Data ◽  
Dynamic Clustering ◽  
Biological Processes ◽  
Time Frequency ◽  
Expression Of Genes

It is well accepted that genes are simultaneously involved in multiple biological processes and that genes are coordinated over the duration of such events. Unfortunately, clustering methodologies that group genes for the purpose of novel gene discovery fail to acknowledge the dynamic nature of biological processes and provide static clusters, even when the expression of genes is assessed across time or developmental stages. By taking advantage of techniques and theories from time frequency analysis, periodic gene expression profiles are dynamically clustered based on the assumption that different spectral frequencies characterize different biological processes. A two-step cluster validation approach is proposed to statistically estimate both the optimal number of clusters and to distinguish significant clusters from noise. The resulting clusters reveal coordinated coexpressed genes. This novel dynamic clustering approach has broad applicability to a vast range of sequential data scenarios where the order of the series is of interest.

Yolk proteins in salmon (Salmo salar) oocytes, eyed eggs, and alevins differing in viability

1990 ◽  
Vol 68 (5) ◽  
pp. 895-900 ◽  
Author(s):  
Thomas Olin ◽  
Alexandra von der Decken
Keyword(s):  
Molecular Weight ◽  
Salmo Salar ◽  
Gel Electrophoresis ◽  
Developmental Stages ◽  
Polyacrylamide Gel Electrophoresis ◽  
Specific Antigen ◽  
Protein Composition ◽  
Polyacrylamide Gel ◽  
Parental Origin ◽  
Yolk Proteins

The developmental stages of oocytes, eyed eggs, and alevins from salmon (Salmo salar) were compared for their yolk protein composition. In oocytes, SDS–polyacrylamide gel electrophoresis showed high amounts of a protein with the molecular weight (Mr) of 94 000. In eyed eggs, the 94 000 protein decreased and was undetectable in the alevins. Furthermore, in eyed eggs the proteins of 67 000, 30 000, and 27 000 increased, while in the alevins the concentration of the 67 000 protein decreased and that of the 39 000 increased. Vitellogenin-specific antigen sites analyzed by immunoblotting were most pronounced with the proteins of 94 000, 67 000, 39 000, 30 000, 23 000, and 19 000. Separation of the yolk proteins by HPLC gave four peaks at 280 nm for all three developmental stages. Each peak consisted of several proteins as analyzed by SDS–polyacrylamide gel electrophoresis. The 7-day-old alevins sampled from groups of different parental origin showed differences in the amount of the 67 000 and 23 000 proteins. Expectancy of survival within the group in connection with a slow disappearance of the 67 000 and 23 000 proteins was statistically significant. A fast disappearance may be used as an indication of, but not as the reason for, a high mortality within one group of alevins.

An approach for isolating high-molecular-weight glutenin subunit genes using monoclonal antibodies

Genome ◽  
2006 ◽  
Vol 49 (2) ◽  
pp. 181-189 ◽  
Author(s):  
H Q Wang ◽  
X Y Zhang
Keyword(s):  
Molecular Weight ◽  
Monoclonal Antibody ◽  
Triticum Aestivum ◽  
Amino Acid ◽  
High Molecular Weight ◽  
Storage Proteins ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Glutenin Subunits ◽  
Sds Page

High-molecular-weight glutenin subunits (HMW-GSs) play an important role in the breadmaking quality of wheat flour. In China, cultivars such as Triticum aestivum 'Xiaoyan No. 6' carrying the 1Bx14 and 1By15 glutenin subunits usually have attributes that result in high-quality bread and noodles. HMW-GS 1Bx14 and 1By15 were isolated by preparative sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and used as an antigen to immunize BALB/c mice. A resulting monoclonal antibody belonging to the IgG1 subclass was shown to bind to all HMW-GSs of Triticum aestivum cultivars, but did not bind to other storage proteins of wheat seeds in a Western blot analysis. After screening a complementary DNA expression library from immature seeds of 'Xiaoyan No. 6' using the monoclonal antibody, the HMW-GS 1By15 gene was isolated and fully sequenced. The deduced amino acid sequence showed an extra stretch of 15 amino acid repeats consisting of a hexapeptide and a nonapeptide in the repetitive domain of this y-type HMW subunit. Bacterial expression of a modified 1By15 gene, in which the coding sequence for the signal peptide was removed and a BamHI site eliminated, gave rise to a protein with mobility identical to that of HMW-GSs extracted from seeds of 'Xiaoyan No. 6' via SDS-PAGE. This approach for isolating genes using specific monoclonal antibody against HMW-GS genes is a good alternative to the extensively used polymerase chain reaction (PCR) technology based on sequence homology of HMW-GSs in wheat and its relatives.Key words: wheat, HMW-GS, monoclonal antibody, immunoscreen.

174 Follicular fluid extracellular vesicles obtained from Holstein cows kept under thermoneutral or heat stress conditions modify gene expression of in vitro-matured oocytes

2019 ◽  
Vol 31 (1) ◽  
pp. 211
Author(s):  
F. M. Dalanezi ◽  
R. A. Ferrazza ◽  
J. C. Ochoa ◽  
H. D. Mogllón ◽  
F. C. Destro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Follicular Fluid ◽  
Cumulus Cells ◽  
Oocyte Quality ◽  
Holstein Cows ◽  
Dna Integrity ◽  
Meiotic Progression ◽  
Expression Of Genes

Heat stress (HS) has a massive impact on bovine reproduction. In cows, some of these deleterious effects involve follicular development and oocyte quality. Extracellular vesicles (EV) secreted by granulosa cells play a critical role in the intrafollicular environment by directly influencing cumulus cells and oocyte functions. The objective of this study was to investigate the effect of follicular fluid EV obtained from Holstein cows kept under thermoneutral (TN) or HS conditions, on in vitro bovine oocyte maturation. Non-lactating Holstein cows were synchronized with the Ovsynch protocol and also received an intravaginal progesterone device. From ovulation day (Day 1), cows were randomly assigned to TN (26°C, 73% humidity; n=12) or HS (36°C, 70% humidity; n=12) environments. On Day 9, 2 follicles (F1 and F2) were individually aspirated and all remained follicles were ablated. Then, on Day 14, newly formed F1 and F2 were also aspirated. Follicular fluid from all follicles from each treatment was pooled and EV were obtained according to Silveira et al. (2017 PLoS One 12, 1-25) and diluted in PBS (100μL of PBS per mL of follicular fluid centrifuged). Pools of 20 cumulus-oocyte complexes (COC) grade 1 or 2 (Stojkovic et al. Biol Reprod 200164, 904-992], predominantly from Bos indicus, were submitted to the following treatment groups: Control (n=4): matured in 90μL of TCM-199 with Eagles’ salts, glutamine, NaHCO3, pyruvate, amikacin, and FSH (base medium); TN (n=4): matured in 81μL of base medium+9μL of TN EV suspension; and HS (n=4): matured in 81μL+9μL of HS EV suspension. All treatments were carried out at 38.5°C for 24h in a humid atmosphere with 5% CO2. After 24h of maturation, COC were evaluated for meiotic progression (Hoechst 33342 stain), DNA integrity (TUNEL stain), and expression of genes related to oocyte quality (TaqMan assay, Applied Biosystems/Thermo Fisher Scientific, Waltham, MA, USA). Results were analysed using ANOVA followed by Tukey post hoc test (P<0.05). When the experimental groups were compared with the control group, there was no treatment effect on meiotic progression, DNA integrity, or gene expression of cumulus cells. In the oocytes of the TN group, the genes HSF1, IGFBP2, BMP15, GDF9, CDCA8, HAS2, RPL15, STAT3,and PFKP were less expressed. We concluded that oocytes matured in the presence of EV from follicular fluid of cows kept under TN conditions had lesser expression of genes related to oocyte quality. This study was supported by FAPESP (Grant #2012/18297-7) and CAPES Foundation of Brazil.

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