Hybrid weakness in a rice interspecific hybrid is nitrogen-dependent, and accompanied by changes in gene expression at both total transcript level and parental allele partitioning

Abstract Background: In this study, sodium nitrate (SNP, a donor of nitric oxide) and methyl jasmonate (MJ) were used as exogenous hormones. The experiment was conducted with the offspring (interspecific hybrid) D110 of ash and ash, and their respective parents (non-interspecific hybrid) D113 and 4-3 as experimental materials. The experiment set up three experimental groups of drought stress, exogenous hormone SNP and MJ, and a control group under normal growth (non-drought stress), to study the physiological indicators and gene expression of manchurian ash. Result: The results showed that under drought stress and exogenous application of hormone SNP or MJ, there were significant differences between hybrids and parents in plant growth, photosynthesis, defense enzyme activity, hormone content and gene expression.Conclusions: This experiment provides a new theoretical support for the existing hormone breeding methods of manchurian ash, which can improve the drought resistance of manchurian ash and increase its survival rate in the wild. Increasing the growth rate and breeding efficiency of manchurian ash brings new ideas.

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Differential expression of alpha- and beta-enolase genes during rat heart development and hypertrophy

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.1995.269.6.h1843 ◽

1995 ◽

Vol 269 (6) ◽

pp. H1843-H1851 ◽

Cited By ~ 12

Author(s):

A. Keller ◽

J. D. Rouzeau ◽

F. Farhadian ◽

C. Wisnewsky ◽

F. Marotte ◽

...

Keyword(s):

Gene Expression ◽

Heart Development ◽

Rat Heart ◽

Cardiac Development ◽

Transcript Level ◽

Glycolytic Enzyme ◽

High Ratio ◽

Control Mechanisms ◽

Nonmuscle Cells ◽

A Minor

We have analyzed the transition between isoforms of the glycolytic enzyme enolase (2-phospho-D-glycerate hydrolyase; EC 4.2.1.11) in rat heart during normal and pathological growth. A striking fall in embryonic alpha-enolase gene expression occurs during cardiac development, mostly controlled at pretranslational steps. In fetal and neonatal hearts, muscle-specific beta-enolase gene expression is a minor contributor to total enolase. Control mechanisms of beta-enolase gene expression must include posttranscriptional steps. Aortic stenosis induces a rapid and drastic decrease in beta-enolase transcript level in cardiomyocytes, followed by the fall in beta-subunit level. In contrast, alpha-enolase transcript level is not significantly altered, although the corresponding subunit level increases in nonmuscle cells. We conclude that, like fetal heart, hypertrophic heart is characterized by a high ratio of alpha- to beta-enolase subunit concentrations. This study indicates that the decrease in beta-enolase gene expression may be linked to beneficial energetic changes in contractile properties occurring during cardiac hypertrophy

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Gene expression amplification by nuclear speckle association

The Journal of Cell Biology ◽

10.1083/jcb.201904046 ◽

2019 ◽

pp. jcb.201904046 ◽

Cited By ~ 7

Author(s):

Jiah Kim ◽

Neha Chivukula Venkata ◽

Gabriela Andrea Hernandez Gonzalez ◽

Nimish Khanna ◽

Andrew S. Belmont

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Liquid Droplet ◽

Transcript Level ◽

Rna Degradation ◽

Nuclear Speckles ◽

Nascent Transcript ◽

Nuclear Compartment ◽

Transcript Levels ◽

Endogenous Genes

Many active genes reproducibly position near nuclear speckles, but the functional significance of this positioning is unknown. Here we show that HSPA1B BAC transgenes and endogenous Hsp70 genes turn on 2–4 min after heat shock (HS), irrespective of their distance to speckles. However, both total HSPA1B mRNA counts and nascent transcript levels measured adjacent to the transgene are approximately twofold higher for speckle-associated alleles 15 min after HS. Nascent transcript level fold-increases for speckle-associated alleles are 12–56-fold and 3–7-fold higher 1–2 h after HS for HSPA1B transgenes and endogenous genes, respectively. Severalfold higher nascent transcript levels for several Hsp70 flanking genes also correlate with speckle association at 37°C. Live-cell imaging reveals that HSPA1B nascent transcript levels increase/decrease with speckle association/disassociation. Initial investigation reveals that increased nascent transcript levels accompanying speckle association correlate with reduced exosome RNA degradation and larger Ser2p CTD-modified RNA polymerase II foci. Our results demonstrate stochastic gene expression dependent on positioning relative to a liquid-droplet nuclear compartment through “gene expression amplification.”

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Gene expression in an interspecific hybrid: Analysis of hemoglobins in donkey, horse, and mule by peptide mapping

Biochemical Genetics ◽

10.1007/bf00484019 ◽

1970 ◽

Vol 4 (1) ◽

pp. 73-85 ◽

Cited By ~ 4

Author(s):

W. Akintunde Isaacs

Keyword(s):

Gene Expression ◽

Interspecific Hybrid ◽

Peptide Mapping ◽

Hybrid Analysis

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Angiogenic Gene Expression in Down Syndrome Fetal Hearts

Fetal Diagnosis and Therapy ◽

10.1159/000441356 ◽

2015 ◽

Vol 40 (1) ◽

pp. 21-27 ◽

Cited By ~ 7

Author(s):

Olga Sánchez ◽

Carmen Domínguez ◽

Aina Ruiz ◽

Irene Ribera ◽

Jaume Alijotas ◽

...

Keyword(s):

Gene Expression ◽

Down Syndrome ◽

Growth Factor ◽

Heart Defects ◽

Hypoxia Inducible Factor ◽

Transcript Level ◽

Heart Tissue ◽

Angiogenic Factors ◽

Heme Oxygenase 1 ◽

Endothelial Growth Factor

Introduction: Forty percent of Down syndrome (DS) fetuses have congenital heart defects (CHD). An abnormal angiogenic environment has been described in euploid fetuses with CHD. However, the underlying pathophysiologic pathway that contributes to CHD in DS remains unknown. The objective was to compare the expression of angiogenic factors and chronic hypoxia genes in heart tissue from DS and euploid fetuses with and without CHD. Methods: The gene expression profile was determined by real-time PCR quantification in heart tissue from 33 fetuses with DS, 23 euploid fetuses with CHD and 23 control fetuses. Results: Angiogenic factors mRNA expression was significantly increased in the DS group compared to the controls (soluble fms-like tyrosine kinase-1, 81%, p = 0.007; vascular endothelial growth factor A, 57%, p = 0.006, and placental growth factor, 32%, p = 0.0227). Significant increases in the transcript level of hypoxia-inducible factor-2α and heme oxygenase 1 were also observed in the DS group compared to the controls. The expression of angiogenic factors was similar in DS fetuses and CHD euploid fetuses with CHD. Conclusion: Abnormal angiogenesis was detected in the hearts of DS fetuses with and without CHD. Our results suggest that DS determines an intrinsically angiogenic impairment that may be present in the fetal heart.

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Gene Expression of Medicago sativa Inoculated with Sinorhizobium meliloti as Modulated by the Xenobiotics Cadmium and Fluoranthene

Zeitschrift für Naturforschung C ◽

10.1515/znc-2000-3-414 ◽

2000 ◽

Vol 55 (3-4) ◽

pp. 222-232 ◽

Cited By ~ 3

Author(s):

Heike Neumann ◽

Dietrich Werner

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Medicago Sativa ◽

Sinorhizobium Meliloti ◽

Rhizobium Meliloti ◽

Root Nodules ◽

Cadmium Concentration ◽

Transcript Level ◽

Northern Hybridization ◽

Fresh Weight

Abstract Alfalfa plants (Medicago sativa cv. Europe) inoculated with Sinorhizobium meliloti 2011 (formerly Rhizobium meliloti, de Lajudie et al., 1994) were cultivated for 14 days under standardized growth conditions in mineral medium with addition of the heavy metal cadmium or the polycyclic aromatic hydrocarbon fluoranthene. These xenobiotics significantly reduced the numbers of root nodules before any visible damage to the plant could be detected. EC10. EC50, and EC90 (effective concentrations reducing nodulation, shoot and root fresh weight by 10, 50, or 90% compared to the control without pollutant) were calculated. EC50 for cadmium ranged from 5.8 jam (nodulation) to more than 20 μᴍ (root fresh weight). Testing fluoranthene resulted in an EC50 of 2.5 μg cm-2 for nodulation, and EC50 values of more than 35 μg cm-2 for shoot and root biomass production, indicating that the effect parameter nodulation is 10-fold more sensitive than shoot and root fresh weight. With m RNA differential display techniques the effects of both xenobiotics on gene expression in alfalfa root systems were studied. 37 differentially displayed transcripts were detected. Two of them, called DDMs1 and DDMs2, were confirmed by northern hybridization to be down-regulated in the presence of the xenobiotics. The expression of transcript DDMs1 was enhanced in alfalfa control plants inoculated with rhizobia, the transcript level was increased 2.5-3-fold compared to non-inoculated plants. This positive effect of nodulation was suppressed, partly by 35 μg cm-2 fluoranthene and totally by 20 μᴍ cadmium. The decrease in DDMsl transcription was highly affected by the cadmium concentration with an EC50 of 5.9 μᴍ . Compared to nodulation, almost identical EC10, EC50. and EC90 values were found for DDMsl expression. Sequence analysis of DDMsl revealed a significant overall homology (50% identity) to a hypothetical protein from Arabidopsis thaliana with high similarity to a copper transporting ATPase. High levels of transcript DDMs2 were observed in control plants with a 50% decrease in the xenobiotic-treated plants. DDM s2 gave a strong homology (82% identity) to the cytoplasmatic 60S ribosomal protein L18 from Arabidopsis thaliana.

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Enterococcus faecalis rnjB Is Required for Pilin Gene Expression and Biofilm Formation

Journal of Bacteriology ◽

10.1128/jb.00725-10 ◽

2010 ◽

Vol 192 (20) ◽

pp. 5489-5498 ◽

Cited By ~ 41

Author(s):

Peng Gao ◽

Kenneth L. Pinkston ◽

Sreedhar R. Nallapareddy ◽

Ambro van Hoof ◽

Barbara E. Murray ◽

...

Keyword(s):

Gene Expression ◽

Enterococcus Faecalis ◽

Drug Targets ◽

Deletion Mutant ◽

Transcript Level ◽

Northern Blotting ◽

Gram Positive ◽

Gene Assay ◽

Functional Features ◽

Pilin Gene

ABSTRACT Pili in Gram-positive bacteria play a major role in the colonization of host tissue and in the development of biofilms. They are promising candidates for vaccines or drug targets since they are highly immunogenic and share common structural and functional features among various Gram-positive pathogens. Numerous publications have helped build a detailed understanding of pilus surface assembly, yet regulation of pilin gene expression has not been well defined. Utilizing a monoclonal antibody developed against the Enterococcus faecalis major pilus protein EbpC, we identified mutants from a transposon (Tn) insertion library which lack surface-exposed Ebp pili. In addition to insertions in the ebp regulon, an insertion in ef1184 (dapA) significantly reduced levels of EbpC. Analysis of in-frame dapA deletion mutants and mutants with the downstream gene rnjB deleted further demonstrated that rnjB was responsible for the deficiency of EbpC. Sequence analysis revealed that rnjB encodes a putative RNase J2. Subsequent quantitative real-time PCR (qRT-PCR) and Northern blotting demonstrated that the ebpABC mRNA transcript level was significantly decreased in the rnjB deletion mutant. In addition, using a reporter gene assay, we confirmed that rnjB affects the expression of the ebpABC operon. Functionally, the rnjB deletion mutant was attenuated in its ability to produce biofilm, similar to that of an ebpABC deletion mutant which lacks Ebp pili. Together, these results demonstrate the involvement of rnjB in E. faecalis pilin gene expression and provide insight into a novel mechanism of regulation of pilus production in Gram-positive pathogens.

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RNA Expression Analysis Using an AntisenseBacillus subtilis Genome Array

Journal of Bacteriology ◽

10.1128/jb.183.24.7371-7380.2001 ◽

2001 ◽

Vol 183 (24) ◽

pp. 7371-7380 ◽

Cited By ~ 74

Author(s):

Jian-Ming Lee ◽

Shehui Zhang ◽

Soumitra Saha ◽

Sonia Santa Anna ◽

Can Jiang ◽

...

Keyword(s):

Gene Expression ◽

Dynamic Range ◽

Expression Patterns ◽

Transcript Level ◽

Open Reading Frames ◽

Biosynthetic Genes ◽

Coding Regions ◽

Intergenic Regions ◽

Differential Gene ◽

Novel Transcripts

ABSTRACT We have developed an antisense oligonucleotide microarray for the study of gene expression and regulation in Bacillus subtilis by using Affymetrix technology. Quality control tests of the B. subtilis GeneChip were performed to ascertain the quality of the array. These tests included optimization of the labeling and hybridization conditions, determination of the linear dynamic range of gene expression levels, and assessment of differential gene expression patterns of known vitamin biosynthetic genes. In minimal medium, we detected transcripts for approximately 70% of the known open reading frames (ORFs). In addition, we were able to monitor the transcript level of known biosynthetic genes regulated by riboflavin, biotin, or thiamine. Moreover, novel transcripts were also detected within intergenic regions and on the opposite coding strand of known ORFs. Several of these novel transcripts were subsequently correlated to new coding regions.

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Regulatory motifs identified from a maize developmental coexpression network

Genome ◽

10.1139/gen-2013-0177 ◽

2014 ◽

Vol 57 (3) ◽

pp. 181-184 ◽

Cited By ~ 3

Author(s):

Gregory S. Downs ◽

Christophe Liseron-Monfils ◽

Lewis N. Lukens

Keyword(s):

Gene Expression ◽

Transcriptional Control ◽

Important Determinant ◽

Gene Expression Pattern ◽

Transcript Level ◽

Regulatory Sequences ◽

Regulatory Motifs ◽

Control Gene Expression ◽

Maize Gene ◽

Upstream Regulatory Sequences

Transcriptional control is an important determinant of plant development, and distinct modules of coordinated genes characterize the maize developmental transcriptome. Upstream regulatory sequences are often the primary factors that control gene expression pattern and abundance. Here, we identify 244 regulatory motifs that are significantly enriched within 24 gene expression modules previously constructed from transcript abundances of 34 876 Zea mays (maize) gene models from embryogenesis to senescence. Within modules, we identify motifs that have not been characterized. In addition, we identify motifs similar to experimentally verified motifs, and the functions of these motifs overlap with predicted module functions. This work demonstrates the power of transcript-level coexpression modules to identify both variants of known regulatory motifs and novel motifs that control a species’ developmental transcriptome.

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Effects of 1-MCP on the Physiological Attributes, Volatile Components and Ester-Biosynthesis-Related Gene Expression during Storage of ‘Jinyan’ Kiwifruit

Horticulturae ◽

10.3390/horticulturae7100381 ◽

2021 ◽

Vol 7 (10) ◽

pp. 381

Author(s):

Qiang Wang ◽

Xiaoxia An ◽

Miaolian Xiang ◽

Xiu Chen ◽

Zhenyu Luo ◽

...

Keyword(s):

Gene Expression ◽

Transcript Level ◽

Solid Content ◽

Soluble Solid Content ◽

Volatile Components ◽

Related Gene ◽

Methyl Butanoate ◽

Soluble Solid ◽

Ester Biosynthesis ◽

Aroma Components

The effects of 1.0 μL/L 1-methylcyclopropene (1-MCP) treatment on aroma quality and ester-biosynthesis-related gene expression of ‘Jinyan’ kiwifruit during room storage were examined, aiming to provide a theoretical basis and technical reference for the postharvest storage of kiwifruit. The results demonstrate that 1-MCP treatment conspicuously inhibited respiration rate, delayed a decrease in fruit firmness and increased soluble solid content (SSC) in ‘Jinyan’ kiwifruit. Compared to the control, the relative content of aroma components markedly changed in 1-MCP treatment kiwifruit during fruit ripening. The characteristic aroma of ‘Jinyan’ kiwifruit included ethyl butanoate, methyl butanoate, E-2-hexanal and hexenal, and 1-MCP treatment significantly reduced the ester content in kiwifruit. During the entire shelf life, the expression levels of AcLOX1, AcLOX5, AcLOX6, AcHPL and AcAAT were significantly inhibited in 1-MCP-treated fruit. However, the transcript level of AcADH was not suppressed by 1-MCP. The lower content of ester volatiles maybe ascribed to the suppression of AcLOXs, AcHPL and AcAAT.

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