scholarly journals Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Youko Oono ◽  
Takayuki Yazawa ◽  
Hiroyuki Kanamori ◽  
Harumi Sasaki ◽  
Satomi Mori ◽  
...  
Keyword(s):  
Metal Ion ◽  
Rice Genome ◽  
Cadmium Stress ◽  
Rna Seq ◽  
Rice Genome Sequence ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Toxic Concentrations ◽  
Cd Exposure

Rice growth is severely affected by toxic concentrations of the nonessential heavy metal cadmium (Cd). To elucidate the molecular basis of the response to Cd stress, we performed mRNA sequencing of rice following our previous study on exposure to high concentrations of Cd (Oono et al., 2014). In this study, rice plants were hydroponically treated with low concentrations of Cd and approximately 211 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence. Many genes, including some identified under high Cd concentration exposure in our previous study, were found to be responsive to low Cd exposure, with an average of about 11,000 transcripts from each condition. However, genes expressed constitutively across the developmental course responded only slightly to low Cd concentrations, in contrast to their clear response to high Cd concentration, which causes fatal damage to rice seedlings according to phenotypic changes. The expression of metal ion transporter genes tended to correlate with Cd concentration, suggesting the potential of the RNA-Seq strategy to reveal novel Cd-responsive transporters by analyzing gene expression under different Cd concentrations. This study could help to develop novel strategies for improving tolerance to Cd exposure in rice and other cereal crops.

scholarly journals Kinetics of Alkaline Phosphatase from Pig Kidney. Influence of complexing agents on stability and activity

1976 ◽  
Vol 153 (2) ◽  
pp. 151-157 ◽  
Author(s):  
B P Ackermann ◽  
J Ahlers
Keyword(s):  
Alkaline Phosphatase ◽  
Metal Ion ◽  
Complexing Agents ◽  
Pig Kidney ◽  
Low Concentrations ◽  
Sequential Addition ◽  
Quantitative Examination ◽  
High Concentrations ◽  
Kinetics Of ◽  
Active Centres

Metal ion-complexing agents, like KCN, EDTA etc., inactivate alkaline phosphatase of pig kidney. This inactivation is reversible at low concentrations of the complexing agents and irreversible at high concentrations. The reversible inhibition is probably due to removal of Zn2+ ions from the active site, where they are necessary for catalytic action, whereas the irreversible inhibition results from the removal of Zn2+ ions necessary for preservation of the structure. The inactivation is pseudo-first order. It depends on the concentration, size and charge of the complexing agents. β-Glycerophosphate and Mg2+ ions protect the enzyme from inactivation by complexing agents. Quantitative examination of the effect of substrate leads to a model that is similar to the “sequential model” proposed by D.E. Koshland, G. Nemethy & D. Filmer (1966) (Biochemistry 5, 365-385) to explain allosteric behavior of enzymes. It describes the sequential addition of two substrate molecules at two active centres of the dimer enzyme. The binding of the substrate molecules is accompanied by changes in the conformation, which lead to stabilization of the enzyme against attack by complexing agents.

scholarly journals Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

2020 ◽  
Author(s):  
Jose J De Vega ◽  
Ned Peel ◽  
Sarah J Purdy ◽  
Sarah Hawkins ◽  
Iain Donnison ◽  
...  
Keyword(s):  
Biomass Yield ◽  
Agronomic Traits ◽  
Biomass Productivity ◽  
Rna Seq ◽  
High Biomass ◽  
Metabolic Genes ◽  
Low Concentrations ◽  
High Starch ◽  
High Concentrations ◽  
Lower Biomass

ABSTRACTMiscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity and low chemical input requirements. Interspecific Miscanthus hybrids with high biomass yield were shown to have low concentrations of starch and sucrose but high concentrations of fructose. We performed a transcriptional RNA-seq analysis between selected Miscanthus hybrids with contrasting values for these phenotypes to clarify how these phenotypes are genetically controlled. We observed that genes directly involved in the synthesis and degradation of starch and sucrose were down-regulated in high yielding Miscanthus hybrids. At the same time, glycolysis and export of triose phosphates were up-regulated in high yielding Miscanthus hybrids. Our results evidence a direct relationship between high expression of essential enzymatic genes in the starch and sucrose pathways, high starch concentrations, and lower biomass production. The strong interconnectivity between genotype, chemotype and agronomic traits opens the door to use the expression of well-characterised genes in the starch and sucrose pathway for the early selection of high biomass yielding genotypes from large Miscanthus populations.

scholarly journals Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

2020 ◽  
Author(s):  
Jose J De Vega ◽  
Ned Peel ◽  
Sarah J Purdy ◽  
Sarah Hawkins ◽  
Iain Donnison ◽  
...  
Keyword(s):  
Biomass Yield ◽  
Agronomic Traits ◽  
Biomass Productivity ◽  
Rna Seq ◽  
High Biomass ◽  
Metabolic Genes ◽  
Low Concentrations ◽  
High Starch ◽  
High Concentrations ◽  
Lower Biomass

Abstract BACKGROUND:Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity and low chemical input requirements. Interspecific Miscanthus hybrids with high biomass yield were shown to have low concentrations of starch and sucrose but high concentrations of fructose. We performed a transcriptional RNA-seq analysis between selected Miscanthus hybrids with contrasting values for these phenotypes to clarify how these phenotypes are genetically controlled. RESULTS:We observed that genes directly involved in the synthesis and degradation of starch and sucrose were down-regulated in high yielding Miscanthus hybrids. At the same time, glycolysis and export of triose phosphates were up-regulated in high yielding Miscanthus hybrids. CONCLUSIONS:Our results evidence a direct relationship between high expression of essential enzymatic genes in the starch and sucrose pathways, high starch concentrations, and lower biomass production. The strong interconnectivity between genotype, chemotype and agronomic traits opens the door to use the expression of well-characterised genes in the starch and sucrose pathway for the early selection of high biomass yielding genotypes from large Miscanthus populations.

scholarly journals Dose- and time-dependent effects of hyaluronidase on structural cells and the extracellular matrix of the skin

2020 ◽  
Vol 25 (1) ◽  
Author(s):  
Bettina Alexandra Buhren ◽  
Holger Schrumpf ◽  
Katharina Gorges ◽  
Oliver Reiners ◽  
Edwin Bölke ◽  
...  
Keyword(s):  
Wound Healing ◽  
Ex Vivo ◽  
Time Dependent ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Dose Dependent ◽  
Genome Wide Expression ◽  
Skin Samples

Abstract Introduction Hyaluronic acid (hyaluronan; HA) is an essential component of the extracellular matrix (ECM) of the skin. The HA-degrading enzyme hyaluronidase (HYAL) is critically involved in the HA-metabolism. Yet, only little information is available regarding the skin’s HA–HYAL interactions on the molecular and cellular levels. Objective To analyze the dose- and time-dependent molecular and cellular effects of HYAL on structural cells and the HA-metabolism in the skin. Materials and methods Chip-based, genome-wide expression analyses (Affymetrix® GeneChip PrimeView™ Human Gene Expression Array), quantitative real-time PCR analyses, enzyme-linked immunosorbent assay (ELISA), immunohistochemistry (DAB), and in vitro wound healing assays were performed to assess dose-dependent and time-kinetic effects of HA and HYAL (bovine hyaluronidase, Hylase “Dessau”) on normal human dermal fibroblasts (NHDF), primary human keratinocytes in vitro and human skin samples ex vivo. Results Genome-wide expression analyses revealed an upregulation of HA synthases (HAS) up to 1.8-fold change in HA- and HYAL-treated NHDF. HA and HYAL significantly accelerated wound closure in an in vitro model for cutaneous wound healing. HYAL induced HAS1 and HAS2 mRNA gene expression in NHDF. Interestingly, low concentrations of HYAL (0.015 U/ml) resulted in a significantly higher induction of HAS compared to moderate (0.15 and 1.5 U/ml) and high concentrations (15 U/ml) of HYAL. This observation corresponded to increased concentrations of HA measured by ELISA in conditioned supernatants of HYAL-treated NHDF with the highest concentrations observed for 0.015 U/ml of HYAL. Finally, immunohistochemical analysis of human skin samples incubated with HYAL for up to 48 h ex vivo demonstrated that low concentrations of HYAL (0.015 U/ml) led to a pronounced accumulation of HA, whereas high concentrations of HYAL (15 U/ml) reduced dermal HA-levels. Conclusion HYAL is a bioactive enzyme that exerts multiple effects on the HA-metabolism as well as on the structural cells of the skin. Our results indicate that HYAL promotes wound healing and exerts a dose-dependent induction of HA-synthesis in structural cells of the skin. Herein, interestingly the most significant induction of HAS and HA were observed for the lowest concentration of HYAL.

scholarly journals Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient

2017 ◽  
Author(s):  
Colleen E. Hannon ◽  
Shelby A. Blythe ◽  
Eric F. Wieschaus
Keyword(s):  
Target Genes ◽  
Positional Information ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Accessible Chromatin ◽  
Anterior Posterior

ABSTRACTIn Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.

scholarly journals Dose- and time-dependent effects of hyaluronidase on structural cells and the extracellular matrix of the skin

2020 ◽  
Author(s):  
Bettina Buhren ◽  
Holger Schrumpf ◽  
Katharina Gorges ◽  
Oliver Reiners ◽  
Edwin Boelke ◽  
...  
Keyword(s):  
Wound Healing ◽  
Ex Vivo ◽  
Time Dependent ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Dose Dependent ◽  
Genome Wide Expression ◽  
Skin Samples

Abstract Hyaluronic acid (hyaluronan; HA) is an essential component of the extracellular matrix (ECM) of the skin. The HA-degrading enzyme hyaluronidase (HYAL) is critically involved in the HA-metabolism. Yet, only little information is available regarding the skin´s HA-HYAL interactions on the molecular and cellular levels.OBJECTIVE To analyze the dose- and time-dependent molecular and cellular effects of HYAL on structural cells and the HA-metabolism in the skin.MATERIALS AND METHODS Chip-based, genome-wide expression analyses (Affymetrix® GeneChip PrimeView™ Human Gene Expression Array), quantitative real-time PCR analyses, enzyme-linked immunosorbent assay (ELISA), immunohistochemistry (DAB), and in vitro wound healing assays were performed to assess dose-dependent and time-kinetic effects of HA and HYAL (bovine hyaluronidase, Hylase “Dessau”) on normal human dermal fibroblasts (NHDF), primary human keratinocytes in vitro and human skin samples ex vivo.RESULTS Genome-wide expression analyses revealed an upregulation of HA synthases (HAS) up to 1.8-fold change in HA- and HYAL-treated NHDF. HA and HYAL significantly accelerated wound closure in an in vitro model for cutaneous wound healing. HYAL induced HAS1 and HAS2 mRNA gene expression in NHDF. Interestingly, low concentrations of HYAL (0.015 U/ml) resulted in a significantly higher induction of HAS compared to moderate (0.15 and 1.5 U/ml) and high concentrations (15 U/ml) of HYAL. This observation corresponded to increased concentrations of HA measured by ELISA in conditioned supernatants of HYAL-treated NHDF with the highest concentrations observed for 0.015 U/ml of HYAL. Finally, immunohistochemical analysis of human skin samples incubated with HYAL for up to 48 h ex vivo demonstrated that low concentrations of HYAL (0.015 U/ml) led to a pronounced accumulation of HA, whereas high concentrations of HYAL (15 U/ml) reduced dermal HA-levels.CONCLUSION HYAL is a bioactive enzyme that exerts multiple effects on the HA-metabolism as well as on the structural cells of the skin. Our results indicate that HYAL promotes wound healing and exerts a dose-dependent induction of HA-synthesis in structural cells of the skin. Herein, interestingly the most significant induction of HAS and HA were observed for the lowest concentration of HYAL.

Effect of 2,4-D on Ametryne Toxicity

Weed Science ◽  
1974 ◽  
Vol 22 (3) ◽  
pp. 285-292 ◽  
Author(s):  
J. R. Diem ◽  
D. E. Davis
Keyword(s):  
Zea Mays ◽  
Acetic Acid ◽  
Glycine Max ◽  
Dry Weight ◽  
Low Concentrations ◽  
High Concentrations ◽  
Eichornia Crassipes ◽  
Dichlorophenoxy Acetic Acid ◽  
Toxic Concentrations ◽  
Species Mixtures

Nontoxic concentrations of 2,4-D [(2,4-dichlorophenoxy)acetic acid] increased the toxicity of ametryne [2-(ethylamino)-4-(isopropylamino)-6-(methylthio)-s-triazine], when applied to the roots of waterhyacinth [Eichornia crassipes(Mart.) Solms], when applied to the roots or foliage of corn (Zea maysL.), and to a lesser extent, when applied to the roots of soybean [Glycine max(L.) Merr.]. Nontoxic concentrations of 2,4-D frequently also increased the absorption of ametryne, water, and radioactive calcium by all three species. Mixtures containing toxic concentrations of 2,4-D with ametryne were not synergistic and sometimes the mixtures were less toxic than ametryne alone. Toxic concentrations of 2,4-D also decreased plant dry weight and the absorption of ametryne, water, and calcium. Low concentrations of ametryne increased the absorption of water and sometimes calcium while high concentrations decreased dry weight and the absorption of water and calcium.

Inhibition of respiration in submitochondrial particles by N,N′-dicyclohexylcarbodiimide: the effect of sodium, potassium, and antibiotics which alter membrane permeability

1969 ◽  
Vol 47 (2) ◽  
pp. 117-124 ◽  
Author(s):  
Robert E. Beyer ◽  
Karl R. Brinker ◽  
Daune L. Crankshaw
Keyword(s):  
Metal Ion ◽  
Nadh Oxidation ◽  
Potassium Ions ◽  
Inner Mitochondrial Membrane ◽  
Submitochondrial Particles ◽  
Sodium Potassium ◽  
Low Concentrations ◽  
Sonic Treatment ◽  
Metal Ion Transport ◽  
High Concentrations

NADH oxidation catalyzed by submitochondrial particles produced by sonic treatment (ETPH) is inhibited by N,N′-dicyclohexylcarbodiimide. The inhibition of electron-transfer activity is released by uncouplers of oxidative phosphorylation, but not by ADP nor by potassium or sodium ions, either in the presence or absence of valinomycin or tyrocidin. Low concentrations of potassium or sodium (0–30 mM) either in the presence or absence of valinomycin or tyrocidin do not significantly increase the rate of NADH oxidation by ETPH. High concentrations of sodium or potassium ions (30–120 mM) cause a significant increase in the rate of NADH oxidation by ETPH. It is suggested that the metal ion transport system is a property of the oriented inner mitochondrial membrane, and that high concentrations of metal ion are required to overcome the low permeability of the ETPH membrane in the inward direction in order to transport the metal ion actively in the outward direction.

scholarly journals Identification and Analysis of Micro-Exon Genes in the Rice Genome

2019 ◽  
Vol 20 (11) ◽  
pp. 2685 ◽  
Author(s):  
Qi Song ◽  
Fang Lv ◽  
Muhammad Tahir ul Qamar ◽  
Feng Xing ◽  
Run Zhou ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stop Codon ◽  
Indica Rice ◽  
Rice Genome ◽  
Protein Structures ◽  
Wide Distribution ◽  
Rna Seq ◽  
Rice Varieties ◽  
Genome Wide ◽  
Alternatively Spliced

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.

scholarly journals Effects of Hyaluronidase on Structural Cells and the Extracellular Matrix of the Skin

2020 ◽  
Author(s):  
Bettina Alexandra Buhren ◽  
Holger Schrumpf ◽  
Katharina Gorges ◽  
Oliver Reiners ◽  
Edwin Boelke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Wound Healing ◽  
Ex Vivo ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Dose Dependent ◽  
Genome Wide Expression ◽  
Skin Samples

Abstract Hyaluronic acid (hyaluronan; HA) is an essential component of the extracellular matrix (ECM) of the skin. The HA-degrading enzyme hyaluronidase (HYAL) is critically involved in the HA-metabolism. Yet, only little information is available regarding the skin´s HA-HYAL interactions on the molecular and cellular levels.OBJECTIVETo analyze the dose- and time-dependent molecular and cellular effects of HYAL on structural cells and the HA-metabolism in the skin.MATERIALS AND METHODSChip-based, genome-wide expression analyses (Affymetrix® GeneChip PrimeView™ Human Gene Expression Array), quantitative real-time PCR analyses, enzyme-linked immunosorbent assay (ELISA), immunohistochemistry (DAB), and in vitro wound healing assays were performed to assess dose-dependent and time-kinetic effects of HA and HYAL (bovine hyaluronidase, Hylase “Dessau”) on normal human dermal fibroblasts (NHDF), primary human keratinocytes in vitro and human skin samples ex vivo.RESULTSGenome-wide expression analyses revealed an upregulation of HA synthases (HAS) up to 1.8-fold change in HA- and HYAL-treated NHDF. HA and HYAL significantly accelerated wound closure in an in vitro model for cutaneous wound healing. HYAL induced HAS1 and HAS2 mRNA gene expression in NHDF. Interestingly, low concentrations of HYAL (0.015 U/ml) resulted in a significantly higher induction of HAS compared to moderate (0.15 and 1.5 U/ml) and high concentrations (15 U/ml) of HYAL. This observation corresponded to increased concentrations of HA measured by ELISA in conditioned supernatants of HYAL-treated NHDF with the highest concentrations observed for 0.015 U/ml of HYAL. Finally, immunohistochemical analysis of human skin samples incubated with HYAL for up to 48 h ex vivo demonstrated that low concentrations of HYAL (0.015 U/ml) led to a pronounced accumulation of HA, whereas high concentrations of HYAL (15 U/ml) reduced dermal HA-levels.CONCLUSIONHYAL is a bioactive enzyme that exerts multiple effects on the HA-metabolism as well as on the structural cells of the skin. Our results indicate that HYAL promotes wound healing and exerts a dose-dependent induction of HA-synthesis in structural cells of the skin. Herein, interestingly the most significant induction of HAS and HA were observed for the lowest concentration of HYAL.

Sign in / Sign up

Export Citation Format

Share Document