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You searched for: Subject "gene expression regulation" Remove constraint Subject: "gene expression regulation"
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1. Regulation mechanism of cyanide production and conversion of Pseudomonas fluorescens commonly used in bio-cyanidation of precious metals from waste printed circuit boards

Author:
Mi Lin; Zichun Yao; Pengcheng Wang; Yonggao Fu; Jujun Ruan
Source:
Resources, conservation, and recycling 2023 v.188 pp. 106670
ISSN:
0921-3449
Subject:
gene expression regulation,   etc   ; Pseudomonas fluorescens; carbon; cyanides; risk; sustainable technology; transcriptome;     Show all 7 Subjects
Abstract:
... Replacing virgin mining with urban mining is an important step to achieve resources recycling and carbon emission reduction. Bio-cyanidation is an environmentally-friendly technology to recover precious metals from waste printed circuit boards, a type of typical urban minerals. However, the limited cyanide-producing ability and the risk of cyanide containing solutions restricts its industrial appl ...
DOI:
10.1016/j.resconrec.2022.106670

2. Renewable biohydrogen production from Clostridium sp. LQ25 using different forms of ferric as electron acceptor

Author:
Shan Zhang; Xiaodan Zhang; Yuan Yuan; Kaiqiang Li; Hongyan Liu
Source:
Science of the total environment 2023 v.855 pp. 158911
ISSN:
0048-9697
Subject:
gene expression regulation,   etc   ; Clostridium; butyrates; citrates; environment; fermentation; ferric hydroxide; glucose; hydrogen production;     Show all 9 Subjects
Abstract:
... Clostridium sp. LQ25 was cultured in different forms of ferric (ferric citrate and ferric hydroxide) as electron acceptors to investigate growth, ferric reduction, hydrogen production, fermentation products and fermentation process. The growth of the strain LQ25 detected by protein was 82.8 ± 2.1 mg/L and 73.5 ± 1.7 mg/L using ferric citrate and ferric hydroxide as electron acceptors, which was 33 ...
DOI:
10.1016/j.scitotenv.2022.158911

3. Transcriptomic responses reveal impaired physiological performance of the pearl oyster following repeated exposure to marine heatwaves

Author:
Guixiang He; Xinwei Xiong; Yalan Peng; Chuangye Yang; Yang Xu; Xiaolong Liu; Jian Liang; Fortunatus Masanja; Ke Yang; Xin Xu; Zhe Zheng; Yuewen Deng; Jonathan Y.S. Leung; Liqiang Zhao
Source:
Science of the total environment 2023 v.854 pp. 158726
ISSN:
0048-9697
Subject:
gene expression regulation,   etc   ; Pinctada; biomineralization; cell proliferation; energy metabolism; environment; oysters; thermal stress; transcriptome; transcriptomics;     Show all 10 Subjects
Abstract:
... Marine heatwaves are predicted to become more intense and frequent in the future, possibly threatening the survival of marine organisms and devastating their communities. While recent evidence reveals the adaptability of marine organisms to heatwaves, substantially overlooked is whether they can also adjust to repeated heatwave exposure, which can occur in nature. By analysing transcriptome, we ex ...
DOI:
10.1016/j.scitotenv.2022.158726

4. Transcriptomic and metabolomic analyses reveal that MYB transcription factors regulate anthocyanin synthesis and accumulation in the disc florets of the anemone form of chrysanthemum morifolium

Author:
Hua Liu; Haixia Chen; Xiaoxi Chen; Jie Lu; Dongliang Chen; Chang Luo; Xi Cheng; Conglin Huang
Source:
Scientia horticulturae 2023 v.307 pp. 110847
ISSN:
0304-4238
Subject:
gene expression regulation,   etc   ; Chrysanthemum morifolium; anthocyanins; biosynthesis; chlorides; cyanidin; disc florets; flower color; metabolomics; pelargonidin; transcriptome; transcriptomics; unigenes;     Show all 13 Subjects
Abstract:
... Chrysanthemum morifolium is a popular flower. The disc florets of most C. morifolium varieties are yellow or colourless, whereas those of the anemone-form are red/pink. To explain this difference, we analysed the metabolomes and transcriptomes of ‘Danfen’ (conventional variety) and ‘Fenlian’ (anemone-form variety). Of the 129,277 assembled unigenes, 59,070 were annotated. A total of 50,325 differe ...
DOI:
10.1016/j.scienta.2021.110847

5. β-Carotene and lutein accumulation, and carotenoid biosynthetic gene expression during fruit development and fruit ripening of A genome banana

Author:
Petcharat Netlak; Ratri Boonruangrod; Charles Ampomah-Dwamena; Andrew C. Allan; Wachiraya Imsabai
Source:
Scientia horticulturae 2023 v.307 pp. 111484
ISSN:
0304-4238
Subject:
gene expression regulation,   etc   ; Musa; bananas; biosynthesis; color; cultivars; diploidy; fruiting; fruits; gene expression; genes; intraspecific hybridization; lutein; pulp; triploidy;     Show all 15 Subjects
Abstract:
... Bananas (Musa spp.) are an important source of pro-vitamin A, derived from carotenoids. Some cultivated bananas originated from intra-specific hybridization resulting in genotypes which are diploid (AA) and triploid (AAA) genomes that are the most important bananas for desserts. The accumulation of carotenoids and transcripts of genes related to carotenoid biosynthesis during fruit development and ...
DOI:
10.1016/j.scienta.2022.111484

6. Transcriptome reveals overview of Ca2+ dose-dependent metabolism disorders in zebrafish larvae after Cd2+ exposure

Author:
Biran Zhu; Ziniu Wang; Lei Lei; Yongyong Guo; Jian Han; Bingsheng Zhou
Source:
Journal of environmental sciences (China) 2023 v.125 pp. 480-491
ISSN:
1001-0742
Subject:
gene expression regulation,   etc   ; Danio rerio; cadmium; calcium; dose response; heavy metals; lipid metabolism; remission; toxicity; toxicology; transcriptome; water hardness; China;     Show all 13 Subjects
Abstract:
... Cadmium (Cd), a ubiquitous environmental hazardous heavy metal, poses a significant threat to the health of aquatic organisms, including teleosts. Although the toxic profile of Cd is well recognized, little is known regarding the overall view of toxic responses to varying aquatic environmental parameters (e.g., water hardness) at an individual level. Herein, differences in water hardness were part ...
DOI:
10.1016/j.jes.2021.12.009

7. Prediction of intestinal stem cell regulatory genes from Drosophila gut damage model created using multiple inducers: Differential gene expression-based protein-protein interaction network analysis

Author:
Seung Hun Lee; Dooseon Hwang; Tae-Won Goo; Eun-Young Yun
Source:
Developmental and comparative immunology 2023 v.138 pp. 104539
ISSN:
0145-305X
Subject:
gene expression regulation,   etc   ; Drosophila melanogaster; genes; homeostasis; innate immunity; intestines; models; oral administration; prediction; protein-protein interactions; sequence analysis; stem cells;     Show all 12 Subjects
Abstract:
... Intestinal tissue functions in innate immunity to prevent the entry of harmful substances, and to maintain homeostasis through the constant proliferation of intestinal stem cells (ISC). To understand the mechanisms which regulate ISC in response to gut damage, we identified 81 differentially expressed genes (DEGs) through RNA-seq analysis after oral administration of three intestinal-damaging subs ...
DOI:
10.1016/j.dci.2022.104539

8. Morphological, physiological, biochemical, and transcriptome studies reveal the importance of transporters and stress signaling pathways during salinity stress in Prunus

Author:
Acharya Biswa R.; Sandhu Devinder; Dueñas Christian; Dueñas Marco; Pudussery Manju V.; Kaundal Amita; Ferreira Jorge F.S.; Suarez Donald L.; Skaggs Todd H.
Source:
Scientific reports 2022 v.12 no.1 pp. 1274
ISSN:
2045-2322
Subject:
gene expression regulation,   etc   ; Prunus; almonds; chlorides; economic feasibility; electrical conductivity; genotype; ion channels; proline; salinity; salt stress; salt tolerance; sequence analysis; transcriptome;     Show all 14 Subjects
Abstract:
... The almond crop has high economic importance on a global scale, but its sensitivity to salinity stress can cause severe yield losses. Salt-tolerant rootstocks are vital for crop economic feasibility under saline conditions. Two commercial rootstocks submitted to salinity, and evaluated through different parameters, had contrasting results with the survival rates of 90.6% for 'Rootpac 40' (tolerant ...
Handle:
10113/7709627
DOI:
10.1038/s41598-022-05202-1

9. Integrated transcriptome and metabolome analysis unveiled the mechanisms of xenia effect and the role of different pollens on aroma formation in ‘Yali’ pear (Pyrus bretschneideri Rehd)

Author:
Wanjun Liu; Ying Zhang; Li Wang; Bilal Ahmad; Xiaoxin Shi; Yan Ren; Chen Liang; Xiangkun Zhang; Yuxing Zhang; Guoqiang Du
Source:
Scientia horticulturae 2023 v.307 pp. 111503
ISSN:
0304-4238
Subject:
gene expression regulation,   etc   ; Pyrus bretschneideri; biosynthesis; cultivars; ethylene; ethylene signaling pathway; flavor; hybrids; metabolites; metabolome; metabolomics; nerolidol; odors; pears; phenotype; pollen; pollination; pollinators; transcriptome; trees;     Show all 20 Subjects
Abstract:
... The flavor of ‘Yali’ pear fruits has substantially declined recently as a result of poor pollination tree selection. Xenia effect is a powerful mechanism for regulating aroma production. To study the effect of different pollens on aroma quality and the molecular basis of xenia effect in ‘Yali’ pear fruits, ‘Hongnanguo’ and ‘Xuehuali’ were used as pollinizers, and the hybrid fruits were named YH an ...
DOI:
10.1016/j.scienta.2022.111503

10. Integrated physiologic and proteomic analysis of Stropharia rugosoannulata mycelia in response to Cd stress

Author:
Qin Dong; Mingjie Chen; Yaru Zhang; Panpan Song; Huanling Yang; Yan Zhao; Changxia Yu; Lei Zha
Source:
Journal of hazardous materials 2023 v.441 pp. 129877
ISSN:
0304-3894
Subject:
gene expression regulation,   etc   ; Stropharia rugosoannulata; antioxidants; bioremediation; biosynthesis; energy; energy metabolism; growth retardation; homeostasis; human health; isoleucine; leucine; mycelium; pollution; proteome; proteomics; soil; toxicity; valine;     Show all 19 Subjects
Abstract:
... Soil Cd pollution seriously threatens environment and human health. Due to its ability to absorb and accumulate Cd in mycelia, Stropharia rugosoannulata could be a potential candidate for bioremediation of Cd-contaminated soils; however, the response mechanism of mycelia to Cd stress is still unclear. In this study, the physiologic and proteomic differences of S. rugosoannulata mycelia under 0.2 m ...
DOI:
10.1016/j.jhazmat.2022.129877

11. Reproductive toxicity of enrofloxacin in Caenorhabditis elegans involves oxidative stress-induced cell apoptosis

Author:
Jiahao Huang; Lizi Liao; Guowei Wang; Zhongkun Du; Zhengxing Wu
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 726-737
ISSN:
1001-0742
Subject:
gene expression regulation,   etc   ; Caenorhabditis elegans; apoptosis; bioaccumulation; chronic exposure; egg hatchability; enrofloxacin; enzyme activity; fluoroquinolones; germ cells; livestock; models; oxidative stress; reproductive toxicology; risk; China;     Show all 16 Subjects
Abstract:
... Fluoroquinolone antibiotics (FQs) that persist and bioaccumulate in the environment have aroused people's great concern. Here, we studied the adverse effects of FQs in soil animals of Caenorhabditis elegans via food-chronically exposure. The result shows C. elegans exposed to FQs exhibited reproductive toxicity with small-brood size and low-egg hatchability. To study the underlying mechanism, we c ...
DOI:
10.1016/j.jes.2022.07.002

12. Determining transcriptomic response of kidneys of olive flounder to viral hemorrhagic septicemia virus infection using next-generation sequencing

Author:
Hyoung Jun Kim; Jeong Su Park; Se Ryun Kwon; Youngjin Park
Source:
Aquaculture 2023 v.562 pp. 738886
ISSN:
0044-8486
Subject:
gene expression regulation,   etc   ; Paralichthys olivaceus; RNA; Viral hemorrhagic septicemia virus; aquaculture; aquaculture industry; chemokines; flounder; interleukins; intraperitoneal injection; kidneys; metabolism; septicemia; tissue culture; transcriptomics; Korean Peninsula;     Show all 16 Subjects
Abstract:
... Viral hemorrhagic septicemia (VHS) in olive flounder (Paralichthys olivaceus) causes considerable economic losses in the flounder aquaculture industry in Korea. This study was aimed to identify the immune-associated genes contributing to VHSV infection progression in the kidneys of the olive flounder. Ten fish were divided into two groups via an intraperitoneal injection with either diethylpyrocar ...
DOI:
10.1016/j.aquaculture.2022.738886

13. Methylome and transcriptome analysis of alters leaf phenotype with autotetraploid in grape

Author:
Xiaodong Xiang; Yukun Gao; Jianghui Cui; Genzeng Ren; Congpei Yin; Jinhua Chang
Source:
Scientia horticulturae 2023 v.307 pp. 111534
ISSN:
0304-4238
Subject:
gene expression regulation,   etc   ; 5-methylcytosine; DNA; Vitis vinifera; anthocyanins; antioxidant activity; autotetraploidy; biosynthesis; bisulfites; cell walls; diploidy; epigenetics; gene expression; genomics; grapes; homeostasis; introns; leaf thickness; leaves; lipid metabolism; methylation; phenotype; photosynthesis; plant hormones; secondary metabolites; transcriptomics;     Show all 26 Subjects
Abstract:
... The doubling of the plant genome causes obvious morphological and physiological changes, and DNA 5-methylcytosine (5mCs) modification is a key epigenetic component that helps neopolyploids overcome challenges and acquire advantages. In the study of autotetraploid grape, we found that leaf thickness, photosynthetic and antioxidant capacity increased and anthocyanin coloring decreased in autotetrapl ...
DOI:
10.1016/j.scienta.2022.111534

14. Formation mechanisms of ethyl acetate and organic acids in Kluyveromyces marxianus L1-1 in Chinese acid rice soup

Author:
Na Liu; Likang Qin; Laili Hu; Song Miao
Source:
Food science and human wellness 2023 v.12 no.1 pp. 45-56
ISSN:
2213-4530
Subject:
gene expression regulation,   etc   ; Kluyveromyces marxianus; acetic acid; acetyl-CoA acetyltransferase; acyl coenzyme A; alcohol dehydrogenase; aldehyde dehydrogenase; ethanol; ethyl acetate; fermentation; food science; gluconeogenesis; glycolysis; humans; hydrolases; lactic acid; proteome; pyruvic acid; rice; soups; starch; sucrose; thioesters; transcriptome;     Show all 24 Subjects
Abstract:
... This study aims to explore the formation mechanism of ethyl acetate and organic acids in acid rice soup (rice-acid soup) inoculated with Kluyveromyces marxianus L1-1 through the complementary analysis of transcriptome and proteome. The quantity of K. marxianus L1-1 varied significantly in the fermentation process of rice-acid soup and the first and third days were the two key turning points in the ...
DOI:
10.1016/j.fshw.2022.07.017

15. A novel milk-derived peptide effectively inhibits Staphylococcus aureus: Interferes with cell wall synthesis, peptidoglycan biosynthesis disruption reaction mechanism, and its application in real milk system

Author:
Yanan Shi; Yufang Li; Kun Yang; Guangqiang Wei; Aixiang Huang
Source:
Food control 2023 v.144 pp. 109374
ISSN:
0956-7135
Subject:
gene expression regulation,   etc   ; DNA repair; Staphylococcus aureus; anti-infective agents; antimicrobial peptides; antimicrobial properties; biosynthesis; buffalo milk; cell walls; food preservation; food safety; glutamic acid; glutamine; metabolites; milk; peptidoglycans; protein synthesis; proteome; proteomics; quantitative polymerase chain reaction; reaction mechanisms; ultrastructure;     Show all 22 Subjects
Abstract:
... BCp12, a novel antimicrobial agent derived from buffalo milk, poses superior antimicrobial activity against Staphylococcus aureus. In the present study, the effect of BCp12 on the cell wall synthesis and molecular pathways of Staphylococcus aureus was studied by the CLSM, SEM and proteomics analyses to facilitate the development of this novel antimicrobial peptide. The results demonstrated that BC ...
DOI:
10.1016/j.foodcont.2022.109374

16. Integrated transcriptome and proteome unveiled distinct toxicological effects of long-term cadmium pollution on the silk glands of Pardosa pseudoannulata

Author:
Bo Lv; Yong Peng; Yuan-de Peng; Zhi Wang; Qi-sheng Song
Source:
Science of the total environment 2023 v.854 pp. 158841
ISSN:
0048-9697
Subject:
gene expression regulation,   etc   ; Erinaceidae; Pardosa; alanine; amino acid metabolism; antioxidants; biomarkers; biosynthesis; cadmium; cell growth; cytoskeleton; environment; glutathione peroxidase; glutathione synthase; growth and development; malondialdehyde; methionine adenosyltransferase; models; paddies; peptides; peroxidase; phosphorylase; proline; protein-protein interactions; proteome; silk; soil pollution; spiders; spidroins; toxicity; toxicology; transcriptome;     Show all 32 Subjects
Abstract:
... Cadmium (Cd) induces severe soil pollution worldwide and exerts adverse effects on paddy field arthropods. Spiders grant a novel perspective to assess the Cd-induced toxicity, yet the impacts of long-term Cd stress on spider silk glands and its underlying mechanism remain elusive. The study showed that Cd stress enervated the antioxidant system in the spider Pardosa pseudoannulata, manifested as t ...
DOI:
10.1016/j.scitotenv.2022.158841

17. Transcriptome analysis and pattern recognition receptors (PRRs) identification in different tissues of adult Pacific oysters infected with Vibrio parahaemolyticus

Author:
Petcharat Namwong; Shuang Wang; Qing Kong; Haijin Mou; Lei Ma; Prapansak Srisapoome
Source:
Aquaculture 2023 v.562 pp. 738824
ISSN:
0044-8486
Subject:
gene expression regulation,   etc   ; Crassostrea gigas; Gram-negative bacteria; Vibrio parahaemolyticus; adults; aquaculture industry; bacterial adhesion; bacterial infections; carbohydrate binding; cytoskeleton; data collection; epithelium; fluorescent antibody technique; food sanitation; galectins; gene expression; genes; host-pathogen relationships; macrophages; mannose; oxidative stress; pathogens; peptidoglycans; peroxidase; phagocytosis; recombinant proteins; shellfish culture; transcriptomics;     Show all 28 Subjects
Abstract:
... Contamination of V. parahaemolyticus in raw product and culture areas of Crassostrea gigas has been a concern in food hygiene and infectious diseases in the shellfish aquaculture industry for decades. Although numerous researchers have presently objective of decreasing pathogen microorganism contaminated load in raw oysters or genetics improvement for prevention, the in-depth information at the mo ...
DOI:
10.1016/j.aquaculture.2022.738824

18. Pathologic, transcriptomic and microbiomic insight into the pathogenesis of intestinal parasitic tapeworm in cultured Chinese soft-shelled turtle (Pelodiscus sinensis)

Author:
Xianwen Zhou; Yu Tian; Li Liu; Lingrui Ge; Hui Zhang; Yixin Liang; Xiaoqing Wang; Yazhou Hu
Source:
Aquaculture 2023 v.562 pp. 738788
ISSN:
0044-8486
Subject:
gene expression regulation,   etc   ; Citrobacter; Edwardsiella; Eucestoda; Pelodiscus sinensis; alanine transaminase; alkaline phosphatase; alpha-linolenic acid; aquaculture; arachidonic acid; aspartate transaminase; blood serum; creatinine; cytochrome P-450; epithelium; fish; glucose; histopathology; intestinal microorganisms; intestines; linoleic acid; lipid metabolism; liver; low density lipoprotein; mechanical damage; metabolic diseases; nutrition; pathogenesis; prediction; protein content; species identification; superoxide dismutase; tapeworms; transcriptomics; xenobiotics; China;     Show all 36 Subjects
Abstract:
... Tapeworms are infamous and highly successful invasive parasites in aquatic animals, especially in fish. However, tapeworm-caused diseases in soft-shelled turtles are rarely discovered. In this study, a case of cultured Chinese soft-shelled turtle (Pelodiscus sinensis) infected with tapeworm in Changde city of China was reported, and the taxonomic identification of the tapeworm and the effects of t ...
DOI:
10.1016/j.aquaculture.2022.738788

19. Exaggerated false positives by popular differential expression methods when analyzing human population samples

Author:
Yumei Li; Xinzhou Ge; Fanglue Peng; Wei Li; Jingyi Jessica Li
Source:
Genome biology 2022 v.23 no.1 pp. 79
ISSN:
1474-760X
Subject:
gene expression regulation,   etc   ; bioinformatics; human population; sequence analysis;     Show all 4 Subjects
Abstract:
... When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates. Expanding the analysis to limma-voom, NOISeq, dearseq, and Wilcoxon rank-sum test, we found that FDR control is often failed except for the Wi ...
DOI:
10.1186/s13059-022-02648-4

20. scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data

Author:
Kun Qian; Shiwei Fu; Hongwei Li; Wei Vivian Li
Source:
Genome biology 2022 v.23 no.1 pp. 82
ISSN:
1474-760X
Subject:
gene expression regulation,   etc   ; gene expression; genome; learning; methodology;     Show all 5 Subjects
Abstract:
... The increasing number of scRNA-seq data emphasizes the need for integrative analysis to interpret similarities and differences between single-cell samples. Although different batch effect removal methods have been developed, none are suitable for heterogeneous single-cell samples coming from multiple biological conditions. We propose a method, scINSIGHT, to learn coordinated gene expression patter ...
DOI:
10.1186/s13059-022-02649-3