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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:
transcriptome,   etc   ; Pseudomonas fluorescens; carbon; cyanides; gene expression regulation; risk; sustainable technology;     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. Integrative analysis based on transcriptome revealed the relation of auxin to turnip hypocotyl-tuber formation

Author:
Yingjuan Huang; Ruicheng Liu; Ruiqi Song; Dong Zhou; Jingwen Chen; Rui Liu; Weiwei Chen; Jianli Yang; Xiaolin Yu; Jiashu Cao; Li Huang
Source:
Scientia horticulturae 2023 v.308 pp. 111536
ISSN:
0304-4238
Subject:
transcriptome,   etc   ; Brassica rapa subsp. oleifera; agronomic traits; hypocotyls; naphthaleneacetic acid; secondary xylem; transcriptomics; turnips;     Show all 8 Subjects
Abstract:
... Turnip (Brassica campestris L. ssp. rapifera Matag syn. B. rapa L.) is characterized by bulbous hypocotyl-tuber, which is an important agronomic trait of the Brassica plants, but the molecular mechanism underlying the development of turnip hypocotyl-tuber has rarely been explored. Contrary to turnip, pak-choi (B. campestris L. ssp. chinensis Makino syn. B. rapa ssp. chinensis) is characterized by ...
DOI:
10.1016/j.scienta.2022.111536

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:
transcriptome,   etc   ; Pinctada; biomineralization; cell proliferation; energy metabolism; environment; gene expression regulation; oysters; thermal stress; 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:
transcriptome,   etc   ; Chrysanthemum morifolium; anthocyanins; biosynthesis; chlorides; cyanidin; disc florets; flower color; gene expression regulation; metabolomics; pelargonidin; 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. Aflatoxin M1 and ochratoxin A induce a competitive endogenous RNA regulatory network of intestinal immunosuppression by whole-transcriptome analysis

Author:
Ya-Nan Gao; Zi-Wei Wang; Xue Yang; Jia-Qi Wang; Nan Zheng
Source:
Science of the total environment 2023 v.854 pp. 158777
ISSN:
0048-9697
Subject:
transcriptome,   etc   ; aflatoxin M1; body weight; environment; human health; immunosuppression; immunotoxicity; intestines; mice; microRNA; milk; ochratoxin A; phosphorylation; risk; transcriptomics;     Show all 15 Subjects
Abstract:
... Aflatoxin M1 (AFM1) and ochratoxin A (OTA) are common mycotoxins in cereal foods and milk products, and may cause serious negative impacts on human health. The intestine is crucial for immune regulation as it protects host homeostatic health from external contaminants; however, the underlying mechanisms of AFM1 and OTA mediated intestinal immunotoxicity remain unclear. In this study, whole transcr ...
DOI:
10.1016/j.scitotenv.2022.158777

6. Sugar accumulation and fruit quality of tomatoes under water deficit irrigation

Author:
Chunmei Bai; Jinhua Zuo; Christopher B. Watkins; Qing Wang; Hao Liang; Yanyan Zheng; Mingchi Liu; Yanhai Ji
Source:
Postharvest biology and technology 2023 v.195 pp. 112112
ISSN:
0925-5214
Subject:
transcriptome,   etc   ; ascorbic acid; color; deficit irrigation; fruit quality; fruits; galactose; metabolism; metabolites; metabolome; starch; sucrose; sweetness; taste; technology; texture; tomatoes;     Show all 17 Subjects
Abstract:
... Agricultural production has improved with the development of water deficit (WD) irrigation technology, but the impact of the application of WD irrigation on product quality is still understudied. The effects of WD irrigation on the transcriptome and metabolome of fruit have been investigated by treating tomato plants with control or WD irrigation during the growing period. WD irrigation promoted t ...
DOI:
10.1016/j.postharvbio.2022.112112

7. 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:
transcriptome,   etc   ; Danio rerio; cadmium; calcium; dose response; gene expression regulation; heavy metals; lipid metabolism; remission; toxicity; toxicology; 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

8. Genome-wide profiling of dysregulated piRNAs and their target genes implicated in oncogenicity of tongue squamous cell carcinoma

Author:
Trisha Chattopadhyay; Pooja Gupta; Rojalin Nayak; Bibekanand Mallick
Source:
Gene 2023 v.849 pp. 146919
ISSN:
0378-1119
Subject:
transcriptome,   etc   ; RNA; antineoplastic agents; carcinogenesis; carcinogenicity; databases; gene expression; genes; geranylgeranyl diphosphate synthase; germ cells; mouth neoplasms; squamous cell carcinoma; tongue;     Show all 13 Subjects
Abstract:
... PIWI-interacting RNAs (piRNAs) are single-stranded, 23–36 nucleotide long RNAs that regulate gene expression in the germline but are also detected in some cancers. However, there are no reports yet on piRNA expression in tongue squamous cell carcinoma (TSCC), the most common oral cancer (80–90% percent of all oral cancers). We performed small RNA and whole transcriptome sequencing in H357 tongue c ...
DOI:
10.1016/j.gene.2022.146919

9. Integrated multi-omic analyses on yellow Flammulina filiformis cultivar reveal postharvest oxidative damage responses

Author:
Yu Fu; Hao Tan; Bo Wang; Weihong Peng; Qun Sun; Yang Yu
Source:
Postharvest biology and technology 2023 v.195 pp. 112111
ISSN:
0925-5214
Subject:
transcriptome,   etc   ; DNA; Flammulina; biosynthesis; catechol oxidase; cell senescence; cultivars; genome; laccase; melanin; mushrooms; oxidative phosphorylation; oxygen; proteolysis; proteome; proteomics; technology; transcriptomics; tyrosine;     Show all 19 Subjects
Abstract:
... Yellow cultivars of Flammulina filiformis are prone to browning, which causes significant yearly loss. This study investigated the critical factors involved and revealed that oxygen plays an essential role in the browning process. Integrated multi-omic analyses, including genome sequencing, transcriptome profiling, and 4D label-free proteome quantification, were incorporated to dissect essential g ...
DOI:
10.1016/j.postharvbio.2022.112111

10. 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:
transcriptome,   etc   ; Prunus; almonds; chlorides; economic feasibility; electrical conductivity; gene expression regulation; genotype; ion channels; proline; salinity; salt stress; salt tolerance; sequence analysis;     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

11. Functional insights of a two-component system sensor kinase GacS in a fish pathogen, Pseudomonas plecoglossicida

Author:
Su-Ming Zhou; Yan Wang; Feng-Ling Shu; Zhen Tao; Xiao Xie; Jia-Song Xie; Rong-Rong Ma; Fei Yin
Source:
Aquaculture 2023 v.562 pp. 738866
ISSN:
0044-8486
Subject:
transcriptome,   etc   ; Larimichthys crocea; Pseudomonas plecoglossicida; adhesion; aquaculture; biofilm; blood serum; chemotaxis; complement; fish; granuloma; kidneys; metabolism; models; mutants; pathogens; phenotype; sequence analysis; transcriptomics; virulence;     Show all 20 Subjects
Abstract:
... Pseudomonas plecoglossicida is an important pathogenic bacterial species in aquaculture, causing visceral granulomas in large yellow croaker (Larimichthys crocea) and several other economically important fish species. The GacS/GacA is a two-component regulatory system (TCS) primarily found in Pseudomonads for its role in virulence, quorum sensing, and biofilm formation. To investigate the potentia ...
DOI:
10.1016/j.aquaculture.2022.738866

12. 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:
transcriptome,   etc   ; Pyrus bretschneideri; biosynthesis; cultivars; ethylene; ethylene signaling pathway; flavor; gene expression regulation; hybrids; metabolites; metabolome; metabolomics; nerolidol; odors; pears; phenotype; pollen; pollination; pollinators; 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

13. Molecular insights into lignin biosynthesis on cadmium tolerance: Morphology, transcriptome and proteome profiling in Salix matsudana

Author:
Miao Yu; Renying Zhuo; Zhuchou Lu; Shaocui Li; Juanjuan Chen; Yujun Wang; Jihong Li; Xiaojiao Han
Source:
Journal of hazardous materials 2023 v.441 pp. 129909
ISSN:
0304-3894
Subject:
transcriptome,   etc   ; Populus; Salix matsudana; biosynthesis; cadmium; callus; cinnamoyl-CoA reductase; cinnamyl alcohol dehydrogenase; genetically modified organisms; lignin; lignin content; phytoremediation; proteome; soil; soil pollution; xylem;     Show all 16 Subjects
Abstract:
... Soil pollution caused by cadmium (Cd) is a serious concern. Phytoremediation is a popular technology in the remediation of Cd-contaminated soil. Salix matsudana var. matsudana f. umbraculifera Rehd. has been characterized as a high Cd-accumulating and tolerant willow (HCW). Here, transcriptome and proteome profiling, along with morphology analyses were performed to explore molecular cross-talk inv ...
DOI:
10.1016/j.jhazmat.2022.129909

14. Physiological and transcriptomic analysis reveals the postharvest ripening differences between “Nantianhuang” and “Brazilian” banana fruit

Author:
Jiao Chen; Yixing Li; Fenfang Li; Debao Yuan; Keqian Hong
Source:
Postharvest biology and technology 2023 v.195 pp. 112138
ISSN:
0925-5214
Subject:
transcriptome,   etc   ; Fusarium wilt; aminocyclopropanecarboxylate oxidase; bananas; cell respiration; climacteric fruits; cultivars; ethylene production; firmness; fruit quality; gene expression; industry; malondialdehyde; pectinesterase; polygalacturonase; starch; technology; transcriptomics;     Show all 18 Subjects
Abstract:
... Banana, as a typical climacteric fruit, undergoes a ripening process which impacts fruit quality. The Nantianhuang (NTH) banana fruit is a new cultivar resistant to Fusarium wilt, whose physiological characteristics and regulation mechanisms of fruit ripening are not clear. Ripening physiology and the related genes of the NTH fruit were compared with the Brazilian banana (BX) and investigated in t ...
DOI:
10.1016/j.postharvbio.2022.112138

15. Biochar application enhanced rice biomass production and lodging resistance via promoting co-deposition of silica with hemicellulose and lignin

Author:
Wei Miao; Fengcheng Li; Jiancheng Lu; Donglei Wang; Mingkai Chen; Liang Tang; Zhengjin Xu; Wenfu Chen
Source:
Science of the total environment 2023 v.855 pp. 158818
ISSN:
0048-9697
Subject:
transcriptome,   etc   ; application rate; biochar; biomass production; cell wall components; cell walls; cultivars; environment; hemicellulose; lignin; organic matter; rice; silica; silicon; soil; soil amendments; stem cells;     Show all 17 Subjects
Abstract:
... Biochar, an environmentally friendly soil amendment, is created via a series of thermochemical processes from carbon-rich organic matter. The biochar addition enhances soil characteristics dramatically and increases crop growth and yields. However, the mechanism by which biochar improves plant lodging resistance, which is heavily influenced by cell walls, remains unknown. Three rice cultivars were ...
DOI:
10.1016/j.scitotenv.2022.158818

16. Metabolic and transcriptional regulatory mechanisms of differential carbohydrates formation from flower buds to flowers of Hemerocallis citrina

Author:
Xiao-Ke Li; Jin-Long Cui; Xue-Mei Qin; Jun-Hong Wang; Meng-Liang Wang
Source:
Scientia horticulturae 2023 v.308 pp. 111553
ISSN:
0304-4238
Subject:
transcriptome,   etc   ; Hemerocallis; alpha-glucosidase; beta-amylase; beta-fructofuranosidase; flowers; fructose; galactose; health services; mannose; metabolism; metabolome; microRNA; nutrient content; phosphoglucomutase; starch; sucrose; transcription (genetics); vegetables;     Show all 19 Subjects
Abstract:
... The flower buds of Hemerocallis citrina that are about to open are an edible vegetable with health care functions of "forgetting worries". However, the flower buds that open into flowers will be discarded due to changes in nutritional composition such as carbohydrates which is still unclear on their difference and formation mechanism from flower buds. In this study, the combined analysis of transc ...
DOI:
10.1016/j.scienta.2022.111553

17. A 24-epibrassinolide treatment and intercropping willow with alfalfa increase the efficiency of the phytoremediation of cadmium-contaminated soil

Author:
Yepu Li; Qi Dong; Danni Wu; Ying Yin; Wenchao Du; Hongyan Guo
Source:
Science of the total environment 2023 v.854 pp. 158471
ISSN:
0048-9697
Subject:
transcriptome,   etc   ; alfalfa; antioxidant activity; cadmium; calcium; calcium channels; catalase; environment; food security; glutathione; greenhouses; human health; paddy soils; phagosomes; phosphates; photosynthesis; phytomass; phytoremediation; pot culture; solubilization;     Show all 20 Subjects
Abstract:
... Cadmium contamination in agricultural soils threatens food security and human health, and that has caused widespread concern worldwide. Willow and alfalfa are widely used for the phytoremediation of cadmium (Cd)-contaminated soil, and willow NJU513 is the promising plant for remediating Cd-contaminated soil. In order to discuss the effect of intercropping willow NJU513 with alfalfa on the phytorem ...
DOI:
10.1016/j.scitotenv.2022.158471

18. 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:
transcriptome,   etc   ; Kluyveromyces marxianus; acetic acid; acetyl-CoA acetyltransferase; acyl coenzyme A; alcohol dehydrogenase; aldehyde dehydrogenase; ethanol; ethyl acetate; fermentation; food science; gene expression regulation; gluconeogenesis; glycolysis; humans; hydrolases; lactic acid; proteome; pyruvic acid; rice; soups; starch; sucrose; thioesters;     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

19. 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:
transcriptome,   etc   ; Erinaceidae; Pardosa; alanine; amino acid metabolism; antioxidants; biomarkers; biosynthesis; cadmium; cell growth; cytoskeleton; environment; gene expression regulation; 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;     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

20. Transcriptome and Genome Analyses Applied to Aquaculture Research

Author:
Patricia Pereiro
Source:
Biology 2022 v.11 no.9 pp. -
ISSN:
2079-7737
Subject:
transcriptome,   etc   ; aquaculture; genome;     Show all 3 Subjects
Abstract:
... The Special Issue “Transcriptome and Genome Analyses Applied to Aquaculture Research” had great success among the researchers specialized in different fields of aquaculture [...] ...
DOI:
10.3390/biology11091312