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1. Identification of co-expressed networks and key genes associated with organic acid in peach fruit

Author:
Qi Wang; Ke Cao; Yong Li; Jinlong Wu; Jiaqi Fan; Tiyu Ding; Irshad Ahmad Khan; Lirong Wang
Source:
Scientia horticulturae 2023 v.307 pp. 111496
ISSN:
0304-4238
Subject:
transcriptomics,   etc   ; citrates; fruiting; genes; malates; peaches; phenotype;     Show all 7 Subjects
Abstract:
... Malate, citrate, and quinate are the major organic acids in ripen peach fruit, the content of which undergoes considerable variations during fruit development and maturation. The molecular mechanisms underlying these variations remain largely unclear. In this study, weighted gene co-expression network analysis (WGCNA) of two accessions in five developmental stages was performed to identify network ...
DOI:
10.1016/j.scienta.2022.111496

2. A mutant of Monascus purpureus obtained by carbon ion beam irradiation yielded yellow pigments using various nitrogen sources

Author:
Xiaofei Jiang; Xunhan Qiu; Jingjing Yang; Song Zhang; Jun Liu; Jiali Ren; Dong Lu; Xiang Zhou; Bo Zhou
Source:
Enzyme and microbial technology 2023 v.162 pp. 110121
ISSN:
0141-0229
Subject:
transcriptomics,   etc   ; Monascus purpureus; biosynthesis; carbon; citrinin; enzymes; irradiation; mutants; nitrogen; pH; polyketides;     Show all 11 Subjects
Abstract:
... The industrial production of monascus yellow pigments (MYPs) has not yet been done due to the lack of high-quality industrial Monascus strains. In this work, we employed carbon ion beam (¹²C⁶⁺) irradiation to screen Monascus strains that produce high-quality extracellular MYPs (extr-MYPs). One genetically stable M. purpureus mutant of BWY-5 with extr-MYPs accumulation was obtained under ¹²C⁶⁺ irra ...
DOI:
10.1016/j.enzmictec.2022.110121

3. Developmental toxicity of TCBPA on the nervous and cardiovascular systems of zebrafish (Danio rerio): A combination of transcriptomic and metabolomics

Author:
Wentao Liu; Yifan Pan; Lu Yang; Yun Xie; Xuanyue Chen; Jing Chang; Weiyu Hao; Lifei Zhu; Bin Wan
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 197-209
ISSN:
1001-0742
Subject:
transcriptomics,   etc   ; Danio rerio; blood; developmental toxicity; flame retardants; focal adhesions; humans; metabolomics; China;     Show all 9 Subjects
Abstract:
... Tetrachlorobisphenol A (TCBPA), a widely used halogenated flame retardant, is frequently detected in environmental compartments and human samples. However, unknown developmental toxicity and mechanisms limit the entire understanding of its effects. In this study, zebrafish (Danio rerio) embryos were exposed to various concentrations of TCBPA while a combination of transcriptomics, behavioral and b ...
DOI:
10.1016/j.jes.2022.04.022

4. 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:
transcriptomics,   etc   ; Brassica rapa subsp. oleifera; agronomic traits; hypocotyls; naphthaleneacetic acid; secondary xylem; transcriptome; 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

5. 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:
transcriptomics,   etc   ; Pinctada; biomineralization; cell proliferation; energy metabolism; environment; gene expression regulation; oysters; thermal stress; transcriptome;     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

6. β-ketoacyl-CoA synthase improves the drought tolerance of root restricted grown grapevines by regulating the cuticular wax biosynthesis

Author:
Boyang Liu; Yanli Sun; Xiangyi Li; Dinghan Guo; Liping Zhao; Chao Ma; Lei Wang; Shiping Wang
Source:
Scientia horticulturae 2023 v.307 pp. 111494
ISSN:
0304-4238
Subject:
transcriptomics,   etc   ; Arabidopsis; Vitis; biosynthesis; cultivars; drought; drought tolerance; endoplasmic reticulum; epicuticular wax; fruits; genome; grapes; water stress;     Show all 13 Subjects
Abstract:
... Drought stress limits fruit ripening and quality of grape cultivar, particularly with the use of root restriction. However, the mechanism involved in the molecular response to water deficit concomitant to agriculture adjustment remains poorly understood. In the present study, the regulation of two grape β-ketoacyl-CoA synthase (KCS) genes obtained with transcriptome analysis whose expression is si ...
DOI:
10.1016/j.scienta.2022.111494

7. 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:
transcriptomics,   etc   ; Chrysanthemum morifolium; anthocyanins; biosynthesis; chlorides; cyanidin; disc florets; flower color; gene expression regulation; metabolomics; pelargonidin; transcriptome; 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

8. Genome-wide identification of B3 superfamily in pecan (Carya illinoensis): In silico and experimental analyses

Author:
Linna Wang; Feng Chen; Yangang Lan; Hongxia Liu; Min Wu; Hanwei Yan; Yan Xiang
Source:
Scientia horticulturae 2023 v.307 pp. 111533
ISSN:
0304-4238
Subject:
transcriptomics,   etc   ; Carya illinoinensis; computer simulation; genes; growth and development; oils; pecans; plant growth; seed development; transcription factors; yeasts;     Show all 11 Subjects
Abstract:
... The B3 superfamily comprises a class of transcription factors containing B3 functional domains that play crucial roles in plant growth and development. However, the identification and analysis of the B3 superfamily have not been reported in pecans. In this study, 75 B3 superfamily members were identified and divided into four families, namely ARF (31), RAV (10), LAV (8), and REM (26). The gene str ...
DOI:
10.1016/j.scienta.2022.111533

9. 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:
transcriptomics,   etc   ; aflatoxin M1; body weight; environment; human health; immunosuppression; immunotoxicity; intestines; mice; microRNA; milk; ochratoxin A; phosphorylation; risk; transcriptome;     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

10. Iron scraps packing rapidly enhances nitrogen removal in an aerobic sludge system and the mechanism

Author:
Xin Yu; Hong Chen; Yunfan Liu; Luying Yu; Kai Wang; Gang Xue
Source:
Science of the total environment 2023 v.856 pp. 159081
ISSN:
0048-9697
Subject:
transcriptomics,   etc   ; Nitrosomonas; Thauera; carbon; denitrification; energy; environment; gene expression; iron; metagenomics; microbial communities; nitrate reduction; nitrification; nitrogen; sludge; total nitrogen;     Show all 16 Subjects
Abstract:
... Simultaneous nitrification and denitrification (SND) has the advantage of energy saving and carbon demand reduction. Here, readily available low-cost iron scraps packing was added to an aerobic sludge system. This successfully enhanced the efficiency of total nitrogen removal from 37.7 ± 13.2 % to 62.7 ± 7.9 % over 2 days. While electrons from iron biocorrosion did not contribute to nitrate reduct ...
DOI:
10.1016/j.scitotenv.2022.159081

11. 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:
transcriptomics,   etc   ; DNA; Flammulina; biosynthesis; catechol oxidase; cell senescence; cultivars; genome; laccase; melanin; mushrooms; oxidative phosphorylation; oxygen; proteolysis; proteome; proteomics; technology; transcriptome; 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

12. Triclosan toxicity in a model cyanobacterium (Anabaena flos-aquae): Growth, photosynthesis and transcriptomic response

Author:
Jiezhang Mo; Linrong Han; Runnan Lv; Michael W.L. Chiang; Rong Fan; Jiahua Guo
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 82-90
ISSN:
1001-0742
Subject:
transcriptomics,   etc   ; Anabaena flos-aquae; Pseudomonas aeruginosa; biofilm; biosynthesis; environmental exposure; fatty acids; growth retardation; nucleotide sequences; photosynthesis; starch; sucrose; toxicity; triclosan; China;     Show all 15 Subjects
Abstract:
... Exposure to triclosan (TCS) has been reported to reduce photosynthetic pigments, suppress photosynthesis, and inhibit growth in both prokaryotic and eukaryotic algae including Anabaena flos-aquae (a model cyanobacterium). In particular, cyanobacteria are more sensitive to TCS toxicity compared to eukaryotic algae possibly due to the structural similarity to bacteria (target organisms); however, wh ...
DOI:
10.1016/j.jes.2022.03.039

13. Omic analysis of anthocyanin synthesis in wine grape leaves under low-temperature

Author:
Qianqian Pang; Wenbin Yu; Ehsan Sadeghnezhad; Xueqin Chen; Pingjing Hong; Tariq Pervaiz; Yanhua Ren; Yanping Zhang; Tianyu Dong; Haifeng Jia; Jinggui Fang
Source:
Scientia horticulturae 2023 v.307 pp. 111483
ISSN:
0304-4238
Subject:
transcriptomics,   etc   ; anthocyanins; autumn; carbohydrate metabolism; cold; energy metabolism; heat; hydrogen peroxide; lipid metabolism; metabolomics; protein kinases; salt stress; sequence analysis; temperature; wine grapes;     Show all 15 Subjects
Abstract:
... Anthocyanins can be induced by environmental factors such as low- temperature, and play an important role in adapting to abiotic stress. In this study, the leaves of 'Cabernet Gernischt' grapes with different colors under natural low-temperature in autumn were collected and grouped into Green (Gre), Light-red (L-Red), Red (Red), and Dark-red (D-Red). Results showed that the total anthocyanin conte ...
DOI:
10.1016/j.scienta.2022.111483

14. 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:
transcriptomics,   etc   ; Larimichthys crocea; Pseudomonas plecoglossicida; adhesion; aquaculture; biofilm; blood serum; chemotaxis; complement; fish; granuloma; kidneys; metabolism; models; mutants; pathogens; phenotype; sequence analysis; transcriptome; 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

15. Mepanipyrim induces visual developmental toxicity and vision-guided behavioral alteration in zebrafish larvae

Author:
Chao Shen; Yimei Cai; Jialing Li; Chengyong He; Zhenghong Zuo
Source:
Journal of environmental sciences (China) 2023 v.124 pp. 76-88
ISSN:
1001-0742
Subject:
transcriptomics,   etc   ; Danio rerio; anilinopyrimidine fungicides; aryl hydrocarbon receptors; developmental toxicity; fruit growing; fungi; genes; light intensity; mepanipyrim; opsin; phototransduction; quantitative polymerase chain reaction; wavelengths; China;     Show all 15 Subjects
Abstract:
... Mepanipyrim, an anilinopyrimidine fungicide, has been extensively used to prevent fungal diseases in fruit culture. Currently, research on mepanipyrim-induced toxicity in organisms is still very scarce, especially visual developmental toxicity. Here, zebrafish larvae were employed to investigate mepanipyrim-induced visual developmental toxicity. Intense light and monochromatic light stimuli-evoked ...
DOI:
10.1016/j.jes.2021.11.008

16. 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:
transcriptomics,   etc   ; Fusarium wilt; aminocyclopropanecarboxylate oxidase; bananas; cell respiration; climacteric fruits; cultivars; ethylene production; firmness; fruit quality; gene expression; industry; malondialdehyde; pectinesterase; polygalacturonase; starch; technology; transcriptome;     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

17. Salicylic acid enhances the resistance of Neoporphyra haitanensis to pathogen Vibrio mediterranei 117-T6

Author:
Shanshan Zhu; Zhen Jin; Juanjuan Chen; Rui Yang; Qijun Luo; Tiegan Wang; Peng Zhang; Haimin Chen
Source:
Aquaculture 2023 v.562 pp. 738773
ISSN:
0044-8486
Subject:
transcriptomics,   etc   ; Porphyra; Vibrio mediterranei; antioxidants; aquaculture; carbon dioxide fixation; carotenoids; catalase; disease resistance; macroalgae; oxidative stress; pathogens; photorespiration; plant hormones; protective effect; salicylic acid; thallus;     Show all 17 Subjects
Abstract:
... The economically important seaweed Porphyra are often infected by various diseases during sea farming. As one of the most important phytohormones in disease resistance, the protective effect of salicylic acid (SA) on Neoporphyra haitanensis during Vibrio mediterranei 117-T6 infection was investigated by biochemical methods and transcriptomic profile analysis. The addition of exogenous SA at a mode ...
DOI:
10.1016/j.aquaculture.2022.738773

18. 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:
transcriptomics,   etc   ; Paralichthys olivaceus; RNA; Viral hemorrhagic septicemia virus; aquaculture; aquaculture industry; chemokines; flounder; gene expression regulation; interleukins; intraperitoneal injection; kidneys; metabolism; septicemia; tissue culture; 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

19. Acid shock protein Asr induces protein aggregation to promote E. coli O157:H7 entering viable but non-culturable state under high pressure carbon dioxide stress

Author:
Hanxu Pan; Dong Yang; Yongtao Wang; Lei Rao; Xiaojun Liao
Source:
Food microbiology 2023 v.109 pp. 104136
ISSN:
0740-0020
Subject:
transcriptomics,   etc   ; Escherichia coli O157; acid tolerance; carbon dioxide; culture media; electron transport chain; food microbiology; food safety; food spoilage; human diseases; public health; reverse transcriptase polymerase chain reaction; risk;     Show all 13 Subjects
Abstract:
... Under stressful conditions, bacteria can enter viable but non-culturable (VBNC) state to survive. VBNC cells lost ability to grow on routine culture medium but are still alive and may revive in suitable conditions. The revived cells can consume nutrients or produce toxins, leading to food spoilage or human illness, posing great risk to food safety and public health. Previously, we have reported th ...
DOI:
10.1016/j.fm.2022.104136

20. Biochemical, transcriptomic and metabolomic responses to total dissolved gas supersaturation and their underlying molecular mechanisms in Yangtze sturgeon (Acipenser dabryanus)

Author:
Yeyu Chen; Xiaoyun Wu; Xiaoqing Liu; Jiansheng Lai; Ya Liu; Mingjiang Song; Feiyang Li; Quan Gong
Source:
Environmental research 2023 v.216 pp. 114457
ISSN:
0013-9351
Subject:
transcriptomics,   etc   ; Acipenser dabryanus; amino acid metabolism; catalase; cell membranes; dissolved gases; energy; fish; flagship species; glycerophospholipids; heat stress; histopathology; liver; metabolites; metabolomics; research; superoxide dismutase; ubiquitin; water power; Yangtze River;     Show all 20 Subjects
Abstract:
... With the rapid development of hydropower facility construction, the total dissolved gas (TDG) generated by dam discharge is seriously threatening the survival of fish and has become an ecological environmental issue of global concern. However, how TDG affects fish physiology and the underlying molecular mechanism remain poorly known. In this study, Acipenser dabryanus, an ancient living fossil tha ...
DOI:
10.1016/j.envres.2022.114457