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Bulked Segregant RNA-Seq Analysis of Pollinated Pistils Reveals Genes Influencing Spikelet Fertility in Rice

Rice science 2024年第5期31卷 556-571,I0031-I0056页

作者： Kanokwan KAEWMUNGKUN Keasinee TONGMARK Sriprapai CHAKHONKAEN Numphet SANGARWUT Theerachai THANANANTA Amorntip MUANGPROM Department of biotechnology Faculty of Science and TechnologyThammasat UniversityRangsit CentreKhlong LuangPathum Thani 12120Thailand National Center for genetic engineering and biotechnology National Science and Technology Development AgencyThailand Science ParkKhlong LuangPathum Thani 12120Thailand

Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F_(5:6) generation plants derived from inter-subspecific crosses(Nipponbare × KDML105) with low(LS) and high seed-setting rates(HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4-5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes(DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS-specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene(CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall(OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion(Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.

关键词： bulked segregant RNA-Seq flavonoid inter-subspecific cross pectin pollinated pistil prezygotic barrier spikelet fertility

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Ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry-characterized extract of Aerides odorata Lour alleviates paracetamol-induced hepatotoxicity in animal model evidenced by biochemical,molecular,and computational studies

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Animal Models and Experimental Medicine 2024年第4期7卷 497-522页

作者： A.M.Abu Ahmed Md.Atiar Rahman Farjana Sharmen A.S.M.Ali Reza Md.Shahidul Islam Md.Mamunur Rashid Md.Khalid Juhani Rafi Tanvir Ahmed Siddiqui Md.Muzahid Ahmed Ezaj Srabonti Saha Md.Nazim Uddin Walla Alelwani Department of genetic engineering and biotechnology University of ChittagongChittagongBangladesh Department of Biochemistry and Molecular Biology University of ChittagongChittagongBangladesh Department of Pharmacy International Islami University ChittagongChittagongBangladesh Institute of Food Science and Technology Bangladesh Council of Scientific and Industrial ResearchDhakaBangladesh Department of Biochemistry College of ScienceUniversity of JeddahJeddahSaudi Arabia

Background:Many kinds of orchids have significant health benefits although ade-quate research on their biological functions is yet to be carried *** study inves-tigated the paracetamol-induced liver damage-protecting effect of epiphytic Aerides odorata methanol extract(AODE).Methods:The protective effects of AODE were studied by analyzing its effect on liver function parameters,messenger RNA(mRNA)expression,and tissue histopatho-logical *** results were confirmed by ligand-receptor interaction of molecular docking and multitarget interaction of network pharmacological ***:AODE significantly(ptor),EGFR(epidermal growth factor receptor),HSP90AA1(heat shock protein 90α),MAPK3(mitogen-activated protein kinase 3),STAT3(signal transducer and activator of transcription 3),CASP3(caspase protein),

关键词： Aerides odorata animal model mRNA expression PCM-induced hepatotoxicity UPLC-qTOF-MS

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A systematic review of global occurrence of emerging mycotoxins in crops and animal feeds,and their toxicity in livestock

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Emerging Contaminants 2024年第3期10卷 32-39页

作者： Oluwatobi Kolawole Wipada Siri-Anusornsak Awanwee Petchkongkaew Christopher Elliott Plant Sciences Group Wageningen University&ResearchDroevendaalsesteeg 46708 PB WageningenNetherlands Microarray Laboratory National Centre for Genetic Engineering and Biotechnology113 Thailand Science ParkPhahonyothin RoadPathum Thani12120Thailand The international Joint Research centre on Food Security 113 Thailand Science ParkPhahonyothin RoadPathum Thani12120Thailand Department of Food Science and Technology Faculty of Agro-IndustryKasetsart UniversityBangkok10900Thailand Scientific Equipment and Research Division Kasetsart University Research and Development Institute(KURDI)Kasetsart UniversityBangkok10900Thailand School of Food Science and Technology Faculty of Science and TechnologyThammasat UniversityPathum Thani12120Thailand

Mycotoxins are the most frequently occurring natural contaminant in food and *** occurrence in crops and animal feed represents an enormous challenge,particularly for livestock farmers in terms of increased production costs,reduced animal performance and *** study investigates the scale of emerging mycotoxins contamination of crops and animal feeds globally,and evaluates their impacts on the health and performance of livestock,especially when they co-occur alongside regulated *** mycotoxins including nivalenol,enniatins,beauvericin,diacetoxyscirpenol,fusaric acid,patulin,moniliformin and sterigmatocystin were found to be the most prevalent contaminants of cereals and other feed commodities *** pooled mean levels for beauvericin,nivalenol,enniatins,moniliformin,sterigmatocystin,diacetoxyscirpenol,fusaric acid,and patulin were 386,421,7,854,204,136,126,370 and 138 mg/kg,*** terms of toxicity,co-occurrence of emerging mycotoxins with each other and also with regulated mycotoxins profoundly impacts livestock performance,even at low ***,there is a need for cumulative risk assessments to evaluate the health risks associated with simultaneous exposure to emerging and regulated mycotoxins and also to develop effective mitigation strategies.

关键词： Emerging mycotoxins Animal feeds Contamination Livestock Systematic review Toxicity Crops Cereals

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Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

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Marine Life Science & Technology 2024年第2期6卷 331-348页

作者： Hao Ling Yongxin Lv Yu Zhang Ning‑Yi Zhou Ying Xu State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State Key of Laboratory of Ocean engineering Shanghai Jiao Tong UniversityShanghai 200240China

Phenolic compounds,as well as other aromatic compounds,have been reported to be abundant in hadal *** high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds,direct microbiological,genetic and biochemical evidence under in situ pressures remain ***,a microbial consortium and a pure culture of Pseudomonas,newly isolated from Mariana Trench sediments,efficiently degraded phenol under pressures up to 70 and 60 MPa,respectively,with concomitant increase in *** analyzing a high-pressure(70 MPa)culture metatranscriptome,not only was the entire range of metabolic processes under high pressure generated,but also genes encod-ing complete phenol degradation via ortho-and meta-cleavage pathways were *** isolate of Pseudomonas also contained genes encoding the complete degradation *** transcribed genes(dmpKLMNOP_(sed))were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous *** addition,key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial *** microbiological,genetic,bioinformatics,and biochemical levels,this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic *** information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

关键词： Hadal trench High hydrostatic pressure Phenolic compounds degradation Piezotolerant microorganisms Widespread distribution

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Gas chromatography mass spectrometry based metabolic profiling reveals biomarkers involved in rice-gall midge interactions

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Journal of Integrative Plant Biology 2014年第9期56卷 837-848页

作者： Ruchi Agarrwal Jagadish Sanmallappa Bentur Suresh Nair international centre for genetic engineering and biotechnology(ICGEB) Directorate of Rice Reearch Agri Biotech Foundation

The Asian rice gall midge（Orseolia oryzae WoodMason） is a serious pest of rice that causes huge loss in *** feeding inside the susceptible host,maggots secrete substances that facilitate the formation of a hollow tube-like structure called gall and prevent panicle *** present investigation was carried out to get an account of biochemical changes occurring in the rice plant upon gall midge *** profiling of host tissues from three rice varieties,namely,TN1,Kavya,and RP2068,exposed to gall midge biotype 1（GMB1）,was carried out using gas chromatography mass spectrometry（GC-MS）.TN1 and GMB1 represented compatible interaction,while Kavya and GMB1 as well as RP2068 and GMB1 represented incompatible *** current study identified several metabolites that could be grouped as resistance,susceptibility,infestation,and host features based on their relative *** may be regarded as biomarkers for insect-plant interaction in general and rice-gall midge interaction in particular.

关键词： Biomarkers gas chromatography mass spectrometry insect-plant interaction metabolic profiling metabolites rice-gall midge interaction

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O-methyltransferase CbzMT catalyzes iterative 3,4-dimethylations for carbazomycin biosynthesis

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engineering Microbiology 2024年第2期4卷 51-61页

作者： Baixin Lin Dashan Zhang Junbo Wang Yongjian Qiao Jinjin Wang Zixin Deng Lingxin Kong Delin You State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences&BiotechnologyShanghai Jiao Tong UniversityShanghai 200030China

Carbazomycins(1-8)are a subgroup of carbazole derivatives that contain oxygen at the C3 and C4 positions and an unusual asymmetric substitution *** of these compounds exhibit antifungal and antioxidant *** date,no systematic biosynthetic studies have been conducted on *** this study,carbazomycins A and B(1 and 2)were isolated from Streptomyces luteosporeus NRRL 2401 using a one-strain-many-compound(OSMAC)-guided natural product mining screen.A biosynthetic gene cluster(BGC)was iden-tified,and possible biosynthetic pathways for 1 and 2 were *** in vivo genetic manipulation of the O-methyltransferase-encoding gene cbzMT proved indispensable for 1 and 2 *** exclusion chro-matography indicated that CbzMT was active as a *** vitro biochemical assays confirmed that CbzMT could repeatedly act on the hydroxyl groups at C3 and C4,producing monomethylated 2 and dimethylated *** carbazomycin B(2)is not easily methylated;however,CbzMT seemingly prefers the dimethy-lation of the dihydroxyl substrate(12)to 1,even with a low conversion *** findings not only improve the understanding of carbazomycin biosynthesis but also expand the inventory of OMT-catalyzing it-erative methylations on different acceptor sites,paving the way for engineering biocatalysts to synthesize new active carbazomycin derivatives.

关键词： One-strain-many-compounds(OSMAC) Carbazole Carbazomycins O-methyltransferase Iterative methylation

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High affinity mouse-human chimeric Fab against Hepatitis B surface antigen

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World Journal of Gastroenterology 2005年第48期11卷 7569-7578页

作者： Biplab Bose Navin Khanna Subrat K Acharya Subrata Sinha Department of Biochemistry international Center for genetic engineering and biotechnology Department of Gastroenterology

AIM： Passive immunotherapy using antibody against hepatitis B surface antigen （HBsAg） has been advocated in certain cases of Hepatitis B infection. We had earlier reported on the cloning and expression of a high affinity scFv derived from a mouse monoclonal （5S） against HBsAg. However this mouse antibody cannot be used for therapeutic purposes as it may elicit anti-mouse immune responses. Chimerization by replacing mouse constant domains with human ones can reduce the immunogenicity of this antibody.METHODS： We cloned the VH and V, genes of this mouse antibody, and fused them with CH1 domain of human IgG1 and C, domain of human kappa chain respectively. These chimeric genes were cloned into a phagemid vector. After initial screening using the phage display system, the chimeric Fab was expressed in soluble form in E. coli.RESULTS： The chimeric Fab was purified from the bacterial periplasmic extract. We characterized the chimeric Fab using several in vitro techniques and it was observed that the chimeric molecule retained the high affinity and specificity of the original mouse monoclonal. This chimeric antibody fragment was further expressed in different strains of E. coli to increase the yield.CONCLUSION： We have generated a mouse-human chimeric Fab against HBsAg without any significant loss in binding and epitope specificity. This chimeric Fab fragment can be further modified to generate a fulllength chimeric antibody for therapeutic uses.

关键词： Chimeric Fab Hepatitis B surface antigen Phage display

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Knights in Action： Lectin Receptor-Like Kinases in Plant Development and Stress Responses

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Molecular Plant 2013年第5期6卷 1405-1418页

作者： Neha Vaid Anca Macovei Narendra Tuteja Plant Molecular Biology Group International Centre for Genetic Engineering and Biotechnology Aruna Asaf Ali Marg New Delhi 110067 India

The Receptor-Like Kinase （RLK） is a vast protein family with over 600 genes in Arabidopsis and 1100 in rice. The Lectin RLK （LecRLK） family is believed to play crucial roles in saccharide signaling as well as stress perception. All the LecRLKs possess three domains： an N-terminal lectin domain, an intermediate transmembrane domain, and a C-terminal kinase domain. On the basis of lectin domain variability, LecRLKs have been subgrouped into three subclasses： L-, G-, and C-type LecRLKs. While the previous studies on LecRLKs were dedicated to classification, comparative structural analysis and expression analysis by promoter-based studies, most of the recent studies on LecRLKs have laid special emphasis on the potential of this gene family in regulating biotic/abiotic stress and developmental pathways in plants, thus mak- ing the prospects of studying the LecRLK-mediated regulatory mechanism exceptionally promising. In this review, we have described in detail the LecRLK gene family with respect to a historical, evolutionary, and structural point of view. Furthermore, we have laid emphasis on the LecRLKs roles in development, stress conditions, and hormonal response. We have also discussed the exciting research prospects offered by the current knowledge on the LecRLK gene family. The multitude of the LecRLK gene family members and their functional diversity mark these genes as both interesting and worthy candidates for further analysis, especially in the field of crop improvement.

关键词： classification hormone signaling Lectin Receptor-Like Kinase membrane protein plant development RLKfamily stress.

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Butein imparts free radical scavenging, anti-oxidative and proapoptotic properties in the flower extracts of Butea monosperma

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BIOCELL 2012年第2期36卷 63-71页

作者： ANURADHA SEHRAWAT VIJAY KUMAR Virology Group International Centre for Genetic Engineering and BiotechnologyAruna Asaf Ali MargNew Delhi 110067India

The flower of Butea monosperma(Lam.)(Fabaceae)has been used in traditional Indian medicine in the treatment of many ailments including liver *** understand the pharmacological basis of its beneficial effects,the extracts of dried flowers in water,methanol,butanol,ethyl acetate and acetone were evaluated for free radical scavenging and pro-apoptotic activities in cell cultures(human hepatoma Huh-7 cell line and immortalized AML-12 mouse hepatocytes).Butrin and butein-the active constituents of flower extracts-were used as reference *** levels of cell injury markers like lactate dehydrogenase,glutathione and lipid peroxidation and primary antioxidant enzymes glutathione S-transferase and catalase were also *** aqueous and butanolic extracts exhibited better 2,2-diphenyl-1-picrylhydrazyl scavenging and cytotoxic activities in hepatoma cells than in immortalized ***,butein inhibited 2,2-diphenyl-1-picrylhydrazyl radical better than *** aqueous and butanolic extracts were further investigated for hepatoprotection against carbon tertrachloride-induced biochemical changes and cell *** extracts,just as butrin and butein,significantly reversed the cellular glutathione levels and lipid peroxidation,and glutathione–S-transferase *** dehydrogenase leakage and cell death were also ***,only butein revived the catalase ***,the butein content of Butea monosperma flower extracts is important for free radical scavenging activity,apoptotic cell death and protection against oxidative injury in hepatic cells.

关键词： butrin cytotoxicity hepatoprotection methanol extract free radical scavenging

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Endosperm ontogeny through the lens of epigenetics

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Molecular Plant 2023年第2期16卷 295-297页

作者： Kajol B.M.Singh Jitendra K.Thakur National Institute of Plant Genome Research New Delhi 110067India international centre for genetic engineering and biotechnology New Delhi 110067India

Endosperm tissue is crucial to seed *** and dicots have evolved different fates for their endosperm:it is usually consumed in dicots during seed development,while monocot seeds retain the endosperm until ***,Wu et al.(2022)addressed the role of divergent epigenetic regulation over the functionally conserved IKU2 gene contributing to silenced or persistent endosperm proliferation and have provided insights into divergent seed ontogeny patterns in ***,we highlight the novel findings from this study and their potential significance.

关键词： maturity finding insight

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