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The transcriptional landscape of the developmental switch from regular pollen maturation towards microspore-derived plant regeneration in barley

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The Crop Journal 2024年第4期12卷 1064-1080页

作者： Anna Nowicka Martin Kovacik Anna Maksylewicz Przemysław Kopec Ewa Dubas Monika Krzewska Agnieszka Springer Robert E.Hoffie Diaaeldin S.Daghma Zbynek Milec Ales Pecinka Jochen Kumlehn Iwona Zur The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences Niezapominajek 2130-239 KrakówPoland Institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional GenomicsŠlechtitelu3177900 OlomoucCzech Republic Department of Cell Biology and genetics Faculty of SciencePalacky UniversityŠlechtitelu°2777900 OlomoucCzech Republic Malopolska Centre of Biotechnology Jagiellonian University30-387 KrakówPoland Leibniz Institute of Plant genetics and Crop Plant Research(IPK)Gatersleben Corrensstraße 306466 Stadt SeelandGermany Institute for Breeding Research on Horticultural Crops Julius Kühn Institute(JKI)-Federal Research Centre for Cultivated PlantsErwin-Baur Straße 2706484 QuedlinburgGermany Global Change Research Institute Czech Academy of Sciences Beˇlidla 986/4a60300 BrnoCzech Republic

Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental ***/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant breeding and genetic ***,the mechanism underlying the developmental switch from regular pollen maturation towards microspore-derived plant regeneration remains poorly ***,RNA-sequencing was employed to elucidate the transcriptional landscapes of four early stages of microspore embryogenesis(ME)in barley cultivars Golden Promise and Igri,which exhibit contrasting responsiveness to microspore-derived plant *** experiments revealed fundamental regulatory networks,specific groups of genes,and transcription factor(TF)families potentially regulating the developmental *** identified a set of candidate genes crucial for genotype-dependent responsiveness/recalcitrance to *** high-resolution temporal transcriptome atlas provides an important resource for future functional studies on the genetic control of microspore developmental transition.

关键词： Hordeum vulgare marker gene Microspore embryogenesis Stress response Transcriptome analysis

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Rescue of white egg 1 mutant by introduction of the wildtype Bombyx kynurenine 3-monooxygenase gene

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Insect Science 2007年第2期14卷 85-92页

作者： GUO-XING QUAN ISAO KOBAYASHI KATSURA KOJIMA KEIRO UCHINO TOSHIO KANDA HIDEKI SEZUTSU TORU SHIMADA TOSHIKI TAMURA Transgenic Silkworm Research Center National Institute of Agrobiological Sciences Tsukuba Ibaraki 305-8634 Japan Biomimetic Laboratory National Institute of Agrobiological Sciences Tsukuba Ibaraki 305-8634 Japan Department of Agricultural and Environmental Biology Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan

In silkworms, the white egg 1 （w-1） mutant, which is characterized by white eyes and white eggs, is deficient in Bombyx kynurenine 3-monooxygenase （KMO） activity. To investigate whether the w-1 mutant phenotype is rescued by introducing the wild-type KMO gene, we constructed transgenic silkworms with the wild-type Bombyx KMO gene under the control of either the cytoplasmic actin gene promoter （A3KMO） or the native KMO gene promoter （KKMO）. We created two transgenic lines with A3KMO and one line with KKMO constructs. The eyes of adults in these lines were brown, and the eggs laid by the transgenic females were also brown. Reverse transcription-polymerase chain reaction（RT-PCR） analysis showed that the A3KMO silkworm lines expressed the transcript in the mid-gut, fat bodies, and Malpighian tubules. The KKMO line expressed the transcript only in the fat bodies and Malpighian tubules. The intensity of eye and egg color in the transgenic lines was proportional to the KMO expression level. Interestingly, transgenic larvae with the A3KMO construct had a light brown larval cuticle, but the KKMO line did not. These results indicate that the wild-type KMO gene can be used as a marker gene for visually screening transgenic silkworms.

关键词： Bombyx mori KMO marker gene transgenic w-1

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Diversity,community structure,and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers:a case study of the Pearl River Estuary

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Marine Life Science & Technology 2023年第3期5卷 415-430页

作者： Shumin Xu Guihao Li Cui He Yi Huang Dan Yu Huiwen Deng Zhuyin Tong Yichong Wang Christine Dupuy Bangqin Huang Zhuo Shen Jie Xu Jun Gong School of Marine Sciences Sun Yat-Sen University(Zhuhai Campus)and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)Zhuhai 519000China Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering Guangzhou 510006China State Key Laboratory of Marine Environmental Science Xiamen UniversityXiamen 361102China BIOFEEL UMRi LIENSsLa Rochelle Université/CNRSLa RochelleFrance Centre for Regional Oceans Department of Civil and Environmental EngineeringFaculty of Science and TechnologyUniversity of MacaoMacaoChina

Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem *** this study,eukaryotic phytoplankton in the Pearl River Estuary,South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment *** was found that 18S abundance poorly explained the variations in total chlorophyll a(Chl-a).However,the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent,suggesting that the ratio has potential as an indicator of the physiological state of *** richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community,but insignifcant or weak for individual phytoplankton ***,the 18S based,rather than the 16S based,community structure had a greater similarity to pigment-based *** to the pigment data,the proportion of haptophytes in the 18S dataset,and diatoms and cryptophytes in the 16S dataset,were *** study highlights that 18S metabarcoding tends to refect biomass-based community organization of eukaryotic *** there were lower copy numbers of plastid 16S than 18S per genome,metabarcoding of 16S probably approximates cell abundance-based community *** in biomass organization of the pigment-based community were sensitive to environmental *** together,multiple methodologies are recommended to be applied to more accurately profle the diversity and community composition of phytoplankton in natural ecosystems.

关键词： Accessory pigments Chloroplast marker gene Metabarcoding Phytoplankton

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Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 899-911页

作者： Yongbing Zhao Jinfeng Shao Yan W.Asmann Department of Quantitative Health Sciences Mayo ClinicJacksonvilleFL 32224USA The Laboratory of Malaria and Vector Research National Institute of Allergy and Infectious DiseasesNational Institutes of HealthRockvilleMD 20852USA

Explainable artificial intelligence aims to interpret how machine learning models make decisions,and many model explainers have been developed in the computer vision ***,understanding of the applicability of these model explainers to biological data is still *** this study,we comprehensively evaluated multiple explainers by interpreting pre-trained models for predicting tissue types from transcriptomic data and by identifying the top contributing genes from each sample with the greatest impacts on model *** improve the reproducibility and interpretability of results generated by model explainers,we proposed a series of optimization strategies for each explainer on two different model architectures of multilayer perceptron(MLP)and convolutional neural network(CNN).We observed three groups of explainer and model architecture combinations with high *** II,which contains three model explainers on aggregated MLP models,identified top contributing genes in different tissues that exhibited tissue-specific manifestation and were potential cancer *** summary,our work provides novel insights and guidance for exploring biological mechanisms using explainable machine learning models.

关键词： Machine learning Model interpretability gene expression marker gene Omics data mining

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Serial changes in expression of functionally clustered genes in progression of liver fibrosis in hepatitis C patients

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World Journal of Gastroenterology 2008年第13期14卷 2010-2022页

作者： Yoshiyuki Takahara Mitsuo Takahashi Qing-Wei Zhang Hirotaka Wagatsuma Maiko Mori Akihiro Tamori Susumu Shiomi Shuhei Nishiguchi Exploratory & Applied Pharmaceutical Research Department Pharmaceutical Company Ajinomoto Co. Inc. 1-1 Suzuki-cho Kawasaki-ku Kawasaki 210-8681 Japan Department of Nuclear Medicine Graduate School of Medicine Osaka City University Osaka Japan Division of Hepatobiliary and Pancreatic Diseases Department of Internal Medicine Hyogo College of Medicine Nishinomiya Japan

AIM: To investigate the relationship of changes in expression of marker genes in functional categories or molecular networks comprising one functional category or multiple categories in progression of hepatic fibrosis in hepatitis C (HCV) patients. METHODS: marker genes were initially identified using DNA microarray data from a rat liver fibrosis model. The expression level of each fibrosis associated marker gene was analyzed using reverse transcription-polymerase chain reaction (RT-PCR) in clinical biopsy specimens from HCV-positive patients (n = 61). Analysis of changes in expression patterns and interactions of marker genes in functional categories was used to assess the biological mechanism of fibrosis. RESULTS: The profile data showed several biological changes associated with progression of hepatic fibrosis. Clustered genes in functional categories showed sequential changes in expression. Several sets of clustered genes, including those related to the extracellular matrix (ECM), inflammation, lipid metabolism, steroid metabolism, and some transcription factors important for hepatic biology showed expression changes in the immediate early phase (F1/F2) of fibrosis. genes associated with aromatic amino acid (AA) metabolism, sulfur-containing AA metabolism and insulin/ Wnt signaling showed expression changes in the middle phase (F2/F3), and some genes related to glucose metabolism showed altered expression in the late phase of fibrosis (F3/F4). Therefore, molecular networks showing serial changes in gene expression are present in liver fibrosis progression in hepatitis C patients. CONCLUSION: Analysis of gene expression profiles from a perspective of functional categories or molecular networks provides an understanding of disease and suggests new diagnostic methods. Selected marker genes have potential utility for biological identification of advanced fibrosis.

关键词： Hepatitis C Liver fibrosis marker gene gene expression RT-PCR Molecular network Metabolism Transcription factor Diagnosis

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ImmuSubset:a database of experimentally validated human and mouse immune cell subsets

ImmuSubset:a database of experimentally validated human and ...

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第十四届全国免疫学学术大会

作者： Yuzhe Hu Huiying Qi Shibin Song Ling Tang Wenling Han Pingzhang Wang Department of Immunology Peking University Health Science Center Peking University Center for Human Disease Genomics Department of Health Informatics and Management Peking University Health Science Center Information and Communication Center Peking University Health Science Center

Many immune cell subsets have been identified in recent *** subsets are labelled by diffe rent molecular markers and combinations of these markers,and exhibit diversified phenotypes and functions involved in diffe rent physiological and pathological processes.H owever,no existing resource or database has recorded all of these immune cell subsets and relevant information,and the true number of identified immune cell subsets remains *** this study,we present a new database,ImmuSubset,that collects information about experimentally validated human and mouse immune cell *** supports queries by cell type and gene symbol or alias,and thus provides a convenient way to view reported immune cell subsets and information about related maker *** current database version covers 16 human and 16 mouse immune cell types,with 2,757 and 2,233 immune cell subsets,respectively,and involves more than 360 and 306 marker genes,*** T cell subsets are the most abundant among both human and mouse cell *** database URL is http://***/immusubset.

关键词： Immune cell subset database marker gene immuno-phenotype

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