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  1. Article ; Online: Adaptive visual detection of industrial product defects

    Haigang Zhang / Dong Wang / Zhibin Chen / Ronghui Pan

    PeerJ Computer Science, Vol 9, p e

    2023  Volume 1264

    Abstract: Visual inspection of the appearance defects on industrial products has always been a research hotspot pursued by industry and academia. Due to the lack of samples in the industrial defect dataset and the serious class imbalance, deep learning technology ... ...

    Abstract Visual inspection of the appearance defects on industrial products has always been a research hotspot pursued by industry and academia. Due to the lack of samples in the industrial defect dataset and the serious class imbalance, deep learning technology cannot be directly applied to industrial defect visual inspection to meet the real application needs. Transfer learning is a good choice to deal with insufficient samples. However, cross-dataset bias is unavoidable during simple knowledge transfer. We noticed that the appearance defects of industrial products are similar, and most defects can be classified as stains or texture jumps, which provides a research basis for building a universal and adaptive industrial defect detection model. In this article, based on the idea of model-agnostic meta-learning (MAML), we propose an adaptive industrial defect detection model through learning from multiple known industrial defect datasets and then transfer it to the novel anomaly detection tasks. In addition, the Siamese network is used to extract differential features to minimize the influence of defect types on model generalization, and can also highlight defect features and improve model detection performance. At the same time, we add a coordinate attention mechanism to the model, which realizes the feature enhancement of the region of interest in terms of two coordinate dimensions. In the simulation experiments, we construct and publish a visual defect dataset of injection molded bottle cups, termed BC defects, which can complement existing industrial defect visual data benchmarks. Simulation results based on BC defects dataset and other public datasets have demonstrated the effectiveness of the proposed general visual detection model for industrial defects. The dataset and code are available at https://github.com/zhg-SZPT/MeDetection.
    Keywords Model-agnostic meta-learning ; Industrial visual inspection ; Convolutional neural network ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Sequence and biochemical analysis of Arabidopsis SP1 protein, a regulator of organelle biogenesis

    Ronghui Pan / Jianping Hu

    Communicative & Integrative Biology, Vol 10, Iss

    2017  Volume 4

    Abstract: Peroxisomes, chloroplasts, and mitochondria are essential eukaryotic organelles that host a suite of metabolic processes crucial to energy metabolism and development. Regulatory mechanisms of the dynamics and biogenesis of these important organelles have ...

    Abstract Peroxisomes, chloroplasts, and mitochondria are essential eukaryotic organelles that host a suite of metabolic processes crucial to energy metabolism and development. Regulatory mechanisms of the dynamics and biogenesis of these important organelles have begun to be discovered in plants. We recently showed that, aside from its previously reported role in targeting chloroplast protein import proteins, the Arabidopsis ubiquitin E3 ligase SP1 (suppressor of ppi1 locus1) negatively regulates peroxisome matrix protein import by promoting the ubiquitination and destabilization of PEX13 and possibly PEX14 and other components of the peroxisome protein import apparatus. Here, we compared protein sequence and domain structure of SP1-like proteins in Arabidopsis and their human homolog, Mitochondrial-Anchored Protein Ligase (MAPL). We further characterized SP1 protein in respect to its membrane topology and ubiquitin E3 ligase activity.
    Keywords chloroplasts ; E3 ubiquitin ligase ; MAPL ; mitochondria ; peroxisomes ; SP1 ; SPL1 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2017-07-01T00:00:00Z
    Publisher Taylor & Francis Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes

    Yanxiang Lin / Pan Li / Yuchan Zhang / Delara Akhter / Ronghui Pan / Zhixi Fu / Mingqing Huang / Xiaobo Li / Yanlei Feng

    BMC Biology, Vol 20, Iss 1, Pp 1-

    2022  Volume 16

    Abstract: Abstract Background The morning glories (Convolvulaceae) are distributed worldwide and produce economically important crops, medicinal herbs, and ornamentals. Members of this family are diverse in morphological characteristics and trophic modes, ... ...

    Abstract Abstract Background The morning glories (Convolvulaceae) are distributed worldwide and produce economically important crops, medicinal herbs, and ornamentals. Members of this family are diverse in morphological characteristics and trophic modes, including the leafless parasitic Cuscuta (dodders). Organelle genomes were generally used for studying plant phylogeny and genomic variations. Notably, plastomes in parasitic plants always show non-canonical features, such as reduced size and accelerated rates. However, few organelle genomes of this group have been sequenced, hindering our understanding of their evolution, and dodder mitogenome in particular. Results We assembled 22 new mitogenomes and 12 new plastomes in Convolvulaceae. Alongside previously known ones, we totally analyzed organelle genomes of 23 species in the family. Our sampling includes 16 leafy autotrophic species and 7 leafless parasitic dodders, covering 8 of the 12 tribes. Both the plastid and mitochondrial genomes of these plants have encountered variations that were rarely observed in other angiosperms. All of the plastomes possessed atypical IR boundaries. Besides the gene and IR losses in dodders, some leafy species also showed gene and intron losses, duplications, structural variations, and insertions of foreign DNAs. The phylogeny reconstructed by plastid protein coding sequences confirmed the previous relationship of the tribes. However, the monophyly of ‘Merremieae’ and the sister group of Cuscuta remained uncertain. The mitogenome was significantly inflated in Cuscuta japonica, which has exceeded over 800 kb and integrated massive DNAs from other species. In other dodders, mitogenomes were maintained in small size, revealing divergent evolutionary strategies. Mutations unique to plants were detected in the mitochondrial gene ccmFc, which has broken into three fragments through gene fission and splicing shift. The unusual changes likely initially happened to the common ancestor of the family and were caused by a foreign insertion from ...
    Keywords Convolvulaceae ; Cuscuta ; Plastid genome ; Mitochondrial genome ; ccmFc ; Horizontal gene transfer ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Author Correction

    Bin Ma / Caiyu Lu / Yiling Wang / Jingwen Yu / Kankan Zhao / Ran Xue / Hao Ren / Xiaofei Lv / Ronghui Pan / Jiabao Zhang / Yongguan Zhu / Jianming Xu

    Nature Communications, Vol 14, Iss 1, Pp 1-

    A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

    2023  Volume 1

    Keywords Science ; Q
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

    Bin Ma / Caiyu Lu / Yiling Wang / Jingwen Yu / Kankan Zhao / Ran Xue / Hao Ren / Xiaofei Lv / Ronghui Pan / Jiabao Zhang / Yongguan Zhu / Jianming Xu

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale ... ...

    Abstract Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome’s functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.
    Keywords Science ; Q
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The OsbHLH002/OsICE1-OSH1 module orchestrates secondary cell wall formation in rice

    Ying Chen / Haoyue Qi / Lijia Yang / Liang Xu / Jiaxuan Wang / Jiazhuo Guo / Liang Zhang / Yuanyuan Tan / Ronghui Pan / Qingyao Shu / Qian Qian / Shiyong Song

    Cell Reports, Vol 42, Iss 7, Pp 112702- (2023)

    2023  

    Abstract: Summary: Transcriptional regulation of secondary cell wall (SCW) formation is strictly controlled by a complex network of transcription factors in vascular plants and has been shown to be mediated by a group of NAC master switches. In this study, we show ...

    Abstract Summary: Transcriptional regulation of secondary cell wall (SCW) formation is strictly controlled by a complex network of transcription factors in vascular plants and has been shown to be mediated by a group of NAC master switches. In this study, we show that in a bHLH transcription factor, OsbHLH002/OsICE1, its loss-of-function mutant displays a lodging phenotype. Further results show that OsbHLH002 and Oryza sativa homeobox1 (OSH1) interact and share a set of common targets. In addition, the DELLA protein SLENDER RICE1, rice ortholog of KNOTTED ARABIDOPSIS THALIANA7, and OsNAC31 interact with OsbHLH002 and OSH1 and regulate their binding capacity on OsMYB61, a key regulatory factor in SCW development. Collectively, our results indicate OsbHLH002 and OSH1 as key regulators in SCW formation and shed light on molecular mechanisms of how active and repressive factors precisely orchestrate SCW synthesis in rice, which may provide a strategy for manipulating plant biomass production.
    Keywords CP: Plants ; CP: Molecular biology ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: RNA-Seq-Based Profiling of pl Mutant Reveals Transcriptional Regulation of Anthocyanin Biosynthesis in Rice ( Oryza sativa L.)

    Ruonan Xu / Ronghui Pan / Yuchan Zhang / Yanlei Feng / Ujjal Kumar Nath / Yinbo Gan / Chunhai Shi / Delara Akhter

    International Journal of Molecular Sciences, Vol 22, Iss 9787, p

    2021  Volume 9787

    Abstract: Purple-colored leaves in plants attain much interest for their important biological functions and could be a potential source of phenotypic marker in selecting individuals in breeding. The transcriptional profiling helps to precisely identify mechanisms ... ...

    Abstract Purple-colored leaves in plants attain much interest for their important biological functions and could be a potential source of phenotypic marker in selecting individuals in breeding. The transcriptional profiling helps to precisely identify mechanisms of leaf pigmentation in crop plants. In this study, two genetically unlike rice genotypes, the mutant purple leaf ( pl ) and wild (WT) were selected for RNA-sequencing and identifying the differentially expressed genes (DEGs) that are regulating purple leaf color. In total, 609 DEGs were identified, of which 513 and 96 genes were up- and down-regulated, respectively. The identified DEGs are categorized into metabolic process, carboxylic acid biosynthesis, phenylpropanoids, and phenylpropanoid biosynthesis process enrichment by GO analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their association with phenylpropanoid synthesis, flavonoid synthesis, and phenylalanine metabolism. To explore molecular mechanism of purple leaf color, a set of anthocyanin biosynthetic and regulatory gene expression patterns were checked by qPCR. We found that OsPAL ( Os02g0626100 , Os02g0626400 , Os04g0518400 , Os05g0427400 and Os02g0627100 ), OsF3H ( Os03g0122300 ), OsC4HL ( Os05g0320700 ), and Os4CL5 ( Os08g0448000 ) are associated with anthocyanin biosynthesis, and they were up-regulated in pl leaves. Two members of regulatory MYB genes ( OsMYB55

    Os05g0553400 and Os08g0428200 ), two bHLH genes ( Os01g0196300 and Os04g0300600 ), and two WD40 genes ( Os11g0132700 and Os11g0610700 ) also showed up-regulation in pl mutant. These genes might have significant and vital roles in pl leaf coloration and could provide reference materials for further experimentation to confirm the molecular mechanisms of anthocyanin biosynthesis in rice.
    Keywords pl ( purple leaf ) mutant ; anthocyanin biosynthesis ; transcriptional analysis ; DEGs ; rice ( Oryza sativa L.) ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 580
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Arabidopsis Forkhead‐Associated Domain Protein 3 negatively regulates peroxisome division

    Desai, Mintu / Ronghui Pan / Jianping Hu

    Journal of integrative plant biology. 2017 July, v. 59, no. 7

    2017  

    Abstract: Peroxisomes are ubiquitous and dynamic eukaryotic organelles capable of altering their abundance in response to environmental and developmental cues, yet the regulatory mechanism of plant peroxisome division/proliferation is unclear. To identify ... ...

    Abstract Peroxisomes are ubiquitous and dynamic eukaryotic organelles capable of altering their abundance in response to environmental and developmental cues, yet the regulatory mechanism of plant peroxisome division/proliferation is unclear. To identify transcriptional regulators of the peroxisome division factor gene PEX11b, we performed a nuclear pull‐down experiment and identified Arabidopsis Forkhead‐Associated Domain Protein 3 (FHA3) as a novel protein that binds to the promoter of PEX11b. Our data supported the conclusion that, in contrast to the previously identified HY5 HOMOLOG (HYH) protein that promotes the transcription of PEX11b, FHA3 is a negative regulator of PEX11b expression and peroxisome division.
    Keywords Arabidopsis ; genes ; peroxisomes ; transcription factors
    Language English
    Dates of publication 2017-07
    Size p. 454-458.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note LETTER
    ZDB-ID 2130095-1
    ISSN 1744-7909 ; 1672-9072
    ISSN (online) 1744-7909
    ISSN 1672-9072
    DOI 10.1111/jipb.12542
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Spermidine Enhances Heat Tolerance of Rice Seeds by Modulating Endogenous Starch and Polyamine Metabolism

    Yuying Fu / Qingqing Gu / Qian Dong / Zhihao Zhang / Cheng Lin / Weimin Hu / Ronghui Pan / Yajing Guan / Jin Hu

    Molecules, Vol 24, Iss 7, p

    2019  Volume 1395

    Abstract: Polyamines have been reported to be involved in grain filling and they might contribute to the construction of heat resistance of some cereals. In this study, the hybrid rice ‘YLY 689’ was used to explore the possible effects of exogenous spermidine (Spd) ...

    Abstract Polyamines have been reported to be involved in grain filling and they might contribute to the construction of heat resistance of some cereals. In this study, the hybrid rice ‘YLY 689’ was used to explore the possible effects of exogenous spermidine (Spd) on seed quality under high temperature during the filling stage. Rice spikes were treated with Spd or its synthesis inhibitor cyclohexylamine (CHA) after pollination, and then the rice plants were transferred to 40 °C for 5-day heat treatment. The results showed that, compared with the control under high temperature, Spd pretreatment significantly improved the germination percentage, germination index, vigor index, seedling shoot height, and dry weight of seeds harvested at 35 days after pollination, while the CHA significantly decreased the seed germination and seedling growth. Meanwhile, Spd significantly increased the peroxidase (POD) activity and decreased the malondialdehyde (MDA) content in seeds. In addition, after spraying with Spd, the endogenous content of spermidine and spermine and the expression of their synthetic genes, spermidine synthase ( SPDSYN) and spermine synthase ( SPMS1 and SPMS2 ), significantly increased, whereas the accumulation of amylose and total starch and the expression of their related synthase genes, soluble starch synthase II-3 ( SS II-3 ) and granules bound starch synthase I ( GBSSI ), also increased to some extent. The data suggests that exogenous Spd pretreatment could alleviate the negative impacts of high temperature stress on rice seed grain filling and improve the rice seed quality to some extent, which might be partly caused by up-regulating endogenous polyamines and starch metabolism.
    Keywords spermidine ; high temperature ; grain filling ; starch ; polyamines ; Organic chemistry ; QD241-441
    Subject code 580
    Language English
    Publishing date 2019-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Evaluation of seed quality based on changes of internal substances during tobacco seed (Nicotiana tabacum L.) development

    Li, Zhan / Fan Li / Genyuan Guo / Yue Gao / Wenguang Ma / Ronghui Pan / Yajing Guan / Jin Hu

    Plant growth regulation. 2018 Dec., v. 86, no. 3

    2018  

    Abstract: Seed quality is closely associated with internal substances during seed development. Tobacco seed varieties Honghua Dajinyuan (HD) and Yunyan97 (Y97) had higher viability and vigor when harvested from 31 to 33 days after pollination (DAP), subsequently ... ...

    Abstract Seed quality is closely associated with internal substances during seed development. Tobacco seed varieties Honghua Dajinyuan (HD) and Yunyan97 (Y97) had higher viability and vigor when harvested from 31 to 33 days after pollination (DAP), subsequently decline slightly on 35 DAP. From 7 to 35 DAP, the moisture content of HD and Y97 decreased sharply from 90 to 30%, and abscisic acid declined more than 80% totally in seeds. Accumulation of oil and protein was accompanied with the consumption of soluble sugar and starch, especially from 7 to 23 DAP. In addition, crude fiber and arginine exhibited an increasing trend, while ash and lysine significantly decreased from 7 to 23 DAP. Generally, the germination percentage (seed viability) in HD and Y97 seed was related to oil, moisture, soluble sugar, protein, starch, ABA, lysine, arginine, seed weight and seed coat color; however, only moisture, oil and protein had a significant correlation with vigor index (seed vigor). Thus, seed viability could be applied to estimate the relationship between internal substances and seed quality, and predict the optimum seed harvest time of tobacco.
    Keywords Nicotiana tabacum ; abscisic acid ; arginine ; color ; crude fiber ; germination ; lysine ; oils ; pollination ; seed coat ; seed development ; seed quality ; seed weight ; seeds ; starch ; sugars ; tobacco ; viability ; vigor ; water content
    Language English
    Dates of publication 2018-12
    Size p. 389-399.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 843025-1
    ISSN 1573-5087 ; 0167-6903
    ISSN (online) 1573-5087
    ISSN 0167-6903
    DOI 10.1007/s10725-018-0437-x
    Database NAL-Catalogue (AGRICOLA)

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