Journal of Plant Biochemistry and Biotechnology最新文献_第2页

Genome-wide identification and characterization of PGIP gene family in Vigna radiata L. Wilczek and its expression in wild non-progenitor, Vigna umbellata L. Thunb. modulate bruchid resistance 全基因组范围内对 Vigna radiata L. Wilczek 中 PGIP 基因家族的鉴定和表征及其在野生非原种 Vigna umbellata L. Thunb. 中的表达调控青枯病抗性

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-29 DOI: 10.1007/s13562-024-00915-y

Ramesh Kumar, Rakesh Pandey, Shalini Purwar, Mukesh Kumar Mishra, Ashutosh Rai, Chandra Mohan Singh

{"title":"Genome-wide identification and characterization of PGIP gene family in Vigna radiata L. Wilczek and its expression in wild non-progenitor, Vigna umbellata L. Thunb. modulate bruchid resistance","authors":"Ramesh Kumar, Rakesh Pandey, Shalini Purwar, Mukesh Kumar Mishra, Ashutosh Rai, Chandra Mohan Singh","doi":"10.1007/s13562-024-00915-y","DOIUrl":"https://doi.org/10.1007/s13562-024-00915-y","url":null,"abstract":"Mungbean [Vigna radiata (L.) R. Wilczek] is an important short duration grain legume. The huge demand of mungbean around the world creates a substantial export potential. Pulse beetles (Callosobruchus spp.) are a key issue of concern among the several threats that limit the production of mungbean, particularly under storage conditions. An investigation was carried out to analyze the polygalacturonase inhibiting protein (PGIP) gene family in mungbean and their possible role in bruchid resistance. A pulse beetle resistant wild ricebean genotype belongs to Vigna umbellata (PRR 2008-2) and a susceptible cultivar from V. radiata (Shikha) were used in present study for gene expression profiling. Total of 41 VrPGIP genes were identified in the mungbean genome. All the genes were randomly distributed over the chromosomes. All the 41 VrPGIP genes were grouped into 06 major clades and had single exon except VrPGIP-37. All the genes comprised of Glyco_Hydro_18 domain. Four candidate genes VrPGIP-17, VrPGIP-18, VrPGIP-21 and VrPGIP-23 were found significantly up-regulated in the PRR 2008-2. These genes may be utilized in the development of resistant varieties against pulse beetle in breeding programme.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"58 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell multi-omics in the medicinal plant Catharanthus roseus: a new era of next generation therapeutics 药用植物长春花的单细胞多组学：下一代疗法的新时代

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-29 DOI: 10.1007/s13562-024-00913-0

Meenakshi Dangwal, Gurparsad Singh Suri, Gurleen Kaur

引用次数: 0

Alternative transcriptomes and plant resilience: technological innovations and biological insights 替代转录组与植物恢复能力：技术创新与生物学见解

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-29 DOI: 10.1007/s13562-024-00909-w

Ashish Kumar Pathak, Raja Jeet, Mathilde Moens, Yogesh Gupta, Vani Sharma, Kaushal Kumar Bhati

{"title":"Alternative transcriptomes and plant resilience: technological innovations and biological insights","authors":"Ashish Kumar Pathak, Raja Jeet, Mathilde Moens, Yogesh Gupta, Vani Sharma, Kaushal Kumar Bhati","doi":"10.1007/s13562-024-00909-w","DOIUrl":"https://doi.org/10.1007/s13562-024-00909-w","url":null,"abstract":"The development of advanced high-throughput sequencing approaches has revealed the biomolecular diversity associated with central genetic dogmas like never before. Big genomics data highlight the hidden complexity of the genetic regulation of cellular machinery and physiological responses to environmental stimuli. The investigation and identification of alternative mRNA forms and protein diversity as adaptation mechanisms to environmental stimuli is one such case of unparallel genetic complexity in plant cells. Alternative splicing and selection of alternative start and stop sites during and after transcription lead to conditional variants across protein families. The biological importance of many such proteins is well understood, especially during reprogramming of plant stress responses and development. Interestingly, valuable methodologies and technical leads in the genome and alternative transcriptome sequencing from animals and model plants are now laying the groundwork for similar studies in crops. However, identifying alternative transcriptomes remains a major challenge for higher plants. Therefore, there is a need for improved library preparation methods and data analysis pipelines. We sought to examine the status of alternative transcriptome-associated studies on plant physiological regulation in response to environmental adaptation. In addition, we evaluated the recent technological advances available for studying alternative transcriptomes in plants.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"11 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluating the dynamics of physical, proximate, mineral and antioxidant compositions during dragon fruit development 评估火龙果发育过程中的物理、近似、矿物质和抗氧化成分的动态变化

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-23 DOI: 10.1007/s13562-024-00916-x

Rahul Sen, Ananta Madhab Baruah

{"title":"Evaluating the dynamics of physical, proximate, mineral and antioxidant compositions during dragon fruit development","authors":"Rahul Sen, Ananta Madhab Baruah","doi":"10.1007/s13562-024-00916-x","DOIUrl":"https://doi.org/10.1007/s13562-024-00916-x","url":null,"abstract":"Current study investigates the changes in physical, nutritional, and antioxidant compositions of two dragon fruit species H. costaricensis (HC) and H. udantus (HU) from 7 days after fruit set (DAFS) to maturity. In both species during development, physical parameters such as length, diameter, weight, volume, and pulp percentage increased, while peel percentage decreased. Mature HC fruits have a spherical shape with a length of 7.91 ± 0.14 cm, while HU fruits were oval, measuring 9.13 ± 0.19 cm. Moisture content declined during maturation, with mature HC and HU fruits containing 82.91 ± 1.23% and 80.53 ± 0.46% moisture, respectively. In both HC and HU, ash content remained around 1%, and dietary fiber content decreased significantly, while crude protein levels increased, reaching 4.04 ± 0.03% in HC and 4.64 ± 0.05% in HU at maturity. Chemical composition analysis indicated increases in total soluble sugars, reducing sugars, and total soluble solids (TSS) during maturation, with mature HC fruits having higher TSS (13.59 ± 0.92 ºBrix) compared to HU fruits (11.91 ± 0.04 ºBrix). Antioxidant activity and total phenolic content peaked during the early developmental stages and in the peel of mature fruits for both species, then decreased as the fruits matured. This study enhances the understanding of dragon fruit's maturation process and nutritional benefits, offering crucial information for optimizing cultivation, postharvest handling, and consumption practices. By identifying key stages for nutrient and antioxidant maximization, these findings may contribute to improved agricultural practices and the development of value-added products from dragon fruit.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"31 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic, biochemical and peptidomics based analysis reveals heat responsive changes in the seedlings of Brassica juncea 基于蛋白质组学、生物化学和肽组学的分析揭示了芥蓝幼苗的热响应变化

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-22 DOI: 10.1007/s13562-024-00914-z

Reema Rani, Ibandalin Mawlong, Balbeer Balbeer, M.S. Sujith Kumar , Pramod Kumar Rai, Vijay Veer Singh

{"title":"Proteomic, biochemical and peptidomics based analysis reveals heat responsive changes in the seedlings of Brassica juncea","authors":"Reema Rani, Ibandalin Mawlong, Balbeer Balbeer, M.S. Sujith Kumar , Pramod Kumar Rai, Vijay Veer Singh","doi":"10.1007/s13562-024-00914-z","DOIUrl":"https://doi.org/10.1007/s13562-024-00914-z","url":null,"abstract":"Heat stress at seedling stage has a crucial impact on Indian mustard growth and productivity. Identifying heat stress responsive proteins can be crucial to understand the heat stress adaptive mechanisms. In this work, biochemical, proteomic, and peptidomics response of the thermotolerant genotype, BPR 543-2 was investigated in the early seedlings of mustard under heat stress treatment. A total of 403, 328 and 369 number of proteins were identified to be expressed exclusively during 0, 4 and 8 h of heat-stress while 89, 119 and 81 were differentially accumulated during 0–4 h, 4 h-8 h and 0–8 h using LC–MS/MS based analysis. Notably, BPR 543-2 expressed elevated levels of heat shock proteins, chaperones, enzymes involved in the metabolism of carbohydrate and energy, cell wall modifications and transcription factors. In addition, using MALDI-TOF-MS, overexpressed proteins involved in DNA repair, signal transduction and metabolic adaptation were identified during different time point of heat stress. Moreover, biochemical analysis revealed high TAC, TF and less turbulence in photosynthetic pigments in stressed samples. Through combined analysis of biochemical, proteomics and peptidomics approaches, it was observed that BPR 543-2 was more resilient to heat stress and experienced fewer significant metabolic disruptions in stressed samples, demonstrating its adaptability to heat stress at early seedling stage. The proteins with differential abundance were functionally annotated in-silico for their subcellular localization, biological and molecular functions. This work demonstrates the usefulness of proteomics and peptidomics-based approaches by providing fresh insights into the mechanism behind the heat-stress adaption mechanisms in Indian mustard. The identified critical proteins provide intriguing targets for developing stress tolerance in heat-sensitive brassica crops. ","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"251 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel deep contrastive convolutional autoencoder based binning approach for taxonomic independent metagenomics data 基于深度对比卷积自动编码器的新颖分选方法，适用于独立于分类的元基因组学数据

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-16 DOI: 10.1007/s13562-024-00911-2

Sharanbasappa D. Madival, Girish Kumar Jha, Dwijesh Chandra Mishra, Sunil Kumar, Neeraj Budhlakoti, Anu Sharma, Krishna Kumar Chaturvedi, S. Kabilan, Mohammad Samir Farooqi, Sudhir Srivastava

{"title":"A novel deep contrastive convolutional autoencoder based binning approach for taxonomic independent metagenomics data","authors":"Sharanbasappa D. Madival, Girish Kumar Jha, Dwijesh Chandra Mishra, Sunil Kumar, Neeraj Budhlakoti, Anu Sharma, Krishna Kumar Chaturvedi, S. Kabilan, Mohammad Samir Farooqi, Sudhir Srivastava","doi":"10.1007/s13562-024-00911-2","DOIUrl":"https://doi.org/10.1007/s13562-024-00911-2","url":null,"abstract":"In this study, we present an innovative binning approach for metagenomics data that combines Natural Language Processing (NLP) with a Deep Contrastive Convolutional Autoencoder (DCAE). We used NLP for feature extraction, specifically focusing on Tetra-nucleotide frequency (TNF) through CountVec and (Term Frequency -Inverse Document Frequency) TF-IDF, further enriched by integrating GC-Content into their respective feature matrices. The DCAE, equipped with advanced convolutional layers and a contrastive loss function, excels at capturing intricate patterns in the data, providing a sophisticated representation for binning. By applying k-means clustering to the latent representations obtained from the DCAE, our approach consistently achieves impressive results. To assess the performance of our method, we utilized three standard benchmark metagenomics datasets: 10s, 25s, and Sharon datasets. Across all datasets, we observed Silhouette Indices exceeding 0.6 and Rand Indices surpassing 0.8, demonstrating the superior performance of our proposed method. Compared to existing methodologies, our approach not only surpasses the Rand Index and Silhouette Index of current unsupervised methods but also performs on par with semi-supervised methods across datasets. This underscores the effectiveness and versatility of our approach in metagenomics analysis.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"407 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative analysis of complete chloroplast genomes of five Anemone species and phylogenetic analysis within Tribe Anemoneae (Ranunculaceae) 五种海葵完整叶绿体基因组的比较分析以及海葵科（毛茛科）内的系统发育分析

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-08-03 DOI: 10.1007/s13562-024-00910-3

Siqi Hu, Wenbo Shi, Yahui Huang, Zirui Zhang, Qianhui Lin, Chao Shi

{"title":"Comparative analysis of complete chloroplast genomes of five Anemone species and phylogenetic analysis within Tribe Anemoneae (Ranunculaceae)","authors":"Siqi Hu, Wenbo Shi, Yahui Huang, Zirui Zhang, Qianhui Lin, Chao Shi","doi":"10.1007/s13562-024-00910-3","DOIUrl":"https://doi.org/10.1007/s13562-024-00910-3","url":null,"abstract":"Anemone plants (Ranunculaceae) are perennial, low-growing herbs that have a long history of traditional medicinal use. However, the phylogenetic relationship of Anemone species and the comprehensive study of the tribe Anemoneae have not been thoroughly examined due to the lack of available molecular resources. In this study, we conducted a comprehensive sequencing and characterization of the complete chloroplast genomes of Anemone species. These genomes exhibited typical quadripartite structures, ranging in length from 156,659 to 162,991 bp. We also identified several highly divergent intergenic regions (trnQ-UUG–psbK, trnfM-CAU–psbC, trnT-GGU–trnC-GCA, trnG-UCC–trnL-UAA, ndhC–trnM-CAU, psbE–petL, trnW-CCA–rpl33, rps12–trnV-GAC, and trnL-UAG–ndhF) and genes (rps16, ndhD, and ycf1) that could potentially serve as phylogenetic markers. We conducted phylogenetic analyses on 125 species from the tribe Anemoneae using chloroplast genome sequences. We obtained consistent topological structures and strong support for the backbone of phylogenetic relationships by employing maximum likelihood and Bayesian inference methods. Our findings suggest that Hepatica forms a monophyletic group, while Anemone s.l. is paraphyletic, based on the phylogenetic trees. Furthermore, the Hepatica + Anemone clade and the Anemoclema + Clematis clade exhibit a sister relationship. Overall, these results provide valuable genetic resources for the identification and phylogenetic studies of Anemone species.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"53 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141882428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alginate-mediated immobilization of jackfruit (Artocarpus heterophyllus) latex serine protease enzyme exhibits improved catalytic properties 藻酸盐介导的固定化菠萝蜜（Artocarpus heterophyllus）胶乳丝氨酸蛋白酶具有更好的催化特性

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-07-29 DOI: 10.1007/s13562-024-00905-0

Suman Natta, Swathi Chintala, Deepak Kumar, Nandita Sahana, Somnath Mandal

{"title":"Alginate-mediated immobilization of jackfruit (Artocarpus heterophyllus) latex serine protease enzyme exhibits improved catalytic properties","authors":"Suman Natta, Swathi Chintala, Deepak Kumar, Nandita Sahana, Somnath Mandal","doi":"10.1007/s13562-024-00905-0","DOIUrl":"https://doi.org/10.1007/s13562-024-00905-0","url":null,"abstract":"Serine proteases have been receiving special attention from the industrial point of view, due to their thermo-stable properties and activity over wide ranges of pH. In the present investigation, a serine protease (49.3 kDa) from jackfruit latex has been purified using chromatographic techniques. Fold purification of the serine protease in the final purification step was 92.41 with 24% yield. The protease is completely inhibited by PMSF, a serine protease-specific inhibitor at a minimal concentration (100 µM). The purified serine protease was immobilized with sodium alginate (2.5%) and calcium chloride (0.3 M) solution. The kinetic studies of immobilized enzyme showed stable activity up to pH 7, and can withstand temperatures up to 45 °C. The immobilization process improves the catalytic efficiency of the enzyme over purified soluble enzyme (for Kcat 1.4 times and for Kcat/Km 1.21 times). Our results depicted that alginate mediated immobilization of serine protease greatly improves the pH and temperature optima which broadens the scope of usage of the enzyme further.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"8 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141863201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptomic analysis of the cytokinin response in industrial hemp (Cannabis sativa L.) leaves 工业大麻（Cannabis sativa L.）叶片细胞分裂素反应的转录组分析

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-07-29 DOI: 10.1007/s13562-024-00907-y

Mengdi Yu, Yushu Chen, Junbao Zhang, Xuesong Wang, Zhongmin Jin, Shanshan Li, Lijie Liu

{"title":"Transcriptomic analysis of the cytokinin response in industrial hemp (Cannabis sativa L.) leaves","authors":"Mengdi Yu, Yushu Chen, Junbao Zhang, Xuesong Wang, Zhongmin Jin, Shanshan Li, Lijie Liu","doi":"10.1007/s13562-024-00907-y","DOIUrl":"https://doi.org/10.1007/s13562-024-00907-y","url":null,"abstract":"Cytokinins (CKs) not only promote the growth of female flowers in industrial hemp but also serve as plant hormones that influence leaf development and regulate various genes, including transcription factors. The molecular mechanism of cytokinin response in industrial hemp leaves remains unclear. In this study, industrial hemp Longma 5 was utilized, with 60 mg·L− 1 and 120 mg·L− 1 of 6-BA sprayed at the three-leaf stage, followed by transcriptome sequencing at the mature stage. 3244 DEGs were identified in the Ctrl (control) vs. B60 (60 mg·L− 1 6-BA treatment) group, including 1714 upregulated genes and 1530 downregulated genes; 7818 DEGs were identified in the Ctrl vs. B120 (120 mg·L− 1 6-BA treatment) group, including 3772 upregulated genes and 4046 downregulated genes. Further analysis showed that these DEGs were primarily enriched in pathways associated with metabolism and energy, including photosynthesis, photosynthesis-antenna protein, and phenylpropanoid biosynthesis. The CTK, auxin, ABA, GA, ETH and JA signaling pathways displayed differential gene expression under 6-BA treatment. A total of 283 transcription factors were categorized into 16 families, suggesting that CKs could enhance the growth and metabolism of industrial hemp. This study lays the groundwork for further exploring the molecular mechanisms of the CTK effect on industrial hemp.","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"191 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141863203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ReDtool: a Python-based command line tool for restriction digestion analysis of large DNA sequences ReDtool：基于 Python 命令行的大型 DNA 序列限制性消化分析工具

IF 1.9 4区生物学

Journal of Plant Biochemistry and Biotechnology Pub Date : 2024-07-24 DOI: 10.1007/s13562-024-00906-z

Guntha Shiva Brahmam, Divya Mishra, Vikash Kumar Yadav

引用次数: 0