Article
Veterinary Sciences
Dawei Wei, Sayed Haidar Abbas Raza, Xingping Wang, Rajwali Khan, Zhaoxiong Lei, Guijie Zhang, Jiupan Zhang, Zhuoma Luoreng, Yun Ma, Muna O. Alamoudi, Bandar Hamad Aloufi, Ahmed Mohajja Alshammari, Ayman Hassan Abd El-Aziz, Majid Alhomrani, Abdulhakeem S. Alamri
Summary: This study investigated the tissue expression patterns and functional promoter of bovine LATS1, and identified the key transcription factors in the core promoter region. It revealed the regulatory mechanisms of bovine LATS1 transcription in mediating skeletal muscle growth. Bovine LATS1 was highly expressed in the longissimus thoracis and upregulated in infancy muscle.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Plant Sciences
Mingming Liu, Ke Li, Shichao Sheng, Mingyu Wang, Panpan Hua, Yanfang Wang, Ping Chen, Kangyu Wang, Mingzhu Zhao, Yi Wang, Meiping Zhang
Summary: This study investigated the MYB transcription factor family in ginseng and identified PgMYB transcripts in Jilin ginseng. The results showed that PgMYB transcripts were classified into different functional subclasses and exhibited spatiotemporally specific expression patterns. Some of these transcripts may be related to salt resistance in ginseng.
Article
Plant Sciences
Madiha Zaynab, Yasir Sharif, Zhaoshi Xu, Sajid Fiaz, Rashid Al-Yahyai, Hamad. A. Yadikar, Najla Amin T. Al Kashgry, Sameer H. Qari, Monther Sadder, Shuangfei Li
Summary: In this study, 30 DUF668 genes were identified in the soybean genome, distributed across fifteen chromosomes. Phylogenetic analysis classified these genes into three groups. Gene structure analysis showed that some of these genes lacked introns. Subcellular localization results indicated that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane.
Article
Entomology
Yudai Masuoka, Wei Cao, Akiya Jouraku, Hiroki Sakai, Hideki Sezutsu, Kakeru Yokoi
Summary: This study identified novel regulatory factors for silk protein genes in Bombyx mori through co-expression network and time-course expression analysis. The results suggest that silk protein production in B. mori is regulated by a complex mechanism, and the newly identified candidate genes can be used to develop methods to enhance silk protein production.
Article
Plant Sciences
Rezwan Tariq, Ammara Hussain, Arslan Tariq, Muhammad Hayder Bin Khalid, Imran Khan, Huseyin Basim, Par K. Ingvarsson
Summary: This study conducts a genome-wide comparison and analysis of NAC transcription factors in mung bean, identifying 81 NAC TFs and investigating their functions in different biological processes. The study also explores the gene structure and co-expression network of VrNACs, revealing their significance in mung bean growth and stress responses.
Article
Biology
Mary Couvillion, Kevin M. Harlen, Kate C. Lachance, Kristine L. Trotta, Erin Smith, Christian Brion, Brendan M. Smalec, L. Stirling Churchman
Summary: This study reveals that a diverse array of factors precisely regulate transcription elongation by balancing Pol II activity.
Article
Plant Sciences
Emil Vatov, Uwe Ludewig, Ulrike Zentgraf
Summary: Gene regulation networks precisely control the expression of genes associated with specific physiological and developmental processes in plants, such as leaf senescence. Transcription factors like WRKY53 and WRKY45 play key roles in activating the gene AtSAG12 during senescence, while other factors like bZIP may have accessory functions in gene regulation. The presence of conserved cis-regulatory elements like bZIP and WRKY binding sites in the promoter regions of orthologs of AtSAG12 varies among closely related species, with differences possibly arising from duplication events and leading to distinct cis-regulatory sites in different locations. This variability in gene regulation is discussed in the context of gene and promoter evolution, genetic variation, and plant adaptability to changing environmental conditions.
Article
Biochemical Research Methods
Neel Patel, William S. Bush
Summary: This study developed a general model of transcription factor influence on gene expression by incorporating both cis and trans gene regulatory features. The models performed significantly better compared to models containing only cis-regulatory features, and the inclusion of long distance chromatin interactions further improved accuracy. The refined effect estimates generated by the models allow for characterization of individual transcription factors' roles across the genome, providing a framework for integrating multiple data types into a single model of transcriptional regulation.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Madiha Zaynab, Hamed A. Ghramh, Yasir Sharif, Sajid Fiaz, Rashid Al-Yahyai, Maryam A. Alahdal, Sameer H. Qari, Kamel Hessini, Xiazi Huang, Shuangfei Li
Summary: The present study conducted a comprehensive analysis of DUF599 genes in potato, revealing their significant roles in plant growth and stress response. The study found that these genes are important in coping with abiotic stresses and can enhance plant tolerance by regulating developmental processes and hormone responses.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Liqin Liao, Ziqi Yao, Jie Kong, Xinheng Zhang, Hongxin Li, Weiguo Chen, Qingmei Xie
Summary: This study conducted transcriptome analysis of five early developmental stages in White Leghorn chicken, covering 17,478 genes with about 807 million clean reads of RNA-sequencing. Comparative analysis of differentially expressed TFs between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development, and morphogenesis. The study identified Zf-C2H2, Homeobox, and bHLH as three dominant transcription factor families in early embryogenesis, and constructed a TFs co-expression network to identify critical TFs.
Article
Biochemistry & Molecular Biology
Ying Guo, Tongli Wang, Fang-Fang Fu, Yousry A. El-Kassaby, Guibin Wang
Summary: The study revealed variations in photosynthetic capacity and related compounds in developing ginkgo leaves. A co-expression network was constructed to demonstrate the regulatory role of transcription factors in the photosynthetic light reaction pathway. This analysis identified candidate genes that could potentially improve photosynthetic capacity and yield in ginkgo trees.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yuexin Zhang, Chao Song, Yimeng Zhang, Yuezhu Wang, Chenchen Feng, Jiaxin Chen, Ling Wei, Qi Pan, Desi Shang, Yanbing Zhu, Jiang Zhu, Shuangsang Fang, Jun Zhao, Yongsan Yang, Xilong Zhao, Xiaozheng Xu, Qiuyu Wang, Jincheng Guo, Chunquan Li
Summary: TcoFBase is a database that collects a large number of resources for mammalian TcoFs, providing detailed annotations and functional analyses, as well as supporting various regulatory analyses to reveal the biological effects and regulatory mechanisms of TcoFs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Vijaykumar Yogesh Muley, Rainer Koenig
Summary: This study compares transcriptional regulatory pairs from multiple databases and finds that TF and TG are common across data resources, but their regulatory pairs are not. The regulatory pairs show weak expression correlation, but significant gene ontology overlap and co-citations in PubMed, with a small number of TF-TG pairs representing transcriptional repression relationships. The assembled TRN provides a valuable resource for benchmarking TRN prediction tools and for researchers in functional genomics, gene expression, and regulation analysis.
Article
Biotechnology & Applied Microbiology
Yuxin Yang, Xueying Zhang, Lifen Wu, Lichao Zhang, Guoxiang Liu, Chuan Xia, Xu Liu, Xiuying Kong
Summary: Wheat heading date is crucial for environmental adaptability and yield component regulation. RNA-Seq analysis identified thousands of differentially expressed genes associated with flowering time. Co-expression networks of key flowering time genes were established, and a potential candidate gene was discovered for further study on the regulatory mechanism of wheat heading date.
Article
Microbiology
Cinthia Soberanes-Gutierrez, Alfredo Castillo-Jimenez, Ernesto Perez-Rueda, Edgardo Galan-Vasquez
Summary: Biological systems respond to environmental disturbances and compounds through complex gene interaction networks. In this study, a gene co-expression network was built for Ustilago maydis using gene expression data, leading to the identification of 13 co-expressed gene modules. These modules enriched with virulence genes were classified into diseases related to corn smut, Invasive candidiasis, among others. Additionally, a large number of hypothetical genes were found to be highly co-expressed with virulence genes, making them potential experimental targets.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Behzad Hajieghrari, Naser Farrokhi
Summary: The study found that evolving microRNA repertoires in the plant domain consist of approximately 4324 potential pre-miRNAs, with the majority being transposons. There is a lack of correlation between the numbers of miRNAs and genome sizes among different plant species. Duplications of MIR paralogs are more evident in Liliopsida compared to dicots.
PLANT MOLECULAR BIOLOGY REPORTER
(2021)
Article
Biochemical Research Methods
Khazar Edrisi Maryan, Habibollah Samizadeh Lahiji, Naser Farrokhi, Paul A. Haynes, Sara Hamzelou, Hassan Hasani Komeleh
Summary: Research comparing protein expression in cold-acclimated canola leaves found that some proteins related to chloroplast function were differentially expressed under early cold acclimation conditions. This provides new insights into plant responses to cold stress.
PLANT MOLECULAR BIOLOGY REPORTER
(2021)
Article
Plant Sciences
Rahele Panahabadi, Asadollah Ahmadikhah, Lauren S. McKee, Paer K. Ingvarsson, Naser Farrokhi
Summary: The genetic variability of MLG and starch contents in rice whole grains was analyzed, revealing a negative correlation between MLG content and grain starch content. A new genome-wide association study identified seven significant QTLs associated with MLG content and two QTLs associated with starch content. Novel genes related to MLG content included a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Mathematical & Computational Biology
Behzad Hajieghrari, Naser Farrokhi, Mojahed Kamalizadeh
Summary: This study introduces a method based on intuitionistic fuzzy for improving the sensitivity of progressive multiple sequence alignments and evaluates system performance using various test methods. The results indicate better performance of the proposed methods in improving alignment sensitivity and accuracy.
NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Behzad Hajieghrari, Naser Farrokhi
Summary: Not all transcribed RNAs encode proteins. Some non-coding RNAs (ncRNAs) are non-functional and result from accidental transcription, while many others play significant roles in the translation process. Gene expression relies on complex networks of diverse gene regulatory pathways, and several ncRNAs act as major components in regulating gene expression either at the transcriptional or posttranscriptional level in a sequence-specific manner. RNA-mediated gene regulation machinery is evolutionarily ancient and highly complex. This review summarizes the current knowledge in the field of RNA-mediated gene silencing.
Article
Spectroscopy
Raha Soltani, Amin Baghizadeh, Hassan Karimi-Maleh, Naser Farrokhi
Summary: The genotypic diversity of 17 cacti species was analyzed using ISSR markers, and representatives were selected for the synthesis and characterization of AuNPs, with successful synthesis achieved in Opuntia pycnacantha.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Plant Sciences
Rahele Panahabadi, Asadollah Ahmadikhah, Lauren S. McKee, Par K. Ingvarsson, Naser Farrokhi
Summary: The genetic variability of cellulose, lignin, and fermentable sugars contents in rice straw was analyzed through a genome-wide association study, identifying genomic regions significantly associated with these components. Candidate genes involved in cell wall metabolism were found to be associated with cellulose, lignin, and fermentable sugar contents. New SNP markers associated with these components were identified, aiding in understanding the genetic basis of biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
Article
Ecology
Zahra Ganji, Foad Fatehi, Fatemeh Habibpour Mehraban, Paul A. Haynes, Vahid Hosseni Naveh, Naser Farrokhi
Summary: This study used proteomics to investigate the response of pistachio seedlings to herbivory by the nymphal stages of the common pistachio psylla. The results showed that pistachio seedlings increase their growth rate as a strategy to cope with herbivory stress. The study provides valuable information for understanding the interaction between plants and herbivores.
ARTHROPOD-PLANT INTERACTIONS
(2022)
Article
Biochemical Research Methods
Hamideh Raeisi, Mohammad Reza Safarnejad, Seyed Mehdi Alavi, Naser Farrokhi, Seyed Ali Elahinia
Summary: In this study, the in planta expression of a specific anti-pthA single-chain variable fragment (scFv) recombinant antibody, scFvG8, was described, and its function was assessed using molecular docking, immunoblotting, and indirect enzyme-linked immunosorbent assay (ELISA). The results confirmed that scFvG8 can suppress the function of pthA effector protein within plant cells and potentially reduce the necrotic leaf area caused by Xanthomonas citri subsp. citri.
TRANSGENIC RESEARCH
(2022)
Article
Medicine, Research & Experimental
Tahereh Tajik, Kaveh Baghaei, Vahid Erfani Moghadam, Naser Farrokhi, Seyed Alireza Salami
Summary: Plant-derived extracellular vesicles (EVs) have gained attention in recent years due to their proven therapeutic properties. In this study, EVs were isolated from two different chemotypes of cannabis and classified as high-CBD and low-CBD EVs. These EVs exhibited different cytotoxicity and anticancer effects. The findings suggest that CDEVs could be an ideal natural vehicle for delivering bioactive phytocannabinoids and a promising strategy in cancer management.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Agronomy
Rahele Panhabadi, Asadollah Ahmadikhah, Naser Farrokhi, Nadali Bagheri
Summary: This study conducted a genome-wide association study (GWAS) to identify genetic regions and candidate genes associated with seed germination and post-germination related seedling traits in rice. The results revealed several significant quantitative trait loci (QTLs) and candidate genes that play a role in regulating these traits.
Correction
Agronomy
Rahele Panahabadi, Asadollah Ahmadikhah, Naser Farrokhi, Nadali Bagheri
Article
Plant Sciences
Rahele Panahabadi, Asadollah Ahmadikhah, Naser Farrokhi
Summary: This study identified genomic regions influencing monosaccharide contents in rice and discovered candidate genes associated with the constituents of rice grain. The findings contribute to enhancing the nutritional value of rice and impacting related industries.
Article
Biotechnology & Applied Microbiology
Behzad Hajieghrari, Naser Farrokhi, Mojahed Kamalizadeh
Summary: This study investigates the evolutionary history and phylogenetic relationship of the DCL protein family in plants. The results show that DCL proteins independently expanded in both eudicots and monocots, with the main duplication events occurring before the split between these two lineages. The divergence of DCL proteins coincided with the start of multicellularization and the need for complex gene regulation. The study also reveals the conservation of functional domains in DCL protein subfamilies, which differ between lineages.
JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Developmental Biology
Sanjana Srinivasan, Xinjian He, Sarah Mirza, Jesse Mager
Summary: Exosome Complex Components 1 and 2 (EXOSC1 and 2) are essential proteins in the RNA Exosome complex that play important roles in early mammalian development. Their absence results in developmental delay and morphological abnormalities in embryos.
GENE EXPRESSION PATTERNS
(2024)