Article
Biotechnology & Applied Microbiology
Bahareh Nikparvar, Margarita Andreevskaya, Ilhan C. Duru, Florentina I. Bucur, Leontina Grigore-Gurgu, Daniela Borda, Anca I. Nicolau, Christian U. Riedel, Petri Auvinen, Nadav Bar
Summary: The pathogen Listeria (L.) monocytogenes exhibits different gene regulation modes in response to high pressure processing, including survival mode, repair mode, and re-growth mode. This allows for the timely activation of transcription factors associated with immediate stress response, followed by repair and re-growth to survive and recover from extreme conditions. The findings provide insights for potential design of specific strategies to target genes or mechanisms to prevent L. monocytogenes recovery during food storage under high pressure conditions.
Article
Agricultural Engineering
Yuping Li, Ziyan Xie, Yun Huang, Jiangyi Zeng, Chao Yang, Ling Yuan, Ying Wang, Yongqing Li
Summary: In this study, the characteristic flavonoids (CFs) of three licorice species were identified through integrated metabolic and transcriptomic analysis. The key regulators of CF biosynthesis were also identified. These findings provide valuable information for understanding the biosynthesis of CFs and future breeding of Glycyrrhiza varieties.
INDUSTRIAL CROPS AND PRODUCTS
(2024)
Review
Cell Biology
Trine V. Dam, Nicolaj I. Toft, Lars Grontved
Summary: The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing rapidly. There are difficulties in diagnosing and treating NAFLD. Further insight into disease mechanisms and gene regulatory mechanisms associated with tissue remodeling is needed. Mapping the cis-regulatory genome and single-cell analysis are emerging technologies that provide more possibilities for research.
Article
Plant Sciences
Chaoqun Xu, Xiang Liu, Guoan Shen, Xuelan Fan, Yue Zhang, Chao Sun, Fengmei Suo, Baolin Guo
Summary: This study reveals the dynamics and regulatory network of prenylated flavonol glycosides (PFGs) biosynthesis in the leaves of the Chinese medicinal herb Epimedium pubescens. Metabolite profiling and transcriptome analysis identified key candidate structural genes and transcription factors (TFs) involved in PFG accumulation. The results provide valuable insights into the molecular regulatory mechanism of PFG biosynthesis, enrich the gene resources, and guide further research on PFG accumulation in Epimedium.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Seungsoo Kim, Joanna Wysocka
Summary: Uncovering the cis-regulatory code that governs gene transcription in a given genome and cellular state remains a central goal of biology. This review discusses the different layers of regulation that influence transcriptional outputs, including the binding of transcription factors to specific DNA sequences, the role of cofactors in facilitating their function, and the complex interplay within regulatory landscapes. The authors propose that a quantitative, mechanistically informed model of transcriptional regulation is essential for ultimately understanding the cis-regulatory code.
Article
Plant Sciences
Wei Liu, Xufang Tian, Ying Feng, Juan Hu, Bo Wang, Shilin Chen, Di Liu, Yifei Liu
Summary: This study provides comprehensive insights into the bHLH gene family in C. chinensis, identifying 143 CcbHLH genes that are unevenly distributed on nine chromosomes. Thirty of these genes are significantly expressed in the rhizomes of C. chinensis, and 11 of them are highly correlated with the contents of various alkaloids. Additionally, yeast one-hybrid experiments confirmed the regulatory roles of CcbHLH001 and CcbHLH0002 in the biosynthesis of BIAs.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Wenjing Hu, Qiaoyu Ren, Yali Chen, Guoliang Xu, Yexiong Qian
Summary: This study identified 140 ZmWRKY proteins encoded by 125 ZmWRKY genes in maize, which were divided into three main groups and further classified into five subgroups. The genes displayed specific exon-intron structures and conserved protein motifs. RNA-seq analysis revealed differential expression patterns of ZmWRKY genes at different developmental stages and under abiotic stress treatments.
Article
Food Science & Technology
Yaqiong Wu, Chunhong Zhang, Zhengjin Huang, Lianfei Lyu, Weilin Li, Wenlong Wu
Summary: Blackberry fruit is rich in anthocyanins, which have nutritional and health benefits. Through transcriptome and metabolome analysis, the molecular mechanisms of flavonoid biosynthesis were identified.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Genetics & Heredity
Xiaodong Zhang, Caixia Li, Zhanchao Hao, Yongjiang Liu
Summary: Angelica dahurica roots have a long history of use in traditional Chinese medicine due to their high coumarin content. In this study, transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were used to identify key genes and gene modules involved in coumarin and terpenoid backbone biosynthesis. KEGG enrichment analysis was also conducted to explore crucial pathways in coumarin biosynthesis. The findings provide valuable insights into the biosynthesis of coumarin in A. dahurica, which can facilitate future research and potential applications in traditional Chinese medicine and synthetic biology strategies.
Article
Agriculture, Multidisciplinary
Gegen Bao, Umair Ashraf, Xiaorong Wan, Qi Zhou, Shengyu Li, Chunling Wang, Longxin He, Xiangru Tang
Summary: This study found that under foliar zinc application, the 2-acetyl-1-pyrroline (2AP) and zinc contents in aromatic rice were substantially increased, leading to improved 2AP biosynthesis through various pathways such as the activation of the PSCS2 gene. Multiple transcription factors (TFs) were involved in regulating the formation of 2AP in fragrant rice under zinc treatments. Further research is needed to explore the relationship between 2AP biosynthesis pathway genes and TFs in aromatic rice.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Review
Plant Sciences
Saet Buyl Lee, Mi Chung Suh
Summary: This study summarizes the regulatory mechanisms underlying cuticular wax biosynthesis in plants, including transcriptional, post-transcriptional, post-translational, and epigenetic levels. The advances in our understanding of these regulatory mechanisms have improved our knowledge of how plants balance carbon metabolic pathways between optimal growth and development and defense against abiotic stresses.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Mingming Dong, Shudan Xue, Ezra S. Bartholomew, Xuling Zhai, Lei Sun, Shuo Xu, Yaqi Zhang, Shuai Yin, Wenyue Ma, Shuying Chen, Zhongxuan Feng, Chao Geng, Xiangdong Li, Xingwang Liu, Huazhong Ren
Summary: This study provides insights into the molecular processes involved in multicellular trichome formation in cucumber and presents a framework for understanding the regulatory network of multicellular trichome formation.
Article
Microbiology
Alberto C. Rodriguez-Sanchez, Luz A. Gonzalez-Salazar, Lorena Rodriguez-Orduna, Andres Cumsille, Agustina Undabarrena, Beatriz Camara, Nelly Selem-Mojica, Cuauhtemoc Licona-Cassani
Summary: In this study, a phylogenetic analysis was proposed to classify biosynthetic gene clusters (BGCs) into regulatory mechanisms based on protein domain information. The study focused on actinobacterial strains from different environments and found that despite environmental variations, the isolated microorganisms shared similar regulatory mechanisms, suggesting the potential to activate new BGCs using known activators.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Peng Zhou, Tara A. Enders, Zachary A. Myers, Erika Magnusson, Peter A. Crisp, Jaclyn M. Noshay, Fabio Gomez-Cano, Zhikai Liang, Erich Grotewold, Kathleen Greenham, Nathan M. Springer
Summary: Changes in gene expression are crucial for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes reveals many alterations in transcript abundance. By analyzing expression responses in multiple genotypes and identifying cis- or trans-regulatory variation, predictive models of gene expression responses for thermal stress-responsive genes can be developed. Models focusing on unmethylated regions near the transcription start sites (TSSs) show improved accuracy, suggesting that different genes may have varying response dynamics to stress.
Review
Biochemistry & Molecular Biology
Shuya Tan, Yueqi Sha, Liwei Sun, Zhonghai Li
Summary: Leaf senescence is a natural process in plants that occurs during aging and is influenced by internal and external factors. Understanding the molecular mechanisms of leaf senescence in response to abiotic stresses is crucial for improving crop resilience and productivity. Research progress has been made in identifying key genes and transcription factors involved, but challenges remain in exploring the regulatory network and developing effective strategies for gene manipulation in crops.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Clark K. Ho, Lola Rahib, James C. Liao, Ganesh Sriram, Katrina M. Dipple
MOLECULAR GENETICS AND METABOLISM
(2015)
Article
Endocrinology & Metabolism
Clark K. Ho, Ganesh Sriram, Katrina M. Dipple
MOLECULAR GENETICS AND METABOLISM
(2016)
Article
Endocrinology & Metabolism
Lilly S. Parr, Ganesh Sriram, Ramin Nazarian, Lola Rahib, Katrina M. Dipple
MOLECULAR GENETICS AND METABOLISM
(2018)
Article
Plant Sciences
Xiaofeng Zhang, Ashish Misra, Shilpa Nargund, Gary D. Coleman, Ganesh Sriram
Article
Biochemical Research Methods
Nazrul Islam, Gen Li, Wesley M. Garrett, Rongshuang Lin, Ganesh Sriram, Bret Cooper, Gary D. Coleman
JOURNAL OF PROTEOME RESEARCH
(2015)
Article
Biotechnology & Applied Microbiology
Yuting Zheng, Andrew H. Quinn, Ganesh Sriram
MICROBIAL CELL FACTORIES
(2013)
Article
Biochemistry & Molecular Biology
Shilpa Nargund, Ganesh Sriram
MOLECULAR BIOSYSTEMS
(2013)
Article
Biochemistry & Molecular Biology
Shilpa Nargund, Ashish Misra, Xiaofeng Zhang, Gary D. Coleman, Ganesh Sriram
MOLECULAR BIOSYSTEMS
(2014)
Article
Microbiology
Ashish Misra, Matthew F. Conway, Joseph Johnnie, Tabish M. Qureshi, Bao Lige, Anne M. Derrick, Eddy C. Agbo, Ganesh Sriram
FRONTIERS IN MICROBIOLOGY
(2013)
Article
Biotechnology & Applied Microbiology
Jaewook Chung, Ganesh Sriram, Carol L. Keefer
BIOTECHNOLOGY LETTERS
(2020)
Article
Biotechnology & Applied Microbiology
Daniel J. Lugar, Sean G. Mack, Ganesh Sriram
Summary: Flux balance analysis (FBA) is a powerful method for predicting cell-wide metabolic activity, but interpreting the resulting flux vector can be challenging. The NetRed algorithm systematically reduces a stoichiometric matrix and flux vector to a more easily interpretable form, providing transparent and lossless simplification for metabolic networks. This reduction allows users to quickly identify metabolites and reaction pathways of interest with simplified presentation.
METABOLIC ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Bilal Moiz, Jonathan Garcia, Sarah Basehore, Angela Sun, Andrew Li, Surya Padmanabhan, Kaitlyn Albus, Cholsoon Jang, Ganesh Sriram, Alisa Morss Clyne
Summary: Disruption of endothelial metabolism is associated with endothelial dysfunction and cardiovascular disease. Targeted metabolic inhibitors may have significant impacts on endothelial metabolism, highlighting the importance of studying systemic metabolic therapeutic effects.
Article
Biotechnology & Applied Microbiology
Sean G. Mack, Ganesh Sriram
Summary: Genome-scale stoichiometric models (GSMs) are widely used to predict and understand cellular metabolism, but parsing flux predictions from GSMs is challenging due to their complexity. NetFlow, an algorithm that leverages genome-scale carbon mapping, quantitatively distinguishes biologically relevant metabolic pathways within flux predictions. By simulating C-13 isotope labeling experiments, NetFlow calculates carbon exchange between metabolites, making pathways easier to interpret and enabling a deeper mechanistic understanding of metabolic phenotypes.
METABOLIC ENGINEERING COMMUNICATIONS
(2021)
Proceedings Paper
Computer Science, Theory & Methods
Joseph Johnnie, Mark Austin, Ganesh Sriram, Matt Conway, Ashish Misra
CONFERENCE ON SYSTEMS ENGINEERING RESEARCH
(2012)