Article
Pharmacology & Pharmacy
Ulrik Kraemer Sundekilde, Caroline Maag Kristensen, Mette Algot Olsen, Henriette Pilegaard, Martin Kroyer Rasmussen
Summary: The circadian rhythm has a significant impact on various physiological processes, including sleep-wake patterns, eating behavior, and hepatic detoxification. This study investigated the role of hepatic peroxisome proliferator-activated receptor gamma coactivator-1 (PGC-1 alpha) in the circadian regulation of cytochrome P450 enzymes (Cyps) in the liver. The results showed that the expression of circadian regulator genes Bmal1 and Clock was influenced by PGC-1 alpha, and the mRNA content of certain Cyps exhibited rhythmic expression. However, no significant circadian regulation was observed at the protein level. Principal component analysis further demonstrated the distinct differences between the control and PGC-1a LKO mice. These findings provide valuable insights into the molecular mechanisms underlying circadian regulation of Cyps and hepatic detoxification.
Article
Multidisciplinary Sciences
Hadar Medini, Amit Zirman, Dan Mishmar
Summary: Mitochondrial dysfunction has been found to play a central role in COVID-19, with significantly reduced mtDNA gene expression in patients observed, suggesting a potential link to the disease. Additionally, elevated expression of ROS-response genes and glycolysis enzymes in patients may indicate a shift towards glycolysis, creating conditions beneficial for SARS-CoV-2 replication.
Review
Biochemistry & Molecular Biology
Jogindra Naik, Prashant Misra, Prabodh Kumar Trivedi, Ashutosh Pandey
Summary: Flavonoids are structurally diverse compounds that play important roles in plants and have health benefits for humans. Various factors such as light, temperature, nutrients, and hormones modulate their biosynthesis. Transcriptional regulators, especially MYB and bHLH family transcription factors, directly regulate the genes involved in flavonoid biosynthesis. Recent studies have also found that stress and hormone signaling pathways regulate some of these factors.
Review
Biochemistry & Molecular Biology
Mengyuan Wang, Qian Li, Lingbo Liu
Summary: Gene expression regulation involves multiple processes and various regulatory factors. This review provides an overview of key factors involved in gene expression regulation, such as transcription factors, chromatin accessibility, histone modifications, DNA methylation, and RNA modifications. Additionally, methods for detecting these regulatory factors are also described.
Article
Biochemical Research Methods
Alba Rubio-Canalejas, Lucas Pedraz, Eduard Torrents
Summary: ReViTA (Reverse in Vitro Transcription Assay) is a novel in vitro transcription-based method used to study gene expression under specific transcription factors. The method was evaluated using two different transcription factors, AlgR and LexA, and demonstrated successful gene expression regulation. ReViTA has the potential to be a rapid and accessible method for studying genes and regulators in various species.
Article
Biochemistry & Molecular Biology
Amala Kaja, Abhinav Adhikari, Saswati Karmakar, Wanwei Zhang, Gerson Rothschild, Uttiya Basu, Surinder K. Batra, Judith K. Davie, Sukesh R. Bhaumik
Summary: The study reveals that human SPT16 is regulated by the proteasome, impacting the transcription of cancer-associated genes, and degradation of SPT16 is impaired in kidney cancer cells, leading to its upregulation.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Review
Genetics & Heredity
Liliana Villao-Uzho, Tatiana Chavez-Navarrete, Ricardo Pacheco-Coello, Eduardo Sanchez-Timm, Efren Santos-Ordonez
Summary: One strategy to overcome crop diseases or abiotic stress is through the use of improved varieties achieved by genetic improvement methods such as conventional breeding, induced mutation, genetic transformation, or gene editing. Promoters, which regulate gene expression, are crucial for transgenic crops to improve specific traits. Many techniques, including RT-PCR, genetic libraries, cloning, and sequencing, are used to identify and isolate promoters for biotechnological crops. Promoter analysis through plant genetic transformation allows for understanding gene regulation and development, highlighting the importance of promoters in ensuring correct gene expression in biotechnological processes.
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
Georgia Katsioudi, Rene Dreos, Enes S. Arpa, Sevasti Gaspari, Angelica Liechti, Miho Sato, Christian H. Gabriel, Achim Kramer, Steven A. Brown, David Gatfield
Summary: The study demonstrates the importance of nonsense-mediated mRNA decay (NMD) in physiological control, particularly in regulating the circadian clock and gene expression.
Article
Cell Biology
Mengjia Li, Penglei Jiang, Kai Cheng, Zehui Zhang, Shuyu Lan, Xiaoxia Li, Lirong Zhao, Yucheng Wang, Xiang Wang, Jing Chen, Tao Ji, Bingshe Han, Junfang Zhang
Summary: The enhancer elements at -34k are crucial for MYB expression, with transcription factor binding and epigenetic modifications playing key roles in this process.
CELL DEATH & DISEASE
(2021)
Article
Plant Sciences
Yadong Fan, Mengyuan Li, Yujie Wu, Xiaoteng Wang, Putong Wang, Li Zhang, Xiaodan Meng, Fanrong Meng, Yongchun Li
Summary: This study identifies and characterizes a type of Trx gene called TaTrxh9 in wheat. TaTrxh9 is involved in the regulation of heading time in wheat, and its expression is correlated with plant development. These findings provide new insights into the biological function of TaTrxh9 and offer potential for molecular breeding targeting early heading in wheat.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Cell Biology
Partho Sen, Syed Bilal Ahmad Andrabi, Tanja Buchacher, Mohd Moin Khan, Ubaid Ullah Kalim, Tuomas Mikael Lindeman, Marina Amaral Alves, Victoria Hinkkanen, Esko Kemppainen, Alex M. Dickens, Omid Rasool, Tuulia Hyotylainen, Riitta Lahesmaa, Matej Oresic
Summary: The study demonstrates specific metabolic changes in human CD4(+) T cells during activation and functional differentiation, highlighting the importance of the de novo sphingolipid pathway in Th17 cell differentiation and effector functions, with serine palmitoyltransferase playing a significant role in the expression of proinflammatory cytokines IL-17A and IL17F by Th17 cells. These findings offer a comprehensive resource for selectively manipulating CD4(+) T cells in conditions characterized by an imbalance of Th17/natural Treg (nTreg) cells.
Article
Multidisciplinary Sciences
Xiaoding Xu, Chuwei Yu, Hongxiu He, Xiangyu Pan, Aijun Hou, Jianxun Feng, Rongrong Tan, Likun Gong, Jing Chen, Jin Ren
Summary: Epigenetic regulations, particularly miR-337-3p, play a crucial role in the pathogenesis of metabolic-associated fatty liver disease (MAFLD). Overexpression of miR-337-3p can ameliorate hepatic lipid accumulation, reduce fasting blood glucose, and improve insulin resistance. Additionally, miR-337-3p may influence multiple genes involved in glycolipid metabolism, providing a potential therapeutic target for MAFLD.
Review
Microbiology
Fernanda Gil de Souza, Jonatas Santos Abrahao, Rodrigo Araujo Lima Rodrigues
Summary: Nucleocytoplasmic large DNA viruses (NCLDV) have unique characteristics and an independent transcriptional apparatus that sparks discussions on their evolutionary aspects. Analyzing their temporal gene expression profile and activated gene sets reveals a common characteristic of this group.
Article
Biochemistry & Molecular Biology
Shivani Nanda, Marc-Antoine Jacques, Wen Wang, Chad L. Myers, L. Safak Yilmaz, Albertha J. M. Walhout
Summary: A new study reveals that three-quarters of metabolic genes in the nematode Caenorhabditis elegans are transcriptionally regulated, and generates a co-regulated subpathway map of metabolism. The researchers also develop a web application to query gene associations with metabolic pathways. This study sheds light on the ubiquity of transcriptional regulation in metabolism and provides a blueprint for similar studies in other organisms.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Neurosciences
Ella Podvalny, Niv Noy, Michal Harel, Stephan Bickel, Gal Chechik, Charles E. Schroeder, Ashesh D. Mehta, Misha Tsodyks, Rafael Malach
JOURNAL OF NEUROPHYSIOLOGY
(2015)
Article
Biochemical Research Methods
Lior Kirsch, Gal Chechik
PLOS COMPUTATIONAL BIOLOGY
(2016)
Article
Computer Science, Artificial Intelligence
Alon Zweig, Gal Chechik
Article
Biochemical Research Methods
Noa Liscovitch, Uri Shalit, Gal Chechik
Article
Anatomy & Morphology
Shlomit Beker, Miri Goldin, Noa Menkes-Caspi, Vered Kellner, Gal Chechik, Edward A. Stern
BRAIN STRUCTURE & FUNCTION
(2016)
Article
Neurosciences
Hadas Taubman, Eilon Vaadia, Rony Paz, Gal Chechik
JOURNAL OF NEUROPHYSIOLOGY
(2013)
Article
Computer Science, Artificial Intelligence
Gregoire Mesnil, Antoine Bordes, Jason Weston, Gal Chechik, Yoshua Bengio
Article
Neurosciences
Ossnat Bar-shira, Gal Chechik
MOLECULAR AND CELLULAR NEUROSCIENCE
(2013)
Article
Multidisciplinary Sciences
Gal Chechik, Israel Nelken
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Biochemistry & Molecular Biology
Noa Liscovitch, Lily Bazak, Erez Y. Levanon, Gal Chechik
Article
Biochemical Research Methods
Lior Kirsch, Noa Liscovitch, Gal Chechik
PLOS COMPUTATIONAL BIOLOGY
(2012)
Article
Biochemical Research Methods
Noa Liscovitch, Gal Chechik
PLOS COMPUTATIONAL BIOLOGY
(2013)
Proceedings Paper
Computer Science, Artificial Intelligence
Niv Cohen, Rinon Gal, Eli A. Meirom, Gal Chechik, Yuval Atzmon
Summary: This paper introduces a new learning setup called Personalized Vision & Language (PerVL) for reasoning about user-specific visual concepts in unstructured language. By expanding the input vocabulary of a pretrained model with new word embeddings, the proposed approach learns personalized visual concepts and effectively applies them in image retrieval and semantic segmentation.
COMPUTER VISION, ECCV 2022, PT XX
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Ramakrishna Vedantam, Samy Bengio, Kevin Murphy, Devi Parikh, Gal Chechik
30TH IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR 2017)
(2017)
Article
Biochemistry & Molecular Biology
Ella Podvalny, Erin Yeagle, Pierre Megevand, Nimrod Sarid, Michal Harel, Gal Chechik, Ashesh D. Mehta, Rafael Malach