Article
Biology
Nico Fuhrmann, Celine Prakash, Tobias S. Kaiser
Summary: Genomic analysis confirms the recent establishment of different ecotypes in marine midges of the genus Clunio, which are characterized by variations in timing of adult emergence, oviposition behavior, and larval habitat. QTL mapping and genome screens reveal that polygenic adaptation from standing genetic variation, particularly involving circadian clock genes, sensory perception genes, and nervous system development genes, plays a central role in ecotype formation. These findings suggest that adaptive ecotype formation can occur rapidly through ongoing gene flow and the re-assortment of existing alleles.
Article
Biochemical Research Methods
Prabina Kumar Meher, Ansuman Mohapatra, Subhrajit Satpathy, Anuj Sharma, Isha Saini, Sukanta Kumar Pradhan, Anil Rai
Summary: A computational method based on Support Vector Machine (SVM) was developed to identify circadian genes, achieving an accuracy of 62.48%. The method was also applied for proteome-wide identification of circadian proteins in two cereal crops and functional annotation with Gene Ontology terms.
Review
Biochemistry & Molecular Biology
Sara M. Ortega-Campos, Eva M. Verdugo-Sivianes, Ana Amiama-Roig, Jose R. Blanco, Amancio Carnero
Summary: The molecular machinery of the circadian clock regulates gene expression and cellular activities to adapt to daily light-dark cycles. Disruption of the circadian rhythm is an independent risk factor for cancer and circadian genes may play dual roles as tumor suppressors and oncogenes. Understanding the molecular basis of the circadian clock can help identify new markers and targets for cancer prognosis and therapy.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2023)
Article
Biochemistry & Molecular Biology
Shir Confino, Talya Dor, Adi Tovin, Yair Wexler, Zohar Ben-Moshe Livne, Michaela Kolker, Odelia Pisanty, Sohyun Kathy Park, Nathalie Geyer, Joel Reiter, Shimon Edvardson, Hagar Mor-Shaked, Orly Elpeleg, Daniela Vallone, Lior Appelbaum, Nicholas S. Foulkes, Yoav Gothilf
Summary: The circadian clock is a mechanism that regulates various physiological rhythms with a period of approximately 24 hours. A mutation in FBXL3 has been found in patients with syndromic developmental delay, morphological abnormalities, and intellectual disability. Using zebrafish as a model, it was discovered that loss of fbxl3a function disrupts the circadian rhythms, locomotor activity, and sleep-wake cycles, but does not cause morphological effects. These findings suggest a conserved role for FBXL3 in the circadian clock system across vertebrates and its acquisition of developmental roles in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Luis M. M. San-Jose, Elvire Bestion, Felix Pellerin, Murielle Richard, Lucie Di Gesu, Jordi Salmona, Laurane Winandy, Delphine Legrand, Camille Bonneaud, Olivier Guillaume, Olivier Calvez, Kathryn R. Elmer, Andrey A. Yurchenko, Hans Recknagel, Jean Clobert, Julien Cote
Summary: Although animal dispersal plays key roles in ecological and evolutionary processes, its genetic basis, particularly in vertebrates, is poorly understood. This study investigated the genetic basis of natal dispersal in the common lizard using quantitative genetics, genome-wide sequencing, and transcriptome sequencing. The results suggest the heritability of dispersal and highlight the involvement of neurotransmitters and circadian pathways in regulating dispersal and shaping dispersal syndromes. These findings have implications for understanding dispersal behavior in vertebrates.
Article
Cell Biology
Robert C. Moseley, Francis Motta, Gerald A. Tuskan, Steven B. Haase, Xiaohan Yang
Summary: This study explores the circadian control of CAM-related genes in plants, investigating the re-phasing of core clock genes and rewiring of phase-specific gene networks. By inferring gene regulatory relationships and constructing gene regulatory networks, the research sheds new light on the mechanisms behind circadian regulation of gene expression in CAM plants.
Article
Ecology
Ricarda Cremer, Alexander Wacker, Anke Schwarzenberger
Summary: Cryptochromes are ancient blue-light photoreceptors that play a role in the circadian clock of organisms. They transfer light information to the clock, which impacts behaviors like diel vertical migration in zooplankton. Changes in light regime, such as anthropogenic Artificial Light At Night, can affect both the circadian clock and the feeding habits of zooplankton, ultimately influencing ecosystem dynamics.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Yu Zhang, Yong Li, Yilin Yuan, Jun Wang, Shiyu Zhang, Run Zhu, Yan Wang, Yinbao Wu, Xindi Liao, Jiandui Mi
Summary: Light plays a crucial role in regulating the central biological clock system. Intermittent photoperiods enhance the circadian rhythms of gut microbes and the expression of clock genes in the hypothalamus, liver, and cecal wall. This regulation is mediated through the melatonin pathway and the production of short-chain fatty acids.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Physics, Multidisciplinary
Ying Li, Guang-Kun Zhang, Yan-Ming Ge
Summary: Cyanobacteria have a circadian clock system consisting of a transcriptional/translational feedback loop and a post-translational oscillator. The protein CikA plays a crucial role in the regulation of the circadian clock, enhancing sensitivity and adaptability. Mathematical models have shown that CikA regulation strengthens the central role of the post-translational oscillator and improves the system's ability to modulate its period against environmental changes.
Review
Biotechnology & Applied Microbiology
Judit Vago, Roland Takacs, Patrik Kovacs, Tibor Hajdu, Daan R. van der Veen, Csaba Matta
Summary: The unique structure and composition of articular cartilage are critical for its function, but they can be disrupted by degeneration or trauma. The low regenerative capacity of the tissue limits its healing response, leading to inflammation and reduced quality of life. Tissue engineering approaches that generate new cartilage can address these limitations by considering the biomechanical microenvironment and entraining the molecular circadian clockwork. This review highlights the importance of the biomechanical microenvironment in advancing cartilage tissue engineering interventions.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Titouan Bonnot, Dawn H. Nagel
Summary: Plants regulate their transcriptome in response to heat stress by modulating gene expression through the circadian clock, highlighting potential regulatory nodes for improving heat stress tolerance.
Article
Biochemistry & Molecular Biology
Zhilong He, Caixia Liu, Xiangnan Wang, Rui Wang, Yun Tian, Yongzhong Chen
Summary: A comparative analysis of leaf transcriptome of two Camellia oleifera cultivars with different photosynthetic characteristics revealed a group of genes related to photosynthesis and hormone regulation. Real-time PCR validation identified key genes in the regulatory network of photosynthesis. The study suggested heat tolerance as a crucial factor affecting photosynthetic differences.
BIOCHEMICAL GENETICS
(2021)
Article
Multidisciplinary Sciences
Nange Jin, Lian-Ming Tian, Iris Fahrenfort, Zhijing Zhang, Friso Postma, David L. Paul, Stephen C. Massey, Christophe P. Ribelayga
Summary: This study utilized rod- or cone-specific gene knockout mice to investigate the functionality of the secondary rod pathway and the additive contribution of different pathways to retinal output.
Article
Biochemistry & Molecular Biology
Hans Christoph Liedtke, Ewan Harney, Ivan Gomez-Mestre
Summary: Research has uncovered differences in gene expression between two species of spadefoot toads in response to a shared environmental risk, particularly genes related to lipid, cholesterol, and steroid biosynthesis and metabolism. These differences may have played a crucial role in the genetic accommodation of developmental plasticity in this biological system.
Review
Physiology
Muege Yalcin, Annakarina Mundorf, Freya Thiel, Sandra Amatriain-Fernandez, Ida Schulze Kalthoff, Jan-Carl Beucke, Henning Budde, Susan Garthus-Niegel, Jutta Peterburs, Angela Relogio
Summary: This article addresses the role of the circadian clock in health and disease, particularly in relation to behavior, cognitive functioning, and mental health. The disruption of circadian rhythms is linked to the onset and progression of various pathologies. The article also highlights the potential use of circadian activators in delaying the progression of certain diseases.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
R. R. Cheng, O. Nordesjo, R. L. Hayes, H. Levine, S. C. Flores, J. N. Onuchic, F. Morcos
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Article
Multidisciplinary Sciences
Michele Di Pierro, Ryan R. Cheng, Erez Lieberman Aiden, Peter G. Wolynes, Jose N. Onuchic
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Multidisciplinary Sciences
Xian-Li Jiang, Emmanuel Martinez-Ledesma, Faruck Morcos
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Qin Zhou, Nikesh Kunder, Jose Alberto De la Paz, Alexandra E. Lasley, Vandita D. Bhat, Faruck Morcos, Zachary T. Campbell
NATURE COMMUNICATIONS
(2018)
Article
Pharmacology & Pharmacy
Hector E. Sanchez-Ibarra, Luisa M. Reyes-Cortes, Xian-Li Jiang, Claudia M. Luna-Aguirre, Dionicio Aguirre-Trevino, Ivan A. Morales-Alvarado, Rafael B. Leon-Cachon, Fernando Lavalle-Gonzalez, Faruck Morcos, Hugo A. Barrera-Saldana
FRONTIERS IN PHARMACOLOGY
(2018)
Article
Multidisciplinary Sciences
Ricardo Nascimento dos Santos, Shahid Khan, Faruck Morcos
ROYAL SOCIETY OPEN SCIENCE
(2018)
Article
Multidisciplinary Sciences
Sarah H. Karml, Sarah H. Holt, Luhua Song, Sagi Tamir, Yuting Luo, Fang Bai, Ammar Adenwalla, Merav Darash-Yahana, Yang-Sung Sohn, Patricia A. Jennings, Rajeev K. Azad, Jose' N. Onuchic, Faruck Morcos, Rachel Nechushtail, Ron Mittler
Article
Multidisciplinary Sciences
Ryan R. Cheng, Ellinor Haglund, Nicholas S. Tiee, Faruck Morcos, Herbert Levine, Joseph A. Adams, Patricia A. Jennings, Jose N. Onuchic
Article
Multidisciplinary Sciences
Dana Krepel, Ryan R. Cheng, Michele Di Pierro, Jose N. Onuchic
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Chemistry, Physical
Ana Mandic, Ryan L. Hayes, Heiko Lammert, Ryan R. Cheng, Jose N. Onuchic
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Biochemistry & Molecular Biology
Vinicius G. Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman-Aiden, Peter G. Wolynes, Michele Di Pierro, Jose N. Onuchic
Summary: The Nucleome Data Bank (NDB) is a web-based platform for simulating and analyzing the 3D organization of genomes, allowing users to generate chromosomal sub-compartment annotations and access experimental and computational structural genomics data for free. Users can also analyze and visualize data through custom-designed web-based tools.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Ryan R. Cheng, Vinicius G. Contessoto, Erez Lieberman Aiden, Peter G. Wolynes, Michele Di Pierro, Jose N. Onuchic
Article
Chemistry, Physical
Kareem M. Mehrabiani, Ryan R. Cheng, Jose N. Onuchic
Summary: Direct Coupling Analysis (DCA) is a global statistical approach that predicts spatial contacts in the three-dimensional structure of a folded protein using information encoded in protein sequence data. DCA can predict the folding of monomers, identify biologically relevant interaction sites in folded proteins, and stabilize interacting spatial contacts in protein complexes. A new Z-score measure has been proposed to filter out statistically significant DCA predictions and improve prediction ability.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Vinicius G. Contessoto, Ryan R. Cheng, Jose N. Onuchic
Summary: Recent efforts have focused on understanding the 3D organization of the genome and how this structure impacts nuclear function. Experimental techniques combining DNA proximity ligation with high-throughput sequencing, such as Hi-C, have improved knowledge about chromatin organization. Theoretical modeling is necessary to determine structural ensembles consistent with experimental data, providing insight into the physical mechanisms governing genome architecture.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)