Review
Biochemistry & Molecular Biology
Tingting Li, Shihua Zhang, Yuxuan Yang, Lingli Zhang, Yu Yuan, Jun Zou
Summary: This paper reviews the progress of research on the co-regulation of bone metabolism by circadian clock genes and microRNAs, aiming to provide new ideas for the prevention and treatment of bone metabolic diseases such as osteoporosis.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2022)
Review
Nutrition & Dietetics
Lauren N. Woodie, Kaan T. Oral, Brianna M. Krusen, Mitchell A. Lazar
Summary: Obesity and metabolic diseases are common in industrialized societies due to circadian disruption caused by shift work, jet lag, and social obligations. The circadian rhythm of the hypothalamic suprachiasmatic nucleus (SCN) plays a critical role in regulating physiological, metabolic, and behavioral processes. However, disruptions in external cues or metabolic flexibility can lead to the development of obesity and metabolic disease. This review explores the circadian rhythm of nutrient metabolism and discusses obesity as a circadian disease.
Article
Genetics & Heredity
Akiko Suzuki, Hiroki Yoshioka, Teng Liu, Aania Gull, Naina Singh, Thanh Le, Zhongming Zhao, Junichi Iwata
Summary: This study reveals the regulatory network of genes and microRNAs (miRNAs) related to amelogenesis imperfecta. miR-16-5p and miR-27b-3p were identified as potential pathogenic miRNAs, as they significantly inhibited ameloblast differentiation by regulating mAIGenes.
FRONTIERS IN GENETICS
(2022)
Review
Medicine, Research & Experimental
Yi Qin, Zhong-hua Chen, Jun-Jie Wu, Zhen-Yu Zhang, Zheng-Dong Yuan, Dan-Yang Guo, Meng-Nan Chen, Xia Li, Feng-Lai Yuan
Summary: The circadian clock plays a crucial role in regulating bone metabolism, including bone loss. Clock-related genes control signaling pathways and transcription factors in osteoblasts and osteoclasts, while also regulating osteocytes and endothelial cells. Furthermore, the regulation of circadian clock genes by novel modulators presents a potential strategy for preventing and treating bone diseases.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Cell Biology
Xiaojie Bai, Yilie Liao, Fangfang Sun, Xia Xiao, Suneng Fu
Summary: The diurnal organization of biological pathways, especially in relation to energy metabolism and inflammation/proliferation pathways, remains to be fully understood. Perturbing the hepatic transcriptome through nutrient regulators has revealed the enduring properties of pathway organization, with G0s2 and Rgs16 genes identified as potential mediators at the metabolism-inflammation interface. These genes play a role in promoting amino acid oxidation, suppressing mitochondrial respiration, and preventing hepatic inflammation and hepatocyte proliferation under both physiological and pathological conditions, such as obesity.
Article
Multidisciplinary Sciences
Jennifer A. Davis, Jodi R. Paul, Stefani D. Yates, Elam J. Cutts, Lori L. McMahon, Jennifer S. Pollock, David M. Pollock, Shannon M. Bailey, Karen L. Gamble
Summary: Changing meal timing can rescue the cognitive and hippocampal impairments induced by HFD, even without altering body composition and total caloric intake. This suggests that short-term time-restricted feeding is an effective intervention for HFD-induced cognitive deficits and hippocampal dysfunction.
Review
Cell Biology
Deeksha Malhan, Britt Schoenrock, Muege Yalcin, Dieter Blottner, Angela Relogio
Summary: Alterations in the circadian system are common in aging on Earth and also observed in astronauts during and after space exploration. However, little is known about the common molecular alterations underlying terrestrial aging and space-related aging. This review focuses on the role of the circadian clock in visual, cardiovascular, central nervous, and musculoskeletal systems and summarizes the known molecular alterations associated with spaceflight.
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
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.
Article
Cell Biology
Holly Kay, Harry Taylor, Gerben van Ooijen
Summary: This study reveals how environmental and endogenous circadian rhythms regulate the selenoproteome in a model eukaryotic cell. The expression of selenoproteins is influenced by rhythmicity under constant circadian conditions, while selenium uptake shows high-amplitude rhythms under environmentally rhythmic conditions. Additionally, selenium deprivation leads to clock gene expression defects under the light/dark cycle.
Article
Immunology
Feng Ling, Caijie Zhang, Xin Zhao, Xiangyang Xin, Shaozhen Zhao
Summary: This study identified key genes associated with circadian rhythms and explored potential drugs related to these genes in diabetic retinopathy (DR). The findings contribute to a better understanding of the pathogenesis of DR and provide insights for future therapeutic interventions.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Cesar Rodriguez-Santana, Javier Florido, Laura Martinez-Ruiz, Alba Lopez-Rodriguez, Dario Acuna-Castroviejo, Germaine Escames
Summary: The circadian clock system plays a crucial role in regulating various physiological processes, and disruptions in this system have been linked to diseases such as cancer. Tumor cells exhibit abnormal circadian machinery, which affects cell cycle, repair mechanisms, and energy metabolism. Melatonin, produced by the pineal gland, has been shown to regulate clock gene expression in cancer cells, suggesting its potential anti-neoplastic effects. This review aims to explore the role of clock genes in cancer and the mechanisms through which melatonin regulates the tumor's circadian machinery, with the goal of proposing future clinical treatments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Christine Merlin
Summary: The molecular mechanism behind organisms' ability to anticipate variations in environmental conditions caused by tides in the intertidal zone has been unknown. A recent study shows that the circadian clock gene bmal1 is necessary for circatidal rhythms.
Article
Multidisciplinary Sciences
Eui Min Jeong, Miri Kwon, Eunjoo Cho, Sang Hyuk Lee, Hyun Kim, Eun Young Kim, Jae Kyoung Kim
Summary: In metazoan organisms, circadian rhythms are regulated by pacemaker neurons organized in a master-slave hierarchy. This study reveals the heterogeneity in molecular clockworks between master pacemakers and slave oscillators, with higher PER synthesis and turnover, as well as lower CLK levels in the master pacemakers. The distinct molecular clockwork of the master pacemakers allows them to generate strong rhythms and adapt flexibly to environmental changes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Agriculture, Multidisciplinary
Run Li, Jie Xiao, Yong Cao, Qingrong Huang, Chi-Tang Ho, Muwen Lu
Summary: This study demonstrates that capsaicin can alleviate circadian desynchrony, inhibit ROS overproduction, and improve mitochondrial function in HepG2 cells, thus regulating lipid metabolism by involving the rhythmic expression of circadian clock genes.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Seung-Jun Lee, Jinah Park, Dong-Joon Lee, Keishi Otsu, Pyunggang Kim, Seiya Mizuno, Min-Jung Lee, Hyun-Yi Kim, Hidemitsu Harada, Satoru Takahashi, Seong-Jin Kim, Han-Sung Jung
Summary: This study investigated the role of MAST4 in spermatogenesis in mice, revealing its importance in the localization to Sertoli cells, phosphorylation of ERM, and maintenance of SSC self-renewal.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Developmental Biology
Keishi Otsu, Hiroko Ida-Yonemochi, Shojiro Ikezaki, Masatsugu Ema, Jiro Hitomi, Hayato Ohshima, Hidemitsu Harada
Summary: Oxygen plays a crucial role in regulating the proliferation of epithelial stem cells by maintaining slow-cycling cells in a relatively hypoxic microenvironment, and the upregulation of HIF1 alpha during hypoxia triggers a downstream signaling pathway that inhibits cell proliferation.
Review
Biology
Joseph Cavataio, Santiago Schnell
Summary: The study discusses the missing critical metadata in the COVID-19 pandemic and identifies key metadata for the COVID-19 fatality rate through analysis. The authors suggest establishing standard-based guidelines for recording and reporting epidemiological data, as well as standardizing nomenclature to improve communication and reproducibility.
MATHEMATICAL BIOSCIENCES
(2021)
Article
Biology
Justin Eilertsen, Santiago Schnell
Summary: The quasi-steady-state approximation is widely used in developing simplified deterministic or stochastic models of enzyme catalyzed reactions. The stochastic extension of this approximation has been shown to be accurate under certain conditions, but recent research has highlighted stricter requirements for its validity in open Michaelis-Menten reaction mechanisms.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Geriatrics & Gerontology
Nicholas D. Urban, Joseph P. Cavataio, Yasmeen Berry, Brandon Vang, Anirudh Maddali, Richard J. Sukpraphrute, Santiago Schnell, Matthias C. Truttmann
Summary: The nematode Caenorhabditis elegans is widely used for studying various biological processes, but differences in experimental conditions and variations in chemical treatments or geographic locations can significantly influence the lifespan of N2 worms, leading to unreliable inter-laboratory comparisons. Standardized experimental protocols and improved reporting standards are needed to increase the reliability and reproducibility of lifespan studies in C. elegans.
EXPERIMENTAL GERONTOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Jan Range, Colin Halupczok, Jens Lohmann, Neil Swainston, Carsten Kettner, Frank T. Bergmann, Andreas Weidemann, Ulrike Wittig, Santiago Schnell, Jurgen Pleiss
Summary: EnzymeML is an XML-based data exchange format that supports comprehensive documentation of enzymatic data, extended by implementing the STRENDA Guidelines. It supports the scientific community with a standardized data exchange format and integrates software tools through a Python API.
Article
Cell Biology
Morgan A. Gingerich, Xueying Liu, Biaoxin Chai, Gemma L. Pearson, Michael P. Vincent, Tracy Stromer, Jie Zhu, Vaibhav Sidarala, Aaron Renberg, Debashish Sahu, Daniel J. Klionsky, Santiago Schnell, Scott A. Soleimanpour
Summary: CLEC16A regulates mitochondrial health through mitophagy and is associated with over 20 human diseases. This study reveals the importance of a C-terminal intrinsically disordered protein region (IDPR) in CLEC16A for mitochondrial quality control. The stability of CLEC16A is dependent on proline bias within the C-terminal IDPR.
Article
Biology
Justin Eilertsen, Kashvi Srivastava, Santiago Schnell
Summary: This paper studies the linear approximation model of noise in chemical reactions, derives the slow scale linear noise approximation from geometric singular perturbation theory, and explains the origins of different ssLNAs reported in the literature. The model is extended to a non-classical singular perturbed problem, disproving commonly-accepted qualifier for the validity of stochastic quasi-steady-state approximation of the Michaelis-Menten reaction mechanism.
JOURNAL OF MATHEMATICAL BIOLOGY
(2022)
Article
Biology
Justin Eilertsen, Santiago Schnell, Sebastian Walcher
Summary: In this study, we present a simplified model for the irreversible Michaelis-Menten reaction mechanism under quasi-steady-state conditions. We complement existing research by identifying local conditions that prevent quasi-steady-state reductions, both in the classical and broader sense. Furthermore, we discuss parameter regions where no quasi-steady-state reduction is applicable and show that these regions are small in a well defined sense. Additionally, we provide local conditions for the accuracy of standard or total quasi-steady-state.
MATHEMATICAL BIOSCIENCES
(2022)
Article
Dentistry, Oral Surgery & Medicine
Marii Azumane, Shojiro Ikezaki, Keishi Otsu, Mika Kumakami-Sakano, Haruno Arai, Hiroyuki Yamada, Paivi Kettunen, Hidemitsu Harada
Summary: This study investigates the molecular mechanisms underlying the maintenance of Hertwig's epithelial root sheath (HERS) and the development of epithelial rests of Malassez (ERM) during root dentin formation. The researchers observed the expression of semaphorin receptors in HERS cells and the activation of RhoA signaling pathway, while TGF-beta signaling pathway promoted cell migration and reduced E-cadherin expression. These findings provide insights into the opposing effects of semaphorin and TGF-beta signaling in controlling HERS maintenance and EMT during root formation.
JOURNAL OF PERIODONTAL RESEARCH
(2023)
Article
Biology
Justin Eilertsen, Santiago Schnell, Sebastian Walcher
Summary: This paper focuses on deriving small parameters to gauge the accuracy of reduction in reaction networks that admit a singular perturbation reduction in a certain range of parameters. These parameters are derived based on local timescale estimates using eigenvalues of the Jacobian near critical manifolds, providing a critical first step toward estimating the accuracy of reduction. Coefficients of the characteristic polynomial are used to derive these parameters, which are related to timescales. The paper presents new parameters for systems of arbitrary dimension, with particular emphasis on reduction to dimension one. The efficacy of the parameters is illustrated through numerical simulations, although certain limitations must be observed.
BULLETIN OF MATHEMATICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Morgan A. Gingerich, Jie Zhu, Biaoxin Chai, Michael P. Vincent, Nuli Xie, Vaibhav Sidarala, Nicholas A. Kotov, Debashish Sahu, Daniel J. Klionsky, Santiago Schnell, Scott A. Soleimanpour
Summary: CLEC16A is an E3 ubiquitin ligase that plays a crucial role in regulating mitochondrial quality control through mitophagy and is associated with various human diseases. A recent study discovered an internal intrinsically disordered protein region (IDPR) within CLEC16A that is essential for its function and turnover. This IDPR is targeted by RNF41 to promote CLEC16A degradation and destabilize the CLEC16A-RNF41-USP8 complex. These findings highlight the importance of the IDPR in controlling the regulatory balance between CLEC16A and RNF41, which could be therapeutically targeted to improve mitochondrial health in disease.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Simone Lauterbach, Hannah Dienhart, Jan Range, Stephan Malzacher, Jan-Dirk Spoering, Doerte Rother, Maria Filipa Pinto, Pedro Martins, Colton E. Lagerman, Andreas S. Bommarius, Amalie Vang Host, John M. Woodley, Sandile Ngubane, Tukayi Kudanga, Frank T. Bergmann, Johann M. Rohwer, Dorothea Iglezakis, Andreas Weidemann, Ulrike Wittig, Carsten Kettner, Neil Swainston, Santiago Schnell, Juergen Pleiss
Summary: The design of biocatalytic reaction systems is complex due to the dependency of kinetic parameters on the enzyme, reaction conditions, and modeling method. Enzymatic experiments and data reusability are challenging, leading to the development of EnzymeML, an XML-based markup language for storing and exchanging enzymatic data. EnzymeML facilitates the communication between experimental platforms, lab notebooks, modeling tools, publication platforms, and enzymatic reaction databases.
Article
Multidisciplinary Sciences
Kanako Ikami, Suzanne Shoffner-Beck, Malgorzata Tyczynska Weh, Santiago Schnell, Shosei Yoshida, Edgar Andres Diaz Miranda, Sooah Ko, Lei Lei
Summary: During mouse gametogenesis, germ cells derived from the same progenitor are connected via intercellular bridges forming germline cysts. In fetal female cysts, branching germ cells that are connected by multiple bridges are preferentially protected from cell death and accumulate cytoplasm and organelles to become primary oocytes. The formation and function of branched cysts in mice provide insights into oocyte determination in germline cysts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Dentistry, Oral Surgery & Medicine
H. Ida-Yonemochi, K. Otsu, T. Irie, A. Ohazama, H. Harada, H. Ohshima
Summary: Autophagy plays a crucial role in the maintenance of dental epithelial stem cells and enamel formation. Deficiency in autophagy may lead to tumorigenesis in dental epithelial cells.
JOURNAL OF DENTAL RESEARCH
(2023)
