Review
Plant Sciences
Joao Antonio Siqueira, Willian Batista-Silva, Agustin Zsogon, Alisdair R. Fernie, Wagner L. Araujo, Adriano Nunes-Nesi
Summary: Through domestication, humans have altered the developmental and circadian clocks of plants, resulting in modern crops with increased productivity and adaptability. However, this domestication has also led to reduced genetic variability and abiotic stress tolerance. The domestication process has likely caused a significant restructuring of plant metabolic timekeeping. We highlight the importance of the contrasting timings among organs in wild relatives of crops for recognizing environmental adversities. Furthermore, we suggest that the connections established among biological clocks during plant domestication may offer a valuable source of genetic variation for improving crop resilience and yield.
TRENDS IN PLANT SCIENCE
(2023)
Article
Biology
Amy Newman, Emma Picot, Sian Davies, Sally Hilton, Isabelle A. Carre, Gary D. Bending
Summary: Aberrant function of plant circadian clock can lead to altered rhythmicity of rhizosphere bacteria and fungi, resulting in changes in the composition of rhizosphere microbiome with potential consequences for plant health.
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
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
Genetics & Heredity
Evan John, Karam B. Singh, Richard P. Oliver, Kar-Chun Tan
Summary: This study compared transcription factors (TFs) across diverse fungal proteomes and analyzed their evolutionary trajectories. The study found that host-associated pathogens have fewer TFs, primarily due to contractions in specific TF lineages. The study also provided new insights into the origin and evolution of virulence-regulating TFs.
FUNGAL GENETICS AND BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Bo-Wei Qin, Lei Zhao, Wei Lin
Summary: Calibrating both anomalous frequency and amplitude of biorhythm prevents physiological dysfunctions or diseases. The authors propose a universal approach to design a frequency-amplitude coordinator rigorously via dynamical systems tools.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Michael J. Rust
Summary: The study on circadian clock suggests that it can function even in non-growing cells using minimal components from cyanobacteria. The findings indicate the potential evolution of the circadian clock to adapt to different cellular conditions.
Review
Biochemistry & Molecular Biology
Weixiang Wang, Xuan Cai, Xiao-Lin Chen
Summary: Ubiquitination is an important cellular regulatory mechanism that modifies proteins, while deubiquitination reverses this modification. Deubiquitinating enzymes play significant roles in fungal pathogens, regulating infection-related morphogenesis, virulence, development, and stress response.
Review
Biochemistry & Molecular Biology
Evrim Yildirim, Rachel Curtis, Dae-Sung Hwangbo
Summary: Biological clocks are essential mechanisms that synchronize physiological and behavioral processes with external cues to ensure organisms' fitness and survival. While the central clock in the brain drives daily activity rhythms, peripheral tissues have their own clock systems generating metabolic and physiological rhythms. The fruit fly Drosophila melanogaster has been a widely studied model organism for investigating the mechanism and functions of circadian clocks.
Review
Plant Sciences
Christian Falter, Sigrun Reumann
Summary: This review summarizes recent research results on the novel peroxisomal functions of filamentous fungi and emphasizes the importance of peroxisomes in the infection of host plants. Peroxisomes play a central role in fungal virulence, producing important metabolic products and housing various enzymes.
MOLECULAR PLANT PATHOLOGY
(2022)
Review
Cell Biology
Namasthee Harris-Gauthier, Shashank Bangalore Srikanta, Nicolas Cermakian
Summary: Living organisms have evolved to synchronize and adapt to daily environmental cycles through circadian rhythms. These rhythms are driven by a molecular clock composed of clock genes and proteins, which regulate the expression of numerous genes. Ubiquitination and deubiquitination play important roles in the regulation of clock proteins and their functions within the circadian clock.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2022)
Review
Endocrinology & Metabolism
Ferdinando Fusco, Nicola Longo, Marco De Sio, Davide Arcaniolo, Giuseppe Celentano, Marco Capece, Roberto La Rocca, Francesco Mangiapia, Gianluigi Califano, Simone Morra, Carmine Turco, Gianluca Spena, Lorenzo Spirito, Giovanni Maria Fusco, Luigi Cirillo, Luigi De Luca, Luigi Napolitano, Vincenzo Mirone, Massimiliano Creta
Summary: The impact of circadian desynchrony on spermatogenesis is significant but current evidence is insufficient due to study heterogeneity.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Review
Cell Biology
Jonathan S. Yi, Nicolas M. Diaz, Shane D'Souza, Ethan D. Buhr
Summary: Most organisms have self-sustained circadian clocks that can be synchronized by environmental stimuli or oscillate indefinitely. In mammals, this is true at the molecular level for most cell types, with a core set of clock genes forming a transcriptional/translational feedback loop (TTFL) with a 24-hour period. The TTFL mechanism varies slightly in different cell types, but all involve similar core clock genes. The clock has unique outputs in different tissues, as cells convert the TTFL timing signals into orchestrated transcriptional oscillations of clock-controlled genes and cellular processes.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Review
Physiology
Siska Wilantri, Hanna Grasshoff, Tanja Lange, Timo Gaber, Luciana Besedovsky, Frank Buttgereit
Summary: Research on 24-h rhythms over the past four decades has revealed their significance for immunity and various diseases through genetic, molecular, and physiological findings. Disruption and misalignment of circadian rhythms have been linked to diseases and abnormal physiological functioning, highlighting their fundamental importance to mammals. This article provides an overview of the molecular regulation of 24-h rhythms, their impact on immunity, the detrimental effects of misalignment, the association between pathological rhythms and rheumatoid arthritis (RA), and the potential use of chronobiological rhythms for chronotherapy in inflammatory autoimmune diseases like RA.
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
Biotechnology & Applied Microbiology
Rafaella Zarate, Duxan Arancibia, Anllely Fernandez, Janetti R. Signorelli, Luis F. Larrondo, Maria Estela Andres, Pedro Zamorano
Summary: This study adapted the Light-On system into a lentiviral platform, allowing precise control of gene expression in neurons. The system showed promising results in both cell lines and cultured rat hippocampal neurons, indicating its potential for biomedical and neuroscience research as well as brain therapies for neurodegenerative diseases.
ELECTRONIC JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Felipe Munoz-Guzman, Valeria Caballero, Luis F. Larrondo
Summary: Eukaryotic circadian oscillators typically operate through a negative feedback loop, with additional transcriptional regulators influencing the expression of core clock components. A study on Neurospora crassa identified a set of 23 transcription factors that, when absent, resulted in significant changes in circadian period. While the exact mechanisms of these regulators remain unclear, they demonstrate the broad impact of light and clock-regulated transcription factors on modulating the circadian clock.
G3-GENES GENOMES GENETICS
(2021)
Article
Microbiology
Vicente Rojas, Francisco Salinas, Andres Romero, Luis F. Larrondo, Paulo Canessa
Summary: This study confirms the interaction between BcWCL1 and BcWCL2 in the absence of light and upon blue-light stimulation, and demonstrates that both proteins are capable of light sensing.
Article
Biology
Marlene Henriquez-Urrutia, Rebecca Spanner, Consuelo Olivares-Yanez, Aldo Seguel-Avello, Rodrigo Perez-Lara, Hector Guillen-Alonso, Robert Winkler, Alfredo Herrera-Estrella, Paulo Canessa, Luis F. Larrondo
Summary: This study confirms the existence of circadian rhythms in Trichoderma atroviride and highlights the importance of these rhythms in the fungal-fungal interaction with Botrytis cinerea. The study also reveals the impact of clock components on various aspects of T. atroviride's lifestyle and the modulation of fungal interactions and dynamics.
Article
Environmental Sciences
Gabriel A. Rojas, Nicolas Saavedra, Kathleen Saavedra, Montserrat Hevia, Cristian Morales, Fernando Lanas, Luis A. Salazar
Summary: This study aimed to evaluate the effects of PAH exposure on systemic pro-inflammatory cytokines and markers of endothelial dysfunction. The results showed that PAHs present in air pollution stimulated the increase in serum inflammatory cytokines and the expression of markers of endothelial dysfunction in the murine model studied.
Article
Biochemical Research Methods
Vicente Rojas, Luis F. Larrondo
Summary: Cell communication is a widespread mechanism in biology for transmitting information about environmental conditions. In this study, cell communication and optogenetics were coupled in yeast to modulate gene expression. The results showed that external light information can be propagated through diffusible signaling molecules to regulate gene expression in a synthetic system involving microbial cells.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Nathan R. Johnson, Luis F. Larrondo, Jose M. Alvarez, Elena A. Vidal
Summary: This study systematically assesses the characteristics and annotation reliability of mi/milRNA in fungi. It finds that less than half of the reported loci meet the basic standards for hairpin RNA discovery. Fungal mi/milRNAs are generally similar in size to animal miRNAs and are frequently associated with protein-coding genes. The study also identifies 25 conserved mi/milRNA loci across multiple species.
Article
Microbiology
Gabriel Perez-Lara, Tomas C. Moyano, Andrea Vega, Luis F. Larrondo, Ruben Polanco, Jose M. Alvarez, Daniel Aguayo, Paulo Canessa
Summary: To comprehensively analyze gene expression in the phytopathogenic fungus Botrytis cinerea, a web-based gene expression browser called BEB was developed. This computationally inexpensive application provides publication-ready heatmaps of transcript levels and allows gene expression clustering and visualization options, along with the ability to download gene expression values for further exploration. The implementation of BEB is transferable to other organisms and allows for comparative transcriptomics and candidate gene identification.
Article
Biochemistry & Molecular Biology
Gabriel Perez-Lara, Consuelo Olivares-Yanez, Harm van Bakel, Luis F. Larrondo, Paulo Canessa
Summary: In this study, the transcriptomic differences between wild-type B. cinerea B05.10 and ? bcwcl1 were compared after a 60 min light pulse. The results showed that the deletion of the white-collar-1 gene caused a lack of response to light pulse in the mutant strain during its interaction with the plant. Additionally, the light-repressed genes in fungus-infected plants were enriched with biological functions associated with plant defense.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Multidisciplinary Sciences
Luis F. Larrondo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Consuelo Olivares-Yanez, Maria P. Alessandri, Loreto Salas, Luis F. Larrondo
Summary: In Neurospora crassa, caffeine and other methylxanthines inhibit phosphodiesterase (PDE) activity, leading to increased cAMP levels and longer circadian period. However, these substances still exert their effects in adenylate cyclase and protein kinase A mutants, suggesting a different mechanism from the canonical PDE-cAMP-PKA signaling axis.
MICROBIOLOGY SPECTRUM
(2023)
Review
Cell Biology
Alyssa Kearly, Andrew D. L. Nelson, Aleksandra Skirycz, Monika Chodasiewicz
Summary: Stress Granules (SGs) and Processing-bodies (P-bodies) are important biomolecular condensates that play crucial roles in maintaining mRNA balance and regulating stress responses. They are composed of proteins and RNAs involved in translation, protein folding, and energy metabolism.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
P. Lemonnier, T. Lawson
Summary: Stomatal conductance plays a crucial role in determining CO2 uptake and water loss in plants, affecting overall water status and productivity. However, the signals coordinating mesophyll demands for CO2, the role of chloroplasts in stomatal function, and other GC metabolic processes in stomatal function remain poorly understood.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Matteo Gionfriddo, Timothy Rhodes, Spencer M. Whitney
Summary: Rubisco is a key enzyme that facilitates the entry of CO2 into the biosphere, but its catalytic properties are slow and error-prone. More effective Rubisco variants have been discovered in certain algae, offering the potential to significantly improve crop productivity. However, incompatibilities in protein folding have hindered the transplantation of these variants into plants. Directed evolution is now being explored to enhance Rubisco catalysis.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Vittoria Clapero, Stephanie Arrivault, Mark Stitt
Summary: The Calvin-Benson cycle has undergone massive selection and co-evolution with carbon-concentrating mechanisms due to changing environmental factors. Metabolite profiling reveals species-specific variations in the operation of the cycle, indicating the influence of different modes of photosynthesis. Connectivity analysis identifies constraints and driving factors for cross-species diversity in the cycle.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Sukhbir Kaur, David D. Roberts
Summary: Thrombospondin-1 modulates cell behavior by interacting with components of the extracellular matrix and cell surface receptors. Its release and expression are influenced by injuries and various diseases, while its sustained presence in the extracellular space is regulated by receptor-mediated clearance. Thrombospondin-1 plays important roles in immune responses.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Richard P. Tucker, Josephine C. Adams
Summary: Thrombospondins (TSPs) play diverse roles in animals and have been found to belong to a superfamily that includes different subgroups such as mega-TSPs, sushi-TSPs, and poriferan-TSPs. Invertebrates encode a greater diversity of TSP superfamily members than vertebrates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
James Petrik, Sylvia Lauks, Bianca Garlisi, Jack Lawler
Summary: Many cancers start with a small nest of transformed cells that can remain dormant. Thrombospondin-1 (TSP-1) initially promotes dormancy by suppressing angiogenesis, but over time, factors promoting angiogenesis become dominant and recruit various cells to form a complex tumor microenvironment. TSPs play a role in the proliferation, migration, and invasion of cells in the tumor microenvironment, as well as influencing the immune characteristics and phenotype of tumor-associated macrophages.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hana Fakim, Christine Vande Velde
Summary: There has been increasing attention to the role of phase-separated biomolecular condensates, specifically stress granules, in neurodegenerative diseases like ALS. ALS-associated mutations in genes involved in stress granule assembly have been found, and stress granule proteins have been detected in pathological inclusions in ALS patient neurons. However, protein components of stress granules are also present in other physiological biomolecular condensates, which have not been adequately discussed in relation to ALS. This review explores the functions of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites beyond stress granules, and discusses the impact of ALS-linked mutations on their ability to phase separate and perform their functions in stress-independent biomolecular condensates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Alexander Lin, Yogambha Ramaswamy, Ashish Misra
Summary: Smooth muscle cells, endothelial cells, and macrophages in blood vessels display remarkable heterogeneity, and their developmental origins may influence their plasticity. Unbiased single cell whole transcriptome analysis techniques are revolutionizing the understanding of cellular diversity and plasticity, providing insights for therapeutic research.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Elton P. Hudson
Summary: The Calvin Benson cycle plays a crucial role in the ecological and biotechnological aspects of bacteria. Recent studies have shed light on the regulation of this cycle in bacteria, with post-transcriptional and post-translational regulation being important in phototrophic bacteria, and transcriptional regulation being prominent in chemolithoautotrophic bacteria. Understanding the regulation of the Calvin Benson cycle has implications for enhancing CO2 fixation and improving the synthesis of desired products. Non-canonical cycles may offer potential benefits for industrial applications.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Xin-Guang Zhu, Haim Treves, Honglong Zhao
Summary: This paper discusses the major regulatory mechanisms over the Calvin Benson Cycle (CBC) that maintain homeostasis of metabolite levels. These mechanisms include redox regulation of enzymes, metabolite regulations (especially allosteric regulations), and balanced activities of enzymes. These regulatory mechanisms are crucial for maintaining high flux and photosynthetic efficiency in CBC.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hunter C. Herriage, Yi-Ting Huang, Brian R. Calvi
Summary: Apoptosis prevents the inappropriate acquisition of extra copies of the genome, known as polyploidy, but the polyploid state can suppress apoptosis. The mechanisms linking apoptosis and polyploid cell cycles are still largely unknown, and studying the regulation of apoptosis in development and cancer could lead to more effective therapies.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Daniel Campbell, Steven Zuryn
Summary: Mitochondrial dynamics play a crucial role in regulating cellular and organismal homeostasis, impacting various aspects of an organism's healthspan. By studying the nematode Caenorhabditis elegans, a comprehensive understanding of the impact of mitochondrial dynamics on homeostasis over a lifetime can be obtained.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Diba Borgmann, Henning Fenselau
Summary: Maintaining blood glucose at an appropriate physiological level requires coordination of multiple organs and tissues, with the vagus nerve playing a key role in central control. Recent studies have revealed the cellular identity, neuroanatomical organization, and functional contributions of vagal neurons in the regulation of systemic glucose metabolism. These findings provide new insights into the precise roles of vagal neurons in coordinating glucose levels and offer potential avenues for treating glucose metabolism disorders.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Tatiana C. Coverdell, Stephen B. G. Abbott, John N. Campbell
Summary: In this article, we review how genetic technology and single-cell genomics are revealing the organizational principles of the efferent vagus in unprecedented detail.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
