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International Journal of Molecular... Mar 2021Cell wall biosynthesis is a complex biological process in plants. In the rapidly growing cells or in the plants that encounter a variety of environmental stresses, the... (Review)
Review
Cell wall biosynthesis is a complex biological process in plants. In the rapidly growing cells or in the plants that encounter a variety of environmental stresses, the compositions and the structure of cell wall can be dynamically changed. To constantly monitor cell wall status, plants have evolved cell wall integrity (CWI) maintenance system, which allows rapid cell growth and improved adaptation of plants to adverse environmental conditions without the perturbation of cell wall organization. Salt stress is one of the abiotic stresses that can severely disrupt CWI, and studies have shown that the ability of plants to sense and maintain CWI is important for salt tolerance. In this review, we highlight the roles of CWI in salt tolerance and the mechanisms underlying the maintenance of CWI under salt stress. The unsolved questions regarding the association between the CWI and salt tolerance are discussed.
Topics: Adaptation, Physiological; Cell Wall; Cellulose; Gene Expression Regulation, Plant; Glycoproteins; Hydrogen-Ion Concentration; Intracellular Space; Oxidation-Reduction; Plant Physiological Phenomena; Salinity; Salt Tolerance; Signal Transduction
PubMed: 33806816
DOI: 10.3390/ijms22063260 -
Trends in Ecology & Evolution Jun 2013Coevolution, the process of reciprocal adaptation and counter-adaptation between ecologically interacting species, affects most organisms and is considered a key force... (Review)
Review
Coevolution, the process of reciprocal adaptation and counter-adaptation between ecologically interacting species, affects most organisms and is considered a key force structuring biological diversity. Our understanding of the pattern and process of coevolution, particularly of antagonistic species interactions, has been hugely advanced in recent years by an upsurge in experimental studies that directly observe coevolution in the laboratory. These experiments pose new questions by revealing novel facets of the coevolutionary process not captured by current theory, while also providing the first empirical tests of longstanding coevolutionary ideas, including the influential Red Queen hypothesis. In this article, we highlight emerging directions for this field, including experimental coevolution of mutualistic interactions and understanding how pairwise coevolutionary processes scale up within species-rich communities.
Topics: Adaptation, Biological; Bacterial Physiological Phenomena; Biological Evolution; Biota; Eukaryota; Symbiosis; Virus Physiological Phenomena
PubMed: 23523051
DOI: 10.1016/j.tree.2013.02.009 -
Cell Cycle (Georgetown, Tex.) Nov 2020Hippo pathway is a chain of kinases consists of a series of protein kinases and transcription factors. Meanwhile, oxidative stress is a condition of elevated... (Review)
Review
Hippo pathway is a chain of kinases consists of a series of protein kinases and transcription factors. Meanwhile, oxidative stress is a condition of elevated concentrations of reactive oxygen species (ROS) that cause molecular damage to vital structures and functions. Both of them are key regulators in cell proliferation, survival, and development. These processes are strictly regulated by highly coordinated mechanisms, including c-Jun n-terminal kinase (JNK) pathway, mTOR pathway and a number of extrinsic and intrinsic factors. Recently, emerging evidence suggests that Hippo pathway is involved in the responses to cellular stresses, including mechanic stress, DNA damage, and oxidative stress, to mediate biological process, such as apoptosis, pyroptosis, and metastasis. But the exact mechanism remains to be further explored. Therefore, the purpose of this review is to summarize recent findings and discuss how Hippo pathway, oxidative stress, and the crosstalk between them regulate some biological process which determines cell fate.
Topics: Animals; Biological Phenomena; Cell Differentiation; Cell Proliferation; Hippo Signaling Pathway; Humans; Oxidation-Reduction; Oxidative Stress; Signal Transduction
PubMed: 33016196
DOI: 10.1080/15384101.2020.1824448 -
Theory in Biosciences = Theorie in Den... Jun 2022Contemporary scientific knowledge is built on both methodological and epistemological reductionism. The discovery of the limitations of the reductionist paradigm in the...
Contemporary scientific knowledge is built on both methodological and epistemological reductionism. The discovery of the limitations of the reductionist paradigm in the mathematical treatment of certain physical phenomena originated the notion of complexity, both as a pattern and process. After clarifying some very general terms and ideas on biological evolution and biological complexity, the article will tackle to seek to summarize the debate on biological complexity and discuss the difference between complexities of living and inert matter. Some examples of the major successes of mathematics applied to biological problems will follow; the notion of an intrinsic limitation in the application of mathematics to biological complexity as a global, relational, and historical phenomenon at the individual and species level will also be advanced.
Topics: Biological Evolution; Knowledge; Mathematics
PubMed: 35583727
DOI: 10.1007/s12064-022-00369-7 -
ACS Chemical Biology Jul 2010Natural products have evolved to encompass a broad spectrum of chemical and functional diversity. It is this diversity, along with their structural complexity, that... (Review)
Review
Natural products have evolved to encompass a broad spectrum of chemical and functional diversity. It is this diversity, along with their structural complexity, that enables nature's small molecules to target a nearly limitless number of biological macromolecules and to often do so in a highly selective fashion. Because of these characteristics, natural products have seen great success as therapeutic agents. However, this vast pool of compounds holds much promise beyond the development of future drugs. These features also make them ideal tools for the study of biological systems. Recent examples of the use of natural products and their derivatives as chemical probes to explore biological phenomena and assemble biochemical pathways are presented here.
Topics: Affinity Labels; Biochemical Phenomena; Biological Phenomena; Biological Products; Chromatography, Liquid; Drug Design; Drug Resistance, Microbial; Enzymes; Mass Spectrometry; Molecular Probes; Proteomics; Small Molecule Libraries
PubMed: 20509672
DOI: 10.1021/cb100105c -
Annual Review of Phytopathology Sep 2023Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth... (Review)
Review
Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology.
Topics: Agrobacterium; Virulence; Biological Evolution; Ecology; Genomics
PubMed: 37164023
DOI: 10.1146/annurev-phyto-021622-125009 -
Cell Mar 2014Cell differentiation is an essential process for the development, growth, reproduction, and longevity of all multicellular organisms, and its regulation has been the... (Review)
Review
Cell differentiation is an essential process for the development, growth, reproduction, and longevity of all multicellular organisms, and its regulation has been the focus of intense investigation for the past four decades. The study of natural and induced stem cells has ushered an age of re-examination of what it means to be a stem or a differentiated cell. Past and recent discoveries in plants and animals, as well as novel experimental manipulations, are beginning to erode many of these established concepts and are forcing a re-evaluation of the experimental systems and paradigms presently being used to explore these and other biological process.
Topics: Animals; Biological Evolution; Cell Differentiation; Humans; Plant Cells; Plants; Pluripotent Stem Cells; Regeneration; Stem Cells
PubMed: 24679530
DOI: 10.1016/j.cell.2014.02.041 -
The Science of the Total Environment Dec 2022Understanding the fate of plastics in the environment is of critical importance for the quantitative assessment of the biological impacts of plastic waste. Specially,... (Review)
Review
Understanding the fate of plastics in the environment is of critical importance for the quantitative assessment of the biological impacts of plastic waste. Specially, there is a need to analyze in more detail the reputed longevity of plastics in the context of plastic degradation through oxidation and fragmentation reactions. Photo-oxidation of plastic debris by solar UV radiation (UVR) makes material prone to subsequent fragmentation. The fragments generated following oxidation and subsequent exposure to mechanical stresses include secondary micro- or nanoparticles, an emerging class of pollutants. The paper discusses the UV-driven photo-oxidation process, identifying relevant knowledge gaps and uncertainties. Serious gaps in knowledge exist concerning the wavelength sensitivity and the dose-response of the photo-fragmentation process. Given the heterogeneity of natural UV irradiance varying from no exposure in sediments to full UV exposure of floating, beach litter or air-borne plastics, it is argued that the rates of UV-driven degradation/fragmentation will also vary dramatically between different locations and environmental niches. Biological phenomena such as biofouling will further modulate the exposure of plastics to UV radiation, while potentially also contributing to degradation and/or fragmentation of plastics independent of solar UVR. Reductions in solar UVR in many regions, consequent to the implementation of the Montreal Protocol and its Amendments for protecting stratospheric ozone, will have consequences for global UV-driven plastic degradation in a heterogeneous manner across different geographic and environmental zones. The interacting effects of global warming, stratospheric ozone and UV radiation are projected to increase UV irradiance at the surface in localized areas, mainly because of decreased cloud cover. Given the complexity and uncertainty of future environmental conditions, this currently precludes reliable quantitative predictions of plastic persistence on a global scale.
Topics: Stratospheric Ozone; Plastics; Ultraviolet Rays; Global Warming; Environmental Pollutants
PubMed: 35970458
DOI: 10.1016/j.scitotenv.2022.158022 -
Genetics Jul 2022Light microscopes are the cell and developmental biologists' "best friend," providing a means to see structures and follow dynamics from the protein to the organism... (Review)
Review
Light microscopes are the cell and developmental biologists' "best friend," providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of Caenorhabditis elegans as a model organism is its transparency, which coupled with its small size means that nearly every biological process can be observed and measured with the appropriate probe and light microscope. Continuous improvement in microscope technologies along with novel genome editing techniques to create transgenic probes have facilitated the development and implementation of a dizzying array of methods for imaging worm embryos, larvae, and adults. In this review, we provide an overview of the molecular and cellular processes that can be visualized in living worms using light microscopy. A partial inventory of fluorescent probes and techniques successfully used in worms to image the dynamics of cells, organelles, DNA, and protein localization and activity is followed by a practical guide to choosing between various imaging modalities, including widefield, confocal, lightsheet, and structured illumination microscopy. Finally, we discuss the available tools and approaches, including machine learning, for quantitative image analysis tasks, such as colocalization, segmentation, object tracking, and lineage tracing. Hopefully, this review will inspire worm researchers who have not yet imaged their worms to begin, and push those who are imaging to go faster, finer, and longer.
Topics: Animals; Animals, Genetically Modified; Biological Phenomena; Caenorhabditis elegans; Fluorescent Dyes; Microscopy
PubMed: 35766819
DOI: 10.1093/genetics/iyac068 -
Integrative Biology : Quantitative... Apr 2016The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the... (Review)
Review
The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.
Topics: Animals; Bacteriophages; Binding Sites; Biological Evolution; Drosophila melanogaster; Escherichia coli; Female; Genetic Drift; Green Fluorescent Proteins; Heterozygote; Humans; Lac Operon; Male; Models, Biological; Phosphorylation; Selection, Genetic; Signal Transduction; Synthetic Biology; Systems Biology
PubMed: 26952708
DOI: 10.1039/c6ib00006a