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American Journal of Physiology.... Apr 2019Homeostasis is a founding principle of integrative physiology. In current systems biology, however, homeostasis seems almost invisible. Is homeostasis a key goal driving... (Review)
Review
Homeostasis is a founding principle of integrative physiology. In current systems biology, however, homeostasis seems almost invisible. Is homeostasis a key goal driving body processes, or is it an emergent mechanistic fact? In this perspective piece, I propose that the integrative physiological and systems biological viewpoints about homeostasis reflect different epistemologies, different philosophies of knowledge. Integrative physiology is concept driven. It attempts to explain biological phenomena by continuous formation of theories that experimentation or observation can test. In integrative physiology, "function" refers to goals or purposes. Systems biology is data driven. It explains biological phenomena in terms of "omics"-i.e., genomics, gene expression, epigenomics, proteomics, and metabolomics-it depicts the data in computer models of complex cascades or networks, and it makes predictions from the models. In systems biology, "function" refers more to mechanisms than to goals. The integrative physiologist emphasizes homeostasis of internal variables such as Pco and blood pressure. The systems biologist views these emphases as teleological and unparsimonious in that the "regulated variable" (e.g., arterial Pco and blood pressure) and the "regulator" (e.g., the "carbistat" and "barostat") are unobservable constructs. The integrative physiologist views systems biological explanations as not really explanations but descriptions that cannot account for phenomena we humans believe exist, although they cannot be observed directly, such as feelings and, ultimately, the conscious mind. This essay reviews the history of the two epistemologies, emphasizing autonomic neuroscience. I predict rapprochement of integrative physiology with systems biology. The resolution will avoid teleological purposiveness, transcend pure mechanism, and incorporate adaptiveness in evolution, i.e., "Darwinian medicine."
Topics: Animals; Biological Evolution; History, 19th Century; History, 20th Century; Homeostasis; Humans; Physiological Phenomena; Physiology; Systems Biology
PubMed: 30649893
DOI: 10.1152/ajpregu.00396.2018 -
International Journal of Molecular... Oct 2022The yeast has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular... (Review)
Review
The yeast has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of and humans and discuss the challenges of using as a model system.
Topics: Biological Phenomena; Biology; Cell Cycle Checkpoints; DNA Damage; Eukaryotic Cells; Humans; Saccharomyces cerevisiae
PubMed: 36232965
DOI: 10.3390/ijms231911665 -
Philosophical Transactions. Series A,... Mar 2011The Anthropocene, an informal term used to signal the impact of collective human activity on biological, physical and chemical processes on the Earth system, is assessed... (Review)
Review
The Anthropocene, an informal term used to signal the impact of collective human activity on biological, physical and chemical processes on the Earth system, is assessed using stratigraphic criteria. It is complex in time, space and process, and may be considered in terms of the scale, relative timing, duration and novelty of its various phenomena. The lithostratigraphic signal includes both direct components, such as urban constructions and man-made deposits, and indirect ones, such as sediment flux changes. Already widespread, these are producing a significant 'event layer', locally with considerable long-term preservation potential. Chemostratigraphic signals include new organic compounds, but are likely to be dominated by the effects of CO(2) release, particularly via acidification in the marine realm, and man-made radionuclides. The sequence stratigraphic signal is negligible to date, but may become geologically significant over centennial/millennial time scales. The rapidly growing biostratigraphic signal includes geologically novel aspects (the scale of globally transferred species) and geologically will have permanent effects.
Topics: Animals; Biodiversity; Climate Change; Ecosystem; Extinction, Biological; Fossils; Geologic Sediments; Geological Phenomena; History, Ancient; Humans; Introduced Species; Time Factors
PubMed: 21282159
DOI: 10.1098/rsta.2010.0315 -
Microbiology Spectrum Sep 2018Transmission is a basic process in biology that can be analyzed in accordance with information theory. A sender or transmitter located in a particular patch of space is... (Review)
Review
Transmission is a basic process in biology that can be analyzed in accordance with information theory. A sender or transmitter located in a particular patch of space is the source of the transmitted object, the message. A receiver patch interacts to receive the message. The "messages" that are transmitted between patches (eventually located in different hierarchical biological levels) are "meaningful" biological entities (biosemiotics). -acting transmission occurs when unenclosed patches acting as emitter and receiver entities of the same hierarchical level are linked (frequently by a vehicle) across an unfit space; -acting transmission occurs between biological individuals of different hierarchical levels, embedded within a close external common limit. To understand the causal frame of transmission events, we analyze the ultimate, but most importantly also the proximate, causes of transmission. These include the repelling, centrifugal "forces" influencing the transmission (emigration) and the attractive, centripetal "energies" involved in the reception (immigration). As transmission is a key process in evolution, creating both genetic-embedded complexity-diversity (-acting transmission, as introgression), and exposure to novel and alternative patches-environments (-acting transmission, as migration), the causal frame of transmission shows the -evolutionary and -evolutionary dimensions of evolution.
Topics: Animal Migration; Bacteria; Bacterial Physiological Phenomena; Biological Evolution; Disease Transmission, Infectious; Genetic Phenomena; Humans; Selection, Genetic
PubMed: 30191806
DOI: 10.1128/microbiolspec.MTBP-0018-2016 -
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 -
Microbiology Spectrum Jul 2017Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most... (Review)
Review
Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most research on fungal dispersal focuses on only a small fraction of species. Thus, any discussion of the dispersal dynamics of fungi as a whole is problematic. While abundant morphological and biogeographic data are available for hundreds of species, researchers have yet to integrate this information into a unifying paradigm of fungal dispersal, especially in the context of long-distance dispersal (LDD). Fungal LDD is mediated by multiple vectors, including meteorological phenomena (e.g., wind and precipitation), plants (e.g., seeds and senesced leaves), animals (e.g., fur, feathers, and gut microbiomes), and in many cases humans. In addition, fungal LDD is shaped by both physical constraints on travel and the ability of spores to survive harsh environments. Finally, fungal LDD is commonly measured in different ways, including by direct capture of spores, genetic comparisons of disconnected populations, and statistical modeling and simulations of dispersal data. To unify perspectives on fungal LDD, we propose a synthetic three-part definition that includes (i) an identification of the source population and a measure of the concentration of source inoculum and (ii) a measured and/or modeled dispersal kernel. With this information, LDD is defined as (iii) the distance found within the dispersal kernel beyond which only 1% of spores travel.
Topics: Animals; Biological Evolution; Environment; Fungi; Plants; Seeds; Wind
PubMed: 28710849
DOI: 10.1128/microbiolspec.FUNK-0047-2016 -
Progress in Biophysics and Molecular... May 2016When quantum physics and biological phenomena are analogously explored, it emerges that biologic causation must also be understood independently of its overt appearance.... (Review)
Review
When quantum physics and biological phenomena are analogously explored, it emerges that biologic causation must also be understood independently of its overt appearance. This is similar to the manner in which Bohm characterized the explicate versus the implicate order as overlapping frames of ambiguity. Placed in this context, the variables affecting epigenetic inheritance can be properly assessed as a key mechanistic principle of evolution that significantly alters our understanding of homeostasis, pleiotropy, and heterochrony, and the purposes of sexual reproduction. Each of these become differing manifestations of a new biological relativity in which biologic space-time becomes its own frame. In such relativistic cellular contexts, it is proper to question exactly who has observer status, and who and what are being observed. Consideration within this frame reduces biology to cellular information sharing through cell-cell communication to resolve ambiguities at every scope and scale. In consequence, it becomes implicit that eukaryotic evolution derives from the unicellular state, remaining consistently adherent to it in a continuous evolutionary arc based upon elemental, non-stochastic physiologic first principles. Furthermore, the entire cell including its cytoskeletal apparatus and membranes that participate in the resolution of biological uncertainties must be considered as having equivalent primacy with genomes in evolutionary terms.
Topics: Animals; Evolution, Molecular; Genomics; Humans; Phenotype
PubMed: 26980522
DOI: 10.1016/j.pbiomolbio.2016.03.001 -
Military Medical Research Jun 2018With the development of radiotherapeutic oncology, computer technology and medical imaging technology, radiation therapy has made great progress. Research on the impact... (Review)
Review
With the development of radiotherapeutic oncology, computer technology and medical imaging technology, radiation therapy has made great progress. Research on the impact and the specific mechanism of radiation on tumors has become a central topic in cancer therapy. According to the traditional view, radiation can directly affect the structure of the DNA double helix, which in turn activates DNA damage sensors to induce apoptosis, necrosis, and aging or affects normal mitosis events and ultimately rewires various biological characteristics of neoplasm cells. In addition, irradiation damages subcellular structures, such as the cytoplasmic membrane, endoplasmic reticulum, ribosome, mitochondria, and lysosome of cancer cells to regulate various biological activities of tumor cells. Recent studies have shown that radiation can also change the tumor cell phenotype, immunogenicity and microenvironment, thereby globally altering the biological behavior of cancer cells. In this review, we focus on the effects of therapeutic radiation on the biological features of tumor cells to provide a theoretical basis for combinational therapy and inaugurate a new era in oncology.
Topics: Biological Phenomena; Genes, Neoplasm; Humans; Immunotherapy; Radiation, Ionizing
PubMed: 29958545
DOI: 10.1186/s40779-018-0167-4 -
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 -
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