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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 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 -
The American Journal of Pathology Apr 2016Advances in DNA and RNA sequencing technologies have completely transformed the field of genomics. High-throughput sequencing (HTS) is now a widely used and accessible... (Review)
Review
Advances in DNA and RNA sequencing technologies have completely transformed the field of genomics. High-throughput sequencing (HTS) is now a widely used and accessible technology that allows scientists to sequence an entire transcriptome or genome in a timely and cost-effective manner. Application of HTS techniques has led to many key discoveries, including the identification of long noncoding RNAs, microDNAs, a family of small extrachromosomal circular DNA species, and tRNA-derived fragments, which are a group of small non-miRNAs that are derived from tRNAs. Furthermore, public sequencing repositories provide unique opportunities for laboratories to parse large sequencing databases to identify proteins and noncoding RNAs at a scale that was not possible a decade ago. Herein, we review how HTS has led to the discovery of novel nucleic acid species and uncovered new biological processes during the course.
Topics: Animals; Biological Phenomena; Genomics; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA; Sequence Analysis, RNA; Transcriptome
PubMed: 26828742
DOI: 10.1016/j.ajpath.2015.10.033 -
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 -
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 -
PloS One 2022To grasp the complexity of biological processes, the biological knowledge is often translated into schematic diagrams of, for example, signalling and metabolic pathways....
To grasp the complexity of biological processes, the biological knowledge is often translated into schematic diagrams of, for example, signalling and metabolic pathways. These pathway diagrams describe relevant connections between biological entities and incorporate domain knowledge in a visual format making it easier for humans to interpret. Still, these diagrams can be represented in machine readable formats, as done in the KEGG, Reactome, and WikiPathways databases. However, while humans are good at interpreting the message of the creators of diagrams, algorithms struggle when the diversity in drawing approaches increases. WikiPathways supports multiple drawing styles which need harmonizing to offer semantically enriched access. Particularly challenging, here, are the interactions between the biological entities that underlie the biological causality. These interactions provide information about the biological process (metabolic conversion, inhibition, etc.), the direction, and the participating entities. Availability of the interactions in a semantic and harmonized format is essential for searching the full network of biological interactions. We here study how the graphically-modelled biological knowledge in diagrams can be semantified and harmonized, and exemplify how the resulting data is used to programmatically answer biological questions. We find that we can translate graphically modelled knowledge to a sufficient degree into a semantic model and discuss some of the current limitations. We then use this to show that reproducible notebooks can be used to explore up- and downstream targets of MECP2 and to analyse the sphingolipid metabolism. Our results demonstrate that most of the graphical biological knowledge from WikiPathways is modelled into the semantic layer with the semantic information intact and connectivity information preserved. Being able to evaluate how biological elements affect each other is useful and allows, for example, the identification of up or downstream targets that will have a similar effect when modified.
Topics: Algorithms; Biological Phenomena; Databases, Factual; Humans; Metabolic Networks and Pathways; Signal Transduction
PubMed: 35436299
DOI: 10.1371/journal.pone.0263057 -
Bioinformatics (Oxford, England) Nov 2017Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that...
MOTIVATION
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications.
RESULTS
For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.
AVAILABILITY AND IMPLEMENTATION
http://reactome.org.
CONTACT
[email protected] or [email protected].
Topics: Biological Phenomena; Computer Graphics; Gene Ontology; Internet; Knowledge Bases; Libraries; Signal Transduction; User-Computer Interface
PubMed: 29077811
DOI: 10.1093/bioinformatics/btx441 -
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