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ELife Mar 2015Over the last two decades, the zebrafish has joined the ranks of premier model organisms for biomedical research, with a full suite of tools and genomic resources. Yet... (Review)
Review
Over the last two decades, the zebrafish has joined the ranks of premier model organisms for biomedical research, with a full suite of tools and genomic resources. Yet we still know comparatively little about its natural history. Here I review what is known about the natural history of the zebrafish, where significant gaps in our knowledge remain, and how a fuller appreciation of this organism's ecology and behavior, population genetics, and phylogeny can inform a variety of research endeavors.
Topics: Animals; Bangladesh; Ecology; Ecosystem; Genetic Variation; Geography; India; Nepal; Phylogeny; Zebrafish
PubMed: 25807087
DOI: 10.7554/eLife.05635 -
Frontiers in Genetics 2021B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they... (Review)
Review
B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they mostly arise through rearrangements and duplications from standard chromosomes. They can occur in single or multiple copies in a cell and are usually present only in a subset of individuals in the population. Because B chromosomes frequently show unstable inheritance, their maintenance in a population is often associated with meiotic drive or other mechanisms that increase the probability of their transmission to the next generation. For all these reasons, B chromosomes have been commonly considered to be nonessential, selfish, parasitic elements. Although it was originally believed that B chromosomes had little or no effect on an organism's biology and fitness, a growing number of studies have shown that B chromosomes can play a significant role in processes such as sex determination, pathogenicity and resistance to pathogens. In some cases, B chromosomes became an essential part of the genome, turning into new sex chromosomes or germline-restricted chromosomes with important roles in the organism's fertility. Here, we review such cases of "cellular domestication" of B chromosomes and show that B chromosomes can be important genomic players with significant evolutionary impact.
PubMed: 34956308
DOI: 10.3389/fgene.2021.727570 -
Endokrynologia Polska 2020Hypoxia-inducible factors (HIFs), as a family of transcription factors involved in the cellular response to hypoxia, are key regulatory factors in the regulation... (Review)
Review
Hypoxia-inducible factors (HIFs), as a family of transcription factors involved in the cellular response to hypoxia, are key regulatory factors in the regulation mechanism of an organism's response to hypoxia. A large number of studies have shown that HIFs are closely related to the angiogenesis, erythropoiesis, cell metabolism, and autophagy of organisms, as well as the occurrence and development of tumours. Therefore, it is of great significance to further study HIFs to understand and treat tumours or other related diseases. This paper summarises the structure, oxygen-dependent degradation mechanism, non-oxygen-dependent degradation mechanism, transcriptional activation mechanism, relevant signalling pathways, and inhibitors of HIFs, in order to provide new clues for the treatment of tumour, vascular, and other related diseases.
Topics: Cell Differentiation; Cell Hypoxia; Cell Proliferation; Humans; Hypoxia; Hypoxia-Inducible Factor 1; Neovascularization, Pathologic; Signal Transduction; Transcription Factors
PubMed: 33202030
DOI: 10.5603/EP.a2020.0064 -
Psychoneuroendocrinology Dec 2022Chronic psychosocial stress increases disease risk and mortality, but the underlying mechanisms remain largely unclear. Here we outline an energy-based model for the...
Chronic psychosocial stress increases disease risk and mortality, but the underlying mechanisms remain largely unclear. Here we outline an energy-based model for the transduction of chronic stress into disease over time. The energetic model of allostatic load (EMAL) emphasizes the energetic cost of allostasis and allostatic load, where the "load" is the additional energetic burden required to support allostasis and stress-induced energy needs. Living organisms have a limited capacity to consume energy. Overconsumption of energy by allostatic brain-body processes leads to hypermetabolism, defined as excess energy expenditure above the organism's optimum. In turn, hypermetabolism accelerates physiological decline in cells, laboratory animals, and humans, and may drive biological aging. Therefore, we propose that the transition from adaptive allostasis to maladaptive allostatic states, allostatic load, and allostatic overload arises when the added energetic cost of stress competes with longevity-promoting growth, maintenance, and repair. Mechanistically, the energetic restriction of growth, maintenance and repair processes leads to the progressive wear-and-tear of molecular and organ systems. The proposed model makes testable predictions around the physiological, cellular, and sub-cellular energetic mechanisms that transduce chronic stress into disease risk and mortality. We also highlight new avenues to quantify allostatic load and its link to health across the lifespan, via the integration of systemic and cellular energy expenditure measurements together with classic allostatic load biomarkers.
PubMed: 36302295
DOI: 10.1016/j.psyneuen.2022.105951 -
Biochemistry. Biokhimiia Dec 2012Endonucleases are the main instruments of obligatory DNA degradation in apoptosis. Many endonucleases have marked processive action; initially they split DNA in... (Review)
Review
Endonucleases are the main instruments of obligatory DNA degradation in apoptosis. Many endonucleases have marked processive action; initially they split DNA in chromatin into very large domains, and then they perform in it internucleosomal fragmentation of DNA followed by its hydrolysis to small fragments (oligonucleotides). During apoptosis, DNA of chromatin is attacked by many nucleases that are different in activity, specificity, and order of action. The activity of every endonuclease is regulated in the cell through its own regulatory mechanism (metal ions and other effectors, possibly also S-adenosylmethionine). Apoptosis is impossible without endonucleases as far as it leads to accumulation of unnecessary (defective) DNA, disorders in cell differentiation, embryogenesis, the organism's development, and is accompanied by various severe diseases. The interpretation of the structure and functions of endonucleases and of the nature and action of their modulating effectors is important not only for elucidation of mechanisms of apoptosis, but also for regulation and control of programmed cell death, cell differentiation, and development of organisms.
Topics: Animals; Apoptosis; DNA; Endonucleases; Humans; Multigene Family
PubMed: 23379520
DOI: 10.1134/S0006297912130032 -
Frontiers in Neuroscience 2021In the natural environment, organisms are constantly exposed to a continuous stream of sensory input. The dynamics of sensory input changes with organism's behaviour and... (Review)
Review
In the natural environment, organisms are constantly exposed to a continuous stream of sensory input. The dynamics of sensory input changes with organism's behaviour and environmental context. The contextual variations may induce >100-fold change in the parameters of the stimulation that an animal experiences. Thus, it is vital for the organism to adapt to the new diet of stimulation. The response properties of neurons, in turn, dynamically adjust to the prevailing properties of sensory stimulation, a process known as "neuronal adaptation." Neuronal adaptation is a ubiquitous phenomenon across all sensory modalities and occurs at different stages of processing from periphery to cortex. In spite of the wealth of research on contextual modulation and neuronal adaptation in visual and auditory systems, the neuronal and computational basis of sensory adaptation in somatosensory system is less understood. Here, we summarise the recent finding and views about the neuronal adaptation in the rodent whisker-mediated tactile system and further summarise the functional effect of neuronal adaptation on the response dynamics and encoding efficiency of neurons at single cell and population levels along the whisker-mediated touch system in rodents. Based on direct and indirect pieces of evidence presented here, we suggest sensory adaptation provides context-dependent functional mechanisms for noise reduction in sensory processing, salience processing and deviant stimulus detection, shift between integration and coincidence detection, band-pass frequency filtering, adjusting neuronal receptive fields, enhancing neural coding and improving discriminability around adapting stimuli, energy conservation, and disambiguating encoding of principal features of tactile stimuli.
PubMed: 34776857
DOI: 10.3389/fnins.2021.770011 -
Cell Stress Feb 2020Cyclical renewal of integumentary organs, including hair, feathers, and teeth occurs throughout an organism's lifetime. Transition from the resting to the initiation...
Cyclical renewal of integumentary organs, including hair, feathers, and teeth occurs throughout an organism's lifetime. Transition from the resting to the initiation stage is critical for each cycle, but the mechanism remains largely unknown. Humans have two sets of dentitions-deciduous and permanent-and tooth replacement occurs only once. Prior to eruption of the permanent tooth (PT), the successional dental lamina (SDL) of the PT can be detected as early as the embryonic stage, even though it then takes about 6-12 years for the SDL to develop to late bell stage. Little is known about the mechanism by which resting SDL transitions into the initiation stage inside the mandible. As a large mammal, the miniature pig, which is also a diphyodont, was a suitable model for our recent study (EMBO J (2020)39: e102374). Using this model, we found that the SDL of PT did not begin the transition into the bud stage until the deciduous tooth (DT) began to erupt.
PubMed: 32190821
DOI: 10.15698/cst2020.03.215 -
Journal of Microbiology & Biology... Aug 2022Bacterial characterization is an important aspect of microbiology that includes experimentally determining growth rates, environmental conditions conducive to growth,...
Bacterial characterization is an important aspect of microbiology that includes experimentally determining growth rates, environmental conditions conducive to growth, and the types of energy sources microorganisms can use. Researchers use this information to help understand and predict an organism's ecological distribution and environmental functions. Microbiology students generally conduct bacterial characterization experiments in their coursework; however, they are frequently restricted to model organisms without ecological relevance and already well-studied physiologies. We present a course-based undergraduate research experience (CURE) curriculum to involve students in characterization of previously untested, ecologically relevant aquatic free-living bacteria (bacterioplankton) cultures to identify the usable nutrient substrates, as well as the temperature and salinity ranges conducive to growth. Students use these results to connect their organism's physiology to the isolation environment. This curriculum also exposes students to advanced microbiology methods such as flow cytometry for measuring cell concentrations, teaches them to use the programming language R for data plotting, and emphasizes scientific communication through writing, speaking, poster creation/presentation, and social media. This CURE is an attractive introduction to scientific research and was successfully tested with 187 students in three semesters at two different universities. Students generated reproducible growth data for multiple strains across these different deployments, demonstrating the utility of the curriculum for research support.
PubMed: 36061319
DOI: 10.1128/jmbe.00068-22 -
General and Comparative Endocrinology Mar 2018Accurate timing and physiological adaptation to anticipate seasonal changes are an essential requirement for an organism's survival. In contrast to all other... (Review)
Review
Accurate timing and physiological adaptation to anticipate seasonal changes are an essential requirement for an organism's survival. In contrast to all other environmental cues, photoperiod offers a highly predictive signal that can be reliably used to activate a seasonal adaptive programme at the correct time of year. Coupled to photoperiod sensing, it is apparent that many organisms have evolved innate long-term timekeeping systems, allowing reliable anticipation of forthcoming environmental changes. The fundamental biological processes giving rise to innate long-term timing, with which the photoperiod-sensing pathway engages, are not known for any organism. There is growing evidence that the pars tuberalis (PT) of the pituitary, which acts as a primary transducer of photoperiodic input, may be the site of the innate long-term timer or "circannual clock". Current research has led to the proposition that the PT-specific thyrotroph may act as a seasonal calendar cell, driving both hypothalamic and pituitary endocrine circuits. Based on this research we propose that the mechanistic basis for the circannual rhythm appears to be deeply conserved, driven by a binary switching cell based accumulator, analogous to that proposed for development. We review the apparent conservation of function and pathways to suggest that these broad principles may apply across the vertebrate lineage and even share characteristics with processes driving seasonal adaptation in plants.
Topics: Animals; Circadian Rhythm; Humans; Hypothalamus; Mammals; Melatonin; Photoperiod; Pituitary Gland; Seasons
PubMed: 28669798
DOI: 10.1016/j.ygcen.2017.06.029 -
American Journal of Physiology. Cell... Sep 2004In the past decade, researchers have defined committed stem or progenitor cells from various tissues, including bone marrow, peripheral blood, brain, liver, and... (Review)
Review
In the past decade, researchers have defined committed stem or progenitor cells from various tissues, including bone marrow, peripheral blood, brain, liver, and reproductive organs, in both adult animals and humans. Whereas most cells in adult organs are composed of differentiated cells, which express a variety of specific phenotypic genes adapted to each organ's environment, quiescent stem or progenitor cells are maintained locally or in the systemic circulation and are activated by environmental stimuli for physiological and pathological tissue regeneration. Recently, endothelial progenitor cells (EPCs) were isolated from peripheral blood CD34, Flk-1, or AC133 antigen-positive cells, which are considered to include a hematopoietic stem cell population, and were shown to be incorporated into foci of neovascularization. This finding, that circulating EPCs may home to sites of neovascularization and differentiate into endothelial cells in situ, is consistent with "vasculogenesis," a critical paradigm for embryonic neovascularization, and suggests that vasculogenesis and angiogenesis may constitute complementary mechanisms for postnatal neovascularization. Previous reports demonstrating therapeutic potential of EPC transplantation in animal models of hindlimb and myocardial ischemia opened the way to the clinical application of cell therapy: the replacement of diseased or degenerating cell populations, tissues, and organs. In this review, we summarize biological features of EPCs and speculate on the utility of EPCs for vascular and general medicine.
Topics: Animals; Blood Vessels; Cell Differentiation; Endothelial Cells; Hematopoietic Stem Cell Transplantation; Hematopoietic Stem Cells; Humans; Neovascularization, Physiologic; Signal Transduction
PubMed: 15308462
DOI: 10.1152/ajpcell.00330.2003