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Scientific Reports Apr 2021Continuous monitoring of large specimens for long durations requires fast volume imaging. This is essential for understanding the processes occurring during the...
Continuous monitoring of large specimens for long durations requires fast volume imaging. This is essential for understanding the processes occurring during the developmental stages of multicellular organisms. One of the key obstacles of fluorescence based prolonged monitoring and data collection is photobleaching. To capture the biological processes and simultaneously overcome the effect of bleaching, we developed single- and multi-color lightsheet based OVSS imaging technique that enables rapid screening of multiple tissues in an organism. Our approach based on OVSS imaging employs quantized step rotation of the specimen to record 2D angular data that reduces data acquisition time when compared to the existing light sheet imaging system (SPIM). A co-planar multicolor light sheet PSF is introduced to illuminate the tissues labelled with spectrally-separated fluorescent probes. The detection is carried out using a dual-channel sub-system that can simultaneously record spectrally separate volume stacks of the target organ. Arduino-based control systems were employed to automatize and control the volume data acquisition process. To illustrate the advantages of our approach, we have noninvasively imaged the Drosophila larvae and Zebrafish embryo. Dynamic studies of multiple organs (muscle and yolk-sac) in Zebrafish for a prolonged duration (5 days) were carried out to understand muscle structuring (Dystrophin, microfibers), primitive Macrophages (in yolk-sac) and inter-dependent lipid and protein-based metabolism. The volume-based study, intensity line-plots and inter-dependence ratio analysis allowed us to understand the transition from lipid-based metabolism to protein-based metabolism during early development (Pharyngula period with a critical transition time, [Formula: see text] h post-fertilization) in Zebrafish. The advantage of multicolor lightsheet illumination, fast volume scanning, simultaneous visualization of multiple organs and an order-less photobleaching makes OVSS imaging the system of choice for rapid monitoring and real-time assessment of macroscopic biological organisms with microscopic resolution.
Topics: Animals; Drosophila; Embryo, Nonmammalian; Fluorescence; Image Processing, Computer-Assisted; Larva; Microscopy, Fluorescence; Optical Devices; Optical Imaging; Photobleaching; Zebrafish
PubMed: 33828140
DOI: 10.1038/s41598-021-86951-3 -
Interdisciplinary Topics in Gerontology 2015Aging is a consequence of an organism's evolution, where specific traits that lead to the organism's development eventually promote aged phenotypes or could lead to... (Review)
Review
Aging is a consequence of an organism's evolution, where specific traits that lead to the organism's development eventually promote aged phenotypes or could lead to age-related diseases. In this sense, one theory that broadly explored development and its association to aging is the developmental aging theory (DevAge), which also encompasses most known age-associated theories. Thus, we employed different systems biology tools to prospect developmental and aging-associated networks for human and murine models for evolutionary comparison. The gathered data suggest a model where proteins related to inflammation, development, epigenetic mechanisms and oxygen homeostasis coordinate the interplay between development and aging. Moreover, the mechanism also appears to be evolutionary conserved in both mammalian models, further corroborating the DevAge molecular model.
Topics: Aging; Animals; Biological Evolution; Epigenesis, Genetic; Humans; Models, Biological; Systems Biology
PubMed: 25341514
DOI: 10.1159/000364932 -
Experimental Physiology Feb 2013Skeletal muscle has been identified as an endocrine organ owing to its capacity to produce and secrete a variety of cytokines (myokines) and other proteins. To date,... (Review)
Review
Skeletal muscle has been identified as an endocrine organ owing to its capacity to produce and secrete a variety of cytokines (myokines) and other proteins. To date, myokines have primarily been studied in response to exercise or metabolic challenges; however, numerous observations suggest that skeletal muscle may also release myokines in response to certain categories of internal or external stress exposure. Internal stress signals include oxidative or nitrosative stress, damaged or unfolded proteins, hyperthermia or energy imbalance. External stress signals, which act as indicators of organismal stress or injury in other cells, employ mediators such as catecholamines, endotoxin, alarmins, ATP and pro-inflammatory cytokines, such as tumour necrosis factor-α and interleukin-1β. External stress signals generally induce cellular responses through membrane receptor systems. In this review, we focus on the regulation of interleukin-6 (IL-6) as a prototypical stress response myokine and highlight evidence that IL-6 gene regulation in muscle is inherently organized to respond to a wide variety of internal and external stressors. Given that IL-6 can initiate protective, anti-inflammatory or restorative processes throughout the organism during life-threatening conditions, we present the argument that skeletal muscle has a physiological function as a sensor and responder to stress. Furthermore, we hypothesize that it may comprise a fundamental component of the organism's acute stress response.
Topics: Animals; Endocrine System; Gene Expression Regulation; Homeostasis; Humans; Interleukin-6; Muscle, Skeletal; Signal Transduction; Stress, Physiological
PubMed: 22941979
DOI: 10.1113/expphysiol.2012.068189 -
Journal of Biological Rhythms Aug 2001Photoperiodism is a process whereby organisms are able to use both absolute measures of day length and the direction of day length change as a basis for regulating... (Review)
Review
Photoperiodism is a process whereby organisms are able to use both absolute measures of day length and the direction of day length change as a basis for regulating seasonal changes in physiology and behavior. The use of day length cues allows organisms to essentially track time-of-year and to "anticipate" relatively predictable annual variations in important environmental parameters. Thus, adaptive types of seasonal biological changes can be molded through evolution to fit annual environmental cycles. Studies of the formal properties of photoperiodic mechanisms have revealed that most organisms use circadian oscillators to measure day length. Two types of paradigms, designated as the external and internal coincidence models, have been proposed to account for photoperiodic time measurement by a circadian mechanism. Both models postulate that the timing of light exposure, rather than the total amount of light, is critical to the organism's perception of day length. In mammals, a circadian oscillator(s) in the suprachiasmatic nucleus of the hypothalamus receives photic stimuli via the retinohypothalamic tract. The circadian system regulates the rhythmic secretion of the pineal hormone, melatonin. Melatonin is secreted at night, and the duration of secretion varies in inverse relation to day length; thus, photoperiod information is "encoded" in the melatonin signal. The melatonin signal is presumably "decoded" in melatonin target tissues that are involved in the regulation of a variety of seasonal responses. Variations in photoperiodic response are seen not only between species but also between breeding populations within a species and between individuals within single breeding populations. Sometimes these variations appear to be the result of differences in responsiveness to melatonin; in other cases, variations in photoperiod responsiveness may depend on differences in patterns of melatonin secretion related to circadian variation. Sites of action for melatonin in mammals are not yet well characterized, but potential targets of particular interest include the pars tuberalis of the pituitary gland and the suprachiasmatic nuclei. Both these sites exhibit uptake of radiolabeled melatonin in various species, and there is some evidence for direct action of melatonin at these sites. However, it appears that there are species differences with respect to the importance and specific functions of various melatonin target sites.
Topics: Animals; Chronobiology Phenomena; Humans; Mammals; Melatonin; Neurosecretory Systems; Photoperiod; Pineal Gland; Seasons
PubMed: 11506375
DOI: 10.1177/074873001129001980 -
Il Giornale Di Chirurgia 2008Traumatic shock is a complex phenomenon that represents the culminating element of a series of events. It is, in fact, the outcome of an imbalance-decompensation of the... (Review)
Review
Traumatic shock is a complex phenomenon that represents the culminating element of a series of events. It is, in fact, the outcome of an imbalance-decompensation of the organism's defence mechanisms, in which the oxygen supply to the mitochondria is hampered by a macro and/or microcirculation failure. Basically, it is a form of hypovolemic shock in which further factors have a role, including the activation of inflammation mediators. It should also be stressed that part of the cellular damage is caused by tissue reperfusion. Good hemodynamic compensation is maintained with loss of up to 30% of the circulation mass but, beyond this amount, a fall of the cardiac index, peripheral pO2, and an increase of blood lactates will ensue. Hypoxia causes capillary injury and increased permeability, resulting in the formation of edema and finally in loss of the self-regulating power of the microcirculation. Moreover, it strongly stimulates pro-inflammatory activation of the macrophages and the release of vasoactive substances, such as prostaglandins and thromboxanes. The inflammatory response is triggered by cascade systems (such as the complement, coagulation, kinins, fibrinolysis), cell elements (endothelium, leukocytes, macrophages, monocytes, mast cells) and the release of mediators (cytokines, proteolytic enzymes, histamine, etc.) and others interacting factors. In severe trauma, the inflammatory process extends beyond the local limits, maintaining and aggravating the state of shock and causing a Systemic Inflammatory Response Syndrome (SIRS), with involvement and injury of healthy organs and tissues even at a distance from the site of trauma, raising a risk of onset of ARDS (Acute Respiratory Distress Syndrome), sepsis, MODS (Multiple Organ Dysfunction Syndrome). Tissue reperfusion (reoxygenation) also induces the production of toxic metabolites, such as hydroxylated anions, superoxide, hydrogen peroxide: peroxidation of the phospholipid cell membranes alters the barrier functions, permitting entry of substances such as calcium, which interfere with the intracellular enzymatic systems.
Topics: Capillary Permeability; Humans; Hypovolemia; Inflammation Mediators; Multiple Organ Failure; Prostaglandins; Respiratory Distress Syndrome; Shock, Septic; Shock, Traumatic; Systemic Inflammatory Response Syndrome; Thromboxanes
PubMed: 18252151
DOI: No ID Found -
The phenoptosis problem: what is causing the death of an organism? Lessons from acute kidney injury.Biochemistry. Biokhimiia Jul 2012Programmed execution of various cells and intracellular structures is hypothesized to be not the only example of elimination of biological systems - the general... (Review)
Review
Programmed execution of various cells and intracellular structures is hypothesized to be not the only example of elimination of biological systems - the general mechanism can also involve programmed execution of organs and organisms. Modern rating of programmed cell death mechanisms includes 13 mechanistic types. As for some types, the mechanism of actuation and manifestation of cell execution has been basically elucidated, while the causes and intermediate steps of the process of fatal failure of organs and organisms remain unknown. The analysis of deaths resulting from a sudden heart arrest or multiple organ failure and other acute and chronic pathologies leads to the conclusion of a special role of mitochondria and oxidative stress activating the immune system. Possible mechanisms of mitochondria-mediated induction of the signaling cascades involved in organ failure and death of the organism are discussed. These mechanisms include generation of reactive oxygen species and damage-associated molecular patterns in mitochondria. Some examples of renal failure-induced deaths are presented with mechanisms and settings determined by some hypothetical super system rather than by the kidneys themselves. This system plays the key role in the process of physiological senescence and termination of an organism. The facts presented suggest that it is the immune system involved in mitochondrial signaling that can act as the system responsible for the organism's death.
Topics: Acute Kidney Injury; Aging; Animals; Cell Death; Humans; Mitochondria; Reactive Oxygen Species; Signal Transduction
PubMed: 22817538
DOI: 10.1134/S0006297912070073 -
Cold Spring Harbor Symposia on... 1993DNA methylation is ancestrally a mechanism for neutralizing potentially damaging DNA elements in the genome. The genomes of most multicellular organisms contain a small... (Review)
Review
DNA methylation is ancestrally a mechanism for neutralizing potentially damaging DNA elements in the genome. The genomes of most multicellular organisms contain a small fraction of methylated DNA that contains the methylated elements, whereas the organism's own genes remain free of methylation. Vertebrates are exceptional among animals in that their genomes, including genes, are predominantly methylated. They retain the ability to inactivate viral DNA but have recruited the DNA methylation system for new functions. Widespread low-density methylation can contribute to lowering of the level of transcriptional "noise" from cryptic or inappropriate promoters. This may be the major advantage of DNA methylation in these organisms and may be sufficiently beneficial to offset the disadvantage of m5C mutability. The other novel feature of DNA methylation in vertebrates is the capacity to de novo methylate certain CpG islands, causing long-term strong repression. These evolutionary innovations may explain the high complexity of vertebrate organs and cell types.
Topics: 5-Methylcytosine; Animals; Binding Sites; Biological Evolution; Cytosine; DNA; Genes, Regulator; Genome; Methylation; Transcription, Genetic; Vertebrates
PubMed: 7956040
DOI: 10.1101/sqb.1993.058.01.033 -
ELife Apr 2021The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive...
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon re-infections. However, differentiation of memory cells is still one of the least understood cell fate decisions. Here, we introduce a mathematical framework to characterize optimal strategies to store memory to maximize the utility of immune response over an organism's lifetime. We show that memory production should be actively regulated to balance between affinity and cross-reactivity of immune receptors for an effective protection against evolving pathogens. Moreover, we predict that specificity of memory should depend on the organism's lifespan, and shorter lived organisms with fewer pathogenic encounters should store more cross-reactive memory. Our framework provides a baseline to gauge the efficacy of immune memory in light of an organism's coevolutionary history with pathogens.
Topics: Adaptive Immunity; Animals; Biological Evolution; Humans; Immunologic Memory; Models, Theoretical
PubMed: 33908347
DOI: 10.7554/eLife.61346 -
Current Opinion in Biotechnology Aug 2013Whether organisms evolve to perform tasks optimally has intrigued biologists since Lamarck and Darwin. Optimality models have been used to study diverse properties such... (Review)
Review
Whether organisms evolve to perform tasks optimally has intrigued biologists since Lamarck and Darwin. Optimality models have been used to study diverse properties such as shape, locomotion, and behavior. However, without access to the genetic underpinnings or the ability to manipulate biological functions, it has been difficult to understand an organism's intrinsic potential and limitations. Now, novel experiments are overcoming these technical obstacles and have begun to test optimality in more quantitative terms. With the use of simple model systems, genetic engineering, and mathematical modeling, one can independently quantify the prevailing selective pressures and optimal phenotypes. These studies have given an exciting view into the evolutionary potential and constraints of biological systems, and hold the promise to further test the limits of predicting future evolutionary change.
Topics: Biological Evolution; Escherichia coli; Models, Genetic; Phenotype; Selection, Genetic; Synthetic Biology
PubMed: 23684729
DOI: 10.1016/j.copbio.2013.04.008 -
Learning & Behavior Jun 2017The animal kingdom contains species with a wide variety of sensory systems that have been selected to function in different environmental niches, but that are also... (Review)
Review
The animal kingdom contains species with a wide variety of sensory systems that have been selected to function in different environmental niches, but that are also subject to modification by experience during an organism's lifetime. The modification of such systems by experience is often called perceptual learning. In rodents, the classic example of perceptual learning is the observation that simple preexposure to two visual stimuli facilitates a subsequent (reinforced) discrimination between them. However, until recently very little behavioral research had investigated perceptual learning with tactile stimuli in rodents, in marked contrast to the wealth of information about plasticity in the rodent somatosensory system. Here we present a selective review of behavioral analyses of perceptual learning with tactile stimuli, alongside evidence concerning the potential bases of such effects within the somatosensory system.
Topics: Animals; Learning; Perception
PubMed: 28432592
DOI: 10.3758/s13420-017-0269-y