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Human Molecular Genetics Oct 2016The genetic code is degenerate. With the exception of two amino acids (Met and Trp), all other amino acid residues are each encoded by multiple, so-called synonymous... (Review)
Review
The genetic code is degenerate. With the exception of two amino acids (Met and Trp), all other amino acid residues are each encoded by multiple, so-called synonymous codons. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in genes/genomes suggested that codon choice might have functional implications beyond amino acid coding. The pattern of non-uniform codon use (known as codon usage bias) varies between organisms and represents a unique feature of an organism. Organism-specific codon choice is related to organism-specific differences in populations of cognate tRNAs. This implies that, in a given organism, frequently used codons will be translated more rapidly than infrequently used ones and vice versa A theory of codon-tRNA co-evolution (necessary to balance accurate and efficient protein production) was put forward to explain the existence of codon usage bias. This model suggests that selection favours preferred (frequent) over un-preferred (rare) codons in order to sustain efficient protein production in cells and that a given un-preferred codon will have the same effect on an organism's fitness regardless of its position within an mRNA's open reading frame. However, many recent studies refute this prediction. Un-preferred codons have been found to have important functional roles and their effects appeared to be position-dependent. Synonymous codon usage affects the efficiency/stringency of mRNA decoding, mRNA biogenesis/stability, and protein secretion and folding. This review summarizes recent developments in the field that have identified novel functions of synonymous codons and their usage.
Topics: Codon; Evolution, Molecular; Genetic Code; Open Reading Frames; Protein Biosynthesis; RNA Stability; RNA, Messenger; RNA, Transfer
PubMed: 27354349
DOI: 10.1093/hmg/ddw207 -
Annual Review of Neuroscience Jul 2020While neurons and circuits are almost unequivocally considered to be the computational units and actuators of behavior, a complete understanding of the nervous system... (Review)
Review
While neurons and circuits are almost unequivocally considered to be the computational units and actuators of behavior, a complete understanding of the nervous system must incorporate glial cells. Far beyond a copious but passive substrate, glial influence is inextricable from neuronal physiology, whether during developmental guidance and synaptic shaping or through the trophic support, neurotransmitter and ion homeostasis, cytokine signaling and immune function, and debris engulfment contributions that this class provides throughout an organism's life. With such essential functions, among a growing literature of nuanced roles, it follows that glia are consequential to behavior in adult animals, with novel genetic tools allowing for the investigation of these phenomena in living organisms. We discuss here the relevance of glia for maintaining circadian rhythms and also for serving functions of sleep.
Topics: Animals; Circadian Rhythm; Drosophila; Humans; Neuroglia; Neurons; Neurotransmitter Agents; Sleep
PubMed: 32075519
DOI: 10.1146/annurev-neuro-091819-094557 -
Dose-response : a Publication of... 2012Organisms are perpetually facing noxious insults but exhibit surprising diverse reaction patterns. Depending on the strength, frequency and quality of the stress stimuli...
Organisms are perpetually facing noxious insults but exhibit surprising diverse reaction patterns. Depending on the strength, frequency and quality of the stress stimuli biological systems may react with increased vitality, future stress resistance or with injury and degeneration. Whereas a multitude of such specific stress responses has been observed in diverse biological systems the underlying molecular mechanisms are mainly unknown. These knowledge restrictions urge the exploration of specific molecular signaling reactions controlling the ambivalent responses of cells and organisms to noxious effects. The adaptive responses of signaling networks to defined stress stimuli need to be investigated in a time-and dose-resolved manner in cellular and organismic models. Anticipated results are expected to significantly advance the understanding of the molecular signatures of stress responses and may also promote ongoing efforts for the effective use of the organism's preventive and regenerative potentials in modern medicine.
PubMed: 22423231
DOI: 10.2203/dose-response.11-012.Wetzker -
Frontiers in Microbiology 2021Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, "species" are biological units of individuation. Niches do... (Review)
Review
Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, "species" are biological units of individuation. Niches do not exist without individual organisms, and every organism has a niche. We use "niche" in the Hutchinsonian sense as an abstraction of a multidimensional environmental space characterized by a variety of conditions, both biotic and abiotic, whose quantitative ranges determine the positive or negative growth rates of the microbial individual, typically a species, but also parts of the communities of species contained in this space. Microbial organisms ("species") constantly diversify, and such diversification (radiation) depends on the possibility of opening up unexploited or insufficiently exploited niches. Niche exploitation frequently implies "niche construction," as the colonized niche evolves with time, giving rise to new potential subniches, thereby influencing the selection of a series of new variants in the progeny. The evolution of niches and organisms is the result of reciprocal interacting processes that form a single unified process. Centrifugal microbial diversification expands the limits of the species' niches while a centripetal or cohesive process occurs simultaneously, mediated by horizontal gene transfers and recombinatorial events, condensing all of the information recovered during the diversifying specialization into "novel organisms" (possible future species), thereby creating a more complex niche, where the selfishness of the new organism(s) establishes a "homeostatic power" limiting the niche's variation. Once the niche's full carrying capacity has been reached, reproductive isolation occurs, as no foreign organisms can outcompete the established population/community, thereby facilitating speciation. In the case of individualization-speciation of the microbiota, its contribution to the animal' gut structure is a type of "niche construction," the result of crosstalk between the niche (host) and microorganism(s). Lastly, there is a parallelism between the hierarchy of niches and that of microbial individuals. The increasing anthropogenic effects on the biosphere (such as globalization) might reduce the diversity of niches and bacterial individuals, with the potential emergence of highly transmissible multispecialists (which are eventually deleterious) resulting from the homogenization of the microbiosphere, a possibility that should be explored and prevented.
PubMed: 33815348
DOI: 10.3389/fmicb.2021.657986 -
Molecular Biology of the Cell May 2019Organoids derived from stem cells or tissues in culture can develop into structures that resemble the in vivo anatomy and physiology of intact organs. Human organoid...
Organoids derived from stem cells or tissues in culture can develop into structures that resemble the in vivo anatomy and physiology of intact organs. Human organoid cultures provide the potential to study human development and model disease processes with the same scrutiny and depth of analysis customary for research with nonhuman model organisms. Resembling the complexity of the actual tissue or organ, patient-derived human organoid studies may accelerate medical research, creating new opportunities for tissue engineering and regenerative medicine, generating knowledge and tools for preclinical studies, including drug development and testing. Biologists are drawn to this system as a new "model organism" to study complex disease phenotypes and genetic variability among individuals using patient-derived tissues. The American Society for Cell Biology convened a task force to report on the potential, challenges, and limitations for human organoid research. The task force suggests ways to ease the entry for new researchers into the field and how to facilitate broader use of this new model organism within the research community. This includes guidelines for reproducibility, culturing, sharing of patient materials, patient consent, training, and communication with the public.
Topics: Animals; Biomedical Research; Cell Culture Techniques; Humans; Models, Biological; Organoids; Regenerative Medicine; Reproducibility of Results; Stem Cells; Tissue Engineering
PubMed: 31034354
DOI: 10.1091/mbc.E19-03-0135 -
Frontiers in Psychology 2020The enactive and ecological approaches to embodied cognitive science are on a collision course. While both draw inspiration from similar views in psychology and... (Review)
Review
The enactive and ecological approaches to embodied cognitive science are on a collision course. While both draw inspiration from similar views in psychology and phenomenology, the two approaches initially held seemingly contradictory views and points of focus. Early enactivists saw value in the ecological approach but insisted that the two schools remain distinct. While ecological psychology challenged the common foes of mental representation and mind-body dualism, it seemingly did so at the cost of the autonomy of the agent. This is evidence that the early enactive and ecological approaches told different stories about how agents and environments interact. Whereas the enactive approach broadly focuses on agency and the organism's resilience to environmental perturbations, the ecological approach insists that organisms are best understood in terms of the organism-environment system and at the ecological scale. Historically, this tension created space for harsh criticisms from both sides and for some ecological psychologists to dismiss enactivism altogether. Despite their differences, both approaches use dynamic systems theory to explain the interactions between embodied agents and the environment or contextual milieu in which they are embedded. This has led some scholars to focus on the complementary elements of each approach and argue that the two schools are allies, thus rejecting the historical disagreements between the two approaches and calling for an ecological-enactive synthesis. The attempts to synthesize the approaches are noteworthy and should be considered steps in the right direction but are potentially problematic. If the two schools are merely synthesized to some form of ecological-enactivism, then something of value from both approaches could be lost. This is analogous to the hasty comparison between two seemingly similar schools of thought found in early attempts at East-West comparative philosophy. I argue that the relationship between the enactive and ecological approaches is both complementary and contrary and is thus best understood in terms of complementarity. Given the complexity of complementarity I will unpack the notion in steps. I will begin with the exploration of analogous concepts in Japanese Philosophy and gradually build a lens through which both agent environment and ecological enactive complementarities can be understood.
PubMed: 32903774
DOI: 10.3389/fpsyg.2020.01347 -
Journal of Clinical Ultrasound : JCU Oct 2022Cardiorenal syndrome is a clinical condition that impacts both the heart and the kidneys. One organ's chronic or acute impairment can lead to the other's chronic or... (Review)
Review
Cardiorenal syndrome is a clinical condition that impacts both the heart and the kidneys. One organ's chronic or acute impairment can lead to the other's chronic or acute dysregulation. The cardiorenal syndrome has been grouped into five subcategories that describe the etiology, pathophysiology, duration, and pattern of cardiac and renal dysfunction. This classification reflects the large spectrum of interrelated dysfunctions and underlines the bidirectional nature of heart-kidney interactions. However, more evidence is needed to apply these early findings in medical practice. Understanding the relationship between these two organs during each organ's impairment has significant clinical implications that are relevant for therapy in both chronic and acute conditions. The epidemiology, definition, classification, pathophysiology, therapy, and outcome of each form of cardiorenal syndrome are all examined in this review.
Topics: Acute Disease; Cardio-Renal Syndrome; Heart; Heart Failure; Humans; Kidney
PubMed: 36218199
DOI: 10.1002/jcu.23265 -
Frontiers in Behavioral Neuroscience 2022Benefits of physical exercise for brain functions are well documented in mammals, including humans. In this review, we will summarize recent research on the effects of... (Review)
Review
Benefits of physical exercise for brain functions are well documented in mammals, including humans. In this review, we will summarize recent research on the effects of species-specific intense locomotion on behavior and brain functions of different invertebrates. Special emphasis is made on understanding the biological significance of these effects as well as underlying cellular and molecular mechanisms. The results obtained in three distantly related clades of protostomes, Nematodes, Molluscs and Artropods, suggest that influence of intense locomotion on the brain could have deep roots in evolution and wide adaptive significance. In , improved learning, nerve regeneration, resistance to neurodegenerative processes were detected after physical activity; in -facilitation of decision making in the novel environment, in -increased endurance, improved sleep and feeding behavior, in -improved orientation in conspecific phonotaxis, enhanced aggressiveness, higher mating success, resistance to some disturbing stimuli. Many of these effects have previously been described in mammals as beneficial results of running, suggesting certain similarity between distantly-related species. Our hypothesis posits that the above modulation of cognitive functions results from changes in the organism's predictive model. Intense movement is interpreted by the organism as predictive of change, in anticipation of which adjustments need to be made. Identifying the physiological and molecular mechanisms behind these adjustments is easier in experiments in invertebrates and may lead to the discovery of novel neurobiological mechanisms for regulation and correction of cognitive and emotional status.
PubMed: 35836487
DOI: 10.3389/fnbeh.2022.928093 -
Oxidative Medicine and Cellular... 2014Liver ischemia/reperfusion injury has been extensively studied during the last decades and has been implicated in the pathophysiology of many clinical entities following... (Review)
Review
Liver ischemia/reperfusion injury has been extensively studied during the last decades and has been implicated in the pathophysiology of many clinical entities following hepatic surgery and transplantation. Apart from its pivotal role in the pathogenesis of the organ's post reperfusion injury, it has also been proposed as an underlying mechanism responsible for the dysfunction and injury of other organs as well. It seems that liver ischemia and reperfusion represent an event with "global" consequences that influence the function of many remote organs including the lung, kidney, intestine, pancreas, adrenals, and myocardium among others. The molecular and clinical manifestation of these remote organs injury may lead to the multiple organ dysfunction syndrome, frequently encountered in these patients. Remote organ injury seems to be in part the result of the oxidative burst and the inflammatory response following reperfusion. The present paper aims to review the existing literature regarding the proposed mechanisms of remote organ injury after liver ischemia and reperfusion.
Topics: Heart Injuries; Humans; Intestinal Mucosa; Intestines; Ischemia; Kidney; Liver; Lung Injury; Oxidative Stress; Pancreas; Reactive Oxygen Species; Reperfusion Injury
PubMed: 24799983
DOI: 10.1155/2014/906965