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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 -
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 -
Frontiers in Cell and Developmental... 2017The long-term maintenance of an organism's homeostasis and health relies on the accurate regulation of organ-organ communication. Recently, there has been growing... (Review)
Review
The long-term maintenance of an organism's homeostasis and health relies on the accurate regulation of organ-organ communication. Recently, there has been growing interest in using the gastrointestinal tract to elucidate the regulatory programs that underlie the complex interactions between organs. Data obtained in this field have dramatically improved our understanding of how organ-organ communication contributes to the regulation of various aspects of the intestine, including its metabolic and physiological status. However, although research uncovering regulatory programs associated with interorgan communication has provided key insights, the underlying mechanisms have not been extensively explored. In this review, we highlight recent findings describing gut-neighbor and neighbor-neighbor communication models in adults and larvae, respectively, with a special focus on how a range of critical strategies concerning continuous interorgan communication and adjustment can be used to manipulate different aspects of biological processes. Given the high degree of similarity between the and mammalian intestinal epithelia, it can be anticipated that further analyses of the gastrointestinal tract will facilitate the discovery of similar mechanisms underlying organ-organ communication in other mammalian organs, such as the human intestine.
PubMed: 28421183
DOI: 10.3389/fcell.2017.00029 -
Frontiers in Cell and Developmental... 2022Epithelial tissues are vital to the function of most organs, providing critical functions such as secretion, protection, and absorption. Cells within an epithelial layer... (Review)
Review
Epithelial tissues are vital to the function of most organs, providing critical functions such as secretion, protection, and absorption. Cells within an epithelial layer must coordinate to create functionally distinct apical, lateral, and basal surfaces in order to maintain proper organ function and organism viability. This is accomplished through the careful targeting of polarity factors to their respective locations within the cell, as well as the strategic placement of post-mitotic cells within the epithelium during tissue morphogenesis. The process of establishing and maintaining epithelial tissue integrity is conserved across many species, as important polarity factors and spindle orientation mechanisms can be found in many phyla. However, most of the information gathered about these processes and players has been investigated in bilaterian organisms such as , and vertebrate species. This review discusses the advances made in the field of epithelial polarity establishment from more basal organisms, and the advantages to utilizing these simpler models. An increasing number of cnidarian model organisms have been sequenced in recent years, such as and . It is now feasible to investigate how polarity is established and maintained in basal organisms to gain an understanding of the most basal requirements for epithelial tissue morphogenesis.
PubMed: 35433674
DOI: 10.3389/fcell.2022.854373 -
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 -
The Veterinary Clinics of North... Mar 2014Holistic veterinary medicine treats the whole patient including all physical and behavioral signs. The root cause of disease is treated at the same time as accompanying... (Review)
Review
Holistic veterinary medicine treats the whole patient including all physical and behavioral signs. The root cause of disease is treated at the same time as accompanying clinical signs. Herbal and nutritional supplements can help support tissue healing and proper organ functioning, thereby reducing the tendency of disease progression over time. Proper selection of homeopathic remedies is based on detailed evaluation of clinical signs. Herbal medicines are selected based on organ(s) affected and the physiologic nature of the imbalance. Many herbal and nutraceutical companies provide support for veterinarians, assisting with proper formula selection, dosing, drug interactions, and contraindications.
Topics: Animals; Axitinib; Cats; Complementary Therapies; Dogs; Imidazoles; Indazoles; Veterinary Medicine
PubMed: 24580996
DOI: 10.1016/j.cvsm.2013.11.003 -
The International Journal of... 2019Dictyostelium is a microorganism found in soils that are known as the battle fields of chemical warfare. Genome analysis of Dictyostelium revealed that it has great... (Review)
Review
Dictyostelium is a microorganism found in soils that are known as the battle fields of chemical warfare. Genome analysis of Dictyostelium revealed that it has great potential for the production of small molecules, including secondary metabolites such as polyketides and terpenes.Polyketides are a large family of secondary metabolites which have a variety of structures. In accordance with their structural variety, polyketides have a plethora of biological activities, including antimicrobial, antifungal, and antitumor activities. Unsurprisingly, they have exceptional medical importance. Polyketides in nature work as protective compounds and /or function in pheromonal communication. Terpenes belong to another family of structurally diverse secondary metabolites which play roles in ecological interactions, including defence against predators and formation of mutually beneficial alliance with other organisms. Polyketides and terpenes work as intra- or inter-species signalling compounds, i.e. they play the role of a chemical language. However, in Dictyostelium, they work as paracrine signalling compounds which control the organism's multicellular morphogenesis. This review is primarily focused on the small molecules that regulate pattern formation in the slug stage of the organism and their biosynthetic pathways. Current in vivo understandings of polyketide DIF-1 induced cell differentiation and DIF-1-dependent/independent pathways are also discussed.
Topics: Cell Differentiation; Cyclic AMP; Dictyostelium; Gene Expression Profiling; Genome; Models, Biological; Polyketide Synthases; Polyketides; STAT Transcription Factors; Signal Transduction; Terpenes; Transcription Factors
PubMed: 31840781
DOI: 10.1387/ijdb.190192ts -
International Journal of Molecular... Mar 2019Circadian timekeeping allows appropriate temporal regulation of an organism's internal metabolism to anticipate and respond to recurrent daily changes in the... (Review)
Review
Circadian timekeeping allows appropriate temporal regulation of an organism's internal metabolism to anticipate and respond to recurrent daily changes in the environment. Evidence from animal genetic models and from humans under circadian misalignment (such as shift work or jet lag) shows that disruption of circadian rhythms contributes to the development of obesity and metabolic disease. Inappropriate timing of food intake and high-fat feeding also lead to disruptions of the temporal coordination of metabolism and physiology and subsequently promote its pathogenesis. This review illustrates the impact of genetically or environmentally induced molecular clock disruption (at the level of the brain and peripheral tissues) and the interplay between the circadian system and metabolic processes. Here, we discuss some mechanisms responsible for diet-induced circadian desynchrony and consider the impact of nutritional cues in inter-organ communication, with a particular focus on the communication between peripheral organs and brain. Finally, we discuss the relay of environmental information by signal-dependent transcription factors to adjust the timing of gene oscillations. Collectively, a better knowledge of the mechanisms by which the circadian clock function can be compromised will lead to novel preventive and therapeutic strategies for obesity and other metabolic disorders arising from circadian desynchrony.
Topics: Animals; Circadian Clocks; Circadian Rhythm Signaling Peptides and Proteins; Energy Metabolism; Humans; Metabolic Diseases
PubMed: 30935034
DOI: 10.3390/ijms20071597