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PLoS Computational Biology May 2017Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism...
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. Transcriptomics has been defined by repeated technological innovations that transform the field. There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA sequencing (RNA-Seq), which uses high-throughput sequencing to capture all sequences. Measuring the expression of an organism's genes in different tissues, conditions, or time points gives information on how genes are regulated and reveals details of an organism's biology. It can also help to infer the functions of previously unannotated genes. Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.
Topics: Animals; Cluster Analysis; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Humans; Image Processing, Computer-Assisted; Mice; Oligonucleotide Array Sequence Analysis; Organ Specificity; RNA; Rats; Sequence Analysis, RNA
PubMed: 28545146
DOI: 10.1371/journal.pcbi.1005457 -
Annual Review of Marine Science Jan 2022To better understand life in the sea, marine scientists must first quantify how individual organisms experience their environment, and then describe how organismal... (Review)
Review
To better understand life in the sea, marine scientists must first quantify how individual organisms experience their environment, and then describe how organismal performance depends on that experience. In this review, we first explore marine environmental variation from the perspective of pelagic organisms, the most abundant life forms in the ocean. Generation time, the ability to move relative to the surrounding water (even slowly), and the presence of environmental gradients at all spatial scales play dominant roles in determining the variation experienced by individuals, but this variation remains difficult to quantify. We then use this insight to critically examine current understanding of the environmental physiology of pelagic marine organisms. Physiologists have begun to grapple with the complexity presented by environmental variation, and promising frameworks exist for predicting and/or interpreting the consequences for physiological performance. However, new technology needs to be developed and much difficult empirical work remains, especially in quantifying response times to environmental variation and the interactions among multiple covarying factors. We call on the field of global-change biology to undertake these important challenges.
Topics: Aquatic Organisms; Oceans and Seas
PubMed: 34314598
DOI: 10.1146/annurev-marine-040221-115454 -
Wiley Interdisciplinary Reviews.... Nov 2020Multicellular organisms have evolved organs and tissues with highly specialized tasks. For instance, nutrients are assimilated by the gut, sensed, processed, stored, and... (Review)
Review
Multicellular organisms have evolved organs and tissues with highly specialized tasks. For instance, nutrients are assimilated by the gut, sensed, processed, stored, and released by adipose tissues and liver to provide energy consumed by peripheral organ activities. The function of each organ is modified by local clues and systemic signals derived from other organs to ensure a coordinated response accommodating the physiological needs of the organism. The intestine, which represents one of the largest interfaces between the internal and external environment, plays a key role in sensing and relaying environmental inputs such as nutrients and microbial derivatives to other organs to produce systemic responses. In turn, gut physiology and immunity are regulated by multiple signals emanating from other organs including the brain and the adipose tissues. In this review, we highlight physiological processes where the gut serves as a key organ in coupling systemic signals or environmental cues with organism growth, metabolism, immune activity, aging, or behavior. Robust strategies involving intraorgan and interorgan signaling pathways have evolved to preserve gut size in homeostatic conditions and restrict growth during damage-induced regenerative phases. Here we review some of the mechanisms that maintain gut size homeostasis and point out known examples of homeostasis-breaking events that promote gut plasticity to accommodate changes in the external or internal environment. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Environmental Control of Stem Cells Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration.
Topics: Adult Stem Cells; Animals; Cell Self Renewal; Drosophila melanogaster; Genetic Fitness; Homeostasis; Regeneration; Signal Transduction
PubMed: 32174007
DOI: 10.1002/wdev.378 -
The Bone & Joint Journal Nov 2022Periprosthetic joint infection (PJI) remains an extremely challenging complication. We have focused on this issue more over the last decade than previously, but there...
Periprosthetic joint infection (PJI) remains an extremely challenging complication. We have focused on this issue more over the last decade than previously, but there are still many unanswered questions. We now have a workable definition that everyone should align to, but we need to continue to focus on identifying the organisms involved. Surgical strategies are evolving and care is becoming more patient-centred. There are some good studies under way. There are, however, still numerous problems to resolve, and the challenge of PJI remains a major one for the orthopaedic community. This annotation provides some up-to-date thoughts about where we are, and the way forward. There is still scope for plenty of research in this area.Cite this article: 2022;104-B(11):1193-1195.
Topics: Humans; Prosthesis-Related Infections; Arthroplasty, Replacement, Hip; Synovial Fluid; Arthroplasty, Replacement, Knee; Biomarkers; Arthritis, Infectious; Sensitivity and Specificity
PubMed: 36317347
DOI: 10.1302/0301-620X.104B11.BJJ-2022-0944 -
Developmental Biology Jul 2019Tissue remodeling is broadly defined as the reorganization or restoration of existing tissues. Tissue remodeling processes are responsible for directing the development... (Review)
Review
Tissue remodeling is broadly defined as the reorganization or restoration of existing tissues. Tissue remodeling processes are responsible for directing the development and maintenance of tissues, organs, and overall morphology of an organism. Therefore, studying the regulatory and mechanistic aspects of tissue remodeling allows one to decipher how tissue structure and function is manipulated in animals. As such, research focused on investigating natural tissue reorganization in animal model organisms has great potential for advancing medical therapies, in conjunction with tissue engineering and regenerative medicine. Here we discuss the molecular and cellular mechanisms responsible for tissue remodeling events that occur across several animal phyla. Notably, this review emphasizes the molecular and cellular mechanisms involved in embryonic and postnatal physiological tissue remodeling events, ranging from metamorphosis to bone remodeling during functional adaptation.
Topics: Animal Structures; Animals; Biological Evolution; Extracellular Matrix; Humans; Metamorphosis, Biological; Models, Animal; Regeneration; Signal Transduction; Tissue Engineering
PubMed: 30974103
DOI: 10.1016/j.ydbio.2019.04.001 -
Frontiers in Psychology 2020Enactivism and ecological psychology converge on the relevance of the environment in understanding perception and action. On both views, perceiving organisms are not...
Enactivism and ecological psychology converge on the relevance of the environment in understanding perception and action. On both views, perceiving organisms are not merely passive receivers of environmental stimuli, but rather form a dynamic relationship with their environments in such a way that shapes how they interact with the world. In this paper, I suggest that while enactivism and ecological psychology enjoy a shared specification of the environment as the cognitive domain, on both accounts, the structure of the environment, itself, is unspecified beyond that of contingent relations with the species-typical sensorimotor capacities of perceiving organisms. This lack of specification creates a considerable gap in theory regarding the organization of organisms as coupled with their environments. I argue that this gap can be filled by drawing from resources in developmental systems theory, namely, specifying the environmental state-space as a developmental niche that shapes and is shaped by individual organisms over developmental and, on a population scale, evolutionary time. Defining the environment as an organism's developmental niche makes it clearer how and why certain contingencies have arisen, in turn, strengthening a joint appeal to both enactivism and ecological psychology as theories asserting complementarity between organisms and their environments.
PubMed: 32733307
DOI: 10.3389/fpsyg.2020.01285 -
Science China. Life Sciences Apr 2015The limited regenerative capacity of several organs, such as central nervous system (CNS), heart and limb in mammals makes related major diseases quite difficult to... (Review)
Review
The limited regenerative capacity of several organs, such as central nervous system (CNS), heart and limb in mammals makes related major diseases quite difficult to recover. Therefore, dissection of the cellular and molecular mechanisms underlying organ regeneration is of great scientific and clinical interests. Tremendous progression has already been made after extensive investigations using several model organisms for decades. Unfortunately, distance to the final achievement of the goal still remains. Recently, zebrafish became a popular model organism for the deep understanding of regeneration based on its powerful regenerative capacity, in particular the organs that are limitedly regenerated in mammals. Additionally, zebrafish are endowed with other advantages good for the study of organ regeneration. This review summarizes the recent progress in the study of zebrafish organ regeneration, in particular regeneration of fin, heart, CNS, and liver as the representatives. We also discuss reasons of the reduced regenerative capacity in higher vertebrate, the roles of inflammation during regeneration, and the difference between organogenesis and regeneration.
Topics: Animals; Models, Animal; Regeneration; Zebrafish
PubMed: 25862658
DOI: 10.1007/s11427-015-4838-z -
Annals of Human Biology 2013All living organisms are made of individual and identifiable cells, whose number, together with their size and type, ultimately defines the structure and functions of an...
BACKGROUND
All living organisms are made of individual and identifiable cells, whose number, together with their size and type, ultimately defines the structure and functions of an organism. While the total cell number of lower organisms is often known, it has not yet been defined in higher organisms. In particular, the reported total cell number of a human being ranges between 10(12) and 10(16) and it is widely mentioned without a proper reference.
AIM
To study and discuss the theoretical issue of the total number of cells that compose the standard human adult organism.
SUBJECTS AND METHODS
A systematic calculation of the total cell number of the whole human body and of the single organs was carried out using bibliographical and/or mathematical approaches.
RESULTS
A current estimation of human total cell number calculated for a variety of organs and cell types is presented. These partial data correspond to a total number of 3.72 × 10(13).
CONCLUSIONS
Knowing the total cell number of the human body as well as of individual organs is important from a cultural, biological, medical and comparative modelling point of view. The presented cell count could be a starting point for a common effort to complete the total calculation.
Topics: Adult; Cell Count; Cell Size; Humans; Models, Biological; Organ Specificity
PubMed: 23829164
DOI: 10.3109/03014460.2013.807878 -
Biomimetics (Basel, Switzerland) Dec 2022MoCLORA (Modular Climbing-and-Legged Robotic Organism Architecture) is a software framework for climbing bio-inspired robotic organisms composed of modular robots...
MoCLORA (Modular Climbing-and-Legged Robotic Organism Architecture) is a software framework for climbing bio-inspired robotic organisms composed of modular robots (legs). It is presented as a modular low-level architecture that coordinates the modules of an organism with any morphology, at the same time allowing exchanges between the physical robot and its digital twin. It includes the basic layers to control and coordinate all the elements, while allowing adding new higher-level components to improve the organism's behavior. It is focused on the control of both the body and the legs of the organism, allowing for position and velocity control of the whole robot. Similarly to insects, which are able to adapt to new situations after the variation on the capacity of any of their legs, MoCLORA allows the control of organisms composed of a variable number of modules, arranged in different ways, giving the overall system the versatility to tackle a wide range of tasks in very diverse environments. The article also presents ROMERIN, a modular climbing and legged robotic organism, and its digital twin, which allows the creation of different module arrangements for testing. MoCLORA has been tested and validated with both the physical robot and its digital twin.
PubMed: 36648797
DOI: 10.3390/biomimetics8010011 -
Biochemistry. Biokhimiia Dec 1999Programmed cell death (apoptosis) is well-established in many multicellular organisms. Apoptosis purifies a tissue from cells that became useless or even harmful for the... (Review)
Review
Programmed cell death (apoptosis) is well-established in many multicellular organisms. Apoptosis purifies a tissue from cells that became useless or even harmful for the organism. Similar phenomena are already described also at subcellular level (suicide of mitochondria, i.e., mitoptosis) as well as at supracellular level (degradation of some organs temporarily appearing in the course of ontogenesis and then disappearing by means of apoptosis of the organ-composing cells). Following the same logic, one may put a question about programmed death of an organism as a mechanism of purification of a kin, community of organisms, or population from individuals who became unwanted for this kin, etc. A putative mechanism of such kind is proposed to be coined "phenoptosis" by analogy with apoptosis and mitoptosis. In a unicellular organism (the bacterium Escherichia coli), three different biochemical mechanisms of programmed death are identified. All of them are actuated by the appearance of phages inside the bacterial cell. This may be regarded as a precedent of phenoptosis which prevents expansion of the phage infection among E. coli cells. Purification of a population from infected individuals looks like an evolutionary invention useful for a species. Such an invention has high chances to be also employed by multicellular organisms. Most probably, septic shock in animals and humans serves as an analog of the phage-induced bacterial phenoptosis. It is hypothesized that the stress-induced ischemic diseases of brain and heart as well as carcinogenesis if they are induced by repeated stresses also represent phenoptoses that, in contrast to sepsis, are age-dependent. There are interrelations of programmed death phenomena at various levels of complexity of the living systems. Thus, extensive mitoptosis in a cell leads to apoptotic death of this cell and extensive apoptosis in an organ of vital importance results in phenoptotic death of an individual. In line with this logic, some cases are already described when inhibition of apoptosis strongly improves the postischemic state of the organism.
Topics: Aging; Animals; Apoptosis; Brain Ischemia; Death; Escherichia coli; Humans; Models, Biological; Myocardial Ischemia; Neoplasms; Reactive Oxygen Species; Reperfusion Injury; Shock, Septic
PubMed: 10648966
DOI: No ID Found