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HSV epigenetics is the epigenetic modification of herpes simplex virus (HSV) genetic code.
As of 2012, an estimated 3. 7 billion people globally were infected with oral herpes simplex virus (HSV-1), and 417 million were living with genital herpes (HSV-2) worldwide (World Health Organization, 2018)
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Epigenetics of human development is the study of how epigenetics (hertiable characteristics that do no involve changes in DNA sequence) effects human development.
Development before birth, including gametogenesis, embryogenesis, and fetal development, is the process of body development from the gametes are formed to eventually combine into a zygote to when the fully developed organism exits the uterus. Epigenetic processes are vital to fetal development due to the need to differentiate from a single cell to a variety of cell types that are arranged in such a way to produce cohesive tissues, organs, and systems
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Human epigenome is the complete set of structural modifications of chromatin and chemical modifications of histones and nucleotides (such as cytosine methylation). These modifications affect according to cellular type and development status. Various studies show that epigenome depends on exogenous factors
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Induced stem cells (iSC) are stem cells derived from somatic, reproductive, pluripotent or other cell types by deliberate epigenetic reprogramming. They are classified as either totipotent (iTC), pluripotent (iPSC) or progenitor (multipotent – iMSC, also called an induced multipotent progenitor cell – iMPC) or unipotent – (iUSC) according to their developmental potential and degree of dedifferentiation. Progenitors are obtained by so-called direct reprogramming or directed differentiation and are also called induced somatic stem cells
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The International Human Epigenome Consortium (IHEC) is a scientific organization, founded in 2010, that helps to coordinate global efforts in the field of Epigenomics. The initial goal was to generate at least 1,000 reference (baseline) human epigenomes from different types of normal and disease-related human cell types.
Structure and funding
IHEC's operations are funded by its full members (national and regional scientific funding agencies), and staffed largely on a volunteer basis by scientists and other experts from participating funding agencies and epigenome mapping projects
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A locus control region (LCR) is a long-range cis-regulatory element that enhances expression of linked genes at distal chromatin sites. It functions in a copy number-dependent manner and is tissue-specific, as seen in the selective expression of β-globin genes in erythroid cells. Expression levels of genes can be modified by the LCR and gene-proximal elements, such as promoters, enhancers, and silencers
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Metabolic imprinting refers to the long-term physiological and metabolic effects that an offspring's prenatal and postnatal environments have on them. Perinatal nutrition has been identified as a significant factor in determining an offspring's likelihood of it being predisposed to developing cardiovascular disease, obesity, and type 2 diabetes amongst other conditions. During pregnancy, maternal glucose can cross the blood-placental barrier meaning maternal hyperglycaemia is associated with foetal hyperglycaemia
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Methylated DNA immunoprecipitation (MeDIP or mDIP) is a large-scale (chromosome- or genome-wide) purification technique in molecular biology that is used to enrich for methylated DNA sequences. It consists of isolating methylated DNA fragments via an antibody raised against 5-methylcytosine (5mC). This technique was first described by Weber M
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In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and the biological sciences
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The missing heritability problem is the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes. This is a problem that has significant implications for medicine, since a person's susceptibility to disease may depend more on the combined effect of all the genes in the background than on the disease genes in the foreground, or the role of genes may have been severely overestimated.
The missing heritability problem was named as such in 2008 (after the "missing baryon problem" in physics)
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NAIL-MS (short for nucleic acid isotope labeling coupled mass spectrometry) is a technique based on mass spectrometry used for the investigation of nucleic acids and its modifications. It enables a variety of experiment designs to study the underlying mechanism of RNA biology in vivo. For example, the dynamic behaviour of nucleic acids in living cells, especially of RNA modifications, can be followed in more detail
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The Epigenomics database at the National Center for Biotechnology Information was a database for whole-genome epigenetics data sets. It was retired on 1 June 2016.
The Epigenomics database
The Epigenomics database of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH) was launched in June 2010 as a means to collect maps of epigenetic modifications and their occurrence across the human genome
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The neurobiological effects of physical exercise are numerous and involve a wide range of interrelated effects on brain structure, brain function, and cognition. A large body of research in humans has demonstrated that consistent aerobic exercise (e. g
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Neuroepigenetics is the study of how epigenetic changes to genes affect the nervous system. These changes may effect underlying conditions such as addiction, cognition, and neurological development.
Mechanisms
Neuroepigenetic mechanisms regulate gene expression in the neuron
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In chromatin, those proteins which remain after the histones have been removed, are classified as non-histone proteins. The non-histone proteins, are a large group of heterogeneous proteins that play a role in organization and compaction of the chromosome into higher order structures. They play vital roles in regulating processes like nucleosome remodeling, DNA replication, RNA synthesis and processing, nuclear transport, steroid hormone action and interphase/mitosis transition
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A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin
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The nucleosome repeat length, (NRL) is the average distance between the centers of neighboring nucleosomes. NRL is an important physical chromatin property that determines its biological function. NRL can be determined genome-wide for the chromatin in a given cell type and state, or locally for a large enough genomic region containing several nucleosomes
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Nutriepigenomics is the study of food nutrients and their effects on human health through epigenetic modifications. There is now considerable evidence that nutritional imbalances during gestation and lactation are linked to non-communicable diseases, such as obesity, cardiovascular disease, diabetes, hypertension, and cancer. If metabolic disturbances occur during critical time windows of development, the resulting epigenetic alterations can lead to permanent changes in tissue and organ structure or function and predispose individuals to disease
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In epigenetics, a paramutation is an interaction between two alleles at a single locus, whereby one allele induces a heritable change in the other allele. The change may be in the pattern of DNA methylation or histone modifications. The allele inducing the change is said to be paramutagenic, while the allele that has been epigenetically altered is termed paramutable
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Pharmacoepigenetics is an emerging field that studies the underlying epigenetic marking patterns that lead to variation in an individual's response to medical treatment.
Background
Due to genetic heterogeneity, environmental factors, and pathophysiological causes, individuals that exhibit similar disease expression may respond differently to identical drug treatments. Selecting treatments based on factors such as age, body-surface area, weight, gender, or disease stage has been shown to incompletely address this problem, so medical professionals are shifting toward using patient genomic data to select optimal treatments
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Position effect is the effect on the expression of a gene when its location in a chromosome is changed, often by translocation. This has been well described in Drosophila with respect to eye color and is known as position effect variegation (PEV). The phenotype is well characterised by unstable expression of a gene that results in the red eye coloration
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In epigenetics, proline isomerization is the effect that cis-trans isomerization of the amino acid proline has on the regulation of gene expression. Similar to aspartic acid, the amino acid proline has the rare property of being able to occupy both cis and trans isomers of its prolyl peptide bonds with ease. Peptidyl-prolyl isomerase, or PPIase, is an enzyme very commonly associated with proline isomerization due to their ability to catalyze the isomerization of prolines
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Protein methylation is a type of post-translational modification featuring the addition of methyl groups to proteins. It can occur on the nitrogen-containing side-chains of arginine and lysine, but also at the amino- and carboxy-termini of a number of different proteins. In biology, methyltransferases catalyze the methylation process, activated primarily by S-adenosylmethionine
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Generally, in progression to cancer, hundreds of genes are silenced or activated. Although silencing of some genes in cancers occurs by mutation, a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see DNA methylation in cancer). DNA methylation causing silencing in cancer typically occurs at multiple CpG sites in the CpG islands that are present in the promoters of protein coding genes
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In biology, reprogramming refers to erasure and remodeling of epigenetic marks, such as DNA methylation, during mammalian development or in cell culture. Such control is also often associated with alternative covalent modifications of histones.
Reprogrammings that are both large scale (10% to 100% of epigenetic marks) and rapid (hours to a few days) occur at three life stages of mammals
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The epigenetics of schizophrenia is the study of how inherited epigenetic changes are regulated and modified by the environment and external factors and how these changes influence the onset and development of, and vulnerability to, schizophrenia. Epigenetics concerns the heritability of those changes, too. Schizophrenia is a debilitating and often misunderstood disorder that affects up to 1% of the world's population
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A sex-determination system is a biological system that determines the development of sexual characteristics in an organism. Most organisms that create their offspring using sexual reproduction have two common sexes and a few less common intersex variations.
In some species there are hermaphrodites
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Sexual differentiation in humans is the process of development of sex differences in humans. It is defined as the development of phenotypic structures consequent to the action of hormones produced following gonadal determination. Sexual differentiation includes development of different genitalia and the internal genital tracts and body hair plays a role in sex identification
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Single cell epigenomics is the study of epigenomics (the complete set of epigenetic modifications on the genetic material of a cell) in individual cells by single cell sequencing. Since 2013, methods have been created including whole-genome single-cell bisulfite sequencing to measure DNA methylation, whole-genome ChIP-sequencing to measure histone modifications, whole-genome ATAC-seq to measure chromatin accessibility and chromosome conformation capture.
Single-cell DNA methylome sequencing
Single cell DNA genome sequencing quantifies DNA methylation
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Silent Information Regulator (SIR) proteins are involved in regulating gene expression. SIR proteins organize heterochromatin near telomeres, ribosomal DNA (rDNA), and at silent loci including hidden mating type loci in yeast. The SIR family of genes encodes catalytic and non-catalytic proteins that are involved in de-acetylation of histone tails and the subsequent condensation of chromatin around a SIR protein scaffold
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Skewed X-chromosome inactivation (skewed X-inactivation) occurs when the X-inactivation of one X chromosome is favored over the other, leading to an uneven number of cells with each chromosome inactivated. It is usually defined as one allele being found on the active X chromosome in over 75% of cells, and extreme skewing is when over 90% of cells have inactivated the same X chromosome. It can be caused by primary nonrandom inactivation, either by chance due to a small cell pool or directed by genes, or by secondary nonrandom inactivation, which occurs by selection
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Sleep epigenetics is the field of how epigenetics (heritable characteristics that do not involve changes in DNA sequence) affects sleep.
Research in the field of epigenetics has time and time again proven the significance of various environmental experiences. Changes in sleep can cause critical changes to the epigenome, while changes to the epigenome can, in turn, have a crucial influence on experiences related to sleep
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Epigenetic effects of smoking concerns how epigenetics (hertiable characteristics that do not involve changes in DNA sequence) contributes to the deleterious effects of smoking. Cigarette smoking has been found to affect global epigenetic regulation of transcription across tissue types. Studies have shown differences in epigenetic markers like DNA methylation, histone modifications and miRNA expression between smokers and non-smokers
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A somatic epitype is a non-heritable epigenetic alteration in a gene. It is similar to conventional epigenetics in that it does not involve changes in the DNA primary sequence. Physically, the somatic epitype corresponds to changes in DNA methylation, oxidative damage (replacement of GTP with oxo-8-dGTP), or changes in DNA-chromatin structure that are not reversed by normal cellular or nuclear repair mechanisms
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Structural inheritance or cortical inheritance is the transmission of an epigenetic trait in a living organism by a self-perpetuating spatial structures. This is in contrast to the transmission of digital information such as is found in DNA sequences, which accounts for the vast majority of known genetic variation.
Examples of structural inheritance include the propagation of prions, the infectious proteins of diseases such as scrapie (in sheep and goats), bovine spongiform encephalopathy ('mad cow disease') and Creutzfeldt–Jakob disease (although the protein-only hypothesis of prion transmission has been considered contentious until recently)
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Sex-determining region Y protein (SRY), or testis-determining factor (TDF), is a DNA-binding protein (also known as gene-regulatory protein/transcription factor) encoded by the SRY gene that is responsible for the initiation of male sex determination in therian mammals (placental mammals and marsupials). SRY is an intronless sex-determining gene on the Y chromosome. Mutations in this gene lead to a range of disorders of sex development with varying effects on an individual's phenotype and genotype
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The TET enzymes are a family of ten-eleven translocation (TET) methylcytosine dioxygenases. They are instrumental in DNA demethylation. 5-Methylcytosine (see first Figure) is a methylated form of the DNA base cytosine (C) that often regulates gene transcription and has several other functions in the genome
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Transgenerational epigenetic inheritance is the transmission of epigenetic markers and modifications from one generation to multiple subsequent generations without altering the primary structure of DNA. Thus, the regulation of genes via epigenetic mechanisms can be heritable; the amount of transcripts and proteins produced can be altered by inherited epigenetic changes. In order for epigenetic marks to be heritable, however, they must occur in the gametes in animals, but since plants lack a definitive germline and can propagate, epigenetic marks in any tissue can be heritable
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Transgenerational epigenetic inheritance in plants involves mechanisms for the passing of epigenetic marks from parent to offspring that differ from those reported in animals. There are several kinds of epigenetic markers, but they all provide a mechanism to facilitate greater phenotypic plasticity by influencing the expression of genes without altering the DNA code. These modifications represent responses to environmental input and are reversible changes to gene expression patterns that can be passed down through generations
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Epigenetics of anxiety and stress–related disorders is the field studying the relationship between epigenetic modifications of genes and anxiety and stress-related disorders, including mental health disorders such as generalized anxiety disorder (GAD), post-traumatic stress disorder, obsessive-compulsive disorder (OCD), and more. These change can lead to transgenerational stress inheritance. Epigenetic modifications play a role in the development and heritability of these disorders and related symptoms
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Transvection is an epigenetic phenomenon that results from an interaction between an allele on one chromosome and the corresponding allele on the homologous chromosome. Transvection can lead to either gene activation or repression. It can also occur between nonallelic regions of the genome as well as regions of the genome that are not transcribed
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X chromosome reactivation (XCR) is the process by which the inactive X chromosome (the Xi) is re-activated in the cells of eutherian female mammals. Therian female mammalian cells have two X chromosomes, while males have only one, requiring X-chromosome inactivation (XCI) for sex-chromosome dosage compensation. In eutherians, XCI is the random inactivation of one of the X chromosomes, silencing its expression
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X-inactivation (also called Lyonization, after English geneticist Mary Lyon) is a process by which one of the copies of the X chromosome is inactivated in therian female mammals. The inactive X chromosome is silenced by being packaged into a transcriptionally inactive structure called heterochromatin. As nearly all female mammals have two X chromosomes, X-inactivation prevents them from having twice as many X chromosome gene products as males, who only possess a single copy of the X chromosome (see dosage compensation)
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C7 protein is an engineered zinc finger protein based on the murine ZFP, Zif268 and discovered by Wu et al. in 1994 (published in 1995). It shares the same zinc finger 2 and zinc finger 3 of Zif268, but differs in the sequence of finger 1
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Cell ablation (from Latin Cellula "small chamber" and Ablatio "removal"). Also known as tissue ablation, cell ablation is a biotechnological tool for studying cell lineage. The process consists of selectively destroying or removing cells in an organism
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Chimeric nucleases are an example of engineered proteins which must comprise a DNA-binding domain to give sequence specificity and a nuclease domain for DNA cleavage.
DNA-binding domains
DNA-binding domains including the basic helix-loop-helix, zinc finger, helix-turn-helix and leucine zipper motifs have been used in construction of sequence-specific nucleases. Of these, zinc fingers have been suggested the most important due to their modularity, allowing construction of a tailor-made DNA-binding domain
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A memetic algorithm (MA) in computer science and operations research, is an extension of the traditional genetic algorithm (GA) or more general evolutionary algorithm (EA). It may provide a sufficiently good solution to an optimization problem. It uses a suitable heuristic or local search technique to improve the quality of solutions generated by the EA and to reduce the likelihood of premature convergence
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In evolutionary computation, Minimum Population Search (MPS) is a computational method that optimizes a problem by iteratively trying to improve a set of candidate solutions with regard to a given measure of quality. It solves a problem by evolving a small population of candidate solutions by means of relatively simple arithmetical operations.
MPS is a metaheuristic as it makes few or no assumptions about the problem being optimized and can search very large spaces of candidate solutions
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The MOEA Framework is an open-source evolutionary computation library for Java that specializes in multi-objective optimization. It supports a variety of multiobjective evolutionary algorithms (MOEAs), including genetic algorithms, genetic programming, grammatical evolution, differential evolution, and particle swarm optimization. As a result, it has been used to conduct numerous comparative studies to assess the efficiency, reliability, and controllability of state-of-the-art MOEAs
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Multi Expression Programming (MEP) is an evolutionary algorithm for generating mathematical functions describing a given set of data. MEP is a Genetic Programming variant encoding multiple solutions in the same chromosome. MEP representation is not specific (multiple representations have been tested)
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Mutation is a genetic operator used to maintain genetic diversity of the chromosomes of a population of a genetic or, more generally, an evolutionary algorithm (EA). It is analogous to biological mutation.
The classic example of a mutation operator of a binary coded genetic algorithm (GA) involves a probability that an arbitrary bit in a genetic sequence will be flipped from its original state
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Natural evolution strategies (NES) are a family of numerical optimization algorithms for black box problems. Similar in spirit to evolution strategies, they iteratively update the (continuous) parameters of a search distribution by following the natural gradient towards higher expected fitness.
Method
The general procedure is as follows: the parameterized search distribution is used to produce a batch of search points, and the fitness function is evaluated at each such point
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Neuroevolution, or neuro-evolution, is a form of artificial intelligence that uses evolutionary algorithms to generate artificial neural networks (ANN), parameters, and rules. It is most commonly applied in artificial life, general game playing and evolutionary robotics. The main benefit is that neuroevolution can be applied more widely than supervised learning algorithms, which require a syllabus of correct input-output pairs
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NeuroEvolution of Augmenting Topologies (NEAT) is a genetic algorithm (GA) for the generation of evolving artificial neural networks (a neuroevolution technique) developed by Kenneth Stanley and Risto Miikkulainen in 2002 while at The University of Texas at Austin. It alters both the weighting parameters and structures of networks, attempting to find a balance between the fitness of evolved solutions and their diversity. It is based on applying three key techniques: tracking genes with history markers to allow crossover among topologies, applying speciation (the evolution of species) to preserve innovations, and developing topologies incrementally from simple initial structures ("complexifying")
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In computational science, particle swarm optimization (PSO) is a computational method that optimizes a problem by iteratively trying to improve a candidate solution with regard to a given measure of quality. It solves a problem by having a population of candidate solutions, here dubbed particles, and moving these particles around in the search-space according to simple mathematical formula over the particle's position and velocity. Each particle's movement is influenced by its local best known position, but is also guided toward the best known positions in the search-space, which are updated as better positions are found by other particles
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The population model of an evolutionary algorithm (EA) describes the structural properties of its population to which its members are subject. A population is the set of all proposed solutions of an EA considered in one iteration, which are also called individuals according to the biological role model. The individuals of a population can generate further individuals as offspring with the help of the genetic operators of the procedure
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In evolutionary algorithms (EA), the term of premature convergence means that a population for an optimization problem converged too early, resulting in being suboptimal. In this context, the parental solutions, through the aid of genetic operators, are not able to generate offspring that are superior to, or outperform, their parents. Premature convergence is a common problem found in evolutionary algorithms in general and genetic algorithms in particular, as it leads to a loss, or convergence of, a large number of alleles, subsequently making it very difficult to search for a specific gene in which the alleles were present
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The promoter based genetic algorithm (PBGA) is a genetic algorithm for neuroevolution developed by F. Bellas and R. J
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Reward-based selection is a technique used in evolutionary algorithms for selecting potentially useful solutions for recombination.
The probability of being selected for an individual is proportional to the cumulative reward obtained by the individual. The cumulative reward can be computed as a sum of the individual reward and the reward, inherited from parents
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Selection is the stage of a genetic algorithm or more general evolutionary algorithm in which individual genomes are chosen from a population for later breeding (e. g. , using the crossover operator)
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In mathematics, the spiral optimization (SPO) algorithm is a metaheuristic inspired by spiral phenomena in nature.
The first SPO algorithm was proposed for two-dimensional unconstrained optimization
based on two-dimensional spiral models. This was extended to n-dimensional problems by generalizing the two-dimensional spiral model to an n-dimensional spiral model
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Algae (UK: , US: ; SG: alga ) is an informal term for a large and diverse group of photosynthetic, eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga which may grow up to 50 metres (160 ft) in length
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Achnanthaceae is a family of algae belonging to the order Achnanthales. Genera:
Achnanthes Bory, 1822
Amphicocconeis M. De Stephano & D
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An algae scrubber is a water filtering device (not to be confused with a scrubber pad used to clean glass) which uses light to grow algae; in this process, undesirable chemicals are removed from the water. Algae scrubbers allow saltwater, freshwater and pond hobbyists to operate their tanks using natural filtration in the form of primary production, much like oceans and lakes.
Concepts
An algae scrubber filters water by moving water rapidly over a rough, highly illuminated surface, which causes algae to start growing in large amounts
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AlgaeBase is a global species database of information on all groups of algae, both marine and freshwater, as well as sea-grass.
History
AlgaeBase began in March 1996, founded by Michael Guiry. By 2005, the database contained about 65,000 names
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An algal bloom or algae bloom is a rapid increase or accumulation in the population of algae in freshwater or marine water systems. It is often recognized by the discoloration in the water from the algae's pigments. The term algae encompasses many types of aquatic photosynthetic organisms, both macroscopic multicellular organisms like seaweed and microscopic unicellular organisms like cyanobacteria
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Algal mats are one of many types of microbial mat that forms on the surface of water or rocks. They are typically composed of blue-green cyanobacteria and sediments. Formation occurs when alternating layers of blue-green bacteria and sediments are deposited or grow in place, creating dark-laminated layers
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Algal viruses are the viruses infecting photosynthetic single-celled eukaryotes, algae. As of 2020, there were 61 viruses known to infect algae. Algae are integral components of aquatic food webs and drive nutrient cycling, so the viruses infecting algal populations also impacts the organisms and nutrient cycling systems that depend on them
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Biliproteins are pigment protein compounds that are located in photosynthesising organisms such as algae and certain insects. They refer to any protein that contains a bilin chromophore. In plants and algae, the main function of biliproteins is to make the process of light accumulation required for photosynthesis more efficient; while in insects they play a role in growth and development
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Ice algae are any of the various types of algal communities found in annual and multi-year sea, and terrestrial lake ice or glacier ice.
On sea ice in the polar oceans, ice algae communities play an important role in primary production. The timing of blooms of the algae is especially important for supporting higher trophic levels at times of the year when light is low and ice cover still exists
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Marine primary production is the chemical synthesis in the ocean of organic compounds from atmospheric or dissolved carbon dioxide. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through chemosynthesis, which uses the oxidation or reduction of inorganic chemical compounds as its source of energy. Almost all life on Earth relies directly or indirectly on primary production
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Microcystin-LR (MC-LR) is a toxin produced by cyanobacteria. It is the most toxic of the microcystins.
Structure
Microcystins are cyclic heptapeptides
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Photosynthetic picoplankton or picophytoplankton is the fraction of the phytoplankton performing photosynthesis composed of cells between 0. 2 and 2 µm in size (picoplankton). It is especially important in the central oligotrophic regions of the world oceans that have very low concentration of nutrients
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Phycotechnology refers to the technological applications of algae, both microalgae and macroalgae.
Uses
Sewage reclamation
Currently micro-algae are being exploited for environmental protection as the species of Chlorella, Chlamydomonas, and Scenedesmus carry out selective uptake, accumulation and biodegradation of pollutants and thus help in remediation. They are used in biological reclamation of sewage since they can immobilize heavy metals from aquatic systems
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Pyrenoids are sub-cellular micro-compartments found in chloroplasts of many algae, and in a single group of land plants, the hornworts. Pyrenoids are associated with the operation of a carbon-concentrating mechanism (CCM). Their main function is to act as centres of carbon dioxide (CO2) fixation, by generating and maintaining a CO2 rich environment around the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)
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https://huggingface.co/datasets/fmars/wiki_stem
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Shelf-Break Fronts are a process by which stratification of the water column occurs. This stratification normally results in thermoclines, since they occur where a sudden change in water depth causes a constriction of the current flow. They can be expressed as a ratio of their potential energy due to maintaining mixed (non-stratified) conditions, to the dissipated energy produced by the current being forced across the sudden change in depth
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https://huggingface.co/datasets/fmars/wiki_stem
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Snow algae are a group of freshwater micro-algae which grow in the alpine and polar regions of the earth. These algae have been observed to come in a variety of colors associated with both the individual species, stage of life or topography/geography. A typical snow algae in the alps and polar regions is Chlamydomonas nivalis
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https://huggingface.co/datasets/fmars/wiki_stem
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Bryophytes () are a group of land plants, sometimes treated as a taxonomic division, that contains three groups of non-vascular land plants (embryophytes): the liverworts, hornworts and mosses. In the strict sense, Bryophyta consists of the mosses only. Bryophytes are characteristically limited in size and prefer moist habitats although they can survive in drier environments
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https://huggingface.co/datasets/fmars/wiki_stem
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Fern allies are a diverse group of seedless vascular plants that are not true ferns. Like ferns, a fern ally disperses by shedding spores to initiate an alternation of generations.
Classification
Originally, three or four groups of plants were considered to be fern allies
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https://huggingface.co/datasets/fmars/wiki_stem
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A fungus (PL: fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from the other eukaryotic kingdoms, which, by one traditional classification, includes Plantae, Animalia, Protozoa, and Chromista.
A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls
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https://huggingface.co/datasets/fmars/wiki_stem
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A lichen ( LY-kən, UK also LITCH-ən) is a composite organism that arises from algae or cyanobacteria living among filaments of multiple fungi species in a mutualistic relationship. Lichens are important actors in nutrient cycling and act as producers which many higher trophic feeders feed on, such as reindeer, gastropods, nematodes, mites, and springtails. Lichens have properties different from those of their component organisms
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https://huggingface.co/datasets/fmars/wiki_stem
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The lycophytes, when broadly circumscribed, are a group of vascular plants that include the clubmosses. They are sometimes placed in a division Lycopodiophyta or Lycophyta or in a subdivision Lycopodiophytina. They are one of the oldest lineages of extant (living) vascular plants; the group contains extinct plants that have been dated from the Silurian (ca
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https://huggingface.co/datasets/fmars/wiki_stem
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A pteridophyte is a vascular plant (with xylem and phloem) that disperses spores. Because pteridophytes produce neither flowers nor seeds, they are sometimes referred to as "cryptogams", meaning that their means of reproduction is hidden.
Ferns, horsetails (often treated as ferns), and lycophytes (clubmosses, spikemosses, and quillworts) are all pteridophytes
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https://huggingface.co/datasets/fmars/wiki_stem
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Thallophytes (Thallophyta, Thallophyto or Thallobionta) are a polyphyletic group of non-motile organisms traditionally described as "thalloid plants", "relatively simple plants" or "lower plants". They form a division of kingdom Plantae that include lichens and algae and occasionally bryophytes, bacteria and slime moulds. Thallophytes have a hidden reproductive system and hence they are also incorporated into the similar Cryptogamae category (together with ferns), as opposed to Phanerogamae
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https://huggingface.co/datasets/fmars/wiki_stem
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Hemimastigophora is a group of single-celled eukaryotic organisms including the Spironemidae, first identified in 1988. Over the next 30 years, different authors proposed placing these organisms in various branches of the eukaryotes. In 2018 Lax et al
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https://huggingface.co/datasets/fmars/wiki_stem
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Spironemidae is a family of heterotrophic flagellates, in the group Hemimastigophora. They vary in size and shape from the ellipsoid Hemimastix amphikineta (14 × 7 μm) to the vermiform Spironema terricola (43 × 3 μm), and are united by the possession of two rows of cilia, called kineties. Phylogenomic analysis shows that Hemimastigophora are a distinct and ancient lineage of eukaryotic organisms, forming a possible sister clade to the supergroup Diaphoretickes
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https://huggingface.co/datasets/fmars/wiki_stem
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Picoeukaryotes are picoplanktonic eukaryotic organisms 3. 0 µm or less in size. They are distributed throughout the world's marine and freshwater ecosystems and constitute a significant contribution to autotrophic communities
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https://huggingface.co/datasets/fmars/wiki_stem
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Raphidiophrys drakena is a species of protist in the genus of Raphidiophrys. It is a unicellular eukaryote with a cell diameter of 26. 7±0
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https://huggingface.co/datasets/fmars/wiki_stem
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Choreocolax polysiphoniae is a minute marine parasitic alga in the division Rhodophyta.
Description
This small parasitic alga grows on the red alga Polysiphonia lanosa. It grows as an irregular sphere on the fronds of the alga, reaching no more than 1 mm in extent
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https://huggingface.co/datasets/fmars/wiki_stem
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Miamiensis avidus is a species of unicellular marine eukaryote that is a parasite of many different types of fish. It is one of several organisms known to cause the fish disease scuticociliatosis and is considered an economically significant pathogen of farmed fish. M
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https://huggingface.co/datasets/fmars/wiki_stem
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Orchitophrya stellarum is a species of single-celled marine ciliates, a member of the class Oligohymenophorea. It is found living freely in the north Atlantic and Pacific Oceans but is also parasitic, being found inside the gonads of starfish.
Biology
Orchitophrya stellarum tolerates a sea temperature range of between 3 °C (37 °F) and 27 °C (81 °F) and a salinity range of between 2 and at least 30 parts per thousand of salt equivalent
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https://huggingface.co/datasets/fmars/wiki_stem
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A supergroup, in evolutionary biology, is a large group of organisms that share one common ancestor and have important defining characteristics. It is an informal, mostly arbitrary rank in biological taxonomy that is often greater than phylum or kingdom, although some supergroups are also treated as phyla.
Eukaryotic supergroups
Since the decade of 2000's, the eukaryotic tree of life (abbreviated as eToL) has been divided into 5–8 major groupings called 'supergroups'
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https://huggingface.co/datasets/fmars/wiki_stem
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Ancyromonas is a genus of basal Eukaryote consisting of heterotrophic flagellates. It includes the species Ancyromonas sigmoides, first described by Saville Kent in 1880. The genus was rediscovered in modern times by Hänel in 1979
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https://huggingface.co/datasets/fmars/wiki_stem
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In Biology, Archezoa is a term that has been introduced by several authors to refer to a group of organisms (a taxon). Authors include Josef Anton Maximilian Perty, Ernst Haeckel and in the 20th century by Thomas Cavalier-Smith (1942–2021) in his classification system. Each author used the name to refer to different arrays of organisms
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https://huggingface.co/datasets/fmars/wiki_stem
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Collodictyonidae (also Diphylleidae) is a group of aquatic, unicellular eukaryotic organisms with two to four terminal flagella. They feed by phagocytosis, ingesting other unicellular organisms like algae and bacteria. The most remarkable fact of this clade is its uncertain position in the tree of life
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https://huggingface.co/datasets/fmars/wiki_stem
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Eolouka is a paraphyletic phylum of protists localized in the clade Discoba. It contains two lineages: Jakobea and Tsukubea, the last containing only one genus, Tsukubamonas.
History of classification
In 1999 Cavalier-Smith proposed a new paraphyletic phylum of flagellates called Loukozoa, containing only the jakobids
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https://huggingface.co/datasets/fmars/wiki_stem
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Fuxianospira gyrata is a Cambrian macroalgae found in the Chengjiang lagerstatte. Preserved in clustered, helicoid groups, the filaments are threadlike, plain and without branches. Brown and smooth in appearance, these structural characteristics display a resemblance to modern brown algae
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https://huggingface.co/datasets/fmars/wiki_stem
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Heliozoa, commonly known as sun-animalcules, are microbial eukaryotes (protists) with stiff arms (axopodia) radiating from their spherical bodies, which are responsible for their common name. The axopodia are microtubule-supported projections from the amoeboid cell body, and are variously used for capturing food, sensation, movement, and attachment. They are similar to Radiolaria, but they are distinguished from them by lacking central capsules and other complex skeletal elements, although some produce simple scales and spines
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https://huggingface.co/datasets/fmars/wiki_stem
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Hyalochlorella marina, the only species in the genus Hyalochlorella and also known as Dermocystidium sp. , is a marine heterotrophic eukaryote with uncertain phylogenic position.
Phylogeny
Hyalochlorella marina was first classified as a fungus under the name Dermocystidium sp
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https://huggingface.co/datasets/fmars/wiki_stem
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Infusoria are minute freshwater life forms including ciliates, euglenoids, protozoa, unicellular algae and small invertebrates. Some authors (e. g
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https://huggingface.co/datasets/fmars/wiki_stem
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