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Topic Review

Most genes contain the information needed to make functional molecules called proteins. Proteins do most of the work in cells and are required for the structure, function, and regulation of the body's tissues and organs.

2.8K
24 Dec 2020

Topic Review

TNF is a gene that plays an essential role in the body, it affects both immune response and inflammation. The gene encodes a protein called tumour necrosis factor alpha (TNFα) [1].

2.8K
05 Nov 2020

Topic Review

Prions are misfolded proteins that have the ability to transmit their misfolded shape onto normal variants of the same protein. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals. It is not known what causes a normal protein to misfold, but the resulting abnormal three-dimensional structure confers infectious properties by collapsing nearby protein molecules into the same shape. The word prion is derived from the term, "proteinaceous infectious particle". In comparison to all other known infectious agents such as viroids, viruses, bacteria, fungi, and parasites, all of which contain nucleic acids (DNA, RNA, or both), the hypothesized role of a protein as an infectious agent stands in contrast. Prion isoforms of the prion protein (PrP), whose specific function is uncertain, are hypothesized as the cause of transmissible spongiform encephalopathies (TSEs), including scrapie in sheep, chronic wasting disease (CWD) in deer, bovine spongiform encephalopathy (BSE) in cattle (commonly known as "mad cow disease") and Creutzfeldt–Jakob disease (CJD) in humans. All known prion diseases in mammals affect the structure of the brain or other neural tissue; all are progressive, have no known effective treatment, and are always fatal. Until 2015, all known mammalian prion diseases were caused by the prion protein (PrP); however, in 2015 it was hypothesized that multiple system atrophy (MSA) was caused by a prion form of alpha-synuclein. Prions are a type of intrinsically disordered protein, which change their conformation unless they are bound to a specific partner such as another protein. With a prion, two protein chains are stabilized if one binds to another in the same conformation. The probability of this happening is low, but once it does the combination of the two is very stable. Then more units can get added, making a sort of "fibril". Prions form abnormal aggregates of proteins called amyloids, which accumulate in infected tissue and are associated with tissue damage and cell death. Amyloids are also responsible for several other neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. A prion disease is a type of proteopathy, or disease of structurally abnormal proteins. In humans, prions are believed to be the cause of Creutzfeldt–Jakob disease (CJD), its variant (vCJD), Gerstmann–Sträussler–Scheinker syndrome (GSS), fatal familial insomnia (FFI), and kuru. There is also evidence suggesting prions may play a part in the process of Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS); these have been termed prion-like diseases. Several yeast proteins have also been identified as having prionogenic properties, as well as a protein involved in modification of synapses during the formation of memories (see Eric Kandel § Molecular changes during learning). Prion replication is subject to epimutation and natural selection just as for other forms of replication, and their structure varies slightly between species. Prion aggregates are stable, and this structural stability means that prions are resistant to denaturation by chemical and physical agents: they cannot be destroyed by ordinary disinfection or cooking. This makes disposal and containment of these particles difficult.

2.8K
14 Nov 2022

Topic Review

Human Satellite DNA Families

Going back to the 1960s, the discovery and classification of three clearly distinguishable human genomic DNA fractions in CsSO4 gradients established the identity of the corresponding classical satellite DNAs I, II, and III. More precisely, a set of repetitive sequences with analogous buoyant densities was found to compose each gradient fraction. These DNA fractions presented a characteristic inter-sequence heterogeneity, which led to a new classification in 1987, as a prime family of simple repeats was identified for each fraction. The three families were described as satellite DNA families I, II, and III and were first reported to be present in all acrocentric chromosomes, as well as in chromosomes 3 and 4. Additionally, the centromeric alpha (α) satellite DNA family was also identified and described, soon becoming the most intensively studied human satDNA sequence. Later on, gamma (γ) and beta (β) satellites were likewise found among the diverse families of human satellite DNAs.

2.6K
13 May 2021

Topic Review

Testis-Determining Factor

An Error has occurred retrieving Wikidata item for infobox Testis-determining factor (TDF), also known as sex-determining region Y (SRY) protein, 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 (DSD) with varying effects on an individual's phenotype and genotype. TDF is a member of the SOX (SRY-like box) gene family of DNA-binding proteins. When complexed with the SF1 protein, TDF acts as a transcription factor that causes upregulation of other transcription factors, most importantly SOX9. Its expression causes the development of primary sex cords, which later develop into seminiferous tubules. These cords form in the central part of the yet-undifferentiated gonad, turning it into a testis. The now-induced Leydig cells of the testis then start secreting testosterone, while the Sertoli cells produce anti-Müllerian hormone. SRY gene effects normally take place 6–8 weeks after fetus formation which inhibits the female anatomical structural growth in males. It also works towards developing the dominant male characteristics.

2.6K
25 Oct 2022

Topic Review

The growth arrest and DNA damage-inducible 45 alpha (GADD45A) gene encodes a 165 aa protein localized in the nucleus, whose level is highest in the G1 phase of the cell cycle, with a substantial reduction in S. The involvement of GADD45A in the cell cycle regulation and interaction with other proteins underline its function in the cellular DNA damage response and maintaining genomic stability, which, in turn, determines its high potential in cancer transformation. The protective role of GADD45A in DNA damage-induced tumorigenesis is the main biological function of this protein, but exact mechanism of it is not known. Emerging evidence suggests that GADD45A may be important in breast cancer and several molecular pathways were reported to underline this importance, including Ras, mitogen-activated protein kinase 8 (MAPK8), JNK (c-Jun N-terminal kinase) and p38. GADD45A may play a tumor-suppressor role by induction of senescence and apoptosis in cancer cells. However, it was also shown that GADD45A may promote tumorigenesis via the GSK3 β (glycogen synthase kinase 3 beta)/β-catenin signaling. Therefore, GADD45A may function as either a tumor promotor or suppressor, depending on the kind of oncogenic stress, and these two functions are mediated by different signaling pathways.

2.5K
01 Nov 2020

Topic Review

Genetics and Human Traits

Each person's fingerprints are unique, which is why they have long been used as a way to identify individuals. Surprisingly little is known about the factors that influence a person's fingerprint patterns. Like many other complex traits, studies suggest that both genetic and environmental factors play a role.

2.5K
24 Dec 2020

Topic Review

Hemoglobin subunit beta

2.5K
22 Dec 2020

Topic Review

European Nucleotide Archive

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database (also known as EMBL-bank). The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank. The ENA has grown out of the EMBL Data Library which was released in 1982 as the first internationally supported resource for nucleotide sequence data. As of early 2012, the ENA and other INSDC member databases each contained complete genomes of 5,682 organisms and sequence data for almost 700,000. Moreover, the volume of data is increasing exponentially with a doubling time of approximately 10 months.

2.4K
28 Nov 2022

Topic Review

Short Interspersed Nuclear Elements (SINEs)

SINEs or Short Interspersed Nuclear Elements are sequences of non-coding DNA present at high frequencies in various eukaryotic genomes. They are a class of retrotransposons, DNA elements that amplify themselves throughout eukaryotic genomes, often through RNA intermediates. Short-interspersed nuclear elements are characterized by their size and method of retrotransposition. The literature differs on the length of the SINEs but there is a general consensus that they often range in length from about 100 to 700 base pairs (more or less, arbitrary cut-offs). Short-interspersed nuclear elements are transcribed by RNA polymerase III which is known to transcribe ribosomal RNA and tRNA, two types of RNA vital to ribosomal assembly and mRNA translation. SINEs, like tRNAs and many small-nuclear RNAs possess an internal promoter and thus are transcribed differently than most protein-coding genes. In other words, short-interspersed nuclear elements have their key promoter elements within the transcribed region itself. Though transcribed by RNA polymerase III, SINEs and other genes possessing internal promoters, recruit different transcriptional machinery and factors than genes possessing upstream promoters. The RNA coded by the short-interspersed nuclear element does not code for any protein product but is nonetheless reverse-transcribed and inserted back into an alternate region in the genome. For this reason, short interspersed nuclear elements are believed to have co-evolved with long interspersed nuclear element (LINEs), as LINEs do in fact encode protein products which enable them to be reverse- transcribed and integrated back into the genome. SINEs are believed to have co-opted the proteins coded by LINEs which are contained in 2 reading frames. Open reading frame 1 (ORF 1) encodes a protein which binds to RNA and acts as a chaperone to facilitate and maintain the LINE protein-RNA complex structure. Open reading frame 2 (ORF 2) codes a protein which possesses both endonuclease and reverse transcriptase activities. This enables the LINE mRNA to be reverse-transcribed into DNA and integrated into the genome based on the sequence-motifs recognized by the protein’s endonuclease domain. Furthermore, SINEs are known to share sequence homology with LINES which gives a basis by which the LINE machinery can reverse transcribe and integrate SINE transcripts. Alternately, some SINEs are believed to use a much more complex system of integrating back into the genome; this system involves the use random double-stranded DNA breaks (rather than the endonuclease coded by related long-interspersed nuclear elements creating an insertion-site). These DNA breaks are utilized to prime reverse transcriptase, ultimately integrating the SINE transcript back into the genome. SINEs nonetheless depend on enzymes coded by other DNA elements and are thus known as non-autonomous retrotransposons as they depend on the machinery of LINEs, which are known as autonomous retrotransposons.

2.4K
22 Nov 2022

Topic Review

Mobile DNA is DNA that able to move to new locations throughout the genome. This process of movement is often called transposion, and the mobile DNA, transposons. Some mobile DNAs move by different mechanisms to transposons, but have similarities.

2.3K
27 Sep 2022

Topic Review

Maximum Genetic Diversity

Maximum Genetic Diversity (MGD) is a scientific hypothesis relating to molecular evolution, which is the study of how and why populations of organisms experience genetic changes over time. MGD starts with the observation that some regions of the genome are more likely to preserve mutations into the next generation than others. This difference in the observed rate of mutation means some regions of the genome appear to mutate faster than others, and is theorized to relate to balancing the preservation of vital information relating to a species' function against its ability to mutate and adapt to new environmental niches. According to MGD, these regions of the genome eventually drift into two rough categories: faster-mutating sections tuned to respond quickly to environmental pressures and allow adaptive radiation, as well as slower-mutating sections involved in an organism's most fundamental instructions. Because MGD asserts that only slow-mutating genes accurately reflect shared evolutionary history, relationships between species can alternatively be calculated by their "maximum genetic diversity," which is determined by measuring the frequency of mutations in specific corresponding regions of orthologous genes instead of using raw overall genetic similarity. Using calculations based on mutations in these slow-mutating genes provides a chart of genetic ancestry that lines up with the fossil record – measurements based on raw genetic similarity yield results that clash with the fossil record. Also due to this grouping into fast and slow, MGD hypothesizes that over time complex organisms become genetically fragile and less tolerant to mutation as their MGD decreases, since an increasing proportion of their genome will have become slow-mutating over time. MGD asserts that this is because increased organismal and social complexity means more of the genome is needed to preserve the expanding instructional manual necessary for complex behavior and function, and so more of an organism's genome must become slow-mutating as the organism increases in complexity, since being slow-mutating preserves and protects those vital instructions. MGD seeks to reconcile the inconsistencies observed around the neutral theory of molecular evolution, whose "original lines of evidence... are now falsified" according to a paper published in Oxford's Molecular Biology and Evolution in 2018. One example of this is that supposedly consistent and neutral mutation rates from proteins across a wide range of species were demonstrably not neutral nor consistent. Another study published in Nature in December 2019 noted that "defining the evolutionary time scales according to the molecular clock is intrinsically biased, especially for proteins of complex organisms." Although a number of other arguments have been proposed against the neutral theory in recent years, there is not a yet a consensus that the neutral theory is entirely falsified and counter-arguments against the role of selection do exist. Furthermore, beyond the fact that MGD is still relatively unknown, it also contradicts the current paradigm in molecular evolution, since the neutral theory's fundamental premises are still nearly ubiquitously utilized in genetic analysis and admixture studies. Additionally, some of the phenomena explained by MGD could theoretically be accounted for by other processes such as gene conversion or concerted evolution. Lastly, even if the neutral theory is disproved, it does not necessarily validate MGD, as alternative theories have been proposed that also incorporate the effects of selection on the genome. And so MGD will have to be more rigorously tested against any alternative theories before becoming widely adopted. However, to date MGD has not been contradicted in peer-reviewed literature, and its assumptions and framework have been confirmed when it comes to examining the ratio of brain-specific proteins in a range of mammals, for classifying and timing the evolutionary genetic structure of a wide range of organisms ranging from yeast to primates, by evaluating the genetic fitness of yeast which become more genetically fragile as they become more fit, by a genetic model that seeks to more accurately model not only the location of mutations but the rate at which they occur, and by the observation that vital slow-mutating genes are more protected by "transcriptional scanning" in mammalian testes than fast-evolving genes involved with responding quickly to environmental challenges.

2.3K
25 Nov 2022

Topic Review

DNA Mismatch Repair Gene Variants

DNA mismatch repair system (MMR) is an integral part of DNA damage response pathway (DDR), responsible for maintenance of genomic integrity. MMR preferably corrects frameshift mutations in microsatellites and mismatched nucleotides generated during DNA replication.

2.3K
26 Oct 2020

Topic Review

Ferroptosis in Liver Diseases

Ferroptosis is an iron-dependent form of cell death characterized by intracellular lipid peroxide accumulation and redox imbalance. Ferroptosis shows specific biological and morphological features when compared to the other cell death patterns. The loss of lipid peroxide repair activity by glutathione peroxidase 4 (GPX4), the presence of redox-active iron and the oxidation of polyunsaturated fatty acid (PUFA)-containing phospholipids are considered as distinct fingerprints of ferroptosis. Several pathways, including amino acid and iron metabolism, ferritinophagy, cell adhesion, p53, Keap1/Nrf2 and phospholipid biosynthesis, can modify susceptibility to ferroptosis. Through the decades, various diseases, including acute kidney injury; cancer; ischemia-reperfusion injury; and cardiovascular, neurodegenerative and hepatic disorders, have been associated with ferroptosis. Here, we provide a short overview of the main biological and biochemical mechanisms of ferroptosis. The contribution of ferroptosis to the spectrum of liver diseases, acute or chronic is also reported. Finally, we discuss the use of ferroptosis as a therapeutic approach against hepatocellular carcinoma, the most common form of primary liver cancer.

2.3K
21 Jul 2020

Topic Review

Whole Genome Amplification in Preimplantation Genetic Testing

Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging.

2.3K
27 Jul 2022

Topic Review

Aneuploidy is the presence of an abnormal number of chromosomes in a cell, for example a human cell having 45 or 47 chromosomes instead of the usual 46. It does not include a difference of one or more complete sets of chromosomes. A cell with any number of complete chromosome sets is called a euploid cell. An extra or missing chromosome is a common cause of some genetic disorders. Some cancer cells also have abnormal numbers of chromosomes. About 68% of human solid tumors are aneuploid. Aneuploidy originates during cell division when the chromosomes do not separate properly between the two cells (nondisjunction). Most cases of aneuploidy in the autosomes result in miscarriage, and the most common extra autosomal chromosomes among live births are 21, 18 and 13. Chromosome abnormalities are detected in 1 of 160 live human births. Autosomal aneuploidy is more dangerous than sex chromosome aneuploidy, as autosomal aneuploidy is almost always lethal to embryos that cease developing because of it.

2.3K
09 Nov 2022

Topic Review

Scarr-Rowe Effect

In behavioral genetics, the Scarr-Rowe effect, also known as the Scarr-Rowe hypothesis, refers to the proposed moderating effect of low socioeconomic status on the heritability of children's IQ. According to this hypothesis, lower socioeconomic status and greater exposure to social disadvantage during childhood leads to a decrease in the heritability of IQ, as compared to children raised in more advantaged environments. It is considered an example of gene–environment interaction. This hypothesized effect was first proposed by Sandra Scarr, who found support for it in a 1971 study of twins in Philadelphia, and these results were replicated by David C. Rowe in 1999. A 2015 meta-analysis found the effect was predominant in the United States while less evident in societies with robust child welfare systems.

2.3K
10 Nov 2022

Topic Review

MED13L Syndrome

MED13L syndrome is a developmental disorder characterized by developmental delay, intellectual disability, and minor differences in facial features. Additionally, some people with this condition have recurrent seizures (epilepsy) or heart abnormalities that are present from birth (congenital heart defects).

2.3K
24 Dec 2020

Topic Review

Hybrid Rye Breeding and Production

Hybrid rye breeding leads to considerably higher grain yield and a higher revenue to the farmer. The basis of hybrid seed production is the CMS-inducing Pampa (P) cytoplasm derived from an Argentinean landrace and restorer-to-fertility (Rf) genes. Breeding is based on inbred line development and intensive testing for line per se performance and general combining ability (GCA). The finally selected inbred lines are used to compose a topcross hybrid with two genetically different seed parent lines (A-P, B-N) and a restorer synthetic composed of two S2 lines (SynRf). European restorer sources show low-to-moderate pollen-fertility levels. This results in higher susceptibility to ergot (Claviceps purpurea) because rye pollen and ergot spores are in strong competition for the unfertilized stigma. Rf genes from non-adapted Iranian primitive rye and old Argentinean cultivars proved to be most effective. The major Rf gene in these sources was localized on chromosome 4RL, which is also a hotspot of restoration in other Triticeae. Commercial hybrids with these Rf genes showed a similar low ergot infection when compared with population cultivars. The great future challenges of climate change, such as increased drought stress tolerance, improved lodging tolerance, as well as the increasing need for resistant varieties can effectively only be met by hybrid breeding.

2.3K
06 May 2022

Topic Review

Heme oxygenase-1

Heme oxygenases (E.C. 1:14:99:33) are vital metabolic enzymes that catalyze the rate-limiting step in the degradation of heme, with the generation of carbon monoxide, biliverdin, and iron. The inducible form, heme oxygenase-1 (HO-1), is a stress protein, whose expression is responsive to a broad spectrum of adverse chemical and physical stimuli. HO-1 is known to provide cytoprotection and can exert anti-inflammatory and immunomodulatory effects in tissues, via heme removal. HO-1 is a potential therapeutic target in inflammatory diseases. The end-products of HO-1 activity, including carbon monoxide, may contribute to HO-1 mediated protection. Carbon monoxide delivery by inhalation at low concentration, as well as through application of carbon monoxide releasing molecules (CORMs), has been explored for therapeutic potential. Recently completed clinical trials have evaluated the safety and feasibility of inhaled CO as a therapy for acute and chronic lung disease,

2.3K
14 Dec 2020

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