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Topic Review
Mitochondrial DNA
Increasing evidence implicates mitochondrial dysfunction in the etiology of Parkinson’s disease (PD). Mitochondrial DNA (mtDNA) mutations represent a possible cause and this mechanism might be shared with the aging process and with other age-related neurodegenerative disorders such as Alzheimer’s disease (AD). We have recently proposed a computerized method for mutated mtDNA characterization able to discriminate between AD and aging. Dealing with mtDNA mutation-based profiling of neurodegenerative disease(s), peripheral blood mtDNA sequences from late-onset PD patients and age-matched controls were analyzed and compared to the revised Cambridge Reference Sequence (rCRS). The chaos game representation (CGR) method, modified to visualize heteroplasmic mutations, was used to display fractal properties of mtDNA sequences and fractal lacunarity analysis was applied to quantitatively characterize PD based on mtDNA mutations. Parameter β, from the hyperbola model function of our lacunarity method, was statistically different between PD and control groups when comparing mtDNA sequence frames corresponding to GenBank np 5713-9713. Our original method, based on CGR and lacunarity analysis, represents a useful tool to analyze mtDNA mutations. Lacunarity parameter β is able to characterize individual mutation profile of mitochondrial genome and could represent a promising index to discriminate between PD and aging.
  • 1.7K
  • 29 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.
  • 1.6K
  • 21 Jul 2020
Topic Review
Sleeping Beauty Transposon System
Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure–function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.
  • 1.6K
  • 27 Jan 2021
Topic Review
Mobile DNA
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.
  • 1.6K
  • 27 Sep 2022
Topic Review
Beta-Catenin
Catenin beta-1, also known as β-catenin, is a protein that in humans is encoded by the CTNNB1 gene. β-catenin is a dual function protein, involved in regulation and coordination of cell–cell adhesion and gene transcription. In humans, the CTNNB1 protein is encoded by the CTNNB1 gene. In Drosophila, the homologous protein is called armadillo. β-catenin is a subunit of the cadherin protein complex and acts as an intracellular signal transducer in the Wnt signaling pathway. It is a member of the catenin protein family and homologous to γ-catenin, also known as plakoglobin. Beta-catenin is widely expressed in many tissues. In cardiac muscle, beta-catenin localizes to adherens junctions in intercalated disc structures, which are critical for electrical and mechanical coupling between adjacent cardiomyocytes. Mutations and overexpression of β-catenin are associated with many cancers, including hepatocellular carcinoma, colorectal carcinoma, lung cancer, malignant breast tumors, ovarian and endometrial cancer. Alterations in the localization and expression levels of beta-catenin have been associated with various forms of heart disease, including dilated cardiomyopathy. β-catenin is regulated and destroyed by the beta-catenin destruction complex, and in particular by the adenomatous polyposis coli (APC) protein, encoded by the tumour-suppressing APC gene. Therefore, genetic mutation of the APC gene is also strongly linked to cancers, and in particular colorectal cancer resulting from familial adenomatous polyposis (FAP).
  • 1.6K
  • 01 Dec 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,
  • 1.6K
  • 14 Dec 2020
Topic Review
Au-Kline Syndrome
Au-Kline syndrome is a condition that affects many body systems. Individuals with this condition typically have weak muscle tone (hypotonia), intellectual disability, and delayed development. Speech is delayed in children with Au-Kline syndrome, and some are able to say only one or a few words or are never able to speak. In addition, affected children learn to walk later than usual, and some are never able to walk on their own.
  • 1.6K
  • 24 Dec 2020
Topic Review
Transplacental Gene Delivery
Transplacental gene delivery (TPGD) is a technique for delivering nucleic acids to fetal tissues via tail-vein injections in pregnant mice. After transplacental transport, administered nucleic acids enter fetal circulation and are distributed among fetal tissues. In 1995, TPGD was established by Tsukamoto et al., and its mechanisms, and potential applications have been further characterized since. In 2019, Nakamura et al. demonstrated that intravenous injection of plasmid DNA containing genome editing component (CRISPR/Cas9 system) produced indels in fetal myocardial cells. In the future, this unique technique will allow manipulation of fetal cell functions in basic studies of fetal gene therapy.
  • 1.6K
  • 31 Jul 2020
Topic Review
Jacobsen Syndrome
Jacobsen syndrome is a condition caused by a loss of genetic material from chromosome 11. Because this deletion occurs at the end (terminus) of the long (q) arm of chromosome 11, Jacobsen syndrome is also known as 11q terminal deletion disorder.
  • 1.6K
  • 23 Dec 2020
Topic Review
HBB Gene
Hemoglobin subunit beta
  • 1.5K
  • 22 Dec 2020
Topic Review
16p12.2 Microdeletion
16p12.2 microdeletion is a chromosomal change in which a small amount of genetic material on chromosome 16 is deleted. The deletion occurs on the short (p) arm of the chromosome at a location designated p12.2. Common characteristics that have been described in people with a 16p12.2 microdeletion include developmental delay, delayed speech, intellectual disability that ranges from mild to profound, weak muscle tone (hypotonia), slow growth resulting in short stature, an usually small head (microcephaly), malformations of the heart, recurrent seizures (epilepsy), and psychiatric and behavioral problems.
  • 1.5K
  • 23 Dec 2020
Topic Review
Childhood Asthma
Asthma is a complex and multifactorial respiratory disease with a high prevalence in the pediatric population. Variation in treatment response to asthma therapies has been described among patients, and difficult-to-treat asthma carries both high healthcare and socioeconomic burden to the patients and society. Omic studies can be used to discover the molecular mechanisms underlying asthma susceptibility and treatment response, contributing to a better knowledge and definition of asthma pathogenesis and therefore, to the development of precision medicine. This entry aims to summarize the recent findings of omic studies of treatment response in childhood asthma. Between 2018-2019 a total of 13 omic studies has been performed involving genomics, epigenomics, transcriptomics, metabolomics, and the microbiome. These have been focused on the response to three common asthma medications: short-acting beta agonists, inhaled corticosteroids, and leukotriene receptor antagonists. Novel associations of different biomarkers with asthma treatment response have been described. However, stronger evidence and more consistent results are required to implement these molecular biomarkers into clinical practice by establishing the most appropriate therapy for each patient.
  • 1.5K
  • 29 Oct 2020
Topic Review
Aneuploidy
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.
  • 1.5K
  • 09 Nov 2022
Topic Review
Genetic Aspects of Seed Longevity
Seed longevity is the most important trait related to the management of gene banks because it governs the regeneration cycle of seeds. Thus, seed longevity is a quantitative trait. Prior to the discovery of molecular markers, classical genetic studies have been performed to identify the genetic determinants of this trait. Post-2000 saw the use of DNA-based molecular markers and modern biotechnological tools, including RNA sequence (RNA-seq) analysis, to understand the genetic factors determining seed longevity.
  • 1.5K
  • 06 May 2022
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.
  • 1.5K
  • 24 Dec 2020
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.
  • 1.5K
  • 22 Nov 2022
Topic Review
Genomic Aberrations
Multiple Myeloma is a genetically heterogeneous disease, arising and progressing through the appearance and accumulation of a tangle of genomic aberrations. In the last decade, cheap and wide applicable sequencing technologies allowed significant advantages in its biological knowledge. Here author focus on genomic events that drive plasma cell disorders. 
  • 1.5K
  • 21 Dec 2020
Topic Review
Prion
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.
  • 1.5K
  • 14 Nov 2022
Topic Review
Chromosome 19
Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 19, one copy inherited from each parent, form one of the pairs.
  • 1.4K
  • 24 Dec 2020
Topic Review
Chromosomal instability in Fanconi anemia
Fanconi anemia (FA), a chromosomal instability syndrome, is caused by inherited pathogenic variants in any of 22 FANC genes, which cooperate in the FA/BRCA pathway. This pathway regulates the repair of DNA interstrand crosslinks (ICLs) through homologous recombination. In FA proper repair of ICLs is impaired and accumulation of toxic DNA double strand breaks occurs. To repair this type of DNA damage, FA cells activate alternative error-prone DNA repair pathways, which may lead to the formation of gross structural chromosome aberrations of which radial figures are the hallmark of FA, and their segregation during cell division are the origin of subsequent aberrations such as translocations, dicentrics and acentric fragments. The deficiency in DNA repair has pleiotropic consequences in the phenotype of patients with FA, including developmental alterations, bone marrow failure and an extreme risk to develop cancer.
  • 1.4K
  • 15 Jan 2021
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