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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.
  • 1.3K
  • 25 Nov 2022
Topic Review
Mammalian Target of Rapamycin
The entry outlines the discovery of mTOR and describes mTOR complex 1 (mTORC1) and mTORC2.
  • 1.3K
  • 26 Oct 2020
Topic Review
Cat Body-type Mutation
Cats, like all living organisms, occasionally have mutations that affect their body type. Sometimes, these cat body-type mutations are striking enough that humans select for and perpetuate them. This is not always in the best interests of the cat, as many of these mutations are harmful; some are even lethal in their homozygous form. This article gives a selection of cat body type mutant alleles and the associated mutations with a brief description.
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  • 29 Sep 2022
Topic Review
Chromosome Conformation Signatures
Epigenetic mechanisms mediate the integration of genetic and environmental factors that are responsible for changes in phenotypes. The organisation of the human genome within three-dimensional space (the 3D genome) is a dynamic epigenetic regulator of phenotypic expression. Mediated through the changing spatial proximity of genomic regions relative to one another in 3D space, ‘chromosome conformations’ have emerged in the past several years as a novel class of molecular switches that regulate cellular and physiological processes. Technological advances in the detection of chromosome conformations have spawned a new class of biomarker - the chromosome conformation signature (CCS) - that identifies chromosomal interactions across multiple genomic loci as a collective marker of distinct epigenomic states. The use of CCSs in basic and clinical research has shown recent applications in identifying disease states, subtyping disease states, and prospectively stratifying individuals according to their likely response to medical intervention.
  • 1.3K
  • 19 Aug 2020
Topic Review
TRNA Modifications in Microorganisms
Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. Modifications to tRNA are installed as post-transcriptional events at multiple locations on the tRNA structure by specialized tRNA-modifying enzymes and can occur at the 2’OH group of the ribose moiety as well as various positions of all A, C, G, and U bases. These modifications are diverse in their chemical structures and functional properties, and respond to nutritional and environmental factors.
  • 1.3K
  • 18 Aug 2020
Topic Review
L1 Syndrome
L1 syndrome describes a group of conditions that primarily affect the nervous system and occur almost exclusively in males. These conditions vary in severity and include, from most severe to least, X-linked hydrocephalus with stenosis of the aqueduct of Sylvius (HSAS), MASA syndrome, spastic paraplegia type 1, and X-linked complicated corpus callosum agenesis.
  • 1.3K
  • 23 Dec 2020
Topic Review
Transposable Elements
Transposable elements (TEs) are mobile DNA sequences that can jump from one genomic locus to another and that have colonized the genomes of all living organisms. While TE mobilization is an important source of genomic innovations that greatly contribute to the host species evolution, it is also a major threat to genome integrity that can lead to pathologies.
  • 1.2K
  • 26 May 2022
Topic Review
CRISPR-Cas9 in Fruit and Vegetable
Fruit and vegetable crops are rich in dietary fibre, vitamins and minerals, which are vital to human health. However, many biotic stressors (such as pests and diseases) and abiotic stressors threaten crop growth, quality, and yield. Traditional breeding strategies for improving crop traits include a series of backcrosses and selection to introduce beneficial traits into fine germplasm, this process is slow and resource-intensive. The new breeding technique known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9) has the potential to improve many traits rapidly and accurately, such as yield, quality, disease resistance, abiotic stress tolerance, and nutritional aspects in crops. Because of its simple operation and high mutation efficiency, this system has been applied to obtain new germplasm resources via gene-directed mutation.
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  • 04 Aug 2021
Topic Review
Pre-mRNA Splicing
Pre-mRNA splicing is an essential process for gene expression in higher eukaryotes, which requires a high order of accuracy. Mutations in splicing factors or regulatory elements in pre-mRNAs often result in many human diseases. Myelodysplastic syndrome (MDS) is a heterogeneous group of chronic myeloid neoplasms characterized by many symptoms and a high risk of progression to acute myeloid leukemia. Recent findings indicate that mutations in splicing factors represent a novel class of driver mutations in human cancers and affect about 50% of Myelodysplastic syndrome (MDS) patients. Somatic mutations in MDS patients are frequently found in genes SF3B1, SRSF2, U2AF1, and ZRSR2. Interestingly, they are involved in the recognition of 3′ splice sites and exons. It has been reported that mutations in these splicing regulators result in aberrant splicing of many genes.
  • 1.2K
  • 12 Aug 2021
Topic Review
47,XYY Syndrome
47,XYY syndrome is characterized by an extra copy of the Y chromosome in each of a male's cells. Although many males with this condition are taller than average, the chromosomal change sometimes causes no unusual physical features. Most males with 47,XYY syndrome have normal production of the male sex hormone testosterone and normal sexual development, and they are usually able to father children.  
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  • 23 Dec 2020
Topic Review
IBMPFD
Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia (IBMPFD) is a condition that can affect the muscles, bones, and brain.
  • 1.2K
  • 04 Jan 2021
Topic Review
KIT Gene
KIT proto-oncogene receptor tyrosine kinase
  • 1.2K
  • 23 Dec 2020
Topic Review
Hypermethioninemia
Hypermethioninemia is an excess of a particular protein building block (amino acid), called methionine, in the blood. This condition can occur when methionine is not broken down (metabolized) properly in the body.
  • 1.2K
  • 23 Dec 2020
Topic Review
Wilson’s Disease
Wilson disease (WD) is a rare disorder caused by mutations in ATP7B, which leads to a defective biliary excretion of copper. Subsequent gradual accumulation of copper in different organs produces an extremely variable clinical picture, which comprises hepatic, neurological psychiatric, ophthalmological, and other disturbances. WD has specific treatment, so that early diagnosis is crucial in order to avoid the progression of the disease and its devastating consequences. The clinical diagnosis of WD is based on the Leipzig scale, which considers clinical, histological, biochemical and genetic data. However, even patients with an initial WD diagnosis based on a high Leipzig score result to suffer from other condition that mimics the WD’s phenotype (Wilson-like).
  • 1.2K
  • 22 Sep 2021
Topic Review
SARS-CoV-2 Genome
An enigmatic localized pneumonia escalated into a worldwide COVID-19 pandemic from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This review aims to consolidate the extensive biological minutiae of SARS-CoV-2 which requires decipherment. Having one of the largest RNA viral genomes, the single strand contains the genes ORF1ab, S, E, M, N and ten open reading frames. Highlighting unique features such as stem-loop formation, slippery frameshifting sequences and ribosomal mimicry, SARS-CoV-2 represents a formidable cellular invader. Hijacking the hosts translational engine, it produces two polyprotein repositories (pp1a and pp1ab), armed with self-cleavage capacity for production of sixteen non-structural proteins. Novel glycosylation sites on the spike trimer reveal unique SARS-CoV-2 features for shielding and cellular internalization. Affording complexity for superior fitness and camouflage, SARS-CoV-2 challenges diagnosis and vaccine vigilance.
  • 1.2K
  • 21 Jan 2021
Topic Review
Genetic Loci Underlying Awn Morphology in Barley
Awns are a transformed leaf blade that extends from the lemmas of the florets, and can contribute significantly to the grain filling via active photosynthesis. Barley awns are highly diverse in morphology, ranging from long to short or awnless types, and from straight to hooded or crooked shapes. The morphological diversity, importance to grain yield and ease of study of barley awns have intrigued plant geneticists for several decades. A large set of genetic loci associated with the development of awns have been identified genetically and mapped to chromosomes.
  • 1.2K
  • 03 Nov 2021
Topic Review
Congenital Insensitivity to Pain
Congenital insensitivity to pain is a condition that inhibits the ability to perceive physical pain.
  • 1.2K
  • 24 Dec 2020
Topic Review
Prion Protein Gene (PRNP) in Dogs
Transmissible spongiform encephalopathies (TSEs) have been reported in a wide range of species. However, TSE infection in natural cases has never been reported in dogs. Previous studies have reported that polymorphisms of the prion protein gene (PRNP) have a direct impact on the susceptibility of TSE. However, studies on polymorphisms of the canine PRNP gene are very rare in dogs. We examined the genotype, allele, and haplotype frequencies of canine PRNP in 204 dogs and analyzed linkage disequilibrium (LD). In addition, to evaluate the impact of nonsynonymous polymorphisms on prion protein (PrP), we carried out in silico analysis.
  • 1.2K
  • 18 Jun 2020
Topic Review
BARD1 and Tumor Development
BARD1 is a very important BRCA1 binding partner and plays a key role in the development of a variety of tumors. Similar to BRCA1, BARD1 has been implicated in the development of breast and gynecological cancers. In addition, BARD1 also plays a role in the development of non-breast and non-gynecological cancers.
  • 1.2K
  • 30 Jul 2020
Topic Review
Fitness
Fitness (often denoted [math]\displaystyle{ w }[/math] or ω in population genetics models) is the quantitative representation of individual reproductive success. It is also equal to the average contribution to the gene pool of the next generation, made by the same individuals of the specified genotype or phenotype. Fitness can be defined either with respect to a genotype or to a phenotype in a given environment or time. The fitness of a genotype is manifested through its phenotype, which is also affected by the developmental environment. The fitness of a given phenotype can also be different in different selective environments. With asexual reproduction, it is sufficient to assign fitnesses to genotypes. With sexual reproduction, recombination scrambles alleles into different genotypes every generation; in this case, fitness values can be assigned to alleles by averaging over possible genetic backgrounds. Natural selection tends to make alleles with higher fitness more common over time, resulting in Darwinian evolution. The term "Darwinian fitness" can be used to make clear the distinction with physical fitness. Fitness does not include a measure of survival or life-span; Herbert Spencer's well-known phrase "survival of the fittest" should be interpreted as: "Survival of the form (phenotypic or genotypic) that will leave the most copies of itself in successive generations." Inclusive fitness differs from individual fitness by including the ability of an allele in one individual to promote the survival and/or reproduction of other individuals that share that allele, in preference to individuals with a different allele. One mechanism of inclusive fitness is kin selection.
  • 1.2K
  • 31 Oct 2022
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