DNA (Mary Ann Liebert, Inc.)最新文献_第2页

Complex Roles of NEIL1 and OGG1: Insights Gained from Murine Knockouts and Human Polymorphic Variants NEIL1和OGG1的复杂作用：从小鼠敲除和人类多态变体中获得的见解

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-12-01 DOI: 10.3390/dna2040020

A. Basu, Deyu Li, R. Lloyd

{"title":"Complex Roles of NEIL1 and OGG1: Insights Gained from Murine Knockouts and Human Polymorphic Variants","authors":"A. Basu, Deyu Li, R. Lloyd","doi":"10.3390/dna2040020","DOIUrl":"https://doi.org/10.3390/dna2040020","url":null,"abstract":"DNA glycosylases promote genomic stability by initiating base excision repair (BER) in both the nuclear and mitochondrial genomes. Several of these enzymes have overlapping substrate recognition, through which a degree of redundancy in lesion recognition is achieved. For example, OGG1 and NEIL1 both recognize and release the imidazole-ring-fragmented guanine, FapyGua as part of a common overall pathway to cleanse the genome of damaged bases. However, these glycosylases have many differences, including their differential breadth of substrate specificity, the contrasting chemistries through which base release occurs, the subsequent steps required to complete the BER pathway, and the identity of specific protein-binding partners. Beyond these differences, the complexities and differences of their in vivo biological roles have been primarily elucidated in studies of murine models harboring a knockout of Neil1 or Ogg1, with the diversity of phenotypic manifestations exceeding what might have been anticipated for a DNA glycosylase deficiency. Pathologies associated with deficiencies in nuclear DNA repair include differential cancer susceptibilities, where Ogg1-deficient mice are generally refractory to carcinogenesis, while deficiencies in Neil1-deficient mice confer cancer susceptibility. In contrast to NEIL1, OGG1 functions as a key transcription factor in regulating inflammation and other complex gene cascades. With regard to phenotypes attributed to mitochondrial repair, knockout of either of these genes results in age- and diet-induced metabolic syndrome. The adverse health consequences associated with metabolic syndrome can be largely overcome by expression of a mitochondrial-targeted human OGG1 in both wild-type and Ogg1-deficient mice. The goal of this review is to compare the roles that NEIL1 and OGG1 play in maintaining genomic integrity, with emphasis on insights gained from not only the diverse phenotypes that are manifested in knockout and transgenic mice, but also human disease susceptibility associated with polymorphic variants.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45416663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

The Domino Effect: Nucleosome Dynamics and the Regulation of Base Excision Repair Enzymes 多米诺效应：核小体动力学与碱基切除修复酶的调节

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-11-10 DOI: 10.3390/dna2040018

Julia C. Cook, S. Delaney

引用次数: 2

DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification 用于三维表面的DNA瓦片自组装：朝向属属识别

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-10-24 DOI: 10.4230/LIPIcs.DNA.29.2

Florent Becker, Shahrzad Heydarshahi

{"title":"DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification","authors":"Florent Becker, Shahrzad Heydarshahi","doi":"10.4230/LIPIcs.DNA.29.2","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.29.2","url":null,"abstract":"We introduce a new DNA tile self-assembly model: the Surface Flexible Tile Assembly Model (SFTAM), where 2D tiles are placed on host 3D surfaces made of axis-parallel unit cubes glued together by their faces, called polycubes. The bonds are flexible, so that the assembly can bind on the edges of the polycube. We are interested in the study of SFTAM self-assemblies on 3D surfaces which are not always embeddable in the Euclidean plane, in order to compare their different behaviors and to compute the topological properties of the host surfaces. We focus on a family of polycubes called cuboids. Order-0 cuboids are polycubes that have six rectangular faces, and order-1 cuboids are made from two order-0 cuboids by substracting one from the other. Thus, order-1 cuboids can be of genus 0 or of genus 1 (then they contain a tunnel). We are interested in the genus of these structures, and we present a SFTAM tile assembly system that determines the genus of a given order-1 cuboid. The SFTAM tile assembly system which we design, contains a specific set $Y$ of tile types with the following properties. If the assembly is made on a host order-1 cuboid $C$ of genus 0, no tile of $Y$ appears in any producible assembly, but if $C$ has genus 1, every terminal assembly contains at least one tile of $Y$. Thus, we are able to distinguish the host surfaces according to their genus, by the tiles used in the assembly. This system is specific to order-1 cuboids but the techniques we use should be generalizable to other families of shapes.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":"1 1","pages":"2:1-2:21"},"PeriodicalIF":0.0,"publicationDate":"2022-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46313622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Multi-Faceted Roles of ERCC1-XPF Nuclease in Processing Non-B DNA Structures ERCC1-XPF核酸酶在非B DNA结构加工中的多面作用

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-10-11 DOI: 10.3390/dna2040017

Tonia T. Li, K. Vasquez

引用次数: 1

Contributing Factors for Mutagenic DNA Lesion Bypass by DNA Polymerase Eta (polη) DNA聚合酶Eta (polη)旁路致突变性DNA损伤的影响因素

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-09-28 DOI: 10.3390/dna2040015

Hunmin Jung

{"title":"Contributing Factors for Mutagenic DNA Lesion Bypass by DNA Polymerase Eta (polη)","authors":"Hunmin Jung","doi":"10.3390/dna2040015","DOIUrl":"https://doi.org/10.3390/dna2040015","url":null,"abstract":"The integrity of DNA replication is under constant threat from various exogenous and endogenous factors along with some epigenetic factors. When there is damage to the genome, cells respond to the damage in two major ways, DNA damage repair and DNA damage tolerance. One of the major mechanisms for DNA damage tolerance is DNA lesion bypass, which is performed by specific DNA polymerases called Y-family DNA polymerases including DNA polymerase eta (polη). Ever since the discovery of polη’s unique role in bypassing cyclobutane pyrimidine dimer (CPD), a wide range of DNA lesions have been experimentally shown to be bypassed by polη. The structural study of polη was greatly boosted by the first elucidation of the N-terminal catalytic domain of polη by X-ray crystallography in 2010. Ever since, a lot of polη catalytic domain crystal structures have been published, which were complexed with an incoming nucleotide and a lesion containing DNA including pyrimidine dimers, cisplatin GpG adduct, 8-oxoguanine (oxoG), 8-oxoadenine (oxoA), N7-methylguanine (N7mG), O6-methylguanine (O6mG), hypoxanthine (HX), and many others. Though polη’s active site is known to be rigid with few conformational changes, there are several contributing factors that could facilitate the lesion bypass such as catalytic metals, syn–anti conformational equilibrium, tautomerization, and specific residues of polη. Each of these components are discussed in detail in this review.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41946895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

The Joint Meeting of the 23rd International Chromosome Conference (ICC) and the 24th International Colloquium in Animal Cytogenetics and Genomics (ICACG) 第23届国际染色体会议（ICC）与第24届动物细胞遗传学与基因组学国际学术讨论会（ICACG）联席会议

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-09-02 DOI: 10.3390/dna2030014

D. Griffin

引用次数: 0

Origin of the Bunun Indigenous People of Taiwan, a Review of Published Material Using Y-Chromosome and Mitochondrial DNA Gene Systems 台湾布农族起源及Y-染色体和线粒体DNA基因系统研究综述

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-09-01 DOI: 10.3390/dna2030013

J. Trejaut

引用次数: 0

W Chromosome Evolution by Repeated Recycling in the Frog Glandirana rugosa 腺蛙W染色体的重复循环进化

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-08-01 DOI: 10.3390/dna2030012

M. Ogata, F. Shams, Yuri Yoshimura, T. Ezaz, I. Miura

{"title":"W Chromosome Evolution by Repeated Recycling in the Frog Glandirana rugosa","authors":"M. Ogata, F. Shams, Yuri Yoshimura, T. Ezaz, I. Miura","doi":"10.3390/dna2030012","DOIUrl":"https://doi.org/10.3390/dna2030012","url":null,"abstract":"The Y or W sex chromosome of a heteromorphic pair is usually heterochromatinised and degenerated. However, whether chromosome degeneration constantly proceeds toward an extreme end is not fully understood. Here, we present a case of intermittent evolution of W chromosomes caused by interpopulation hybridisation in the Japanese soil-frog, Glandirana rugosa. This species includes two heteromorphic sex chromosome systems, which are separated into geographic populations, namely the XY and ZW groups. In this study, to uncover the evolutionary mechanisms of the heterogeneous W chromosomes, we genetically investigated the geographic differentiation of the ZW populations along with the closely located XY populations. Analysis of mitochondrial cytochrome b sequences detected three distinct clades, named ZW1, ZW2, and ZW3. High throughput analyses of nuclear genomic DNA showed that autosomal alleles of XY populations were deeply introgressed into the ZW3 sub-group. Based on the genotypes of sex-linked single nucleotide polymorphisms, W-borne androgen receptor gene expression, and WW developmental mortality, we concluded that the X chromosomes were recycled to W chromosomes. Upon inclusion of two cases from another group, Neo-ZW, we observed that the X chromosomes were recycled independently at least four times to the new W chromosomes: a repetition of degeneration and resurrection.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42618826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

The Efficacy of Hyaluronic Acid Binding (HAB) in the Treatment of Male Infertility: A Systematic Review of the Literature 透明质酸结合(HAB)治疗男性不育症的疗效:文献系统综述

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-07-18 DOI: 10.3390/dna2030011

Róisín Ní Dhuifin, D. Griffin, T. Moodley

{"title":"The Efficacy of Hyaluronic Acid Binding (HAB) in the Treatment of Male Infertility: A Systematic Review of the Literature","authors":"Róisín Ní Dhuifin, D. Griffin, T. Moodley","doi":"10.3390/dna2030011","DOIUrl":"https://doi.org/10.3390/dna2030011","url":null,"abstract":"Hyaluronic acid (HA)-binding is reported to predict the fertilising capacity of spermatozoa, while HA-bound sperm selection is reported to reduce the incidence of miscarriage. However, the clinical effectiveness of these techniques remains uncertain. This work investigated the prognostic value of sperm-HA binding (HAB) as a predictor of treatment outcomes, and whether HAB-sperm selection for Invitro fertilisation (IVF)/intracytoplasmic sperm injection (ICSI) improves clinical outcomes or reduces miscarriage rates. A systematic review of the literature was carried out. A modified version of the Downs and Black Checklist was used to assess bias and study quality on eleven selected studies. No significant correlations were found between HAB score and fertilisation, clinical pregnancy, or live birth rates (low-quality evidence). Three studies reported a significant reduction in the incidence of miscarriage, including a Cochrane review (low-quality evidence). While the prognostic value of HAB scores is currently undetermined, there is evidence that HAB-sperm selection prior to insemination reduces the incidence of miscarriage following ART. Moreover, there are no reports of detrimental effects of HAB-sperm selection on treatment outcomes when compared with conventional IVF or ICSI. Therefore, it is unclear why it is assigned as a treatment “add-on” with a red light by the HFEA, and why its routine use is not recommended.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42853175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria 具有连续平衡点的大种群协议的实数计算

DNA (Mary Ann Liebert, Inc.) Pub Date : 2022-06-14 DOI: 10.48550/arXiv.2206.06594

Xiang Huang, Rachel N. Huls

{"title":"Computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria","authors":"Xiang Huang, Rachel N. Huls","doi":"10.48550/arXiv.2206.06594","DOIUrl":"https://doi.org/10.48550/arXiv.2206.06594","url":null,"abstract":"Bournez, Fraigniaud, and Koegler defined a number in [0,1] as computable by their Large-Population Protocol (LPP) model, if the proportion of agents in a set of marked states converges to said number over time as the population grows to infinity. The notion, however, restricts the ordinary differential equations (ODEs) associated with an LPP to have only finitely many equilibria. This restriction places an intrinsic limitation on the model. As a result, a number is computable by an LPP if and only if it is algebraic, namely, not a single transcendental number can be computed under this notion. In this paper, we lift the finitary requirement on equilibria. That is, we consider systems with a continuum of equilibria. We show that essentially all numbers in [0,1] that are computable by bounded general-purpose analog computers (GPACs) or chemical reaction networks (CRNs) can also be computed by LPPs under this new definition. This implies a rich series of numbers (e.g., the reciprocal of Euler's constant, $pi/4$, Euler's $gamma$, Catalan's constant, and Dottie number) are all computable by LPPs. Our proof is constructive: We develop an algorithm that transfers bounded GPACs/CRNs into LPPs. Our algorithm also fixes a gap in Bournez et al.'s construction of LPPs designed to compute any arbitrary algebraic number in [0,1].","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":"1 1","pages":"7:1-7:22"},"PeriodicalIF":0.0,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43434089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0