Academic literature on the topic 'Gene overlaps'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Gene overlaps.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "Gene overlaps"
1
Decrulle, Antoine L., Antoine Frénoy, Thomas A. Meiller-Legrand, Aude Bernheim, Chantal Lotton, Arnaud Gutierrez, and Ariel B. Lindner. "Engineering gene overlaps to sustain genetic constructs in vivo." PLOS Computational Biology 17, no. 10 (October 8, 2021): e1009475. http://dx.doi.org/10.1371/journal.pcbi.1009475.
Full textAbstract:
Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time.
2
Muñoz-Baena, Laura, and Art F. Y. Poon. "Using networks to analyze and visualize the distribution of overlapping genes in virus genomes." PLOS Pathogens 18, no. 2 (February 24, 2022): e1010331. http://dx.doi.org/10.1371/journal.ppat.1010331.
Full textAbstract:
Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated open reading frames (ORFs) in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. Antisense overlaps in which one of the ORFs was encoded in the same frame on the opposite strand (−0) tend to be longer. Next, we develop a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family. In the absence of an unambiguous partition of ORFs by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent ORFs are adjacent in one or more genomes, and (2) that these ORFs overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.
3
Lartey, R. T., T. C. Voss, and U. Melcher. "Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications." Molecular Biology and Evolution 13, no. 10 (December 1, 1996): 1327–38. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025579.
Full text
4
Makałowska, Izabela, Chiao-Feng Lin, and Krisitina Hernandez. "Birth and death of gene overlaps in vertebrates." BMC Evolutionary Biology 7, no. 1 (2007): 193. http://dx.doi.org/10.1186/1471-2148-7-193.
Full text
5
Jain, Kanika, Tyler H. Stanage, Elizabeth A. Wood, and Michael M. Cox. "The Escherichia coli serS gene promoter region overlaps with the rarA gene." PLOS ONE 17, no. 4 (April 15, 2022): e0260282. http://dx.doi.org/10.1371/journal.pone.0260282.
Full textAbstract:
Deletion of the entire gene encoding the RarA protein of Escherichia coli results in a growth defect and additional deficiencies that were initially ascribed to a lack of RarA function. Further work revealed that most of the effects reflected the presence of sequences in the rarA gene that affect expression of the downstream gene, serS. The serS gene encodes the seryl aminoacyl-tRNA synthetase. Decreases in the expression of serS can trigger the stringent response. The sequences that affect serS expression are located in the last 15 nucleotides of the rarA gene.
6
Pribyl, T., C. Campagnoni, S. Amur-Umarjee, K. Kampf, B. Garbay, V. Handley, and A. Campagnoni. "Identification and characterization of Golli, a gene which overlaps the MBP gene." Neurochemistry International 21 (January 1992): C1. http://dx.doi.org/10.1016/0197-0186(92)92037-5.
Full text
7
Brauburger, Kristina, Yannik Boehmann, Verena Krähling, and Elke Mühlberger. "Transcriptional Regulation in Ebola Virus: Effects of Gene Border Structure and Regulatory Elements on Gene Expression and Polymerase Scanning Behavior." Journal of Virology 90, no. 4 (December 9, 2015): 1898–909. http://dx.doi.org/10.1128/jvi.02341-15.
Full textAbstract:
ABSTRACTThe highly pathogenic Ebola virus (EBOV) has a nonsegmented negative-strand (NNS) RNA genome containing seven genes. The viral genes either are separated by intergenic regions (IRs) of variable length or overlap. The structure of the EBOV gene overlaps is conserved throughout all filovirus genomes and is distinct from that of the overlaps found in other NNS RNA viruses. Here, we analyzed how diverse gene borders and noncoding regions surrounding the gene borders influence transcript levels and govern polymerase behavior during viral transcription. Transcription of overlapping genes in EBOV bicistronic minigenomes followed the stop-start mechanism, similar to that followed by IR-containing gene borders. When the gene overlaps were extended, the EBOV polymerase was able to scan the template in an upstream direction. This polymerase feature seems to be generally conserved among NNS RNA virus polymerases. Analysis of IR-containing gene borders showed that the IR sequence plays only a minor role in transcription regulation. Changes in IR length were generally well tolerated, but specific IR lengths led to a strong decrease in downstream gene expression. Correlation analysis revealed that these effects were largely independent of the surrounding gene borders. Each EBOV gene contains exceptionally long untranslated regions (UTRs) flanking the open reading frame. Our data suggest that the UTRs adjacent to the gene borders are the main regulators of transcript levels. A highly complex interplay between the differentcis-acting elements to modulate transcription was revealed for specific combinations of IRs and UTRs, emphasizing the importance of the noncoding regions in EBOV gene expression control.IMPORTANCEOur data extend those from previous analyses investigating the implication of noncoding regions at the EBOV gene borders for gene expression control. We show that EBOV transcription is regulated in a highly complex yet not easily predictable manner by a set of interactingcis-active elements. These findings are important not only for the design of recombinant filoviruses but also for the design of other replicon systems widely used as surrogate systems to study the filovirus replication cycle under low biosafety levels. Insights into the complex regulation of EBOV transcription conveyed by noncoding sequences will also help to interpret the importance of mutations that have been detected within these regions, including in isolates of the current outbreak.
8
Kepler, T. B., M. Borrero, B. Rugerio, S. K. McCray, and S. H. Clarke. "Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement." Journal of Immunology 157, no. 10 (November 15, 1996): 4451–57. http://dx.doi.org/10.4049/jimmunol.157.10.4451.
Full textAbstract:
Abstract Diversity in the Ag binding receptors of B and T cells is achieved through a process of genomic rearrangement involving selection of recombination sites and, in adult mice, addition of nontemplated (N) nucleotides. We have analyzed 543 Ig heavy chain nonproductive rearrangements, involving a single variable region gene segment, from adult and perinatal mice. We infer several fundamental and novel features of the recombination mechanism. N regions are formed predominantly from the DNA plus strand or from the DNA minus strand polymerizations, rather than as a concatenation of the two. Homologous overlaps of as few as one nucleotide between gene segments cause significant skewing of recombination sites. The V(H) recombination site spectrum differs in perinatal and adult mice, with sites representing overlap between V(H) and D over-represented in the perinatal mice, and sites representing overlaps between V(H) and the N strand polymerized onto the D segment over-represented in the adult mice. Thus, in V(D)J joining, N nucleotide addition and recombination site choice are highly interdependent events.
9
Chen, Quan, Xianghong J. Zhou, and Fengzhu Sun. "Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists." Journal of Computational Biology 22, no. 2 (February 2015): 111–23. http://dx.doi.org/10.1089/cmb.2014.0149.
Full text
10
Ray, Bryan L., Charles I. White, and James E. Haber. "The TSM1 gene of Saccharomyces cerevisiae overlaps the MAT locus." Current Genetics 20, no. 1-2 (July 1991): 25–31. http://dx.doi.org/10.1007/bf00312761.
Full textDissertations / Theses on the topic "Gene overlaps"
1
Reich, Jennifer G. "Functional overlap in gene duplications in the yeast Saccharomyces cerevisiae." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ59268.pdf.
Full text
2
Li, Ai. "Generalizations of the topological overlap measure for neighborhood analysis and module detection in gene and protein networks." Diss., Restricted to subscribing institutions, 2007. http://proquest.umi.com/pqdweb?did=1481673641&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
Full text
3
Silva, Alex Eduardo da. "Avaliação genotípica de pacientes com polineuropatia inflamatória desmielinizante crônica: estudo da duplicação/deleção do gene PMP22." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/17/17140/tde-25112014-142430/.
Full textAbstract:
Introdução: Polineuropatias são doenças do sistema nervoso periférico com etiologias variadas. Dentre elas são freqüentes as inflamatórias e as hereditárias, com prevalência de 0,67-7,7/100000 e 7,9-82,3/100000 para polineuropatia inflamatória desmielinizante crônica (PIDC) e Doença de Charcot-Marie-Tooth (CMT), respectivamente. Existem poucas evidências de sobreposição entre estas duas doenças e também algumas dificuldades diagnósticas em situações específicas. Objetivos: Estudar a freqüência de mutações (duplicações e deleções) do gene PMP22 em uma coorte de pacientes inicialmente diagnosticados como PIDC ou suspeitos de apresentarem as duas condições, os sinais e sintomas sugestivos da sobreposição e os fatores implicados em erro de classificação da neuropatia. Métodos: 111 pacientes com diagnóstico de PIDC foram estudados. DNA foi isolado a partir de leucócitos de sangue periférico segundo protocolo padrão. Duplicações e deleções do gene PMP22 foram avaliadas através de marcadores polimórficos do DNA localizados dentro do cromossomo 17p11.2-12, o qual contém o gene PMP22. Achados clínicos e laboratoriais também foram estudados e comparados entre os grupos. Resultados: Dentre os 111 pacientes estudados, mutações no PMP22 foram encontradas em 10 (9%), sendo duplicações em 9 pacientes e deleção em 1 paciente. Concomitância entre PIDC e CMT foi verificada em 4 pacientes (3,6%), todos com duplicação do PMP22. Os outros 6 pacientes foram diagnosticados como CMT puro (5) ou Neuropatia Hereditária Susceptível à Compressão (1), visto que não apresentaram melhora com o uso de tratamento imunomodulador e/ou imunossupressor (5 casos) ou foi estabelecido diagnóstico alternativo associado (1). Os outros 101 pacientes não tiveram duplicação nem deleção deste gene e, portanto, tinham PIDC apenas. Idade média dos pacientes com PIDC/CMT foi de 23,8±18,0 anos e 43,6±19,3 anos para pacientes sem mutações (p=0,04). Houve diferença estatísticamente significativa na resposta ao tratamento entre os grupos PIDC/CMT X CMT (p=0,008) e PIDC X CMT (p=0,00). Ausência de história familiar e presença de doenças e hábitos ligados ao desenvolvimento de neuropatias periféricas, como diabetes mellitus e ingesta de bebidas alcoólicas, por exemplo, bem como achados atípicos na eletroneuromiografia e na biópsia de nervo podem ter contribuído para a confusão diagnóstica nos casos de CMT puro. Conclusões: Alguns pacientes podem desenvolver PIDC em associação com CMT e se beneficiam do tratamento. A neuropatia hereditária poderia predispor à neuropatia inflamatória, uma vez que estes pacientes tendem a apresentar essa condição em idades mais precoces. Cautela deve ser dispensada àqueles pacientes com suspeita diagnóstica de PIDC que não têm os achados clássicos ou não melhoram com o tratamento, uma vez que podem apresentar outras etiologias para a neuropatia, dentre elas uma neuropatia hereditária, como a CMT.Introduction: Polyneuropathies are peripheral nervous system disorders with a wide range of etiologies. Among them, inflammatory and hereditary are frequent with prevalence of 0.67-7.7/100000 and 7.9-82.3/100000, for chronic inflammatory demyelinating polyneuropathy (CIDP) and Charcot-Marie-Tooth disease (CMT), respectively. There are a few evidence of ovelapping between these two conditions and also some diagnostic difficulties in specific situations. Objectives: To study the frequency of mutations in PMP22 gene (duplications and delections) among a cohort of patients initially diagnosed as CIDP or suspected to have both conditions, the signs and symptoms related to this ovelapping and factors implicated in misdiagnose. Methods: 111 patients with an initially CIDP suspected diagnosis were studied. DNA was isolated from peripheral blood leucocytes following a standard salting-out protocol. Duplications and delections in the PMP22 gene were analysed by polymorphic DNA markers located within the chromosome 17p11.2-12, wich contains the PMP22 gene. Clinical and laboratory findings were also studied and compared within groups. Results: Among 111 patients studied, 10 (9%) were found to harbor mutations in PMP22 gene, specifically duplications in nine and delection in one. We therefore diagnosed CIDP plus CMT in four patients (3.6%), all of them with a duplicated PMP22 gene. The other six patients were diagnosed as pure CMT (5) or Hereditary Neuropathy with liability to Pressure Palsy (1), as they did not improved with the use of immunomodulatory and/or immunosupressive treatment (five cases) or were found to have alternative associated diagnosis (one patient). The other 101 patients did not show duplication nor delection in this gene, so they had CIDP. Mean age of patients with CIDP/CMT were 23.8±18.0 years and 43.6±19.3 years for patients without mutations (p=0.04). There were statistically significant difference in treatmet response between groups CIDP/CMT X CMT (p=0.008) and CIDP X CMT (p=0.00). The lack of family history and presence of other diseases and habits linked to the development of peripheral neuropathies, as diabetes mellitus and alcohol intake, for instance, as well as atypical findings in electrodiagnostic studies and nerve biopsy may have contributed to misdiagnose in the pure CMT cases. Conclusions: Some patients may develop CIDP in association with CMT and have benefit from treatment. The hereditary neuropathy may predispose to the inflammatory neuropathy as these patients tend to show this condition at younger ages. Caution should be dispensed to those patients with a suspected diagnose of CIDP who do not have the classical disease findings or do not improve with treatment, as they can have alternative etiologies for the neuropathy, among them a hereditary neuropathy as CMT disease.
4
Sandré, Marion. "Constances et spécificités des dysfonctionnements interactionnels dans le genre "débat politique télévisé" : une application au débat de l'entre-deux tours de l'élection présidentielle de 2007." Thesis, Montpellier 3, 2010. http://www.theses.fr/2010MON30034/document.
Full textAbstract:
Ce travail s’inscrit en sciences du langage, dans le champ de l’analyse du discours, et utilise les outils de l’analyse conversationnelle et interactionnelle. L’objectif est de montrer la corrélation entre l’objet d’étude – le dysfonctionnement interactionnel – et le genre du discours – le débat politique télévisé. Le corpus choisi est le débat de l’entredeuxtours de l’élection présidentielle de 2007, entre Ségolène Royal et Nicolas Sarkozy. La transcription intégrale de cette interaction permet de recenser l’ensemble des dysfonctionnements et de les classer. Il existe ainsi deux types de dysfonctionnement : les ratés du système des tours (interruption, chevauchement, silence prolongé entre deuxtours) et la non-pertinence de l'enchaînement (échange tronqué, seconde partie de paire non pertinente). Chacun de ces dysfonctionnements est étudié en fonction des visées auxquelles il obéit (coopérer, polémique, gérer l’interaction…), et par rapport à la stratégie globale à laquelle il participe. L’analyse précise de chaque catégorie de dysfonctionnement interactionnel permet de montrer les constantes et les spécificités de ces phénomènes discursifs. En outre, cette analyse porte sur la relation interpersonnelle et mobilise les notions de face et d’ethos, l’image des candidats locuteurs s’élaborantaussi au travers de ces dysfonctionnements. Plus largement, le but de cette étude est d’esquisser une cartographie des dysfonctionnements interactionnels pouvant servir de modèle à d’autres analyses. Les études futures pourront porter sur d’autres débats ou d’autres genres du discours, afin de mener une étude comparative, en utilisant les outils mis en évidence dans ce travailThe second-round debate of presidential elections has been a significant event in French politics since 1974. The final TV debate of 2007, during which presidential candidates Ségolène Royal and Nicolas Sarkozy confronted each other, constitutes the corpus of the present study. The analysis focuses on turn-taking dysfunctions : interruption, overlapand problematic sequence. The aim of this study is to understand the function of these discursive devices in this TV political debate. First, the detailed transcription shows many turn-taking dysfunctions. Second, the analysis of the data reveals different types of interruption (intentional or not, with or without simultaneous speech, isolated or with others interruptions), different types of overlap (when two speakers begin together, when the current speaker continues speaking after the overlap or when he lets the next speaker talk) and different types of problematic sequence (when the next speaker does not answer at all or does not answer well to the first speaker). Third, each type is precisely examined. The discourse analysis demonstrates how the debater uses them to defend himself or to criticize the other person. Furthermore, as turn-taking dysfunctions are conversational insults, the discourse surrounding them is analysed as a way to save face and to build the discursive ethos. The results of this study may help the field of linguistics to understand the discursive strategies of politicians. More generally, it presents a model to analyse every type of turn-taking dysfunction. Future research might focus on other TV political debates and other discursive genres (interviews, TV programmes with politicians) so as to carry out a comparative analysis
5
Elmansy, Dalia F. "Computational Methods to Characterize the Etiology of Complex Diseases at Multiple Levels." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1583416431321447.
Full text
6
Frénoy, Antoine. "Second order selection pressures promoting the evolution and maintenance of cooperation in microbial and in silico systems." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05T050/document.
Full textAbstract:
Cette thèse s'intéresse aux liens entre l'évolution de la coopération et la sélection de second ordre. Dans une première partie, nous montrons comment des organismes digitaux adaptent leurs génomes pour encoder les gènes liées à la coopération d'une manière plus contrainte (suppression d'évolvabilité), notamment à l'aide d'opérons et d'overlaps impliquant aussi des gènes essentiels. Dans une deuxième partie, nous testons expérimentalement cette vision des overlaps de gènes comme "contrainte évolutive" grâce à des outils d'algorithmique et de biologie synthétique que nous avons développés. Dans une troisième partie, nous utilisons des simulations par agents pour montrer comment une forme de division du travail peut être interprétée comme un système coopératif à la lumière de la théorie évolutive moderne. Dans une dernière partie, nous montrons que la dispersion spatiale des allèles coopératives obtenue par des phénomènes de "genetic hitchiking" joue un rôle important dans l'évolution de la coopération, quand bien même ce mécanisme de dispersion s'applique aussi à des allèles non coopératives, grâce à la "relatedness" (aux loci codant pour la coopération) crée par l'invasion locale de mutations bénéfiques (à des loci non liés à la coopération) et par l'équilibre complexe entre ces mutations bénéfiques et la robustesse mutationnelle. L'ensemble de ces résultats appelle à une prise en compte plus importante des pressions sélectives de second ordre dans l'étude de l'évolution sociale, et au développement de modèles plus réalistes qui permettraient d'intégrer de telles forces évolutives. Nous insistons également sur l'importance du paysage mutationnel dans l'étude des populations bactériennes, et montrons le potentiel croissant de la biologie synthétique comme outil d'étude de ce paysage et de l'évolution microbienne en généralIn the first part, I show how digital organisms adapt their genomes to encode cooperation-related genes in a more constrained way (evolvability suppression), especially using operons and overlaps also involving essential genes. In the second part, we experimentally test this view of gene overlaps as an evolutionary constraint, using both algorithmic and synthetic biology tools that we have developed. In the third part, I use agent-based simulations to show how a form of division of labour can be interpreted as a cooperative system in the light of modern evolutionary theory. In the final part, I show that the patterns of dispersal of cooperative alleles due to hitchhiking phenomena play an important role in the evolution of cooperation. The last result holds even though the hitchhiking mechanisms also applies to non-cooperative alleles, thanks to the relatedness (at cooperation-related loci) created by the local invasion of beneficial mutations (at loci not related to cooperation). The beneficial mutations form a complex and interesting equilibrium with mutational robustness, which I investigate using in silico evolution. On the whole, these results call for a more careful consideration of the second-order selection pressures in the study of social evolution, and show the necessity for more realistic models allowing to integrate such evolutionary forces. My thesis research specifically highlights the importance of the mutational landscape in the study of microbial populations and shows the increasing potential of synthetic biology as a tool to study such landscape and microbial evolution in general
7
Reich, Jennifer G. "Functional overlap in gene duplications of the yeast Saccharomyces cerevisiae." Thesis, 2000. http://spectrum.library.concordia.ca/1315/1/MQ59268.pdf.
Full textAbstract:
The Saccharomyces cerevisiae genome contains many duplicated regions of DNA. The presence of extra copies of some genes can result in certain genes performing similar or identical functions as their duplicated counterparts. This study reveals phenotypes for functionally overlapping genes and classifies selected duplicated genes as functionally overlapping or divergent. A region of DNA on chromosomes I and XV containing 12 duplicated genes was examined. Mutants were created containing deletions of one or both members of every gene pair and subjected to several functional tests. Gene pairs were classified as functionally overlapping when both members had to be deleted to observe a "synthetic" phenotype. Gene pairs were considered to be functionally divergent when the removal of one member of a gene pair revealed a mutant phenotype, as the remaining member was unable to "rescue" the phenotype.
8
Kaufman, Liana. "Identification of Non-syndromic Intellectual Disability Genes and Their Overlap with Autism." Thesis, 2011. http://hdl.handle.net/1807/29568.
Full textAbstract:
Non-syndromic intellectual disability (NS-ID) is a widespread neurodevelopmental disorder in which the major phenotypic manifestation is low IQ. Given the known genetic overlaps between the two conditions, it was hypothesize that autosomal recessive NS-ID (NS-ARID) genes may also play a role in autism. In this thesis, autism probands with CNVs overlapping NS-ARID genes were screened for additional mutations by sequencing. In addition, TRAPPC9 was identified as a novel cause of NS-ARID in two unrelated consanguineous families. TRAPPC9 (NIBP) is believed to function in the NF-kB pathway and the TRAPP complex. Multiple probands with developmental delays and CNVs overlapping TRAPPC9 were also identified. A potential mechanism for the CNV-related phenotype is that TRAPPC9 may be partially paternally imprinted in brain, and overlapping CNVs may cause loss of regulation. Identification of genes for autism and ID will translate into earlier diagnosis and better clinical care for this population in the future.
9
Fernandes, Maria Isabel Mou Sequeira. "Anti and pro-longevity genes differentiation and overlap with age-related diseases." Master's thesis, 2015. http://hdl.handle.net/10451/20358.
Full textAbstract:
Tese de mestrado, Bioinformática e Biologia Computacional (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2015Envelhecimento, longevidade e doenças associadas à idade (DAIs) são processos interligados e apresentam algumas semelhanças. A determinação e caracterização dos genes partilhados pelo envelhecimento ou longevidade e DAIs - genes AD - podem fornecer mais pistas acerca dos processos de regulação do envelhecimento e das DAIs, sendo este o propósito biomédico da pesquisa na área do envelhecimento. Na área da longevidade, existe já a distinção entre dois tipos de genes: anti e pró-longevidade. São considerados anti-longevidade genes cuja sobre-expressão promove a diminuição do tempo de vida; enquanto que a sobre-expressão de genes pró-longevidade está associada a um aumento do tempo de vida. No presente trabalho, foi realizado um tratamento do enviesamento presente na investigação e foram comparados os resultados das análises com e sem tratamento. O enviesamente presente na investigação resulta do conhecimento à priori que temos, por exemplo acerca de genes, e que nos conduz a uma seleção tendenciosa dos genes a estudar. Com o objetivo de definir quais os genes AD, foram realizadas análises de sobreposição sob quatro perspetivas: no genoma, no interactoma, incluindo os parceiros de primeira ordem considerando interações proteína-proteína e incluindo os genes co-expressos definidos por dados de RNA-Seq. Foram realizadas análises de algumas características e de mecanismos para os seguintes conjuntos de genes: genes AD, genes associados ao envelhecimento ou a doenças excluindo os comuns, genes anti-longevidade, genes pro-longevidade, genes associados ao envelhecimento e genes associados a doenças. Adicionalmente, para definir os genes mais comuns, foi analisada a frequência dos genes AD ao longo das DAIs. Suportado pelos resultados obtidos, a exclusão dos genes menos estudados conduz a resultados mais precisos e a definição do número mínimo de publicações pode ser um método para reduzir o enviesamento presente na investigação. O presente trabalho evidencia a associação entre envelhecimento e DAIs, assim como entre genes anti ou pró-longevidade e DAIs. Os genes envelhecimento-doença revelaram envolvimento nos principais mecanismos de envelhecimento e doenças conhecidos. As comparações do comprimento do gene, comprimento e massa da proteína, assim como da taxa de evolução molecular (dN/dS) não demonstraram nenhum padrão de distinção entre genes anti e pró-longevidade, apresentando apenas duas diferenças significativas: i) o comprimento da proteína codificada por genes anti-longevidade é o maior, na mosca da fruta e, ii) a taxa dN/dS dos genes anti-longevidade é a maior, na minhoca. Os genes envelhecimento-doenças apresentam um maior número de conexões com outros genes, o que frisa a sua importância nas redes do envelhecimento e DAIs.
Ageing, longevity and age-related diseases (ARDs) are interconnected processes and they present some similarities. The determination and characterization of common genes between ageing or longevity and ARDs - AD-genes - can provide more clues about the regulation processes involved in ageing and diseases which is the biomedical purpose of ageing research. In the longevity research, there is already a distinction between two types of genes: anti and pro-longevity. The anti-longevity genes are those whose over-expression is associated to a decrease in the life span, while the pro-longevity genes over-expression is associated to an increase in life span. In the present work, a research bias treatment and a comparison between analyses with and without this was performed. The research bias results from the à priori knowledge, for example about genes, which leads us to make a biased selection of the genes to study. In order to find AD-genes, overlap analyses were done from four perspectives: the genome, the interactome, including first order proteinprotein interactions partners, and including co-expressed genes from RNA-Seq data. Analysis of some features and functional enrichment was applied to characterize the following gene sets: AD-genes, noncommon ageing or disease genes, anti-longevity genes, pro-longevity genes, ageing genes and ARDs genes. Additionally the frequency of genes among the ARDs was analysed for AD-genes in order to define the most common genes. Supported by the obtained results, the exclusion of less studied genes leads to more accurate results and the setting of a minimum number of publications can be a method to reduce the research bias. The present work evidenced the association between ageing and ARDs, as well as the relation between anti or pro-longevity and ARDs. The AD-genes were revealed to be more involved with the main known ageing and diseases mechanisms. The comparisons of gene length, protein length and mass, as well as the molecular evolutionary (dn/ds) ratio didn't show any pattern of difference between anti and prolongevity genes, showing only two significant differences: i) the length of proteins coded by anti-longevity genes is the highest in fruit fly and, ii) the dn/ds ratio of anti-longevity genes is the highest in roundworm. The AD-genes show a higher number of connections which highlight their importance in ageing and ARDs networks.
10
Beinhoff, Malte. "Molecular and functional characterization of potential pathogenicity related genes from Verticillium longisporum." Doctoral thesis, 2011. http://hdl.handle.net/11858/00-1735-0000-0006-AB46-F.
Full textBooks on the topic "Gene overlaps"
1
Christa, Landert, ed. "Wenn du absolut nach Amerika willst, so gehe in Gottesnamen!": Erinnerungen an den California Trail, John A. Sutter und den Goldrausch 1846-1849. 2nd ed. Zürich: Limmat-Verlag, 2011.
Find full text
2
Siebert, Stefan, Sengupta Raj, and Alexander Tsoukas. The genetics of axial spondyloarthritis. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198755296.003.0004.
Full textAbstract:
Family and twin studies have long suggested a large genetic component in ankylosing spondylitis (AS). The genetic association with HLA-B27 remains one of the strongest single gene variant associations reported in any complex polygenic disease. The exact mechanism by which HLA-B27 contributes to AS remains unknown, with three main theories proposed: the arthritogenic peptide, endoplasmic reticulum stress with unfolded protein response, and homodimerization theories. Genome-wide association studies have identified a number of other important susceptibility genes for AS, several of which overlap with other spondyloarthritis conditions. Of these, ERAP1 and IL-23R, are covered in more detail, highlighting their functional importance.
3
Smith-Hicks, C. L., and S. Naidu. Rett Syndrome. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0054.
Full textAbstract:
Rett Syndrome (RTT) is a neurodevelopmental disorder that predominantly affects females but males with RTT have been identified. RTT was first described by an Austrian pediatrician, Andreas Rett. Rett syndrome was mapped to chromosome Xq28 in 1998 and a year later it was determined to be due to mutations in the MeCP2 gene at this locus. Identification of the gene led to the broadening of the clinical phenotype and further characterization into classic and atypical forms of the disease that overlap with Autism spectrum disorders during the period of regression. More than 95% of individuals with classic RTT have mutations in the MeCP2 gene.
4
Holdt, Lesca M., and Daniel Teupser. Genetic background of atherosclerosis and its risk factors. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199656653.003.0002.
Full textAbstract:
This chapter is concerned with how atherosclerosis risk is modulated by a complex interplay between genetic and environmental risk factors. The contribution of genetics to the variability of atherosclerosis risk is estimated as 50%. Recent genome-wide association studies have led to the identification of over 50 gene variants which modulate atherogenesis. Risk factors for atherosclerosis are also partly genetically determined and some of the variants which play a role in atherogenesis overlap with those modulating its risk factors. However, the current relevance of these findings for clinical practice is limited, mainly due to the small effect sizes of identified risk variants with insufficient discriminatory power, and a large portion of the genetic contribution to atherosclerosis is still unknown. The major promise therefore lies in understanding the pathophysiology of newly identified genes with the perspective of novel therapeutic approaches.
5
Kan, Carol, and Ma-Li Wong. Genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198789284.003.0004.
Full textAbstract:
An association between type 2 diabetes mellitus (T2DM) and depression has been reported in epidemiological studies. Finding a genetic overlap between T2DM and depression will provide evidence to support a common biological pathway to both disorders. Genetic correlations observed from twin studies indicate that a small magnitude of the variance in liability can be attributed to genetic factors. However, no genetic overlap has been observed between T2DM and depression in genome-wide association studies using both the polygenic score and the linkage disequilibrium score regression approaches. Clarifying the shared heritability between these two complex traits is an important next step towards better therapy and treatment. Another area that needs to be explored is gene–environment interaction, since genotypes can affect an individual’s responses to the environment and environment can differentially affect genotypes expression.
6
Garcia-Pavia, Pablo, and Fernando Dominguez. Left ventricular non-compaction: genetics and embryology. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0362.
Full textAbstract:
Left ventricular non-compaction (LVNC) is a rare disorder that is considered an ‘unclassified cardiomyopathy’ by the European Society of Cardiology. Several different gene mutations related to LVNC have been identified, involving sarcomeric, cytoskeletal, Z-line, ion channel, mitochondrial, and signalling proteins. However, there is broad genetic overlap between LVNC and other inherited cardiac diseases such as dilated cardiomyopathy and hypertrophic cardiomyopathy. LVNC could also be part of multisystemic genetic entities such as Barth syndrome, or accompany congenital heart defects.
7
Levinson, Douglas F., and Walter E. Nichols. Genetics of Depression. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0024.
Full textAbstract:
Major depressive disorder (MDD) is a common and heterogeneous complex trait. Twin heritability is 35%–40%, perhaps higher in severe/recurrent cases. Adverse life events (particularly during childhood) increase risk. Current evidence suggests some overlap in genetic factors among MDD, bipolar disorder, and schizophrenia. Large genome-wide association studies (GWAS) are now proving successful. Polygenic effects of common SNPs are substantial. Findings implicate genes with effects on synaptic development and function, including two obesity-associated genes (NEGR1 and OLFM4), but not previous “candidate genes.” It can now be expected that larger GWAS samples will produce additional associations that shed new light on MDD genetics.
8
Straaijer, Robin. The usage guide. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198808206.003.0002.
Full textAbstract:
Drawing on data from the Hyper Usage Guide of English (HUGE) database (Straaijer 2014), this chapter sets the context for the other chapters of the collection by exploring the usage guide as a genre since the earliest publication in 1770. While modern usage guides overlap in form and content with other genres of works about language, there are distinct characteristics that identify them as a separate genre. After this genre had slowly been evolving for 150 years, H. W. Fowler’s Dictionary of Modern English Usage (1926) became a model for future publications. However, the usage guide remains a strongly author-driven genre, resulting in much variation in form and content. After continued development and professionalization from the mid-twentieth century onwards, two subtypes within the genre seem to have emerged: one striving for comprehensiveness and the other offering entertaining narrative. This variety may account for the enduring popularity of the genre.
9
Franks, David D. Sex Differences in the Human Brain. Edited by Rosemary L. Hopcroft. Oxford University Press, 2018. http://dx.doi.org/10.1093/oxfordhb/9780190299323.013.6.
Full textAbstract:
In this chapter, the different meanings of the terms sex and gender are discussed: Sex is biological, and gender has to do with social roles. Biological differences such as genes are discussed next, including a discussion of whether these differences should be considered as either/or distinctions or as continuums. Differences in social skills are discussed. Next, differences in the brain’s gray and white matter are explored. Various parts of the brain and the abilities they support are then presented. How sex differences in the brain complement each other is explored, as well as differences and overlaps. The implications for single-sex education are presented. Reasons to discuss brain differences and other differences follow, including sleep problems, anorexia, and bulimia. A subsection on memory and emotion follows.
10
Oxley, Cristal, and Argyris Stringaris. Comorbidity. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198739258.003.0022.
Full textAbstract:
Anxiety and depression often co-occur in children with ADHD and this comorbidity can also occur across the lifespan. Such comorbidity is associated with adverse outcomes across several domains. The origin of the overlap between these disorders is discussed, including the role of shared risk factors such as common genes, environmental factors, potential association with a third disorder, or as a separate nosological entity. Abnormalities in neurochemistry and findings from imaging studies are discussed. Key components of clinical assessment are discussed together with differential diagnoses, including challenges that clinicians may encounter. Treatment approaches for comorbid ADHD with emotional disorders are outlined.
Book chapters on the topic "Gene overlaps"
1
Harju, Tero, Ion Petre, and Grzegorz Rozenberg. "Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs." In Aspects of Molecular Computing, 202–12. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-24635-0_14.
Full text
2
Makita, Naomasa. "Phenotypic Overlap of Lethal Arrhythmias Associated with Cardiac Sodium Mutations: Individual-Specific or Mutation-Specific?" In Genes and Cardiovascular Function, 185–96. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4419-7207-1_18.
Full text
3
Li, Gang, Bing-Xue Dong, Yu-Huan Liu, Chang-Jie Li, and Li-Ping Zhang. "Gene Synthesis Method Based on Overlap Extension PCR and DNAWorks Program." In Synthetic Biology, 9–17. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-625-2_2.
Full text
4
Mayrhofer, Patrick, and Renate Kunert. "Cloning of Single-Chain Antibody Variants by Overlap-Extension PCR for Evaluation of Antibody Expression in Transient Gene Expression." In Methods in Molecular Biology, 57–69. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6972-2_4.
Full text
5
Orwig, Marcy Leasum, and Anish Dave. "The Conflict of Genre: Disciplinary Terminology and Conceptual Overlap in the Context of the Annual Report." In Communication and Conflict Studies, 57–70. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-32746-0_4.
Full text
6
Zhong, Chao, Chun You, Ping Wei, and Yi-Heng Percival Zhang. "Simple Cloning by Prolonged Overlap Extension-PCR with Application to the Preparation of Large-Size Random Gene Mutagenesis Library in Escherichia coli." In Methods in Molecular Biology, 49–61. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6343-0_4.
Full text
7
Nishizawa, Mikio, Tetsuya Okuyama, and Richi Nakatake. "The Natural Antisense Transcript-Targeted Regulation Technology Using Sense Oligonucleotides and Its Application." In Oligonucleotides - Overview and Applications [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.108281.
Full textAbstract:
Natural antisense transcripts (NATs or AS transcripts) are frequently transcribed from many eukaryotic genes and post-transcriptionally regulate gene expression. The AS transcript is classified as noncoding RNA and acts as a regulatory RNA in concert with RNA-binding proteins that bind to cis-controlling elements on the mRNA, microRNAs, and drugs. The AS transcript that overlaps with mRNA regulates mRNA stability by interacting with mRNA, and the network of mRNAs, AS transcripts, microRNAs, and RNA-binding proteins finely tunes the output of gene regulation, i.e., mRNA levels. We found that single-stranded ‘sense’ oligonucleotides corresponding to an mRNA sequence decreased the mRNA levels by interfering with the mRNA-AS transcript interactions of several genes, such as inducible nitric oxide synthase (iNOS) and interferon-alpha1 (IFN-A1) genes. In contrast, AntagoNAT oligonucleotides, which are complementary to AS transcripts, are sense oligonucleotides when they overlap with mRNA, but they increase the levels of specific mRNAs. Collectively, the sense oligonucleotide is a powerful tool for decreasing or increasing mRNA levels. The natural antisense transcript-targeted regulation (NATRE) technology using sense oligonucleotides is a method with a unique modality for modulating cytosolic mRNA levels and may be used to treat human diseases in which AS transcripts are involved.
8
Q. Clement, Jade. "Gene Expression Profile of HDF in SMG Partially Overlaps with That in the NASA Twins Study." In Gene Expression and Phenotypic Traits. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.88957.
Full text
9
Ali, Zafar, Uzma Abdullah, and Ambrin Fatima. "Intellectual Disabilities." In Omics Technologies for Clinical Diagnosis and Gene Therapy: Medical Applications in Human Genetics, 269–82. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/9789815079517122010019.
Full textAbstract:
Intellectual disability (ID) is caused by the disruption of neurodevelopmental processes. Its diagnosis and severity are defined in terms of an Intelligence Quotient score of <70. ID has diverse presentations and clinical overlaps with other cognitive disorders such as autism spectrum disorder and microcephaly. ID has a diverse etiology encompassing both environmental and genetic insults to the developing brain. The precise diagnosis is challenging but crucial for prognosis and risk assessment for future pregnancies. The suspected cases of genetic ID often follow a strategic series of tests for diagnosis. There is no effective cure for this disorder except in the cases of early diagnosed metabolic disorders. The available therapies are mostly aimed at easing the symptoms and improving the quality of life.
10
Richards, Rashna Wadia. "“You’re Nobody’s Mommy”." In Cinematic TV, 111–53. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780190071257.003.0004.
Full textAbstract:
Chapter 3 focuses on televisual appropriations of broader thematic conventions. It begins with genre and its troubled relationship with intertextuality. Due to its common association with the formulaic, genre might appear to contradict the multifaceted energies of intertextuality. Far from being merely a classificatory framework, however, genre too can be seen as a theory of intersection and entanglement. This chapter carefully teases out an alternative understanding of genre as overlap. It analyzes Damages (FX, 2007–10; Audience Network, 2011–12) as a legal drama that overlaps with the puzzle film and the maternal melodrama. These overlaps, Chapter 3 concludes, also enable reflection on the looseness of genres and their unexpected kinship with intertextuality.
Conference papers on the topic "Gene overlaps"
1
Banerjee, Nilanjana, Vinay Varadan, Sitharthan Kamalakaran, and Angel Janevski. "Towards identification of thematic overlaps in gene sets." In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2009. http://dx.doi.org/10.1109/gensips.2009.5174372.
Full text
2
Boudewijn, Ilse M., Alen Faiz, Katrina Steiling, Erica van der Wiel, Eef Telenga, Susan Hoonhorst, Nick ten Hacken, et al. "A nasal gene expression profile differentiates individuals with and without COPD and overlaps bronchial gene expression." In ERS International Congress 2017 abstracts. European Respiratory Society, 2017. http://dx.doi.org/10.1183/1393003.congress-2017.pa4470.
Full text
3
Bosacoma, Adelaida, Daniel Aguilar, Tanja Paul, Isabel Blanco, Olga Tura-Ceide, Joan Albert Barberà, and Victor I. Peinado. "The Gene Signature of Lungs from Guinea Pigs Exposed to Cigarette Smoke Overlaps with that of Human with COPD." In ERS International Congress 2020 abstracts. European Respiratory Society, 2020. http://dx.doi.org/10.1183/13993003.congress-2020.2707.
Full text
4
Sadler, J. Evan. "THE MOLECULAR BIOLOGY OF VON WILLEBRAND FACTOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643930.
Full textAbstract:
Human von Willebrand factor (vWF) is a plasma glycoprotein that is synthesized by endothelial cells and megakaryocytes, and perhaps by syncytiotrophoblast of placenta. The biosynthesis of vWF is very complex, involving proteolytic processing, glycosyla-tion, disulfide bond formation, and sulfation. Mature vWF consists of a single subunit of ∼ 250,000 daltons that is assembled into multimer ranging from dimers to species of over 10 million daltons. vWF performs its essential hemostatic function through several binding interactions, forming a bridge between specific receptors on the platelet surface and components of damaged vascular subendothelial connective tissue. Inherited deficiency of vWF, or von Willebrand disease (vWD), is the most common genetically transmitted bleeding disorder worldwide. The last two years has been a time of very rapid progress in understanding the molecular biology of vWF. Four research groups have independently isolated and sequenced the 9 kilobase full-length vWF cDNA. The predicted protein sequence has provided a foundation for understanding the biosynthetic processing of vWF, and has clarified the relationship between vWF and a 75-100 kilodalton plasma protein of unknown function, von Willebrand antigen II (vWAgll)/ vWAgll is co-distributed with vWF in endothelial cells and platelets, and is deficient in patients with vWD. The cDNA sequence of vWF shows that vWAgll is a rather large pro-peptide for vWF, explaining the biochemical and genetic association between the two proteins. vWF has a complex evolutionary history marked by many separate gene segment duplications. The primary structure of the protein contains four distinct types of repeated domains present in two to four copies each. Repeated domains account for over 90 percent of the protein sequence. This sequence provides a framework for ordering the functional domains that have been defined by protein chemistry methods. A tryptic peptide from the amino-terminus of vWF that overlaps domain D3 binds to factor VIII and also appears to bind to heparin. Peptides that include domain A1 bind to collagens, to heparin, and to platelet glycoprotein Ib. A second collagen binding site appears to lie within domain A3. The vWF cDNA has been expressed in heterologous cells to produce small amounts of functionally and structurally normal vWF, indicating that endothelial cells are not unique in their ability to process and assemble vWF multimers. Site-directed mutagenesis has been used to show that deletion of the propeptide of vWF prevents the formation of multimers. Cloned cDNA probes have been employed to isolate vWF genomic DNA from cosmid and λ-phage libraries, and the size of the vWF gene appears to be ∼ 150 kilobases. The vWF locus has been localized to human chromosome 12p12—pter. Several intragenic RFLPs have been characterized. With them, vWF has been placed on the human genetic linkage map as the most telomeric marker currently available for the short arm of chromosome 12. A second apparently homologous locus has been identified on chromosome 22, but the relationship of this locus to the authentic vWF gene is not yet known. The mechanism of vWD has been studied by Southern blotting of genomic DNA with cDNA probes in a few patients. Three unrelated pedigrees have been shown to have total deletions of the vWF gene as the cause of severe vWD (type III). This form of gene deletion appears to predispose to the development of inhibitory alloantibodies to vWF during therapy with cryoprecipitate. During the next several years recombinant DNA methods will continue to contribute our understanding of the evolution, biosynthesis, and structure-function relationships of vWF, as well as the mechanism of additional variants of vWD at the level of gene structure.
5
Laug, Walter E. "HETEROGENOUS EXPRESSION OF PLASMINOGEN ACTIVATOR (PA) GENES IN THE HUMAN SARCOMA CELL LINE HT1080." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644395.
Full textAbstract:
Tumor cell derived PA activities are of crucial importance for tissue invasion and destruction by tumor cells. Therefore, we studied the expression of the PA genes in HT1080 cells using immunoenzymatic methods and specific PA gene probes.Immunenzymatic methods allowed only for the detection of urokinase like PA (u-PA) activities in HT1080 cells which was suppressed by treatment of the cells with dexamethasone (10-7 m). Despite the lack of u-PA activities, the cells still degraded extracellular tissue glycoproteins. Northern blot analysis with specific PA gene probe showed that HT1080 cells express both tissue type PA (t-PA) and u-PA. The enzymatic activities of t-PA were most likely masked by the simultaneous production of inhibitors of PA (PAI). Treatment of HT1080 cells with dexamethasone resulted in increased transcription of t-PA and decreased expression of the u-PA gene, explaining the unchanged tissue destruction by dexamethasone treated HT1080 cells.Cell clones secreting either large or small amounts of enzymatic PA activities were isolated from the parental HT1080 cell line using a fibrin agarose overlay technique.The expression of the u-PA gene was enhanced in high secreting PA clones compared to low secreting PA clones when analyzed on Northern blots. This heterogenous expression of the u-PA gene within the HT1080 cell line was confirmed by in situ hybridization with a specific u-PA gene probe.These findings demonstrate that PA gene expression can be missed with immunenzymatic methods due to simultaneous production of inhibitors of PA. In addition our results show that the expression of a given PA gene may be heterogenous on the cellular level within an established tumor cell line. These findings, therefore, suggest cellular variation of PA gene expression in tumor which may be of fundamental importance for tissue invasion and metastasis by cancer cells.
6
Saferali, A., J. H. Yun, S. Lee, R. Chase, P. Castaldi, and C. P. Hersh. "Gene Expression Signature of Asthma COPD Overlap." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4555.
Full text
7
Badia, Bruno de Mattos Lombardi, Roberta Ismael Lacerda Machado, Wladimir Bocca Vieira de Rezende Pinto, Igor Braga Farias, José Marcos Vieira de Albuquerque Filho, Paulo Victor Sgobbi de Souza, Márcio Luiz Escórcio Bezerra, and Acary Souza Bulle Oliveira. "Blurred Lines – Is the distinction between CIDP and CMT always clear?" In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.015.
Full textAbstract:
Introduction: Charcot-Marie-Tooth disease (CMT) is a group of inherited sensorymotor neuropathies with variable age of onset, clinical and neurophysiological patterns but often with a chronic slow progression. Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is an immune-mediated neuropathy with a relapsing clinical course and typically good response to corticosteroids or other therapies. The distinction between these two conditions can be made with aid of clinical history, neurophysiological studies and genetic testing in the vast majority of cases. However, an overlap between them can occur. Methods: We describe four Brazilian patients under clinical follow-up at our service with genetic diagnosis of CMT and clinical and neurophysiological features compatible with a concurrent CIDP diagnosis. Results: Four cases of different CMT subtypes with co-occurrence of an immunemediated neuropathy compatible with CIDP were reported. The patients were all unrelated, two males and two females, age range from 3 to 45 years. The genetic mutations were the following: hemizygous pathogenic variant c.514C>T (p.Pro172Ser) in GJB1 gene (CMT1X), duplication of PMP22 gene (CMT1A), simple heterozygous pathogenic variant c.188_190delCCT (p.Ser64del) in MPZ gene (CMT1B) and homozygous pathogenic variant c.122T>C (p.Ile41Thr) in FIG4 gene (CMT4J). All four patients presented with relapsing or subacute worsening of neurological symptoms, demyelinating non-uniform features in neurophysiological studies including conduction blocks and elevated cerebrospinal fluid (CSF) protein levels without pleocytosis. Three patients (3/4) improved after treatment with corticosteroids, immunoglobulin or cyclophosphamide with variable clinical response. Conclusion: CMT and CIDP are different conditions involving the peripheral nervous system and the distinction between them usually is possible with the appropriate assessment. The overlap between them is possible and we report four cases with this association.
8
Sarbazi-Azad, Saeed, and Mohammad Saniee Abadeh. "Gene Selection for Cancer Classification from Microarray Data Using Data Overlap Measure." In 2018 25th National and 3rd International Iranian Conference on Biomedical Engineering (ICBME). IEEE, 2018. http://dx.doi.org/10.1109/icbme.2018.8703565.
Full text
9
Ying, Li, Lei Na, and Ma Jian. "Statistical Analysis of Gene Co-Expression Networks by Maximal Overlap Discrete Wavelet Transform." In 2009 2nd International Conference on Biomedical Engineering and Informatics. IEEE, 2009. http://dx.doi.org/10.1109/bmei.2009.5305153.
Full text
10
Wald, Randall, Taghi Khoshgoftaar, and David Dittman. "A New Fixed-Overlap Partitioning Algorithm for Determining Stability of Bioinformatics Gene Rankers." In 2012 Eleventh International Conference on Machine Learning and Applications (ICMLA). IEEE, 2012. http://dx.doi.org/10.1109/icmla.2012.149.
Full textReports on the topic "Gene overlaps"
1
Horwitz, Benjamin A., and Barbara Gillian Turgeon. Fungal Iron Acquisition, Oxidative Stress and Virulence in the Cochliobolus-maize Interaction. United States Department of Agriculture, March 2012. http://dx.doi.org/10.32747/2012.7709885.bard.
Full textAbstract:
Our project focused on genes for high affinity iron acquisition in Cochliobolus heterostrophus, a necrotrophic pathogen of maize, and their intertwined relationship to oxidative stress status and virulence of the fungus on the host. An intriguing question was why mutants lacking the nonribosomal peptide synthetase (NRPS) gene (NPS6) responsible for synthesis of the extracellular siderophore, coprogen, are sensitive to oxidative stress. Our overall objective was to understand the mechanistic connection between iron stress and oxidative stress as related to virulence of a plant pathogen to its host. The first objective was to examine the interface where small molecule peptide and reactive oxygen species (ROS) mechanisms overlap. The second objective was to determine if the molecular explanation for common function is common signal transduction pathways. These pathways, built around sensor kinases, response regulators, and transcription factors may link sequestering of iron, production of antioxidants, resistance to oxidative stress, and virulence. We tested these hypotheses by genetic manipulation of the pathogen, virulence assays on the host plant, and by following the expression of key fungal genes. An addition to the original program, made in the first year, was to develop, for fungi, a genetically encoded indicator of redox state based on the commercially available Gfp-based probe pHyper, designed for animal cell biology. We implemented several tools including a genetically encoded indicator of redox state, a procedure to grow iron-depleted plants, and constructed a number of new mutants in regulatory genes. Lack of the major Fe acquisition pathways results in an almost completely avirulent phenotype, showing how critical Fe acquisition is for the pathogen to cause disease. Mutants in conserved signaling pathways have normal ability to regulate NPS6 in response to Fe levels, as do mutants in Lae1 and Vel1, two master regulators of gene expression. Vel1 mutants are sensitive to oxidative stress, and the reason may be underexpression of a catalase gene. In nps6 mutants, CAT3 is also underexpressed, perhaps explaining the sensitivity to oxidative stress. We constructed a deletion mutant for the Fe sensor-regulator SreA and found that it is required for down regulation of NPS6 under Fe-replete conditions. Lack of SreA, though, did not make the fungus over-sensitive to ROS, though the mutant had a slow growth rate. This suggests that overproduction of siderophore under Fe-replete conditions is not very damaging. On the other hand, increasing Fe levels protected nps6 mutants from inhibition by ROS, implying that Fe-catalyzed Fenton reactions are not the main factor in its sensitivity to ROS. We have made some progress in understanding why siderophore mutants are sensitive to oxidative stress, and in doing so, defined some novel regulatory relationships. Catalase genes, which are not directly related to siderophore biosynthesis, are underexpressed in nps6 mutants, suggesting that the siderophore product (with or without bound Fe) may act as a signal. Siderophores, therefore, could be a target for intervention in the field, either by supplying an incorrect signal or blocking a signal normally provided during infection. We already know that nps6 mutants cause smaller lesions and have difficulty establishing invasive growth in the host. Lae1 and Vel1 are the first factors shown to regulate both super virulence conferred by T-toxin, and basic pathogenicity, due to unknown factors. The mutants are also altered in oxidative stress responses, key to success in the infection court, asexual and sexual development, essential for fungal dissemination in the field, aerial hyphal growth, and pigment biosynthesis, essential for survival in the field. Mutants in genes encoding NADPH oxidase (Nox) are compromised in development and virulence. Indeed the triple mutant, which should lack all Nox activity, was nearly avirulent. Again, gene expression experiments provided us with initial evidence that superoxide produced by the fungus may be most important as a signal. Blocking oxidant production by the pathogen may be a way to protect the plant host, in interactions with necrotrophs such as C. heterostrophus which seem to thrive in an oxidant environment.
2
Horwitz, Benjamin, and Barbara Gillian Turgeon. Secondary Metabolites, Stress, and Signaling: Roles and Regulation of Peptides Produced by Non-ribosomal Peptide Synthetases. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696522.bard.
Full textAbstract:
Fungal pathogens of plants produce a diverse array of small molecules. Often referred to as secondary metabolites because they were thought to be dispensable for basic functions, they may indeed have central roles as signals for the fungal cell, and in interactions with the host. We have identified more than a dozen genes encoding nonribosomal peptide synthetases (NPS) in Cochliobolusheterostrophus, the agent of southern corn leaf blight. The aim of this project was to identify roles of these genes in stress responses and signaling. The first objective was to test a complete collection of C. heterostrophus nonribosomal peptide synthetase (NRPS)-encoding gene deletion mutant and wildtype (WT) strains for sensitivity to various agents of oxidative (ROS) and nitrosative (RNOS) stress, in vitro. The second objective and next step in this part of the project was to study the relevance of sensitivity to ROS and RNOS in the host pathogen interaction, by measuring the production of ROS and RNOS in planta, when plants are inoculated with wild type and mutant strains. A third objective was to study expression of any genes shown to be involved in sensitivity to ROS or RNOS, in vitro and in planta. Another objective was to determine if any of the genes involved in oxidative or nitrosative stress responses are regulated by components of signal transduction pathways (STP) that we have identified and to determine where mechanisms overlap. Study of the collection of nps mutants identified phenotypes relevant for virulence, development and oxidative stress resistance for two of the genes, NPS2 and NPS6. Mutants in genes related to RNOS stress have no virulence phenotypes, while some of those related to ROS stress have reduced virulence as well as developmental phenotypes, so we focused primarily on ROS stress pathways. Furthermore, the identification of NPS2 and NPS6 as encoding for NRPS responsible for siderophore biosynthesis lent a new focus to the project, regulation by Fe. We have not yet developed good methods to image ROS in planta and work in this direction is continuing. We found that NPS6 expression is repressed by Fe, responding over the physiological Fe concentration range. Studying our collection of mutants, we found that conserved MAPK and G protein signal transduction pathways are dispensable for Fe regulation of NPS6, and initiated work to identify other pathways. The transcription factor SreA is one candidate, and is responsible for part, but not all, of the control of NPS6 expression. The results of this project show that the pathogen contends with oxidative stress through several signaling pathways. Loss of the siderophore produced by Nps6 makes the fungus sensitive to oxidative stress, and decreases virulence, suggesting a central role of the ability to sequester and take up extracellular iron in the host-pathogen interaction. Siderophores, and manipulation of Fe levels, could be targets for new strategies to deal with fungal pathogens of maize and other plants.
3
Pirone, Thomas P., Benjamin Raccah, and Nor Chejanovsky. Vector Specificity in Potyvirus Transmission: Role of the Helper Component. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7586456.bard.
Full textAbstract:
Objectives: The overall objective of this research was to gain a better understanding of how potyviruses interact with their aphid vectors. The aim was to design new approaches for prevention of potyvirus spread by aphids. The sub-objectives included: (1). Determination of which of the HCs of different potyviruses effect efficient transmission by specific aphid vectors; (2). Determine regions in the HC that play a role in their compatibility with the vector; (3). Determine the factors within the aphid stylets that modify HC activity in transmission. Background of the topic: Background to the topic: Potyviruses are typical non persistent viruses. They are retained within the vector’s stylets and rapidly lost by the vector. Some potyviruses greatly differ in their ability to be transmitted by different aphid species. The present work centered on analyzing factors that may modify the interactions between the "helper component"(HC), the virions and the aphid species involved. Major conclusions, solutions and achievements: It was established that specificity of transmission may depend on aphid species used. It was also shown that specificity may depend on the affinity between HC and virion. However, the attempts to create activechimericTEV/TuMVHCs or ZYMV/TuMVHCs to identify the regions that determine interaction with a specific vector(s), were not successful. More progress was attained in objective 3: In Kentucky, tests were conducted to ascertain retention tobacco vein mottling virus (TVMV) HC in the stylets of L. erysimicompared to that in M. persicae. Ultra-thin section of stylets of aphids that fed on either TuMVHC or TVMVHC antibodies were treated with gold-labeled goat anti-rabbit antibodies.TuMV was seen in 25% the stylets of L. erysimi when they acquired TuMVHC but not when they acquired TVMVHC. In M. persicae, TVMVHC was present in 30% of the stylets. . Transmission with TuMVHC was not affected by treatment with L. erysimi saliva whereas transmission with PVYHC (which also is not functional in L. erysimi) was consistently reduced by about half. Saliva from M. persicaehad essentially no effect on either HC. The possible role aphid cuticle proteins (which are found on the stylets surface) in the association with the potyviralHC was investigated in Israel. This was done adopting two approaches: (a) isolation of cuticular proteins from aphid cuticle; (b) screening for genes encoding cuticular proteins. In the first approach, we succeeded in extracting proteins from whole homogenized M. persicaeusing concentrated urea. The extracted protein served for preparation of anti cuticular antibodies. In overlay experiments it was found that cuticular proteins specifically bind to ZYMVHC. In addition, a cDNA library of M. persicae has been prepared. Genes encoding for cuticular proteins were ascertained using antibodies to cuticular proteins. This allowed reporting the sequence of the first cuticular gene of aphids and comparing it in six aphid species. Implications, scientific and agricultural: Achievements: (1) Proofs were provided for the role of the specificity of the aphid species to the HC of certain potyviruses; (2) aphid’s saliva was found to affects transmission efficiency; (3) cuticle protein genes were isolated for the first time from aphid species and an association of cuticle protein with the potyviralHC was discerned. Agricultural and/or economic impact of the research findings: At this stage of research, our finding do not bear an agricultural or economic impact.