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https://www.readbyqxmd.com/read/29771304/laboratory-evolution-for-forced-glucose-xylose-co-consumption-enables-identification-of-mutations-that-improve-mixed-sugar-fermentation-by-xylose-fermenting-saccharomyces-cerevisiae
#1
Ioannis Papapetridis, Maarten D Verhoeven, Sanne J Wiersma, Maaike Goudriaan, Antonius J A van Maris, Jack T Pronk
Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilization of these sugars in batch cultures of Saccharomyces cerevisiae. To force simultaneous utilization of xylose and glucose, the genes encoding glucose-6-phosphate isomerase (PGI1) and ribulose-5-phosphate epimerase (RPE1) were deleted in a xylose-isomerase-based xylose-fermenting strain with a modified oxidative pentose-phosphate pathway...
May 15, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29769396/bulk-electroporation-mediated-gene-transfer-into-xenopus-tadpole-brain
#2
Cristina Sáenz de Miera, Ethan Parr, Robert J Denver
In vivo gene transfer is a powerful tool for investigating protein function and gene regulation in living organisms. Delivery of plasmid DNA to the brain of Xenopus tadpoles by bulk electroporation-mediated (EM) gene transfer can be used to study the effects of ectopic gene expression on development, physiology, and behavior. It can also be used to mark cells for lineage tracing, investigate the in vivo function of gene regulatory elements when linked to a reporter gene, and introduce mutations into the genome of transfected cells, among other applications...
May 16, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29766388/molecular-evolution-of-metaplasia-to-adenocarcinoma-in-the-esophagus
#3
REVIEW
William M Grady, Ming Yu
Esophageal adenocarcinoma (EAC) develops from Barrett's esophagus (BE), a condition where the normal squamous epithelia is replaced by specialized intestinal metaplasia in response to chronic gastroesophageal acid reflux. In a minority of individuals, BE can progress to low- and high-grade dysplasia and eventually to intra-mucosal and then invasive carcinoma. BE provides researchers with a unique model to characterize the process by which a carcinoma arises from its precursor lesion. Molecular studies of BE have demonstrated that it is not simply a metaplastic tissue, but rather it harbors frequent alterations that are also present in dysplastic BE and in EAC...
May 15, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29754204/diagnosing-arvc-in-pediatric-patients-applying-the-revised-task-force-criteria-importance-of-imaging-12-lead-ecg-and-genetics
#4
Michael Steinmetz, Ulrich Krause, Peter Lauerer, Frank Konietschke, Randolph Aguayo, Christian Oliver Ritter, Andreas Schuster, Joachim Lotz, Thomas Paul, Wieland Staab
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a potentially lethal disease that is well described in adults. In pediatric patients, however, identification of patients at risk of adverse events of ARVC remains a challenge. We aimed to determine which criteria of the revised Task Force Criteria (rTFC), alone or combined, have an impact on diagnosis of ARVC when compared to disease-specific genetic mutations in pediatric patients ≤ 18 years. Between September 2010 and December 2013, 48 consecutive young patients ≤ 18 years of age (mean 14, range of 12...
May 12, 2018: Pediatric Cardiology
https://www.readbyqxmd.com/read/29752281/increased-fgf8-signaling-promotes-chondrogenic-rather-than-osteogenic-development-in-the-embryonic-skull
#5
Linnea Schmidt, Aftab Taiyab, Vida Senkus Melvin, Kenneth L Jones, Trevor Williams
The bones of the cranial vault are formed directly from mesenchymal cells through intramembranous ossification rather than via a cartilage intermediate. Formation and growth of the skull bones involves the interaction of multiple cell:cell signaling pathways, with Fibroblast Growth Factors (FGFs) and their receptors exerting prominent influence. Mutations within this pathway are the most frequent cause of craniosynostosis, which is a common human craniofacial developmental abnormality characterized by the premature fusion of the cranial sutures...
May 10, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29746888/nearly-neutral-evolution-in-ifnl3-gene-retains-the-immune-function-to-detect-and-clear-the-viral-infection-in-hcv
#6
Pratichi Singh, J Febin Prabhu Dass
IFNL3 gene plays a crucial role in immune defense against viruses. It induces the interferon stimulated genes (ISGs) with antiviral properties by activating the JAK-STAT pathway. In this study, we investigated the evolutionary force involved in shaping the IFNL3 gene to perform its downstream function as a regulatory gene in HCV clearance. We have selected 25 IFNL3 coding sequences with human gene as a reference sequence and constructed a phylogeny. Furthermore, rate of variation, substitution saturation test, phylogenetic informativeness and differential selection were also analysed...
May 7, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29743200/experimental-evolution-as-a-high-throughput-screen-for-genetic-adaptations
#7
Vaughn S Cooper
Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving populations are influenced by all population genetic forces, including selection, mutation, drift, and recombination, and the relative contributions of these forces may be seen as mysterious. Here, I describe why the outcomes of experimental evolution should be viewed with greater certainty because the force of selection typically dominates...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29741611/crispr-cas9-editing-in-human-pluripotent-stem-cell-cardiomyocytes-highlights-arrhythmias-hypocontractility-and-energy-depletion-as-potential-therapeutic-targets-for-hypertrophic-cardiomyopathy
#8
Diogo Mosqueira, Ingra Mannhardt, Jamie R Bhagwan, Katarzyna Lis-Slimak, Puspita Katili, Elizabeth Scott, Mustafa Hassan, Maksymilian Prondzynski, Stephen C Harmer, Andrew Tinker, James G W Smith, Lucie Carrier, Philip M Williams, Daniel Gaffney, Thomas Eschenhagen, Arne Hansen, Chris Denning
Aims: Sarcomeric gene mutations frequently underlie hypertrophic cardiomyopathy (HCM), a prevalent and complex condition leading to left ventricle thickening and heart dysfunction. We evaluated isogenic genome-edited human pluripotent stem cell-cardiomyocytes (hPSC-CM) for their validity to model, and add clarity to, HCM. Methods and results: CRISPR/Cas9 editing produced 11 variants of the HCM-causing mutation c.C9123T-MYH7 [(p.R453C-β-myosin heavy chain (MHC)] in 3 independent hPSC lines...
May 8, 2018: European Heart Journal
https://www.readbyqxmd.com/read/29739937/networks-of-genetic-similarity-reveal-non-neutral-processes-shape-strain-structure-in-plasmodium-falciparum
#9
Qixin He, Shai Pilosof, Kathryn E Tiedje, Shazia Ruybal-Pesántez, Yael Artzy-Randrup, Edward B Baskerville, Karen P Day, Mercedes Pascual
Pathogens compete for hosts through patterns of cross-protection conferred by immune responses to antigens. In Plasmodium falciparum malaria, the var multigene family encoding for the major blood-stage antigen PfEMP1 has evolved enormous genetic diversity through ectopic recombination and mutation. With 50-60 var genes per genome, it is unclear whether immune selection can act as a dominant force in structuring var repertoires of local populations. The combinatorial complexity of the var system remains beyond the reach of existing strain theory and previous evidence for non-random structure cannot demonstrate immune selection without comparison with neutral models...
May 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29739933/recurrent-hotspot-mutations-in-hras-q61-and-pi3k-akt-pathway-genes-as-drivers-of-breast-adenomyoepitheliomas
#10
Felipe C Geyer, Anqi Li, Anastasios D Papanastasiou, Alison Smith, Pier Selenica, Kathleen A Burke, Marcia Edelweiss, Huei-Chi Wen, Salvatore Piscuoglio, Anne M Schultheis, Luciano G Martelotto, Fresia Pareja, Rahul Kumar, Alissa Brandes, Dan Fan, Thais Basili, Arnaud Da Cruz Paula, John R Lozada, Pedro Blecua, Simone Muenst, Achim A Jungbluth, Maria P Foschini, Hannah Y Wen, Edi Brogi, Juan Palazzo, Brian P Rubin, Charlotte K Y Ng, Larry Norton, Zsuzsanna Varga, Ian O Ellis, Emad A Rakha, Sarat Chandarlapaty, Britta Weigelt, Jorge S Reis-Filho
Adenomyoepithelioma of the breast is a rare tumor characterized by epithelial-myoepithelial differentiation, whose genetic underpinning is largely unknown. Here we show through whole-exome and targeted massively parallel sequencing analysis that whilst estrogen receptor (ER)-positive adenomyoepitheliomas display PIK3CA or AKT1 activating mutations, ER-negative adenomyoepitheliomas harbor highly recurrent codon Q61 HRAS hotspot mutations, which co-occur with PIK3CA or PIK3R1 mutations. In two- and three-dimensional cell culture models, forced expression of HRASQ61R in non-malignant ER-negative breast epithelial cells with or without a PIK3CAH1047R somatic knock-in results in transformation and the acquisition of the cardinal features of adenomyoepitheliomas, including the expression of myoepithelial markers, a reduction in E-cadherin expression, and an increase in AKT signaling...
May 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29734251/myd88-card11-and-cd79b-oncogenic-mutations-are-rare-events-in-the-indian-cohort-of-de-novo-nodal-diffuse-large-b-cell-lymphoma
#11
Vaishali Aggarwal, Ashim Das, Amanjit Bal, Radhika Srinivasan, Reena Das, Gaurav Prakash, Pankaj Malhotra, Subhash Varma
Diffuse large B-cell lymphoma (DLBCL) has a heterogenous biological behavior, and the western literature has reported activating oncogenic mutations in myeloid differentiation primary response gene 88 (MYD88), in conjunction with B-cell receptor signaling pathway genes, CARD11 and CD79B as the driving force for activating the NF-κB pathway implicated in the pathogenesis of DLBCL. The mutation profile of MYD88 genes was evaluated by Sanger sequencing in a cohort of 97 patients [DLBCL (N=55), non-DLBCL lymphomas (N=30), reactive lymphadenopathy (N=10), and 2 cases of lymphoplasmacytic lymphoma (positive control)]...
May 4, 2018: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/29716942/mechanosensitive-gene-regulation-by-myocardin-related-transcription-factors-is-required-for-cardiomyocyte-integrity-in-load-induced-ventricular-hypertrophy
#12
Michael A Trembley, Pearl Quijada, Esperanza Agullo-Pascual, Kevin M Tylock, Mert Colpan, Ronald A Dirkx, Jason R Myers, Deanne M Mickelsen, Karen de Mesy Bentley, Eli Rothenberg, Christine S Moravec, Jeffrey D Alexis, Carol C Gregorio, Robert T Dirksen, Mario Delmar, Eric M Small
Background -Hypertrophic cardiomyocyte (CM) growth and dysfunction accompanies various forms of heart disease. The mechanisms responsible for transcriptional changes that impact cardiac physiology and the transition to heart failure (HF) are not well understood. The intercalated disc (ID) is a specialized intercellular junction coupling CM electrical activity and force transmission, and is gaining attention as a mechanosensitive signaling hub and hotspot for causative mutations in cardiomyopathy. Methods -Transmission electron microscopy, confocal microscopy, and single-molecule localization microscopy (SMLM) were used to examine changes in ID structure and protein localization in the murine and human heart...
May 1, 2018: Circulation
https://www.readbyqxmd.com/read/29713479/pulmonary-involvement-in-fabry-disease-effect-of-plasma-globotriaosylsphingosine-and-time-to-initiation-of-enzyme-replacement-therapy
#13
Daniel Franzen, Sarah R Haile, David C Kasper, Thomas P Mechtler, Andreas J Flammer, Pierre A Krayenbühl, Albina Nowak
Introduction: Anderson-Fabry disease (AFD) is an X-linked lysosomal storage disorder caused by mutations of GLA gene leading to reduced α-galactosidase activity and resulting in a progressive accumulation of globotriaosylceramide (Gb3) and its deacylated derivative, globotriaosyl-sphingosine (Lyso-Gb3). Plasma Lyso-Gb3 levels serve as a disease severity and treatment monitoring marker during enzyme replacement therapy (ERT). Methods: Adult patients with AFD who had yearly pulmonary function tests between 1999 and 2015 were eligible for this observational study...
2018: BMJ Open Respiratory Research
https://www.readbyqxmd.com/read/29712824/green-function-of-correlated-genes-in-a-minimal-mechanical-model-of-protein-evolution
#14
Sandipan Dutta, Jean-Pierre Eckmann, Albert Libchaber, Tsvi Tlusty
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated the search for physical links between the observed genetic and dynamic cooperativity. We outline here a simplified theory of protein, which relates sequence correlations to physical interactions and to the emergence of mechanical function. Our protein is modeled as a strongly coupled amino acid network with interactions and motions that are captured by the mechanical propagator, the Green function...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29709087/identification-of-sarcomeric-variants-in-probands-with-a-clinical-diagnosis-of-arrhythmogenic-right-ventricular-cardiomyopathy-arvc
#15
Brittney Murray, Edgar T Hoorntje, Anneline S J M Te Riele, Crystal Tichnell, Jeroen F van der Heijden, Harikrishna Tandri, Maarten P van den Berg, Jan D H Jongbloed, Arthur A M Wilde, Richard N W Hauer, Hugh Calkins, Daniel P Judge, Cynthia A James, J Peter van Tintelen, Dennis Dooijes
AIMS: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiomyopathy characterized by ventricular arrhythmias and sudden death. Currently 60% of patients meeting Task Force Criteria (TFC) have an identifiable mutation in one of the desmosomal genes. As much overlap is described between other cardiomyopathies and ARVC, we examined the prevalence of rare, possibly pathogenic sarcomere variants in the ARVC population. METHODS: One hundred and thirty-seven (137) individuals meeting 2010 TFC for a diagnosis of ARVC, negative for pathogenic desmosomal variants, TMEM43, SCN5A, and PLN were screened for variants in the sarcomere genes (ACTC1, MYBPC3, MYH7, MYL2, MYL3, TNNC1, TNNI3, TNNT2 and TPM1) through either clinical or research genetic testing...
April 30, 2018: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/29702698/comprehensive-behavioral-analysis-of-the-cdkl5-knockout-mice-revealed-significant-enhancement-in-anxiety-and-fear-related-behaviors-and-impairment-in-both-acquisition-and-long-term-retention-of-spatial-reference-memory
#16
Kosuke Okuda, Keizo Takao, Aya Watanabe, Tsuyoshi Miyakawa, Masashi Mizuguchi, Teruyuki Tanaka
Mutations in the Cyclin-dependent kinase-like 5 (CDKL5) gene cause severe neurodevelopmental disorders. Recently we have generated Cdkl5 KO mice by targeting exon 2 on the C57BL/6N background, and demonstrated postsynaptic overaccumulation of GluN2B-containing N-methyl-D-aspartate (NMDA) receptors in the hippocampus. In the current study, we subjected the Cdkl5 KO mice to a battery of comprehensive behavioral tests, aiming to reveal the effects of loss of CDKL5 in a whole perspective of motor, emotional, social, and cognition/memory functions, and to identify its undetermined roles...
2018: PloS One
https://www.readbyqxmd.com/read/29690995/two-complement-receptor-one-alleles-have-opposing-associations-with-cerebral-malaria-and-interact-with-%C3%AE-thalassaemia
#17
D Herbert Opi, Olivia Swann, Alexander Macharia, Sophie Uyoga, Gavin Band, Carolyne M Ndila, Ewen Harrison, Mahamadou A Thera, Abdoulaye K Kone, Dapa A Diallo, Ogobara K Doumbo, Kirsten E Lyke, Christopher Plowe, Joann M Moulds, Mohammed Shebbe, Neema Mturi, Norbert Peshu, Kathryn Maitland, Ahmed Raza, Dominic P Kwiatkowski, Kirk A Rockett, Thomas Williams, J Alexandra Rowe
Malaria has been a major driving force in the evolution of the human genome. In sub-Saharan African populations, two neighbouring polymorphisms in the Complement Receptor One ( CR1 ) gene, named Sl2 and McCb , occur at high frequencies, consistent with selection by malaria. Previous studies have been inconclusive. Using a large case-control study of severe malaria in Kenyan children and statistical models adjusted for confounders, we estimate the relationship between Sl2 and McCb and malaria phenotypes, and find they have opposing associations...
April 25, 2018: ELife
https://www.readbyqxmd.com/read/29688316/diagnostic-and-therapeutic-strategies-for-arrhythmogenic-right-ventricular-dysplasia-cardiomyopathy-patient
#18
Weijia Wang, Cynthia A James, Hugh Calkins
Arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is a rare inherited heart muscle disease characterized by ventricular tachyarrhythmia, predominant right ventricular dysfunction, and sudden cardiac death. Its pathophysiology involves close interaction between genetic mutations and exposure to physical activity. Mutations in genes encoding desmosomal protein are the most common genetic basis. Genetic testing plays important roles in diagnosis and screening of family members. Syncope, palpitation, and lightheadedness are the most common symptoms...
April 23, 2018: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/29686627/burst-like-transcription-of-mutant-and-wildtype-myh7-alleles-as-possible-origin-of-cell-to-cell-contractile-imbalance-in-hypertrophic-cardiomyopathy
#19
Judith Montag, Kathrin Kowalski, Mirza Makul, Pia Ernstberger, Ante Radocaj, Julia Beck, Edgar Becker, Snigdha Tripathi, Britta Keyser, Christian Mühlfeld, Kirsten Wissel, Andreas Pich, Jolanda van der Velden, Cristobal G Dos Remedios, Andreas Perrot, Antonio Francino, Francesco Navarro-López, Bernhard Brenner, Theresia Kraft
Hypertrophic Cardiomyopathy (HCM) has been related to many different mutations in more than 20 different, mostly sarcomeric proteins. While development of the HCM-phenotype is thought to be triggered by the different mutations, a common mechanism remains elusive. Studying missense-mutations in the ventricular beta-myosin heavy chain (β-MyHC, MYH7 ) we hypothesized that significant contractile heterogeneity exists among individual cardiomyocytes of HCM-patients that results from cell-to-cell variation in relative expression of mutated vs...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29666399/genotype-b-of-killer-cell-immunoglobulin-like-receptor-is-related-with-gastric-cancer-lesions
#20
Eric G Hernandez, Oswaldo Partida-Rodriguez, Margarita Camorlinga-Ponce, Miriam Nieves-Ramirez, Irma Ramos-Vega, Javier Torres, Martha Perez-Rodriguez
NK cells are important in innate immunity for their capacity to kill infected or cancer cells. The killer cell immunoglobulin-like receptors (KIR) are a family of polymorphic genes with inhibitory and activating functions. The main driving force for gastric cancer (GC) development is a chronic response, which causes an increase of NK cells in the gastric mucosa. The aim of this work was to study polymorphisms in KIR genes in patients with either GC or non-atrophic gastritis (NAG). We studied 242 patients (130 with NAG and 112 with GC) and contrasted with 146 asymptomatic individuals...
April 17, 2018: Scientific Reports
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