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Mutational robustness

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https://www.readbyqxmd.com/read/28727984/gba-analysis-in-next-generation-era-pitfalls-challenges-and-possible-solutions
#1
Stefania Zampieri, Silvia Cattarossi, Bruno Bembi, Andrea Dardis
Mutations in the gene encoding the lysosomal enzyme acid β-glucosidase (GBA) are responsible for Gaucher disease and represent the main genetic risk factor for developing Parkinson disease. In past years, next-generation sequencing (NGS) technology has been applied for the molecular analysis of the GBA gene, both as a single gene or as part of gene panels. However, the presence of complex gene-pseudogene rearrangements, resulting from the presence of a highly homologous pseudogene (GBAP1) located downstream of the GBA gene, makes NGS analysis of GBA challenging...
July 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28727779/contemporary-status-of-insecticide-resistance-in-the-major-aedes-vectors-of-arboviruses-infecting-humans
#2
REVIEW
Catherine L Moyes, John Vontas, Ademir J Martins, Lee Ching Ng, Sin Ying Koou, Isabelle Dusfour, Kamaraju Raghavendra, João Pinto, Vincent Corbel, Jean-Philippe David, David Weetman
Both Aedes aegytpi and Ae. albopictus are major vectors of 5 important arboviruses (namely chikungunya virus, dengue virus, Rift Valley fever virus, yellow fever virus, and Zika virus), making these mosquitoes an important factor in the worldwide burden of infectious disease. Vector control using insecticides coupled with larval source reduction is critical to control the transmission of these viruses to humans but is threatened by the emergence of insecticide resistance. Here, we review the available evidence for the geographical distribution of insecticide resistance in these 2 major vectors worldwide and map the data collated for the 4 main classes of neurotoxic insecticide (carbamates, organochlorines, organophosphates, and pyrethroids)...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28724579/novel-bivalent-viral-vectored-vaccines-induce-potent-humoral-and-cellular-immune-responses-conferring-protection-against-stringent-influenza-a-virus-challenge
#3
Claire M Tully, Senthil Chinnakannan, Caitlin E Mullarkey, Marta Ulaszewska, Francesca Ferrara, Nigel Temperton, Sarah C Gilbert, Teresa Lambe
Seasonal influenza viruses are a common cause of acute respiratory illness worldwide and generate a significant socioeconomic burden. Influenza viruses mutate rapidly, necessitating annual vaccine reformulation because traditional vaccines do not typically induce broad-spectrum immunity. In addition to seasonal infections, emerging pandemic influenza viruses present a continued threat to global public health. Pandemic influenza viruses have consistently higher attack rates and are typically associated with greater mortality compared with seasonal strains...
July 19, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28724573/a-single-dose-of-peripherally-infused-egfrviii-directed-car-t-cells-mediates-antigen-loss-and-induces-adaptive-resistance-in-patients-with-recurrent-glioblastoma
#4
Donald M O'Rourke, MacLean P Nasrallah, Arati Desai, Jan J Melenhorst, Keith Mansfield, Jennifer J D Morrissette, Maria Martinez-Lage, Steven Brem, Eileen Maloney, Angela Shen, Randi Isaacs, Suyash Mohan, Gabriela Plesa, Simon F Lacey, Jean-Marc Navenot, Zhaohui Zheng, Bruce L Levine, Hideho Okada, Carl H June, Jennifer L Brogdon, Marcela V Maus
We conducted a first-in-human study of intravenous delivery of a single dose of autologous T cells redirected to the epidermal growth factor receptor variant III (EGFRvIII) mutation by a chimeric antigen receptor (CAR). We report our findings on the first 10 recurrent glioblastoma (GBM) patients treated. We found that manufacturing and infusion of CAR-modified T cell (CART)-EGFRvIII cells are feasible and safe, without evidence of off-tumor toxicity or cytokine release syndrome. One patient has had residual stable disease for over 18 months of follow-up...
July 19, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28723063/using-cooperatively-folded-peptides-to-measure-interaction-energies-and-conformational-propensities
#5
Maziar S Ardejani, Evan T Powers, Jeffery W Kelly
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state in aqueous solution. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively yet are small enough to be chemically synthesized to measure such quantities...
July 19, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28720893/nanoplasmonic-fiber-tip-probe-detects-significant-reduction-of-intracellular-alzheimer-s-disease-related-oligomers-by-curcumin
#6
Feng Liang, Yu Wan, Diane Schaak, Joseph Ward, Xunuo Shen, Rudolph E Tanzi, Can Zhang, Qimin Quan
Considerable evidence shows critical roles of intracellular pathogenic events of Alzheimer's disease (AD). In particular, intracellular amyloid-β accumulation and oligomerization are early AD pathologic processes, which may lead to changes in inflammatory molecules and other AD-related pathological components. Curcumin and its analogs have been identified as potential drug candidates for AD. However, the effects of curcumin on intracellular AD pathologic processes remain largely unknown. Here we utilized a recently developed nanoplasmonic fiber tip probe (nFTP) technology and investigated whether curcumin leads to intracellular AD pathologic changes...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720853/complete-chloroplast-genome-sequences-of-lilium-insights-into-evolutionary-dynamics-and-phylogenetic-analyses
#7
Yun-Peng Du, Yu Bi, Feng-Ping Yang, Ming-Fang Zhang, Xu-Qing Chen, Jing Xue, Xiu-Hai Zhang
Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720156/fmr1-cgg-repeat-expansion-mutation-detection-and-linked-haplotype-analysis-for-reliable-and-accurate-preimplantation-genetic-diagnosis-of-fragile-x-syndrome
#8
Indhu-Shree Rajan-Babu, Mulias Lian, Felicia S H Cheah, Min Chen, Arnold S C Tan, Ethiraj B Prasath, Seong Feei Loh, Samuel S Chong
Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification...
July 19, 2017: Expert Reviews in Molecular Medicine
https://www.readbyqxmd.com/read/28719389/genetic-contribution-to-neurodevelopmental-outcomes-in-congenital-heart-disease-are-some-patients-predetermined-to-have-developmental-delay
#9
Caitlin K Rollins, Jane W Newburger, Amy E Roberts
PURPOSE OF REVIEW: Neurodevelopmental impairment is common in children with moderate to severe congenital heart disease (CHD). As children live longer and healthier lives, research has focused on identifying causes of neurodevelopmental morbidity that significantly impact long-term quality of life. This review will address the role of genetic factors in predicting neurodevelopmental outcome in CHD. RECENT FINDINGS: A robust literature suggests that among children with various forms of CHD, those with known genetic/extracardiac anomalies are at highest risk of neurodevelopmental impairment...
July 14, 2017: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/28719194/molecular-modeling-of-the-major-dna-adduct-formed-from-the-food-mutagen-ochratoxin-a-in-nari-2-base-deletion-duplexes-impact-of-sequence-context-and-adduct-ionization-on-conformational-preference-and-mutagenicity
#10
Preetleen Kathuria, Purshotam Sharma, Richard A Manderville, Stacey D Wetmore
Exposure to ochratoxin A (OTA), a possible human carcinogen, leads to many different DNA mutations. As a first step toward understanding the structural basis of OTA-induced mutagenicity, the present work uses a robust computational approach and a slipped mutagenic intermediate model previously studied for C(8)-dG aromatic amine adducts to analyze the conformational features of post-replication 2-base deletion DNA duplexes containing OT-dG, the major OTA lesion at the C(8) position of guanine. Specifically, a total of 960 ns of molecular dynamics simulations (excluding trial simulations) were carried out on four OT-dG ionization states in three sequence contexts within oligomers containing the NarI recognition sequence, a known hotspot for deletion mutations induced by related adducts formed from known carcinogens...
July 18, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28716709/isolation-and-characterization-of-the-5-flanking-region-of-the-human-pdxk-gene
#11
ShuoHao Huang, ZhengQing Liu, ZhenQiao Ma, JianYun Zhang, LongQuan Huang
Pyridoxal kinase is a key enzyme for the biosynthesis of pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the catalytically active form of vitamin B6, and acts as a cofactor in >140 different enzyme reactions. It is still unknown how the kinase synthesis is regulated in the cells, and nothing has been reported about the gene promoter. In the present study, based on the bioinformatics analysis of the 5'-flanking region of the human PDXK gene, we cloned the promoter region by PCR. Through the construction of a series of luciferase expression vectors containing the human PDXK promoter region, we characterized the promoter in terms of its structure and function...
July 14, 2017: Gene
https://www.readbyqxmd.com/read/28716278/single-step-blood-direct-pcr-a-robust-and-rapid-method-to-diagnose-triplet-repeat-disorders
#12
Inder Singh, Vishnu Swarup, Sunil Shakya, Vinay Goyal, Mohammed Faruq, Achal Kumar Srivastava
OBJECTIVE: DNA extraction prior to polymerase chain reaction (PCR) amplification in genetic diagnoses of triplet repeat disorders (TRDs) is tedious and labour-intensive and has the limitations of sample contamination with foreign DNA, including that from preceding samples. Therefore, we aimed to develop a rapid, robust, and cost-effective method for expeditious genetic investigation of TRDs from whole blood as a DNA template. METHODS: Peripheral blood samples were collected from 70 clinically suspected patients of progressive ataxia...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28715716/ronin-influences-the-dna-damage-response-in-pluripotent-stem-cells
#13
Bryce A Seifert, Marion Dejosez, Thomas P Zwaka
Early mammalian embryonic cells must maintain a particularly robust DNA repair system, as mutations at this developmental point have detrimental consequences for the organism. How the repair system can be tuned to fulfill such elevated requirements is largely unknown, but it may involve transcriptional regulation. Ronin (Thap11) is a transcriptional regulator responsible for vital programs in pluripotent cells. Here, we report that this protein also modulates the DNA damage response of such cells. We show that conditional Ronin knockout sensitizes embryonic stem cells (ESCs) to UV-C-induced DNA damage in association with Atr pathway activation and G2/M arrest...
July 3, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28712498/safety-security-and-policy-considerations-for-plant-genome-editing
#14
Jeffrey D Wolt
Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28712454/crispr-cas9-mediated-scanning-for-regulatory-elements-required-for-hprt1-expression-via-thousands-of-large-programmed-genomic-deletions
#15
Molly Gasperini, Gregory M Findlay, Aaron McKenna, Jennifer H Milbank, Choli Lee, Melissa D Zhang, Darren A Cusanovich, Jay Shendure
The extent to which non-coding mutations contribute to Mendelian disease is a major unknown in human genetics. Relatedly, the vast majority of candidate regulatory elements have yet to be functionally validated. Here, we describe a CRISPR-based system that uses pairs of guide RNAs (gRNAs) to program thousands of kilobase-scale deletions that deeply scan across a targeted region in a tiling fashion ("ScanDel"). We applied ScanDel to HPRT1, the housekeeping gene underlying Lesch-Nyhan syndrome, an X-linked recessive disorder...
July 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28708563/evolving-spatial-clusters-of-genomic-regions-from-high-throughput-chromatin-conformation-capture-data
#16
Xiangtao Li, Shijing Ma, Ka-Chun Wong
High-throughput chromosome-conformation-capture (Hi-C) methods have revealed a multitude of structural insights into interphase chromosomes. In this paper, we elucidate the spatial clusters of genomic regions from Hi-C contact maps by formulating the underlying problem as a global optimization problem. Given its nonconvex objective and nonnegativity constraints, we implement several evolutionary algorithms and compare their performance with non-negative matrix factorization, revealing novel insights into the problem...
July 11, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28707884/rapid-and-programmable-protein-mutagenesis-using-plasmid-recombineering
#17
Sean Andrew Higgins, Sorel Ounkap, David F Savage
Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. However, current techniques enabling comprehensive protein mutagenesis are based on PCR and require in vitro reactions involving specialized protocols and reagents. This has complicated efforts to rapidly and reliably produce desired comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space...
July 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28706145/reverse-phase-protein-array-rppa-combined-with-computational-analysis-to-unravel-relevant-prognostic-factors-in-non-small-cell-lung-cancer-nsclc-a-pilot-study
#18
Vienna Ludovini, Rita Chiari, Lorenzo Tomassoni, Chiara Antonini, Elisa Baldelli, Sara Baglivo, Annamaria Sigillino, Francesca Romana Tofanetti, Guido Bellezza, K Alex Hodge, Emanuel Petricoin, Mariaelena Pierobon, Lucio Crinò, Fortunato Bianconi
In this work high throughput technology and computational analysis were used to study two stage IV lung adenocarcinoma patients treated with standard chemotherapy with markedly different survival (128 months vs 6 months, respectively) and whose tumor samples exhibit a dissimilar protein activation pattern of the signal transduction. Tumor samples of the two patients were subjected to Reverse Phase Protein Microarray (RPPA) analysis to explore the expression/activation levels of 51 signaling proteins. We selected the most divergent proteins based on the ratio of their RPPA values in the two patients with short (s-OS) and long (l-OS) overall survival (OS) and tested them against a EGFR-IGF1R mathematical model...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28704069/potent-synchronization-of-peripheral-circadian-clocks-by-glucocorticoid-injections-in-per2-luc-clock-clock-mice
#19
Mayo Kamagata, Yuko Ikeda, Hiroyuki Sasaki, Yuta Hattori, Shinnosuke Yasuda, Shiho Iwami, Miku Tsubosaka, Ryosuke Ishikawa, Ai Todoh, Konomi Tamura, Yu Tahara, Shigenobu Shibata
In mammals, the central clock (the suprachiasmatic nuclei, SCN) is entrained mainly by the light-dark cycle, whereas peripheral clocks in the peripheral tissues are entrained/synchronized by multiple factors, including feeding patterns and endocrine hormones such as glucocorticoids. Clock-mutant mice (Clock/Clock), which have a mutation in a core clock gene, show potent phase resetting in response to light pulses compared with wild-type (WT) mice, owing to the damped and flexible oscillator in the SCN. However, the phase resetting of the peripheral clocks in Clock/Clock mice has not been elucidated...
July 13, 2017: Chronobiology International
https://www.readbyqxmd.com/read/28701330/oral-administration-of-pyrophosphate-inhibits-connective-tissue-calcification
#20
Dóra Dedinszki, Flóra Szeri, Eszter Kozák, Viola Pomozi, Natália Tőkési, Tamás Róbert Mezei, Kinga Merczel, Emmanuel Letavernier, Ellie Tang, Olivier Le Saux, Tamás Arányi, Koen van de Wetering, András Váradi
Various disorders including pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI), which are caused by inactivating mutations in ABCC6 and ENPP1, respectively, present with extensive tissue calcification due to reduced plasma pyrophosphate (PPi). However, it has always been assumed that the bioavailability of orally administered PPi is negligible. Here, we demonstrate increased PPi concentration in the circulation of humans after oral PPi administration. Furthermore, in mouse models of PXE and GACI, oral PPi provided via drinking water attenuated their ectopic calcification phenotype...
July 12, 2017: EMBO Molecular Medicine
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