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https://www.readbyqxmd.com/read/28931241/association-of-a-novel-mutation-in-the-plasmodium-falciparum-chloroquine-resistance-transporter-with-decreased-piperaquine-sensitivity
#1
Sonia Agrawal, Kara A Moser, Lindsay Morton, Michael P Cummings, Ankita Parihar, Ankit Dwivedi, Amol C Shetty, Elliott F Drabek, Christopher G Jacob, Philipp P Henrich, Christian M Parobek, Krisada Jongsakul, Rekol Huy, Michele D Spring, Charlotte A Lanteri, Suwanna Chaorattanakawee, Chanthap Lon, Mark M Fukuda, David L Saunders, David A Fidock, Jessica T Lin, Jonathan J Juliano, Christopher V Plowe, Joana C Silva, Shannon Takala-Harrison
Background: Amplified copy number in the plasmepsin II/III genes within Plasmodium falciparum has been associated with decreased sensitivity to piperaquine. To examine this association and test whether additional loci might also contribute, we performed a genome-wide association study of ex vivo P. falciparum susceptibility to piperaquine. Methods: Plasmodium falciparum DNA from 183 samples collected primarily from Cambodia was genotyped at 33716 genome-wide single nucleotide polymorphisms (SNPs)...
August 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28931069/methylation-associated-transcriptional-repression-of-elovl5-in-novel-colorectal-cancer-cell-lines
#2
Arnoud Boot, Jan Oosting, Jaap D H van Eendenburg, Peter J K Kuppen, Hans Morreau, Tom van Wezel
Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines...
2017: PloS One
https://www.readbyqxmd.com/read/28930842/type-4b-hereditary-hemochromatosis-associated-with-a-novel-mutation-in-the-slc40a1-gene-a-case-report-and-a-review-of-the-literature
#3
Wei Zhang, Tingxia Lv, Jian Huang, Xiaojuan Ou
RATIONALE: Hereditary hemochromatosis can be divided into HFE- and non-HFE-related based on genetic mutations in different genes. HFE-related hemochromatosis is the most common inherited genetic disease in European populations but rare in Asia-pacific region. Recently, non-HFE-related hemochromatosis has been reported in patients from the Asian countries. PATIENT CONCERNS: We report the case of a 48-year-old Chinese Han woman who presented with abnormal liver function, diabetes mellitus, hyperferritinemia, and high transferrin saturation, with severe iron overload in parenchymal cells, Kupffer cells, and periportal fibrosis on liver biopsy...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28930610/rps6ka4-mir1237-and-aurkc-promoter-regions-are-differentially-methylated-in-wilms-tumor
#4
Hanna S Pereira, Sheila C Soares Lima, Paulo S de Faria, Leila Ca Cardoso, Hector N Seuanez
Wilms' tumor (WT) is the most frequent renal cancer in childhood, the occurrence of which is characterized by a relatively low frequency of associated mutations. While epigenetic alterations have been postulated to play a relevant role in the emergence of this tumor, the mechanisms involved in WT development remain largely unknown. In this study, the DNA methylation profile of WT was characterized with Beadchip array. Comparisons between WT with normal kidney identified 827 differentially methylated regions, most of which were attributable in hypermethylation in CpG islands...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28929973/vermont-a-multi-perspective-visual-interactive-platform-for-mutational-analysis
#5
Alexandre V Fassio, Pedro M Martins, Samuel da S Guimarães, Sócrates S A Junior, Vagner S Ribeiro, Raquel C de Melo-Minardi, Sabrina de A Silveira
BACKGROUND: A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease association and effects on protein structure and function. Therefore, reliable computational approaches are needed to support the understanding of mutations and their impacts. Here, we present VERMONT 2.0, a visual interactive platform that combines sequence and structural parameters with interactive visualizations to make the impact of protein point mutations more understandable...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929533/crystal-structure-of-a-novel-prolidase-from-deinococcus-radiodurans-identifies-new-subfamily-of-bacterial-prolidases
#6
Venkata N Are, Sahayog N Jamdar, Biplab Ghosh, Venuka Durani Goyal, Ashwani Kumar, Sanchit Neema, Rekha Gadre, Ravindra D Makde
Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1...
September 20, 2017: Proteins
https://www.readbyqxmd.com/read/28929138/cryoem-structure-of-mxb-reveals-a-novel-oligomerization-interface-critical-for-hiv-restriction
#7
Frances J D Alvarez, Shaoda He, Juan R Perilla, Sooin Jang, Klaus Schulten, Alan N Engelman, Sjors H W Scheres, Peijun Zhang
Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, each of which has eluded structural determination due to difficulties in protein preparation. We report that maltose binding protein-fused, full-length wild-type MxB purifies as oligomers and further self-assembles into helical arrays in physiological salt. Guanosine triphosphate (GTP), but not guanosine diphosphate, binding results in array disassembly, whereas subsequent GTP hydrolysis allows its reformation...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28928870/the-impact-of-microsatellite-instability-status-and-sidedness-of-the-primary-tumor-on-the-effect-of-cetuximab-containing-chemotherapy-in-patients-with-metastatic-colorectal-cancer
#8
Seung Tae Kim, Su-Jin Lee, Jeeyun Lee, Se Hoon Park, Joon Oh Park, Ho Yeong Lim, Won Ki Kang, Young Suk Park
Background: Colorectal cancer (CRC) has been reconsidered as a heterogeneous disease. Among advances of genomic analysis in CRC, the sidedness of tumors (left-sided colon vs. right-sided colon) and microsatellite instability (MSI)-high (H) tumors have been highlighted. Methods: We analyzed 153 CRC patients who were available for evaluation of MSI status and had been treated with cetuximab-containing chemotherapy between April 2008 and January 2013. KRAS mutational status was available in all 153 patients, but BRAF mutational status was only available in 72 patients (47...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28928742/a-streamlined-approach-to-antibody-novel-germline-allele-prediction-and-validation
#9
Ben S Wendel, Chenfeng He, Peter D Crompton, Susan K Pierce, Ning Jiang
Advancements in high-throughput sequencing and molecular identifier-based error correction have opened the door to antibody repertoire sequencing with single mutation precision, increasing both the breadth and depth of immune response characterization. However, improvements in sequencing technology cannot resolve one key aspect of antibody repertoire sequencing accuracy: the possibility of undocumented novel germline alleles. Somatic hypermutation (SHM) calling requires a reference germline sequence, and the antibody variable region gene alleles collected by the IMGT database, although large in number, are not comprehensive...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28928741/cxcl12-mediates-aberrant-costimulation-of-b-lymphocytes-in-warts-hypogammaglobulinemia-infections-myelokathexis-immunodeficiency
#10
Giuliana Roselli, Elisa Martini, Vassilios Lougaris, Raffaele Badolato, Antonella Viola, Marinos Kallikourdis
The Warts, Hypogammaglobulinemia, Infections, Myelokathexis (WHIM) syndrome is an immunodeficiency caused by mutations in chemokine receptor CXCR4. WHIM patient adaptive immunity defects remain largely unexplained. We have previously shown that WHIM-mutant T cells form unstable immunological synapses, affecting T cell activation. Here, we show that, in WHIM patients and WHIM CXCR4 knock-in mice, B cells are more apoptosis prone. Intriguingly, WHIM-mutant B cells were also characterized by spontaneous activation...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28928732/facile-affinity-maturation-of-antibody-variable-domains-using-natural-diversity-mutagenesis
#11
Kathryn E Tiller, Ratul Chowdhury, Tong Li, Seth D Ludwig, Sabyasachi Sen, Costas D Maranas, Peter M Tessier
The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs) that are permissive to mutagenesis while maintaining antigen binding...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28928627/a-novel-truncation-mutation-in-crybb1-associated-with-autosomal-dominant-congenital-cataract-with-nystagmus
#12
Yan Rao, Sufang Dong, Zuhua Li, Guohua Yang, Chunyan Peng, Ming Yan, Fang Zheng
PURPOSE: To identify the potential candidate genes for a large Chinese family with autosomal dominant congenital cataract (ADCC) and nystagmus, and investigate the possible molecular mechanism underlying the role of the candidate genes in cataractogenesis. METHODS: We combined the linkage analysis and direct sequencing for the candidate genes in the linkage regions to identify the causative mutation. The molecular and bio-functional properties of the proteins encoded by the candidate genes was further explored with biophysical and biochemical studies of the recombinant wild-type and mutant proteins...
2017: Molecular Vision
https://www.readbyqxmd.com/read/28928474/using-experimental-evolution-to-identify-druggable-targets-that-could-inhibit-the-evolution-of-antimicrobial-resistance
#13
Heer H Mehta, Amy G Prater, Yousif Shamoo
With multi-drug and pan-drug-resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics...
September 20, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28928406/hemoglobin-enhances-mirna-144-expression-and-autophagic-activation-mediated-inflammation-of-microglia-via-mtor-pathway
#14
Zhenyu Wang, Bangqing Yuan, Fenlan Fu, Shaokuan Huang, Zhao Yang
Intracerebral hemorrhage promotes autophagic activation of microglia and enhances neuroinflammation. MiRNAs are key factors to autophagy, contributed to negatively and posttranscriptionally regulate gene expression and function. However, the specific miRNAs involved in the intracerebral hemorrhage mediated microglia autophagic activation are unidentified. In this experiment, microglia was treated with hemoglobin. And then, miRNA-144 expression, autophagic activation and inflammation of microglia were detected...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928215/influenza-virus-hemagglutinin-stalk-specific-antibodies-in-human-serum-are-a-surrogate-marker-for-in-vivo-protection-in-a-serum-transfer-mouse-challenge-model
#15
Henning Jacobsen, Madhusudan Rajendran, Angela Choi, Haakon Sjursen, Karl A Brokstad, Rebecca J Cox, Peter Palese, Florian Krammer, Raffael Nachbagauer
The immunogenicity of current influenza virus vaccines is assessed by measuring an increase of influenza virus-specific antibodies in a hemagglutination inhibition assay. This method exclusively measures antibodies against the hemagglutinin head domain. While this domain is immunodominant, it has been shown that hemagglutination inhibition titers do not always accurately predict protection from disease. In addition, several novel influenza virus vaccines that are currently under development do not target the hemagglutinin head domain, but rather more conserved sites, including the hemagglutinin stalk...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28928082/mir-338-3p-confers-5-fluorouracil-resistance-in-p53-mutant-colon-cancer-cells-by-targeting-the-mammalian-target-of-rapamycin
#16
Jia Han, Jie Li, Kaijie Tang, Huahua Zhang, Bo Guo, Ni Hou, Chen Huang
Evidence demonstrate that p53 mutations and microRNAs (miRs) are important components of 5-FU resistance in colorectal cancer (CRC). miR-338-3p has been reported associated with cancer prognosis. However whether or not it influences chemotherapy sensitivity and the underlying mechanisms have not been elucidated. Here, three types of human colon cancer cell lines, HT29 (mutant p53), HCT116 (wild-type p53), and HCT116 p53(-/-) (deficient p53), were treated with 5-FU. We showed that expression of miR-338-3p was correlated with apoptosis and 5-FU resistance in colon cancer cells...
September 16, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28927821/a-novel-ikaros-haploinsufficiency-kindred-with-unexpectedly-late-and-variable-b-cell-maturation-defects
#17
Delfien J Bogaert, Hye Sun Kuehn, Carolien Bonroy, Katherine R Calvo, Joke Dehoorne, Arnaud V Vanlander, Marieke De Bruyne, Urszula Cytlak, Venetia Bigley, Frans De Baets, Elfride De Baere, Sergio D Rosenzweig, Filomeen Haerynck, Melissa Dullaers
We report on the first truncating IKZF1 mutation associated with IKAROS haploinsufficiency and illustrate an unexpectedly late and variable block in central and peripheral B cell development in two patients and their asymptomatic mother.
September 16, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28927585/whole-genome-and-transcriptome-sequencing-of-prostate-cancer-identify-new-genetic-alterations-driving-disease-progression
#18
Shancheng Ren, Gong-Hong Wei, Dongbing Liu, Liguo Wang, Yong Hou, Shida Zhu, Lihua Peng, Qin Zhang, Yanbing Cheng, Hong Su, Xiuqing Zhou, Jibin Zhang, Fuqiang Li, Hancheng Zheng, Zhikun Zhao, Changjun Yin, Zengquan He, Xin Gao, Haiyen E Zhau, Chia-Yi Chu, Jason Boyang Wu, Colin Collins, Stanislav V Volik, Robert Bell, Jiaoti Huang, Kui Wu, Danfeng Xu, Dingwei Ye, Yongwei Yu, Lianhui Zhu, Meng Qiao, Hang-Mao Lee, Yuehong Yang, Yasheng Zhu, Xiaolei Shi, Rui Chen, Yang Wang, Weidong Xu, Yanqiong Cheng, Chuanliang Xu, Xu Gao, Tie Zhou, Bo Yang, Jianguo Hou, Li Liu, Zhensheng Zhang, Yao Zhu, Chao Qin, Pengfei Shao, Jun Pang, Leland W K Chung, Jianfeng Xu, Chin-Lee Wu, Weide Zhong, Xun Xu, Yingrui Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Jun Wang, Haojie Huang, Yinghao Sun
BACKGROUND: Global disparities in prostate cancer (PCa) incidence highlight the urgent need to identify genomic abnormalities in prostate tumors in different ethnic populations including Asian men. OBJECTIVE: To systematically explore the genomic complexity and define disease-driven genetic alterations in PCa. DESIGN, SETTING, AND PARTICIPANTS: The study sequenced whole-genome and transcriptome of tumor-benign paired tissues from 65 treatment-naive Chinese PCa patients...
September 15, 2017: European Urology
https://www.readbyqxmd.com/read/28927527/dna-mismatch-repair-and-its-many-roles-in-eukaryotic-cells
#19
REVIEW
Dekang Liu, Guido Keijzers, Lene Juel Rasmussen
DNA mismatch repair (MMR) is an important DNA repair pathway that plays critical roles in DNA replication fidelity, mutation avoidance and genome stability, all of which contribute significantly to the viability of cells and organisms. MMR is widely-used as a diagnostic biomarker for human cancers in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays novel roles in eukaryotic cells, several of which are not yet well-defined or understood...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28927463/towards-precision-medicine-discovering-novel-gynecological-cancer-biomarkers-and-pathways-using-linked-data
#20
Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation...
September 19, 2017: Journal of Biomedical Semantics
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