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David S Lynch, Wei Jia Zhang, Rahul Lakshmanan, Justin A Kinsella, Günes Altiokka Uzun, Merih Karbay, Zeynep Tüfekçioglu, Hasmet Hanagasi, Georgina Burke, Nicola Foulds, Simon R Hammans, Anupam Bhattacharjee, Heather Wilson, Matthew Adams, Mark Walker, James A R Nicoll, Jeremy Chataway, Nick Fox, Indran Davagnanam, Rahul Phadke, Henry Houlden
Importance: Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) is a frequent cause of adult-onset leukodystrophy known to be caused by autosomal dominant mutations in the CSF1R (colony-stimulating factor 1) gene. The discovery that CSF1R mutations cause ALSP led to more accurate prognosis and genetic counseling for these patients in addition to increased interest in microglia as a target in neurodegeneration. However, it has been known since the discovery of the CSF1R gene that there are patients with typical clinical and radiologic evidence of ALSP who do not carry pathogenic CSF1R mutations...
October 17, 2016: JAMA Neurology
Huangai Li, Hideki Kondo, Thomas Kühne, Yukio Shirako
In this study, we investigated the barley yellow mosaic virus (BaYMV, genus Bymovirus) factor(s) responsible for breaking eIF4E-mediated recessive resistance genes (rym4/5/6) in barley. Genome mapping analysis using chimeric infectious cDNA clones between rym5-breaking (JT10) and rym5-non-breaking (JK05) isolates indicated that genome-linked viral protein (VPg) is the determinant protein for breaking the rym5 resistance. Likewise, VPg is also responsible for overcoming the resistances of rym4 and rym6 alleles...
2016: Frontiers in Plant Science
Max E Kraner, Katrin Link, Michael Melzer, Arif B Ekici, Steffen Uebe, Pablo Tarazona, Ivo Feussner, Jörg Hofmann, Uwe Sonnewald
Plasmodesmata (PD) are microscopic pores connecting plant cells and enable cell-to-cell transport. Currently, little is known about the molecular mechanisms regulating PD formation and development. To uncover components of PD development we made use of the 17 kDa movement protein (MP17) encoded by the Potato leafroll virus (PLRV). The protein is required for cell-to-cell movement of the virus and localises to complex PD. Forward genetic screening for Arabidopsis mutants with altered PD-binding of MP17 revealed several mutant lines, while molecular genetics, biochemical and microscopic studies allowed further characterisation...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Feng Zhang, Youchun Wang
Cell culture is an important research method in virology. Although many attempts were tried to culture HEV in cells, only two cell culture systems were considered to have high enough efficient for usage. Concentration of virus stocks, host cells, and medium components affect the culture efficient, and the genetic mutations during HEV passage were found to be associated with the increased virulence in cell culture. As an alternative method for traditional cell culture, the infectious cDNA clones were constructed...
2016: Advances in Experimental Medicine and Biology
Eva Heger, Alexandra Theis, Klaus Remmel, Hauke Walter, Alejandro Pironti, Elena Knops, Veronica Di Cristanziano, Björn Jensen, Stefan Esser, Rolf Kaiser, Nadine Lübke
Phenotypic resistance analysis is an indispensable method for determination of HIV-1 resistance and cross-resistance to novel drug compounds. Since integrase inhibitors are essential components of recent antiretroviral combination therapies, phenotypic resistance data, in conjunction with the corresponding genotypes, are needed for improving rules-based and data-driven tools for resistance prediction, such as HIV-Grade and geno2pheno[integrase]. For generation of phenotypic resistance data to recent integrase inhibitors, a recombinant phenotypic integrase susceptibility assay was established...
October 10, 2016: Journal of Virological Methods
Gabriel Cabot, Carla López-Causapé, Alain A Ocampo-Sosa, Lea M Sommer, María Ángeles Domínguez, Laura Zamorano, Carlos Juan, Fe Tubau, Cristina Rodríguez, Bartolomé Moyà, Carmen Peña, Luis Martínez-Martínez, Patrick Plesiat, Antonio Oliver
Whole genome sequencing (WGS) was used for the characterization of the, frequently extensively-drug resistant (XDR), P. aeruginosa high-risk clone ST175. A total of eighteen ST175 isolates recovered from 8 different Spanish hospitals were analyzed; four isolates from four different French hospitals were included for comparison. The typical resistance profile of ST175 included penicillins, cephalosporins, monobactams, carbapenems, aminoglycosides, and fluoroquinolones. In the phylogenetic analysis, the four French isolates clustered together with the two isolates from one of the Spanish regions...
October 10, 2016: Antimicrobial Agents and Chemotherapy
Hong-Hao Yu, Heng Zhao, Yu-Bo Qing, Wei-Rong Pan, Bao-Yu Jia, Hong-Ye Zhao, Xing-Xu Huang, Hong-Jiang Wei
Dystrophinopathy, including Duchenne muscle dystrophy (DMD) and Becker muscle dystrophy (BMD) is an incurable X-linked hereditary muscle dystrophy caused by a mutation in the DMD gene in coding dystrophin. Advances in further understanding DMD/BMD for therapy are expected. Studies on mdx mice and dogs with muscle dystrophy provide limited insight into DMD disease mechanisms and therapeutic testing because of the different pathological manifestations. Miniature pigs share similar physiology and anatomy with humans and are thus an excellent animal model of human disease...
October 9, 2016: International Journal of Molecular Sciences
TaeHyung Kim, Marc S Tyndel, Hyeoung Joon Kim, Jae-Sook Ahn, Seung Hyun Choi, Hee Jeong Park, Yeo-Kyeoung Kim, Soo Young Kim, Jeffrey H Lipton, Zhaolei Zhang, Dennis Dong Hwan Kim
Somatic mutations commonly detected in a variety of myeloid neoplasms have not been systematically investigated in chronic myeloid leukemia (CML). We performed targeted deep sequencing on a total of 300 serial samples from 100 CML patients; thirty-seven patients carried mutations. Sixteen of these had evidence of mutations originating from preleukemic clones. Using unsupervised hierarchical clustering, we identified five distinct patterns of mutation dynamics arising following tyrosine kinase inhibitor (TKI) therapy...
October 12, 2016: Blood
Sun Jiji, Zhao Xiaoxu, Qiao Lihua, Mei Shuang, Nie Zhipeng, Zhang Qinghai, Ji Yanchun, Jiang Pingping, Guan Min-Xin
Mitochondrial DNA (mtDNA) mutations cause a variety of mitochondrial DNA-based diseases which have been studied using Lymphoblastoid cell lines (LCLs) and transmitochondrial cybrids. Individual genetic information is preserved permanently in LCLs while the development of transmitochondrial cybrids provide ex-vivo cellular platform to study molecular mechanism of mitochondrial DNA-based diseases. The cytoplasmic donor cells for previous transmitochondrial cybrids come from patient's tissue or platelet directly...
July 20, 2016: Yi Chuan, Hereditas
Xie Dejian, Shi Minglei, Zhang Yan, Wang Tianyi, Shen Wenlong, Ye Bingyu, Li Ping, He Chao, Zhang Xiangyuan, Zhao Zhihu
The CCCTC-binding factor (CTCF) is the main insulator protein described in vertebrates. It plays fundamental roles during diverse cellular processes. CTCF gene knockout mice led to death during embryonic development. To further explore the functions of CTCF, we employed a CRISPR/Cas9-based genome engineering strategy to in-frame insert the mitosis-special degradation domain (MD) of cyclin B into the upstream open reading frame of CTCF gene. Fusion protein is designed to degrade during mitosis leaded by MD. As a control group, mutation of a single arginine (R42A) within the destruction box inactivates the MD leading to constitutive expression of MD(*)-CTCF...
July 20, 2016: Yi Chuan, Hereditas
Thomas Stiehl, Christoph Lutz, Anna Marciniak-Czochra
BACKGROUND: Leukemias are malignant proliferative disorders of the blood forming system. Sequencing studies demonstrate that the leukemic cell population consists of multiple clones. The genetic relationship between the different clones, referred to as the clonal hierarchy, shows high interindividual variability. So far, the source of this heterogeneity and its clinical relevance remain unknown. We propose a mathematical model to study the emergence and evolution of clonal heterogeneity in acute leukemias...
October 12, 2016: Biology Direct
Arnold L Demain, Evan Martens
We are pleased to dedicate this paper to Dr Julian E Davies. Julian is a giant among microbial biochemists. He began his professional career as an organic chemistry PhD student at Nottingham University, moved on to a postdoctoral fellowship at Columbia University, then became a lecturer at the University of Manchester, followed by a fellowship in microbial biochemistry at Harvard Medical School. In 1965, he studied genetics at the Pasteur Institute, and 2 years later joined the University of Wisconsin in the Department of Biochemistry...
October 12, 2016: Journal of Antibiotics
Maria Doitsidou, Sophie Jarriault, Richard J Poole
The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy...
October 2016: Genetics
Donna J Palmer, Nathan C Grove, Jordan Ing, Ana M Crane, Koen Venken, Brian R Davis, Philip Ng
Helper-dependent adenoviral vectors mediate high efficiency gene editing in induced pluripotent stem cells without needing a designer nuclease thereby avoiding off-target cleavage. Because of their large cloning capacity of 37 kb, helper-dependent adenoviral vectors with long homology arms are used for gene editing. However, this makes vector construction and recombinant analysis difficult. Conversely, insufficient homology may compromise targeting efficiency. Thus, we investigated the effect of homology length on helper-dependent adenoviral vector targeting efficiency at the cystic fibrosis transmembrane conductance regulator locus in induced pluripotent stem cells and found a positive correlation...
October 11, 2016: Molecular Therapy. Nucleic Acids
Dominik Schulz, Markus Wirth, Guido Piontek, Anna Maria Stefanie Buchberger, Jürgen Schlegel, Rudolf Reiter, Gabriele Multhoff, Anja Pickhard
Despite remarkable successes with targeted therapies in the treatment of cancer, resistance can occur which limits the clinical outcome. In this study, we generated and characterized resistant cell clones derived from two different head and neck squamous cell carcinoma (HNSCC) cell lines (Cal27, UD-SCC-5) by long-term exposure to five targeted- and chemotherapeutics (afatinib, MK2206, BEZ235, olaparib and cisplatin). The resistant tumor cell clones showed an increased ERK1/2 expression and an altered expression of the stem-cell markers CD44, ALDH1, Oct4, Sox2, Nanog and Bmi1...
2016: American Journal of Cancer Research
Xiaoyu Wang, Huoqing Huang, Xiangming Xie, Rui Ma, Yingguo Bai, Fei Zheng, Shuai You, Bingyu Zhang, Huifang Xie, Bin Yao, Huiying Luo
A xylanase gene of GH 10, Tlxyn10A, was cloned from Talaromyces leycettanus JCM12802 and expressed in Pichia pastoris. Purified recombinant TlXyn10A was acidic and hyperthermophilic, and retained stable over the pH range of 2.0-6.0 and at 90°C. Sequence analysis of TlXyn10A identified seven residues probably involved in substrate contacting. Three mutants (TlXyn10A_P, _N and _C) were then constructed by substituting some or all of the residues with corresponding ones of hyperthermal Xyl10C from Bispora sp...
October 3, 2016: Bioresource Technology
Song Jiao, Xu Li, Huimin Yu, Huan Yang, Xue Li, Zhongyao Shen
Surfactin-family lipopeptides are green biosurfactants with substantial industrial potential. The major problem prohibiting surfactin use is the low titer of the wild producer, Bacillus subtilis. Using transcriptomic analysis, four strong promoters, PgroE, Pcdd, PrplK and PsspE, were identified and cloned from the genome of B. subtilis THY-7, a novel surfactin producer that has been identified from soil with a 0.55 g/L surfactin titer. An optimal promoter, PgroE, was selected to replace the native THY-7 surfactin synthase (SrfA) promoter through single-cross homologous recombination; however, the resulting engineered strain containing the PgroE substitution did not synthesize surfactin...
October 10, 2016: Biotechnology and Bioengineering
Gene Kurosawa, Mariko Kondo, Yoshikazu Kurosawa
When the technology for constructing human antibody (Ab) libraries using a phage-display system was developed, many researchers in Ab-related fields anticipated that it would be widely applied to the development of pharmaceutical drugs against various diseases, including cancers. However, successful examples of such applications are very limited. Moreover, researchers who utilize phage-display technology now show divergent ways of thinking about phage Ab libraries. For example, there is debate about what should be the source of VH and VL genes for the construction of libraries to cover the whole repertoire of Abs present in the human body...
October 5, 2016: Biochemical and Biophysical Research Communications
W J Yang, Z Yu, R Lyu, Z J Li, H Li, W J Xiong, S H Yi, W Liu, L G Qiu
Objective: To investigate the IGHV mutational status and its differences from Caucasian in splenic marginal zone lymphoma (SMZL). Methods: A retrospective study on 40 SMZL cases were performed to detect the V-D-J sequence of IGHV by plasmid cloning sequencing, comparing the data with the most homologous germ line V sequence in database, identifying the stereotype of patients through cluster analysis and alignment. The clinical and laboratory characteristics were compared between the patients with IGHV mutation and without mutations...
September 14, 2016: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
Meer T Alam, Shrestha S Ray, Camille N Chun, Zahara G Chowdhury, Mohammed H Rashid, Valery E Madsen Beau De Rochars, Afsar Ali
In October of 2010, an outbreak of cholera was confirmed in Haiti for the first time in more than a century. A single clone of toxigenic Vibrio cholerae O1 biotype El Tor serotype Ogawa strain was implicated as the cause. Five years after the onset of cholera, in October, 2015, we have discovered a major switch (ranging from 7 to 100%) from Ogawa serotype to Inaba serotype. Furthermore, using wbeT gene sequencing and comparative sequence analysis, we now demonstrate that, among 2013 and 2015 Inaba isolates, the wbeT gene, responsible for switching Ogawa to Inaba serotype, sustained a unique nucleotide mutation not found in isolates obtained from Haiti in 2012...
October 2016: PLoS Neglected Tropical Diseases
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