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https://www.readbyqxmd.com/read/28636132/trpc1-and-trpc3-dependent-ca-2-signaling-in-mouse-cortical-astrocytes-affects-injury-evoked-astrogliosis-in-vivo
#1
Thabet Belkacemi, Alexander Niermann, Laura Hofmann, Ulrich Wissenbach, Lutz Birnbaumer, Petra Leidinger, Christina Backes, Eckart Meese, Andreas Keller, Xianshu Bai, Anja Scheller, Frank Kirchhoff, Stephan E Philipp, Petra Weissgerber, Veit Flockerzi, Andreas Beck
Following brain injury astrocytes change into a reactive state, proliferate and grow into the site of lesion, a process called astrogliosis, initiated and regulated by changes in cytoplasmic Ca(2+) . Transient receptor potential canonical (TRPC) channels may contribute to Ca(2+) influx but their presence and possible function in astrocytes is not known. By RT-PCR and RNA sequencing we identified transcripts of Trpc1, Trpc2, Trpc3, and Trpc4 in FACS-sorted glutamate aspartate transporter (GLAST)-positive cultured mouse cortical astrocytes and subcloned full-length Trpc1 and Trpc3 cDNAs from these cells...
June 21, 2017: Glia
https://www.readbyqxmd.com/read/28630229/observing-clonal-dynamics-across-spatiotemporal-axes-a-prelude-to-quantitative-fitness-models-for-cancer
#2
Andrew W McPherson, Fong Chun Chan, Sohrab P Shah
The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones...
June 19, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28630215/mechanisms-of-primary-drug-resistance-in-fgfr1-amplified-lung-cancer
#3
Florian Malchers, Meryem Seda Ercanoglu, Daniel Schütte, Roberta Castiglione, Verena Tischler, Sebastian Michels, Ilona Dahmen, Johannes Brägelmann, Roopika Menon, Johannes M Heuckmann, Julie George, Sascha Ansén, Martin L Sos, Alex Soltermann, Martin Peifer, Jurgen Wolf, Reinhard Büttner, Roman K Thomas
<br />The 8p12-p11 locus is frequently amplified in squamous cell lung cancer (SQLC); the receptor tyrosine kinase fibroblast growth factor receptor 1 (FGFR1) being one of the most prominent targets of this amplification. Thus, small molecules inhibiting FGFRs have been employed to treat FGFR1-amplified SQLC. However, only about 11% of such FGFR1-amplified tumors respond to single agent FGFR inhibition and several tumors exhibited insufficient tumor shrinkage, compatible with the existence of drug-resistant tumor cells...
June 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28630184/occurrence-of-clinically-important-lineages-including-the-st131-c1-m27-subclone-among-extended-spectrum-%C3%AE-lactamase-producing-escherichia-coli-in-wastewater
#4
Ryota Gomi, Tomonari Matsuda, Yasufumi Matsumura, Masaki Yamamoto, Michio Tanaka, Satoshi Ichiyama, Minoru Yoneda
Contamination of environmental waters by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBLEC) is of great concern. Wastewater treatment plants (WWTPs) and hospitals release large amounts of ESBLEC into the environment. In the present study, we isolated ESBLEC strains from wastewater collected from a WWTP and a hospital in Japan and performed whole-genome sequencing to characterize these strains. Genomic analysis of 54 strains (32 from the WWTP and 22 from hospital wastewater) revealed the occurrence of clinically important clonal groups with extraintestinal pathogenic E...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28623774/discrepancy-in-braf-status-among-patients-with-metastatic-malignant-melanoma-a-meta-analysis
#5
REVIEW
Antonis Valachis, Gustav J Ullenhag
The incidence of malignant melanoma is growing rapidly. Approximately half of the cases are BRAF mutated, making treatment with kinase inhibitors a (MEK and BRAF inhibitors) preferred choice in the advanced setting. The vast majority of these patients will benefit from the treatment. It is therefore of vital importance that the BRAF analysis is reliable and reflects the true nature of the tumour. Intraindividual tumour BRAF heterogeneity may exist, and changes of BRAF status over time might occur. We reviewed the literature by searching the PubMed database and 630 potentially relevant studies were identified...
June 14, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28618430/extreme-assay-sensitivity-in-molecular-diagnostics-further-unveils-intratumour-heterogeneity-in-metastatic-colorectal-cancer-as-well-as-artifactual-low-frequency-mutations-in-the-kras-gene
#6
Sara Mariani, Luca Bertero, Simona Osella-Abate, Cristiana Di Bello, Paola Francia di Celle, Vittoria Coppola, Anna Sapino, Paola Cassoni, Caterina Marchiò
BACKGROUND: Gene mutations in the RAS family rule out metastatic colorectal carcinomas (mCRCs) from anti-EGFR therapies. METHODS: We report a retrospective analysis by Sequenom Massarray and fast COLD-PCR followed by Sanger sequencing on 240 mCRCs. RESULTS: By Sequenom, KRAS and NRAS exons 2-3-4 were mutated in 52.9% (127/240) of tumours, while BRAF codon 600 mutations reached 5% (12/240). Fast COLD-PCR found extra mutations at KRAS exon 2 in 15/166 (9%) of samples, previously diagnosed by Sequenom as wild-type or mutated at RAS (exons 3-4) or BRAF genes...
June 15, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28618197/analysis-of-mutant-allele-fractions-in-driver-genes-in-colorectal-cancer-biological-and-clinical-insights
#7
Rodrigo Dienstmann, Elena Elez, Guillem Argiles, Ignacio Matos, Enrique Sanz-Garcia, Carolina Ortiz, Teresa Macarulla, Jaume Capdevila, Maria Alsina, Tamara Sauri, Helena Verdaguer, Marta Vilaro, Fiorella Ruiz-Pace, Cristina Viaplana, Ariadna Garcia, Stefania Landolfi, Hector G Palmer, Paolo Nuciforo, Jordi Rodon, Ana Vivancos, Josep Tabernero
Sequencing of tumors is now routine and guides personalized cancer therapy. Mutant allele fractions (MAFs, or the 'mutation dose') of a driver gene may reveal the genomic structure of tumors and influence response to targeted therapies. We performed a comprehensive analysis of MAFs of driver alterations in unpaired primary and metastatic colorectal cancer (CRC) at our institution from 2010 to 2015 and studied their potential clinical relevance. Out of 763 CRC samples, 622 had detailed annotation on overall survival in the metastatic setting (OSmet) and 89 received targeted agents matched to KRAS (MEK inhibitors), BRAF (BRAF inhibitors) or PIK3CA mutations (PI3K pathway inhibitors)...
June 15, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28614790/genomic-landscape-and-evolution-of-metastatic-chromophobe-renal-cell-carcinoma
#8
Jozefina Casuscelli, Nils Weinhold, Gunes Gundem, Lu Wang, Emily C Zabor, Esther Drill, Patricia I Wang, Gouri J Nanjangud, Almedina Redzematovic, Amrita M Nargund, Brandon J Manley, Maria E Arcila, Nicholas M Donin, John C Cheville, R Houston Thompson, Allan J Pantuck, Paul Russo, Emily H Cheng, William Lee, Satish K Tickoo, Irina Ostrovnaya, Chad J Creighton, Elli Papaemmanuil, Venkatraman E Seshan, A Ari Hakimi, James J Hsieh
Chromophobe renal cell carcinoma (chRCC) typically shows ~7 chromosome losses (1, 2, 6, 10, 13, 17, and 21) and ~31 exonic somatic mutations, yet carries ~5%-10% metastatic incidence. Since extensive chromosomal losses can generate proteotoxic stress and compromise cellular proliferation, it is intriguing how chRCC, a tumor with extensive chromosome losses and a low number of somatic mutations, can develop lethal metastases. Genomic features distinguishing metastatic from nonmetastatic chRCC are unknown. An integrated approach, including whole-genome sequencing (WGS), targeted ultradeep cancer gene sequencing, and chromosome analyses (FACETS, OncoScan, and FISH), was performed on 79 chRCC patients including 38 metastatic (M-chRCC) cases...
June 15, 2017: JCI Insight
https://www.readbyqxmd.com/read/28604461/chemosensitivity-of-brca1-mutated-ovarian-cancer-cells-and-established-cytotoxic-agents
#9
Caroline van Haaften, Jaap van Eendenburg, Arnoud Boot, Willem E Corver, Lucien Haans, Tom van Wezel, J Baptist Trimbos
OBJECTIVE: Serous adenocarcinomas that arise in patients with inherited mutations in the tumor suppressor genes BRCA1 and BRCA2 are initially well treatable with platinum/paclitaxel. For recurrent disease in patients with BRCA1 or BRCA2 mutations, olaparib treatment is available. To study additional therapeutic regimens, a better understanding of the cellular and molecular mechanisms of the tumors in in vitro models is important. METHODS/MATERIALS: From a high-grade serous ovarian tumor of a BRCA1 mutation carrier, we established 3 distinct cell line subclones, OVCA-TR3...
June 10, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/28602946/whole-genome-analysis-reveals-unexpected-dynamics-of-mutant-subclone-development-in-a-patient-with-jak2-v617f-positive-chronic-myeloid-leukemia
#10
I Sloma, M Mitjavila-Garcia, O Feraud, F Griscelli, N Oudrhiri, S El Marsafy, E Gobbo, D Divers, A Proust, D M Smadja, C Desterke, A Carles, Y Ma, M Hirst, M A Marra, C J Eaves, A Bennaceur-Griscelli, A G Turhan
We report here the first use of whole genome sequencing (WGS) to examine the initial clonal dynamics in an unusual patient with chronic myeloid leukemia (CML) who presented in chronic phase (CP) with doubly marked BCR-ABL1(+)/JAK2(V617F)-mutant cells and over a 9 year period progressed into an accelerated phase (AP) and then terminal blast phase (BP). WGS showed the diagnostic cells also contained mutations in ASXL1, SEC23B, MAD1L1 and RREB1, as well as 12,000 additional uncommon DNA variants. WGS of endothelial cells generated from circulating precursors revealed many of these were shared with the CML clone...
June 7, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28598822/patient-specific-molecular-alterations-are-associated-with-metastatic-clear-cell-renal-cell-cancer-progressing-under-tyrosine-kinase-inhibitor-therapy
#11
Steffen Dietz, Holger Sültmann, YueJun Du, Eva Reisinger, Anja Lisa Riediger, Anna-Lena Volckmar, Albrecht Stenzinger, Matthias Schlesner, Dirk Jäger, Markus Hohenfellner, Stefan Duensing, Carsten Grüllich, Sascha Pahernik
The availability of tyrosine kinase inhibitors (TKI) during the past ten years has led to improved response and overall survival of patients suffering from metastatic clear cell renal cell carcinoma (ccRCC). However, most of these tumors will eventually progress due to resistance evolving under therapy. The objective of this pilot study was to determine whether molecular alterations in ccRCC tissues sampled over the course of the disease might be suggestive of potential therapies. We performed whole exome sequencing of nine samples from four patients in the MORE (Molecular Renal Cancer Evolution) trial...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28596419/intra-tumor-heterogeneity-novel-approaches-for-resolving-genomic-architecture-and-clonal-evolution
#12
Ravi G Gupta, Robert A Somer
High-throughput genomic technologies have revealed a remarkably complex portrait of intra-tumor heterogeneity in cancer and have shown that tumors evolve through a reiterative process of genetic diversification and clonal selection. This discovery has challenged the classical paradigm of clonal dominance and brought attention to subclonal tumor cell populations that contribute to the cancer phenotype. Dynamic evolutionary models may explain how these populations grow within the ecosystem of tissues, including linear, branching, neutral and punctuated patterns...
June 8, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28588200/fluorometric-evaluation-of-cyp3a4-expression-using-improved-transgenic-heparg-cells-carrying-a-dual-colour-reporter-for-cyp3a4-and-cyp3a7
#13
Takafumi Ueyama, Saori Tsuji, Takemi Sugiyama, Masako Tada
Primary human hepatocytes are necessary to evaluate cytotoxicity, drug metabolism, and drug-drug interactions for candidate compounds in early-phase drug discovery and development. However, these analyses are often hampered by limited resources and functional or genetic variation among lots. HepaRG human hepatocellular carcinoma cells can differentiate into mature hepatocyte-like cells (HepLCs) that possess similar metabolic activity to human hepatocytes. We previously established transgenic HepaRG cells carrying a dual reporter that express red fluorescent protein (RFP) under the transcriptional regulation of CYP3A7 in the hepatoblast-like cell state and enhanced green fluorescent protein (EGFP) under the transcriptional regulation of CYP3A4 following HepLC differentiation...
June 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28584139/genomic-analysis-of-multidrug-resistant-escherichia-coli-from-north-carolina-community-hospitals-ongoing-circulation-of-ctx-m-producing-st131-h30rx-and-st131-h30r1-strains
#14
Hajime Kanamori, Christian M Parobek, Jonathan J Juliano, James R Johnson, Brian D Johnston, Timothy J Johnson, David J Weber, William A Rutala, Deverick J Anderson
Escherichia coli sequence type 131 (ST131) predominates globally among multidrug-resistant (MDR) E. coli We used whole-genome sequencing (WGS) to investigate 63 MDR E. coli isolates from 7 North Carolina community hospitals (2010-2015). Of these, 39 (62%) represented ST131, including 37 (95%) from the ST131-H30R subclone: 10 (27%) from its H30R1 subset, and 27 (69%) from its H30Rx subset. ST131 core genomes differed by a median of 15 single-nucleotide variants (SNVs) overall (range, 0-490), vs. only 7 within H30R1 (range, 3-12 SNVs) and 11 within H30Rx (range, 0-21)...
June 5, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28581503/between-region-genetic-divergence-reflects-the-mode-and-tempo-of-tumor-evolution
#15
Ruping Sun, Zheng Hu, Andrea Sottoriva, Trevor A Graham, Arbel Harpak, Zhicheng Ma, Jared M Fischer, Darryl Shibata, Christina Curtis
Given the implications of tumor dynamics for precision medicine, there is a need to systematically characterize the mode of evolution across diverse solid tumor types. In particular, methods to infer the role of natural selection within established human tumors are lacking. By simulating spatial tumor growth under different evolutionary modes and examining patterns of between-region subclonal genetic divergence from multiregion sequencing (MRS) data, we demonstrate that it is feasible to distinguish tumors driven by strong positive subclonal selection from those evolving neutrally or under weak selection, as the latter fail to dramatically alter subclonal composition...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28580925/crystal-structure-of-the-multiple-antibiotic-resistance-regulator-marr-from-clostridium-difficile
#16
J W Peng, H Yuan, X S Tan
Regulators of multiple antibiotic resistance (MarRs) are key players against toxins in prokaryotes. MarR homologues have been identified in many bacterial and archaeal species which pose daunting antibiotic resistance issues that threaten public health. The continuous prevalence of Clostridium difficile infection (CDI) throughout the world is associated with the abuse of antibiotics, and antibiotic treatments of CDI have limited effect. In the genome of C. difficile strain 630, the marR gene (ID 4913953) encodes a MarR protein...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28576485/highly-efficient-one-step-scarless-protein-tagging-by-type-iis-restriction-endonuclease-mediated-precision-cloning
#17
Zhen Xu, Yan-Ning Rui, Julien Balzeau, Miriam R Menezes, Airu Niu, John P Hagan, Dong H Kim
Protein tagging with a wide variety of epitopes and/or fusion partners is used routinely to dissect protein function molecularly. Frequently, the required DNA subcloning is inefficient, especially in cases where multiple constructs are desired for a given protein with unique tags. Additionally, the generated clones have unwanted junction sequences introduced. To add versatile tags into the extracellular domain of the transmembrane protein THSD1, we developed a protein tagging technique that utilizes non-classical type IIS restriction enzymes that recognize non-palindromic DNA sequences and cleave outside of their recognition sites...
May 30, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28575848/identification-of-srf-e2f1-fusion-transcript-in-ewsr-negative-myoepithelioma-of-the-soft-tissue
#18
Milena Urbini, Annalisa Astolfi, Valentina Indio, Giuseppe Tarantino, Salvatore Serravalle, Maristella Saponara, Margherita Nannini, Alessandro Gronchi, Marco Fiore, Roberta Maestro, Monica Brenca, Angelo Paolo Dei Tos, Gian Paolo Dagrada, Tiziana Negri, Silvana Pilotti, Paolo Giovanni Casali, Guido Biasco, Andrea Pession, Silvia Stacchiotti, Maria Abbondanza Pantaleo
Myoepithelial neoplasms (MN) are rare and not well-circumstanced entities displaying a heterogeneous spectrum of genetic abnormalities, including EWSR1, FUS and PLAG1 rearrangements. However, in the remaining MN no other fusion gene has been described and knowledge concerning secondary acquired molecular alterations is still poor. Therefore, we screened 5 cases of MN of the soft tissue by RNA sequencing with the aim of identifying novel fusion transcripts.A novel SRF-E2F1 fusion was detected in two cases: one was negative for other fusions while the other showed also the presence of FUS-KLF17...
May 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28575024/efficient-method-for-site-directed-mutagenesis-in-large-plasmids-without-subcloning
#19
Louay K Hallak, Kelly Berger, Rita Kaspar, Anna R Kwilas, Federica Montanaro, Mark E Peeples
Commonly used methods for site-directed DNA mutagenesis require copying the entire target plasmid. These methods allow relatively easy modification of DNA sequences in small plasmids but become less efficient and faithful for large plasmids, necessitating full sequence verification. Introduction of mutations in larger plasmids requires subcloning, a slow and labor-intensive process, especially for multiple mutations. We have developed an efficient DNA mutagenesis technique, UnRestricted Mutagenesis and Cloning (URMAC) that replaces subcloning steps with quick biochemical reactions...
2017: PloS One
https://www.readbyqxmd.com/read/28574839/advances-in-single-cell-rna-sequencing-and-its-applications-in-cancer-research
#20
REVIEW
Sibo Zhu, Tao Qing, Yuanting Zheng, Li Jin, Leming Shi
Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years' development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection...
May 16, 2017: Oncotarget
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