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https://www.readbyqxmd.com/read/28103009/fully-automated-one-step-synthesis-of-single-transcript-talen-pairs-using-a-biological-foundry
#1
Ran Chao, Jing Liang, Ipek Tasan, Tong Si, Linyang Ju, Huimin Zhao
Transcription activator-like effector nuclease (TALEN) is a programmable genome editing tool with wide applications. Since TALENs perform cleavage of DNA as heterodimers, a pair of TALENs must be synthesized for each target genome locus. Conventionally, TALEN pairs are either expressed on separate vectors or synthesized separately and then subcloned to the same vector. Neither approach allows high-throughput construction of TALEN libraries for large-scale applications. Here we present an assembly scheme to synthesize and express a pair of TALENs in a single transcript format with the help of a P2A self-cleavage sequence...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28096848/immunogenicity-and-efficacy-of-live-l-tarentolae-expressing-kmp11-ntgp96-gfp-fusion-as-a-vaccine-candidate-against-experimental-visceral-leishmaniasis-caused-by-l-infantum
#2
Vahid Nasiri, Abdolhossein Dalimi, Fatemeh Ghaffarifar, Azam Bolhassani
BACKGROUND: The aim of present study was to evaluate the protective efficacy of live recombinant L. tarentolae expressing KMP11-NTGP96-GFP fusion as candidates for live engineered recombinant vaccine against visceral leishmaniasis in BALB/c mice. METHODS: KMP-11 and NT-GP96 genes cloned into the pJET1.2/blunt cloning vector and then into pEGFP-N1 expression vector. The KMP-11, NT-GP96 and GFP fused in pEGFP-N1 and subcloned into Leishmanian pLEXSY-neo vector. Finally this construct was transferred to L...
April 2016: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28096247/order-matters-the-order-of-somatic-mutations-influences-cancer-evolution
#3
David G Kent, Anthony R Green
Cancers evolve as a consequence of multiple somatic lesions, with competition between subclones and sequential subclonal evolution. Some driver mutations arise either early or late in the evolution of different individual tumors, suggesting that the final malignant properties of a subclone reflect the sum of mutations acquired rather than the order in which they arose. However, very little is known about the cellular consequences of altering the order in which mutations are acquired. Recent studies of human myeloproliferative neoplasms show that the order in which individual mutations are acquired has a dramatic impact on the cell biological and molecular properties of tumor-initiating cells...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28096240/coevolution-of-leukemia-and-host-immune-cells-in-chronic-lymphocytic-leukemia
#4
Noelia Purroy, C J Wu
Cumulative studies on the dissection of changes in driver genetic lesions in cancer across the course of the disease have provided powerful insights into the adaptive mechanisms of tumors in response to the selective pressures of therapy and environmental changes. In particular, the advent of next-generation-sequencing (NGS)-based technologies and its implementation for the large-scale comprehensive analyses of cancers have greatly advanced our understanding of cancer as a complex dynamic system wherein genetically distinct subclones interact and compete during tumor evolution...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28092686/epigenomic-reprogramming-during-pancreatic-cancer-progression-links-anabolic-glucose-metabolism-to-distant-metastasis
#5
Oliver G McDonald, Xin Li, Tyler Saunders, Rakel Tryggvadottir, Samantha J Mentch, Marc O Warmoes, Anna E Word, Alessandro Carrer, Tal H Salz, Sonoko Natsume, Kimberly M Stauffer, Alvin Makohon-Moore, Yi Zhong, Hao Wu, Kathryn E Wellen, Jason W Locasale, Christine A Iacobuzio-Donahue, Andrew P Feinberg
During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28089908/human-aml-ipscs-reacquire-leukemic-properties-after-differentiation-and-model-clonal-variation-of-disease
#6
Mark P Chao, Andrew J Gentles, Susmita Chatterjee, Feng Lan, Andreas Reinisch, M Ryan Corces, Seethu Xavy, Jinfeng Shen, Daniel Haag, Soham Chanda, Rahul Sinha, Rachel M Morganti, Toshinobu Nishimura, Mohamed Ameen, Haodi Wu, Marius Wernig, Joseph C Wu, Ravindra Majeti
Understanding the relative contributions of genetic and epigenetic abnormalities to acute myeloid leukemia (AML) should assist integrated design of targeted therapies. In this study, we generated induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements and found that they retained leukemic mutations but reset leukemic DNA methylation/gene expression patterns. AML-iPSCs lacked leukemic potential, but when differentiated into hematopoietic cells, they reacquired the ability to give rise to leukemia in vivo and reestablished leukemic DNA methylation/gene expression patterns, including an aberrant MLL signature...
December 26, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/28078253/effects-of-eicosapentaenoic-acid-and-docosahexaenoic-acid-on-mitochondrial-dna-replication-and-pgc-1%C3%AE-gene-expression-in-c2c12-muscle-cells
#7
Mak-Soon Lee, Yoonjin Shin, Sohee Moon, Seunghae Kim, Yangha Kim
Mitochondrial biogenesis is a complex process requiring coordinated expression of nuclear and mitochondrial genomes. The peroxisome proliferator-activated receptor gamma co-activator 1-alpha (PGC-1α) is a key regulator of mitochondrial biogenesis, and it controls mitochondrial DNA (mtDNA) replication within diverse tissues, including muscle tissue. The aim of this study was to investigate the effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on mtDNA copy number and PGC-1α promoter activity in C2C12 muscle cells...
December 2016: Preventive Nutrition and Food Science
https://www.readbyqxmd.com/read/28076468/phenotypic-diversity-and-selection-maintain-leishmania-amazonensis-infectivity-in-balb-c-mouse-model
#8
Benoît Espiau, Virginia Vilhena, Armelle Cuvillier, Aldina Barral, Gilles Merlin
Leishmania are protozoan parasites that show remarkable diversity, as revealed by the various clinical forms of leishmaniasis, which can range from mild skin lesions to severe metastatic cutaneous/mucosal lesions. The exact nature and extent of Leishmania phenotypic diversity in establishing infection is not fully understood. In order to try to understand some aspects of this diversity, we subcutaneously infected BALB/c mice with first and second generation subclones of a L. amazonensis strain isolated from a patient (BA125) and examined in vivo lesion growth rate and antimony susceptibility...
January 1, 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28076454/a-broad-ph-range-and-processive-chitinase-from-a-metagenome-library
#9
S S Thimoteo, A Glogauer, H Faoro, E M de Souza, L F Huergo, B M Moerschbacher, F O Pedrosa
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil was functionally screened for chitinase activity leading to the isolation and identification of a chitinase gene named metachi18A. The metachi18A gene was subcloned and overexpressed in Escherichia coli BL21 and the MetaChi18A chitinase was purified by affinity chromatography as a 6xHis-tagged fusion protein...
January 5, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28074063/direct-in-vivo-evidence-for-increased-proliferation-of-cll-cells-in-lymph-nodes-compared-to-bone-marrow-and-peripheral-blood
#10
T M Herndon, S-S Chen, N S Saba, J Valdez, C Emson, M Gatmaitan, X Tian, T E Hughes, C Sun, D C Arthur, M Stetler-Stevenson, C M Yuan, C U Niemann, G E Marti, G Aue, S Soto, M Z H Farooqui, S E M Herman, N Chiorazzi, A Wiestner
Chronic Lymphocytic Leukemia (CLL) is a progressive malignancy of mature B-cells that involves the peripheral blood (PB), lymph nodes (LNs) and bone marrow (BM). While the majority of CLL cells are in a resting state, small populations of proliferating cells exist; however, the anatomical site of active cell proliferation remains to be definitively determined. Based on findings that CLL cells in LNs have increased expression of B-cell activation genes, we tested the hypothesis that the fraction of 'newly born' cells would be highest in the LNs...
January 11, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28061803/evaluation-of-mlva-for-epidemiological-typing-and-outbreak-detection-of-esbl-producing-escherichia-coli-in-sweden
#11
Lisa Helldal, Nahid Karami, Christina Welinder-Olsson, Edward R B Moore, Christina Åhren
BACKGROUND: To identify the spread of nosocomial infections and halt outbreak development caused by Escherichia coli that carry multiple antibiotic resistance factors, such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases, is becoming demanding challenges due to the rapid global increase and constant and increasing influx of these bacteria from the community to the hospital setting. Our aim was to assess a reliable and rapid typing protocol for ESBL-E. coli, with the primary focus to screen for possible clonal relatedness between isolates...
January 6, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28060758/exosomes-as-mediators-of-platinum-resistance-in-ovarian-cancer
#12
Jennifer Crow, Safinur Atay, Samagya Banskota, Brittany Artale, Sarah Schmitt, Andrew K Godwin
Exosomes have been implicated in the cell-cell transfer of oncogenic proteins and genetic material. We speculated this may be one mechanism by which an intrinsically platinum-resistant population of epithelial ovarian cancer (EOC) cells imparts its influence on surrounding tumor cells. To explore this possibility we utilized a platinum-sensitive cell line, A2780 and exosomes derived from its resistant subclones, and an unselected, platinum-resistant EOC line, OVCAR10. A2780 cells demonstrate a ~2-fold increase in viability upon treatment with carboplatin when pre-exposed to exosomes from platinum-resistant cells as compared to controls...
January 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060738/the-prognostic-value-of-clonal-heterogeneity-and-quantitative-assessment-of-plasma-circulating-clonal-ig-vdj-sequences-at-diagnosis-in-patients-with-follicular-lymphoma
#13
Clémentine Sarkozy, Sarah Huet, Victoria E H Carlton, Bettina Fabiani, Alain Delmer, Fabrice Jardin, Marie-Helene Delfau-Larue, Maya Hacini, Vincent Ribrag, Stéphanie Guidez, Malek Faham, Gilles Salles
Recent advances in next-generation sequencing (NGS) have enabled the quantitation of circulating tumour DNA (ctDNA) encoding the clonal rearranged V(D)J immunoglobulin locus. We aimed to evaluate the clonal heterogeneity of follicular lymphoma (FL) in the tumour and the plasma at diagnosis and to assess the prognostic value of the ctDNA level. Plasma samples at diagnosis were available for 34 patients registered in the PRIMA trial (NCT00140582). One tumour clonotype or more could be detected for 29 (85%) and 25 (74%) patients, respectively, in the tumour or plasma samples...
January 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28056180/clonality-inference-from-single-tumor-samples-using-low-coverage-sequence-data
#14
Nilgun Donmez, Salem Malikic, Alexander W Wyatt, Martin E Gleave, Colin C Collins, S Cenk Sahinalp
Inference of intra-tumor heterogeneity can provide valuable insight into cancer evolution. Somatic mutations detected by sequencing can help estimate the purity of a tumor sample and reconstruct its subclonal composition. Although several methods have been developed to infer intra-tumor heterogeneity, the majority of these tools rely on variant allele frequencies as estimated via ultra-deep sequencing from multiple samples of the same tumor. In practice, obtaining sequencing data from a large number of samples per patient is only feasible in a few cancer types such as liquid tumors, or in rare cases involving solid tumors selected for research...
January 5, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28054381/rhabdoid-component-emerging-as-a-subclonal-evolution-of-paediatric-glioneuronal-tumours
#15
A Bertrand, C Rondenet, J Masliah-Planchon, P Leblond, A de la Fourchardière, D Pissaloux, K Aït-Raïs, D Lequin, A Jouvet, P Freneaux, H Sevestre, D Ranchere-Vince, A Tauziede-Espariat, C-A Maurage, K Silva, G Pierron, O Delattre, P Varlet, D Frappaz, F Bourdeaut
Atypical teratoid/rhabdoid tumors (AT/RT) are high-grade tumors partially composed of rhabdoid cells (1). The 1-year overall survival rate is 41% (2). Rhabdoid cells have large eccentric nuclei, a single prominent nucleolus, and abundant cytoplasm with eosinophilic inclusions. The immunohistochemical profile of these cells frequently includes loss of nuclear BAF47 expression due to loss of the SMARCB1 locus combined with a mutation of the other allele (3). This article is protected by copyright. All rights reserved...
January 5, 2017: Neuropathology and Applied Neurobiology
https://www.readbyqxmd.com/read/28049639/clonal-evolution-leading-to-ibrutinib-resistance-in-chronic-lymphocytic-leukemia
#16
Inhye E Ahn, Chingiz Underbayev, Adam Albitar, Sarah E M Herman, Xin Tian, Irina Maric, Diane C Arthur, Laura Wake, Stefania Pittaluga, Constance M Yuan, Maryalice Stetler-Stevenson, Susan Soto, Janet Valdez, Pia Nierman, Jennifer Lotter, Liqiang Xi, Mark Raffeld, Mohammed Farooqui, Maher Albitar, Adrian Wiestner
Disease progression in patients with chronic lymphocytic leukemia (CLL) treated with ibrutinib has been attributed to histologic transformation or acquired mutations in BTK and PLCG2 The rate of resistance and clonal composition of progressive disease are incompletely characterized. We report on CLL patients treated with single-agent ibrutinib on an investigator-initiated phase 2 trial. With median follow-up of 34 months, fifteen (17.9%) of 84 evaluable patients progressed. Relapsed/refractory disease at study entry, TP53 aberration, advanced Rai stage, and high β-2 microglobulin were independently associated with inferior progression-free survival (P<...
January 3, 2017: Blood
https://www.readbyqxmd.com/read/28049479/sequence-conservation-of-plasmodium-vivax-glutamate-dehydrogenase-among-korean-isolates-and-its-application-in-seroepidemiology
#17
Bomin Seol, Hyun-Il Shin, Jung-Yeon Kim, Bo-Young Jeon, Yoon-Joong Kang, Jhang-Ho Pak, Tong-Soo Kim, Hyeong-Woo Lee
BACKGROUND: Glutamate dehydrogenase of malaria parasites (pGDH) is widely used in rapid diagnostic tests for malaria. Variation in the pGDH gene among Korean isolates of Plasmodium vivax was analysed, and a recombinant pGDH protein was evaluated for use as antigens for the serodiagnosis of vivax malaria. METHODS: Genomic DNA was purified from blood samples of 20 patients and the pGDH gene of P. vivax was sequenced. Recombinant protein was prepared to determine the antigenicity of pGDH by enzyme-linked immunosorbent assay (ELISA)...
January 3, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28049408/detailed-simulation-of-cancer-exome-sequencing-data-reveals-differences-and-common-limitations-of-variant-callers
#18
Ariane L Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
BACKGROUND: Next-generation sequencing of matched tumor and normal biopsy pairs has become a technology of paramount importance for precision cancer treatment. Sequencing costs have dropped tremendously, allowing the sequencing of the whole exome of tumors for just a fraction of the total treatment costs. However, clinicians and scientists cannot take full advantage of the generated data because the accuracy of analysis pipelines is limited. This particularly concerns the reliable identification of subclonal mutations in a cancer tissue sample with very low frequencies, which may be clinically relevant...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28044227/a-novel-versatile-family-iv-carboxylesterase-exhibits-high-stability-and-activity-in-a-broad-ph-spectrum
#19
Amélie Dukunde, Dominik Schneider, Mingji Lu, Silja Brady, Rolf Daniel
OBJECTIVES: To investigate the properties of a novel metagenome-derived member of the hormone-sensitive lipase family of lipolytic enzymes. RESULTS: A forest soil metagenome-derived gene encoding an esterase (Est06) belonging to the hormone-sensitive lipase family of lipolytic enzymes was subcloned, heterologously expressed and characterized. Est06 is a polypeptide of 295 amino acids with a molecular mass of 31 kDa. The deduced protein sequence shares 61% similarity with a hypothetical protein from the marine symbiont Candidatus Entotheonella sp...
January 2, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28041846/change-in-ighv-mutational-status-of-cll-suggests-origin-from-multiple-clones
#20
Afaf Osman, Christopher D Gocke, Douglas E Gladstone
BACKGROUND: Fluorescence in situ hybridization and immunoglobulin (Ig) heavy-chain variable-region (IgHV) mutational status are used to predict outcome in chronic lymphocytic leukemia (CLL). Although DNA aberrations change over time, IgHV sequences and mutational status are considered stable. PATIENTS AND METHODS: In a retrospective review, 409 CLL patients, between 2008 and 2015, had IgHV analysis: 56 patients had multiple analyses performed. Seven patients' IgHV results changed: 2 from unmutated to mutated and 5 from mutated to unmutated IgHV sequence...
November 21, 2016: Clinical Lymphoma, Myeloma & Leukemia
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