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https://www.readbyqxmd.com/read/28922540/ape1-ref-1-knockdown-in-pancreatic-ductal-adenocarcinoma-characterizing-gene-expression-changes-and-identifying-novel-pathways-using-single-cell-rna-sequencing
#1
Fenil Shah, Emery Goossens, Nadia M Atallah, Michelle Grimard, Mark R Kelley, Melissa L Fishel
Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1 or APE1) is a multifunctional protein that regulates numerous transcription factors associated with cancer-related pathways. Because APE1 is essential for cell viability, generation of APE1 knockout cell lines and determining a comprehensive list of genes regulated by APE1 has not been possible. To circumvent this challenge, we utilized single-cell RNA Sequencing to identify differentially expressed genes in relation to APE1 protein levels within the cell...
September 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28922104/interleukin-2-interferon-gamma-gene-polymorphisms-in-recurrent-aphthous-stomatitis
#2
Shamsolmoulouk Najafi, Hila Yousefi, Mahsa Mohammadzadeh, Alireza Zare Bidoki, Elham Farhadi, Nima Rezaei
Recurrent aphthous stomatitis (RAS) is the most common oral ulcerative inflammatory disease with unknown etiology. IL-2 and IFN-γ are secreted by Th1 cells and the elevated levels of them have been reported in RAS. Single nucleotide polymorphisms (SNPs) of IL-2 and IFN-γ genes could alter the cytokine production. The aim of this study was to investigate frequencies of IL-2 and IFN-γ alleles and genotypes in a group of patients with minor-RAS (MiRAS). PCR-SSP method used to type genomic DNA of 64 Iranian patients with MiRAS for IL-2 gene (G -330 T) and (G +166 T) and IFN-γ gene at position UTR5644 (A/T)...
2017: Prague Medical Report
https://www.readbyqxmd.com/read/28917838/human-smoothened-inhibits-human-immunodeficiency-virus-type-1-infection
#3
Takeshi Yoshida, Akiko Hamano, Asuka Ueda, Hiroaki Takeuchi, Shoji Yamaoka
Human SMOOTHENED (SMO) was identified by expression cloning as a new host factor that inhibits HIV-1 infection. Forced expression of SMO inhibited HIV-1 replication and infection with a single-round lentiviral vector, but not infection with a murine leukemia virus-based retroviral vector in human MT-4 T cells. Quantitative PCR analyses revealed that stable expression of SMO impaired formation of the integrated form of lentiviral DNA, but did not interrupt reverse transcription. This inhibition was evident in MT-4 and HUT102 human T cell lines expressing low levels of SMO mRNA, but not in SupT1 or Jurkat T cell lines expressing higher levels of SMO mRNA...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28915574/comparative-study-of-whole-genome-amplification-and-next-generation-sequencing-performance-of-single-cancer-cells
#4
Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P McMullin, Denis A Smirnov, Weimin Li, Maria Geffken, Klaus Pantel, Simon A Joosse
BACKGROUND: Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS: In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28911154/prognostic-significance-of-circulating-ret-m918t-mutated-tumor-dna-in-patients-with-advanced-medullary-thyroid-carcinoma
#5
Gilbert J Cote, Caitlin Evers, Mimi I Hu, Elizabeth G Grubbs, Michelle D Williams, Tao Hai, Dzifa Y Duose, Michal R Houston, Jacquelin H Bui, Meenakshi Mehrotra, Steven G Waguespack, Naifa L Busaidy, Maria E Cabanillas, Mouhammed Amir Habra, Rajyalakshmi Luthra, Steven I Sherman
Context: Interpretation of calcitonin measurement to predict the prognosis of medullary thyroid carcinoma (MTC) requires multiple measurements over an extended time period, making it an imperfect biomarker for evaluating prognosis or disease behavior. Single circulating cell-free DNA (cfDNA) values have been shown to be a valuable prognostic marker for several solid tumors. Objective: We tested the hypothesis that cfDNA containing the RET M918T mutation could be detected in the blood of patients with advanced MTC whose tumor harbored an M918T mutation and would be able to predict overall survival more reliably than calcitonin...
September 1, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28910385/improving-the-characterization-of-endothelial-progenitor-cell-subsets-by-an-optimized-facs-protocol
#6
Karin Huizer, Dana A M Mustafa, J Clarissa Spelt, Johan M Kros, Andrea Sacchetti
The characterization of circulating endothelial progenitor cells (EPCs) is fundamental to any study related to angiogenesis. Unfortunately, current literature lacks consistency in the definition of EPC subsets due to variations in isolation strategies and inconsistencies in the use of lineage markers. Here we address critical points in the identification of hematopoietic progenitor cells (HPCs), circulating endothelial cells (CECs), and culture-generated outgrowth endothelial cells (OECs) from blood samples of healthy adults (AB) and umbilical cord (UCB)...
2017: PloS One
https://www.readbyqxmd.com/read/28910279/longitudinal-multiparameter-single-cell-analysis-of-macaques-immunized-with-pneumococcal-protein-conjugated-or-unconjugated-polysaccharide-vaccines-reveals-distinct-antigen-specific-memory-b-cell-repertoires
#7
Bin Jia, Lisa K McNeil, Christopher D Dupont, Konstantinos Tsioris, Rachel M Barry, Ingrid L Scully, Adebola O Ogunniyi, Christopher Gonzalez, Michael W Pride, Todd M Gierahn, Paul A Liberator, Kathrin U Jansen, J Christopher Love
BACKGROUND: The efficacy of protein-conjugated pneumococcal polysaccharide vaccines has been well characterized for children. The level of protection conferred by unconjugated polysaccharide vaccines remains less clear, particularly for elderly individuals who have had prior antigenic experience through immunization with unconjugated polysaccharide vaccines or natural exposure to Streptococcus pneumoniae. METHODS: We compared the magnitude, diversity and genetic biases of antigen-specific memory B cells in two groups of adult cynomolgus macaques that were immunized with a 7-valent conjugated vaccine and boosted after five years with either a 13-valent pneumococcal polysaccharide conjugate vaccine (13vPnC) or a 23-valent unconjugated pneumococcal polysaccharide vaccine (23vPS) using microengraving (a single-cell analysis method) and single-cell RT-PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28903012/in-vitro-chondrotoxicity-of-nonsteroidal-anti-inflammatory-drugs-and-opioid-medications
#8
Geoffrey D Abrams, Wenteh Chang, Jason L Dragoo
BACKGROUND: A variety of medications are administered to the intra-articular space for the relief of joint pain. While amide-type local anesthetics have been extensively studied, there is minimal information regarding the potential chondrotoxicity of nonsteroidal anti-inflammatory drugs (NSAIDs) and opioid medications. PURPOSE: To investigate the in vitro chondrotoxicity of single-dose equivalent concentrations of ketorolac, morphine, meperidine, and fentanyl on human chondrocytes...
September 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28902926/down-regulation-of-single-stranded-dna-binding-protein-1-expression-induced-by-hcmv-infection-promotes-lipid-accumulation-in-cells
#9
N Guo, N Zhang, L Yan, X Cao, F Lv, J Wang, Y Wang, H Cong
The objective of this study was to observe the infection of human cytomegalovirus (HCMV) to human umbilical vein endothelial cells, and its effect on the expression of single-stranded DNA-binding protein (SSBP1) and on lipid metabolism in endothelial cells. We screened the differential expression of mRNAs after HCMV infection by suppression subtractive hybridization and the expression levels of SSBP1 mRNA and protein after HCMV infection by real-time PCR and western blot. After verification of successful infection by indirect immunofluorescent staining and RT-PCR, we found a differential expression of lipid metabolism-related genes including LDLR, SCARB, CETP, HMGCR, ApoB and LPL induced by HCMV infection...
September 12, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28901422/association-between-endothelin%C3%A2-1-and-fibromyalgia-syndrome
#10
Seong-Su Nah, Hwayoung Lee, Yeongseon Hong, Jiyun Im, Hansol Won, Sung-Hae Chang, Hyung-Ki Kim, Jun-Tack Kwon, Hak-Jae Kim
Fibromyalgia syndrome (FMS) is characterized by widespread chronic musculoskeletal pain, stiffness and pressure hyperalgesia at soft tissue tender points. Patients with FMS may exhibit a tendency towards cold extremities and cold‑induced vasospasm. Endothelin‑1 (EDN1) is a potent vasoconstrictor that is mainly produced by endothelial cells. The present study aimed to determine whether plasma expression levels avvnd single‑nucleotide polymorphism (SNP; rs1800541) of the EDN1 gene were associated with FMS and/or any of its clinical variables...
August 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28900479/loss-of-tff1-promotes-pro-inflammatory-phenotype-with-increase-in-the-levels-of-ror%C3%AE-t-t-lymphocytes-and-il-17-in-mouse-gastric-neoplasia
#11
Mohammed Soutto, Mohamed Saleh, Mohamed S Arredouani, Blanca Piazuelo, Abbes Belkhiri, Wael El-Rifai
Background: TFF1 deficiency induces a mucosal pro-inflammatory phenotype that contributes to gastric tumorigenesis in mouse and human. Methods: We utilized the Tff1-KO mouse model to assess the impact of TFF1 loss on immune cells infiltration in the stomach. We used single cell suspension, flow cytometry, immunohistochemistry, and quantitative PCR (qPCR) assays. Results: The Tff1-KO gastric mucosa demonstrated high chronic inflammatory scores (score: 3-4) at age 2 months, which exacerbated at age 8 months (score: 4-6)...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28900421/efficacy-analysis-of-combinatorial-sirnas-against-hiv-derived-from-one-double-hairpin-rna-precursor
#12
Chang Liu, Zhipin Liang, Xiaohong Kong
Combinatorial small interfering RNA duplexes (siRNAs) have the potential to be a gene therapy against HIV-1, and some studies have reported that transient combinatorial siRNA expression represses HIV replication, but the effects of long-term siRNA expression on HIV replication have not been studied in detail. In this study, HIV-1 replication under the influence of stable combinatorial siRNA expression from a single RNA transcript was analyzed. First, a series of cassettes encoding short hairpin RNA (shRNA)/long hairpin RNA (lhRNA)/double long hairpins (dlhRNA) was constructed and subjected to an analysis of inhibitory efficacy...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28894165/evolution-analysis-of-heterogeneous-non-small-cell-lung-carcinoma-by-ultra-deep-sequencing-of-the-mitochondrial-genome
#13
Wafa Amer, Csaba Toth, Erik Vassella, Jeannine Meinrath, Ulrike Koitzsch, Anne Arens, Jia Huang, Hannah Eischeid, Alexander Adam, Reinhard Buettner, Andreas Scheel, Stephan C Schaefer, Margarete Odenthal
Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893911/molecular-and-functional-characterization-of-the-endothelial-atp-sensitive-potassium-channel
#14
Qadeer Aziz, Yiwen Li, Naomi Anderson, Leona Ojake, Elena Tsisanova, Andrew Tinker
ATP-sensitive potassium (KATP) channels are widely expressed in the cardiovascular system where they regulate a range of biological activities by linking cellular metabolism with membrane excitability. KATP channels in vascular smooth muscle have a well-defined role in regulating vascular tone. KATP channels are also thought to be expressed in vascular endothelial cells (ECs), but their presence and function in this context is less clear. As a result, we aimed to investigate the molecular composition and physiological role of endothelial KATP channels...
September 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28893570/phytoestrogenic-effect-of-inula-racemosa-hook-f-a-cardioprotective-root-drug-in-traditional-medicine
#15
Kalachaveedu Mangathayaru, Divya Raghavan, Srivani Telapolu, Sarah Kuruvilla, Kedike Balakrishna
ETHNOPHARMACOLOGICAL RELEVANCE: Roots of Inula racemosa are used as a cardio protective in Ayurveda in India, being prescribed as a medicine for precordial chest pain, cough and dyspnoea, both singly and as a poly herbal. AIM: Evaluation of Phytoestrogenic activity of the root extracts of Inula racemosa and compounds isolated therefrom in vivo, in silico and in vitro. MATERIALS AND METHODS: Alcohol (IrA) and hexane (IrH) extracts characterized by HPTLC/GC-MS analysis respectively and processed for compound isolation were evaluated for estrogenic activity (100 &250mg/kg bw) by the Immature rat uterotrophic assay using ethinylestradiol (EE -30µg/kg bw) as standard drug...
September 8, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28892497/improved-dop-pcr-idop-pcr-a-robust-and-simple-wga-method-for-efficient-amplification-of-low-copy-number-genomic-dna
#16
Konstantin A Blagodatskikh, Vladimir M Kramarov, Ekaterina V Barsova, Alexey V Garkovenko, Dmitriy S Shcherbo, Andrew A Shelenkov, Vera V Ustinova, Maria R Tokarenko, Simon C Baker, Tatiana V Kramarova, Konstantin B Ignatov
Whole-genome amplification (WGA) techniques are used for non-specific amplification of low-copy number DNA, and especially for single-cell genome and transcriptome amplification. There are a number of WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which is a very simple, fast and inexpensive WGA technique. Although DOP-PCR has been regarded as one of the pioneering methods for WGA, it only provides low genome coverage and a high allele dropout rate when compared to more modern techniques...
2017: PloS One
https://www.readbyqxmd.com/read/28888816/the-repeat-structure-of-two-paralogous-genes-yersinia-ruckeri-invasin-yrinv-and-a-y-ruckeri-invasin-like-molecule-yrilm-sheds-light-on-the-evolution-of-adhesive-capacities-of-a-fish-pathogen
#17
Agnieszka Wrobel, Claudio Ottoni, Jack C Leo, Snorre Gulla, Dirk Linke
Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule)...
September 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28885682/selective-targeting-of-m-type-potassium-channel-kv7-4-demonstrates-its-key-role-in-regulating-of-dopaminergic-neuronal-excitability-and-depression-like-behaviour
#18
Li Li, Hui Sun, Jie Ding, Chenxu Niu, Min Su, Ludi Zhang, Yingmin Li, Chuan Wang, Nikita Gamper, Xiaona Du, Hailin Zhang
BACKGROUND AND PURPOSE: The mesolimbic dopamine (DA) system originating in the ventral tegmental area (VTA) is implicated in the development of depression, and firing patterns of VTA DA neurons are key determinants in this process. Here, we describe a crucial role of the M-type potassium channel Kv7.4 in modulation of VTA DA neuronal excitability and in the development of depressive behaviour in mice. EXPERIMENTAL APPROACH: We used Kv7.4 knock-out mice and a social defeat model of depression in combination with various electrophysiological techniques (patch clamp recording and in vivo single unit recordings), immunohistochemistry, single-cell PCR and behavioural analyses (social interaction time and glucose preference tests) to investigate VTA circuits involved in development of depression-like behaviour...
September 8, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28885603/functional-characterization-of-selected-universal-stress-protein-from-salvia-miltiorrhiza-smusp-in-escherichia-coli
#19
Xiao-Fan Wang, Jiao Su, Na Yang, Hui Zhang, Xiao-Yan Cao, Jie-Fang Kang
The multigene universal stress protein (USP) family is evolutionarily conserved. Members play indispensable roles in plant tolerance to abiotic stresses. Although relatively well-characterized in model plants, such as Arabidopsis thaliana and Oryzasativa, this family has not been investigated in Salvia miltiorrhiza, an important herbal plant for which yields can be limited by various abiotic stresses. Here, we identified 32 USP family members in the S. miltiorrhiza genome, and used phylogenetic analysis to sort these SmUSPs into four groups...
September 8, 2017: Genes
https://www.readbyqxmd.com/read/28880020/novel-gp64-envelope-variants-for-improved-delivery-to-human-airway-epithelial-cells
#20
P L Sinn, B-Y Hwang, N Li, J L S Ortiz, E Shirazi, K R Parekh, A L Cooney, D V Schaffer, P B McCray
Lentiviral vectors pseudotyped with the baculovirus envelope protein GP64 transduce primary cultures of human airway epithelia (HAE) at their apical surface. Our goal in this study was to harness a directed evolution approach to develop a novel envelope glycoprotein with increased transduction properties for HAE. Using error-prone PCR, a library of GP64 mutants was generated and used to prepare a diverse pool of lentiviral virions pseudotyped with GP64 variants. The library was serially passaged on HAE and three GP64 mutations were recovered...
September 7, 2017: Gene Therapy
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