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Immuno sequencing

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https://www.readbyqxmd.com/read/28346477/disruption-of-sorcs2-reveals-differences-in-the-regulation-of-stereociliary-bundle-formation-between-hair-cell-types-in-the-inner-ear
#1
Andrew Forge, Ruth R Taylor, Sally J Dawson, Michael Lovett, Daniel J Jagger
Behavioural anomalies suggesting an inner ear disorder were observed in a colony of transgenic mice. Affected animals were profoundly deaf. Severe hair bundle defects were identified in all outer and inner hair cells (OHC, IHC) in the cochlea and in hair cells of vestibular macular organs, but hair cells in cristae were essentially unaffected. Evidence suggested the disorder was likely due to gene disruption by a randomly inserted transgene construct. Whole-genome sequencing identified interruption of the SorCS2 (Sortilin-related VPS-10 domain containing protein) locus...
March 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28287596/generation-of-fluorescent-protein-fusions-in-candida-species
#2
Sara Gonia, Judith Berman, Cheryl A Gale
Candida species, prevalent colonizers of the intestinal and genitourinary tracts, are the cause of the majority of invasive fungal infections in humans. Thus, molecular and genetic tools are needed to facilitate the study of their pathogenesis mechanisms. PCR-mediated gene modification is a straightforward and quick approach to generate epitope-tagged proteins to facilitate their detection. In particular, fluorescent protein (FP) fusions are powerful tools that allow visualization and quantitation of both yeast cells and proteins by fluorescence microscopy and immunoblotting, respectively...
March 4, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28245399/-single-nucleotide-polymorphism-of-mitochondrial-dna-d-loop-region-in-peripheral-blood-lymphocytes-of-immuno-related-pancytopenia-patients
#3
Qiu-Fan Zhou, Shu-Mei Xu, Hua-Quan Wang, Li-Min Xing, Rong Fu, Zong-Hong Shao
OBJECTIVE: To explore the single nucleotide polymorphism(SNP) of mitochondrial DNA (mtDNA) D-LOOP region in peripheral blood lymphocytes of immuno-related pancytopenia (IRP) patients and its correlation with immune parameters. METHODS: The D-LOOP region in mitochondrial DNA of lymphocytes in peripheral blood mononuclear cells from 43 patients with untreated IRP was detected by polymerase chain reaction(PCR). The PCR products were sequenced by the pros and cons direct sequencing methods...
February 2017: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/28216140/expression-profiles-of-cancer-stem-cell-markers-cd133-cd44-musashi-1-and-epcam-in-the-cardiac-mucosa-barrett-s-esophagus-early-esophageal-adenocarcinoma-advanced-esophageal-adenocarcinoma-sequence
#4
Anna Mokrowiecka, Lothar Veits, Christina Falkeis, Jacek Musial, Radzislaw Kordek, Mariusz Lochowski, Jozef Kozak, Agnieszka Wierzchniewska-Lawska, Michael Vieth, Ewa Malecka-Panas
INTRODUCTION: Barrett's esophagus (BE), which develops as a result of gastroesophageal reflux disease, is a preneoplastic condition for esophageal adenocarcinoma (EAC). A new hypothesis suggests that cancer is a disease of stem cells, however, their expression and pathways in BE - EAC sequence are not fully elucidated yet. AIMS: We used a panel of putative cancer stem cells markers to identify stem cells in consecutive steps of BE-related cancer progression. METHODS: Immunohistochemistry was performed on formalin-fixed, paraffin-embedded blocks from 58 patients with normal cardiac mucosa (n=5), BE (n=14), early EAC (pT1) from mucosal resection (n=17) and advanced EAC (pT1-T4) from postoperative specimens (n=22)...
December 30, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28213174/evidence-of-the-presence-of-a-calmodulin-sensitive-plasma-membrane-ca-2-atpase-in-trypanosoma-equiperdum
#5
María Carolina Pérez-Gordones, José Rubén Ramírez-Iglesias, Vincenza Cervino, Graciela L Uzcanga, Gustavo Benaim, Marta Mendoza
Trypanosoma equiperdum belongs to the subgenus Trypanozoon, which has a significant socio-economic impact by limiting animal protein productivity worldwide. Proteins involved in the intracellular Ca(2+) regulation are prospective chemotherapeutic targets since several drugs used in experimental treatment against trypanosomatids exert their action through the disruption of the parasite intracellular Ca(2+) homeostasis. Therefore, the plasma membrane Ca(2+)-ATPase (PMCA) is considered as a potential drug target...
February 14, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28174236/merkel-cell-carcinomas-arising-in-autoimmune-disease-affected-patients-treated-with-biological-drugs-including-tnf
#6
John C Rotondo, Ilaria Bononi, Andrea Puozzo, Marcello Govoni, Valentina Foschi, Giovanni Lanza, Roberta Gafà, Antoine Touzè, Pauline Gaboriaud, Rita Selvatici, Fernanda Martini, Mauro Tognon
PURPOSE: The purpose of this investigation was to characterize Merkel cell carcinomas (MCC) arising in patients affected by auto-immune diseases, treated with biologic drugs. EXPERIMENTAL DESIGN: Serum samples from MCC patients were analyzed for the presence and titer of antibodies against antigens of the oncogenic Merkel cell polyomavirus (MCPyV). IgG antibodies against the viral oncoproteins Large T (LT) and small t (ST) antigens and the viral capsid protein 1 were analyzed by indirect E...
February 7, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28152598/immuno-affinity-capture-followed-by-tmpp-n-terminus-tagging-to-study-catabolism-of-therapeutic-proteins
#7
Majlinda Kullolli, Dan A Rock, Ji Ma
Characterization of in vitro and in vivo catabolism of therapeutic proteins has increasingly become an integral part of discovery and development process for novel proteins. Unambiguous and efficient identification of catabolites can not only facilitate accurate understanding of pharmacokinetic profiles of drug candidates, but also enables follow up protein engineering to generate more catabolically stable molecules with improved properties (pharmacokinetics and pharmacodynamics). Immunoaffinity capture (IC) followed by top-down intact protein analysis using either matrix-assisted laser desorption/ionization or electrospray ionization mass spectrometry analysis have been the primary methods of choice for catabolite identification...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28132690/mutations-in-extl3-cause-neuro-immuno-skeletal-dysplasia-syndrome
#8
Machteld M Oud, Paul Tuijnenburg, Maja Hempel, Naomi van Vlies, Zemin Ren, Sacha Ferdinandusse, Machiel H Jansen, René Santer, Jessika Johannsen, Chiara Bacchelli, Marielle Alders, Rui Li, Rosalind Davies, Lucie Dupuis, Catherine M Cale, Ronald J A Wanders, Steven T Pals, Louise Ocaka, Chela James, Ingo Müller, Kai Lehmberg, Tim Strom, Hartmut Engels, Hywel J Williams, Phil Beales, Ronald Roepman, Patricia Dias, Han G Brunner, Jan-Maarten Cobben, Christine Hall, Taila Hartley, Polona Le Quesne Stabej, Roberto Mendoza-Londono, E Graham Davies, Sérgio B de Sousa, Davor Lessel, Heleen H Arts, Taco W Kuijpers
EXTL3 regulates the biosynthesis of heparan sulfate (HS), important for both skeletal development and hematopoiesis, through the formation of HS proteoglycans (HSPGs). By whole-exome sequencing, we identified homozygous missense mutations c.1382C>T, c.1537C>T, c.1970A>G, and c.2008T>G in EXTL3 in nine affected individuals from five unrelated families. Notably, we found the identical homozygous missense mutation c.1382C>T (p.Pro461Leu) in four affected individuals from two unrelated families. Affected individuals presented with variable skeletal abnormalities and neurodevelopmental defects...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28130119/a-new-microneme-protein-of-neospora-caninum-ncmic8-is-involved-in-host-cell-invasion
#9
Jing Wang, Di Tang, Wensheng Li, Jianhai Xu, Qun Liu, Jing Liu
Microneme proteins play an important role in the invasion process of Apicomplexan parasites through adhesion to host cells. We discovered a new N. caninum protein, NcMIC8, which is highly identical to TgMIC8. The NcMIC8 sequence has 2049 bp and no intron in the open reading fragment. It has a molecular weight of 73.8 kDa and contains a signal peptide, a transmembrane region, a low complexity region and 10 epidermal growth factor (EGF) domains. Immuno-fluorescence assay showed that NcMIC8 is located in the microneme...
April 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28107671/recent-sequence-variation-in-probe-binding-site-affected-detection-of-respiratory-syncytial-virus-group-b-by-real-time-rt-pcr
#10
Everlyn Kamau, Charles N Agoti, Clement S Lewa, John Oketch, Betty E Owor, Grieven P Otieno, Anne Bett, Patricia A Cane, D James Nokes
BACKGROUND: Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. OBJECTIVES: Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. STUDY DESIGN: Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples...
March 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28106467/follicular-lymphoma-a-b-cell-malignancy-addicted-to-epigenetic-mutations
#11
Koorosh Korfi, Sara Ali, James A Heward, Jude Fitzgibbon
While follicular lymphoma (FL) is exquisitely responsive to immuno-chemotherapy, many patients follow a relapsing remitting clinical course driven in part by a common precursor cell (CPC) population. Advances in next generation sequencing have provided valuable insights into the genetic landscape of FL and its clonal evolution in response to therapy, implicating perturbations of epigenetic regulators as a hallmark of the disease. Recurrent mutations of histone modifiers KMT2D, CREBBP, EP300, EZH2, ARIDIA, and linker histones are likely early events arising in the CPC pool, rendering epigenetic based therapies conceptually attractive for treatment of indolent and transformed FL...
January 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28063307/sharpin-facilitates-p53-degradation-in-breast-cancer-cells
#12
Huijie Yang, Sifan Yu, Weilong Wang, Xin Li, Yingxiang Hou, Zhenhua Liu, Yuanyuan Shi, Kun Mu, Gang Niu, Juntao Xu, Hui Wang, Jian Zhu, Ting Zhuang
The ubiquitin binding protein SHAPRIN is highly expressed in human breast cancer, one of the most frequent female malignancies worldwide. Here, we perform SHARPIN depletion in breast cancer cells together with RNA sequencing. The global expression profiling showed p53 signaling as a potential SHARPIN target. SHARPIN depletion decreased cell proliferation, which effect could be rescue by p53 knocking down. Depletion SHARPIN significantly increases p53 protein level and its target genes in multiple breast cancer cell lines...
February 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28059484/assessment-of-il-18-serum-level-and-its-promoter-polymorphisms-in-the-saudi-coronary-artery-disease-cad-patients
#13
Nasimudeen R Jabir, Chelapram K Firoz, Mohammad A Kamal, Ghazi A Damanhouri, Mohammed Nabil Alama, Qamre Alam, Absarul Haque, Hussein A Almehdar, Shams Tabrez
The purpose of the current study was to find out the possible polymorphic site at the promoter region of IL-18 gene in Saudi CAD patients. We have also measured serum IL-18 level to find out, the likely association between its level and polymorphic site. The present study included total 200 subjects (100 confirmed CAD patients both men and women and 100 healthy control individuals). Serum concentration of IL-18 was measured by enzyme linked immuno-sorbent assay. For SNPs analysis, sanger method of DNA sequencing was followed...
January 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28043417/in-silico-structure-analysis-and-epitope-prediction-of%C3%A2-e3-cr1-beta-protein-of-human-adenovirus-e%C3%A2-for%C3%A2-vaccine-design
#14
Noman Ibna Amin Patwary, Md Saiful Islam, Md Sohel, Ismot Ara, Mohd Omar Faruk Sikder, Shah Md Shahik
BACKGROUND: Human Adenoviruses are divided into 7 species of Human Adenovirus A to G based on DNA genome homology. The Human Adenovirus E (HAdVs-E) genome is a linear, double-stranded DNA containing 38 protein-coding genes. Wild-type adenoviruses type E, are linked to a number of slight illnesses. The most important part of HAdVs-E is E3 CR1-beta protein which controls the host immune response and viral attachment. METHOD: We use numerous bio-informatics and immuno-informatics implements comprising sequence and construction tools for construction of 3D model and epitope prediction for HAdVs-E...
December 2016: Biomedical Journal
https://www.readbyqxmd.com/read/28038990/putative-dna-modification-methylase-dr_c0020-of-deinococcus-radiodurans-is-an-atypical-sam-dependent-c-5-cytosine-dna-methylase
#15
Nayana A Patil, Bhakti Basu, Deepti D Deobagkar, Shree K Apte, Dileep N Deobagkar
BACKGROUND: Control of cellular processes by epigenetic modification of cytosine in DNA is widespread among living organisms, but, is hitherto unknown in the extremely radioresistant microbe D. radiodurans. METHODS: C-5 methyl cytosines (m(5)C) were detected by immuno-blotting with m(5)C-specific antibody. Site of cytosine methylation by DR_C0020 encoded protein was investigated by bisulfite sequencing. The DR_C0020 knockout mutant (Δdcm), constructed by site directed mutagenesis, was assessed for effect on growth, radiation resistance and proteome...
March 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28005999/characterization-of-chinese-haemophilus-parasuis-isolates-by-traditional-serotyping-and-molecular-serotyping-methods
#16
Lina Ma, Liyan Wang, Yuefeng Chu, Xuerui Li, Yujun Cui, Shengli Chen, Jianhua Zhou, Chunling Li, Zhongxin Lu, Jixing Liu, Yongsheng Liu
Haemophilus parasuis is classified mainly through serotyping, but traditional serotyping always yields non-typable (NT) strains and unreliable results via cross-reactions. Here, we surveyed the serotype prevalence of Chinese H. parasuis isolates using traditional serotyping (gel immuno-diffusion test, GID) and molecular serotyping (multiplex PCR, mPCR). We also investigated why discrepant results between these methods were obtained, and investigated mPCR failure through whole-genome sequencing. Of the 100 isolate tested, 73 (73%) and 93 (93%) were serotyped by the GID test and mPCR, respectively, with a concordance rate of 66% (66/100)...
2016: PloS One
https://www.readbyqxmd.com/read/27990137/immuno-affinity-selex-for-simple-rapid-and-cost-effective-aptamer-enrichment-and-identification-against-aflatoxin-b1
#17
Keerthana Setlem, Bhairab Mondal, Shylaja Ramlal, Joseph Kingston
Aflatoxins are naturally occurring mycotoxins that contaminate food and agro commodities, leading to acute and chronic health conditions in human and animals. In the present work, an attempt was made to generate high-affinity single stranded DNA aptamers that specifically bind to Aflatoxin B1 (AFB1) by a modified Systemic Evolution of Ligands by Exponential Enrichment (SELEX) procedure with the aid of Immunoaffinity columns. Ten rounds of SELEX and alternating three counter SELEX rounds with a cocktail of related and other mycotoxins were performed to enhance the specificity...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27960591/immuno-oncology-for-renal-cell-carcinoma-treatment-future-perspectives-for-combinations-and-sequences-with-molecularly-targeted-agents
#18
Camillo Porta, Ilaria Toscani, Anna M Czarnecka, Cezary A Szczylik
From a theoretical viewpoint, combining molecularly targeted agents endowed with antiangiogenic properties with immunotherapy makes sense in treatment of metastatic renal cell carcinoma (RCC); this neoplasm is highly angiogenesis-dependent, as well as potentially immunogenic. Areas covered: The authors performed a literature search looking for clinical trials aimed at evaluating efficacy and tolerability of combinations (or sequences) of molecularly targeted agents and different immunotherapeutic approaches in metastatic RCC...
February 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/27923825/rational-selection-of-syngeneic-preclinical-tumor-models-for-immunotherapeutic-drug-discovery
#19
Suzanne I S Mosely, John E Prime, Richard C A Sainson, Jens-Oliver Koopmann, Dennis Y Q Wang, Danielle M Greenawalt, Miika J Ahdesmaki, Rebecca Leyland, Stefanie Mullins, Luciano Pacelli, Danielle Marcus, Judith Anderton, Amanda Watkins, Jane Coates Ulrichsen, Philip Brohawn, Brandon W Higgs, Matthew McCourt, Hazel Jones, James A Harper, Michelle Morrow, Viia Valge-Archer, Ross Stewart, Simon J Dovedi, Robert W Wilkinson
Murine syngeneic tumor models are critical to novel immuno-based therapy development, but the molecular and immunologic features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Across a panel of commonly used murine syngeneic tumor models, we showed variable responsiveness to immunotherapies. We used array comparative genomic hybridization, whole-exome sequencing, exon microarray analysis, and flow cytometry to extensively characterize these models, which revealed striking differences that may underlie these contrasting response profiles...
December 6, 2016: Cancer Immunology Research
https://www.readbyqxmd.com/read/27871874/functional-and-immuno-reactive-characterization-of-a-previously-undescribed-peptide-from-the-venom-of-the-scorpion-centruroides-limpidus
#20
Timoteo Olamendi-Portugal, Rita Restano-Cassulini, Lidia Riaño-Umbarila, Baltazar Becerril, Lourival D Possani
A previously undescribed toxic peptide named Cl13 was purified from the venom of the Mexican scorpion Centruroides limpidus. It contains 66 amino acid residues, including four disulfide bonds. The physiological effects assayed in 7 different subtypes of voltage gated Na(+)-channels, showed that it belongs to the β-scorpion toxin type. The most notorious effects were observed in subtypes Nav1.4, Nav1.5 and Nav1.6. Although having important sequence similarities with two other lethal toxins from this scorpion species (Cll1m and Cll2), the recently developed single chain antibody fragments (scFv) of human origin were not capable of protecting against Cl13...
January 2017: Peptides
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