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Immuno sequencing

John Moat, Athanasios Rizoulis, Graeme Fox, Mathew Upton
The domestic environment can be a source of pathogenic bacteria. We show here that domestic shower hoses may harbour potentially pathogenic bacteria and fungi. Well-developed biofilms were physically removed from the internal surface of shower hoses collected in four locations in England and Scotland. Amplicon pyrosequencing of 16S and 18S rRNA targets revealed the presence of common aquatic and environmental bacteria, including members of the Actinobacteria, Alphaproteobacteria, Bacteroidetes and non-tuberculous Mycobacteria...
October 2016: Journal of Water and Health
Tsuyoshi Hamada, NaNa Keum, Reiko Nishihara, Shuji Ogino
Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality...
October 13, 2016: Journal of Gastroenterology
M Brasino, J N Cha
Here we describe novel covalent conjugates of antibody-phage for the detection of multiple cancer biomarkers using real time immuno-polymerase chain reaction (immuno-PCR). While the conventional process of immuno-PCR utilizes DNA-conjugated antibodies, chemical modification of antibodies not only reduces antibody affinity but also creates a heterogeneous population of products. However, phage naturally encapsulate genomic DNA, which can be used as a PCR template. To produce covalently conjugated antibody-phage constructs without recombinant antibody expression or chemical modification of antibodies, we incorporated a photocrosslinkable non-canonical amino acid within an antibody-binding domain displayed on one of the phage coat proteins...
October 12, 2016: Analyst
Samina Rahmatpour, Amjad Hayat Khan, Rasoul Nasiri Kalmarzi, Masoumeh Rajabibazl, Gholamreza Tavoosidana, Elahe Motevaseli, Nosratollah Zarghami, Esmaeil Sadroddiny
In vivo and in vitro tests are the two major ways of identifying the triggering allergens in sensitized individuals with allergic symptoms. Both methods are equally significant in terms of sensitivity and specificity. However, in certain circumstances, in vitro methods are highly preferred because they circumvent the use of sensitizing drugs in patients. In current study, we described a highly sensitive immuno-PCR (iPCR) assay for serum IgE specific to Bermuda allergens. Using oligonucleotide-labelled antibody, we used iPCR for the sensitive detection of serum IgE...
October 5, 2016: Molecular and Cellular Probes
Martina Rudgalvyte, Juhani Peltonen, Merja Lakso, Garry Wong
Methylmercury (MeHg) is a persistent environmental pollutant that occurs in the food chain, at occupational sites, and via medical procedures. Exposure in humans and animal models results in renal, neuro, and reproductive toxicities. In this study, we demonstrate that chronic exposure to MeHg (10μM) causes epigenetic landscape modifications of histone H3K4 trimethylation (H3K4me3) marks in Caenorhabditis elegans using chromatin immuno-precipitation sequencing (ChIP-seq). The modifications correspond to the locations of 1467 genes with enhanced and 508 genes with reduced signals...
October 4, 2016: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
Fabian Lorenzo-Diaz, Cris Fernández-Lopez, Pierre-Emmanuel Douarre, Adrian Baez-Ortega, Carlos Flores, Philippe Glaser, Manuel Espinosa
Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance...
October 2016: Open Biology
Antonio Filippi, Elisa Petrussa, Uros Rajcevic, Vladka Čurin Šerbec, Sabina Passamonti, Giovanni Renzone, Andrea Scaloni, Marco Zancani, Angelo Vianello, Enrico Braidot
In the present study, an antibody raised against a peptide sequence of rat bilitranslocase (anti-peptide Ab) was tested on microsomal proteins obtained from red grape berry skin. Previously, this antibody had demonstrated to recognize plant membrane proteins associated with flavonoid binding and transport. Immuno-proteomic assays identified a number of proteins reacting with this particular antibody, suggesting that the flavonoid binding and interaction may be extended not only to carriers of these molecules, but also to enzymes with very different functions...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Eva Löser, Daniel Latreille, Nicola Iovino
This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq)...
2016: Methods in Molecular Biology
Sabrina Nusrat Sabah, Md Amran Gazi, Rahvia Alam Sthity, Amena Binte Husain, Salwa Abdul Quyyum, Mustafizur Rahman, Md Rezaul Islam
Human papillomavirus (HPV) is a DNA virus that belongs to the papillomavirus family and is capable of infecting humans. Currently, few vaccines are available to prevent infection by HPV. However, they are not so much effective and provide little benefit to women who have already been infected with HPV. The aim of this study was to design epitope-based vaccines of HPV58 by targeting E6 and E7 proteins of HPV58. Proteomic sequences were retrieved from different isolates at different time periods and later analyzed by performing alignment of these sequences...
September 17, 2016: Interdisciplinary Sciences, Computational Life Sciences
Afreenish Hassan, Anam Naz, Ayesha Obaid, Rehan Zafar Paracha, Kanwal Naz, Faryal Mehwish Awan, Syed Aun Muhmmad, Hussnain Ahmed Janjua, Jamil Ahmad, Amjad Ali
BACKGROUND: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets...
2016: BMC Genomics
Jackie Kleynhans, Gerhard Pietersen
Citrus tristeza virus (CTV) is the most economically important virus found on citrus and influences production worldwide. The 3' half of the RNA genome is generally conserved amongst sources, whereas the 5' portion is more divergent, allowing for the classification of the virus into a number of genotypes based on sequence diversity. The acknowledged genotypes of CTV are continually being expanded, and thus far include T36, T30, T3, VT, B165, HA16-5, T68 and RB. The genotype composition of the CTV populations of a potential cross protection source in Mexican lime was studied whilst comparing different techniques of viral population characterization...
November 2016: Journal of Virological Methods
James W Larrick, Mark R Alfenito, Jamie K Scott, Paul W H I Parren, Dennis R Burton, Andrew R M Bradbury, Cynthia A Lemere, Anne Messer, James S Huston, Paul J Carter, Trudi Veldman, Kerry A Chester, Janine Schuurman, Gregory P Adams, Janice M Reichert
Antibody Engineering & Therapeutics, the largest meeting devoted to antibody science and technology and the annual meeting of The Antibody Society, will be held in San Diego, CA on December 11-15, 2016. Each of 14 sessions will include six presentations by leading industry and academic experts. In this meeting preview, the session chairs discuss the relevance of their topics to current and future antibody therapeutics development. Session topics include bispecifics and designer polyclonal antibodies; antibodies for neurodegenerative diseases; the interface between passive and active immunotherapy; antibodies for non-cancer indications; novel antibody display, selection and screening technologies; novel checkpoint modulators / immuno-oncology; engineering antibodies for T-cell therapy; novel engineering strategies to enhance antibody functions; and the biological Impact of Fc receptor engagement...
August 24, 2016: MAbs
Mohammad Mahdi Forghanifard, Abolfazl Rad, Moein Farshchian, Maryam Khaleghizadeh, Mehran Gholamin, Meysam Moghbeli, Mohammad Reza Abbaszadegan
: Overexpression of MAGEA4 oncogene has been demonstrated in different malignancies; however, little is known about its exact mechanism for overexpression. TWIST1, as a bHLH transcription factor, activates a cell migration-invasion program involved in both embryonic and tumor development. Since MAGEA4 overexpression was statistically correlated to TWIST1, we aimed to elucidate the probable regulatory role of TWIST1 on MAGEA4 expression in KYSE30 cells. METHODS: Expression pattern of MAGEA4 and TWIST1 was analyzed in 55 ESCC patients using relative comparative real-time PCR...
August 17, 2016: Molecular Carcinogenesis
Rebecca L Skalsky, Sarah A Barr, Andrew J Jeffery, Tiffany Blair, Ryan Estep, Scott W Wong
UNLABELLED: Japanese macaque (JM) rhadinovirus (JMRV) is a novel, gamma-2 herpesvirus that was recently isolated from JM with inflammatory demyelinating encephalomyelitis (JME). JME is a spontaneous and chronic disease with clinical characteristics and immunohistopathology comparable to those of multiple sclerosis in humans. Little is known about the molecular biology of JMRV. Here, we sought to identify and characterize the small RNAs expressed during lytic JMRV infection using deep sequencing...
October 15, 2016: Journal of Virology
Giovanni Franzo, Martì Cortey, Joaquim Segalés, Joseph Hughes, Michele Drigo
Since its first description, PCV2 has emerged as one of the most economically relevant diseases for the swine industry. Despite the introduction of vaccines effective in controlling clinical syndromes, PCV2 spread was not prevented and some potential evidences of vaccine immuno escape have recently been reported ("Complete genome sequence of a novel porcine circovirus type 2b variant present in cases of vaccine failures in the United States" (Xiao and Halbur, 2012) [1], "Genetic and antigenic characterization of a newly emerging porcine circovirus type 2b mutant first isolated in cases of vaccine failure in Korea" (Seo et al...
September 2016: Data in Brief
G Gremel, R J Lee, M R Girotti, A K Mandal, S Valpione, G Garner, M Ayub, S Wood, D G Rothwell, A Fusi, A Wallace, G Brady, C Dive, N Dhomen, P Lorigan, R Marais
BACKGROUND: The application of precision medicine in oncology requires in-depth characterisation of a patient's tumours and the dynamics of their responses to treatment. PATIENTS AND METHODS: We used next-generation sequencing of circulating cell-free DNA (cfDNA) to monitor the response of a KIT p.L576P-mutant metastatic vaginal mucosal melanoma to sequential targeted, immuno- and chemotherapy. RESULTS: Despite a KIT mutation, the response to imatinib was mixed...
October 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Aleksandra Lipka, Grzegorz Panasiewicz, Marta Majewska, Martyna Bieniek-Kobuszewska, Alexander P Saveljev, Andrey P Pankratov, Bozena Szafranska
This study describes the identification and a broad-based characterization of the pregnancy-associated glycoprotein (PAG) genes expressed in the synepitheliochorial placenta of the Alces alces (Aa; N = 51). We used: (1) both size measurements (cm) of various Aa embryos/fetuses (crown-rump length) and placentomes (PLCs); (2) PCR, Southern and sequencing; (3) Western-blot for total placental glycoproteins; (4) deglycosylation of total cotyledonary proteins; and (5) double heterologous IHC for cellular immune-localization of the PAGs as pregnancy advanced (50-200 days post coitum)...
July 15, 2016: Theriogenology
Peter Berger, Adrian J Lapthorn
Antigenic domains are defined to contain a limited number of neighboring epitopes recognized by antibodies (Abs) but their molecular relationship remains rather elusive. We thoroughly analyzed the antigenic surface of the important pregnancy and tumor marker human chorionic gonadotropin (hCG), a cystine knot (ck) growth factor, and set antigenic domains and epitopes in molecular relationships to each other. Antigenic domains on hCG, its free hCGα and hCGβ subunits are dependent on appropriate inherent molecular features such as molecular accessibility and protrusion indices that determine bulging structures accessible to Abs...
August 2016: Molecular Immunology
Yasmin A Begum, K A Talukder, Ishrat J Azmi, Mohammad Shahnaij, A Sheikh, Salma Sharmin, A-M Svennerholm, Firdausi Qadri
BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is a common cause of bacterial infection leading to acute watery diarrhea in infants and young children as well as in travellers to ETEC endemic countries. Ciprofloxacin is a broad-spectrum antimicrobial agent nowadays used for the treatment of diarrhea. This study aimed to characterize ciprofloxacin resistant ETEC strains isolated from diarrheal patients in Bangladesh. METHODS: A total of 8580 stool specimens from diarrheal patients attending the icddr,b Dhaka hospital was screened for ETEC between 2005 and 2009...
2016: PloS One
István Nagy, Roland Wilhelm Knispel, Christine Kofler, Massimiliano Orsini, Marius Boicu, Sándor Varga, Elisabeth Weyher-Stingl, Na Sun, Ruben Fernandez-Busnadiego, József Kukolya, Stephan Nickell, Wolfgang Baumeister
Cytosolic, globular droplets with an average diameter of 50 nm were observed in vitrified Thermoplasma acidophilum cells by means of cryo-electron tomography. These droplets were isolated by column chromatography and immunoprecipitation protein purification methods. Subsequent chemical and biochemical analyses identified lipid and protein components, respectively. Two major lipid components, comigrating menaquinones at the solvent front and the slower migrating Thermoplasma polar lipid U4, were detected by TLC experiments...
September 2016: FEMS Microbiology Letters
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