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Immuno sequencing

G R Gowane, Najif Akram, S S Misra, Ved Prakash, Arun Kumar
The objective of this study was to assess the genetic diversity of the Sirohi goat for DQB and DQB1 loci, and to study their association with antibody response induced by the Peste des petits ruminants (PPR) vaccine. A total of 360 Sirohi kids were studied using single stranded confirmation polymorphism (SSCP) followed by polymerase chain reaction sequence-based typing (PCR-SBT) for DQB and DQB1 diversities. The competitive enzyme-linked immuno-sorbent assay (C-ELISA) was used to evaluate immune response post-PPR vaccination...
June 2018: Journal of Genetics
Qiguo Zhang, Liangqi Cai, Mian Wang, Xiaoping Ke, Xiaoyan Zhao, Yijin Huang
Keloids are skin fibroproliferative tumors characterized by locally invasive growth of fibroblasts and excessive collagen deposition. The objective of this study is to investigate the molecular basis of the keloid scar by studying the mutation of related genes. We performed gene screening of mechanoreceptors by quantitative polymerase chain reaction (qPCR), Sanger sequencing to detect the CXCR1gene mutation, and immuno-histochemistry to determine CXCR1 protein expression. Among the genes encoding mechanoreceptors, the expression of CXCR1 mRNA was significantly higher in keloid scar tissues than in the surrounding tissues of normal controls (P < 0...
June 21, 2018: Archives of Dermatological Research
Seyed Reza Banihashemi, Ahmad Zavaran Hosseini, Fatemeh Rahbarizadeh, Davoud Ahmadvand
Objectives: CD19 is a transmembrane glycoprotein of immunoglobulin superfamily. In order to treat lymphoma, monoclonal antibodies (mAb) can target different antigens, including CD19, CD20 and CD22 on the surface of B-cells. Along with biotechnology progress, a new generation of antibodies is introduced, with the purpose of eliminating the defects of the previous generation. Among the most developed one are nanobodies (Nb). Nbs are a unique kind of camelid single domain antibody fragments with a broad range of medical applications...
May 2018: Iranian Journal of Basic Medical Sciences
Krithika Bhuvaneshwar, Lei Song, Subha Madhavan, Yuriy Gusev
An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN, which allows for not only the detection and quantification of viral RNA, but also variants in the viral transcripts. The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups...
2018: Frontiers in Microbiology
Jessie A G van Buggenum, Jan P Gerlach, Sabine E J Tanis, Mark Hogeweg, Pascal W T C Jansen, Jesse Middelwijk, Ruud van der Steen, Michiel Vermeulen, Hendrik G Stunnenberg, Cornelis A Albers, Klaas W Mulder
Cell-based small molecule screening is an effective strategy leading to new medicines. Scientists in the pharmaceutical industry as well as in academia have made tremendous progress in developing both large-scale and smaller-scale screening assays. However, an accessible and universal technology for measuring large numbers of molecular and cellular phenotypes in many samples in parallel is not available. Here we present the immuno-detection by sequencing (ID-seq) technology that combines antibody-based protein detection and DNA-sequencing via DNA-tagged antibodies...
June 19, 2018: Nature Communications
Arjan P Palstra, Jeroen Kals, Ainhoa Blanco Garcia, Ron P Dirks, Marnix Poelman
Seaweeds may represent immuno-stimulants that could be used as health-promoting fish feed components. This study was performed to gain insights into the immunomodulatory effects of dietary seaweeds in Atlantic salmon. Specifically tested were 10% inclusion levels of Laminaria digitata (SW1) and a commercial blend of seaweeds (Oceanfeed® ) (SW2) against a fishmeal based control diet (FMC). Differences between groups were assessed in growth, feed conversion ratio and blood parameters hematocrit and hemoglobin...
2018: Frontiers in Physiology
Jee Youn Hwang, Kesavan Markkandan, Kyudong Han, Mun Gyeong Kwon, Jung Soo Seo, Seung-Il Yoo, Seong Don Hwang, Bo Young Ji, Maeng-Hyun Son, Jun-Hyung Park
Olive flounder (Paralichthys olivaceus) is one of the most economically important aquaculture fish. However, its production is often affected by various diseases, especially viral hemorrhagic septicemia virus (VHSV) that cause serious economic losses. In this study, we sequenced the whole transcriptome of the P. olivaceus using Illumina RNA-sEq. De novo assembly of control and virus-infected cDNA libraries of head kidney at 13 and 20 °C was accomplished with 2,007,532,438 raw reads, resulting in 244,578 unigenes with an average length of 533 bp and found 65,535 candidate coding unigenes with homology to other species by BLAST analysis...
March 2018: Genes & Genomics
Elena Gayo, Vincenzo Cuteri, Laura Polledo, Giacomo Rossi, Juan F García Marín, Silvia Preziuso
Small Ruminant Lentiviruses (SRLVs) are widespread in many countries and cause economically relevant, slow, and persistent diseases in sheep and goats. Monitoring the genetic diversity of SRLVs is useful to improve the diagnostic tools used in the eradication programs. In this study, SRLVs detected in Spanish Assaf sheep with different grades of lymphoproliferative mastitis were sequenced. Genetic characterization showed that most samples belonged to type A and were closer to Spanish SRLV isolates previously classified as A2/A3...
June 9, 2018: Viruses
John Smestad, Luke Erber, Yue Chen, L James Maher
Succinylation is a post-translational protein acylation modification that converts the cationic lysine side chain to an anion with large potential impacts on protein structure and function. Here we characterize the epigenome-wide distribution of succinyllysine marks in chromatin using chromatin immuno-precipitation sequencing (ChIP-seq). We estimate that more than one-third of all nucleosomes contain lysine succinylation marks and demonstrate a potential role of chromatin succinylation in modulating gene expression...
April 27, 2018: iScience
Jashan P Abraham, Dominic J Barker, James Robinson, Giuseppe Maccari, Steven G E Marsh
The IMGT/HLA Database has provided a repository for information regarding polymorphism in the genes of the immune system since 1998. In 2003, it was absorbed into the Immuno Polymorphism Database (IPD). The IPD project has enabled us to create and maintain a platform for curating and publishing locus-specific databases which are either involved directly with, or relate to, the function of the Major Histocompatibility Complex across a number of species. In collaboration with specialist groups and nomenclature committees individual sections have been curated prior to their submission to the IPD for online publication...
2018: Methods in Molecular Biology
Sunantha Sethuraman, Merin Thomas, Lauren A Gay, Rolf Renne
Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi's Sarcoma-associated herpes virus (KSHV) and Epstein-Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs...
May 29, 2018: Nucleic Acids Research
Kanokkarn Pothong, Chalit Komalamisra, Thareerat Kalambaheti, Dorn Watthanakulpanich, Timothy P Yoshino, Paron Dekumyoy
BACKGROUND: Paragonimus heterotremus is the main causative agent of paragonimiasis in Thailand. In Western blot diagnostic assays for paragonimiasis, the 35 kDa band present in crude P. heterotremus somatic extracts represents one of the known diagnostic bands. This study aimed to use a P. heterotremus cDNA library to create a recombinant version of this antigen for use in immunodiagnosis of paragonimiasis. METHODS: To accomplish this aim a cDNA expression library was constructed from adult worm mRNA and immuno-screened using antibodies from mice that had been immunized with the 35 kDa antigen...
May 30, 2018: Parasites & Vectors
Simon Hirschberger, Ludwig Christian Hinske, Simone Kreth
MicroRNAs (miRNAs), small noncoding RNA molecules, have emerged as important regulators of almost all cellular processes. By binding to specific sequence motifs within the 3´- untranslated region of their target mRNAs, they induce either mRNA degradation or translational repression. In the human immune system, potent miRNAs and miRNA-clusters have been discovered, that exert pivotal roles in the regulation of gene expression. By targeting cellular signaling hubs, these so-called immuno-miRs have fundamental regulative impact on both innate and adaptive immune cells in health and disease...
May 22, 2018: Cancer Letters
Eloy Povedano, Alejandro Valverde, Víctor Ruiz-Valdepeñas Montiel, María Pedrero, Paloma Yáñez-Sedeño, Rodrigo Barderas, Pablo San Segundo-Acosta, Alberto Peláez-García, Marta Mendiola, David Hardisson, Susana Campuzano, José Manuel Pingarron
We report a rapid and sensitive electrochemical strategy for the detection of gene-specific 5-methylcytosine DNA methylation. Magnetic beads (MBs) modified with an antibody specific for 5-methylcytosines (5-mC) are employed for the selective capture of any 5-mC methylated single-stranded (ss)DNA sequence. A flanking region next to the 5-mCs of the captured methylated ssDNA is recognized by selective hybridization with a synthetic biotinylated DNA sequence, further labeled with an HRP streptavidin conjugate...
May 9, 2018: Angewandte Chemie
Yi Li, Lye Lin Lock, Yuzhu Wang, Shih-Hao Ou, David Stern, Arne Schön, Ernesto Freire, Xuankuo Xu, Sanchayita Ghose, Zheng Jian Li, Honggang Cui
Many one-dimensional (1D) nanostructures are constructed by self-assembly of peptides or peptide conjugates containing a short β-sheet sequence as the core building motif essential for the intermolecular hydrogen bonding that promotes directional, anisotropic growth of the resultant assemblies. While this molecular engineering strategy has led to the successful production of a plethora of bioactive filamentous β-sheet assemblies for interfacing with biomolecules and cells, concerns associated with effective presentation of α-helical epitopes and their function preservation have yet to be resolved...
April 16, 2018: Biomaterials
Benjamin A Weinberg, Joanne Xiu, Jimmy J Hwang, Anthony F Shields, Mohamed E Salem, John L Marshall
PURPOSE: The treatment of patients with advanced gastric and gastroesophageal junction (G/GEJ) adenocarcinomas has been transformed by the U.S. Food and Drug Administration approval of pembrolizumab. Tumor and adjacent tissue must stain positively for the programmed cell death ligand 1 (PD-L1) protein by companion diagnostic testing. However, some patients with PD-L1-negative tumors also benefit from pembrolizumab. High microsatellite instability (MSI) and tumor mutational load (TML) are positive predictive biomarkers for immune checkpoint inhibition (ICI) in other tumors...
April 27, 2018: Oncologist
Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia Payton, Amit Singh
The ability to express a gene of interest in a spatio-temporal manner using Gal4-UAS system has allowed the use of Drosophila model to study various biological phenomenon. During Drosophila eye development, a synchronous wave of differentiation called Morphogenetic furrow (MF) initiates at the posterior margin resulting in differentiation of retinal neurons. This synchronous differentiation is also observed in the differentiating retina of vertebrates. Since MF is highly dynamic, it can serve as an excellent model to study patterning and differentiation...
2018: PloS One
Yoshio Takei, Noriko Nemoto, Toru Kameya, Hideaki Tamaki, Osamu Katsumata, Susumu Hyodo, Makoto Kusakabe
Atrial and B-type natriuretic peptides (ANP and BNP) are cardiac hormones important for cardiovascular and body fluid regulation. In some teleost species, an additional member of the natriuretic peptide family, ventricular NP (VNP), has been identified. In this study, we examine tissue distribution of these three NPs in the eel heart. Quantitative real-time PCR showed that anp is almost exclusively expressed in atria, bnp equally in atria and ventricles and vnp three-fold more in ventricles than in atria. The amount of bnp transcript overall in the heart was 1/10 those of anp and vnp...
April 25, 2018: Cell and Tissue Research
Ana C Borsanelli, David F Lappin, Lorenzo Viora, David Bennett, Iveraldo S Dutra, Bernd W Brandt, Marcello P Riggio
Periodontitis is an infectious polymicrobial, immuno-inflammatory disease of multifactorial aetiology that has an impact on the health, production and welfare of ruminants. The objective of the present study was to determine the microbial profiles present in the gingival sulcus of cattle considered periodontally healthy and in the periodontal pocket of animals with periodontitis lesions using high-throughput bacterial 16S rRNA gene sequencing. Subgingival biofilm samples were collected from 40 cattle with periodontitis and 38 periodontally healthy animals...
May 2018: Veterinary Microbiology
Joseph P Gallant, Raquel Asunción Lima-Cordón, Silvia A Justi, Maria Carlota Monroy, Toni Viola, Lori Stevens
Rational drug design creates innovative therapeutics based on knowledge of the biological target to provide more effective and responsible therapeutics. Chagas disease, endemic throughout Latin America, is caused by Trypanosoma cruzi, a protozoan parasite. Current therapeutics are problematic with widespread calls for new approaches. Researchers are using rational drug design for Chagas disease and one target receiving considerable attention is the T. cruzi trans-sialidase protein (TcTS). In T. cruzi, trans-sialidase catalyzes the transfer of sialic acid from a mammalian host to coat the parasite surface membrane and avoid immuno-detection...
April 21, 2018: Infection, Genetics and Evolution
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