|Development of an Automated Platform for HT Cloning and Expression|
Stefano Bonacci; Sara Iozzi; Scilla Buccato; Manuele Martinelli; John Telford; Domenico Maione; Roberto Petracca
Biomolecular protocols covering the whole cloning process were implemented in liquid handler robots. When compared to the manual approach, it was found that automation significantly speeds up HT cloning.
|Metal Polymers, A Glue to Immobilise Proteins Onto Synthetic Surfaces|
Abernethy N, Chung E, Fontanelle BT, Gao Y, Jennins D, Koudijs MM, Lim D, Yang L, Ling T, Vukovic P, Wong A, Maeji, NJ
The main objective of this work was to develop a surface chemistry which maintains protein function and orientation per unit surface area, regardless of the surface used.
| Gene Expression Profiling: qPCR Toolkit for Quality Control|
Švec D., Jacobsson J., Sjöback R., Kubista M.
TATAA Biocenter explain how they developed and optimized high-throughput gene expression qPCR with ValidPrime quality control, compensating for inter-run variations.
|Antigen Determination in Autoimmune Hepatitis Type1|
Naveen L Gupta, S Nayak, S Shakeyavar
Objectives of this project were to exploit the database in indian setting to determine nuclear antigens as target for antinuclear antibodies (ANA) in patients of autoimmune hapatitis (AIH) type1.
|Is it possible to quantify and rank the quality of several lists of significant genes found with gene expression profiling by different methods?|
Joachim R. Grün (1), Andreas Grützkau (1), Biljana Smiljanovic (1), Thomas Häupl (2), Gerd-Rüdiger Burmester (2), Andreas Radbruch (1)
High Performance Chip Data Analysis (HPCDA) improves expression profiling of Affymetrix chips via Bioretis database: you can easily use the default parameters and are sure to get the optimum of true positive results, independant of number of significant genes in your dataset. Gene List Significance Index (GLSI) quantifies quality of gene lists. With GLSI its easily judged which normalization/analyzing method gives better results. HPCDA score ranks by relevance.
|Identification of novel autoantigensin patients with liver autoimmune diseases by Protein MicroArray|
C. Zingaretti1, M. Arigò1, A. Cardaci1, A. Sinisi1, L. Muratori3, P. Colombatto4, F. Bonino2, P. Invernizzi5, , A.L. Zignego6 MC. Crosti1, M. Moro1, J. Geginat1, Pagani M.1, R. De Francesco1, S. Abrignani1. & M. Bombaci1
The characterization of autoimmune disease-specific biomarkers are of primary importance for the development of diagnostic tools and the comprehension of pathogenetic mechanisms leading to autoimmunity. To this aim a protein microarray was employed to analyze serum samples from patients with autoimmune hepatitis (e.g. AIH & PBC) and of healthy as controls. A panel of autoantigens able to discriminate among the groups of patients was identified for potential use as biomarkers.
|Intronic polymorphisms in Daucus carota AOX2b generate putative genotype specific miRNA|
Hélia G. Cardoso, Maria Doroteia Campos, Birgit Arnholdt-Schmitt
A study in the carrot alternative oxidase gene DcAOX2b from several individual plant genotypes of D. carota cv. Rotin revealed the frequent occurrence of intron length polymorphisms (ILPs). Here we will present an in silico analysis performed in order to identify putative miRNA sites at three different sizes of intron 1. The overall research approach aims to develop functional marker candidates for carrot plant breeding.
|Gene expression analysis of CD14+ monocytes immunomagnetically separated directly from whole blood: adaptation of protocols towards clinical trial requirements|
Gregor Winkels1, Ines Dischinger1, Katharina Bublitz1, Evert Luesink2, Nanguneri R. Nirmala2, Frank Staedtler2, Keith J. Johnson2, Alena Fitz1, Sabrina Schmitz1, Dirk Dietrich1, Sonja Balzer1, Sabine Classen1, Silvia Rüberg1, Uwe Janssen1, and Bernhard Gerstmayer1
Peripheral blood is widely used as starting material for biomarker discovery and validation using molecular biology technologies. The vast majority of currently published transcriptome data is based on RNA derived either from stabilized whole blood or peripheral blood mononuclear cells (PBMCs). Here, gene expression profiling studies and SOPs for fast, easy and specific manual or automated isolation of monocytes directly from whole blood are being described.
|Integrated In Silico Analysis of NGS Prostate Cancer Data via High-Resolution RNA-Seq Analysis|
Sandeep Sanga , Antoaneta Vladimirova, Aubree Hoover
The goal: To get novel insights into the mechanisms of prostate adenocarcinoma by leveraging next generation sequencing (NGS) data, particularly human transcriptome data, through in silico data analysis and interpretation by Ingenuity’s IPA® software. CLC Genomics Workbench and CLC Genomics Server helped us assess short read RNA-Seq data.