Search results for " microarray"

Peptide microarrays enable rapid mimotope optimization for pharmacokinetic analysis of the novel therapeutic antibody IMAB362.

2014

As membrane proteins play an important role in a variety of life-threatening diseases, the development of therapeutic monoclonal antibodies against membrane proteins is of significant interest. Among many other requirements, the process of antibody drug development requires a set of tailor-made assays for the characterization of the antibodies and for monitoring their activity. Designing assays to characterize antibodies directed to membrane proteins is challenging, because the natural targets are often not available in a format that is compatible with a biochemical assay setup. Thus, alternatives that mimic the targeted membrane proteins are needed. In this study, we developed optimal pept…

Therapeutic and diagnostic applications of nanoparticles.

2011

Nanoparticles are sphere-like biocompatible materials made of inert silica, metal or crystals of a few nanometers in size. They are emerging as a novel class of therapeutics for cancer treatment. Being more selective and specific toward their targets, nanoparticles have the ability to enhance the anticancer effects and to simultaneously reduce systemic toxicity compared with conventional therapeutics. Furthermore, they offer the potential to overcome drug resistance leading to higher intracellular drug accumulation. Nowadays, nanotechnologies are applied to molecular diagnostics and incorporated in cutting-edge molecular diagnostic methods, such as DNA and protein microarray biochips. Nanot…

Control of dataset bias in combined Affymetrix cohorts of triple negative breast cancer

2014

AbstractHeterogenous subtypes of breast cancer need to be analyzed separately. Pooling of datasets can provide reasonable sample sizes but dataset bias is an important concern. We assembled a combined dataset of 579 Affymetrix microarrays from triple negative breast cancer (TNBC) in Gene Expression Omnibus (GEO) series GSE31519. We developed a method for selecting comparable datasets and to control for the amount of dataset bias of individual probesets.

Printing Biology: engineering analytical platforms by molecular inks

2021

Extracorporeal shock wave-mediated changes in proliferation, differentiation, and gene expression of human osteoblasts.

2008

The goal of this study was to determine whether cell proliferation, differentiation, and gene expression of primary human osteoblasts (hOB) are influenced by shock wave application (SWA).Osteoblast cultures were isolated from cancellous bone fragments and treated with 500 impulses of energy flux densities of 0.06 mJ/mm, 0.18 mJ/mm, 0.36 mJ/mm, and 0.50 mJ/mm. Twenty-four hours and 96 hours after SWA cell proliferation, alkaline phosphatase activity, and mineralization were analyzed. The global gene expression profiling was determined 96 hours after SWA employing Affymetrix HG-U133A microarrays.After 24 hours, hOB showed a dose-dependent increase in cell proliferation from 68.7% (at 0.06 mJ/…

Global transcriptional profiling ofCandida albicans cwt1 null mutant

2007

CaCwt1p is a Candida albicans putative transcriptional factor homologue to Rds2p in Saccharomyces cerevisiae. The lack of this protein in S. cerevisiae leads to a pleiotropic resistance to drugs and defects in cell wall architecture that are also detectable in C. albicans. It is also known that CaCwt1p is mainly expressed in the stationary growth phase of this fungus. In order to elucidate the role of CWT1, transcriptome analysis of the mutant strain was performed in exponential and stationary growth phases. A total of 460 genes were found to be up- or downregulated in the mutant strain growing exponentially, and 666 genes presented a misregulation when cwt1 cells reached the stationary pha…

RPPanalyzer Toolbox: An improved R package for analysis of reverse phase protein array data

2014

Analysis of large-scale proteomic data sets requires specialized software tools, tailored toward the requirements of individual approaches. Here we introduce an extension of an open-source software solution for analyzing reverse phase protein array (RPPA) data. The R package RPPanalyzer was designed for data preprocessing followed by basic statistical analyses and proteomic data visualization. In this update, we merged relevant data preprocessing steps into a single user-friendly function and included a new method for background noise correction as well as new methods for noise estimation and averaging of replicates to transform data in such a way that they can be used as input for a new t…

Proteomic Strategies and their Application in Cancer Research

2006

The understanding of carcinogenesis and tumor progression on a molecular basis needs a detailed study of proteins as effector molecules and as critical components of the multiple interconnected signaling pathways that drive the neoplastic phenotype. Thus, the proteomic approach represents a powerful tool for the challenge of the post-genomic era. The term “cancer proteome” refers to the collection of proteins expressed by a given cancer cell and should be considered as a highly dynamic entity within the cell, which affects a variety of cellular activities. The emerging proteomic analysis platforms including 2D-PAGE, mass spectrometry technologies, and protein microarrays represent powerful…

Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data

2013

Background The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. Technologies like mass spectrometry are commonly being used in proteomic research. Mass spectrometry signals show the proteomic profiles of the individuals under study at a given time. These profiles correspond to the recording of a large number of proteins, much larger than the number of individuals. These variables come in addition to or to complete classical clinical variables. The objective of this study is to evaluate and compare the predictive ability of new and existing models combining mass spectrometry data and classical clinical variables. This study was co…

Proteomic Approaches in Colon Cancer: Promising Tools for New Cancer Markers and Drug Target Discovery

2005

Novel technologies are needed from which to identify new and more efficient biomarkers and improved molecular targets for the expedient and accurate diagnosis and treatment of colorectal cancer. Many advances have been made in direct and virtual imaging for detection of polyps and malignant-type lesions. These require tissue verification before definitive intervention. Inclusion of a simple serum test, more accurate than CEA, especially for early cancer detection, would make virtual imaging much more successful. Proteomics, the study of the proteins and protein pathways involved in disease, is a new dimension in preclinical and clinical development. Mass spectrometric analysis of serum prot…