Search results for "Tandem repeat"

Establishment and comparative characterization of novel squamous cell non-small cell lung cancer cell lines and their corresponding tumor tissue.

2010

Abstract Background Cell lines play an important role for studying tumor biology and novel therapeutic agents. Particularly in pulmonary squamous cell carcinoma (SCC) the availability of cell lines is limited and knowledge about their representativeness for corresponding tumor tissue is scanty. Materials and methods We established three novel SCC cell lines from fresh tumor tissue of 28 donors, including 8 SCC. Two cell lines were derived from different localizations of the same donor, i.e. primary tumor and lymph node metastasis. This represents a so far unique combination in lung cancer. The genotypes, gene expression profiles and mutational status of epidermal growth factor receptor ( EG…

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

2020

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new lev…

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences

2020

Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses f…

Tumor-Associated MUC1 Tandem-Repeat Glycopeptide Microarrays to Evaluate Serum- and Monoclonal-Antibody Specificity

2009

Biochemistry and molecular biology techniques for person characterization

2008

Using the traditional serological tests and the most novel techniques for DNA fingerprinting, forensic scientists scan different traits that vary from person to person and use the data to include or exclude suspects based on matching with the evidence obtained in a criminal case. Although the forensic application of these methods is well known, the procedures and techniques used to obtain these results are not so well studied. Here, we report a laboratory exercise aimed to familiarize the students in several of the methods and markers employed for people individualization. With this exercise, students have to characterize themselves and an unknown sample according to the following character…

Molecular Co-operation between Protein PAM and Streptokinase for Plasmin Acquisition by Streptococcus pyogenes

1998

Bacterial surface-associated plasmin formation is believed to contribute to invasion, although the underlying molecular mechanisms are poorly understood. To define the components necessary for plasmin generation on group A streptococci we used strain AP53 which exposes an M-like protein ("PAM") that contains a plasminogen-binding sequence with two 13-amino acid residues long tandem repeats (a1 and a2). Utilizing an Escherichia coli-streptococcal shuttle vector, we replaced a 29-residue long sequence segment of Arp4, an M-like protein that does not bind plasminogen, with a single (a1) or the combined a1a2 repeats of PAM. When expressed in E. coli, the purified chimeric Arp/PAM proteins both …

A Synthetic Vaccine Consisting of a Tumor-Associated Sialyl-TN-MUC1 Tandem-Repeat Glycopeptide and Tetanus Toxoid: Induction of a Strong and Highly S…

2009

Titelbild: Tumor-Associated MUC1 Tandem-Repeat Glycopeptide Microarrays to Evaluate Serum- and Monoclonal-Antibody Specificity (Angew. Chem. 44/2009)

2009

Biomimetic synthesis of the tumor-associated (2,3)-sialyl-T antigen and its incorporation into glycopeptide antigens from the mucins MUC1 and MUC4.

2004

Glycoproteins on epithelial tumor cells often exhibit aberrant glycosylation profiles. The incomplete formation of the glycan side chains resulting from a down-regulated glucosamine transfer and a premature sialylation results in additional peptide epitopes, which become accessible to the immune system in mucin-type glycoproteins. These cancer-specific structure alterations are considered to be a promising basis for selective immunological attack on tumor cells. Among the tumor-associated saccharide antigens, the (2,3)-sialyl-T antigen has been identified as the most abundant glycan, found in several different carcinoma cell lines. According to a linear biomimetic strategy, the (2,3)-sialyl…

Common genomic structure for the Lepidoptera cadherin-like genes.

2005

A cadherin-like protein present in the midgut epithelial cells of Lepidoptera is associated with insect resistance to Bacillus thuringiensis Cry toxins. We describe for the first time the genes that encode the cadherin-like proteins in Ostrinia nubilalis, Helicoverpa armigera, and Bombyx mori, and analyze their organization. These genes encompass 19.6 kb, 20.0 kb, and 41.8 kb of genomic DNA, respectively, and despite the size heterogeneity, they are all composed of 35 exons that are linked by 34 introns. In contrast to the high variability noted for the sizes of the introns, the sizes of the coding exons were almost completely preserved among the three species, because the intronic sequence…