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Tissue microarrays (TMAs) have been commonly used to study protein expression by immunohistochemistry (IHC). However, limited data exist on the validity of using TMAs to study gene amplification. In this study, we evaluated the feasibility of using breast carcinoma TMAs to study HER-2 gene amplification by fluorescence in situ hybridization (FISH). In addition, hormonal receptor status (ER and PR) and HER-2 protein overexpression by IHC were also studied, and results were compared with whole tissue sections. FISH for HER-2 was performed on formalin-fixed paraffin-embedded tissue from 114 invasive breast carcinomas both on whole tissue sections and on TMAs containing the same tumors. The TMA was created using 0.6-mm tissue cores with four sampled cores per tumor from the same tissue block used for whole section FISH. The PathVysion HER-2 probe kit was used for the FISH analysis. A ratio of HER-2:Chromosome17 > or =2.0 was interpreted as positive for gene amplification. The ER or PR was interpreted as positive when nuclear staining was detected in more than 10% of tumor cells. The HER-2 IHC (HercepTest; DAKO Corp, Carpinteria, CA) results were interpreted as 0, 1+, 2+, and 3+ according to standard criteria. The FISH results in the TMA and whole sections were concordant in 99 out of 101 successfully analyzed cases (99%). The FISH scores were consistent among the two to four cores in the majority of the cases. ER and PR results were concordant between whole sections and TMA cores in 97% (107/110) and 89% (97/109) cases, respectively. The overall concordance for HER-2 status by IHC between whole sections and TMA cores was 86% (94 out of 109 cases). TMAs are a reliable approach to study HER-2 gene amplification in a high throughput manner.
Diagn Mol Pathol 2004 Dec
PMID:Feasibility of using tissue microarrays for the assessment of HER-2 gene amplification by fluorescence in situ hybridization in breast carcinoma. 1553 11

We describe a rapid and robust assay to genotype mitochondrial deoxyribonucleic acid (mtDNA) coding region single nucleotide polymorphism (SNPs) using the SNaPshot (Applied Biosystems, Foster City, CA) minisequencing reaction kit. A protocol for mtDNA SNaPshot typing is described in detail, although we emphasize that this method allows great flexibility in the implementation of whatever set of mtDNA SNPs. We discuss the utility of our selection of mtDNA SNPs for molecular anthropologists and forensic geneticists. Firstly, these SNPs allow allocating common mitochondrial West Eurasian haplotypes into their corresponding branches of the mtDNA skeleton, with special attention to the subdivision of sequences belonging to haplogroup H, the most frequent European haplogroup (40-50%) and the worst phylogenetically characterized in the first and second hypervariable segments (HVS-I/II; by far, the most common segments analyzed by sequencing). Second, the polymorphic positions selected for this multiplex reaction considerably increase the discrimination power of current mitochondrial analysis in the forensic field. The method shows high accuracy and robustness, avoiding both the use of alternative time-consuming classical strategies (i.e., restriction fragment length polymorphism typing) and the requirement of high quantities of DNA template.
Methods Mol Biol 2005
PMID:SNaPshot typing of mitochondrial DNA coding region variants. 1557 Jan 9

We describe a method for the simultaneous typing of Y-chromosome single nucleotide polymorphism (SNP) markers by means of multiplex polymerase chain reaction (PCR) strategies that allow the detection of 35 Y chromosome SNPs on 25 amplicons from 100 to 200 pg of chromosomal deoxyribonucleic acid (DNA). Multiplex PCR amplification of the DNA was performed with slight modifications of standard PCR conditions. Single-base extension (SBE) was performed using the SNaPshot kit containing fluorescently labeled ddNTPs. The extended primers were detected on an ABI 3100 sequencer. The most important factors for the creation of larger SNP typing PCR multiplexes include careful selection of primers for the primary amplification and the SBE reaction, use of DNA primers with homogenous composition, and balancing the primer concentrations for both the amplification and the SBE reactions.
Methods Mol Biol 2005
PMID:Typing of Y chromosome SNPs with multiplex PCR methods. 1557 Jan 10

Single nucleotide polymorphisms (SNPs) are the most frequent polymorphisms described in the human genome, and their analysis is becoming an extensive routine in molecular biology, not only in the forensic field, but also in population and clinical genetics. In particular, SNPs located on the Y chromosome have a specific utility as forensic tools, and based on this fact, we have designed a strategy that allows us to identify the most frequent haplogroups in European populations. We selected 29 markers among the 245 binary polymorphisms described in the Y-Chromosome Consortium tree. The whole set was grouped into four multiplexes in a hierarchical way, allowing us to determine the final haplogroup using only one or two multiplexes. In this way, we only type in the best-case nine SNPs, and in the worst possible combination 17 SNPs, to define the haplogroup. The selected strategy to type the SNPs was a single-base extension method using the SNaPshot multiplex kit from Applied Biosystems, and detailed practical procedures are described here. With this hierarchical strategy adapted for European populations the massive typing of SNPs was avoided, and therefore the time and money involved in the study was also reduced.
Methods Mol Biol 2005
PMID:Y chromosome SNP analysis using the single-base extension: a hierarchical multiplex design. 1557 Jan 11

The cancer risk assessment process as currently proposed by the U.S. Environmental Protection Agency allows for the use of mechanistic data to inform the low-dose tumor response in humans and in laboratory animals. The aim is to reduce the reliance on defaults that introduce a relatively high level of uncertainty to the risk estimates. The types of data required for this purpose are those that help identify key events in tumor formation following exposure to environmental chemicals. Informative biomarkers of tumor responses could then be developed for describing the shape of a dose-response curve at low doses (i.e., a qualitative assessment) and for predicting tumor frequency at these low doses (i.e., a quantitative assessment). A number of recently developed molecular approaches could aid in the development of qualitatively and quantitatively informative biomarkers. An overview of these with examples of their use is presented. These methods include quantitative gene expression array techniques, quantitative proteomic assays, and the assessment of DNA alterations at the single gene level and at the genome level of detection. It is most likely that a combination of approaches at different levels of cellular organization (i.e., DNA, RNA, and protein) will be the most productive for biomarker development. The rapid progress that is being made will make this tool kit even more applicable for the cancer risk assessment process.
Environ Mol Mutagen
PMID:Mechanistic data and cancer risk assessment: the need for quantitative molecular endpoints. 1564 41

The cross-fertilization of biology, chemistry, material sciences, and solid-state physics is opening up a great variety of new opportunities for innovation in nanosciences. One of the key challenges is the technological utilization of self-assembly systems wherein molecules spontaneously associate under equilibrium conditions into reproducible supramolecular aggregates. The attractiveness of such processes lies in their capability to build uniform, ultrasmall functional units and the possibility of exploiting such structures at meso- and macroscopic scale for life and nonlife science applications. The use of crystalline bacterial cell-surface proteins (S-layer proteins) provided innovative approaches for the assembly of supramolecular structures and devices with dimensions of a few to tens of nanometers. S-layers have proven to be particularly suited as building blocks in a molecular construction kit involving all major classes of biological molecules. The immobilization of biomolecules in an ordered fashion on solid substrates and their controlled confinement in definite areas of nanometer dimensions are key requirements for many applications including the development of bioanalytical sensors, biochips, molecular electronics, biocompatible surfaces, and signal processing among functional membranes, cells, and integrated circuits.
Methods Mol Biol 2005
PMID:Nanotechnology with S-layer proteins. 1565 81

Ceruloplasmin (CP) is the major plasma antioxidant and copper transport protein. Monoclonal antibodies (mAbs) against human CP were produced and characterized. A total of five hybridoma cell lines were established (CP2, CP10, CP20, CP25, CP30). From the epitope mapping analysis, two subgroups of mAbs recognize different peptide fragments were identified. When the purified CP was incubated with the mAbs, the ferroxidase activity of CP was inhibited up to a maximum 57 %. Immunoblotting with various tissue homogenates indicated that all the mAbs specifically recognize a single protein band of 130 kDa. They also appear to be extensively cross-reactive among different mammalian including human and avian sources. These results demonstrated that only one type of immunologically similar CP is present in all of the mammalian tissues including human. The CP mAbs could be of great benefit to design the diagnostic kit for CP-related diseases such as Wilson's disease.
J Biochem Mol Biol 2005 Jan 31
PMID:Production and characterization of monoclonal antibodies against human ceruloplasmin. 1571 49

Adrenomedullin (AM) is a regulatory peptide widely expressed, along its receptors, in cells and tissues, of which it controls many basic and specific functions acting in an autocrine-paracrine manner. However, the unequivocal demonstration of the physiological relevance of the regulatory role of AM would require the study of cells where endogenous AM system had been suppressed. Hence, we developed a protocol to silence the human AM gene by transfection with short interfering RNAs (siRNAs). Eight possible AM-siRNA sequences were designed: six siRNAs were synthesized in our laboratory and two were provided by Ambion. As positive control the suppression of the glyceraldehyde-3-phosphate dehydrogenase (GADPH) gene was tested using the Ambion Silencer GADPH siRNA kit. Cultured human embryonal kidney cell line HEK-293 and human umbilical vein endothelial cells (HUVECs) were transfected using either the Qiagen or the Ambion transfection reagent, and transfection visualization, carried out using Cy3-labeled siRNA and examining red fluorescence within the cells, showed that the former reagent was the most efficient. AM-gene silencing was determined in HUVECs by measuring AM mRNA levels in transfected and control cells by real-time polymerase chain reaction. Only Ambion siRNAs were effective, and the best AM-gene silencing (about 80%) was observed 48 or 72 h after transfection with 3 or 6 microg of siRNAs. The conclusion is drawn that siRNA technology can be useful in the investigations on AM functions, but that the complete suppression of the AM-gene transcription is very difficult to obtain.
Int J Mol Med 2005 Apr
PMID:Human adrenomedullin gene silencing by short interfering RNAs: a preliminary study. 1575 17

This study was conducted to determine if an oral squamous cell carcinoma alters mRNA expression of serotonin transporter (5-HTT) in the central nervous system. KB cell line derived from a human oral squamous cell carcinoma was inoculated into nude mice, and mRNA expression level of 5-HTT in the dorsal raphe nucleus (DRN) was examined by in situ hybridization when the tumor mass reached to -10% of total body weight. Plasma leptin levels were determined by radioimmunoassay method using a commercial kit. 5-HTT mRNA level was significantly decreased in the DRN of tumor bearing mice, compared to the age-matching non-tumor control. Plasma leptin level decreased concomitantly in tumor bearing mice. These results suggest that oral carcinoma may suppress 5-HTT gene expression in the central nervous system, perhaps in relation with decreased plasma leptin level.
Exp Mol Med 2005 Feb 28
PMID:Serotonin transporter mRNA expression in the dorsal raphe nucleus of a tumor bearing mouse. 1576 Dec 54

A single-stage polymerase-based procedure is described that allows extensive modifications of DNA. The version described here uses the QuikChange Site-Directed Mutagenesis System kit supplied by Stratagene. The original protocol is replaced by a single-stage method in which linear production of complementary strands is accomplished in separate single primer reactions. This has proved effective in introducing insertions and deletions into large gene/vector combinations without subcloning.
Mol Biotechnol 2005 Mar
PMID:A single-stage polymerase-based protocol for the introduction of deletions and insertions without subcloning. 1576


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