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Imaging mass spectrometry of intact proteins from alcohol-preserved tissue specimens: bypassing formalin fixation.
Chaurand P, Latham JC, Lane KB, Mobley JA, Polosukhin VV, Wirth PS, Nanney LB, Caprioli RM
(2008) J Proteome Res 7: 3543-55
MeSH Terms: Animals, Brain, Carcinoma, Lewis Lung, Desiccation, Electrophoresis, Ethanol, Fixatives, Formaldehyde, Kidney, Liver, Lung, Mice, Paraffin Embedding, Proteome, Solubility, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tissue Preservation
Show Abstract · Added March 5, 2014
Imaging mass spectrometry is becoming a key technology for the investigation of the molecular content of biological tissue sections in direct correlation with the underlying histology. Much of our work has been done with fresh-frozen tissue sections that has undergone minimal protein degradation between the time a tissue biopsy is sampled and the time it is snap-frozen so that no preserving or fixing agents need to be added to the frozen biopsy. However, in many sampling environments, immediate flash freezing may not be possible and so we have explored the use of ethanol-preserved, paraffin-embedded tissue specimens for proteomic analyses. Solvent-only preserved tissue specimens provide long-term preservation at room temperature, generation of high quality histological sections and little if any chemical alteration of the proteins. Using mouse organs, several key steps involved in the tissue dehydration process have been investigated to assess the potential of such preserved specimens for profiling and imaging mass spectrometry investigations.
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17 MeSH Terms
Helicobacter pylori genotyping and sequencing using paraffin-embedded biopsies from residents of colombian areas with contrasting gastric cancer risks.
Sicinschi LA, Correa P, Peek RM, Camargo MC, Delgado A, Piazuelo MB, Romero-Gallo J, Bravo LE, Schneider BG
(2008) Helicobacter 13: 135-45
MeSH Terms: Adult, Antigens, Bacterial, Bacterial Proteins, Bacterial Typing Techniques, Biopsy, DNA, Bacterial, Gastritis, Genotype, Helicobacter Infections, Helicobacter pylori, Humans, Paraffin Embedding, Stomach Neoplasms
Show Abstract · Added March 5, 2014
BACKGROUND - cagA-positive and vacA s1 and m1 genotypes of Helicobacter pylori are associated with an elevated risk of gastric cancer (GC). We determined these genotypes using paraffin-embedded gastric biopsy specimens harvested from infected individuals and compared genotype distributions in two Colombian populations residing in geographic regions with a high and low incidence of GC.
METHODS - DNA from paraffin-embedded gastric biopsies from 107 adults was amplified using primers specific for cagA, for the cag'empty site', for the s and m alleles of vacA, and for H. pylori 16S rRNA.
RESULTS - H. pylori infection was detected by molecular assays in 97 (90.7%) biopsies. Complete genotyping of cagA and vacA was achieved in 94 (96.9%) cases. The presence of cagA was detected in 78 of 97 cases (80.4%); when considered separately, cagA and vacA s regions were not significantly associated with a particular geographic area. The vacA m1 allele and s1m1 genotypes were more common in the area of high risk for GC (p = .037 and p = .044, respectively), while the vacA m2 allele and s2m2 genotypes were more prevalent in the low-risk area. The prevalence of the combination of cagA-positive, vacA s1m1 genotypes was 84.3% and 60.5% for high and low risk areas, respectively (p = .011).
CONCLUSIONS - H. pylori cagA and vacA genotyping from paraffin-embedded gastric biopsies permitted reliable typability and discrimination. The more virulent cagA-positive s1m1 strains, as well as vacA m1 genotype, were more prevalent in high risk than in low risk areas, which may contribute to the difference in GC risk between those two regions.
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13 MeSH Terms
Differential expression of cone opsin mRNA levels following experimental retinal detachment and reattachment.
Rex TS, Lewis GP, Geller SF, Fisher SK
(2002) Mol Vis 8: 114-8
MeSH Terms: Animals, Cats, Cloning, Molecular, DNA Primers, DNA, Complementary, Disease Models, Animal, Gene Expression, In Situ Hybridization, Paraffin Embedding, Polymerase Chain Reaction, RNA, Messenger, Retinal Cone Photoreceptor Cells, Retinal Detachment, Retinal Rod Photoreceptor Cells, Rod Opsins
Show Abstract · Added January 20, 2015
PURPOSE - To identify changes in S- and M-sensitive cone opsin gene expression following retinal detachment (RD) and reattachment.
METHODS - Cat retinas were detached for 1, 3, 7, or 28 days, or reattached after 1 h, 1 day, or 3 days of RD and fixed in 4% paraformaldehyde. Pieces of mid-peripheral retina were removed from the same region of each detached, normal (attached), and reattached retina and embedded in paraffin. Paraffin sections (8 mm) were processed for in situ hybridization using S- or M-cone opsins, rod opsin, or phosducin riboprobes in vitro transcribed from cat partial cDNAs. Labeled cells were counted to obtain the number of labeled cells/mm retina.
RESULTS - The number of cells labeled with the anti-sense cone opsin riboprobes, and the intensity of this label, decreased after RD. The number of cones labeled with the anti-sense S-opsin riboprobe decreased to 42% of normal at 3 days of RD. The number of M-opsin mRNA-positive cones decreased to 4% of normal at 3 days of RD. The number of cells positive for M-opsin or S-opsin mRNA recovered to near normal levels after reattachment. Phosducin and rod opsin mRNA labeling was near normal in surviving rod photoreceptors after RD.
CONCLUSIONS - Cones and rods behave differently after detachment. There are significant obstacles to overcome in order to study the responses of cones after RD because surviving cells no longer label with antibodies used as cone markers in normal retina. The results of this study show that: (1) After RD, surviving cones decrease their expression of opsin mRNA while rods do not; (2) Upon reattachment of the retina, the cones once again begin to express their opsins; (3) Most cones survive short-term detachments; and (4) Defects in cone-based vision after reattachment may not be based mainly on the loss of cones but due to other changes in these cells, for example, reduced phototransduction and/or changes in synaptic connectivity to second order neurons.
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15 MeSH Terms
Alterations in lipoxygenase and cyclooxygenase-2 catalytic activity and mRNA expression in prostate carcinoma.
Shappell SB, Manning S, Boeglin WE, Guan YF, Roberts RL, Davis L, Olson SJ, Jack GS, Coffey CS, Wheeler TM, Breyer MD, Brash AR
(2001) Neoplasia 3: 287-303
MeSH Terms: Adenocarcinoma, Arachidonic Acid, Blotting, Northern, Chromatography, High Pressure Liquid, Cyclooxygenase 2, Dinoprostone, Humans, Hydroxyeicosatetraenoic Acids, Immunoenzyme Techniques, In Situ Hybridization, Isoenzymes, Lipoxygenase, Male, Membrane Proteins, Paraffin Embedding, Prostaglandin-Endoperoxide Synthases, Prostatic Neoplasms, RNA, Messenger, RNA, Neoplasm
Show Abstract · Added December 10, 2013
Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic acid (AA) metabolizing enzymes in prostate adenocarcinoma (Pca) development or progression. The goal of this study was to more fully characterize lipoxygenase (LOX) and cyclooxygenase-2 (COX-2) gene expression and AA metabolism in benign and malignant prostate using snap-frozen tissues obtained intraoperatively and mRNA analyses and enzyme assays. Formation of 15-hydroxyeicosatetraenoic acid (15-HETE) was detected in 23/29 benign samples and 15-LOX-2 mRNA was detected in 21/25 benign samples. In pairs of pure benign and Pca from the same patients, 15-HETE production and 15-LOX-2 mRNA were reduced in Pca versus benign in 9/14 (P=.04) and 14/17 (P=.002), respectively. Under the same conditions, neither 5-HETE nor 12-HETE formation was detectable in 29 benign and 24 tumor samples; with a more sensitive assay, traces were detected in some samples, but there was no clear association with tumor tissue. COX-2 mRNA was detected by nuclease protection assay in 7/16 benign samples and 5/16 tumors. In benign and tumor pairs from 10 patients, COX-2 was higher in tumor versus benign in only 2, with similar results by in situ hybridization. Paraffin immunoperoxidase for COX-2 was performed in whole mount sections from 87 additional radical prostatectomy specimens, with strong expression in ejaculatory duct as a positive control and corroboration with in situ hybridization. No immunostaining was detected in benign prostate or tumor in 45% of cases. Greater immunostaining in tumor versus benign was present in only 17% of cases, and correlated with high tumor grade (Gleason score 8 and 9 vs. 5 to 7). In conclusion, reduced 15-LOX-2 expression and 15-HETE formation is the most characteristic alteration of AA metabolism in Pca. Increased 12-HETE and 5-HETE formation in Pca were not discernible. Increased COX-2 expression is not a typical abnormality in Pca in general, but occurs in high-grade tumors.
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19 MeSH Terms