Genomes and Genes
Summary: A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)
Publications288 found, 100 shown here
- FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatinPaul G Giresi
Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
Genome Res 17:877-85. 2007..demonstrate a simple procedure for the isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements)...
- RNA expression analysis from formalin fixed paraffin embedded tissuesSusan M Farragher
Almac Diagnostics, Craigavon, 19 Seagoe Industrial Estate, Armagh BT635QD, UK
Histochem Cell Biol 130:435-45. 2008..This paper reviews the progress in this field and discusses the unique opportunities that exist for the application of these techniques in the development of personalized medicine...
- Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samplesCraig April
Illumina, Inc, San Diego, California, United States of America
PLoS ONE 4:e8162. 2009..We have developed a gene expression assay (Whole-Genome DASL), capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE) specimens...
- MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimensLihong Weng
Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
J Pathol 222:41-51. 2010..To our knowledge, this is the first study to demonstrate that FFPE specimens can be used reliably for miRNA deep-sequencing analysis, making future large-scale clinical cohort/trial-based studies possible...
- Histone demethylation mediated by the nuclear amine oxidase homolog LSD1Yujiang Shi
Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
Cell 119:941-53. 2004..Lysine demethylation occurs via an oxidation reaction that generates formaldehyde. Importantly, RNAi inhibition of LSD1 causes an increase in H3 lysine 4 methylation and concomitant ..
- Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cellsJinghuan Li
Department of Histopathology, University of Dublin, Trinity College, Dublin, Ireland
BMC Biotechnol 7:36. 2007..This study analyzed 160 miRNAs in paired snap frozen and FFPE cells to investigate if miRNAs may be successfully detected in archival specimens...
- TRPA1 mediates formalin-induced painColleen R McNamara
Hydra Biosciences, Inc, 790 Memorial Drive, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 104:13525-30. 2007....
- Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissuesMaria Filippa Addis
Porto Conte Ricerche Srl, Tramariglio, Alghero, Sassari, Italy
Proteomics 9:3815-23. 2009..An evaluation of the extent of modifications introduced on proteins by formalin fixation and crosslink reversal, and their impact on quality of MS results, is also reported...
- Is exposure to formaldehyde in air causally associated with leukemia?--A hypothesis-based weight-of-evidence analysisLorenz R Rhomberg
Gradient, Cambridge, Massachusetts 02138, USA
Crit Rev Toxicol 41:555-621. 2011Recent scientific debate has focused on the potential for inhaled formaldehyde to cause lymphohematopoietic cancers, particularly leukemias, in humans...
- Reproductive and developmental toxicity of formaldehyde: a systematic reviewAnh Duong
School of Public Health, University of California, Berkeley, CA 94720, USA
Mutat Res 728:118-38. 2011b>Formaldehyde, the recently classified carcinogen and ubiquitous environmental contaminant, has long been suspected of causing adverse reproductive and developmental effects, but previous reviews were inconclusive, due in part, to ..
- miRNA in situ hybridization in formaldehyde and EDC-fixed tissuesJohn T G Pena
Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10065, USA
Nat Methods 6:139-41. 2009..We showed that in situ hybridization (ISH) using conventional formaldehyde fixation results in substantial microRNA loss from mouse tissue sections, which can be prevented by fixation ..
- Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissueLorenza Mittempergher
Divisions of Experimental Therapy, Molecular Biology, Surgical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
PLoS ONE 6:e17163. 2011..To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material...
- Formaldehyde-inactivated whole-virus vaccine protects a murine model of enterovirus 71 encephalomyelitis against diseaseKien Chai Ong
Department of Pathology, University of Malaya, 50603 Kuala Lumpur, Malaysia
J Virol 84:661-5. 2010..b>Formaldehyde-inactivated whole-virus vaccines derived from EV71 clinical isolates and a mouse-adapted virus (MAV) were ..
- Urine formaldehyde level is inversely correlated to mini mental state examination scores in senile dementiaZhiqian Tong
State Key Lab of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
Neurobiol Aging 32:31-41. 2011It is widely known that exogenous formaldehyde exposure induces human cognitive impairment and animal memory loss; and recent studies show that formaldehyde at pathological levels induces Aβ deposition and misfolding of tau protein to ..
- Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimensRaji Pillai
Pathwork Diagnostics, Inc, Redwood City, California 94063 4737, USA
J Mol Diagn 13:48-56. 2011..3% concordance between laboratories. The Tissue of Origin Test makes the benefits of microarray-based gene expression tests for tumor diagnosis available for use with the most common type of histology specimen (ie, FFPE)...
- Tumor tissue-derived formaldehyde and acidic microenvironment synergistically induce bone cancer painZhiqian Tong
Neuroscience Research Institute, Peking University, Beijing, China
PLoS ONE 5:e10234. 2010..Accumulated evidence shows that endogenous formaldehyde concentrations are elevated in the blood or urine of patients with breast, prostate or bladder cancer...
- Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samplesYaguang Xi
Cancer Genomics Laboratory, Mitchell Cancer Institute, Mobile, Alabama 36688, USA
RNA 13:1668-74. 2007..There are no significant differences of representative miRNA expression among 40 colorectal cancer FFPE specimens. This study provides a foundation for miRNA investigation using FFPE samples in cancer and other types of diseases...
- Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosisK F Becker
Technische Universitat, Institut fur Pathologie, Munchen, Germany
J Pathol 211:370-8. 2007..This technique may also be used to identify, characterize, and validate known and new protein markers in a variety of human diseases...
- Formaldehyde-based whole-mount in situ hybridization method for planariansBret J Pearson
Department of Neurobiology and Anatomy, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
Dev Dyn 238:443-50. 2009..Here, we describe a formaldehyde-based WISH method for the freshwater planarian Schmidtea mediterranea developed by systematically comparing and ..
- Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysisMichal R Schweiger
Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
PLoS ONE 4:e5548. 2009..However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies...
- Proteomic analysis of formalin-fixed prostate cancer tissueBrian L Hood
Laboratory of Proteomics and Analytical Technologies, SAIC Frederick, Inc, National Cancer Institute, Frederick, MD 21702, USA
Mol Cell Proteomics 4:1741-53. 2005....
- Evidence for the involvement of spinal cord glia in subcutaneous formalin induced hyperalgesia in the ratL R Watkins
Department of Psychology, University of Colorado at Boulder, 80309, USA
Pain 71:225-35. 1997..Taken together, the present series of experiments suggest an important role for spinal glial cells in the cascade of events that are initiated by descending signals following s.c. administration of formalin...
- Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissueStephen M Hewitt
Tissue Array Research Program, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4605, USA
Arch Pathol Lab Med 132:1929-35. 2008..High-quality nucleic acids can be obtained from formalin-fixed, paraffin-embedded tissue, but greater attention to all steps in the process of tissue handling and preparation is required...
- Mortality from lymphohematopoietic malignancies and brain cancer among embalmers exposed to formaldehydeMichael Hauptmann
Department of Bioinformatics and Statistics, Netherlands Cancer Institute, Amsterdam, The Netherlands
J Natl Cancer Inst 101:1696-708. 2009..found in surveys of anatomists, pathologists, and funeral industry workers, all of whom may have worked with formaldehyde. We investigated the relation of mortality to work practices and formaldehyde exposure levels among these ..
- Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysisRobert W Sprung
Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 8575, USA
Mol Cell Proteomics 8:1988-98. 2009..No covalent peptide modifications attributable to formaldehyde chemistry were detected by analyses of the MS/MS datasets, which suggests that undetected, cross-linked ..
- Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assayNic Waddell
The Queensland Institute of Medical Research, Brisbane, Australia
J Pathol 221:452-61. 2010....
- Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarraysDiana Abdueva
Department of Pathology, Children s Hospital Los Angeles, Research Institute and Keck School of Medicine, University of Southern California, Los Angeles, California, USA
J Mol Diagn 12:409-17. 2010..This study provides guidelines for application of these methods in the discovery, validation, and clinical application of microarray expression profiling with FFPE material...
- Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assayMark Abramovitz
VM Institute of Research, Montreal, Quebec, Canada
Biotechniques 44:417-23. 2008....
- Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissuesS I Hwang
Department of Cell Biology, Center for Vascular Biology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
Oncogene 26:65-76. 2007..We propose that this general strategy provides a roadmap for successful identification of critical molecular targets of multiple cancer types...
- Effect of inhaled formaldehyde on learning and memory of miceZ Lu
College of Life Science, Central China Normal University, Wuhan, China
Indoor Air 18:77-83. 2008In this study, we investigated the effect of inhaled formaldehyde on learning and memory capacity...
- Use of LC-MS/MS and stable isotopes to differentiate hydroxymethyl and methyl DNA adducts from formaldehyde and nitrosodimethylamineKun Lu
Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
Chem Res Toxicol 25:664-75. 2012b>Formaldehyde is a known human and animal carcinogen that forms DNA adducts, and causes mutations. While there is widespread exposure to formaldehyde in the environment, formaldehyde is also an essential biochemical in all living cells...
- Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samplesGalen Hostetter
Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ 85004, USA
Nucleic Acids Res 38:e9. 2010..3. Finally we present data on derivative of log ratio, a particular sensitive detector of measurement variance, for 216 sequential hybridizations to assess protocol reliability over a wide range of FFPE samples...
- Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)Paul G Giresi
Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, CB 3280, 408 Fordham Hall, Chapel Hill, NC 27599 3280, USA
Methods 48:233-9. 2009..a simple procedure for the genome-wide isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)...
- Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometryPaweł Ostasiewicz
Department for Proteomics and Signal Transduction at Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
J Proteome Res 9:3688-700. 2010..Thus, FFPE biobank material can be analyzed by quantitative proteomics at the level of proteins and post-translational modifications...
- Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimensEsteban Braggio
Department of Biochemistry, Mayo Clinic, Scottsdale, Arizona, USA
Clin Cancer Res 17:4245-53. 2011....
- Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometryRita Casadonte
Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
Nat Protoc 6:1695-709. 2011..For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis...
- Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneityMartin Kerick
Max Planck Institute for Molecular Genetics, Ihnestr, Berlin, Germany
BMC Med Genomics 4:68. 2011..However, these technologies need to be further improved with regard to reproducibility and applicability to clinical samples and settings...
- Producing reverse phase protein microarrays from formalin-fixed tissuesClaudia Wolff
Institut fur Pathologie, Technische Universitat Munchen, Munich, Germany
Methods Mol Biol 785:123-40. 2011..In this chapter, we describe a protein extraction protocol established in our laboratory combined with the use of reverse phase protein microarray...
- Combined analysis of chromosomal aberrations and glutathione S-transferase M1 and T1 polymorphisms in pathologists occupationally exposed to formaldehydeAlfredo Santovito
Department of Animal and Human Biology, University of Torino, Via Accademia Albertina n 13, 10123, Turin, Italy
Arch Toxicol 85:1295-302. 2011The formaldehyde (FA) genotoxic potential in occupationally exposed individuals is conflicting...
- Optimization of formaldehyde cross-linking for protein interaction analysis of non-tagged integrin beta1Cordula Klockenbusch
The Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T1Z3, Canada
J Biomed Biotechnol 2010:927585. 2010b>Formaldehyde cross-linking of protein complexes combined with immunoprecipitation and mass spectrometry analysis is a promising technique for analysing protein-protein interactions, including those of transient nature...
- Genotoxicity biomarkers in occupational exposure to formaldehyde--the case of histopathology laboratoriesCarina Ladeira
Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Portugal
Mutat Res 721:15-20. 2011b>Formaldehyde, classified by the IARC as carcinogenic in humans and experimental animals, is a chemical agent that is widely used in histopathology laboratories...
- Formaldehyde and tobacco smoke as alkylating agents: the formation of N-methylenvaline in pathologists and in plastic laminate workersRoberto Bono
Department of Public Health and Microbiology, University of Torino, Torino, Italy
Sci Total Environ 414:701-7. 2012Aim of this study was to investigate the relationships between the concentration of formaldehyde in air and the alkylation of hemoglobin to form a terminal N-methylenvaline residue in three occupationally exposed groups: a) technicians of ..
- Mortality from lymphohematopoietic malignancies among workers in formaldehyde industries: the National Cancer Institute CohortLaura E Beane Freeman
Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
J Natl Cancer Inst 101:751-61. 2009b>Formaldehyde exposure is associated with leukemia in some epidemiological studies...
- Multicentre validation study of nucleic acids extraction from FFPE tissuesSerena Bonin
ACADEM Department University of Trieste and ICGEB, University of Trieste, Cattinara Hospital, 34149 Trieste, Italy
Virchows Arch 457:309-17. 2010..The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories...
- Incomplete follow-up in the National Cancer Institute's formaldehyde worker study and the impact on subsequent reanalyses and causal evaluationsGary M Marsh
Center for Occupational Biostatistics and Epidemiology and Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
Regul Toxicol Pharmacol 58:233-6. 2010..performed reanalyses of the National Cancer Institute cohort study on nasopharyngeal cancer (NPC) risk among formaldehyde exposed workers (Hauptmann et al., 2004). Both reanalyses (Marsh and Youk, 2005; Marsh et al...
- Histology without formalin?René J Buesa
Ann Diagn Pathol 12:387-96. 2008..With a fast penetration, formaldehyde is a slow and reversible fixative that requires 24 to 48 hours to completely bind to tissue; thus, any surgical ..
- The generation of formaldehyde in cigarettes--Overview and recent experimentsRichard R Baker
Group Research and Development, British American Tobacco, Regent s Park Road, Southampton SO15 8TL, UK
Food Chem Toxicol 44:1799-822. 2006..One exception to this generalisation is formaldehyde, which is generated from saccharides used as tobacco ingredients...
- Treatment of maternal blood samples with formaldehyde does not alter the proportion of circulatory fetal nucleic acids (DNA and mRNA) in maternal plasmaSatheesh Kumar Reddy Chinnapapagari
Department of Research, University Women s Hospital, Basel, Switzerland
Clin Chem 51:652-5. 2005
- Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissueElla R Thompson
VBCRC Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
Hum Mutat 26:384-9. 2005..This advance will open up vast archival tissue resources to high-resolution genetic analysis and unlock a wealth of biological information...
- Formaldehyde: integrating dosimetry, cytotoxicity, and genomics to understand dose-dependent transitions for an endogenous compoundMelvin E Andersen
Program in Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709, USA
Toxicol Sci 118:716-31. 2010b>Formaldehyde (FA), an endogenous cellular aldehyde, is a rat nasal carcinogen...
- Enhanced formaldehyde detoxification by overexpression of glutathione-dependent formaldehyde dehydrogenase from ArabidopsisHakima Achkor
Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
Plant Physiol 132:2248-55. 2003The ADH2 gene codes for the Arabidopsis glutathione-dependent formaldehyde dehydrogenase (FALDH), an enzyme involved in formaldehyde metabolism in eukaryotes...
- Clinical proteomic applications of formalin-fixed paraffin-embedded tissuesJosip Blonder
Laboratory of Proteomics and Analytical Technologies, SAIC Frederick, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD 21702, USA
Clin Lab Med 29:101-13. 2009..The almost inexhaustible supply of these tissues will enable proteomic laboratories access to clinically important specimens that will undoubtedly lead to a number of important discoveries in the near future...
- The function neutralizing anti-TrkA antibody MNAC13 reduces inflammatory and neuropathic painGabriele Ugolini
Lay Line Genomics, Via di Castel Romano 100, 00128 Rome, Italy
Proc Natl Acad Sci U S A 104:2985-90. 2007..This study represents a direct demonstration that neutralizing antibodies directed against the TrkA receptor may display potent analgesic effects in inflammatory and chronic pain...
- Lack of dramatic enrichment of fetal DNA in maternal plasma by formaldehyde treatmentGrace T Y Chung
Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
Clin Chem 51:655-8. 2005
- Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRMLasse S Kristensen
Institute of Human Genetics, University of Aarhus, The Bartholin Building, Aarhus C, Denmark
BMC Cancer 9:453. 2009..Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM...
- Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomasGayatry Mohapatra
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
Acta Neuropathol 121:529-43. 2011..In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues...
- Quantitation of p95HER2 in paraffin sections by using a p95-specific antibody and correlation with outcome in a cohort of trastuzumab-treated breast cancer patientsJeff Sperinde
diaDexus, South San Francisco, CA, USA
Clin Cancer Res 16:4226-35. 2010..We sought to show that quantitative p95HER2 levels would correlate with outcome in trastuzumab-treated HER2-positive metastatic breast cancer...
- Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissuesMartina Doleshal
Asuragen, Inc, Austin, TX 78744, USA
J Mol Diagn 10:203-11. 2008....
- Epidemiological studies of formaldehyde exposure and risk of leukemia and nasopharyngeal cancer: a meta-analysisAnnette M Bachand
Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
Crit Rev Toxicol 40:85-100. 2010The authors conducted meta-analyses of the epidemiological literature on formaldehyde exposure and risk of leukemia and risk of nasopharyngeal cancer...
- A temporal threshold for formaldehyde crosslinking and fixationLars Schmiedeberg
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
PLoS ONE 4:e4636. 2009b>Formaldehyde crosslinking is in widespread use as a biological fixative for microscopy and molecular biology...
- Protein unlocking procedures of formalin-fixed paraffin-embedded tissues: application to MALDI-TOF imaging MS investigationsMaurizio Ronci
Centro Studi Sull Invecchiamento, Chieti, Italy
Proteomics 8:3702-14. 2008..A multivariate statistical evaluation is presented and discussed according to molecular spatial distributions and tissue morphology...
- Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR)Thi Thu Huyen Nguyen
Institute for Microbiology, Ernst Moritz Arndt University of Greifswald, D 17487 Greifswald, Germany
Mol Microbiol 71:876-94. 2009..We analysed the global expression profile of Bacillus subtilis to the toxic carbonyls methylglyoxal (MG) and formaldehyde (FA)...
- Treatment of inflammatory and neuropathic pain by uncoupling Src from the NMDA receptor complexXue Jun Liu
Program in Neurosciences and Mental Health, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
Nat Med 14:1325-32. 2008....
- Local genotoxic effects of formaldehyde in humans measured by the micronucleus test with exfoliated epithelial cellsGünter Speit
Universitat Ulm, Abteilung Humangenetik, D 89070 Ulm, Germany
Mutat Res 613:1-9. 2006b>Formaldehyde (FA) is genotoxic in vitro in cultured mammalian cells. When FA reaches the nuclear DNA, it forms DNA-protein cross-links (DPX)...
- KRAS genotyping of paraffin-embedded colorectal cancer tissue in routine diagnostics: comparison of methods and impact of histologyWilko Weichert
Institut fur Pathologie, Charite Universitatsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany
J Mol Diagn 12:35-42. 2010....
- Occupational exposure to formaldehyde, hematotoxicity, and leukemia-specific chromosome changes in cultured myeloid progenitor cellsLuoping Zhang
School of Public Health, University of California at Berkeley, Berkeley, California 94720, USA
Cancer Epidemiol Biomarkers Prev 19:80-8. 2010There are concerns about the health effects of formaldehyde exposure, including carcinogenicity, in light of elevated indoor air levels in new homes and occupational exposures experienced by workers in health care, embalming, ..
- Formaldehyde exposure and asthma in children: a systematic reviewGerald McGwin
Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Environ Health Perspect 118:313-7. 2010Despite multiple published studies regarding the association between formaldehyde exposure and childhood asthma, a consistent association has not been identified...
- Formaldehyde and leukemia: epidemiology, potential mechanisms, and implications for risk assessmentLuoping Zhang
School of Public Health, University of California, Berkeley, California 94720 7356, USA
Environ Mol Mutagen 51:181-91. 2010b>Formaldehyde is widely used in the United States and other countries. Occupational and environmental exposures to formaldehyde may be associated with an increased risk of leukemia in exposed individuals...
- Cancer effects of formaldehyde: a proposal for an indoor air guideline valueGunnar Damgård Nielsen
National Research Centre for the Working Environment, Lersø Parkallé 105, 2100, Copenhagen Ø, Denmark
Arch Toxicol 84:423-46. 2010b>Formaldehyde is a ubiquitous indoor air pollutant that is classified as "Carcinogenic to humans (Group 1)" (IARC, Formaldehyde, 2-butoxyethanol and 1-tert-butoxypropanol-2-ol...
- Analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue: an illustration with breast cancer tissuesMuhammad G Kibriya
Department of Health Studies, The University of Chicago, 5841 S, Maryland Avenue, MC 2007, Chicago, IL 60637, USA
BMC Genomics 11:622. 2010..We used a whole genome DASL assay (addressing 18,391 genes) on a total of 72 samples from paired breast tumor and surrounding healthy tissues from both FF and FFPE samples...
- 'Tissue surrogates' as a model for archival formalin-fixed paraffin-embedded tissuesCarol B Fowler
Department of Biophysics, Armed Forces Institute of Pathology, Rockville, MD 20850, USA
Lab Invest 87:836-46. 2007..been hampered by inefficient methods to extract proteins from archival tissue and by an incomplete knowledge of formaldehyde-induced modifications in proteins...
- Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samplesJ S Hall
Translational Radiobiology Group, School of Cancer and enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
Br J Cancer 104:971-81. 2011..This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples...
- Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarraysKim Linton
Cancer Research UK Department of Medical Oncology, the Christie NHS Foundation Trust, Manchester, UK
Biotechniques 47:587-96. 2009..While larger series are needed to confirm high correspondence between fresh-frozen and FFPE expression patterns, these data suggest that both Plus 2.0 and Exon arrays are suitable platforms for FFPE microarray expression analyses...
- Metastatic colorectal cancer KRAS genotyping in routine practice: results and pitfallsAude Lamy
Laboratory of Tumor Genetics, University Hospital, Rouen, France
Mod Pathol 24:1090-100. 2011..The tumor heterogeneity observed in some patients indicates that it should be more appropriate to perform KRAS genotyping on metastases if sample is available...
- Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomicsOmid Azimzadeh
Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Institute of Radiation Biology, 85764 Neuherberg, Germany
J Proteome Res 9:4710-20. 2010..This study will facilitate the development of future proteomic analysis of FFPE tissue and provide a tool for the validation in archival samples of biomarkers of exposure, prognosis and disease...
- Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome withinBrian L Hood
Laboratory of Proteomics and Analytical Technologies, SAIC Frederick, Inc, National Cancer Institute, Frederick, MD 21702, USA
Proteomics 6:4106-14. 2006..Although these developments are quite new, the ability to conduct MS-based proteomic analyses of FFPE tissues opens heretofore intractable clinical samples for discovery-based biomarker research...
- In vivo stabilization of preinitiation complexes by formaldehyde cross-linkingLEOS VALASEK
Institute of Microbiology, AS CR, Prague, Czech Republic
Methods Enzymol 429:163-83. 2007..Therefore, we developed an alternative method for PIC stabilization using formaldehyde (HCHO) to cross-link factors associated with 40S ribosomal subunits in vivo before the disruption of the yeast ..
- Efficient method for the proteomic analysis of fixed and embedded tissuesDarryl Erik Palmer-Toy
Harvard Partners Center for Genetics and Genomics, Cambridge, Massachusetts, USA
J Proteome Res 4:2404-11. 2005..Moreover, we demonstrate that a high level of sequence coverage can be observed for proteins of interest...
- Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometryMarshall S Scicchitano
Department of Safety Assessment, 709 Swedeland Road, Mail Stop UE0364, King of Prussia, PA 19406, USA
J Histochem Cytochem 57:849-60. 2009..These findings demonstrate that formalin fixation, paraffin processing, and LCM do not negatively impact protein quality and quantity as determined by MS and that FFPE samples are amenable to global proteomic analysis...
- Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissuesBrian M Balgley
Calibrant Biosystems, Gaithersburg, Maryland 20878, USA
J Proteome Res 8:917-25. 2009....
- Formaldehyde exposure and leukemia: a new meta-analysis and potential mechanismsLuoping Zhang
School of Public Health, 50 University Hall, University of California, Berkeley, CA 94720 7356, USA
Mutat Res 681:150-68. 2009b>Formaldehyde is an economically important chemical, to which more than 2 million U.S. workers are occupationally exposed...
- DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: heating under the influence of pHShan Rong Shi
Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
J Histochem Cytochem 50:1005-11. 2002..These findings may lead to a more effective protocol for DNA extraction from archival paraffin-embedded tissues and may also provide enhanced understanding of changes that occur during formalin-induced modification of nucleic acids...
- Mortality among a cohort of garment workers exposed to formaldehyde: an updateL E Pinkerton
Industrywide Studies Branch, Division of Surveillance, Hazard Evaluations and Field Studies, The National Institute for Occupational Safety and Health, Cincinnati, Ohio 45226, USA
Occup Environ Med 61:193-200. 2004To evaluate the mortality experience of 11 039 workers exposed to formaldehyde for three months or more in three garment plants. The mean time weighted average formaldehyde exposure at the plants in the early 1980s was 0...
- Social modulation of pain as evidence for empathy in miceDale J Langford
Department of Psychology and Centre for Research on Pain, McGill University, Montreal, QC H3A 1B1, Canada
Science 312:1967-70. 2006..Finally, observation of a cagemate in pain altered pain sensitivity of an entirely different modality, suggesting that nociceptive mechanisms in general are sensitized...
- Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChipChristina Thirlwell
Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
Methods 52:248-54. 2010..Here, we describe a protocol for the analysis of FFPE samples using the Infinium HumanMethylation27 BeadChip...
- AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coliPål Ø Falnes
Centre for Molecular Biology and Neuroscience, and Institute of Medical Microbiology, University of Oslo, National Hospital, 0027 Oslo, Norway
Nature 419:178-82. 2002..This mechanism represents a new pathway for DNA repair and the third type of DNA damage reversal mechanism so far discovered...
- Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1Gregory J Crowther
Department of Chemical Engineering, University of Washington, Box 355014, Seattle, Washington 98195 5014, USA
J Bacteriol 190:5057-62. 2008..In these bacteria, two routes are possible for generating methylene H4F from formaldehyde during methylotrophic growth: one involving the reaction of formaldehyde with H4F to generate methylene H4F and ..
- DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solutionShan Rong Shi
Department of Pathology, University of Southern California Keck School of Medicine HMR 204, 2011 Zonal Avenue, Los Angeles 90033, USA
Histochem Cell Biol 122:211-8. 2004..1 M alkaline solution is a simpler and more effective heat-induced retrieval protocol for DNA extraction. Combination with some chemicals (detergents) may further significantly improve efficiency of the heat-induced retrieval technique...
- Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimensTong Guo
Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
J Histochem Cytochem 55:763-72. 2007..This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique...
- Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometryShan Rong Shi
Department of Pathology, University of Southern California Keck School of Medicine HMR 204, 2011 Zonal Avenue, Los Angeles, CA 90033, USA
J Histochem Cytochem 54:739-43. 2006....
- Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissuesHaifeng Xu
Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, Maryland 20878, USA
J Proteome Res 7:1098-108. 2008..Because single peptide hits are often regarded with skepticism, it is notable that all proteins tested by IHC stained positive...
- Successful protein extraction from over-fixed and long-term stored formalin-fixed tissuesClaudia Wolff
Institute of Pathology, Technische Universitat Munchen, Munich, Germany
PLoS ONE 6:e16353. 2011..Because tissue fixation times vary in the routine clinical setting and pathology archives contain billions of FFPE tissues blocks, our data are highly relevant for research, diagnosis, and treatment of disease...
- Reliability and reproducibility of PCR-based testing of O6-methylguanine-DNA methyltransferase gene (MGMT) promoter methylation status in formalin-fixed and paraffin-embedded neurosurgical biopsy specimensM Preusser
Department of Internal Medicine I, Medical University, Austria
Clin Neuropathol 27:388-90. 2008..To analyze the reliability and reproducibility of PCR-based testing of O6-methylguanine-DNA methyltransferase gene (MGMT) promoter methylation status in formalin-fixed and paraffin-embedded (FFPE) neurosurgical biopsy specimens...
- Development of a microarray platform for FFPET profiling: application to the classification of human tumorsSven Duenwald
Translational Sciences, Department of Molecular Profiling, Merck Research Laboratories, Seattle, WA 98109, USA
J Transl Med 7:65. 2009..Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications...
- Whole genome amplification for array comparative genomic hybridization using DNA extracted from formalin-fixed, paraffin-embedded histological sectionsJian Huang
International Agency for Research on Cancer, Lyon, France
J Mol Diagn 11:109-16. 2009..0001). These results suggest that genetic analyses are possible using WGA-DNA extracted from paraffin sections, but that they should be performed with a carefully optimized and controlled protocol...
- An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samplesXiao Zhang
Department of Pathology and Molecular Medicine, Queen s Laboratory for Molecular Pathology, Kingston, ON, Canada
J Mol Diagn 10:513-9. 2008..669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling...
- Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challengesNiroshini J Nirmalan
Clinical and Biomedical Proteomics Group, Cancer Research UK Clinical Centre, St James s University Hospital, Beckett Street, Leeds, UK
Mol Biosyst 4:712-20. 2008..Here, we critically review the current status of research in the field, highlighting challenges which need to be addressed for robust quantitative application of protocols to ensure confident high impact inferences can be made...
- Housing characteristics and indoor concentrations of nitrogen dioxide and formaldehyde in Quebec City, CanadaNicolas L Gilbert
Air Health Effects Division, Health Canada, 269 Laurier Avenue West, PL 4903B, Ottawa, Ontario, Canada K1A 0K9
Environ Res 102:1-8. 2006Concentrations of nitrogen dioxide and formaldehyde were determined in a study of 96 homes in Quebec City, Canada, between January and April 2005...
- Reversal of pathological pain through specific spinal GABAA receptor subtypesJulia Knabl
Institute of Experimental and Clinical Pharmacology and Toxicology, University of Erlangen Nurnberg, D 91054 Erlangen, Germany
Nature 451:330-4. 2008..These results provide a rational basis for the development of subtype-selective GABAergic drugs for the treatment of chronic pain, which is often refractory to classical analgesics...
- Formaldehyde and cancer risk: a quantitative review of cohort studies through 2006C Bosetti
Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
Ann Oncol 19:29-43. 2008Occupational exposure to formaldehyde has been associated with excess risk of nasopharyngeal and selected other cancers.
- Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analysesMaricris Macabeo-Ong
Oral Pathology, Department of Stomatology, University of California San Francisco, California 94143 0424, USA
Mod Pathol 15:979-87. 2002..However, results for some markers are adversely affected by prolonged formalin fixation times...
- Nanopore Biosensor for Kinetics of Reparative Antibodies on Plasma MembranesSang Hyun Oh; Fiscal Year: 2010..Fixation of any kind (methanol, formaldehyde, freezing) destroys the complex membrane antigen...
- Innate immune evasion and/or antagonism by eastern equine encephalitis virusKATHERINE RYMAN; Fiscal Year: 2007....
- True Direct Single Molecule RNA SequencingPATRICE MARIE MILOS; Fiscal Year: 2010....
- Developing an inactivated whole cell H. pylori vaccineGARY NABORS; Fiscal Year: 2006..This trial will position the vaccine for more highly powered Phase 1 or early Phase 2 trials, and thus will move H. pylori vaccination one step closer to being a reality. ..
- Immunoprotective monoclonals to B. anthracis sporesALISON O BRIEN; Fiscal Year: 2003..actually bind to the surface of spores and decrease the level of spore germination, taken with the fact that formaldehyde-inactivated spores can serve as a protective vaccine against anthrax in guinea pigs, led us to the following ..
- Molecular signatures of melanoma histology and progression: A Population Based AAbrar A Qureshi; Fiscal Year: 2010..Thus we aim to significantly improve the current paradigm for diagnosis and therapy for melanoma by eventually reducing mortality from this deadly skin cancer. ..
- Molecular signatures of melanoma histology and progression: A Population Based AAbrar Qureshi; Fiscal Year: 2009..Thus we aim to significantly improve the current paradigm for diagnosis and therapy for melanoma by eventually reducing mortality from this deadly skin cancer. ..
- Early Diagnosis of Oral Carcinoma Using Mutant PP32R1GERALD KOCHEVAR; Fiscal Year: 2006..Identification of the intracellular protein ligands will provide a specific functional context for mutant PP32R1S. ..
- RSV Upper Airway Infection and Otitis MediaJoan Durbin; Fiscal Year: 2009..Our group has found a new vaccine against this virus, and want to test whether immunity to RSV can protect against the process that causes bacterial ear infections. ..
- RSV Upper Airway Infection and Otitis MediaJOAN E contact DURBIN; Fiscal Year: 2010..Our group has found a new vaccine against this virus, and want to test whether immunity to RSV can protect against the process that causes bacterial ear infections. ..
- PAIN, OPIOID ANALGESIA AND BLOOD PRESSURE CONTROLBradley Taylor; Fiscal Year: 2002..The results of these studies will facilitate our understanding of the mechanisms that contribute to chronic pain in the hypertensive patient. ..
- TUMOR MARKERS TO PREDICT TREATMENT RESPONSELynn Dressler; Fiscal Year: 2005..Two subcontracts are included in this proposal, one to support the CALGB Pathology Coordinating Office functions at OSU relevant to this study and the other in support of the molecular studies being performed by USC. ..
- REGULATION OF C1 METABOLISM IN METHYLOTROPHSMary Lidstrom; Fiscal Year: 2007..A distinguishing feature of methylotrophic metabolism is the generation and consumption of formaldehyde as a central intermediate, the starting point for all of metabolism...
- Develop & Validate An Ultrasound Tissue Preservation De*Zhenqing Zhu; Fiscal Year: 2006..Long-term stability of tissue morphology and mRNA integrity in USFFPE tissues is slightly better than that in conventional FFPE tissues. ..
- REGULATION OF C1 METABOLISM IN METHYLOTROPHSMary Lidstrom; Fiscal Year: 2003..From a cell biology perspective, their ability to funnel all of their cell carbon through a toxic intermediate (formaldehyde) make them of interest in terms of how they balance formaldehyde production and consumption under a wide regime ..