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  • 1
    Language: English
    In: Journal of Infectious Diseases, June 15, 2010, Vol.201(12), p.S114(12)
    Keywords: Chlamydia Trachomatis -- Research ; Chlamydia Trachomatis -- Physiological Aspects ; Sexually Transmitted Diseases -- Research ; Sexually Transmitted Diseases -- Physiological Aspects ; T Cells -- Research ; T Cells -- Physiological Aspects ; Immune Response -- Research ; Immune Response -- Physiological Aspects
    ISSN: 0022-1899
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  • 2
    Language: English
    In: The Journal of infectious diseases, 01 March 2002, Vol.185(5), pp.627-31
    Description: Nontypeable Haemophilus influenzae (NTHI) is an important cause of lower respiratory tract infections in patients with chronic obstructive pulmonary disease. Recent findings suggest that the major outer membrane protein P2 should be reconsidered as a vaccine candidate for NTHI. A P2-based vaccine would require a relative degree of sequence stability of the gene encoding P2 (ompP2) during colonization. To characterize the sequence stability of ompP2 during colonization of the human respiratory tract, ompP2 genes from 13 sets of isolates that persisted in patients with chronic obstructive pulmonary disease (mean colonization, 7 months) were sequenced. In 9 sets of isolates, ompP2 did not change. Sequence changes were noted in 4 sets of isolates. Most of these changes occurred within areas of repetitive DNA, suggesting that this type of DNA has a role in antigenic variation of P2. The sequence of ompP2 is relatively stable during persistence of NTHI in the human host.
    Keywords: Bacterial Proteins ; Genetic Variation ; Sequence Analysis, DNA ; Bacterial Outer Membrane Proteins -- Genetics ; Haemophilus Influenzae -- Classification ; Porins -- Genetics ; Respiratory Tract Infections -- Microbiology
    ISSN: 0022-1899
    E-ISSN: 15376613
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  • 3
    Language: English
    In: The Journal of infectious diseases, 01 July 2003, Vol.188(1), pp.114-7
    Description: An adult with chronic obstructive pulmonary disease was monitored prospectively for 2 years. Nontypeable Haemophilus influenzae was isolated from sputum cultures at 22 of 23 monthly clinic visits. Analysis of the isolates, by pulsed-field gel electrophoresis (PFGE), revealed that the patient was colonized by 3 different strains during the 2-year period. The gene encoding outer-membrane protein (OMP) P2, ompP2, was amplified from sputum samples and selected strains obtained from this patient. Analysis of the ompP2 sequences, in combination with the PFGE patterns, indicated that ompP2 horizontal transfer between 2 strains occurred in the respiratory tract, between clinic visits 13 and 14. Observation of ompP2 horizontal transfer in the human respiratory tract has important implications for both the understanding of ompP2 diversity among strains and the future design of OMP P2-based vaccines.
    Keywords: Bacterial Outer Membrane Proteins -- Genetics ; Gene Transfer, Horizontal -- Genetics ; Haemophilus Infections -- Complications ; Haemophilus Influenzae -- Genetics ; Pulmonary Disease, Chronic Obstructive -- Complications
    ISSN: 0022-1899
    E-ISSN: 15376613
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  • 4
    In: Journal of Bacteriology, March, 1997, Vol.179(5-6), p.1764(10)
    Description: The nucleotide sequence of the gene encoding the major outer membrane protein (MOMP) of Haemophilus ducreyi was analyzed by sodium dodecyl sulfate-polyacrilamide gel electrophoresis. Nucleotide sequence analysis of the MOMP gene of Haemophilus ducreyi indicated the presence of two OmpA homologs that were encoded by momp and ompA2 genes. Southern blot analysis also indicated the high degree of similarity between MOMP and OmpA2 which existed in tandem in the different strains of Haemophilus ducreyi.
    Keywords: Pathogenic Bacteria -- Genetic Aspects ; Membrane Proteins -- Analysis ; Bacterial Proteins -- Analysis
    ISSN: 0021-9193
    E-ISSN: 10985530
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  • 5
    In: PLoS ONE, 2018, Vol.13(6)
    Description: The presence of cancer stem cells (CSCs) and the induction of epithelial-to-mesenchymal transition (EMT) in tumors are associated with tumor aggressiveness, metastasis, drug resistance, and poor prognosis, necessitating the development of reagents for unambiguous detection of CSC- and EMT-associated proteins in tumor specimens. To this end, we generated novel antibodies to EMT- and CSC-associated proteins, including Goosecoid, Sox9, Slug, Snail, and CD133. Importantly, unlike several widely used antibodies to CD133, the anti-CD133 antibodies we generated recognize epitopes distal to known glycosylation sites, enabling analyses that are not confounded by differences in CD133 glycosylation. For all target proteins, we selected antibodies that yielded the expected target protein molecular weights by Western analysis and the correct subcellular localization patterns by immunofluorescence microscopy assay (IFA); binding selectivity was verified by immunoprecipitation−mass spectrometry and by immunohistochemistry and IFA peptide blocking experiments. Finally, we applied these reagents to assess modulation of the respective markers of EMT and CSCs in xenograft tumor models by IFA. We observed that the constitutive presence of human hepatocyte growth factor (hHGF) in the tumor microenvironment of H596 non-small cell lung cancer tumors implanted in homozygous hHGF knock-in transgenic mice induced a more mesenchymal-like tumor state (relative to the epithelial-like state when implanted in control SCID mice), as evidenced by the elevated expression of EMT-associated transcription factors detected by our novel antibodies. Similarly, our new anti-CD133 antibody enabled detection and quantitation of drug-induced reductions in CD133-positive tumor cells following treatment of SUM149PT triple-negative breast cancer xenograft models with the CSC/focal adhesion kinase (FAK) inhibitor VS-6063. Thus, our novel antibodies to CSC- and EMT-associated factors exhibit sufficient sensitivity and selectivity for immunofluorescence microscopy studies of these processes in preclinical xenograft tumor specimens and the potential for application with clinical samples.
    Keywords: Research Article ; Research And Analysis Methods ; Research And Analysis Methods ; Research And Analysis Methods ; Research And Analysis Methods ; Research And Analysis Methods ; Research And Analysis Methods ; Biology And Life Sciences ; Medicine And Health Sciences ; Biology And Life Sciences ; Medicine And Health Sciences ; Biology And Life Sciences ; Research And Analysis Methods ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Clinical chemistry, January 2016, Vol.62(1), pp.48-69
    Description: For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope-labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays. The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials-in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry-is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.
    Keywords: Clinical Laboratory Techniques ; Mass Spectrometry ; Proteomics ; Specimen Handling ; Peptides -- Analysis
    ISSN: 00099147
    E-ISSN: 1530-8561
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  • 7
    Language: English
    In: Cell, 28 July 2016, Vol.166(3), pp.755-765
    Description: To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC. Layering proteomic and genomic data from ovarian tumors provides insights into how signaling pathways correspond to specific genome rearrangements and points to the benefit of using protein signatures for assessing prognosis and treatment stratification.
    Keywords: Biology
    ISSN: 0092-8674
    E-ISSN: 1097-4172
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  • 8
    In: Nature Biotechnology, 2009, Vol.27(7), p.633
    Description: Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low mug/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.
    Keywords: Blood Proteins -- Analysis ; Mass Spectrometry -- Methods;
    ISSN: 1087-0156
    E-ISSN: 15461696
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  • 9
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