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1.  Putative Inv Is Essential for Basolateral Invasion of Caco-2 Cells and Acts Synergistically with OmpA To Affect In Vitro and In Vivo Virulence of Cronobacter sakazakii ATCC 29544 
Infection and Immunity  2014;82(5):1755-1765.
Cronobacter sakazakii is an opportunistic pathogen that causes neonatal meningitis and necrotizing enterocolitis. Its interaction with intestinal epithelium is important in the pathogenesis of enteric infections. In this study, we investigated the involvement of the inv gene in the virulence of C. sakazakii ATCC 29544 in vitro and in vivo. Sequence analysis of C. sakazakii ATCC 29544 inv revealed that it is different from other C. sakazakii isolates. In various cell culture models, an Δinv deletion mutant showed significantly lowered invasion efficiency, which was restored upon genetic complementation. Studying invasion potentials using tight-junction-disrupted Caco-2 cells suggested that the inv gene product mediates basolateral invasion of C. sakazakii ATCC 29544. In addition, comparison of invasion potentials of double mutant (ΔompA Δinv) and single mutants (ΔompA and Δinv) provided evidence for an additive effect of the two putative outer membrane proteins. Finally, the importance of inv and the additive effect of putative Inv and OmpA were also proven in an in vivo rat pup model. This report is the first to demonstrate two proteins working synergistically in vitro, as well as in vivo in C. sakazakii pathogenesis.
doi:10.1128/IAI.01397-13
PMCID: PMC3993460  PMID: 24549330
2.  OCCUPATIONAL RADIATION DOSES TO OPERATORS PERFORMING FLUOROSCOPICALLY-GUIDED PROCEDURES 
Health physics  2012;103(1):80-99.
In the past 30 years, the numbers and types of fluoroscopically-guided (FG) procedures have increased dramatically. The objective of the present study is to provide estimated radiation doses to physician specialists, other than cardiologists, who perform FG procedures. We searched Medline to identify English-language journal articles reporting radiation exposures to these physicians. We then identified several primarily therapeutic FG procedures that met specific criteria: well-defined procedures for which there were at least five published reports of estimated radiation doses to the operator, procedures performed frequently in current medical practice, and inclusion of physicians from multiple medical specialties. These procedures were percutaneous nephrolithotomy (PCNL), vertebroplasty, orthopedic extremity nailing for treatment of fractures, biliary tract procedures, transjugular intrahepatic portosystemic shunt creation (TIPS), head/neck endovascular therapeutic procedures, and endoscopic retrograde cholangiopancreatography (ERCP). We abstracted radiation doses and other associated data, and estimated effective dose to operators. Operators received estimated doses per patient procedure equivalent to doses received by interventional cardiologists. The estimated effective dose per case ranged from 1.7 – 56μSv for PCNL, 0.1 – 101 μSv for vertebroplasty, 2.5 – 88μSv for orthopedic extremity nailing, 2.0 – 46μSv for biliary tract procedures, 2.5 – 74μSv for TIPS, 1.8 – 53μSv for head/neck endovascular therapeutic procedures, and 0.2 – 49μSv for ERCP. Overall, mean operator radiation dose per case measured over personal protective devices at different anatomic sites on the head and body ranged from 19 – 800 (median = 113) μSv at eye level, 6 – 1180 (median = 75)μSv at the neck, and 2 – 1600 (median = 302) μSv at the trunk. Operators’ hands often received greater doses than the eyes, neck or trunk. Large variations in operator doses suggest that optimizing procedure protocols and proper use of protective devices and shields might reduce occupational radiation dose substantially.
doi:10.1097/HP.0b013e31824dae76
PMCID: PMC3951010  PMID: 22647920
interventional procedure; fluoroscopically-guided procedure; occupational exposure; radiation protection
3.  Quantitative proteomics of extracellular vesicles derived from human primary and metastatic colorectal cancer cells 
Journal of Extracellular Vesicles  2012;1:10.3402/jev.v1i0.18704.
Cancer cells actively release extracellular vesicles (EVs), including exosomes and microvesicles, into surrounding tissues. These EVs play pleiotropic roles in cancer progression and metastasis, including invasion, angiogenesis, and immune modulation. However, the proteomic differences between primary and metastatic cancer cell-derived EVs remain unclear. Here, we conducted comparative proteomic analysis between EVs derived from human primary colorectal cancer cells (SW480) and their metastatic derivatives (SW620). Using label-free quantitation, we identified 803 and 787 proteins in SW480 EVs and SW620 EVs, respectively. Based on comparison between the estimated abundance of EV proteins, we identified 368 SW480 EV-enriched and 359 SW620 EV-enriched proteins. SW480 EV-enriched proteins played a role in cell adhesion, but SW620 EV-enriched proteins were associated with cancer progression and functioned as diagnostic indicators of metastatic cancer; they were overexpressed in metastatic colorectal cancer and played roles in multidrug resistance. As the first proteomic analysis comparing primary and metastatic cancer-derived EVs, this study increases our understanding of the pathological function of EVs in the metastatic process and provides useful biomarkers for cancer metastasis.
doi:10.3402/jev.v1i0.18704
PMCID: PMC3760640  PMID: 24009881
colorectal cancer; microvesicles; exosomes; ectosomes; metastasis; biomarker; secretome; APEX; label-free quantitative proteomics; nanoparticle tracking analysis
4.  Coronary artery calcification screening: estimated radiation dose and cancer risk 
Archives of internal medicine  2009;169(13):1188-1194.
Background
Multi-detector computed tomography (MDCT) has been proposed as a tool for routine screening for coronary artery calcification (CAC) in asymptomatic individuals. As proposed, such screening could involve tens of millions of individuals, but detailed estimates of radiation doses and potential risk of radiation-induced cancer are not currently available. We estimated organ-specific radiation doses and associated cancer risks from CAC screening with MDCT, according to age, frequency and scan protocol.
Methods
Radiation doses to adult patients were calculated from a range of available protocols using Monte Carlo radiation transport. Radiation risk models, derived using data from Japanese atomic bomb survivors and medically-exposed cohorts, were used to estimate the excess lifetime risk of radiation-induced cancer.
Results
Radiation dose from a single CAC CT scan varied more than 10-fold (effective dose range=0.8 to 10.5 mSv) depending on the protocol. In general higher radiation doses were associated with higher x-ray tube current, higher tube potential, and spiral scanning with low pitch, and retrospective gating. The wide dose variation also resulted in wide variation in estimated radiation-induced cancer risk. Assuming screening every five years from age 45-75 for men and from age 55-75 for women, the estimated excess lifetime cancer risk using the median dose of 2.3 mSv (0.8-10.5 mSv) was 42 cases/100,000 for men (range 14-200) and 62 cases/100,000 for women (range 21-300).
Conclusions
These radiation risk estimates can be compared to potential benefits from screening, when such estimates are available. Doses and hence risks can be minimized by using optimized protocols.
doi:10.1001/archinternmed.2009.162
PMCID: PMC2765044  PMID: 19597067
5.  Low C24-OH and C22-OH sulfatides in human renal cell carcinoma 
Journal of Mass Spectrometry  2014;49(5):409-416.
Histopathologic diagnosis of renal cell carcinoma (RCC) may sometimes be difficult with small biopsy samples. We applied histology-directed matrix-assisted laser desorption/ionization mass spectrometry to RCC samples to evaluate whether and how lipid profiles are different between RCC and normal tissue. We evaluated 59 RCC samples and 24 adjacent normal tissue samples collected from patients who underwent surgery. Five peaks were significantly differently expressed (p < 10−7) between RCCs and adjacent normal tissue samples. C24-OH sulfatide (ST-OH {18:1/24:0}[M-H]−; m/z 906.7 in the negative ion mode) and C22-OH sulfatide (ST-OH {18:1/22:0}[M-H]−; m/z 878.6 in the negative ion mode) were most significantly underexpressed in RCC samples, compared with adjacent normal tissue samples. With 100 random training-to-test partitions within these samples, the median prediction accuracy (RCC vs. normal) ranged from 96.3% to 100% at p cutoff values for feature selection ranging from 0.001 to 10−7. Two oncocytoma samples were predicted as normal tissue by five lipids that were differentially expressed between RCC and normal tissue at p < 10−7. Clear-cell, papillary, and chromophobe RCCs were different in lipid profiles. Permutation p- values for 0.632+ bootstrap cross-validated misclassification rates were less than 0.05 for all the classifiers. Thus, lipid profiles differentiate RCC from normal tissue and may possibly classify the histology of RCC. © 2014 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons, Ltd.
doi:10.1002/jms.3358
PMCID: PMC4274961  PMID: 24809902
renal cell carcinoma; lipid; MALDI; mass spectrometry; sulfatide
6.  Phosphatidylcholine Alteration Identified Using MALDI Imaging MS in HBV-Infected Mouse Livers and Virus-Mediated Regeneration Defects 
PLoS ONE  2014;9(8):e103955.
In this study, we investigated whether hepatitis B virus (HBV) causes the alteration of lipid metabolism and composition during acute infection and liver regeneration in a mouse model. The liver controls lipid biogenesis and bile acid homeostasis. Infection of HBV causes various liver diseases and impairs liver regeneration. As there are very few reports available in the literature on lipid alterations by HBV infection or HBV-mediated liver injury, we have analyzed phospholipids that have important roles in liver regeneration by using matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS) in the livers of HBV model mice. As a result, we identified different phosphatidylcholines (PCs) showing significant changes in their composition as well as cationized ion adduct formation in HBV-infected mouse livers which are associated with virus-mediated regeneration defects. To find the factor of altered PCs, the expression kinetics of enzymes was also examined that regulate PC biosynthesis during liver regeneration. It is noteworthy that the expression of choline-phosphate cytidylyltransferase A (PCYT1A) was significantly delayed in wild type HBV-expressing livers. Moreover, the amount of hepatic total PC was also significantly decreased in wt HBV-expressing mice. These results suggest that infection of HBV alters the composition of PCs which may involve in HBV-mediated regeneration defects and liver disease.
doi:10.1371/journal.pone.0103955
PMCID: PMC4125171  PMID: 25101682
7.  Analysis of the Phospholipid Profile of Metaphase II Mouse Oocytes Undergoing Vitrification 
PLoS ONE  2014;9(7):e102620.
Oocyte freezing confers thermal and chemical stress upon the oolemma and various other intracellular structures due to the formation of ice crystals. The lipid profiles of oocytes and embryos are closely associated with both, the degrees of their membrane fluidity, as well as the degree of chilling and freezing injuries that may occur during cryopreservation. In spite of the importance of lipids in the process of cryopreservation, the phospholipid status in oocytes and embryos before and after freezing has not been investigated. In this study, we employed mass spectrometric analysis to examine if vitrification has an effect on the phospholipid profiles of mouse oocytes. Freshly prepared metaphase II mouse oocytes were vitrified using copper grids and stored in liquid nitrogen for 2 weeks. Fresh and vitrified-warmed oocytes were subjected to phospholipid extraction procedure. Mass spectrometric analyses revealed that multiple species of phospholipids are reduced in vitrified-warmed oocytes. LIFT analyses identified 31 underexpressed and 5 overexpressed phospholipids in vitrified mouse oocytes. The intensities of phosphatidylinositol (PI) {18∶2/16∶0} [M−H]− and phosphatidylglycerol (PG) {14∶0/18∶2} [M−H]− were decreased the most with fold changes of 30.5 and 19.1 in negative ion mode, respectively. Several sphingomyelins (SM) including SM {d38∶3} [M+H]+ and SM {d34∶0} [M+K]+ were decreased significantly in positive ion mode. Overall, the declining trend of multiple phospholipids demonstrates that vitrification has a marked effect on phospholipid profiles of oocytes. These results show that the identified phospholipids can be used as potential biomarkers of oocyte undergoing vitrification and will allow for the development of strategies to preserve phospholipids during oocyte cryopreservation.
doi:10.1371/journal.pone.0102620
PMCID: PMC4102530  PMID: 25033391
8.  Historical Review of Cancer Risks in Medical Radiation Workers 
Radiation research  2010;174(6):793-808.
Epidemiologic studies of medical radiation workers have found excess risks of leukemia, skin and female breast cancer in those employed before 1950, but little consistent evidence of cancer risk increases subsequently. Occupational radiation-related dose-response, risk estimates for recent years, and lifetime cancer risk data are limited for radiologists and radiologic technologists and lacking for physicians and technologists performing or assisting with fluoroscopically-guided procedures. Based on data from 80 mostly small studies of cardiologists and substantially fewer studies of physicians in other specialties, estimated effective doses to physicians per interventional procedure vary by more than an order of magnitude. There is an urgent need to expand the limited base of information on average annual occupational radiation exposures and time-trends in doses received by medical radiation workers, to assess lifetime cancer risks of radiologists and radiologic technologists in the existing cohorts, and to initiate long-term follow-up studies of cancer and other radiation-associated disease risks in physicians and technologists performing or assisting with interventional procedures. Such studies will help to optimize standardized protocols for radiologic procedures, determine if current radiation protection measures are adequate, provide guidance on cancer screening needs, and yield valuable insights on cancer risks associated with chronic radiation exposure.
doi:10.1667/RR2014.1
PMCID: PMC4098897  PMID: 21128805
radiologists; interventional radiologists; radiologic technologists; interventional cardiologists; neoplasms; reviews
9.  Imaging Mass Spectrometry in Papillary Thyroid Carcinoma for the Identification and Validation of Biomarker Proteins 
Journal of Korean Medical Science  2014;29(7):934-940.
Direct tissue imaging mass spectrometry (IMS) by matrix-assisted laser desorption ionization and time-of-flight (MALDI-TOF) mass spectrometry has become increasingly important in biology and medicine, because this technology can detect the relative abundance and spatial distribution of interesting proteins in tissues. Five thyroid cancer samples, along with normal tissue, were sliced and transferred onto conductive glass slides. After laser scanning by MALDI-TOF equipped with a smart beam laser, images were created for individual masses and proteins were classified at 200-µm spatial resolution. Based on the spatial distribution, region-specific proteins on a tumor lesion could be identified by protein extraction from tumor tissue and analysis using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using all the spectral data at each spot, various intensities of a specific peak were detected in the tumor and normal regions of the thyroid. Differences in the molecular weights of expressed proteins between tumor and normal regions were analyzed using unsupervised and supervised clustering. To verify the presence of discovered proteins through IMS, we identified ribosomal protein P2, which is specific for cancer. We have demonstrated the feasibility of IMS as a useful tool for the analysis of tissue sections, and identified the tumor-specific protein ribosomal protein P2.
Graphical Abstract
doi:10.3346/jkms.2014.29.7.934
PMCID: PMC4101781  PMID: 25045225
Pathology; Proteins; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Thyroid Gland; Neoplasms
10.  Lipid Peroxidation Product 4-Hydroxy-2-Nonenal Promotes Seeding-Capable Oligomer Formation and Cell-to-Cell Transfer of α-Synuclein 
Antioxidants & Redox Signaling  2013;18(7):770-783.
Abstract
Aims: Abnormal accumulation of α-synuclein aggregates is one of the key pathological features of many neurodegenerative movement disorders and dementias. These pathological aggregates propagate into larger brain regions as the disease progresses, with the associated clinical symptoms becoming increasingly severe and complex. However, the factors that induce α-synuclein aggregation and spreading of the aggregates remain elusive. Herein, we have evaluated the effects of the major lipid peroxidation byproduct 4-hydroxy-2-nonenal (HNE) on α-synuclein oligomerization and cell-to-cell transmission of this protein. Results: Incubation with HNE promoted the oligomerization of recombinant human α-synuclein via adduct formation at the lysine and histidine residues. HNE-induced α-synuclein oligomers evidence a little β-sheet structure and are distinct from amyloid fibrils at both conformation and ultrastructure levels. Nevertheless, the HNE-induced oligomers are capable of seeding the amyloidogenesis of monomeric α-synuclein under in vitro conditions. When neuronal cells were treated with HNE, both the translocation of α-synuclein into vesicles and the release of this protein from cells were increased. Neuronal cells can internalize HNE-modified α-synuclein oligomers, and HNE treatment increased the cell-to-cell transfer of α-synuclein proteins. Innovation and Conclusion: These results indicate that HNE induces the oligomerization of α-synuclein through covalent modification and promotes the cell-to-cell transfer of seeding-capable oligomers, thereby contributing to both the initiation and spread of α-synuclein aggregates. Antioxid. Redox Signal. 18, 770–783.
doi:10.1089/ars.2011.4429
PMCID: PMC3555112  PMID: 22867050
11.  Nonintegrin Laminin Receptor Precursor Protein Is Expressed on Olfactory Stem and Progenitor Cells 
The Journal of comparative neurology  2007;502(3):10.1002/cne.21328.
The biochemical identification and immunocytochemical characterization of a cell surface antigen, expressed on globose basal cells (GBCs) of the rodent olfactory epithelium (OE), are described. The monoclonal antibody (MAb) GBC-3 recognizes a surface protein, confirmed by both live cell staining and fluorescence-activated cell sorting. Two-dimensional SDS-PAGE/Western blot followed by tandem mass spectrometry demonstrates that the cell surface GBC-3 antigen is the 40 kDa laminin receptor precursor protein. The MAb GBC-3 labels the vast majority of cells among the GBC population and does not stain either sustentacular cells or horizontal basal cells (HBCs) in the normal rat OE. After epithelial lesion by exposure to methyl bromide, the remaining cells, which are mostly GBCs, are heavily stained by GBC-3, and colabeled with GBC-3 and sustentacular cell or HBC markers. GBC-3 will be a potentially useful tool for identifying and characterizing GBCs.
doi:10.1002/cne.21328
PMCID: PMC3882313  PMID: 17366606
2D IEF/SDS-PAGE; tandem mass spectrometry; cell surface marker; nonintegrin laminin receptors; tissue stem cells; progenitors
12.  Integration analysis of quantitative proteomics and transcriptomics data identify potential targets of frizzled-8 protein-related antiproliferative factor in vivo 
BJU international  2012;110(11C):E1138-E1146.
Objectives
To enhance our understanding of the interstitial cystitis urine biomarker antiproliferative factor (APF), as well as interstitial cystitis biology more generally at the systems level, we reanalyzed recently published large-scale quantitative proteomics and in vivo transcriptomics data sets using an integration analysis tool that we have developed.
Materials and methods
To identify more differentially expressed genes with a lower false discovery rate from a previously published microarray data set, an integrative hypothesis-testing statistical approach was applied.
For validation experiments, expression and phosphorylation levels of select proteins were evaluated by western blotting.
Results
Integration analysis of this transcriptomics data set with our own quantitative proteomics data set identified 10 genes that are potentially regulated by APF in vivo from 4140 differentially expressed genes identified with a false discovery rate of 1%.
Of these, five (i.e. JUP, MAPKSP1, GSPT1, PTGS2/COX-2 and XPOT) were found to be prominent after network modelling of the common genes identified in the proteomics and microarray studies.
This molecular signature reflects the biological processes of cell adhesion, cell proliferation and inflammation, which is consistent with the known physiological effects of APF.
Lastly, we found the mammalian target of rapamycin pathway was down-regulated in response to APF.
Conclusions
This unbiased integration analysis of in vitro quantitative proteomics data with in vivo quantitative transcriptomics data led to the identification of potential downstream mediators of the APF signal transduction pathway.
doi:10.1111/j.1464-410X.2012.11299.x
PMCID: PMC3461241  PMID: 22738385
APF; integration analysis; interstitial cystitis; microarray; SILAC
13.  Staphylococcus aureus Extracellular Vesicles Carry Biologically Active β-Lactamase 
Gram-positive bacteria naturally produce extracellular vesicles. However, little is known regarding the functions of Gram-positive bacterial extracellular vesicles, especially in the bacterial community. Here, we investigated the role of Staphylococcus aureus extracellular vesicles in interbacterial communication to cope with antibiotic stress. We found that S. aureus liberated BlaZ, a β-lactamase protein, via extracellular vesicles. These extracellular vesicles enabled other ampicillin-susceptible Gram-negative and Gram-positive bacteria to survive in the presence of ampicillin. However, S. aureus extracellular vesicles did not mediate the survival of tetracycline-, chloramphenicol-, or kanamycin-susceptible bacteria. Moreover, S. aureus extracellular vesicles did not contain the blaZ gene. In addition, the heat-treated S. aureus extracellular vesicles did not mediate the survival of ampicillin-susceptible bacteria. The β-lactamase activities of S. aureus soluble and extracellular vesicle-associated BlaZ were similar, but only the extracellular vesicle-associated BlaZ was resistant to protease digestion, which suggests that the enzymatic activity of BlaZ in extracellular vesicles is largely protected by the vesicle structure. Our observations provide evidence of the important role of S. aureus extracellular vesicles in antibiotic resistance, which allows the polymicrobial community to continue to evolve and prosper against antibiotics.
doi:10.1128/AAC.00522-12
PMCID: PMC3716153  PMID: 23529736
14.  Estradiol induces cytochrome P450 2B6 expression at high concentrations: Implication in estrogen-mediated gene regulation in pregnancy 
Biochemical Pharmacology  2012;84(1):93-103.
Pregnancy alters the rate and extent of drug metabolism, but little is known about the underlying molecular mechanism. We have found that 17β-estradiol (E2) upregulates expression of the major drug-metabolizing enzyme CYP2B6 in primary human hepatocytes. Results from promoter reporter assays in HepG2 cells revealed that E2 activates constitutive androstane receptor (CAR) and enhances promoter activity of CYP2B6, for which high concentrations of E2 reached during pregnancy were required. E2 triggered nuclear translocation of CAR in primary rat hepatocytes that were transiently transfected with human CAR as well as in primary human hepatocytes, further confirming transactivation of CAR by E2. E2-activated estrogen receptor (ER) also enhanced CYP2B6 promoter activity. The DNA-binding domain of ER was not required for the induction of CYP2B6 promoter activity by E2, suggesting involvement of a non-classical mechanism of ER action. Results from deletion and mutation assays as well as electrophorectic mobility shift and supershift assays revealed that two AP-1 binding sites (−1782/−1776 and −1664/−1658 of CYP2B6) are critical for ER-mediated activation of the CYP2B6 promoter by E2. Concurrent activation of both ER and CAR by E2 enhanced CYP2B6 expression in a synergistic manner. Our data demonstrate that at high concentrations reached during pregnancy, E2 activates both CAR and ER that synergistically induce CYP2B6 expression. These results illustrate pharmacological activity of E2 that would likely become prominent during pregnancy.
doi:10.1016/j.bcp.2012.03.016
PMCID: PMC3376749  PMID: 22484313
Cytochrome P450 2B6; estradiol; nuclear receptors; pregnancy
15.  Cholesterol Modulates Cell Signaling and Protein Networking by Specifically Interacting with PDZ Domain-Containing Scaffold Proteins 
Nature communications  2012;3:1249.
Cholesterol is known to modulate the physical properties of cell membranes but its direct involvement in cellular signaling has not been thoroughly investigated. Here we show that cholesterol specifically binds many PDZ domains found in scaffold proteins, including the N-terminal PDZ domain of NHERF1/EBP50. This modular domain has a cholesterol-binding site topologically distinct from its canonical protein-binding site and serves as a dual specificity domain that bridges the membrane and juxta-membrane signaling complexes. Disruption of the cholesterol binding activity of NHERF1 largely abrogates its dynamic colocalization with and activation of cystic fibrosis transmembrane conductance regulator, one of its binding partners in the plasma membrane of mammalian cells. At least seven more PDZ domains from other scaffold proteins also bind cholesterol and have cholesterol-binding sites, suggesting that cholesterol modulates cell signaling through direct interactions with these scaffold proteins. This mechanism may provide an alternative explanation for the formation of signaling platforms in cholesterol-rich membrane domains.
doi:10.1038/ncomms2221
PMCID: PMC3526836  PMID: 23212378
16.  EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles 
Journal of Extracellular Vesicles  2013;2:10.3402/jev.v2i0.20384.
Secretion of extracellular vesicles is a general cellular activity that spans the range from simple unicellular organisms (e.g. archaea; Gram-positive and Gram-negative bacteria) to complex multicellular ones, suggesting that this extracellular vesicle-mediated communication is evolutionarily conserved. Extracellular vesicles are spherical bilayered proteolipids with a mean diameter of 20–1,000 nm, which are known to contain various bioactive molecules including proteins, lipids, and nucleic acids. Here, we present EVpedia, which is an integrated database of high-throughput datasets from prokaryotic and eukaryotic extracellular vesicles. EVpedia provides high-throughput datasets of vesicular components (proteins, mRNAs, miRNAs, and lipids) present on prokaryotic, non-mammalian eukaryotic, and mammalian extracellular vesicles. In addition, EVpedia also provides an array of tools, such as the search and browse of vesicular components, Gene Ontology enrichment analysis, network analysis of vesicular proteins and mRNAs, and a comparison of vesicular datasets by ortholog identification. Moreover, publications on extracellular vesicle studies are listed in the database. This free web-based database of EVpedia (http://evpedia.info) might serve as a fundamental repository to stimulate the advancement of extracellular vesicle studies and to elucidate the novel functions of these complex extracellular organelles.
doi:10.3402/jev.v2i0.20384
PMCID: PMC3760654  PMID: 24009897
nanocosmos; communicasomes; exosomes; microvesicles; outer membrane vesicles; membrane vesicles; web portals; phylogenetic analyses
17.  Myocardial perfusion scans: projected population cancer risks from current levels of use in the U.S 
Circulation  2010;122(23):2403-2410.
Background
Myocardial perfusion scans contribute up to 20% of the estimated annual collective radiation dose to the U.S. population. We estimated potential future cancer risk from these scans by age at exposure and current frequency of use in the U.S.
Methods and Results
Usage patterns were determined from national survey data, and radionuclide dosage was based on current guidelines. Cancer risk projection models were generated based on the National Research Council Biologic Effects of Ionizing Radiation VII report, under the assumption that risk has a linear relationship with radiation exposure even at low doses. The mean projected number of radiation-related incident cancers and 95% uncertainty intervals (UI) were estimated using Monte Carlo simulations. Estimated risks for a scan performed at age 50 years ranged from 2 cancers/10,000 scans (95%UI:1–15) for a positron emission tomography ammonia-13 test to 25 (95%UI:9–58) cancers/10,000 scans for a dual-isotope (thallium-201+technetium-99m) scan. Risks were 50% lower at age 70 years, but were similar for males and females. Combination of cancer risk estimates with data on frequency of use suggested that the 9.1 million myocardial perfusion scans performed annually in the U.S. could result in 7400 (95%UI:3300–13700) additional future cancers.
Conclusions
The lifetime cancer risk from a single myocardial perfusion scan is small, and should be balanced against likely benefit and appropriateness of the test. The estimates depend on a number of assumptions including life-expectancy. They apply directly to asymptomatic individuals with life-expectancies similar to the general population. For individuals with a symptomatic clinical profile, on whom such scans are typically performed, the risks will be lower because of shorter life-expectancy.
doi:10.1161/CIRCULATIONAHA.110.941625
PMCID: PMC3548424  PMID: 21098448
nuclear medicine; perfusion; radioisotopes; cancer risks; computed tomography
18.  Radiation-related cancer risks from CT colonography screening: a risk-benefit analysis 
Objective
The purpose of this study was to estimate the ratio of cancers prevented to induced (benefit-risk ratio) for CT colonography screening every five years from age 50-80.
Materials and methods
Radiation-related cancer risk was estimated using risk projection models based on the National Research Council's BEIR VII committee's report and screening protocols from the American College of Radiology Imaging Network's National CT Colonography Trial. Uncertainty limits (UL) were estimated using Monte-Carlo simulation methods. Comparative modelling with three colorectal cancer microsimulation models was used to estimate the potential reduction in colorectal cancer cases and deaths.
Results
The estimated mean effective dose per CT colonography screen was 8mSv for females and 7mSv for males. The estimated number of radiation-related cancers from CT colonography screening every 5 years from age 50-80 was 150 cases/100,000 individuals (95%UL:80-280) for males and females. The estimated number of colorectal cancers prevented by CT colonography every 5 years from age 50-80 ranged across the three microsimulation models from 3580 to 5190/100,000, yielding a benefit-risk ratio that varied from 24:1(95%UL=13:1-45:1) to 35:1(95%UL=19:1-65:1). The benefit-risk ratio for cancer deaths was even higher than the ratio for cancer cases. Inclusion of radiation-related cancer risks from CT scans following-up extracolonic findings did not materially alter the results.
Conclusions
Concerns have been raised about recommending CT colonography as a routine screening tool because of the potential harms, including the radiation risks. Based on these models the benefits from CT colonography screening every five years from age 50-80 clearly outweigh the radiation risks.
doi:10.2214/AJR.10.4907
PMCID: PMC3470483  PMID: 21427330
19.  Radiation exposure from CT scans in childhood and subsequent risk of leukaemia and brain tumours: a retrospective cohort study 
Lancet  2012;380(9840):499-505.
Summary
Background
Although CT scans are very useful clinically, potential cancer risks exist from associated ionising radiation, in particular for children who are more radiosensitive than adults. We aimed to assess the excess risk of leukaemia and brain tumours after CT scans in a cohort of children and young adults.
Methods
In our retrospective cohort study, we included patients without previous cancer diagnoses who were first examined with CT in National Health Service (NHS) centres in England, Wales, or Scotland (Great Britain) between 1985 and 2002, when they were younger than 22 years of age. We obtained data for cancer incidence, mortality, and loss to follow-up from the NHS Central Registry from Jan 1, 1985, to Dec 31, 2008. We estimated absorbed brain and red bone marrow doses per CT scan in mGy and assessed excess incidence of leukaemia and brain tumours cancer with Poisson relative risk models. To avoid inclusion of CT scans related to cancer diagnosis, follow-up for leukaemia began 2 years after the first CT and for brain tumours 5 years after the first CT.
Findings
During follow-up, 74 of 178 604 patients were diagnosed with leukaemia and 135 of 176 587 patients were diagnosed with brain tumours. We noted a positive association between radiation dose from CT scans and leukaemia (excess relative risk [ERR] per mGy 0·036, 95% CI 0·005–0·120; p=0·0097) and brain tumours (0·023, 0·010–0·049; p<0·0001). Compared with patients who received a dose of less than 5 mGy, the relative risk of leukaemia for patients who received a cumulative dose of at least 30 mGy (mean dose 51·13 mGy) was 3·18 (95% CI 1·46–6·94) and the relative risk of brain cancer for patients who received a cumulative dose of 50–74 mGy (mean dose 60·42 mGy) was 2·82 (1·33–6·03).
Interpretation
Use of CT scans in children to deliver cumulative doses of about 50 mGy might almost triple the risk of leukaemia and doses of about 60 mGy might triple the risk of brain cancer. Because these cancers are relatively rare, the cumulative absolute risks are small: in the 10 years after the first scan for patients younger than 10 years, one excess case of leukaemia and one excess case of brain tumour per 10 000 head CT scans is estimated to occur. Nevertheless, although clinical benefits should outweigh the small absolute risks, radiation doses from CT scans ought to be kept as low as possible and alternative procedures, which do not involve ionising radiation, should be considered if appropriate.
Funding
US National Cancer Institute and UK Department of Health.
doi:10.1016/S0140-6736(12)60815-0
PMCID: PMC3418594  PMID: 22681860
20.  CT Scans in Young People in Great Britain: Temporal and Descriptive Patterns, 1993–2002 
Background. Although using computed tomography (CT) can be greatly beneficial, the associated relatively high radiation doses have led to growing concerns in relation to potential associations with risk of future cancer. Very little has been published regarding the trends of CT use in young people. Therefore, our objective was to assess temporal and other patterns in CT usage among patients aged under 22 years in Great Britain from 1993 to 2002. Methods. Electronic data were obtained from the Radiology Information Systems of 81 hospital trusts within Great Britain. All included patients were aged under 22 years and examined using CT between 1993 and 2002, with accessible radiology records. Results. The number of CT examinations doubled over the study period. While increases in numbers of recorded examinations were seen across all age groups, the greatest increases were in the older patients, most notably those aged 15–19 years of age. Sixty percent of CT examinations were of the head, with the percentages varying with calendar year and patient age. Conclusions. In contrast to previous data from the North of England, the doubling of CT use was not accompanied by an increase in numbers of multiple examinations to the same individual.
doi:10.1155/2012/594278
PMCID: PMC3390133  PMID: 22792457
21.  Inducible Clostridium perfringens bacteriophages ΦS9 and ΦS63 
Bacteriophage  2012;2(2):89-97.
Two inducible temperate bacteriophages ΦS9 and ΦS63 from Clostridium perfringens were sequenced and analyzed. Isometric heads and long non-contractile tails classify ΦS9 and ΦS63 in the Siphoviridae family, and their genomes consist of 39,457 bp (ΦS9) and 33,609 bp (ΦS63) linear dsDNA, respectively. ΦS63 has 3′-overlapping cohesive genome ends, whereas ΦS9 is the first Clostridium phage featuring an experimentally proven terminally redundant and circularly permuted genome. A total of 50 and 43 coding sequences were predicted for ΦS9 and ΦS63, respectively, organized into 6 distinct lifestyle-associated modules typical for temperate Siphoviruses. Putative functions could be assigned to 26 gene products of ΦS9, and to 25 of ΦS63. The ΦS9 attB attachment and insertion site is located in a non-coding region upstream of a putative phosphorylase gene. Interestingly, ΦS63 integrates into the 3′ part of sigK in C. perfringens, and represents the first functional skin-element-like phage described for this genus. With respect to possible effects of lysogeny, we did not obtain evidence that ΦS9 may influence sporulation of a lysogenized host. In contrast, interruption of sigK, a sporulation associated gene in various bacteria, by the ΦS63 prophage insertion is more likely to affect sporulation of its carrier.
doi:10.4161/bact.21363
PMCID: PMC3442830  PMID: 23050219
Clostridium perfringens; prophage; attachment site; sporulation; skin-element
22.  Protein and lipid MALDI profiles classify breast cancers according to the intrinsic subtype 
BMC Cancer  2011;11:465.
Background
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of common solid tumors. Using recently developed MALDI matrices for lipid profiling, we evaluated whether direct tissue MALDI MS analysis on proteins and lipids may classify human breast cancer samples according to the intrinsic subtype.
Methods
Thirty-four pairs of frozen, resected breast cancer and adjacent normal tissue samples were analyzed using histology-directed, MALDI MS analysis. Sinapinic acid and 2,5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid were manually deposited on areas of each tissue section enriched in epithelial cells to identify lipid profiles, and mass spectra were acquired using a MALDI-time of flight instrument.
Results
Protein and lipid profiles distinguish cancer from adjacent normal tissue samples with the median prediction accuracy of 94.1%. Luminal, HER2+, and triple-negative tumors demonstrated different protein and lipid profiles, as evidenced by permutation P values less than 0.01 for 0.632+ bootstrap cross-validated misclassification rates with all classifiers tested. Discriminatory proteins and lipids were useful for classifying tumors according to the intrinsic subtype with median prediction accuracies of 80.0-81.3% in random test sets.
Conclusions
Protein and lipid profiles accurately distinguish tumor from adjacent normal tissue and classify breast cancers according to the intrinsic subtype.
doi:10.1186/1471-2407-11-465
PMCID: PMC3218066  PMID: 22029885
protein; lipid; breast cancer; MALDI
23.  Discovery of the serum biomarker proteins in severe preeclampsia by proteomic analysis 
Experimental & Molecular Medicine  2011;43(7):427-435.
Preeclapsia (PE) is a severe disorder that occurs during pregnancy, leading to maternal and fetal morbidity and mortality. PE affects about 3-8% of all pregnancies. In this study, we conducted liquid chromatographymass spectrometry/mass spectrometry (LC-MS/MS) to analyze serum samples depleted of the six most abundant proteins from normal and PE-affected pregnancies to profile serum proteins. A total of 237 proteins were confidently identified with < 1% false discovery rate from the two groups of duplicate analysis. The expression levels of those identified proteins were compared semiquantitatively by spectral counting. To further validate the candidate proteins with a quantitative mass spectrometric method, selective reaction monitoring (SRM) and enzyme linked immune assay (ELISA) of serum samples collected from pregnant women with severe PE (n = 8) or normal pregnant women (n = 5) was conducted. α2-HS-glycoprotein (AHSG), retinol binding protein 4 (RBP4) and α-1-microglobulin/bikunin (AMBP) and Insulin like growth factor binding protein, acid labile subunit (IGFBP-ALS) were confirmed to be differentially expressed in PE using SRM (P < 0.05). Among these proteins, AHSG was verified by ELISA and showed a statistically significant increase in PE samples when compared to controls.
doi:10.3858/emm.2011.43.7.047
PMCID: PMC3158502  PMID: 21646846
α2HS-glycoprotein; biomarkers; pre-eclampsia; spectrometry, mass, electrospray ionization; proteomics; serum
24.  CT colonography: perforation rates and potential radiation risks 
CT colonography has emerged as a potential screening tool for colorectal cancer that could provide good efficacy combined with greater acceptability than optical colonosocopy and fecal occult blood testing. Some organizations have raised concerns about potential harms, including perforation rates, radiation dose and the risk of radiation-related cancer, and have not recommended that it be currently used as a screening tool in the general population. In this paper we review the current evidence for these potential harms for CT colonography, and compare them to potential harms from the alternatives including colonoscopy and double-contrast barium enema.
doi:10.1016/j.giec.2010.02.003
PMCID: PMC2956272  PMID: 20451817
Computed tomography; colorectal cancer; screening; radiation; risk; perforation; colonography
25.  Outer Membrane Proteins A (OmpA) and X (OmpX) Are Essential for Basolateral Invasion of Cronobacter sakazakii▿  
Applied and Environmental Microbiology  2010;76(15):5188-5198.
Cronobacter sakazakii is an opportunistic pathogen that actively invades host eukaryotic cells. To identify invasion factors responsible for the intestinal translocation of C. sakazakii, we constructed for the first time outer membrane protein X (OmpX) and A (OmpA) deletion mutants using the lambda Red recombination system. The ompX and ompA deletion mutants showed significantly reduced invasion of human enterocyte-like epithelial Caco-2 and human intestinal epithelial INT-407 cells, and significantly fewer mutant cells were recovered from the livers and spleens of rat pups. Furthermore, compared with intact target cells, the invasion and initial association potentials of the mutants increased at a rate similar to that of the wild type in tight-junction-disrupted target cells, suggesting that OmpX and OmpA are involved in basolateral invasion by C. sakazakii. This is the first report of C. sakazakii virulence determinants that are essential for basolateral invasion and that may be critical for the virulence of C. sakazakii.
doi:10.1128/AEM.02498-09
PMCID: PMC2916488  PMID: 20543055

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