Search tips
Search criteria

Results 1-25 (147)

Clipboard (0)

Select a Filter Below

more »
Year of Publication
more »
1.  Retention of asbestos fibres in lungs of workers with asbestosis, asbestosis and lung cancer, and mesothelioma in Asbestos township. 
OBJECTIVE: To conduct a mineralogical study on the particles retained in the necropsied lungs of a homogenous group of asbestos miners and millers from Asbestos township (and a local reference population) and to consider the hypothesis that there is a difference in size between fibres retained in the lungs of patients with asbestosis with and without lung cancer. METHODS: Samples of lung tissue were obtained from 38 patients with asbestosis without lung cancer, 25 with asbestosis and lung cancer, and 12 with mesothelioma, from necropsied Quebec chrysotile miners and millers from Asbestos township. Fibre concentrations in the lungs of these patients were compared with those in tissue from necropsies carried out on a local reference population: men who had died of either accidental death or acute myocardial infarction between 1990 and 1992. 23 were born before 1940 and 26 after 1940. RESULTS: Geometric mean (GM) concentrations were higher in cases than in the controls for chrysotile fibres 5 to 10 microns long in patients with asbestosis with or without lung cancer; for tremolite fibres 5 to 10 microns long in all patients; for crocidolite, talc, or anthophyllite fibres 5 to 10 microns long in patients with mesothelioma; for chrysotile and tremolite fibres > or = 10 microns long in patients with asbestosis; and crocidolite, talc, or anthophyllite fibres > or = 10 microns long in patients with mesothelioma. However, median concentrations of each type of fibre in the lungs did not show any significant differences between the three disease groups. Average length to diameter ratios of the fibres were calculated to be larger in patients with asbestosis and lung cancer than in those without lung cancer for crocidolite fibres > or = 10 microns long, for chrysotile, amosite, and tremolite fibres 5 to 10 microns long, and for chrysotile and crocidolite fibres < 5 microns long. However, there was no statistical difference in the median length to diameter ratios for any type of fibres across the disease groups when they were calculated in each patient. Cumulative smoking index (pack-years) was higher in the group with asbestosis and lung cancer but was not statistically different from the two other disease groups. CONCLUSION: Lung cancers occurred in workers with asbestosis from Asbestos township who had an equal concentration of retained fibres but a tendency to a higher length to diameter ratio of amphiboles. These workers had a 29% higher average cumulative smoking index.
PMCID: PMC1128612  PMID: 8994398
2.  Epidemiology of Candida kefyr in Patients with Hematologic Malignancies 
Journal of Clinical Microbiology  2014;52(6):1830-1837.
Candida kefyr is an emerging pathogen among patients with hematologic malignancies (HM). We performed a retrospective study at Johns Hopkins Hospital to evaluate the epidemiology of C. kefyr colonization and infection in HM patients between 2004 and 2010. Eighty-three patients were colonized and/or infected with C. kefyr, with 8 (9.6%) having invasive candidiasis (IC). The yearly incidence of C. kefyr colonization and candidemia increased over the study period (P < 0.01), particularly after 2009. In 2010, C. kefyr caused 16.7% of candidemia episodes. The monthly incidence of C. kefyr was higher during the summer throughout the study. In a cohort of patients with acute myelogenic leukemia receiving induction chemotherapy, risks for C. kefyr colonization included the summer season (odds ratio [OR], 3.1; P = 0.03); administration of an azole (OR, 0.06; P < 0.001) or amphotericin B (OR, 0.35; P = 0.05) was protective. Fingerprinting of 16 isolates by repetitive sequence-based PCR showed that all were different genotypes. The epidemiology of C. kefyr candidemia was evaluated in another hospital in Montreal, Canada; data confirmed higher rates of C. kefyr infection in the summer. C. kefyr appears to be increasing in HM patients, with prominent summer seasonality. These findings raise questions about the effect of antifungal agents and health care exposures (e.g., yogurt) on the epidemiology of this yeast.
PMCID: PMC4042816  PMID: 24622105
3.  Alginate Hydrogel Protects Encapsulated Hepatic HuH-7 Cells against Hepatitis C Virus and Other Viral Infections 
PLoS ONE  2014;9(10):e109969.
Cell microencapsulation in alginate hydrogel has shown interesting applications in regenerative medicine and the biomedical field through implantation of encapsulated tissue or for bioartificial organ development. Although alginate solution is known to have low antiviral activity, the same property regarding alginate gel has not yet been studied. The aim of this work is to investigate the potential protective effect of alginate encapsulation against hepatitis C virus (HCV) infection for a hepatic cell line (HuH-7) normally permissive to the virus. Our results showed that alginate hydrogel protects HuH-7 cells against HCV when the supernatant was loaded with HCV. In addition, alginate hydrogel blocked HCV particle release out of the beads when the HuH-7 cells were previously infected and encapsulated. There was evidence of interaction between the molecules of alginate hydrogel and HCV, which was dose- and incubation time-dependent. The protective efficiency of alginate hydrogel towards HCV infection was confirmed against a variety of viruses, whether or not they were enveloped. This promising interaction between an alginate matrix and viruses, whose chemical mechanisms are discussed, is of great interest for further medical therapeutic applications based on tissue engineering.
PMCID: PMC4195705  PMID: 25310111
4.  Epidemic cycles driven by host behaviour 
Host immunity and demographics (the recruitment of susceptibles via birthrate) have been demonstrated to be a key determinant of the periodicity of measles, pertussis and dengue epidemics. However, not all epidemic cycles are from pathogens inducing sterilizing immunity or are driven by demographics. Many sexually transmitted infections are driven by sexual behaviour. We present a mathematical model of disease transmission where individuals can disconnect and reconnect depending on the infectious status of their contacts. We fit the model to historic syphilis (Treponema pallidum) and gonorrhea (Neisseria gonorrhoeae) incidence in the USA and explore potential intervention strategies against syphilis. We find that cycles in syphilis incidence can be driven solely by changing sexual behaviour in structured populations. Our model also explains the lack of similar cycles in gonorrhea incidence even if the two infections share the same propagation pathways. Our model similarly illustrates how sudden epidemic outbreaks can occur on time scales smaller than the characteristic demographic time scale of the population and that weaker infections can lead to more violent outbreaks. Behaviour also appears to be critical for control strategies as we found a bigger sensitivity to behavioural interventions than antibiotic treatment. Thus, behavioural interventions may play a larger role than previously thought, especially in the face of antibiotic resistance and low intervention efficacies.
PMCID: PMC4235258  PMID: 25100316
syphilis; network model; epidemic cycles; human behaviour
5.  Clostridium difficile infection after adult autologous stem cell transplantation: A multicenter study of epidemiology and risk factors 
We sought to describe the epidemiology of Clostridium difficile infection (CDI) among adult recipients of autologous hematopoietic stem cell transplantation (auto HSCT) within the first year after HSCT in centers with variable epidemiology of hyper-toxigenic strains. A multicenter, retrospective nested case-control study was conducted among 873 auto HSCT recipients at Johns Hopkins Hospital (JHH, Baltimore, MD) and Hôpital Maisonneuve-Rosemont (HMR, Montreal, Canada) between 1/2003-12/2008. Despite center differences in the prevalence of NAP-1 strains over the time period (21-43% JHH; 80-84% HMR), the 1-year incidence of CDI was similar (6.2% JHH; 5.7% HMR). The median time to infection was 11 days (interquartile range [IQR] 1 to 27). In case control analysis, the following were predictors for CDI: grade 2 or higher mucositis (odds ratio [OR]: 3.00, P=0.02) and receipt of a 4th generation cephalosporin (OR: 2.76, P=0.04). Mucositis was the strongest predictor of risk for CDI in multivariate analysis (adjusted OR [AOR]: 2.77; P=0.03). CDI is a common and early complication of auto HSCT. Treatment-related gastrointestinal mucosal damage, in addition to the potentially modifiable risk of antimicrobial exposure, influence risk for CDI early post-auto HSCT.
PMCID: PMC3806308  PMID: 23916741
Clostridium difficile; stem cell transplantation; mucositis; antibiotics; NAP-1
6.  Impact of KIT exon 10 M541L allelic variant on the response to imatinib in aggressive fibromatosis: analysis of the desminib series by competitive allele specific Taqman PCR technology 
BMC Cancer  2014;14(1):632.
Aggressive fibromatosis (AF) is a rare fibroblastic proliferative disease with a locally aggressive behavior and no distant metastasis, characterized by driver mutations in CTNNB1 or the APC gene. When progressive and/or symptomatic AF is not amenable to local management, a variety of medical treatments may be efficient, including imatinib mesylate. The phase II “Desminib trial” included 40 patients with AF to evaluate the toxicity and efficacy of imatinib resulting in a 65% tumor control rate at 1 year. We investigated a potential predictive value of KIT exon 10 M541L variant (KITL541) on this prospective series.
DNA was extracted in sufficient quantity from 33 patients included in the Desminib trial. The detection of KITL541 was performed by Competitive Allele-Specific Taqman® PCR technology. Chi-2 analyses were performed to search for a correlation between KIT status and tumor response. Progression free (PFS) and overall survival (OS) were compared by log-rank test after Kaplan-Meier analysis.
In 6 out of 33 cases (18%), the technique failed to determine the mutational status; 5 patients (19%) harboured KITL541 and 22 patients (81%) were classified as KIT wild type. Compared with total cohort, KITL541 frequency did not distinguish between different clinical characteristics. In the KITL541 and the KITWT subgroups, the tumor control rate at 1 year was 100% and 68%, respectively (p = 0.316). The median PFS of patients harboring KITL541 or not is 29.9 and 24.5 months, respectively (p = 0.616), and the median OS is not reached, in any of the groups.
Our results do not support a predictive effect of KITL541 on the efficacy of imatinib for patients with AF.
PMCID: PMC4161827  PMID: 25174682
Aggressive fibromatosis; KIT exon 10 M541L allelic variant; Imatinib
7.  MicroRNAs as emerging biomarkers and therapeutic targets for pancreatic cancer 
World Journal of Gastroenterology : WJG  2014;20(32):11199-11209.
Despite tremendous efforts from scientists and clinicians worldwide, pancreatic adenocarcinoma (PDAC) remains a deadly disease due to the lack of early diagnostic tools and reliable therapeutic approaches. Consequently, a majority of patients (80%) display an advanced disease that results in a low resection rate leading to an overall median survival of less than 6 months. Accordingly, robust markers for the early diagnosis and prognosis of pancreatic cancer, or markers indicative of survival and/or metastatic disease are desperately needed to help alleviate the dismal prognosis of this cancer. In addition, the discovery of new therapeutic targets is mandatory to design effective treatments. In this review, we will highlight the translational studies demonstrating that microRNAs may soon translate into clinical applications as long-awaited screening tools and therapeutic targets for PDAC.
PMCID: PMC4145758  PMID: 25170204
MicroRNAs; Biomarkers; Pancreatic cancer; Therapeutic targets; Precancerous lesions
8.  Climate change and habitat fragmentation drive the occurrence of Borrelia burgdorferi, the agent of Lyme disease, at the northeastern limit of its distribution 
Evolutionary Applications  2014;7(7):750-764.
Lyme borreliosis is rapidly emerging in Canada, and climate change is likely a key driver of the northern spread of the disease in North America. We used field and modeling approaches to predict the risk of occurrence of Borrelia burgdorferi, the bacteria causing Lyme disease in North America. We combined climatic and landscape variables to model the current and future (2050) potential distribution of the black-legged tick and the white-footed mouse at the northeastern range limit of Lyme disease and estimated a risk index for B. burgdorferi from these distributions. The risk index was mostly constrained by the distribution of the white-footed mouse, driven by winter climatic conditions. The next factor contributing to the risk index was the distribution of the black-legged tick, estimated from the temperature. Landscape variables such as forest habitat and connectivity contributed little to the risk index. We predict a further northern expansion of B. burgdorferi of approximately 250–500 km by 2050 – a rate of 3.5–11 km per year – and identify areas of rapid rise in the risk of occurrence of B. burgdorferi. Our results will improve understanding of the spread of Lyme disease and inform management strategies at the most northern limit of its distribution.
PMCID: PMC4227856  PMID: 25469157
climate change; emergence; habitat fragmentation; Lyme disease; range shift; white-footed mouse
9.  Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum 
BMC Genomics  2014;15(1):629.
Fusarium Head Blight (FHB) caused primarily by Fusarium graminearum (Fg) is one of the major diseases of small-grain cereals including bread wheat. This disease both reduces yields and causes quality losses due to the production of deoxynivalenol (DON), the major type B trichothecene mycotoxin. DON has been described as a virulence factor enabling efficient colonization of spikes by the fungus in wheat, but its precise role during the infection process is still elusive. Brachypodium distachyon (Bd) is a model cereal species which has been shown to be susceptible to FHB. Here, a functional genomics approach was performed in order to characterize the responses of Bd to Fg infection using a global transcriptional and metabolomic profiling of B. distachyon plants infected by two strains of F. graminearum: a wild-type strain producing DON (Fgdon+) and a mutant strain impaired in the production of the mycotoxin (Fgdon-).
Histological analysis of the interaction of the Bd21 ecotype with both Fg strains showed extensive fungal tissue colonization with the Fgdon+ strain while the florets infected with the Fgdon- strain exhibited a reduced hyphal extension and cell death on palea and lemma tissues. Fungal biomass was reduced in spikes inoculated with the Fgdon- strain as compared with the wild-type strain. The transcriptional analysis showed that jasmonate and ethylene-signalling pathways are induced upon infection, together with genes encoding putative detoxification and transport proteins, antioxidant functions as well as secondary metabolite pathways. In particular, our metabolite profiling analysis showed that tryptophan-derived metabolites, tryptamine, serotonin, coumaroyl-serotonin and feruloyl-serotonin, are more induced upon infection by the Fgdon+ strain than by the Fgdon- strain. Serotonin was shown to exhibit a slight direct antimicrobial effect against Fg.
Our results show that Bd exhibits defense hallmarks similar to those already identified in cereal crops. While the fungus uses DON as a virulence factor, the host plant preferentially induces detoxification and the phenylpropanoid and phenolamide pathways as resistance mechanisms. Together with its amenability in laboratory conditions, this makes Bd a very good model to study cereal resistance mechanisms towards the major disease FHB.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-629) contains supplementary material, which is available to authorized users.
PMCID: PMC4124148  PMID: 25063396
Fusarium Head Blight; Brachypodium distachyon; Transcriptome; Metabolic profiling; Serotonin
10.  Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics 
PLoS ONE  2014;9(7):e102561.
A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.
PMCID: PMC4102501  PMID: 25033299
11.  The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity 
Cell  2013;156(0):183-194.
The physical nature of the bacterial cytoplasm is poorly understood even though it determines cytoplasmic dynamics and hence cellular physiology and behavior. Through single-particle tracking of protein filaments, plasmids, storage granules and foreign particles of different sizes, we find that the bacterial cytoplasm displays properties characteristic of glass-forming liquids and changes from liquid-like to solid-like in a component size-dependent fashion. As a result, the motion of cytoplasmic components becomes disproportionally constrained with increasing size. Remarkably, cellular metabolism fluidizes the cytoplasm, allowing larger components to escape their local environment and explore larger regions of the cytoplasm. Consequently, cytoplasmic fluidity and dynamics dramatically change as cells shift between metabolically active and dormant states in response to fluctuating environments. Our findings provide insight into bacterial dormancy and have broad implications to our understanding of bacterial physiology as the glassy behavior of the cytoplasm impacts all intracellular processes involving large components.
PMCID: PMC3956598  PMID: 24361104
12.  Scaling of Traction Forces with the Size of Cohesive Cell Colonies 
Physical review letters  2012;108(19):198101.
To understand how the mechanical properties of tissues emerge from interactions of multiple cells, we measure traction stresses of cohesive colonies of 1–27 cells adherent to soft substrates. We find that traction stresses are generally localized at the periphery of the colony and the total traction force scales with the colony radius. For large colony sizes, the scaling appears to approach linear, suggesting the emergence of an apparent surface tension of the order of 10−3 N/m. A simple model of the cell colony as a contractile elastic medium coupled to the substrate captures the spatial distribution of traction forces and the scaling of traction forces with the colony size.
PMCID: PMC4098718  PMID: 23003091
13.  A prognostic nomogram for prediction of recurrence in desmoid fibromatosis 
Annals of surgery  2013;258(2):347-353.
To construct a postoperative nomogram to estimate the risk of local recurrence for patients with desmoid tumors.
The standard management of desmoid tumors is resection, but many recur locally. Other options include observation or novel chemotherapeutics, but little guidance exists on selecting treatment.
Patients undergoing resection during 1982-2011 for primary or locally recurrent desmoids were identified from a single-institution prospective database. Cox regression analysis was used to assess risk factors and to create a recurrence nomogram, which was validated using an international, multi-institutional dataset.
Desmoids were treated surgically in 495 patients (median follow-up 60 months). Of 439 patients undergoing complete gross resection, 100 (23%) had recurrence. Five-year local recurrence–free survival (LRFS) was 69%. Eight patients died of disease, all after R2 resection. Adjuvant radiation was not associated with improved LRFS. In multivariate analysis, factors associated with recurrence were extremity location, young age, and large tumor size, but not margin. Abdominal wall tumors had the best outcome (5-year LRFS 91%). Age, site, and size were used to construct a nomogram with concordance index 0.703 in internal validation and 0.659 in external validation. Integration of additional variables (R1 margin, gender, depth, and primary vs. recurrent presentation) did not importantly improve concordance (internal concordance index 0.707).
A postoperative nomogram including only size, site, and age predicts local recurrence and can aid in counseling patients. Systemic therapies may be appropriate for young patients with large, extremity desmoids, but surgery alone is curative for most abdominal wall lesions.
PMCID: PMC4096320  PMID: 23532110
15.  Atazanavir and Other Determinants of Hyperbilirubinemia in a Cohort of 1150 HIV-Positive Patients: Results from 9 Years of Follow-Up 
AIDS Patient Care and STDs  2013;27(7):378-386.
Hyperbilirubinemia is common among patients exposed to atazanavir (ATV), but its long-term significance is not well documented. The objective was to analyze hyperbilirubinemia (incidence, regression, determinants, and outcome) among 1150 HIV-positive patients followed-up in a prospective cohort between 2003 and 2012. Cumulative incidence of hyperbilirubinemia grades 3–4 and its probability of regression were estimated using Kaplan-Meier method. Cox proportional hazards model was used to study the determinants. Generalized estimating equation (GEE) regression was used to evaluate the association between hyperbilirubinemia grades 3–4 and adverse health outcome. Eight years cumulative incidence of hyperbilirubinemia was 83.6% (95% CI:79.0–87.7) and 6.6% (95% CI:4.7–9.2) among ATV users and non-users, respectively. This clinical outcome fluctuated considerably, as most patients exposed to ATV (91%) regressed, transiently, to lower grade at some point during follow-up. Determinants were atazanavir (HR=147.90, 95% CI: 33.64–604.18), ritonavir (HR=5.18, 95% CI:2.33–11.48), zidovudine (HR=2.62, 95% CI:1.07–6.46), and age (HR=1.04 95% CI:1.01–1.08). Alcohol consumption and others non-antiretroviral medications including hepatotoxic and recreational drugs were not available for analyses. Incidence of hyperbilirubinemia was very high among ATV users and, although regression to lower grade was frequent in the clinical follow-up of these patients, this was usually transient as the mean level of bilirubin stayed at a relatively high level. Importantly, long-term hyperbilirubinemia was not associated with adverse health outcome.
PMCID: PMC3704117  PMID: 23829329
16.  Pathway analysis for genetic association studies: to do, or not to do? That is the question 
BMC Proceedings  2014;8(Suppl 1):S103.
In Genetic Analysis Workshop 18 data, we used a 3-stage approach to explore the benefits of pathway analysis in improving a model to predict 2 diastolic blood pressure phenotypes as a function of genetic variation. At stage 1, gene-based tests of association in family data of approximately 800 individuals found over 600 genes associated at p<0.05 for each phenotype. At stage 2, networks and enriched pathways were estimated with Cytoscape for genes from stage 1, separately for the 2 phenotypes, then examining network overlap. This overlap identified 4 enriched pathways, and 3 of these pathways appear to interact, and are likely candidates for playing a role in hypertension. At stage 3, using 157 maximally unrelated individuals, partial least squares regression was used to find associations between diastolic blood pressure and single-nucleotide polymorphisms in genes highlighted by the pathway analyses. However, we saw no improvement in the adjusted cross-validated R2. Although our pathway-motivated regressions did not improve prediction of diastolic blood pressure, merging gene networks did identify several plausible pathways for hypertension.
PMCID: PMC4144468  PMID: 25519357
17.  Dynamic peripheral traction forces balance stable neurite tension in regenerating Aplysia bag cell neurons 
Scientific Reports  2014;4:4961.
Growth cones of elongating neurites exert force against the external environment, but little is known about the role of force in outgrowth or its relationship to the mechanical organization of neurons. We used traction force microscopy to examine patterns of force in growth cones of regenerating Aplysia bag cell neurons. We find that traction is highest in the peripheral actin-rich domain and internal stress reaches a plateau near the transition between peripheral and central microtubule-rich domains. Integrating stress over the area of the growth cone reveals that total scalar force increases with area but net tension on the neurite does not. Tensions fall within a limited range while a substantial fraction of the total force can be balanced locally within the growth cone. Although traction continuously redistributes during extension and retraction of the peripheral domain, tension is stable over time, suggesting that tension is a tightly regulated property of the neurite independent of growth cone dynamics. We observe that redistribution of traction in the peripheral domain can reorient the end of the neurite shaft. This suggests a role for off-axis force in growth cone turning and neuronal guidance.
PMCID: PMC4019958  PMID: 24825441
18.  Role of Transportation in Spread of Porcine Epidemic Diarrhea Virus Infection, United States 
Emerging Infectious Diseases  2014;20(5):872-874.
After porcine epidemic diarrhea virus (PEDV) was detected in the United States in 2013, we tested environmental samples from trailers in which pigs had been transported. PEDV was found in 5.2% of trailers not contaminated at arrival, , suggesting that the transport process is a source of transmission if adequate hygiene measures are not implemented.
PMCID: PMC4012813  PMID: 24750785
Porcine Epidemic Diarrhea Virus; PEDV; viruses; Cornaviridae; transport; lairage; biosecurity; epidemic; fomite
19.  ABRF Research Group Development and Characterization of a Proteomics Normalization Standard Consisting of 1,000 Stable Isotope Labeled Peptides 
The ABRF Proteomics Standards Research Group (sPRG) is reporting the progress of a two-year study (2012–2014) which focuses on the generation of interassay, interspecies, and interlaboratory peptide standard that can be used for normalization of protein abundance measurements in mass spectrometry based quantitative proteomics analyses. The standard has been formulated as two mixtures: 1,000 stable isotope 13C/15N-labeled (SIL) synthetic peptides alone, and peptides mixed with a tryptic digest of a HEK 293 cell lysate. The sequences of the synthetic peptides were derived from 552 proteins conserved across proteomes of commonly analyzed species: Homo sapiens, Mus musculus and Rattus norvegicus. The selected peptides represent a full range of hydrophobicities and isoelectric points, typical of tryptic peptides derived from complex proteomic samples. The standard was designed to represent proteins of various concentrations, spanning three orders of magnitude. First year efforts were focused on selection of appropriate protein and peptide candidates, peptide synthesis, quality assessment and LC-MS/MS evaluation conducted in laboratories of sPRG members. Using a variety of instrumental configurations and bioinformatics approaches, a thorough characterization of all 1,000 peptides was established. In the second year, the group launched the study to the entire proteomics community. A lyophilized mixture of HEK 293 tryptic digest cell lysate spiked with the 1,000 SIL peptide standards was provided to each participant. Also provided were a Skyline tutorial, tutorial datasets, three MS/MS spectral libraries generated from linear ion-trap (CID), Q-TOF/QQQ (CID), or Orbitrap (HCD) instrumentation, and a Panorama data repository. Participants were asked to analyze the sample in triplicate and calculate ratios of the spiked SIL to endogenous peptides and coefficients of variance for each peptide. Over 40 datasets were returned, and results following thorough characterization of the standard using various instrumental configurations will be reported.
PMCID: PMC4162257
20.  Histoplasmosis and subcutaneous nodules in a kidney transplant recipient: erythema nodosum versus fungal panniculitis 
Erythema nodosum (EN)-like lesions are a rare occurrence after solid organ transplantation. Differential diagnosis includes infective panniculitis, which can be a feature of progressive disseminated histoplasmosis (PDH), an uncommon but severe form affecting primarily immunocompromised hosts. We report on a fatal case of PDH, which presented as fungal panniculitis masquerading as EN in a renal allograft recipient 25 years after transplantation. We discuss the clinical, histopathological, and microbiological characteristics of this rare complication, with focus on its distinction from EN. This case emphasizes the central role of biopsy in transplant recipients presenting with cutaneous lesions, and the importance of clinicopathologic correlation and complementary microbiological investigations.
PMCID: PMC3618553  PMID: 23331504
histoplasmosis; progressive disseminated histoplasmosis; solid organ transplantation; renal transplant; kidney transplant; erythema nodosum; fungal panniculitis; infective panniculitis; granulomatous panniculitis
21.  Evaluation of a Method for Nitrotyrosine Site Identification and Relative Quantitation Using a Stable Isotope-Labeled Nitrated Spike-In Standard and High Resolution Fourier Transform MS and MS/MS Analysis 
The overproduction of reactive oxygen and nitrogen species (ROS and RNS) can have deleterious effects in the cell, including structural and possible activity-altering modifications to proteins. Peroxynitrite is one such RNS that can result in a specific protein modification, nitration of tyrosine residues to form nitrotyrosine, and to date, the identification of nitrotyrosine sites in proteins continues to be a major analytical challenge. We have developed a method by which 15N-labeled nitrotyrosine groups are generated on peptide or protein standards using stable isotope-labeled peroxynitrite (O15NOO−), and the resulting standard is mixed with representative samples in which nitrotyrosine formation is to be measured by mass spectrometry (MS). Nitropeptide MS/MS spectra are filtered using high mass accuracy Fourier transform MS (FTMS) detection of the nitrotyrosine immonium ion. Given that the nitropeptide pair is co-isolated for MS/MS fragmentation, the nitrotyrosine immonium ions (at m/z = 181 or 182) can be used for relative quantitation with negligible isotopic interference at a mass resolution of greater than 50,000 (FWHM, full width at half-maximum). Furthermore, the standard potentially allows for the increased signal of nitrotyrosine-containing peptides, thus facilitating selection for MS/MS in a data-dependent mode of acquisition. We have evaluated the methodology in terms of nitrotyrosine site identification and relative quantitation using nitrated peptide and protein standards.
PMCID: PMC4013627  PMID: 24736779
nitration; oxidative stress; immonium ion; high resolution mass spectrometry; liquid chromatography (LC)-MS/MS; FTMS
22.  Incidence of invasive aspergillosis following remission–induction chemotherapy for acute leukemia: a retrospective cohort study in a single Canadian tertiary care centre 
CMAJ Open  2014;2(2):E86-E93.
The decision to use universal primary antimould prophylaxis to prevent invasive aspergillosis in patients with acute leukemia depends on the incidence of infection at individual centres. We determined our institution’s incidence of invasive aspergillosis among patients who received remission–induction chemotherapy for acute leukemia to evaluate the potential benefits of primary antimould prophylaxis.
We conducted this retrospective cohort study at a Canadian tertiary care centre. From the central pharmacy registries, we retrieved records for all adult patients for whom remission–induction chemotherapy for acute leukemia was prescribed between 2008 and 2010. We retrieved clinical, microbiologic, pathologic and radiologic data from the patients’ medical charts. The primary outcome was a diagnosis of probable or proven invasive aspergillosis up to 180 days after resolution of aplasia.
We retrieved records for 123 patients with acute leukemia. Twenty-two of these patients did not receive the prescribed chemotherapy and were excluded from the analysis. Of the 101 patients included, 77 (76.2%) had acute myeloid leukemia. Overall, 136 courses of chemotherapy were administered, with more than 1 course administered to 26 (25.7%) of the 101 patients. In 9 of the patients (8.9%; 95% confidence interval 4.2%–16.2%), invasive aspergillosis was diagnosed (3 proven and 6 probable cases) a median of 19 (range 11–34) days after initiation of chemotherapy. In 7 (78%) of these 9 patients, invasive aspergillosis occurred during the first course of chemotherapy. Three patients died within the first year after diagnosis of invasive aspergillosis.
We found a high incidence (8.9%) of invasive aspergillosis at our centre. This finding triggered the introduction of targeted antimould prophylaxis for patients with acute leukemia who were undergoing remission–induction chemotherapy.
PMCID: PMC4114061  PMID: 25077134
23.  Interlaboratory studies and initiatives developing standards for proteomics 
Proteomics  2013;13(6):10.1002/pmic.201200532.
Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This view-point article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG).
PMCID: PMC3863631  PMID: 23319436
LC-MS/MS; Mass spectrometry-based proteomics; Phosphopeptides; Post-translational modifications; Protein identification
24.  Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex 
Mobile DNA  2014;5:1.
Transposable elements (TEs) play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. The population dynamics and distribution of TEs are influenced by their mode of transposition, the availability of niches in host genomes, and host population dynamics. Theories predict an increase in the number of TE insertions following hybridization or polyploidization. Evolution of TEs in hybrids and polyploids has mostly been studied in plants; few studies have examined the impacts of hybridization and/or polyploidization on TEs in animals. Hybrids and polyploids have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex.
The polymorphism of Pokey insertion sites did not depend solely on either the ploidy level or the genetic background of their host; therefore, it may be the result of interactions between these parameters and other parameters such as Pokey activity, selection and/or drift. No significant effect of ploidy level was found on the number of Pokey insertions using TE display and qPCR. However, the load of Pokey insertion sites and the number of unique insertion sites were slightly (but not significantly) higher in polyploids than in diploids.
These results suggest a lack of increase in the number of Pokey insertions following polyploidization but higher availability of Pokey insertion sites in polyploids than in diploids. Compared to previous TE display and qPCR results, the load of Pokey insertions in hybrid diploids was higher than in non-hybrid sexual and asexual diploids, which suggests an increase in the density of Pokey insertions following hybridization.
PMCID: PMC3882798  PMID: 24382139
Daphnia pulex; Hybrids; Insertion site polymorphism; Load; Pokey; Polyploids; Transposable element
25.  Poleward Expansion of the White-Footed Mouse (Peromyscus leucopus) under Climate Change: Implications for the Spread of Lyme Disease 
PLoS ONE  2013;8(11):e80724.
The white-footed mouse (Peromyscus leucopus) is an important reservoir host for Borrelia burgdorferi, the pathogen responsible for Lyme disease, and its distribution is expanding northward. We used an Ecological Niche Factor Analysis to identify the climatic factors associated with the distribution shift of the white-footed mouse over the last 30 years at the northern edge of its range, and modeled its current and potential future (2050) distributions using the platform BIOMOD. A mild and shorter winter is favouring the northern expansion of the white-footed mouse in Québec. With more favorable winter conditions projected by 2050, the distribution range of the white-footed mouse is expected to expand further northward by 3° latitude. We also show that today in southern Québec, the occurrence of B. burgdorferi is associated with high probability of presence of the white-footed mouse. Changes in the distribution of the white-footed mouse will likely alter the geographical range of B. burgdorferi and impact the public health in northern regions that have yet to be exposed to Lyme disease.
PMCID: PMC3832455  PMID: 24260464

Results 1-25 (147)