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1.  Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge 
Microbiome  2014;2:22.
The bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs). Our study represents the first survey of the nasopharynx during a known, controlled viral challenge. We aimed to gain a better understanding of the composition and dynamics of the nasopharyngeal microbiome during viral infection.
Rhinovirus illnesses were induced by self-inoculation using the finger to nose or eye natural transmission route in ten otherwise healthy young adults. Nasal lavage fluid samples (NLF) samples were collected at specific time points before, during, and following experimental rhinovirus inoculation. Bacterial DNA from each sample (N = 97 from 10 subjects) was subjected to 16S rRNA sequencing by amplifying the V1-V2 hypervariable region followed by sequencing using the 454-FLX platform.
This survey of the nasopharyngeal microbiota revealed a highly complex microbial ecosystem. Taxonomic composition varied widely between subjects and between time points of the same subject. We also observed significantly higher diversity in not infected individuals compared to infected individuals. Two genera – Neisseria and Propionibacterium – differed significantly between infected and not infected individuals. Certain phyla, including Firmicutes, Actinobacteria, and Proteobacteria, were detected in all samples.
Our results reveal the complex and diverse nature of the nasopharyngeal microbiota in both healthy and viral-challenged adults. Although some phyla were common to all samples, differences in levels of diversity and selected phyla were detected between infected and uninfected participants. Deeper, species-level metagenomic sequencing in a larger sample is warranted.
PMCID: PMC4098959  PMID: 25028608
Microbiota; nasopharynx; longitudinal; sequencing; rhinovirus illness
2.  Predictors of Adherence to Home Rehabilitation Exercises Following Anterior Cruciate Ligament Reconstruction 
Rehabilitation psychology  2013;58(1):64-72.
Although home exercises are commonly prescribed following anterior cruciate ligament (ACL) reconstruction and are considered important in obtaining successful rehabilitation outcomes, little is known about factors associated with the completion of such exercises. Consequently, this study was designed to identify predictors of adherence to home rehabilitation exercises after ACL surgery.
Research Method/Design
Participants (33 women, 58 men) completed indices of athletic identity, neuroticism, optimism, and pessimism before ACL surgery and measures of daily pain, negative mood, stress, and home exercise completion for 42 days postoperatively.
Participants reported a high level of adherence to the prescribed regimen. Home exercise completion increased significantly over time as the number of sets of prescribed home exercises declined. Personal factors were not predictive of home exercise completion. Participants completed fewer home exercises on days when they experienced more stress or negative mood.
Day-to-day variations in negative mood and stress may contribute to adherence to prescribed home exercises.
PMCID: PMC4045843  PMID: 23438001
compliance; knee; surgery; psychology
3.  Nomenclature for alleles of the thiopurine methyltransferase gene 
Pharmacogenetics and genomics  2013;23(4):242-248.
The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors’ articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website ( serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G > A) from TPMT*24 to TPMT*30 and position 611 (T > C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged.
PMCID: PMC3727893  PMID: 23407052
allele; nomenclature; pharmacogenetics; thiopurine methyltransferase
4.  Select Neurocognitive Impairment in HIV-Infected Women: Associations with HIV Viral Load, Hepatitis C Virus, and Depression, but Not Leukocyte Telomere Length 
PLoS ONE  2014;9(3):e89556.
Through implementation of combination antiretroviral therapy (cART) remarkable gains have been achieved in the management of HIV infection; nonetheless, the neurocognitive consequences of infection remain a pivotal concern in the cART era. Research has often employed norm-referenced neuropsychological scores, derived from healthy populations (excluding many seronegative individuals at high risk for HIV infection), to characterize impairments in predominately male HIV-infected populations.
Using matched-group methodology, we assessed 81 HIV-seropositive (HIV+) women with established neuropsychological measures validated for detection of HIV-related impairments, as well as additional detailed tests of executive function and decision-making from the Cambridge Neuropsychological Test Automated Battery (CANTAB).
On validated tests, the HIV+ women exhibited impairments that were limited to significantly slower information processing speed when compared with 45 HIV-seronegative (HIV−) women with very similar demographic backgrounds and illness comorbidities. Additionally, select executive impairments in shifting attention (i.e., reversal learning) and in decision-making quality were revealed in HIV+ participants. Modifiers of neurocognition in HIV-infected women included detectable HIV plasma viral load, active hepatitis C virus co-infection, and self-reported depression symptoms. In contrast, leukocyte telomere length (LTL), a marker of cellular aging, did not significantly differ between HIV+ and HIV− women, nor was LTL associated with overall neurocognition in the HIV+ group.
The findings suggest that well-managed HIV infection may entail a more circumscribed neurocognitive deficit pattern than that reported in many norm-referenced studies, and that common comorbidities make a secondary contribution to HIV-related neurocognitive impairments.
PMCID: PMC3942358  PMID: 24595021
5.  Impaired musical ability in people with schizophrenia 
Assessment of the musical ability of people with schizophrenia has attracted little interest despite the diverse and substantive findings of impairments in sound perception and processing and the therapeutic effect of music in people with the illness. The present study investigated the musical ability of people with schizophrenia and the association with psychiatric symptoms and cognition.
We recruited patients with chronic schizophrenia and healthy controls for participation in our study. To measure musical ability and cognitive function, we used the Montreal Battery of Evaluation of Amusia (MBEA) and the Brief Assessment of Cognition in Schizophrenia (BACS). We carried out a mediation analysis to investigate a possible pathway to a deficit in musical ability.
We enrolled 50 patients and 58 controls in the study. The MBEA global score in patients with schizophrenia was significantly lower than that in controls (p < 0.001), and was strongly associated with both the composite cognitive function score (r = 0.645, p < 0.001) and the negative symptom score (r = −0.504, p < 0.001). Further analyses revealed direct and indirect effects of negative symptoms on musical ability. The indirect effects were mediated through cognitive impairment.
The relatively small sample size did not permit full evaluation of the possible effects of age, sex, education, medication and cultural influences on the results.
Examining the associations between musical deficits, negative symptoms and cognitive imapirment in patients with schizophrenia may identify shared biological mechanisms.
PMCID: PMC3937280  PMID: 24119791
6.  Identification of Cinnabarinic Acid as a Novel Endogenous Aryl Hydrocarbon Receptor Ligand That Drives IL-22 Production 
PLoS ONE  2014;9(2):e87877.
The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.
PMCID: PMC3912126  PMID: 24498387
7.  Personalized Risk Assessment of Drug-Related Harm Is Associated with Health Outcomes 
PLoS ONE  2013;8(11):e79754.
The Independent Scientific Committee on Drugs (ISCD) assigned quantitative scores for harm to 20 drugs. We hypothesized that a personalized, ISCD-based Composite Harm Score (CHS) would be associated with poor health outcomes in polysubstance users.
A prospective community sample (n=293) of adults living in marginal housing was assessed for substance use. The CHS was calculated based on the ISCD index, and the personal substance use characteristics over four weeks. Regression models estimated the association between CHS and physical, psychological, and social health outcomes.
Polysubstance use was pervasive (95.8%), as was multimorbid illness (median 3, possible range 0–12). The median CHS was 2845 (interquartile range 1865–3977). Adjusting for age and sex, every 1000-unit CHS increase was associated with greater mortality (odds ratio [OR] 1.47, 95% confidence interval [CI] 1.07–2.01, p = 0.02), and persistent hepatitis C infection (OR 1.29, 95% CI 1.02–1.67, p = 0.04). The likelihood of substance-induced psychosis increased 1.39-fold (95% CI 1.13–1.67, p = 0.001). The amount spent on drugs increased 1.51-fold (1.40–1.62, p < 0.001) and the odds of having committed a crime increased 1.74-fold (1.46–2.10, p < 0.001). Multimorbid illness increased 1.43-fold (95% CI 1.26–1.63, p < 0.001).
Greater CHS predicts poorer physical, psychological, and social health, and may be a useful quantitative, personalized measure of risk for drug-related harm.
PMCID: PMC3819243  PMID: 24223192
8.  Indoor tanning and risk of early-onset basal cell carcinoma 
Despite a rise in incidence of basal cell carcinoma (BCC) among young people and the ubiquity of indoor tanning in this population, few epidemiologic studies have investigated this exposure-disease relationship.
Evaluate the association between indoor tanning and early-onset BCC.
BCC cases (n=376) and controls with minor benign skin conditions (n=390) under age 40 were identified through Yale Dermatopathology. Participants provided information on ever indoor tanning, age of initiation, frequency, duration, burns while tanning, and type of tanning device during an in-person interview. We calculated odds ratios (OR) and 95% confidence intervals (CI) using multivariate logistic regression with never indoor tanners as the referent group.
Ever indoor tanning was associated with a 69% increased risk of early-onset BCC (95% CI=1.15-2.48). This association was stronger among women (OR=2.14, 95% CI=1.31-3.47), for multiple BCCs (OR=2.16, 95% CI=1.26-3.70), and for BCCs on the trunk and extremities (OR=2.81, 95% CI=1.57-5.02). Risk increased dose-dependently with years used regular indoor tanning devices (p-trend=0.003), number of overall burns (p-trend=<0.001) and burns to biopsy site (p-trend=<0.001) from indoor tanning. Approximately one-quarter (27%) of early-onset BCCs (or 43% among women) could be prevented if individuals never tanned indoors.
Potential recall bias of indoor tanning by cases and generalizability of the control population suggest replication in other studies is warranted.
Indoor tanning was a strong risk factor for early-onset BCC, particularly among women. Indoor tanning should continue to be targeted by both policy-based and behavioral interventions, as the impact on BCC-associated morbidity may be substantial.
PMCID: PMC3307842  PMID: 22153793
basal cell carcinoma; epidemiology; indoor tanning; case-control; skin cancer; risk factors
9.  Beneficial Effects of Autologous Bone Marrow-Derived Mesenchymal Stem Cells in Naturally Occurring Tendinopathy 
PLoS ONE  2013;8(9):e75697.
Tendon injuries are a common age-related degenerative condition where current treatment strategies fail to restore functionality and normal quality of life. This disease also occurs naturally in horses, with many similarities to human tendinopathy making it an ideal large animal model for human disease. Regenerative approaches are increasingly used to improve outcome involving mesenchymal stem cells (MSCs), supported by clinical data where injection of autologous bone marrow derived MSCs (BM-MSCs) suspended in marrow supernatant into injured tendons has halved the re-injury rate in racehorses. We hypothesized that stem cell therapy induces a matrix more closely resembling normal tendon than the fibrous scar tissue formed by natural repair. Twelve horses with career-ending naturally-occurring superficial digital flexor tendon injury were allocated randomly to treatment and control groups. 1X107 autologous BM-MSCs suspended in 2 ml of marrow supernatant were implanted into the damaged tendon of the treated group. The control group received the same volume of saline. Following a 6 month exercise programme horses were euthanized and tendons assessed for structural stiffness by non-destructive mechanical testing and for morphological and molecular composition.
BM-MSC treated tendons exhibited statistically significant improvements in key parameters compared to saline-injected control tendons towards that of normal tendons and those in the contralateral limbs. Specifically, treated tendons had lower structural stiffness (p<0.05) although no significant difference in calculated modulus of elasticity, lower (improved) histological scoring of organisation (p<0.003) and crimp pattern (p<0.05), lower cellularity (p<0.007), DNA content (p<0.05), vascularity (p<0.03), water content (p<0.05), GAG content (p<0.05), and MMP-13 activity (p<0.02).
Treatment with autologous MSCs in marrow supernatant therefore provides significant benefits compared to untreated tendon repair in enhancing normalisation of biomechanical, morphological, and compositional parameters. These data in natural disease, with no adverse findings, support the use of this treatment for human tendon injuries.
PMCID: PMC3783421  PMID: 24086616
10.  Integration-specific In Vitro Evaluation of Lentivirally Transduced Rhesus CD34+ Cells Correlates With In Vivo Vector Copy Number 
Hematopoietic stem cell (HSC) gene therapy using integrating vectors has a potential leukemogenic risk due to insertional mutagenesis. To reduce this risk, a limitation of ≤2 average vector copy number (VCN) per cell is generally accepted. We developed an assay for VCN among transduced CD34+ cells that reliably predicts in vivo VCN in 16 rhesus recipients of CD34+ cells transduced with a green fluorescent protein (GFP) (or yellow fluorescent protein (YFP))-encoding lentiviral vector. Using GFP (or YFP)-specific probe/primers by real-time PCR, VCN among transduced CD34+ cells had no correlation with VCN among granulocytes or lymphocytes in vivo assayed 6 months post-transplantation. This was a likely result of residual plasmids present in the vector preparation. We then designed self-inactivating long terminal repeat (SIN-LTR)-specific probe/primers, which detect only integrated provirus. Evaluation with SIN-LTR probe/primers resulted in a positive correlation of VCN among transduced CD34+ cells with granulocytes and lymphocytes in vivo. The transduced CD34+ cells had higher VCN (25.1 ± 5.6) as compared with granulocytes (2.8 ± 1) and lymphocytes (2.4 ± 0.7). In summary, an integrated provirus-specific real-time PCR system demonstrated nine- to tenfold higher VCN in transduced CD34+ cells in vitro, as compared with VCN in vivo. Therefore, the restriction of ≤2 VCN before infusion might unnecessarily limit gene transfer efficacy.
PMCID: PMC4098567  PMID: 24045711
CD34+ cells; hematopoietic stem cell transplantation; large animal model; lentiviral vector
11.  Increased Immune Gene Expression and Immune Cell Infiltration in High Grade Astrocytoma Distinguish Long from Short-Term Survivors 
Survival in the majority of high grade astrocytoma (HGA) patients is very poor, with only a rare population of long-term survivors. A better understanding of the biological factors associated with long-term survival in HGA would aid development of more effective therapy and survival prediction. Factors associated with long-term survival have not been extensively studied using unbiased genome-wide expression analyses. In the present study, gene expression microarray profiles of HGA from long-term survivors were interrogated for discovery of survival-associated biological factors. Ontology analyses revealed that increased expression of immune function-related genes was the predominant biological factor that positively correlated with longer survival. A notable T-cell signature was present within this prognostic immune gene-set. Using immune cell-specific gene classifiers, both T-cell and myeloid linage-associated genes were shown to be enriched in HGA from long versus short-term survivors. Association of immune function and cell-specific genes with survival was confirmed independently in a larger publicly available glioblastoma gene expression microarray dataset. Histology was used to validate the results of microarray analyses in a larger cohort of long-term survivors of HGA. Multivariate analyses demonstrated that increased immune cell infiltration was a significant independent variable contributing to longer survival, as was Karnofsky/Lansky performance score. These data provide evidence of a prognostic anti-tumor adaptive immune response and rationale for future development of immunotherapy in HGA.
PMCID: PMC3411857  PMID: 22802421
12.  Relationship of Tc-99m Tetrofosmin Gated Rest SPECT Myocardial Perfusion Imaging to Death and Hospitalization in Heart Failure Patients: Results from the Nuclear Ancillary Study of the HF-ACTION Trial 
American heart journal  2011;161(6):1038-1045.
We hypothesized that the severity of resting perfusion abnormalities assessed by the summed rest score (SRS) would be associated with a higher rate of adverse outcomesin patients with heart failure (HF) and reduced left ventricular (LV) ejection fraction (EF).
A subset of 240 subjects from HF-ACTION underwent resting Tc99m tetrofosmin gated single photon emission computed tomography (SPECT) myocardial perfusion imaging(MPI). Images were evaluated using a 17-segment model to derive the SRS and additional nuclear variables.
After adjusting for pre-specified covariates, SRS was significantly associated with the primary endpoint (hazard ratio [HR] 0.98; 95% confidence interval [CI] 0.97–1.00, P=0.04), with a higher SRS corresponding to lower risk of an event. This association was not present in the unadjusted analysis. The relationship between SRS and the primary outcome was likely due to a higher event ratein patients with ischemic HF and a low SRS. The LV phase standard deviation (SD) was not predictive of the primary outcome (HR 1.00; 95% CI 0.99–1.01, P=0.49). In a post hoc analysis, nuclear variables provided incremental prognostic information when added to clinical information (P=0.006).
Gated SPECT MPI provides important information in patients with HF and reduced LVEF. In the adjusted analysis, SRS has an unexpected relationship with the primary endpoint. Phase SD was not associated with the primary endpoint. Rest gated SPECT MPI provides incrementally greater prognostic information than clinical information alone.
PMCID: PMC3739977  PMID: 21641348
heart failure; SPECT; outcomes; coronary artery disease; cardiomyopathy
13.  Detection of early FXTAS motor symptoms using the CATSYS computerised neuromotor test battery 
Journal of medical genetics  2008;45(5):290-297.
Carriers of the FMR1 premutation allele are at a significantly increased risk for a late-onset neurodegenerative disorder, fragile X-associated tremor/ataxia syndrome (FXTAS). This disorder is distinct from fragile X syndrome (FXS) in its molecular aetiology and clinical presentation. The primary features of FXTAS are late-onset intention tremor and gait ataxia. Associated features include parkinsonism, neuropsychological dysfunction, autonomic dysfunction and peripheral neuropathy.
To investigate the usefulness of a quantitative neurological test battery implemented through the CATSYS instrument to identify preclinical symptoms of FXTAS.
Both premutation carriers with 70–199 repeats (62 men) and their low-repeat allele carrier siblings (27 men), identified through families with an individual affected with FXS, were tested.
As expected, because of its sensitivity, use of the instrument allowed identification of tremor in 23% of men who had not self-reported tremor, and ataxia in 30% of men who had not self-reported ataxia. Among subjects with self-reported tremor and ataxia, we found significant concordance between measures of the CATSYS system and the self-report.
Rates of these traits among premutation carriers and low-repeat allele carrier siblings could be identified, and are presented in this paper, along with the minimum estimates of age-related prevalence.
PMCID: PMC3696494  PMID: 18234731
14.  Droplet-Based Pyrosequencing Using Digital Microfluidics 
Analytical chemistry  2011;83(22):8439-8447.
The feasibility of implementing pyrosequencing chemistry within droplets using electrowetting-based digital microfluidics is reported. An array of electrodes patterned on a printed-circuit board was used to control the formation, transportation, merging, mixing, and splitting of submicroliter-sized droplets contained within an oil-filled chamber. A three-enzyme pyrosequencing protocol was implemented in which individual droplets contained enzymes, deoxyribonucleotide triphosphates (dNTPs), and DNA templates. The DNA templates were anchored to magnetic beads which enabled them to be thoroughly washed between nucleotide additions. Reagents and protocols were optimized to maximize signal over background, linearity of response, cycle efficiency, and wash efficiency. As an initial demonstration of feasibility, a portion of a 229 bp Candida parapsilosis template was sequenced using both a de novo protocol and a resequencing protocol. The resequencing protocol generated over 60 bp of sequence with 100% sequence accuracy based on raw pyrogram levels. Excellent linearity was observed for all of the homopolymers (two, three, or four nucleotides) contained in the C. parapsilosis sequence. With improvements in microfluidic design it is expected that longer reads, higher throughput, and improved process integration (i.e., “sample-to-sequence” capability) could eventually be achieved using this low-cost platform.
PMCID: PMC3690483  PMID: 21932784
15.  Immunogenicity and clinical protection against equine influenza by gene-based DNA vaccination of ponies 
Vaccine  2012;30(26):3965-3974.
Equine influenza A (H3N8) virus is a leading cause of infectious respiratory disease in horses causing widespread morbidity and economic losses. As with influenza in other species, equine influenza strains continuously mutate, requiring constant re-evaluation of current vaccines and development of new vaccines. Current inactivated (killed) vaccines, while efficacious, only offer limited protection against multiple strains and require frequent boosts. Ongoing research into new vaccine technologies, including gene-based vaccines, aims to increase the neutralization potency, breadth, and duration of protective immunity of new or existing vaccines. In these hypothesis-generating experiments, we demonstrate that a DNA vaccine expressing the hemagglutinin protein of equine H3N8 influenza virus generates homologous and heterologous immune responses, and protects against clinical disease and viral replication following homologous H3N8 infection in horses. Furthermore, we demonstrate that a needle-free delivery device is as efficient and effective as conventional parenteral injection using a needle and syringe. The observed trends in this study drive the hypothesis that DNA vaccines offer a safe, effective, and promising alternative approach for veterinary vaccines against influenza, and applicable to combat equine influenza.
PMCID: PMC3474358  PMID: 22449425
Influenza; Equine; DNA Vaccine; Immunogenicity; Protection
16.  A Variant in the Glucokinase Regulatory Protein (GCKR) Gene is Associated with Fatty Liver in Obese Children and Adolescents 
Hepatology (Baltimore, Md.)  2011;55(3):781-789.
Recently the SNP identified as rs1260326, in the glucokinase regulatory protein (GCKR) was associated with hypertriglyceridemia in adults. Since accumulation of triglycerides in hepatocytes represents the hallmark of the steatosis, we aimed to investigate whether this variant might be associated with fatty liver (hepatic fat content, HFF%). Moreover, since recently rs738409 in the PNPLA3 and rs2854116 in the APOC3 were associated with fatty liver recently, we explored how the GCKR SNP and these two variants jointly influence hepatosteatosis.
Methods and Results
We studied 455 obese children and adolescents (181 Caucasians, 139 African Americans and 135 Hispanics). All underwent an OGTT and fasting lipoprotein subclasses measurement by proton NMR. A subset of 142 children underwent a fast gradient MRI to measure the HFF%.
The rs1260326 was associated with elevated triglycerides (Caucasians p=0.00014; African Americans p=0.00417) large VLDL (Caucasians p=0.001; African Americans p=0.03) and with fatty liver (Caucasians p= 0.034; African Americans p= 0.00002; and Hispanics p= 0.016). The PNPLA3, but not the APOC3 rs2854116 SNP, was associated with fatty liver but not with triglycerides levels. There was a joint effect between the PNPLA3 and GCKR SNPs, explaining 32% of HFF% variance Caucasians (p=0.00161), 39.0% in African Americans (p=0.00000496), and 15% in Hispanics (p=0.00342).
The rs1260326 in GCKR is associated with hepatic fat accumulation along with large VLDL, and triglycerides levels. GCKR and PNPLA3 act together to convey susceptibility to fatty liver in obese youths.
PMCID: PMC3288435  PMID: 22105854
GCKR; PNPLA3; SNPs; obesity; youths
17.  Functional and physical interaction between the mismatch repair and FA-BRCA pathways 
Human Molecular Genetics  2011;20(22):4395-4410.
Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure and an increased risk for leukemia and cancer. Fifteen proteins thought to function in the repair of DNA interstrand crosslinks (ICLs) comprise what is known as the FA-BRCA pathway. Activation of this pathway leads to the monoubiquitylation and chromatin localization of FANCD2 and FANCI. It has previously been shown that FANCJ interacts with the mismatch repair (MMR) complex MutLα. Here we show that FANCD2 interacts with the MMR proteins MSH2 and MLH1. FANCD2 monoubiquitylation, foci formation and chromatin loading are greatly diminished in MSH2-deficient cells. Human or mouse cells lacking MSH2 or MLH1 display increased sensitivity and radial formation in response to treatment with DNA crosslinking agents. Studies in human cell lines and Drosophila mutants suggest an epistatic relationship between FANCD2, MSH2 and MLH1 with regard to ICL repair. Surprisingly, the interaction between MSH2 and MLH1 is compromised in multiple FA cell lines, and FA cell lines exhibit deficient MMR. These results suggest a significant role for MMR proteins in the activation of the FA pathway and repair of ICLs. In addition, we provide the first evidence for a defect in MMR in FA cell lines.
PMCID: PMC3196888  PMID: 21865299
18.  Host phenotype characteristics and MC1R in relation to early-onset basal cell carcinoma 
Basal cell carcinoma (BCC) incidence is increasing, particularly among adults under age 40. Pigment-related characteristics are associated with BCC in older populations, but epidemiologic studies among younger individuals and analyses of phenotype-genotype interactions are limited. We examined self-reported phenotypes and melanocortin 1 receptor gene (MC1R) variants in relation to early-onset BCC. BCC cases (n=377) and controls with benign skin conditions (n=390) under age 40 were identified through Yale’s Dermatopathology database. Factors most strongly associated with early-onset BCC were skin reaction to first summer sun for one hour [severe sunburn vs. tan odds ratio (OR)=12.27, 95% confidence interval (CI)=4.08–36.94] and skin color (very fair vs. olive OR=11.06, 95% CI=5.90–20.74). Individuals with two or more MC1R non-synonymous variants were 3.59 times (95% CI=2.37–5.43) more likely to have BCC than those without non-synonymous variants. All host characteristics and MC1R were more strongly associated with multiple BCC cases status (37% of cases) than single BCC case status. MC1R, number of moles, skin reaction to first summer sun for one hour, and hair and skin color were independently associated with BCC. BCC risk conferred by MC1R tended to be stronger among those with darker pigment phenotypes, traditionally considered to be at low-risk of skin cancer.
PMCID: PMC3305835  PMID: 22158557
19.  Differential Acetylcholine Release in the Prefrontal Cortex and Hippocampus During Pavlovian Trace and Delay Conditioning 
Pavlovian trace conditioning critically depends on the medial prefrontal cortex (mPFC) and hippocampus (HPC), whereas delay conditioning does not depend on these brain structures. Given that the cholinergic basal forebrain system modulates activity in both the mPFC and HPC, it was reasoned that the level of acetylcholine (ACh) release in these regions would show distinct profiles during testing in trace and delay conditioning paradigms. To test this assumption, microdialysis probes were implanted unilaterally into the mPFC and HPC of rats that were pre-trained in appetitive trace and delay conditioning paradigms using different conditional stimuli in the two tasks. On the day of microdialysis testing, dialysate samples were collected during a quiet baseline interval before trials were initiated, and again during performance in separate blocks of trace and delay conditioning trials in each animal. ACh levels were quantified using high performance liquid chromatography and electrochemical detection techniques. Consistent with our hypothesis, results showed that ACh release in the mPFC was greater during trace conditioning than during delay conditioning. The level of ACh released during trace conditioning in the HPC was also greater than the levels observed during delay conditioning. While ACh efflux in both the mPFC and HPC selectively increased during trace conditioning, ACh levels in the mPFC during trace conditioning testing showed the greatest increases observed. These results demonstrate a dissociation in cholinergic activation of the mPFC and HPC during performance in trace but not delay appetitive conditioning, where this cholinergic activity may contribute to attentional mechanisms, adaptive response timing, or memory consolidation necessary for successful trace conditioning.
PMCID: PMC3148348  PMID: 21514394
microdialysis; attention; cholinergic system; nucleus basalismagnocellularis; medial septal area
20.  A New Real-Time PCR Assay for Improved Detection of the Parasite Babesia microti 
Journal of Clinical Microbiology  2012;50(3):903-908.
Babesiosis is an emerging zoonosis with important public health implications, as the incidence of the disease has risen dramatically over the past decade. Because the current gold standard for detection of Babesia is microscopic examination of blood smears, accurate identification requires trained personnel. Species in the genus cannot be distinguished microscopically, and Babesia can also be confused with the early trophozoite stage (ring forms) of Plasmodium parasites. To allow more accurate diagnosis in a format that is accessible to a wider variety of laboratories, we developed a real-time PCR assay targeting the 18S rRNA gene of Babesia microti, the dominant babesiosis pathogen in the United States. The real-time PCR is performed on DNA extracted from whole-blood specimens and detects Babesia microti with a limit of detection of ∼100 gene copies in 5 μl of blood. The real-time PCR assay was shown to be 100% specific when tested against a panel of 24 organisms consisting of Babesia microti, other Babesia species, Plasmodium species, tick-borne and other pathogenic bacteria, and other blood-borne parasites. The results using clinical specimens show that the assay can detect infections of lower parasitemia than can be detected by microscopic examination. This method is therefore a rapid, sensitive, and accurate method for detection of Babesia microti in patient specimens.
PMCID: PMC3295123  PMID: 22170915
21.  Intra-individual stability over time of standardized anti-Müllerian hormone in FMR1 premutation carriers 
Human Reproduction (Oxford, England)  2011;26(8):2185-2191.
Carriers of a premutation (CGG repeat length 55–200) in the fragile X mental retardation (FMR1) gene are at risk for primary ovarian insufficiency (FXPOI). The anti-Müllerian hormone (AMH) level acts as a useful marker of ovarian follicle reserve and, thus, may serve to predict when this ovarian reserve becomes too low to sustain ovarian function. We investigated the intra-individual variation of AMH levels over time for premutation carriers compared with non-carriers.
We determined AMH levels in blood samples from 240 women ascertained through fragile X families, of which 127 were premutation carriers and 113 were non-carriers. Linear mixed models were used to assess the effect of age and premutation status on AMH levels and to determine a modeled AMH value. The stability over time of the deviation of observed AMH levels from modeled levels, referred to as standardized AMH values, was assessed through correlation coefficients of 41 longitudinal samples.
At all ages, premutation carriers exhibited lower AMH levels. For all women, AMH was found to decrease by 10% per year. The added effect of having a premutation decreased AMH levels by 54%. The deviation of an individual's AMH level from the modeled value showed a reasonable intra-individual correlation. The Pearson correlation coefficient of two samples taken at different ages was 0.36 (P = 0.05) for non-carriers and 0.69 (P = 0.01) for carriers.
We developed a unique standardized AMH value, taking FMR1 premutation status and the subject's age into account, which appears to be stable over time and may serve as a predictor for FXPOI after further longitudinal assessment.
PMCID: PMC3137386  PMID: 21576079
anti-Müllerian hormone (AMH); premutation carriers; FMR1 gene; fragile X-associated primary ovarian insufficiency (FXPOI); ovarian reserve
22.  Accelerated Lymphocyte Reconstitution and Long-Term Recovery Following Transplantation of Lentiviral Transduced Rhesus CD34+ Cells Mobilized by G-CSF and Plerixafor 
Experimental hematology  2011;39(7):795-805.
Granulocyte colony-stimulating factor (G-CSF) in combination with plerixafor produces significant mobilization of CD34+ cells in rhesus macaques. We sought to evaluate whether these CD34+ cells can stably reconstitute blood cells with lentiviral gene marking.
We performed hematopoietic stem cell (HSC) transplantation using G-CSF and plerixafor-mobilized rhesus CD34+ cells transduced with a lentiviral vector, and these data were compared to those of G-CSF and stem cell factor (SCF) mobilization.
G-CSF and plerixafor mobilization resulted in CD34+ cell yields that were 2-fold higher than yields with G-CSF and SCF. CD123 (IL-3 receptor) expression was greater in G-CSF and plerixafor-mobilized CD34+ cells when compared to G-CSF alone. Animals transplanted with G-CSF and plerixafor-mobilized cells showed engraftment of all lineages, similar to animals who received G-CSF and SCF-mobilized grafts. Lymphocyte engraftment was accelerated in animals receiving the G-CSF and plerixafor-mobilized CD34+ cells. One animal in the G-CSF and plerixafor group developed cold agglutinin associated skin rash during the first 3 months of rapid lymphocyte recovery. One year after transplantation, all animals had 2–10% transgene expression in all blood cell lineages.
G-CSF and plerixafor-mobilized CD34+ cells accelerate lymphocyte engraftment and contain HSC capable of reconstituting multi-lineage blood cells. These findings indicate important differences to consider in plerixafor based HSC mobilization protocols in rhesus macaques.
PMCID: PMC3143244  PMID: 21549175
hematopoietic stem cell transplantation; hematopoietic stem cell mobilization; lentivirus vector
23.  Polychlorinated Biphenyl (PCB) Exposure and Diabetes: Results from the Anniston Community Health Survey 
Environmental Health Perspectives  2012;120(5):727-732.
Background: Polychlorinated biphenyls (PCBs) manufactured in Anniston, Alabama, from 1929 to 1971 caused significant environmental contamination. The Anniston population remains one of the most highly exposed in the world.
Objectives: Reports of increased diabetes in PCB-exposed populations led us to examine possible associations in Anniston residents.
Methods: Volunteers (n = 774) from a cross-sectional study of randomly selected households and adults who completed the Anniston Community Health Survey also underwent measurements of height, weight, fasting glucose, lipid, and PCB congener levels and verification of medications. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the relationships between PCBs and diabetes, adjusting for diabetes risk factors. Participants with prediabetes were excluded from the logistic regression analyses.
Results: Participants were 47% African American, 70% female, with a mean age of 54.8 years. The prevalence of diabetes was 27% in the study population, corresponding to an estimated prevalence of 16% for Anniston overall; the PCB body burden of 35 major congeners ranged from 0.11 to 170.42 ppb, wet weight. The adjusted OR comparing the prevalence of diabetes in the fifth versus first quintile of serum PCB was 2.78 (95% CI: 1.00, 7.73), with similar associations estimated for second through fourth quintiles. In participants < 55 years of age, the adjusted OR for diabetes for the highest versus lowest quintile was 4.78 (95% CI: 1.11, 20.6), whereas in those ≥ 55 years of age, we observed no significant associations with PCBs. Elevated diabetes prevalence was observed with a 1 SD increase in log PCB levels in women (OR = 1.52; 95% CI: 1.01, 2.28); a decreased prevalence was observed in men (OR = 0.68; 95% CI: 0.33, 1.41).
Conclusions: We observed significant associations between elevated PCB levels and diabetes mostly due to associations in women and in individuals < 55 years of age.
PMCID: PMC3346783  PMID: 22334129
diabetes; epidemiology; polychlorinated biphenyls (PCBs); POPs
24.  Lifetime history of indoor tanning in young people: a retrospective assessment of initiation, persistence, and correlates 
BMC Public Health  2012;12:118.
Despite educational and public health campaigns to convey the risks of indoor tanning, many individuals around the world continue to engage in this behavior. Few descriptive studies of indoor tanning have collected information pertaining to the lifetime history of indoor tanning, thereby limiting our ability to understand indoor tanning patterns and potentially target interventions for individuals who not only initiate, but continue to persistently engage in indoor tanning.
In-person interviews elicited detailed retrospective information on lifetime history of indoor tanning among white individuals (n = 401) under age 40 seen by a dermatologist for a minor benign skin condition. These individuals were controls in a case-control study of early-onset basal cell carcinoma. Outcomes of interest included ever indoor tanning in both males and females, as well as persistent indoor tanning in females - defined as females over age 31 who tanned indoors at least once in the last three or all four of four specified age periods (ages 11-15, 16-20, 21-30 and 31 or older). Multivariate logistic regression was used to identify sociodemographic and lifestyle correlates of ever and persistent indoor tanning in females.
Approximately three-quarters (73.3%) of females and 38.3% of males ever tanned indoors, with a median age of initiation of 17.0 and 21.5, respectively. Among indoor tanners, 39.3% of females and 21.7% of males reported being burned while indoor tanning. Female ever indoor tanners were younger, had darker color eyes, and sunbathed more frequently than females who never tanned indoors. Using unique lifetime exposure data, 24.7% of female indoor tanners 31 and older persistently tanned indoors starting as teenagers. Female persistent indoor tanners drank significantly more alcohol, were less educated, had skin that tanned with prolonged sun exposure, and sunbathed outdoors more frequently than non-persistent tanners.
Indoor tanning was strikingly common in this population, especially among females. Persistent indoor tanners had other high-risk behaviors (alcohol, sunbathing), suggesting that multi-faceted behavioral interventions aimed at health promotion/disease prevention may be needed in this population.
PMCID: PMC3340300  PMID: 22324969
Indoor tanning; Correlates; Epidemiology; Skin cancer prevention
25.  Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype 
G3: Genes|Genomes|Genetics  2012;2(2):279-286.
Basal cell carcinomas (BCCs) are the most common cancers in the United States. The histologic appearance distinguishes several subtypes, each of which can have a different biologic behavior. In this study, global miRNA expression was quantified by high-throughput sequencing in nodular BCCs, a subtype that is slow growing, and infiltrative BCCs, aggressive tumors that extend through the dermis and invade structures such as cutaneous nerves. Principal components analysis correctly classified seven of eight infiltrative tumors on the basis of miRNA expression. The remaining tumor, on pathology review, contained a mixture of nodular and infiltrative elements. Nodular tumors did not cluster tightly, likely reflecting broader histopathologic diversity in this class, but trended toward forming a group separate from infiltrative BCCs. Quantitative polymerase chain reaction assays were developed for six of the miRNAs that showed significant differences between the BCC subtypes, and five of these six were validated in a replication set of four infiltrative and three nodular tumors. The expression level of miR-183, a miRNA that inhibits invasion and metastasis in several types of malignancies, was consistently lower in infiltrative than nodular tumors and could be one element underlying the difference in invasiveness. These results represent the first miRNA profiling study in BCCs and demonstrate that miRNA gene expression may be involved in tumor pathogenesis and particularly in determining the aggressiveness of these malignancies.
PMCID: PMC3284335  PMID: 22384406
miR-150; miR-183; histopathology; skin cancer; expression profiling

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