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26.  The anti-inflammatory drug BAY 11-7082 suppresses the MyD88-dependent signalling network by targeting the ubiquitin system 
Biochemical Journal  2013;451(Pt 3):427-437.
The compound BAY 11-7082 inhibits IκBα [inhibitor of NF-κB (nuclear factor κB)α] phosphorylation in cells and has been used to implicate the canonical IKKs (IκB kinases) and NF-κB in >350 publications. In the present study we report that BAY 11-7082 does not inhibit the IKKs, but suppresses their activation in LPS (lipopolysaccharide)-stimulated RAW macrophages and IL (interleukin)-1-stimulated IL-1R (IL-1 receptor) HEK (human embryonic kidney)-293 cells. BAY 11-7082 exerts these effects by inactivating the E2-conjugating enzymes Ubc (ubiquitin conjugating) 13 and UbcH7 and the E3 ligase LUBAC (linear ubiquitin assembly complex), thereby preventing the formation of Lys63-linked and linear polyubiquitin chains. BAY 11-7082 prevents ubiquitin conjugation to Ubc13 and UbcH7 by forming a covalent adduct with their reactive cysteine residues via Michael addition at the C3 atom of BAY 11-7082, followed by the release of 4-methylbenzene-sulfinic acid. BAY 11-7082 stimulated Lys48-linked polyubiquitin chain formation in cells and protected HIF1α (hypoxia-inducible factor 1α) from proteasomal degradation, suggesting that it inhibits the proteasome. The results of the present study indicate that the anti-inflammatory effects of BAY 11-7082, its ability to induce B-cell lymphoma and leukaemic T-cell death and to prevent the recruitment of proteins to sites of DNA damage are exerted via inhibition of components of the ubiquitin system and not by inhibiting NF-κB.
PMCID: PMC3685219  PMID: 23441730
lymphoma; linear ubiquitin assembly complex (LUBAC); myeloid differentiation factor 88 (MyD88); nuclear factor κB (NF-κB); proteasome; ubiquitin conjugating 13 (Ubc13); DAPI, 4′,6-diamidino-2-phenylindole; DLBCL, diffuse large B-cell lymphoma; DMEM, Dulbecco’s modified Eagle’s medium; ERK, extracellular-signal-regulated kinase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFP, green fluorescent protein; HEK, human embryonic kidney; HIF1α, hypoxia-inducible factor 1α; HOIP, haem-oxidized IRP2 ligase-1-interacting protein; HRMS, high-resolution mass spectra; HTLV-1, human T-cell lymphotropic virus 1; IL, interleukin; IL-1R, IL-1 receptor; IRAK, IL-receptor-associated kinase; IκB, inhibitor of NF-κB; IKK, IκB kinase; JNK, c-Jun N-terminal kinase; K48-pUb, Lys48-linked polyubiquitin; K63-pUb, Lys63-linked polyubiquitin; LPS, lipopolysaccharide; LUBAC, linear ubiquitin assembly complex; MALDI–TOF, matrix-assisted laser-desorption ionization–time-of-flight; MAPK, mitogen-activated protein kinase; MS/MS, tandem MS; MyD88, myeloid differentiation factor 88; NEDD8, neural-precursor-cell-expressed developmentally down-regulated 8; NEMO, NF-κB essential modifier; NF-κB, nuclear factor κB; PAMP, pathogen-associated molecular pattern; pUb, polyubiquitin; RBR, RING-between-RING, TAB, TAK1-binding protein; TAK1, transforming growth factor β-activated kinase 1; TBK1, tumour-necrosis-factor-receptor-associated factor-associated NF-κB activator-binding kinase 1; TRAF, tumour-necrosis-factor-receptor-associated factor; Ubc, ubiquitin conjugating; UBE, ubiquitin-activating enzyme
27.  Development of a Community-Sensitive Strategy to Increase Availability of Fresh Fruits and Vegetables in Nashville’s Urban Food Deserts, 2010–2012 
Food deserts, areas that lack full-service grocery stores, may contribute to rising rates of obesity and chronic diseases among low-income and racial/ethnic minority residents. Our corner store project, part of the Centers for Disease Control and Prevention’s Communities Putting Prevention to Work initiative, aimed to increase availability of healthful foods in food deserts in Nashville, Tennessee.
Community Context
We identified 4 food deserts in which most residents are low-income and racially and ethnically diverse. Our objectives were to develop an approach to increase availability of fresh fruits and vegetables, low-fat or nonfat milk, and 100% whole-wheat bread in Nashville’s food deserts and to engage community members to inform our strategy.
Five corner stores located in food deserts met inclusion criteria for our intervention. We then conducted community listening sessions, proprietor surveys, store audits, and customer-intercept surveys to identify needs, challenges to retailing the products, and potential intervention strategies.
Few stores offered fresh fruits, fresh vegetables, low-fat or nonfat milk, or 100% whole-wheat bread, and none stocked items from all 4 categories. Major barriers to retailing healthful options identified by community members are mistrust of store owners, history of poor-quality produce, and limited familiarity with healthful options. Store owners identified neighborhood crime as the major barrier. We used community input to develop strategies.
Engaging community residents and understanding neighborhood context is critical to developing strategies that increase access to healthful foods in corner stores.
PMCID: PMC3725846  PMID: 23886044
28.  Association of enrolment in primary care networks with diabetes care and outcomes among First Nations and low-income Albertans 
Open Medicine  2012;6(4):e155-e165.
The prevalence of diabetes mellitus and its complications is higher among First Nations people and people with low socio-economic status (SES). Previous studies in Alberta have shown that provision of care through Primary Care Networks (PCNs) is associated with better quality of care and better outcomes for people with diabetes, possibly because of greater utilization of chronic disease management programs. However, it is unknown whether First Nations individuals and those in lower SES groups experience these benefits.
We used administrative and laboratory data for a population-based cohort analysis of Alberta residents under 65 years of age with diabetes. The primary outcome, assessed over a 1-year period, was admission to hospital or emergency department visit for a diabetes-specific ambulatory care sensitive condition (ACSC). Secondary outcomes were 2 quality-of-care indicators (likelihood of measurement of glycated hemoglobin [HbA1c] and or retinal screening) and 2 measures of health care utilization (visits to specialist and primary care physicians). We used negative binomial regression to determine the association between care within a PCN and hospital admission or emergency department visit for diabetes-specific ACSCs. We also assessed outcomes in 3 populations of interest (individuals receiving a health care subsidy [household income less than $39 250 and not eligible for Income Support], those receiving Income Support, and First Nations individuals) relative to the remainder of the population, controlling for whether care was provided in a PCN and adjusting for several baseline characteristics.
We identified a total of 106 653 patients with diabetes eligible for our study, of whom 43 327 (41%) received care in a PCN. Receiving care through a PCN was associated with lower rates of ACSC-related hospital admission or emergency department visits for all groups of interest, which suggests that PCNs had similar effects across each group. However, regardless of where care was provided, First Nations and low-SES patients had more than twice the adjusted rates of hospital admission or emergency department visits for diabetes-specific ACSCs than the general population and were less likely to receive guideline-recommended care, including measurement of HbA1c and retinal screening.
Care in a PCN was associated with lower risks of hospital admission or emergency department visits for diabetes-specific ACSCs, even within vulnerable groups such as First Nations people and those of low SES. However, differences in outcomes and quality-of-care indicators persisted for First Nations individuals and those of low SES, relative to the general population, irrespective of where care was provided.
PMCID: PMC3654512  PMID: 23687531
29.  Atg13 and FIP200 act independently of Ulk1 and Ulk2 in autophagy induction 
Autophagy  2011;7(12):1424-1433.
Under normal growth conditions the mammalian target of rapamycin complex 1 (mTORC1) negatively regulates the central autophagy regulator complex consisting of Unc-51-like kinases 1/2 (Ulk1/2), focal adhesion kinase family-interacting protein of 200 kDa (FIP200) and Atg13. Upon starvation, mTORC1-mediated repression of this complex is released, which then leads to Ulk1/2 activation. In this scenario, Atg13 has been proposed as an adaptor mediating the interaction between Ulk1/2 and FIP200 and enhancing Ulk1/2 kinase activity. Using Atg13-deficient cells, we demonstrate that Atg13 is indispensable for autophagy induction. We further show that Atg13 function strictly depends on FIP200 binding. In contrast, the simultaneous knockout of Ulk1 and Ulk2 did not have a similar effect on autophagy induction. Accordingly, the Ulk1-dependent phosphorylation sites we identified in Atg13 are expendable for this process. This suggests that Atg13 has an additional function independent of Ulk1/2 and that Atg13 and FIP200 act in concert during autophagy induction.
PMCID: PMC3327613
Atg13; autophagy; FIP200; Ulk1; Ulk2
30.  Change in Hematologic Indices over Time in Pediatric Inflammatory Bowel Disease Treated with Azathioprine 
Drugs in R&d  2012;10(4):213-217.
Azathioprine leads to changes in mean corpuscular volume (MCV) and white blood cell (WBC) indices reflecting efficacy or toxicity. Understanding the interactions between bone marrow stem cells and azathioprine could highlight abnormal response patterns as forerunners for hematologic malignancies. This study gives a statistical description of factors influencing the relationship between MCV and WBC in children with inflammatory bowel disease treated with azathioprine. We found that leukopenia preceded macrocytosis. Macrocytosis is therefore not a good predictor of leukopenia. Further studies will be necessary to determine the subgroup of patients at increased risk of malignancies based on bone marrow response.
PMCID: PMC3586161  PMID: 21171667
31.  Change in Hematologic Indices over Time in Pediatric Inflammatory Bowel Disease Treated with Azathioprine 
Drugs in R&D  2012;10(4):213-217.
Azathioprine leads to changes in mean corpuscular volume (MCV) and white blood cell (WBC) indices reflecting efficacy or toxicity. Understanding the interactions between bone marrow stem cells and azathioprine could highlight abnormal response patterns as forerunners for hematologic malignancies. This study gives a statistical description of factors influencing the relationship between MCV and WBC in children with inflammatory bowel disease treated with azathioprine. We found that leukopenia preceded macrocytosis. Macrocytosis is therefore not a good predictor of leukopenia. Further studies will be necessary to determine the subgroup of patients at increased risk of malignancies based on bone marrow response.
PMCID: PMC3586161  PMID: 21171667
32.  Identification of the Amino Acids 300–600 of IRS-2 as 14-3-3 Binding Region with the Importance of IGF-1/Insulin-Regulated Phosphorylation of Ser-573 
PLoS ONE  2012;7(8):e43296.
Phosphorylation of insulin receptor substrate (IRS)-2 on tyrosine residues is a key event in IGF-1/insulin signaling and leads to activation of the PI 3-kinase and the Ras/MAPK pathway. Furthermore, phosphorylated serine/threonine residues on IRS-2 can induce 14-3-3 binding. In this study we searched IRS-2 for novel phosphorylation sites and investigated the interaction between IRS-2 and 14-3-3. Mass spectrometry identified a total of 24 serine/threonine residues on IRS-2 with 12 sites unique for IRS-2 while the other residues are conserved in IRS-1 and IRS-2. IGF-1 stimulation led to increased binding of 14-3-3 to IRS-2 in transfected HEK293 cells and this binding was prevented by inhibition of the PI 3-kinase pathway and an Akt/PKB inhibitor. Insulin-stimulated interaction between endogenous IRS-2 and 14-3-3 was observed in rat hepatoma cells and in mice liver after an acute insulin stimulus and refeeding. Using different IRS-2 fragments enabled localization of the IGF-1-dependent 14-3-3 binding region spanning amino acids 300–600. The 24 identified residues on IRS-2 included several 14-3-3 binding candidates in the region 300–600. Single alanine mutants of these candidates led to the identification of serine 573 as 14-3-3 binding site. A phospho-site specific antibody was generated to further characterize serine 573. IGF-1-dependent phosphorylation of serine 573 was reduced by inhibition of PI 3-kinase and Akt/PKB. A negative role of this phosphorylation site was implicated by the alanine mutant of serine 573 which led to enhanced phosphorylation of Akt/PKB in an IGF-1 time course experiment. To conclude, our data suggest a physiologically relevant role for IGF-1/insulin-dependent 14-3-3 binding to IRS-2 involving serine 573.
PMCID: PMC3422239  PMID: 22912850
33.  Distribution, genetic analysis and conservation priorities for rare Texas freshwater molluscs in the genera Fusconaia and Pleurobema (Bivalvia: Unionidae) 
Aquatic Biosystems  2012;8:12.
Freshwater bivalves in the order Unionoida are considered to be one of the most endangered groups of animals in North America. In Texas, where over 60% of unionids are rare or very rare, 15 species have been recently added to the state’s list of threatened species, and 11 are under consideration for federal listing. Due to insufficient survey efforts in the past decades, however, primary data on current distribution and habitat requirement for most of these rare species are lacking, thus challenging their protection and management. Taxonomic identification of endemic species based on shell morphology is challenging and complicates conservation efforts. In this paper we present historic and current distributional data for three rare Texas species, Fusconaia askewi, F. lananensis, and Pleurobema riddellii, collected during our 2003–2011 state-wide surveys and suggest appropriate conservation measures. In addition, we tested the genetic affinities of Fusconaia and similar species collected from eastern Texas and western Louisiana using cox1 and nad1 sequences.
We found that F. askewi still inhabits four river basins in eastern and northeastern Texas and can be locally abundant, while P. riddellii was found only in one river basin. Pleurobema riddellii was well-separated from F. askewi and grouped with the P. sintoxia clade. The sequences for F. lananensis were very similar to those for F. askewi, with a maximum difference of just over 1% for nad1 and only 0.7% for cox1, similar to the variation between F. askewi alleles. Except for one low difference (1.55%) with the partial cox1 sequence for F. burkei, all other Fusconaia populations, including those from the Calcasieu drainage, differed by over 2.3% for both genes.
Our study suggested that F. lananensis is not a valid species, and it is likely that only one Fusconaia species (F. askewi or its probable senior synonym F. chunii) is currently present in East Texas, thus simplifying conservation efforts. Distribution range of both these regional endemics (F. askewi and P. riddellii) has been reduced in the last 80 years.
PMCID: PMC3422191  PMID: 22731520
Freshwater molluscs; Fusconaia askewi; Fusconaia lananensis; Pleurobema riddellii; Molecular identification; Taxonomy; Distribution; Habitat requirements; Conservation priorities
34.  Morbidity of the Arterial Switch Operation 
The Annals of Thoracic Surgery  2012;93(6):1977-1983.
The arterial switch operation (ASO) has become a safe, reproducible surgical procedure with low mortality in experienced centers. We examined morbidity, which remains significant, particularly for complex ASO.
From 2003 to 2011, 101 consecutive patients underwent ASO, arbitrarily classified as “simple” (n = 52) or “complex” (n = 49). Morbidity was measured in selected complications and postoperative hospitalization. Three outcomes were analyzed: ventilation time, postextubation hospital length of stay, and a composite morbidity index, defined as ventilation time + postextubation hospital length of stay + occurrence of selected major complications. Complexity was measured with the comprehensive Aristotle score.
The operative mortality was zero. Twenty-five major complications occurred in 23 patients: 6 of 25 (12%) in simple ASO and 19 of 49 (39%) in complex ASO (p = 0.002). The most frequent complication was unplanned reoperation (15 vs 6, p = 0.03). No patients required permanent pacing. The complex group had a significantly higher morbidity index and longer ventilation time and postextubation hospital length of stay. In multivariate analysis, factors independently predicting higher morbidity were the comprehensive Aristotle score, arch repair, bypass time, and malaligned commissures. Myocardial infarction caused one sudden late death at 3 months. Late coronary failure was 2%. Overall survival was 99% at a mean follow-up of 49 ± 27 months.
In this consecutive series without operative mortality, morbidity was significantly higher in complex ASO. The only anatomic incremental risk factors for morbidity were aortic arch repair and malaligned commissures, but not primary diagnosis, weight less than 2.5 kg, or coronary patterns.
PMCID: PMC3381339  PMID: 22365263
35.  PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65 
Open Biology  2012;2(5):120080.
Missense mutations in PTEN-induced kinase 1 (PINK1) cause autosomal-recessive inherited Parkinson's disease (PD). We have exploited our recent discovery that recombinant insect PINK1 is catalytically active to test whether PINK1 directly phosphorylates 15 proteins encoded by PD-associated genes as well as proteins reported to bind PINK1. We have discovered that insect PINK1 efficiently phosphorylates only one of these proteins, namely the E3 ligase Parkin. We have mapped the phosphorylation site to a highly conserved residue within the Ubl domain of Parkin at Ser65. We show that human PINK1 is specifically activated by mitochondrial membrane potential (Δψm) depolarization, enabling it to phosphorylate Parkin at Ser65. We further show that phosphorylation of Parkin at Ser65 leads to marked activation of its E3 ligase activity that is prevented by mutation of Ser65 or inactivation of PINK1. We provide evidence that once activated, PINK1 autophosphorylates at several residues, including Thr257, which is accompanied by an electrophoretic mobility band-shift. These results provide the first evidence that PINK1 is activated following Δψm depolarization and suggest that PINK1 directly phosphorylates and activates Parkin. Our findings indicate that monitoring phosphorylation of Parkin at Ser65 and/or PINK1 at Thr257 represent the first biomarkers for examining activity of the PINK1-Parkin signalling pathway in vivo. Our findings also suggest that small molecule activators of Parkin that mimic the effect of PINK1 phosphorylation may confer therapeutic benefit for PD.
PMCID: PMC3376738  PMID: 22724072
PINK1; Parkin; Parkinson's disease
36.  Early migration characteristics of a hydroxyapatite-coated femoral stem: an RSA study 
International Orthopaedics  2009;35(4):483-488.
Measurement of early stem subsidence can be used to predict the likelihood of long-term femoral component loosening and clinical failure. Data that examines the early migration pattern of clinically proven stems will provide clinicians with useful baseline data with which to compare new stem designs. This study was performed to evaluate the early migration pattern of a hydroxyapatite-coated press-fit femoral component that has been in use for over ten years. We enrolled 30 patients who underwent THA for osteoarthritis. The median age was 70 years (range, 55–80 years). Patients were clinically assessed using the Harris hip score. Radiostereometric analysis was used to evaluate stem migration at three to four days, six months, one year and two years. We observed a mean subsidence of 0.73 mm at six months, 0.62 mm at one year and 0.58 mm at two years and a mean retroversion of 1.82° at six months, 1.90° at one year and 1.59° at two years. This data suggests that subsidence is confined to the first six months after which there was no further subsidence. The results from this study can be compared with those from novel cementless stem designs to help predict the long-term outcome one may expect from new cementless stem designs.
PMCID: PMC3066322  PMID: 20012862
37.  Heparin-Induced Thrombocytopenia Associated with Massive Intracardiac Thrombosis: A Case Report 
Case Reports in Hematology  2012;2012:257023.
A 60-years old patient was admitted to a community hospital with septic arthritis. He was treated with antibiotics and subcutaneous unfractionated heparin (UH) was used for venous thromboprophylaxis. After three days, he developed leg deep venous thrombosis and was treated with IV heparin. One day later, the patient developed pulmonary emboli, which was found using ventilation/perfusion scan. He was transferred to the University Hospital for further management. Upon arrival, antibiotic and intravenous UH were continued. Trans-Esophageal Echocardiogram showed a thrombus in the right atrium, a small portion of which extended to the left atrium through a patent foramen ovale. Another large thrombus was noted in the right ventricle, which extended to the pulmonary artery. Review of the patient's medical records revealed a halving of his platelet count three days following the heparin administration. Therefore, HIT seemed very likely. Intravenous UH was stopped and an emergency thrombectomy was performed. ELISA testing of HIT antibodies came negative. This made HIT diagnosis unlikely and the patient received dalteparin. A week later, as the platelet count declined again, HIT antibodies' testing using ELISA and C-14 serotonin release was repeated, and both assays were positive. Argatroban was restarted and the platelet count normalized.
PMCID: PMC3420555  PMID: 22937322
38.  Enrolment in primary care networks: impact on outcomes and processes of care for patients with diabetes 
Primary care networks are a newer model of primary care that focuses on improved access to care and the use of multidisciplinary teams for patients with chronic disease. We sought to determine the association between enrolment in primary care networks and the care and outcomes of patients with diabetes.
We used administrative health care data to study the care and outcomes of patients with incident and prevalent diabetes separately. For patients with prevalent diabetes, we compared those whose care was managed by physicians who were or were not in a primary care network using propensity score matching. For patients with incident diabetes, we studied a cohort before and after primary care networks were established. Each cohort was further divided based on whether or not patients were cared for by physicians enrolled in a network. Our primary outcome was admissions to hospital or visits to emergency departments for ambulatory care sensitive conditions specific to diabetes.
Compared with patients whose prevalent diabetes is managed outside of primary care networks, patients in primary care networks had a lower rate of diabetes-specific ambulatory care sensitive conditions (adjusted incidence rate ratio 0.81, 95% confidence interval [CI] 0.75 to 0.87), were more likely to see an ophthalmologist or optometrist (risk ratio 1.19, 95% CI 1.17 to 1.21) and had better glycemic control (adjusted mean difference −0.067, 95% CI −0.081 to −0.052).
Patients whose diabetes was managed in primary care networks received better care and had better clinical outcomes than patients whose condition was not managed in a network, although the differences were very small.
PMCID: PMC3273535  PMID: 22143232
39.  O-GlcNAcylation of TAB1 modulates TAK1-mediated cytokine release 
The EMBO Journal  2012;31(6):1394-1404.
O-GlcNAcylation of TAB1 modulates TAK1-mediated cytokine release
The protein kinase TAK1 plays an important role in pro-inflammatory cytokine signalling. Interleukin-1- and osmotic stress-induced O-GlcNAcylation of its regulatory subunit TAB1 is required for full TAK1 activation to induce downstream cytokine production, linking this protein modification to innate immunity signalling.
Transforming growth factor (TGF)-β-activated kinase 1 (TAK1) is a key serine/threonine protein kinase that mediates signals transduced by pro-inflammatory cytokines such as transforming growth factor-β, tumour necrosis factor (TNF), interleukin-1 (IL-1) and wnt family ligands. TAK1 is found in complex with binding partners TAB1–3, phosphorylation and ubiquitination of which has been found to regulate TAK1 activity. In this study, we show that TAB1 is modified with N-acetylglucosamine (O-GlcNAc) on a single site, Ser395. With the help of a novel O-GlcNAc site-specific antibody, we demonstrate that O-GlcNAcylation of TAB1 is induced by IL-1 and osmotic stress, known inducers of the TAK1 signalling cascade. By reintroducing wild-type or an O-GlcNAc-deficient mutant TAB1 (S395A) into Tab1−/− mouse embryonic fibroblasts, we determined that O-GlcNAcylation of TAB1 is required for full TAK1 activation upon stimulation with IL-1/osmotic stress, for downstream activation of nuclear factor κB and finally production of IL-6 and TNFα. This is one of the first examples of a single O-GlcNAc site on a signalling protein modulating a key innate immunity signalling pathway.
PMCID: PMC3321193  PMID: 22307082
cytokine; glycobiology; innate immunity; O-GlcNAc; signal transduction
40.  Medication compliance aids: a qualitative study of users' views 
Despite the rapid rise in the use of multicompartmental compliance aids (MCAs), little is known about the role they play in self-management of medication.
To explore the perceived benefits of MCAs for people using them to manage their own or a relative's medication.
Design of study
Qualitative study using in-depth interviews.
West Northumberland.
Recruitment was via posters and leaflets in general practices and community pharmacies. In-depth interviews were conducted using a topic guide.
Nineteen people were interviewed. Three overarching themes emerged in relation to medicine taking: disruption, organisation, and adherence, which impacted on control. The medication regime had caused disruption to their lives and this had led to the purchase of an MCA. The MCA enabled them to organise their medication, which they believed had improved the efficiency of medicine taking and saved time. Although the MCA did not prompt them to take their medication, they could see whether they had actually taken it or not, which alleviated their anxiety. To meet their individual needs and lifestyles, some had developed broader systems of medication management, incorporating the MCA. For a small cost – the initial outlay for the MCA and time spent loading it – they gained control over the management of their medication and their condition.
This group found the use of an MCA to be beneficial, but advice and support regarding how best to manage their medication and on the most appropriate design to suit their needs would be helpful.
PMCID: PMC3026148  PMID: 21276336
medication adherence; medication systems; qualitative research
41.  TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists* 
Molecular & Cellular Proteomics : MCP  2011;11(4):R111.015040.
Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring.
PMCID: PMC3322582  PMID: 22159873
42.  VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics 
Nucleic Acids Research  2011;40(Database issue):D729-D734.
VectorBase ( is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.
PMCID: PMC3245112  PMID: 22135296
43.  Discovery of catalytically active orthologues of the Parkinson's disease kinase PINK1: analysis of substrate specificity and impact of mutations 
Open biology  2011;1(3):110012.
Missense mutations of the phosphatase and tensin homolog (PTEN)-induced kinase 1 (PINK1) gene cause autosomal-recessive Parkinson's disease. To date, little is known about the intrinsic catalytic properties of PINK1 since the human enzyme displays such low kinase activity in vitro. We have discovered that, in contrast to mammalian PINK1, insect orthologues of PINK1 we have investigated—namely Drosophila melanogaster (dPINK1), Tribolium castaneum (TcPINK1) and Pediculus humanus corporis (PhcPINK1)—are active as judged by their ability to phosphorylate the generic substrate myelin basic protein. We have exploited the most active orthologue, TcPINK1, to assess its substrate specificity and elaborated a peptide substrate (PINKtide, KKWIpYRRSPRRR) that can be employed to quantify PINK1 kinase activity. Analysis of PINKtide variants reveal that PINK1 phosphorylates serine or threonine, but not tyrosine, and we show that PINK1 exhibits a preference for a proline at the +1 position relative to the phosphorylation site. We have also, for the first time, been able to investigate the effect of Parkinson's disease-associated PINK1 missense mutations, and found that nearly all those located within the kinase domain, as well as the C-terminal non-catalytic region, markedly suppress kinase activity. This emphasizes the crucial importance of PINK1 kinase activity in preventing the development of Parkinson's disease. Our findings will aid future studies aimed at understanding how the activity of PINK1 is regulated and the identification of physiological substrates.
PMCID: PMC3352081  PMID: 22645651
biochemistry; Parkinson's disease; kinase
44.  Second-generation Highly Cross-linked X3™ Polyethylene Wear: A Preliminary Radiostereometric Analysis Study 
First-generation highly cross-linked polyethylene liners have reduced the incidence of wear particle-induced osteolysis. However, failed acetabular liners have shown evidence of surface cracking, mechanical failure, and oxidative damage. This has led to the development of second-generation highly cross-linked polyethylene, which has improved wear and mechanical properties and resistance to oxidation in vitro. Owing to its recent introduction, there are no publications describing its clinical performance.
We assessed early clinical wear of a second-generation highly cross-linked polyethylene liner and compared its clinical performance with the published results of hip simulator tests and with first-generation highly cross-linked polyethylene annealed liners.
Patients and Methods
Twenty-one patients were enrolled in a prospective cohort study. Clinical outcome and femoral head penetration were measured for 19 patients at 6 months and 1 and 2 years postoperatively.
The median proximal head penetration was 0.009 mm and 0.024 mm at 1 and 2 years, respectively. The median two-dimensional (2-D) head penetration was 0.083 mm and 0.060 mm at 1 and 2 years, respectively. The median proximal wear rate between 1 and 2 years was 0.015 mm/year.
The wear rate calculated was similar to the in vitro wear rate reported for this material; however, it was less than the detection threshold for this technique. Although longer followup is required for wear to reach a clinically quantifiable level, this low level of wear is encouraging for the future clinical performance of this material.
Level of Evidence
Level IV, therapeutic study. See the Guidelines for Authors for a complete description of levels of evidence.
PMCID: PMC3049610  PMID: 20151231
45.  Dasatinib sensitizes KRAS mutant colorectal tumors to cetuximab 
Oncogene  2010;30(5):561-574.
KRAS mutation is a predictive biomarker for resistance to cetuximab (Erbitux®) in metastatic colorectal cancer (mCRC). This study sought to determine if KRAS mutant CRC lines could be sensitized to cetuximab using dasatinib (BMS-354825, sprycel®) a potent, orally bioavailable inhibitor of several tyrosine kinases, including the Src Family Kinases. We analyzed 16 CRC lines for: 1) KRAS mutation status, 2) dependence on mutant KRAS signaling, 3) expression level of EGFR and SFKs. From these analyses, we selected three KRAS mutant (LS180, LoVo, and HCT116) cell lines, and two KRAS wild type cell lines (SW48 and CaCo2). In vitro, using Poly-D-Lysine/laminin plates, KRAS mutant cell lines were resistant to cetuximab whereas parental controls showed sensitivity to cetuximab. Treatment with cetuximab and dasatinib showed a greater anti-proliferative effect on KRAS mutant line as compared to either agent alone both in vitro and in vivo. To investigate potential mechanisms for this anti-proliferative response in the combinatorial therapy we performed Human Phospho-kinase Antibody Array analysis measuring the relative phosphorylation levels of phosphorylation of 39 intracellular proteins in untreated, cetuximab, dasatinib or the combinatorial treatment in LS180, LoVo and HCT116 cells. The results of this experiment showed a decrease in a broad spectrum of kinases centered on the β-catenin pathway, the classical MAPK pathway, AKT/mTOR pathway and the family of STAT transcription factors when compared to the untreated control or monotherapy treatments. Next we analyzed tumor growth with cetuximab, dasatinib or the combination in vivo. KRAS mutant xenografts showed resistance to cetuximab therapy, whereas KRAS wild type demonstrated an anti-tumor response when treated with cetuximab. KRAS mutant tumors exhibited minimal response to dasatinib monotherapy. However, as in vitro, KRAS mutant lines exhibited a response to the combination of cetuximab and dasatinib. Combinatorial treatment of KRAS mutant xenografts resulted in decreased cell proliferation as measured by Ki67 and higher rates of apoptosis as measured by TUNEL. The data presented herein indicate that dasatinib can sensitize KRAS mutant CRC tumors to cetuximab and may do so by altering the activity of several key-signaling pathways. Further, these results suggest that signaling via the EGFR and SFKs may be necessary for cell proliferation and survival of KRAS mutant CRC tumors. This data strengthen the rationale for clinical trials in this genetic setting combining cetuximab and dasatinib.
PMCID: PMC3025039  PMID: 20956938
Cetuximab; resistance; KRAS mutation; dasatinib; EGFR; SRC; colorectal cancer
46.  Absolute quantification of microbial proteomes at different states by directed mass spectrometry 
The developed, directed mass spectrometry workflow allows to generate consistent and system-wide quantitative maps of microbial proteomes in a single analysis. Application to the human pathogen L. interrogans revealed mechanistic proteome changes over time involved in pathogenic progression and antibiotic defense, and new insights about the regulation of absolute protein abundances within operons.
The developed, directed proteomic approach allowed consistent detection and absolute quantification of 1680 proteins of the human pathogen L. interrogans in a single LC–MS/MS experiment.The comparison of 25 extensive, consistent and quantitative proteome maps revealed new insights about the proteome changes involved in pathogenic progression and antibiotic defense of L. interrogans, and about the regulation of protein abundances within operons.The generated time-resolved data sets are compatible with pattern analysis algorithms developed for transcriptomics, including hierarchical clustering and functional enrichment analysis of the detected profile clusters.This is the first study that describes the absolute quantitative behavior of any proteome over multiple states and represents the most comprehensive proteome abundance pattern comparison for any organism to date.
Over the last decade, mass spectrometry (MS)-based proteomics has evolved as the method of choice for system-wide proteome studies and now allows for the characterization of several thousands of proteins in a single sample. Despite these great advances, redundant monitoring of protein levels over large sample numbers in a high-throughput manner remains a challenging task. New directed MS strategies have shown to overcome some of the current limitations, thereby enabling the acquisition of consistent and system-wide data sets of proteomes with low-to-moderate complexity at high throughput.
In this study, we applied this integrated, two-stage MS strategy to investigate global proteome changes in the human pathogen L. interrogans. In the initial discovery phase, 1680 proteins (out of around 3600 gene products) could be identified (Schmidt et al, 2008) and, by focusing precious MS-sequencing time on the most dominant, specific peptides per protein, all proteins could be accurately and consistently monitored over 25 different samples within a few days of instrument time in the following scoring phase (Figure 1). Additionally, the co-analysis of heavy reference peptides enabled us to obtain absolute protein concentration estimates for all identified proteins in each perturbation (Malmström et al, 2009). The detected proteins did not show any biases against functional groups or protein classes, including membrane proteins, and span an abundance range of more than three orders of magnitude, a range that is expected to cover most of the L. interrogans proteome (Malmström et al, 2009).
To elucidate mechanistic proteome changes over time involved in pathogenic progression and antibiotic defense of L. interrogans, we generated time-resolved proteome maps of cells perturbed with serum and three different antibiotics at sublethal concentrations that are currently used to treat Leptospirosis. This yielded an information-rich proteomic data set that describes, for the first time, the absolute quantitative behavior of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date. Using this unique property of the data set, we could quantify protein components of entire pathways across several time points and subject the data sets to cluster analysis, a tool that was previously limited to the transcript level due to incomplete sampling on protein level (Figure 4). Based on these analyses, we could demonstrate that Leptospira cells adjust the cellular abundance of a certain subset of proteins and pathways as a general response to stress while other parts of the proteome respond highly specific. The cells furthermore react to individual treatments by ‘fine tuning' the abundance of certain proteins and pathways in order to cope with the specific cause of stress. Intriguingly, the most specific and significant expression changes were observed for proteins involved in motility, tissue penetration and virulence after serum treatment where we tried to simulate the host environment. While many of the detected protein changes demonstrate good agreement with available transcriptomics data, most proteins showed a poor correlation. This includes potential virulence factors, like Loa22 or OmpL1, with confirmed expression in vivo that were significantly up-regulated on the protein level, but not on the mRNA level, strengthening the importance of proteomic studies. The high resolution and coverage of the proteome data set enabled us to further investigate protein abundance changes of co-regulated genes within operons. This suggests that although most proteins within an operon respond to regulation synchronously, bacterial cells seem to have subtle means to adjust the levels of individual proteins or protein groups outside of the general trend, a phenomena that was recently also observed on the transcript level of other bacteria (Güell et al, 2009).
The method can be implemented with standard high-resolution mass spectrometers and software tools that are readily available in the majority of proteomics laboratories. It is scalable to any proteome of low-to-medium complexity and can be extended to post-translational modifications or peptide-labeling strategies for quantification. We therefore expect the approach outlined here to become a cornerstone for microbial systems biology.
Over the past decade, liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) has evolved into the main proteome discovery technology. Up to several thousand proteins can now be reliably identified from a sample and the relative abundance of the identified proteins can be determined across samples. However, the remeasurement of substantially similar proteomes, for example those generated by perturbation experiments in systems biology, at high reproducibility and throughput remains challenging. Here, we apply a directed MS strategy to detect and quantify sets of pre-determined peptides in tryptic digests of cells of the human pathogen Leptospira interrogans at 25 different states. We show that in a single LC–MS/MS experiment around 5000 peptides, covering 1680 L. interrogans proteins, can be consistently detected and their absolute expression levels estimated, revealing new insights about the proteome changes involved in pathogenic progression and antibiotic defense of L. interrogans. This is the first study that describes the absolute quantitative behavior of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date.
PMCID: PMC3159967  PMID: 21772258
absolute quantification; directed mass spectrometry; Leptospira interrogans; microbiology; proteomics
47.  Performance of Cavopulmonary Palliation at Elevated Altitude 
Circulation  2008;118(14 Suppl):S177-S181.
Outcomes of patients undergoing cavopulmonary palliation for single ventricle physiology may be impacted by living at altitude, as the passive pulmonary circulation is dependent on the resistance of the pulmonary vascular bed. The objective of this study is to identify risk factors for failure of cavopulmonary palliation at elevated altitude.
Methods and Results
Between January 1995 and March 2007, 122 consecutive patients living at a mean altitude of 1600 m (range 305 to 2570) underwent a bidirectional Glenn (BDG). There was one in-hospital mortality and 7 late deaths. 52 have proceeded to the Fontan procedure. Survival after BDG was 92.4% at 5 years. Freedom from palliation failure, defined as death, transplant, BDG/Fontan takedown, or revision was 81% at 5 years. At a mean follow-up of 39.8 months, 90 patients (75%) were in New York Heart Association class I. Patients with failing cavopulmonary circulation had higher pre-BDG pulmonary artery pressure (PAP) (18.3±6.1 mm Hg versus 14.8±5.1 mm Hg, P=0.016) and higher pre-BDG transpulmonary gradient (TPG) (11.2±6.2 mm Hg versus 7.7±4.3 mm Hg, P=0.014). Post-BDG, patients with palliation failure had increased PAP (15.0±5.7 mm Hg versus 10.8±2.8 mm Hg, P=0.008) and indexed pulmonary vascular resistance (PVRI) (2.43±1.0 Wood U · m2 versus 1.52±0.9 Wood U · m2, P=0.007).
The majority of patients at moderate altitude have favorable outcomes after BDG or Fontan palliation. Risk factors for palliation failure at elevated altitude include PAP >15 mm Hg, TPG >8 mm Hg, and PVRI >2.5 Wood U · m2.
PMCID: PMC3129266  PMID: 18824752
Fontan procedure; single ventricle; altitude
48.  Outcomes of Reparative and Transplantation Strategies for Multilevel Left Heart Obstructions With Mitral Stenosis 
The Annals of thoracic surgery  2008;86(4):1305-1310.
Conventional management for multilevel left heart obstructions and mitral stenosis (Shone’s complex) involves multiple operations that carry additive risks. This study reviews our experience with reconstructive and transplantation approaches for Shone’s complex.
Between 1987 and 2007, 43 patients with mitral stenosis and one or more left-sided obstructions were identified: supramitral ring (n = 13), subaortic stenosis (n = 25), aortic stenosis (n = 24), hypoplastic arch (n = 20), and coarctation (n = 38). Thirty patients underwent a staged reparative approach, including 27 mitral and 51 left ventricular outflow tract operations. Thirteen patients were referred for transplantation. Patients with severe hypoplasia of the left ventricle were excluded.
There was one in-hospital death (2.5%) and six late deaths (14.2%). Actuarial 5- and 10-year survival for staged surgical and transplantation was 88% vs 61.3% and 83.1% vs 61.3% (p = 0.035). At a mean follow-up of 7.9 years, freedom from mitral reoperation was 83.3% and freedom from reoperation for subaortic stenosis was 78.0%. Wait-list mortality was 13.3% (2 of 13). Wait-list time exceeding 90 days was an incremental risk factor for death after transplantation (p = 0.005).
Despite the challenges of a reparative strategy for Shone’s complex, favorable survival and durability outcomes can be expected. Heart transplantation, although avoiding the pitfalls of staged repair, confers increased risks from ongoing physiologic derangements due to uncorrected left heart inflow and outflow obstructions during the wait for donor heart availability.
PMCID: PMC3128450  PMID: 18805182
49.  Visualization and Biochemical Analyses of the Emerging Mammalian 14-3-3-Phosphoproteome* 
Molecular & Cellular Proteomics : MCP  2011;10(10):M110.005751.
Hundreds of candidate 14-3-3-binding (phospho)proteins have been reported in publications that describe one interaction at a time, as well as high-throughput 14-3-3-affinity and mass spectrometry-based studies. Here, we transcribed these data into a common format, deposited the collated data from low-throughput studies in MINT (, and compared the low- and high-throughput data in VisANT graphs that are easy to analyze and extend. Exploring the graphs prompted questions about technical and biological specificity, which were addressed experimentally, resulting in identification of phosphorylated 14-3-3-binding sites in the mitochondrial import sequence of the iron-sulfur cluster assembly enzyme (ISCU), cytoplasmic domains of the mitochondrial fission factor (MFF), and endoplasmic reticulum-tethered receptor expression-enhancing protein 4 (REEP4), RNA regulator SMAUG2, and cytoskeletal regulatory proteins, namely debrin-like protein (DBNL) and kinesin light chain (KLC) isoforms. Therefore, 14-3-3s undergo physiological interactions with proteins that are destined for diverse subcellular locations. Graphing and validating interactions underpins efforts to use 14-3-3-phosphoproteomics to identify mechanisms and biomarkers for signaling pathways in health and disease.
PMCID: PMC3205853  PMID: 21725060
50.  Outcome of Extracorporeal Membrane Oxygenation for Early Primary Graft Failure After Pediatric Heart Transplantation 
We sought to analyze the indications and outcome of extracorporeal membrane oxygenation (ECMO) for early primary graft failure and determine its impact on long-term graft function and rejection risk.
Early post-operative graft failure requiring ECMO can complicate heart transplantation.
A retrospective review of all children requiring ECMO in the early period after transplantation from 1990 to 2007 was undertaken.
Twenty-eight (9%) of 310 children who underwent transplantation for cardiomyopathy (n = 5) or congenital heart disease (n = 23) required ECMO support. The total ischemic time was significantly longer for ECMO-rescued recipients compared with our overall transplantation population (276 ± 86 min vs. 242 ± 70 min, p < 0.01). The indication for transplantation, for ECMO support, and the timing of cannulation had no impact on survival. Hyperacute rejection was uncommon. Fifteen children were successfully weaned off ECMO and discharged alive (54%). Mean duration of ECMO was 2.8 days for survivors (median 3 days) compared with 4.8 days for nonsurvivors (median 5 days). There was 100% 3-year survival in the ECMO survivor group, with 13 patients (46%) currently alive at a mean follow-up of 8.1 ± 3.8 years. The graft function was preserved (shortening fraction 36 ± 7%), despite an increased number of early rejection episodes (1.7 ± 1.6 vs. 0.7 ± 1.3, overall transplant population, p < 0.05) and hemodynamically comprising rejection episodes (1.3 ± 1.9 vs. 0.7 ± 1.3, overall transplant population, p < 0.05).
Overall survival was 54%, with all patients surviving to at least 3 years after undergoing transplantation. None of the children requiring >4 days of ECMO support survived. Despite an increased number of early and hemodynamically compromising rejections, the long-term graft function is similar to our overall transplantation population.
PMCID: PMC3117294  PMID: 19679252
extracorporeal membrane oxygenation; child; heart transplantation; right-sided heart failure; left-sided heart failure; hypertension pulmonary

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