Multiplexed quantitation via isobaric chemical tags (e.g., tandem mass tags (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ)) has the potential to revolutionize quantitative ...proteomics. However, until recently the utility of these tags was questionable due to reporter ion ratio distortion resulting from fragmentation of coisolated interfering species. These interfering signals can be negated through additional gas-phase manipulations (e.g., MS/MS/MS (MS3) and proton-transfer reactions (PTR)). These methods, however, have a significant sensitivity penalty. Using isolation waveforms with multiple frequency notches (i.e., synchronous precursor selection, SPS), we coisolated and cofragmented multiple MS2 fragment ions, thereby increasing the number of reporter ions in the MS3 spectrum 10-fold over the standard MS3 method (i.e., MultiNotch MS3). By increasing the reporter ion signals, this method improves the dynamic range of reporter ion quantitation, reduces reporter ion signal variance, and ultimately produces more high-quality quantitative measurements. To demonstrate utility, we analyzed biological triplicates of eight colon cancer cell lines using the MultiNotch MS3 method. Across all the replicates we quantified 8 378 proteins in union and 6 168 proteins in common. Taking into account that each of these quantified proteins contains eight distinct cell-line measurements, this data set encompasses 174 704 quantitative ratios each measured in triplicate across the biological replicates. Herein, we demonstrate that the MultiNotch MS3 method uniquely combines multiplexing capacity with quantitative sensitivity and accuracy, drastically increasing the informational value obtainable from proteomic experiments.
Although most tissues in an organism are genetically identical, the biochemistry of each is optimized to fulfill its unique physiological roles, with important consequences for human health and ...disease. Each tissue's unique physiology requires tightly regulated gene and protein expression coordinated by specialized, phosphorylation-dependent intracellular signaling. To better understand the role of phosphorylation in maintenance of physiological differences among tissues, we performed proteomic and phosphoproteomic characterizations of nine mouse tissues. We identified 12,039 proteins, including 6296 phosphoproteins harboring nearly 36,000 phosphorylation sites. Comparing protein abundances and phosphorylation levels revealed specialized, interconnected phosphorylation networks within each tissue while suggesting that many proteins are regulated by phosphorylation independently of their expression. Our data suggest that the “typical” phosphoprotein is widely expressed yet displays variable, often tissue-specific phosphorylation that tunes protein activity to the specific needs of each tissue. We offer this dataset as an online resource for the biological research community.
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► Comprehensive survey of protein expression and phosphorylation in nine murine tissues ► Each tissue displays distinctive protein phosphorylation and expression profiles ► Little correlation is observed among protein expression and phosphorylation levels ► Most phosphoproteins are multiply phosphorylated by kinases from multiple lineages
Left ventricular assist devices (LVADs) are becoming a more frequent life-support intervention. Gaining an understanding of risk factors for infection and management strategies is important for ...treating these patients. We conducted a systematic review and meta-analysis of studies describing infections in continuous-flow LVADs. We evaluated incidence, risk factors, associated microorganisms, and outcomes by type of device and patient characteristics. Our search identified 90 distinct studies that reported LVAD infections and outcomes. Younger age and higher body mass index were associated with higher rates of LVAD infections. Driveline infections were the most common infection reported and the easiest to treat with fewest long-term consequences. Bloodstream infections were not reported as often, but they were associated with stroke and mortality. Treatment strategies varied and did not show a consistent best approach. LVAD infections are a significant cause of morbidity and mortality in LVAD patients. Most research comes from secondary analyses of other LVAD studies. The lack of infection-oriented research leaves several areas understudied. In particular, bloodstream infections in this population merit further research. Providers need more research studies to make evidence-based decisions about the prevention and treatment of LVAD infections.
Quantitative mass spectrometry methods offer near-comprehensive proteome coverage; however, these methods still suffer with regards to sample throughput. Multiplex quantitation via isobaric chemical ...tags (e.g., TMT and iTRAQ) provides an avenue for mass spectrometry-based proteome quantitation experiments to move away from simple binary comparisons and toward greater parallelization. Herein, we demonstrate a straightforward method for immediately expanding the throughput of the TMT isobaric reagents from 6-plex to 8-plex. This method is based upon our ability to resolve the isotopic shift that results from substituting a (15)N for a (13)C. In an accommodation to the preferred fragmentation pathways of ETD, the TMT-127 and -129 reagents were recently modified such that a (13)C was exchanged for a (15)N. As a result of this substitution, the new TMT reporter ions are 6.32 mDa lighter. Even though the mass difference between these reporter ion isotopologues is incredibly small, modern high-resolution and mass accuracy analyzers can resolve these ions. On the basis of our ability to resolve and accurately measure the relative intensity of these isobaric reporter ions, we demonstrate that we are able to quantify across eight samples simultaneously by combining the (13)C- and (15)N-containing reporter ions. Considering the structure of the TMT reporter ion, we believe this work serves as a blueprint for expanding the multiplexing capacity of the TMT reagents to at least 10-plex and possibly up to 18-plex.
Subtalar joint (STJ) dysfunction can contribute to movement disturbances. Vibration energy with color Doppler imaging (VECDI) may be useful for detecting STJ stiffness changes.
(1) Support ...proof-of-concept that VECDI could detect STJ stiffness differences; (2) Establish STJ stiffness range in asymptomatic volunteers; (3) Examine relationships between STJ stiffness and foot mobility; and (4) Assess VECDI precision and reliability for examining STJ stiffness.
After establishing cadaveric testing model proof-of-concept, STJ stiffness (threshold units, ΔTU), ankle complex passive range-of-motion (PROM) and midfoot-width-difference (MFWDiff) data were collected in 28 asymptomatic subjects in vivo. Three reliability measurements were collected per variable; Rater-1 collected on all subjects and rater-2 on the first ten subjects. Subjects were classified into three STJ stiffness groups.
Cadaveric VECDI measurement intra-rater reliability was 0.80. A significantly lower STJ ΔTU (p = .002) and ankle complex PROM (p < .001) was observed during the screw fixation versus normal condition. A fair correlation (r = 0.660) was observed between cadaveric ΔTU and ankle complex PROM. In vivo VECDI measurements demonstrated good intra-rater (0.76-0.84) versus poor inter-rater (-3.11) reliability. Significant positive correlations were found between STJ stiffness and both dorsum (r = .440) and posterior (r = .390) PROM. MFWDiff exhibited poor relationships with stiffness (r = .103) and either dorsum (r = .256) or posterior (r = .301) PROM. STJ stiffness ranged from 2.33 to 7.50 ΔTUs, categorizing subjects' STJ stiffness as increased (n = 6), normal (n = 15), or decreased (n = 7). Significant ANOVA main effects for classification were found based on ΔTU (p< .001), dorsum PROM (p = .017), and posterior PROM (p = .036). Post-hoc tests revealed significant: (1) ΔTU differences between all stiffness groups (p < .001); (2) dorsum PROM differences between the increased versus normal (p = .044) and decreased (p = .017) stiffness groups; and (3) posterior PROM differences between the increased versus decreased stiffness groups (p = .044). A good relationship was found between STJ stiffness and dorsum PROM in the increased stiffness group (r = .853) versus poor, nonsignificant relationships in the normal (r = -.042) or decreased stiffness (r = -.014) groups.
PROM may not clinically explain all aspects of joint mobility. Joint VECDI stiffness assessment should be considered as a complimentary measurement technique.
Protein phosphorylation modulates a myriad of biological functions, and its regulation is vital for proper cellular activity. Mass spectrometry is the enabling tool for phosphopeptide analysis, where ...recent instrumentation advances in both speed and sensitivity in linear ion trap and orbitrap technologies may yield more comprehensive phosphoproteomic analyses in less time. Protein phosphorylation analysis by MS relies on structural information derived through controlled peptide fragmentation. Compared with traditional, ion-trap-based collision-induced dissociation (CID), a more recent type of fragmentation termed HCD (higher energy collisional dissociation) provides beam type CID tandem MS with detection of fragment ions at high resolution in the orbitrap mass analyzer. Here we compared HCD to traditional CID for large-scale phosphorylation analyses of murine brain under three separate experimental conditions. These included a same-precursor analysis where CID and HCD scans were performed back-to-back, separate analyses of a phosphotyrosine peptide immunoprecipitation experiment, and separate whole phosphoproteome analyses. HCD generally provided higher search engine scores with more peptides identified, thus out-performing CID for back-to-back experiments for most metrics tested. However, for phosphotyrosine IPs and in a full phosphoproteome study of mouse brain, the greater acquisition speed of CID-only analyses provided larger data sets. We reconciled our results with those in direct contradiction from Nagaraj N, D'Souza RCJ et al. (J. Proteome Res. 9:6786, 2010). We conclude, for large-scale phosphoproteomics, CID fragmentation with rapid detection in the ion trap still produced substantially richer data sets, but the back-to-back experiments demonstrated the promise of HCD and orbitrap detection for the future.
To (1) evaluate whether exercise therapy is effective for managing neck pain, and (2) investigate the relationship between exercise therapy dosage and treatment effect.
Intervention systematic review ...with meta-analysis and meta-regression.
An electronic search of 6 databases was completed for trials assessing the effects of exercise therapy on neck pain.
We included randomized controlled trials that compared exercise therapy to a no-exercise therapy control for treating neck pain. Two reviewers screened and selected studies, extracted outcomes, assessed article risk of bias, and rated the quality of evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.
Data were pooled using random-effects meta-analysis. We used meta-regression to analyze the effect of exercise dosage on neck pain and disability.
Fourteen trials were included in the review. Seven trials were at high risk of bias, 4 were at unclear risk of bias, and 3 were at low risk of bias. Exercise therapy was superior to control for reducing pain (visual analog scale mean difference, -15.32 mm) and improving disability (Neck Disability Index mean difference, -3.64 points). Exercise dosage parameters did not predict pain or disability outcomes.
Exercise was beneficial for reducing pain and disability, regardless of exercise therapy dosage. Therefore, optimal exercise dosage recommendations remain unknown. We encourage clinicians to use exercise when managing mechanical neck pain.
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Left ventricular assist devices (LVAD) are increasingly being used both as a bridge to transplantation and for long-term myocardial surrogate destination therapy in patients with end-stage heart ...failure. Primarily owing to the presence of a driveline that connects the device to an external battery through an open skin incision, the rates of LVAD-related infections (LVADRIs) are high, ranging from 30 to 50%. LVADRIs can be broadly classified into driveline infection, pump pocket infection, bloodstream infection and endocarditis/pump or cannula infection. Diagnostic evaluation and management of these complicated infections can be quite challenging for clinicians involved in the care of these patients. Here, the authors summarize the current epidemiology, microbiology, diagnostic approach and management strategies for each type of LVADRI. The authors also review current concepts regarding antibiotic prophylaxis for LVAD implantation. Finally, the authors highlight the gaps in the knowledge of LVADRI and provide directions for future studies.
Ehrlichiosis is a clinically important, emerging zoonosis. Only Ehrlichia chaffeensis and E. ewingii have been thought to cause ehrlichiosis in humans in the United States. Patients with suspected ...ehrlichiosis routinely undergo testing to ensure proper diagnosis and to ascertain the cause.
We used molecular methods, culturing, and serologic testing to diagnose and ascertain the cause of cases of ehrlichiosis.
On testing, four cases of ehrlichiosis in Minnesota or Wisconsin were found not to be from E. chaffeensis or E. ewingii and instead to be caused by a newly discovered ehrlichia species. All patients had fever, malaise, headache, and lymphopenia; three had thrombocytopenia; and two had elevated liver-enzyme levels. All recovered after receiving doxycycline treatment. At least 17 of 697 Ixodes scapularis ticks collected in Minnesota or Wisconsin were positive for the same ehrlichia species on polymerase-chain-reaction testing. Genetic analyses revealed that this new ehrlichia species is closely related to E. muris.
We report a new ehrlichia species in Minnesota and Wisconsin and provide supportive clinical, epidemiologic, culture, DNA-sequence, and vector data. Physicians need to be aware of this newly discovered close relative of E. muris to ensure appropriate testing, treatment, and regional surveillance. (Funded by the National Institutes of Health and the Centers for Disease Control and Prevention.).
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