PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

Background: It is possible to identify thousands of phosphopeptides and -proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires a number of manual steps.Results: Toward automating the analysis steps, we have developed and implemented a software, PhosFox, which enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons. Importantly, PhosFox detects uniquely phosphorylated peptides and proteins in one sample compared to another. It also distinguishes differences in phosphorylation sites between phosphorylated proteins in different samples. Using two case study examples, a qualitative phosphoproteome dataset from human keratinocytes and a quantitative phosphoproteome dataset from rat kidney inner medulla, we demonstrate here how PhosFox facilitates an efficient and in-depth phosphoproteome data analysis. PhosFox was implemented in the Perl programming language and it can be run on most common operating systems. Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox.Conclusions: PhosFox facilitates efficient and more in-depth comparisons between phosphoproteins in case-control settings. The open source implementation is easily extendable to accommodate additional features for widespread application use cases

Timing is everything: Drivers of interannual variability in blue whale migration.

Blue whales need to time their migration from their breeding grounds to their feeding grounds to avoid missing peak prey abundances, but the cues they use for this are unknown. We examine migration timing (inferred from the local onset and cessation of blue whale calls recorded on seafloor-mounted hydrophones), environmental conditions (e.g., sea surface temperature anomalies and chlorophyll a), and prey (spring krill biomass from annual net tow surveys) during a 10 year period (2008-2017) in waters of the Southern California Region where blue whales feed in the summer. Colder sea surface temperature anomalies the previous season were correlated with greater krill biomass the following year, and earlier arrival by blue whales. Our results demonstrate a plastic response of blue whales to interannual variability and the importance of krill as a driving force behind migration timing. A decadal-scale increase in temperature due to climate change has led to blue whales extending their overall time in Southern California. By the end of our 10-year study, whales were arriving at the feeding grounds more than one month earlier, while their departure date did not change. Conservation strategies will need to account for increased anthropogenic threats resulting from longer times at the feeding grounds

The use the a high intensity neutrino beam from the ESS proton linac for measurement of neutrino CP violation and mass hierarchy

It is proposed to complement the ESS proton linac with equipment that would enable the production, concurrently with the production of the planned ESS beam used for neutron production, of a 5 MW beam of 10$^{23}$ 2.5 GeV protons per year in microsecond short pulses to produce a neutrino Super Beam, and to install a megaton underground water Cherenkov detector in a mine to detect $\nu_e$ appearance in the produced $\nu_\mu$ beam. Results are presented of preliminary calculations of the sensitivity to neutrino CP violation and the mass hierarchy as a function of the neutrino baseline. The results indicate that, with 8 years of data taking with an antineutrino beam and 2 years with a neutrino beam and a baseline distance of around 400 km, CP violation could be discovered at 5 $\sigma$ (3 $\sigma$) confidence level in 48% (73%) of the total CP violation angular range. With the same baseline, the neutrino mass hierarchy could be determined at 3 $\sigma$ level over most of the total CP violation angular range. There are several underground mines with a depth of more than 1000 m, which could be used for the creation of the underground site for the neutrino detector and which are situated within or near the optimal baseline range

The Anti-Sigma Factor MucA of Pseudomonas aeruginosa: Dramatic Differences of a mucA22 vs. a ΔmucA Mutant in Anaerobic Acidified Nitrite Sensitivity of Planktonic and Biofilm Bacteria in vitro and During Chronic Murine Lung Infection

Mucoid mucA22 Pseudomonas aeruginosa (PA) is an opportunistic lung pathogen of cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) patients that is highly sensitive to acidified nitrite (A-NO2-). In this study, we first screened PA mutant strains for sensitivity or resistance to 20 mM A-NO2- under anaerobic conditions that represent the chronic stages of the aforementioned diseases. Mutants found to be sensitive to A-NO2- included PA0964 (pmpR, PQS biosynthesis), PA4455 (probable ABC transporter permease), katA (major catalase, KatA) and rhlR (quorum sensing regulator). In contrast, mutants lacking PA0450 (a putative phosphate transporter) and PA1505 (moaA2) were A-NO2- resistant. However, we were puzzled when we discovered that mucA22 mutant bacteria, a frequently isolated mucA allele in CF and to a lesser extent COPD, were more sensitive to A-NO2- than a truncated ΔmucA deletion (Δ157–194) mutant in planktonic and biofilm culture, as well as during a chronic murine lung infection. Subsequent transcriptional profiling of anaerobic, A-NO2--treated bacteria revealed restoration of near wild-type transcript levels of protective NO2- and nitric oxide (NO) reductase (nirS and norCB, respectively) in the ΔmucA mutant in contrast to extremely low levels in the A-NO2--sensitive mucA22 mutant. Proteins that were S-nitrosylated by NO derived from A-NO2- reduction in the sensitive mucA22 strain were those involved in anaerobic respiration (NirQ, NirS), pyruvate fermentation (UspK), global gene regulation (Vfr), the TCA cycle (succinate dehydrogenase, SdhB) and several double mutants were even more sensitive to A-NO2-. Bioinformatic-based data point to future studies designed to elucidate potential cellular binding partners for MucA and MucA22. Given that A-NO2- is a potentially viable treatment strategy to combat PA and other infections, this study offers novel developments as to how clinicians might better treat problematic PA infections in COPD and CF airway diseases

A beta 2-Integrin/MRTF-A/SRF Pathway Regulates Dendritic Cell Gene Expression, Adhesion, and Traction Force Generation

beta 2-integrins are essential for immune system function because they mediate immune cell adhesion and signaling. Consequently, a loss of beta(2)-integrin expression or function causes the immunodeficiency disorders, Leukocyte Adhesion Deficiency (LAD) type I and III. LAD-III is caused by mutations in an important integrin regulator, kindlin-3, but exactly how kindlin-3 regulates leukocyte adhesion has remained incompletely understood. Here we demonstrate that mutation of the kindlin-3 binding site in the beta 2-integrin (TTT/AAA-beta 2-integrin knock-in mouse/KI) abolishes activation of the actin-regulated myocardin related transcription factor A/serum response factor (MRTF-A/SRF) signaling pathway in dendritic cells and MRTF-A/SRF-dependent gene expression. We show that Ras homolog gene family, member A (RhoA) activation and filamentous-actin (F-actin) polymerization is abolished in murine TTT/AAA-beta 2-integrin KI dendritic cells, which leads to a failure of MRTF-A to localize to the cell nucleus to coactivate genes together with SRF. In addition, we show that dendritic cell gene expression, adhesion and integrin-mediated traction forces on ligand coated surfaces is dependent on the MRTF-A/SRF signaling pathway. The participation of beta 2-integrin and kindlin-3-mediated cell adhesion in the regulation of the ubiquitous MRTF-A/SRF signaling pathway in immune cells may help explain the role of beta 2-integrin and kindlin-3 in integrin-mediated gene regulation and immune system function

Acute Clopidogrel Use and Outcomes in Patients With Non–ST-Segment Elevation Acute Coronary Syndromes Undergoing Coronary Artery Bypass Surgery

OBJECTIVES We sought to characterize patterns of clopidogrel use before coronary artery bypass grafting (CABG) and examine the drug's impact on risks for postoperative transfusions among patients with non-ST-segment elevation acute coronary syndromes (NSTE ACS). BACKGROUND Adherence in community practice to American College of Cardiology/American Heart Association guidelines for clopidogrel use among NSTE ACS patients has not been previously characterized. METHODS We evaluated 2,858 NSTE ACS patients undergoing CABG at 264 hospitals participating in the CRUSADE (Can Rapid Risk Stratification of Unstable Angina Patients Suppress Adverse Outcomes With Early Implementation of the ACC/AHA Guidelines) Initiative. We examined the patterns of acute clopidogrel therapy and its association with bleeding risks among those having early CABG ≤5 days and again among those having late surgery >5 days after catheterization. RESULTS Within 24 h of admission, 852 patients (30%) received clopidogrel. In contrast to national guidelines, 87% of clopidogrel-treated patients underwent CABG ≤5 days after treatment. Among those receiving CABG within ≤5 days of last treatment, the use of clopidogrel was associated with a significant increase in blood transfusions (65.0% vs. 56.9%, adjusted odds ratio [OR] 1.36, 95% confidence interval [CI] 1.10 to 1.68) as well as the need for transfusion of ≥4 U of blood (27.7% vs. 18.4%, OR 1.70, 95% CI 1.32 to 2.19). In contrast, acute clopidogrel therapy was not associated with higher bleeding risks if CABG was delayed >5 days (adjusted OR 1.18, 95% CI 0.54 to 2.58). CONCLUSIONS Despite guideline recommendations, the overwhelming majority of NSTE ACS patients treated with acute clopidogrel needing CABG have their surgery within ≤5 days of treatment. A failure to delay surgery is associated with increased blood transfusion requirements that must be weighed against the potential clinical and economic impacts of such delays

Intra-aortic balloon counterpulsation in US and non-US centres: results of the Benchmark® Registry

Aims To examine differences in patient characteristics and outcomes in 19 636 patients enrolled in the USA and 3027 patients enrolled in other countries undergoing intra-aortic balloon pump (IABP) counterpulsation. Methods and results Indications for IABP use; a larger percentage of US patients were identified as ‘early support and stabilization for angiography or angioplasty' (21.1% US vs 11.8% non-US), and ‘pre-operative support for high-risk CABG' (15.9% vs 6.6%). A smaller percentage of US patients vs non-US patients were identified as ‘weaning from cardiopulmonary bypass' (14.3% vs 28.2%), and ‘refractory ventricular failure' (6.2% vs 9.8%). One out of five patients in both groups was listed as ‘cardiogenic shock' (18.9% US vs 20.2% non-US). All cause, risk-adjusted, in-hospital mortality (20.1% vs 28.7%; P<0.001), and mortality with IABP in place (10.8% vs 18.0%; P<0.001) were lower at US vs non-US sites. In both US and non-US institutions, IABP associated complication rates, such as IABP-related mortality (0.05% vs 0.07%), major limb ischaemia (0.9% vs 0.8%), and severe bleeding (0.9% vs 0.8%), were low. Conclusions IABP counterpulsation is deployed at an earlier clinical stage in US patients. Mortality rates are higher for non-US patients, particularly for patients with non-surgery cardiac interventions, even after adjusting for risk factors. Complication rates were low. Physicians should therefore not be reluctant to use IABP in high-risk patients undergoing cardiac procedure

Predator-Induced Vertical Behavior of a Ctenophore

Although many studies have focused on Mnemiopsis leidyi predation, little is known about the role of this ctenophore as prey when abundant in native and invaded pelagic systems. We examined the response of the ctenophore M. leidyi to the predatory ctenophore Beroe ovata in an experiment in which the two species could potentially sense each other while being physically separated. On average, M. leidyi responded to the predator’s presence by increasing variability in swimming speeds and by lowering their vertical distribution. Such behavior may help explain field records of vertical migration, as well as stratified and near-bottom distributions of M. leidyi

The Impact of For-Profit Hospital Status on the Care and Outcomes of Patients With Non–ST-Segment Elevation Myocardial Infarction Results From the CRUSADE Initiative

ObjectivesWe sought to determine whether for-profit status influenced hospitals’ care or outcomes among non–ST-segment elevation myocardial infarction (NSTEMI) patients.BackgroundWhile for-profit hospitals potentially have financial incentives to selectively care for younger, healthier patients, perform highly reimbursed procedures, reduce costs by limiting access to expensive medications, and encourage shorter in-patient length of stay, there are limited data available to investigate these issues objectively.MethodsUsing data from the CRUSADE (Can Rapid risk stratification of Unstable angina patients Suppress ADverse outcomes with Early implementation of the American College of Cardiology/American Heart Association guidelines) Initiative, we investigated whether for-profit status influenced hospitals’ patient case mix, care, or outcomes among 145,357 patients with NSTEMI treated between January 1, 2001, and December 31, 2005, at 532 U.S. hospitals. Impact of for-profit status on care and outcomes was analyzed overall and after adjustment for clinical and facility factors using regression modeling.ResultsPatients (n = 11,658) treated at 58 for-profit hospitals were of similar age and gender, but were more likely to be nonwhite (black, Asian, Hispanic, and other) and have health maintenance organization/private insurance, diabetes mellitus, congestive heart failure, hypertension, and renal insufficiency compared with 133,699 patients treated at 474 nonprofit hospitals. For-profit hospitals were less likely to use discharge beta-blockers, but all other treatments were similar including the use of interventional procedures (cardiac catheterization and revascularization procedures) compared with nonprofit centers. In-hospital length of stay and mortality were also similar by hospital type.ConclusionsWe found no evidence that for-profit hospitals selectively treat less sick patients, provide less evidence-based care, limit in-hospital stays, or have patients with worse acute outcomes than nonprofit centers