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Find video protocols related to scientific articles indexed in Pubmed.
Identification of a misfolded region in superoxide dismutase 1 that is exposed in amyotrophic lateral sclerosis.
J. Biol. Chem.
PUBLISHED: 08-27-2014
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Mutations and aberrant post-translational modifications within Cu,Zn-superoxide dismutase (SOD1) cause this otherwise protective enzyme to misfold, leading to amyotrophic lateral sclerosis (ALS). The C4F6 antibody selectively binds misfolded SOD1 in spinal cord tissues from postmortem human ALS cases, as well as from an ALS-SOD1 mouse model, suggesting that the C4F6 epitope reports on a pathogenic conformation that is common to misfolded SOD1 variants. To date, the residues and structural elements that comprise this epitope have not been elucidated. Using a chemical cross-linking and mass spectrometry approach, we identified the C4F6 epitope within several ALS-linked SOD1 variants, as well as an oxidized form of WT SOD1, supporting the notion that a similar misfolded conformation is shared among pathological SOD1 proteins. Exposure of the C4F6 epitope was modulated by the SOD1 electrostatic (loop VII) and zinc binding (loop IV) loops and correlated with SOD1-induced toxicity in a primary microglia activation assay. Site-directed mutagenesis revealed Asp(92) and Asp(96) as key residues within the C4F6 epitope required for the SOD1-C4F6 binding interaction. We propose that stabilizing the functional loops within SOD1 and/or obscuring the C4F6 epitope are viable therapeutic strategies for treating SOD1-mediated ALS.
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Phosphorylation within the cysteine-rich region of dystrophin enhances its association with ?-dystroglycan and identifies a potential novel therapeutic target for skeletal muscle wasting.
Hum. Mol. Genet.
PUBLISHED: 07-31-2014
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Mutations in dystrophin lead to Duchenne muscular dystrophy, which is among the most common human genetic disorders. Dystrophin nucleates assembly of the dystrophin-glycoprotein complex (DGC), and a defective DGC disrupts an essential link between the intracellular cytoskeleton and the basal lamina, leading to progressive muscle wasting. In vitro studies have suggested that dystrophin phosphorylation may affect interactions with actin or syntrophin, yet whether this occurs in vivo or affects protein function remains unknown. Utilizing nanoflow liquid chromatography mass spectrometry, we identified 18 phosphorylated residues within endogenous dystrophin. Mutagenesis revealed that phosphorylation at S3059 enhances the dystrophin-dystroglycan interaction and 3D modeling utilizing the Rosetta software program provided a structural model for how phosphorylation enhances this interaction. These findings demonstrate that phosphorylation is a key mechanism regulating the interaction between dystrophin and the DGC and reveal that posttranslational modification of a single amino acid directly modulates the function of dystrophin.
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Serum-induced differentiation of human meibomian gland epithelial cells.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 05-29-2014
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We hypothesize that culturing immortalized human meibomian gland epithelial cells in serum-containing medium will induce their differentiation. The purpose of this investigation was to begin to test our hypothesis, and explore the impact of serum on gene expression and lipid accumulation in human meibomian gland epithelial cells.
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Clinical measures associated with dynamic balance and functional movement.
J Strength Cond Res
PUBLISHED: 04-24-2014
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Decreased balance and impaired functional movement have been linked with increased injury risk. The purpose of our study was to determine the association between specific measures of power, strength, flexibility, balance, and endurance compared with more global measures of dynamic balance, using the Y-Balance Test (YBT), and functional movement, using the functional movement screen (FMS), in healthy soldiers. Our participants (n = 64; 53 men, 11 women) were healthy active duty service members (25.2 ± 3.8 years, 25.1 ± 3.1 kg·m(-2)). Seventeen tests with 38 associated measures of strength, power, flexibility, endurance, balance, and functional measures were assessed. A significant Pearson product moment correlation (r > 0.2 and p < 0.01) was used to narrow the number of variables of interest. Two hierarchical stepwise regression analyses were performed to determine the most parsimonious set of variables associated with the YBT and FMS performance scores. Our results included a 4 variable model (F = 13.4, p < 0.001) that was associated with YBT scores (R = 0.72, R2 = 0.51). Superior performance on the YBT was associated with better performance on the FMS lunge and upper trunk mobility tests, decreased number of hops during a 6-m hop test, and greater gastrocnemius flexibility. A second 4 variable model (F = 11.813, p < 0.001) was associated with FMS scores (R = 0.70, R2 = 0.50). Superior performance on the FMS was associated with greater anterior reach on the YBT, greater distance on the crossover hop test, increased hamstring flexibility, and higher levels of self-reported function through the lower-extremity functional scale. Physical fitness leaders and clinicians could use these models to inform decision making when developing and assessing the outcomes of a personalized intervention program for those with low FMS and YBT scores.
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Median and ulnar neuropathies in US Army dental personnel at Fort Sam Houston, Texas.
US Army Med Dep J
PUBLISHED: 04-08-2014
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Dental personnel have an increased prevalence of upper-extremity (UE) musculoskeletal (MSK) disorders, including carpal tunnel syndrome (CTS). Military dental personnel report more UE MSK complaints than their civilian counterparts. Literature using nerve conduction studies (NCS) to diagnose UE neuropathy in dental personnel is lacking.
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Inhibition of heat shock protein 90 alleviates steatosis and macrophage activation in murine alcoholic liver injury.
J. Hepatol.
PUBLISHED: 03-28-2014
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Heat shock protein 90 (hsp90) is an emerging therapeutic target in chronic liver diseases. Hsp90 plays an important role in liver immune cell activation; however its role in alcoholic liver disease (ALD) remains elusive. Here we hypothesize that hsp90 is crucial in alcohol induced steatosis and pro-inflammatory cytokine production. To test this hypothesis, we employed a pharmacological inhibitor of hsp90, 17-DMAG (17-Dimethylamino-ethylamino-17-demethoxygeldanamycin) in an in vivo mouse model of acute and chronic alcoholic liver injury.
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Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 02-12-2014
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The most common data collection in shotgun proteomics is via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest. An alternative to DDA is data-independent acquisition (DIA), a process in which a specified range in m/z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum, thus potentially offering a more comprehensive analysis of peptides than DDA. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified with an electrodynamic ion funnel, and an LTQ Velos. These instruments represent both older (LTQ) and newer (LTQ Velos) ion trap designs (i.e., linear versus dual ion traps, respectively), and allow direct comparison of peptide identifications using both DDA and DIA analysis. Further, as the LTQ Velos has an enhanced "S-lens" ion guide to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different design to the S-lens. We find that the ion funnel enabled LTQ identifies more proteins in the insoluble fraction of a yeast lysate than the other two instruments in DIA mode, whereas the faster scanning LTQ Velos performs better in DDA mode. We explore reasons for these results, including differences in scan speed, source ion optics, and linear ion trap design.
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As the egg turns: monitoring egg attendance behavior in wild birds using novel data logging technology.
PLoS ONE
PUBLISHED: 01-01-2014
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Egg turning is unique to birds and critical for embryonic development in most avian species. Technology that can measure changes in egg orientation and temperature at fine temporal scales (1 Hz) was neither readily available nor small enough to fit into artificial eggs until recently. Here we show the utility of novel miniature data loggers equipped with 3-axis (i.e., triaxial) accelerometers, magnetometers, and a temperature thermistor to study egg turning behavior in free-ranging birds. Artificial eggs containing egg loggers were deployed in the nests of three seabird species for 1-7 days of continuous monitoring. These species (1) turned their eggs more frequently (up to 6.5 turns h(-1)) than previously reported for other species, but angular changes were often small (1-10° most common), (2) displayed similar mean turning rates (ca. 2 turns h(-1)) despite major differences in reproductive ecology, and (3) demonstrated distinct diurnal cycling in egg temperatures that varied between 1.4 and 2.4 °C. These novel egg loggers revealed high-resolution, three-dimensional egg turning behavior heretofore never measured in wild birds. This new form of biotechnology has broad applicability for addressing fundamental questions in avian breeding ecology, life history, and development, and can be used as a tool to monitor birds that are sensitive to disturbance while breeding.
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Median and ulnar neuropathies in u.s. Army medical command band members.
Med Probl Perform Art
PUBLISHED: 12-17-2013
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Musicians have been reported as having a high prevalence of upper-extremity musculoskeletal disorders, including carpal tunnel syndrome. The purpose of this study was to determine the presence of median and ulnar neuropathies in U.S. Army Medical Command (MEDCOM) Band members at Fort Sam Houston, Texas.
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Y-balance test: a reliability study involving multiple raters.
Mil Med
PUBLISHED: 11-05-2013
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The Y-balance test (YBT) is one of the few field expedient tests that have shown predictive validity for injury risk in an athletic population. However, analysis of the YBT in a heterogeneous population of active adults (e.g., military, specific occupations) involving multiple raters with limited experience in a mass screening setting is lacking. The primary purpose of this study was to determine interrater test-retest reliability of the YBT in a military setting using multiple raters. Sixty-four service members (53 males, 11 females) actively conducting military training volunteered to participate. Interrater test-retest reliability of the maximal reach had intraclass correlation coefficients (2,1) of 0.80 to 0.85 with a standard error of measurement ranging from 3.1 to 4.2 cm for the 3 reach directions (anterior, posteromedial, and posterolateral). Interrater test-retest reliability of the average reach of 3 trails had an intraclass correlation coefficients (2,3) range of 0.85 to 0.93 with an associated standard error of measurement ranging from 2.0 to 3.5cm. The YBT showed good interrater test-retest reliability with an acceptable level of measurement error among multiple raters screening active duty service members. In addition, 31.3% (n = 20 of 64) of participants exhibited an anterior reach asymmetry of >4cm, suggesting impaired balance symmetry and potentially increased risk for injury.
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Immunodepletion plasma proteomics by tripleTOF 5600 and Orbitrap elite/LTQ-Orbitrap Velos/Q exactive mass spectrometers.
J. Proteome Res.
PUBLISHED: 09-19-2013
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Plasma proteomic experiments performed rapidly and economically using several of the latest high-resolution mass spectrometers were compared. Four quantitative hyperfractionated plasma proteomics experiments were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments. Each experiment compared two iTRAQ isobaric-labeled immunodepleted plasma proteomes, provided as 30 labeled peptide fractions, and 480 LC-MS/MS runs delivered >250 GB of data in 2 months. Several analysis algorithms were compared. At 1% false discovery rate, the relative comparative findings concluded that the Thermo Scientific Q Exactive Mass Spectrometer resulted in the highest number of identified proteins and unique sequences with iTRAQ quantitation. The confidence of iTRAQ fold-change for each protein is dependent on the overall ion statistics (Mascot Protein Score) attainable by each instrument. The benchmarking also suggested how to further improve the mass spectrometry parameters and HPLC conditions. Our findings highlight the special challenges presented by the low abundance peptide ions of iTRAQ plasma proteome because the dynamic range of plasma protein abundance is uniquely high compared with cell lysates, necessitating high instrument sensitivity.
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Cumulative human impacts on marine predators.
Nat Commun
PUBLISHED: 02-26-2013
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Stressors associated with human activities interact in complex ways to affect marine ecosystems, yet we lack spatially explicit assessments of cumulative impacts on ecologically and economically key components such as marine predators. Here we develop a metric of cumulative utilization and impact (CUI) on marine predators by combining electronic tracking data of eight protected predator species (n=685 individuals) in the California Current Ecosystem with data on 24 anthropogenic stressors. We show significant variation in CUI with some of the highest impacts within US National Marine Sanctuaries. High variation in underlying species and cumulative impact distributions means that neither alone is sufficient for effective spatial management. Instead, comprehensive management approaches accounting for both cumulative human impacts and trade-offs among multiple stressors must be applied in planning the use of marine resources.
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Interlaboratory studies and initiatives developing standards for proteomics.
Proteomics
PUBLISHED: 02-19-2013
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Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This viewpoint article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG).
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GABAergic neuroactive steroids and resting-state functional connectivity in postpartum depression: a preliminary study.
J Psychiatr Res
PUBLISHED: 01-28-2013
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Postpartum depression (PPD) affects up to 1 in 8 women. The early postpartum period is characterized by a downward physiological shift from relatively elevated levels of sex steroids during pregnancy to diminished levels after parturition. Sex steroids influence functional brain connectivity in healthy non-puerperal subjects. This study tests the hypothesis that PPD is associated with attenuation of resting-state functional connectivity (rs-fc) within corticolimbic regions implicated in depression and alterations in neuroactive steroid concentrations as compared to healthy postpartum women. Subjects (n = 32) were prospectively evaluated during pregnancy and in the postpartum with repeated plasma neuroactive steroid measurements and mood and psychosocial assessments. Healthy comparison subjects (HCS) and medication-free subjects with unipolar PPD (PPD) were examined using functional magnetic resonance imaging (fMRI) within 9 weeks of delivery. We performed rs-fc analysis with seeds placed in the anterior cingulate cortex (ACC), and bilateral amygdala (AMYG), hippocampi (HIPP) and dorsolateral prefrontal cortices (DLPFCs). Postpartum rs-fc and perinatal neuroactive steroid plasma concentrations, quantified by liquid chromatography/mass spectrometry, were compared between groups. PPD subjects showed attenuation of connectivity for each of the tested regions (i.e. ACC, AMYG, HIPP and DLPFC) and between corticocortical and corticolimbic regions vs. HCS. Perinatal concentrations of pregnanolone, allopregnanolone and pregnenolone were not different between groups. This is the first report of a disruption in the rs-fc patterns in medication-free subjects with PPD. This disruption may contribute to the development of PPD, at a time of falling neuroactive steroid concentrations.
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Reliability of lower quarter physical performance measures in healthy service members.
US Army Med Dep J
PUBLISHED: 08-02-2011
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Measures of endurance, flexibility, strength, and power may be of value in predicting injury risk, but application to the military setting has been limited. The purpose of this study was to assess the reliability and precision of lower quarter physical performance measures among novice raters.
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Contemporary and historical separation of transequatorial migration between genetically distinct seabird populations.
Nat Commun
PUBLISHED: 05-03-2011
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Pelagic seabirds are highly mobile, reducing the likelihood of allopatric speciation where disruption of gene flow between populations is caused by physically insurmountable, extrinsic barriers. Spatial segregation during the non-breeding season appears to provide an intrinsic barrier to gene flow among seabird populations that otherwise occupy nearby or overlapping regions during breeding, but how this is achieved remains unclear. Here we show that the two genetically distinct populations of Cooks petrel (Pterodroma cookii) exhibit transequatorial separation of non-breeding ranges at contemporary (ca. 2-3 yrs) and historical (ca. 100 yrs) time scales. Segregation during the non-breeding season per se appears as an unlikely barrier to gene flow. Instead we provide evidence that habitat specialization during the non-breeding season is associated with breeding asynchrony which, in conjunction with philopatry, restricts gene flow. Habitat specialization during breeding and non-breeding likely promotes evolutionary divergence between these two populations via local adaptation.
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Substrate specificity and ligand interactions of CYP26A1, the human liver retinoic acid hydroxylase.
Mol. Pharmacol.
PUBLISHED: 04-26-2011
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All-trans-retinoic acid (atRA) is the active metabolite of vitamin A. atRA is also used as a drug, and synthetic atRA analogs and inhibitors of retinoic acid (RA) metabolism have been developed. The hepatic clearance of atRA is mediated primarily by CYP26A1, but design of CYP26A1 inhibitors is hindered by lack of information on CYP26A1 structure and structure-activity relationships of its ligands. The aim of this study was to identify the primary metabolites of atRA formed by CYP26A1 and to characterize the ligand selectivity and ligand interactions of CYP26A1. On the basis of high-resolution tandem mass spectrometry data, four metabolites formed from atRA by CYP26A1 were identified as 4-OH-RA, 4-oxo-RA, 16-OH-RA and 18-OH-RA. 9-cis-RA and 13-cis-RA were also substrates of CYP26A1. Forty-two compounds with diverse structural properties were tested for CYP26A1 inhibition using 9-cis-RA as a probe, and IC(50) values for 10 inhibitors were determined. The imidazole- and triazole-containing inhibitors [S-(R*,R*)]-N-[4-[2-(dimethylamino)-1-(1H-imidazole-1-yl)propyl]-phenyl]2-benzothiazolamine (R116010) and (R)-N-[4-[2-ethyl-1-(1H-1,2,4-triazol-1-yl)butyl]phenyl]-2-benzothiazolamine (R115866) were the most potent inhibitors of CYP26A1 with IC(50) values of 4.3 and 5.1 nM, respectively. Liarozole and ketoconazole were significantly less potent with IC(50) values of 2100 and 550 nM, respectively. The retinoic acid receptor (RAR) ? agonist CD1530 was as potent an inhibitor of CYP26A1 as ketoconazole with an IC(50) of 530 nM, whereas the RAR? and RAR? agonists tested did not significantly inhibit CYP26A1. The pan-RAR agonist 4-[(E)-2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl]benzoic acid and the peroxisome proliferator-activated receptor ligands rosiglitazone and pioglitazone inhibited CYP26A1 with IC(50) values of 3.7, 4.2, and 8.6 ?M, respectively. These data demonstrate that CYP26A1 has high ligand selectivity but accepts structurally related nuclear receptor agonists as inhibitors.
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Dynamic habitat models: using telemetry data to project fisheries bycatch.
Proc. Biol. Sci.
PUBLISHED: 03-23-2011
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Fisheries bycatch is a recognized threat to marine megafauna. Addressing bycatch of pelagic species however is challenging owing to the dynamic nature of marine environments and vagility of these organisms. In order to assess the potential for species to overlap with fisheries, we propose applying dynamic habitat models to determine relative probabilities of species occurrence for specific oceanographic conditions. We demonstrate this approach by modelling habitats for Laysan (Phoebastria immutabilis) and black-footed albatrosses (Phoebastria nigripes) using telemetry data and relating their occurrence probabilities to observations of Hawaii-based longline fisheries in 1997-2000. We found that modelled habitat preference probabilities of black-footed albatrosses were high within some areas of the fishing range of the Hawaiian fleet and such preferences were important in explaining bycatch occurrence. Conversely, modelled habitats of Laysan albatrosses overlapped little with Hawaii-based longline fisheries and did little to explain the bycatch of this species. Estimated patterns of albatross habitat overlap with the Hawaiian fleet corresponded to bycatch observations: black-footed albatrosses were more frequently caught in this fishery despite being 10 times less abundant than Laysan albatrosses. This case study demonstrates that dynamic habitat models based on telemetry data may help to project interactions with pelagic animals relative to environmental features and that such an approach can serve as a tool to guide conservation and management decisions.
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Clinical and electrodiagnostic abnormalities of the median nerve in Army dental assistants before and after training as preventive dental specialists.
US Army Med Dep J
PUBLISHED: 03-17-2011
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Dentists and dental hygienists have been reported as having a high prevalence of upper-extremity musculoskeletal disorders, including carpal tunnel syndrome. Unfortunately, previous research has not involved the impact of preventive dental specialist training on dental assistants. Therefore, the purpose of this study was to determine the presence of median and ulnar neuropathies in US Army dental assistants before and after training as preventive dental specialists.
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Automated lipid A structure assignment from hierarchical tandem mass spectrometry data.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 03-05-2011
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Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS(n)) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS(n) spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS(n) spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS(n ) data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS(n) spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS(n) spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.
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Faster, quantitative, and accurate precursor acquisition independent from ion count.
Anal. Chem.
PUBLISHED: 02-22-2011
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Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Recently, we demonstrated the superior performance of a data-independent method we termed precursor acquisition independent from ion count (PAcIFIC). Here, we report a faster, accurate, multiplexed, and quantitative PAcIFIC method. Our results show that the time needed to perform such analysis can be decreased by 33% to 66% using modern ion trap instruments and that high mass accuracy can be applied to such a strategy. Quantification capability is demonstrated on protein standards and a whole bacterial cell lysate using isobaric tagging. Finally, we confirm in yeast the dynamic range capabilities of such a method where proteins down to less than 50 copies per cell can be monitored without sample prefractionation.
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New structural proteins of Halobacterium salinarum gas vesicle revealed by comparative proteomics analysis.
J. Proteome Res.
PUBLISHED: 01-25-2011
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The Halobacterium salinarum gas vesicle (GV) is an extremely stable intracellular organelle with air trapped inside a proteinaceous membrane. Reported here is a comparative proteomics analysis of GV and GV depleted lysate (GVD) to reveal the membrane structural proteins. Ten proteins encoded by gvp-1 (gvpMLKJIHGFED-1 and gvpACNO-1) and five proteins encoded by gvp-2 (gvpMLKJIHGFED-2 and gvpACNO-2) gene clusters for the biogenesis of spindle- and cylindrical-, respectively, shaped GV were identified by LC-MS/MS. The peptides of GvpA1, I1, J1, A2, and J2 were exclusively identified in purified GV, GvpD1, H1, L1, and F2 only in GVD, and GvpC1, N1, O1, F1, H2, and O2 in both samples. The identification of GvpA1, C1, F1, J1, and A2 in GV is in agreement with their previously known structural function. In addition, the detection of GvpI1, N1, O1, H2, J2, and O2 in GV suggested they are new structural proteins. Among these, the structural role of GvpI1 and N1 in GV was further validated by immuno-detection of protein A-tagged GvpI1 and N1 fusion proteins in purified GV. Thus, LC-MS/MS could reveal at least a half dozen gas vesicle structural proteins in the predominant spindle-shaped GV that may be helpful for studying its biogenesis.
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Genetic variation shapes protein networks mainly through non-transcriptional mechanisms.
PLoS Biol.
PUBLISHED: 01-03-2011
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Networks of co-regulated transcripts in genetically diverse populations have been studied extensively, but little is known about the degree to which these networks cause similar co-variation at the protein level. We quantified 354 proteins in a genetically diverse population of yeast segregants, which allowed for the first time construction of a coherent protein co-variation matrix. We identified tightly co-regulated groups of 36 and 93 proteins that were made up predominantly of genes involved in ribosome biogenesis and amino acid metabolism, respectively. Even though the ribosomal genes were tightly co-regulated at both the protein and transcript levels, genetic regulation of proteins was entirely distinct from that of transcripts, and almost no genes in this network showed a significant correlation between protein and transcript levels. This result calls into question the widely held belief that in yeast, as opposed to higher eukaryotes, ribosomal protein levels are regulated primarily by regulating transcript levels. Furthermore, although genetic regulation of the amino acid network was more similar for proteins and transcripts, regression analysis demonstrated that even here, proteins vary predominantly as a result of non-transcriptional variation. We also found that cis regulation, which is common in the transcriptome, is rare at the level of the proteome. We conclude that most inter-individual variation in levels of these particular high abundance proteins in this genetically diverse population is not caused by variation of their underlying transcripts.
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Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics.
Neuron
PUBLISHED: 05-19-2010
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The Purkinje cell degeneration (pcd) mouse is a recessive model of neurodegeneration, involving cerebellum and retina. Purkinje cell death in pcd is dramatic, as >99% of Purkinje neurons are lost in 3 weeks. Loss of function of Nna1 causes pcd, and Nna1 is a highly conserved zinc carboxypeptidase. To determine the basis of pcd, we implemented a two-pronged approach, combining characterization of loss-of-function phenotypes of the Drosophila Nna1 ortholog (NnaD) with proteomics analysis of pcd mice. Reduced NnaD function yielded larval lethality, with survivors displaying phenotypes that mirror disease in pcd. Quantitative proteomics revealed expression alterations for glycolytic and oxidative phosphorylation enzymes. Nna proteins localize to mitochondria, loss of NnaD/Nna1 produces mitochondrial abnormalities, and pcd mice display altered proteolytic processing of Nna1 interacting proteins. Our studies indicate that Nna1 loss of function results in altered bioenergetics and mitochondrial dysfunction.
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Surface acoustic wave nebulization of peptides as a microfluidic interface for mass spectrometry.
Anal. Chem.
PUBLISHED: 04-07-2010
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We describe the fabrication of a surface acoustic wave (SAW) device on a LiNbO(3) piezoelectric transducer for the transfer of nonvolatile analytes to the gas phase at atmospheric pressure (a process referred to as nebulization or atomization). We subsequently show how such a device can be used in the field of mass spectrometry (MS) detection, demonstrating that SAW nebulization (SAWN) can be performed either in a discontinuous or pulsed mode, similar to that for matrix assisted laser desorption ionization (MALDI) or in a continuous mode like electrospray ionization (ESI). We present data showing the transfer of peptides to the gas phase, where ions are detected by MS. These peptide ions were subsequently fragmented by collision-induced dissociation, from which the sequence was assigned. Unlike MALDI mass spectra, which are typically contaminated with matrix ions at low m/z, the SAWN generated spectra had no such interference. In continuous mode, the SAWN plume was sampled on a microsecond time scale by a linear ion trap mass spectrometer and produced multiply charged peptide precursor ions with a charge state distribution shifted to higher m/z compared to an identical sample analyzed by ESI. The SAWN technology also provides the opportunity to re-examine a sample from a flat surface, repeatedly. The process can be performed without the need for capillaries, which can clog, reservoirs, which dilute the sample, and electrodes, which when in direct contact with sample, cause unwanted electrochemical oxidation. In both continuous and pulsed sampling modes, the quality of precursor ion scans and tandem mass spectra of peptides was consistent across the plumes lifetime.
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xComb: a cross-linked peptide database approach to protein-protein interaction analysis.
J. Proteome Res.
PUBLISHED: 03-23-2010
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We developed an informatic method to identify tandem mass spectra composed of chemically cross-linked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and X!Tandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community.
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Shearwater foraging in the Southern Ocean: the roles of prey availability and winds.
PLoS ONE
PUBLISHED: 03-15-2010
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Sooty (Puffinus griseus) and short-tailed (P. tenuirostris) shearwaters are abundant seabirds that range widely across global oceans. Understanding the foraging ecology of these species in the Southern Ocean is important for monitoring and ecosystem conservation and management.
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A review of seabird energetics using the doubly labeled water method.
Comp. Biochem. Physiol., Part A Mol. Integr. Physiol.
PUBLISHED: 01-26-2010
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The doubly labeled water (DLW) method has been essential for understanding animal energetics of free-ranging individuals. The first published studies on free-ranging seabirds were conducted on penguins in the early 1980s. Since then, nearly 50 seabird species with representatives from each major taxonomic order have been studied using DLW. Although the basic methodology has not changed, there are at least nine different equations, varying with respect to assumptions on fractionation and the total body water pool, to estimate field metabolic rate (FMR) from isotopic water turnover. In this review, I show that FMR can vary by as much as 45% depending on the equation used to calculate CO(2) production in five albatross species. Energy budgets derived from DLW measurements are critical tools for understanding patterns of energy use and allocation in seabirds. However, they depend on accurate and representative measurements of FMR, so analyses that include greater partitioning of activity specific FMR yield more realistic cost estimates. I also show how the combined use of DLW and biologging methods can 1) provide greater clarity for explaining observed variation in FMR measurements within a species and 2) allow FMRs to be viewed in a wider physiological, behavioral, or ecological context. Finally, I update existing allometric equations with new FMR data. These updates reaffirm that albatrosses have the lowest at-sea FMRs per equivalent body mass and that individuals of other seabird orders have FMRs ranging between 1.39 and 2.24 times higher than albatrosses.
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Deciphering diatom biochemical pathways via whole-cell proteomics.
Aquat. Microb. Ecol.
PUBLISHED: 10-16-2009
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Diatoms play a critical role in the oceans carbon and silicon cycles; however, a mechanistic understanding of the biochemical processes that contribute to their ecological success remains elusive. Completion of the Thalassiosira pseudonana genome provided blueprints for the potential biochemical machinery of diatoms, but offers only a limited insight into their biology under various environmental conditions. Using high-throughput shotgun proteomics, we identified a total of 1928 proteins expressed by T. pseudonana cultured under optimal growth conditions, enabling us to analyze this diatoms primary metabolic and biosynthetic pathways. Of the proteins identified, 70% are involved in cellular metabolism, while 11% are involved in the transport of molecules. We identified all of the enzymes involved in the urea cycle, thereby describing the complete pathway to convert ammonia to urea, along with urea transporters, and the urea-degrading enzyme urease. Although metabolic exchange between these pathways remains ambiguous, their constitutive presence suggests complex intracellular nitrogen recycling. In addition, all C(4) related enzymes for carbon fixation have been identified to be in abundance, with high protein sequence coverage. Quantification of mass spectra acquisitions demonstrated that the 20 most abundant proteins included an unexpectedly high expression of clathrin, which is the primary structural protein involved in endocytic transport. This result highlights a previously overlooked mechanism for the inter- and intra-cellular transport of nutrients and macromolecules in diatoms, potentially providing a missing link to organelle communication and metabolite exchange. Our results demonstrate the power of proteomics, and lay the groundwork for future comparative proteomic studies and directed analyses of specifically expressed proteins and biochemical pathways of oceanic diatoms.
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Proteomics on Fixed Tissue Specimens - A Review.
Curr Proteomics
PUBLISHED: 10-16-2009
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The vast majority of clinical tissue samples are formalin-fixed and paraffin-preserved. This type of preservation has been considered an obstacle to protein extraction from these tissues. However, these are the very tissue samples that have associated patient histories, diagnoses and outcomes - ideal samples in the quest to translate bench research into clinical applications. Thus, until recently, these valuable specimens have been unavailable for proteomic analysis.Over the last decade, researchers have been exploring efficient methods to undo protein cross-linking caused by standard tissue fixatives and extract proteins from archived tissue specimens. These methods have been applied in different clinical proteomic studies. In this report, we attempt to review the development of these techniques, summarize the proteomic findings, and discuss the impact on future clinical proteomics.
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Identification, cloning, expression, and purification of Francisella lpp3: an immunogenic lipoprotein.
Microbiol. Res.
PUBLISHED: 09-02-2009
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The severe and fatal human disease, tularemia, results from infection with the Gram-negative pathogen Francisella tularensis. Identification of surface outer membrane proteins, specifically lipoproteins, has been of interest for vaccine development and understanding the initiation of disease. We sought to identify Francisella live vaccine strain lipoproteins that could be a component of a subunit vaccine and have adjuvant properties as TLR2 agonists. We have identified a membrane lipoprotein of Francisella LVS isolated by sarkosyl extraction and gel filtration chromatography that is recognized by sera from LVS-vaccinated individuals and tularemia patients, indicating its potential diagnostic value. Sequencing of the protein by mass spectrometry indicated that it encodes the FTL_0645 open reading frame of F. holarctica LVS, which is 100% identical/homologous to FTT1416c of F. tularensis Schu S4. The predicted 137 amino acid lipoprotein encoded by FTL_0645 ORF, was expressed in Escherichia coli, purified, and demonstrated to be a lipoprotein. This recombinant lipoprotein, named Flpp3, was able to activate TLR2 and induce an immunogenic response in mice, suggesting that the E. coli-expressed Flpp3 is palmitoylated and closely resembles the native protein in structure and immunogenicity. Taken together, these data suggest that Flpp3 could be a candidate for inclusion in a F. tularensis vaccine.
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Tandem mass spectrometry investigation of ADP-ribosylated kemptide.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 08-29-2009
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Bacterial adenosine diphosphate-ribosyltransferases (ADPRTs) are toxins that play a significant role in pathogenicity by inactivating host proteins through covalent addition of ADP-ribose. In this study we used ADP-ribosylated Kemptide (LRRASLG) as a standard to examine the effectiveness of three common tandem mass spectrometry fragmentation methods for assignment of amino acid sequence and site of modification. Fragmentation mechanisms investigated include low-energy collision-induced dissociation (CID), infrared multiphoton dissociation (IRMPD), and electron-capture dissociation (ECD); all were performed on a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer. We show that ECD, but neither CID nor IRMPD, of ADP-ribosylated Kemptide produces tandem mass spectra that are interpretable with regard to amino acid sequence assignment and site of modification. Examination of CID and IRMPD tandem mass spectra of ADP-ribosylated Kemptide revealed that fragmentation was primarily focused to the ADP-ribose region, generating several potential diagnostic ions for use in discovery of ADP-ribosylated proteins. Because of the lower relative sensitivity of ECD during data-dependent acquisition to CID, we suggest a 2-fold strategy where CID and IRMPD are first used to detect ADP-ribosylated peptides, followed by sequence assignment and location of modification by ECD analysis.
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Bringing home the trash: do colony-based differences in foraging distribution lead to increased plastic ingestion in Laysan albatrosses?
PLoS ONE
PUBLISHED: 08-24-2009
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When searching for prey, animals should maximize energetic gain, while minimizing energy expenditure by altering their movements relative to prey availability. However, with increasing amounts of marine debris, what once may have been optimal foraging strategies for top marine predators, are leading to sub-optimal diets comprised in large part of plastic. Indeed, the highly vagile Laysan albatross (Phoebastria immutabilis) which forages throughout the North Pacific, are well known for their tendency to ingest plastic. Here we examine whether Laysan albatrosses nesting on Kure Atoll and Oahu Island, 2,150 km apart, experience different levels of plastic ingestion. Twenty two geolocators were deployed on breeding adults for up to two years. Regurgitated boluses of undigestable material were also collected from chicks at each site to compare the amount of plastic vs. natural foods. Chicks from Kure Atoll were fed almost ten times the amount of plastic compared to chicks from Oahu despite boluses from both colonies having similar amounts of natural food. Tracking data indicated that adults from either colony did not have core overlapping distributions during the early half of the breeding period and that adults from Kure had a greater overlap with the putative range of the Western Garbage Patch corroborating our observation of higher plastic loads at this colony. At-sea distributions also varied throughout the year suggesting that Laysan albatrosses either adjusted their foraging behavior according to constraints on time away from the nest or to variation in resources. However, in the non-breeding season, distributional overlap was greater indicating that the energy required to reach the foraging grounds was less important than the total energy available. These results demonstrate how a marine predator that is not dispersal limited alters its foraging strategy throughout the reproductive cycle to maximize energetic gain and how this has led to differences in plastic ingestion.
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Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean.
Anal. Chem.
PUBLISHED: 07-04-2009
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Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Here, we demonstrate the superior performance of a data-independent method we term precursor acquisition independent from ion count (PAcIFIC). Our results show that almost the entire, predicted, soluble bacterial proteome can be thoroughly analyzed by PAcIFIC without the need for any sample fractionation other than the C18-based liquid chromatograph used to introduce the peptide mixture into the mass spectrometer. Importantly, we also show that PAcIFIC provides unique performance for analysis of human plasma in terms of the number of proteins identified (746 at FDR < or = 0.5%) and achieved dynamic range (8 orders of magnitude at FDR < or = 0.5%), without any fractionation other than immuno-depletion of the seven most abundant proteins.
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Shotgun proteomics implicates extracellular matrix proteins and protease systems in neuronal development induced by astrocyte cholinergic stimulation.
J. Neurochem.
PUBLISHED: 04-21-2009
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Astrocytes play an important role in neuronal development through the release of soluble factors that affect neuronal maturation. Shotgun proteomics followed by gene ontology analysis was used in this study to identify proteins present in the conditioned medium of primary rat astrocytes. One hundred and thirty three secreted proteins were identified, the majority of which were never before reported to be produced by astrocytes. Extracellular proteins were classified based on their biological and molecular functions; most of the identified proteins were involved in neuronal development. Semi-quantitative proteomic analysis was carried out to identify changes in the levels of proteins released by astrocytes after stimulation with the cholinergic agonist carbachol, as we have previously reported that carbachol-treated astrocytes elicit neuritogenesis in hippocampal neurons through the release of soluble factors. Carbachol up-regulated secretion of 15 proteins and down-regulated the release of 17 proteins. Changes in the levels of four proteins involved in neuronal differentiation (thrombospondin-1, fibronectin, plasminogen activator inhibitor-1, and plasminogen activator urokinase) were verified by western blot or ELISA. In conclusion, this study identified a large number of proteins involved in neuronal development in the astrocyte secretome and implicated extracellular matrix proteins and protease systems in neuronal development induced by astrocyte cholinergic stimulation.
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Precursor ion independent algorithm for top-down shotgun proteomics.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 03-21-2009
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We present a precursor ion independent top-down algorithm (PIITA) for use in automated assignment of protein identifications from tandem mass spectra of whole proteins. To acquire the data, we utilize data-dependent acquisition to select protein precursor ions eluting from a C4-based HPLC column for collision induced dissociation in the linear ion trap of an LTQ-Orbitrap mass spectrometer. Gas-phase fractionation is used to increase the number of acquired tandem mass spectra, all of which are recorded in the Orbitrap mass analyzer. To identify proteins, the PIITA algorithm compares deconvoluted, deisotoped, observed tandem mass spectra to all possible theoretical tandem mass spectra for each protein in a genomic sequence database without regard for measured parent ion mass. Only after a protein is identified, is any difference in measured and theoretical precursor mass used to identify and locate post-translation modifications. We demonstrate the application of PIITA to data generated via our wet-lab approach on a Salmonella typhimurium outer membrane extract and compare these results to bottom-up analysis. From these data, we identify 154 proteins by top-down analysis, 73 of which were not identified in a parallel bottom-up analysis. We also identify 201 unique isoforms of these 154 proteins at a false discovery rate (FDR) of <1%.
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Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics.
Prostate
PUBLISHED: 01-01-2009
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Functional development of the prostate is governed by stromal mesenchyme induction and epithelial response. Stromal/epithelial signaling can be mediated through direct cell-cell contact and diffusible factors and their cell surface receptors. These inducers are likely secreted or membrane-associated extracellular proteins. Given the importance of intercellular communication, it is possible that diseases like cancer could arise from a loss of this communication. One approach to gain a molecular understanding of stromal cells is to identify, as a first step, secreted stromal signaling factors. We proposed to do this by comparative analysis between bladder and prostate.
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Cross-linking mass spectrometry and mutagenesis confirm the functional importance of surface interactions between CYP3A4 and holo/apo cytochrome b(5).
Biochemistry
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Cytochrome b(5) (cyt b(5)) is one of the key components in the microsomal cytochrome P450 monooxygenase system. Consensus has not been reached about the underlying mechanism of cyt b(5) modulation of CYP catalysis. Both cyt b(5) and apo b(5) are reported to stimulate the activity of several P450 isoforms. In this study, the surface interactions of both holo and apo b(5) with CYP3A4 were investigated and compared for the first time. Chemical cross-linking coupled with mass spectrometric analysis was used to identify the potential electrostatic interactions between the protein surfaces. Subsequently, the models of interaction of holo/apo b(5) with CYP3A4 were built using the identified interacting sites as constraints. Both cyt b(5) and apo b(5) were predicted to bind to the same groove on CYP3A4 with close contacts to the B-B loop of CYP3A4, a substrate recognition site. Mutagenesis studies further confirmed that the interacting sites on CYP3A4 (Lys96, Lys127, and Lys421) are functionally important. Mutation of these residues reduced or abolished cyt b(5) binding affinity. The critical role of Arg446 on CYP3A4 in binding to cyt b(5) and/or cytochrome P450 reductase was also discovered. The results indicated that electrostatic interactions on the interface of the two proteins are functionally important. The results indicate that apo b(5) can dock with CYP3A4 in a manner analogous to that of holo b(5), so electron transfer from cyt b(5) is not required for its effects.
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The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus.
Cell
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In addition to sculpting eukaryotic transcripts by removing introns, pre-mRNA splicing greatly impacts protein composition of the emerging mRNP. The exon junction complex (EJC), deposited upstream of exon-exon junctions after splicing, is a major constituent of spliced mRNPs. Here, we report comprehensive analysis of the endogenous human EJC protein and RNA interactomes. We confirm that the major "canonical" EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions and that the majority of exon junctions carry an EJC. Unexpectedly, we find that endogenous EJCs multimerize with one another and with numerous SR proteins to form megadalton sized complexes in which SR proteins are super-stoichiometric to EJC core factors. This tight physical association may explain known functional parallels between EJCs and SR proteins. Further, their protection of long mRNA stretches from nuclease digestion suggests that endogenous EJCs and SR proteins cooperate to promote mRNA packaging and compaction.
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Physical performance assessment in military service members.
J Am Acad Orthop Surg
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Few established measures allow effective quantification of physical performance in severely injured service members. We sought to establish preliminary normative data in 180 healthy, active-duty service members for physical performance measures that can be readily implemented in a clinical setting. Interrater and test-retest reliability and minimal detectable change (MDC) values were also determined. Physical performance testing included self-selected walking velocity on level and uneven terrain, timed stair ascent, the sit-to-stand five times test, the four-square step test, and the 6-minute walk test. Data analysis included descriptive statistics, intraclass correlation coefficients, and MDC. Interrater and test-retest reliability were excellent for all measures (intraclass correlation coefficients >0.75). MDC values for timed measures were <0.3 seconds for interrater comparisons and <1.5 seconds for between-day comparisons. Physical performance measures had a narrow range of normal performance and were reliable and stable between days.
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Transcription factor Foxp3 and its protein partners form a complex regulatory network.
Nat. Immunol.
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The transcription factor Foxp3 is indispensible for the differentiation and function of regulatory T cells (T(reg) cells). To gain insights into the molecular mechanisms of Foxp3-mediated gene expression, we purified Foxp3 complexes and explored their composition. Biochemical and mass-spectrometric analyses revealed that Foxp3 forms multiprotein complexes of 400-800 kDa or larger and identified 361 associated proteins, ?30% of which were transcription related. Foxp3 directly regulated expression of a large proportion of the genes encoding its cofactors. Some transcription factor partners of Foxp3 facilitated its expression. Functional analysis of the cooperation of Foxp3 with one such partner, GATA-3, provided additional evidence for a network of transcriptional regulation afforded by Foxp3 and its associates to control distinct aspects of T(reg) cell biology.
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Clinical and electrodiagnostic abnormalities of the median nerve in US Army Dental Assistants at the onset of training.
US Army Med Dep J
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PURPOSE/HYPOTHESIS: Dental personnel including dentists, dental hygienists, and dental assistants have been reported as having a high prevalence of upper-extremity musculoskeletal disorders, including carpal tunnel syndrome. Previous research has not involved dental assistant students at the onset of dental training. Therefore, the purpose of this study was to determine the presence of median and ulnar neuropathies in US Army dental assistants at the onset of their training.
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Serine/threonine acetylation of TGF?-activated kinase (TAK1) by Yersinia pestis YopJ inhibits innate immune signaling.
Proc. Natl. Acad. Sci. U.S.A.
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The Gram-negative bacteria Yersinia pestis, causative agent of plague, is extremely virulent. One mechanism contributing to Y. pestis virulence is the presence of a type-three secretion system, which injects effector proteins, Yops, directly into immune cells of the infected host. One of these Yop proteins, YopJ, is proapoptotic and inhibits mammalian NF-?B and MAP-kinase signal transduction pathways. Although the molecular mechanism remained elusive for some time, recent work has shown that YopJ acts as a serine/threonine acetyl-transferase targeting MAP2 kinases. Using Drosophila as a model system, we find that YopJ inhibits one innate immune NF-?B signaling pathway (IMD) but not the other (Toll). In fact, we show YopJ mediated serine/threonine acetylation and inhibition of dTAK1, the critical MAP3 kinase in the IMD pathway. Acetylation of critical serine/threonine residues in the activation loop of Drosophila TAK1 blocks phosphorylation of the protein and subsequent kinase activation. In addition, studies in mammalian cells show similar modification and inhibition of hTAK1. These data present evidence that TAK1 is a target for YopJ-mediated inhibition.
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FANCJ/BACH1 acetylation at lysine 1249 regulates the DNA damage response.
PLoS Genet.
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BRCA1 promotes DNA repair through interactions with multiple proteins, including CtIP and FANCJ (also known as BRIP1/BACH1). While CtIP facilitates DNA end resection when de-acetylated, the function of FANCJ in repair processing is less well defined. Here, we report that FANCJ is also acetylated. Preventing FANCJ acetylation at lysine 1249 does not interfere with the ability of cells to survive DNA interstrand crosslinks (ICLs). However, resistance is achieved with reduced reliance on recombination. Mechanistically, FANCJ acetylation facilitates DNA end processing required for repair and checkpoint signaling. This conclusion was based on the finding that FANCJ and its acetylation were required for robust RPA foci formation, RPA phosphorylation, and Rad51 foci formation in response to camptothecin (CPT). Furthermore, both preventing and mimicking FANCJ acetylation at lysine 1249 disrupts FANCJ function in checkpoint maintenance. Thus, we propose that the dynamic regulation of FANCJ acetylation is critical for robust DNA damage response, recombination-based processing, and ultimately checkpoint maintenance.
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Automation to improve efficiency of field expedient injury prediction screening.
J Strength Cond Res
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Musculoskeletal injuries are a primary source of disability in the U.S. Military. Physical training and sports-related activities account for up to 90% of all injuries, and 80% of these injuries are considered overuse in nature. As a result, there is a need to develop an evidence-based musculoskeletal screen that can assist with injury prevention. The purpose of this study was to assess the capability of an automated system to improve the efficiency of field expedient tests that may help predict injury risk and provide corrective strategies for deficits identified. The field expedient tests include survey questions and measures of movement quality, balance, trunk stability, power, mobility, and foot structure and mobility. Data entry for these tests was automated using handheld computers, barcode scanning, and netbook computers. An automated algorithm for injury risk stratification and mitigation techniques was run on a server computer. Without automation support, subjects were assessed in 84.5 ± 9.1 minutes per subject compared with 66.8 ± 6.1 minutes per subject with automation and 47.1 ± 5.2 minutes per subject with automation and process improvement measures (p < 0.001). The average time to manually enter the data was 22.2 ± 7.4 minutes per subject. An additional 11.5 ± 2.5 minutes per subject was required to manually assign an intervention strategy. Automation of this injury prevention screening protocol using handheld devices and netbook computers allowed for real-time data entry and enhanced the efficiency of injury screening, risk stratification, and prescription of a risk mitigation strategy.
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LPS remodeling is an evolved survival strategy for bacteria.
Proc. Natl. Acad. Sci. U.S.A.
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Maintenance of membrane function is essential and regulated at the genomic, transcriptional, and translational levels. Bacterial pathogens have a variety of mechanisms to adapt their membrane in response to transmission between environment, vector, and human host. Using a well-characterized model of lipid A diversification (Francisella), we demonstrate temperature-regulated membrane remodeling directed by multiple alleles of the lipid A-modifying N-acyltransferase enzyme, LpxD. Structural analysis of the lipid A at environmental and host temperatures revealed that the LpxD1 enzyme added a 3-OH C18 acyl group at 37 °C (host), whereas the LpxD2 enzyme added a 3-OH C16 acyl group at 18 °C (environment). Mutational analysis of either of the individual Francisella lpxD genes altered outer membrane (OM) permeability, antimicrobial peptide, and antibiotic susceptibility, whereas only the lpxD1-null mutant was attenuated in mice and subsequently exhibited protection against a lethal WT challenge. Additionally, growth-temperature analysis revealed transcriptional control of the lpxD genes and posttranslational control of the LpxD1 and LpxD2 enzymatic activities. These results suggest a direct mechanism for LPS/lipid A-level modifications resulting in alterations of membrane fluidity, as well as integrity and may represent a general paradigm for bacterial membrane adaptation and virulence-state adaptation.
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Long-term correction of very long-chain acyl-coA dehydrogenase deficiency in mice using AAV9 gene therapy.
Mol. Ther.
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Very long-chain acyl-coA dehydrogenase (VLCAD) is the rate-limiting step in mitochondrial fatty acid oxidation. VLCAD-deficient mice and patients clinical symptoms stem from not only an energy deficiency but also long-chain metabolite accumulations. VLCAD-deficient mice were treated systemically with 1 × 10(12) vector genomes of recombinant adeno-associated virus 9 (rAAV9)-VLCAD. Biochemical correction was observed in vector-treated mice beginning 2 weeks postinjection, as characterized by a significant drop in long-chain fatty acyl accumulates in whole blood after an overnight fast. Changes persisted through the termination point around 20 weeks postinjection. Magnetic resonance spectroscopy (MRS) and tandem mass spectrometry (MS/MS) revealed normalization of intramuscular lipids in treated animals. Correction was not observed in liver tissue extracts, but cardiac muscle extracts showed significant reduction of long-chain metabolites. Disease-specific phenotypes were characterized, including thermoregulation and maintenance of euglycemia after a fasting cold challenge. Internal body temperatures of untreated VLCAD(-/-) mice dropped below 20 °C and the mice became lethargic, requiring euthanasia. In contrast, all rAAV9-treated VLCAD(-/-) mice and the wild-type controls maintained body temperatures. rAAV9-treated VLCAD(-/-) mice maintained euglycemia, whereas untreated VLCAD(-/-) mice suffered hypoglycemia following a fasting cold challenge. These promising results suggest rAAV9 gene therapy as a potential treatment for VLCAD deficiency in humans.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.