Protein phosphorylation is one of the most widespread post-translational modifications in biology
. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine ...phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes
. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible
. Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.
Warming climates are rapidly transforming lake ecosystems worldwide, but the breadth of changes in tropical lakes is poorly documented. Sustainable management of freshwater fisheries and biodiversity ...requires accounting for historical and ongoing stressors such as climate change and harvest intensity. This is problematic in tropical Africa, where records of ecosystem change are limited and local populations rely heavily on lakes for nutrition. Here, using a ∼1,500-y paleoecological record, we show that declines in fishery species and endemic molluscs began well before commercial fishing in Lake Tanganyika, Africa’s deepest and oldest lake. Paleoclimate and instrumental records demonstrate sustained warming in this lake during the last ∼150 y, which affects biota by strengthening and shallowing stratification of the water column. Reductions in lake mixing have depressed algal production and shrunk the oxygenated benthic habitat by 38% in our study areas, yielding fish and mollusc declines. Late-20th century fish fossil abundances at two of three sites were lower than at any other time in the last millennium and fell in concert with reduced diatom abundance and warming water. A negative correlation between lake temperature and fish and mollusc fossils over the last ∼500 y indicates that climate warming and intensifying stratification have almost certainly reduced potential fishery production, helping to explain ongoing declines in fish catches. Long-term declines of both benthic and pelagic species underscore the urgency of strategic efforts to sustain Lake Tanganyika’s extraordinary biodiversity and ecosystem services.
Glioblastoma is the most common primary malignant brain tumor in adults and is associated with poor survival. The Ivy Foundation Early Phase Clinical Trials Consortium conducted a randomized, ...multi-institution clinical trial to evaluate immune responses and survival following neoadjuvant and/or adjuvant therapy with pembrolizumab in 35 patients with recurrent, surgically resectable glioblastoma. Patients who were randomized to receive neoadjuvant pembrolizumab, with continued adjuvant therapy following surgery, had significantly extended overall survival compared to patients that were randomized to receive adjuvant, post-surgical programmed cell death protein 1 (PD-1) blockade alone. Neoadjuvant PD-1 blockade was associated with upregulation of T cell- and interferon-γ-related gene expression, but downregulation of cell-cycle-related gene expression within the tumor, which was not seen in patients that received adjuvant therapy alone. Focal induction of programmed death-ligand 1 in the tumor microenvironment, enhanced clonal expansion of T cells, decreased PD-1 expression on peripheral blood T cells and a decreasing monocytic population was observed more frequently in the neoadjuvant group than in patients treated only in the adjuvant setting. These findings suggest that the neoadjuvant administration of PD-1 blockade enhances both the local and systemic antitumor immune response and may represent a more efficacious approach to the treatment of this uniformly lethal brain tumor.
Protecting the upper airway from microbial infection is an important function of the immune system. Proper detection of these pathogens is paramount for sinonasal epithelial cells to be able to ...prepare a defensive response. Toll-like receptors and, more recently, bitter taste receptors and sweet taste receptors have been implicated as sensors able to detect the presence of these pathogens and certain compounds that they secrete. Activation of these receptors also triggers innate immune responses to prevent or counteract infection, including mucociliary clearance and the production and secretion of antimicrobial compounds (e.g., defensins).
To provide an overview of the current knowledge of the role of innate immunity in the upper airway, the mechanisms by which it is carried out, and its clinical relevance.
A literature review of the existing knowledge of the role of innate immunity in the human sinonasal cavity was performed.
Clinical and basic science studies have shown that the physical epithelial cell barrier, mucociliary clearance, and antimicrobial compound secretion play pivotal innate immune roles in defending the sinonasal cavity from infection. Clinical findings have also linked dysfunction of these defense mechanisms with diseases, such as chronic rhinosinusitis and cystic fibrosis. Recent discoveries have elucidated the significance of bitter and sweet taste receptors in modulating immune responses in the upper airway.
Numerous innate immune mechanisms seem to work in a concerted fashion to keep the sinonasal cavity free of infection. Understanding sinonasal innate immune function and dysfunction in health and disease has important implications for patients with respiratory ailments, such as chronic rhinosinusitis and cystic fibrosis.
There is a growing body of evidence demonstrating improved outcomes for patients with CNS neoplasms treated at academic centers (ACs) versus nonacademic centers (non-ACs), which represents a ...potential healthcare disparity within neurosurgery. In this paper, the authors sought to investigate the relationship between facility type and surgical outcomes in meningioma patients.
The National Cancer Database was queried for adult patients diagnosed with intracranial meningioma between 2004 and 2019. Patients were stratified by facility type, and the Mann-Whitney U-test and Fisher exact test were used for bivariate comparisons of continuous and categorical variables, respectively. Multivariate logistic regression was used to assess whether demographic variables were associated with treatment at ACs. Furthermore, multivariate Cox proportional hazards models were used to determine whether facility type was associated with overall survival (OS) outcomes.
Data on 139,304 patients (74% male, 84% White) were retrieved. Patients were stratified by facility type, with 50,349 patients (36%) treated at ACs and 88,955 patients (64%) treated at non-ACs. Patients treated at ACs were more likely to have private insurance (41% vs 34%, p < 0.001) and less likely to have Medicare (46% vs 57%, p < 0.001). Patients treated at ACs were more likely to have larger tumors (36.91 mm vs 33.57 mm, p < 0.001) and more likely to undergo surgery (47% vs 34%, p < 0.001). Interestingly, patients treated at ACs had decreased comorbidities (Charlson Comorbidity Index rating 0: 74% vs 69%) and similar income levels (income ≥ $46,000: 44% vs 43%). With respect to survival outcomes, patients treated at ACs demonstrated a higher median OS at 10 years than patients treated at non-ACs (65.2% vs 54.1%). The association of improved OS in patients treated at ACs continued to be true when adjusting for all other clinical and demographic variables (HR 0.900, 95% CI 0.882-0.918; p < 0.001).
The results of this study indicate that facility type is associated with disparate survival outcomes in the treatment of intracranial meningiomas. Namely, patients treated at non-ACs appear to have a survival disadvantage even when controlling for additional comorbidities.
Acute traumatic coagulopathy has been associated with shock and tissue injury, and may be mediated via activation of the protein C pathway. Patients with acute traumatic coagulopathy have prolonged ...PT and PTT, and decreased activity of factors V and VIII; they are also hypocoagulable by thromboelastometry (ROTEM) and other viscoelastic assays. To test the etiology of this phenomenon, we hypothesized that such coagulopathy could be induced in vitro in healthy human blood with the addition of activated protein C (aPC).
Whole blood was collected from 20 healthy human subjects, and was "spiked" with increasing concentrations of purified human aPC (control, 75, 300, 2000 ng/mL). PT/PTT, factor activity assays, and ROTEM were performed on each sample. Mixed effect regression modeling was performed to assess the association of aPC concentration with PT/PTT, factor activity, and ROTEM parameters.
In all subjects, increasing concentrations of aPC produced ROTEM tracings consistent with traumatic coagulopathy. ROTEM EXTEM parameters differed significantly by aPC concentration, with stepwise prolongation of clotting time (CT) and clot formation time (CFT), decreased alpha angle (α), impaired early clot formation (a10 and a20), and reduced maximum clot firmness (MCF). PT and PTT were significantly prolonged at higher aPC concentrations, with corresponding significant decreases in factor V and VIII activity.
A phenotype of acute traumatic coagulopathy can be induced in healthy blood by the in vitro addition of aPC alone, as evidenced by viscoelastic measures and confirmed by conventional coagulation assays and factor activity. This may lend further mechanistic insight to the etiology of coagulation abnormalities in trauma, supporting the central role of the protein C pathway. Our findings also represent a model for future investigations in the diagnosis and treatment of acute traumatic coagulopathy.
Gastrointestinal complications are an important problem of antithrombotic therapy. Proton-pump inhibitors (PPIs) are believed to decrease the risk of such complications, though no randomized trial ...has proved this in patients receiving dual antiplatelet therapy. Recently, concerns have been raised about the potential for PPIs to blunt the efficacy of clopidogrel.
We randomly assigned patients with an indication for dual antiplatelet therapy to receive clopidogrel in combination with either omeprazole or placebo, in addition to aspirin. The primary gastrointestinal end point was a composite of overt or occult bleeding, symptomatic gastroduodenal ulcers or erosions, obstruction, or perforation. The primary cardiovascular end point was a composite of death from cardiovascular causes, nonfatal myocardial infarction, revascularization, or stroke. The trial was terminated prematurely when the sponsor lost financing.
We planned to enroll about 5000 patients; a total of 3873 were randomly assigned and 3761 were included in analyses. In all, 51 patients had a gastrointestinal event; the event rate was 1.1% with omeprazole and 2.9% with placebo at 180 days (hazard ratio with omeprazole, 0.34, 95% confidence interval CI, 0.18 to 0.63; P<0.001). The rate of overt upper gastrointestinal bleeding was also reduced with omeprazole as compared with placebo (hazard ratio, 0.13; 95% CI, 0.03 to 0.56; P = 0.001). A total of 109 patients had a cardiovascular event, with event rates of 4.9% with omeprazole and 5.7% with placebo (hazard ratio with omeprazole, 0.99; 95% CI, 0.68 to 1.44; P = 0.96); high-risk subgroups did not show significant heterogeneity. The two groups did not differ significantly in the rate of serious adverse events, though the risk of diarrhea was increased with omeprazole.
Among patients receiving aspirin and clopidogrel, prophylactic use of a PPI reduced the rate of upper gastrointestinal bleeding. There was no apparent cardiovascular interaction between clopidogrel and omeprazole, but our results do not rule out a clinically meaningful difference in cardiovascular events due to use of a PPI. (Funded by Cogentus Pharmaceuticals; ClinicalTrials.gov number, NCT00557921.).
Quantifying the timing and intensity of migratory movements is imperative for understanding impacts of changing landscapes and climates on migratory bird populations. Billions of birds migrate in the ...Western Hemisphere, but accurately estimating the population size of one migratory species, let alone hundreds, presents numerous obstacles. Here, we quantify the timing, intensity, and distribution of bird migration through one of the largest migration corridors in the Western Hemisphere, the Gulf of Mexico (the Gulf). We further assess whether there have been changes in migration timing or intensity through the Gulf. To achieve this, we integrate citizen science (eBird) observations with 21 years of weather surveillance radar data (1995–2015). We predicted no change in migration timing and a decline in migration intensity across the time series. We estimate that an average of 2.1 billion birds pass through this region each spring en route to Nearctic breeding grounds. Annually, half of these individuals pass through the region in just 18 days, between April 19 and May 7. The western region of the Gulf showed a mean rate of passage 5.4 times higher than the central and eastern regions. We did not detect an overall change in the annual numbers of migrants (2007–2015) or the annual timing of peak migration (1995–2015). However, we found that the earliest seasonal movements through the region occurred significantly earlier over time (1.6 days decade−1). Additionally, body mass and migration distance explained the magnitude of phenological changes, with the most rapid advances occurring with an assemblage of larger‐bodied shorter‐distance migrants. Our results provide baseline information that can be used to advance our understanding of the developing implications of climate change, urbanization, and energy development for migratory bird populations in North America.
We quantify the timing, intensity, and distribution of bird migration through one of the largest migration corridors in the Western Hemisphere, the Gulf of Mexico, by integrating citizen science (eBird) observations with weather surveillance radar data. We estimate that an average of 2.1 billion birds pass through this region each spring, with half of these individuals pass through the region in just 18 days, between April 19 and May 7. We did not detect an overall change in the annual numbers of migrants (2007–2015) or the annual timing of peak migration (1995–2015).
A strong temperature dependence of oxygen K-edge x-ray absorption fine structure features was observed for supercooled and normal liquid water droplets prepared from the breakup of a liquid microjet. ...Analysis of the data over the temperature range 251 to 288 kelvin (-22° to + 15°C) yields a value of 1.5 ± 0.5 kilocalories per mole for the average thermal energy required to effect an observable rearrangement between the fully coordinated ("ice-like") and distorted ("broken-donor") local hydrogen-bonding configurations responsible for the pre-edge and post-edge features, respectively. This energy equals the latent heat of melting of ice with hexagonal symmetry (ice Ih) and is consistent with the distribution of hydrogen bond strengths obtained for the "overstructured" ST2 model of water.
Graphene, a honeycomb sp2 hybridized carbon lattice, is a promising building block for hybrid-nanomaterials due to its electrical, mechanical, and optical properties. Graphene can be readily obtained ...through mechanical exfoliation, solution-based deposition of reduced graphene oxide (rGO), and chemical vapor deposition (CVD). The resulting graphene films’ topology is two-dimensional (2D) surface. Recently, synthesis of three-dimensional (3D) graphitic networks supported or templated by nanoparticles, foams, and hydrogels was reported. However, the resulting graphene films lay flat on the surface, exposing 2D surface topology. Out-of-plane grown carbon nanostructures, such as vertically aligned graphene sheets (VAGS) and vertical carbon nanowalls (CNWs), are still tethered to 2D surface. 3D morphology of out-of-plane growth of graphene hybrid-nanomaterials which leverages graphene's outstanding surface-to-volume ratio has not been achieved to date. Here we demonstrate highly controlled synthesis of 3D out-of-plane single- to few-layer fuzzy graphene (3DFG) on a Si nanowire (SiNW) mesh template. By varying graphene growth conditions (CH4 partial pressure and process time), we control the size, density, and electrical properties of the NW templated 3DFG (NT-3DFG). 3DFG growth can be described by a diffusion-limited-aggregation (DLA) model. The porous NT-3DFG meshes exhibited high electrical conductivity of ca. 2350 S m−1. NT-3DFG demonstrated exceptional electrochemical functionality, with calculated specific electrochemical surface area as high as ca. 1017 m2 g−1 for a ca. 7 μm thick mesh. This flexible synthesis will inspire formation of complex hybrid-nanomaterials with tailored optical and electrical properties to be used in future applications such as sensing, and energy conversion and storage.
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