A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer

Genetic and Serologic Properties of Zika Virus Associated with an Epidemic, Yap State, Micronesia, 2007

One-sentence summary for table of contents: The full coding region nucleic acid sequence and serologic properties of the virus were identified

Pretreatment with phenoxybenzamine attenuates the radial artery's vasoconstrictor response to α-adrenergic stimuli

AbstractBackgroundAlthough the radial artery bypass conduit has excellent intermediate-term patency, it has a proclivity to vasospasm. We tested the hypothesis that brief pretreatment of a radial artery graft with the irreversible adrenergic antagonist phenoxybenzamine attenuates the vasoconstrictor response to the vasopressors phenylephrine and norepinephrine compared with the currently used papaverine/lidocaine.MethodsSegments of human radial artery grafts were obtained after a 30-minute intraoperative pretreatment with a solution containing 20 mL of heparinized blood, 0.4 mL of papaverine (30 mg/mL), and 1.6 mL of lidocaine (1%). The segments were transported to the laboratory and placed into a bath containing Krebs-Henseleit solution and 10, 100, or 1000 μmol/L phenoxybenzamine or vehicle. The segments were tested in organ chambers for contractile responses to increasing concentrations of phenylephrine and norepinephrine (0.5-15 μmol/L).ResultsContractile responses to 15 μmol/L phenylephrine in control radial artery segments averaged 44.2% ± 9.1% of the maximal contractile response to 30 mmol/L KCl. Papaverine/lidocaine modestly attenuated contraction to 15 μmol/L phenylephrine (32.1% ± 5.9%; P = .22), but 1000 μmol/L phenoxybenzamine completely abolished radial artery contraction (−7.2% ± 4.4%; P < .001). The effect of 10 and 100 μmol/L phenoxybenzamine on attenuating vasocontraction was intermediate between 1000 μmol/L phenoxybenzamine and papaverine/lidocaine. Responses to 15 μmol/L norepinephrine in control radial artery segments averaged 54.7% ± 7.5% of maximal contraction to 30 mmol/L KCl. Papaverine/lidocaine modestly attenuated the contraction response of radial artery segments (35.6% ± 5.1%; P = .04). In contrast, 1000 μmol/L phenoxybenzamine showed the greatest attenuation of norepinephrine-induced contraction (−10.5% ± 2.0%; P < .001).ConclusionsA brief pretreatment of the human radial artery bypass conduit with 1000 μmol/L phenoxybenzamine completely attenuates the vasoconstrictor responses to the widely used vasopressors norepinephrine and phenylephrine. Papaverine/lidocaine alone did not block vasoconstriction to these α-adrenergic agonists

Extracellular superoxide dismutase (SOD3) regulates oxidative stress at the vitreoretinal interface

Oxidative stress is a pathogenic feature in vitreoretinal disease. However, the ability of the inner retina to manage metabolic waste and oxidative stress is unknown. Proteomic analysis of antioxidants in the human vitreous, the extracellular matrix opposing the inner retina, identified superoxide dismutase-3 (SOD3) that localized to a unique matrix structure in the vitreous base and cortex. To determine the role of SOD3, Sod3-/- mice underwent histological and clinical phenotyping. Although the eyes were structurally normal, at the vitreoretinal interface Sod3-/- mice demonstrated higher levels of 3-nitrotyrosine, a key marker of oxidative stress. Pattern electroretinography also showed physiological signaling abnormalities within the inner retina. Vitreous biopsies and epiretinal membranes collected from patients with diabetic vitreoretinopathy (DVR) and a mouse model of DVR showed significantly higher levels of nitrates and/or 3-nitrotyrosine oxidative stress biomarkers suggestive of SOD3 dysfunction. This study analyzes the molecular pathways that regulate oxidative stress in human vitreous substructures. The absence or dysregulation of the SOD3 antioxidant at the vitreous base and cortex results in increased oxidative stress and tissue damage to the inner retina, which may underlie DVR pathogenesis and other vitreoretinal diseases

MHCII glycosylation modulates Bacteroides fragilis carbohydrate antigen presentation

N-linked glycans on class II MHC molecules are required for the presentation of glycoantigens, but not peptide antigens

SCIPP: An Expanded Community of Practice - Community Publishing

SCIPP redefines and expands the existing notions about what makes for a vibrant and robust community of practice by partnering CSUSB students and professors with K-12 students, parents, and educators, along with committed community partners. SCIPP encourages curiosity in ways that leads to critical thinking, exploration, risk taking , confidence building, open-mindedness, and other personal traits that equip them with the softskills to be active, critical, and creative contributors to our communities. SCIPP pedagogy embraces our students\u27 collective wisdom and focuses on relational building where multi-directional communication is promoted and students are viewed as equal stakeholders in their own educations. SCIPP puts collaboration into action which in turn fosters community-based lifelong learning. SCIPP provides the open intellectual space for future university students (our K-12 students) to engage with existing university students in meaningful ways so as to sustain interconnected partnerships facilitating community engagement. It supports parents as experts in the education of their children and acknowledges parents as the first conduits to spark their children’s imagination while they actively participate in education enriching activities and programs. Everyone involved is committed to creating a secure and open atmosphere for dreaming, sharing, and learning. Together we explore the aspects of community publishing through collaborative learning in formal and informal settings relating to digital and printed medias

Ephemeris and hazard assessment for near-Earth asteroid (101955) Bennu based on OSIRIS-REx data

Small bodies such as the near-Earth asteroid Bennu drift in their orbit due to thermal radiation forces (the Yarkovsky effect). Ground-based observations have indicated a nonzero probability of Bennu impacting Earth, depending on how its orbit evolves. Thus, among the goals of the OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer) mission to Bennu were to precisely measure the Yarkovsky effect and refine the impact hazard assessment for this body. Here we address these objectives. Using OSIRIS-REx spacecraft tracking data, we derive meter-level constraints on the distance between Earth and Bennu from January 2019 to October 2020. While these data greatly improve the knowledge of the trajectory of Bennu, they also require an unprecedented fidelity for the modeling of an asteroid’s trajectory. In particular, special care is needed to take into account the contribution of 343 small-body perturbers and the uncertainty in their masses. Radiation effects such as the Poynting–Robertson drag, so far only considered for interplanetary dust dynamics, now become a consideration for modeling the trajectory of a 500-m asteroid such as Bennu. By employing a thermophysical model based on OSIRIS-REx’s characterization of Bennu, we estimate a semimajor axis drift of−284.6 ± 0.2m/yr (signal-to-noise ratio∼1400) at epoch 2011 January 1 caused by the Yarkovsky effect. The largest source of modeling error is solar wind drag, which may lower the magnitude of the semimajor axis drift from the Yarkovsky effect by up to 0.16 m/yr. The Yarkovsky-related semimajor axis drift varies by roughly±1m/yr as the orbit of Bennu evolves due to planetary perturbations from 1900 to 2135. The Yarkovsky thermophysical model proves to be extremely accurate by predicting a bulk density estimate within 0.1% of that estimated through gravity science analysis. Compared to the information available before the OSIRIS-REx mission, the knowledge of the circumstances of the scattering Earth encounter that will occur in 2135 improves by a factor of 20, thus allowing us to rule out many previously possible impact trajectories. However, there remain some impact trajectories compatible with the data. Prior to the spacecraft encounter, the overall impact probability through 2200 was 3.7 × 10−4 (1 in 2700). As a result of our analysis, the cumulative impact probability through 2300 becomes 5.7 × 10−4 (1 in 1750) and the most significant individual impact solution is for September 2182, with an impact probability of 3.7 × 10−4 (1 in 2700). Both Bennu and (29075) 1950 DA have a Palermo scale value of −1.42 and share the distinction as the currently most hazardous object in the asteroid catalog

Is the Hyporheic Zone Relevant beyond the Scientific Community?

Rivers are important ecosystems under continuous anthropogenic stresses. The hyporheic zone is a ubiquitous, reactive interface between the main channel and its surrounding sediments along the river network. We elaborate on the main physical, biological, and biogeochemical drivers and processes within the hyporheic zone that have been studied by multiple scientific disciplines for almost half a century. These previous efforts have shown that the hyporheic zone is a modulator for most metabolic stream processes and serves as a refuge and habitat for a diverse range of aquatic organisms. It also exerts a major control on river water quality by increasing the contact time with reactive environments, which in turn results in retention and transformation of nutrients, trace organic compounds, fine suspended particles, and microplastics, among others. The paper showcases the critical importance of hyporheic zones, both from a scientific and an applied perspective, and their role in ecosystem services to answer the question of the manuscript title. It identifies major research gaps in our understanding of hyporheic processes. In conclusion, we highlight the potential of hyporheic restoration to efficiently manage and reactivate ecosystem functions and services in river corridors