Experimental Methods in Cryogenic Spectroscopy: Stark Effect Measurements in Substituted Myoglobin

Dawning from well-defined tertiary structure, the active regions of enzymatic proteins exist as specifically tailored electrostatic microenvironments capable of facilitating chemical interaction. The specific influence these charge distributions have on ligand binding dynamics, and their impact on specificity, reactivity, and biological functionality, have yet to be fully understood. A quantitative determination of these intrinsic fields would offer insight towards the mechanistic aspects of protein functionality. This work seeks to investigate the internal molecular electric fields that are present at the oxygen binding site of myoglobin. Experiments are performed at 1 K on samples located within a glassy matrix, using the high-resolution technique spectral hole-burning. The internal electric field distributions can be explored by implementing a unique mathematical treatment for analyzing the effect that externally applied electric fields have on the spectral hole profiles. Precise control of the light field, the temperature, and the externally applied electric field at the site of the sample is crucial. Experimentally, the functionality of custom cryogenic temperature confocal scanning microscope was extended to allow for collection of imaging and spectral data with the ability to modulate the polarization of the light at the sample. Operation of the instrumentation was integrated into a platform allowing for seamless execution of input commands with high temporal inter-instrument resolution for collection of data streams. For the regulated control and cycling of the sample temperature. the thermal characteristics of the research Dewar were theoretically modeled to systematically predict heat flows throughout the system. A high voltage feedthrough for delivering voltages of up to 5000 V to the sample as positioned within the Dewar was developed. The burning of spectral holes with this particular experimental setup is highly repeatable. The quantum mechanical treatment that is employed during analysis of the experimental data requires the state energies and the transition dipole moments of the porphyrin probe. The configuration interaction, as well as the coupled-cluster approaches, have been investigated for their ability to produce realistic valuations for these calculated quantities as gauged by their ability to accurately reproduce valuations for spectroscopically observable transition energies. A capacitive cell, for the determination of a material’s dielectric permittivity, necessary for defining the magnitude of the externally applied electric field at the sample, was developed and shown to successfully yield permittivity valuations for various media in accordance with those reported the literature, while offering the ability to provide measures for permittivities over the temperature range of 1-300 K

Content analysis of promotional material for asthma-related products and therapies on Instagram

BACKGROUND: Increasingly, social media is a source for information about health and disease self-management. We conducted a content analysis of promotional asthma-related posts on Instagram to understand whether promoted products and services are consistent with the recommendations found in the Global Initiative for Asthma (GINA) 2019 guidelines. METHODS: We collected every Instagram post incorporating a common, asthma-related hashtag between September 29, 2019 and October 5, 2019. Of these 2936 collected posts, we analyzed a random sample of 266, of which, 211 met our inclusion criteria. Using an inductive, qualitative approach, we categorized the promotional posts and compared each post\u27s content with the recommendations contained in the 2019 GINA guidelines. Posts were categorized as consistent with GINA if the content was supported by the GINA guidelines. Posts that promoted content that was not recommended by or was unrelated to the guidelines were categorized as not supported by GINA . RESULTS: Of 211 posts, 89 (42.2%) were promotional in nature. Of these, a total of 29 (32.6%) were categorized as being consistent with GINA guidelines. The majority of posts were not supported by the guidelines. Forty-one (46.1%) posts promoted content that was not recommended by the current guidelines. Nineteen (21.3%) posts promoted content that was unrelated to the guidelines. The majority of unsupported content promoted non-pharmacological therapies (n = 39, 65%) to manage asthma, such as black seed oil, salt-room therapy, or cupping. CONCLUSIONS: The majority of Instagram posts in our sample promoted products or services that were not supported by GINA guidelines. These findings suggest a need for providers to discuss online health information with patients and highlight an opportunity for providers and social media companies to promote evidence-based asthma treatments and self-management advice online

Diatom control of the autotrophic community and particle export in the eastern Bering Sea during the recent cold years (2008–2010)

The southeastern Bering Sea has exhibited shifts in climate since the start of the 21st century. The regional climate shifts are manifested in the duration and areal extent of seasonal sea-ice coverage. During a recent cold period (2008–2010) with extensive spring sea-ice cover over the southeastern shelf of the Bering Sea, a total of 77 water column and 24 sediment trap profiles were collected over the shelf and shelf break and analyzed for autotrophic pigment concentrations and elemental (carbon, nitrogen, phosphorus, and silicon) concentrations in suspended and exported particulate material. These results are used to establish the seasonal succession of the autotrophic community and the control that both phytoplankton and zooplankton exert on export production. In spring (April to mid-June), total chlorophyll a (TChl a) concentrations were generally low (i.e., \u3c 1 μg L–1); however, localized phytoplankton blooms near the marginal ice zone (MIZ) lead to elevated spring average TChl a concentrations (i.e., \u3e5 μg L–1). In summer (mid-June to late July), photic zone chlorophyll a concentrations were typically \u3c1 μg L–1 over the shelf and at the shelf break. Diatoms represented the greatest contribution to TChl a (regional averages of 71%–96% in spring and 25%–75% in summer) and autotrophic biomass in spring and summer. This algal class also represented 50%–99% of TChl a associated with particles sinking from the photic zone. The relatively high proportion of phaeophorbide a in sediment trap material indicates that sinking of zooplankton fecal pellets facilitate the export of particles through the water column. Further, zooplankton grazing may be an important process that returns regenerated nutrients to the water column based on the elemental composition of suspended and sinking particles. In colder than average years, the emergence of diatom blooms in the spring MIZ supports the production of abundant large zooplankton, which are a primary food source for juvenile pelagic fishes of economically important species. Therefore, processes in colder than average years may be essential for the transfer of particulate organic carbon from the surface waters and the success of the economically important pelagic fisheries

The timing of hypertonic saline (HTS) and airway clearance techniques (ACT) in adults with Cystic Fibrosis (CF) during pulmonary exacerbation: Pilot data form a randomised crossover study.

BACKGROUND: Streamlining the timing of treatments in cystic fibrosis (CF) is important to optimise adherence while ensuring efficacy. The optimal timing of treatment with hypertonic saline (HTS) and airway clearance techniques (ACT) is unknown. OBJECTIVES: This study hypothesised that HTS before ACT would be more effective than HTS during ACT as measured by Lung Clearance Index (LCI). METHODS: Adults with CF providing written informed consent were randomised to a crossover trial of HTS before ACT or HTS during ACT on consecutive days. ACT treatment consisted of Acapella Duet. Patients completed LCI and spirometry at baseline and 90 min post treatment. Mean difference (MD) and 95% CIs were reported. RESULTS: 13 subjects completed the study (mean (SD) age 33 (12) years, forced expiratory volume in 1second % (FEV1%) predicted 51% (22), LCI (no. turnovers) 14 (4)). Comparing the two treatments (HTS before ACT vs HTS during ACT), the change from baseline to 90 min post treatment in LCI (MD (95% CI) -0.02 (-0.63 to 0.59)) and FEV1% predicted (MD (95% CI) -0.25 (-2.50 to 1.99)) was not significant. There was no difference in sputum weight (MD (95% CI) -3.0 (-14.9 to 8.9)), patient perceived ease of clearance (MD (95% CI) 0.4 (-0.6 to 1.3) or satisfaction (MD (95% CI) 0.4 (-0.6 to 1.5)). The time taken for HTS during ACT was significantly shorter (MD (95% CI) 14.7 (9.8 to 19.6)). CONCLUSIONS: In this pilot study, HTS before ACT was no more effective than HTS during ACT as measured by LCI. TRIAL REGISTRATION NUMBER: NCT01753869; Pre-results

Engineered SH2 domains with tailored specificities and enhanced affinities for phosphoproteome analysis

Protein phosphorylation is the most abundant post-translational modification in cells. Src homology 2 (SH2) domains specifically recognize phosphorylated tyrosine (pTyr) residues to mediate signaling cascades. A conserved pocket in the SH2 domain binds the pTyr side chain and the EF and BG loops determine binding specificity. By using large phage-displayed libraries, we engineered the EF and BG loops of the Fyn SH2 domain to alter specificity. Engineered SH2 variants exhibited distinct specificity profiles and were able to bind pTyr sites on the epidermal growth factor receptor, which were not recognized by the wild-type Fyn SH2 domain. Furthermore, mass spectrometry showed that SH2 variants with additional mutations in the pTyr-binding pocket that enhanced affinity were highly effective for enrichment of diverse pTyr peptides within the human proteome. These results showed that engineering of the EF and BG loops could be used to tailor SH2 domain specificity, and SH2 variants with diverse specificities and high affinities for pTyr residues enabled more comprehensive analysis of the human phosphoproteome. Statement: Src Homology 2 (SH2) domains are modular domains that recognize phosphorylated tyrosine embedded in proteins, transducing these post-translational modifications into cellular responses. Here we used phage display to engineer hundreds of SH2 domain variants with altered binding specificities and enhanced affinities, which enabled efficient and differential enrichment of the human phosphoproteome for analysis by mass spectrometry. These engineered SH2 domain variants will be useful tools for elucidating the molecular determinants governing SH2 domains binding specificity and for enhancing analysis and understanding of the human phosphoproteome

Student Recital (May 1, 2013)

Etude No. 1 / Everett “Vic” Firth Dan Maloney, snare drum French Suite No. 2, BWV 813 / Johann Sebastian Bach Air David Smith, piano Night and Day / Cole Porter What is This Thing Called Love / C. Porter Colin Sullivan, baritone Left Behind / Duncan Sheik Jack Cappadona, tenor Yesterday’s / Otto Harbach Fools Rush In (Where Angels Fear to Tread) / Johnny Mercer Danni Vitorino, tenor You Walk With Me / David Yazbeck Jack Cappadona, tenor Danni Vitorino, tenor Ulrica’s Aria from un ballo in Maschera / Guiseppe Verdi Va! Laisse couler mes larmes / Jules Massenet Diane Card, alto Sonata No, 4 in C Major, BWV 1033 / J. S. Bach Andante Allegro Marie Doyon, flute Three Songs of the Sea, Op. 1 / Roger Quilter The Sea-Bird Moonlight By The Sea Thomas Manning, baritone The Ballad of Baby Doe / Douglas Moore Willow Song Jordan Ennis, soprano Adieu Notre Petite Table / J. Massenet Ach ich fuhl’s from Die Zauberflote, K. 620 / Wolfgang Amadeus Mozart Mary Sanker, soprano Se tu m’ami (If You Love Me) / Alessandro Parisotti I Attempt From Love’s Sickness / Henry Purcell Justine Smigel, soprano Ave Maria / Franz Schubert A Quiet Girl / Leonard Bernstein Michael Bradley, baritone The Point of No Return / Andrew Lloyd Weber Michael Bradley, baritone Stephanie Blood, soprano My Lovely Celia / George Monro I Have Dreamed from The King and I / Richard Rogers Richard Moran, tenor Adelita / Francisco Tarrega Cancion Del Emperador / Luis De Navaex Bryan Picher, guitar Cello Suite No. 1, BWV 1007 / J. S. Bach Prelude Mark Gavin, guitarhttps://vc.bridgew.edu/student_concerts/1042/thumbnail.jp

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment