Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins

This is the peer reviewed version of the following article: Jo, S., Song, K. C., Desaire, H., MacKerell, A. D., & Im, W. (2011). Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins. Journal of Computational Chemistry, 32(14), 3135–3141. http://doi.org/10.1002/jcc.21886, which has been published in final form at http://doi.org/10.1002/jcc.21886. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMMGUI, http://www.charmm-gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three-dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N-/O-glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM-GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics

Human Vault Nanoparticle Targeted Delivery of Antiretroviral Drugs to Inhibit Human Immunodeficiency Virus Type 1 Infection.

"Vaults" are ubiquitously expressed endogenous ribonucleoprotein nanoparticles with potential utility for targeted drug delivery. Here, we show that recombinant human vault nanoparticles are readily engulfed by certain key human peripheral blood mononuclear cells (PBMC), predominately dendritic cells, monocytes/macrophages, and activated T cells. As these cell types are the primary targets for human immunodeficiency virus type 1 (HIV-1) infection, we examined the utility of recombinant human vaults for targeted delivery of antiretroviral drugs. We chemically modified three different antiretroviral drugs, zidovudine, tenofovir, and elvitegravir, for direct conjugation to vaults. Tested in infection assays, drug-conjugated vaults inhibited HIV-1 infection of PBMC with equivalent activity to free drugs, indicating vault delivery and drug release in the cytoplasm of HIV-1-susceptible cells. The ability to deliver functional drugs via vault nanoparticle conjugates suggests their potential utility for targeted drug delivery against HIV-1

Transmission spectroscopy of the lowest-density gas giant: metals and a potential extended outflow in HAT-P-67b

Extremely low-density exoplanets are tantalizing targets for atmospheric characterization because of their promisingly large signals in transmission spectroscopy. We present the first analysis of the atmosphere of the lowest-density gas giant currently known, HAT-P-67 b. This inflated Saturn-mass exoplanet sits at the boundary between hot and ultrahot gas giants, where thermal dissociation of molecules begins to dominate atmospheric composition. We observed a transit of HAT-P-67 b at high spectral resolution with CARMENES and searched for atomic and molecular species using cross-correlation and likelihood mapping. Furthermore, we explored potential atmospheric escape by targeting H$\alpha$ and the metastable helium line. We detect Ca II and Na I with significances of 13.2$\sigma$ and 4.6$\sigma$, respectively. Unlike in several ultrahot Jupiters, we do not measure a day-to-night wind. The large line depths of Ca II suggest that the upper atmosphere may be more ionized than models predict. We detect strong variability in H$\alpha$ and the helium triplet during the observations. These signals suggest the possible presence of an extended planetary outflow that causes an early ingress and late egress. In the averaged transmission spectrum, we measure redshifted absorption at the $\sim 3.8\%$ and $\sim 4.5\%$ level in the H$\alpha$ and He I triplet lines, respectively. From an isothermal Parker wind model, we derive a mass loss rate of $\dot{M} \sim 10^{13}~\rm{g/s}$ and an outflow temperature of $T \sim 9900~\rm{K}$. However, due to the lack of a longer out-of-transit baseline in our data, additional observations are needed to rule out stellar variability as the source of the H$\alpha$ and He signals.Comment: The Astronomical Journal, in press. 17 pages, 9 figure

The GstLAL Search Analysis Methods for Compact Binary Mergers in Advanced LIGO's Second and Advanced Virgo's First Observing Runs

After their successful first observing run (September 12, 2015 - January 12, 2016), the Advanced LIGO detectors were upgraded to increase their sensitivity for the second observing run (November 30, 2016 - August 26, 2017). The Advanced Virgo detector joined the second observing run on August 1, 2017. We discuss the updates that happened during this period in the GstLAL-based inspiral pipeline, which is used to detect gravitational waves from the coalescence of compact binaries both in low latency and an offline configuration. These updates include deployment of a zero-latency whitening filter to reduce the over-all latency of the pipeline by up to 32 seconds, incorporation of the Virgo data stream in the analysis, introduction of a single-detector search to analyze data from the periods when only one of the detectors is running, addition of new parameters to the likelihood ratio ranking statistic, increase in the parameter space of the search, and introduction of a template mass-dependent glitch-excision thresholding method.Comment: 12 pages, 7 figures, to be submitted to Phys. Rev. D, comments welcom

Bridging the Gap: An Impact Study of Eight Developmental Summer Bridge Programs in Texas

Developmental summer bridge programs are a popular strategy for increasing college readiness among recent high school graduates. Aimed at providing an alternative to traditional developmental education, these programs provide accelerated and focused learning opportunities in order to help students acquire the knowledge and skills needed for college success. The current study uses an experimental design to evaluate the outcomes of eight developmental summer bridge programs offered in Texas during the summer of 2009. At each college, students who consented to participate in the study were randomly assigned to either a program group that was eligible to participate in a developmental summer bridge program or a control group that was eligible to use any other services that the college provided. Based on a program model developed by the Texas Higher Education Coordinating Board, the developmental summer bridge programs in this study included four common features: accelerated instruction in developmental math, reading, and/or writing; academic support; a “college knowledge” component; and the opportunity to earn a $400 stipend