Biophysical Studies of Hairpin Polyamides with Broad-Spectrum Activity Against High-Risk Human Papillomaviruses

Human papillomavirus is a small dsDNA virus that infects mucosal and cutaneous epithelial tissues. Persistent infection with high-risk HPV is the main etiological agent in the development of cervical cancer worldwide. Although prophylactic vaccines against HPV are available, these preventative measures are type-specific and are ineffective against existing infections. Thus, there is a pressing need for antiviral drugs with a broad-spectrum activity against HPV to eradicate existing infections, no matter the subtype. Our group and collaborators have synthesized an extensive library of novel N-methylpyrrole/N-methylimidazole (Py/Im) hairpin polyamides (PAs) with broad-spectrum activities against three prevalent oncogenic-HPV types (HPV16, HPV18 and HPV31) without apparent cytotoxicity. Because Py/Im polyamides can be rationally designed to bind the minor groove of dsDNA in a sequence-dependent manner, these small molecules are attractive candidates as modulators of gene expression, as molecular probes for diagnostics and as antiviral agents for the selective elimination of dsDNA viruses. Despite the promise of applying these agents to treat HPV infections, much regarding their mechanism of action remains unexplained. Therefore, the overall goal of this dissertation is to investigate the DNA-binding properties of potent anti-HPV PAs under cell-free conditions and in HPV-harboring keratinocytes. Chapter 2 describes biophysical studies of anti-HPV hairpin polyamides (PA1 and PA25) using deoxyribonuclease I footprinting and affinity cleavage to interrogate the sequence specificity, binding sites and dissociation constants within the HPV18 Long Control Region. Chapter 3 extends these analyses to a new structural class of hairpin polyamides with tetramethylguanidinium (PA30) and guanidinium (PA31) substitutions on the N-terminus of PA1. Chapter 4 presents a detailed procedure to determine the genome-wide binding events of DNA-binding molecules in cell-free conditions using hydroxyl radical footprinting coupled to massively parallel DNA sequencing (·OH-Seq). In Chapter 5, ·OH-Seq and COSMIC-Seq have been employed to assess the binding occupancies of anti-HPV hairpin polyamides across the viral genomes in keratinocytes harboring HPV16 episomes. A deeper understanding of the molecular underpinnings of the ability of antiviral hairpin PAs to eliminate the HPV viral load may facilitate the development of a new generation of broad-spectrum antiviral treatments against this deadly virus

A scintillating plastic fiber tracking detector for neutron and proton imaging and spectroscopy

We report the results of recent calibration data analysis of a prototype scintillating fiber tracking detector system designed to perform imaging, spectroscopy and particle identification on 20 to 250 MeV neutrons and protons. We present the neutron imaging concept and briefly review the detection principle and the prototype description. The prototype detector system records ionization track data on an event-by-event basis allowing event selection criteria to be used in the off-line analysis. Images of acrylic phantoms from the analysis of recent proton beam calibrations (14 to 65 MeV range) are presented as demonstrations of the particle identification, imaging and energy measurement capabilities. The measured position resolution is c 500 pm. The measured energy resolution (AE/E, FWHM) is 14.2% at 35 MeV. An effective technique for track identification and data compression is presented. The detection techniques employed can be applied to measurements in a variety of disciplines including solar and atmospheric physics, radiation therapy and nuclear materials monitoring. These applications are discussed briefly as are alternative detector configurations and future development plans

Effect Of High-optical Excitation On The Ultrafast Electron Dynamics In Stacked-monolayer Graphene Samples

We report on transient absorption experiments performed at high optical excitation fluences and used to study the ultrafast dynamics in graphene. We employed a degenerated scheme of pump and probe at 800 nm (1.55 eV). The time resolution of our measurements was limited by the pulse duration similar to 100 fs. The samples were prepared by chemical vapor deposition (CVD) as single-layers on silica and, then staked layer-by-layer in order to make a stack of up to 5 graphene monolayers. We observed saturable absorption (SA) and fluence-dependent relaxation times. We see that the ultrafast carrier dynamics is composed by two decay mechanisms, one with response time of about 200 fs and a slower process of about 1 ps. The fast decay, due to both carrier-carrier and carrier-optical phonon scattering, becomes slower when the density of excited carrier was increased. We implemented a theoretical model and found that both the optical phonon rate emission and the optical phonon lifetime are affect by the pump fluence.9835Conference on Ultrafast Bandgap PhotonicsAPR 18-20, 2016Baltimore, M

The rejuvenating power of the Buena Vista Social Club

26S proteasome, a major regulatory protease in eukaryotes, consists of a 20S proteolytic core particle (CP) capped by a 19S regulatory particle (RP). The 19S RP is divisible into base and lid sub-complexes. Even within the lid, subunits have been demarcated into two modules: module 1 (Rpn5, Rpn6, Rpn8, Rpn9 and Rpn11), which interacts with both CP and base sub-complexes and module 2 (Rpn3, Rpn7, Rpn12 and Rpn15) that is attached mainly to module 1. We now show that suppression of RPN11 expression halted lid assembly yet enabled the base and 20S CP to pre-assemble and form a base-CP. A key role for Regulatory particle non-ATPase 11 (Rpn11) in bridging lid module 1 and module 2 subunits together is inferred from observing defective proteasomes in rpn11–m1, a mutant expressing a truncated form of Rpn11 and displaying mitochondrial phenotypes. An incomplete lid made up of five module 1 subunits attached to base-CP was identified in proteasomes isolated from this mutant. Re-introducing the C-terminal portion of Rpn11 enabled recruitment of missing module 2 subunits. In vitro, module 1 was reconstituted stepwise, initiated by Rpn11–Rpn8 heterodimerization. Upon recruitment of Rpn6, the module 1 intermediate was competent to lock into base-CP and reconstitute an incomplete 26S proteasome. Thus, base-CP can serve as a platform for gradual incorporation of lid, along a proteasome assembly pathway. Identification of proteasome intermediates and reconstitution of minimal functional units should clarify aspects of the inner workings of this machine and how multiple catalytic processes are synchronized within the 26S proteasome holoenzymes

DNA Binding Polyamides and the Importance of DNA Recognition in their use as Gene-Specific and Antiviral Agents

There is a long history for the bioorganic and biomedical use of N-methyl-pyrrole-derived polyamides (PAs) that are higher homologs of natural products such as distamycin A and netropsin. This work has been pursued by many groups, with the Dervan and Sugiyama groups responsible for many breakthroughs. We have studied PAs since about 1999, partly in industry and partly in academia. Early in this program, we reported methods to control cellular uptake of polyamides in cancer cell lines and other cells likely to have multidrug resistance efflux pumps induced. We went on to discover antiviral polyamides active against HPV31, where SAR showed that a minimum binding size of about 10 bp of DNA was necessary for activity. Subsequently we discovered polyamides active against two additional high-risk HPVs, HPV16 and 18, a subset of which showed broad spectrum activity against HPV16, 18 and 31. Aspects of our results presented here are incompatible with reported DNA recognition rules. For example, molecules with the same cognate DNA recognition properties varied from active to inactive against HPVs. We have since pursued the mechanism of action of antiviral polyamides, and polyamides in general, with collaborators at NanoVir, the University of Missouri-St. Louis, and Georgia State University. We describe dramatic consequences of β-alanine positioning even in relatively small, 8-ring polyamides; these results contrast sharply with prior reports. This paper was originally presented by JKB as a Keynote Lecture in the 2nd International Conference on Medicinal Chemistry and Computer Aided Drug Design Conference in Las Vegas, NV, October 2013

Bioelectricity Generated by Microbial Fuel Cells from Spearmint (Mentha Spicata) and Ribbon Plant (Chlorophytum Comosum)

Clean energy such as bioelectricity, a sustainable energy, obtains electricity associated with biological processes that do not generate greenhouse gases. The research aimed to produce bioelectricity using microbial fuel cells (MFCs) that transform chemical energy stored in organic matter into electricity. Peppermint (Mentha spicata) and ribbon plant (Chlorophytum comosum) MFC were designed in the district of Yanacancha, Chupaca-Junín. For the experimental process, microbial fuel cells were built, 3 batteries for mint and 3 batteries for ribbon plant, using graphite rods as electrodes. The initial characterization of the soil used in the pile was carried out, and then the global solar radiation was measured during the operation of the pile. In the investigation, a greater bioelectricity was achieved when the pH and temperature of the soil of the microbial fuel cell were 7.04 and 10.80 °C in peppermint MFC and 6.43 and 12.83 °C in tape MFC where bioelectricity of 245.37 mV was generated, 601.15x10-6 W in peppermint MFC and 505.45 mV, 2552.52x10-6 W in ribbon MFC respectively, so the ribbon microbial fuel cell (MFC) was the most efficient for bioelectricity generation

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Integrated Carbon Budget Models for the Everglades Terrestrial-Coastal-Oceanic Gradient: Current Status and Needs for Inter-Site Comparisons

Recent studies suggest that coastal ecosystems can bury significantly more C than tropical forests, indicating that continued coastal development and exposure to sea level rise and storms will have global biogeochemical consequences. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) site provides an excellent subtropical system for examining carbon (C) balance because of its exposure to historical changes in freshwater distribution and sea level rise and its history of significant long-term carbon-cycling studies. FCE LTER scientists used net ecosystem C balance and net ecosystem exchange data to estimate C budgets for riverine mangrove, freshwater marsh, and seagrass meadows, providing insights into the magnitude of C accumulation and lateral aquatic C transport. Rates of net C production in the riverine mangrove forest exceeded those reported for many tropical systems, including terrestrial forests, but there are considerable uncertainties around those estimates due to the high potential for gain and loss of C through aquatic fluxes. C production was approximately balanced between gain and loss in Everglades marshes; however, the contribution of periphyton increases uncertainty in these estimates. Moreover, while the approaches used for these initial estimates were informative, a resolved approach for addressing areas of uncertainty is critically needed for coastal wetland ecosystems. Once resolved, these C balance estimates, in conjunction with an understanding of drivers and key ecosystem feedbacks, can inform cross-system studies of ecosystem response to long-term changes in climate, hydrologic management, and other land use along coastlines

Public health utility of cause of death data : applying empirical algorithms to improve data quality

Background: Accurate, comprehensive, cause-specific mortality estimates are crucial for informing public health decision making worldwide. Incorrectly or vaguely assigned deaths, defined as garbage-coded deaths, mask the true cause distribution. The Global Burden of Disease (GBD) study has developed methods to create comparable, timely, cause-specific mortality estimates; an impactful data processing method is the reallocation of garbage-coded deaths to a plausible underlying cause of death. We identify the pattern of garbage-coded deaths in the world and present the methods used to determine their redistribution to generate more plausible cause of death assignments. Methods: We describe the methods developed for the GBD 2019 study and subsequent iterations to redistribute garbage-coded deaths in vital registration data to plausible underlying causes. These methods include analysis of multiple cause data, negative correlation, impairment, and proportional redistribution. We classify garbage codes into classes according to the level of specificity of the reported cause of death (CoD) and capture trends in the global pattern of proportion of garbage-coded deaths, disaggregated by these classes, and the relationship between this proportion and the Socio-Demographic Index. We examine the relative importance of the top four garbage codes by age and sex and demonstrate the impact of redistribution on the annual GBD CoD rankings. Results: The proportion of least-specific (class 1 and 2) garbage-coded deaths ranged from 3.7% of all vital registration deaths to 67.3% in 2015, and the age-standardized proportion had an overall negative association with the Socio Demographic Index. When broken down by age and sex, the category for unspecified lower respiratory infections was responsible for nearly 30% of garbage-coded deaths in those under 1 year of age for both sexes, representing the largest proportion of garbage codes for that age group. We show how the cause distribution by number of deaths changes before and after redistribution for four countries: Brazil, the United States, Japan, and France, highlighting the necessity of accounting for garbage-coded deaths in the GBD

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)