Chemistry of a Dehydrogenase and Di-heme Enzyme Related to Tryptophan Oxidation

Tryptophan is an essential amino acid that is used as a building block to construct proteins, the biosynthetic precursor for several essential molecules, and is modified to serve as a cofactor in some enzymes. This dissertation focuses on two enzymes involved in tryptophan oxidation, AMSDH and MauG. AMSDH is a dehydrogenase in the kynurenine pathway, which is the main metabolic route for tryptophan catabolism. In addition to breaking down tryptophan, the kynurenine pathway is also involved in regulating the innate immune response, NAD biosynthesis, and some neurodegenerative. As such, enzymes of the kynurenine pathway are of fundamental interest for study. This work leveraged a bacterial homologue of human AMSDH to solve its crystal structure in various forms, including several catalytic intermediates. The knowledge gained from the bacterial enzyme was then used to identify and verify human ALDH8A1 as the human AMSDH. MauG is the enzyme responsible for catalyzing the formation of the tryptophan-derived cofactor of methylamine dehydrogenase. It is a diheme enzyme that utilizes hydrogen peroxide perform long-range oxidations on its protein substrate. MauG possesses the remarkable ability to store two oxidizing equivalents as a bis-Fe(IV) species that is stabilized through a type III charge resonance phenomenon. The nature of the charge resonance phenomenon was investigated with exogenous small molecules, radical traps, and temperature dependent studies. Finally, a cryogenic method for generating radicals was developed to study the electronic structure of model compounds similar to the substrate of MauG

Numerical Tests of the Fokas Method for Helmholtz-type Partial Differential Equations: Dirichlet to Neumann Maps

A method for solving boundary value problems for linear partial differential equations in convex polygons developed by A.S. Fokas in the late 1990s is introduced. In order to solve well-posed boundary value problems using the novel Fokas approach, certain global relations must be derived. These global relations yield so-called Dirichlet to Neumann maps which not only allow us to solve Helmholtz-type PDEs using the Fokas method, but they are also of interest in their own right. Given a convex polygon and a prescribed set of boundary conditions associated with a PDE, the Dirichlet to Neumann map enables us to numerically recover unknown boundary conditions with relatively high accuracy without solving the PDE on the interior. The numerical implementation of the Dirichlet to Neumann map is shown to be an efficient and accurate method for resolving unknown boundary conditions. The map is also analyzed and certain parameters are optimized. With an accurate Dirichlet to Neumann map, solving the modified Helmholtz and the Helmholtz equations via the Fokas method becomes possible

Trade Promotion Authority (TPA): Frequently Asked Questions

This report answers frequently asked questions regarding the Trade Promotion Authority (TPA) program which requires international trade agreements that reduce tariff or non-tariff barriers to trade in ways that require changes in U.S. law, to be implemented only through the enactment of legislation. If the trade agreement and the process of negotiating it meet certain requirements, TPA allows Congress to consider the required implementing bill under expedited procedures, pursuant to which the bill may come to the floor without action by the leadership, and can receive a guaranteed up-or-down vote with no amendments

Re-investigating Tilaurakot's Ancient Fortifications: a preliminary report of excavations through the northern rampart at Tilaurakot(Nepal)

First paragraph: Urban settlements defined by fortification complexes have long been identified as one of the key indicators of the emergence and spread of the Early Historic Tradition across South Asia (Coningham 1995). Whilst performing defensive functions, city walls and moats are also thought to have prevented disruption to a settlement from natural forces, such as erosion and flooding (Narain and Roy 1977: 7, Coningham 1999: 54), as well as protecting settlements and crops grown within a city's boundary from wild animals (Coningham 1999: 56). Furthermore, some have argued that ramparts and moats also fulfilled symbolic functions and a number of settlement layouts have been thought to exhibit cosmomagical symbolism (Wheatley 1971: 481), with urban forms constructed as microcosms of the universe. Indeed, there are a number of South Asian examples where urban rampart and moat complexes are believed to have formed key cosmological motifs, representing the ocean and mountain range surrounding the universe (Coningham 2000). With a central role thus implied for the royal palace as representing Mount Meru, the dwelling of the Gods at the centre of the universe, this also portrayed the temporal ruler as a universal ruler or chakravartin (Wheatley 1971: 437, Coningham 2000: 350). Early Historic texts, such as the Arthasastra and Manasara, provided clear instructions for the construction of moats and ramparts, with the Arthasastra stating that a city should be quadrangular, surrounded by three moats and a rampart {Arthasastra 2.3.4-6) and be internally demarcated by cardinally orientated roads and gateways {Arthasastra 2.4.1-2). Similarly, the Manasara suggested that cities should be furnished with a quadrangular wall with an accompanying ditch surrounding the settlement with a gate at each cardinal direction {Manasara 9.107-109). It is now clear from its urban plan, that Tilaurakot, in southern Nepal, seemingly aligns with these precepts as it possesses an almost quadrangular fortification (Figure 1) and the results of recent geophysical survey suggest that cardinally-orientated roads were laid out in a grid within the city (Coningham et al. 2015)

“What if There's Something Wrong with Her?”‐How Biomedical Technologies Contribute to Epistemic Injustice in Healthcare

While there is a steadily growing literature on epistemic injustice in healthcare, there are few discussions of the role that biomedical technologies play in harming patients in their capacity as knowers. Through an analysis of newborn and pediatric genetic and genomic sequencing technologies (GSTs), I argue that biomedical technologies can lead to epistemic injustice through two primary pathways: epistemic capture and value partitioning. I close by discussing the larger ethical and political context of critical analyses of GSTs and their broader implications for just and equitable healthcare delivery

Impact of computed tomography perfusion imaging on the response to tenecteplase in ischemic stroke: analysis of two randomized controlled trials

Background: We pooled 2 clinical trials of tenecteplase compared with alteplase for the treatment of acute ischemic stroke, 1 that demonstrated superiority of tenecteplase and the other that showed no difference between the treatments in patient clinical outcomes. We tested the hypotheses that reperfusion therapy with tenecteplase would be superior to alteplase in improving functional outcomes in the group of patients with target mismatch as identified with advanced imaging. Methods: We investigated whether tenecteplase-treated patients had a different 24-hour reduction in the National Institutes of Health Stroke Scale and a favorable odds ratio of a modified Rankin scale score of 0 to 1 versus 2 to 6 compared with alteplase-treated patients using linear regression to generate odds ratios. Imaging outcomes included rates of vessel recanalization and infarct growth at 24 hours and occurrence of large parenchymal hematoma. Baseline computed tomography perfusion was analyzed to assess whether patients met the target mismatch criteria (absolute mismatch volume >15 mL, mismatch ratio >1.8, baseline ischemic core <70 mL, and volume of severely hypoperfused tissue <100 mL). Patients meeting target mismatch criteria were analyzed as a subgroup to identify whether they had different treatment responses from the pooled group. Results: Of 146 pooled patients, 71 received alteplase and 75 received tenecteplase. Tenecteplase-treated patients had greater early clinical improvement (median National Institutes of Health Stroke Scale score change: tenecteplase, 7; alteplase, 2; P=0.018) and less parenchymal hematoma (2 of 75 versus 10 of 71; P=0.02). The pooled group did not show improved patient outcomes when treated with tenecteplase (modified Rankin scale score 0–1: odds ratio, 1.77; 95% confidence interval, 0.89–3.51; P=0.102) compared with alteplase therapy. However, in patients with target mismatch (33 tenecteplase, 35 alteplase), treatment with tenecteplase was associated with greater early clinical improvement (median National Institutes of Health Stroke Scale score change: tenecteplase, 6; alteplase, 1; P<0.001) and better late independent recovery (modified Rankin scale score 0–1: odds ratio, 2.33; 95% confidence interval, 1.13–5.94; P=0.032) than those treated with alteplase. Conclusions: Tenecteplase may offer an improved efficacy and safety profile compared with alteplase, benefits possibly exaggerated in patients with baseline computed tomography perfusion–defined target mismatch. Clinical Trial Registration: URL: http://www.clinicaltrials.gov. Unique identifier: NCT01472926. URL: https://www.anzctr.org.au. Unique identifier: ACTRN12608000466347

Tissue Effects in a Randomized Controlled Trial of Short-term Finasteride in Early Prostate Cancer.

BackgroundIn the Prostate Cancer Prevention Trial, finasteride selectively suppressed low-grade prostate cancer and significantly reduced the incidence of prostate cancer in men treated with finasteride compared with placebo. However, an apparent increase in high-grade disease was also observed among men randomized to finasteride. We aimed to determine why and hypothesized that there is a grade-dependent response to finasteride.MethodsFrom 2007 to 2012, we randomized dynamically by intranet-accessible software 183 men with localized prostate cancer to receive 5mg finasteride or placebo daily in a double-blind study during the 4-6weeks preceding prostatectomy. As the primary end point, the expression of a predefined molecular signature (ERβ, UBE2C, SRD5A2, and VEGF) differentiating high- and low-grade tumors in Gleason grade (GG) 3 areas of finasteride-exposed tumors from those in GG3 areas of placebo-exposed tumors, adjusted for Gleason score (GS) at prostatectomy, was compared. We also determined androgen receptor (AR) levels, Ki-67, and cleaved caspase 3 to evaluate the effects of finasteride on the expression of its downstream target, cell proliferation, and apoptosis, respectively. The expression of these markers was also compared across grades between and within treatment groups. Logistic regression was used to assess the expression of markers.FindingsWe found that the predetermined molecular signature did not distinguish GG3 from GG4 areas in the placebo group. However, AR expression was significantly lower in the GG4 areas of the finasteride group than in those of the placebo group. Within the finasteride group, AR expression was also lower in GG4 than in GG3 areas, but not significantly. Expression of cleaved caspase 3 was significantly increased in both GG3 and GG4 areas in the finasteride group compared to the placebo group, although it was lower in GG4 than in GG3 areas in both groups.InterpretationWe showed that finasteride's effect on apoptosis and AR expression is tumor grade dependent after short-term intervention. This may explain finasteride's selective suppression of low-grade tumors observed in the PCPT

Comparing mismatch strategies for patients being considered for ischemic stroke tenecteplase trials

Background: Currently there are multiple variations of imaging-based patient selection mismatch methods in ischemic stroke. In the present study, we sought to compare the two most common mismatch methods and identify if there were different effects on the outcome of a randomized clinical trial depending on the mismatch method used. Aims: Investigate the effect of clinical and imaging-based mismatch criteria on patient outcomes of a pooled cohort from randomized trials of intravenous tenecteplase versus alteplase. Methods: Baseline clinical and imaging scores were used to categorize patients as meeting either the DAWN mismatch (baseline NIHSS ≥ 10, and age cut-offs for ischemic core volume) or DEFUSE 2 mismatch criteria (mismatch volume > 15 mL, mismatch ratio > 1.8 and ischemic core < 70 mL). We then investigated whether tenecteplase-treated patients had favorable odds of less disability (on modified Rankin scale, mRS) compared to those treated with alteplase, for clinical and imaging mismatch, respectively. Results: From 146 pooled patients, 71 received alteplase and 75 received tenecteplase. The overall pooled group did not show improved patient outcomes when treated with tenecteplase (mRS 0-1 OR 1.77, 95% CI 0.89–3.51, p = 0.102) compared with alteplase. A total of 39 (27%) patients met both clinical and imaging mismatch criteria, 25 (17%) patients met only imaging criteria, 36 (25%) met only clinical mismatch criteria and, finally, 46 (31%) did not meet either of imaging or mismatch criteria. Patients treated with tenecteplase had more favorable outcomes when they met either imaging mismatch (mRS 0–1, OR 2.33, 95% CI 1.13–5.94, p = 0.032) or clinical mismatch criteria (mRS 0–1, OR 2.15, 95% CI 1.142, 8.732, p = 0.027) but with differing proportions. Conclusion: Target mismatch selection was more inclusive and exhibited in a larger treatment effect between tenecteplase and alteplase

Instrumental performance and results from testing of the BLAST-TNG receiver, submillimeter optics, and MKID arrays

Polarized thermal emission from interstellar dust grains can be used to map magnetic fields in star forming molecular clouds and the diffuse interstellar medium (ISM). The Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry (BLASTPol) flew from Antarctica in 2010 and 2012 and produced degree-scale polarization maps of several nearby molecular clouds with arcminute resolution. The success of BLASTPol has motivated a next-generation instrument, BLAST-TNG, which will use more than 3000 linear polarization sensitive microwave kinetic inductance detectors (MKIDs) combined with a 2.5m diameter carbon fiber primary mirror to make diffraction-limited observations at 250, 350, and 500 $\mu$m. With 16 times the mapping speed of BLASTPol, sub-arcminute resolution, and a longer flight time, BLAST-TNG will be able to examine nearby molecular clouds and the diffuse galactic dust polarization spectrum in unprecedented detail. The 250 $\mu$m detector array has been integrated into the new cryogenic receiver, and is undergoing testing to establish the optical and polarization characteristics of the instrument. BLAST-TNG will demonstrate the effectiveness of kilo-pixel MKID arrays for applications in submillimeter astronomy. BLAST-TNG is scheduled to fly from Antarctica in December 2017 for 28 days and will be the first balloon-borne telescope to offer a quarter of the flight for "shared risk" observing by the community.Comment: Presented at SPIE Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy VIII, June 29th, 201

A high-resolution mRNA expression time course of embryonic development in zebrafish.

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3' ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl