Rheostats and Toggle Switches for Modulating Protein Function

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author’s publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.The millions of protein sequences generated by genomics are expected to transform protein engineering and personalized medicine. To achieve these goals, tools for predicting outcomes of amino acid changes must be improved. Currently, advances are hampered by insufficient experimental data about nonconserved amino acid positions. Since the property “nonconserved” is identified using a sequence alignment, we designed experiments to recapitulate that context: Mutagenesis and functional characterization was carried out in 15 LacI/GalR homologs (rows) at 12 nonconserved positions (columns). Multiple substitutions were made at each position, to reveal how various amino acids of a nonconserved column were tolerated in each protein row. Results showed that amino acid preferences of nonconserved positions were highly context-dependent, had few correlations with physico-chemical similarities, and were not predictable from their occurrence in natural LacI/GalR sequences. Further, unlike the “toggle switch” behaviors of conserved positions, substitutions at nonconserved positions could be rank-ordered to show a “rheostatic”, progressive effect on function that spanned several orders of magnitude. Comparisons to various sequence analyses suggested that conserved and strongly co-evolving positions act as functional toggles, whereas other important, nonconserved positions serve as rheostats for modifying protein function. Both the presence of rheostat positions and the sequence analysis strategy appear to be generalizable to other protein families and should be considered when engineering protein modifications or predicting the impact of protein polymorphisms

Bartolomeu: An SDN rebalancing system across multiple interdomain paths

Bartolomeu is a solution to enable stub networks to perform adaptive egress traffic load balancing across multiple interdomain routes by spreading the traffic across available paths according to a passive measurement of their performance. It defines a BGP-SDN architecture that increases the number of BGP routes that can be used by stub networks. Bartolomeu measures the available capacity of each path to any destination prefix, and allocates to each path a number of large flows that is proportional to its capacity. This strategy reduces the mean sojourn time, i.e., mean time to flow completion, compared to state-of-the-art traffic balancing techniques as ECMP. We develop a mathematical model to compute this time and compare with ECMP and single path (fast path) selection. An analysis of the traffic traces of two content providers was performed to ensure that our solution is deployable. An experiment with traffic exchange over the Internet is used to show that Bartolomeu can provide gains with real interfering traffic. A discrete-event simulator fed with the traces captured is used to asses Bartolomeu's gains with prefixes with different number of flows, and flows with different sizes and arrival time. We observe in this experiment that Bartolomeu can reduce the sojourn time, compared to ECMP, by half when path rates differ in a factor of 3, or to a sixth when path rates differ in a factor of 10. We compute the maximum number of per-flow entries and the maximum entry change request rate to show that the resources required fit in with the specifications of the current generation of SDN switches.The work of Pedro Rodrigues Torres-Jr. was partially supported by the Fundación Carolina, program Mobilidad SEGIB 2019. The work of Alberto García-Martínez was supported by the 5G-TRANSFORMER project, H2020-761536. The work of and Marcelo Bagnulo was supported in part by the 5G-TRANSFORMER project, and by the Spanish Ministry of Economy and Competitiveness under 5GCity project, TEC2016-76795-C6-3-R

Chemotherapy-induced apoptosis, autophagy and cell cycle arrest are key drivers of synergy in chemo-immunotherapy of epithelial ovarian cancer

Epithelial ovarian cancer (EOC) is the most lethal of all gynecological malignancies in the UK. Recent evidence has shown that there is potential for immunotherapies to be successful in treating this cancer. We have previously shown the effective application of combinations of traditional chemotherapy and CAR (chimeric antigen receptor) T cell immunotherapy in in vitro and in vivo models of EOC. Platinum-based chemotherapy synergizes with ErbB-targeted CAR T cells (named T4), significantly reducing tumor burden in mice. Here, we show that paclitaxel synergizes with T4 as well, and look into the mechanisms behind the effectiveness of chemo-immunotherapy in our system. Impairment of caspase activity using pan-caspase inhibitor Z-VAD reveals this chemotherapy-induced apoptotic pathway as an essential factor in driving synergy. Mannose-6-phosphate receptor-mediated autophagy and the arrest of cell cycle in G2/M are also shown to be induced by chemotherapy and significantly contributing to the synergy. Increased expression of PD-1 on T4 CAR T cells occurred when these were in culture with ovarian tumor cells; on the other hand, EOC cell lines showed increased PD-L1 expression following chemotherapy treatment. These findings provided a rationale to look into testing PD-1 blockade in combination with paclitaxel and T4 immunotherapy. Combination of these three agents in mice resulted in significant reduction of tumor burden, compared to each treatment alone. In conclusion, the mechanism driving synergy in chemo-immunotherapy of EOC is multifactorial. A deeper understanding of such process is needed to better design combination therapies and carefully stratify patients

Characterization of street food consumption in palermo: possible effects on health

<p>Abstract</p> <p>Background</p> <p>Street Food (SF) consists of out-of-home food consumption and has old, historical roots with complex social-economic and cultural implications. Despite the emergence of modern fast food, traditional SF persists worldwide, but the relationship of SF consumption with overall health, well-being, and obesity is unknown.</p> <p>Methods</p> <p>This is an observational, cross-sectional study. The study was performed in Palermo, the largest town of Sicily, Italy. Two groups were identified: consumers of SF (n = 687) and conventional restaurant food (RES) consumers (n = 315). Study subjects answered a questionnaire concerning their health conditions, nutritional preferences, frequency of consumption of SF and a score relative to SF consumption ranging from 0 to 20 was calculated.</p> <p>Results</p> <p>Body mass index (BMI, kg/m²) was significantly and independently correlated with the score of street food consumption (r = 0,103; p < 0.002). The prevalence of different diseases, including hypertension and type 2 diabetes, and the use of medications did not differ between the two groups. Milza (a sandwich stuffed with thin slice of bovine spleen and lung) consumers had a significantly higher prevalence of hypertension (12.2% vs 6.2% in non consumers; p < 0.005) and in this subgroup the use of anti-hypertensive drugs was inversely correlated with the frequency of milza consumption (r = 0.11; P = 0.010).</p> <p>Conclusions</p> <p>This study suggests that SF consumption in Palermo is associated with a higher BMI and higher prevalence of hypertension in milza consumers. Further studies should evaluate whether frequent SF consumers have unfavourable metabolic and cardiovascular profile.</p

Changes in heart failure medications in patients hospitalised and discharged

BACKGROUND: To date, evidence-based recommendations help doctors to manage patients with heart failure (HF). However, the implementation of these recommendations in primary care is still problematic as beneficial drugs are infrequently prescribed. The aim of the study was to determine whether admission to hospital increases usage of beneficial HF medication and if this usage is maintained directly after discharge. METHODS: The study was conducted from November 2002 until January 2004. In 77 patients hospitalised with heart failure (HF), the medication prescribed by the referring general practitioner (GP) and drug treatment directed by the hospital physicians was documented. Information regarding the post-discharge (14 d) therapy by the GP was evaluated via a telephone interview. Ejection fraction values, comorbidity and specifics regarding diagnostic or therapeutic intervention were collected by chart review. RESULTS: When compared to the referring GPs, hospital physicians prescribed more ACE-inhibitors (58.4% vs. 76.6%; p = 0.001) and beta-blockers of proven efficacy in HF (metoprolol, bisoprolol, carvedilol; 58.4% vs. 81.8%). Aldosterone antagonists were also administered more frequently in the hospital setting compared to general practice (14.3% vs. 37.7%). The New York Heart Association classification for heart failure did not influence whether aldosterone antagonists were administered either in primary or secondary care. Fourteen days after discharge, there was no significant discontinuity in discharge medication. CONCLUSION: Patients suffering from HF were more likely to receive beneficial medication in hospital than prior to admission. The treatment regime then remained stable two weeks after discharge. We suggest that findings on drug continuation in different cardiovascular patients might be considered validated for patients with HF

Update on the correlation of the highest energy cosmic rays with nearby extragalactic matter

Data collected by the Pierre Auger Observatory through 31 August 2007 showed evidence for anisotropy in the arrival directions of cosmic rays above the Greisen-Zatsepin-Kuz'min energy threshold, \nobreak{$6\times 10^{19}$eV}. The anisotropy was measured by the fraction of arrival directions that are less than $3.1^\circ$ from the position of an active galactic nucleus within 75 Mpc (using the V\'eron-Cetty and V\'eron $12^{\rm th}$ catalog). An updated measurement of this fraction is reported here using the arrival directions of cosmic rays recorded above the same energy threshold through 31 December 2009. The number of arrival directions has increased from 27 to 69, allowing a more precise measurement. The correlating fraction is $(38^{+7}_{-6})$, compared with $21$ expected for isotropic cosmic rays. This is down from the early estimate of $(69^{+11}_{-13})$. The enlarged set of arrival directions is examined also in relation to other populations of nearby extragalactic objects: galaxies in the 2 Microns All Sky Survey and active galactic nuclei detected in hard X-rays by the Swift Burst Alert Telescope. A celestial region around the position of the radiogalaxy Cen A has the largest excess of arrival directions relative to isotropic expectations. The 2-point autocorrelation function is shown for the enlarged set of arrival directions and compared to the isotropic expectation.Comment: Accepted for publication in Astroparticle Physics on 31 August 201

The Fluorescence Detector of the Pierre Auger Observatory

The Pierre Auger Observatory is a hybrid detector for ultra-high energy cosmic rays. It combines a surface array to measure secondary particles at ground level together with a fluorescence detector to measure the development of air showers in the atmosphere above the array. The fluorescence detector comprises 24 large telescopes specialized for measuring the nitrogen fluorescence caused by charged particles of cosmic ray air showers. In this paper we describe the components of the fluorescence detector including its optical system, the design of the camera, the electronics, and the systems for relative and absolute calibration. We also discuss the operation and the monitoring of the detector. Finally, we evaluate the detector performance and precision of shower reconstructions.Comment: 53 pages. Submitted to Nuclear Instruments and Methods in Physics Research Section