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

Communities organizing to promote equity: engaging local communities in public health responses to health inequities exacerbated by COVID-19–protocol paper

BackgroundThe COVID-19 pandemic has disproportionately impacted rural and under-resourced urban communities in Kansas. The state’s response to COVID-19 has relied on a highly decentralized and underfunded public health system, with 100 local health departments in the state, few of which had prior experience engaging local community coalitions in a coordinated response to a public health crisis.MethodsTo improve the capacity for local community-driven responses to COVID-19 and other public health needs, the University of Kansas Medical Center, in partnership with the Kansas Department of Health and Environment, will launch Communities Organizing to Promote Equity (COPE) in 20 counties across Kansas. COPE will establish Local Health Equity Action Teams (LHEATs), coalitions comprised of community members and service providers, who work with COPE-hired community health workers (CHWs) recruited to represent the diversity of the communities they serve. CHWs in each county are tasked with addressing unmet social needs of residents and supporting their county’s LHEAT. LHEATs are charged with implementing strategies to improve social determinants of health in their county. Monthly, LHEATs and CHWs from all 20 counties will come together as part of a learning collaborative to share strategies, foster innovation, and engage in peer problem-solving. These efforts will be supported by a multilevel communications strategy that will increase awareness of COPE activities and resources at the local level and successes across the state. Our mixed methods evaluation design will assess the processes and impact of COPE activities as well as barriers and facilitators to implementation using aspects of both the Consolidated Framework for Implementation Research (CFIR) and Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) models.DiscussionThis protocol is designed to expand community capacity to strategically partner with local public health and social service partners to prioritize and implement health equity efforts. COPE intentionally engages historically resilient communities and those living in underserved rural areas to inform pragmatic strategies to improve health equity

Study of downward Terrestrial Gamma-ray Flashes with the surface detector of the Pierre Auger Observatory

The surface detector (SD) of the Pierre Auger Observatory, consisting of 1660 water-Cherenkov detectors (WCDs), covers 3000 km2 in the Argentinian pampa. Thanks to the high efficiency of WCDs in detecting gamma rays, it represents a unique instrument for studying downward Terrestrial Gamma-ray Flashes (TGFs) over a large area. Peculiar events, likely related to downward TGFs, were detected at the Auger Observatory. Their experimental signature and time evolution are very different from those of a shower produced by an ultrahigh-energy cosmic ray. They happen in coincidence with low thunderclouds and lightning, and their large deposited energy at the ground is compatible with that of a standard downward TGF with the source a few kilometers above the ground. A new trigger algorithm to increase the TGF-like event statistics was installed in the whole array. The study of the performance of the new trigger system during the lightning season is ongoing and will provide a handle to develop improved algorithms to implement in the Auger upgraded electronic boards. The available data sample, even if small, can give important clues about the TGF production models, in particular, the shape of WCD signals. Moreover, the SD allows us to observe more than one point in the TGF beam, providing information on the emission angle

Sex difference and intra-operative tidal volume: Insights from the LAS VEGAS study

BACKGROUND: One key element of lung-protective ventilation is the use of a low tidal volume (VT). A sex difference in use of low tidal volume ventilation (LTVV) has been described in critically ill ICU patients.OBJECTIVES: The aim of this study was to determine whether a sex difference in use of LTVV also exists in operating room patients, and if present what factors drive this difference.DESIGN, PATIENTS AND SETTING: This is a posthoc analysis of LAS VEGAS, a 1-week worldwide observational study in adults requiring intra-operative ventilation during general anaesthesia for surgery in 146 hospitals in 29 countries.MAIN OUTCOME MEASURES: Women and men were compared with respect to use of LTVV, defined as VT of 8 ml kg-1 or less predicted bodyweight (PBW). A VT was deemed 'default' if the set VT was a round number. A mediation analysis assessed which factors may explain the sex difference in use of LTVV during intra-operative ventilation.RESULTS: This analysis includes 9864 patients, of whom 5425 (55%) were women. A default VT was often set, both in women and men; mode VT was 500 ml. Median [IQR] VT was higher in women than in men (8.6 [7.7 to 9.6] vs. 7.6 [6.8 to 8.4] ml kg-1 PBW, P < 0.001). Compared with men, women were twice as likely not to receive LTVV [68.8 vs. 36.0%; relative risk ratio 2.1 (95% CI 1.9 to 2.1), P < 0.001]. In the mediation analysis, patients' height and actual body weight (ABW) explained 81 and 18% of the sex difference in use of LTVV, respectively; it was not explained by the use of a default VT.CONCLUSION: In this worldwide cohort of patients receiving intra-operative ventilation during general anaesthesia for surgery, women received a higher VT than men during intra-operative ventilation. The risk for a female not to receive LTVV during surgery was double that of males. Height and ABW were the two mediators of the sex difference in use of LTVV.TRIAL REGISTRATION: The study was registered at Clinicaltrials.gov, NCT01601223

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Mining Evolutionary Data to Reveal the Layered Architecture of Protein Function

Revolutionary advances in sequencing technology have dramatically expanded the set of known, naturally-occurring protein sequences. Protein sequences arise from an evolutionary process and during evolution proteins experience pressure to maintain and diversity their functions via mutation. Some mutations arise merely from neutral drift, but other changes enable organisms to adapt to their unique niche. Positions that are important for structure or function are expected to be mutationally constrained during evolution. To that end, many algorithms have been devised to identify mutational constraints in the evolutionary record in order to predict the location of functionally important sites. Accurate prediction of functionally important positions would have important practical implications. For example, individual humans each carry about 10,000 exomic sequence polymorphisms. Which of these are functionally and/or clinically significant? Similarly, protein engineers may target such sites for mutagenesis to derive variant functions. To detect these constraints, homologous proteins must first be sorted into protein families, based on sequence similarity, which typically indicates structural and functional similarity. Protein family multiple sequence alignments (MSAs) can then be computationally analyzed to understand the family in light of its evolutionary history. MSA analyses have detect various evolutionary patterns that are thought to confer functional significance. For example, positions that are absolutely conserved across a family are commonly inferred to play important structural or functional roles and, consequently, be intolerant to mutation. Other analyses attempt to identify important non-conserved positions, some of which must be functionally significant for the family to evolve functional variations. One important example is “co-evolutionary” analyses, which seek pairs of positions that vary in a coordinated manner across evolution. MSA analyses make a number of simplifying assumptions to abstract away the full complexity of real proteins. Here, we have (1) assessed the validity of some of these assumptions, and (2) investigated strategies to maximize the usefulness of existing tools in identifying functionally important positions, in light of their limitations, and (3) evaluated the ability of existing tools to identify known-significant positions. To that end, we have applied MSA analyses to the LacI/GalR bacterial transcription regulator family as our primary model system. Our studies have proceeded in three phases. First, preceding work indicated that published predictions based on a small LacI/GalR MSA fail to identify several functionally-significant positions in the 18-amino acid linker of LacI/GalR proteins. We have investigated whether making better use of these tools — by expanding the set of sequence in the LacI/GalR MSA and sorting the family based on external experimental knowledge — can improve predictive accuracy. Interestingly, comparison of existing predictions to all available experimental data also suggests that — contrary to a common assumption — functionally neutral positions may be much more rare than previously thought. Second, LacI/GalR proteins exhibit substantial functional diversity, even though their structures are extremely similar. One question is: how can a common structure support high levels of functional diversity? We have used conservation and co-evolutionary analyses to determine whether (a) functionally significant positions are dictated by the tertiary structure — an assumption of most MSA analyses — or (b) whether the structure serves as an accommodating scaffold, by permitting multiple subfamily-specific networks of functionally significant positions. Finally, alternative co-evolutionary algorithms disagree about which pairs of positions are evolutionarily-linked. However, we have analyzed alternative co-evolution networks using graph theory and have observed that the eigenvector network centrality (a) improves agreement between diverse analyses, and (b) can identify functionally significant positions in protein families. Thus, eigenvector centrality may be a useful framework for interpreting co-evolution analyses. Taken together, our studies provide tools to make best use of existing MSA analyses and indicate that future tools should avoid making several common assumptions

Adjuvant pembrolizumab versus placebo in resected stage III melanoma (EORTC 1325-MG/KEYNOTE-054): health-related quality-of-life results from a double-blind, randomised, controlled, phase 3 trial

International audienceBackground: The European Organisation for Research and Treatment of Cancer (EORTC) 1325-MG/KEYNOTE-054 trial in patients with resected, high-risk stage III melanoma demonstrated improved recurrence-free survival with adjuvant pembrolizumab compared with placebo (hazard ratio 0·57 [98·4% CI 0·43-0·74]; p<0·0001). This study reports the results from the health-related quality-of-life (HRQOL) exploratory endpoint.Methods: This double-blind, randomised, controlled, phase 3 trial was done at 123 academic centres and community hospitals across 23 countries. Patients aged 18 years or older with previously untreated histologically confirmed stage IIIA, IIIB, or IIIC resected cutaneous melanoma, and an Eastern Cooperative Oncology Group performance status score of 1 or 0 were eligible. Patients were randomly assigned (1:1) using a central interactive voice-response system on the basis of a minimisation technique stratified for stage and geographic region to receive intravenously 200 mg pembrolizumab or placebo. Treatment was administered every 3 weeks for 1 year, or until disease recurrence, unacceptable toxicity, or death. The primary endpoint of the trial was recurrence-free survival (reported elsewhere). HRQOL was a prespecified exploratory endpoint, with global health/quality of life (GHQ) over 2 years measured by the EORTC QLQ-C30 as the primary analysis. Analyses were done in the intention-to-treat population. This study is registered with ClinicalTrials.gov, NCT02362594, and EudraCT, 2014-004944-37, and long-term follow-up is ongoing.Findings: Between Aug 26, 2015, and Nov 14, 2016, 1019 patients were assigned to pembrolizumab (n=514) or placebo (n=505). Median follow-up was 15·1 months (IQR 12·8-16·9) at the time of this analysis. HRQOL compliance was greater than 90% at baseline, greater than 70% during the first year, and greater than 60% thereafter for both groups. Because of low absolute compliance numbers at later follow-up, the analysis was truncated to week 84. Baseline GHQ scores were similar between groups (77·55 [SD 18·20] in the pembrolizumab group and 76·54 [17·81] in the placebo group) and remained stable over time. The difference in average GHQ score between the two groups over the 2 years was -2·2 points (95% CI -4·3 to -0·2). The difference in average score during treatment was -1·1 points (95% CI -3·2 to 0·9) and the difference in average score after treatment was -2·2 points (-4·8 to 0·4). These differences are within the 5-point clinical relevance threshold for the QLQ-C30 and are therefore clinically non-significant.Interpretation: Pembrolizumab does not result in a clinically significant decrease in HRQOL compared with placebo when given as adjuvant therapy for patients with resected, high-risk stage III melanoma. These results support the use of adjuvant pembrolizumab in this setting