MinD-RNase E interplay controls localization of polar mRNAs in E. coli

The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.

The PfRCR complex bridges malaria parasite and erythrocyte during invasion

The symptoms of malaria occur during the blood stage of infection, when parasites invade and replicate within human erythrocytes. The PfPCRCR complex1, containing PfRH5 (refs. 2,3), PfCyRPA, PfRIPR, PfCSS and PfPTRAMP, is essential for erythrocyte invasion by the deadliest human malaria parasite, Plasmodium falciparum. Invasion can be prevented by antibodies3-6 or nanobodies1 against each of these conserved proteins, making them the leading blood-stage malaria vaccine candidates. However, little is known about how PfPCRCR functions during invasion. Here we present the structure of the PfRCR complex7,8, containing PfRH5, PfCyRPA and PfRIPR, determined by cryogenic-electron microscopy. We test the hypothesis that PfRH5 opens to insert into the membrane9, instead showing that a rigid, disulfide-locked PfRH5 can mediate efficient erythrocyte invasion. We show, through modelling and an erythrocyte-binding assay, that PfCyRPA-binding antibodies5 neutralize invasion through a steric mechanism. We determine the structure of PfRIPR, showing that it consists of an ordered, multidomain core flexibly linked to an elongated tail. We also show that the elongated tail of PfRIPR, which is the target of growth-neutralizing antibodies6, binds to the PfCSS-PfPTRAMP complex on the parasite membrane. A modular PfRIPR is therefore linked to the merozoite membrane through an elongated tail, and its structured core presents PfCyRPA and PfRH5 to interact with erythrocyte receptors. This provides fresh insight into the molecular mechanism of erythrocyte invasion and opens the way to new approaches in rational vaccine design.

Shodagor women cooperate across domains of work and childcare to solve an adaptive problem

Across human societies, women's economic production and their contributions to childcare are critical in supporting reproductive fitness for themselves, their spouses and children. Yet, the necessity of performing both work and childcare tasks presents women with an adaptive problem in which they must determine how best to allocate their time and energy between these tasks. Women often use cooperative relationships with alloparents to solve this problem, but whether or not women cooperate across different domains (e.g. work and childcare) to access alloparents remains relatively under-explored. Using social network data collected with Shodagor households in Bangladesh, we show that women who need childcare help in order to work draw on cooperative work partners as potential alloparents, and that all women rely heavily on kin, but not reciprocal cooperation for childcare help. These results indicate that Shodagor women strategize to create work and childcare relationships in ways that help solve the adaptive problem they face. We discuss the implications of our results and the example provided by Shodagor women for a broader understanding of women's cooperative relationships, including the importance of socio-ecological circumstances and gendered divisions of labour in shaping women's cooperative strategies. This article is part of the theme issue 'Cooperation among women: evolutionary and cross-cultural perspectives'.

The impact of market integration on arranged marriages in Matlab, Bangladesh

Success in marriage markets has lasting impacts on women's wellbeing. By arranging marriages, parents exert financial and social powers to influence spouse characteristics and ensure optimal marriages. While arranging marriages is a major focus of parental investment, marriage decisions are also a source of conflict between parents and daughters in which parents often have more power. The process of market integration may alter parental investment strategies, however, increasing children's bargaining power and reducing parents' influence over children's marriage decisions. We use data from a market integrating region of Bangladesh to (a) describe temporal changes in marriage types, (b) identify which women enter arranged marriages and (c) determine how market integration affects patterns of arranged marriage. Most women's marriages were arranged, with love marriages more recent. We found few predictors of who entered arranged vs. love marriages, and family-level market integration did not predict marriage type at the individual level. However, based on descriptive findings, and findings relating women's and fathers' education to groom characteristics, we argue that at the society-level market integration has opened a novel path in which daughters use their own status, gained via parental investments, to facilitate good marriages under conditions of reduced parental assistance or control.

A Machine Learning Algorithm to Discriminating Between Bipolar and Major Depressive Disorders Based on Resting EEG Data

Distinguishing major depressive disorder (MDD) from bipolar disorder (BD) is a crucial clinical challenge due to the lack of known biomarkers. Conventional methods of diagnosis rest exclusively on symptomatic presentation, and personal and family history. As a result, BD-depressed episode (BD-DE) is often misdiagnosed as MDD, and inappropriate therapy is given. Electroencephalography (EEG) has been widely studied as a potential source of biomarkers to differentiate these disorders. Previous attempts using machine learning (ML) methods have delivered insufficient sensitivity and specificity for clinical use, likely as a consequence of the small training set size, and inadequate ML methodology. We hope to overcome these limitations by employing a training dataset of resting-state EEG from 71 MDD and 71 BD patients. We introduce a robust 3 steps ML technique: 1) a multi-step preprocessing method is used to improve the quality of the EEG signal 2) symbolic transfer entropy (STE), which is an effective connectivity measure, is applied to the resultant EEG signals 3) the ML algorithm uses the extracted STE features to distinguish MDD from BD patients. Clinical Relevance--- The accuracy of our algorithm, derived from a large sample of patients, suggests that this method may hold significant promise as a clinical tool. The proposed method delivered total accuracy, sensitivity, and specificity of 84.9%, 83.4%, and 87.1%, respectively.

Drought stress enhances the efficiency of floral dip method of Agrobacterium-mediated transformation in Arabidopsis thaliana

The Agrobacterium-mediated floral dip protocol is the most extensively used transformation method for a model plant Arabidopsis thaliana. Several useful methods for Agrobacterium tumefaciens-mediated transformations of Arabidopsis are existing, but they are time consuming and with low transformation efficiency. Here, we developed a transgenic Arabidopsis lines TET12p::TET12-RFP in a short period of time and enhanced transformation efficiency by using a modified transformation method by applying drought stress after floral dip. In this protocol, Agrobacterium cells carrying TET12p::TET12-RFP recombinant vectors were resuspended in a solution of 5% sucrose, 0.05% (v/v) silwet L-77 to transform female gametes of developing Arabidopsis inflorescences. Treated Arabidopsis were then applied with different levels of drought stresses to stimulate plants for the utilization of maximum plant energy in seed maturation process. The applied stresses achieved the fast maturation of already treated inflorescences while stopped the growing of newly arising untreated inflorescence, thus decreased the chances of wrong collection of untransformed seeds. Consequently, the collected seeds were mostly transgenic with a transformation frequency of at least 10%, thus the screening for positive transformants selection was more advantageous on a selective medium as compared to a classical floral dip method. Within 2-3 months, two hundred of individual transgenic plants were produced from just 10 infiltrated plants. This study concludes that application of drought stresses in a specific stage of plant is a beneficial strategy for achieving the transgenic Arabidopsis in a short period of time with high transformation efficiency.

Are fathers a good substitute for mothers? Paternal care and growth rates in Shodagor children

Biparental care is a hallmark of human social organization, though paternal investment varies between and within societies. The facultative nature of paternal care in humans suggests males should invest when their care improves child survival and/or quality, though testing this prediction can be challenging because of the difficulties of empirically isolating paternal effects from those of other caregivers. Additionally, the broader context in which care is provided, vis-à-vis care from mothers and others, may lead to different child outcomes. Here, we examine the effects of paternal care on child growth among Shodagor fisher-traders, where fathers provide high levels of both additive and substitutive care, relative to mothers. We modeled seasonal z-scores and velocities for height, weight, and body mass index (BMI) outcomes using linear mixed models. Our evidence indicates that, as predicted, the context of paternal care is an important predictor of child outcomes. Results show that environmental seasonality and alloparental help contribute to a nuanced understanding of the impact of Shodagor paternal care on child physiology.

Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45

Peptide-protein docking is challenging due to the considerable conformational freedom of the peptide. CAPRI rounds 38-45 included two peptide-protein interactions, both characterized by a peptide forming an additional beta strand of a beta sheet in the receptor. Using the Rosetta FlexPepDock peptide docking protocol we generated top-performing, high-accuracy models for targets 134 and 135, involving an interaction between a peptide derived from L-MAG with DLC8. In addition, we were able to generate the only medium-accuracy models for a particularly challenging target, T121. In contrast to the classical peptide-mediated interaction, in which receptor side chains contact both peptide backbone and side chains, beta-sheet complementation involves a major contribution to binding by hydrogen bonds between main chain atoms. To establish how binding affinity and specificity are established in this special class of peptide-protein interactions, we extracted PeptiDBeta, a benchmark of solved structures of different protein domains that are bound by peptides via beta-sheet complementation, and tested our protocol for global peptide-docking PIPER-FlexPepDock on this dataset. We find that the beta-strand part of the peptide is sufficient to generate approximate and even high resolution models of many interactions, but inclusion of adjacent motif residues often provides additional information necessary to achieve high resolution model quality.

A spike with which to beat COVID-19?

This month’s Under the Lens discusses how structural studies of the SARS-CoV-2 spike glycoprotein might guide a path towards a vaccine.

This month’s Under the Lens discusses how structural studies of the SARS-CoV-2 spike glycoprotein might guide a path towards a vaccine.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

National Clinical Guidance for the Management of Cardiovascular Intervention in the COVID-19 Pandemic: From Bangladesh Society of Cardiovascular Interventions (BSCI)

Since the first recorded case of SARS-CoV-2 in Bangladesh on 8th March 2020, COVID-19 has spread widely through different regions of the country, resulting in a necessity to re-evaluate the delivery of cardiovascular services, particularly procedures pertaining to interventional cardiology in resource-limited settings. Given its robust capacity for human-to-human transmission and potential of being a nosocomial source of infection, the disease has specific implications on healthcare systems and health care professionals faced with performing essential cardiac procedures in patients with a suspected or confirmed diagnosis of COVID-19. The limited resources in terms of cardiac catheterization laboratories that can be designated to treat only COVID positive patients are further compounded by the additional challenges of unavailability of widespread rapid testing on-site at tertiary cardiac hospitals in Bangladesh. This document prepared for our nation by the Bangladesh Society of Cardiovascular Interventions (BSCI) is intended to serve as a clinical practice guideline for cardiovascular health care professionals, with a focus on modifying standard practice of care during the COVID-19 pandemic, in order to ensure continuation of adequate and timely treatment of cardiovascular emergencies avoiding hospital-based transmission of SARS-COV-2 among healthcare professionals and the patients. This is an evolving document based on currently available global data and is tailored to healthcare systems in Bangladesh with particular focus on, but not limited to, invasive cardiology facilities (cardiac catheterization, electrophysiology & pacing labs). This guideline is limited to the provision of cardiovascular care, and it is expected that specific targeted pharmaco-therapeutics against SARS-CoV-2 be prescribed as stipulated by the National Guidelines on Clinical Management of Corona virus Disease 2019 (COVID-19) published by the Director General of Health Services, Ministry of Health and Family Welfare of Bangladesh.

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking

Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template-based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template-based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https://tbm.cluspro.org, is demonstrated by predicting the protein-protein targets of rounds 38 to 45 of CAPRI.

Septic patients with cancer: Do prehospital antibiotics improve survival? A sub-analysis of the PHANTASi trial

BACKGROUND

Sepsis in patients with cancer is increasingly common and associated with high mortality. To date, no studies have examined the effectiveness of prehospital antibiotics in septic patients with cancer. This study aimed without and to evaluate the effect of prehospital antibiotics in septic patients with cancer.

METHODS

We conducted a post-hoc sub-analysis of the PHANTASi (PreHospital ANTibioitcs Against Sepsis) trial database: a randomised controlled trial which enrolled patients with suspected sepsis who were transported to the emergency department by ambulance. Patients in the intervention group were administered prehospital intravenous antibiotics while those in the control group received usual care. We compared patients who had cancer to those who did not. Primary outcome was 28-day mortality; among the secondary outcomes, we included in-hospital mortality and 90-day mortality.

RESULTS

357(13.4%) of the 2658 included patients had cancer in the past five years, of which, 209 (58.5%) were included in the intervention and 148 (41.5%) usual care groups; 28-day mortality was significantly higher in patients who were diagnosed with cancer in the past five years than those without cancer in the past five years: 15.2% vs. 7.1%, respectively (p < 0.001). Prehospital antibiotics in the group of patients with cancer in the last five years yielded no significant effect on survival. There were however, significantly fewer 30-day readmissions (p = 0.031) in the intervention group of cancer patients (12.2% vs 5.7%).

CONCLUSION

Prehospital antibiotics did not improve overall survival. However, there was a significant reduction in 30-day readmissions.

Health related quality of life in sepsis survivors from the Prehospital Antibiotics Against Sepsis (PHANTASi) trial

BACKGROUND

Due to the rise in incidence, the long term effect of sepsis are becoming more evident. There is increasing evidence that sepsis may result in an impaired health related quality of life. The aim of this study was to investigate whether health related quality of life is impaired in sepsis survivors and which clinical parameters are associated with the affected health related quality of life.

METHODS

We analyzed 880 Short Form 36 (SF-36) questionnaires that were sent to sepsis survivors who participated in the Prehospital Antibiotics Against Sepsis (PHANTASi) trial. These questionnaires were sent by email, 28 days after discharge. Data entry and statistical analyses were performed in SPSS. The data from the general Dutch population, was obtained from the Netherlands Cancer Institute (NKI-AVL) and served as a control group. Subsequently, 567 sepsis survivors were matched to 567 controls. Non-parametric Wilcoxon signed-rank test was performed to compare these two groups. Within the group, we sought to explain the diminished health related quality of life by factor analysis.

RESULTS

We found that sepsis survivors have a worse health related quality of life compared to the general Dutch population. This negative effect was more evident for the physical component than the mental component of health related quality of life. We found that health related quality of life was significantly altered by advancing age and female sex. We also found that the total length of stay (in the hospital) and (previous) comorbidity negatively affect the physical component of health related quality of life.

CONCLUSION

In our study we found that health related quality of life in sepsis survivors, 28 days after discharge, is severely diminished in comparison with the general Dutch population. The physical domain is severely affected, whereas the mental domain is less influenced. The length of stay, comorbidity, advancing age and female sex all have a negative effect on the Physical Component Scale of the health related quality of life.

Deep tubewell microbial water quality and access in arsenic mitigation programs in rural Bangladesh

The objective of this paper is to determine whether deep tubewells installed through arsenic mitigation efforts in rural Bangladesh provide better drinking water microbial quality compared to shallow tubewells. We conducted a stratified random cross-sectional survey of 484 households to assess microbial contamination of deep tubewell water at source and at point of use (POU) compared to shallow tubewell water using the Compartment Bag Test. In addition, we measured storage time, distance, travel time and ownership status among both sets of users to assess deep tubewell efficacy and under what conditions they offer poorer or better water quality. Differences in tubewell characteristics were compared using non-parametric Mann-Whitney U tests and two-proportion Z-tests. Prevalence ratios of microbial contamination stratified by water quality, storage time and distance to tubewells and ownership were estimated using unadjusted Mantel-Haenszel tests. There was no significant difference in microbial contamination between shallow and deep tubewells at source. The presence of POU water microbial contamination in storage containers in deep tubewell households was 1.11 times the prevalence in shallow tubewell storage containers (95% CI = 0.97-1.27). Deep tubewell users stored water longer and walked significantly farther to obtain water compared to shallow tubewell users. Among deep tubewell households, those residing farther away from the source were 1.24 times as likely to drink contaminated water from storage containers compared to those located nearby (95% CI = 1.04-1.48). Our findings suggest that deep tubewells have comparable water quality to shallow tubewells at source, but increasing distance from the household exacerbates risk of microbial contamination at POU.

Evaluation of blood culture epidemiology and efficiency in a large European teaching hospital

Background

Blood cultures remain the gold standard for detecting bacteremia despite their limitations. The current practice of blood culture collection is still inefficient with low yields. Limited focus has been given to the association between timing of specimen collection at different time points during admission and their yield.

Methods

We carried out a retrospective observational study by analyzing all 3,890 sets of cultures collected from the 1,962 admitted patients over the seven-month period of this study. We compared the blood culture yield between the early group (≤24 hours after admission) and the late group (> 24 hours of admission). We also investigated the effect of prehospital oral antibiotics and pre-analytical time on the first cultures in the emergency department. Epidemiology and efficiency of blood cultures were studied for each medical specialty.

Results

In total, 3,349(86.1%) blood cultures were negative and 541(13.9%) were positive for one or more microorganisms. After correcting for contamination, the overall yield was 290 (7.5%). The early group (n = 1,490) yielded significantly more true-positive cultures (10.1% versus 5.8%, P<0.001) than the late group (n = 2,400). The emergency department had a significantly higher yield than general wards, 11.2% versus 5.7% (p<0.001). Prehospital oral antibiotic use and pre-analytical time did not affect the yield of first cultures at the emergency department (p = 0.735 and 0.816 respectively). The number of tests needed to obtain one true-positive culture varied between departments, ranging from 7 to 45.

Conclusion

This study showed that blood cultures are inefficient in detecting bacteremia. Cultures collected during 24 hours after admission yielded more positive results than those collected later. Significant variations in blood culture epidemiology and efficiency per specialty suggest that guidelines should be reevaluated. Future studies should aim at improving blood culture yield, implementing educational programs to reduce contamination and cost-effective application of modern molecular diagnostic technologies.

Abstract P6-07-03: A live tissue platform allows dynamic measurement of neovascularization and prediction of clinical response in human breast cancer samples, ex vivo

Background: Outgrowth of new blood vessels (neovascularization) allows tumors to supply themselves with oxygen and nutrients, and to rapidly metastasize throughout the body. Triple negative breast cancer (TNBC) is particularly susceptible to neovascularization. However, success with anti-angiogenics is highly variable and often patient-specific. This is particularly true as anti-angiogenics are being combined with immunotherapies. Thus, there is a huge unmet need for clinicians to test and predict clinical efficacy of anti-angiogenics at the individual patient level, prior to treatment.

Methods: Here, we characterize a patient-autologous, ex-vivo tumor model, termed CANscript, as a platform to study the intratumor microvascular density (iMVD) of breast cancer samples (N=15). To profile iMVD we used immunohistochemical (IHC) analysis of CD34, an early biomarker of neovascularization. We then introduced anticancer and anti-angiogenic agents (e.g. Avastin) for 72 hours, and subsequently quantified phenotypic response to drugs by testing viability, cell death, proliferation and morphology. These quantitative data were then fed into a machine learning algorithm that provides a clinical response prediction (M-Score).

Results: We determined that ex-vivo culture reliably retains baseline heterogeneity of iMVD based on expression of CD34+ nodes per visual field by IHC. Furthermore, we show that anticancer and anti-angiogenic agents will dynamically alter iMVD, ex-vivo, in a patient-specific manner. Finally, we show that prediction of clinical response using the 'M-Score' algorithm associates with diminished expression of CD34 per visual field of IHC after drug pressure.

Summary: Neovascularization and iMVD are features of aggressive cancers, such as TNBC. CANscript provides a rapid assessment of clinical response to anticancer drugs, many of which induce their antitumor effect by targeting the tumor vasculature. We show that pharmacodynamics of antiangiogenics can be captured during acute ex-vivo culture under drug pressure, which associate to clinical response prediction. Therefore, we highlight the ability of CANscript as a platform to predict clinical response to anti-angiogenic drugs, and may therefore be a logical 'testing ground' to predict clinical efficacy of antiangiogenic drugs combined with immunotherapies.

Citation Format: Smalley M, Alam N, Murmu N, Somashekhar S, Ulaganathan B, Thayakumar A, Maciejko L, Ganesh J, Lawson M, Gertje H, Shanthappa BU, Goldman A. A live tissue platform allows dynamic measurement of neovascularization and prediction of clinical response in human breast cancer samples, ex vivo [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-07-03.

Association of Prolonged QTc Dispersion with Diastolic Dysfunction of the Left Ventricle in Patients with Non ST Segment Elevation Myocardial Infarction

Diastolic function usually declines before systolic function, and this precedes clinical signs in patients with acute coronary syndrome. Therefore, diagnosis of diastolic dysfunction is very important for early diagnosis, follow-up, treatment, and prognostic evaluation in heart failure with preserved ejection fraction (HFpEF) patients. The main objective of the study was to find out association between prolonged QTc dispersion and left ventricular diastolic dysfunction in Non ST Segment Elevation Myocardial Infarction (NSTEMI) patients in HFpEF. This cross sectional analytical study was conducted in the Department of Cardiology and 60 patients were included as study population from August 2015 to July 2016. Then the study population was divided into two groups, each group consisted of 30 patients. NSTEMI patients with prolonged QTc dispersion treated as Group I and NSTEMI patients with normal QTc dispersion treated as Group II. The study shows 20.0% vs. 26.6% patients had detected as Grade I in Group I and Group II respectively with statistically insignificant association (p=0.16). On the contrary, 30.0% vs. 13.4% patients had detected as Grade II in Group I and Group II respectively with statistically significant association (p=0.001). Again, 40.0% vs. 10.0% patients had detected as Grade III in Group I and Group II respectively with statistically significant association (p=0.001). QTc dispersion was found sequentially significant increased (p=0.007) among 3 grades of LVDD (63.6±4.9 vs. 79.4±8.6 vs. 98.2±28.8). QTc dispersion in surface ECG which is a cheap, non-invasive, easily available tool can help us predicting left ventricular diastolic dysfunction in patients with NSTEMI.

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT

Summary

We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide’s final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions.

Availability and Implementation

The method is available as part of the protein-protein docking server ClusPro at https://peptidock.cluspro.org/nousername.php.

Supplementary information

Supplementary data are available at Bioinformatics online.

Protein-peptide docking: opportunities and challenges

Peptides have recently attracted much attention as promising drug candidates. Rational design of peptide-derived therapeutics usually requires structural characterization of the underlying protein-peptide interaction. Given that experimental characterization can be difficult, reliable computational tools are needed. In recent years, a variety of approaches have been developed for 'protein-peptide docking', that is, predicting the structure of the protein-peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and/or conformation. In this review, we provide an overview of protein-peptide docking methods and outline their capabilities, limitations, and applications in structure-based drug design. Key challenges are also briefly discussed, such as modeling of large-scale conformational changes upon binding, scoring of predicted models, and optimal inclusion of varied types of experimental data and theoretical predictions into an integrative modeling process.

Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite

Pepsin-family aspartic peptidases are biosynthesized as inactive zymogens in which the propeptide blocks the active site until its proteolytic removal upon enzyme activation. Here, we describe a novel dual regulatory function for the propeptide using a set of crystal structures of the parasite cathepsin D IrCD1. In the IrCD1 zymogen, intramolecular autoinhibition by the intact propeptide is mediated by an evolutionarily conserved exosite on the enzyme core. After activation, the mature enzyme employs the same exosite to rebind a small fragment derived from the cleaved propeptide. This fragment functions as an effective natural inhibitor of mature IrCD1 that operates in a pH-dependent manner through a unique allosteric inhibition mechanism. The study uncovers the propeptide-binding exosite as a target for the regulation of pepsin-family aspartic peptidases and defines the structural requirements for exosite inhibition.

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as validated on a small but representative set of peptide-protein complex structures well resolved by X-ray crystallography. Our approach opens up the way to high-resolution modeling of many more peptide-protein interactions and to the detailed study of peptide-protein association in general. PIPER-FlexPepDock is freely available to the academic community as a server at http://piperfpd.furmanlab.cs.huji.ac.il.

Peptide-protein interactions are crucial components of various important biological processes in living cells. High-resolution structural information of such interactions provides insight about the underlying biophysical principles governing the interactions, and a starting point for their targeted manipulations. Accurate docking algorithms can help fill the gap between the vast number of these interactions and the small number of experimentally solved structures. However, the accuracies of the existing protocols have been limited, in particular for ab initio docking when no information about the peptide beyond its sequence is available. Here we introduce PIPER-FlexPepDock, a fragment-based global docking protocol for high-resolution modeling of peptide-protein interactions. Integration of accurate and efficient representation of the peptide using fragment ensembles, their fast and exhaustive rigid-body docking, and their subsequent accurate flexible refinement, enables peptide-protein docking of remarkable accuracy. The validation on a representative benchmark set of crystallographically solved high-resolution peptide-protein complexes demonstrates significantly improved performance over all existing docking protocols. This opens up the way to the modeling of many more peptide-protein interactions, and to a more detailed study of peptide-protein association in general.

Prognostic value of early warning scores in the emergency department (ED) and acute medical unit (AMU): A narrative review

BACKGROUND

A wide array of early warning scores (EWS) have been developed and are used in different settings to detect which patients are at risk of deterioration. The aim of this review is to provide an overview of studies conducted on the value of EWS on predicting intensive care (ICU) admission and mortality in the emergency department (ED) and acute medical unit (AMU).

METHODS

A literature search was conducted in the bibliographic databases PubMed and EMBASE, from inception to April 2017. Two reviewers independently screened all potentially relevant titles and abstracts for eligibility.

RESULTS

42 studies were included. 36 studies reported on mortality as an endpoint, 13 reported ICU admission and 9 reported the composite outcome of mortality and ICU admission. For mortality prediction National Early Warning Score (NEWS) was the most accurate score in the general ED population and in those with respiratory distress, Mortality in Emergency Department Sepsis score (MEDS) had the best accuracy in patients with an infection or sepsis. ICU admission was best predicted with NEWS, however in patients with an infection or sepsis Modified Early Warning Score (MEWS) yielded better results for this outcome.

CONCLUSION

MEWS and NEWS generally had favourable results in the ED and AMU for all endpoints. Many studies have been performed on ED and AMU populations using heterogeneous prognostic scores. However, future studies should concentrate on a simple and easy to use prognostic score such as NEWS with the aim of introducing this throughout the (pre-hospital and hospital) acute care chain.

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility

CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites. These rounds have also provided us the opportunity to reassess the success criteria, to better reflect the quality of a peptide-protein complex model. Using all models submitted to CAPRI, we analyze the correlation between current classification criteria and the ability to retrieve critical interface features, such as hydrogen bonds and hotspots. We find that loosening the backbone (and ligand) RMSD threshold, together with a restriction on the side chain RMSD measure, allows us to improve the selection of high-accuracy models. We also suggest a new measure to assess interface hydrogen bond recovery, which is not assessed by the current CAPRI criteria. Finally, we find that surprisingly much can be learned from rather inaccurate models about binding hotspots, suggesting that the current status of peptide-protein docking methods, as reflected by the submitted CAPRI models, can already have a significant impact on our understanding of protein interactions. Proteins 2017; 85:445-462. © 2016 Wiley Periodicals, Inc.

Review of Experimental Modelling in Vascular Access for Hemodialysis

This paper reviews applications of experimental modelling in vascular access for hemodialysis. Different techniques that are used in in-vitro experiments are bulk pressure and flow rate measurements, Laser Doppler Velocimetry and Vector Doppler Ultrasound point velocity measurements, and whole-field measurements such as Particle Image Velocimetry, Ultrasound Imaging Velocimetry, Colour Doppler Ultrasound, and Planar Laser Induced Fluorescence. Of these methods, the ultrasound techniques can also be used in-vivo, to provide realistic boundary conditions to in-vitro experiments or numerical simulations. In the reviewed work, experimental modelling is mainly used to support computational models, but also in some cases as a tool on its own. It is concluded that, to further advance the utility of computational modelling in vascular access research, a rigorous verification and validation procedure should be adopted. Experimental modelling can play an important role in both in-vitro validation, and the quantification of the accuracy, uncertainty, and reproducibility of in-vivo measurement methods.

Acute medical units: The way to go? A literature review

BACKGROUND

Acute healthcare chains in the Netherlands are increasingly under pressure because of rising emergency department (ED) admissions, relative bed shortages and government policy changes. In order to improve acute patient flow and quality of care through hospitals, an acute medical unit (AMU) might be a solution, as demonstrated in the UK. However, limited information is available concerning AMUs in the Netherlands. Therefore, the aims of this study were to METHODS: A systematic literature search was performed searching 3 electronic databases: PubMed, Cochrane and EMBASE. All 106 hospitals in the Netherlands were contacted, inquiring about the status of an ED, the AMU or future plans to start one.

RESULTS

The literature search resulted in 31 studies that met inclusion criteria. In general, these studies reported significant benefits on number of admissions, hospital length of stay (LOS), mortality, other wards and readmissions. Among the Dutch hospitals with an ED, 33 out of 93 implemented an AMU or similar ward, these are however organized heterogeneously. Following current trends, more AMUs are expected to be realized in the future.

CONCLUSION

In order to improve the current strain on the Dutch acute healthcare system, an AMU could potentially provide benefits. However, uniform guideline is warranted to optimize and compare quality of care throughout the Netherlands.

Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors

FIH-mediated post-translational modification through asparaginyl hydroxylation of eukaryotic proteins impacts regulation of protein-protein interaction. We have identified the FIH recognition motif in 11 Legionella pneumophila translocated effectors, YopM of Yersinia, IpaH4.5 of Shigella and an ankyrin protein of Rickettsia. Mass spectrometry analyses of the AnkB and AnkH effectors of L. pneumophila confirm their asparaginyl hydroxylation. Consistent with localization of the AnkB effector to the Legionella-containing vacuole (LCV) membrane and its modification by FIH, our data show that FIH and its two interacting proteins, Mint3 and MT1-MMP are acquired by the LCV in a Dot/Icm type IV secretion-dependent manner. Chemical inhibition or RNAi-mediated knockdown of FIH promotes LCV-lysosomes fusion, diminishes decoration of the LCV with polyubiquitinated proteins, and abolishes intra-vacuolar replication of L. pneumophila. These data show acquisition of the host FIH by a pathogen-containing vacuole and that asparaginyl-hydroxylation of translocated effectors is indispensable for their function.

Long-term health related quality of life in patients with sepsis after intensive care stay: A systematic review

Sepsis is a major health care issue and sepsis survivors are often confronted with long-term complications after admission to the intensive care unit (ICU) which may negatively influence their health related quality of life (HRQOL). This study aimed to systematically evaluate the outcome in terms of HRQOL in patients with sepsis after ICU discharge. A literature search was conducted in the bibliographic databases PubMed, EMBASE, and CINAHL, including reference lists of published guidelines, reviews and associated articles. Sixteen studies were included, thirteen (81.3%) reported that sepsis survivors suffer from impaired HRQOL in physical and mental domains which persist from months to years after a sepsis episode. More focus on improving long-term outcomes for patients surviving sepsis and the ICU is needed.

Structure-Based Identification of HDAC8 Non-histone Substrates

HDAC8 is a member of the family of histone deacetylases (HDACs) that catalyze the deacetylation of acetyl lysine residues within histone and non-histone proteins. The recent identification of novel non-histone HDAC8 substrates such as SMC3, ERRα, and ARID1A indicates a complex functionality of this enzyme in cellular homeostasis. To discover additional HDAC8 substrates, we developed a comprehensive, structure-based approach based on Rosetta FlexPepBind, a protocol that evaluates peptide-binding ability to a receptor from structural models of this interaction. Here we adapt this protocol to identify HDAC8 substrates using peptide sequences extracted from proteins with known acetylated sites. The many new in vitro HDAC8 peptide substrates identified in this study suggest that numerous cellular proteins are HDAC8 substrates, thus expanding our view of the acetylome and its regulation by HDAC8.

Tendon grafts: their natural history, biology and future development

The use of tendon grafts has diminished as regimes of primary repairs and rehabilitation have improved, but they remain important in secondary reconstruction. Relatively little is known about the cellular biology of grafts, and the general perception is that they have little biological activity. The reality is that there is a wealth of cellular and molecular changes occurring with the process of engraftment that affect the quality of the repair. This review highlights the historical perspectives and modern concepts of graft take, reviews the different attachment techniques and revisits the biology of pseudosheath formation. In addition, we discuss some of the future directions in tendon reconstruction by grafting, which include surface modification, vascularized tendon transfer, allografts, biomaterials and cell-based therapies.

What are we waiting for? Factors influencing completion times in an academic and peripheral emergency department

BACKGROUND

A long completion time in the Emergency Department (ED) is associated with higher morbidity and in-hospital mortality. A completion time of more than four hours is a frequently used cut-off point. Mostly, older and sicker patients exceed a completion time of four hours on the ED. The primary aim was to examine which factors currently contribute to overcrowding and a time to completion of more than four hours on the EDs of two different hospitals, namely: the VU Medical Center (VUmc), an academic level 1 trauma centre and the St. Antonius Hospital, a large community hospital in Nieuwegein. In addition, we compared the differences between these hospitals.

METHODS

In this observational study, the time steps in the process of diagnosing and treatment of all patients visiting the EDs of the two hospitals were measured for four weeks. Patients triaged as Emergency Severity Index (ESI) category 2/3 or Manchester Triage System (MTS) orange/yellow were followed more closely and prospectively by researchers for detailed information in the same period from 12.00-23.00 hrs.

RESULTS

In the VUmc, 89% of the patients had a completion time of less than four hours. The average completion time (n = 2262) was 2:10 hours, (median 1:51 hours, range: 0:05-12:08). In the St. Antonius Hospital, 77% of patients had a completion time shorter than four hours (n = 1656). The average completion time in hours was 2:49 (n = 1655, median 2:34, range: 0:08-11:04). In the VUmc, a larger percentage of ESI 1, 2 and 3 patients did not achieve the 4-hour target (14%, 20% and 19%) compared with ESI 4 and 5 patients (2.7% and 0%), p < 0.001. At the St. Antonius Hospital, a greater percentage of orange and yellow categorised patients exceeded four hours on the ED (32% and 28%) compared with red (8%) and green/blue (13%), p < 0.001. For both hospitals there was a significant dependency between exceeding four hours on the ED and the following: whether a consultation was performed (p < 0.001), the number of radiology tests performed (p < 0.001), and an age above 65 years.

CONCLUSION

Factors leading to ED stagnation were similar in both hospitals, namely old age, treatment by more than one speciality and undergoing radiological tests. Uniform remedial measures should be taken on a nationwide level to deal with these factors to reduce stagnation in the EDs.

Patient age, remission status and HCT-CI in a combined score are prognostic for patients with AML undergoing allogeneic hematopoietic cell transplantation in CR1 and CR2

For AML, older age, advanced disease and increased hematopoietic cell transplant comorbidity index (HCT-CI) are associated with worse prognosis following allogeneic hematopoietic cell transplantation (HCT). This single-center retrospective study investigated the influence of pre-transplant characteristics on outcomes of 387 patients undergoing allogeneic HCT for AML in CR1 and CR2. The multivariable analysis model for overall survival (OS) included age (hazard ratio (HR)=2.24 for ages 31-64 years and HR=3.23 for age ⩾65 years compared with age ⩽30 years, P=0.003), remission status (HR=1.49 for CR2 compared with CR1, P=0.005) and HCT-CI score (HR=1.47 for ⩾3 compared with <3, P=0.005). Transplant year was significantly associated with OS (P=0.001) but this did not influence the model. A weighted score was developed with age ⩽30, CR1 and HCT-CI score <3 receiving 0 points each, and CR2 and HCT-CI score ⩾3 receiving 1 point each. Ages 31-64 received 2 points, age ⩾65 received 3 points. Scores were grouped as follows: scores 0-1 (low risk, n=36), score 2 (intermediate-low risk, n=147), score 3 (intermediate-high risk, n=141) and scores 4-5 (high risk, n=63) with 3-year OS of 71%, 55%, 42% and 29% for scores 0-1, 2, 3 and 4-5, respectively (P<0.0001). The score predicted nonrelapse mortality (P=0.03) but not cumulative incidence of relapse (P=0.18). This model should be validated for the pre-HCT assessment of AML patients in CR1 and CR2.

Outcomes of patients with therapy-related AML/myelodysplastic syndrome (t-AML/MDS) following hematopoietic cell transplantation

We studied outcomes of 65 consecutive patients with therapy-related AML/myelodyplastic syndrome (t-AML/MDS) who underwent allogeneic hematopoietic cell transplantation (HCT). Previously published scores of HCT-CI, CIBMTR, EBMT and Comorbidity-age index were also evaluated. Median follow-up of survivors was 72 months (range 16-204). At 2 years, overall survival (OS) was 34% (95% confidence interval (CI) 23-45). Nineteen patients (29%) had monosomal karyotype (MK). Patients with MK had an OS of 21% (95% CI 7-41) at 2 years. Abnormal adverse cytogenetics, unrelated donor, bone marrow graft and CIBMTR score were significant risk factors for OS on univariate analysis. On multivariate analysis, abnormal adverse cytogenetics (hazard ratio (HR) 2.7; 95% CI 1.02-7.2; P-value=0.02) and unrelated donor (HR 2.7; 95% CI 1.5-5.0; P-value=0.0013) were independent factors for survival. Non-relapse mortality (NRM) at 2 years was 31% (95% CI 15-47). Donor type was the only factor that was significant for NRM with matched related donors having an NRM of 20% (95% CI 0-42) whereas unrelated donors had NRM of 60% (95% CI 40-80; P-value=0.0007). In conclusion, patients with t-AML/MDS have poor OS. Unrelated donor is a significant risk factor for both higher NRM and decreased OS. Cytogenetics are predictive for OS.