Population-level impact of beliefs and attitudes on vaccine decision-making in South Africa: results from the COVID-19 Vaccine Survey (2021/2022)

OBJECTIVES

In addition to being home to more than seven million HIV-infected individuals, South Africa also has a high burden of COVID-19 and related comorbidities worldwide. We aimed to identify the most influential "beliefs" and "attitudes" on vaccine decision-making behavior.

STUDY DESIGN

This study used panel data from cross-sectional surveys.

METHODS

We used the data from Black South Africans who participated in the "COVID-19 Vaccine Surveys" (November 2021 and February/March 2022) in South Africa. Besides standard risk factor analysis, such as multivariable logistic regression models, we also used the modified version of population attributable risk percent and estimated the population-level impacts of beliefs and attitudes on vaccine decision-making behavior using the methodology in multifactorial setting.

RESULTS

A total of 1399 people (57% men and 43% women) who participated in both surveys were analyzed. Of these, 336 (24%) reported being vaccinated in survey 2. Overall low perceived risk, concerns around efficacy, and safety were identified as the most influential factors and associated with 52%-72% (<40 years) and 34%-55% (40+ years) of the unvaccinated individuals.

CONCLUSION

Our findings highlighted the most influential beliefs and attitudes on vaccine decision-making and their population-level impacts, which are likely to have significant public health implications exclusively for this population.

Exploring CRD mobility during RAS/RAF engagement at the membrane

During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.

TB testing in HIV-positive patients prior to antiretroviral treatment

BACKGROUND: TB diagnosis in patients with HIV is challenging due to the lower sensitivities across tests. Molecular tests are preferred and the Xpert^® MTB/RIF assay has limitations in lower-income settings. We evaluated the performance of loop-mediated isothermal amplification (LAMP) and the lipoarabinomannan (LAM) test in HIV-positive, ART-naïve clinic patients.METHODS: A total of 783 eligible patients were enrolled; three spot sputum samples of 646 patients were tested using TB-LAMP, Xpert, smear microscopy and culture, while 649 patients had TB-LAM testing. Sensitivity, specificity, and negative and positive predictive values were estimated with 95% confidence intervals.RESULTS: Sensitivities for smear microscopy, TB-LAMP and Xpert were respectively 50%, 63% and 74% compared to culture, with specificities of respectively 99.2%, 98.5% and 97.5%. An additional eight were positive on TB-LAM alone. Seventy TB patients (9%) were detected using standard-of-care testing, an additional 27 (3%) were detected using study testing. Treatment was initiated in 57/70 (81%) clinic patients, but only in 56% (57/97) of all those with positive TB tests; 4/8 multidrug-resistant samples were detected using Xpert.CONCLUSION: TB diagnostics continue to miss cases in this high-burden setting. TB-LAMP was more sensitive than smear microscopy, and if followed by culture and drug susceptibility testing as required, can diagnose TB in HIV-positive patients. TB-LAM is a useful add-in test and both tests at the point-of-care would maximise yield.

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes

Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell's organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1's life cycle.

Array programming with NumPy

Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves¹ and in the first imaging of a black hole². Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis.

NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.

Scalable Analysis of Authentic Viral Envelopes on FRONTERA

Enveloped viruses, such as SARS-CoV-2, infect cells via fusion of their envelope with the host membrane. By employing molecular simulations to characterize viral envelopes, researchers can gain insights into key determinants of infection. Here, the Frontera supercomputer is leveraged for large-scale modeling and analysis of authentic viral envelopes, whose lipid compositions are complex and realistic. Visual Molecular Dynamics (VMD) with support for MPI is employed, overcoming previous computational limitations and enabling investigation into virus biology at an unprecedented scale. The techniques applied here to an authentic HIV-1 envelope at two levels of spatial resolution (29 million particles and 280 million atoms) are broadly applicable to the study of other viruses. The authors are actively employing these techniques to develop and characterize an authentic SARS-CoV-2 envelope. A general framework for carrying out scalable analysis of simulation trajectories on Frontera is presented, expanding the utility of the machine in humanity’s ongoing fight against infectious diseases.

SciPy 1.0: fundamental algorithms for scientific computing in Python

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

SciPy 1.0: fundamental algorithms for scientific computing in Python

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

SciPy 1.0: fundamental algorithms for scientific computing in Python

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

The clinical prognostic significance of myocardial performance index (MPI) in stable placental-mediated disease

AIM

To determine whether a single elevated myocardial performance index (MPI) value in the third trimester of pregnancy is a marker for later adverse obstetric outcomes in stable placental-mediated disease, defined as well-controlled pre-eclampsia (PE) on a single agent and/or uncompensated intra-uterine growth restriction (IUGR).

METHODS

Fifty-five foetuses whose mothers had stable placental-mediated disease, either mild pre-eclampsia controlled on a single agent, and/or uncompensated IUGR in the third trimester, attending the Foetal Unit at Inkosi Albert Luthuli Hospital, Durban, South Africa were prospectively recruited with 55 matched controls. Recorded data for the subjects included demographic data of maternal age and parity, sonographic data of estimated foetal weight (EFW) and amniotic fluid index (AFI), myocardial performance index (MPI), and foetal Doppler data of the umbilical artery (UA), middle cerebral artery (MCA) and ductus venosus (DV).

RESULTS

The mean gestational age in the controls, the IUGR and any PE cases was 31.4, 31.8 and 31.0 weeks, respectively. The distribution of MPI values was significantly lower in the controls compared to all other groups. The highest standardised MPI values were observed in the PE-IUGR group, where a median of 5.62 was observed. The only significant differences observed between the PE and IUGR groups was the UA resistance index (p = 0.01), where the IUGR cases tended to have higher UA values compared to the combined PE group. Borderline statistical significance was observed for the MCA resistance index values ( p = 0.05) between these groups. The overall adverse event rate in the cases was 49%. The highest rate was observed in the PE + IUGR group, where eight out of 12 (67%) experienced adverse events. MPI z-scores served as a good marker of adverse events, as evidenced by the total area under the curve (AUC) of 0.90 on the ROC curve. A cut-off value of 4.5 on the MPI z-score conferred a sensitivity of 89% and specificity of 68% for an adverse event later in pregnancy. In univariate logistic regression, MPI z-score, AFI, EFW, UA Doppler, CPR category, DV Doppler and MCA Doppler were assessed separately as potential predictors of adverse outcome. The only significant predictor of adverse outcome was MPI z-score.

CONCLUSIONS

A single elevated value of the MPI ( z-score > 4.5) in the third trimester in stable placental-mediated disease was a strong indicator of adverse obstetric outcomes later in pregnancy. This has the potential to be incorporated in conjunction with standard monitoring models in stable placental-mediated disease to predict an adverse event later in pregnancy and thus to reduce perinatal morbidity and mortality.

How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins

The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.

In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.

Detecting Mycobacterium tuberculosis using the loop-mediated isothermal amplification test in South Africa

SETTING

In South Africa, KwaZulu-Natal is the epicentre of the human immunodeficiency virus (HIV) epidemic, where approximately 70% of people with tuberculosis (TB) are co-infected with HIV. Undiagnosed TB contributes to high mortality in HIV-infected patients. Delays in diagnosing TB and treatment initiation result in prolonged transmission and increased infectiousness.

OBJECTIVE

To evaluate the LoopampTM MTBC Detection kit (TB-LAMP; based on the loop-mediated isothermal amplification assay), smear microscopy and Xpert test with the gold standard of mycobacterial culture.

METHODS

Sputum samples were collected from 705 patients with symptoms of pulmonary TB attending a primary health care clinic.

RESULTS

The TB-LAMP assay had significantly higher sensitivity than smear microscopy (72.6% vs. 45.4%, P < 0.001), whereas specificity was slightly lower (99% vs. 96.8%, P = 0.05), but significantly higher than Xpert (92.9%, P = 0.004). There was no significant difference in sensitivity of smear-positive, culture-positive and smear-negative, culture-positive sputum samples using TB-LAMP vs. Xpert (respectively 95.9%/55.9% vs. 97.6%/66.1%; P =0.65, P = 0.27). The positive predictive value of TB-LAMP was significantly higher than that of Xpert (87.5% vs. 77.0%; P = 0.02), but similar to that of smear microscopy (94.2%; P = 0.18). The negative predictive value was respectively 91.9%, 92.5% (P = 0.73) and 83.1% (P = 0.0001).

CONCLUSION

Given its ease of operability, the TB-LAMP assay could be implemented as a point-of-care test in primary health care settings, and contribute to reducing treatment waiting times and TB prevalence.

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes

Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies of an inwardly rectifying potassium (Kir) channel which forms specific interactions with the regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency of protein molecules to cluster has the effect of organizing the membrane into dynamic compartments. At the same time, the diversity of lipids present has a marked effect on the clustering behavior of ion channels. Sub-diffusion of proteins and lipids is observed. Protein crowding alters the sub-diffusive behavior of proteins and lipids such as PIP2 which interact tightly with Kir channels. Protein crowding also affects bilayer properties, such as membrane undulations and bending rigidity, in a PIP2-dependent manner. This interplay between the diffusion and the dynamic organization of Kir channels may have important implications for channel function.

Triamcinolone injection for treatment of Mitrofanoff stomal stenosis: Optimizing results and reducing cost of care

INTRODUCTION

Stomal stenosis is the most common complication after the creation of a continent catheterizable channel (CCC), but is challenging to treat.

OBJECTIVE

To describe early experience with triamcinolone injection for the treatment of stomal stenosis.

MATERIALS AND METHODS

A retrospective review was performed of patients who had undergone a triamcinolone injection (40 mg/ml) for the treatment of stomal stenosis at the present institution. The primary outcome of success was defined as a patient-reported or caregiver-reported return to ease with catheterization, and avoidance of stomal revision or indwelling catheter. The cost of care with various techniques for the treatment of stomal stenosis was also assessed by representing the cost as a percentage of charges for a re-operative Monti ileovesicostomy.

RESULTS

A total of 22 injections were performed in 18 CCCs of 17 patients. Demographic and clinical data are provided in the Summary Table. Thirteen CCCs (72%) were successfully treated with a single injection. Three patients (10%) required a total of five repeat injections at a median of 5.1 months between injections (IQR, 4.6-12.4). One patient required a stomal revision at 34.9 months after the initial injection, while one patient also required a Chait cecostomy catheter. The median length of time for ease with catheterization was 11.6 months (IQR, 3.5-18.0) after the initial injection, and 10.4 months (IQR, 4.5-16.0) after any injection. No adverse effects or complications occurred from the injection. There were no variables associated with failure after the initial or any injection on univariate analysis. Represented as a percentage of charges for a reoperative Monti ileovesicostomy, the cost of care was 11.3% for a stomal revision, 5.8% for triamcinolone injection in the operating room, and 0.3% as an office-based procedure.

DISCUSSION

The success rate for triamcinolone injection favorably compared with other options for the treatment of stomal stenosis. It surpassed the reported success rate of stomal dilation and approached that of stomal revision. Other studies have similarly observed a minimal risk of adverse effects and complications from both topical and intralesional corticosteroids. The limitations of the present study included its retrospective design at a single institution. A larger cohort of patients with a longer follow-up is necessary to determine its long-term durability.

CONCLUSIONS

Triamcinolone injection was an effective and well-tolerated option for the treatment of stomal stenosis in any cutaneous stoma, thereby avoiding the need for a more invasive and costly stomal revision.

Assessment of fetal myocardial performance in severe early onset pre-eclampsia (EO-PET) with and without intrauterine growth restriction across deteriorating stages of placental vascular resistance and links to adverse outcomes

OBJECTIVE

To determine whether fetuses in severe early onset pre-eclampsia (EO-PET) with or without intrauterine growth restriction has cardiac dysfunction across deteriorating stages of placental vascular resistance and whether this dysfunction influences perinatal outcome.

STUDY DESIGN

This was a prospective cross-sectional study performed in a tertiary care university medical centre. Sixty pregnant patients with severe early-onset pre-eclampsia between 27 and 32 weeks were recruited and matched with 60 patients having normal pregnancies. An analysis of cardiac function using the myocardial performance index (MPI) and early ventricular filling (E) and late active atrial contraction (A) ratios (E/A ratios) in the study group was performed compared to controls and further analysis was performed based on worsening placental vascular resistance and presence of growth restriction.

RESULTS

MPI values were increased in the pre-eclamptic group, irrespective if growth restriction co-exists, compared to controls (0.61 vs 0.38, p<0.001). Its median value progressively increased with worsening placental vascular resistance. For adverse perinatal outcome cut-off MPI values have been suggested. The E/A ratios were significantly decreased in the pre-eclamptic group compared to controls (0.66 vs 0.79, p<0.0001). No adverse outcomes were noted in the control group.

CONCLUSION

Fetal cardiac function is significantly impaired in pregnancies complicated by severe early onset pre-eclampsia, irrespective if growth restriction co-exists and worsens with deteriorating grades of placental vascular resistance. The MPI can potentially be integrated into routine fetal surveillance techniques.

Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane

The cytoskeleton underlying cell membranes may influence the dynamic organization of proteins and lipids within the bilayer by immobilizing certain transmembrane (TM) proteins and forming corrals within the membrane. Here, we present coarse-grained resolution simulations of a biologically realistic membrane model of asymmetrically organized lipids and TM proteins. We determine the effects of a model of cytoskeletal immobilization of selected membrane proteins using long time scale coarse-grained molecular dynamics simulations. By introducing compartments with varying degrees of restraints within the membrane models, we are able to reveal how compartmentalization caused by cytoskeletal immobilization leads to reduced and anomalous diffusional mobility of both proteins and lipids. This in turn results in a reduced rate of protein dimerization within the membrane and of hopping of membrane proteins between compartments. These simulations provide a molecular realization of hierarchical models often invoked to explain single-molecule imaging studies of membrane proteins.

Computational virology: From the inside out

Viruses typically pack their genetic material within a protein capsid. Enveloped viruses also have an outer membrane made up of a lipid bilayer and membrane-spanning glycoproteins. X-ray diffraction and cryoelectron microscopy provide high resolution static views of viral structure. Molecular dynamics (MD) simulations may be used to provide dynamic insights into the structures of viruses and their components. There have been a number of simulations of viral capsids and (in some cases) of the inner core of RNA or DNA packaged within them. These simulations have generally focussed on the structural integrity and stability of the capsid and/or on the influence of the nucleic acid core on capsid stability. More recently there have been a number of simulation studies of enveloped viruses, including HIV-1, influenza A, and dengue virus. These have addressed the dynamic behaviour of the capsid, the matrix, and/or of the outer envelope. Analysis of the dynamics of the lipid bilayer components of the envelopes of influenza A and of dengue virus reveals a degree of biophysical robustness, which may contribute to the stability of virus particles in different environments. Significant computational challenges need to be addressed to aid simulation of complex viruses and their membranes, including the need to integrate structural data from a range of sources to enable us to move towards simulations of intact virions. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Longitudinal assessment of health related quality of life of HIV infected patients treated for tuberculosis and HIV in a high burden setting

INTRODUCTION

Assessment of patients receiving treatment for human immunodeficiency virus (HIV) and tuberculosis (TB) using a Health Related Quality of Life (HRQoL) instrument is important to get the subjective view of the patients' wellbeing.

METHODS

We used the Functional Assessment of HIV Infection (FAHI) HRQoL instrument to collect perceived wellness information at baseline, month 3, 6 and 12 from patients enrolled in a pharmacokinetic study between March 2007 and April 2008. Composite domain scores at each time point and their relationship with the rate of adverse events (AEs) and serious adverse events were compared between treatment arms.

RESULTS

Out of the 82 patients enrolled, 76 were analysed. There was a significant increase in total score in all groups between baseline, month 3, 6 and 12 (all p values < 0.0001), and over time (p < 0.001). Adjusting for baseline total score, baseline CD4 count had a significant effect on the total score over time (p = 0.002) and the rate of change in total score over time, that is; interaction effect (p < 0.001). There was no difference in each domain scores between participants that received ART with TB treatment and those that received TB treatment only. Respiratory AEs had a significant effect on HRQoL.

CONCLUSION

We found that assessment of HRQoL of participants in TB-HIV treatment using the FAHI instrument was useful in evaluating treatment responses. It showed improvement consistent with decrease in adverse events and signs and symptoms of TB. Number and type of AEs was related to lower HRQoL in spite of TB cure.

The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope

The dengue virion is surrounded by an envelope of membrane proteins surrounding a lipid bilayer. We have combined the cryoelectron microscopy structures of the membrane proteins (PDB: 3J27) with a lipid bilayer whose composition is based on lipidomics data for insect cell membranes, to obtain a near-atomic resolution computational model of the envelope of the dengue virion. A coarse-grained molecular dynamics simulation on the microsecond timescale enables analysis of key biophysical properties of the dengue outer envelope. Properties analyzed include area per lipid values (for a spherical virion with a mixed lipid composition), bilayer thickness, and lipid diffusion coefficients. Despite the absence of cholesterol from the lipid bilayer, the virion exhibits biophysical robustness (slow lipid diffusion alongside stable bilayer thickness, virion diameter, and shape) that matches the cholesterol-rich membrane of influenza A, with similarly anomalous diffusion of lipids. Biophysical robustness of the envelope may confer resilience to environmental perturbations.

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The dengue virus envelope is a lipid bilayer plus an outer layer of membrane proteins

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The structures of the proteins plus lipidomics data were used to model the envelope

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Microsecond MD simulations revealed the dynamic behavior of the lipid bilayer

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Protein interactions confer “raft-like” robustness on a cholesterol-free membrane

Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion

The influenza virus is surrounded by an envelope composed of a lipid bilayer and integral membrane proteins. Understanding the structural dynamics of the membrane envelope provides biophysical insights into aspects of viral function, such as the wide-ranging survival times of the virion in different environments. We have combined experimental data from X-ray crystallography, nuclear magnetic resonance spectroscopy, cryo-electron microscopy, and lipidomics to build a model of the intact influenza A virion. This is the basis of microsecond-scale coarse-grained molecular dynamics simulations of the virion, providing simulations at different temperatures and with varying lipid compositions. The presence of the Forssman glycolipid alters a number of biophysical properties of the virion, resulting in reduced mobility of bilayer lipid and protein species. Reduced mobility in the virion membrane may confer physical robustness to changes in environmental conditions. Our simulations indicate that viral spike proteins do not aggregate and thus are competent for multivalent immunoglobulin G interactions.

Determination of the myocardial performance index in deteriorating grades of intrauterine growth restriction and its link to adverse outcomes

AIM

The aim of this study is to determine the fetal modified myocardial performance index (Mod-MPI) and E-wave/A-wave peak velocities (E/A ratio) in deteriorating grades of intrauterine growth restriction (IUGR) and its link to adverse outcomes defined as perinatal death, hypoxic ischemic encephalopathy, neonatal resuscitation, neonatal cord pH <7.15, intraventricular hemorrhage and bronchopulmonary dysplasia.

METHOD

Forty three pregnant women with IUGR defined as the abdominal circumference <10th percentile for gestational age and umbilical resistance index >2 standard deviations in the third trimester of pregnancy were matched for gestational age and maternal age with 43 women with appropriate-for-gestational-age fetuses. The IUGR group was subdivided on the basis of multivessel Doppler anomalies into different grades of growth restriction. Mod-MPI and E/A ratio were determined and linked to perinatal outcome.

RESULTS

The median Mod-MPI was significantly higher in growth-restricted fetuses compared with controls (0.59 vs 0.37, p < 0.001) and increased with severity of IUGR, the classification of which was based on degree of abnormality of the umbilical resistance index, presence of arterial redistribution and degree of abnormality of the ductus venosus (DV) Doppler indices. A cut-off Mod-MPI value of 0.54 conferred a sensitivity of 87% [confidence interval (CI): 66-97%], specificity of 75% (CI: 55-91%) and a likelihood ratio (LR) of 3.47 for an adverse outcome. A cut-off Mod-MPI value of 0.67 conferred a sensitivity of 100% (CI: 54-100%), specificity of 81% (CI: 65-92%) and LR of 5.28 for perinatal death. No abnormal outcomes occurred in controls. In logistic regression analysis, the MPI remained a significant predictor of adverse outcome after adjusting for gestational age of delivery, fetal weight, E/A ratio, maternal age, DV Doppler indices, amniotic fluid index and umbilical artery resistance index [adjusted odds ratio, 95% CI: 2.60 (1.15-5.83), p-value 0.02]. MPI fared significantly better than the E/A ratio as a predictor of adverse outcome (area under the receiver operating characteristic curve of 0.94 and 0.76, p < 0.001).

CONCLUSION

Fetal myocardial performance deteriorates with severity of growth restriction. There is an association between severity of the MPI elevation and rates of adverse perinatal outcome. The Mod-MPI and E/A ratio have the potential to be integrated into routine surveillance techniques of the growth-restricted fetus. © 2014 John Wiley & Sons, Ltd.

Oestradiol and diet modulate energy homeostasis and hypothalamic neurogenesis in the adult female mouse

Leptin and oestradiol have overlapping functions in energy homeostasis and fertility, and receptors for these hormones are localised in the same hypothalamic regions. Although, historically, it was assumed that mammalian adult neurogenesis was confined to the olfactory bulbs and the hippocampus, recent research has found new neurones in the male rodent hypothalamus. Furthermore, some of these new neurones are leptin-sensitive and affected by diet. In the present study, we tested the hypothesis that diet and hormonal status modulate hypothalamic neurogenesis in the adult female mouse. Adult mice were ovariectomised and implanted with capsules containing oestradiol (E2 ) or oil. Within each group, mice were fed a high-fat diet (HFD) or maintained on standard chow (STND). All animals were administered i.c.v. 5-bromo-2'-deoxyuridine (BrdU) for 9 days and sacrificed 34 days later after an injection of leptin to induce phosphorylation of signal transducer of activation and transcription 3 (pSTAT3). Brain tissue was immunohistochemically labelled for BrdU (newly born cells), Hu (neuronal marker) and pSTAT3 (leptin sensitive). Although mice on a HFD became obese, oestradiol protected against obesity. There was a strong interaction between diet and hormone on new cells (BrdU+) in the arcuate, ventromedial hypothalamus and dorsomedial hypothalamus. HFD increased the number of new cells, whereas E2 inhibited this effect. Conversely, E2 increased the number of new cells in mice on a STND diet in all hypothalamic regions studied. Although the total number of new leptin-sensitive neurones (BrdU-Hu-pSTAT3) found in the hypothalamus was low, HFD increased these new cells in the arcuate, whereas E2 attenuated this induction. These results suggest that adult neurogenesis in the hypothalamic neurogenic niche is modulated by diet and hormonal status and is related to energy homeostasis in female mice.

Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.

Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: characterization via multiscale molecular dynamics simulations

Receptor tyrosine kinases are single-pass membrane proteins that form dimers within the membrane. The interactions of their transmembrane domains (TMDs) play a key role in dimerization and signaling. Fibroblast growth factor receptor 3 (FGFR3) is of interest as a G380R mutation in its TMD is the underlying cause of ~99% of the cases of achondroplasia, the most common form of human dwarfism. The structural consequences of this mutation remain uncertain: the mutation shifts the position of the TMD relative to the lipid bilayer but does not alter the association free energy. We have combined coarse-grained and all-atom molecular dynamics simulations to study the dimerization of wild-type, heterodimer, and mutant FGFR3 TMDs. The simulations reveal that the helices pack together in the dimer to form a flexible interface. The primary packing mode is mediated by a Gx3G motif. There is also a secondary dimer interface that is more highly populated in heterodimer and mutant configurations that may feature in the molecular mechanism of pathology. Both coarse-grained and atomistic simulations reveal a significant shift of the G380R mutant dimer TMD relative to the bilayer to allow interactions of the arginine side chain with lipid headgroup phosphates.

Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking

G-protein coupled receptors (GPCRs) comprise a large family of membrane proteins with rich functional diversity. Signaling through the apelin receptor (AR or APJ) influences the cardiovascular system, central nervous system and glucose regulation. Pathophysiological involvement of apelin has been shown in atherosclerosis, cancer, human immunodeficiency virus-1 (HIV-1) infection and obesity. Here, we present the high-resolution nuclear magnetic resonance (NMR) spectroscopy-based structure of the N-terminus and first transmembrane (TM) segment of AR (residues 1-55, AR55) in dodecylphosphocholine micelles. AR55 consists of two disrupted helices, spanning residues D14-K25 and A29-R55(1.59). Molecular dynamics (MD) simulations of AR built from a hybrid of experimental NMR and homology model-based restraints allowed validation of the AR55 structure in the context of the full-length receptor in a hydrated bilayer. AR55 structural features were functionally probed using mutagenesis in full-length AR through monitoring of apelin-induced extracellular signal-regulated kinase (ERK) phosphorylation in transiently transfected human embryonic kidney (HEK) 293A cells. Residues E20 and D23 form an extracellular anionic face and interact with lipid headgroups during MD simulations in the absence of ligand, producing an ideal binding site for a cationic apelin ligand proximal to the membrane-water interface, lending credence to membrane-catalyzed apelin-AR binding. In the TM region of AR55, N46(1.50) is central to a disruption in helical character. G42(1.46), G45(1.49) and N46(1.50), which are all involved in the TM helical disruption, are essential for proper trafficking of AR. In summary, we introduce a new correlative NMR spectroscopy and computational biochemistry methodology and demonstrate its utility in providing some of the first high-resolution structural information for a peptide-activated GPCR TM domain.

Comparing early treatment outcomes of MDR-TB in decentralised and centralised settings in KwaZulu-Natal, South Africa

SETTING

In KwaZulu-Natal, South Africa, a setting endemic for tuberculosis (TB) and the human immunodeficiency virus (HIV), prolonged hospitalisation for the treatment of the growing number of multidrug-resistant TB (MDR-TB) patients is neither possible nor effective.

OBJECTIVE

To compare early treatment outcomes in patients with MDR-TB with and without HIV co-infection at four decentralised rural sites with a central urban referral hospital.

DESIGN

This is an operational, prospective cohort study of patients between 1 July 2008 and 30 November 2009, where culture conversion, time to culture conversion, survival and predictors of these outcomes were analysed.

RESULTS

Of 860 patients with MDR-TB, 419 were at the decentralised sites and 441 at the central hospital. Overall, 71% were HIV co-infected. In the 17-month study period, there was a higher proportion of culture conversion at the decentralised sites compared with the centralised hospital (54% vs. 24%, P < 0.001, OR 3.76, 95%CI 2.81-5.03). The median time to treatment initiation was significantly shorter at the decentralised sites compared with the centralised hospital (72 vs. 93 days, P < 0.001). There was no significant difference in survival following treatment initiation.

CONCLUSION

In this study, early treatment outcomes suggest that decentralised care for MDR-TB patients is superior to that in a centralised setting.

Interpretation of biomolecular NMR spin relaxation parameters

Biomolecular nuclear magnetic resonance (NMR) spin relaxation experiments provide exquisite information on the picosecond to nanosecond timescale motions of bond vectors. Spin-lattice (T1) and spin-spin (T2) relaxation times and the steady-state nuclear Overhauser effect (NOE) are the first set of parameters extracted from typical 15N or 13C NMR relaxation experiments. Therefore, verifying that T1, T2, and NOE are consistent with theoretical predictions is an important step before carrying out the more detailed model-free and reduced spectral density mapping analyses commonly employed. In this mini-review, we discuss the essential motional parameters used to describe biomolecular dynamics in the context of a variety of examples of folded and intrinsically disordered proteins and peptides in aqueous and membrane mimetic environments. Estimates of these parameters can be used as input for an online interface, introduced herein, allowing plotting of trends of T1, T2, and NOE with magnetic field strength. The plots may serve as a first-check to the spectroscopist preparing to embark on a detailed NMR relaxation analysis.

Solid-State NMR Studies of Chemically Lithiated CF

Three types of fluorinated carbon, all in their original form and upon sequential chemical lithiations via n-butyllithium, were investigated by (13)C and (19)F solid-state NMR methods. The three starting CF(x) materials [where x = 1 (nominally)] were fiber based, graphite based, and petroleum coke based. The aim of the current study was to identify, at the atomic/molecular structural level, factors that might account for differences in electrochemical performance among the different kinds of CF(x). Differences were noted in the covalent F character among the starting compounds and in the details of LiF production among the lithiated samples.

182. ROLE OF CRISP4 IN ION CHANNEL REGULATION AND MALE REPRODUCTION

CRISPs are a group of 3 proteins found in mammals (4 in the mouse) which show a strong expression bias in the male reproductive organs. Whilst the function of most CRISPs are yet to be elucidated, mouse CRISP2 is a known regulator of the ion channel, ryanodine receptor. CRISP4 is most abundantly produced by the principal cells of the epididymis and are secreted into the lumen, where they adhere to sperm during epididymal transit. In this study we examined the role of CRISP4 ion channel regulation in mouse spermatozoa through cell assays and mouse models. The identification of the Transient Receptor Potential (TRP) ion channel, TRPM8 to interact with CRISP4 was confirmed using stably-transfected CHO cell lines. Production of CRISP4 KO mouse model, whilst males are fertile, they exhibit a subtle infertility phenotype characterized by a reduced ability to capacitate and undergo the acrosome reaction. This data is further emphasized by the ability of TRPM8 agonists, icillin and menthol, to inhibit the acrosome reaction in mouse spermatozoa that could be prevented by the addition of recombinant CRISP4 crisp domain. Corresponding to these data, CRISP4 is localized to the tail and head of mouse spermatozoa. In conclusion, we have demonstrated that CRISP4 is a regulator of TRPM8 in mouse spermatozoa, and due to its expression and localization pattern is an important protein in sperm epididymal maturation.

Structural and functional characterization of transmembrane segment IX of the NHE1 isoform of the Na+/H+ exchanger

The Na(+)/H(+) exchanger isoform 1 (NHE1) is an integral membrane protein that regulates intracellular pH by removing one intracellular H(+) in exchange for one extracellular Na(+). It has a large N-terminal membrane domain of 12 transmembrane segments and an intracellular C-terminal regulatory domain. We characterized the cysteine accessibility of amino acids of the putative transmembrane segment IX (residues 339-363). Each residue was mutated to cysteine in a functional cysteineless NHE1 protein. Of 25 amino acids mutated, 5 were inactive or nearly so after mutation to cysteine. Several of these showed aberrant targeting to the plasma membrane and reduced expression of the intact protein, whereas others were expressed and targeted correctly but had defective NHE1 function. Of the active mutants, Glu(346) and Ser(351) were inhibited >70% by positively charged [2-(trimethylammonium)-ethyl]methanethiosulfonate but not by anionic [2-sulfonatoethyl]methanethiosulfonate, suggesting that they are pore lining and make up part of the cation conduction pathway. Both mutants also had decreased affinity for Na(+) and decreased activation by intracellular protons. The structure of a peptide representing amino acids 338-365 was determined by using high resolution NMR in dodecylphosphocholine micelles. The structure contained two helical regions (amino acids Met(340)-Ser(344) and Ile(353)-Ser(359)) kinked with a large bend angle around a pivot point at amino acid Ser(351). The results suggest that transmembrane IX is critical with pore-lining residues and a kink at the functionally important residue Ser(351).

425. Expression of mammalian cysteine-rich secretory proteins in the mouse model

Mammalian cysteine rich secretory proteins are a family of four proteins exhibiting a high amino acid sequence similarity and belonging to the CAP (Cysteine rich secretory proteins, Antigen-5 proteins and the plant Pathogenesis related-1 proteins) superfamily of proteins. They are designated CRISP 1, 2, 3 and 4. Structurally, mammalian CRISP’s are characterised by 16 cysteine residues involved in intra-molecular di-sulfide bonds and the formation of 2 domains, ie., the CRISP domain (CD) and CAP domain. Whilst studies on mouse CRISP2 suggest that the CD is involved in ion channel regulation, studies on non-mammalian CAP superfamily members suggest that the CAP domain is involved in proteolytic activity.They are predominantly expressed and localised in the male reproductive tract, however, the EST expression databases suggest that mammalian CRISPs are expressed more widely than in the male reproductive tract. The objective of this study was therefore to conclusively define the expression and localisation of each CRISP protein in a mammalian system.A reverse transcription PCR expression profile and immunohistochemical analysis of 16 mouse tissue was conducted to establish the expression and localisation of each of the four CRISPs. These data showed that although the CRISPs have a strong expression and localisation bias to the male reproductive tract, they are widely distributed throughout the body in mice, including the ovary, uterus, and mammary gland. Whilst each CRISP has a clear expression profile, there was a striking localisation of androgen regulated CRISPs (1, 3, 4) in immune tissue including the spleen and thymus. Such a localisation raises the spectre of a role for CRISPs in the normal physiology and disease of several organs.

Fetal ocular movements and retinal cell differentiation: analysis employing DNA microarrays

As developmental biologists we study the role of fetal movements in providing continuity between prenatal and postnatal life. There are two major categories of fetal motility. The first category consists of movements that have an obvious effect on the survival or development of the fetus (e.g., changes of position, sucking and swallowing). The second category consists of fetal movements that anticipate postnatal functions. For example, fetal ocular movements (FOMs) predict postnatal eye function (e.g., motion vision) of the newborn and therefore represent an important indicator of fetal health. However, while the clinical significance of fetal motility is obvious, its biological significance is elusive. We propose to use retina of genetically modified mouse embryos to study the biological role of FOMs in the genesis of cell diversity and organ functional maturation. Our results have already demonstrated the importance of fetal eye motility in the differentiation of cholinergic amacrine cells (CACs) in the retina (Kablar, 2003). Apparently, these cells are sensitive to motion and also responsible for motion vision. In the current report, we suggest employing the unique opportunity provided by the mouse Myf5-/-:MyoD-/- knock-outs that lack skeletal musculature and FOMs, microarray analysis and the follow-up experiments to identify a group of candidate genes that are essential for the molecular regulation of CAC differentiation and in turn for the functional maturation of the visual system towards its ability to perform motion vision. Finally, the molecules identified via this approach may be important in the mechanochemical signal transduction pathways employed during the process of conversion of a mechanical stimulus into an instruction understandable by the developing retinal neurons and glia cells.