Addressing ethical issues in H3Africa research – the views of research ethics committee members

In June 2014, the H3Africa Working Group on Ethics organised a workshop with members of over 40 research ethics committees from across Africa to discuss the ethical challenges raised in H3Africa research, and to receive input on the proposed H3Africa governance framework. Prominent amongst a myriad of ethical issues raised by meeting participants were concerns over consent for future use of samples and data, the role of community engagement in large international collaborative projects, and particular features of the governance of sample sharing. This report describes these concerns in detail and will be informative to researchers wishing to conduct genomic research on diseases pertinent to the African research context.     

A screen for Neurospora knockout mutants displaying growth rate dependent branch density

Branch density (the spatial distribution of branch initiation points along a growing hypha) in wild-type Neurospora has been shown to remain constant at different growth rates due to a hypothesized system which compensates for hyphal growth rate. Here we report the results of a survey of the Neurospora knockout library for mutants affecting this proposed growth rate compensation system. The mutants identified fail to maintain branching homeostasis?at different growth rates, thus showing growth rate-dependent branch density. The gene functions highlighted by this screen are diverse with several emerging themes including: ubiquitin-binding proteins, kinases, metal binding/metal metabolism proteins, reactive oxygen species (ROS) control proteins, and clock-associated/clock-controlled proteins. Other than their common influence on branch density homeostasis, the relationships between these gene functions and how they interact to influence branching are unclear.     

Protein charge determination and implications for interactions in cell extracts

Decades of dilute‐solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behavior under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ～2‐fold lower than predicted from primary structure analysis. Cytochrome c charge was tuned by sulfate binding and was rendered anionic in E. coli extracts due to interactions with macroanions. Mutants in which three or four cationic residues were replaced with glutamate were charge‐neutral and “inert” in extracts. A comparison of the interaction propensities of cytochrome c and the mutants emphasizes the role of negative charge in stabilizing physiological environments. Charge–charge repulsion and preferential hydration appear to prevent aggregation. The implications for molecular organization in vivo are discussed.     

New insights into the location and form of sclerostin

Sclerostin is widely reported to be a monomeric osteocyte specific protein. In this study we have investigated whether sclerostin is produced in different forms and in which cell and tissue types they are produced.     

Proteomic Analysis of the Extracellular Matrix Produced by Mesenchymal Stromal Cells: Implications for Cell Therapy Mechanism

Mesenchymal stromal cells (MSCs) transiently transfected with notch1 intracellular domain (NICD) are beneficial for neurological disorders as observed in several preclinical studies. Extracellular matrix (ECM) derived from NICD-transfected MSCs has been previously shown to support in vitro neural cell growth and survival better than that of un-transfected MSCs. To understand the underlying mechanism(s) by which NICD-transfected MSC-derived ECM supports neural cell growth and survival, we investigated the differences in NICD-transfected MSC- and MSC-derived ECM protein quantity and composition. To compare the ECM derived from MSCs and NICD-transfected MSCs, the proteins were sequentially solubilized using sodium dodecyl sulfate (SDS) and urea, quantified, and compared across four human donors. We then analyzed ECM proteins using either in-gel digests or in-solution surfactant-assisted trypsin digests (SAISD) coupled with reverse phase nano-liquid chromatography and tandem mass spectrometry (nLC-MS/MS). Analyses using nLC-MS/MS identified key components of ECM from NICD-transfected MSCs and un-transfected MSCs and revealed significant differences in their respective compositions. This work provides a reproducible method for identifying and comparing in vitro cell-derived ECM proteins, which is crucial for exploring the mechanisms underlying cellular therapy.     

The use of geographic information systems to map and assess ecosystem services

In recent years, geographic information systems (GIS) have become a powerful tool for mapping and assessing the provision of ecosystem services within a landscape. GIS can help land managers and conservationists visualize spatial and temporal patterns and changes in ecosystem services and estimate the potential impact from projected changes in land use or management or climatic conditions on the provision of these services. The end-goal of ecosystem service assessment is usually to estimate marginal values of ecosystem services to inform decisions where trade-offs in ecosystem service provision will affect human well-being. Because our ability to estimate the provision of ecosystem services underlies our ability to estimate their societal values, the theoretical bases of GIS approaches and models for assessing ecosystem services need to be well understood before they are employed for decision-making purposes. This paper reviews GIS approaches and software developed for the assessment of ecosystem services and highlights their strengths and weaknesses in the context of different end uses.     

Experimental investigations of the human oesophagus: anisotropic properties of the embalmed muscular layer under large deformation

Biomechanics and Modeling in Mechanobiology - The oesophagus is a primarily mechanical organ whose material characterisation would aid in the investigation of its pathophysiology, help in the field...     

Preoperative testing before low-risk surgical procedures

Background:There is concern about increasing utilization of low-value health care services, including preoperative testing for low-risk surgical procedures. We investigated temporal trends, explanatory factors, and institutional and regional variation in the utilization of testing before low-risk procedures.Methods:For this retrospective cohort study, we accessed linked population-based administrative databases from Ontario, Canada. A cohort of 1 546 223 patients 18 years or older underwent a total of 2 224 070 low-risk procedures, including endoscopy and ophthalmologic surgery, from Apr. 1, 2008, to Mar. 31, 2013, at 137 institutions in 14 health regions. We used hierarchical logistic regression models to assess patient- and institution-level factors associated with electrocardiography (ECG), transthoracic echocardiography, cardiac stress test or chest radiography within 60 days before the procedure.Results:Endoscopy, ophthalmologic surgery and other low-risk procedures accounted for 40.1%, 34.2% and 25.7% of procedures, respectively. ECG and chest radiography were conducted before 31.0% (95% confidence interval [CI] 30.9%–31.1%) and 10.8% (95% CI 10.8%–10.8%) of procedures, respectively, whereas the rates of preoperative echocardiography and stress testing were 2.9% (95% CI 2.9%–2.9%) and 2.1% (95% CI 2.1%–2.1%), respectively. Significant variation was present across institutions, with the frequency of preoperative ECG ranging from 3.4% to 88.8%. Receipt of preoperative ECG and radiography were associated with older age (among patients 66–75 years of age, for ECG, adjusted odds ratio [OR] 18.3, 95% CI 17.6–19.0; for radiography, adjusted OR 2.9, 95% CI 2.8–3.0), preoperative anesthesia consultation (for ECG, adjusted OR 8.7, 95% CI 8.5–8.8; for radiography, adjusted OR 2.2, 95% CI 2.1–2.2) and preoperative medical consultation (for ECG, adjusted OR 6.8, 95% CI 6.7–6.9; for radiography, adjusted OR 3.6, 95% CI 3.5–3.6). The median ORs for receipt of preoperative ECG and radiography were 2.3 and 1.6, respectively.Interpretation:Despite guideline recommendations to limit testing before low-risk surgical procedures, preoperative ECG and chest radiography were performed frequently. Significant variation across institutions remained after adjustment for patient- and institution-level factors.In response to concerns about increasing utilization of low-value health care services, the American Board of Internal Medicine Foundation launched the Choosing Wisely campaign in the United States in 2012.¹ The goal of the campaign is to encourage conversations between physicians and patients about low-value care by defining “top 5” lists of tests, treatments and procedures that may be unnecessary or unsupported by evidence.¹ Subsequent Choosing Wisely campaigns have followed in other countries, including Canada starting in April 2014.^2,3 Of interest for health policy-makers, payers and clinicians are current utilization rates for the procedures mentioned in these recommendations. Establishing baseline rates permits an understanding of the extent of the problem of low-value care, which in turn allows monitoring of the effect of initiatives such as Choosing Wisely on utilization rates over time.One Choosing Wisely item included by many specialty societies is the recommendation to avoid routinely performing preoperative testing (including chest radiography, echocardiography and cardiac stress tests) for patients undergoing low-risk surgery.^4–6 This recommendation was previously included in the 2007 American College of Cardiology/American Heart Association guidelines on perioperative cardiovascular evaluation for noncardiac surgery⁷ and was reconfirmed in a recent update.⁸ Avoiding preoperative investigations in this setting is supported by evidence that routine testing in patients undergoing low-risk surgery does not improve outcomes or change management and may lead to further unnecessary downstream testing, cancellation of surgery, and increases in patient anxiety and cost.^7,9–12 To date, neither the rate of preoperative testing across a large and diverse jurisdiction nor the degree of variation at regional and institutional levels, where data may be “actionable,” is well understood.The objectives of this study were to determine utilization rates of preoperative tests before hospital-based low-risk surgical procedures at the jurisdictional, regional and institutional level. In addition, we aimed to evaluate temporal trends of preoperative testing over a 5-year period. We hypothesized that there would be significant regional and institutional variation in preoperative cardiac testing before low-risk surgery and that patients with prior cardiac comorbidities would have a higher rate of preoperative testing than those without such comorbidities.     

The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America

A comprehensive study of the phylogeography and population genetics of the largest wild artiodactyl in the arid and cold‐temperate South American environments, the guanaco (Lama guanicoe) was conducted. Patterns of molecular genetic structure were described using 514 bp of mtDNA sequence and 14 biparentally inherited microsatellite markers from 314 samples. These individuals originated from 17 localities throughout the current distribution across Peru, Bolivia, Argentina and Chile. This confirmed well‐defined genetic differentiation and subspecies designation of populations geographically separated to the northwest (L. g. cacsilensis) and southeast (L. g. guanicoe) of the central Andes plateau. However, these populations are not completely isolated, as shown by admixture prevalent throughout a limited contact zone, and a strong signal of expansion from north to south in the beginning of the Holocene. Microsatellite analyses differentiated three northwestern and 4–5 southeastern populations, suggesting patterns of genetic contact among these populations. Possible genetic refuges were identified, as were source‐sink patterns of gene flow at historical and recent time scales. Conservation and management of guanaco should be implemented with an understanding of these local population dynamics while also considering the preservation of broader adaptive variation and evolutionary processes.     

Defensin-driven viral evolution

Enteric alpha-defensins are potent effectors of innate immunity that are abundantly expressed in the small intestine. Certain enteric bacteria and viruses are resistant to defensins and even appropriate them to enhance infection despite neutralization of closely related microbes. We therefore hypothesized that defensins impose selective pressure during fecal-oral transmission. Upon passaging a defensin-sensitive serotype of adenovirus in the presence of a human defensin, mutations in the major capsid protein hexon accumulated. In contrast, prior studies identified the vertex proteins as important determinants of defensin antiviral activity. Infection and biochemical assays suggest that a balance between increased cell binding and a downstream block in intracellular trafficking mediated by defensin interactions with all of the major capsid proteins dictates the outcome of infection. These results extensively revise our understanding of the interplay between defensins and non-enveloped viruses. Furthermore, they provide a feasible rationale for defensins shaping viral evolution, resulting in differences in infection phenotypes of closely related viruses.