Conformation of Circular DNA in 2 Dimensions

The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW value (in the present case $\nu=3/4$), and that the topology and dimensionality of the system strongly influences the cross-over between the rigid regime and the self-avoiding regime at a scale $L\approx 8 \ell_p$. Additionally, the bond correlation function scales with the molecular length $L$ as predicted. For molecular lengths $L\leq5 \ell_p$, circular DNA behaves like a stiff molecule with approximately elliptic shape.Comment: 4 pages, 5 figure

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA-DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes

Small Angle Scattering by Fractal Aggregates: A Numerical Investigation of the Crossover Between the Fractal Regime and the Porod Regime

Fractal aggregates are built on a computer using off-lattice cluster-cluster aggregation models. The aggregates are made of spherical particles of different sizes distributed according to a Gaussian-like distribution characterised by a mean $a_0$ and a standard deviation $\sigma$. The wave vector dependent scattered intensity $I(q)$ is computed in order to study the influence of the particle polydispersity on the crossover between the fractal regime and the Porod regime. It is shown that, given $a_0$, the location $q_c$ of the crossover decreases as $\sigma$ increases. The dependence of $q_c$ on $\sigma$ can be understood from the evolution of the shape of the center-to-center interparticle-distance distribution function.Comment: RevTex, 4 pages + 6 postscript figures, compressed using "uufiles", published in Phys. Rev. B 50, 1305 (1994

Real-time monitoring of protein conformational changes using a nano-mechanical sensor.

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice

The Swiss Tropical and Public Health Institute: past, present and future

Compared internationally, the history of the Swiss Tropical and Public Health Institute (Swiss TPH) is unusual. Founded in 1944, at a time of utmost isolation, it was a response to specific needs of the government of Switzerland during the Second World War. In 1943, the Swiss Federal Council approached universities in Switzerland and asked them to submit project proposal that had the potential to mitigate possible post-war unemployment and threatening economic isolation. Members of the University of Basel proposed to establish a Swiss Tropical Institute (today: Swiss TPH). With its harbour at the River Rhine, Basel was an important international transport hub. The city was and still is the headquarters of important pharmaceutical companies, such as Novartis Pharma AG and F. Hoffmann-La Roche AG, which were looking for new markets overseas. Last but not least, scientific expeditions to Africa were rather common in the 19(th) and the beginning of the 20(th) century for members of Basel's bourgeoisie. Initially, Swiss TPH focused primarily on basic research into diseases of poverty, but over the years it has developed into an important player in public, international and global health. This article sees the development of the institute as a reflection of the visions of its directors from the founder Professor Rudolf Geigy to Professor Jurg Utzinger, who is the current Swiss TPH director. It includes interviews with the four latest of them, discussing their experiences and attempts to adapt the institute to an ever changing global environment. From these lessons learnt we hope to gain insights that could be relevant for today's leaders of scientific institutes; foster public-private partnerships and contribute to solve some of the most pressing global health challenges

Health impact assessment and climate change: a scoping review

Climate change has various adverse impacts on public health, ranging from heat-related illness to an increased risk of undernutrition in low-income countries. Health impact assessment (HIA) has been advocated as a valuable tool to systematically identify and quantify the effects of climate change on public health and to inform and evaluate the impact of disease-specific adaptation measures as well as health co-benefits of mitigation measures. We conducted a scoping review to map out peer-reviewed literature on HIA in the context of climate change. Web of Science, Scopus and PubMed were searched without language or time restriction. Publications were included in the full text screening that presented or discussed the application of HIA for investigating health impacts of climate change, or associated adaptation and mitigation measures. In total, 76 peer-reviewed publications from 26 countries were included and characterized. There was a paucity of studies on HIA in the context of climate change from low- and middle-income countries. The most investigated climate change effects were related to temperature and air-pollution. Consequently, associated health impacts, such as respiratory or cardiovascular morbidity and mortality, were examined most frequently. Research-driven HIAs with a quantitative methodological approach were the predominant choice to assess health impacts of climate change. Only one in five publications applied a classical step-by-step HIA approach. While quantitative assessment of health impacts associated with climate change seems to be a well established field of research, the few publications applying a step-by-step HIA approach to systematically anticipate potential health impacts of climate change in a given context point at a missed opportunity for strengthening intersectoral collaboration to maximize health (co-) benefits of climate mitigation and adaptation measures. To promote the use of step-by-step HIA in regions that are most affected by climate change, HIA teaching and training efforts are urgently needed

The sensuous secrets of shelter: how recollections of food stimulate Irish men's reconstructions of their early formative residential experiences in Leicester, Sheffield and Manchester

This paper examines the intersection between food, recollection and Irish migrants’ reconstructions of their housing pathways in the three English cities of Leicester (East Midlands), Sheffield (South Yorkshire) and Manchester (North). Previous studies have acknowledged more implicitly the role of memory in representing the Irish migrant experience in England. Here, we adopt a different stance. We explore the mnemonic power of food to encode, decode and recode Irish men’s reconstructions of their housing pathways in England when constructing and negotiating otherness. In doing so, we apply a ‘Proustian anthropological’ approach in framing the men’s representations of their formative residential experiences in the boarding houses of the three English cities during the 1950s and 1960s are examined. The extent to which food provided in the boarding houses was used as an instrument of discipline and control is examined. The relevance of food related acts of resistance, food insecurity and acts of hedonic meat-centric eating in constructing the men’s sociocultural identity are also explored

Quantification of annual settlement growth in rural mining areas using machine learning

Studies on annual settlement growth have mainly focused on larger cities or incorporated data rarely available in, or applicable to, sparsely populated areas in sub-Saharan Africa, such as aerial photography or night-time light data. The aim of the present study is to quantify settlement growth in rural communities in Burkina Faso affected by industrial mining, which often experience substantial in-migration. A multi-annual training dataset was created using historic Google Earth imagery. Support vector machine classifiers were fitted on Landsat scenes to produce annual land use classification maps. Post-classification steps included visual quality assessments, majority voting of scenes of the same year and temporal consistency correction. Overall accuracy in the four studied scenes ranged between 58.5% and 95.1%. Arid conditions and limited availability of Google Earth imagery negatively affected classification accuracy. Humid study sites, where training data could be generated in proximity to the areas of interest, showed the highest classification accuracies. Overall, by relying solely on freely and globally available imagery, the proposed methodology is a promising approach for tracking fast-paced population dynamics in rural areas where population data is scarce. With the growing availability of longitudinal high-resolution imagery, including data from the Sentinel satellites, the potential applications of the methodology presented will further increase in the futur

Industrial mining and HIV risk: evidence from 39 mine openings across 16 countries in sub-Saharan Africa

OBJECTIVES: The aim of this study was to assess the impact of natural resource extraction projects on HIV transmission risks in local communities in sub-Saharan Africa. DESIGN: Difference-in-differences design using repeated cross-sectional data from around newly opened mines. METHODS: We combined data on mine openings with HIV data from the Demographic and Health Surveys (DHS). Using logistic regression models, we compared HIV related indicators between mining (i.e. up to 10 km distance from the mine) and comparison (i.e. 10-50 km) areas before and after mine opening to identify their impact on HIV prevalence, sexual behavior and HIV knowledge. RESULTS: A total of 33,086 individuals across 39 mine openings were analyzed. Adjusting for baseline differences and temporal trends in the study regions, mine opening increased the odds of HIV infection almost two-fold (odds ratio (OR): 1.93, 95% confidence interval (CI): 1.19-3.14). Strongest effects were seen in high-prevalence countries and in the 20-29 years age group. In mining communities around operational mines there was a tendency towards lower HIV knowledge (OR: 0.81, 95% CI: 0.63-1.04). New mine openings increased the odds of risky sexual behaviors, such as having multiple sex partners (OR: 1.61, 95% CI: 1.02-2.55), high-risk sexual partners (OR: 1.45, 95% CI: 1.03-2.05) and unprotected sex with high-risk partners (OR: 1.77, 95% CI: 1.18-2.67). CONCLUSION: The findings suggest that in our sample of households surrounding industrial mines, HIV infection risks substantially increase upon mine opening. Existing strategies for addressing mining-related risks for HIV transmission seem to be insufficient. Further efforts for mitigating and monitoring impacts of mines are needed. Video Abstract: http://links.lww.com/QAD/C557

Scoping review of the inclusion of economic analysis in impact studies of natural resource extraction projects

The extraction of natural resources, such as minerals, oil, and gas, can have profound economic effects. The application of economic analysis methods in impact studies of resource extraction projects holds potential to inform decision-making in order to optimise gains and minimise negative externalities. This paper aims to identify and characterise peer-reviewed publications that report on economic studies implemented as part of impact assessments of resource extraction projects. We conducted a systematic scoping review in PubMed and Scopus of articles published between 1998 and 2020. Out of 1,579 raw hits, we identified 13 articles describing 15 economic analyses of resource extraction projects. Half of the identified papers presented economic analyses conducted in the context of mining and oil/gas projects. The majority of the identified studies dealt with the cost and/or benefits of environmental and/or social impacts. Only one study investigated economic aspects associated with potential health impacts. Given the small number of papers identified, economic analysis of impacts associated with natural resource extraction projects seems to be a small field of published research. Yet the inclusion of economic analysis in impact assessment of resource extraction projects holds promise to better harness benefits for local communities and governments while minimising negative externalities. © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group