An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

open access articlePseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms

Trapping in irradiated p-on-n silicon sensors at fluences anticipated at the HL-LHC outer tracker

The degradation of signal in silicon sensors is studied under conditions expected at the CERN High-Luminosity LHC. 200 $\mu$m thick n-type silicon sensors are irradiated with protons of different energies to fluences of up to $3 \cdot 10^{15}$ neq/cm$^2$. Pulsed red laser light with a wavelength of 672 nm is used to generate electron-hole pairs in the sensors. The induced signals are used to determine the charge collection efficiencies separately for electrons and holes drifting through the sensor. The effective trapping rates are extracted by comparing the results to simulation. The electric field is simulated using Synopsys device simulation assuming two effective defects. The generation and drift of charge carriers are simulated in an independent simulation based on PixelAV. The effective trapping rates are determined from the measured charge collection efficiencies and the simulated and measured time-resolved current pulses are compared. The effective trapping rates determined for both electrons and holes are about 50% smaller than those obtained using standard extrapolations of studies at low fluences and suggests an improved tracker performance over initial expectations

Review and meta-analysis of organic matter in cultivated soils in southern Africa

Soil organic matter (SOM) is tightly linked to soil quality, but cultivation generally causes a decline in SOM, reducing soil quality and releasing carbon dioxide into the atmosphere. Internationally, countries are expected to reduce their greenhouse gas (GHG) emissions, and compile and update GHG inventories. Many developing countries, such as those in southern Africa, do not have reliable information regarding SOM levels in cultivated soils, changes over time and best management practices to maintain or even restore SOM. A review was conducted to collate published research on SOM [or its indicator elements, carbon (C) and nitrogen (N)] in cultivated fields in southern Africa. A total of 84 publications were assessed, and information such as date, location, SOM/soil organic carbon (SOC) and clay content and key findings were recorded. Most of the publications (90 %) were published post-1990. The spatial distribution of these studies is very non-uniform. A decline of 25–53 % in SOC due to cultivation was evident for cultivated fields in different precipitation zones in southern Africa, with SOC ranging from 0.7 to 2.5 %. These values correlate relatively well with existing SOC maps. A strong correlation between SOC and clay content in natural soil is weakened following cultivation. Carbon sequestration and GHG emission dynamics under various management systems and for different climatic regions, as well as how field crop production can play a role in mitigating climate change, are poorly understood. Intensified monitoring by multi-institutional collaboration is recommended to address this issue.ARC and the Water Research Commission (Project K5/2501).http://link.springer.com/journal/107052017-01-29hb201

Cultural Capital and Self-Rated Health in Low Income Women: Evidence from the Urban Health Study, Beirut, Lebanon

This paper examines the association between cultural capital and self-rated psychosocial health among poor, ever-married Lebanese women living in an urban context. Both self-rated general and mental health status were assessed using data from a cross-sectional survey of 1,869 women conducted in 2003. Associations between self-rated general and mental health status and cultural capital were obtained using χ(2) tests and odds ratios from binary logistic regression models. Cultural capital had significant associations with self-perceived general and mental health status net of the effects of social capital, SES, demographics, community and health risk factors. For example, the odds ratios for poor general and mental health associated with low cultural capital were 4.5 (CI: 2.95–6.95) and 2.9 (CI: 2.09–4.05), respectively, as compared to participants with high cultural capital. As expected, health risk factors were significantly associated with both measures of health status. However, demographic and community variables were associated with general health but not with mental health status. The findings pertaining to social capital and measures of SES were mixed. Cultural capital was a powerful and significant predictor of self-perceived general and mental health among women living in poor urban communities