Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

Pathogen access to host nutrients in infected tissues is fundamental for pathogen growth and virulence, disease progression, and infection control. However, our understanding of this crucial process is still rather limited because of experimental and conceptual challenges. Here, we used proteomics, microbial genetics, competitive infections, and computational approaches to obtain a comprehensive overview of Salmonella nutrition and growth in a mouse typhoid fever model. The data revealed that Salmonella accessed an unexpectedly diverse set of at least 31 different host nutrients in infected tissues but the individual nutrients were available in only scarce amounts. Salmonella adapted to this situation by expressing versatile catabolic pathways to simultaneously exploit multiple host nutrients. A genome-scale computational model of Salmonella in vivo metabolism based on these data was fully consistent with independent large-scale experimental data on Salmonella enzyme quantities, and correctly predicted 92% of 738 reported experimental mutant virulence phenotypes, suggesting that our analysis provided a comprehensive overview of host nutrient supply, Salmonella metabolism, and Salmonella growth during infection. Comparison of metabolic networks of other pathogens suggested that complex host/pathogen nutritional interfaces are a common feature underlying many infectious diseases.     

Metabolic profiling of human saliva before and after induced physiological stress by ultra-high performance liquid chromatography–ion mobility–mass spectrometry

A method has been developed for metabolite profiling of the salivary metabolome based on protein precipitation and ultra-high performance liquid chromatography coupled with ion mobility-mass spectrometry (UHPLC–IM–MS). The developed method requires 0.5 mL of human saliva, which is easily obtainable by passive drool. Standard protocols have been established for the collection, storage and pre-treatment of saliva. The use of UHPLC allows rapid global metabolic profiling for biomarker discovery with a cycle time of 15 min. Mass spectrometry imparts the ability to analyse a diverse number of species reproducibly over a wide dynamic range, which is essential for profiling of biofluids. The combination of UHPLC with IM–MS provides an added dimension enabling complex metabolic samples to be separated on the basis of retention time, ion mobility and mass-to-charge ratio in a single chromatographic run. The developed method has been applied to targeted metabolite identification and untargeted metabolite profiling of saliva samples collected before and after exercise-induced physiological stress. δ-Valerolactam has been identified as a potential biomarker on the basis of retention time, MS/MS spectrum and ion mobility drift time.     

The growth-ring variations of alpine shrub Rhododendron przewalskii reflect regional climate signals in the alpine environment of Miyaluo Town in Western Sichuan Province,China

Rhododendron przewalskii is an important dwarf shrub species in alpine environments of western Sichuan that offers a unique opportunity to expand current dendrochronological networks into extreme environments beyond the survival limit of trees. Our objectives in this study are to evaluate the dendroclimatological potentials of R. przewalskii and determine the major limiting climate factor for the species’ growth rings. We sampled 25 cross-sections of R. przewalskii at an elevation of 4050 m, about 150 m above treeline, on Zhegu Mountain of Miyaluo in western Sichuan of southeastern Tibetan Plateau. R. przewalskii has well-defined growth rings such that most stem sections could be cross-dated. The resulting 61-year long standard chronology (A.D. 1949–2009) was derived from 38 series from 19 cross-sections. Response analysis revealed that radial growth of the Zhegu Mountain R. przewalskii is significantly and negatively correlated to late winter temperature (January–February), mainly driven by maximum temperatures. This correlation indicates that colder daytime temperatures during late-winter lead to improved growth the following growing season. Minimum winter temperatures do not appear important for radial growth of this population. R. przewalskii ring widths are also strongly correlated to late-winter maximum temperatures over the southeastern Tibetan Plateau region. April maximum and July minimum temperatures are positively and significantly correlated to radial growth suggesting that warm April days and warm July nights promote current-season radial growth. In contrast, radial growth is only negatively correlated to April precipitation, indicating that wet soil conditions inhibit total radial increment. The main differences of R. przewalskii compared to tree species living at high-altitude nearby regions is that R. przewalskii has a weaker positive growth response to summer temperature and winter minimum temperature, but a much stronger negative response to winter temperature. Due to the strong climatic signal recorded in the growth curves of R. przewalskii, this dwarf shrub should be useful for climate–growth studies in alpine regions where no forests are present.     

Control of (Multi)Drug Resistance and Tuberculosis Incidence over 23 Years in the Context of a Well-Supported Tuberculosis Programme in Rural Malawi

Background

The rise in tuberculosis (TB) incidence following generalized HIV epidemics can overwhelm TB control programmes in resource-limited settings, sometimes accompanied by rising rates of drug resistance. This has led to claims that DOTS-based TB control has failed in such settings. However, few studies have described the effect of a sustained and well-supported DOTS programme on TB incidence and drug resistance over a long period. We present long-term trends in incidence and drug resistance in rural Malawi.

Methods

Karonga District in northern Malawi has an adult HIV prevalence of ∼10%. A research group, the Karonga Prevention Study, collaborates with the National Tuberculosis Programme to support core TB control activities. Bacteriological, demographic and clinical (including HIV status) information from all patients starting TB treatment in the District have been recorded since 1988. During that period isolates from each culture-positive TB patient were exported for drug sensitivity testing. Antiretroviral therapy (ART) has been widely available since 2005.

Results

Incidence of new smear-positive adult TB peaked at 124/100,000/year in the mid-90s, but has since fallen to 87/100,000/year. Drug sensitivity information was available for 95% (3132/3307) of all culture-positive cases. Initial resistance to isoniazid was around 6% with no evidence of an increase. Fewer than 1% of episodes involved a multi-drug resistant strain.

Discussion

In this setting with a generalised HIV epidemic and medium TB burden, a well-supported DOTS programme enhanced by routine culture and drug sensitivity testing may well have reduced TB incidence and maintained drug resistance at low levels.     

Development of Nascent Focal Adhesions in Spreading Cells

The eukaryotic cell develops organelles to sense and respond to the mechanical properties of its surroundings. These mechanosensing organelles aggregate into symmetry-breaking patterns to mediate cell motion and differentiation on substrate. The spreading of a cell plated onto a substrate is one of the simplest paradigms in which angular symmetry-breaking assemblies of mechanical sensors are seen to develop. We review evidence for the importance of the edge of the cell-extracellular matrix adhesion area in the aggregation of mechanosensors and develop a theoretical model for the clustering of mechanosensors into nascent focal adhesions on this contact ring. To study the spatial patterns arising on this topological feature, we use a one-dimensional lattice model with a nearest-neighbor interaction between individual integrin-mediated mechanosensors. We find the effective Ginzburg-Landau free energy for this model and determine the spectrum of spatial modes as the cell spreads and increases its contact area with the substrate. To test our model, we compare its predictions with measured distributions of paxillin in spreading fibroblasts.     

BlackOPs: increasing confidence in variant detection through mappability filtering

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.     

Subsurface behavior of bottlenose dolphins (Tursiops truncatus) interacting with fish trawl nets in northwestern Australia: Implications for bycatch mitigation

Most studies of delphinid‐trawler interactions have documented the surface behavior of dolphins feeding on discarded bycatch, but not their subsurface behavior around demersal trawl gear. Using video cameras mounted inside trawl nets, we recorded the subsurface behavior of common bottlenose dolphins (Tursiops truncatus) in a demersal fish trawl fishery in northwestern Australia. Footage from 36 trawls across the fishery was analyzed to determine the extent of dolphin‐gear interactions and the behavior of dolphins inside the nets. Interaction rates were high, with dolphins present inside and outside the nets during 29 and 34 trawls, respectively, and for up to 99% of the trawl duration. The proportion of foraging behaviors exhibited inside the nets was higher than the proportions of traveling and socializing behaviors. Twenty‐nine individuals were identified inside the net, seven of which returned repeatedly within and between trawls and fishing trips, but were observed primarily in the same localized areas in which they were first recorded. Our results suggest that entering trawl nets may be a frequently occurring, yet specialized behavior exhibited by a small subset of trawler‐associated dolphins. We propose that gear modifications, not spatial or temporal adjustments to fishing effort, have the greatest potential to reduce dolphin bycatch.