Portrait of a Pathogen: The Mycobacterium tuberculosis Proteome In Vivo

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a facultative intracellular pathogen that can persist within the host. The bacteria are thought to be in a state of reduced replication and metabolism as part of the chronic lung infection. Many in vitro studies have dissected the hypothesized environment within the infected lung, defining the bacterial response to pH, starvation and hypoxia. While these experiments have afforded great insight, the picture remains incomplete. The only way to study the combined effects of these environmental factors and the mycobacterial response is to study the bacterial response in vivo.We used the guinea pig model of tuberculosis to examine the bacterial proteome during the early and chronic stages of disease. Lungs were harvested thirty and ninety days after aerosol challenge with Mtb, and analyzed by liquid chromatography-mass spectrometry. To date, in vivo proteomics of the tubercle bacillus has not been described and this work has generated the first large-scale shotgun proteomic data set, comprising over 500 unique protein identifications. Cell wall and cell wall processes, and intermediary metabolism and respiration were the two major functional classes of proteins represented in the infected lung. These classes of proteins displayed the greatest heterogeneity indicating important biological processes for establishment of a productive bacterial infection and its persistence. Proteins necessary for adaptation throughout infection, such as nitrate/nitrite reduction were found at both time points. The PE-PPE protein class, while not well characterized, represented the third most abundant category and showed the most consistent expression during the infection.Cumulatively, the results of this work may provide the basis for rational drug design - identifying numerous Mtb proteins, from essential kinases to products involved in metal regulation and cell wall remodeling, all present throughout the course of infection

At the Crossroads of Sustainability: The Natural Recompositioning of Architecture

It is widely acknowledged that the mantra of sustainability has triggered a fundamental reversal in the core of design practice: If the original purpose of architecture was to protect humans from the destructive actions of nature,today it should protect nature from the damaging actions of humans. But sustainable design is far from being a coherent body of fully totalized ideas:it has a broad spectrum of disputing interpretations that oscillate between the deterministic models of energy control and technological efficiencies, and the moralistic and romantic approaches that attempt to see in nature and natural processes a fundamental way to de-escalate the global urban footprint and its associated patterns of consumption. However, mainstream green design has been evolving by progressively absorbing the narrative of deep ecology. Nature has been being integrated into architecture literally, by inserting vegetation onto buildings; digitally, by bringing environmental data into the design process (climate records, wind streams, sun rotation and air flows are computed, modelled and effectually shape architectures), and transcendentally, by claiming that sustainable architecture nurtures “the existing and evolving connections between spiritual and material consciousness.” The acknowledgement of the inexorable affiliation between architecture and the environment is, of course, not exactly new. What is distinctive today is the reification of the role of nature in architecture as an ideological stance, now totally intertwined with state-of-art data processing and the market-driven tools brought by Natural Capitalism. This paper will examine emblematic “green” buildings produced by leading architects such as Pelli Clarke Pelli, William McDonough, Stefano Boeri, Norman Foster and BIG in the light of Tim Morton’s, Slavoj Zizek and Bruno Latour’s critique of nature. It will illustrate how, despite being able to successfully forge new creative freedoms by exploring hybridizations between the domains of design and science, sustainability’s self-righteous “naturalistic” narrative is enabling a vision of the architect as an “expert manager” focused on producing projects of ecologic “beautification” while assumed to be “saving the world,” effectively depoliticizing the architectural practice. Nevertheless, these examples attest that there is a vast and fertile field of ideas to be explored and in this regard it is important to underline that we are still in the embryonic outset of the engagement of architecture with sustainability

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

BACKGROUND: Whole genome sequencing (WGS) is becoming an important part of epidemiological investigations of infectious diseases due to greater resolution and cost reductions compared to traditional typing approaches. Many public health and clinical teams will increasingly use WGS to investigate clusters of potential pathogen transmission, making it crucial to understand the benefits and assumptions of the analytical methods for investigating the data. We aimed to understand how different approaches affect inferences of transmission dynamics and outline limitations of the methods. METHODS: We comprehensively searched electronic databases for studies that presented methods used to interpret WGS data for investigating tuberculosis (TB) transmission. Two authors independently selected studies for inclusion and extracted data. Due to considerable methodological heterogeneity between studies, we present summary data with accompanying narrative synthesis rather than pooled analyses. RESULTS: Twenty-five studies met our inclusion criteria. Despite the range of interpretation tools, the usefulness of WGS data in understanding TB transmission often depends on the amount of genetic diversity in the setting. Where diversity is small, distinguishing re-infections from relapses may be impossible; interpretation may be aided by the use of epidemiological data, examining minor variants and deep sequencing. Conversely, when within-host diversity is large, due to genetic hitchhiking or co-infection of two dissimilar strains, it is critical to understand how it arose. Greater understanding of microevolution and mixed infection will enhance interpretation of WGS data. CONCLUSIONS: As sequencing studies have sampled more intensely and integrated multiple sources of information, the understanding of TB transmission and diversity has grown, but there is still much to be learnt about the origins of diversity that will affect inferences from these data. Public health teams and researchers should combine epidemiological, clinical and WGS data to strengthen investigations of transmission

Characterization of extensively drug-resistant tuberculosis cases from Valle del Cauca, Colombia.

Contains fulltext : 124253.pdf (publisher's version ) (Open Access)1 december 201

Identification of promoter-binding proteins of the <i>fbp</i> A and C genes in <i>Mycobacterium tuberculosis</i>

The antigen 85 (Ag85) complex of Mycobacterium tuberculosis represents a promising candidate as a novel drug target and pathogenesis factor. Ag85 comprises three proteins Ag85A, B and C, (encoded by the genes fbpA, B, and C), which participate in cell wall biosynthesis, and interact with the host macrophage as fibronectin-binding proteins (fbps). Ag85 is also involved in the response to isoniazid (INH) treatment. The objective of this study was to identify potential fbp gene activators involved in the over-expression of fbp genes in response to INH. The biotinylated upstream promoter regions of fbpA and fbpC were used together with streptavidin-coated magnetic beads in DNA-binding assays, to isolate proteins with high-binding affinities from cytosolic extracts of INH-treated M. tuberculosis. Resolution of the DNA-binding proteins by 1D SDS-PAGE revealed 6 proteins with high-affinity for the fbpA promoter, and 7 with specificity the fbpC promoter. Mass spectrometric analyses [LC-ES(MS/MS)] identified proteins associated with drug resistance and stress/treatment responses, intermediary metabolism and cellular division, hypothetical proteins including a member of the MarR family of bacterial transcriptional regulators. The DNA-binding MarR protein shows potential as an authentic activator of fbp genes and functional validation of this factor is warranted

Dataset associated with "Laboratory evaluation of low-cost PurpleAir PM monitors and in-field correction using co-located portable filter samplers"

This dataset consists of data collected during two laboratory evaluations of PurpleAir monitors and one field deployment of PurpleAir monitors co-located with portable filter samplers.The pre-deployment laboratory evaluation took place on 2018-08-20. The post-deployment laboratory evaluation took place on 2018-12-17. The goals of these evaluations were to: (a) assess whether the PurpleAir monitors responded linearly to NIST Urban Particulate Matter concentrations ranging from approximately 0 to 75 micrograms per cubic meter, (b) obtain laboratory-derived gravimetric correction factors for fine particulate matter (PM2.5) concentrations reported by PurpleAir monitors, (c) determine whether the response of the PurpleAir monitors to NIST Urban Particulate Matter changed over the duration of the field deployment, and (d) evaluate the precision of co-located PurpleAir monitors.The field deployment took place in Fort Collins, Colorado, USA between 2018-10-22 and 2018-12-06. The goals of the field deployment were to: (a) determine whether gravimetric correction factors derived from periodic co-locations with portable filter samplers (called "ASPEN boxes") improved the accuracy of 72-hour average PM2.5 concentrations reported by PurpleAir monitors (relative to conventional PM2.5 filter samplers operated at 16.7 L/min) and (b) compare 72-hour average PM2.5 concentrations measured using portable filter samplers and conventional filter samplers.The files associated with this dataset include: (1) the raw data recorded by the PurpleAir monitors during the two laboratory evaluations and the field deployment; (2) the raw data recorded by a tapered element oscillating microbalance (TEOM) during the two laboratory evaluations; (3) the raw data recorded by the ASPEN boxes during the field deployment; (4) a summary file describing the time-averaged concentrations reported by the PurpleAir monitors and the TEOM during the discrete concentration steps that comprised each laboratory evaluation; and (5) a summary file describing the average PM2.5 concentrations measured using the PurpleAir monitors, ASPEN boxes, and conventional filter samplers at each field site during each 72-hour sample period.Low-cost aerosol monitors can provide more spatially- and temporally-resolved data on ambient fine particulate matter (PM2.5) concentrations than are typically available from regulatory monitoring networks; however, low-cost monitors—which do not measure PM2.5 mass directly and tend to be sensitive to variations in particle size and refractive index—sometimes produce inaccurate concentration estimates. We investigated laboratory- and field-based approaches for calibrating low-cost PurpleAir monitors against gravimetric filter samples. First, we investigated the linearity of the PurpleAir response to NIST Urban PM and derived a laboratory-based gravimetric correction factor. Then, we co-located PurpleAir monitors with portable filter samplers at 15 outdoor sites spanning a 3×3-km area in Fort Collins, CO, USA. We evaluated whether PM2.5 correction factors derived from periodic co-locations with portable filter samplers improved the accuracy of PurpleAir monitors (relative to reference filter samplers operated at 16.7 L/min). We also compared 72-hour average PM2.5 concentrations measured using portable and reference filter samplers. Both before and after field deployment, the coefficient of determination for a linear model relating NIST Urban PM concentrations measured by a tapered element oscillating microbalance and the PurpleAir monitors (PM2.5 ATM) was 0.99; however, an F-test identified a significant lack of fit between the model and the data. The laboratory-based correction factor did not translate to the field. Correction factors derived in the field from monthly, weekly, semi-weekly, and concurrent co-locations with portable filter samplers increased the fraction of 72-hour average PurpleAir PM2.5 concentrations that were within 20% of the reference concentrations from 15% (for uncorrected measurements) to 45%, 59%, 56%, and 70%, respectively. Furthermore, 72-hour average PM2.5 concentrations measured using portable and reference filter samplers agreed (bias ≤ 20% for 71% of samples). These results demonstrate that periodic co-location with portable filter samplers can improve the accuracy of 72-hour average PM2.5 concentrations reported by PurpleAir monitors.This work was funded by the National Oceanic and Atmospheric Administration under grant no. 1305M218CNRMW0048