The Frequencies of IFNγ+IL2+TNFα+ PPD-Specific CD4+CD45RO+ T-Cells Correlate with the Magnitude of the QuantiFERON? Gold In-Tube Response in a Prospective Study of Healthy Indian Adolescents

Background

QuantiFERON-TB Gold In-Tube (QFT) is an IFNγ-release assay used in the diagnosis of Mycobacterium tuberculosis (MTB) infection. The risk of TB progression increases with the magnitude of the MTB-specific IFNγ-response. QFT reversion, also associated with low Tuberculin Skin Test responses, may therefore represent a transient immune response with control of M. tuberculosis infection. However, studies at the single cell level have suggested that the quality (polyfunctionality) of the T-cell response is more important than the quantity of cytokines produced.

Objective

To explore the quality and/or magnitude of mycobacteria-specific T-cell responses associated with QFT reversion and persistent QFT-positivity.

Methods

Multi-color flowcytometry on prospectively collected peripheral blood mononuclear cells was applied to assess mycobacteria-specific T-cell responses in 42 QFT positive Indian adolescents of whom 21 became QFT negative (reverters) within one year. Ten QFT consistent negatives were also included as controls.

Results

There was no difference in the qualitative PPD-specific CD4+ T-cell response between QFT consistent positives and reverters. However, compared with QFT consistent positives, reverters displayed lower absolute frequencies of polyfunctional (IFNγ+IL2+TNFα+) CD4+ T-cells at baseline, which were further reduced to the point where they were not different to QFT negative controls one year later. Moreover, absolute frequencies of these cells correlated well with the magnitude of the QFT-response.

Conclusion

Whereas specific polyfunctional CD4+ T-cells have been suggested to protect against TB progression, our data do not support that higher relative or absolute frequencies of PPD-specific polyfunctional CD4+ T-cells in peripheral blood can explain the reduced risk of TB progression observed in QFT reverters. On the contrary, absolute frequencies of these cells correlated with the QFT-response, suggesting that this readout reflects antigenic load.     

Application of Bayesian decomposition for analysing microarray data

MOTIVATION: Microarray and gene chip technology provide high throughput tools for measuring gene expression levels in a variety of circumstances, including cellular response to drug treatment, cellular growth and development, tumorigenesis, among many other processes. In order to interpret the large data sets generated in experiments, data analysis techniques that consider biological knowledge during analysis will be extremely useful. We present here results showing the application of such a tool to expression data from yeast cell cycle experiments. RESULTS: Originally developed for spectroscopic analysis, Bayesian Decomposition (BD) includes two features which make it useful for microarray data analysis: the ability to assign genes to multiple coexpression groups and the ability to encode biological knowledge into the system. Here we demonstrate the ability of the algorithm to provide insight into the yeast cell cycle, including identification of five temporal patterns tied to cell cycle phases as well as the identification of a pattern tied to an approximately 40 min cell cycle oscillator. The genes are simultaneously assigned to the patterns, including partial assignment to multiple patterns when this is required to explain the expression profile. AVAILABILITY: The application is available free to academic users under a material transfer agreement. Go to http://bioinformatics.fccc.edu/ for more details.     

Metal accumulation in two contiguous eutrophic peri-urban lakes,Chivero and Manyame,Zimbabwe

Concentrations of aluminium, cadmium, chromium, cobalt, copper, iron, lead, nickel and zinc were determined in surface water, benthic sediments, and the gills, liver and stomach muscle tissues of Oreochromis niloticus and Clarias gariepinus in peri-urban lakes Chivero and Manyame, Zimbabwe. Five sites were sampled in each lake once per month in November 2015, February, May, August and November 2016. Pollution load index detected no metal contamination, whereas the geo-accumulation index reflected heavy to extreme sediment pollution, with Fe, Cd, Zn, Cr, Ni and Cu present in both lakes. Significant spatial temporal variations were detected for Al, Cr, Cu and Pb across sites within and between the two lakes. High Fe, Al and Cr concentrations in water and sediments in lakes Chivero and Manyame derive from geogenic background sources in addition to anthropogenic loads and intensity. Elevated concentrations of Al, Pb, Cu, Cd, Fe and Zn detected in gills, liver and stomach tissue of catfish corroborate concentrations in water and sediments, and pose the highest ecological and health risk for hydrobionts in lakes Chivero and Manyame. Contiguity of peri-urban lakes exposes them to similar threats, necessitating creative water management strategies, which ensure ecological continuity.     

Cellular uptake and in situ binding of a peptide agonist for calmodulin

We have used the method of inverted hydropathy to develop peptides that interact with EF hands of calmodulin (CaM). Previously we have shown these peptides specifically interact with their desired target in a productive manner, in that they activated CaM in the absence of Ca(2+). Therefore, we sought to determine whether these peptides would enter cells, remain intact, and interact with CaM in the interior of the cell. Using several techniques we have demonstrated cellular uptake, stability, and an intracellular interaction with CaM with fluorescein-labeled and radiolabeled peptides in Jurkat T cells. The results suggest that these peptides may be useful in the study and the manipulation of Ca(2+)-mediated pathways in cells.     

FuGEFlow: data model and markup language for flow cytometry

Background  

Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata.     

Market Assessment of Tuberculosis Diagnostics in Brazil in 2012

Background

Improved diagnostics for the diagnosis of tuberculosis (TB) are urgently needed. However, test developers and investors require market size data to support new product development. This study assessed the served available market for TB diagnostics in Brazil in 2012 and the market segmentation in the public and private sectors.

Methods

Data were collected on test volumes done in the public and private sectors for the diagnosis of latent and active TB, drug susceptibility testing and treatment follow-up. Tests included were tuberculin skin tests, interferon-gamma releases assays, smear microscopy, solid and liquid cultures, nucleic acid amplification tests and phenotypic drug susceptibility tests. The data were collected by means of an electronic survey via the Brazilian State laboratories and from sales information provided by manufacturers. Test costs for the public sector were calculated using a components approach, while costs for the private sector were based on prices paid by patients. The overall market value (expenditure) for the entire country was calculated using the public sector test costs.

Results

During 2012, an estimated total of 2.4 million TB diagnostic tests were done in Brazil, resulting in an estimated overall market value of USD 17.2 million. The public sector accounted for 91% of the test volumes and 88% of the market value. Smear microscopy was the most commonly test (n = 1.3 million; 55% of total) at an estimated value of USD 3.7 million. Culture overall (n = 302,761) represented 13% of test volumes and 40% (USD 6.9 million) of the market value. On average, USD 208 was spent on TB diagnostics for every notified TB patient in Brazil, in 2012.

Conclusion

The TB diagnostics market value in Brazil in 2012 was over USD 17 million. These study results will help test developers to understand the current and potential market for replacement or add-on diagnostic technologies.