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Fig. 2 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 2. Verification of the biotinylation of recombinant P. relictum MSP-1. Purified recombinant P. relictum MSP-1 protein was labeled with biotin. Biotinylation of MSP-1 was confirmed using an enzyme (streptavidin alkaline phosphatase)-linking assay and absorbance read at 405 nm indicated the presence of biotinylated MSP-1. Black column represents biotinylated MSP-1 protein. Hatched column and white column represent negative controls containing non-biotinylated MSP-1 and PBS, respectively. Grey column represents the positive control containing streptavidin alkaline-phosphatase (SAP) and its substrate p-nitrophenyl phosphate (PNPP). Each reaction was performed in triplicate, and the data shown represent means of three independent experiments with standard error bars and levels of statistical significance (****: P <0.0001).

Fig. 3 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 3. Biotin-labeled MSP-1 protein titration curve. Serially diluted (300 ng/ μL to 0.003 ng/μL) biotinylated MSP-1 was used for coating the surfaces of the reaction wells overnight at 4 ◦C. The amount of biotinylated MSP-1 immobilized on the surface of the well was proportional to the intensity of the colored product generated which in turn was proportional to the absorbance value measured at 405 nm wavelength. Reactions were performed in triplicate, and the data shown represent means of three independent experiments with standard error bars.

Fig. 7. MSP-1 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 7. MSP-1 capture antigen-based ELISA analysis of 370 sera samples collected from 11 penguins during three consecutive seasons of Spring (March to May), Summer (June to August) and Fall (September to November). (A) ELISA absorbance readings for the 370 sera samples collected from Spring to Fall are arranged in ascending order. Time of collection is indicated by color. Light grey represents Spring, dark grey represents Summer, and black represents Fall. Black dashed line indicates the single cut-off point (0.488) determined by change-point analysis. (B) Left: percentage of positive (A405 ≥ 0.488) and negative (A405 <0.488) sera samples; Right: distribution of positive samples in Spring (March to May), Summer (June to August), and Fall (September to November). (C) Percentage of penguin sera samples that tested positive (A405> = 0.488) in each month from March to November.

Fig. 5. P. relictum MSP-1 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 5. P. relictum MSP-1 capture antigen-based ELISA analysis of test sera from penguins. Sera samples (370 total) from eleven penguins collected from Spring through Fall season were used as test samples in the assay to determine anti-P. relictum antibodies level. Light grey, dark grey, and black columns represent penguin sera samples collected in Spring, Summer, and Fall, respectively. Panel A–K represents ELISA results for individual penguins' sera collected at different time points from Spring to Fall. Panel L represents average ELISA absorbances for all 11 penguins at different sampling points. Each sample was assayed in triplicate, and the data shown represent means of three independent experiments with standard error bars.

Fig. 4 in Giardia duodenalis in a clinically healthy population of captive zoo chimpanzees: Rapid antigen testing, diagnostic real-time PCR and faecal microbiota profiling

Fig. 4. | Faecal bacterial community profile of captive chimpanzees infected with Giardia duodenalis detected by rapid antigen test. (A) Relative abundance of colour coded bacterial phyla separated based on presence (+) or absence (‒) of Giardia using rapid antigen test (RAT). The sample identity is located at the bottom of the graph with two labels (C20, C3) shaded indicating samples that were found as Giardia positive by real-time PCR. (B) Alpha diversity based on observed OTU and Shannon's index plotted as box plot and evaluated using t-tests. (C) Principal coordinates analysis (PCoA) 2D plot using first two principal components from Bray-Curtis dissimilarity matrix at the genus taxonomic levels. The clustering between Giardia positive (RAT+) and negative (RAT-) samples was tested using ANOSIM. (D) Linear discriminant analysis effect size (LEfSe) used plot of significant factors discriminating G. duodenalis positive from negative sample. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Giardia duodenalis in a clinically healthy population of captive zoo chimpanzees: Rapid antigen testing, diagnostic real-time PCR and faecal microbiota profiling

Fig. 3. | Faecal bacterial community profile of captive chimpanzees infected with Giardia duodenalis as detected by rapid antigen test and real-time PCR combined. (A) Relative abundance of colour coded bacterial phyla separated based on presence (+) or absence (‒) of Giardia. The sample identity is located at the bottom of the graph. (B) Alpha diversity based on observed OTU and Shannon's index plotted as box plot and evaluated using t-tests. (C) Principal coordinates analysis (PCoA) 2D plot using first two principal components from Bray-Curtis dissimilarity matrix at the genus taxonomic levels. The clustering between Giardia positive (+) and negative (‒) samples was tested using ANOSIM. (D) Linear discriminant analysis effect size (LEfSe) used plot of significant factors discriminating G. duodenalis positive from negative sample. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Giardia duodenalis in a clinically healthy population of captive zoo chimpanzees: Rapid antigen testing, diagnostic real-time PCR and faecal microbiota profiling

Fig. 2. | Results of Giardia duodenalis rapid antigen test applied on faecal samples from chimpanzees. A positive result for the Giardia duodenalis rapid antigen test (RAT, Anigen Rapid Giardia AG Test Kit) is represented by the line in the 'T' position in the window along with the positive control line in the 'C' position.

Fig. 1 in Giardia duodenalis in a clinically healthy population of captive zoo chimpanzees: Rapid antigen testing, diagnostic real-time PCR and faecal microbiota profiling

Fig. 1. Captive chimpanzees and their enclosure in Sydney, Australia. (A) Main chimpanzee open air exhibit with multiple climbing structures. (B) View from the other direction showing entry to the indoor area at the end of the exhibit. (C) smaller exhibit with mesh covering and more climbing and sleeping structures. (D) Members of the chimpanzee troop at the Taronga Zoo.

opencc-by-4.0Aug 2024View details →

Altered T-cell Reactivity to β-amyloid-related Antigens in Early Alzheimer's Disease

The code generated during this study is available at this online repository with free access. Further information and requests for resources should be directed to and will be fulfilled by the Lead Contact, Dr. Christoph Gericke (christoph.gericke@irem.uzh.ch).

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Regression models generated by APRANK (computational prioritization of antigenic proteins and peptides from complete pathogen proteomes)

Availability of highly parallelized immunoassays has renewed interest in the discovery of serology-based biomarkers for infectious diseases. Protein and peptide microarrays now provide a high-throughput platform for immunological screening of potential antigens and B-cell epitopes. However, there is still a need to prioritize relevant probes when designing these arrays. In this work we describe a computational method called APRANK (Antigenic Protein and Peptide Ranker) which integrates multiple molecular features to prioritize antigenic targets starting from a given pathogen proteome. These features include subcellular localization, presence of repetitive motifs, natively disordered regions, secondary structure, transmembrane spans and predicted interaction with the immune system. We applied this method to the prioritization of potential diagnostic antigens and peptides in a number of pathogen proteomes and human diseases: Borrelia burgdorferi (Lyme disease), Brucella melitensis (Brucellosis), Coxiella burnetii (Q fever), Escherichia coli (Gastroenteritis), Francisella tularensis (Tularemia), Leishmania braziliensis (Leishmaniasis), Leptospira interrogans (Leptospirosis), Mycobacterium leprae (Leprae), Mycobacterium tuberculosis (Tuberculosis), Plasmodium falciparum (Malaria), Porphyromonas gingivalis (Periodontal disease), Staphylococcus aureus (Bacteremia), Streptococcus pyogenes (Group A Streptococcal infections), Toxoplasma gondii (Toxoplasmosis) and Trypanosoma cruzi (Chagas Disease). After training a linear regression model the method achieves good to excellent performance on most species, measured by the enrichment of validated antigens at the top of the ranking. An unbiased validation using independent data sets shows APRANK is successful in predicting antigenicity for all pathogen species tested. We make APRANK available to facilitate the identification of novel diagnostic antigens in infectious diseases.

opencc-zeroJun 2021View details →

opencc-by-4.0Dec 2020View details →

Diagnostic accuracy of a novel enzyme‑linked immunoassay for the detection of IgG and IgG4 against Strongyloides stercoralis based on the recombinant antigens NIE/SsIR.

Background: The diagnosis of strongyloidiasis is challenging. Serological tests are acknowledged to have high sensitivity, but issues due to cross-reactions with other parasites, native parasite antigen supply and intrinsic test variability do occur. Assays based on recombinant antigens could represent an improvement. The aim of this study was to assess the sensitivity and specificity of two novel immunoglobulin (Ig)G and IgG4 enzyme-linked immunosorbent assays (ELISAs) based on the recombinant antigens NIE/SsIR for the diagnosis of strongyloidiasis. Methods: This was a retrospective diagnostic accuracy study. We included serum samples collected from immigrants from strongyloidiasis endemic areas for whom there was a matched result for Strongyloides stercoralis on agar plate culture and/or PCR assay, or a positive microscopy for S. stercoralis larvae. For the included samples, results were also available from an in-house indirect fluorescent antibody test (IFAT) and a commercial (Bordier ELISA; Bordier Affinity Products SA) ELISA. We excluded: (i) samples with insufficient serum volume; (ii) samples from patients treated with ivermectin in the previous 6 months; and (iii) sera from patients for whom only routine coproparasitology was performed after formol–ether concentration, if negative for S. stercoralis larvae. The performance of the novel assays was assessed against: (i) a primary reference standard, with samples classified as negative/positive on the basis of the results of fecal tests; (ii) a composite reference standard (CRS), which also considered patients to be positive who had concordant positive results for the IFAT and Bordier ELISA or with a single “high titer” positive result for the IFAT or Bordier ELISA. Samples with a single positive test, either for the IFAT or Bordier ELISA, at low titer, were considered to be “indeterminate,” and analyses were carried out with and without their inclusion. Results: When assessed against the primary reference standard, the sensitivities of the IgG and IgG4 ELISAs were 92% (95% confidence interval [CI]: 88–97%) and 81% (95% CI: 74–87%), respectively, and the specificities were 91% (95% CI: 88–95%) and 94% (95% CI: 91–97%), respectively. When tested against the CRS, the IgG ELISA performed best, with 78% sensitivity (95% CI: 72–83%) and 98% specificity (95% CI: 96–100%), when a cut-off of 0.675 was applied and the indeterminate samples were excluded from the analysis. Conclusion: The NIE-SsIR IgG ELISA demonstrated better accuracy than the IgG4 assay and was deemed promising particularly for serosurveys in endemic areas.

opencc-by-4.0Dec 2021View details →

Correlation of the kinetics of viral antigen and genomic RNA with restoration of normal cell homeostasis

The main objective of the studies within COCID Work Package 6 is to understand basic mechanisms by which viral replication machineries are removed from cells after pharmacological interruption of viral replication using functional as well as imaging techniques, including soft X-ray tomography. In this document, we highlight the progress in establishing the HCV replication models (replicons), the antiviral treatment chosen to eliminate viral structures from the host cells and the correlation between elimination of the viral replication machinery and restoration of a normal host cell homeostasis, using markers of HCV-induced stress. These data are essential to frame the experimental setup chosen for the imaging process required in subsequent stps of the project.

opencc-by-4.0Jan 2023View details →

Underlying data of Impact of shipping temperature on cell viability and T cell responses to bacterial antigens

Abstract Background: Interferon-γ (IFN-γ) secretion by T cells is a key correlate of immune protection against many pathogens including tuberculosis and the neglected tropical disease melioidosis. Clinical studies in tropical regions of immune responses to pathogens and vaccine monitoring studies require the collection of samples in resource-limited rural areas and subsequent shipment to central laboratories for downstream assays and long-term storage. Here, we studied the impact of two different shipping temperatures on the viability, composition and function of peripheral blood mononuclear cells (PBMC) using multi-colour flow cytometry and IFN-g enzyme-linked immunospot assay (IFN-g ELISpot), in order to provide guidance on sample shipment conditions for future clinical studies. Methods: Paired peripheral blood mononuclear cell (PBMC) samples from recovered melioidosis patients were stored in liquid nitrogen (-196°C) and then shipped from Bangkok, Thailand to Oxford, UK at either -80°C (dry ice) or -196°C (dry shipper).  After thawing, cell viability and composition were assessed by flow cytometry and antigen specific responses to Burkholderia pseudomallei (BP) were measured using IFN-g ELISpot. Results: We observed modest lowering of viability in the majority of samples and a reduction in IFN-g responses to BP which correlated to a decrease of monocytes and NK cells in samples shipped at -80°C compared to -196°C. Despite being lower in magnitude antigen-specific responses remained detectable in the majority of samples. Conclusions:Here we demonstrate that shipment of cryopreserved PBMC at -196°C has a benefit on cell viability, recovery and T cell responses to bacterial antigens, although useful information can still be obtained from samples shipped at -80°C, thus providing important guidance for sample management in future clinical trials.

opencc-by-4.0May 2023View details →

[Dataset] Pattern and repeatability of ascarid-specific antigen excretion through chicken faeces, and the diagnostic accuracy of copro-antigen measurements as compared with McMaster egg counts and plasma and egg yolk antibody measurements in laying hens

Comprehensive data examining the pattern and repeatability of ascarid-specific antigen excretion in chicken faeces and the diagnostic accuracy of copro-antigen measurements compared to McMaster egg counts and antibody measurements in laying hens. The dataset consists of observations and measurements obtained from a controlled study involving laying hens infected with mixed Ascaridia galli and Heterakis gallinarum. A total of 179 individual hens were monitored between wpi 2 and 18 and their fecal samples/blood samples were collected at specific time points. Faecel samples were repeatedly collected four(4) consecutive times in one wpi.Hence antigen measurements is 4 X 179 = 716 measurements

opencc-by-4.0May 2023View details →

Pan-cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics

CPTAC PAN-cancer Data Repository Welcome to the CPTAC PAN-cancer Data Repository! This repository serves as a data repository for the CPTAC PAN-cancer effort, which focuses on cancer target discovery. It contains various data sets related to protein abundance estimation, derived TMT-TPA, iBAQ, iBAQ-derived copy number, and differential protein expression for CPTAC ten indications. ## Contents The repository includes the following data: - FragPipe Output: Protein abundance estimation data generated using the FragPipe software. - Derived TMT-TPA: Data derived from Tandem Mass Tag (TMT) based Total Protein Approach (TPA). - iBAQ: Data representing intensity-based absolute quantification (iBAQ) of proteins. - iBAQ-derived Copy Number: Data derived from iBAQ analysis for copy number estimation. - Differential Protein Expression: Data indicating differential expression of proteins between tumor and NAT. ## Data Organization The data in this repository is organized in a structured manner to facilitate easy access and navigation. The repository structure is as follows: FragPipe/ [fragpipe_data_files] Derived_TMT_TPA/ [derived_tmt_tpa_data_files] iBAQ/ [ibaq_data_files] iBAQ-derived_copy_number/ [ibaq_copy_number_data_files] Differential_protein_expression/ [differential_expression_data_files]

opencc-by-4.0Aug 2023View details →

The cell-associated magnesium content is affected in Salmonella mutants defective for SigmaS/RpoS and O-antigen synthesis

In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of quiescent cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence.                    Our recent work has shown that a ΔrpoS mutation reduces the magnesium content of Salmonella (Metaane et al. 2022, PLoS ONE 17(3): e0265511).  The O-antigen of LPS is a Mg2+ reservoir that can be used under magnesium deprivation.        We show here that eventhough the cell-associated magnesium content is affected when Salmonella lacks the entire O-antigen, an effect of the ΔrpoS mutation can be still observed.      We have also shown that the amount of intracellular free Mg2+ is slightly reduced in the ΔrpoS mutant compared to the wild-type strain (Metaane et al 2023, PLoS ONE 18(9): e0291736).     This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).

opencc-by-4.0Nov 2021View details →

Fig 2 in Soluble total antigen derived from Toxoplasma gondii RH strain prevents apoptosis, but induces anti-apoptosis in human monocyte cell line

Fig 2. This schematic overview suggests signaling pathways of apoptosis. Apoptosis is induced through either the extrinsic pathway or intrinsic pathway. Toxoplasma gondii can prevent cell apoptosis via inhibition of cytochrome c release from the mitochondria into the cytosol, inhibition of cas-3, -6, -7, and -9 via blocking the mitochondrial pathway, and blocking cas-8 by external pathways. The parasite may also suppress pro-apoptotic protein (Bax) and induce anti-apoptotic Bcl-2 proteins and is able to activate transcription factors STAT6 and STAT3-miR-17-92-Bim pathway to inhibit apoptosis. Some proteins of T. gondii such as ROP18 plays a role in Fas/ CD95-mediated apoptosis to inhibit this process. Similarly ROP16 phosphorylates STAT3 and STAT6 to inhibit cell death. Original (S. Nemati).

opencc-by-4.0Nov 2021View details →

Fig 1 in Soluble total antigen derived from Toxoplasma gondii RH strain prevents apoptosis, but induces anti-apoptosis in human monocyte cell line

Fig 1. The comparison of the expression levels of Bcl-2 (A), Mcl-1 (B), Cas-7 (C), Cas-3 (D), and Bax (E) in THP-1 cell line regarding different concentrations of the soluble total antigen of Toxoplasma gondii (Nicolle et Manceaux, 1908) STAg. NS: not significant; * P value <0.05; ** P value <0.01; *** P value <0.001.