Polyclonal Aptamers for Specific Fluorescence Labeling and Quantification of the Health Relevant Human Gut Bacterium Parabacteroides distasonis

Single-stranded DNA aptamers as affinity molecules for the rapid, reliable detection of intestinal bacteria are of particular interest to equip health systems with novel robust and cheap diagnostic tools for monitoring the success of supplementation strategies with selected probiotic gut bacteria in the fight against major widespread threats, such as obesity and neurodegenerative diseases. The human gut bacterium Parabacteroides distasonis (P. distasonis) is positively associated with diseases such as obesity, non-alcoholic fatty liver disease and multiple sclerosis with reduced cell counts in these diseases and is thus a promising potential probiotic bacterium for future microbial supplementation. In this paper we report on the evolution of a specific polyclonal aptamer library by the fluorescence based FluCell-SELEX directed against whole cells of P. distasonis that specifically and efficiently binds and labels P. distasonis. The aptamer library showed high binding affinity and was suited to quantitatively discriminate P. distasonis from other prominent gut bacteria also in mixtures. We believe that this library against a promising probiotic bacterium as a prototype may open new routes towards the development of novel biosensors for the easy and efficient quantitative monitoring of microbial abundance in human microbiomes in general

Applied Climate-Change Analysis: The Climate Wizard Tool

Background: Although the message of ‘‘global climate change’’ is catalyzing international action, it is local and regional changes that directly affect people and ecosystems and are of immediate concern to scientists, managers, and policy makers. A major barrier preventing informed climate-change adaptation planning is the difficulty accessing, analyzing, and interpreting climate-change information. To address this problem, we developed a powerful, yet easy to use, web-based tool called Climate Wizard (http://ClimateWizard.org) that provides non-climate specialists with simple analyses and innovative graphical depictions for conveying how climate has and is projected to change within specific geographic areas throughout the world. Methodology/Principal Findings: To demonstrate the Climate Wizard, we explored historic trends and future departures (anomalies) in temperature and precipitation globally, and within specific latitudinal zones and countries. We found the greatest temperature increases during 1951–2002 occurred in northern hemisphere countries (especially during January–April), but the latitude of greatest temperature change varied throughout the year, sinusoidally ranging from approximately 50uN during February-March to 10uN during August-September. Precipitation decreases occurred most commonly in countries between 0–20uN, and increases mostly occurred outside of this latitudinal region. Similarly, a quantile ensemble analysis based on projections from 16 General Circulation Models (GCMs) for 2070–2099 identified the median projected change within countries, which showed both latitudinal and regional patterns in projected temperature and precipitation change. Conclusions/Significance: The results of these analyses are consistent with those reported by the Intergovernmental Panel on Climate Change, but at the same time, they provide examples of how Climate Wizard can be used to explore regionally and temporally-specific analyses of climate change. Moreover, Climate Wizard is not a static product, but rather a data analysis framework designed to be used for climate change impact and adaption planning, which can be expanded to include other information, such as downscaled future projections of hydrology, soil moisture, wildfire, vegetation, marine conditions, disease, and agricultural productivity

Applied Climate-Change Analysis: The Climate Wizard Tool

Although the message of "global climate change" is catalyzing international action, it is local and regional changes that directly affect people and ecosystems and are of immediate concern to scientists, managers, and policy makers. A major barrier preventing informed climate-change adaptation planning is the difficulty accessing, analyzing, and interpreting climate-change information. To address this problem, we developed a powerful, yet easy to use, web-based tool called Climate Wizard (http://ClimateWizard.org) that provides non-climate specialists with simple analyses and innovative graphical depictions for conveying how climate has and is projected to change within specific geographic areas throughout the world.To demonstrate the Climate Wizard, we explored historic trends and future departures (anomalies) in temperature and precipitation globally, and within specific latitudinal zones and countries. We found the greatest temperature increases during 1951-2002 occurred in northern hemisphere countries (especially during January-April), but the latitude of greatest temperature change varied throughout the year, sinusoidally ranging from approximately 50 degrees N during February-March to 10 degrees N during August-September. Precipitation decreases occurred most commonly in countries between 0-20 degrees N, and increases mostly occurred outside of this latitudinal region. Similarly, a quantile ensemble analysis based on projections from 16 General Circulation Models (GCMs) for 2070-2099 identified the median projected change within countries, which showed both latitudinal and regional patterns in projected temperature and precipitation change.The results of these analyses are consistent with those reported by the Intergovernmental Panel on Climate Change, but at the same time, they provide examples of how Climate Wizard can be used to explore regionally- and temporally-specific analyses of climate change. Moreover, Climate Wizard is not a static product, but rather a data analysis framework designed to be used for climate change impact and adaption planning, which can be expanded to include other information, such as downscaled future projections of hydrology, soil moisture, wildfire, vegetation, marine conditions, disease, and agricultural productivity

Glatiramer acetate treatment does not modify the clinical course of (NZB × BXSB)F1 lupus murine model

Glatiramer acetate (GA, copolymer-1, Copaxone®), a therapy approved for treatment of multiple sclerosis (MS), prevents and reverses experimental autoimmune encephalomyelitis, the animal model of MS. In central nervous system autoimmune disease, GA is thought to act through modulation of antigen-presenting cells, such as monocytes, mediating an antigen-independent Th2 shift and development of FoxP3+ regulatory T cells. Recent reports indicate that GA may also be effective in models of other autoimmune diseases such as uveoretinitis, inflammatory bowel disease and graft rejection. To date, the potential effect of GA in lupus animal models has not been described. (NZB × BXSB)F1, male mice bearing Y-linked autoimmune acceleration , is a lupus-prone mouse model which is associated with a monocytosis accelerating disease progression. These mice were treated with GA before disease onset until death and both mortality rate and biological parameters were assessed to investigate whether GA may be beneficial in this spontaneous model of systemic lupus erythematosus. GA exerted no beneficial effect on the median survival after up to 7 months of treatment. Humoral and cellular parameters used as markers for lupus progression, such as anti-chromatin, anti-double-stranded DNA and anti-erythrocytes antibodies, hematocrit and monocytosis, were similarly unchanged. Our study demonstrates that GA has no significant effect on the progression of the (NZB × BXSB)F1 lupus-prone animal model. These results reinforce the hypothesis that GA may exert its beneficial effect in some specific autoimmune diseases onl

Accuracy of a method based on atomic absorption spectrometry to determine inorganic arsenic in food : Outcome of the collaborative trial IMEP-41

Peer reviewedPublisher PD

Differential activation of anti-erythrocyte and anti-DNA autoreactive B lymphocytes by the Yaa mutation

An as-yet-unidentified mutation, Y-linked autoimmune acceleration (Yaa), is responsible for the accelerated development of lupus-like autoimmune syndrome in mice. In view of a possible role for Yaa as a positive regulator of BCR signaling, we have explored whether the expression of the Yaa mutation affects the development and activation of transgenic autoreactive B cells expressing either 4C8 IgM anti-RBC or Sp6 IgM anti-DNA. In this study, we show that the expression of the Yaa mutation induced a lethal form of autoimmune hemolytic anemia in 4C8 transgenic C57BL/6 mice, likely as a result of activation of 4C8 anti-RBC autoreactive B cells early in life. This was further supported, although indirectly, by increased T cell-independent IgM production in spleens of nontransgenic C57BL/6 mice bearing the Yaa mutation. In contrast, Yaa failed to induce activation of Sp6 anti-DNA autoreactive B cells, consistent with a lack of increased IgM anti-DNA production in nontransgenic C57BL/6 Yaa mice. Our results suggest that Yaa can activate autoreactive B cells in a BCR-dependent manner, related to differences in the form and nature of autoantigens

BSA Hydrogel Beads Functionalized with a Specific Aptamer Library for Capturing Pseudomonas aeruginosa in Serum and Blood

Systemic blood stream infections are a major threat to human health and are dramatically increasing worldwide. Pseudomonas aeruginosa is a WHO-alerted multi-resistant pathogen of extreme importance as a cause of sepsis. Septicemia patients have significantly increased survival chances if sepsis is diagnosed in the early stages. Affinity materials can not only represent attractive tools for specific diagnostics of pathogens in the blood but can prospectively also serve as the technical foundation of therapeutic filtration devices. Based on the recently developed aptamers directed against P. aeruginosa, we here present aptamer-functionalized beads for specific binding of this pathogen in blood samples. These aptamer capture beads (ACBs) are manufactured by crosslinking bovine serum albumin (BSA) in an emulsion and subsequent functionalization with the amino-modified aptamers on the bead surface using the thiol- and amino-reactive bispecific crosslinker PEG(4)-SPDP. Specific and quantitative binding of P. aeruginosa as the dedicated target of the ACBs was demonstrated in serum and blood. These initial but promising results may open new routes for the development of ACBs as a platform technology for fast and reliable diagnosis of bloodstream infections and, in the long term, blood filtration techniques in the fight against sepsis

A Polyclonal Aptamer Library for the Specific Binding of the Gut Bacterium Roseburia intestinalis in Mixtures with Other Gut Microbiome Bacteria and Human Stool Samples

Roseburia intestinalis has received attention as a potential probiotic bacterium. Recent studies have demonstrated that changes in its intestinal abundance can cause various diseases, such as obesity, enteritis and atherosclerosis. Probiotic administration or fecal transplantation alter the structure of the intestinal flora, offering possibilities for the prevention and treatment of these diseases. However, current monitoring methods, such as 16S rRNA sequencing, are complex and costly and require specialized personnel to perform the tests, making it difficult to continuously monitor patients during treatment. Hence, the rapid and cost-effective quantification of intestinal bacteria has become an urgent problem to be solved. Aptamers are of emerging interest because their stability, low immunogenicity and ease of modification are attractive properties for a variety of applications. We report a FluCell-SELEX polyclonal aptamer library specific for R. intestinalis isolated after seven evolution rounds, that can bind and label this organism for fluorescence microscopy and binding assays. Moreover, R. intestinalis can be distinguished from other major intestinal bacteria in complex defined mixtures and in human stool samples. We believe that this preliminary evidence opens new avenues towards aptamer-based electronic biosensors as new powerful and inexpensive diagnostic tools for the relative quantitative monitoring of R. intestinalis in gut microbiomes

FluCell-SELEX Aptamers as Specific Binding Molecules for Diagnostics of the Health Relevant Gut Bacterium Akkermansia muciniphila

Based on their unique properties, oligonucleotide aptamers have been named a gift of biological chemistry to life science. We report the development of DNA aptamers as the first high-affinity binding molecules available for fast and rapid labeling of the human gut bacterium Akkermansia muciniphila with a certain impact on Alzheimer´s disease. Fast and reliable analyses of the composition of microbiomes is an emerging field in microbiology. We describe the molecular evolution and biochemical characterization of a specific aptamer library by a FluCell-SELEX and the characterization of specific molecules from the library by bioinformatics. The aptamer AKK13.1 exerted universal applicability in different analysis techniques in modern microbiology, including fluorimetry, confocal laser scanning microscopy and flow cytometry. It was also functional as a specific binding entity hybridized to anchor primers chemically coupled via acrydite-modification to the surface of a polyacrylamide-hydrogel, which can be prototypically used for the construction of affinity surfaces in sensor chips. Together, the performance and methodological flexibility of the aptamers presented here may open new routes not only to develop novel Akkermansia-specific assays for clinical microbiology and the analyses of human stool samples but may also be an excellent starting point for the construction of novel electronic biosensors