Monomeric serum immunoglobulin A (IgA) can contribute to the development of various autoimmune diseases, but the regulation of serum IgA effector functions is not well defined. Here, we show that the ...two IgA subclasses (IgA1 and IgA2) differ in their effect on immune cells due to distinct binding and signaling properties. Whereas IgA2 acts pro-inflammatory on neutrophils and macrophages, IgA1 does not have pronounced effects. Moreover, IgA1 and IgA2 have different glycosylation profiles, with IgA1 possessing more sialic acid than IgA2. Removal of sialic acid increases the pro-inflammatory capacity of IgA1, making it comparable to IgA2. Of note, disease-specific autoantibodies in patients with rheumatoid arthritis display a shift toward the pro-inflammatory IgA2 subclass, which is associated with higher disease activity. Taken together, these data demonstrate that IgA effector functions depend on subclass and glycosylation, and that disturbances in subclass balance are associated with autoimmune disease.
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•Microbial Enhanced Oil Recovery with Halanerobium sp. was performed in sandpacks.•Sucrose consumption with 10 % carbonate was 8 times higher compared to pure quartz.•1 % of carbonate ...and sulfide maintained microbial growth and led to 21.6 % more oil.•Superficial mineral dissolution by microbially produced acids was confirmed by XPS.•Acid neutralization capacity of rock is proposed as a screening criterion for MEOR.
Microbial enhanced oil recovery (MEOR) is an economically attractive tertiary recovery technique and fermentative bacteria are frequently suggested for MEOR, partly because microbially produced organic acids have the potential for rock matrix dissolution.
In this study, the metabolic activity and the community shift of a diverse microbiome of a high-salinity oilfield upon supplying MEOR nutrients was investigated in dynamic sandpacks set-up with and without crude oil using pure quartz sand and two types of reservoir rock. Geochemical characterization of the porous media included specific surface area (SSA), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). During the experiments, substrate and metabolites, incremental oil and differential pressure were monitored and the microbial community shift was investigated via Illumina sequencing.
Fermentative Halanaerobiales outcompeted other microbes and led to an incremental oil recovery of 24.5 ± 9.6%OOIP in reservoir rock. Microbial-induced dissolution of surface minerals was indicated by a decrease in SSA and surface-bound ferrous iron and concluded to be an important MEOR mechanism. Fermentation of sucrose was primarily limited by an insufficient acid neutralization capacity (ANC), but a carbonate content of 12% sustainably buffered the pH in a favorable growth range. Even minor amounts of other non-inert minerals (1% pyrite and calcite) facilitated microbial growth significantly, resulting in six-fold higher acetate production rates compared to quartz sand. Besides emphasizing the relevance of accessory minerals in MEOR, our results imply that the ANC could serve as potential screening parameter for predicting the performance of fermentation-based MEOR in the field.
Genetically encoded fluorescent biosensors have emerged as a powerful tool to support phenotypic screenings of microbes. Optical analyses of fluorescent sensor signals from colonies grown on solid ...media can be challenging as imaging devices need to be equipped with appropriate filters matching the properties of fluorescent biosensors. Toward versatile fluorescence analyses of different types of biosensor signals derived from arrayed colonies, we investigate here the use of monochromator equipped microplate readers as an alternative to imaging approaches. Indeed, for analyses of the LacI-controlled expression of the reporter mCherry in
or promoter activity using GFP as reporter in
, an improved sensitivity and dynamic range was observed for a microplate reader-based analyses compared to their analyses via imaging. The microplate reader allowed us to capture signals of ratiometric fluorescent reporter proteins (FRPs) with a high sensitivity and thereby to further improve the analysis of internal pH via the pH-sensitive FRP mCherryEA in
colonies. Applicability of this novel technique was further demonstrated by assessing redox states in
colonies using the FRP Mrx1-roGFP2. By the use of a microplate reader, oxidative redox shifts were measured in a mutant strain lacking the non-enzymatic antioxidant mycothiol (MSH), indicating its major role for maintaining a reduced redox state also in colonies on agar plates. Taken together, analyses of biosensor signals from microbial colonies using a microplate reader allows comprehensive phenotypic screenings and thus facilitates further development of new strains for metabolic engineering and systems biology.
Souring induced by sulfate reducing microorganisms (SRM) represents a severe problem in the petroleum industry. In addition to conventional biocides and nitrate, alternative SRM inhibitors such as ...molybdate have been proposed recently for controlling microbial souring. We used oilfield-derived microbial consortia, rock and fluids to test molybdate as a specific SRM inhibitor for a microbial enhanced oil recovery (MEOR) application where souring might occur as a side effect. SRM cells were quantified and dissolved molybdate, sulfate and gaseous hydrogen sulfide were measured under different dynamic conditions in sandpacks with and without residual oil. In batch experiments, 0.5 mM molybdate inhibited SRM growth whereas hydrogen sulfide and mineral precipitations were observed in bottles amended with 100 mM nitrate. However, significant molybdate adsorption onto reservoir rock occurred and maximum Langmuir saturation was estimated to be ≥ 34 μmol g−1. Residual oil allowed a further propagation of molybdate into sandpacks, but a pH < 6 and sulfide concentrations >11 μMH2S aq limited the efficiency of molybdate due to rapid adsorption. Under favorable souring conditions, we also observed the localized formation of macroscopic iron sulfide precipitations. These resulted in a four-fold permeability decrease after the injection of SRM substrates for 40 days and a calculated mean sulfate reduction rate of 52 μM h−1. However, delayed sulfate reduction in molybdate-preflushed sandpacks suggests an inhibitory effect even if molybdate is partially adsorbed. Sulfate reduction was not detected when molybdate was continuously injected with MEOR nutrients into sandpacks demonstrating its inhibitory efficiency in case it is applied in early phases of field operations with a potential risk of souring.
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•Anaerobic sandpack experiments to investigate molybdate as inhibitor for microbial souring were set up.•a pH < 6 resulted in rapid molybdate adsorption, while residual oil allowed further propagation of molybdate.•0.5 mM molybdate led to a sustained inhibition of sulfate reducing microorganisms (SRM).•Microbial sulfate reduction and mineral precipitations were observed with 100 mM nitrate.•Molybdate adsorption onto reservoir rock was significant with ≥34 μmolMoO4*g−1rock.
ChIP-seq experiments detect the chromatin occupancy of known transcription factors in a genome-wide fashion. The comparisons of several species-specific ChIP-seq libraries done for different ...transcription factors have revealed a complex combinatorial and context-specific co-localization behavior for the identified binding regions. In this study we have investigated human derived ChIP-seq data to identify common cis-regulatory principles for the human transcription factor c-Fos. We found that in four different cell lines, c-Fos targeted proximal and distal genomic intervals show prevalences for either AP-1 motifs or CCAAT boxes as known binding motifs for the transcription factor NF-Y, and thereby act in a mutually exclusive manner. For proximal regions of co-localized c-Fos and NF-YB binding, we gathered evidence that a characteristic configuration of repeating CCAAT motifs may be responsible for attracting c-Fos, probably provided by a nearby AP-1 bound enhancer. Our results suggest a novel regulatory function of NF-Y in gene-proximal regions. Specific CCAAT dimer repeats bound by the transcription factor NF-Y define this novel cis-regulatory module. Based on this behavior we propose a new enhancer promoter interaction model based on AP-1 motif defined enhancers which interact with CCAAT-box characterized promoter regions.
Biological disease-modifying anti-rheumatic drugs (bDMARDs) can be tapered in some rheumatoid arthritis (RA) patients in sustained remission. The purpose of this study was to assess the feasibility ...of building a model to estimate the individual flare probability in RA patients tapering bDMARDs using machine learning methods.
Longitudinal clinical data of RA patients on bDMARDs from a randomized controlled trial of treatment withdrawal (RETRO) were used to build a predictive model to estimate the probability of a flare. Four basic machine learning models were trained, and their predictions were additionally combined to train an ensemble learning method, a stacking meta-classifier model to predict the individual flare probability within 14 weeks after each visit. Prediction performance was estimated using nested cross-validation as the area under the receiver operating curve (AUROC). Predictor importance was estimated using the permutation importance approach.
Data of 135 visits from 41 patients were included. A model selection approach based on nested cross-validation was implemented to find the most suitable modeling formalism for the flare prediction task as well as the optimal model hyper-parameters. Moreover, an approach based on stacking different classifiers was successfully applied to create a powerful and flexible prediction model with the final measured AUROC of 0.81 (95%CI 0.73-0.89). The percent dose change of bDMARDs, clinical disease activity (DAS-28 ESR), disease duration, and inflammatory markers were the most important predictors of a flare.
Machine learning methods were deemed feasible to predict flares after tapering bDMARDs in RA patients in sustained remission.
Cell-to-cell heterogeneity in products secretion is a bottleneck for diverse applications in bioengineering, including controlled drug release, biomaterial assembly, and production of recombinant ...proteins in bioprocesses.Experimental approaches aiming at characterizing cell-to-cell differences in gene expression and protein accumulation can be partially adapted to address heterogeneity in protein secretion.Significant technological bottlenecks need to be addressed to establish an efficient single cell analysis pipeline.Techniques designed for directing cell collective behavior (e.g., microfluidics or flow cytometry with feedback control) could be adapted for directing product secretion by cells.
Cell-to-cell heterogeneity presents challenges across various fields, from biomedicine to bioproduction, where precise cellular responses are vital. While single cell technologies have significantly enhanced our understanding of population heterogeneity, the predominant focus has been on monitoring intracellular compounds. Recognizing the added complexity introduced by the secretion system, in this review, we first provide a systematic overview of the distinct steps necessary for driving protein secretion. We discuss the various sources of noise acting from the synthesized preprotein to the secretory protein released based on a Gram-positive cellular system as a model. We next explore the applicability of single cell technologies for monitoring protein secretion throughout these functional stages. We also emphasize the importance of applying these single cell technologies for monitoring protein secretion during bioproduction.
Cell-to-cell heterogeneity presents challenges across various fields, from biomedicine to bioproduction, where precise cellular responses are vital. While single cell technologies have significantly enhanced our understanding of population heterogeneity, the predominant focus has been on monitoring intracellular compounds. Recognizing the added complexity introduced by the secretion system, in this review, we first provide a systematic overview of the distinct steps necessary for driving protein secretion. We discuss the various sources of noise acting from the synthesized preprotein to the secretory protein released based on a Gram-positive cellular system as a model. We next explore the applicability of single cell technologies for monitoring protein secretion throughout these functional stages. We also emphasize the importance of applying these single cell technologies for monitoring protein secretion during bioproduction.
Only limited data are available regarding the immunogenicity of the BNT162b2 mRNA vaccine in HIV-1
patients. Therefore, we investigated the humoral immune response after BNT162b2-mRNA vaccination or ...SARS-CoV-2 infection in HIV-1
patients on antiretroviral therapy compared to HIV-1-uninfected subjects. Serum and saliva samples were analysed by SARS-CoV-2 spike-specific IgG and IgA ELISAs and a surrogate neutralization assay. While all subjects developed anti-spike IgG and IgA and neutralizing antibodies in serum after two doses of BNT162b2 mRNA vaccine, the HIV-1
subjects displayed significantly lower neutralizing capacity and anti-spike IgA in serum compared to HIV-1-uninfected subjects. Serum levels of anti-spike IgG and neutralizing activity were significantly higher in vaccinees compared to SARS-CoV-2 convalescents irrespective of HIV-1 status. Among SARS-CoV-2 convalescents, there was no significant difference in spike-specific antibody response between HIV-1
and uninfected subjects. In saliva, anti-spike IgG and IgA antibodies were detected both in vaccinees and convalescents, albeit at lower frequencies compared to the serum and only rarely with detectable neutralizing activity. In summary, our study demonstrates that the BNT162b2 mRNA vaccine induces SARS-CoV-2-specific antibodies in HIV-1-infected patients on antiretroviral therapy, however, lower vaccine induced neutralization activity indicates a lower functionality of the humoral vaccine response in HIV-1
patients.
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