Quinone-mediated extracellular electron transfer processes in ex situ biomethanation reactors

Redox mediators are used in a wide diversity of systems including biological ones. We investigated the effect of adding an artificial quinone (2,7-AQDS) as external redox molecule to an anaerobic digester system dominated by hydrogenotrophic methanogens. When oxidized AQDS was present, the methanogens diverted electrons from H2 to reduce AQDS instead of CO2. The AQDS reduction process was accompanied by a temporary CH4 inhibition, which was re-established several days after the full reduction of AQDS to AH2QDS. The presence of AQDS furthermore resulted in a community shift from Methanobacterium as the dominant methanogen to a more diverse community of methanogens. Protein expression profiles showed a shift in cofactor preference of the adapted community, as a potential response mechanism to AQDS inhibition. AH2QDS was only used as electron donor to a limited extent. Stable isotope incorporation experiments here indicated that the acetogen Acetoanaerobium used AH2QDS to reduce CO2 into acetate.</p

Cellulolytic and Xylanolytic Microbial Communities Associated With Lignocellulose-Rich Wheat Straw Degradation in Anaerobic Digestion

The enzymatic hydrolysis of lignocellulosic polymers is generally considered the rate-limiting step to methane production in anaerobic digestion of lignocellulosic biomass. The present study aimed to investigate how the hydrolytic microbial communities of three different types of anaerobic digesters adapted to lignocellulose-rich wheat straw in continuous stirred tank reactors operated for 134 days. Cellulase and xylanase activities were monitored weekly using fluorescently-labeled model substrates and the enzymatic profiles were correlated with changes in microbial community compositions based on 16S rRNA gene amplicon sequencing to identify key species involved in lignocellulose degradation. The enzymatic activity profiles and microbial community changes revealed reactor-specific adaption of phylogenetically different hydrolytic communities. The enzymatic activities correlated significantly with changes in specific taxonomic groups, including representatives of Ruminiclostridium, Caldicoprobacter, Ruminofilibacter, Ruminococcaceae, Treponema, and Clostridia order MBA03, all of which have been linked to cellulolytic and xylanolytic activity in the literature. By identifying microorganisms with similar development as the cellulase and xylanase activities, the proposed correlation method constitutes a promising approach for deciphering essential cellulolytic and xylanolytic microbial groups for anaerobic digestion of lignocellulosic biomass

High-efficiency genome editing via 2A-coupled co-expression of fluorescent proteins and zinc finger nucleases or CRISPR/Cas9 nickase pairs

Targeted endonucleases including zinc finger nucleases (ZFNs) and clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas9 are increasingly being used for genome editing in higher species. We therefore devised a broadly applicable and versatile method for increasing editing efficiencies by these tools. Briefly, 2A peptide-coupled co-expression of fluorescent protein and nuclease was combined with fluorescence-activated cell sorting (FACS) to allow for efficient isolation of cell populations with increasingly higher nuclease expression levels, which translated into increasingly higher genome editing rates. For ZFNs, this approach, combined with delivery of donors as single-stranded oligodeoxynucleotides and nucleases as messenger ribonucleic acid, enabled high knockin efficiencies in demanding applications, including biallelic codon conversion frequencies reaching 30–70% at high transfection efficiencies and ∼2% at low transfection efficiencies, simultaneous homozygous knockin mutation of two genes with ∼1.5% efficiency as well as generation of cell pools with almost complete codon conversion via three consecutive targeting and FACS events. Observed off-target effects were minimal, and when occurring, our data suggest that they may be counteracted by selecting intermediate nuclease levels where off-target mutagenesis is low, but on-target mutagenesis remains relatively high. The method was also applicable to the CRISPR/Cas9 system, including CRISPR/Cas9 mutant nickase pairs, which exhibit low off-target mutagenesis compared to wild-type Cas9

Interleukin-12 and -23 Control Plasticity of CD127+ Group 1 and Group 3 Innate Lymphoid Cells in the Intestinal Lamina Propria

SummaryHuman group 1 ILCs consist of at least three phenotypically distinct subsets, including NK cells, CD127+ ILC1, and intraepithelial CD103+ ILC1. In inflamed intestinal tissues from Crohn’s disease patients, numbers of CD127+ ILC1 increased at the cost of ILC3. Here we found that differentiation of ILC3 to CD127+ ILC1 is reversible in vitro and in vivo. CD127+ ILC1 differentiated to ILC3 in the presence of interleukin-2 (IL-2), IL-23, and IL-1β dependent on the transcription factor RORγt, and this process was enhanced in the presence of retinoic acid. Furthermore, we observed in resection specimen from Crohn’s disease patients a higher proportion of CD14+ dendritic cells (DC), which in vitro promoted polarization from ILC3 to CD127+ ILC1. In contrast, CD14− DCs promoted differentiation from CD127+ ILC1 toward ILC3. These observations suggest that environmental cues determine the composition, function, and phenotype of CD127+ ILC1 and ILC3 in the gut

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Prognostic implications of nonobstructive coronary plaques in patients with non-ST-segment elevation myocardial infarction: a multidetector computed tomography study

ObjectivesWe sought to determine whether the amount of noncalcified plaque (NCP) in nonobstructive coronary lesions as detected by multidetector computed tomography (MDCT) was a predictor of future coronary events.BackgroundPatients presenting with non–ST-segment elevation myocardial infarction (NSTEMI) frequently have multiple coronary plaques, which may be detected with MDCT.MethodsWe included 312 consecutive patients presenting with NSTEMI, who underwent 64-slice MDCT coronary angiography and coronary artery calcium scoring before invasive coronary angiography. All patients were treated according to current guidelines based on an invasive treatment approach. Quantitative measurements of plaque composition and volume were performed by MDCT in all nonobstructive coronary lesions. The endpoint was cardiac death, acute coronary syndrome, or symptom-driven revascularization.ResultsAfter a median follow-up of 16 months, 23 patients had suffered a cardiac event. Age, male sex, and diabetes mellitus were all associated with an increasing amount of NCP. In a multivariate regression analysis for events, the total amount of NCP in nonobstructive lesions was independently associated with an increased hazard ratio (1.18/100-mm3 plaque volume increase, p = 0.01). Contrary to this, neither Agatston score nor the amount of calcium in nonobstructive lesions was associated with an increased risk.ConclusionsMultidetector computed tomography plaque imaging identified patients at increased risk of recurrent coronary events after NSTEMI by measuring the total amount of NCP in nonobstructive lesions. The amount of calcified plaque was not associated with an increased risk