Modular RNA motifs for orthogonal phase separated compartments.

Recent discoveries in biology have highlighted the importance of protein and RNA-based condensates as an alternative to classical membrane-bound organelles. Here, we demonstrate the design of pure RNA condensates from nanostructured, star-shaped RNA motifs. We generate condensates using two different RNA nanostar architectures: multi-stranded nanostars whose binding interactions are programmed via linear overhangs, and single-stranded nanostars whose interactions are programmed via kissing loops.

Longitudinal integrated clerkships from start to finish: A medical curriculum innovation.

Stellenbosch University embarked on a renewal of its MBChB programme guided by an updated set of core values developed by the multidisciplinary curriculum task team. These values acknowledged the important role of (among others) context and generalism in the development of our graduates as doctors of the future for South Africa. This report describes the overall direction of the renewed curriculum focusing on two of the innovative educational methods for Family Medicine and Primary Health Care training that enabled us to respond to these considerations.

Dynamic control of DNA condensation.

Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract.

Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter.

The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes.

gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of .

An anaerobic bacterial strain, designated strain M3/9, was isolated from a laboratory-scale biogas fermenter fed with maize silage supplemented with 5 % wheat straw. Cells were straight, non-motile rods, which stained Gram-negative. Optimal growth occurred between 30 and 40°C, at pH 7.

The novel oligopeptide utilizing species M3/9, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses.

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously, species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative strain, M3/9 was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail.

Fueling DNA Self-Assembly via Gel-Released Regulators.

The development of responsive, multicomponent molecular materials requires means to physically separate yet easily couple distinct processes. Here we demonstrate methods to use molecules and reactions loaded into microliter-sized polyacrylamide hydrogels (mini-gels) to control the dynamic self-assembly of DNA nanotubes. We first characterize the UV-mediated release of DNA molecules from mini-gels, changing diffusion rates and minimizing spontaneous leakage of DNA.

The Growth Rate of DNA Condensate Droplets Increases with the Size of Participating Subunits.

Liquid-liquid phase separation (LLPS) is a common phenomenon underlying the formation of dynamic membraneless organelles in biological cells, which are emerging as major players in controlling cellular functions and health. The bottom-up synthesis of biomolecular liquid systems with simple constituents, like nucleic acids and peptides, is useful to understand LLPS in nature as well as to develop programmable means to build new amorphous materials with properties matching or surpassing those observed in natural condensates. In particular, understanding which parameters determine condensate growth kinetics is essential for the synthesis of condensates with the capacity for active, dynamic behaviors.

Dynamic self-assembly of compartmentalized DNA nanotubes.

Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets.

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics.

Background: Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

The Role of ING2-E5A in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses.

Members of the genera and were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, ING2-E5A was isolated from a biogas reactor sample and sequenced on the PacBio and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5A in close proximity to and species (family Dysgonomonadaceae).

Rationally designed rare earth separation by selective oxalate solubilization.

A simple, environmentally benign, and efficient chemical separation of rare earth oxalates (CSEREOX) within two rare earth element (REE) subgroups has been developed. The protocol allows for selective solubilization of water-insoluble oxalates of rare earth elements, and results in efficient REE extraction even at low initial concentrations (<5%) from processed magnet wastes.

Draft Genome Sequence of a New Bacterium Isolated from Anaerobic Digestion of Biomass.

Here, we present the genome sequence and annotation of the novel bacterial strain HV4-5-C5C, which may represent a new genus within the family (order ). This strain is a potential keystone species in the hydrolysis of complex polymers during anaerobic digestion of biomass.

Complete Genome Sequence of a New sp. Isolated from Anaerobic Digestion and Biomethanation.

Here, we present the genome sequence and annotation of the bacterial strain HV4-5-A1G, a potentially new species. Based on its genomic data, this strain may act as a keystone microorganism in the hydrolysis of complex polymers, as well as in the different acidogenesis and acetogenesis steps during anaerobic digestion.

Complete Genome Sequence of a New Bacterium Isolated from Anaerobic Biomass Digestion.

Here, we present the genome sequence and annotation of HV4-6-C5C, a bacterial strain isolated from a mesophilic two-stage laboratory-scale leach bed biogas reactor system. Strain HV4-6-C5C may represent a new genus of the family and may have a key role in acidogenesis and acetogenesis steps during anaerobic biomass digestion.

Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems.

Synthetic biology brings engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry.

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants.

Background: In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were analyzed using a high-resolution metaproteomics pipeline.

Results: Examined methanogenesis archaeal communities were either mixotrophic or strictly hydrogenotrophic in syntrophy with bacterial acetate oxidizers.

Screening of microbial communities associated with endive lettuce during postharvest processing on industrial scale.

In this study, the composition of the microbial community on endive lettuce () was evaluated during different postharvest processing steps. Microbial community structure was characterized by culture-dependent and culture-independent methods. Endive lettuce was sampled exemplarily at four different stages of processing (raw material, cut endive lettuce, washed endive lettuce, and spin-dried (ready to pack) endive lettuce) and analysed by plate count analysis using non-selective and selective agar plates with subsequent identification of bacteria colonies by matrix-assisted laser desorption/ionization time-of light mass spectrometry (MALDI-TOF MS).

Characterization of genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.

Background: Previous studies on the , recently assigned to the novel archaeal phylum , reported on the dominance of these within the anaerobic carbohydrate cycle performed by the deep marine biosphere. For the first time, members of this phylum were identified also in mesophilic and thermophilic biogas-forming biofilms and characterized in detail.

Results: Metagenome shotgun libraries of biofilm microbiomes were sequenced using the Illumina MiSeq system.

str. M3/6 isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

str. M3/6 is a recently described species within the family (phylum ), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters.

Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.

A new bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family outside recently described genera.

sp. nov., isolated from a thermophilic industrial-scale biogas plant.

A novel strictly anaerobic bacterium, designated strain BA2-13, was isolated from a thermophilic industrial-scale biogas plant. Cells were rod-shaped and Gram-stain-positive. Growth occurred at temperatures of 25 to 50 °C and between pH 6.

Engineering DNA nanotubes for resilience in an TXTL system.

Deoxyribonucleic acid (DNA) nanotechnology is a growing field with potential intracellular applications. In this work, we use an cell-free transcription-translation (TXTL) system to assay the robustness of DNA nanotubes in a cytoplasmic environment. TXTL recapitulates physiological conditions as well as strong linear DNA degradation through the RecBCD complex, the major exonuclease in .

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.

Background: To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences.

Results: Novel cellulolytic, hydrolytic, and acidogenic/acetogenic as well as methanogenic originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production.