Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome.

Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C).

Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases.

Motivation: Gene expression data are commonly used at the intersection of cancer research and machine learning for better understanding of the molecular status of tumour tissue. Deep learning predictive models have been employed for gene expression data due to their ability to scale and remove the need for manual feature engineering. However, gene expression data are often very high dimensional, noisy and presented with a low number of samples.

Variational Autoencoders for Cancer Data Integration: Design Principles and Computational Practice.

International initiatives such as the Molecular Taxonomy of Breast Cancer International Consortium are collecting multiple data sets at different genome-scales with the aim to identify novel cancer bio-markers and predict patient survival. To analyze such data, several machine learning, bioinformatics, and statistical methods have been applied, among them neural networks such as autoencoders. Although these models provide a good statistical learning framework to analyze multi-omic and/or clinical data, there is a distinct lack of work on how to integrate diverse patient data and identify the optimal design best suited to the available data.

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.

TRPV1 is a physiological regulator of μ-opioid receptors.

Opioids are powerful analgesics, but also carry significant side effects and abuse potential. Here we describe a modulator of the μ-opioid receptor (MOR1), the transient receptor potential channel subfamily vanilloid member 1 (TRPV1). We show that TRPV1 binds MOR1 and blocks opioid-dependent phosphorylation of MOR1 while leaving G protein signaling intact.

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.

Measuring G-protein-coupled Receptor Signaling via Radio-labeled GTP Binding.

G-Protein-Coupled Receptors (GPCRs) are a large family of transmembrane receptors that play critical roles in normal cellular physiology and constitute a major pharmacological target for multiple indications, including analgesia, blood pressure regulation, and the treatment of psychiatric disease. Upon ligand binding, GPCRs catalyze the activation of intracellular G-proteins by stimulating the incorporation of guanosine triphosphate (GTP). Activated G-proteins then stimulate signaling pathways that elicit cellular responses.

Genome sequence of Methanobacterium congolense strain Buetzberg, a hydrogenotrophic, methanogenic archaeon, isolated from a mesophilic industrial-scale biogas plant utilizing bio-waste.

Methanogenic Archaea are of importance at the end of the anaerobic digestion (AD) chain for biomass conversion. They finally produce methane, the end-product of AD. Among this group of microorganisms, members of the genus Methanobacterium are ubiquitously present in anaerobic habitats, such as bioreactors.

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality.

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.

Background: One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood.

Results: The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea.

Inositol hexakisphosphate (IP6) generated by IP5K mediates cullin-COP9 signalosome interactions and CRL function.

The family of cullin-RING E3 Ligases (CRLs) and the constitutive photomorphogenesis 9 (COP9) signalosome (CSN) form dynamic complexes that mediate ubiquitylation of 20% of the proteome, yet regulation of their assembly/disassembly remains poorly understood. Inositol polyphosphates are highly conserved signaling molecules implicated in diverse cellular processes. We now report that inositol hexakisphosphate (IP6) is a major physiologic determinant of the CRL-CSN interface, which includes a hitherto unidentified electrostatic interaction between the N-terminal acidic tail of CSN subunit 2 (CSN2) and a conserved basic canyon on cullins.

Dual investigation of methanogenic processes by quantitative PCR and quantitative microscopic fingerprinting.

Monitoring of methanogenic communities in anaerobic digesters using molecular-based methods is very attractive but can be cost-intensive. A new and fast quantification method by microscopic image analysis was developed to accompany molecular-based methods. This digitalized method, called quantitative microscopic fingerprinting (QMF), enables quantification of active methanogenic cells (N mL(-1)) by their characteristic auto-fluorescence based on coenzyme F420 .

Effect of shoe flexibility on plantar loading in children learning to walk.

Background: In a previous pilot study of "cruisers" (nonindependent ambulation), "early walkers" (independent ambulation for 0-5 months), and "experienced walkers" (independent ambulation for 6-12 months), developmental age significantly affected the children's stability when walking and performing functional activities. We sought to examine how shoe structural characteristics affect plantar pressure distribution in early walkers.

Methods: Torsional flexibility was evaluated in four shoe designs (UltraFlex, MedFlex, LowFlex, and Stiff based on decreasing relative flexibility) with a structural testing machine.

Potential impact of process parameters upon the bacterial diversity in the mesophilic anaerobic digestion of beet silage.

The impact of the process parameters hydraulic retention time (HRT), organic loading rate (OLR) and substrate upon bacterial diversity was analyzed. Therefore, a controlled anaerobic fermentation (1755 days) of beet silage, only initially inoculated with manure, was monitored by the amplified "ribosomal DNA" restriction analysis. More than 85% of detected operational taxonomic units (OTUs) could not be assigned to described Bacteria.

Neural and synaptic defects in slytherin, a zebrafish model for human congenital disorders of glycosylation.

Congenital disorder of glycosylation type IIc (CDG IIc) is characterized by mental retardation, slowed growth and severe immunodeficiency, attributed to the lack of fucosylated glycoproteins. While impaired Notch signaling has been implicated in some aspects of CDG IIc pathogenesis, the molecular and cellular mechanisms remain poorly understood. We have identified a zebrafish mutant slytherin (srn), which harbors a missense point mutation in GDP-mannose 4,6 dehydratase (GMDS), the rate-limiting enzyme in protein fucosylation, including that of Notch.

Mesophilic fermentation of renewable biomass: does hydraulic retention time regulate methanogen diversity?

The present long-term study (about 1,100 days) monitored the diversity of methanogens during the mesophilic, anaerobic digestion of beet silage. Six fermentor samples were analyzed by ribosomal RNA gene restriction analysis, fluorescence in situ hybridization, and fluorescence microscopy. Hydrogenotrophic methanogens dominated within the population in all samples analyzed.

Mechanisms underlying metabolic and neural defects in zebrafish and human multiple acyl-CoA dehydrogenase deficiency (MADD).

In humans, mutations in electron transfer flavoprotein (ETF) or electron transfer flavoprotein dehydrogenase (ETFDH) lead to MADD/glutaric aciduria type II, an autosomal recessively inherited disorder characterized by a broad spectrum of devastating neurological, systemic and metabolic symptoms. We show that a zebrafish mutant in ETFDH, xavier, and fibroblast cells from MADD patients demonstrate similar mitochondrial and metabolic abnormalities, including reduced oxidative phosphorylation, increased aerobic glycolysis, and upregulation of the PPARG-ERK pathway. This metabolic dysfunction is associated with aberrant neural proliferation in xav, in addition to other neural phenotypes and paralysis.

Effect of functional foot orthoses on first metatarsophalangeal joint dorsiflexion in stance and gait.

Reduction in first metatarsophalangeal joint maximum degree of dorsiflexion with dorsiflexion of the first ray has been proposed to be the predominant cause of hallux abducto valgus and hallux rigidus. We sought to determine whether orthoses made from a cast with the first ray plantarflexed and a 4-mm medial skive could increase the maximum degree of dorsiflexion in patients with functional hallux limitus in stance and gait. Forty-eight feet of 27 subjects were casted for orthoses with the first ray plantarflexed and in the customary neutral rearfoot position with locked midtarsal joint.