Biology subjects

Muller, B.

Publications and source records attributed to Muller, B..

12 recordsLinked to original sources

bioRxiv2024

LRRK2 G2019S variant is associated with transcriptional changes in Parkinson's disease human myeloid cells under proinflammatory environment

The G2019S mutation in the leucine-rich repeat kinase 2 (LRRK2) gene is a major risk factor for the development of Parkinsons disease (PD). LRRK2, although ubiquitously expressed, is highly abundant in cells of the innate immune system. Given the importance of central and peripheral immune cells in the development of PD, we sought to investigate the consequences of the G2019S mutation on microglial and monocyte transcriptome and function. We have generated large-scale transcriptomic profiles of isogenic human induced microglial cells (iMGLs) and patient derived monocytes carrying the G2019S mutation under baseline culture conditions and following exposure to the proinflammatory factors IFN{gamma} and LPS. We demonstrate that the G2019S mutation exerts a profound impact on the transcriptomic profile of these myeloid cells, and describe corresponding functional differences in iMGLs. The G2019S mutation led to an upregulation in lipid metabolism and phagolysosomal pathway genes in untreated and LPS/IFN{gamma} stimulated iMGLs, which was accompanied by an increased phagocytic capacity of myelin debris. We also identified dysregulation of cell cycle genes, with a downregulation of the E2F4 regulon. Transcriptomic characterization of human-derived monocytes carrying the G2019S mutation confirmed alteration in lipid metabolism associated genes. Altogether, these findings reveal the influence of G2019S on the dysregulation of the myeloid cell transcriptome under proinflammatory conditions.

genetics↗

bioRxiv2023

Bioaugmentation strategies based on bacterial and methanogenic cultures to relieve stress in anaerobic digestion of protein-rich substrates

Anaerobic co-digestion of protein-rich substrates is a prominent strategy for converting valuable feedstocks into methane, but it releases ammonia, which can inhibit methanogenesis. This study developed a cutting-edge combined culturomic and metagenomic approach to investigate the microbial composition of an ammonia-tolerant biogas plant. Newly-isolated microorganisms were used for bioaugmentation of stressed batch reactors fed with casein, maize silage and their combination. A co-culture enriched with proteolytic bacteria was isolated, selected and compared with the proteolytic collection strain Pseudomonas lundensis DSM6252. The co-culture and P. lundensis were combined with the ammonia-resistant archaeon Methanoculleus bourgensis MS2 to boost process stability. A microbial population pre-adapted to casein was also tested for evaluating the digestion of protein-rich feedstock. The promising results suggest combining proteolytic bacteria and M. bourgensis could exploit microbial co-cultures to improve anaerobic digestion stability and ensure stable productivity even under the harshest of ammonia conditions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/571062v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@623848org.highwire.dtl.DTLVardef@5d2311org.highwire.dtl.DTLVardef@a95f70org.highwire.dtl.DTLVardef@1b8beb6_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- High ammonia release from protein-rich substrates inhibits anaerobic digestion - Newly isolated bacterial strains from anaerobic digester were obtained - Proper bioaugmentation alleviates stress in casein and maize silage co-digestion - Bioaugmentation with a hydrolytic/hydrogenotrophic co-culture enhances CH4 yields

bioengineering↗

bioRxiv2023

The human microglia responsome: a resource to better understand microglia states in health and disease

Microglia, the immune cells of the brain, are increasingly implicated in neurodegenerative disorders through genetic studies. However, how genetic risk factors for these diseases are related to microglial gene expression, microglial function, and ultimately disease, is still largely unknown. Microglia change rapidly in response to alterations in their cellular environment, which is regulated through changes in transcriptional programs, which are as yet poorly understood. Here, we compared the effects of a set of inflammatory and restorative stimuli (lipopolysaccharide, interferon-gamma, resiquimod, tumor necrosis factor-alpha, adenosine triphosphate, dexamethasone, and interleukin-4) on human microglial cells from 67 different donors (N = 398 samples) at the gene and transcript level. We show that microglia from different anatomical brain regions show distinct responses to inflammatory stimuli. We observed a greater overlap between human stimulated microglia and human monocytes than with mouse microglia. We define specific microglial signatures across conditions which are highly relevant for a wide range of biological functions and complex human diseases. Finally, we used our stimulation signatures to interpret associations from Alzheimers disease (AD) genetic studies and microglia by integrating our inflammatory gene expression profiles with common genetic variants to map cis-expression QTLs (eQTLs). Together, we provide the most comprehensive transcriptomic database of the human microglia responsome. HighlightsO_LIRNA-sequencing of 398 human microglial samples exposed to six different triggers. C_LIO_LIMicroglia from different anatomical regions show distinct stimulation responses. C_LIO_LIResponses in human microglia show a greater overlap with human monocytes than murine microglia. C_LIO_LIMapping of response Quantitative Trait Loci identifies interactions between genotype and effect of stimulation on gene expression. C_LIO_LIOur atlas provides a reference map for interpreting microglia signatures in health and disease. C_LI

neuroscience↗

bioRxiv2022

Synthetic extremophiles: Species-specific formulations for microbial therapeutics and beyond.

Microorganisms have been used for millennia to produce food and medicine and are now being developed as products themselves to treat disease and boost crop production. However, as required for these new applications, maintaining high viability throughout manufacturing, transportation and use remains a significant challenge requiring sophisticated cold-chains and packaging. In fact, we found that commercial microbial products (probiotics) provide a poor solution to this challenge, in particular for key industrial organisms like E. coli. To overcome this technological gap, we report the development of synthetic extremophiles of industrially important gram-negative bacteria (E. coli Nissle 1917, Ensifer meliloti), gram positive bacteria (Lactobacillus plantarum) and yeast (Saccharomyces boulardii). Specifically, we developed a high throughput pipeline to define species-specific materials that allow these organisms to survive drying, elevated temperatures, organic solvents and even ionizing radiation. We enhanced the stability of E.coli Nissle 1917 by >4 orders of magnitude over commercial formulations and demonstrate the capacity to remain viable while undergoing tableting and pharmaceutical methodologies involving organic solvents. The development of synthetic materials-based enhanced stabilization stands to transform our capacity to apply micro-organisms in extreme environments including those found on Earth as well as in space. One-Sentence SummaryFragile therapeutic bacteria can be made to survive the manufacturing extremes normally reserved for small molecule drugs.

microbiology↗

bioRxiv2021

Chromosome-level genome assembly and transcriptome- based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14

Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size is 20,534,857 bp with a GC content of 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. In total we annotated 9,464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes. SignificanceThis obtained high-quality draft genome provides the suitable framework needed for genetic manipulations, and future studies of lipid metabolism and evolution of oleaginous yeasts. The identified extrachromosomal circular DNA may be useful for developing efficient episomal vectors for the manipulation of Rhodotorula yeasts. Data depositionThis project has been deposited at ENA under the accession PRJEB-40807.

microbiology↗

bioRxiv2021

Profiling acetogenic community dynamics in anaerobic digesters - comparative analyses using next-generation sequencing and T-RFLP

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional T-RFLP of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/427894v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@14ac78org.highwire.dtl.DTLVardef@1472ea3org.highwire.dtl.DTLVardef@46fc19org.highwire.dtl.DTLVardef@50ce7a_HPS_FORMAT_FIGEXP M_FIG C_FIG ONE SENTENCE SUMMARYOur high-throughput FTHFS gene AmpSeq method for barcoded samples and unsupervised analysis with AcetoScan accurately reveals temporal dynamics of acetogenic community structure in anaerobic digesters.

microbiology↗

bioRxiv2020

Population structure and transmission of Mycobacterium bovis in Ethiopia

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis (M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

genomics↗

bioRxiv2020

A novel method for tri-clustering dynamic functional network connectivity (dFNC) identifies significant schizophrenia effects across multiple states in distinct subgroups of individuals

BackgroundBrain imaging data collected from individuals are highly complex with unique variation; however, such variation is typically ignored in approaches that focus on group averages or even supervised prediction. State-of-the-art methods for analyzing dynamic functional network connectivity (dFNC) subdivide the entire time course into several (possibly overlapping) connectivity states (i.e., sliding window clusters). Though, such an approach does not factor in the homogeneity of underlying data and may end up with a less meaningful subgrouping of the dataset. MethodsDynamic-N-way tri-clustering (dNTiC) incorporates a homogeneity benchmark to approximate clusters that provide a more apples-to-apples comparison between groups within analogous subsets of time-space and subjects. dNTiC sorts the dFNC states by maximizing similarity across individuals and minimizing variance among the pairs of components within a state. ResultsResulting tri-clusters show significant differences between schizophrenia (SZ) and healthy control (HC) in distinct brain regions. Compared to HC, SZ in most tri-clusters show hypoconnectivity (low positive) among subcortical, default mode, cognitive control but hyper-connectivity (high positive) between sensory networks. In tri-cluster 3, HC subjects show significantly stronger connectivity among sensory networks and anticorrelation between subcortical and sensory networks compared to SZ. Results also provide statistically significant difference in reoccurrence time between SZ and HC subjects for two distinct dFNC states. ConclusionsOutcomes emphasize the utility of the proposed method for characterizing and leveraging variance within high-dimensional data to enhance the interpretability and sensitivity of measurements in the study of a heterogeneous disorder like schizophrenia and in unconstrained experimental conditions such as resting fMRI.

neuroscience↗

bioRxiv2019

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei.

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the PHO-regulated alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a >5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical PHO regulon control.

microbiology↗

bioRxiv2019

Application of extracellular flux analysis for determining mitochondrial function in mammalian oocytes and early embryos

1.BackgroundMitochondria provide the major source of ATP for mammalian oocyte maturation and early embryo development. Oxygen Consumption Rate (OCR) is an established measure of mitochondrial function. OCR by mammalian oocytes and embryos has generally been restricted to overall uptake and detailed understanding of the components of OCR dedicated to specific molecular events remains lacking.\n\nResultsHere, extracellular flux analysis (EFA) was applied to small groups of bovine, equine, mouse and human oocytes and bovine early embryos to measure OCR. Using EFA, we report the changes in mitochondrial activity during the processes of oocyte maturation, fertilization, and pre-implantation development to blastocyst stage in response to physiological demands in mammalian embryos. Crucially, we describe the real time partitioning of overall OCR to spare capacity, proton leak, non-mitochondrial and coupled respiration - showing that while there are alterations in activity over the course of development to respond to physiological demand, the overall efficiency is unchanged.\n\nConclusionEFA is shown to be able to measure mitochondrial function in small groups of mammalian oocytes and embryos in a manner which is robust, rapid and easy to use. EFA is non-invasive and allows real-time determination of the impact of compounds on OCR, facilitating an assessment of the parameters of mitochondrial activity. This provides proof-of-concept for EFA as an accessible system with which to study oocyte and embryo metabolism.

developmental biology↗

bioRxiv2018

Optimized breath detection algorithm in Electrical Impedance Tomography

ObjectiveThis paper define a method for optimizing the breath delineation algorithms used in Electrical Impedance Tomography (EIT). In lung EIT the identification of the breath phases is central for generating tidal impedance variation images, subsequent data analysis and clinical evaluation. The optimisation of these algorithms is particularly important in neonatal care since the existing breath detectors developed for adults may give insufficient reliability in neonates due to their very irregular breathing pattern.\n\nApproachOur approach is generic in the sense that it relies on the definition of a gold standard and the associated definition of detector sensitivity and specificity, an optimisation criterion and a set of detector parameters to be investigated. The gold standard has been defined by 11 clinicians with previous experience with EIT and the performance of our approach is described and validated using a neonatal EIT dataset acquired within the EU-funded CRADL project.\n\nMain resultsThree different algorithms are proposed that are improving the breath detector performance by adding conditions on 1) maximum tidal breath rate obtained from zero-crossings of the EIT breathing signal, 2) minimum tidal impedance amplitude and 3) minimum tidal breath rate obtained from Time-Frequency (TF) analysis.\n\nSignificanceBased on the gold standard, the most crucial parameters of the proposed algorithms are optimised by using a simple exhaustive search and a weighted metric defined in connection with the Receiver Operating Characterics (ROC). This provides a practical way to achieve any desirable trade-off between the sensitivity and the specificity of the detectors.

bioengineering↗

bioRxiv2017

Improved Kinect sensor based motion capturing system for gait assessment

Optical motion capturing systems are expensive and require substantial dedicated space to be set up. On the other hand, they provide unsurpassed accuracy and reliability. In many situations however flexibility is required and the motion capturing system can only temporarily be placed. The Microsoft Kinect v2 sensor is comparatively cheap and with respect to gait analysis promising results have been published. We here present a motion capturing system that is easy to set up, flexible with respect to the sensor locations and delivers high accuracy in gait parameters comparable to a gold standard motion capturing system (VICON). Further, we demonstrate that sensor setups which track the person only from one-side are less accurate and should be replaced by two-sided setups. With respect to commonly analyzed gait parameters, especially step width, our system shows higher agreement with the VICON system than previous reports.

neuroscience↗