Project description:Bacterial membrane vesicles have been implicated in a broad range of functions in microbial communities from pathogenesis to gene transfer. Though first thought to be a phenomenon associated with Gram-negative bacteria, vesicle production in Staphylococcus aureus, Lactobacillus plantarum, and other Gram-positives has recently been described. Here we characterize MVs from three different Lactobacillus species (L. acidophilus, L. casei, and L. reuteri), determining that the size and protein composition of Lactobacillus-derived MVs have both similarities and differences with those produced by Gram-negative bacteria. Using proteomics, we identified more than 80 protein components from Lactobacillus-derived MVs, including some that were enriched in the vesicles themselves. For each species, vesicular proteins were categorized based on biological pathway and examined for subcellular localization signals in an effort to identify possible sorting mechanisms for MV proteins. Additionally, differences between MVs of other Lactobacillus species and Gram positive bacteria were highlighted. Information in this study will assist in elucidation of the formation and functions of MVs, as well as the development of therapeutic tools for vaccines, diagnosis, and therapeutic delivery.
Project description:Masel2000 - Drugs to stop prion aggregates
and other amyloids
Encoded non-curated model.
Issues:
- Missing initial concentration for species y, yb and z
- Not reproducible figures
This model is described in the article:
Designing drugs to stop the
formation of prion aggregates and other amyloids.
Masel J, Jansen VA.
Biophys. Chem. 2000 Dec; 88(1-3):
47-59
Abstract:
Amyloid protein aggregates are implicated in many
neurodegenerative diseases, including Alzheimer's disease and
the prion diseases. Therapeutics to block amyloid formation are
often tested in vitro, but it is not clear how to extrapolate
from these experiments to a clinical setting, where the
effective drug dose may be much lower. Here we address this
question using a theoretical kinetic model to calculate the
growth rate of protein aggregates as a function of the dose of
each of three categories of drug. We find that therapeutics
which block the growing ends of amyloids are the most
promising, as alternative strategies may be ineffective or even
accelerate amyloid formation at low drug concentrations. Our
mathematical model can be used to identify and optimise an
end-blocking drug in vitro. Our model also suggests an
alternative explanation for data previously thought to prove
the existence of an entity known as protein X.
This model is hosted on
BioModels Database
and identified by:
MODEL1410310000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
Project description:Bulk RNA-sequencing of the mesendoderm progenitors before aggregation. Mesendoderm progenitors aggregates can lead to the formation of cardiac microtissues, multilineage and gut organoids in different batches. Despite batch-to-batch differences in spheroid phenotype, all spheroids (n>200) within a single batch derived from the same initial differentiation of progenitor cells manifested identical morphologies and cellularity.
Project description:Schizophrenia (SZ) and autism spectrum disorders (ASD) are highly heritable neuropsychiatric/neurodevelopmental disorders, although environmental factors, such as maternal immune activation (MIA), play a role as well. Inflammatory cytokines appear to mediate the effects of MIA on neurogenesis and behavior in animal models. However, drugs and cytokines that trigger MIA can also induce a febrile reaction, which could have independent effects on neurogenesis through heat shock (HS)-regulated cellular stress pathways. However, this has not been well-studied. As a first step towards addressing the role of fever in MIA, we used a recently described model of human brain development in which induced pluripotent stem cells (iPSCs) differentiate into 3-dimensional neuronal aggregates that resemble a first trimester telencephalon. RNA-seq was carried out on aggregates that were heat shocked at 39oC for 24 hours, along with their control partners maintained at 37oC. Overall, 186 genes showed significant differences in expression following HS (p<0.05), including known HS-inducible genes, as expected, as well as those coding for NGFR and a number of SZ and ASD candidates, including SMARCA2, DPP10, ARNT2, AHI1 and ZNF804A. The degree to which the expression of these genes decrease or increase during HS is similar to that found in copy loss and copy gain CNVs, although the effects of HS are likely to be more transient. RNA-seq was carried out on neuronal aggregates as described by Mariani et al. with slight modification (PMID:22761314). For the heat shock experiment, a group of 49 day old aggregates was placed in an incubator set at 39C for 24 hours, while control sets of aggregates were maintained at 37C. The incubator conditions were otherwise unchanged. After detaching the aggregates, total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. Lastly, RNAseq profiles of HS and Control were compared
Project description:Extracellular Mycobacterium tuberculosis (Mtb) aggregates can evade phagocytosis and intracellular host-cell defenses by inducing macrophage killing. We showed that Mtb aggregates require a functional ESX-1 type VII secretion system and production of the surface-exposed lipid phthiocerol dimycocerosate (PDIM) to induce cell death upon contact with macrophages. We used quantitative proteomics to compare the secretome of a panel of Mtb mutant strains that induce or do not induce macrophage death and identified secreted bacteria factors involved in macrophage death induction.
Project description:Cytoplasmic aggregates of TDP-43 are found in neuronal and skeletal muscle diseases yet it is not understood how these protein aggregates relate to the biological function of TDP-43. By examining normal skeletal muscle formation, we discovered TDP-43 redistributes from the nucleus into the cytoplasm and forms higher-ordered aggregates. These skeletal muscle TDP-43 aggregates adopt an amyloid-like structure capable of binding RNA. In skeletal muscle, TDP-43 binds UG-rich, sarcomeric mRNAs and oligomerizes on these long mRNA transcripts facilitating amyloid formation. Tissue specific genetic deletion of TDP-43 in skeletal muscle disrupts the formation and maintenance of the sarcomere and mislocalizes sarcomeric mRNAs. Thus, cytoplasmic, amyloid-like TDP-43 aggregates that traffic mRNAs could serve as a precursor to pathological TDP-43 aggregates common in degenerative neuromuscular disease.
Project description:Some commensal bacteria stimulate the immune system but do not present specific antigenicity. Such adjuvant effects have been reported for the bacterial species Lactobacillus plantarum. To study in vivo human responses to L. plantarum, a randomised double-blind placebo-controlled cross-over study was performed. Healthy adults were provided preparations of living and heat-killed L. plantarum bacteria, biopsies were taken from the intestinal mucosa and altered transcriptional profiles were analysed. Transcriptional profiles of human epithelia displayed striking differences upon exposure to living L. plantarum bacteria harvested at different growth phases. Modulation of NF-κB-dependent pathways was central among the major altered cellular responses. This unique in vivo study shows which cellular pathways are associated with the induction of immune tolerance in mucosal tissues towards common adjuvanticity possessing lactobacilli. Keywords: mucosal response of healthy adult humans to lactic acid bacteria
Project description:Oculopharyngeal muscular dystrophy (OPMD) is an autosomal dominant disease caused by an alanine tract expansion mutation in Poly(A)-binding protein nuclear 1 (expPABPN1). To model OPMD in a myogenic and physiological context, we generated mouse myoblast cell clones stably expressing either human wild type (WT) or expPABPN1 at low levels. The transgene expression is induced upon myotube differentiation and results in formation of insoluble nuclear PABPN1 aggregates that are similar to the in vivo aggregates. Quantitative analysis of PABPN1 protein in myotube cultures revealed that expPABPN1 accumulation and aggregation is greater than that of the WT protein. In a comparative study we found that aggregation of expPABPN1 is more affected by inhibition of proteasome activity, as compared with the WT PABPN1 aggregation. Consistent with this, in myotubes cultures expressing expPABPN1 deregulation of the proteasome was identified as the most significantly deregulated pathway. Differences in the accumulation of soluble WT and expPABPN1 were consistent with differences in ubiquitination and protein turnover. This study indicates, for the first time, that in myotubes the ratio of soluble to insoluble expPABPN1 is significantly lower compared to that of the WT protein. We suggest that this difference can contribute to muscle weakness in OPMD. Clones on IM2 mouse myotubes that stably express Ala10-PABPN1-FLAG (WTA, WTD) or Ala17-PABPN1-FLAG (D7E). The transgene expression level in D7E and WTA are similar. WTA and WTD reflects differences in expression levels. RNA was extracted from myotubes of WTA, WTD and D7E in triplicates. cDNA synthesis and lebeling was preformed with the Illumina cDNA labeling kit.
Project description:Probiotic bacteria, specific representatives of bacterial species that are a common part of the human microbiota, are proposed to deliver health benefits to the consumer by modulation of intestinal function via largely unknown molecular mechanisms. To explore in vivo mucosal responses of healthy adults to probiotics, we obtained transcriptomes in an intervention study following a double-blind placebo-controlled cross-over design. In the mucosa of the proximal small intestine of healthy volunteers, probiotic strains from the species Lactobacillus acidophilus, L. casei and L. rhamnosus each induced differential gene regulatory networks and pathways in the human mucosa. Comprehensive analyses revealed that these transcriptional networks regulate major basal mucosal processes, and uncovered remarkable similarity to response profiles obtained for specific bioactive molecules and drugs. This study elucidates how intestinal mucosa of healthy humans perceive different probiotics and provides avenues for rationally designed tests of clinical applications. Keywords: mucosal response of healthy adult humans to lactic acid bacteria
Project description:Most bacteria can form biofilms, which typically have a life cycle from cells initially attaching to a surface before aggregation and growth produces biomass and an extracellular matrix before finally cells disperse. To maximise fitness at each stage of this life cycle, and given the different events taking place within a biofilm, temporal regulation of gene expression is essential. We recently described the genes required for optimal fitness over time during biofilm formation in Escherichia coli using a massively parallel transposon mutagenesis approach called TraDIS-Xpress. We have now repeated this study in Salmonella enterica serovar Typhimurium to determine the similarities and differences in biofilm formation through time between these species. This work deepens understanding of the core requirements for biofilm formation in the Enterobacteriaceae whilst also identifying some genes with specialised roles in biofilm formation in each species.