The Role of Genomic Context in Bacterial Growth Homeostasis

The growth of bacteria is a complex but well-orchestrated dance involving the repetitive and reproducible production of their diverse cellular components in order to divide. A lot can go astray and therefore the cell has developed several strategies in order to ensure everything remains synchronized. This problem is only further complicated as the cells adjust their growth rate to their living conditions resulting in ripple effects throughout the cell physiology. One notable change is that as nutrient availability and quality increases so too does the average size and the concentration of ribosomes in the cell. The latter enables the production of the largest macromolecule faction in the cell (proteins) including the production of more ribosomes required to maintain the protein synthesis requirements. With the increase in volume of the cell comes a required increase in surface area, and a disbalance between these two would result in untenable levels of internal pressure. How then do bacteria ensure that volume growth is synchronized with the production of cell envelope components so that cell homeostasis is maintained, especially in the face of fluctuating growth rate? Genomic context is known to assist in co-regulation of genes thereby synchronizing them to respond to different cellular stimuli. As the bacterial genome is highly fluid, the existence of conserved genomic contexts suggests important loci of co-regulation. Could it be in these gene clusters that a possible link between growth and surface expansion is found? To answer this question this thesis undertook three missions, firstly we established a genome comparison tool (www.GenCoDB.org) that will take advantage of the ever-growing availability of bacterial genomes to assist us in the analysis, comparison, and quantification of genome contexts. This will rely on novel strategies in order to: accommodate the breadth of genome data available in a computationally efficient manner, reduce the effect of sampling bias that plague most bacterial datasets and ensure candidates are considered significant for their evolutionary context. The availability of GenCoDB is sure to facilitate genomic context research in the microbiology community and improve accessibility to non-bioinformatics to this wellspring of important biological data. With the swath of genomic neighbourhood data, we then sought to understand and analyse the evolution of conserved gene clusters in order to narrow down possible volume-surface regulating candidates. By tracking the evolution of gene clusters throughout the Bacteria kingdom we found that co-orientation is strongly conserved, however, this does not influence the subsequent context around the cluster nor the expansion of the cluster. We found that vertical transmission and not horizontal gene transfer was found to be the driving factor of gene cluster occurrence in chromosomes and that the origin and terminus are hotspots for cluster maintenance. Finally, we found that despite the apparent frequency of operon organization in gene clusters, gene clusters appear to be maintained due to other selective pressures such as within-cluster protein-protein interactions and the essential status of their genes. We suggest that operons are a consequence and not a cause co-localization over evolutionary time. We identified a single gene cluster candidate that met all the requirements we believe are required for cell growth homeostasis of synchronized surface and volume expansion. These requirements were a broad conservation within Bacteria, and a connection between ribosome-associated proteins (growth) with cell envelope synthesizes. In agreement with our evolution studies we found that whilst the cluster was co-regulated this did not appear to be the selective pressure that brought these different processes together. Instead we found a potential role of genomic channelling, linking the production of pyrimidines with the synthesis of the cell envelope which is reliant on the co-localization of this cluster. Together, this work will forward the understanding of chromosome evolution in Bacteria and the potential implications of genomic context in metabolite utilization. It challenges the roles that operons and horizontal gene transfer play in the long-term evolution of gene order and it provides a new quantitative and statistical resource providing access to over 1.9 million gene neighbourhoods

Biomarkers and Bioassays for Cardiovascular Diseases: Present and Future

Stratification of cardiac patients arriving at the emergency department is now being made according to the levels of acute cardiac biomarkers (i.e. cardiac troponin (cTn) or creatine kinase myocardial band (CK-MB)). Ongoing efforts are undertaken in an attempt to identify and validate additional cardiac biomarkers, for example, interleukin-6, soluble CD40L, and C-reactive protein, in order to further risk stratify patients with acute coronary syndrome. Several studies have also now shown an association of platelet transcriptome and genomic single nucleotide polymorphisms with myocardial infarction by using advanced genomic tools. A number of markers, such as myeloid-related protein 14 (MRP-14), cyclooxygenase-1 (COX-1), 5-lipoxygenase activating protein (FLAP), leukotriene A4 hydrolase (LTA4H) and myocyte enhancing factor 2A (MEF2A), have been linked to acute coronary syndromes, including myocardial infarction. In the future, these novel markers may pave the way toward personalized disease-prevention programs based on a person’s genomic, thrombotic and cardiovascular profiles. Current and future biomarkers and bioassays for identifying at-risk patients will be discussed in this review

Project Florida: Federated Learning Made Easy

We present Project Florida, a system architecture and software development kit (SDK) enabling deployment of large-scale Federated Learning (FL) solutions across a heterogeneous device ecosystem. Federated learning is an approach to machine learning based on a strong data sovereignty principle, i.e., that privacy and security of data is best enabled by storing it at its origin, whether on end-user devices or in segregated cloud storage silos. Federated learning enables model training across devices and silos while the training data remains within its security boundary, by distributing a model snapshot to a client running inside the boundary, running client code to update the model, and then aggregating updated snapshots across many clients in a central orchestrator. Deploying a FL solution requires implementation of complex privacy and security mechanisms as well as scalable orchestration infrastructure. Scale and performance is a paramount concern, as the model training process benefits from full participation of many client devices, which may have a wide variety of performance characteristics. Project Florida aims to simplify the task of deploying cross-device FL solutions by providing cloud-hosted infrastructure and accompanying task management interfaces, as well as a multi-platform SDK supporting most major programming languages including C++, Java, and Python, enabling FL training across a wide range of operating system (OS) and hardware specifications. The architecture decouples service management from the FL workflow, enabling a cloud service provider to deliver FL-as-a-service (FLaaS) to ML engineers and application developers. We present an overview of Florida, including a description of the architecture, sample code, and illustrative experiments demonstrating system capabilities

Acute urticaria caused by the injection of goat-derived hyaluronidase

Hyaluronidase is a goat testicular protein that hydrolyzes hyaluronic acid, a structural component of the intercellular matrix. It is commonly used as a spreading factor to improve the diffusion of drugs, including local anesthetics and chemotherapeutics. We experienced a 55-yr-old female with generalized urticaria that developed within 1 hr after the epidural injection of hyaluronidase. She had a history of allergic rhinitis, and had suffered from post-herpetic neuralgia and a herniated disc for several years. To relieve her pain, she had been given epidural injections consisting of mepivacaine hydrochloride, triamcinolone acetonide, and morphine sulfate biweekly for one year. Hyaluronidase had been administered several times with these drugs before this episode of generalized urticaria. Skin prick testing showed a positive response to 1,500 IU/mL of hyaluronidase extract, as compared to histamine. The patient's serum hyaluronidase-specific IgE level, determined using an enzyme-linked immunosorbent assay (ELISA), was markedly elevated, as compared to unexposed healthy controls. An IgE immunoblot analysis using hyaluronidase extract and the patient's serum showed IgE binding components at 31 and 21 kDa, whereas no corresponding IgE binding component was found in healthy controls. An ELISA inhibition test showed significant, dose-dependent inhibition with the serial addition of hyaluronidase extract. This is the first case of an IgE-medicated allergic reaction to goat (Naemorhedus goral raddenus) hyaluronidase, demonstrated by skin testing and a specific IgE and immunoblot assay

Enabling a robust scalable manufacturing process for therapeutic exosomes through oncogenic immortalization of human ESC-derived MSCs

10.1186/1479-5876-9-47Journal of Translational Medicine9