Observation of a Degenerate Fermi Gas Trapped by a Bose-Einstein Condensate

We report on the formation of a stable quantum degenerate mixture of fermionic $^6$Li and bosonic $^{133}$Cs in an optical trap by sympathetic cooling near an interspecies Feshbach resonance. New regimes of the quantum degenerate mixtures are identified. With moderate attractive interspecies interactions, we show that a degenerate Fermi gas of Li can be fully confined in the Cs condensate without external potentials. For stronger attraction where mean-field collapse is expected, no such instability is observed. In this case, we suggest the stability is a result of dynamic equilibrium, where the interspecies three-body loss prevents the collapse. Our picture is supported by a rate equation model, and the crossover between the thermalization rate and the observed inelastic loss rate in the regime where the mean-field collapse is expected to occur.Comment: 6 Pages, 4 Figure

Photoacoustic ultrasound sources from diffusion-limited aggregates

Metallic diffusion-limited aggregate (DLA) films are well-known to exhibit near-perfect broadband optical absorption. We demonstrate that such films also manifest a substantial and relatively material-independent photoacoustic response, as a consequence of their random nanostructure. We theoretically and experimentally analyze photoacoustic phenomena in DLA films, and show that they can be used to create broadband air- coupled acoustic sources. These sources are inexpensive and simple to fabricate, and work into the ultrasonic regime. We illustrate the device possibilities by building and testing an optically-addressed acoustic phased array capable of producing virtually arbitrary acoustic intensity patterns in air.Comment: 5 pages, 5 figure

Understanding the Drought Stress Rescue Pathway of Pseudomonas simiae Strain WCS417 using a Forward Genetic Screen

With a rapidly growing human population, sustainable and climate-resilient agriculture is crucial to our continued survival. Due to the increase in global warming, abiotic stresses such as drought have become more prevalent, significantly reducing crop productivity. Emerging innovative products containing cultures of microbes, labeled as biostimulants or biocontrol strains, have the potential to improve a plant’s response to such stressors. However, the molecular mechanisms by which these microbial-based products relieve drought stress remain unknown. Here, we used Pseudomonas simiae WCS417, a plant growth promoting rhizobacterium, to understand the mechanism of drought rescue of the model plant Arabidopsis thaliana. We hypothesized that specific P. simiae WCS417 genes conferred a fitness advantage to A. thaliana, allowing for it to thrive under drought stress conditions. Using a randomly barcoded-transposon library of WCS417 and in vitro assays, 2000 mutants were screened to define the genes responsible for conferring the drought rescue phenotype, resulting in 19 mutants displaying a loss in this phenotype. After rescreening and sequencing, three genes were implicated in conferring the drought rescue phenotype. The mutant strains were identified to be auxotrophic and involved in the amino acid synthesis of cysteine and tryptophan, which, when mutated, led to decreased colonization by WCS417 of A. thaliana. Furthermore, our results also indicate that colonization efficiency is important for drought rescue of A. thaliana by WCS417. Future studies can exploit these properties to aid farmers across the world increase agricultural outputs in drought-stricken regions and ensure self-subsistence.Bachelor of Scienc

Novel computational approaches to research longitudinal microRNA-mRNA expression datasets

Ph. D. Thesis.microRNAs (miRNAs) regulate many biological processes and are used as biomarkers for the classification of diseases, conditions and developmental stages. miRNAs function by targeting and negatively regulating specific mRNAs. One limitation of utilising miRNAs in experimental work is the complex and often redundant behaviour of miRNA-mRNA interactions; as a single miRNA can regulate many mRNAs and one mRNA can be regulated by multiple miRNAs. This complexity stifles the potential of miRNAs. However, miRNAmRNA expression datasets are becoming generated more frequently and they can help to garner greater understanding of how miRNAs regulate biological systems. Furthermore, researchers are generating longitudinal datasets as these can elude to greater understanding of how biological conditions change over time. Thus there is a rise of longitudinal miRNA-mRNA expression datasets. However, extracting useful information from increasingly sophisticated datasets is a challenge in biological research. Exploration of such datasets using computational techniques, such as big data bioinformatics, kinetic modelling and machine learning could help in identifying interesting miRNA-mRNA interactions. During this PhD I asked if these methodologies can be used to gain insights from a range of longitudinal miRNA-mRNA expression datasets. Hence, I developed an R/Bioconductor tool called TimiRGeN to integrate, analyse and generate small networks from longitudinal miRNA-mRNA datasets. Datasets from kidney fibrosis, chondrogenesis dataset, breast cancer and Huntington’s disease (HD) were analysed with TimiRGeN. Results from the chondrogenesis dataset analysis were taken forward to generate a multimiRNA kinetic model. With help from my collaborators this model was validated and predictions were made. Using the HD dataset, machine learning (ML) techniques trained models to detect if samples have disease or wild type conditions. Overall, I have developed and used multiple computational techniques to increase knowledge gained from longitudinal miRNA-mRNA datasets, and I believe the results show these techniques can contribute to miRNA research

Xanthogranulomatous pyelonephritis: a case review of two cases

Xanthogranulomatous pyelonephirits is a chronic destructive granulomatous inflammation of the renal parenchyma. It was first described by Schlagenhaufer in 1916 and then Oberling named the disease as Xanthogranulomatous pyelonephritis in 1935. It represents 1% of all renal infections. In this report we present two cases of Xanthogranulomatous pyelonephritis along with radiological assessment

Evaluation of endometrial pathologies with high resolution transvaginal ultrasound

Background: The purpose of this study is to evaluate endometrial lesions on the basis of their appearances by high resolution trans-vaginal ultrasound. High resolution trans-vaginal sonography is useful for diagnosis of various endometrial lesions. Broad spectrum of endometrial lesions can be accurately imaged by various available modalities of which ultrasound is easily available, reliable, non-invasive and cost effective modality.Methods: In these study cases with complaints of abnormal uterine bleeding, suspected retained products, white discharge, dysmenorrhea and habitual abortions were evaluated with trans-vaginal ultrasound. Lesions were carefully studied and evaluated. Philips HD-11 and Accuson Siemens ultrasound machines with trans-vaginal probes were used.Results: In all 121 cases, trans-abdominal and trans-vaginal high resolution ultrasound was performed for different lesions in endometrium. Age group of females was between 18 to 65 years. Different uterine lesions were studied. Out of which most commonly encountered lesions were endometrial hyperplasia followed by polyps and least common lesion was AV malformation.Conclusions: High resolution trans-vaginal ultrasound helped in staging and management in cases of ca. endometrium. Hence trans-vaginal ultrasound should be 1st choice of investigation for diagnosis of endometrial lesions

TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis

Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks (GRNs) provide a valuable means to disentangle the complexity of microRNA (miRNA)-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal miRNA-mRNA datasets. Results: We present TimiRGeN, an R package that uses time point-based differential expression results to identify miRNA-mRNA interactions influencing signaling pathways of interest. miRNA-mRNA interactions can be visualized in R or exported to PathVisio or Cytoscape. The output can be used for hypothesis generation and directing in vitro or further in silico work such as GRN construction

Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis.

Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA, and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA-mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work in human cells demonstrated alteration of miR-199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targets FZD6, ITGA3 and CAV1 were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterise a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNAs

Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis

Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA, and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA–mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work in human cells demonstrated alteration of miR199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targets FZD6, ITGA3 and CAV1 were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterise a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNA