No description available.

<p>Peptidoglycan (PG) remodelling and cell division are two important cellular processes that are the major target of antibiotics. Due to rising resistance, the need for new antibiotics today has never been greater. Therefore it is important to fill the gaps in our understanding of these two important processes in order to discover new and promising antibiotic targets. Peptidoglycan synthesis and remodelling is a highly coordinated event that involves a wide number of enzymes and processes which are not well understood. N-acetylmuramoyl-L-alanine amidases, whose function is to cleave the amide linkage between the stem peptides and the lactyl moiety of N-acetylmuramic acid, is a major class of PG-active proteins. Their role in daughter cell separation during cell division is well established in <em>Escherichia coli</em> however little is known about it in other systems. Using enzymatic assays we characterize AmiC as a novel amidase in <em>Pseudomonas aeruginosa. </em>Through mutational analysis and microscopy we show that AmiB and AmiC are required for daughter cell separation. A deletion of both enzymes results in a cell chaining phenotype with abnormal cell morphology. Transmission electron microscopy reveals that the double mutant is arrested at the septal peptidoglycan separation step. In addition to cell chaining, the ∆<em>amiB/amiC</em> mutant exhibits a significant increase in susceptibility to antibiotics. We also demonstrate that the LysM motif of AmiB is not required for its role in cell separation. Furthermore, the <em>amiB</em> mutant has significantly shorter cells than the wildtype indicating an additional role for the enzyme in the cell. Lastly, through a novel bioinformatics strategy we identify PA5047 as a potential PG amidase.</p> / Bachelor of Science (BSc)

Microfluidics, the manipulation of fluids at nanoliter scale, has emerged to offer an ideal platform for biological analysis of a low number of cells. The technological advances in microfluidics have allowed both forming of valves, mixers and pumps and integrating of optic and electronic components into microfluidic devices to construct complete and functional systems. In this dissertation, I present novel microfluidic techniques and their applications in cellular probes delivery, cell separation and epigenetic study. In the first part of the dissertation, electroporation is implemented on microfluidic platform to generate uniform delivery of "exposed" nanoparticle or protein into cells. In contrast to endocytosis, electroporation is a physical method to breach cell membrane and does not involve vesicle encapsulation of delivered probes, which means these probes have exposed surface in the cytosol. Such trait enables the use of delivered nanoparticle and protein for intracellular targeting of native biomolecules. Laser-induced fluorescent microscopy was used for single particle illuminating to track single molecules in cells. Microfluidic device provide integrated platform for conducting electroporation, cell culture and imaging. In the second part, microfluidic immunomagnetic cell separation is introduced. I showed two new approaches to enhance immunomagnetic cell separation based on (1) uniquely microfabricated paramagnetic patterns inside separation channels; and (2) using combination of nonmagnetic beads and magnetic beads for selection of tumor initiating cells based on two markers of opposite preference in one step. Enhancement in cell isolation (high capture efficiency or high selection purity) is experimentally observed and the former is explained by computational model. In the final part of the dissertation, microfluidic device incorporating valves and mixers for sensitive study of chromosome conformation is presented. This device has small reaction chamber minimizing sample requirement, and allows multiple steps of biological analysis in a single chip avoiding sample loss during sample transfer. Several orders of magnitude improved detection sensitivity is achieved with our microfluidics based method. I envision all novel techniques discussed in this dissertation have great potential in application of disease prognosis, diagnosis and treatment. / Ph. D.

No description available.

Cancer study and drug selection research attract more and more researchers, which need a significant laboratory technique, named cell injection. Hundreds of cells are loaded on devices and injected to investigate the behavior of the cells. Traditionally, cell injection is performed manually, which leads to human fatigue, is time-consuming and has a low success rate. Therefore, a system which can replicate the actions of what technicians do, such as to aspirate cells, transfer cells, immobilize cells, and release cells automatically, is needed. This system must be accurate, reliable, and efficient and operate without human intervention. A cell-transfer-cover and a cell-holder have been fabricated and a cell injection system has been set up to investigate the performance of the newly created device. Simulations and experiments have proven that this system would carry out the entire process of cell injection with the result of enhancing the speed of this important activity.

Cancer study and drug selection research attract more and more researchers, which need a significant laboratory technique, named cell injection. Hundreds of cells are loaded on devices and injected to investigate the behavior of the cells. Traditionally, cell injection is performed manually, which leads to human fatigue, is time-consuming and has a low success rate. Therefore, a system which can replicate the actions of what technicians do, such as to aspirate cells, transfer cells, immobilize cells, and release cells automatically, is needed. This system must be accurate, reliable, and efficient and operate without human intervention. A cell-transfer-cover and a cell-holder have been fabricated and a cell injection system has been set up to investigate the performance of the newly created device. Simulations and experiments have proven that this system would carry out the entire process of cell injection with the result of enhancing the speed of this important activity.

Anticorpos monoclonais (AcMos) para uso terapêutico correspondem a uma área importante na indústria de biofármacos, em especial os AcMos humanos, que apresentam menor probabilidade de elicitar imunogenicidade. O objetivo deste trabalho consistiu em obter AcMos humanos antitetânicos através da separação de linfócitos B produtores de anticorpos específicos utilizando o antígeno ou de plasmablastos. As células foram coletadas de doadores após vacinação e separadas por equipamento de cell sorter. As regiões variáveis dos anticorpos foram amplificadas e clonadas em vetores de expressão, que foram usados para transfectar transitoriamente células HEK293-F. O uso da toxina tetânica conjugada independentemente com dois marcadores, biotina e Alexa Fluor® 647, possibilitou a separação específica de linfócitos B produtores de AcMos antitetânicos, que foram avaliados por ELISA, western blotting e pela inibição da ligação da toxina ao gangliosídio GT1b. O ensaio in vivo mostrou proteção total dos animais contra a toxina tetânica quando três AcMos foram usados em conjunto. / Monoclonal antibodies (mAbs) for therapeutic use correspond to a major area of the biopharmaceutical industry, especially human mAbs that are less prone to elicit immunogenicity. The objective of this work was to obtain anti-tetanus human mAbs through separation of memory B lymphocytes producing specific antibodies stained with the antigen or plasmablasts. Cells were collected from peripheral blood of donors after vaccination and separated through cell sorting. The variable regions of the antibodies were amplified and cloned in expression vectors for transient transfection of HEK293-F cells. The staining with the tetanus toxin labeled independently with two markers, biotin and Alexa Fluor® 647 allowed the separation of specific B lymphocytes producing anti-tetanus mAbs. The antibodies expressed were evaluated by ELISA, western blotting and the inhibition of the binding of the tetanus toxin to the ganglioside GT1b. The in vivo neutralization assay showed that a pool of three different mAbs were able to protect mice against the tetanus toxin.

Using mixed-culture fermentation, the carboxylate platform produces carboxylic acids, which are chemically converted into chemicals and fuels. To optimize the mixed-acid fermentation, different bioreactor configurations and operating modes were investigated. Intermittent air exposure did not affect fermentation performance and bacterial profiles, but reduced the high-molecular-weight carboxylic acids. The microbial flora contained strict and facultative microbes, suggesting the presence of a facultative anaerobic community existing in a biofilm. Compared to countercurrent trains, propagated fixed-bed fermentations have similar selectivity and acid distribution, but lower yield, conversion, productivity, and acid concentration. One- to six-stage countercurrent fermentations were operated with similar conditions. Fewer stages increased conversion, whereas more stages increased acid concentration and selectivity. One to four stages achieved similar yield, and four to six stages achieved similar maximum acid concentration. Maximum conversion was achieved with a single stage. Recycling residual biomass retained microorganisms and nutrients and increased yield and productivity. Relative to lower biomass reflux, higher reflux increased conversion, decreased selectivity, and did not affect yield. The recommended carbon-nitrogen ratio is ~24 g carbon/g nitrogen. In four-stage fermentations, recycle to the second fermentor and in parallel to the first three fermentors was optimal. Fermentations with excess or insufficient nitrogen had higher selectivity, but decreased yield and conversion. The glucose-utilization assay is a rapid and repeatable method for determining the amount of microbial activity in a sample. This method determined ~25% efficiency of a new cell separation method. In continuous fermentation, compared to no cell recycle, recycling cellular biomass increased selectivity and yield, but decreased conversion. Compared to lower cell reflux, higher reflux increased productivity, yield, and conversion, but decreased selectivity. Compared to residual biomass recycle, cell recycle had increased selectivity and yield, but decreased conversion. A new method to screen and rank inoculum sources from natural environments was successfully developed and tested.

Anticorpos monoclonais (AcMos) para uso terapêutico correspondem a uma área importante na indústria de biofármacos, em especial os AcMos humanos, que apresentam menor probabilidade de elicitar imunogenicidade. O objetivo deste trabalho consistiu em obter AcMos humanos antitetânicos através da separação de linfócitos B produtores de anticorpos específicos utilizando o antígeno ou de plasmablastos. As células foram coletadas de doadores após vacinação e separadas por equipamento de cell sorter. As regiões variáveis dos anticorpos foram amplificadas e clonadas em vetores de expressão, que foram usados para transfectar transitoriamente células HEK293-F. O uso da toxina tetânica conjugada independentemente com dois marcadores, biotina e Alexa Fluor® 647, possibilitou a separação específica de linfócitos B produtores de AcMos antitetânicos, que foram avaliados por ELISA, western blotting e pela inibição da ligação da toxina ao gangliosídio GT1b. O ensaio in vivo mostrou proteção total dos animais contra a toxina tetânica quando três AcMos foram usados em conjunto. / Monoclonal antibodies (mAbs) for therapeutic use correspond to a major area of the biopharmaceutical industry, especially human mAbs that are less prone to elicit immunogenicity. The objective of this work was to obtain anti-tetanus human mAbs through separation of memory B lymphocytes producing specific antibodies stained with the antigen or plasmablasts. Cells were collected from peripheral blood of donors after vaccination and separated through cell sorting. The variable regions of the antibodies were amplified and cloned in expression vectors for transient transfection of HEK293-F cells. The staining with the tetanus toxin labeled independently with two markers, biotin and Alexa Fluor® 647 allowed the separation of specific B lymphocytes producing anti-tetanus mAbs. The antibodies expressed were evaluated by ELISA, western blotting and the inhibition of the binding of the tetanus toxin to the ganglioside GT1b. The in vivo neutralization assay showed that a pool of three different mAbs were able to protect mice against the tetanus toxin.

Clonal haematopoiesis of indeterminate potential, or CHIP are a family of mutations present in the general population. CHIP-mutations are prevalent in the haematopoietic stem cells and in the more mature cell populations, T-lymphocytes, B-lymphocytes and myeloid cells (CD3+, CD19+ and CD33+ cells) in blood. By separating these cell populations using magnetic isolation, extracting DNA from the cell populations, and detecting the same mutation in all cell populations, one can prove the presence of CHIP-mutations in a hematopoietic stem cell. At least 50 ng good quality DNA is needed for the gene analysis to detect CHIP-mutations. The magnet separated cell population may be very small, so the DNA extraction method must be optimized to achieve enough DNA yield. The main purpose of the method development was to compare two storage methods before DNA-extractions, and then three different DNA-quantification methods after the DNA-extractions. After the best storage and quantification methods were identified, five samples of cryo-preserved viable cells were used to isolate cell populations using magnetic beads covered in specific antibodies and a magnetic field, and then quantified. Results of the study showed that the best way was to store the cells in ATL-buffer and Proteinase K. To quantify DNA, qPCR was the most accurate method, since the other methods showed incorrect results because of the low DNA concentrations. Magnet cell separation was partly successful. All except one of the DNA yields from the cell separation protocols reached the critical amount of DNA, but some yields were not pure yields of the sought-after cell population. In general, the method must be worked on more with further research.