No description available.

A full length cDNA clone of Brassica napus 3-oxoacyl-ACP reductase (β-ketoacyl-ACP reductase; E.C. 1.1.1.100; βKR) and the Escherichia coli gene for the same enzyme, have been over-expressed in E. coli. Both the Brassica napus seed and Escherichia coli βKR proteins have been purified by a rapid two-step, single chromatography matrix method. Glutaraldehyde cross-linking studies show the plant βKR is expressed as a tetramer and the E. coli enzyme is expressed as a dimer. The secondary structure of the two proteins was predicted via analysis of circular dichroism spectra, which also show dilution dependent unfolding of a-helical structure in the plant enzyme, a possible explanation for the dilution inactivation of βKRs. Ultrafiltration substrate binding studies and a bireactant initial velocity study show that Brassica napus βKR employs a fixed order ternary complex mechanism with NADPH binding to the enzyme first. One-dimensional western blot analysis indicates two isoforms of βKR (28 kDa and 31 kDa) in crude B. napus seed extracts. Further analysis using two- dimensional western blots demonstrates the presence of four major isoforms. Comparison with 2D blots from B. campestris suggests that one of the major isoforms has originated from that source. The crystal structure of the E. coli βKR enzyme is also discussed.

Diss. (sammanfattning) Uppsala : Univ., 2002. / Härtill 4 uppsatser.

No description available.

No description available.

Cyclophilins (Cyp) are proteins that catalyze the interconversion of trans/cis isomers of proline belonging to the peptidyl-prolyl isomerases family (PPIase). In addition to their PPIase activity, Cyps have diverse biological roles and have been implicated in a number of different diseases such as HIV-1 and HCV. Although several Cyp inhibitors have been reported in the literature, none are able to inhibit with high specificity various Cyp isoforms. To facilitate the development of isoform-specific Cyp ligands, we have pursued detailed studies of Cyp dynamics and ligand binding thermodynamics using molecular simulations, biophysical assays and protein X-ray crystallography. Research efforts were focussed on the identification of novel Cyp inhibitors using X-ray crystallographic studies and Surface Plasmon Resonance (SPR) experiments on fragments from an in-house bespoke library of small compounds. These biophysical studies revealed a number of fragments that are able to bind to diverse Cyp isoforms with high micromolar – low millimolar activity. To further examine the binding of these fragments to cyclophilins, identify interactions with the proteins and explain specificity trends from SPR and X-ray results, molecular dynamics (MD) simulations and free energy calculations were pursued. Models of apo and holo Cyps in complex with fragments that we had experimentally tested were set up using the Amber, AmberTools and FESetup software. Free energy calculations were performed using the thermodynamic integration (TI) technique with the Sire/OpenMM software. The results were analysed with custom scripts. Correlations between computed and measured binding energies, and calculated and observed binding modes were analysed to help develop guidelines for the development of isoform specific cyclophilin ligands. A detailed comparison of the merits and drawbacks of the experimental and computational techniques used in this work has also been made, and strategies for effective combination of the methodologies in structure-based projects are outlined.

The ability of neurons to dynamically regulate their response to changing inputs is essential for the correct development and function of a nervous system capable of learning and memory. The post synaptic compartment of excitatory synapses contains a dense proteinaceous complex of molecules that link excitatory glutamatergic neurotransmission to downstream signalling pathways that ultimately result in modification of the synapse. One of the most abundant of such postsynaptic signalling molecules, synaptic GTPase activation protein, SynGAP, represents a key signalling link between the activation of the NMDA sensitive glutamate receptor to outcomes such as the structural rearrangement of synaptic sites and altered synaptic content of AMPA type glutamate receptors, molecular processes that underly learning and memory. The primary finding of this thesis is that different isoforms of SynGAP, which varies at it N terminus through alternative transcription start sites and at its C terminus through alternative splicing, can differentially affect the function of the synapse. Using primary murine neuronal cultures we show that despite being crucial for the survival of the mouse the absence of SynGAP does not effect mean dendritic spine morphology and density or miniature excitiatory post synaptic currents under a range of experimental conditions (days in vitro 10 – 14, with and without serum, high and low cell plating density). In order to examine the effects of different SynGAP isoforms we cloned two full length transcripts (SynGAP A-alpha-2 and SynGAP Ealpha- 1) which were used to construct a range of isoforms. Whole cell patch clamping of SynGAP transfected neurons revealed that the post synaptic expression of SynGAPs which terminate as an alpha-1 isoform can lead to the elimination of mEPSCs, while isoforms that terminate as an alpha-2 isoform can lead to synaptic strengthening. The magnitude of the effect in both cases is determined by the identity of the N terminus of the protein; SynGAP A-alpha-1 has the largest synaptic weakening effect and SynGAP B-and C alpha-2 strenghten the synapse. The changes in miniature electrophysiological properties are not mirrored by changes in dendritic spine morphology, whole cell AMPA/NMDA currents, or synaptic responsiveness to stimulation suggesting an undefined novel mechanism of action. SynGAPs A, B and C appear to be under the control of different promoters which are differentially regulated by development and synaptic activity, thus the differential function of SynGAP N and C terminal combinations could play a part in the activity dependent regulation of synaptic strength.

The REarranged in Transfection (RET) tyrosine kinase is an important signalling protein for the development of neural crest-derived tissues such as the enteric and sympathetic nervous systems. RET is constitutively activated in multiple human tumour types, such as thyroid carcinomas and some non-small cell lung cancers. RET has 3 distinct isoforms, RET9, RET43 and RET51, which are named after the lengths of their unique C-terminal tails. Here, we investigate the role of RET in the TT thyroid carcinoma cell line, where it is a driver of tumourigenesis, and in the MiaPaCa-2 pancreatic carcinoma cell line, where RET is not driving tumour initiation, but may nonetheless have a profound effect on tumour progression. We generated lentiviral constructs for shRNAs that target either RET9 or RET51 specifically, or a common region shared by all RET isoforms. TT and MiaPaCa-2 cells were transduced using these lentiviral particles to create stable cell lines containing knockdowns of total RET, RET9, or RET51. Using a variety of morphological and biochemical assays, we found that RET expression is critical for TT cell survival, and that both RET9 and RET51 play significant roles in driving cell proliferation in TT cells. Conversely, RET is not critical for MiaPaCa-2 cell survival, and RET knockdown had no effect on MiaPaCa-2 proliferation. MiaPaCa-2 cells instead underwent dramatic morphological changes, from their normal spindle-like mesenchymal appearance to an increasingly flattened and epithelioid character, in response to RET9, RET51 or total-RET knockdown. The observed morphological changes were coupled with significantly reduced invasiveness through matrigel towards a source of chemoattractant, suggesting a critical role for RET in mediating cell invasiveness. These results suggest that RET may not only drive tumourigenesis, but can also enhance disease progression when expressed in other tumour types. We predict that RET may play critical roles in perineural invasion in pancreatic cancers, a process where cells invade along peripheral nerve fibers by following an increasing concentration of chemoattractants secreted by nerve and glial cells. Thus, RET may be a valuable target to slow, or stop this process, which would have significant clinical implications in a wide variety of cancers. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2013-08-30 11:45:41.969

Master of Science / Department of Animal Sciences and Industry / Timothy G. Rozell / Since vascularization of the theca layer increases as follicles progress in size through preantral and antral stages, the principal angiogenic factor, vascular endothelial growth factor A (VEGFA), may influence follicle growth via regulation of angiogenesis. However, VEGFA may also influence follicular development through nonangiogenic mechanisms since its expression has been localized to nonvascular follicles and cells. Alternative mRNA splicing of 8 exons from the VEGFA gene results in the formation of different VEGFA isoforms. Each isoform has unique properties and is identified by the number of amino acids within the mature protein. Proangiogenic isoforms are encoded by exon 8a while a sister set of isoforms with antiangiogenic properties are encoded by exon 8b. The antiangiogenic isoforms comprise the majority of VEGFA expressed in most tissues while expression of the proangiogenic VEGFA isoforms is upregulated in tissues undergoing active angiogenesis. The Vegfa angiogenic isoforms (Vegfa_120, Vegfa_164, and Vegfa_188) were detected in developing rat ovaries, and quantitative RT-PCR determined that Vegfa_120 and Vegfa_164 mRNA was more abundant after birth, while Vegfa_188 mRNA was highest at embryonic day 16. The antiangiogenic isoforms, Vegfa_165b and Vegfa_189b, were amplified and sequenced from rat ovaries and quantitative RT-PCR determined that Vegfa_165b mRNA was more abundant around embryonic day 18, but Vegfa_189b lacked a distinct pattern of abundance. VEGFA and its receptors were localized to pregranulosa and granulosa cells of all follicle stages and to theca cells of advanced-stage follicles. Antiangiogenic VEGFA isoforms were localized to pregranulosa and granulosa cells of all follicle stages and to theca cells of advanced-stage follicles. To determine the role of VEGFA in developing ovaries, postnatal day 3/4 rat ovaries were cultured with VEGFR-TKI, a tyrosine kinase inhibitor that blocks signaling through the VEGFA receptors, FLT1 and KDR. Ovaries treated with VEGFR-TKI had vascular development reduced by 94%. In addition, treated ovaries had more primordial follicles, fewer early primary, transitional, and secondary follicles, and greater total follicle numbers compared with control ovaries. This suggests that VEGFA promotes follicle recruitment and early follicular development. These effects may be dependent upon increased ovarian vascularization or they may be mediated by nonvascular mechanisms.

This study was conducted at the University of Massachusetts Medical Center in the Volkert laboratory. Human alkyl adenine DNA glycosylase (hAAG) is a DNA repair enzyme that repairs alkylated DNA bases. hAAG was cloned in 1991 and a second isoform was classified in 1994. The difference between the two isoforms of hAAG is an alternate spliced first exon. Both isoforms of the hAAG gene were present in the Volkert laboratory collection, however the second isoform (hAAG-2) was phenotypically different than the first and became the first focus of this study. Using the improperly functioning isoform as a template, and constructing a 5' primer with the identical upstream sequence as the functioning isoform (hAAG-1), a phenotypically similar gene was constructed by PCR. The new isoform (hAAG-2) was cloned into an expression vector and its activity as a DNA repair agent was studied. A second version of hAAG-2 was also constructed, incorporating a histidine tag for protein purification and identification purposes. Efforts included using the ability of hAAG to complement glycosylase deficient alkA tagA E. coli double mutant strains to assess and to compare the ability of the two isoforms of hAAG and to determine if the histidine tag affected function. The ability of hAAG to rescue cells from exposure to a variety of DNA damaging agents was studied by inducing each isoform and analyzing the sensitivity of the cells to increased doses of DNA damaging agents. Both hAAG-1 and hAAG-2 were able to restore the wild type resistance of the alkA and tag genes when exposed to the alkylating agents MNNG and MMS. In order to study the ability of hAAG to repair alkyl lesions larger than methyl groups, it was necessary to inactivate the uvrA dependent nucleotide excision repair gene. In E. coli, methyl lesions are repaired primarily by glycosylases, while nucleotide excision repairs bulky lesions. Thus, in order to detect hAAG activity on these types of damage, it was necessary to inactivate the bacterial uvrA gene. Each isoform of hAAG was transformed into a triple mutant strain deficient in alkA tagA and uvrA, then exposed to CNU, BCNU, and Mitomycin C. Each of these DNA damaging agent caused increased toxicity in the presence of hAAG. hAAG-1 expressed in the alkA tag double mutant strain was exposed to Mitomycin C and showed greater resistance than hAAG-1 expressed in the alkA tag uvrA triple mutant. In fact, in the nucleotide excision proficient strain, expression increased Mitomycin C resistance above that seen in the control, suggesting that glycosylase activity may function in a partnership with nucleotide excision repair and that the two isoforms of hAAG have subtle differences. An ompT protease knockout host strain was constructed using P1-transduction and used to examine protein products. hAAG-2 was inserted into the pBlueScript plasmid so that the gene could be regulated by the T7 promoter for use beyond the scope of this thesis. A protein synthesis time course assay was conducted to determine the expression levels of hAAG-1 and hAAG-2 when induced by IPTG. Immunoblot detection of the histidine tag was used to measure expression levels of each isoform.