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Dissertations / Theses on the topic 'Biochemical interactions'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

Fergus, Andrew Paul. "The biochemical interactions of the chloroquines." Thesis, Northumbria University, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358281.

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2

Ljunggren, Joel. "Biochemical Interactions of Some Saproxylic Fungi." Licentiate thesis, Mittuniversitetet, Avdelningen för naturvetenskap, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:miun:diva-25068.

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Interactions are all around us, and as humans we may use words and gestures to communicate our intentions. At the micro level of fungi, communications are replaced by chemical signals and structure. These interactions fall into three distinctive categories: synergistic, where organisms help each other, as is the case with ectomycorrhizal fungi and tree roots, deadlock, or combat, where organisms fight for or defend a resource. When it comes to fungi-tree interactions, the fungi group of basidiomycetes fall into the latter category. At the onset of fungal infection, a living tree defends itself by producing resinous substances such as terpenes. These compounds are frequently found in hydrodistilled turpentine, which makes turpentine a prime source of antifungal compounds. A D-optimal design of fractionated turpentine together with gas chromatography (GC) coupled to a mass spectrometer was employed to find the most biologically active constituent of turpentine. Growth rate of Coniophora puteana was used to assess the efficacy of the mixed fractions. The partial least squares projection model had an excellent predictive power (R2 = 0.988, Q2 = 0.825) and validity. A putative sesquiterpene was identified as the most active compound for inhibiting fungal growth. The model was corroborated by an external validation assay employing preparative GC. After the death of a tree, fungi are no longer hindered by secondary metabolites from the tree. Instead, other interspecies interactions and intraspecies interactions, such as fungi-fungi interactions, occur. We found that when the white-rot fungus Heterobasidion parviporum and brown-rot fungus Gloeophyllum sepiarium interact with each other, amino acids are used to a higher extent. Amino acids may be used to produce antifungal compounds to hinder the other species from growing. Lysine in particular was utilized to a greater extent during interaction. Glutamine was the only amino acid that increased in concentration. Glutamine might be exuded or converted by enzymes from already existing glutamic acid. Dry weights suggest that the fungi were in a deadlock and that nutrient limitation might be a determining factor. It seemed that H. parviporum was favoured by a decrease in pH while the opposite pattern may be true for G. sepiarium.
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3

Wang, Shao-Fang. "Biochemical and biophysical studies of MDM2-ligand interactions." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/9527.

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MDM2, murine double minute 2, is a RING type-E3 ligase protein and also an oncogene. MDM2 plays a critical role in determining the steady levels and activity of p53 in cells using two mechanisms. The N-terminal domain of MDM2 binds to the transactivation domain of p53 and inhibits its transcriptional activity. The RING domain of MDM2 plays a role in the ubiquitination (and degradation) of p53. Several proteins are responsible for the ubiquitination mechanism including the ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). Since the E2-E3 interaction is essential for ubiquitination, the protein-protein recognition site is a potential drug target. Two different MDM2 RING constructs were expressed and purified: MDM2RING (residues 386-491) and MDM2RING△C (residues 386-478). Both constructs were characterised using dynamic light scattering, size exclusion chromatography, mass spectrometry, NMR and electron microscopy. E3 ligase activity in vitro was also studied. Taken together these results showed that the MDM2RING construct formed a concentration-dependent oligomeric structure. In contrast, the MDM2RING△C construct formed a dimer at all concentrations. Both MDM2RING and MDM2RING △ C retain E3 ligase activity. However, the MDM2RING△C construct is less active. Full length E2 enzyme UbcH5a was also purified. Various biophysical techniques were used to study its interaction with MDM2 as well as with potential small molecule inhibitors as in principle, small molecules which disrupt the interaction between MDM2 and UbcH5a, could prevent/promote ubiquitination of p53. The dimerisation of MDM2 is important for its E3 activity and the C8-binding site potentially provides a second druggable site. In this work, peptide 9, which has the same sequence as the C-terminus of MDMX (an MDM2 homologue) was found to inhibit MDM2 E3 activity. Various biological techniques including NMR, fluorescence anisotropy, and electrospray mass spectrometry were used to investigate the interaction between two inhibitory peptides and MDM2. A major part of project involved virtual screening (VS) to search for small molecules which can affect MDM2-dependent ubiquitination. Three potential targets were considered: (1) the C8-binding site of MDM2; (2) the UbcH5a-binding site of MDM2; and (3) the MDM2-binding site of UbcH5a. Several small molecules were identified using our virtual screening database-mining and docking programs that were shown to affect MDM2-dependent ubiquitination of p53. In terms of understanding the complex biochemical mechanism of MDM2 this work provides two interesting and functionally relevant observations: (i) the MDM2 RING△C construct is a dimer as this would not be expected form the existing studies, and has less E3 ligase activity than MDM2RING; (ii) small molecules that bind MDM2 on the E2 binding site enhanced E3 ligase activity. One model to explain these observations is that binding of small molecule activators family to the RING induces a change in the conformation of the Cterminal tail residues which may enhance E2 binding.
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4

Peters, Daniel. "Structural and biochemical investigation of protein-RNA interactions." Thesis, University of York, 2014. http://etheses.whiterose.ac.uk/6784/.

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Non-coding RNAs (ncRNAs) are nucleic acids that do not code for protein. Rather, they have evolved highly specialised secondary structures and catalytic mechanisms that place them at the heart of regulating gene expression. The function of ncRNAs is often mediated or dependent on their interactions with RNA binding proteins. The study of both the structure and function of these proteins is crucial for understanding the biological role of the protein-RNA complexes. In this thesis, the structure and function of two RNA binding proteins: Lin28 and dihydrouridine synthase C (DusC) were investigated using X-ray crystallography and biophysical techniques. In both systems, the specific recognition of target molecules is important for function. The aim of the study was therefore to use structural and functional data to elucidate the molecular basis of these protein-RNA interactions. There are three main findings: (1) specific recognition of microRNAs by Lin28 is dependent on the interaction of the Zinc Knuckle domain of the protein with a 3’ GGAG motif; (2) non-specific, electrostatic interactions between the cold-shock domain of Lin28 and RNA suggest a transcriptome scanning mechanism for recognising Lin28 targets; and (3) modification of specific nucleotide positions within tRNA by DusC is dependent on the orientation in which the tRNA is bound, which is determined by minor changes in the protein structure. These findings have helped to elucidate the mechanisms, and hence biological functions, of these RNA binding proteins. Both proteins have been previously associated with cancer. Through greater understanding of the molecular basis of these protein-RNA interactions, the production of novel therapeutic agents can be informed, which can help to combat disease. This data will therefore aid future efforts to treat and prevent the cancers caused by the aberrant actions of these RNA binding proteins.
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5

Dehner, Alexander. "Protein interactions studied by biochemical and NMR spectroscopic methods." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972765476.

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6

Que, Jaimmie. "Biochemical protein interactions of Gliotactin at the tricellular junction." Thesis, University of British Columbia, 2006. http://hdl.handle.net/2429/32230.

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The septate junction is an occluding junction in invertebrates, similar in function to tight junctions, playing a role in epithelial barriers, and in apical/basal polarity. Septate junction interactions are still being characterized as new component proteins are discovered. One septate junction protein, Gliotactin, was discovered in Drosophila to correlate with the mislocalization of characteristic septate junction proteins in a Gliotactin null animal. However, Gliotactin is the only component found exclusively at the level of septate junctions at tricellular junctions in epithelia. The tricellular junctions are the structure at the convergence of three cells and a potential organizing factor of the septate junction. This led to the question, what is Gliotactin's role in the organization of the tricellular and septate junctions? To study this, we looked at Gliotactin interactors, and attempted to elucidate a model of tricellular and septate junction protein interactions. Previous attempts at finding Gliotactin interactors were made using in vitro systems or by using transgenic animals using an over-expressed epitope-tagged Gliotactin, that showed that Gliotactin interacts with known septate junction proteins in a calcium dependent manner. This thesis aims to further explore Gliotactin interactions with the hypothesis that native Gliotactin in Drosophila interacts in a calcium dependant manner with septate junction proteins, Discs Large, and Neurexin IV. Using co-immunoprecipitation and GST pulldowns, on native Gliotactin protein in Drosophila, I have shown that Gliotactin does not interact with Neurexin IV but does interact with Discs Large in a calcium-dependent manner. This is significant in that, to date, there has been no known interactor of Discs Large or of native Gliotactin at the tricellular junction. I also present data on unidentified potential Gliotactin interactors seen in a GST pulldown assay. The data presented in this thesis has contributed to a new working model of the tricellular junction and the role of Gliotactin.
Science, Faculty of
Zoology, Department of
Graduate
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7

Torvinen, Maria. "Adenosine receptor/dopamine receptor interactions : molecular and biochemical aspects /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-298-1/.

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8

Chandrasekaran, Aarthi. "Glycans in host-pathogen interactions : an integrated biochemical investigation." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/61219.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2009.
Cataloged from PDF version of thesis.
Includes bibliographical references.
The epithelial cell-extracellular matrix interface primarily comprises of complex glycans and glycoconjugates. The widespread distribution of these glycans on the epithelial cell surface makes them ideal targets for interaction with microbial pathogens. In this thesis, a framework of integrated approaches was developed to characterize the structure-function relationships of host cell surface glycans and examine their role in mediating hostpathogen interactions. The first part of the thesis involves a study of the effect of secreted bacterial sphingomyelinases on the epithelial cell surface proteoglycan (a large glycan- protein conjugate), syndecan-1 and on epithelial tight junctions. The findings presented in this work suggest mechanisms by which sphingomyelinases could enhance bacterial virulence by regulating epithelial cell function. The second part of the thesis investigates the glycan binding requirements that govern the human adaptation and transmission of influenza A viruses by characterizing the molecular interactions between sialylated glycan-receptors and viral hemagglutinin (HA). The study puts forth the concept that the topology or shape (going beyond the chemical c2-3 versus a2-6 sialic acid linkage) adopted by the sialylated glycans is the critical determinant for efficient human adaptation of these viruses. In conclusion, this thesis provides insights into the molecular mechanisms of host-pathogen interactions and enables development of improved strategies for targeted antimicrobial therapies.
by Aarthi Chandrasekaran.
Ph.D.
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9

Lo, Thomas Tzan Hong. "Structural and biochemical analyses of BRCA2 and RAD51 interactions." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616022.

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10

Vo, Uybach. "Biochemical and biophysical studies to characterise the Ras:Sos:nucleotide interactions." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/biochemical-and-biophysical-studies-to-characterise-the-rassosnucleotide-interactions(691827f9-00d8-445a-ab3f-e5b236f918ba).html.

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Ras proteins are mutated in 30% of all human tumours contributing to several malignant phenotypes including abnormal cell growth, proliferation and apoptosis. The activity of Ras is controlled by the inter-conversion between GTP- and GDP- bound forms. This conversion is partly regulated by the binding of protein Son of Sevenless (Sos), a guanine nucleotide exchange factor. The mechanism of Ras activation via its interactions with Sos remains unclear making it challenging as an effective drug target. The aim of this work is to use Nuclear Magnetic Resonance (NMR) spectroscopy and other biophysical methods to understand the molecular activation of Ras via its interactions with Sos. In this thesis, the backbone and Cβ, as well as the partial side-chain NMR assignment for human K-Ras•GDP were completed at pH 7.4. We also revealed significant chemical shift differences between apo, GDP and GTPϒS-bound H-Ras states from the TROSY spectra. In addition, the monitoring of shift perturbations for H-Ras reveals several residues that appear to be central in Sos binding and may provide a starting point in the search for possible inhibition sites for future drug design. To gain a further understanding into the binding events of the Ras:Sos complex, we have expressed and purified the Sos construct containing the REM and Cdc25 domains (SosCat) for titration studies. Here, we have implemented a relatively novel approach to study large complexes (Stoffregen et al. 2012), by selectively labelling the [13C-] Met and Ile methyl groups of SosCat. This approach has provided an assignment for eight reporter signals. In addition, monitoring the shift perturbations of Met [13C-] methyls in the NMR spectra allowed us to examine individual residues at the two Ras binding sites (allosteric and catalytic sites) of SosCat. Disruption of H-Ras•GTPγS binding at the allosteric site (via SosCat W729E mutant) significantly weakens the interactions of Ras at the catalytic site. The data suggests a positive co-operative binding mechanism between the allosteric and catalytic sites, which is consistent with the allosteric feedback model. We have also measured the binding affinities of SosCat (by NMR spectroscopy and fluorescence) with wild type and Ras mutants using different GTP analogues. Our 15N-relaxation data of the H-Ras•GTPϒS:SosCat complex reveal dynamical changes in several regions of Ras other than the P-loop, switch I and II regions. In addition, the backbone NMR relaxation studies revealed that a complex between H-Ras•GTPϒS and SosCat proteins is dynamic and transiently formed. The reported work could be a significant step towards understanding the activation of Ras via its interactions with Sos; and in time the data may influence new anti-cancer treatments.
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11

Wang, Fei. "Biochemical Studies Of Interactions Between Prion Protein And Lipids." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1227725062.

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12

Steele, Bridgett L. Thompson Nancy L. "Total internal reflection fluorescence microscopy for characterizing biochemical interactions." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2725.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2009.
Title from electronic title page (viewed Mar. 10, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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13

Cridland, Peter James. "An investigation of the protein-protein interactions of human DNA topoisomerase II." Thesis, University of Newcastle Upon Tyne, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364796.

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14

Ludwig, Cornelia. "Structural and biochemical studies of PCNA and its molecular interactions." Thesis, University of Edinburgh, 2008. http://hdl.handle.net/1842/12483.

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Proliferating cell nuclear antigen (PCNA) plays a key role in DNA replication and repair. In this thesis I have determined the crystal structure of S. pombe PCNA on its own and in complex with a peptide derived from the natural inhibitor of PCNA in humans, p21. Using the p21 peptide as a template, chemical libraries were screened for small drug-like molecules that are able to mimic the protein-protein interaction between human PCNA and p21 and tested for binding using various fluorescence-based methods. Binding of selected compounds could not be observed, however, which may have been due to poor solubility of the compounds as well as a lack of assays sensitive enough to pick up on ligands with low affinity. Not all direct PCNA binding proteins bind to the above mentioned pocket and PCNA:protein co-crystal structures of these examples without the PIP-box motif are not available so far, so information on the mode of binding in those cases is not accessible yet. Therefore, I tried to narrow down and characterize the PCNA binding site of Gadd45. This protein does not contain a PIP-motif, but previously was shown using yeast-two hybrid technology to bind directly to PCNA via its C-terminus. In vitro binding of the two full-length proteins could not be confirmed, due to the inherent instability of Gadd45, which also has been reported by others. GST-tagged truncations of the C-terminus of Gadd45 were expressed and purified and binding to PCNA was studied using SPR. These results are at odds with the published binding data and suggest that either the interaction between PCNA and Gadd45 is not direct and needs to mediated by a third factor or Gadd45 binds to PCNA via a different part than the C-termination (as also suggested in the literature).
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15

El-Shetehy, Mohamed H. "Molecular and Biochemical Signaling Underlying Arabidopsis-Bacterial/Virus/Fungal Interactions." UKnowledge, 2016. http://uknowledge.uky.edu/plantpath_etds/19.

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Systemic acquired resistance (SAR) is a form of inducible defense response triggered upon localized infection that confers broad-spectrum disease resistance against secondary infections. Several factors are known to regulate SAR and these include phenolic phytohormone salicylic acid (SA), phosphorylated sugar glycerol-3-phosphate (G3P), and dicarboxylic acid azelaic acid (AzA). This study evaluated a role for free radicals nitric oxide (NO) and reactive oxygen species (ROS) in SAR. Normal accumulation of both NO and ROS was required for normal SAR and mutations preventing NO/ROS accumulation and/or biosynthesis compromised SAR. A role for NO and ROS was further established using pharmacological approaches. Notably, both NO and ROS conferred SAR in a concentration dependent manner. This was further established using genetic mutants that accumulated high levels of NO. NO/ROS acted upstream of G3P and in parallel to SA. Collectively, these results suggest that NO and ROS are essential components of the SAR pathway.
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16

Hyndman, Matthew Eric. "Biochemical and functional interactions of methyltetrahydrofolate and homocysteine in vascular disease." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/NQ64814.pdf.

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17

Dornevil, Kednerlin. "Interactions of Metals and Radicals: A Biochemical Perspective in Tryptophan Dioxygenase." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/chemistry_theses/43.

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An intriguing mystery about tryptophan 2, 3-dioxygenase is its hydrogen peroxide-triggered enzyme reactivation from the resting ferric oxidation state to the catalytically active ferrous form. In this study, we found that such an odd Fe(III) reduction by an oxidant depends on the presence of L-Trp, which ultimately serves as the reductant for the enzyme. In the peroxide reaction with tryptophan 2, 3-dioxygenase, a previously unknown catalase-like activity was detected. A ferryl species (δ = 0.055 mm/s and ΔEQ = 1.755 mm/s) and a protein-based free radical (g = 2.0028 and 1.72 millitesla linewidth) were characterized by Mössbauer and EPR spectroscopy, respectively. This is the first compound ES-type of ferryl intermediate from a heme-based dioxygenase characterized by EPR and Mössbauer spectroscopy. Density functional theory calculations revealed the contribution of secondary ligand sphere to the spectroscopic properties of the ferryl species. A Trp-Trp dimer and a monooxygenated L-Trp were both observed as the enzyme reactivation by-products by mass spectrometry. Together, these results lead to the unraveling of an over 60-year old mystery of peroxide reactivation mechanism.
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18

Klemm, Juli Dawn. "Structural and biochemical studies of Oct-1 POU domain-DNA interactions." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32667.

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19

Breitman, Maryana I. "Biochemical characterization of COPI and its interactions with ARF1 G-protein /." Access full-text from WCMC, 2007. http://proquest.umi.com/pqdweb?did=1481657561&sid=15&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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20

Parrott, David L. Jr. "Physiological and Biochemical Aspects of Agrobacterium-Wheat (Triticum Aestivum L.) Interactions." DigitalCommons@USU, 2003. https://digitalcommons.usu.edu/etd/1346.

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Agrobacterium tumefaciens and A. rhizogenes are the causal agents of gall or hairy root disease, but normally the bacteria do not cause disease in wheat. However, both bacteria grew without inhibition when exposed to intact or wounded wheat roots or embryos, and they colonized wheat root surfaces to levels similar to dicotyledonous plants. A. tumefaciens and A. rhizogenes induced 23% cell death after a 1-h exposure to wheat embryo cells grown in 7.4 mM O2, while the extent of cell death at 2.1 mM 02 was 8%. Contact with A. tumefaciens or A. rhizogenes caused cultured wheat embryo and root cells to rapidly produce H202, which decreased when embryos and roots were cultured at 2.1 mM O2. Browning and autofluorescence, and an increase in ferulic acid in cell walls, were observed in wheat embryo and root epidermal cells exposed to Agrobacterium, but . neither lignin nor callose was detected. Agrobacterium appeared to induce resistance-like responses in wheat that may limit transformation efficiency. The inability to regenerate wheat plants using tissue culture has been a limitation to high efficiency transformation. Regeneration via somatic embryogenesis was improved significantly by simulating the in ovulo environment to which the immature wheat embryos are exposed. Triticum embryo culture medium (TEC) improved callus formation, somatic embryo formation, and regeneration from somatic embryos while reducing precocious germination when compared to growth on Murashige and Skoog medium. Regeneration frequencies were improved when embryos were cultured at the O2 concentration found in the wheat ovule (2.1 mM O2) rather than atmospheric 02concentration (7.4 mM O2). Agrobacterium-mediated transformation of wheat was limited by tissue necrosis following co-cultivation, and by poor plant regeneration. Reduction of necrosis and increased plant regeneration were accomplished by amending the culture medium with antioxidant compounds and by reducing the O2 tension in which the wheat embryos were cu1tured. Twelve days past anthesis (DPA), wheat embryos were co-cultivated with Agrobacterium tumefaciens strains WAg 11 or EHA 101, incubated on TEC medium containing antioxidant compounds (catalase, cysteine and ascorbic acid), and cultured at 2.1 mM O2 concentrations. Transformation was documented in 6.0% ofregeneratedA. tumefaciens WAg 11 exposed wheat plants using the firefly luciferase (luc) reporter system.
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21

Tomlinson, Emma Elizabeth. "Characterization and biochemical interactions of the human C-terminal binding protein, CtBP1." Thesis, University of Birmingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.409071.

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22

Mishra, Vidhi. "Structural and Biochemical Studies of Protein-Ligand Interactions: Insights for Drug Development." University of Toledo / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1384637704.

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23

Lin, Ralph Shih-Ying 1969. "Biochemical characterization of zinc-dependent interactions between p̳56l̳c̳k̳ and CD4, and DTT-sensitive interactions between TGF-beta receptor subunits." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/85245.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Biology, 1999.
Double underscored "p" is subscript and double underscored "lck" is superscript in title on t.p.
Includes bibliographical references.
by Ralph Shih-Ying Lin.
Ph.D.
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24

Narayanan, Saravanakumar. "Biochemical and NMR characterization of aggregating proteins and their interactions with molecular charperones." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972765158.

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25

Nouri, Kazem [Verfasser]. "Biochemical Characterization of RHO GTPases-IQGAPs and NPM1-US11/Rev interactions / Kazem Nouri." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2017. http://d-nb.info/1139491148/34.

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26

Sanders, Philip Gordon Thomas. "A biochemical analysis of regulatory interactions between the Notch and Wingless signalling pathways." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614348.

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27

Rabu, Amir. "Biochemical and biophysical characterisation of heat shock protein 90 and its domain interactions." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/11286.

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This thesis describes the study of the Hsp90 proteins from Homo sapiens (Hsp90α) and Caenorhabditis elegans. The attempt to crystallise the C-terminal proteins is also described. The overall goal of the project was to biochemically and biophysically characterise various Hsp90 constructs and use this information to elucidate the biological role of this important family of proteins. The C-terminal domain of human Hsp90α. The work involved over-expression, purification and characterisation of the C-terminus of human Hsp90 α protein. The over-expression and purification led to the production of two reproducibly pure C-terminal human Hsp90 α protein constructs. The characterisation of these proteins focused on the interaction of the C-terminus with the immunophilin Cyp40 and also with ligands such as ATP and novobiocin. C. elegans Hsp90. The work involved the cloning, over-expression and purification of the N and C-terminus of C. elegans Hsp90.  The cloning of genes for the N and C-termini was successful. Purification of the proteins only led to the production of one C-terminal protein but no purified N-terminal protein could be obtained. Similar characterisation studies were carried out to the C-terminus of C. elegans Hsp90. As for the human C-terminal protein, the C. elegans C-terminal protein was found to bind to Cyp40 with a dissociation constant in the micromolar concentration range. The protein also binds to ATP and novobiocin with an affinity very similar to that of the C-terminal proteins of human Hsp90α. The C-terminus of C. elegans also exhibits ATPase activity but the activity was ten-fold lower than that of the C-terminal of human Hsp90α. The work presented in this thesis provides conclusive evidence of the existence of an ATP binding site in the C-terminal domains of the Hsp90 class of proteins. The biological relevance of this finding is also discussed.
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28

Mao, Chunhong 1965. "A genetic and biochemical analysis of cooperative protein-DNA interactions in bacteriophage HK022." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/289256.

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Cooperative binding of specific DNA-binding proteins to DNA plays a crucial role in gene regulation. To understand the molecular basis of cooperative protein-DNA interactions and their role in gene regulation, the lambdoid phage HK022 was used as a model system to study cooperative binding of HK022 CI repressor to DNA. HK022 CI repressor binds to two adjacent operators with a high degree of cooperativity. In this work, a combination of genetics and biochemistry was used to study cooperative binding of HK022 CI regressor by analyzing the effects of changing either the DNA binding sites or the protein on cooperativity. In the first part of this dissertation, the effect of changing the spacing between the two adjacent operators (O(R)1 and O(R)2) on cooperativity and on the conformation of the complex was examined. The highest cooperativity was observed with wild type spacing of 9 bp, implying that the wild type spacing confers the most favorable cooperative interaction. Considerable cooperativity was retained for most spacing variants, but was abolished when the operators lay on opposite faces of the DNA helix. Almost all spacing variants conferred changes in the conformation of the DNA-protein complex. The major conclusions from this study are that: (1) the protein-DNA complex is flexible enough to allow some cooperativity in most spacing variants; (2) a protein-DNA complex involving the same specific binding sites and the same protein molecules can adopt many different conformations, depending on the spacing between the binding sites. In the second part of this investigation, a genetic screen was developed to isolate HK022 repressor mutants which are defective in cooperative binding to adjacent operators, but are normal in binding to a single operator, so as to identify the amino acids in CI responsible for the cooperative interactions. Five mutants (IL153, RS225, RG225, FS233, and +QK) were isolated from this screen. The cooperativity parameter o for these mutant proteins (except IL153) was determined by in vitro DNase I footprinting assay. The results indicated that +QK was a relatively strong mutant, with a reduction of about 20 fold in o; the others were weaker, reducing o about 4 to 5 fold. Two double mutant combinations (+QK-RS225 and +QK-RG225) conferred greater cooperativity defects than the single mutants. One double mutant (RS225-IL153) restored nearly wild type cooperativity indicating that those two single mutations suppress each other perhaps by a lock-and-key mechanism. The cooperativity mutants were used to demonstrate the importance of cooperativity for HK022 phage immunity and the lysis-lysogeny decision.
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Ibrahim, Khalid Subhi. "Biochemical interactions between the gut microbiome and host in obesity/type II diabetes." Thesis, Glasgow Caledonian University, 2017. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.743906.

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Li, Meng, and 李猛. "Diversity of anammox bacteria in coastal and ocean sediments and interactions among ammonia oxidizers and nitrite reducers." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46924681.

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31

Satia, Karishma. "Biochemical, biophysical and interaction studies of the stress responsive protein hSTRAP." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/biochemical-biophysical-and-interaction-studies-of-the-stress-responsive-protein-hstrap(e0e00e4b-de43-4b65-b680-ae8a7126f02d).html.

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STRAP (Stress responsive activator of p300) is a 440 amino acid protein, predicted to have 6 TPR (Tetra-Tri-Co-Peptide Repeats) motifs, known to mediate protein-protein interactions. STRAP has been shown to form a complex with proteins p300 and JMY (Junctional Mediatory Protein), and is implicated in the DNA damage, heat shock response pathway, regulation of the Glucocorticoid receptor and in the function of p53.The aims of this project were to clone, express and purify full length and truncated human STRAP (hSTRAP) variants in high quantities. Full length and shorter hSTRAP fragments, which contain different combinations of the predicted TPR motifs and hence cover different regions, would be then structurally characterised by various structural and biophysical experiments. Another important aim was to identify interacting partners of hSTRAP in breast cancer and to map the position of their interaction sites to different parts of the protein. To this direction GST- and His- tagged full length hSTRAP, as well as His- tagged truncated hSTRAP protein variants have been successfully cloned, expressed and purified. Independent and reproducible biochemical pull-down assays have been carried out in MCF7 breast cancer cells, followed by mass spectrometry-based proteomics analysis which identified 25 hSTRAP-interacting partners from various signaling pathways such as regulation of the actin cytoskeleton and translation. In addition, crystallization trials were carried out using pure His-hSTRAP(1-440) protein, which were unfortunately un-successful. Various hSTRAP protein variants have been characterized by CD, showing that hSTRAP(1-150), His-hSTRAP(1-440), hSTRAP(1-219), hSTRAP(151-284) and hSTRAP(285-440) comprise of alpha and β structures, but the hSTRAP protein variants show no clear cooperative unfolding transitions, suggestive of molten globule states. NMR on hSTRAP(1-219), hSTRAP(1-150) and hSTRAP(151-284) have shown these proteins are not folded at a tertiary structure level. We conclude that a protocol has been established to clone, express and purify various hSTRAP variants and the thermal and secondary structure characteristics of each have been determined, although the 3D structure could not be solved. Pull-down assays followed by proteomic analysis have shown that hSTRAP is implicated in many aspects of cellular regulation.
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Boëchat, Iola Gonçalves. "Biochemical composition of protists." Doctoral thesis, Humboldt-Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, 2005. http://dx.doi.org/10.18452/15184.

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Trotz der Schlüsselstellung heterotropher Protisten als Bindeglied zwischen dem mikrobiellen und dem klassischen Nahrungsnetz ist noch wenig über ihre biochemische Zusammensetzung und ihren Nährwert bekannt. In der vorliegenden Doktorarbeit wurde untersucht ob die biochemische Zusammensetzung von Protisten (1) von deren Nahrungsgrundlage (Alge oder Bakterien) und Ernährungsweise (Autotrophie, Mixotrophie oder Heterotrophie) abhängt und (2) ihre Nahrungsqualität für räuberisches Rotatorien (Keratella quadrata) bedingt. Die Fettsäure-, Sterol- und Aminosäurezusammensetzung vier heterotropher Protisten spiegelte generell die ihrer Nahrung wider. Es trat jedoch eine Akkumulation dieser biochemischen Substanzen in den Protisten auf. Auch die Ernährungsweise eines Flagellaten (Ochromonas sp.) beeinflusste stark dessen biochemische Zusammensetzung, insbesondere die Konzentrationen an mehrfach ungesättigten Fettsäuren (PUFAs). Bei der Untersuchung des Nährwertes vier heterotropher Protisten für K. quadrata wurden signifikante Korrelationen zwischen verschiedenen PUFAs, drei Sterolen und einer Aminosäure (Leucin) der Protisten und der Eiproduktion der Rotatorien festgestellt. Auch die experimentelle Supplementierung eines Flagellaten mit einer PUFA (Docosahexaensäure, DHA) erhöhte seinen Nährwert für die Rotatorien signifikant. Die Ergebnisse verdeutlichen die Fähigkeit heterotropher Protisten, die biochemische Zusammensetzung organischer Materie schon auf einer unteren Ebene des aquatischen Nahrungsnetzes zu verändern, nämlich beim Übergang zwischen Algen/Bakterien und dem Mesozooplankton. Hier können biochemische Änderungen weitreichende Folgen für den Stoff- und Energiefluß des gesamten Nahrungsnetzes nach sich ziehen.
Heterotrophic protists are an important link between the microbial and the classical food web. However, little is known about their biochemical composition and nutritional quality as prey. In this thesis, I analysed (1) whether the biochemical composition of the protists depends on their dietary resources (bacterial or algal food) or trophic mode (autotrophy, mixotrophy or heterotrophy), and (2) whether the biochemical composition of protists determines their nutritional quality as prey for a rotifer species (Keratella quadrata). The fatty acid, sterol, and amino acid composition of four heterotrophic protists generally resembled the dietary composition, but the protists accumulated these compounds. Moreover, the trophic mode strongly affected the composition of a flagellate (Ochromonas sp.), especially that of polyunsaturated fatty acids (PUFAs). When investigating the nutritional quality of four protist species for K. quadrata, several PUFAs, three sterols (desmosterol, ergosterol, stigmastanol), and one amino acid (leucine) of the protists were significantly correlated with the rotifer’s egg production. Moreover, the nutritional quality of a heterotrophic flagellate for the rotifer was significantly enhanced by artificially supplementing the flagellate with a PUFA (docosahexaenoic acid, DHA). The thesis highlights the ability of heterotrophic protists to modify the biochemical composition of organic matter at an early stage in aquatic food webs, i.e. at the interface between algae/bacteria and mesozooplankton. Biochemical modifications at this stage may profoundly affect matter and energy transfer through the entire food web.
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Watson, Joanna. "Structural and biochemical insight into the interactions of Cdc42 with TOCA1 and N-WASP." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/268520.

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Cdc42 is a member of the Rho family of small GTPases, which, together with its homologues RhoA and Rac1, controls a multitude of cellular functions via the actin cytoskeleton. Cdc42 exerts its effects on the cytoskeleton via effector proteins of the Wiskott-Aldrich Syndrome (WASP) family and the Transducer of Cdc42-dependent Actin assembly (TOCA) family. The WASP family and their activation by Cdc42 have been thoroughly studied in vitro and are well understood. Conversely, understanding of the TOCA family remains limited by a lack of biochemical, biophysical and structural insight. An investigation of the TOCA1-Cdc42 interaction is described here, revealing a relatively low affinity interaction with a dissociation constant in the micromolar range. This is 10-100x weaker than other Rho-effector interactions and suggests that TOCA1 must first be co-localised with Cdc42 to achieve stable binding in vivo. The solution NMR structure of the Cdc42 binding HR1 domain of TOCA1 provides the first structural data on this protein and reveals some interesting structural features that may relate to binding affinity and specificity. A structural model of the Cdc42-HR1 complex provides further insight into differential specificities and affinities of GTPase-effector interactions. NMR and actin polymerisation assays provide insight into the pathway of Cdc42/TOCA1/WASP-dependent actin assembly, suggesting unidirectional displacement of TOCA1 by N-WASP. A comparison of the Cdc42- TOCA1 model with an NMR structure of Cdc42 in complex with the GTPase binding domain of WASP reveals a possible mechanism by which an ‘effector handover’ from TOCA1 to N-WASP could take place. Small GTPases such as Cdc42 are lipid modified and membrane anchored via their C- termini in vivo, so in vitro studies using truncated, unmodified GTPases are limited in their biological interpretation. This project also aimed to develop methods to study full length and membrane-anchored GTPases in vitro. Lipid modified protein was produced, which showed a weak affinity for liposomes, and so structural studies of membrane anchored protein are within reach. Further method development is now required to achieve stable membrane anchoring of lipid modified GTPases for detailed NMR studies.
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Fraundorfer, Paul F. "Functional and biochemical characterization of trimetoquinol (TMQ) analog interactions with [beta]-adrenergic receptor subtypes /." The Ohio State University, 1993. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487843314696234.

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35

Triantafilou, Kathy. "Homotypic and heterotypic interactions of HLA-DR, CD74 and CD14 molecules : biochemical and fluorescence imaging analysis." Thesis, University of Essex, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285855.

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36

Chiu, Chi-ngong Philip, and 趙志昂. "An investigation into the biochemical and biological properties of zona-binding inhibitory factor 1 from human follicular fluid." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B31245249.

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Tsaltas, Dimitrios. "Biochemical, structural and molecular characterization of resistant interactions between Pseudomonas syringa pv. phaseolicola and Phaseolus vulgaris." Thesis, Imperial College London, 2003. http://hdl.handle.net/10044/1/7287.

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Bansal, Prashali [Verfasser], and Fulvia [Akademischer Betreuer] Bono. "Biochemical and mass spectrometric analysis of interactions in Drosophila mRNA localization / Prashali Bansal ; Betreuer: Fulvia Bono." Tübingen : Universitätsbibliothek Tübingen, 2019. http://d-nb.info/1180382358/34.

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Saleh, Sherif Aly Abdelgawad. "Genetic and biochemical interactions of the S7 ATPase of the 26S proteasome and the KDEL receptor." Thesis, University of Nottingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.250605.

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40

Branfield, Lauren Elizabeth. "Structural and biochemical analysis of protein/RNA interactions during the initiation of dengue virus genome replication." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/21365/.

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41

Bastidas, Oscar H. "Computational All Atom Energy Density Landscape Mappings of Intra-protein Interactions from Static and Dynamic Ensemble Structure Data." VCU Scholars Compass, 2017. http://scholarscompass.vcu.edu/etd/4955.

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Understanding the energetic and dynamic behavior of natural protein fluctuations is critical to elucidating important information associated with a multitude of protein functions including signaling processes, enzyme behavior, aggregation pathways etc... This information is also critically important in the development of novel and effective strategies aimed at target proteins associated with pathologies and disease. In order to obtain such useful information, tools and techniques are lacking that: 1) permit the efficient quantitative analysis of fluctuation behavior of existing protein structure ensembles and 2) permit computationally generated natural fluctuation states of proteins at relatively large timescales demanded by the need for biologically relevant results. This thesis presents such methods as well as the results of their application to a case study of Aβ40 and pathogenic Aβ42 where we identify key differences in energy interactions between those two isoforms. Additionally, our detailed atom-level analysis, was able to identify very minute differences in Ramachandran angles between the two strains as the cause for these interaction energy differences. We also demonstrate the efficacy of our implicit solvent algorithm in recovering independently, experimentally identified domain motion over a variety of protein systems. Such a system that is medically significant is the HIV-1 protease for which we identified significant motion of a flap domain known to be pharmaceutically important to the protease’s active site in drug targeting strategies. Lastly, we employ the insights thus acquired from the Aβ40/42 case study to see if Aβ42 aggregation inhibitors can be rationally developed and then tested in vitro for their efficacy. Results were very promising with Aβ42 aggregate sizes being significantly reduced by statistically significant margins by the inhibitor compounds. Due to these encouraging results, we have consequently obtained a provisional patent application for our inhibitors.
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George, Derick G. "Molecular and Biochemical interactions between the Noctuid Stem Borer Busseola fusca and its Host Plant Zea mays." Thesis, University of Newcastle Upon Tyne, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515089.

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43

Mee, Christopher James. "Biochemical and thermodynamic analysis of the interactions of GRP78 with its substrate peptides and nucletide exchange factors." Thesis, University of Newcastle Upon Tyne, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.519641.

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44

Seid, Charlotte A. "Genetic and biochemical interactions between the DNA replication initiator and a chromosome architecture protein in Bacillus subtilis." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/92594.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2014.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 204-228).
I described the co-association, in vitro interaction, and epistatic relationship between the DNA replication initiator DnaA and the nucleoid-associated protein Rok in Bacillus subtilis. Using ChIP-seq, I characterized the genome-wide association of DnaA and its regulator YabA. I found that DnaA and YabA associated with over 30 chromosomal regions that were bound by Rok, and association of DnaA and YabA with these regions was dependent on Rok. The DNA-binding domain of DnaA was dispensable for association of DnaA with these chromosomal regions. This indirect Rok-dependent association contrasted with the canonical sequence-specific binding of DnaA to eight chromosomal regions containing clusters of DnaA boxes. I found that association of YabA with Rok-dependent regions did not require DnaA, in contrast to the DnaA-dependent association of YabA with DnaA box cluster regions. Furthermore, I showed an in vitro interaction between DnaA and Rok using purified proteins in an electrophoretic mobility shift assay. DnaA depended on Rok for association with a DNA probe, recapitulating the dependence observed at this chromosomal region in vivo. DnaA and Rok are both transcription factors and regulate some of the same genes. I analyzed global gene expression to determine the genetic relationship between these two transcriptional regulators. In general, rok was epistatic to dnaA; that is, the gene expression effects of DnaA depended on Rok, consistent with the ChIP-seq dependence. I investigated a potential role for Rok in regulating replication initiation, but I did not detect a replication phenotype of a rok null mutant under various conditions. I found that a rok null mutation did not detectably affect DnaA or YabA protein levels, and I showed that the stationary phase growth defect of this strain was dependent on comK, a downstream target of Rok. Additionally, I determined that a putative regulator of replication initiation, the pyruvate dehydrogenase enzyme PdhC, affected replication via its metabolic function but was not a direct regulator of replication initation.
by Charlotte A. Seid.
Ph. D.
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Pokatong, Wilbur Donald Raymond. "Molecular biology and biochemical assessment of acetolactate synthase (ALS)-mediated protein-protein interactions in Arabidopsis thaliana (L.) Heynh." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/NQ63911.pdf.

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Bao, Leyuan. "Genetic, biochemical and cellular studies on VEGF receptor protein-protein interactions and intracellular signalling in human endothelial cells." Thesis, University of Leeds, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555858.

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The vascular endothelial growth factor receptor 2 (VEGFR2) plays a key role in angiogenesis and vascular physiology in higher eukaryotes such as vertebrates. Although intracellular signalling pathways linked to VEGFR2 activation have been well characterised, there is a lack of knowledge on membrane and cytosolic effectors that interact with VEGFR2. To address this problem, I have used a novel membrane protein yeast 2-hybrid (Y2H) screen to identify novel factors that interact with membrane VEGFR2. By screening a human primary endothelial cDNA library, six potential VEGFR2-binding proteins were isolated. One candidate was the SlOO calcium-binding protein A6 (SlOOA6). SlOOA6 is an abundant protein present in both the nucleus and cytoplasm of endothelial cells. The interaction between VEGFR2 and SlOOA6 was found to be calcium-dependent. Calcium dependent-translocation of S lOOA6 from the nucleus caused eo-distribution with VEGFR2 in punctate vesicles. Depletion of SI OOA6 protein levels using RNA interference perturbed VEGF-A-stimulated VEGFR2 activation and phosphorylation, cell proliferation, cell migration and angiogenesis. Taken together, the work in this thesis suggests that S lOOA6 is a novel binding partner for VEGFR2 and regulates intracellular signalling and angiogenesis. Thus SlOOA6 could be a new target in the treatment of vascular disease.
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Mbajiorgu, Ejikeme Felix. "Interactions of ethanol and chloroquine in the protein-mulnourished male sprague dawley rats : haemotological, biochemical and testicular effects." Thesis, University of Limpopo (Turfloop Campus), 2010. http://hdl.handle.net/10386/751.

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Nair, Manoj Sadasivan. "Mechanism of Action of Insecticidal Crystal Toxins from Bacillus thuringiensis: Biophysical and Biochemical Analyses of the Insertion of Cry1A Toxins into Insect Midgut Membranes." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1218558470.

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Granberg, Åsa. "Microbotryum violaceum on Silene dioica : understanding traits that influence plant-pathogen interactions." Doctoral thesis, Umeå universitet, Ekologi, miljö och geovetenskap, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1387.

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The dynamics of a plant-pathogen interaction vary both within and among species. Both spatial structuring and specific genetic and life-history characteristics will affect the interaction and the outcome of a potential co-evolution between the two organisms. In this thesis I have studied the interaction between the wild perennial herb Silene dioica and its automictic, obligate anther smut Microbotryum violaceum MvSd. From the plant perspective, I have examined different aspects of biochemical resistance in S. dioica to M. violaceum MvSd. From the pathogen perspective, I have focused on the breeding system of M. violaceum MvSd and its connection to fitness and distribution of genetic diversity. I have used varying methods; glasshouse trails involving inoculation of plants with the pathogen, classical Mendelian analysis involving controlled crosses between plants, microscopic studies of spores and molecular DNA-analysis. With the results I demonstrate that resistance to M. violaceum MvSd in S. dioica can be specific to the attacking pathogen strain and also spatially highly diverse both within and among populations within a metapopulation. Together, these factors are likely to delay the establishment of the disease within host populations and reduce the spread and amount of disease, once it has been established. The results also suggest that the specific resistance expressed against two different M. violaceum MvSd strains were determined by separate gene systems and that, in both cases, the resistance was simply inherited. This implies a potential for relatively rapid response to M. violaceum-induced selection in S. dioica populations variable for resistance. My results also show that automixis clearly is the predominating breeding system of M. violaceum MvSd, similarly to what earlier has been shown for M. violaceum MvSl. Furthermore, I found lower levels of neutral genetic diversity in M. violaceum MvSd in the northern parts of Sweden, compared to what has been found in populations in more southern Europe. This result is consistent with predictions that populations in the outer regions of a species distribution have lower levels of genetic variation. Moreover, populations were highly differentiated in northern Sweden, which could have been generated by high selfing rates, genetic drift and high population turnover rates, all factors that coincide with life-history and ecology of M. violaceum MvSd. However, despite the general low variability in neutral genetic markers, I did find variation in fitness related traits, both within and among populations, as well as differences in infection ability between strains, suggesting there is a potential for co-evolution between S. dioica and M. violaceum MvSd in the area. To summarize, this thesis reflect a plant-pathogen system that is highly influenced by constant colonisation-extinction dynamics, which is likely to have influenced both the genetics of resistance in the plant and the breeding system of the pathogen and thus also the interaction between the two organisms.
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Duke, Jamie L. "Structural analysis of the EGR family of transcription factors : templates for predicting protein-DNA interactions /." Link to online version, 2006. https://ritdml.rit.edu/dspace/handle/1850/2296.

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