Dissertations / Theses on the topic 'In-Silico identification'
To see the other types of publications on this topic, follow the link: In-Silico identification.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'In-Silico identification.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Tiwari, Vijay, Derek Stuffle, and Aruna Kilaru. "Identification and In-Silico Analysis of Fatty Acid Amide Hydrolases in Tomato." Digital Commons @ East Tennessee State University, 2015. https://dc.etsu.edu/etsu-works/4797.
Full textAbstract:
N-acylethanolamines (NAEs) are a family of signaling lipids derived from a minor membrane lipid constituent N-acylphosphatidylethanolamine (NAPE). In Arabidopsis, NAE mediates physiological functions such as seedling growth, flowering, and response to stress via abscisic acid (ABA) –dependent and –independent signaling pathways. The function of NAEs is terminated by a highly conserved fatty acid amide hydrolase (FAAH). Studies in model plant Arabidopsis showed the significant role of NAEs that makes it relevant to elucidate the conserved metabolic pathway of NAEs in crop species such as tomato. It is hypothesized that there is a functional FAAH in tomato that hydrolyzes NAEs. To test this hypothesis, AtFAAH was used as a template to identify putative FAAH sequences in tomato, using BLASTX. Six SlFAAH sequences with the conserved amidase signature sequence and the catalytic triad, formed by Lys205, Ser281, and Ser305 in AtFAAH, were identified. Phylogenetic analysis of putative SlFAAH homologs and other FAAH family proteins (Arabidopsis, rice and moss), using CLUSTALW, revealed the two sequences that are closely related to the functionally characterized AtFAAH1. Using molecular visualization system (PyMOL), protein structures of putative SlFAAH1and 2 were predicted and compared with AtFAAH; both sequences showed similar domain structure to AtFAAH, with minor differences in spatial arrangement. For further biochemical characterization, full-length coding sequence of SlFAAH1 and SlFAAH2 were isolated and cloned into a heterologous expression system. The expressed protein will be characterized for its hydrolytic activity against radiolabelled NAE substrates. Furthermore, transcript levels for SlFAAH1 and SlFAAH2 will be quantified and correlated with the NAE levels in various tissues to predict their role in tissue-specific NAE hydrolysis. Together, these molecular and biochemical characterization studies in tomato are expected to further validate the conserved nature of NAE metabolic pathway in plants.
2
Salentin, Sebastian. "In Silico Identification of Novel Cancer Drugs with 3D Interaction Profiling." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-226435.
Full textAbstract:
Cancer is a leading cause of death worldwide. Development of new cancer drugs is increasingly costly and time-consuming. By exploiting massive amounts of biological data, computational repositioning proposes new uses for old drugs to reduce these development hurdles. A promising approach is the systematic analysis of structural data for identification of shared binding pockets and modes of action.
In this thesis, I developed the Protein-Ligand Interaction Profiler (PLIP), which characterizes and indexes protein-ligand interactions to enable comparative analyses and searching in all available structures. Following, I applied PLIP to identify new treatment options in cancer: the heat shock protein Hsp27 confers resistance to drugs in cancer cells and is therefore an attractive target with a postulated drug binding site. Starting from Hsp27, I used PLIP to define an interaction profile to screen all structures from the Protein Data Bank (PDB). The top prediction was experimentally validated in vitro. It inhibits Hsp27 and significantly reduces resistance of multiple myeloma cells against the chemotherapeutic agent bortezomib.
Besides computational repositioning, PLIP is used in docking, binding mode analysis, quantification of interactions and many other applications as evidenced by over 12,000 users so far. PLIP is provided to the community online and as open source.
3
Gómez-Porras, Judith Lucia. "In silico identification of genes regulated by abscisic acid in Arabidopsis thaliana (L.) Heynh." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=980562899.
Full text
4
Szolkiewicz, Michal Jerzy. "Homology-based in silico identification of putative protein-ligand interactions in the malaria parasite." Diss., University of Pretoria, 2014. http://hdl.handle.net/2263/41019.
Full textAbstract:
Malaria is still one of the most proli c communicable diseases in the world with more
than 200 million infections annually, its greatest e ect is felt in the poor nations with-in
sub-saharan Africa and south-east Asia. It is especially fatal for women and children where
out of the 660 000 fatalities in 2010, 86% were below the age of 5.
In the past decade the global fatality rate due to malaria has been signi cantly reduced,
primarily due to proliferation of vector control using treated nets and indoor residual spraying
of DDT. There have, however, been few innovations in anti-malarial therapeutics and with
the threat of the spread of drug resistant strains a need still exists to develop novel drugs to
combat malaria infections. One of the major hinderances to drug development is the huge cost
of the drug development process, where candidate failures late in development are extremely
costly. This is where post-genomic information has the potential of adding great value. By
using all available data pertaining to a disease, one gains higher discerning power to select
good drug candidates and identify risks early in development before serious investments are
made. This need provided the motivation for the development of Discovery; a tool to aid in
the identi cation of protein targets and viable lead compounds for the treatment of malaria.
Discovery was developed at the University of Pretoria to be a platform for a large spectrum
of biological data focused on the malaria causing Plasmodium parasite. It conglomerates
various data types into a web-based interface that allows searching using logical lters or
by using protein or chemical start points. In 2010 it was decided to rebuild Discovery to improve it's functionality and optimize query times. Also, since its inception various new
datasources became available speci cally related to bio-active molecules, these include the ChEMBL database and TCAMS dataset of bio-active molecules and the focus of this project
was the integration of said datasets into Discovery. Large quantities of high quality bioactivity
data have never been available in the public domain and this has opened up the
opportunity to gain even greater insight into the activity of chemical compounds in malaria.
Due to conserved structural/functional similarities of proteins between di erent species it
is possible to derive predictions about a malaria protein or a chemicals activity in malaria
due to experiments carried out on other organisms. These comparisons can be leveraged to
highlight potential new compounds that were previously not considered or prevent wasting
resources persuing potential compounds that pose threats of toxicity to humans. This project
has resulted in a web based system that allows one to search through the chemical space of
the malaria parasite. Allowing them to view sets of predicted protein-ligand interactions for
a given protein based on that proteins similarity to those existing in the bio-active molecule
databases.Dissertation (MSc)--University of Pretoria, 2014.
gm2014
Biochemistry
unrestricted
5
Musyoka, Thommas Mutemi. "Combined in silico approaches towards the identification of novel malarial cysteine protease inhibitors." Thesis, Rhodes University, 2017. http://hdl.handle.net/10962/4488.
Full textAbstract:
Malaria an infectious disease caused by a group of parasitic organisms of the Plasmodium genus remains a severe public health problem in Africa, South America and parts of Asia. The leading causes for the persistence of malaria are the emergence of drug resistance to common antimalarial drugs, lack of effective vaccines and the inadequate control of mosquito vectors. Worryingly, accumulating evidence shows that the parasite has developed resistant to the current first-line treatment based on artemisinin. Hence, the identification and characterization of novel drug targets and drugs with unique mode of action remains an urgent priority. The successful sequencing and assembly of genomes from several Plasmodium species has opened an opportune window for the identification of new drug targets. Cysteine proteases are one of the major drug targets to be identified so far. The use of cysteine protease inhibitors coupled with gene manipulation studies has defined specific and putative roles of cysteine proteases which include hemoglobin degradation, erythrocyte rupture, immune evasion and erythrocyte invasion, steps which are central for the completion of the Plasmodium parasite life cycle. In an aim to discover potential novel antimalarials, this thesis focussed on falcipains (FPs), a group of four papain-like cysteine proteases from Plasmodium falciparum. Two of these enzymes, FP-2 and FP-3 are the major hemoglobinases and have been validated as drug targets. For the successful elimination of malaria, drugs must be safe and target both human and wild Plasmodium infective forms. Thus, an incipient aim was to identify protein homologs of these two proteases from other Plasmodium species and the host (human). From BLASTP analysis, up to 16 FP-2 and FP-3 homologs were identified (13 plasmodial proteases and 3 human cathepsins). Using in silico characterization approaches, the intra and inter group sequence, structural, phylogenetic and physicochemical differences were determined. To extend previous work (MSc student) involving docking studies on the identified proteins using known FP-2 and FP-3 inhibitors, a South African natural compound and its ZINC analogs, molecular dynamics and binding free energy studies were performed to determine the stabilities and quantification of the strength of interactions between the different protein-ligand complexes. From the results, key structural elements that regulate the binding and selectivity of non-peptidic compounds onto the different proteins were deciphered. Interaction fingerprints and energy decomposition analysis identified key residues and energetic terms that are central for effective ligand binding. This research presents novel insight essential for the structure-based molecular drug design of more potent antimalarial drugs.
6
Lee, Adam. "The in silico identification and analysis of ancient and recent endogenous retroviruses in mammalian genomes." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/39972.
Full textAbstract:
Recent advances in DNA sequencing technologies have led to a vast plethora of vertebrate genomes being made available for bioinformatic analysis and investigation. This has presented retrovirologists with many new opportunities to study endogenous retroviruses (ERVs) - selfish genetic element (SGEs) endogenised within the genomic DNA of their hosts. Many of these ERVs exist as molecular fossils of past germline infections by their exogenous counterparts, representing approximately 8-10% of mammalian genomes. While the majority are thought to be inactive today, one particular retroviral group - HERV-K(HML-2) - has been implicated in recent activity. In this thesis, efficient, synergistic in silico techniques have been implemented, with which intensive, genome-wide retroviral screens were performed. This has culminated in the identification of 11 novel, insertionally polymorphic human ERVs (HERVs), belonging to the HERV-K(HML-2) lineage, in two high- coverage archaic hominid genomes. This thesis also identifies the oldest ERV described to date - orthologous across all placental mammals - estimated to have endogenised in the germline of an ancestral mammal, 128-140 million years ago. Three SGEs, found to be endogenised within this ancient ERV, have also been described and assigned a minimum age of 104 million years, making these the oldest, definitively dated SGEs. This thesis also presents a computer program for renaming all identified ERVs in vertebrate genomes, according to a newly designed nomenclature standard to be implemented globally, that aims to unambiguously catalogue all the ERVs identified, to date.
7
Tahir, Shifa. "A docking-based method for in silico epitope determination." Thesis, Tours, 2018. http://www.theses.fr/2018TOUR4008.
Full textAbstract:
Le développement des anticorps thérapeutiques s'est rapidement accéléré dans les 10 dernières années et concerne un nombre croissant de pathologies. La connaissance de l'épitope, à savoir la région de la cible à laquelle l'anticorps se fixe, est essentielle pour la compréhension des effets fonctionnels de ce dernier. Nous avons développé une méthode in silico, MAbTope, qui permet une prédiction précise de cet épitope, quand bien même aucune structure 3D de l'anticorps d’intérêt n'est résolue. Cette méthode se base sur une méthode d'amarrage protéine-protéine développée auparavant dans l’équipe BIOS. Le jeu d'apprentissage a été fortement enrichi en complexes anticorps-cibles, de nouvelles fonctions de score spécifiques ont été mises au point, et le plus important, l'objectif de l'apprentissage-machine a été modifié pour optimiser non plus la conformation de !'assemblage, mais la prédiction de l'épitope. Nous montrons que la méthode qui en résulte permet une prédiction précise et robuste de l'épitope, que la structure 3D de l'anticorps soit connue ou non. Nous montrons également comment les prédictions peuvent être facilement exploitées pour la validation expérimentale. Enfin, nous montrons comment la méthode peut être utilisée pour étudier à haut-débit le recouvrement d'épitopes par des anticorps ayant la même cibleThe development of therapeutic antibodies has been rapidly increasing in the last 10 years, with application to an increasing number of pathologies. The knowledge of the epitope, the region of the antigen to which the antibody binds, is crucial for understanding its functional effects. We have developed an in silico method, MAbTope, which allows the accurate prediction of the epitope, regardless of the availability of the 3D structure of the antibody of interest. This method is based on a protein-protein docking method previously developed in the BIOS group. The learning dataset was enlarged in antibody-antigen complexes, new specific scoring functions have been designed, and very importantly, the objective of machine-learning was switched from the conformational perspective towards the epitope determination perspective. We show that the resulting method allows robust and accurate prediction, whether or not the 3D structure of the antibody is available. We also show how the predictions can be easily exploited for experimental validation. Finally, we show how this method can be used for high-throughput epitope binning
8
Zhang, Jin. "In silico Identification of Thyroid Disrupting Chemicals : among industrial chemicals and household dust contaminants." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-125631.
Full textAbstract:
Thyroid disruptions by xenobiotics have been associated with a broad spectrum of severe adverse human health effects, such as impaired brain development and metabolic syndrome. Ingestion of indoor dust and contact with industrial chemicals are two significant human exposure routes of thyroid hormone disrupting chemicals (THDCs), raising serious concerns for human health. However, it is a laborious and costly process to identify THDCs using conventional experimental methods, due to the number of chemicals in commerce and the varieties of potential disruption mechanisms. In this thesis, we are aimed at in silico identification of novel THDCs targeting transthyretin (TTR) and thyroid hormone receptor (THR) among dust contaminants and commonly used industrial chemicals. In vitro assays were used to validate the in silico prediction results. Co-crystallization and molecular dynamics (MD) simulations were applied to reveal binding modes of THDCs at the studied biological targets and to explain their intermolecular recognition. The main findings presented in this thesis are: 1. Over 144 environmental pollutants have been confirmed as TTR-binders in vitro and these cover a wide range of environmental pollutants and show distinct chemical profiles including a large group of halogenated aromatic compounds and a second group of per- and polyfluoroalkyl substances. (Paper I) 2. In total 485 organic contaminants have been reported to be detected in household dust. The developed QSAR classification model predicted 7.6% of these dust contaminants and 53.1% of their metabolites as potential TTR-binders, which emphasizes the importance of metabolic bioactivation. After in vitro validation, four novel TTR binders with IC50 ≤ 10 µM were identified, i.e. perfluoroheptanesulfonic acid, 2,4,2',4'-tetrahydroxybenzophenone (BP2), 2,4,5-trichlorophenoxyacetic acid, and 3,5,6-trichloro-2-pyridinol. (Paper II) 3. The development of a robust structure-based virtual screening (VS) protocol resulted in the prediction of 31 dust contaminants as potential binders to THRβ1 including musk compounds, PFASs, and bisphenol A derivatives. The in vitro experiments confirmed four compounds as weak binders to THRβ1, i.e. 2,4,5-trichlorophenoxyacetic acid, bisphenol A (3-chloro-2-hydroxypropyl) (2,3-dihydroxypropyl) ether, 2,4,2',4'-tetrahydroxybenzophenone, and 2,4-dichlorophenoxyacetic acid. (Paper III) 4. We revealed the binding conformations of perfluorooctanesulfonic acid, perfluorooctanoic acid, and BP2 in the thyroxine binding sites (TBSs) of TTR by co-crystallizing TTR with the three compounds. A VS protocol was developed based on the TTR complex structures that predicted 192 industrial chemicals as potential binders to TTR. Seven novel TTR binders were confirmed by in vitro experiments including clonixin, 2,6-dinitro-p-cresol (DNPC), triclopyr, fluroxypyr, bisphenol S, picloram, and mesotrione. We further co-crystallized TTR with PBS, clonixin, DNPC, and triclopyr, and their complex structures showed that the compounds bind in the TBSs as proposed by the VS protocol. In summary, 13 indoor dust contaminants and industrial chemicals were identified as THDCs using a combination of in silico and in vitro approaches. To the best of our knowledge, none of these compounds has previously been reported to bind to TTR or THR. The identifications of these THDCs improve our understanding on the structure-activity relationships of THDCs. The crystal structures of TTR-THDC complexes and the information on THDC-Target intermolecular interactions provide a better understanding on the mechanism-of-actions behind thyroid disruption. The dataset compiled and in silico methods developed serve as a basis for identification of more diverse THDCs in the future and a tool for guiding de novo design of safer replacements.
9
Ludaka, Namhla. "Identification of biomarkers associated with cervical cancer: a combined in silico and molecular approach." University of the Western Cape, 2014. http://hdl.handle.net/11394/4363.
Full textAbstract:
>Magister Scientiae - MScCervical cancer is the leading cause of cancer mortality among black women in South Africa. It is estimated that this disease kills approximately 8 women in South Africa every day. Cervical cancer is caused by the human papillomavirus (HPV) with the most common screening method for cervical cancer being Papanicolaou (Pap) smear, test amongst others. However, less than 20% of South African women go for these tests. There are several reasons why women do not go for these tests but the invasiveness of the test is one of the major causes for the low rate of screening. Lateral flow devices offer medical diagnosis at the point- of-care, allowing for the quick initiation of the appropriate therapeutic response. These tests are more cost-effective for the healthcare delivery industry, and can potentially be used by patients to self-test in the privacy of their homes and allow them to make informed decisions about their health. Therefore, the aim of this study was to use computational methods to identify serum biomarkers for cervical cancer that can be used to develop a point-of-care diagnostic device for cervical cancer. An in silico approach was used to identify genes implicated in the initiation and development of cervical cancer. Several bioinformatics tools were employed to extract a list of genes from publicly available cancer repositories. Multiple gene enrichment analysis tools were employed to analyze the selected candidate genes. Through this pipeline, ~28190 genes were identified from the various databases and were further refined to only 10 genes. The 10 genes were identified as potential cervical cancer biomarkers. A subcellular compartmentalization analysis clustered the proteins encoded by these genes as cell surface, secretory granules and extracellular space/matrix proteins. The selected candidate genes were predicted to be specific for cervical cancer tissue in a cancer tissue specificity meta-analysis study. The expression levels of the candidate genes were compared relative to each other and a graph constructed using gene expression data generated by GeneHub-GEPIS and TiGER databases. Further gene enrichment analysis was performed such as protein-protein interactions, transcription factor analysis, pathway analysis and co-expression analysis, with 9 out of the10 of the candidate genes showing co-expression. A gene expression analysis done on cervical cancer cell lines, other cancer cell lines and normal fibroblast cell line revealed differential expression of the candidate genes. Three candidate genes were significantly expressed in cervical cancer, while the seven remaining genes showed over expression in other cancer types. The study serves as basis for future investigations to diagnosis of cervical cancer, as well as for cancers. Thus, they could also serve as potential drug targets for cancer therapeutics and diagnostics.
10
Kellett, Kathryn Emily. "Development of chemical sensors for rapid identification of amphetamine-related new psychoactive substances." Thesis, University of Hertfordshire, 2017. http://hdl.handle.net/2299/17686.
Full textAbstract:
A molecular receptor for mephedrone, an amphetamine-like NPS, was developed using host-guest chemistry and pharmacophoric design. The in-field detection of new psychoactive substances (NPS) is an area that has garnered considerable attention in the last few years. With the continuously expanding number of NPS on the market, traditional detection mechanisms lack the selectivity needed. In this project a new methodology has been developed for the design of host molecules for use in in-field detection, based on biomimetic design. To understand what a sensory molecular needs to be selective against, GC-MS and HPLC analysis were employed to identify and quantify thirteen aminoindane internet samples. It was found that the composition of internet samples varies greatly in terms of concentration of active ingredient, with a range of 17-95 % w/w of active ingredient identified. It was also found that caffeine was the most common cutting agent with a range of 27.7-30.2 % w/w identified. This highlights the need for both selectivity and sensitivity in detection mechanisms. Using the principles of biomimetic design, a methodology for the treatment of protein-ligand interactions was developed. Protein-ligand binding data collected from the Protein Databank was analysed for mephedrone related structures and common cutting agents, identified through aminoindane internet sample analysis and literature sources. From this work a three-point pharmacophoric model was developed, upon which two host molecules were considered, macrocyclic calixarenes and acyclic anthraquinones. Both contained the three binding interactions deduced from the pharmacophore design; two p-stacking interactions and one hydrogen bond acceptor. The final host molecule taken forward for testing was 1,8-dibenzylthiourea anthracene (Probe 1). The binding affinity of Probe 1 to mephedrone was tested using 1H-NMR. An estimated association constant of 104 M-1 was calculated, with a 1:1 binding stoichiometry. Along with ESI-MS and DFT calculations, it was found that mephedrone binds to Probe 1 in a concerted fashion with a three-point binding geometry, with two hydrogen bonds and one p-stacking interaction. A modest optical response using fluorescence spectroscopy was also observed between mephedrone and Probe 1 at high molar concentrations. A more pronounced response was observed upon addition of high molar concentrations of flephedrone. 1H-NMR showed that Probe 1 selectively bound mephedrone over methamphetamine as well as the four most common cutting agents identified from literature: lidocaine, caffeine, paracetamol and benzocaine, which have been shown to cause false positives in previous studies. Probe 1 showed significant selectivity for the β-ketoamine arrangement. This is supported by the systematic analysis of mephedrone, methamphetamine, mephedrone precursor and flephedrone. This is the first time this has been achieved using host-guest chemistry. A protocol was developed to successfully detect mephedrone via Probe 1 using NMR spectroscopy in a simulated street sample containing two of the most common cutting agents, benzocaine and caffeine. To further aid future design of small host molecules a methodology for the in silico analysis of small molecule host-guest binding using metadynamics was explored. Solvent interactions with the host and guest molecules were observed, highlighting the importance of solvent choice in binding studies. Metadynamics shows potential to be used in further work for improving the approach in which host molecules are designed in future.
11
Martin, Darius Riziki. "The identification of aptamers against serum biomarkers of human tuberculosis." University of the Western Cape, 2018. http://hdl.handle.net/11394/6778.
Full textAbstract:
>Magister Scientiae - MScTuberculosis (TB) is a global health problem and rated as the second leading cause of death after HIV/AIDS. Transmission of TB from one person to the next is very rapid in crowded communities. Therefore, it is crucial to identify people who are infected as quickly as possible not only to provide treatment but also to prevent the spread of the disease. Current TB diagnostic tests such as the culture and sputum smear tests are time-consuming, while rapid tests make use of antibodies that are costly and have low sensitivity and stability. Great improvement has been observed when aptamers are used in place of antibodies in rapid diagnostic tests such as lateral flow devices (LFDs). Therefore, the current study aims to synthesize and identify aptamers against serum biomarkers for development of rapid TB diagnostic tests such as a lateral flow assay. Several TB serum biomarkers have been identified and can be used for the diagnosis of TB. TB biomarkers expressed in serum samples were identified through in silico approach. The biomarkers were expressed in bacterial systems using recombinant DNA technology. The recombinant proteins were purified by affinity chromatography and further used as targets for the selection of aptamers using Systemic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers for the selected biomarkers were synthesized based on magnetic-bead based SELEX and characterized by electrophoretic mobility shift assay (EMSA), Surface Plasmon resonance (SPR) and MicroScale Thermophoresis (MST). Six putative TB serum biomarker proteins were selected from literature, namely, Insulin-like Growth Factor Binding Protein 6 (IGFBP6), Interferon-stimulated Gene 15 (ISG15), Calcium Binding Protein (S100A9), Retinol Binding Protein 4 (RBP4), Granzyme A (GrA), and Transgelin-2 (TAGLN2). The biomarkers were recombinantly expressed and purified after which they were used as targets in SELEX for aptamers synthesis. Aptamers were analysed by in silico method and the ones with highly conserved motifs were selected. The selected aptamers were synthesized and later characterized. The aptamers that show high affinity and specificity for the biomarkers will be used for the fabrication of a rapid lateral flow device for TB screening. Such a test would allow for a short diagnostic turnaround time, and hence expedite treatment.
12
Gómez-Porras, Judith Lucia. "In silico identification of genes regulated by abscisic acid in Arabidopsis thaliana (L.) Heynh." Phd thesis, Universität Potsdam, 2005. http://opus.kobv.de/ubp/volltexte/2006/740/.
Full textAbstract:
Abscisic acid (ABA) is a major plant hormone that plays an important role during plant growth and development. During vegetative growth ABA mediates (in part) responses to various environmental stresses such as cold, drought and high salinity. The response triggered by ABA includes changes in the transcript level of genes involved in stress tolerance. The aim of this project was the In silico identification of genes putatively regulated by ABA in A. thaliana. In silico predictions were combined with experimental data in order to evaluate the reliability of computational predictions.Taking advantage of the genome sequence of A. thaliana publicly available since 2000, 1 kb upstream sequences were screened for combinations of cis-elements known to be involved in the regulation of ABA-responsive genes. It was found that around 10 to 20 percent of the genes of A. thaliana might be regulated by ABA.
Further analyses of the predictions revealed that certain combinations of cis-elements that confer ABA-responsiveness were significantly over-represented compared with results in random sequences and with random expectations. In addition, it was observed that other combinations that confer ABA-responsiveness in monocotyledonous species might not be functional in A. thaliana. It is proposed that ABA-responsive genes in A. thaliana show pairs of ABRE (abscisic acid responsive element) with MYB binding sites, DRE (dehydration responsive element) or with itself.
The analysis of the distances between pairs of cis-elements suggested that pairs of ABREs are bound by homodimers of ABRE binding proteins. In contrast, pairs between MYB binding sites and ABRE, or DRE and ABRE showed a distance between cis-elements that suggested that the binding proteins interact through protein complexes and not directly.
The comparison of computational predictions with experimental data confirmed that the regulatory mechanisms leading to the induction or repression of genes by ABA is very incompletely understood. It became evident that besides the cis-elements proposed in this study to be present in ABA-responsive genes, other known and unknown cis-elements might play an important role in the transcriptional regulation of ABA-responsive genes. For example, auxin-related cis elements, or the cis-elements recognized by the NAM-family of transcription factors (Non-Apical meristem).
This work documents the use of computational and experimental approaches to analyse possible interactions between cis-elements involved in the regulation of ABA-responsive genes. The computational predictions allowed the distinction between putatively relevant combinations of cis-elements from irrelevant combinations of cis-elements in ABA-responsive genes. The comparison with experimental data allowed to identify certain cis-elements that have not been previously associated to the ABA-mediated transcriptional regulation, but that might be present in ABA-responsive genes (e.g. auxin responsive elements). Moreover, the efforts to unravel the gene regulatory network associated with the ABA-signalling pathway revealed that NAM-transcription factors and their corresponding binding sequences are important components of this network.
Pflanzen reagieren auf aeußere Stresseinwirkung (z.B. Trockenheit oder Hitze) u.a. mit der Bildung bestimmter Hormone. Diese Hormone wiederum bewirken eine Vielzahl komplexer Reaktionen (z.B. im Stoffwechsel und in der Genexpression), die zum Ziel haben, die Pflanzen widerstandsfaehiger gegen die Stresssituation zu machen. Ein wichtiges Stresshormon ist die Abzisinsaeure (ABA, fuer engl. „abscisic acid“). Experimentell koennen Pflanzen durch die Gabe von ABA zu Reaktionen gezwungen werden, die normalerweise nur unter Stressbedingungen beobachtet werden. Hierzu zaehlen vor allem eine Reduktion der Spaltoeffnungen in den Blaettern, um den Wasserverlust infolge von Transpiration zu minimieren, und eine massive Umprogrammierung der Genexpression.
In der vorliegenden Arbeit wurde der Einfluss von ABA auf die Genexpression in der Modellpflanze Arabidopsis thaliana untersucht. Hierzu wurden bioinformatorische und experimentelle Ansaetze verknuepft. Die bioinformatorischen Ansaetze bedienten sich der bekannten Sequenz des Genoms von A. thaliana. Mit Hilfe verschiedener geeigneter Computerprogramme wurden im Genom Gene identifiziert, deren Expression potentiell durch ABA reguliert wird. Die so erhaltenen Vorhersagen der verschiedenen Programme wurden miteinander und mit eigenen als auch mit publizierten experimentellen Daten verglichen, um die Qualitaet der Vorhersagen zu beurteilen.
Die wichtigste Schlussfolgerung aus den Ergebnissen dieser Arbeit ist, dass gegenwaertig bioinformatorische Ansaetze allein nicht ausreichen, um biologische Prozesse zufriedenstellend zu analysieren. In der vorliegenden Arbeit ermoeglichte erst eine Kombination aus bioinformatorischen und experimentellen Ansaetzen die Generierung neuer, abgesicherter Hypothesen zur ABA-induzierten Umprogrammierung der Genexpression.
13
Verardo, Lucas Lima. "Differentially expressed genes and miRNA identification in pig skeletal muscle." Universidade Federal de Viçosa, 2011. http://locus.ufv.br/handle/123456789/4757.
Full textAbstract:
Made available in DSpace on 2015-03-26T13:42:23Z (GMT). No. of bitstreams: 1
texto completo.pdf: 636309 bytes, checksum: ca1e7c510537c62820f228b759c5a23d (MD5)
Previous issue date: 2011-07-25Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
O suíno (Sus scrofa) é considerado um animal de grande importância para produção de carne, sendo seu potencial de crescimento muscular objeto de grande interesse e geralmente associado com características determinadas na fase pré-natal durante a miogênese. Para o estudo de genes responsáveis por estas características, as etiquetas de sequências expressas (Expressed Sequence Tags - EST) fornecem informações diretas sobre o transcriptoma e indiretas sobre a relação entre o genoma e diferentes fenótipos, proporcionando o conhecimento sobre genes diferencialmente expressos (GDE) bem como sequências genômicas transcritas para o controle da expressão gênica como, por exemplo, alguns RNAs não codificantes. Características de tecidos musculares em suínos podem ser influenciadas diretamente por genes, e estes sendo regulados como, por exemplo, através de miRNAs, em diferentes fases de desenvolvimento. O presente trabalho teve como objetivo a identificação e a anotação in sílico de GDE e sequências não codificantes, com enfoque aos miRNAs, de bibliotecas de cDNA construídas a partir do músculo esquelético semi-membranoso de três diferentes raças de suínos (Duroc, Large White e naturalizada brasileira Piau) bem como a análise dos níveis de expressão dos genes identificados e miRNAs em sete fases de desenvolvimento do Longissimus Dorsi (21, 40, 70 e 90 dias pré-natal e 107, 121 e 171 dias pós-natal) de animais de linha comercial. Foram identificados 34 GDE sendo 21 pertencentes a uma rede gênica musculo-específica. Destes, 13 genes tiveram seus perfis de expressão analisados com o uso do qRT-PCR durante os sete períodos citados, formando quatro grupos de expressão semelhantes, um com maior expressão na fase pós-natal e três na fase pré-natal. Nas análises das sequências não codificantes um resultado importante foi a identificação de dois novos miRNAs em suínos, os quais tiveram suas sequências maduras similares aos miRNAs hsa-miR-1207-5p e hsa-miR-665 foram classificadas como verdadeiras pelo programa MiPred e formaram estruturas secundárias. Destes, encontrou-se 289 e 214 genes regulados por eles respectivamente, dos quais quatro são músculo-específicos. Os novos miRNAs tiveram seus perfis de expressão analisados com o uso do PCR em tempo real durante os sete períodos citados juntamente com outros três já identificados em suínos. Seus níveis de expressão mostraram diferenças entre os estágios pré- e pós-natal. Estes estudos podem fornecer valiosas informações possibilitando um maior entendimento dos mecanismos moleculares envolvidos no desenvolvimento muscular. As análises de GDE em fases pré e pós-natal sugerem a presença de genes atuando especificamente em determinados estágios de desenvolvimento do músculo, contribuindo para melhor explicar suas funções. A identificação de dois novos miRNAs, somados a outros já identificados e postados nos bancos de dados em suínos, podem contribuir para um maior entendimento dos modos de regulação gênica, sendo de importância para os estudos de genética e melhoramento animal, permitindo o entendimento da fisiologia da deposição de músculo para produção de carne em suínos.
The pig (Sus scrofa) is considered an important animal for meat production. This interest revolves around the potential for muscle growth, which usually is associated with certain characteristics during prenatal myogenesis. To study the genes responsible for these characteristics, expressed sequence tags (EST) provide direct information about the transcriptome and indirectly on the relationship between the genome and different phenotypes, supplying knowledge about differentially expressed genes (DEG) as well as other transcribed genomic sequences for the control of gene expression, e.g., some non-coding RNAs. Characteristics of muscle tissue in pigs may have been directly influenced by genes, and those being regulated, for example, by miRNAs, in different stages of development. This study aimed to identify by in silico annotation, DEG and non-coding sequences, focusing on miRNAs, using cDNA libraries constructed from semi-membranous skeletal muscle of three different pig breeds (Duroc, Large White and naturalized Brazilian Piau ) as well as analysis of gene expression profiles of identified genes and miRNAs during seven stages of development (21, 40, 70 and 90 days prenatal and 107, 121 and 171 days postnatal) from commercial line animals Longissimus Dorsi muscle. Twenty-one identified genes out of 34 DEGs belongs to the muscle-specific path. From these, 13 genes had their expression profiles analyzed by qRT-PCR during the seven periods, forming four clusters of similar expression, with one having greater expression in the postnatal period and three in the prenatal. In the analysis of non-coding sequences, an important result was the identification of two new miRNAs in pigs, which had their sequences similar to mature miRNAs hsa-miR-1207- 5p and hsa-miR-665 which had their precursor sequences forming secondary structures and classified as real precursor sequence by MiPred program. From these, we found 289 genes and 214 respectively regulated by them, of which four are muscle-specific. The new miRNAs and other three which have been identified in previous studies in pigs had their expression levels analyzed by quantitative real time PCR during the mentioned seven periods. Their levels of expression differed between pre-and postnatal stages. These studies may provide valuable information allowing a better understanding of the molecular mechanisms involved in muscle development. Analyses of DEG in the pre-and postnatal periods suggest the presence of genes acting specifically on certain stages of muscle development, contributing to better explain their functions. The identification of two new miRNAs, together with other previously identified and posted on the databases in pigs, may contribute to a better understanding of gene regulation and is important for studies of genetics and animal breeding, allowing the understanding of the muscle deposition physiology to meat production in pigs.
14
Jean, Géraldine. "In silico methods for genome rearrangement analysis : from identification of common markers to ancestral reconstruction." Thesis, Bordeaux 1, 2008. http://www.theses.fr/2008BOR13704/document.
Full textAbstract:
L'augmentation du nombre de génomes totalement séquencés rend de plus en plus efficace l'étude des mécanismes évolutifs à partir de la comparaison de génomes contemporains. L'un des principaux problèmes réside dans la reconstruction d'architectures de génomes ancestraux plausibles afin d'apporter des hypothèses à la fois sur l'histoire des génomes existants et sur les mécanismes de leur formation. Toutes les méthodes de reconstruction ancestrale ne convergent pas nécessairement vers les mêmes résultats mais sont toutes basées sur les trois mêmes étapes : l'identification des marqueurs communs dans les génomes contemporains, la construction de cartes comparatives des génomes, et la réconciliation de ces cartes en utilisant le critère de parcimonie maximum. La qualité importante des données à analyser nécessite l'automatisation des traitements et résoudre ces problèmes représente de formidables challenges computationnels. Affiner le modèles et outils mathématiques existants par l'ajout de contraintes biologiques fortes rend les hypothèses établies biologiquement plus réalistes. Dans cette thèse, nous proposons une nouvelle méthode permettant d'identifier des marqueurs communs pour des espèces évolutivement distantes. Ensuite, nous appliquons sur les cartes comparatives reconstituées une nouvelle méthode pour la reconstruction d'architectures ancestrales basée sur les adjacences entre les marqueurs calculés et les distances génomiques entre les génomes contemporains. Enfin, après avoir corrigé l'algorithme existant permettant de déterminer une séquence optimale de réarrangements qui se sont produits durant l'évolution des génomes existants depuis leur ancêtre commun, nous proposons un nouvel outil appelé VIRAGE qui permet la visualisation animée des scénarios de réarrangements entre les espècesAbstract
15
Khan, Firdous. "Identification of miRNA's as specific biomarkers in prostate cancer diagnostics : a combined in silico and molecular approach." University of the Western Cape, 2015. http://hdl.handle.net/11394/4746.
Full textAbstract:
Philosophiae Doctor - PhDThere are over 100 different types of cancer, and each of these cancers are classified by the type of cell that it initially affects. For the purpose of this research we will be focussing on prostate cancer (PC). Prostate cancer is the second most common form of cancer in men around the world and annually approximately 4500 men in South Africa are diagnosed making PC a global epidemic. Prostate cancer is a type of cancer which starts in the prostate it is normally a walnut-sized gland found right below the bladder. PC follows a natural course, starting as a tiny group of cancer cells that can grow into a tumour. In some men if PC is not treated it may spread to surrounding tissue by a process called direct invasion/ spread and could lead to death. Current diagnostic tests for prostate cancer have low specificity and poor sensitivity. Although many PC's are slow growing there is currently no test to distinguish between these and cancers that will become aggressive and life threatening. Therefore the need for a less invasive early detection method with the ability to overcome the lack of specificity and sensitivity of current available diagnostic test is required. Biomarkers have recently been identified as a viable option for early detection of disease for example biological indicators ie. DNA, RNA, proteins and microRNAs (miRNAs). Since first described in the 1990s, circulating miRNAs have provided an active and rapidly evolving area of research that has the potential to transform cancer diagnostics and prognostics. In particular, miRNAs could provide potentially new biomarkers for PC as diagnostic molecules. Circulating miRNAs are highly stable and are both detectable and quantifiable in a range of accessible bio-fluids, having the potential to be useful as diagnostic, prognostic and predictive biomarkers. In this study we aimed to identify miRNAs as potential biomarkers to detect and distinguish between various types of PC in its earliest stage. The major objectives of the study were to identify miRNAs and their gene targets that play a critical role in disease onset and progression to further understand their mechanism of action in PC using several in silico methods, and to validate the potential diagnostic miRNAs using qRT-PCR in several cell lines. The identification of specific miRNAs and their targets was done using an "in-house" designed pipeline. Bioinformatic analyses was done using a number of databases including STRING, DAVID, DIANA and mFold database, and these combined with programming and statistical analyses was used for the identification of potential miRNAs specific to PC. Our study identified 40 miRNAs associated with PC using our "in-house" parameters in comparison to the 20-30 miRNAs known to be involved in PC found in public databases e.g. miRBase. A comparison between our parameters and those used in public databases showed a higher degree of specificity for the identification PC-associated miRNAs. These selected miRNAs were analysed using different bioinformatics tools, and were confirmed to be novel miRNAs associated with PC. The identified miRNAs were experimentally validated using qRT-PCR to generate expression profiles for PC as well as various other cancers. Prostate lines utilised in this study included PNT2C2 (normal) which was compared to BPH1 (Benign) and LNCaP (Metastatic). In the study the expression profiles of eight potential miRNA biomarkers for the detection of PC was determined using qRT-PCR, and to distinguish PC from other cancers. QRT-PCR data showed that miRNA-3 and -5 were up-regulated in the BPH1 and LNCaP when compared to PNT2C2. In addition miRNA-8 was also shown to be up-regulated in LNCaP. Based on these results it was shown that a miRNA profile could be established to distinguish between BPH1 and the LNCaP prostate cell lines. The results suggest that one miRNA as a diagnostic marker may be sufficient to differentiate between different cancer cell lines. Furthermore by creating a unique profile for each cancer cell line by using a combination of miRNAs could be a suitable approach as well. Finally, it was shown that through the use of a single or combination of all eight miRNAs a unique profile for all the cancer cell lines tested in this study can be created. This is an important finding which could have potential diagnostic or prognostic implications in clinical practice.
16
Le, Guédard Marina. "Identification et caractérisation de quatre lysolipide acyltransférases de S. Cerevisiae : études in silico, in vitro et in vivo." Bordeaux 2, 2008. http://www.theses.fr/2008BOR21567.
Full textAbstract:
Les lysolipide acytransférases, capables de convertir des lysolipides en lipides, apparaissent comme des enzymes clefs impliquées dans les phénomènes de régulation de l'homéostasie membranaire puisqu'elles sont susceptibles de contrôler à la fois la quantité (import) et la qualité ("remodelage") des lipides membranaires. Malgré leur importance, ces enzymes avaient été peu étudiées tant chez la levure que chez les végétaux. L'objectif de cette thèse a consisté à étudier la diversité des gènes de lysolipide acytransférases d'un organisme modèle (S. Cerevisiae) et à caractériser les enzymes correspondantes (activités, localisation subcellulaire. . . ). Une étude "bioinformatique" a permis d'identifier quatre protéines de S. Cerevisiae pouvant correspondre à des lysolipide acytransférases. Il s'agit des protéines Ydr018cp, Ybr042cp, Ypr139cp et Yor298wp. Les résultats obtenus lors de cette étude ont mis en évidence que trois de ces protéines possèdent des activités lysophosphatidique acyltransférases in vitro dont deux, Ydr018cp et Yor298wp, catalyseraient plutôt l'incorporation d'acides gras à 16 atomes de carbone, tandis que la troisième, Ypr139cp, présenterait une activité incorporant plutôt les acides gras à 18 atomes de carbone. Quant à Ybr042cp, les résultats ont montré que cette enzyme présente une activité sn2-acyl-lysophosphatidylinositol acyltransférase permettant l'incorporation d'acide stéarique en position sn1 du P1 néo-synthétisé. La présence de cette protéine explique à elle seule le fait que le P1 de levure contienne beaucoup plus d'acide stéarique que les autres phospholipidesLysolipid acyltransferases, which are able to convert lysolipids into lipids, appear as key enzymes implicated in membrane homeostasis regulation since they are likely to control, at the same time, quantity (transport) and quality ("remodeling") of membrane lipids. In spite of their importance, these enzymes had not been much studied in yeast or in plants. The objective of this thesis was to study the diversity of lysolipid acyltransferase genes in the model organism S. Cerevisiae and to characterize their corresponding enzymes (activities, sub-cellular localization). A bioinformatic study allowed to identify four S. Cerevisiae proteins Ydr018cp, Ybr042cp, ypr139cp and Yor298w, as putative lysolipid acyltransferases. Results obtained during this study showed that three of these proteins have indeed lysophosphatidic acyltransferase activities in vitro. Ydr018cp and Yor298wp, catalyze the incorporation of fatty acids containing C16 and Ypr139cp shows incorporation of C18 faty acids. As for Ybr042cp, results showed that this enzyme has a sn2-acyl-lysophosphatidylinositol acyltransferase activity which allows the incorporation of stearic acid in sn1 position of neo-synthetized P1. The presence of this protein explains why yeasts P1 contains much more stearic acid that other phospholipids
17
Ferrara, Najua Ali. "Identification of novel miRNAs as diagnostic molecules for detection of breast cancer using in silico approaches." University of the Western cape, 2017. http://hdl.handle.net/11394/5675.
Full textAbstract:
Magister Scientiae - MScBreast cancer (BC) is the most common cancer in women worldwide, and is the second most common cancer in the world, responsible for more than 500 000 deaths annually. Estimates are that 1 in 8 women will develop BC in their lifetime. In South Africa, BC in women affects about 16.6 % of the population and could see a 78 % increase in cases by 2030. The failure of conventional diagnostic tools to detect BC from an early onset has revealed the need for diagnostic tools that would enable early diagnosis of BC. The current diagnostic tools include breast self-examination, mammography magnetic resonance imaging, ultrasonography and serum biomarkers; BRACA1, BRACA2, HER2. These conventional methods lack sensitivity, specificity and positive predictive value, and some of these diagnostic tools may be expensive and quite invasive. Therefore, novel diagnostic tools such as microRNAs which address the short comings of current methods are required for early diagnosis as well as BC management. MicroRNAs are a class of non-coding RNA molecules, which are important in RNA stability and gene expression. Various methodologies have been employed to identify novel microRNAs for diagnostics such as bioinformatics, also referred to as in silico analysis. The aim of this study is to identify novel microRNAs that can potentially detect BC at its earliest stage.
18
Anthony, Yancke. "Identification and validation of micrornas for diagnosing type 2 diabetes : an in silico and molecular approach." University of the Western Cape, 2015. http://hdl.handle.net/11394/4713.
Full textAbstract:
>Magister Scientiae - MScType 2 diabetes mellitus (T2DM), a metabolic disease characterized by chronic hyperglycemia, is the most prevalent form of diabetes globally, affecting approximately 95 % of the total number of people with diabetes i.e. approximately 366 million. Furthermore, it is also the most prevalent form in South Africa (SA), affecting approximately 3.5 million individuals. This disease and its adverse complications can be delayed or prevented if detected early. Standardized diagnostic tests for T2DM have a few limitations which include the inability to predict the future risk of normal glucose tolerance individuals developing T2DM, they are dependent on blood glucose concentration, its invasiveness, and they cannot specify between T1DM and T2DM. Therefore, there is a need for biomarkers which could be used as a tool for the early and specific detection of T2DM. MicroRNAs are small non-coding RNA molecules which play a key role in controlling gene expression and certain biological processes. Studies show that dysregulation of microRNAs may lead to various diseases including T2DM, and thus, may be useful biomarkers for disease detection. Therefore, identifying biomarkers like microRNAs as a tool for the early and specific detection of T2DM, have great potential for diagnostic purposes. The main focus of this investigation, therefore, is the early detection of T2DM by the identification and validation of novel biomarkers. Furthermore, based on previous studies, the aim of the investigation was to identify differentially expressed miRNAs as well as identify their potential target genes associated with the onset and progression of T2DM. An in silico approach was used to identify miRNAs found to be differentially expressed in the serum/plasma of T2DM individuals. Three publically available target prediction software were used for target gene prediction of the identified miRNA. The target genes were subjected to functional analysis using a web-based software, namely DAVID. Functions which were clustered with an enrichment score > 1.3 were considered significant. The ranked target genes mostly had gene ontologies linked with “transcription regulation”, “neuron signalling, and “metal ion binding”. The ranked target genes were then split into two lists – an up-regulated (ur) miRNA targeted gene list and a down-regulated (dr) miRNA targeted gene list. The in silico method used in this investigation produced a final total of 4 miRNAs: miR-dr-1, miR-ur-1, miR-ur-2, and miR-ur-3. Based on the bioinformatics results, miR-dr-1 and its target genes LDLR, PPARA and CAMTA1, seemed the most promising miRNA for biomarker validation, due to the function of the target genes being associated with T2DM onset and progression. The expression levels of the miRNAs were then profiled in kidney tissue of male Wistar rats that were on a high fat diet (HFD), streptozotocin (STZ)-induced T1DM, and non-diabetic control rats via qRT-PCR analysis. The hypothesis was that similar miRNA expression would be found in the HFD kidney samples compared to serum expression levels of the miRNA obtained from the two databases, since kidneys are involved in cleansing the blood from impurities. This hypothesis proved to be true for all miRNAs except for miR-ur-2. Additionally, miR-ur-1 seemed the most significant miRNA due to it having different expression ratios for T1DM and T2DM (i.e. -7.65 and 4.2 fold, respectively). Future work, therefore, include validation of the predicted target genes to the miRNAs of interest i.e. miR-dr-1: PPARA and LDLR and miR-ur-1: CACNB2, using molecular approaches such as the luciferase assays and western blots.
19
Abdullah, Gadija. "The detection of meningococcal disease through identification of antimicrobial peptides using an in silico model creation." University of the Western Cape, 2019. http://hdl.handle.net/11394/7079.
Full textAbstract:
Philosophiae Doctor - PhDNeisseria meningitidis (the meningococcus), the causative agent of meningococcal disease (MD) was identified in 1887 and despite effective antibiotics and partially effective vaccines, Neisseria meningitidis (N. meningitidis) is the leading cause worldwide of meningitis and rapidly fatal sepsis usually in otherwise healthy individuals. Over 500 000 meningococcal cases occur every year. These numbers have made bacterial meningitis a top ten infectious cause of death worldwide. MD primarily affects children under 5 years of age, although in epidemic outbreaks there is a shift in disease to older children, adolescents and adults. MD is also associated with marked morbidity including limb loss, hearing loss, cognitive dysfunction, visual impairment, educational difficulties, developmental delays, motor nerve deficits, seizure disorders and behavioural problems. Antimicrobial peptides (AMPs) are molecules that provide protection against environmental pathogens, acting against a large number of microorganisms, including bacteria, fungi, yeast and virus. AMPs production is a major component of innate immunity against infection. The chemical properties of AMPs allow them to insert into the anionic cell wall and phospholipid membranes of microorganisms or bind to the bacteria making it easily detectable for diagnostic purposes. AMPs can be exploited for the generation of novel antibiotics, as biomarkers in the diagnosis of inflammatory conditions, for the manipulation of the inflammatory process, wound healing, autoimmunity and in the combat of tumour cells. Due to the severity of meningitis, early detection and identification of the strain of N. meningitidis is vital. Rapid and accurate diagnosis is essential for optimal management of patients and a major problem for MD is its diagnostic difficulties and experts conclude that with an early intervention the patient’ prognosis will be much improved. It is becoming increasingly difficult to confirm the diagnosis of meningococcal infection by conventional methods. Although polymerase chain reaction (PCR) has the potential advantage of providing more rapid confirmation of the presence of the bacterium than culturing, it is still time consuming as well as costly. Introduction of AMPs to bind to N. meningitidis receptors could provide a less costly and time consuming solution to the current diagnostic problems. World Health Organization (WHO) meningococcal meningitis program activities encourage laboratory strengthening to ensure prompt and accurate diagnosis to rapidly confirm the presence of MD. This study aimed to identify a list of putative AMPs showing antibacterial activity to N. meningitidis to be used as ligands against receptors uniquely expressed by the bacterium and for the identified AMPs to be used in a Lateral Flow Device (LFD) for the rapid and accurate diagnosis of MD.
20
Bechaux, Julia. "Identification de peptides à activité biologique issus de matrices carnées porcines ayant subi un traitement enzymatique." Thesis, Université Clermont Auvergne (2017-2020), 2019. http://www.theses.fr/2019CLFAC043.
Full textAbstract:
La biomasse animale issue de la filière porcine, qui est faiblement valorisée, nécessite la mise en œuvre de nouveaux procédés de diversification. L’identification de peptides bioactifs (PBs) est une voie prometteuse pour la valorisation de cette biomasse. Cela permet d’un point de vue environnemental de mieux rentabiliser les consommations en ressources naturelles (surface de culture, eau, énergie) ayant servi à l’alimentation des porcs, en fournissant un débouché économiquement intéressant à ces sous-produits. D’autre part, la génération de peptides bioactifs utilisables dans les domaines de la pharmacologie, la cosmétique, ou l’alimentation s’inscrit dans la demande croissante des consommateurs pour l’élaboration de molécules plus naturelles. L’objectif de ce projet est d’identifier des conditions d’hydrolyse optimales permettant de générer, à partir de sous-produits porcins, de nouvelles molécules bioactives à visée nutritionnelle ou médicale. Une étude de potentialité in silico est menée sur quatre matrices porcines (cœur, foie, poumon et muscle) afin d’évaluer leur capacité à générer des PBs, après hydrolyse enzymatique. De plus, la stabilité des peptides générés est testée en condition de digestion gastro-intestinale via l’utilisation d’un modèle statique. Finalement, le développement de la méthode à l’échelle pilote est réalisé. Les études in silico ont permis de sélectionner le couple d’enzymes papaïne/subtilisine présentant une forte potentialité dans la génération de peptides avec une activité antioxydante, antidiabétique (iDPP4) et antihypertensive (iECA) pour les quatre matrices d’étude. La validation in vitro, a confirmé la présence des activités antioxydante et iDPP4 dans les quatre hydrolysats générés avec la papaïne et la subtilisine. Il est noté que l’activité biologique des hydrolysats de cœur, de foie et de poumon est exacerbée au cours de la digestion gastro-intestinale. Les expérimentations sur la digestion d’un palet de porc supplémenté en hydrolysat de cœur ont montré que i) la température de cuisson (70°C ou 90°C) impacte peu le niveau des activités iDPP4 et antioxydante au cours de la digestion, ii) la supplémentation permet d’augmenter significativement l’activité iDPP4 par rapport à un échantillon témoin. Un effet plus modeste de cette supplémentation sur l’activité antioxydante a été observé et iii) l’activité antioxydante des palets de porc supplémentés augmente significativement (+40%) entre le compartiment gastrique et intestinal. Enfin, la méthodologie de génération des peptides bioactifs est transposable à l’échelle pilote moyennant l’utilisation d’enzymes commerciales et de paramètres d’hydrolyse adaptés. Les fractions peptidiques présentant une bioactivité significative pourront être valorisées comme ingrédients aromatiques et servir pour supplémenter des produits alimentaires dans le but d’obtenir des allégations de santéThe poorly valorized animal biomass from the pig sector requires the implementation of new recovery processes. The identification of bioactive peptides (BPs) is a promising way to valorize this biomass. From an environmental point of view, it is possible to reduce the consumption of natural resources (surface of culture, water, energy) having used for the feeding of the pigs, by providing an economically interesting outlet to these by-products. On the other hand, the generation of bioactive peptides that can be used in the fields of pharmacology, cosmetics or food is part of the growing consumer demand for the development of more natural molecules. The objective of this project is to identify optimal hydrolysis conditions allowing generating, from porcine by-products, new bioactive molecules for nutritional or medical purposes. An in silico potency study is conducted on four porcine products (heart, liver, lung and muscle) to evaluate their ability to generate PBs, based on the use of different enzymes. In addition, the stability of the generated peptides is evaluated in the gastrointestinal tract using an in vitro static model. Finally, the method for the generation of BPs is developed at a pilot scale. In silico studies allowed to select the papain / subtilisin pair of enzymes for the generation of the highest number of peptides with antioxidant, antidiabetic (DPP4i) and antihypertensive (ACEi) activities. In vitro validation confirmed the presence of antioxidant and DPP4i activities in the four hydrolysates generated with papain and subtilisin. The biological activity of heart, liver and lung hydrolysates increases during gastrointestinal digestion. Experiments on the digestion of a pork patty supplemented with heart hydrolysate have shown that i) the cooking temperature (70°C or 90°C) slightly modulates iDPP4 and antioxidant activities during digestion, ii) supplementation significantly increases iDPP4 activity compared to a control sample. A moderate effect of this supplementation on the antioxidant activity was observed and iii) the antioxidant activity of the supplemented pork patty increases significantly (+ 40%) between the gastric and intestinal compartment. In addition, the methodology for the generation of bioactive peptides is possible on a pilot scale with commercial enzymes and adapted hydrolysis parameters. Peptide fractions with significant bioactivity can be valued as aromatic ingredients and to supplement a food product for obtaining health claims
21
Russell, Steven Arthur. "Machine learning and in silico modeling for improved identification of peptides from shotgun proteomic Ms/Ms spectra /." Connect to full text via ProQuest. IP filtered, 2005.
Find full textAbstract:
Thesis (Ph.D. in Bioinformatics) -- University of Colorado, 2005.Typescript. Includes bibliographical references (leaves 116-124). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
22
Eshibona, Nasr O. M. "Identification of novel miRNAs as diagnostic and prognostic biomarkers for prostate cancer using an in silico approach." University of the Western Cape, 2017. http://hdl.handle.net/11394/5993.
Full textAbstract:
Magister Scientiae - MSc (Biotechnology)Cancer is known as uncontrollable cell growth which results in the formation of tumours in the areas that are affected by the cancer. There are two types of tumours: benign and malignant. This study focus is on prostate cancer (PCa) as one of the most common cancers in men around the world. A previous study has reported that there were 27,132 new cases of cancer in South Africa in 2010. Out of those, 4652 were prostate cancer cases, which make it a considerable issue. The prostate is a gland that forms part of the male reproductive system. Prostate cancer is more apparent in men over the age of 65 years however it can be present in men of a lower age. However it is rare in men under 45 years of age. Prostate cancer start as a small group of cancer cells that can grow into a mature tumour. In the advanced stages, the tumour cells can spread to other tissue by metastases and can lead to death. Current diagnostic tools include Digital Rectal Examination (DRE), the Prostate-Specific Antigen test (PSA) ultra sound, and biopsy.
23
Kruczkiewicz, Peter. "A comparative genomic framework for the in silico design and assessment of molecular typing methods using whole-genome sequence data with application to Listeria monocytogenes." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, c2013, 2013. http://hdl.handle.net/10133/3391.
Full textAbstract:
Although increased genome sequencing e orts have increased our understanding of genomic
variability within many bacterial species, there has been limited application of this knowledge
towards assessing current molecular typing methods and developing novel molecular typing
methods. This thesis reports a novel in silico comparative genomic framework where the
performance of typing methods is assessed on the basis of the discriminatory power of the
method as well as the concordance of the method with a whole-genome phylogeny. Using
this framework, we designed a comparative genomic ngerprinting (CGF) assay for Listeria
monocytogenes through optimized molecular marker selection. In silico validation and assessment
of the CGF assay against two other molecular typing methods for L. monocytogenes (multilocus
sequence typing (MLST) and multiple virulence locus sequence typing (MVLST)) revealed that
the CGF assay had better performance than these typing methods. Hence, optimized molecular
marker selection can be used to produce highly discriminatory assays with high concordance to
whole-genome phylogenies. The framework described in this thesis can be used to assess current
molecular typing methods against whole-genome phylogenies and design the next generation of
high-performance molecular typing methods from whole-genome sequence data.xiii, 100 leaves : ill. ; 29 cm
24
Lambert, Caroline L. "Identification and Description of Burkholderia pseudomallei Proteins that Bind HostComplement-Regulatory Proteins via in silico and in vitro Analyses." University of Toledo Health Science Campus / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=mco1533315186098586.
Full text
25
Abruquah, Harry H. "Identification of host-pathogen interacting molecules of Campylobacter jejuni using phage display technology and in silico sequence analysis." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10813/.
Full textAbstract:
Campylobacter jejuni is the leading cause of human gastroenteritis world-wide, and the antecedent infection in Guillain-Barré syndrome. Although much progress has been made regarding its virulence determinants,our understanding of the molecular basis of C. jejuni pathogenesis still lags behind that of other enteric pathogens. Bacterial pathogenesis is often dependent on proteinaceous virulence factors transported to the bacterial cell surface or released into the external environment. Understanding the molecular basis of interactions between these proteins and host cells is necessary in understanding and controlling infections. Background: Previously identified adhesins of C. jejuni NCTC11168 have still not provided us with a total understanding of the pathogenesis of campylobacteriosis. It is hypothesized that as yet unidentified C. jejuni surface proteins interact with host proteins contributing to colonisation and pathogenesis. This study sought to screen the genome of C. jejuni NCTC11168 to identify additional genes that may code for other adhesins using phage display technology and in silico sequence analysis. Methods: A phage display library was constructed by the insertion of randomly fragmented chromosomal DNA of C. jejuni NCTC11168 into the phagemid vector pG8SAET. Following affinity panning of the library against holo- and apo-lactoferrin, enriched clones were screened with ELISA to identify affinity-binding clones. Several phage clones were randomly selected and their C. jejuni DNA inserts sequenced and analysed with bio-informatic tools. In order to identify novel autotransporter proteins of C. jejuni, the amino acid sequences of previously described adhesion-associated autotransporters were employed in BLAST searches of the predicted coding sequences of C. jejuni NCTC11168 genome database. Results: Screening of the phage display library resulted in the identification of C. jejuni NCTC11168 gene, Cj0609c, encoding a putative periplasmic protein, designated LimC, predicted to be a member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. Searching the genome of C. jejuni NCTC11168, Cj0628 was identified as coding a protein with characteristics of autotransporters, designated CapA. CapA was demonstrated to be surface-exposed, mutants of which had a lowered ability to associate with or invade Caco-2 cells and failed to colonize chicken guts, indicating that CapA plays a role in host association and colonization by Campylobacter. Conclusion: LimC may be involved in binding of C. jejuni to lactoferrin for iron acquisition in vivo, and/or play further role in adhesion, colonization and internalisation of C. jejuni into host cells. CapA also plays a role in adhesion. Further characterization of these proteins should contribute to our understanding of the pathogenesis of C. jejuni.
26
Padilla, Sirera Natàlia. "Novel approaches for in silico identification of pathogenic variants in BRCA1 and BRCA2 hereditary breast and ovarian cancer predisposition genes." Doctoral thesis, Universitat Autònoma de Barcelona, 2020. http://hdl.handle.net/10803/670705.
Full textAbstract:
Variants germinals a les proteïnes BRCA1 i BRCA2 poden alterar la funció protectora d’aquestes a l’ADN, incrementant el risc de desenvolupar càncer de mama i ovari hereditari (HBOC). Identificació d’aquells individus portadors de variants patogèniques permet canalitzar-los en programes específics de prevenció i vigilància, augmentant les seves taxes de supervivència. Per això, en primer lloc, cal identificar quines de les variants són patogèniques. Malauradament, no sempre hi ha prou informació per arribar a una conclusió. En aquesta situació, els predictors de patogenicitat dissenyats per estimar computacionalment el dany causat per les variants poden proporcionar una valuosa informació.
En aquest treball presentem una nova família de predictors de patogenicitat per BRCA1 i BRCA2. Aquests predictors difereixen en el seu objectiu: un està entrenat per estimar l’impacte molecular de les variants sobre la funció HDR de BRCA1 i BRCA2, i l’altre està entrenat per estimar la significació clínica d’una variant, és a dir, si la seva classificació és patogènica o neutra. Els seus rendiments han estat provats i són comparables als d’altres mètodes àmpliament utilitzats en el camp. Addicionalment, vam presentar els predictors al repte ENIGMA de la 5a Avaluació Crítica de la Interpretació del Genoma (CAGI), trobant que els nostres mètodes, especialment aquells que estimen l’impacte funcional de les variants, es classifiquen en les primeres posicions en comparació amb les altres eines.
Per tal de difondre aquesta família de predictors a la comunitat científica, hem construït el lloc web BRASS (https://www.biotoclin.org/BRASS), on els usuaris poden analitzar les seves variants de BRCA1 i BRCA2 amb canvi de sentit. Els usuaris més avançats també poden interpretar les prediccions mitjançant una mètrica de fiabilitat i diversos gràfics contextualitzant la seva puntuació amb la d’un conjunt de variants curades manualment.
Independentment, hem aplicat els nostres coneixements sobre predictors de patogenicitat en un gran projecte internacional per caracteritzar un nou trastorn neurològic pediàtric causat per variants patogèniques a la histona H3.3. Vam combinar l’ús de predictors de patogenicitat estàndard amb evidències d’anàlisis estructurals i càlculs biofísics per proporcionar una visió mecanicista de l’impacte de les variants causals.Variantes germinales en las proteínas BRCA1 y BRCA2 pueden alterar la función protectora de estas en el ADN, incrementando el riesgo de desarrollar cáncer de mama y ovario hereditario (HBOC). Identificación de aquellos individuos portadores de variantes patogénicas permite canalizarlos hacia programas específicos de prevención y vigilancia, aumentando sus tasas de supervivencia. Para ello, en primer lugar, es necesario identificar cuáles de las variantes son patogénicas. Desafortunadamente, no siempre hay suficiente información para llegar a una conclusión. En esta situación, los predictores de patogenicidad diseñados para estimar computacionalmente el daño causado por las variantes pueden proporcionar una valiosa información. En este trabajo presentamos una nueva familia de predictores de patogenicidad para BRCA1 y BRCA2. Estos predictores difieren en su objetivo: uno está entrenado para estimar el impacto molecular de las variantes en la función HDR de BRCA1 y BRCA2, y el otro está entrenado para estimar la significancia clínica de una variante, es decir, si su clasificación es patogénica o neutra. Sus rendimientos han sido probados y son comparables a los de los métodos ampliamente utilizados en el campo. Además, presentamos los predictores al desafío ENIGMA de la 5ª Evaluación Crítica de la Interpretación del Genoma (CAGI), encontrando que nuestros métodos, especialmente aquellos que estiman el impacto funcional de las variantes, se clasifican en las primeras posiciones en comparación con las otras herramientas. Para difundir esta familia de predictores a la comunidad científica, hemos construido el sitio web BRASS (https://www.biotoclin.org/BRASS), donde los usuarios pueden analizar sus variantes de BRCA1 y BRCA2 con cambio de sentido. Los usuarios más avanzados también pueden interpretar las predicciones utilizando una métrica de confiabilidad y varios gráficos que contextualizan su puntuación a la de un conjunto de variantes seleccionadas manualmente. De forma independiente, aplicamos nuestro conocimiento sobre los predictores de patogenicidad en un gran proyecto internacional para caracterizar un nuevo trastorno neurológico pediátrico causado por variantes patogénicas en la histona H3.3. Combinamos el uso de predictores patogénicos estándar con evidencia de análisis estructurales y cálculos biofísicos para proporcionar una visión mecanicista del impacto de las variantes causales.
Germline variants in BRCA1 and BRCA2 can disrupt the DNA protective role of these proteins resulting in an increased risk of developing hereditary breast and ovarian cancer (HBOC). Identification of those individuals carrying pathogenic variants will allow channeling them into specific programs of prevention and surveillance, incrementing their survival rates. For this purpose, first, it is necessary to identify which of the variants are pathogenic. Unfortunately, there is not always enough information to reach a conclusion. In this situation, pathogenicity predictors designed to computationally estimate the damage caused by variants, can provide valuable information. Here, we present a novel family of pathogenicity predictors for BRCA1 and BRCA2. These predictors differ in their objective: one is trained to estimate the molecular impact of variants on the HDR function of BRCA1 and BRCA2, and the other is trained to estimate the clinical significance of a variant, that is, whether it should be classified as pathogenic or neutral. Their performances have been tested and are comparable to those of widely used predictors in the field. Additionally, we presented them to the ENIGMA challenge from the 5th Critical Assessment of Genome Interpretation (CAGI), finding that our predictors, especially those estimating the functional impact of variants, ranked in the top positions compared to other tools. In order to disseminate this family of predictors to the scientific community, we have built the BRASS website (https://www.biotoclin.org/BRASS), where users can analyze their missense BRCA1 and BRCA2 variants. More advanced users can also interpret the predictions using a reliability metric and several plots contextualizing the score to that of a set of manually curated variants. Independently, we applied our knowledge about pathogenicity predictors in a large international effort to characterize a novel pediatric neurologic disorder caused by pathogenic variants in histone H3.3. We combined the use of standard pathogenic predictors with evidence from structural analyses and biophysical computations to provide a mechanistic view of the impact of the causative variants.
27
Leung, Po-shan. "In silico analysis of 16S ribosomal RNA gene sequencing based methods for identification of medically important Gram-positive cocci /." View the Table of Contents & Abstract, 2007. http://sunzi.lib.hku.hk/hkuto/record/B38348159.
Full text
28
胡國良 and Kwok-leung Wu. "In silico analysis of 16S ribosomal RNA gene sequencing based methods for identification of medically important Gram-positive rods." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40721802.
Full text
29
Leung, Po-shan, and 梁寶珊. "In silico analysis of 16S ribosomal RNA gene sequencing based methods for identification of medically important Gram-positive cocci." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B45011382.
Full text
30
Diallo, Bakary N'tji. "In silico study of Plasmodium 1-deoxy-dxylulose 5-phosphate reductoisomerase (DXR) for identification of novel inhibitots from SANCDB." Thesis, Rhodes University, 2018. http://hdl.handle.net/10962/64012.
Full text
31
Zahra, Latib. "Identification of novel microRNAs as potential biomarkers for the early diagnosis of ovarian cancer using an in-silico approach." University of the Western Cape, 2019. http://hdl.handle.net/11394/7415.
Full textAbstract:
Philosophiae Doctor - PhDOvarian cancer (OC) is the most fatal gynaecologic malignancy that is generally diagnosed in the advanced stages, resulting in a low survival rate of about 40%. This emphasizes the need to identify a biomarker that can allow for accurate diagnosis at stage I. MicroRNAs (miRNAs) are appealing as biomarkers due to their stability, non-invasiveness, and differential expression in tumour tissue compared to healthy tissue. Since they are non-coding, their biological functions can be uncovered by examining their target genes and thus identifying their regulatory pathways and processes. This study aimed to identify miRNAs and genes as candidate biomarkers for early stage OC diagnosis, through two distinct in silico approaches. The first pipeline was based on sequence similarity between miRNAs with a proven mechanism in OC and miRNAs with no known role. This resulted in 9 candidate miRNAs, that have not been previously implicated in OC, that showed 90-99% similarity to a miRNA involved in OC. Following a series of in silico experimentations, it was uncovered that these miRNAs share 12 gene targets that are expressed in the ovary and also have proven implications in the disease. Since the miRNAs target genes contribute to OC onset and progression, it strengthens the notion that the miRNAs may be dysregulated as well. Using TCGA, the second pipeline involved analysing patient clinical data along with implementing statistical measures to isolate miRNAs and genes with high expression in OC. This resulted in 26 miRNAs and 25 genes being shortlisted as the potential candidates for OC management. It was also noted that targeting interactions occur between 15 miRNAs and 16 genes identified through this pipeline. In total, 35 miRNAs and 37 genes were identified from both pipelines.
32
Wu, Kwok-leung. "In silico analysis of 16S ribosomal RNA gene sequencing based methods for identification of medically important Gram-positive rods." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B40721802.
Full text
33
Thelingwani, Roslyn. "Integration of In Silico and In Vitro ADMET properties in lead identification and optimization of compounds for the treatment of parasitic diseases." Doctoral thesis, University of Cape Town, 2012. http://hdl.handle.net/11427/6889.
Full textAbstract:
Parasitic infections are the major causes of illness and death in tropical regions especially in Africa. The main parasitic diseases include leishmaniasis, filariasis, malaria, river blindness, Chagas disease and schistosomiasis. With the absence of vaccines, treatment relies mainly on chemotherapy hence the need for efficacious and safe medicines. Many of the medicines currently used have low efficacy and cause side effects. Some are also being lost to drug resistance. To address the inadequacy of treatment options for infectious diseases, a number of initiatives have been started to promote drug discovery and development in Africa. In parallel they have been collaboration between African institutions and leading pharmaceutical companies as well as other relevant R & D organizations. This has led to the need to modernize African approaches to drug discovery and development with respect to the integration of medicinal chemistry, pharmacology and pharmacokinetics as reflected in the processes of Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET). However, scientific and technological expertise in pharmacokinetics for drug discovery is under developed in Africa.
34
Tanaka, Sunao. "In silico analysis-based identification of the target residue of integrin α6 for metastasis inhibition of basal-like breast cancer." Kyoto University, 2020. http://hdl.handle.net/2433/253190.
Full text
35
Penkler, David Lawrence. "In silico analysis of human Hsp90 for the identification of novel anti-cancer drug target sites and natural compound inhibitors." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1018938.
Full textAbstract:
The 90-KDa heat shock protein (Hsp90) is part of the molecular chaperone family, and as such it is involved in the regulation of protein homeostasis within cells. Specifically, Hsp90 aids in the folding of nascent proteins and re-folding of denatured proteins. It also plays an important role in the prevention of protein aggregation. Hsp90’s functionality is attributed to its several staged, multi-conformational ATPase cycle, in which associated client proteins are bound and released. Hsp90 is known to be associated with a wide array of client proteins, some of which are thought to be involved in multiple oncogenic processes. Indeed Hsp90 is known to be directly involved in perpetuating the stability and function of multiple mutated, chimeric and over-expressed signalling proteins that are known to promote the growth and survival of cancer cells. Hsp90 inhibitors are thus thought to be promising therapeutic agents for cancer treatment. A lack of a 3D structure of human Hsp90 however has restricted Hsp90 inhibitor development in large to in vivo investigations. This study, aims to investigate and calculate hypothetical homology models of the full human Hsp90 protein, and to probe these structural models for novel drug target sites using several in silico techniques. A multi-template homology modelling methodology was developed and in conjunction with protein-protein docking techniques, two functionally important human Hsp90 structural models were calculated; the nucleotide free “v-like” open and nucleotide bound closed conformations. Based on the conservation of ligand binding, virtual screening experiments conducted on both models using 316 natural compounds indigenous to South Africa, revealed three novel putative target sites. Two binding pockets in close association with important Hsp90-Hop interaction residues and a single binding pocket on the dimerization interface in the C-terminal domain. Targeted molecular docking experiments at these sites revealed two compounds (721395-11-5 and 264624-39-7) as putative inhibitors, both showing strong binding affinities for at least one of the three investigated target sites. Furthermore both compounds were found to only violate one Lipinski’s rules, suggesting their potential as candidates for further drug development. The combined work described here provides a putative platform for the development of next generation inhibitors of human Hsp90.
36
Younesi, Erfan [Verfasser]. "A Knowledge-based Integrative Modeling Approach for In-Silico Identification of Mechanistic Targets in Neurodegeneration with Focus on Alzheimer’s Disease / Erfan Younesi." Bonn : Universitäts- und Landesbibliothek Bonn, 2014. http://d-nb.info/1052582060/34.
Full text
37
David, Marion. "Identification and functional characterization of an ABC transporter of Haemonchus contortus, the P-glycoprotein 13." Thesis, Toulouse 3, 2016. http://www.theses.fr/2016TOU30206/document.
Full textAbstract:
Les lactones macrocycliques (LM) sont des anthelminthiques (AH) à effet paralysant très utilisés chez les animaux et les humains contre les nématodes parasites. Cependant, leur succès thérapeutique est compromis par la résistance croissante aux LM, qui pourrait être en partie dû aux ABC transporteurs P-glycoprotéines (Pgps) sélectionnés et surexprimés chez les nématodes résistants aux LM. Dans ce travail, nous avons étudié plus précisément la P-glycoprotéine 13 du parasite de petits ruminants, Haemonchus contortus. Son orthologue chez le modèle nématode C. elegans, Cel-Pgp-13, est exprimé dans les amphides, structures qui ont été associées à la sensibilité aux AH chez C. elegans et H. contortus. Pour prédire la capacité des Pgps de nematode à transporter des drogues, incluant des LM et autres AH, nous avons développé un modèle de docking in silico. Nous avons utilisé la structure cristallographique de C. elegans Pgp-1 (Cel-Pgp-1), et nous avons montré la liaison avec une forte affinité de plusieurs ligands décrits comme activateurs de sa fonction ATPasique. Nous avons aussi décrit une forte affinité des LM, et un site spécifique de liaison de ces composés à Cel-Pgp-1. Cette approche représente un outil important pour prédire les interactions entre AH, et pour concevoir rationnellement de nouveaux inhibiteurs compétitifs des Pgps de nématode, dans le but d'améliorer les stratégies thérapeutiques. Sur la base de cette approche, nous avons prédit la structure 3D de Hco-Pgp-13 à partir du cristal de Cel-Pgp-1 afin d'étudier son intéraction avec des substrats potentiels, en particulier les LM. Nous avons trouvé des affinités similaires pour différents composés précédemment testés sur Cel-Pgp-1. In vitro, la mesure de l'activité ATPasique montre que l'actinomycine D est un substrat de Hco-Pgp-13. Nos données démontrent la présence possible d'un domaine de reconnaissance multispécifique sur ce transporteur de parasite. La détermination par immunofluorescence de l'expression de Hco-Pgp-13 a montré une distribution tissulaire large indiquant que Hco-Pgp-13 pourrait jouer un role important dans le transport de substrats endogènes et/ou exogènes. En conclusion, ce travail permet de mieux comprendre le rôle des Pgps de nématodes dans le transport de médicaments AH, tant au niveau de l'organisme modèle C. elegans que du nématode parasite H. contortus. Cette étude suggère la conservation de la fonction de tranporteur ABC multidrogue dans ces espèces. La localisation de Hco-Pgp-13 sur les structures amphidiales, et son éventuelle implication dans la résistance aux médicaments et à la survie de H. contortus à l'exposition à des composés AH, restent à préciserMacrocyclic lactones (ML) are paralyzing anthelmintics used in animals and humans against parasite nematodes. However, their therapeutic success is compromised by the spread of ML resistance. This might be at least partly due to P-glycoproteins (Pgps) ABC transporters that are selected and overexpressed in ML-resistant nematodes. Deciphering the role of the 10 Pgps expressed in the parasite of small ruminants Haemonchus contortus is thus of major importance to guaranty anthelmintic (AH) efficacy of various drugs. Here we focused on Hco-Pgp-13 due to the expression in the amphids of its closest ortholog in the model nematode C. elegans. Indeed, the amphids represent a putative entry route of drugs to reach AH targets in the nervous system and have been linked to AH susceptibility in C. elegans and H. contortus. In order to predict the capacity of nematode Pgps to transport drugs, including ML and otherAH, we have developed an in silico drug docking model. We have used C. elegans Pgp-1 (Cel-Pgp-1) crystal structure and have showed a high affinity binding of several ligands that have been shown to be activators of its ATPase function. ML were also found to bind with high affinity to Cel-Pgp-1, on a specific binding site. This approach provides a valuable tool to predict drug-drug interactions and to rationally design new competitive inhibitors of nematode Pgps, in order to improve anthelmintic therapeutics. We then predicted a putative 3D structure of Hco-Pgp-13 based on the recently released crystal of Cel-Pgp-1, with which it presented a high homology. This allowed the study of the interaction of Hco-Pgp-13 with potential substrates, in particular ML. We found similar affinities for various drugs previously tested on Cel-Pgp-1, supporting the good homology of these two proteins. Together with in vitro ATPase assay experiments that confirmed the substrate status of actinomycin D, this indicates a possible multispecifc recognition capacity of this parasitic transporter. The determination of Hco-Pgp-13 localization using immunohistochemistry showed a wide tissue expression consistent with a critical role for Hco-Pgp-13 in endogenous and/or exogenous substrate transport. In conclusion, this work provides insights into the role of nematode Pgps in transporting AH drugs, both at the level of the model organism C. elegans and of the parasitic nematode H. contortus. This suggests a high homology of function conserved between ABC tranporters in these species. The localization of such protein on amphidial structures and its possible involvement in drug resistance and survival of H. contortus to exposure to AH compounds remain to be precised
38
Sergent, Jacques-Aurélien. "Modulation de l'expression du gène CFTR par le produit du gène FIC1 responsable de la cholestase familiale intra-hépatique progressive de type 1 : identification des mécanismes moléculaires impliqués." Cergy-Pontoise, 2008. http://www.theses.fr/2008CERG0365.
Full textAbstract:
La cholestase intra-hépatique familiale progressive de type 1 (PFIC1) est une maladie génétique rare due à un défaut de sécrétion des acides biliaires provoquée par des mutations du gène ATP8B1. Les patients PFIC1 souffrent de nombreuses manifestations extra-hépatiques dont certaines sont communes aux patients mucoviscidosiques. Le niveau d'expression de plusieurs gènes parmi lesquels figure CFTR, gène responsable de la mucoviscidose, est diminué chez les patients PFIC1. Notre étude a donc porté sur l'analyse des interactions/régulations entre CFTR et ATP8B1. Elle a montré que la protéine ATP8B1 subissait plusieurs maturations et que l'une des formes de cette protéine interagit physiquement avec une forme immature de la protéine CFTR. De plus un segment d'ATP8B1 semble réadressé au noyau où il pourrait jouer un rôle de régulateur der transcription des gènes dont l'expression est diminuée chez les patients PFIC1Progressive familial intrahepatic cholestasis type 1 is a rare genetic disease due ta a defect in bile acids secretion provoked by mutations in ATP8B1 gene. PFIC1 patients developed many extra-hepatic manifestations, sorne of them are shared with Cystic Fibrosis patients. Many genes present a low level of expression in PFIC1 patients suggesting that ATP8B1 should regulate these genes; among them was identified CFTR, involved in Cystic fibrosis. The aim of our study was to analyze regulation and detect interactions between CFTR and ATP8B1. We have shown that ATP8B1 protein could be maturated and one of the generated forms is interacting with immature CFTR. Moreover, a segment of ATP8B1 seems to be readdressed to the nucleus to be a gene regulator, explaining the decreased level observed for sorne genes for PFIC1 patients
39
Rieper, Stefanie [Verfasser]. "Potential of Phytonutrients to act as Mimetics for Caloric Restriction – Identification of the Transcriptional and Functional Overlap in silico / Stefanie Rieper." Kiel : Universitätsbibliothek Kiel, 2017. http://d-nb.info/1128646137/34.
Full text
40
Salentin, Sebastian [Verfasser], Michael [Akademischer Betreuer] Schroeder, Michael [Gutachter] Schroeder, and Andrew [Gutachter] Torda. "In Silico Identification of Novel Cancer Drugs with 3D Interaction Profiling / Sebastian Salentin ; Gutachter: Michael Schroeder, Andrew Torda ; Betreuer: Michael Schroeder." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://d-nb.info/1163944246/34.
Full text
41
Salentin, Sebastian [Verfasser], Michael [Akademischer Betreuer] Schroeder, Michael Gutachter] Schroeder, and Andrew [Gutachter] [Torda. "In Silico Identification of Novel Cancer Drugs with 3D Interaction Profiling / Sebastian Salentin ; Gutachter: Michael Schroeder, Andrew Torda ; Betreuer: Michael Schroeder." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-226435.
Full text
42
Lombe, Chipampe Patricia. "Identification of microRNAs as a class of biomarkers for the early diagnosis of prostate cancer : an in silico and molecular approach." University of the Western Cape, 2015. http://hdl.handle.net/11394/4863.
Full textAbstract:
>Magister Scientiae - MScProstate cancer (PCa) is the second most common form of cancer in men around the world. In many parts of Africa, data on prostate cancer is sparse. This is attributed to poor access to testing and diagnostics. The International Agency for Research on Cancer (GLOBOCAN) estimated that 28,000 deaths occurred as a result of PCa in Africa in 2008, 4500 of which were in South Africa. This figure (28,000) is predicated a rise to 57,000 over the next two decades. Currently, the most commonly used diagnostic tests for PCa are the DRE and PSA tests. The former is highly invasive and both have low specificity and poor sensitivity. Therefore, the need for a less invasive early detection method with the ability to overcome the lack of specificity and sensitivity is required. Biomarkers have recently been identified as a viable option for early detection of disease. Examples of biological indicators for disease are miRNAs. miRNAs are small non-coding RNA molecules which play a key role in controlling gene expression and certain biological processes. Studies have shown that aberrantly expressed miRNAs are a hallmark of several diseases like cancer. miRNA expression has been shown to be associated with tumour development, progression and response to therapy, suggesting their possible use as diagnostic, prognostic and predictive biomarkers. The study aimed to investigate the potential of miRNAs implicated in prostate cancer as putative biomarkers for the disease and evaluating these miRNAs in a panel of prostate as well as several other cancer cell lines using qRT-PCR. An in silico approach was used to identify 13 putative miRNAs implicated in prostate cancer of which 8 were further analysed in a parallel study and 5 in this study. Two publicly available target prediction software were used for target gene prediction of the 5 identified miRNAs. The target genes were subjected to functional analysis using web-based software, DAVID. Functions which were clustered with an enrichment score of 1.3 and greater were considered significant. Targets with gene ontologies linked to “transcription regulation”, “regulation of “apopotosis”, “extracellular region” and “metal ion binding” were considered for further analyses. Protein gene interaction analysis was performed to determine the pathways the target genes are involved in using STRING. Expression profile analysis of the genes in various tissues was also carried out using in silico methods through the TiGER and GeneHub-GEPIS databases. Analysis using DAVID resulted in 9 gene targets for the 5 miRNAs. It was found that miR3 seemed the most promising miRNA for biomarker validation based on the in silico analyses. Its target gene MNT was found to be abundantly expressed in prostate tissue from the TiGER results. The GeneHub-GEPIS results also indicated that the gene’s expression is up-regulated during prostate cancer. The expression levels of the miRNAs analysed using qRT-PCR indicated that miR3 is significantly over-expressed in prostate cancer cells when compared to the other cancer cell lines used in this study, corroborating the results observed from the in silico analyses. Another miRNA with interesting results was miR5. It was predicted to target two genes, YWHAZ and TNFSF13B. In TiGER, both were found to be expressed in prostate tissue. The genes were also found to be up regulated during prostate cancer in GeneHub-GEPIS. The expression level of miR5 in LNCaP was 15.32; it was significantly up-regulated in the cell line using qRT-PCR. However, miR5 was also present in HEPG2-7.06, MCF7-0.79, HT29-1.61 and H157-3.59. Thus, it was concluded it can be used as a biomarker in combination with other miRNAs. The miRNA miR2 was found to target the actin filament protein encoding gene AFAP1. The gene was predicted to be upregulated with a DEU of 33.25 in GeneHuB-GEPIS. The qRT-PCR analysis showed that the expression ratio in LNcaP was 8.79. However, miR2 expression was up-regulated in MCF7-0.85 and HT29-1.09 as well. The expression level of miR1 in BHP1 was found to be 4.85. It can be considered as an indicator for benign prostate hyperplasia. Future work would include investigating the expression of miR3 in a larger panel of cancer cells as well as in patient samples. In addition, analysis of the UTR sequences of the miRNAs targets experimentally to prove that the target genes identified using in silico methods, are indeed regulated by these miRNAs. Furthermore, performing gene “knock-out” studies on the genes that code for the miRNAs to study their roles in prostate cancer development.
43
Barinov, Aleksandr. "An in silico approach to the identification of proteins involved in bacteria-host interactions : a case-study of lactobacillus delbrueckii ssp. bulgaricus and related lactobacilli." Paris 11, 2009. http://www.theses.fr/2009PA112055.
Full textAbstract:
Les interactions bactéries-hôte constituent un domaine de recherche en pleine expansion. Pendant longtemps, les efforts se sont portés sur les interactions bactéries pathogènes-hôte mais depuis peu, il y a un intérêt grandissant pour le rôle bénéfique joué par les bactéries non-pathogènes dans le tractus digestif. Des études de plus en plus nombreuses décrivent le rôle des bactéries commensales sur la balance énergétique de l’hôte, les réponses immunitaires et l’homéostasie intestinale selon des mécanismes non encore élucidés. Les objectifs de ces travaux de thèse étaient de mieux comprendre ces interactions bactéries commensales avec l’hôte en se basant sur des analyses in silico des donnée issues de programmes de séquençage. Nous avons démontré comment ce type d’analyse pouvait s’appliquer à la détermination des mécanismes moléculaires impliqués dans les interactions microbiote-hôte. Les principaux résultats de ces travaux peuvent être classés en trois parties. La première concerne le développement et la validation de SurfG+, un nouvel outil d’analyse de séquences de protéines pour prédire les protéines potentiellement exposées à la surface de bactéries à Gram positif. La deuxième partie de résultats décrit l’application de l’outil SurfG+ aux protéomes de lactobacilles dont les génomes sont séquencés. Nous avons ainsi mis en évidence des différences significatives au niveau de leurs protéines de surface notamment en terme de nombre de protéines sécrétées et ancrées à la paroi. Enfin, dans la troisième partie, nous avons montré comment ces outils d’analyse in silico peuvent être exploités dans l’analyse fonctionnelle des protéines. Dans cette partie, nous étudions les effets immuno-modulateurs potentiels de protéines de surface de Lactobacillus delbrueckii subsp. Bulgaricus ATCC 11842Bacteria-host cell interactions is an area of growing interest. While pathogenic bacteria and their interaction with the human host traditionally received much attention, there is a growing interest for the beneficial role that non-pathogenic bacteria play at these interfaces and in the GI tract in particular. Growing number of studies indicate that intestinal bacteria influence host energy balance, immune responses and contribute to gut homeostasis, however the mechanisms underlying this dialogue still remains largely unexplored. The work presented in this thesis aims to review the present knowledge on bacteria-host interactions in the GI tract, and to demonstrate the importance of in silico analyses that are widely used in the modern era of genome sequencing to broaden our knowledge. It also shows how this information can be applied for functional studies aiming to decipher molecular mechanisms involved in bacteria-host interactions. The main results presented in this thesis can be divided into three parts. The first part deals with the development and validation of a new protein sequence analysis method to predict potentially surface exposed (PSE) proteins from Gram-positive bacteria. The second part describes the application of the newly developed prediction method to the proteomes of sequenced lactobacilli revealing important differences in their predicted surface protein content. Finally, in the third part we demonstrated how the application of the in silico tools may be applied for functional protein studies. In this part, we focus on the potential immune modulation effects of surface exposed proteins from Lactobacillus delbrueckii subsp. Bulgaricus ATCC 11842
44
Sauvage, Virginie. "Identification et caractérisation d'une famille de gènes codant pour des protéines ABC tranporteurs chez Toxoplasma gondii." Reims, 2005. http://www.theses.fr/2005REIMM207.
Full textAbstract:
La toxoplasmose est une zoonose due à un parasite intracellulaire obligatoire, Toxoplasma gondii. L'infection généralement bénigne peut cependant être responsable de formes cliniques sévères particulièrement en cas de transmission congénitale et chez l'immunodéprimé. Les différents schémas de traitement de la toxoplasmose reposent sur un nombre limité de médicaments et des échecs thérapeutiques ont été rapportés dans le traitement de la toxoplasmose congénitale ou celui des formes graves survenant chez les patients immunodéprimés. L'implication de protéines de transport responsables d'une réduction de l'accumulation des médicaments à l'intérieur du parasite, phénomène décrit chez Plasmodium, pourrait participer à ces échecs. Suite à l'émergence des résistances aux antiparasitaires, de nombreux gènes codant pour des protéines ABC transporteurs de type Pgp (ABCB) et MRP (ABCC) ont été identifiés et caractérisés chez de nombreux parasites protozoaires. Chez T. Gondii, des travaux précédents ont montré que différents inhibiteurs de Pgp, notamment le vérapamil et la cyclosporine A, réduisent l'invasion parasitaire de façon significative. Par conséquent, nous avons étudié le transport actif de xénobiotiques et sa modulation par le vérapamil et la cyclosporine A sur des parasites extra- et intracellulaires. L'utilisation de sondes fluorescentes (JC-1 et Daunorubicine) a permis de montrer, par spectrofluorimétrie et microscopie confocale, une inhibition des échanges moléculaires en présence de ces deux inhibiteurs à la fois dans les parasites vivants extra- et intracellulaires. Ces résultats ont suggéré l'existence d'une P-glycoprotéine homologue localisée au niveau du complexe membranaire du parasite. A la vue de ces résultats, l'identification de protéines de type ABC transporteur chez T. Gondii, a été abordée dans un premier temps par une approche utilisant des amorces dégénérées dirigées contre les motifs consensus, ce qui nous a permis d'isoler une séquence de 393 pb, nommée TgABC1, correspondant au site ATPasique d'une putative protéine ABC dont nous avons vérifié l'expression par RT-PCR au stade tachyzoïte des trois types de souches (I, II, III). En parallèle, nous avons exploré la banque de données de T. Gondii, ToxoDB récemment finalisée. Une recherche par homologies de séquences (Blastp) utilisant les protéines ABC caractérisées chez l'homme et les protozoaires a permis d'identifier 24 0RFs. Quinze d'entre eux ont été classés dans 5 des 7 familles ABC humaines: 6 ABCB, 2 ABCC, 1 ABCE, 1 ABCF et 5 ABCG. Les 9 ORFs restant correspondent à 4 protéines SMC, 4 ABCH et une protéine de structure atypique, non classable. La présence de transcrits ABC a été détectée aux stades tachyzoïte (I, II, III) et bradyzoïte (II, III) pour tous les gènes étudiés, suggérant une implication importante des protéines correspondantes dans la biologie du parasite. Ces gènes pourraient constituer de nouvelles cibles thérapeutiques. A notre connaissance, il s'agit de la première identification d'une famille de gènes codant pour des protéines ABC transporteur chez T. Gondii@Toxoplasma gondii is a protozoan intracellular parasite responsible for widespread infections. Toxoplasmosis is generally asymptomatic or causes very mild symptoms, but it can be severe in two populations, namely congenitally infected children and immunocompromised patients. Treatments of toxoplasmosis are limited, and failure due to drug resistance were reported in case of congenital or severe toxoplasmosis. One explanation could be due to implication of proteins in transport leading to reduction of drug concentrations into parasite, as described in Plasmodium. Several genes encoding for ABC transporters of Pgp (ABCB) and MRP (ABCC) type, were identified and characterized among protozoan parasites (ie P. Falciparum). In T. Gondii, previous studies showed that different Pgp inhibitors, such as verapamil and cyclosporine A, significantly decreased parasite invasion. Hence, we investigated the active transport of xenobiotics (JC-1 and Daunorubicine; fluorescent probes) and its modulation by verapamil and cyclosporine A on extra- and intracellular parasites. We have observed that these two Pgp inhibitors increase both extracellular and intracellular dye accumulation in living T. Gondii, pointing to the existence of a transmembrane transport mediated by a Pgp homologue localized on the parasite membrane complex. To further this study, degenerate oligonucleotide primers directed against consensus motifs were used in a PCR-based approach to clone a member of the ABC genes in T. Gondii. The isolated nucleotide sequence displayed a 393 bp open reading frame which was named T. Gondii ABC1 gene (TgABC1) corresponding to the ATP-binding site of a putative ABC protein. TgABC1 gene expression was detected by RT-PCR in the tachyzoite stage of T. Gondii genotypes I, II and III. Finally, the recent completion of the T. Gondii genome (ToxoDB) has permitted to retrieve 24 putative ABC proteins by BLAST comparison. For this, we used human and protozoan ABC sequences, and ATP-binding consensus motifs to screen the T. Gondii TwinScan2 predicted proteins database. Fifteen of them clustered into 5 of the 7 families of human ABC proteins: 6 ABCB, 2 ABCC, 1 ABCE, 1 ABCF and 5 ABCG. The 9 remaining ORFs were represented by 4 SMC proteins, 4 ABCH, and 1 member of atypical structure. The presence of ABC transcripts was detected in tachyzoite (I, II, III) and bradyzoite (II, III) stages, for all genes studied. Further research on the implication of these ABC proteins will increase our knowledge of the basic biology of Toxoplasma and provide the opportunity to identify novel therapeutic targets. To our knowledge, this is the first report of ABC protein-encoding genes family in T. Gondii
45
Corsi, Flavia. "Towards the in silico reconstruction of protein interaction networks : identification of DNA- and RNA-protein interfaces, and construction of a database of multiple interactions of proteins." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS452.pdf.
Full textAbstract:
Cette thèse porte sur la caractérisation et la prédiction des interfaces protéine-ADN et -ARN, et des comparaisons avec les interfaces protéine-protéine. Nous avons créé un ensemble non-redondant et représentatif de 187 complexes protéine-ADN à haute résolution, comprenant aussi les conformations non liées de 82 protéines. Cette base de données peut servir de référence dans le domaine. Nous avons mené une analyse exhaustive des propriétés de séquence et structurels des interfaces protéine-ADN/ARN et nous les avons comparé avec les propriétés des interfaces protéine-protéine et celles des régions protéiques non-interagissantes. Nous avons développé JET2DNA et JET2RNA, nouvelles méthodes pour la prediction des sites de liaison protéine-ADN/ARN à la surface des protéines. En combinant quatre descripteurs biologiquement pertinents, elles surpassent des méthodes par apprentissage machine. Elles permettent aussi de découvrir des sites de liaison alternatifs avec l'ADN/ARN et de déchiffrer leurs propriétés. Afin de donner un aperçu global de la plasticité des protéines interagissant avec l'ADN, nous avons construit la base de données protéine-(protéine)-ADN (P(P)DNAdb). Elle inclut les 187 complexes protéine-ADN de notre ensemble de référence, les forme libres des protéines et les structures des autres complexes où ces protéines, ou des homologues proches, sont impliqués. L'utilisateur peut accéder aux propriétés des interfaces, visualiser les changements de conformation associés à la liaison avec des partenaires différents et localiser les résidus interagissants avec l'ADN dans les autres structures de la même protéineThis thesis focuses on the characterization and prediction of DNA- and RNA-binding sites on protein structures, with some comparisons with protein-protein ones. We compiled and manually curated a non-redundant and representative set of 187 high resolution protein-DNA complexes, with the available 82 protein unbound conformations, that could be used as a reference benchmark. We conducted a comprehensive analysis of sequence- and structure-based properties of protein-DNA/RNA interfaces and compared them with respect to protein-protein interfaces and to non-interacting protein regions. We developed JET2DNA and JET2RNA, new methods for predicting DNA- and RNA-binding sites on protein surfaces. Combining four biologically meaningful descriptors, they outperform other machine-learning methods, in terms of predictive power and robustness to conformational changes. Our tools demonstrated to be instrumental in discovering alternative DNA/RNA-binding sites and in deciphering their properties. This could be very helpful for drug design and repurposing. To give a comprehensive view of plasticity of DNA-binding proteins and structural information on their multiple interactions, we constructed the Protein-(Protein)-DNA database (P(P)DNAdb). It comprises the 187 protein-DNA complexes in our benchmark, protein unbound forms and structures of other complexes where the proteins, or closed homologs, were in contact with other proteins. The user can access properties of the interfaces, visualize conformational changes associated to the binding of different partners and the location of the DNA-binding residues on the unbound structures and on the complexes with the other protein partners
46
Gutowski, Lukasz [Verfasser], and Klaus [Akademischer Betreuer] Kümmerer. "Fate of Pesticides in the Aquatic Environment: Determination and Identification of Dead End Degradation Products of Selected Pesticides and a Hydrological Tracer by Combination of Experimental and In Silico Methods / Lukasz Gutowski. Betreuer: Klaus Kümmerer." Lüneburg : Universitätsbibliothek der Leuphana Universität Lüneburg, 2015. http://d-nb.info/1080361367/34.
Full text
47
Gilardin, Laurent. "Identification des épitopes T d’ADAMTS13 chez les patients atteints de Purpura Thrombotique Thrombocytopénique The ADAMTS13¹²³⁹-¹²⁵³ peptide is a dominant HLA-DR1-restricted CD4⁺ T-cell epitope Purpura Thrombotique Thrombocytopénique : physiopathologie, clinique, pronostic et traitement In silico calculated affinity of FVIII-derived peptides for HLA class II alleles predicts inhibitor development in haemophilia A patients with missense mutations in the F8 gene In silico prediction of immuno-dominant T-cell epitopes on human therapeutic factor VIII Predictive immunogenicity of Refacto AF Complement C3 is a novel modulator of the anti-factor VIII immune response Anti-ADAMTS13 Autoantibodies against Cryptic Epitopes in Immune-Mediated Thrombotic Thrombocytopenic Purpura." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS520.
Full textAbstract:
Le purpura thrombotique thrombocytopénique (PTT) est une maladie autoimmune rare et grave caractérisée par la présence d’anticorps dirigés contre ADAMTS13 (A13), une protéase impliquée dans l’hémostase primaire. L’implication des lymphocytes T CD4⁺ spécifiques d’ADAMTS13, dans la physiopathologie de la maladie est suggérée par une restriction pour l’haplotype HLA-DRB1*11 (DR11), l’isotype IgG des anticorps. Dans ce travail, nous avons cherché à identifier les épitopes T d’A13. Tout d’abord, nous avons sélectionné in silico les peptides d’A13 susceptibles d’être présentés par les molécules HLA-DR11. Ensuite, l’étude de la liaison de ces peptides à des molécules HLA-DR11 par des tests ELISA compétitifs a permis d’identifier les peptides les plus affins. Enfin, nous avons déterminé les peptides d’ADAMTS13 reconnus par les lymphocytes T CD4⁺ de donneurs sains et de patients porteurs de l’haplotype DR11. Ces travaux ont également été reproduits pour l’haplotype HLA-DR1 et dans un modèle murin de souris transgéniques humanisées exprimant l’haplotype HLA-DR1. Les résultats de ce travail nous permettent d’envisager d’isoler des lymphocytes T CD4⁺ spécifiques d’ADAMTS13 chez les patients afin de mieux les caractériser aux différents stades de la maladie et de suivre leur évolution sous traitement dans le but de mieux anticiper les rechutesThrombotic thrombocytopenic purpura (TTP) is a rare and severe disease characterized by auto-antibodies directed against ADAMTS13 (A13), a plasmatic protein involved in haemostasis. The implication of CD4⁺ T cells in the pathogenesis of the disease is suggested by the existence of a restriction to particular HLA-DR alleles and by the IgG isotype of the antibodies. In this study, we wished to determine the T cell epitopes of A13. First, we selected in silico the immunodominant peptides, based on their binding capacity to HLA-DR11 molecules. Second, their binding capacity to purified HLA-DR11 molecules using a ELISA competitive assay led us to identify the best binder peptides. Finally, we determined the peptides recognized by human CD4⁺ T cells from DR11 healthy donors and patients. These results were reproduced for the HLA-DR1 haplotype and in a transgenic humanized HLA-DR1 mouse model. In a perspective point of view, our results will allow us to further isolate the specific CD4⁺ T cells in order to characterize them at different steps of the disease and during follow-up to better anticipate relapses
48
Hung, Hsing-Shen. "In silico identification of Trichomonade xylosyltransferase via genomewide scanning." 2006. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0006-0408200620203000.
Full text
49
Hung, Hsing-Shen, and 洪幸伸. "In silico identification of Trichomonade xylosyltransferase via genomewide scanning." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/gqxyke.
Full textAbstract:
碩士國立臺北科技大學
有機高分子研究所
94
Trichomonas vaginalis (T. vaginalis ) is an causative agent of trichomoniasis, which is a pivotal and emerging cofactor affecting HIV transmission. The parasite has a dense glycocalyx. The novel finding on the structure of N-linked core structure from T. vaginalis glycalyx (K.Y. Hwa et al, unpublished data) triggers this study, in searching of enzymes synthesizing the new structure. For this reason we inferred that T. vaginalis should possess of xylosyltransferase. To take the time and cost advantages of bioinformatics approach, we have used several different methods to construct theoretical modeling based primarily on HMM, from known sequences of xylosyltransferase genes characterized from other species. We then use the derived model to search for xylosyltransferase genes, by in silico screening of EST genome database of T. vaginalis. Our results had detected 8 sequences with high similarity to beta-1, 2 xylosyltransferase. To further confirm the identity of these sequences, we have used pair-wide BLAST against non-redundant protein bank to see if what would be the genes with high similarity to the 8 candidate sequences. As expected, the similar genes with highest score, are from xylosyltransferase. The identification of the novel xylosyltranferase can be applied for industrial usage in biotechnology. To extend our research, we have also use the sequence to examine a fundamental question on evolution of eukaryotes. Comparative analyses of rRNA sequences have used to construct the “universal tree of life” , a phylogentic tree, which shown a division of living organisms into three major domains: Eucarya, Archaea, and Bacteria. In the rRNA phylogenetic tree, the earliest eukaryotic cells are Archaezoa, which are amitochondriate organisms such as the Diplomonads (Giardia) and Parabasalia (Trichomonads). However recent data using phylogenetic methods based on protein-coding genes have shown that classical methods of molecular phylogeny using rRNA genes may fail to delineate phylogenetic relationships between the three major domains or between major lineages of these domains. Our results had detected eight sequences with high similarity to beta-1, 2 xylosyltransferase. We then, constructed a phylogenetic tree with xylosyltransferase coding regions. Interestingly, the phylogenetic tree based on the “hypothetical” xylosyltransferase protein coding sequences, is similar to the one based on rRNA sequences. Based on the structure similarity in core structure of N-linked glycan and the phylogenic method, we conclude that trichomonads might be the most ancient eukaryote.
50
Salentin, Sebastian. "In Silico Identification of Novel Cancer Drugs with 3D Interaction Profiling." Doctoral thesis, 2017. https://tud.qucosa.de/id/qucosa%3A30374.
Full textAbstract:
Cancer is a leading cause of death worldwide. Development of new cancer drugs is increasingly costly and time-consuming. By exploiting massive amounts of biological data, computational repositioning proposes new uses for old drugs to reduce these development hurdles. A promising approach is the systematic analysis of structural data for identification of shared binding pockets and modes of action.
In this thesis, I developed the Protein-Ligand Interaction Profiler (PLIP), which characterizes and indexes protein-ligand interactions to enable comparative analyses and searching in all available structures. Following, I applied PLIP to identify new treatment options in cancer: the heat shock protein Hsp27 confers resistance to drugs in cancer cells and is therefore an attractive target with a postulated drug binding site. Starting from Hsp27, I used PLIP to define an interaction profile to screen all structures from the Protein Data Bank (PDB). The top prediction was experimentally validated in vitro. It inhibits Hsp27 and significantly reduces resistance of multiple myeloma cells against the chemotherapeutic agent bortezomib.
Besides computational repositioning, PLIP is used in docking, binding mode analysis, quantification of interactions and many other applications as evidenced by over 12,000 users so far. PLIP is provided to the community online and as open source.