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Development of novel droplet-based microfluidic strategies for the molecular diagnosis of cancer / Développement de nouvelles techniques de microfuidique en gouttes pour la détection des biomarqueurs de cancerPekin, Deniz 26 February 2013 (has links)
Le cancer constitue un problème majeur de santé publique en France. La nécessité de disposer d’un test capable de détecter très précocement une tumeur, avant même qu’elle ne soit décelable par l’imagerie (et surtout avant les métastases) ne fait pas doute. Pour l’heure, la voie la plus prometteuse pour détecter la maladie demeure la mise au point des tests simples, fiables, rapides et hautement sensibles, reposant sur le dosage de marqueurs génétiques (des biomarqueurs). Nous avons développé une procédure non-invasive, innovante et au moins 1000 fois plus sensible que les méthodes actuelles (0,0005% de séquences mutées détectées parmi un excès de séquences non-mutées), pour le criblage des biomarqueurs spécifiques des cancers. Elle peut facilement être utilisée pour le diagnostic, le pronostique ou la prédiction des procédures de gestion clinique des patients souffrant du cancer colorectal et par après pour les patients souffrant d’autres types de cancer. Cette méthode est basée sur l’utilisation des millions de microgouttelettes en tant qu’autant de bioréacteurs indépendants. Apportant ainsi la possibilité d’analyse chaque molécule d’ADN indépendamment, elle permettra de détecter spécifiquement une minorité de séquences mutantes au sein d’une forte quantité de séquences non mutées et avec un débit important. Nous avons développé cette stratégie pour la détection des mutations de l’oncogène KRAS (responsables des non-réponses aux thérapies ciblées) et nous l’avons validé avec la détection de mutations KRAS dans les échantillons de plasma sanguin et de tumeur des patients atteints d’un cancer colorectal métastatique. Notre méthode trouvera son utilité non seulement dans le domaine du diagnostic précoce des cancers, mais aussi dans cas de la prédiction de la réponse aux traitements ciblés grâce à la détection de biomarqueurs spécifiques. / The aim of this work is to establish novel strategies for the highly sensitive screening of cancer biomarkers in biological samples.To achieve this goal, we developed droplet-based microfluidic dPCR technique. Using a limiting dilution, individual DNA molecules are encapsulated within monodisperse droplets of a water-in-oil emulsion created with a microfluidic device. Fluorescent TaqMan® probes targeting the screened cancer biomarkers allow the detection of mutations. We focused on the mutations in the human KRAS gene for the development of our test. This method is also transposable in a multiplexed format for the parallel detection of multiple mutations in clinical samples.The developed technique allowed the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of un-mutated KRAS genes and enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines. We validated our technique by screening for KRAS mutations in the blood plasma and tumor samples from patients with metastatic colorectal cancer.
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Nanostructured Gold-Modified Laser Scribed Graphene Biosensor Based on Molecularly Imprinted PolymersAljedaibi, Abdulrahman 07 1900 (has links)
Recently, laser scribed graphene (LSG) technology has shown great potential for the development of a plethora of sensing platforms due to its high sensitivity, 3D porous structure, and flexibility. Molecularly imprinted polymers (MIPs) have shown high potential as recognition elements for many applications such as biosensing. Hence, we report in this thesis a novel biosensing platform that utilizes nanostructured gold to enhance the performance of LSG sensors coupled with a biomimetic MIP biosensor. To the best of our knowledge, this is the first report of a nanostructured gold modified MIP based LSG biosensor to detect HER-2, which is an important breast cancer biomarker. HER-2 positive breast cancer is more aggressive and does not respond to the same treatment as standard breast cancer. As such, a simple and accurate sensing approach is highly needed for early detection of this type of cancer biomarkers. The LSG sensor platform was fabricated by irradiation of polyimide substrates using a CO2 laser under optimized conditions. Nanostructured gold was electrodeposited onto LSG to enhance its sensitivity and active surface area. Deposition parameters such as deposition voltage, deposition time, and gold chloride (HAuCl4) concentration were optimized to yield complete nanostructured gold coverage and enhanced electrical conductivity of LSG-Au electrodes. A deposition voltage of -0.9 V at 50 mM HAuCl4 for 4 minutes proved to be the optimal condition for gold deposition to yield a 150% peak current enhancement. To fabricate our MIP biosensor, 3,4-
ethylenedioxythiophene (EDOT) was chosen from several functional monomers to form PEDOT due to its high conductivity and synergy with nanostructured gold. Electropolymerization of EDOT is performed after adsorbing 0.4mg/mL of HER-2 on the LSG-Au electrode for 20 min. The efficiency of LSG-Au-MIP was optimized by choosing an appropriate extraction agent and HER-2 concentration to be adsorbed on gold. The developed sensing strategy could differentiate between three rebinding concentrations of 10 ng/mL, 100ng/mL, and 200 ng/mL, which is sufficient to determine the HER-2 status of breast cancer since the clinical cut-off is 30.5ng/mL. The developed sensing strategy showed a high degree of novelty and could be useful for the non-invasive detection of cancer biomarkers.
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<b>Role of MicroRNA in Canine Diffuse Large B-Cell Lymphoma</b>Nelly O Elshafie IV (17104207) 06 October 2023 (has links)
<p dir="ltr">Lymphoma is a prevalent malignancy in dogs. Diffuse large B-cell Lymphoma (DLBCL) is the common subtype that represents about 50% of the clinically seen lymphoma cases. DLBCL diagnosis relies on cytological examination of a fine needle aspirate and histological evaluation by immunohistochemistry (IHC) in most common practices. This workflow is sufficient to confirm the diagnosis; however, it may be challenging to differentiate reactive and neoplastic forms in some controversial cases. In such cases, PCR-based clonality assays and flow cytometry (FC) can help with more conclusive diagnoses. So, finding more biomarkers that can detect and track DLBCL early and over time is a must for a final diagnosis and helps us learn more about how DLBCL starts at the molecular level. MicroRNAs (miRNAs), the small non-coding RNAs, regulate gene expression by binding to the 3'-untranslated region of protein-coding RNAs, leading to either RNA degradation or translational repression. They can switch on and off genes to regulate physiological and pathological processes. MicroRNA stability features and tissue availability make them promising biomarkers for identifying and sub-classifying patients and sequentially evaluating the disease status or the response toward a specific medicine. This dissertation investigates the small RNA sequence analysis, the differentially expressed miRNAs between healthy and DLBCL-affected lymph nodes, and the miRNA profile in DLBCL cases with different outcomes.</p>
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Bioinformatics analysis of epigenetic variants associated with melanomaMurat, Katarzyna January 2018 (has links)
The field of cancer genomics is currently being enhanced by the power of
Epigenome-wide association studies (EWAS). Over the last couple of years
comprehensive sequence data sets have been generated, allowing analysis
of genome-wide activity in cohorts of different individuals to be increasingly
available. Finding associations between epigenetic variation and phenotype
is one of the biggest challenges in biomedical research. Laboratories lacking
dedicated resources and programming experience require bioinformatics
expertise which can be prohibitively costly and time-consuming. To address
this, we have developed a collection of freely available Galaxy tools
(Poterlowicz, 2018a), combining analytical methods into a range of convenient
analysis pipelines with graphical user-friendly interface.The tool suite
includes methods for data preprocessing, quality assessment and differentially
methylated region and position discovery. The aim of this project was to
make EWAS analysis flexible and accessible to everyone and compatible with
routine clinical and biological use. This is exemplified by my work undertaken
by integrating DNA methylation profiles of melanoma patients (at baseline and
mitogen-activated protein kinase inhibitor MAPKi treatment) to identify novel
epigenetic switches responsible for tumour resistance to therapy (Hugo et
al., 2015). Configuration files are publicly published on our GitHub repository
(Poterlowicz, 2018b) with scripts and dependency settings also available to
download and install via Galaxy test toolshed (Poterlowicz, 2018a). Results
and experiences using this framework demonstrate the potential for Galaxy to
be a bioinformatics solution for multi-omics cancer biomarker discovery tool.
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Physical activity and breast cancerLahart, I. M. January 2014 (has links)
Background: Breast cancer is the most frequently diagnosed cancer and a leading cause of cancer death among females, both worldwide and in the UK. Although, UK incidence of breast cancer is rising, breast cancer mortality rates are falling, due largely to early detection and improved treatment. As a result there are more women living with a diagnosis of breast cancer than ever before. Due mainly to side-effects of adjuvant therapy, breast cancer patients may require diagnostic, therapeutic, supportive or palliative services many years post-diagnosis, which poses a major challenge to already stretched healthcare services. Accordingly, effective and inexpensive interventions that can alleviate treatment side-effects, improve health, quality of life and potentially reduce risk of early mortality are required for breast cancer patients. Awareness of the positive influence that physical activity can have on breast cancer development and outcome is an important determinant of physical activity levels. A higher level of physical activity before and after breast cancer diagnosis is related to a lower risk of all-cause and breast cancer-related mortality. Randomised controlled trials have reported beneficial effects of physical activity interventions on outcomes relating to health, quality of life and mortality risk among breast cancer survivors. Aims: The present project aimed to: 1) assess awareness of the role of physical activity on breast cancer risk and the sufficiency of physical activity undertaken in women attending the NHS breast screening programme (NHSBSP), 2) compare physical activity levels of women at different stages of breast cancer pathway, 3) investigate the effects of a low-cost six-month home-based physical activity intervention on physical activity, body mass, health-related quality of life (HRQoL), insulin resistance and blood lipid profiles of breast cancer survivors and 4) assess the effects of our home-based intervention on cardiorespiratory fitness in a subset of breast cancer survivors. Methods: A total of 309 volunteers (188 NHSBSP attendees, 41 breast cancer patients undergoing chemotherapy and 80 post-treatment breast cancer survivors) participated in the current project. Physical activity was assessed via the International Physical activity Questionnaires (IPAQ). In studies one and two, Body mass and body mass index (BMI) were assessed directly in chemotherapy patients and breast cancer survivors, and indirectly from self-reported values in NHSBSP attendees. While in study three, body fat percentage was measured via bioelectrical impedance analysis, HRQoL was assessed using the Functional Assessment of Cancer Therapy-Breast (FACT-B) questionnaire and fasting blood samples were taken to measure lipid, glucose and insulin concentrations at baseline and post-six month home-based physical activity intervention. In study four, a random subsample of 32 breast cancer survivors undertook an exercise tolerance test to establish peak oxygen uptake values. Results: A high proportion (70%) of NHSBSP attendees engaged in low-moderate levels of physical activity and performed low amounts of recreational physical activity. Attendees demonstrated high awareness (75%) of the role of physical activity in reducing breast cancer risk but those categorised as “low activity” were significantly unaware of insufficiency of activity (p<0.05). Chemotherapy patients and breast cancer survivors had significantly lower levels of total physical activity than NHSBSP attendees (p<0.001 and p<0.05, respectively). The randomised controlled trial revealed significant improvements in total physical activity, body mass (p<0.05), BMI (p<0.05) HRQoL (breast cancer subscale, p<0.01; trial outcome index, p<0.05) and total (p<0.01) and low-density lipoprotein (p<0.05) cholesterol concentrations in the intervention group compared to usual care, and significant improvements in cardiorespiratory fitness (p<0.05) in a subsample of breast cancer survivors allocated to intervention. Conclusions: Physical activity interventions that incorporate strategies aimed at increasing awareness of recommended physical activity guidelines may be required in populations at risk of breast cancer. A relatively large proportion of women at risk of breast cancer may not be sufficiently exposed to the potential benefits of physical activity on breast cancer outcomes. Post-treatment breast cancer patients may be more receptive to physical activity interventions as the negative effects of chemotherapy begin to resolve, and therefore, may benefit from physical activity interventions. Results suggest that a low-cost home-based physical activity intervention with counselling and telephone support can improve the health and HRQoL of breast cancer survivors, which may in turn potentially reduce risk of breast cancer and cardiovascular disease-related mortality. Given the encouraging results and its highly portable and feasible nature, our intervention represents a promising tool for use in health and community settings to benefit large numbers of breast cancer survivors. The current project supports the inclusion of physical activity promotion as an integral component for the management and care of breast cancer survivors.
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Applications of Monolithic Capillary Electrochromatography (CEC): Method Development and Quantitation of Metabolites in Prostate Tissue and Insights into Chiral Recognition MechanismLu, Yang 06 January 2017 (has links)
Capillary electrochromatography (CEC) is a major capillary electrophoresis (CE) mode that have been interfaced to mass spectrometry (MS) for sensitive and selective analysis of chiral compounds. This research expands CEC applications in cancer biomarker and chiral CE analysis. Chapter 1 is a review of liquid chromatography-mass spectrometry (LC/MS), gas chromatography-mass spectrometry (GC/MS), and capillary electrophoresis mass spectrometry (CE/MS) for analysis of metabolites in prostate cancer diagnostics and therapies. In this chapter, a literature survey was performed within the databases PubMed, 4 Caplus/Webline and Web of Sciences. A total 17 studies reporting on various analytical platforms for metabolite identification in prostate cancer research, which often include case-control comparison were identified and reviewed. Chapter 2 described the analysis of metabolite biomarkers in prostate cancer tissues by capillary electrochromatography mass spectrometry. In this chapter, a capillary CEC–MS/MS method was developed for the simultaneous determination and separation of eight proofs of concept (POC) metabolites (betaine, malate, proline, N-acetyl aspartate, N-acetylglucosamine, uracil, xanthine, and alanine) as potential prostate cancer diagnostic markers. A polymeric monolith column with a hydrophilic crosslinker and strong anion-exchange mixed-mode has been fabricated by an in situ copolymerization of vinyl benzyl trimethylammonium chloride, and bisphenol A glycerolate dimethacrylate (BisGMA) in the presence of methanol and dodecyl alcohol as porogens and AIBN as initiator. After CEC separation, samples were analyzed by a triple–quadrupole mass spectrometer operated in positive ion mode. After optimization, the data showed that the CEC-MS/MS method using monolithic column achieved a much better chromatographic selectivity compared to coated columns and increased sensitivity than bare fused silica column The effect of mobile phase pH, ACN percentage and additive were studies. Under the optimum mobile phase conditions, this method was carried out to separate and detect eight metabolites in the biopsy sample. The LOD for the metabolites is between 50nM-100nM. This method has successfully used to examine patients’ prostate cancer with an accuracy of 95%. Chapter 3 demonstrates Insights into Chiral Recognition Mechanisms in CEC using linear salvation energy relationship. By varying the linker (amide and carbamate), head group (alanine, leucine, and valine) and chain length (C8, C10 and C12) of the amino acid bound surfactants; monolithic column was made to ultimately understand the factors governing chiral stationary solid phase. Through the comparison of system parameters, we can see that surfactant head group, linker and chain length affect the separation of achiral and chiral compounds. Also, with the same type surfactant, data was presented to show how the trend of LSER parameters and how it affects separation between in CEC. This study showed the predictive capability of LSER to understand the aforementioned intermolecular processes controlling retention and by doing so, be able to quantitatively predict the experimental conditions to achieve an acceptable chiral separation.
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Συσχέτιση αλληλομορφών της μικροδορυφορικής θέσης DG8S737 της χρωμοσωμικής περιοχής 8q24 με επιθετικό καρκίνο του προστάτη σε ελληνικό πληθυσμόΚατσένης, Νικόλαος 08 May 2012 (has links)
Ο καρκίνος του προστάτη αποτελεί σημαντικό πρόβλημα της δημόσιας υγείας ιδιαίτερα στο δυτικό κόσμο. Είναι ο πιο συχνός σπλαχνικός καρκίνος και ο δεύτερος πιο θανατηφόρος μετά τον καρκίνο του πνεύμονα.
Η εισαγωγή και χρήση του PSA από τα τέλη της δεκαετίας του ’80 προσέθεσε ένα ισχυρό διαγνωστικό εργαλείο στα χέρια των κλινικών, το οποίο αναχαίτισε τη μέχρι τότε αυξητική τάση του αριθμού των θανάτων οφειλομένων στον καρκίνο του προστάτη. Το PSA ωστόσο χαρακτηρίζεται από χαμηλή ειδικότητα αλλά και ευαισθησία, χαρακτηριστικά που επιβάλλουν περιορισμούς στη χρήση του. Εξάλλου δεν προβλέπει το βαθμό της επιθετικότητας ενός αδενοκαρκινώματος του προστάτη, συμβάλοντας στο φαινόμενο της υπερδιάγνωσης αλλά κυρίως της υπερθεραπείας του καρκίνου του προστάτη. Κατά συνέπεια είναι απαραίτητη η ανάπτυξη μοριακών εργαλείων (δεικτών) οι οποίοι θα διαγιγνώσκουν τη νόσο με μεγαλύτερη ασφάλεια αλλά κυρίως θα μας δίνουν προγνωστικές πληροφορίες για τη βιολογική συμπεριφορά του όγκου, προλαμβάνοντας μια άσκοπη θεραπευτική παρέμβαση.
Ενδιαφέρον πεδίο αναζήτησης τέτοιων δεικτών αποτελεί η χρωμοσωμική περιοχή 8q24. Ο μικροδορυφόρος DG8S737 εδράζεται στην περιοχή 8q24 και έχει δειχθεί, σε διαφορετικούς πληθυσμούς, ότι συγκεκριμένο αλληλόμορφό του σχετίζεται με επιθετικό, κλινικά σημαντικό καρκίνο του προστάτη.
Στη συγκεκριμένη μελέτη ανιχνεύονται οι συχνότητας των αλληλομόρφων του μικροδορυφόρου DG8S737 σε μια ομάδα γενικού πληθυσμού (control) και σε μια ομάδα ασθενών οι οποίοι πάσχουν από επιθετικό καρκίνο του προστάτη.
Τα αποτελέσματα επιβεβαιώνουν την τάση του αλληλομόρφου -8 να ανιχνεύεται συχνότερα σε ασθενείς παρά σε υγιείς. Εξάλλου παρατηρήθηκε για πρώτη φορά η ίδια τάση και για το αλληλόμορφο -10.
Αυτά τα αποτελέσματα ενισχύουν το δυναμικό χρήσης του DG8S737 ως δείκτη για το μέτρο της επιθετικότητας του καρκίνου του προστάτη. / Prostate cancer represents a major public health issue in western world. It is the most frequently diagnosed visceral cancer whereas it is second in mortality.
The use of PSA since the late 80s restrained the rising tendency of mortality of prostate cancer. PSA though, lacks in specificity. Besides it contributes to the phenomenon of overdiagnosis which leads to overtreatment of prostate cancer. Consequently it is necessary for novel biomarkers to emerge in order to diagnose more accurately and predict the aggressiveness of prostate cancer.
The 8q24 region of chromosome 8 is a region which could harbor potential biomarkers for prostate cancer. The microsatellite DG8S737 in that region has a number of alleles, one of which has the tendency to be more often detected in patients with aggressive prostate cancer.
We have studied the frequencies of alleles of DG8S737 in a group of patients with aggressive prostate cancer as well as in a group of control volunteers. The results confirm the findings of previous studies. The allele -8 of DG8S737 has been detected more often in patients than in healthy volunteers. A new finding is that allele -10 also is more frequently detected in the patients group rather than the control group.
The results confirm previous findings and enforce the potential use of DG8S737 as novel biomarker for the aggressive prostate cancer.
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Lectinas vegetais: de moléculas de defesa de plantas às suas diversas aplicações biotecnológicas / Vegetable lectins: from plant defense molecules to the various biotechnological applicationsOliveira, Jaqueline Franciele Caetano de 06 July 2018 (has links)
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Previous issue date: 2018-07-06 / Lectins are proteins belonging to a diverse superfamily, which has as its main characteristic, the capacity to specifically and selectively recognize carbohydrates. They are present in a great variety of microorganisms, such as viruses, bacteria, fungi, plants, and animals. Due to its ability to recognize a large number of glycans, they behave as mediators in many biological processes, as in cell migration, immunologic defense and in bacterial, protozoan and viral infections. Among all, plant lectins are the most studied, showing structural heterogeneities, mainly on its carbohydrates binding sites, what grants several biological activities to these proteins, among them, the antimicrobial, insecticide, mitogenic, anti-tumoral and anti-inflammatory activities. On the last decades, a large number of studies have demonstrated the application of lectins as a potential biotechnological tool on diverse fields like on agriculture, being used at the genetic improvement of grains; on biochemistry, where it’s used at pre-purification of glycoproteins, and on the histochemistry, applied at the distinction between normal and tumoral cells. Nowadays, one of the researched applications is the potential of lectins as a carcinogenic agent, so as its uses on the discovery of biomarkers. The present study shows a brief history of the plant lectins, their functional characteristics, and structural, their biotechnological applications, such as in the biomarkers discovery, covering too, some of the techniques employed to this function, like the Lectin Affinity Chromatography (LAC), Lectin Microarrays and the Antibody-Lectin Sandwich Array. / As lectinas são proteínas pertencentes a uma diversificada superfamília, que possui como principal característica a capacidade de reconhecer carboidratos de modo específico e seletivo. Estão presentes nos mais variados organismos, tais como, vírus, bactérias, fungos, vegetais e animais. Devido à sua habilidade de reconhecer uma grande quantidade de glicanos, são mediadoras em diversos processos biológicos, como migração celular, defesa imunológica, infecção por bactérias, vírus e protozoários. As lectinas de plantas são as mais estudadas e revelam-se com heterogeneidades estruturais principalmente na constituição de seus sítios de ligação ao carboidrato, o que lhes confere múltiplas atividades biológicas, dentre elas, a ação antimicrobiana, a ação inseticida, a ação mitogênica, a ação antitumoral e a anti-inflamatória. Nas últimas décadas, um grande número de publicações tem demonstrado a aplicação das lectinas como ferramenta biotecnológica potencial em diferentes áreas, como na agricultura, para melhoria genética de cultura de grãos; na bioquímica, utilizadas na pré-purificação de glicoproteínas e na histoquímica, para distinguir células tumorais das normais. Umas das aplicações amplamente pesquisadas na atualidade é o potencial das lectinas como agentes carcinogênicos, como também a sua utilização na descoberta de biomarcadores. Neste trabalho, apresentamos uma visão geral sobre as lectinas, incluindo um breve histórico das lectinas vegetais, suas características funcionais e estruturais básicas, suas atividades com potenciais aplicações biotecnológicas dentre elas a inseticida, a antimicrobiana e a antitumoral, bem como o emprego dessas proteínas na descoberta de biomarcadores tumorais. Algumas técnicas utilizadas para essa finalidade como a cromatografia de afinidade com lectina imobilizada (LAC - Lectin Affinity Chromatography) e os microarranjos de lectinas e lectinas/anticorpo no formato sanduíche (ALSA - Antibody-Lectin Sandwich Array) são apresentadas.
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ANÁLISE MORFOLÓGICA DE ISOFORMAS DE MIOSINA NÃO MUSCULAR TIPO II EM CARCINOMA EPIDERMÓIDEDias, Otávio Francisco Gomes 29 August 2012 (has links)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Cell migration is a prominent feature in cancer metastasis and the characterization of proteins related to migration is important in order to understand the behavior of tumor cells and their invasiveness during tumor progression. Among the proteins involved in cell migration, isoforms of non-muscle myosin type II play a pivotal role in several events related to cell migration, such as contractility, adhesion and cellular signaling. There are three isoforms of myosin type II that can be expressed in mammalian cells: myosin IIA (MIIA), myosin IIB (MIIB) and myosin IIC (MIIC). However, few studies have been conducted to characterize the expression and distribution patterns in cells of different types of tumors, including oral squamous cell carcinoma. The aim of the study was to analyze the expression and distribution of isoforms of myosin II (A, B and C) in surgical fragments of squamous cell carcinoma. Fragments of surgical specimen were collected from different regions of the tumor: a tumor-free zone, the center of the tumor and the invasion zone. These samples (n = 4) were fixed, crioprotected, cut on criostat, submitted to immunolocalization of MIIA, MIIB and MIIC and analyzed on confocal microscopy. The three isoforms of myosin II were expressed differently and showed distinct distribution in accordance with the region of the tumor sample. MIIA and MIIC were overexpressed at the center zone when compared with the free zone, whereas strong staining revealed MIIB at the zone invasion. Based on these observations, the isoforms of myosin IIC and IIA appeared to be more associated with tumor proliferation while MIIB appeared to be more involved in the invasive behavior of tumor, indicating that the isoforms can participate in different ways regulating the behavior and development of tumor type analyzed. / A migração celular é uma característica proeminente na metástase do câncer e a caracterização de proteínas relacionadas com a migração é importante para que se compreenda o comportamento de células tumorais e sua capacidade de invasão durante a progressão tumoral. Entre as proteínas envolvidas na migração celular, as isoformas de miosina não-muscular do tipo II desempenham um papel central em vários eventos relacionados com a migração de células, como a contratilidade, a adesão e a sinalização celular. Existem três isoformas de miosina do tipo II que podem ser expressas em células de mamíferos: miosina IIA (MIIA), miosina IIB (MIIB) e miosina IIC (MIIC). Entretanto, poucos estudos têm sido realizados para caracterizar a sua expressão e padrões de distribuição em células de diferentes tipos de tumores, incluindo carcinoma epidermóide. O objetivo do estudo foi analisar a expressão e distribuição de isoformas de miosina II (A, B e C) em fragmentos de peça cirúrgica de carcinoma epidermóide. Os fragmentos de peça cirúrgica foram coletados a partir de distintas regiões do tumor: a zona livre de tumor, o centro do tumor e a zona de invasão. Estas amostras (n = 4) foram fixadas, crioprotegidas, cortadas em criostato, submetidas à imunolocalização de MIIA, MIIB e MIIC e analisadas em microscopia confocal. As três isoformas de miosina II foram expressas diferentemente e apresentaram distribuição distinta de acordo com a região da amostra de tumor. MIIA e MIIC foram superexpressas na zona central quando comparadas com a zona livre, ao passo que MIIB revelou forte marcação para região de zona de invasão. Com base nas presentes observações, as isoformas de miosina IIA e IIC pareceram estar mais associadas ao evento de proliferação tumoral ao passo que MIIB pareceu mostrar-se mais envolvida com o comportamento invasivo do tumor, indicando que as isoformas podem participar de formas distintas na regulação do comportamento e do desenvolvimento do tipo de tumor analisado.
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Statistical methods for analyzing sequencing data with applications in modern biomedical analysis and personalized medicineManimaran, Solaiappan 13 March 2017 (has links)
There has been tremendous advancement in sequencing technologies; the rate at which sequencing data can be generated has increased multifold while the cost of sequencing continues on a downward descent. Sequencing data provide novel insights into the ecological environment of microbes as well as human health and disease status but challenge investigators with a variety of computational issues. This thesis focuses on three common problems in the analysis of high-throughput data. The goals of the first project are to (1) develop a statistical framework and a complete software pipeline for metagenomics that identifies microbes to the strain level and thus facilitating a personalized drug treatment targeting the strain; and (2) estimate the relative content of microbes in a sample as accurately and as quickly as possible.
The second project focuses on the analysis of the microbiome variation across multiple samples. Studying the variation of microbiomes under different conditions within an organism or environment is the key to diagnosing diseases and providing personalized treatments. The goals are to (1) identify various statistical diversity measures; (2) develop confidence regions for the relative abundance estimates; (3) perform multi-dimensional and differential expression analysis; and (4) develop a complete pipeline for multi-sample microbiome analysis.
The third project is focused on batch effect analysis. When analyzing high dimensional data, non-biological experimental variation or “batch effects” confound the true associations between the conditions of interest and the outcome variable. Batch effects exist even after normalization. Hence, unless the batch effects are identified and corrected, any attempts for downstream analyses, will likely be error prone and may lead to false positive results. The goals are to (1) analyze the effect of correlation of the batch adjusted data and develop new techniques to account for correlation in two step hypothesis testing approach; (2) develop a software pipeline to identify whether batch effects are present in the data and adjust for batch effects in a suitable way.
In summary, we developed software pipelines called PathoScope, PathoStat and BatchQC as part of these projects and validated our techniques using simulation and real data sets.
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