Massively parallel high throughput sequencers are transforming the scientific research by reducing the cost and time necessary to sequence entire genomes. The goal of this project is to produce preliminary genome assemblies of calliphorid flies using Life Technologies’ Ion Torrent sequencing and Illumina’s MiSeq sequencing. I located, assembled, and annotated a novel mitochondrial genome for one such fly, the little studied Chrysomya pacifica that is central to one hypothesis about blow fly evolution. With sequencing data from Chrysomya megacephala, its forensically relevant sister species, much insight can be gained by alignments, sequence and protein analysis, and many more tools within the CLC Genomics Workbench software program. I present these analyses here of these recently diverged species.

Depuis leur apparition, les séquenceurs haut débit ont révolutionné l'étude des transcriptomes à l'échelle du génome. En effet, ils offrent la possibilité de générer des millions, voire des milliards de séquences, appelées reads. Des nouvelles approches transcriptomiques, telles que la Digital Gene Expression (DGE) et le RNA-Sequencing (RNA-Seq), permettent aujourd'hui de répertorier, de quantifier, voire reconstruire tous les transcrits d'une cellule, même les plus rares. Parmi ce type de transcrits se trouvent des ARN non-codants régulateurs ; des variants d'épissages créateurs de protéines ; et aussi des chimères (par fusion de gènes ou trans-épissage). La caractérisation de l'ensemble de ces transcrits représente un réel défi algorithmique, mais suscite aussi un défi biologique car certains peuvent être impliqués dans de nombreux processus cellulaires physiologiques et pathologiques et sont fréquemment décrits dans les cancers.Dans ce travail, nous proposons des algorithmes et des méthodes pour la caractérisation et l'annotation des transcriptomes. Tout d'abord, nous proposons une étude statistique sur la DGE afin d'évaluer l'impact des erreurs de séquences lors de l'analyse des reads. À partir de cette analyse, nous avons développé un pipeline d'annotation pour la DGE. Par le biais de ce premier travail, nous avons pu démontrer que de nombreuses informations étaient partagées entre les reads. Cela nous a amené à concevoir la structure d'indexation Gk arrays qui permet d'organiser une quantité massive de reads de façon à pouvoir interroger rapidement la structure sous forme de requêtes. Enfin, en s'appuyant sur les Gk arrays, nous avons développé CRAC qui est un logiciel spécialisé dans le traitement du RNA-Seq. En intégrant sa propre phase de mapping, CRAC est capable de distinguer les phénomènes biologiques des erreurs de séquences. Ilpermet notamment l'identification de chimères qui sont souvent très faiblement exprimées dans un transcriptome et sont par nature complexe à détecter avec des parties localisées à différents endroits sur le génome. / Since their introduction, high-throughput sequencers have revolutionized transcriptomic studies at genome scale. Indeed, they have the ability to generate millions, or even billions of short sequences, called reads. New transcriptomic approaches, such as Digital Gene Expression (DGE) and RNA-sequencing (RNA-Seq), enable the identification, quantification, and reconstitution of all transcripts of the cell, even rare ones. Among these transcripts are regulatory non-coding RNAs, alternative splice variants, which code for novel proteins, but also non colinear transcripts termed chimeras (generated by either gene fusion or trans-splicing). The characterization of these transcripts constitutes a sheer algorithmic,but also a biological challenge due to their differences in nature, their diverse implications in physiological and cellular processes, and for some their role in cancer development.In this work, we focus on algorithms and methods for the characterization and annotation of transcriptomes. First, we proposed a statistical study on DGE to assess the impact of sequence errors on the analysis. Therefrom, we developed a pipeline for the DGE annotation. Through this initial work,we demonstrated that a lot of information is shared between the reads. This property led us to design, the Gk arrays, an indexing data structure for organizing huge amounts of reads in memory and algorithms to quickly query this structure. Finally, based on the Gk arrays we have conceived, CRAC,a software specialised in the RNA-Seq processing. By integrating its own mapping process, CRAC is able to distinguish the biological phenomena from sequence errors. Moreover, it allows to identify chimeric RNAs, which may be weakly expressed in a transcriptome and are inherently complex to detect since their fragments originate from different places on the genome.

Le lymphome est un cancer des ganglions lymphatiques, lieu de prolifération et différenciation des cellules immunitaires en particulier des lymphocytes B qui sont des cellules productrices d'anticorps. Les lymphomes résultent de l’accumulation de mutations génétiques dans le génome d’une cellule B normale contribuant à la transformation en cellule B maligne. Cette cellule B dite transformée prolifère alors pour engendrer un clone de cellules B malignes qui s’accumulent au niveau des ganglions lymphatiques, formant alors une tumeur appelée ‘lymphome B’ (pour cancer lymphoïde issu de la transformation maligne des lymphocytes B). Le ganglion lymphatique normal a une structure histologique qui se décompose ainsi, du centre à la périphérie : le centre germinatif, la zone du manteau et la zone marginale. Les lymphomes B sont classés en différents sous-types histologiques en fonction de leur origine topographique au niveau du ganglion lymphatique et de leurs caractéristiques bio cliniques spécifiques. Parmi ces sous-types, une forme particulièrement agressive peut être distinguée : le lymphome à cellules du manteau. Ce sous-type de lymphome est caractérisé par des rechutes successives et une survie qui est généralement courte (médiane de survie de 4 à 5 ans) même si certains patients, avec des formes plus indolentes de lymphomes à cellules du manteau, présentent des survies prolongées (médiane de survie de 7 à 10 ans). Des biomarqueurs prédictifs de la courte survie manquent aujourd’hui, ce qui rend difficile la prise en charge optimisée des patients. Ce projet s’intéresse à cette question. Plus précisément, nous nous proposons de rechercher des mutations génétiques associées à la résistance thérapeutique. Notre approche sera basée sur le séquençage ciblé à haut débit du génome de cellules B tumorales issus de patients présentant des cas classiques du lymphomes à cellules du manteau mais aussi des cas plus particuliers comme ceux présentant des résistances thérapeutiques précoces, par exemple. Par cette approche dite de ‘cartographie’ à l’échelle du génome, nous espérons identifier des nouveaux prédicteurs moléculaires de la survie chez ces patients atteints de lymphome à cellules du manteau et également apporter de nouvelles connaissances dans l’interconnexion entre la génétique et l’épigénétique dans cette maladie. / Lymphoma is a cancer of the lymph nodes which are organs in which immune cells, particularly the antibody producing B cells, proliferate and differentiate before circulating in the blood and tissues to fight infection. B cell lymphoid cancers – ‘B cell lymphoma’ arise as a consequence of the occurrence of gene mutations in B cells. By affecting the functions of key B cell genes, these mutations drive the malignant transformation of the affected B cells which then begin to divide abnormally eventually destroying normal lymph node organization and function. The lymph node is divided into distinct micro-anatomical compartments or zones which are called (from the inner to outer most compartment – germinal centre, mantle zone, and marginal zone). B cell lymphoma classification follows this general organization and classifies tumours depending on the compartment of origin of the particular tumour B cell population. This classification thus defines lymphoma according to a ‘histological subtype’ with defined clinic-biological features. Among these subtypes, mantle cell lymphoma (MCL) is a particularly aggressive form of B lymphoid cancer. This type of lymphoma is characterised by successive relapses and short survival (median is 4 to 5 years), although some patients can show long survival. Predictive biomarkers of this clinical behavior are lacking. This project aims to address this question. More specifically we propose to perform whole ‘exome’ sequencing – i.e. sequencing of all protein coding sections of all known protein coding genes in the genome – of the tumour B cell DNA from patients who show refractory or early relapsing disease compared to patients who show relatively long survival. By doing this genome scale study we hope to identify new gene mutations that can serve as molecular predictors of survival and bring new knowledges in the understanding between genetics and epigenetics in MCL.

abstract: This study explores the impact of a professional development (PD) activity conducted for teachers of the Next Generation Science Standards (NGSS) at 15 American-curriculum international schools. The intervention involved teachers utilizing the 3D-PAST screening tool to systematically evaluate the alignment of teacher-designed assessments with the constructs of the NGSS and best practices in science instruction. Data about the way the intervention enhanced or challenged teachers’ understanding of the NGSS were collected via a multiple methods approach. The New Framework of Science Education Survey of Teacher Understanding (NFSE-STU) was used in a retrospective pretest-posttest fashion to assess changes in teachers’ understanding of NGSS constructs. Subsequently, interviews were conducted with participants which provided data that expanded upon the NFSE-STU findings. The Refined Consensus Model of Pedagogical Content Knowledge (RCM-PCK) was used to interpret the findings and situate the study within the extant literature on teacher PCK. The intervention was found to have a statistically significant effect on teachers’ understanding of the NGSS in all areas measured by the NFSE-STU. Additionally, data suggest that the intervention elicited changes in teachers’ classroom practices and improved collaborative professional practices. Also highlighted in the analysis was the significance of the relationship between the intervention moderator and the participants as a strong predictor of the way the intervention was perceived by teachers. The findings strongly support the suggestion that international school administrators seeking to maximize the impact of science teacher professional development should consider PD activities that train teachers in the use of aids to align NGSS assessments, because doing so simultaneously enhances teacher understanding of the NGSS while encouraging meaningful changes to professional practice. The study contributes to the nascent body of literature utilizing the RCM-PCK to situate understanding of science-teacher PCK, and fills a void in literature examining PD in American curriculum international schools, and highlights issues with potential to serve as foci for additional cycles of action research in the areas of international schools, science teacher and NGSS-related professional development, and the use of tools similar to 3D-PAST within other teaching disciplines. / Dissertation/Thesis / Doctoral Dissertation Leadership and Innovation 2020

We will combine hands-on science investigations with supporting literacy activities to help students tell the “whole story” of force and motion.

<p>Worldwide concern on fossil fuels depletion and adverse impact on environment pushed researchers to find an alternative energy source. Among various potential systems, electrochemical energy storage devices have attracted significant attraction due to short charge/discharge time, easy relocation, and relatively cheap cost compared to large storage systems. Much research has been reported to suggest a material for electrochemical storage systems. Carbon is a key part of human life in terms of energy source, building materials, daily clothing and foods. The extraordinary characteristics of carbon materials, including good conductivity, good structure stability, relatively low cost, and sustainability, draw interest to carbon application in energy storage systems. </p> <p>The introduction of lithium ion batteries (LIB), using graphite as an anode material, fulfilled the need of alternative energy source and elevated the technologies into next level high-performance applications such as portable devices. While the technology advancement in high performance electronics fosters the development of advanced lithium ion batteries, the introduction of electric vehicles and large intermittent systems seeks energy storage devices with high capacity, sustainability, and low cost. In this thesis, the impact of the characteristics of carbon material on energy storage system performance is studied. The work presented in this thesis not only suggests a cost-effective carbon synthesis for advanced LIB, but also addresses how the carbon structure impact and resolves the systematic issue associated with next generation energy storage systems.</p> <p>Chapter 3 describes a facile, one-step, solvent-free ‘dry autoclaving’ synthesis method utilizing coffee oil as the carbon precursor to obtain micrometer diameter spheroidal carbon particles for lithium ion battery anodes. The spheroidal morphology resulted from the evaporation of liquid oil into a liquid/gas phase interphase at elevated temperature (700 ^oC), followed by solid/gas sublimation interactions during cooling (below 350 ^oC) in a closed autoclave. A mechanism of spheroidal carbon formation is proposed considering the precursor’s composition and chemical interactions during autoclaving. The prepared carbon from dry autoclave has shown successful LIB performance and structure stability after 250 cycles.</p> <p>Chapter 4 illustrates the temperature effect on the structure of biomass derived carbon. In this study, due to its abundance and high porosity, pistachio shells were selected as the primary carbon source and carbonized at a range from 700 to 1500 °C. The temperature effect on carbon structure was analyzed by XRD, Raman, BET, and electron microscopy. To propose an advanced lithium ion battery, pistachio shell-derived carbon was applied as an anode material for a sodium ion battery (SIB). The correlation of carbon structure and SIB electrochemical performance is presented. Pistachio shell carbonized at 1000 °C resulted in highly amorphous structure with specific surface area (760.9 m²/g) and stable cycle performance (225 mAh g^-1 at 10 mA g^-1). With support from Raman, XRD, and BET, the storage mechanism has been studied as well.</p> <p> Chapter 5 describes the impact of carbon structure on resolving the polysulfide shuttling effect in lithium sulfur (Li-S) batteries. Lithium sulfur batteries have received tremendous attention due to its high theoretical capacity (1672 mAh g^-1), sulfur abundance, and low cost. However, main systemic issues, associated with polysulfide shuttling and low Coulombic efficiency, hinder the practical use of sulfur electrodes in commercial batteries. The work in this thesis demonstrated an effective strategy of decorating nano-MnO₂ (less than 10 wt. %) onto a sulfur reservoir in order to further capture the out-diffused polysulfides via chemical interaction, and thereby improve the electrochemical performance of sulfur electrodes without increasing the mass burden of the total battery configuration. Pistachio shell-derived sustainable carbon (PC) was employed as an effective sulfur container due to its structural characteristics (interconnected macro channels and micropores). With the aids of the structural benefits of PC scaffold and the uniform decoration of nano-MnO₂, the polysulfide shuttling effect was significantly suppressed and cycling performance of a sulfur cathode was dramatically improved over 250 cycles.</p> This thesis offers a new prospect in the study of carbon materials applications in various energy storage systems. This concept can be further extended to other applications, such as lithium metal batteries. The intercalation property of carbon structure can reduce the local current density, reducing the risk of lithium dendrite growth, which is the most critical issue of lithium metal battery.

Hlavným cieľom tejto práce je návrh nového algoritmu k spracovaniu unikátnych molekulárnych indexov bez mapovania na referenčný genóm. O tieto náhodné oligonukleotidové sekvencie neustále vzrastá záujem, pretože uľahčujú rozpoznávať PCR chyby a skresľovanie údajov. Keďže používanie technológií sekvenovania novej generácie neustále rastie, je vynaložené veľké úsilie vyvíjať nástroje pre analýzu produkovaných dát. V súčasnosti sú nástroje na riešenie týchto chýb relatívne časovo náročné a zložité z dôvodu výpočtovo náročného zarovnania. Najdôležitejšie obmedzenie týchto nástrojov spočíva v skutočnosti, že pri spracovávaní duplikátov sú povolené multi-mapované čítania. Tieto čítania sú zvyčajne ignorované, čo môže viesť k zníženiu kvantitatívnej presnosti a spôsobiť zavádzajúcu interpretáciu výsledkov daného sekvenovania. V snahe vyriešiť tento problém je v tejto práci uvedený nový prístup, ktorý umožňuje odhad absolútneho počtu jedinečných molekúl s relatívne rýchlym a spoľahlivým spôsobom.

The purpose of this study was to explore the ways in which educators address climate change and the impacts of human activity on the environment in conjunction with the Next Generation Science Standards. This study utilized qualitative methods, a phenomenological methodology informed by Moustakas, and a Systems Theory and Ecojustice Education conceptual framework. The central research questions was: in what ways do educators who are implementing the Next Generation Science Standards address climate change and the impacts of human activity on the environment? The supporting research questions were: in what ways do educators who are implementing the Next Generation Science Standards perceive their roles and responsibilities in addressing climate change and the impacts of human activity on the environment? in what ways do educators who are implementing the Next Generation Science Standards interpret the associated Earth and Human Activity standards prior to enactment? and, how do educators who are implementing the Next Generation Science Standards teach climate change and the impacts of human activity on the environment?Eight participants were purposely selected using criterion sampling. All participants taught in grades six-twelve, had at least five years teaching experience, and worked in the Sacramento Valley region of California. Data collection consisted of interviews, observations, and document analyses. During the data analysis, horizontalization was utilized which led to the illumination of the following themes: Climate change is an existential crisis, Examination and refinement of pedagogy, Perceptions on Next Generation Science Standards pedagogy, Inquiry-based pedagogical methods, Pedagogical resources, Fostering relevancy to students, and Steps toward an eco-ethical consciousness. The conclusions drawn are: context is key, confusion persists and teachers need guidance and support, adopted curricula and content standards are inadequate, systems thinking and eco-ethical mindsets are vital, teachers are essential for survivability, and more needs to happen. The recommendations from this study are of relevance to policy makers, administrators, curricula and standard developers, teachers, and anyone else interested in mitigating the impacts of human activity on the environment.

Hlavním cílem této diplomové práce je analýza diferenciální exprese genů na základě negativního binomického modelu. Úvodní část je věnována teoretickému základu, pojednává o sekvenování RNA, sekvenování nové generace, výhodách a možném využití, formátu fastQ aj. Následující část už se zabývá samotnou praktickou částí, zde byl vybrán vhodný set genů, které budou později analyzovány a příslušná data byla stažena. Tato data byla zarovnána k lidskému genomu verze 37 Burrowsovou-Wheelerovou transformací s využitím bowtie mapovače, byly tak vytvořeny soubory ve formátu SAM. Toto soubory dat byly později setříděny pomocí nástroje SAMtools. Následně byly v programovém prostředí Matlab (verze R2013b) vytvořeny anotované objekty genů s využitím služby Ensembl´s BioMart. Dále byla určena genová exprese a byly odhadnuty faktory velikosti knihovny. Na závěr byly odhadnuty parametry negativního binomického rozložení a byla vyhodnocena diferenciální exprese genů.

Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.