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Université de Neuchâtel
1.
Geiser, Céline.
Genome evolution and mechanisms underlying reproductive
isolation in the polyploid "Biscutella laevigata".
Degree: 2014, Université de Neuchâtel
URL: http://doc.rero.ch/record/257452 
► Malgré des avancées phénoménales en biologie évolutive, les mécanismes qui mènent à la spéciation, le berceau de la biodiversité, ne sont toujours pas complètement déchiffrés.…
(more)
▼ Malgré des avancées phénoménales en biologie
évolutive, les mécanismes qui mènent à la spéciation, le berceau de
la biodiversité, ne sont toujours pas complètement déchiffrés. La
polyploïdie, c’est-à-dire la multiplication du patrimoine
chromosomique (par exemple doublé pour la tétraploïdie), est un
phénomène récurrent, en particulier chez les plantes. Toutes les
plantes à fleurs actuelles, avec leur incroyable diversité, ont
connu au moins deux événements de polyploïdie dans leur histoire
évolutive. Malgré cela il n’a jamais été possible de formellement
associer la polyploïdie à des capacités adaptives accrues et son
rôle dans la diversification des espèces reste controversé. Un
mécanisme qui pourrait amener à des nouveautés chez le polyploïde
est lié à de nouvelles fonctions émergentes des gènes dupliqués.
C’est à ce mécanisme que je m’intéresse dans la première partie de
ma thèse. En recomposant des séquences transcrites grâce aux
nouvelles technologies de séquençage profond j’ai étudié les
différents événements de polyploïdie qui ont influencé l’évolution
d’une espèce alpine, la lunetière lisse tétraploïde
(<i>Biscutella laevigata</i>). En analysant les forces
sélectives agissant sur les gènes dupliqués j’ai pu déterminer des
groupes fonctionnels potentiellement importants dans l’évolution de
cette espèce. D’une part une partie des groupes fonctionnels
préférentiellement retenus en deux copies, après un événement de
polyploïdie récent, sont liés à l’écologie. D’autre part des copies
de gènes sous sélection positive, c’est-à-dire probablement
impliqués dans un processus de diversification, ont été mis en
évidence. Ces gènes sont liés au cytosquelette et pourraient être
associés à une adaptation à la polyploïdie ou au stress.
Dans la deuxième partie de ma thèse je me suis intéressée aux
divers mécanismes impliqués dans la spéciation commençante entre
deux groupes d’une même population alpine de lunetière lisse
tétraploïde (<i>Biscutella laevigata</i>). L’étude de
la spéciation consiste à étudier les mécanismes qui conduisent à
une cessation de flux de gènes entre deux groupes taxonomiques,
c’est-à-dire l’isolement reproductif. Pour déchiffrer les divers
mécanismes qui sous-tendent l’isolement reproductif, les suivis en
population naturelle ainsi que des approches expérimentales sur le
terrain se sont avérés être des outils essentiels. Tout d’abord la
stucture génétique de cette population a révélé une zone hybride
entre deux groupes. J’ai pu démontrer qu’une barrière principale
qui sous-tend la divergence génétique est un décalage de floraison
entre les deux groupes. Ces deux groupes semblent être adaptés à
deux environnements distincts ce qui pourrait participer à
l’isolement reproductif. Néanmoins, il n’a pas été possible de
démontrer l’adaptation locale expérimentalement.
Advisors/Committee Members: Christian (Dir.), Félix (Codir.).
Subjects/Keywords: next generation sequencing
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APA (6th Edition):
Geiser, C. (2014). Genome evolution and mechanisms underlying reproductive
isolation in the polyploid "Biscutella laevigata". (Thesis). Université de Neuchâtel. Retrieved from http://doc.rero.ch/record/257452
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Geiser, Céline. “Genome evolution and mechanisms underlying reproductive
isolation in the polyploid "Biscutella laevigata".” 2014. Thesis, Université de Neuchâtel. Accessed March 07, 2021.
http://doc.rero.ch/record/257452.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Geiser, Céline. “Genome evolution and mechanisms underlying reproductive
isolation in the polyploid "Biscutella laevigata".” 2014. Web. 07 Mar 2021.
Vancouver:
Geiser C. Genome evolution and mechanisms underlying reproductive
isolation in the polyploid "Biscutella laevigata". [Internet] [Thesis]. Université de Neuchâtel; 2014. [cited 2021 Mar 07].
Available from: http://doc.rero.ch/record/257452.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Geiser C. Genome evolution and mechanisms underlying reproductive
isolation in the polyploid "Biscutella laevigata". [Thesis]. Université de Neuchâtel; 2014. Available from: http://doc.rero.ch/record/257452
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Sydney
2.
Nafisinia, Michael.
Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics
.
Degree: 2017, University of Sydney
URL: http://hdl.handle.net/2123/16867
► The focus of this thesis was the identification of the genetic bases of Mendelian and mitochondrial respiratory chain disorders in a cohort of paediatric patients,…
(more)
▼ The focus of this thesis was the identification of the genetic bases of Mendelian and mitochondrial respiratory chain disorders in a cohort of paediatric patients, to better understand their pathogenesis. Genetic disorders are caused by mutations in the mitochondrial or nuclear genomes and may be influenced to a lesser or greater degree by environmental factors. To date, nearly 3000 genes have been implicated in ~ 4,400 Mendelian phenotypes. However, despite this, the genetic bases for almost 50% of all known Mendelian phenotypes remains to be definitively elucidated. Mitochondrial respiratory chain disorders are the most common group of inborn errors of metabolism and can be caused by mutations in either mitochondrial DNA or nuclear DNA. The genetic heterogeneity of these disorders makes diagnosis challenging, adding distress to families already dealing with the trauma of an extremely ill family member. Mutations in mitochondrial DNA or nuclear DNA genes can result in impaired function of the respiratory chain causing broad symptoms including neuropathy, cardiomyopathy, muscle weakness, fatigue, cognitive impairment, visual and auditory impairment, to name a few. Despite the advances in gene screening techniques, the genetic bases of many respiratory chain disorders remains unidentified. This study had two phases: identification of the likely disease-causing variants in paediatric patients with suspected Mendelian or mitochondrial inherited disorders due to mitochondrial or nuclear DNA mutations, and implementation of functional studies to confirm pathogenicity and gain insights into possible disease mechanisms of the identified variants. Nine patients with suspected Mendelian disorders and two patients with a suspected mitochondrial disorder were studied in this project. Using whole exome sequencing (WES) in collaboration with other institutes or groups within Australia and overseas, we were able to efficiently identify the genetic basis of Mendelian and mitochondrial respiratory chain disorders in the majority of the paediatric patients studied in this project. In collaboration with bioinformaticians and clinician colleagues, we implemented sophisticated filtering pipelines, with candidate causative variants being narrowed down from the very expansive WES data. We then performed functional assays to determine the functional impact of the identified variants. These functional assays included immunoblotting and blue native polyacrylamide gel electrophoresis to measure protein expression and assembly. Further, in the case of the mitochondrial respiratory chain disorders, we measured the effect of the variant on the protein levels of mitochondrial respiratory chain complexes in patient fibroblast samples. We also measured respiratory chain complex enzyme activities using dipstick assays (for complex I and complex IV) or traditional spectrophotometric assays (for complexes I, II, III, and IV). In this PhD project, we have successfully identified four disease variants in NDUFV1 (OMIM: 161015), RARS…
Subjects/Keywords: Next generation sequencing
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APA (6th Edition):
Nafisinia, M. (2017). Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics
. (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/16867
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Nafisinia, Michael. “Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics
.” 2017. Thesis, University of Sydney. Accessed March 07, 2021.
http://hdl.handle.net/2123/16867.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Nafisinia, Michael. “Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics
.” 2017. Web. 07 Mar 2021.
Vancouver:
Nafisinia M. Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics
. [Internet] [Thesis]. University of Sydney; 2017. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/2123/16867.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Nafisinia M. Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics
. [Thesis]. University of Sydney; 2017. Available from: http://hdl.handle.net/2123/16867
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Universiteit Utrecht
3.
Hoek, G. van de.
Identifying novel genes involved in congenital anomalies of the kidney and urinary tract.
Degree: 2013, Universiteit Utrecht
URL: http://dspace.library.uu.nl:8080/handle/1874/287149
► The recent collation of a large patient cohort encompassing the complete CAKUT spectrum, the advent of next generation sequencing (NGS) and progress in bioinformatic developmental…
(more)
▼ The recent collation of a large patient cohort encompassing the complete CAKUT spectrum, the advent of
next generation sequencing (NGS) and progress in bioinformatic developmental gene network modeling have created the opportunity to identify novel genetic causes, characterize complex genotype-phenotype relationships and develop rapid and reliable gene diagnostic tools for CAKUT. The studies on CAKUT genetics will have important implications for affected patients and their families. The elucidation of the complex genetics of disease transmission through studies of exome-wide genetic variability will pave the way towards individualized and more effective genetic counseling of families affected by CAKUT.
Advisors/Committee Members: Renkema, K.
Subjects/Keywords: Kidney disease; next generation sequencing
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APA (6th Edition):
Hoek, G. v. d. (2013). Identifying novel genes involved in congenital anomalies of the kidney and urinary tract. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/287149
Chicago Manual of Style (16th Edition):
Hoek, G van de. “Identifying novel genes involved in congenital anomalies of the kidney and urinary tract.” 2013. Masters Thesis, Universiteit Utrecht. Accessed March 07, 2021.
http://dspace.library.uu.nl:8080/handle/1874/287149.
MLA Handbook (7th Edition):
Hoek, G van de. “Identifying novel genes involved in congenital anomalies of the kidney and urinary tract.” 2013. Web. 07 Mar 2021.
Vancouver:
Hoek Gvd. Identifying novel genes involved in congenital anomalies of the kidney and urinary tract. [Internet] [Masters thesis]. Universiteit Utrecht; 2013. [cited 2021 Mar 07].
Available from: http://dspace.library.uu.nl:8080/handle/1874/287149.
Council of Science Editors:
Hoek Gvd. Identifying novel genes involved in congenital anomalies of the kidney and urinary tract. [Masters Thesis]. Universiteit Utrecht; 2013. Available from: http://dspace.library.uu.nl:8080/handle/1874/287149
University of Rochester
4.
Glass, Carolyn.
Identifying a Potential Molecular Therapeutic Target for
MLL-AF9 Leukemia.
Degree: PhD, 2014, University of Rochester
URL: http://hdl.handle.net/1802/28976
► Leukemia is the most common form of cancer among children and adolescents, and approximately 2,000 infants per year are diagnosed within their first year of…
(more)
▼ Leukemia is the most common form of cancer among
children and adolescents, and
approximately 2,000 infants per year
are diagnosed within their first year of life. Infant
survival
rates are poor, reaching only 25-45% with current chemotherapy
regimens. The
Mixed Lineage Leukemia (MLL) gene translocation is
present in 70-80% of infant
leukemia cases and is the most
significant biomarker for poor prognosis. MLL-gene
translocations
produce oncogenic fusion proteins, such as MLL-AF9 that bind and
overactivate transcription of genes involved in normal
hematopoiesis. One such gene that
the MLL-AF9 fusion protein
directly binds is MDS1-EVI1 (Myelodysplastic Syndrome-
Ecotropic
Virus Integration Site 1), a transcription factor critical for
normal hematopoiesis.
For our first aim, we determined whether
MDS1-EVI1 DNA binding via specific zinc
finger domains is required
for MLL-AF9 leukemogenesis and identified genome-wide
target
genes. We discovered that MDS1-EVI1 DNA binding via its Zinc Finger
1 domain,
is necessary for the development of MLL-AF9 leukemia in
a mouse model. Using highthroughput
sequencing techniques we
identified several interesting key genes involving
embryogenesis
and cellular proliferation to be markedly upregulated in MDS1-EVI1
positive MLL- infant leukemia cells from primary patients.
Furthermore, we found several
target genes to be significantly
overexpressed that may serve as potential druggable targets
for
novel therapies, or even potentially existing drug compounds.
Furthermore, we
explored whether MDS1-EVI1 HMT activity
contributes to MLL-leukemia. For our
second aim, we examined
whether MDS1-EVI1 PR-domain HMT activity was aberrant in
MLL-leukemic cells. A histone methyltransferase (HMT) assay did not
demonstrate a
significant difference in HMT activity in the
presence of the MDS1-EVI1 PR-domain, and
thus is not likely the
major driving force of the PR-domain that induces
MLLleukemogenesis.
In conclusion, we elucidated the one of the
main mechanism by which
MDS1-EVI1 contributes to malignant
transformation in MLL-infant leukemic cells, and
have identified
critical molecular genes and pathways that may serve as future
druggable
targets.
Subjects/Keywords: Leukemia; Next Generation Sequencing
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APA (6th Edition):
Glass, C. (2014). Identifying a Potential Molecular Therapeutic Target for
MLL-AF9 Leukemia. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/28976
Chicago Manual of Style (16th Edition):
Glass, Carolyn. “Identifying a Potential Molecular Therapeutic Target for
MLL-AF9 Leukemia.” 2014. Doctoral Dissertation, University of Rochester. Accessed March 07, 2021.
http://hdl.handle.net/1802/28976.
MLA Handbook (7th Edition):
Glass, Carolyn. “Identifying a Potential Molecular Therapeutic Target for
MLL-AF9 Leukemia.” 2014. Web. 07 Mar 2021.
Vancouver:
Glass C. Identifying a Potential Molecular Therapeutic Target for
MLL-AF9 Leukemia. [Internet] [Doctoral dissertation]. University of Rochester; 2014. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1802/28976.
Council of Science Editors:
Glass C. Identifying a Potential Molecular Therapeutic Target for
MLL-AF9 Leukemia. [Doctoral Dissertation]. University of Rochester; 2014. Available from: http://hdl.handle.net/1802/28976
Cornell University
5.
Al Abri, Mohammed.
Development Of Genomic Methods And Tools For An Equine Model.
Degree: PhD, Animal Science, 2015, Cornell University
URL: http://hdl.handle.net/1813/40974
► The advent of genomic analysis has identified regions of functional significance in several mammalian species. However, for horses, relatively little such work was done compared…
(more)
▼ The advent of genomic analysis has identified regions of functional significance in several mammalian species. However, for horses, relatively little such work was done compared to other farm animals. The current archive of genetic variations in the horse is mostly based on the Thoroughbred mare upon which the reference sequence (EquCab2.0) was generated. Thus, more investigation of the equine genomic architecture is critical to better understand the equine genome. Chapter 2 of this dissertation represents an analyses of
next generation sequencing data of six horses from a diverse genetic background. I have utilized the most advanced techniques to identify, and annotate genetic variants including single nucleotide polymorphism, copy number variations and structural variations pertaining to these horse breeds. The analysis discovered thousands of novel SNPs and INDELs and hundreds of CNVs and SVs in each of the horses. These newly identified variants where formatted as online tracks and should provide a foundational database for future studies in horse genomics. Chapter three of the thesis discusses a genome wide association study aimed at the discovery of QTLs affecting body size variation in horses. I used the Illumina Equine SNP50 BeadChip to genotype 48 horses from diverse breeds and representing the extremes in body size in horses. Unlike most association studies, I have utilized a dominant model to identify these QTLs. The analysis revealed an association in chromosome one at the ANKRD1 gene (involved in muscle myocytes and cardiomyocyte growth and differentiation). In chapter four, I represent the results of a genomic study in which 36 Egyptian Arabian horses were genotyped using the Illumina Equine SNP70 BeadChip. The study was conducted to elucidate the genetic background of the herd, relatedness within the herd and to estimate genomic inbreeding values. I was able to re-establish the genetic links between the horses and to confirm their Egyptian ancestry among other Arabian horse bloodlines. Genomic inbreeding values were highly correlated with the pedigree estimated ones. Altogether, our results signify the benefit of using this BeadChip technology to infer relationships within herds and ancestry of herds and to estimate inbreeding in herds lacking pedigree recording.
Advisors/Committee Members: Brooks,Samantha A. (chair), Boyko,Adam R. (committee member), Booth,James (committee member), Mezey,Jason G. (committee member).
Subjects/Keywords: Horse; Genomics; Next generation sequencing
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APA (6th Edition):
Al Abri, M. (2015). Development Of Genomic Methods And Tools For An Equine Model. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/40974
Chicago Manual of Style (16th Edition):
Al Abri, Mohammed. “Development Of Genomic Methods And Tools For An Equine Model.” 2015. Doctoral Dissertation, Cornell University. Accessed March 07, 2021.
http://hdl.handle.net/1813/40974.
MLA Handbook (7th Edition):
Al Abri, Mohammed. “Development Of Genomic Methods And Tools For An Equine Model.” 2015. Web. 07 Mar 2021.
Vancouver:
Al Abri M. Development Of Genomic Methods And Tools For An Equine Model. [Internet] [Doctoral dissertation]. Cornell University; 2015. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1813/40974.
Council of Science Editors:
Al Abri M. Development Of Genomic Methods And Tools For An Equine Model. [Doctoral Dissertation]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/40974
6.
Bankale, Sheyi.
Unheard stories : navigating 'Next Level'.
Degree: PhD, 2017, University of Derby
URL: http://hdl.handle.net/10545/621518
► "To publish art – to literally make it public – was a political act, one that challenged the art world and the world at large"…
(more)
▼ "To publish art – to literally make it public – was a political act, one that challenged the art world and the world at large" (Gwen Allen). This critical appraisal on the published journal Next Level reports the result of my research relating to the body of my work from 2005 to 2016. More specifically, I will survey the creative production of the contemporary photography journal Next Level, currently consisting of seven city editions from a volume of twenty-four editions. This acknowledgement is not intended to emphasise the subjectivity of the journal as a limitation, but rather to provide focus to the lens through which I have been looking at my data with important findings about the outcomes of measurable theoretical, critical and artistic approaches. The journal Next Level periodically publishes a number of editions that present the collection of original data about photography art communities through the exploration of various cities around the world. These editions are developed from data collected through on-the-ground research that is central to this evaluation, which is an examination of and response to a large range of data drawn from seven cities, providing new information. This provides a pivot for the work around which my ideas are put across in a meaningful, comparable and communicable way, creating a mapping of each city, always enabling and never limiting. This methodology of gathering data, consisting of governmental cultural reports, museum archives, catalogues, comment books and newsletters, visual artists’ curriculum vitaes (CVs), interviews and rich contextual material, in turn provides primary research for students, photography professionals, photography enthusiasts and future photography historians. By countering the standard framework of research and production, my work is theoretically, critically and artistically traced, not by making things new, but by comprehensively questioning the characteristics that have shaped things in new ways. This framework manifests itself in the preliminary research and creative practice that provided the foundation for the complete scope of the entire space in the journal, which I present alongside this critical appraisal. Through the dissemination of current photographic discourse, I discuss current traditions and new perceptions through various articles and features. These editorial pieces relating to local communities of contemporary art photography look in particular at their cultural outputs in response to the rise of globalisation. Through the roles of artist-as-editor and curator, the journal is an artefact that I have shaped, utilising print production as part of its aesthetic dimension. I have published and distributed between 8,000 and 20,000 copies per edition to 37 countries. The readership of the journal thus has access to viewpoints that are revealing and politically reflective of specific manifestations of power, representation and the unheard stories that are altering various aspects of the conventions of current photographic discourse.
Subjects/Keywords: 778; Next Level; Photography
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APA (6th Edition):
Bankale, S. (2017). Unheard stories : navigating 'Next Level'. (Doctoral Dissertation). University of Derby. Retrieved from http://hdl.handle.net/10545/621518
Chicago Manual of Style (16th Edition):
Bankale, Sheyi. “Unheard stories : navigating 'Next Level'.” 2017. Doctoral Dissertation, University of Derby. Accessed March 07, 2021.
http://hdl.handle.net/10545/621518.
MLA Handbook (7th Edition):
Bankale, Sheyi. “Unheard stories : navigating 'Next Level'.” 2017. Web. 07 Mar 2021.
Vancouver:
Bankale S. Unheard stories : navigating 'Next Level'. [Internet] [Doctoral dissertation]. University of Derby; 2017. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/10545/621518.
Council of Science Editors:
Bankale S. Unheard stories : navigating 'Next Level'. [Doctoral Dissertation]. University of Derby; 2017. Available from: http://hdl.handle.net/10545/621518
7.
Ortogero, Nicole.
Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species.
Degree: 2014, University of Nevada – Reno
URL: http://hdl.handle.net/11714/2832
► Small non-protein-coding RNAs are essential, ubiquitous molecules found in every cell. Their functions range from post-transcriptional regulation of mRNA expression to epigenetic control of the…
(more)
▼ Small non-protein-coding RNAs are essential, ubiquitous molecules found in every cell. Their functions range from post-transcriptional regulation of mRNA expression to epigenetic control of the genome. Small noncoding RNAs also have crucial functions in the ribosome and spliceosome. Block of small RNA biogenesis and inactivation of effector complex proteins lead to embryonic lethality and loss of cell function. Because of their necessity in biological processes, they are of great interest in current research. Although small RNA research is in full throttle, many ambiguities and obstacles in this field still need to be addressed. This work resolves some of these roadblocks and expands our knowledge of existing small RNAs and their expression in somatic and germ cells. To properly characterize the function of small RNAs in a cell, it is essential to define the small RNA transcriptome. This can be accomplished through
next-generation sequencing of small RNA. Unfortunately, current work in small RNA tends to concentrate on only one type of small RNA, predominantly miRNA, due to their already defined function, biogenesis, and structure. In addition,
next-generation sequencing data generate millions of reads, and it is complicated to consider the entire small RNA transcriptome, as no comprehensive annotation pipeline is currently available. To further this field, we set out to define a small RNA annotation pipeline. To aid in this effort, we developed a graphic user interface program for small RNA data processing and annotation. We validated this pipeline by defining the Sertoli small RNA transcriptome with
next-generation sequencing data. Sertoli cells represent the predominant somatic cell type within the testis and are considered "nurse cells" to developing male germ cells. Male gametes, sperm, are produced through spermatogenesis in the testis. Sertoli cells are in direct contact with all developing germ cells during spermatogenesis and normal Sertoli cell functions are required for normal germ cell development. Small RNAs help regulate dynamic transcriptomes, and we hypothesized that the Sertoli small RNA transcriptome needs to be dynamic due to the different germ cell stages Sertoli cells support. Indeed, all small RNA classes were found within the Sertoli cell and many novel RNAs were also identified in this study. Altogether, we successfully defined the entire small RNA transcriptome of Sertoli cells and developed a small RNA annotation pipeline for the comprehensive annotation of known and novel small RNAs. In our research of small RNAs, we identified a class of somatic small RNAs approximately 30 nucleotides long. In the male gonad a similar population has been defined as PIWI-interacting RNAs or piRNAs. piRNAs are approximately 30 nucleotides long and associate with PIWI proteins. Because PIWI proteins are germ cell exclusive, the somatic counterparts discovered cannot be considered piRNAs. Instead we termed them piRNA-like or pilRNA for their similarities to piRNAs. Our aims of this…
Advisors/Committee Members: Yan, Wei (advisor), Hennig, Grant (committee member), Singer, Cherie (committee member), Zeh, David (committee member), Lu, Minggen (committee member).
Subjects/Keywords: Next Generation Sequencing; Small RNA
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APA ·
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MLA ·
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CSE |
Export
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Manager
APA (6th Edition):
Ortogero, N. (2014). Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species. (Thesis). University of Nevada – Reno. Retrieved from http://hdl.handle.net/11714/2832
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ortogero, Nicole. “Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species.” 2014. Thesis, University of Nevada – Reno. Accessed March 07, 2021.
http://hdl.handle.net/11714/2832.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ortogero, Nicole. “Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species.” 2014. Web. 07 Mar 2021.
Vancouver:
Ortogero N. Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species. [Internet] [Thesis]. University of Nevada – Reno; 2014. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/11714/2832.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ortogero N. Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species. [Thesis]. University of Nevada – Reno; 2014. Available from: http://hdl.handle.net/11714/2832
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Minnesota
8.
Cradic, Kendall.
Next Generation Sequencing: Applications for the Clinic.
Degree: PhD, Biomedical Informatics and Computational Biology, 2016, University of Minnesota
URL: http://hdl.handle.net/11299/182252
► Genomic information from the patient is becoming increasingly important for diagnosis of many diseases. Next Generation Sequencing (NGS), while commonly used as a research tool,…
(more)
▼ Genomic information from the patient is becoming increasingly important for diagnosis of many diseases. Next Generation Sequencing (NGS), while commonly used as a research tool, is steadily making its way into clinical labs. One advantage of NGS is found in the observations that can be made, in addition to primary sequence, by analyzing raw data. This project is focused on the development of three such applications that have diagnostic utility. The first is a method to determine the phase of compound heterozygotes; an important problem when recessive genes contain more than one mutation. The second is a process designed to identify and interpret chromosomal rearrangements that are related to disease. And finally, the third is a technique used to calculate the copy number of mitochondrial DNA. These methods were developed for use in the clinical lab and can have a practical role in diagnosing disease.
Subjects/Keywords: haplotyping; next generation sequencing
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APA (6th Edition):
Cradic, K. (2016). Next Generation Sequencing: Applications for the Clinic. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/182252
Chicago Manual of Style (16th Edition):
Cradic, Kendall. “Next Generation Sequencing: Applications for the Clinic.” 2016. Doctoral Dissertation, University of Minnesota. Accessed March 07, 2021.
http://hdl.handle.net/11299/182252.
MLA Handbook (7th Edition):
Cradic, Kendall. “Next Generation Sequencing: Applications for the Clinic.” 2016. Web. 07 Mar 2021.
Vancouver:
Cradic K. Next Generation Sequencing: Applications for the Clinic. [Internet] [Doctoral dissertation]. University of Minnesota; 2016. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/11299/182252.
Council of Science Editors:
Cradic K. Next Generation Sequencing: Applications for the Clinic. [Doctoral Dissertation]. University of Minnesota; 2016. Available from: http://hdl.handle.net/11299/182252
University of Melbourne
9.
Orlowski, Christian.
Epigenetic responses to external stimuli in murine embryonic stem cells.
Degree: 2012, University of Melbourne
URL: http://hdl.handle.net/11343/37286
► The epigenetic mechanisms underlying the nuclear plasticity of embryonic stem cells have been a focus of intensive research in the past several years. The emergence…
(more)
▼ The epigenetic mechanisms underlying the nuclear plasticity of embryonic stem cells have been a focus of intensive research in the past several years. The emergence of massively parallel sequencing technology has enabled investigators to examine epigenetic responses to stimuli such as signals that trigger stem cell differentiation on a genome-wide scale. Histone modifications represent an essential mechanism that defines the chromatin architecture responsible for regulating the global transcriptional profile of a cell. Though our understanding of the role of histone modifications in stem cell differentiation has grown substantially over the last decade, many of their mechanisms remain elusive, particularly in terms of defining the many multiple developmental lineages a stem cell may take during the course of differentiation. Every lineage and cell type has a unique global epigenetic signature, but this signature is often highly dynamic and comprised of a complex interplay encompassing multiple levels of epigenetic regulation.
Histone H3 lysine monomethylation (H3K4me1) represents a class of histone modifications that is typically associated with transcriptional activation. Histone H3 lysine trimethylation (H3K4me3), for instance, is tightly associated with gene transcription. H3K4me1’s role in the transcriptional status of genes has been less clear than H3K4me3, though it is known that H3K4me1 is a distinctive marker of distal regulatory regions such as transcriptional enhancer elements. H3K4me1 is to a comparatively lesser extent important to and associated with proximal regulatory promoter activation, as has been demonstrated in particular cases such as insulin gene activation and myogenesis. The histone lysine methyltransferase (HKMT) Set7/9 is capable of catalyzing monomethylation of histone H3 lysine 4 at gene promoters. It is not certain whether Set7/9 has any regulatory role in the deposition of H3K4me1 at distal regulatory elements.
This study investigated the global epigenetic effects of inducing early vascular differentiation in pluripotent murine embryonic stem cells (mESCs) with respect to H3K4me1 and its relationship to the changing transcriptome, principally by utilizing mRNA-sequencing and ChIP-sequencing technology. Furthermore, this study addressed the role of Set7/9 in regulating the genome-wide distribution of H3K4me1 in Sca-1+ vascular progenitor cells (VPCs) using an RNA interference technique. Through the determination of the genome-wide distribution of H3K4me1 at the proximal as well as distal regulatory regions associated with genes, this study identified that differentiation-induced H3K4me1 changes were often defined by a large proportion of promoter regions exhibiting a distinctive gain in H3K4me1, whereas Sca-1+ VPCs with ablated Set7/9 function demonstrated the reverse. In both scenarios, putative enhancers identified by H3K4me1 enrichment were also identified as having undergone substantial changes…
Subjects/Keywords: bioinformatics; next generation sequencing; epigenetics
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Chicago ·
MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Orlowski, C. (2012). Epigenetic responses to external stimuli in murine embryonic stem cells. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/37286
Chicago Manual of Style (16th Edition):
Orlowski, Christian. “Epigenetic responses to external stimuli in murine embryonic stem cells.” 2012. Doctoral Dissertation, University of Melbourne. Accessed March 07, 2021.
http://hdl.handle.net/11343/37286.
MLA Handbook (7th Edition):
Orlowski, Christian. “Epigenetic responses to external stimuli in murine embryonic stem cells.” 2012. Web. 07 Mar 2021.
Vancouver:
Orlowski C. Epigenetic responses to external stimuli in murine embryonic stem cells. [Internet] [Doctoral dissertation]. University of Melbourne; 2012. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/11343/37286.
Council of Science Editors:
Orlowski C. Epigenetic responses to external stimuli in murine embryonic stem cells. [Doctoral Dissertation]. University of Melbourne; 2012. Available from: http://hdl.handle.net/11343/37286
University of Southern California
10.
Pakfar, Tina M.
Tailoring philanthropic strategies to new generational
cohorts.
Degree: Doctor of Policy, Planning & Development, Public Policy / Planning, 2013, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/254846/rec/6315
► Demographic changes are currently altering the philanthropic landscape. The traditional generations of donors are aging and, as a consequence, development professionals will have to reach…
(more)
▼ Demographic changes are currently altering the
philanthropic landscape. The traditional generations of donors are
aging and, as a consequence, development professionals will have to
reach out to the
next generation of possible donors. The
Next
Generation, comprised of individuals born between 1965 and 1980,
referred to as Generation X, and individuals born between 1981 and
2000, referred to as Millennials (also known as Generation Y), need
to be approached in ways that differ from previous generations. For
example, the
next generation seeks greater personal involvement in
their endeavors. This article explores the utility of nonprofit
organizations creating internal giving circles to better recruit
and engage the
Next Generation. The paper concludes by discussing
the social implications that make giving circles a viable tool for
development professionals seeking to create and maintain
sustainable philanthropic models.
Advisors/Committee Members: Myrtle, Robert C. (Committee Chair), Esparza, Nicole (Committee Member), Jordan-Marsh, Maryalice (Committee Member).
Subjects/Keywords: philanthropy; giving circles; Next Generation
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MLA ·
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Export
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Manager
APA (6th Edition):
Pakfar, T. M. (2013). Tailoring philanthropic strategies to new generational
cohorts. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/254846/rec/6315
Chicago Manual of Style (16th Edition):
Pakfar, Tina M. “Tailoring philanthropic strategies to new generational
cohorts.” 2013. Doctoral Dissertation, University of Southern California. Accessed March 07, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/254846/rec/6315.
MLA Handbook (7th Edition):
Pakfar, Tina M. “Tailoring philanthropic strategies to new generational
cohorts.” 2013. Web. 07 Mar 2021.
Vancouver:
Pakfar TM. Tailoring philanthropic strategies to new generational
cohorts. [Internet] [Doctoral dissertation]. University of Southern California; 2013. [cited 2021 Mar 07].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/254846/rec/6315.
Council of Science Editors:
Pakfar TM. Tailoring philanthropic strategies to new generational
cohorts. [Doctoral Dissertation]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/254846/rec/6315
Duquesne University
11.
Domencic, Joseph.
Writing The Next Galileo, a Children's Musical.
Degree: MM, Music Technology, 2014, Duquesne University
URL: https://dsc.duq.edu/etd/492
► This thesis details my process in writing the book, music and lyrics to a one-act children's musical entitled The Next Galileo; it also includes an…
(more)
▼ This thesis details my process in writing the book, music and lyrics to a one-act children's musical entitled The
Next Galileo; it also includes an analysis of key aspects of the work. It begins with background on the project's genesis, followed by the early stages of the creative process, including chapters on the story's themes and structure. It continues by analyzing important musical elements of the piece as well as giving specifics about the compositional process. After describing the benefits of the music technologies and digital media utilized, it concludes with information about ongoing plans for the work, including its scheduled tour of Western Pennsylvania schools in 2015.
Advisors/Committee Members: Lynn Purse, Lynn Purse, William Purse, Judith Bowman.
Subjects/Keywords: Children's; Galileo; Musical; Next; Writing
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Domencic, J. (2014). Writing The Next Galileo, a Children's Musical. (Thesis). Duquesne University. Retrieved from https://dsc.duq.edu/etd/492
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Domencic, Joseph. “Writing The Next Galileo, a Children's Musical.” 2014. Thesis, Duquesne University. Accessed March 07, 2021.
https://dsc.duq.edu/etd/492.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Domencic, Joseph. “Writing The Next Galileo, a Children's Musical.” 2014. Web. 07 Mar 2021.
Vancouver:
Domencic J. Writing The Next Galileo, a Children's Musical. [Internet] [Thesis]. Duquesne University; 2014. [cited 2021 Mar 07].
Available from: https://dsc.duq.edu/etd/492.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Domencic J. Writing The Next Galileo, a Children's Musical. [Thesis]. Duquesne University; 2014. Available from: https://dsc.duq.edu/etd/492
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of New South Wales
12.
Deveson, Ira.
Three (largely unrelated) experiments in the age of next-generation sequencing.
Degree: Biotechnology & Biomolecular Sciences, 2017, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/58940
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true
► Next generation sequencing (NGS) enables researchers to identify instances of genetic variation and measure gene expression in an unbiased, global fashion. In this thesis I…
(more)
▼ Next generation sequencing (NGS) enables researchers to identify instances of genetic variation and measure gene expression in an unbiased, global fashion. In this thesis I describe three experiments that apply NGS in quite distinct contexts. Together these illustrate the strengths and broad utility of this revolutionary technology.Experiment 1. I have developed a set of synthetic DNA standards – termed sequins – that emulate human genetic features and constitute qualitative and quantitative spike- in controls for NGS. I have used this approach to represent common and clinically relevant genetic variation, ranging from single nucleotide variants to large structural rearrangements. Here I describe the design and validation of sequin controls, and demonstrate their capacity to measure and mitigate biases during NGS analysis.Experiment 2. In many vertebrates sex is determined by external environmental cues rather than by sex chromosomes. In reptiles, for instance, temperature-dependent sex determination (TSD) is common. I have used the Australian central bearded dragon, in which chromosomal sex determination is overridden at high temperatures to produce sex-reversed female offspring, as a unique model to identify TSD-specific features of the transcriptome. Here I show that an intron is retained in mature transcripts from each of two Jumonji-family chromatin modifier genes, JARID2 and JMJD3, in female dragons that have been sex-reversed by temperature, but not in normal chromosomal females or males. I also observed sex-associated differential retention of the equivalent introns expressed in alligators and turtles, indicative of a reptile-wide mechanism that may control TSD.Experiment 3. The human transcriptome is so large, diverse and dynamic that, even after a decade of investigation by RNA sequencing (RNA-Seq), we are yet to resolve its true dimensions. I have performed targeted single-molecule and short-read RNA- Seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. This analysis identifies a fundamental distinction between the architecture of protein-coding and noncoding gene content. Unlike their coding counterparts, noncoding exons undergo universal alternative splicing to produce a seemingly limitless variety of isoforms. I propose that noncoding exons are functionally modular, with combinatorial alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.
Advisors/Committee Members: Mattick, John, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW, Janitz, Michael, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW, Timothy, Mercer, Clinical School - St Vincent's Hospital, Faculty of Medicine, UNSW.
Subjects/Keywords: Next-generation sequencing; Genomics; Transcriptomics
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APA ·
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MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Deveson, I. (2017). Three (largely unrelated) experiments in the age of next-generation sequencing. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Deveson, Ira. “Three (largely unrelated) experiments in the age of next-generation sequencing.” 2017. Doctoral Dissertation, University of New South Wales. Accessed March 07, 2021.
http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true.
MLA Handbook (7th Edition):
Deveson, Ira. “Three (largely unrelated) experiments in the age of next-generation sequencing.” 2017. Web. 07 Mar 2021.
Vancouver:
Deveson I. Three (largely unrelated) experiments in the age of next-generation sequencing. [Internet] [Doctoral dissertation]. University of New South Wales; 2017. [cited 2021 Mar 07].
Available from: http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true.
Council of Science Editors:
Deveson I. Three (largely unrelated) experiments in the age of next-generation sequencing. [Doctoral Dissertation]. University of New South Wales; 2017. Available from: http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true
Universitat de Valencia
13.
Muñoz Vidal, Javier I.
The NEXT path to neutrino inverse hierarchy
.
Degree: 2018, Universitat de Valencia
URL: http://hdl.handle.net/10550/66537
► De todas las partículas que componen el universo, quizás la más común de ellas sea también la más misteriosa, el neutrino. Ahora mismo miles de…
(more)
▼ De todas las partículas que componen el universo, quizás la más común de ellas sea también la más misteriosa, el neutrino. Ahora mismo miles de millones de estas partículas nos atraviesan sin percibirlo, y detectar una sola de ellas necesita de enormes detectores enterrados a gran profundidad. Postuladas por primera vez por Wolfgang Pauli en 1930, fueron bautizadas en 1934 como ”pequeños neutrones” por Enrico Fermi, aludiendo a dos de sus principales características: su pequeña masa y su ausencia de carga eléctrica. A mediados de los años 70, los neutrinos fueron incluidos en el Modelo Estándar bajo las premisas de: carecer de masa y carga eléctrica, experimentar únicamente la fuerza nuclear débil, ser los neutrinos distintos de sus antipartículas y la existencia de 3 familias con números leptónicos conservados por separado.
Sin embargo, los experimentos de oscilaciones de neutrinos llevados a cabo durante las últimas décadas han demostrado que los neutrinos tienen masa y se mezclan, abriendo un nuevo campo en la física más allá del Modelo Estándar. Una de las maneras de acomodar estas masas en la teoría es que los neutrinos podrían ser partículas de Majorana, es decir, idénticas a sus antipartículas, al contrario que el resto de fermiones, y violar la conservación del número leptónico. De ser así, los neutrinos pudieran tener relación con la asimetría materia-antimateria del universo vía leptogénesis, así como ser una elegante explicación de la pequeñez de su masa a través del mecanismo ”see-saw”. Ante esta situación, es fácil entender que los neutrinos sean en la actualidad uno de los campos de moda de la investigación en física a nivel mundial y multitud de experimentos traten de arrojar luz sobre su naturaleza.
El método más sensible para establecer la naturaleza de los neutrinos es la búsqueda de una hipotética y extremadamente rara transición nuclear llamada desintegración doble beta sin emisión de neutrinos (0νββ) en el que un núcleo de número atómico Z y número másico A se transforma en su isóbaro de número atómico Z + 2 emitiendo únicamente dos electrones:
X (A,Z) → X (A,Z+2) + e− + e−
Aunque la versión del proceso que incluye emisión de neutrinos ha sido observada y medida en varios isótopos, la versión sin neutrinos del proceso aún no lo ha sido a día de hoy. El mecanismo físico más simple que lo describe es el intercambio virtual de un neutrino ligero de tipo Majorana, de manera que toda la energía disponible en la desintegración (Qββ) se reparta entre los dos electrones emitidos. Precisamente ésta, sería la señal característica del proceso y por tanto el objetivo de todo experimento que pretenda encontrarlo. La semivida de este proceso llevaría implícita una medida indirecta de la masa de los neutrinos.
Los experimentos actuales han seguido distintas aproximaciones tecnológicas buscando la mejor resolución energética y la menor actividad de ruido posible que maximicen su sensibilidad. Las técnicas más prometedoras son los bolómetros, las TPCs, los semiconductores y los centelleadores.…
Advisors/Committee Members: Gómez Cadenas, Juan José (advisor).
Subjects/Keywords: Neutrino;
Neutrino mass;
Double beta decay;
Majorana;
NEXT;
Canfranc;
NEXT-100
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APA ·
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MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Muñoz Vidal, J. I. (2018). The NEXT path to neutrino inverse hierarchy
. (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/66537
Chicago Manual of Style (16th Edition):
Muñoz Vidal, Javier I. “The NEXT path to neutrino inverse hierarchy
.” 2018. Doctoral Dissertation, Universitat de Valencia. Accessed March 07, 2021.
http://hdl.handle.net/10550/66537.
MLA Handbook (7th Edition):
Muñoz Vidal, Javier I. “The NEXT path to neutrino inverse hierarchy
.” 2018. Web. 07 Mar 2021.
Vancouver:
Muñoz Vidal JI. The NEXT path to neutrino inverse hierarchy
. [Internet] [Doctoral dissertation]. Universitat de Valencia; 2018. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/10550/66537.
Council of Science Editors:
Muñoz Vidal JI. The NEXT path to neutrino inverse hierarchy
. [Doctoral Dissertation]. Universitat de Valencia; 2018. Available from: http://hdl.handle.net/10550/66537
University of Otago
14.
Sutton, Jolene Theresa.
Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines
.
Degree: 2013, University of Otago
URL: http://hdl.handle.net/10523/4335
► Theory predicts that rapid decreases in population size (“population bottlenecks”) will result in initial decreases in allelic diversity through a random sampling of individuals from…
(more)
▼ Theory predicts that rapid decreases in population size (“population bottlenecks”) will result in initial decreases in allelic diversity through a random sampling of individuals from the source population, followed by subsequent losses through genetic drift (random sampling of alleles from one generation to the
next) if population sizes remain small. Years of empirical research based on neutral genetic diversity (i.e. the diversity of alleles or loci for which mutations do not result in changes to fitness) supports this theory. However, it has been argued that selection will maintain diversity at functionally important genes, even through severe bottlenecks. The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response, and due to strong balancing selection, is one of the most polymorphic regions of the entire genome. Despite 20 years of research in natural populations, empirical studies offer highly contradictory explanations of the relative roles of selection and genetic drift in shaping MHC variation during population bottlenecks. Many studies conclude that “drift outweighs selection”, rendering MHC diversity effectively neutral during population declines, while several others have found evidence that balancing selection can maintain MHC diversity during these events, even while neutral diversity is lost. A few studies have concluded that in small populations, selection can accelerate the rate of loss for adaptive diversity. In this thesis, I test for signals of balancing selection and genetic drift in shaping post-bottleneck MHC diversity, in an effort to inform the debate in this research field. I also examine factors that influence the impact of population bottlenecks, and which may have led to the disparity among previous study results. I focus my research on threatened New Zealand passerines, which provide a model study system due to their bottleneck histories, as well as availability of both pre- and post-bottleneck samples. To achieve my goals, I compare genetic diversity at MHC class II B loci and at microsatellite loci.
I first synthesise the results of previous studies that examined MHC and neutral genetic diversity in bottlenecked populations for multiple vertebrate taxa. Based on meta-analytical techniques, I conclude that bottleneck events generally result in loss of both MHC and neutral genetic diversity, and that MHC diversity can be lost at a faster rate than neutral diversity in natural populations. I find that a key factor in shaping genetic diversity is bottleneck duration, with prolonged bottlenecks resulting in the greatest impacts. In a subsequent chapter, I go on to characterise MHC class II B diversity in contemporary populations of New Zealand South Island and North Island saddlebacks. I find evidence of historic balancing selection, which helps to identify classical MHC allele sequences (under strong selection) from those of non-classical loci (not under strong selection). I also find that South Island saddlebacks have less MHC diversity than…
Advisors/Committee Members: Jamieson, Ian G (advisor).
Subjects/Keywords: Philesturnus;
Petroica;
next generation sequencing;
immunogenetics
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APA ·
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Sutton, J. T. (2013). Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines
. (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/4335
Chicago Manual of Style (16th Edition):
Sutton, Jolene Theresa. “Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines
.” 2013. Doctoral Dissertation, University of Otago. Accessed March 07, 2021.
http://hdl.handle.net/10523/4335.
MLA Handbook (7th Edition):
Sutton, Jolene Theresa. “Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines
.” 2013. Web. 07 Mar 2021.
Vancouver:
Sutton JT. Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines
. [Internet] [Doctoral dissertation]. University of Otago; 2013. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/10523/4335.
Council of Science Editors:
Sutton JT. Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines
. [Doctoral Dissertation]. University of Otago; 2013. Available from: http://hdl.handle.net/10523/4335
University of California – Riverside
15.
Cacho, Ashley.
Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model.
Degree: Applied Statistics, 2016, University of California – Riverside
URL: http://www.escholarship.org/uc/item/98x9v8rn
► The emergence of high-throughput sequencing (HTS) technology has greatly influenced research in biological sciences including clinical applications such as in the understanding of disease etiology…
(more)
▼ The emergence of high-throughput sequencing (HTS) technology has greatly influenced research in biological sciences including clinical applications such as in the understanding of disease etiology and pharmacogenomics. One widely used sequencing machine is the Illumina platform which uses a novel sequencing-by-synthesis method that involves chemical and optical imaging processes. The conversion of fluorescence intensity measures resulting from image processing to nucleotide bases is what is known as base-calling. The complex nature of sequencing-by-synthesis generates biases that affect accuracy of the sequenced DNA. Consequently, further analysis of sequences such as in genome assembly and variant detection may be directly influenced. Considering recently published methods to perform base-calling, it is evident that many methods perform transformations to the intensity data to reduce and/or eliminate biases. Thus, there is a need to model the original intensity data to maintain the information inherent within the data. Our novel method based on a Random Effects Mixture model, REMix, aims to capture the sequencing process while using the original data provided by the sequencing machine. Real data results demonstrate that REMix has the best balance of performance with respect to the validation metrics that are considered.
Subjects/Keywords: Statistics; Bioinformatics; base-calling; next-generation sequencing
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APA ·
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MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Cacho, A. (2016). Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/98x9v8rn
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Cacho, Ashley. “Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model.” 2016. Thesis, University of California – Riverside. Accessed March 07, 2021.
http://www.escholarship.org/uc/item/98x9v8rn.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cacho, Ashley. “Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model.” 2016. Web. 07 Mar 2021.
Vancouver:
Cacho A. Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model. [Internet] [Thesis]. University of California – Riverside; 2016. [cited 2021 Mar 07].
Available from: http://www.escholarship.org/uc/item/98x9v8rn.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cacho A. Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model. [Thesis]. University of California – Riverside; 2016. Available from: http://www.escholarship.org/uc/item/98x9v8rn
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Cornell University
16.
Ouyang, Christine.
Solvent-Based Development Of Photoresists For Next-Generation Lithography.
Degree: PhD, Materials Science and Engineering, 2013, Cornell University
URL: http://hdl.handle.net/1813/34221
► As feature sizes continue to shrink, the need for new materials and new processes for next-generation lithography becomes more urgent. Although aqueous base development has…
(more)
▼ As feature sizes continue to shrink, the need for new materials and new processes for
next-generation lithography becomes more urgent. Although aqueous base development has been the industry standard for over twenty years, there are still several issues that need to be overcome. First, the high surface tension of aqueous base developers can lead to pattern collapse of high aspect ratio patterns and limit resolution. The toxicity of aqueous base developers has also raised concerns about the environment. In order to reduce the problems related to aqueous development, solvents or materials with desirable properties must be used. Recently, there has also been growing interest in solvent-based negative-tone development (NTD) due to its better performance in printing certain feature types. Therefore, solvent-based development of photoresists was investigated in this study. One approach to reduce the pattern collapse problem and environmental issues of the lithographic process is through the use of environmentally friendly solvents with low surface tension. Supercritical carbon dioxide (scCO2) and linear methyl siloxanes (LMS) are green solvents that have low toxicity, low surface tension, low viscosity and can be recycled. Solvent-based development of both polymeric and molecular glass resists with positive- and negative-tone images have been successfully demonstrated in both solvents. High-resolution and high aspect ratio patterns were obtained with no pattern collapse observed using both solvents. As there is little iii understanding about the solvent power of linear methyl siloxanes, the dissolution behavior of polymers and molecular glasses in linear methyl siloxanes was also studied. Besides using low surface tension developers to mitigate pattern collapse problem, another approach is by using materials with high etch resistance that eliminates the use of thick films. Also, because of the low intensity of current EUV light source, the
next-generation resists need to demonstrate high sensitivity and optimum absorbance. Inorganic metal oxide nanoparticles based on zirconium oxide (ZrO2) and hafnium oxide (HfO2) with organic ligands have been synthesized for EUV lithography. These nanoparticle resists can be developed as negative-tone patterns using an organic solvent and high-resolution patterns were achieved. The patterning performance of these nanoparticles in different organic solvents was also evaluated. iv
Advisors/Committee Members: Ober, Christopher Kemper (chair), Giannelis, Emmanuel P (committee member), Jarrow, Robert A. (committee member).
Subjects/Keywords: photoresists; Next-generation lithography; Environmentally friendly
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APA (6th Edition):
Ouyang, C. (2013). Solvent-Based Development Of Photoresists For Next-Generation Lithography. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/34221
Chicago Manual of Style (16th Edition):
Ouyang, Christine. “Solvent-Based Development Of Photoresists For Next-Generation Lithography.” 2013. Doctoral Dissertation, Cornell University. Accessed March 07, 2021.
http://hdl.handle.net/1813/34221.
MLA Handbook (7th Edition):
Ouyang, Christine. “Solvent-Based Development Of Photoresists For Next-Generation Lithography.” 2013. Web. 07 Mar 2021.
Vancouver:
Ouyang C. Solvent-Based Development Of Photoresists For Next-Generation Lithography. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1813/34221.
Council of Science Editors:
Ouyang C. Solvent-Based Development Of Photoresists For Next-Generation Lithography. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/34221
University of Michigan
17.
Lo, Yan Yancy.
Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies.
Degree: PhD, Biostatistics, 2015, University of Michigan
URL: http://hdl.handle.net/2027.42/116761
► Current genetics studies rely heavily on next-generation sequencing (NGS) techniques. This dissertation addresses methodological developments and statistical strategies to efficiently and accurately analyze the large…
(more)
▼ Current genetics studies rely heavily on
next-generation sequencing (NGS) techniques. This dissertation addresses methodological developments and statistical strategies to efficiently and accurately analyze the large amounts of NGS data, thereby to understand the genetic contributions to diseases.
In chapter 2, we evaluated the benefits of different variant calling strategies by performing a comparative analysis of calling methods on large-scale exonic sequencing datasets. We found that individual-based analyses identified the most high quality singletons, but had lower genotype accuracy at common variants than population-based and LD-aware analyses. Therefore, we recommend population-based analyses for high quality variant calls with few missing genotypes, complemented by individual-based analyses to obtain the most singleton variants.
In chapters 3 and 4, we addressed the issue of overlapping read pairs in NGS studies arising from short fragments. In chapter 3, we proposed novel models to separately estimate machine and fragment errors of a NGS experiment from overlapping read pairs. Using a Markov chain Monte Carlo algorithm, our models suggested that machine and fragment errors were largely predicted by the reported quality scores of the overlapping bases and were uniform across individual samples from the same experiment. In chapter 4, we proposed an algorithm, RESCORE, to resolve the fragment dependence while retaining machine error estimates in overlapping reads. When compared to soft-clipping the overlapping regions, RESCORE increased the recalibrated base quality scores for the majority of overlapping bases, leading to a decrease in estimated false positive rate of novel variant discovery.
In chapter 5, we presented an application of whole-genome sequencing for understanding the evolutionary history of uropathogenic Escherichia coli (UPEC). We sequenced 14 UPEC and 5 commensals at >190x, and found a deep split between UPEC and commensal E. coli. We observed high between-strain diversity, which suggests multiple origins of pathogenicity. We detected no selective advantage of virulence genes over other genomic regions. These results suggest that UPEC acquired uropathogenicity a long time ago and used it opportunistically to cause extraintestinal infections. In summary, this dissertation presented practical strategies for NGS studies that will contribute to further genetic advances.
Advisors/Committee Members: Zoellner, Sebastian K (committee member), Foxman, Betsy (committee member), Abecasis, Goncalo (committee member), Kang, Hyun Min (committee member), Johnson, Timothy D (committee member).
Subjects/Keywords: next-generation sequencin; Genetics; Health Sciences
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APA (6th Edition):
Lo, Y. Y. (2015). Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/116761
Chicago Manual of Style (16th Edition):
Lo, Yan Yancy. “Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies.” 2015. Doctoral Dissertation, University of Michigan. Accessed March 07, 2021.
http://hdl.handle.net/2027.42/116761.
MLA Handbook (7th Edition):
Lo, Yan Yancy. “Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies.” 2015. Web. 07 Mar 2021.
Vancouver:
Lo YY. Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies. [Internet] [Doctoral dissertation]. University of Michigan; 2015. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/2027.42/116761.
Council of Science Editors:
Lo YY. Statistical Methods, Analyses and Applications for Next-Generation Sequencing Studies. [Doctoral Dissertation]. University of Michigan; 2015. Available from: http://hdl.handle.net/2027.42/116761
Vanderbilt University
18.
Hutchinson, Katherine Emily.
Identification of Novel Targets for Therapy in Solid Tumors.
Degree: PhD, Cancer Biology, 2015, Vanderbilt University
URL: http://hdl.handle.net/1803/15255
► Solid tumor treatment paradigms have drastically improved in recent decades through direct targeting of the protein products of somatic, constitutively active “driver” mutations and their…
(more)
▼ Solid tumor treatment paradigms have drastically improved in recent decades through direct targeting of the protein products of somatic, constitutively active “driver” mutations and their effector signaling pathways. Prior to these advances, metastatic solid tumors were primarily managed through administration of traditional cytotoxic chemotherapy. A prime example of this success is evident in melanomas expressing alterations at codon V600 of the serine-threonine kinase, BRAF. Compared to the chemotherapeutic standard-of-care in metastatic melanoma, dacarbazine, patients with BRAF V600E/K/M/R/D-mutated tumors exhibit significantly higher response and survival rates when treated with V600-variant specific small molecule inhibitors, vemurafenib and dabrafenib. However, potential driver mutations have not been identified for all tumors, and a large fraction of tumors are still “driver negative”. Herein, we sought to uncover new ‘drivers’ in pan-negative melanoma and pancreatic acinar cell carcinoma (PACC). While approximately 70% of melanomas harbor actionable driver alterations, the remaining one-third of patients are considered pan-negative. No driver alterations have yet been identified in patients with PACC, likely due to the rarity of this tumor type. Through whole-genome sequencing (WGS), we identified BRAF non-V600 alterations (L597, K601) in pan-negative melanomas that activate the mitogen-activation protein kinase (MAPK) signaling pathway and confer sensitivity to MEK1/2 inhibitors. Using comprehensive targeted,
next-generation sequencing platforms, we identified MAPK-pathway activating RAF fusions in both pan-negative melanomas and PACCs. Finally, efforts to distinguish further pan-negative melanomas from one another revealed that a subset of pan-negative melanomas exhibit baseline activation of the ERBB family receptor tyrosine kinases (RTKs) EGFR, HER2 and HER3, suggesting a potential avenue for ERBB kinase inhibition in this disease. Collectively, this work describes the identification of novel and clinically actionable targets in previously un-druggable cancer subtypes.
Advisors/Committee Members: Graham Carpenter (committee member), Jeffrey A. Sosman (committee member), Ann Richmond (committee member), William Pao (committee member), Jin Chen (Committee Chair).
Subjects/Keywords: next-generation sequencing; targeted therapy; cancer; melanoma
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APA (6th Edition):
Hutchinson, K. E. (2015). Identification of Novel Targets for Therapy in Solid Tumors. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/15255
Chicago Manual of Style (16th Edition):
Hutchinson, Katherine Emily. “Identification of Novel Targets for Therapy in Solid Tumors.” 2015. Doctoral Dissertation, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/15255.
MLA Handbook (7th Edition):
Hutchinson, Katherine Emily. “Identification of Novel Targets for Therapy in Solid Tumors.” 2015. Web. 07 Mar 2021.
Vancouver:
Hutchinson KE. Identification of Novel Targets for Therapy in Solid Tumors. [Internet] [Doctoral dissertation]. Vanderbilt University; 2015. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/15255.
Council of Science Editors:
Hutchinson KE. Identification of Novel Targets for Therapy in Solid Tumors. [Doctoral Dissertation]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/15255
Penn State University
19.
Zhang, Zhenhai.
DATAMINING OF GENOME-WIDE NUCLEOSOME DATA
GENERATED BY NEXT-GENERATION SEQUENCING
.
Degree: 2011, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/11443
► The fundamental building block of eukaryotic genomes is the nucleosome, which consists of 147 base pairs DNA sequence and four core histones with possible exchange…
(more)
▼ The fundamental building block of eukaryotic genomes is the nucleosome, which consists of 147 base pairs DNA sequence and four core histones with possible exchange of histone variants, such as H2Av. Both the position and composition of nucleosomes provide important roles during genome compaction and gene regulation. MNase Chromatin ImmunoPrecipitation followed by
next-generation sequencing (ChIP-Seq) allows scientists to investigate genome-wide nucleosome positions in a near base pair resolution.
Chapter 2 summarizes principles, concepts, and philosophies in producing computer scripts, which I developed to process and analyze genomic MNase ChIP-seq data. The resulting pipelines and script toolkits led to the successful analysis in Chapter 3, 4, and 5.
For example, while MNase ChIP-seq has revealed that the H2Av histone variant preferentially marks euchromatin promoter regions in fly, thus far no parallel study has been conducted on heterochromatic regions. In chapter 3 of this thesis, I compared the H2Av nucleosome patterns around same genomic features between euchromatin and heterochromatin. I found that different genomic features have each have a unique H2Av nucleosome organization. This study provided insight into the how nucleosomes are organized in the framework of the typically more compact and transcriptionally silent heterochromatin.
High-throughput sequencing efforts in yeast also showed that nucleosomes are organized in a uniformly spaced array at 5’ end of genes. The mechanism underlying this array formation is far from understood and remains controversial. In chapter 4 of this thesis, I investigated the contributions of DNA sequence, statistical positioning, and ATP-dependent trans-acting factors to genome-wide nucleosome positioning. The genomic DNA sequence defines the thermo-dynamic landscape for nucleosome occupancy and this study shows that the position of the first nucleosome in the array is most dependent on DNA sequence. In collaboration with others I discovered a novel ATP-driven packing mechanism against a genomic barrier that drives nucleosome organization at the 5’ end of most genes. Poly (dA:dT) tracks in 5’ nucleosome-free promoter regions (NFRs) generally excluded nucleosome binding, thereby forming one genomic barrier. ATP-dependent chromatin remodelers pack nucleosomes against this barrier to form regularly spaced arrays. The effect of chromatin remodelers lasts for about four nucleosomes into each genic array, after which the underlying DNA sequence directs nucleosome placement. This new mechanism replaces three other prevailing mechanisms of nucleosome organization (DNA-encoded, statistical positioning, and transcription), and suggests that the packing mechanism creates nucleosome organizing centers that function to buffer nucleosome density and positioning against transient changes in nucleosome level that might occur during transcription and DNA replication.
Advisors/Committee Members: Benjamin Franklin Pugh, Dissertation Advisor/Co-Advisor, Benjamin Franklin Pugh, Committee Chair/Co-Chair, David Scott Gilmour, Committee Member, Debashis Ghosh, Committee Member, Yu Zhang, Committee Member.
Subjects/Keywords: Next-generation sequencing; data mining; ChIP-Seq
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Zhang, Z. (2011). DATAMINING OF GENOME-WIDE NUCLEOSOME DATA
GENERATED BY NEXT-GENERATION SEQUENCING
. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11443
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zhang, Zhenhai. “DATAMINING OF GENOME-WIDE NUCLEOSOME DATA
GENERATED BY NEXT-GENERATION SEQUENCING
.” 2011. Thesis, Penn State University. Accessed March 07, 2021.
https://submit-etda.libraries.psu.edu/catalog/11443.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zhang, Zhenhai. “DATAMINING OF GENOME-WIDE NUCLEOSOME DATA
GENERATED BY NEXT-GENERATION SEQUENCING
.” 2011. Web. 07 Mar 2021.
Vancouver:
Zhang Z. DATAMINING OF GENOME-WIDE NUCLEOSOME DATA
GENERATED BY NEXT-GENERATION SEQUENCING
. [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Mar 07].
Available from: https://submit-etda.libraries.psu.edu/catalog/11443.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zhang Z. DATAMINING OF GENOME-WIDE NUCLEOSOME DATA
GENERATED BY NEXT-GENERATION SEQUENCING
. [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11443
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Guelph
20.
Cairns, Alexander Philip.
The Growth Potential of the 'Next-11': The Importance of Emerging Markets for Canadian Agrifood Trade.
Degree: MS, Department of Food, Agricultural and Resource Economics, 2011, University of Guelph
URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3030
► The capacity of Canada’s export-oriented agrifood sectors to cope with contemporary challenges may hinge on their ability to identify new export markets. This thesis uses…
(more)
▼ The capacity of Canada’s export-oriented agrifood sectors to cope with contemporary challenges may hinge on their ability to identify new export markets. This thesis uses an import demand model, developed by Hallak (2006), to assess how per capita expenditure on Canadian agrifood exports is influenced by income growth and the presence of a preferential trade agreement for a group of emerging economies, known as ‘the
Next-11.’ Results reveal that while as a group the
Next-11 does not appear to be distinct from other income groups or the BRICs in terms of their expenditures on agrifood imports, Vietnam and South Korea demonstrate expenditure elasticities notably higher then other
Next-11 and BRIC members. Finally, the findings cast doubt on the capacity of PTAs to enhance Canadian agrifood trade. However, this result may be indicative of Canada’s longstanding commitment to multilateral trade liberalization and the corresponding delay in the adoption of PTAs.
Advisors/Committee Members: Meilke, Karl D. (advisor).
Subjects/Keywords: Next-11; Agrifood trade; Heckman Selection Model
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APA (6th Edition):
Cairns, A. P. (2011). The Growth Potential of the 'Next-11': The Importance of Emerging Markets for Canadian Agrifood Trade. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3030
Chicago Manual of Style (16th Edition):
Cairns, Alexander Philip. “The Growth Potential of the 'Next-11': The Importance of Emerging Markets for Canadian Agrifood Trade.” 2011. Masters Thesis, University of Guelph. Accessed March 07, 2021.
https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3030.
MLA Handbook (7th Edition):
Cairns, Alexander Philip. “The Growth Potential of the 'Next-11': The Importance of Emerging Markets for Canadian Agrifood Trade.” 2011. Web. 07 Mar 2021.
Vancouver:
Cairns AP. The Growth Potential of the 'Next-11': The Importance of Emerging Markets for Canadian Agrifood Trade. [Internet] [Masters thesis]. University of Guelph; 2011. [cited 2021 Mar 07].
Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3030.
Council of Science Editors:
Cairns AP. The Growth Potential of the 'Next-11': The Importance of Emerging Markets for Canadian Agrifood Trade. [Masters Thesis]. University of Guelph; 2011. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3030
University of Guelph
21.
Taidi, Saina.
Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes.
Degree: MS, Department of Integrative Biology, 2012, University of Guelph
URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951
► This thesis employs three bioindicator species of mayfly (Insecta: Ephemeroptera) and three of caddisfly (Insecta: Trichoptera) as models to develop a reliable biodiversity and biomonitoring…
(more)
▼ This thesis employs three bioindicator species of mayfly (Insecta: Ephemeroptera) and three of caddisfly (Insecta: Trichoptera) as models to develop a reliable biodiversity and biomonitoring assessment approach by using quantitative PCR (qPCR) and
next generation sequencing (NGS) technology. Quantitative PCR was employed to assess the efficiency of species-specific PCR primers in amplifying their target species versus other taxa from closely or distantly related taxonomic groups from benthic habitats. Results showed qPCR can be used as a practical test for evaluating PCR primers for amplifying specific taxa in mixed environmental samples although it might be influenced by amplification bias. Target specific primers are an alternate to presumably universal primers. Each primer set can be tested and optimized using qPCR prior to use in
next-generation sequencing. qPCR results showed corroboration with 454 pyrosequence data and hence it can be used in experimental design procedure for NGS based biomonitoring which could indicate that qPCR is a useful tool for selecting primers in the NGS amplicon preparation.
Advisors/Committee Members: Hajibabaei, Mehrdad (advisor).
Subjects/Keywords: Next generation sequencing; DNA barcoding; Biomonitoring
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APA (6th Edition):
Taidi, S. (2012). Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951
Chicago Manual of Style (16th Edition):
Taidi, Saina. “Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes.” 2012. Masters Thesis, University of Guelph. Accessed March 07, 2021.
https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951.
MLA Handbook (7th Edition):
Taidi, Saina. “Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes.” 2012. Web. 07 Mar 2021.
Vancouver:
Taidi S. Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes. [Internet] [Masters thesis]. University of Guelph; 2012. [cited 2021 Mar 07].
Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951.
Council of Science Editors:
Taidi S. Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes. [Masters Thesis]. University of Guelph; 2012. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951
University of Edinburgh
22.
Emelianova, Katie.
Using next generation sequencing to investigate the generation of diversity in the genus Begonia.
Degree: PhD, 2017, University of Edinburgh
URL: http://hdl.handle.net/1842/29584
► Begonia is one of the most diverse genera on the planet, with a species count approaching 2000 and a distribution across tropics in South America,…
(more)
▼ Begonia is one of the most diverse genera on the planet, with a species count approaching 2000 and a distribution across tropics in South America, Africa and South East Asia. The genus has occupied a vast range of niches; many highly variable growth forms can be found across the distribution, and species exhibit very diverse morphologies, even in closely related species. A recent study has revealed a putative whole genome duplication (WGD) event in the evolutionary history of Begonia, which has prompted an interest in investigating the impact gene and genome duplication has had on the diversification of Begonia. To answer questions about phenotypic and ecological diversification in Begonia, two species from South America, B. conchifolia and B. plebeja were chosen as study species based on their close phylogenetic relationship and divergent ecology and phenotype. RNA-seq data for six tissues from B. conchifolia and B. plebeja was generated using the Illumina sequencing platform, and normalised relative expression data was obtained by mapping reads to transcripts predicted from the B. conchifolia draft genome. A bioinformatics pipeline was devised to compare expression profiles across 6 different tissues between duplicated gene pairs shared between B. conchifolia and B. plebeja. Gene duplicate pairs were selected as candidates if they showed divergent expression in one species but not in another. Such duplicate pairs are suggestive of neofunctionalization in one species, providing evidence of a potential basis for phenotypic divergence and diversification between B. conchifolia and B. plebeja. Two duplicate pairs were identified as showing such divergent expression patterns as well as being functionally ecologically relevant, Chalcone Synthase and 3-Ketoacyl-CoA synthase, involved in anthocyanin biosynthesis and wax biosynthesis respectively. Investigation of expression and duplication patterns in both gene families showed the candidate gene families to be strikingly different. While 3-Ketoacyl-CoA synthase showed deeper duplications shared with outgroup taxa, Chalcone Synthase appeared to be expanded very recently, with a burst of duplications specific to the genus. 3-Ketoacyl-CoA synthase showed examples of partitioned expression by tissue for different gene family members, with at least five members of the gene family being highly expressed in one or two tissues only. Chalcone Synthase, however, showed dominance of one basal gene family member. Other Chalcone Synthase members, though expressed at lower levels, showed some evidence of reciprocal silencing in B. plebeja, though this pattern was not observed in B. conchifolia. Further investigation of the Chalcone Synthase gene family revealed lineage specific duplication in B. plebeja, and more extensive differential duplication patterns were found across other South American Begonias. Additionally, signals of positive selection were found in two branches on the Chalcone Synthase phylogeny.
Subjects/Keywords: 583; Begonia; plant evolution; next generation sequencing
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APA (6th Edition):
Emelianova, K. (2017). Using next generation sequencing to investigate the generation of diversity in the genus Begonia. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/29584
Chicago Manual of Style (16th Edition):
Emelianova, Katie. “Using next generation sequencing to investigate the generation of diversity in the genus Begonia.” 2017. Doctoral Dissertation, University of Edinburgh. Accessed March 07, 2021.
http://hdl.handle.net/1842/29584.
MLA Handbook (7th Edition):
Emelianova, Katie. “Using next generation sequencing to investigate the generation of diversity in the genus Begonia.” 2017. Web. 07 Mar 2021.
Vancouver:
Emelianova K. Using next generation sequencing to investigate the generation of diversity in the genus Begonia. [Internet] [Doctoral dissertation]. University of Edinburgh; 2017. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1842/29584.
Council of Science Editors:
Emelianova K. Using next generation sequencing to investigate the generation of diversity in the genus Begonia. [Doctoral Dissertation]. University of Edinburgh; 2017. Available from: http://hdl.handle.net/1842/29584
Erasmus University Rotterdam
23.
L.C. Chaitanya (Lakshmi).
Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis.
Degree: 2016, Erasmus University Rotterdam
URL: http://hdl.handle.net/1765/94499
► Traditionally, routine forensic casework is based on comparative grounds. DNA profiles obtained from crime-scenes are compared with those of potential suspects or DNA profiles deposited…
(more)
▼ Traditionally, routine forensic casework is based on comparative grounds. DNA profiles
obtained from crime-scenes are compared with those of potential suspects or DNA profiles
deposited in forensic DNA databases. The principal limitation of such comparative approach
is that trace donors unknown to the investigators with their DNA profiles cannot be identified.
The recent advancements in Forensic DNA Phenotyping can provide investigative leads to
help find previously unknown individuals by inferring externally visible characteristics and
biogeographic ancestry prediction without comparative DNA testing. Some predictive DNA
tests for appearance and ancestry were previously developed by our group, but their forensic
validation, as prerequisite for casework application, was mostly missing thus far. For other
appearance traits the genetic knowledge was previously not advanced enough to develop
predictive DNA tests. Moreover, the genotyping technology capable of tolerating quality
and quantity issues of trace DNA and at the same time allowing the parallel analysis of large
number of DNA markers was previously not available, which limited previously developed
forensic ancestry DNA tests.
The major aims of this thesis therefore are to:
- forensically validate DNA test systems for predicting appearance and ancestry that were
recently developed by our group i.e., IrisPlex for eye color prediction, HIrisPlex for hair and
eye color prediction, and a set of mtDNA multiplexes for maternal ancestry prediction;
- develop and forensically validate a new DNA test system for skin color prediction in
combination with eye and hair color prediction from trace DNA;
- develop and forensically validate a new DNA test system for complete mitogenome
analysis providing maximum-resolution maternal lineage and maternal ancestry inference
from trace DNA.
Subjects/Keywords: Phenotyping; HIrisPlex; Next Generation Sequencing; Mitochondrial DNA
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APA (6th Edition):
(Lakshmi), L. C. (2016). Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis. (Thesis). Erasmus University Rotterdam. Retrieved from http://hdl.handle.net/1765/94499
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
(Lakshmi), L.C. Chaitanya. “Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis.” 2016. Thesis, Erasmus University Rotterdam. Accessed March 07, 2021.
http://hdl.handle.net/1765/94499.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
(Lakshmi), L.C. Chaitanya. “Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis.” 2016. Web. 07 Mar 2021.
Vancouver:
(Lakshmi) LC. Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis. [Internet] [Thesis]. Erasmus University Rotterdam; 2016. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1765/94499.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
(Lakshmi) LC. Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis. [Thesis]. Erasmus University Rotterdam; 2016. Available from: http://hdl.handle.net/1765/94499
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
24.
Davey, Susan Rosemary.
A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies.
Degree: Thesis (D.B.M.S.), 2018, University of the West of England, Bristol
URL: https://uwe-repository.worktribe.com/output/864032
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794
► Patients who require platelet transfusion support but have become sensitised to Human Leucocyte Antigens (HLA) or Human Platelet Antigens (HPA) require suitably matched or selected…
(more)
▼ Patients who require platelet transfusion support but have become sensitised to Human Leucocyte Antigens (HLA) or Human Platelet Antigens (HPA) require suitably matched or selected products to avoid adverse transfusion reactions resulting from antibodies reacting with the transfused product. Provision of compatible products for these patients is often challenging, and requires significant resources from the blood service. This study set out to develop and implement next generation sequencing (NGS) technology to enhance the HLA and HPA definition of both platelet donors and recipients. An NGS based method was designed and developed for high throughput, allele level HLA class I genotyping and used to evaluate the impact of NGS technology on the selection of platelet donors using HLA epitope matching (HEM). In addition, an alternative NGS approach was designed to simultaneously sequence the six genes that code for glycoproteins expressing HPA in order to define all known HPA systems in both donor and patient samples. Allele level HLA-A, -B and –C genotypes were generated for 519 platelet donors by NGS. A critical evaluation of algorithms used to predict alleles from low to medium resolution HLA types demonstrated that NGS was more accurate when determining HLA epitopes for the selection of platelets by HEM. The HLA genotyping data obtained was used to establish previously undefined HLA allele and haplotype frequencies at third field resolution in the English platelet donor population. This thesis also includes the first reported NGS based method for the simultaneous genotyping of HPA-1 to HPA-29, with the additional capability of novel HPA detection. NGS has been shown to significantly improve the definition of both HLA and HPA genetic systems and will provide a number of future benefits for laboratories and the patients they support, including provision of well matched transfusion products, the detection of rare or novel polymorphisms and increased knowledge of HLA and HPA frequencies.
Subjects/Keywords: 615.3; Next Generation Sequencing; HPA; Genotyping; HLA
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APA (6th Edition):
Davey, S. R. (2018). A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies. (Doctoral Dissertation). University of the West of England, Bristol. Retrieved from https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794
Chicago Manual of Style (16th Edition):
Davey, Susan Rosemary. “A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies.” 2018. Doctoral Dissertation, University of the West of England, Bristol. Accessed March 07, 2021.
https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794.
MLA Handbook (7th Edition):
Davey, Susan Rosemary. “A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies.” 2018. Web. 07 Mar 2021.
Vancouver:
Davey SR. A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies. [Internet] [Doctoral dissertation]. University of the West of England, Bristol; 2018. [cited 2021 Mar 07].
Available from: https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794.
Council of Science Editors:
Davey SR. A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies. [Doctoral Dissertation]. University of the West of England, Bristol; 2018. Available from: https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794
25.
Al Turki, Saeed.
Integrated approaches to elucidate the genetic architecture of congenital heart defects.
Degree: PhD, 2014, University of Cambridge
URL: https://doi.org/10.17863/CAM.16352
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265
► Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development.…
(more)
▼ Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development. Without surgical and medical interventions, most of the severe CHD cases would not survive after the first year of life. The improved health care for CHD patients has increased CHD prevalence significantly, and it has been estimated that the population of adults with CHD is growing ~5% per year. Understanding the causes of CHD would greatly help improve our knowledge of the pathophysiology, family counseling and planning and possibly prevention and treatment in the future. The aim of my thesis was to identify novel or known CHD genes enriched for rare coding genetic variants in isolated CHD cases and learn about the relative performance of different study designs. High-throughput next generation sequencing (NGS) was used to sequence all coding genes (whole exome) coupled with various analytical pipelines and tools to identify candidate genes in different family-based study designs. Since there is no general consensus on the underlying genetic model of isolated CHD, I developed a suite of software tools to enable different family-based exome analyses of de novo and inherited variants (chapter 2) and then piloted these tools in several gene discovery projects where the mode of inheritance was already known to identify previously described and novel pathogenic genes, before applying them to an analysis of families with two or more siblings with CHD. Based on the tools developed in chapter 2, I designed a two-stage study to investigate isolated parent-offspring trios with Tetralogy of Fallot (chapter 3). In the first stage, I used whole exome sequence data from 30 trios to identify genes with de novo coding variants. This analysis identified six de novo loss-of-function and 13 de novo missense variants. Only one gene showed recurrent de novo mutations in NOTCH1, a well known CHD gene that has mostly been associated with left ventricle outflow tract malformations (LVOT). Besides NOTCH1, the de novo analysis identified several possibly pathogenic novel genes such as ZMYM2 and ARHGAP35, that harbor de novo loss-of-function variants (frameshift and stop gain, respectively). In the second stage of the study, I designed custom baits to capture 122 candidate genes for additional sequencing using NGS in a larger sample size of 250 parent-offspring trios with isolated Tetralogy of Fallot and identified six de novo variants in four genes, half of them are loss-of-function variants. Both of NOTCH1 and its ligand JAG1 harbor two additional de novo mutations (two stop gains in NOTCH1 and one missense and a splice donor in JAG1). The analysis showed a strongly significant over-representation of de novo loss-of-function variants in NOTCH1 (P=3.8 ×10-9). To assess alternative family-based study design in CHD, I combined the analysis from 13 isolated parent-offspring trios with 112 unrelated index cases of isolated atrioventricular septal defects (AVSD) in chapter 4.…
Subjects/Keywords: 616.1; Congenital heart defects; Next generation sequencing
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Al Turki, S. (2014). Integrated approaches to elucidate the genetic architecture of congenital heart defects. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265
Chicago Manual of Style (16th Edition):
Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Doctoral Dissertation, University of Cambridge. Accessed March 07, 2021.
https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265.
MLA Handbook (7th Edition):
Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Web. 07 Mar 2021.
Vancouver:
Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Internet] [Doctoral dissertation]. University of Cambridge; 2014. [cited 2021 Mar 07].
Available from: https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265.
Council of Science Editors:
Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Doctoral Dissertation]. University of Cambridge; 2014. Available from: https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265
Boston College
26.
Indap, Amit R.
Discovering rare variants from populations to
families.
Degree: PhD, Biology, 2013, Boston College
URL: http://dlib.bc.edu/islandora/object/bc-ir:101399
► Partitioning an individual's phenotype into genetic and environmental components has been a major goal of genetics since the early 20th century. Formally, the proportion of…
(more)
▼ Partitioning an individual's phenotype into genetic
and environmental components has been a major goal of genetics
since the early 20th century. Formally, the proportion of
phenotypic variance attributable to genetic variation in the
population is known as heritability. Genome wide association
studies have explained a modest percentage of variability of
complex traits by genotyping common variants. Currently, there is
great interest in what role rare variants play in explaining the
missing heritability of complex traits. Advances of
next generation
sequencing and genomic enrichment technologies over the past
several years have made it feasible to re-sequence large numbers of
individuals, enabling the discovery of the full spectrum of genetic
variation segregating in the human population, including rare
variants. The four projects that comprise my dissertation all
revolve around the discovery of rare variants from
next generation
sequencing datasets. In my first project, I analyzed data from the
exon sequencing pilot of the 1000 Genomes Project, where I
discovered variants from exome capture sequencing experiments in a
worldwide sample of nearly 700 individuals. My results show that
the allele frequency spectrum of the dataset has an excess of rare
variants. My
next project demonstrated the applicability of using
whole-genome amplified DNA (WGA) in capture sequencing. WGA is a
method that amplifies DNA from nanogram starting amounts of
template. In two separate capture experiments I compared the
concordance of call sets, both at the site and genotype level, of
variant calls derived from WGA and genomic DNA. WGA derived calls
have excellent concordance metrics, both at the site and genotypic
level, suggesting that WGA DNA can be used in lieu of genomic DNA.
The results of this study have ramifications for medical sequencing
experiments, where DNA stocks are a finite quantity and
re-collecting samples maybe too expensive or not possible. My third
project kept its focus on capture sequencing, but in a different
context. Here, I analyzed sequencing data from Mendelian exome
study of non-sensorineural hearing loss (NSHL). A subset of 6
individuals (5 affected, 1 unaffected) from a family of European
descent were whole exome sequenced in an attempt to uncover the
causative mutation responsible for the loss of hearing phenotype in
the family. Previous linkage analysis uncovered a linkage region on
chr12, but no mutations in previous candidate genes were found,
suggesting a novel mutation segregates in the family. Using a
discrete filtering approach with a minor allele frequency cutoff, I
uncovered a putative causative non-synonymous mutation in a gene
that encodes a transmembrane protein. The variant perfectly
segregates with the phenotype in the family and is enriched in
frequency in an unrelated cohort of individuals. Finally, for my
last project I implemented a variant calling method for family
sequencing datasets, named Pgmsnp, which incorporates Mendelian
relationships of family members using a Bayesian network…
Advisors/Committee Members: Gabor T. Marth (Thesis advisor).
Subjects/Keywords: bioinformatics; human genetics; next generation sequencing
Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Indap, A. R. (2013). Discovering rare variants from populations to
families. (Doctoral Dissertation). Boston College. Retrieved from http://dlib.bc.edu/islandora/object/bc-ir:101399
Chicago Manual of Style (16th Edition):
Indap, Amit R. “Discovering rare variants from populations to
families.” 2013. Doctoral Dissertation, Boston College. Accessed March 07, 2021.
http://dlib.bc.edu/islandora/object/bc-ir:101399.
MLA Handbook (7th Edition):
Indap, Amit R. “Discovering rare variants from populations to
families.” 2013. Web. 07 Mar 2021.
Vancouver:
Indap AR. Discovering rare variants from populations to
families. [Internet] [Doctoral dissertation]. Boston College; 2013. [cited 2021 Mar 07].
Available from: http://dlib.bc.edu/islandora/object/bc-ir:101399.
Council of Science Editors:
Indap AR. Discovering rare variants from populations to
families. [Doctoral Dissertation]. Boston College; 2013. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101399
27.
Al Turki, Saeed.
Integrated approaches to elucidate the genetic architecture of congenital heart defects.
Degree: PhD, 2014, University of Cambridge
URL: https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt
;
https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf
;
https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt
;
https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg
► Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development.…
(more)
▼ Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development. Without surgical and medical interventions, most of the severe CHD cases would not survive after the first year of life. The improved health care for CHD patients has increased CHD prevalence significantly, and it has been estimated that the population of adults with CHD is growing ~5% per year. Understanding the causes of CHD would greatly help improve our knowledge of the pathophysiology, family counseling and planning and possibly prevention and treatment in the future.
Several lines of evidence from humans and animal models have supported a substantial genetic component for CHD. However, gene discovery in CHD has been difficult due to the extreme locus heterogeneity and the lack of a distinct genotype–phenotype correlation. Currently, genetic causes are identified in fewer than 20-‐30% of the cases, most of which are syndromic while the isolated CHD cases remain largely without explanation.
The aim of my thesis was to identify novel or known CHD genes enriched for rare coding genetic variants in isolated CHD cases and learn about the relative performance of different study designs. High-throughput next generation sequencing (NGS) was used to sequence all coding genes (whole exome) coupled with various analytical pipelines and tools to identify candidate genes in different family-based study designs.
Since there is no general consensus on the underlying genetic model of isolated CHD, I developed a suite of software tools to enable different family-based exome analyses of de novo and inherited variants (chapter 2) and then piloted these tools in several gene discovery projects where the mode of inheritance was already known to identify previously described and novel pathogenic genes, before applying them to an analysis of families with two or more siblings with CHD.
Based on the tools developed in chapter 2, I designed a two-stage study to investigate isolated parent-offspring trios with Tetralogy of Fallot (chapter 3). In the first stage, I used whole exome sequence data from 30 trios to identify genes with de novo coding variants. This analysis identified six de novo loss-of-function and 13 de novo missense variants. Only one gene showed recurrent de novo mutations in NOTCH1, a well known CHD gene that has mostly been associated with left ventricle outflow tract malformations (LVOT). Besides NOTCH1, the de novo analysis identified several possibly pathogenic novel genes such as ZMYM2 and ARHGAP35, that harbor de novo loss-of-function variants (frameshift and stop gain, respectively).
In the second stage of the study, I designed custom baits to capture 122 candidate genes for additional sequencing using NGS in a larger sample size of 250 parent-offspring trios with isolated Tetralogy of Fallot and identified six de novo variants in four genes, half of them are loss-of-function variants. Both of NOTCH1 and its ligand JAG1 harbor two…
Subjects/Keywords: Congenital heart defects; Next generation sequencing
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Al Turki, S. (2014). Integrated approaches to elucidate the genetic architecture of congenital heart defects. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg
Chicago Manual of Style (16th Edition):
Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Doctoral Dissertation, University of Cambridge. Accessed March 07, 2021.
https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg.
MLA Handbook (7th Edition):
Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Web. 07 Mar 2021.
Vancouver:
Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Internet] [Doctoral dissertation]. University of Cambridge; 2014. [cited 2021 Mar 07].
Available from: https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg.
Council of Science Editors:
Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Doctoral Dissertation]. University of Cambridge; 2014. Available from: https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg
University of Manitoba
28.
Xu, Minqi.
Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer.
Degree: Pathology, 2017, University of Manitoba
URL: http://hdl.handle.net/1993/32390
► Introduction: Modern care of patients with lung cancer requires rapid and accurate diagnosis leading to personalized therapies for individual patients based on molecular characteristics of…
(more)
▼ Introduction: Modern care of patients with lung cancer requires rapid and accurate diagnosis leading to personalized therapies for individual patients based on molecular characteristics of their tumour. Detecting mutations that predict response to drug quickly and accurately is an essential part of this process.
Next generation sequencing (NGS) technologies provide an alternative approach for detecting mutated oncogenes in cancer. We hypothesize that NGS is equal if not superior to standard methods for identifying targetable mutations in the EGFR and ALK genes in lung cancer.
Methods: DNA and RNA from 38 formalin fixed paraffin embedded lung cancer samples (37 non-small cell lung cancer (NSCLC) and one small cell lung cancer (SCLC)) archived in Diagnostic Services Manitoba were collected and analyzed using gene enrichment methods from Archer Diagnostics followed by sequencing on the Illumina MiSeq NGS machine. Targeted DNA sequencing to detect the EGFR mutation was performed on 19 samples while targeted RNA sequencing was applied to 20 samples to identify the ALK gene rearrangement. The NGS results were compared with and confirmed by current clinical standard molecular tests for EGFR (real-time PCR) and ALK (immunohistochemistry and FISH).
Results: Three cases were positive for the EGFR mutation and two other samples harbored the EML4-ALK fusion genes as determined by NGS. The concordance between NGS and real-time PCR for EGFR mutation detection was 88.9%. Additionally, the NGS methodology also provided profiles of other genes commonly mutated in NSCLC including KRAS and TP53. The consistency for ALK fusion testing was 100% between NGS and FISH.
Conclusion: This study provides support that NGS is a promising diagnostic tool for mutation detection in NSCLC and holds strong potential for an alternative approach to identifying clinically relevant targets such as EGFR and ALK. Furthermore, NGS provides more information on cancer driven gene mutations than other traditional methods.
Advisors/Committee Members: Qing, Gefei (Pathology) (supervisor), Myal, Yvonne (Pathology).
Subjects/Keywords: next generation sequencing; lung cancer; ALK; EGFR
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Xu, M. (2017). Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer. (Masters Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/32390
Chicago Manual of Style (16th Edition):
Xu, Minqi. “Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer.” 2017. Masters Thesis, University of Manitoba. Accessed March 07, 2021.
http://hdl.handle.net/1993/32390.
MLA Handbook (7th Edition):
Xu, Minqi. “Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer.” 2017. Web. 07 Mar 2021.
Vancouver:
Xu M. Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer. [Internet] [Masters thesis]. University of Manitoba; 2017. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1993/32390.
Council of Science Editors:
Xu M. Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer. [Masters Thesis]. University of Manitoba; 2017. Available from: http://hdl.handle.net/1993/32390
University of Connecticut
29.
Farmer, Justin P.
Efficiency and Safety of a Continuous Rotation Instrumentation System and a Reciprocating Motion Instrumentation System: A Randomized Clinical Trial.
Degree: Master of Dental Science, Dental Science, 2015, University of Connecticut
URL: https://opencommons.uconn.edu/gs_theses/790
► Introduction: It has been suggested that single-file reciprocating systems, such as WaveOne, are capable of more rapid root canal instrumentation compared to systems that…
(more)
▼ Introduction: It has been suggested that single-file reciprocating systems, such as WaveOne, are capable of more rapid root canal instrumentation compared to systems that utilize multi-file continuous rotation. The purpose of this study was to evaluate the efficiency and safety of WaveOne and ProTaper
Next instrumentation systems
in vivo in a randomized clinical trial. The null hypothesis was that no differences would be seen in canal preparation time, working length control, or occurrence of adverse events. Materials and Methods: A total of 89 teeth requiring primary non-surgical endodontic treatment were included in the study. Root canal therapy was performed per routine clinical procedures. Following glide path creation, teeth were randomized into groups according to instrumentation system to be used: WaveOne or ProTaper
Next. Time required for cleaning and shaping was recorded. Discrepancies between the final working length and the initial master cone length and any occurrence of adverse events were also recorded. Differences between groups and tooth types were evaluated with regression models and least squares mean analyses. Results: No overall difference was found between instrumentation systems for average time required per tooth or per canal to complete instrumentation. WaveOne required significantly less time to instrument premolar teeth and teeth with a single canal compared to ProTaper
Next. No significant differences could be detected between WaveOne and ProTaper
Next in regard to working length control. No adverse events occurred in the sample in either treatment group. Conclusions: WaveOne and ProTaper
Next perform with similar efficiency for most tooth types. WaveOne and ProTaper
Next can be used safely and predictably to instrument root canals in a clinical setting.
Advisors/Committee Members: Robert Aseltine, PhD, Kamran Safavi, DMD, MEd, Blythe Kaufman, DMD, MDS.
Subjects/Keywords: WaveOne; ProTaper Next; Reciprocating Motion; Instrumentation Time
Record Details
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Farmer, J. P. (2015). Efficiency and Safety of a Continuous Rotation Instrumentation System and a Reciprocating Motion Instrumentation System: A Randomized Clinical Trial. (Masters Thesis). University of Connecticut. Retrieved from https://opencommons.uconn.edu/gs_theses/790
Chicago Manual of Style (16th Edition):
Farmer, Justin P. “Efficiency and Safety of a Continuous Rotation Instrumentation System and a Reciprocating Motion Instrumentation System: A Randomized Clinical Trial.” 2015. Masters Thesis, University of Connecticut. Accessed March 07, 2021.
https://opencommons.uconn.edu/gs_theses/790.
MLA Handbook (7th Edition):
Farmer, Justin P. “Efficiency and Safety of a Continuous Rotation Instrumentation System and a Reciprocating Motion Instrumentation System: A Randomized Clinical Trial.” 2015. Web. 07 Mar 2021.
Vancouver:
Farmer JP. Efficiency and Safety of a Continuous Rotation Instrumentation System and a Reciprocating Motion Instrumentation System: A Randomized Clinical Trial. [Internet] [Masters thesis]. University of Connecticut; 2015. [cited 2021 Mar 07].
Available from: https://opencommons.uconn.edu/gs_theses/790.
Council of Science Editors:
Farmer JP. Efficiency and Safety of a Continuous Rotation Instrumentation System and a Reciprocating Motion Instrumentation System: A Randomized Clinical Trial. [Masters Thesis]. University of Connecticut; 2015. Available from: https://opencommons.uconn.edu/gs_theses/790
George Mason University
30.
Sharma, Anima.
A Study of RNA Editing in Human Peripheral Blood Mononuclears and Endotheliocytes by NextGen Sequencing
.
Degree: 2013, George Mason University
URL: http://hdl.handle.net/1920/8492
► RNA editing is a process of post-transcriptional modification of the nucleotide sequence in a transcript that leads to a change in the information content of…
(more)
▼ RNA editing is a process of post-transcriptional modification of the nucleotide sequence in a transcript that leads to a change in the information content of the RNA. The alteration of nucleotides in the mRNA can have several consequences at the molecular level, including modified protein products as well as creation or deletion of splice sites. Two types of RNA editing have been known to take place in mRNA: Adenosine (A) to Inosine (I) and Cytidine (C) to Uridine (U), both of which involve deamination of the nucleotide with the help of deaminase enzymes. The “A to I” RNA editing is facilitated by deaminating enzymes known as ADARs (Adenosine Deaminase that Act on RNA). ADARs specifically recognize double stranded RNA structure or RNA duplex structure as their substrate. Though previous studies have shown some evidence of low level sporadic occurrence of RNA editing in other human tissues, brain remains to be the only tissue where RNA editing has been studied systematically. In this study, we investigated “A to I” RNA editing in human PBMCs (peripheral blood mononuclear cells). We were also interested in looking at RNA editing in the umbilical endotheliocytes that are capable of producing interferons. Specifically, the cDNA derived from PBMCs and endothelial cells, was sequenced by NextGen sequencing. The PBMCs’ genomic DNA was sequenced by Sanger sequencing and the sequences were analyzed. Since inosine is recognized as guanosine (G) by most enzymes, A-to-I substitution leads to A-to-G transition in the edited substrate and therefore, any kind of “A to I” RNA editing event will be detected as A to G changes in the transcripts. The multiple sequence alignment tool SeqmanPro was used to assemble all the transcripts together, which revealed that the A to G change frequency was significantly high over 14% in TLR2 at a specific site, in most of the samples of PBMCs and endotheliocytes. At the same consensus position 26, the PMBCs genomic DNA possessed an Adenosine, which was confirmed by the distinct peak in the chromatogram obtained from Sequencher software. The presence of these A to G mismatches within the transcripts, therefore, suggests that “A to I” RNA editing takes place in PBMCs and in endothelial cells.
Advisors/Committee Members: Baranova, Ancha (advisor).
Subjects/Keywords: RNA editing;
next gene sequencing;
TLR2;
ADAR
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APA ·
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MLA ·
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Export
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APA (6th Edition):
Sharma, A. (2013). A Study of RNA Editing in Human Peripheral Blood Mononuclears and Endotheliocytes by NextGen Sequencing
. (Thesis). George Mason University. Retrieved from http://hdl.handle.net/1920/8492
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Sharma, Anima. “A Study of RNA Editing in Human Peripheral Blood Mononuclears and Endotheliocytes by NextGen Sequencing
.” 2013. Thesis, George Mason University. Accessed March 07, 2021.
http://hdl.handle.net/1920/8492.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Sharma, Anima. “A Study of RNA Editing in Human Peripheral Blood Mononuclears and Endotheliocytes by NextGen Sequencing
.” 2013. Web. 07 Mar 2021.
Vancouver:
Sharma A. A Study of RNA Editing in Human Peripheral Blood Mononuclears and Endotheliocytes by NextGen Sequencing
. [Internet] [Thesis]. George Mason University; 2013. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1920/8492.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Sharma A. A Study of RNA Editing in Human Peripheral Blood Mononuclears and Endotheliocytes by NextGen Sequencing
. [Thesis]. George Mason University; 2013. Available from: http://hdl.handle.net/1920/8492
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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Open Access Theses and Dissertations
