subject:(Transcriptome analysis)

University of Illinois – Urbana-Champaign

1. Nixon, Scott Evan. Study of phenotypic and gene expression response to bacterial challenge.

Degree: PhD, Informatics, 2015, University of Illinois – Urbana-Champaign

► In the mouse model of Bacillus Calmette-Guérin (BCG)-induced inflammation, focus is placed upon phenotypic and gene-expression responses to the original challenge. Studies of the phenotypic… (more)

Subjects/Keywords: Behavior; Transcriptome; Functional Analysis

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APA (6^th Edition):

Nixon, S. E. (2015). Study of phenotypic and gene expression response to bacterial challenge. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/78763

Chicago Manual of Style (16^th Edition):

Nixon, Scott Evan. “Study of phenotypic and gene expression response to bacterial challenge.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/78763.

MLA Handbook (7^th Edition):

Nixon, Scott Evan. “Study of phenotypic and gene expression response to bacterial challenge.” 2015. Web. 03 Mar 2021.

Vancouver:

Nixon SE. Study of phenotypic and gene expression response to bacterial challenge. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/78763.

Council of Science Editors:

Nixon SE. Study of phenotypic and gene expression response to bacterial challenge. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/78763

2. Read, Robert W. The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation.

Degree: 2013, University of Nevada – Reno

URL: http://hdl.handle.net/11714/3063

► Diatoms are ubiquitous microorganisms important in the global carbon cycle, because of their significant primary productivity. These phytoplankton require the nutrient silica to form their… (more)

▼ Diatoms are ubiquitous microorganisms important in the global carbon cycle, because of their significant primary productivity. These phytoplankton require the nutrient silica to form their outer cell wall, however, surface concentrations of Si(OH)4, can be a limiting resource in oceanic regions, such as the Southern Ocean. Therefore, it is essential to identify how these microorganisms react to reduced silica concentrations. Here I report transcriptome sequencing results for the ubiquitous diatom Chaetoceros socialis in response to silica limitation. Using short paired-end sequencing, 92015 transcripts were assembled that were homologous to 6129 genes in the fully sequenced diatom Thalassiosira pseudonana. Silica concentrations in this experiment did not alter growth rate until day 5 and samples for differential gene expression were taken on day 2 when the growth rates of the two cultures were similar, and on day 5 when the growth rates of the cultures were different. Of the 92015 transcripts, there were 2238 transcripts corresponding to 344 homologous T. pseudonana genes (p-value 0.01) that showed a log2 fold change of greater than two in the silica stressed cultures compared to the silica replete cultures. Furthermore, there were 1758 transcripts corresponding to 100 homologous T. pseudonana genes that showed a log2 fold change of greater than two in the silica replete cultures compared to the stressed cultures, indicating an early response to silica stress. Differential expression analysis indicated genes associated with the pathways of glycolysis, the TCA cycle, and oxidative phosphorylation were all up-regulated in the reduced silica cultures compared to silica replete cultures. In the stressed cultures, transcripts in fatty acid biosynthesis were up-regulated, while transcripts in B-oxidation were down-regulated, suggesting that lipid content in the diatom may increase under silica limited conditions. Silica transporter transcripts also showed significant log2 changes, consistent with previous work. These data suggest that silica stress causes the cell to increase the concentration of high energy lipids, increase the concentration of ATP in order to carry out unfavorable reactions, such as fatty acid biosynthesis, and repurpose carbohydrate carbon skeletons into higher energy lipids. The up-regulation of silica transporter transcripts in the silica stressed cells showed there are fundamental differences in the diatom cell, as the organism transitions from internal silica regulation to extracellular silica regulation, even though growth rate does not change. These results demonstrate that C. socialis has developed an early, robust cellular response to silica limitation, which affects several different biochemical pathways within the cells, and may have implications for tuning diatoms to being better producers of biofuels Advisors/Committee Members: Grzymski, Joseph J. (advisor), Shintani, David K. (committee member), AuCoin, David P. (committee member).

Subjects/Keywords: Diatoms; Differential Expression; Nutrient Analysis; Sequencing; Transcriptome

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APA (6^th Edition):

Read, R. W. (2013). The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation. (Thesis). University of Nevada – Reno. Retrieved from http://hdl.handle.net/11714/3063

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Read, Robert W. “The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation.” 2013. Thesis, University of Nevada – Reno. Accessed March 03, 2021. http://hdl.handle.net/11714/3063.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Read, Robert W. “The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation.” 2013. Web. 03 Mar 2021.

Vancouver:

Read RW. The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation. [Internet] [Thesis]. University of Nevada – Reno; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/11714/3063.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Read RW. The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation. [Thesis]. University of Nevada – Reno; 2013. Available from: http://hdl.handle.net/11714/3063

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Pretoria

3. [No author]. Gene expression profiling of polyamine-depleted Plasmodium falciparum .

Degree: 2008, University of Pretoria

URL: http://upetd.up.ac.za/thesis/available/etd-12132007-103643/

► Polyamines play an important role in DNA, RNA and protein synthesis as well as a variety of other biological processes (cell division, differentiation and death)… (more)

▼ Polyamines play an important role in DNA, RNA and protein synthesis as well as a variety of other biological processes (cell division, differentiation and death) as outlined in Chapter 1. Assaraf and co-workers (1984) demonstrated that treatment with DFMO resulted in the inhibition of polyamine biosynthesis as well as schizogony arrest in P. falciparum. However, they did not elaborate on any other consequences that polyamine depletion could exert on the parasite. This dissertation aims to elucidate the significance of the inhibition of polyamine biosynthesis within P. falciparum by using differential transcriptome profiling. Suppression subtractive hybridisation generated transcripts which were potentially up-and down-regulated due to endogenous polyamine depletion within the human malaria parasite P. falciparum. The resulting transcripts were subjected to a restriction enzyme analysis and those with unique digestion profiles were selected and sequenced. The sequences were analysed using PlasmoDB to identify the genomic sequences to which they were best matched. To confirm that the selected transcripts were indeed differentially expressed a reverse virtual Northern dot blot was performed. Transcripts for proteins involved in protein processing, methionine and polyamine metabolism, various transporters, proteins involved in cellular differentiation and signal transduction were found to be upregulated in the absences of polyamines. This could be suggestive of a metabolic response induced by the parasite in order to overcome this deficiency. Polyamines seem to influence protein synthesis and haemoglobin degradation as well since depletion of endogenous polyamines within the parasite seems to result in increased food vacuole acidification, haemoglobin degradation, transport of proteins to the cytoplasm and protein synthesis and stabilisation. The majority of downregulated transcripts were found to be involved in cell-cell adhesion and erythrocyte invasion, protein processing and transport indicating that these processes are dependent on polyamines. Further validation of these findings by microarray as well as proteomic analysis will need to be undertaken. These results validate that polyamines do play an essential role in the cellular biology of the parasite. They also confirm that the inhibition of polyamine biosynthesis is a viable route to undertake in the search for new and improved antimalarial targets. This would be especially useful if it was combined with other antimalarials and their synergistic effects were investigated by transcriptomic, proteomic and bioinformatic analysis Advisors/Committee Members: Prof A I Louw (advisor), Dr L Birkholtz (advisor).

Subjects/Keywords: Suppression subtractive hybridisation; Malaria; Transcriptome analysis; Polyamines; Differential expression; UCTD

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APA (6^th Edition):

author], [. (2008). Gene expression profiling of polyamine-depleted Plasmodium falciparum . (Masters Thesis). University of Pretoria. Retrieved from http://upetd.up.ac.za/thesis/available/etd-12132007-103643/

Chicago Manual of Style (16^th Edition):

author], [No. “Gene expression profiling of polyamine-depleted Plasmodium falciparum .” 2008. Masters Thesis, University of Pretoria. Accessed March 03, 2021. http://upetd.up.ac.za/thesis/available/etd-12132007-103643/.

MLA Handbook (7^th Edition):

author], [No. “Gene expression profiling of polyamine-depleted Plasmodium falciparum .” 2008. Web. 03 Mar 2021.

Vancouver:

author] [. Gene expression profiling of polyamine-depleted Plasmodium falciparum . [Internet] [Masters thesis]. University of Pretoria; 2008. [cited 2021 Mar 03]. Available from: http://upetd.up.ac.za/thesis/available/etd-12132007-103643/.

Council of Science Editors:

author] [. Gene expression profiling of polyamine-depleted Plasmodium falciparum . [Masters Thesis]. University of Pretoria; 2008. Available from: http://upetd.up.ac.za/thesis/available/etd-12132007-103643/

Texas A&M University

4. Kianifariz, Mahnaz. Transcriptome Analysis during Stem Development and in the A1 Cytoplasmic Male Sterility System of Sorghum.

Degree: PhD, Molecular and Environmental Plant Sciences, 2017, Texas A&M University

URL: http://hdl.handle.net/1969.1/161494

► Sorghum (Sorghum bicolor (L) Moench) exhibits efficient use of water, nitrogen and energy resources and is grown throughout the world as a cereal, forage, syrup… (more)

▼ Sorghum (Sorghum bicolor (L) Moench) exhibits efficient use of water, nitrogen and energy resources and is grown throughout the world as a cereal, forage, syrup and more recently energy crop. A high-throughput RNA sequencing method (RNA-seq) was used to examine transcriptional dynamics during stem development of two genotypes of sorghum, i.e., BTx623 and R07020. A comparative transcriptome analysis of immature panicles was also conducted between a set of cytoplasmic male sterile (CMS) A1-lines, iso-cytoplasmic maintainer B-lines, and F1 sorghum hybrids. By comparing stem nodal segments each at unique stages of cell wall deposition, more than 500 differentially expressed genes (DEGs) were identified that were annotated as being involved in processes related to cell wall biosynthesis. Categories of DEGs included genes involved in cellulose, hemicellulose, and lignin biosynthesis, transcription factors, glycosyl transferases and cell wall proteins. In non-elongating mature nodal segments actively laying down secondary cell walls, transcriptome profiles revealed inter-related biosynthetic pathways that were highly enriched in DEGs involved in phenylpropanoid metabolism and flavonoid biosynthesis. In immature nodal segments in the rapidly elongating region of the stem, a series of pathways enriched in DEGs were detected that are critical for the primary growth of stems including starch and sucrose metabolism and DNA replication. A co-expression network analysis identified a number of transcription factors with connectivity to lignin biosynthesis genes, which indicates a possible role for these transcription factors as regulators of lignin biosynthesis in sorghum. A number of DEGs were found by comparing nuclear gene expression of CMS A1-lines with associated B-lines and F1 hybrids. In general, a larger proportion of DEGs were down-regulated in CMS A1-lines when compared to pollen-fertile B-lines and F1 hybrids. GO categories whose genes were down-regulated in CMS A1-lines included metabolic processes, lipid biosynthetic/metabolic process, and oxidation/reduction. Examination of these DEGs (and their homologs) within these categories provided evidence that the down-regulation of these genes may relate to the production of viable pollen in fertile panicles. In pollen-sterile panicles of CMS A1-lines, up-regulated genes included several stress-related genes such as heat shock and linoleic acid biosynthesis genes. Advisors/Committee Members: Klein, Patricia E. (advisor), Klein, Robert R. (advisor), Rooney, William L. (committee member), Zhang, Xiuren (committee member).

Subjects/Keywords: Sorghum; Transcriptome analysis; Cell wall; Cytoplasmic male sterility; Fertility restoration

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APA (6^th Edition):

Kianifariz, M. (2017). Transcriptome Analysis during Stem Development and in the A1 Cytoplasmic Male Sterility System of Sorghum. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/161494

Chicago Manual of Style (16^th Edition):

Kianifariz, Mahnaz. “Transcriptome Analysis during Stem Development and in the A1 Cytoplasmic Male Sterility System of Sorghum.” 2017. Doctoral Dissertation, Texas A&M University. Accessed March 03, 2021. http://hdl.handle.net/1969.1/161494.

MLA Handbook (7^th Edition):

Kianifariz, Mahnaz. “Transcriptome Analysis during Stem Development and in the A1 Cytoplasmic Male Sterility System of Sorghum.” 2017. Web. 03 Mar 2021.

Vancouver:

Kianifariz M. Transcriptome Analysis during Stem Development and in the A1 Cytoplasmic Male Sterility System of Sorghum. [Internet] [Doctoral dissertation]. Texas A&M University; 2017. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/1969.1/161494.

Council of Science Editors:

Kianifariz M. Transcriptome Analysis during Stem Development and in the A1 Cytoplasmic Male Sterility System of Sorghum. [Doctoral Dissertation]. Texas A&M University; 2017. Available from: http://hdl.handle.net/1969.1/161494

University of Guelph

5. Zhan, Shuhua. Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana.

Degree: PhD, Department of Plant Agriculture, 2012, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3274

► Small RNAs (sRNAs), circa 21-26nt RNA molecules, are a novel class of regulatory molecules that influence many aspects of plant biology. The first objective of… (more)

▼ Small RNAs (sRNAs), circa 21-26nt RNA molecules, are a novel class of regulatory molecules that influence many aspects of plant biology. The first objective of this thesis was to utilize computational approaches both to investigate how microRNAs (miRNAs), a type of sRNA, as a class affect their target transcripts’ accumulation and to identify novel miRNAs in Arabidopsis thaliana. The second objective of this thesis was to examine the regulation of protein coding (PC) cis natural antisense transcripts (cis-NATs), which have the potential to make double stranded RNA. Computational analysis of the expression of miRNA-regulated genes demonstrated that the transcriptomes of the inflorescences of plants defective in miRNA biogenesis were similar to normal leaf tissues and dissimilar to normal pollen and seed. Thus, miRNAs cause the plant transcriptome to shift from a vegetative to reproductive state. Known miRNA targets fail to explain miRNA-defective mutant transcriptome patterns. Novel computational approaches were used to discover five new mature miRNAs. Interestingly, two miRNAs have different functions but are encoded by perfect complements of the same precursor molecule. Genome-wide analysis of cis-NAT abundances revealed that protein coding (PC) cis-NATs tend to be co-expressed, broadly expressed, and highly expressed across diverse abiotic stress conditions. These expression patterns were negatively associated with sRNAs because sRNAs were under-represented within PC cis-NATs compared to PC non-cis-NATs. sRNAs also mapped to cis-NATs and non-cis-NATs at similar frequencies in mutants defective in nat-siRNA biogenesis relative to other genotypes. We suggest a common euchromatin environment and possibly antisense RNA stabilization of mRNA transcripts may contribute to the high level, breadth, and co-expression of cis-NATs. However, cis-NATs are correlated less frequently than expected, and cis-NAT transcript abundances often differ more than expected. In addition, sRNAs matched PC cis-NATs relative to PC non-cis-NATs more frequently in abiotic stress conditions than in control conditions. Thus, although sRNAs do not have a widespread role in regulating cis-NATs, sRNAs may have a focused role in regulating cis-NAT transcript abundances. Advisors/Committee Members: Dr. Lukens, Lewis (advisor).

Subjects/Keywords: small RNAs; microRNAs; cis-NATs; transcriptome analysis; Arabidopsis thaliana

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APA (6^th Edition):

Zhan, S. (2012). Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3274

Chicago Manual of Style (16^th Edition):

Zhan, Shuhua. “Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana.” 2012. Doctoral Dissertation, University of Guelph. Accessed March 03, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3274.

MLA Handbook (7^th Edition):

Zhan, Shuhua. “Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana.” 2012. Web. 03 Mar 2021.

Vancouver:

Zhan S. Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana. [Internet] [Doctoral dissertation]. University of Guelph; 2012. [cited 2021 Mar 03]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3274.

Council of Science Editors:

Zhan S. Genome-wide expression analysis and regulation of microRNAs and cis natural antisense transcripts in Arabidopsis thaliana. [Doctoral Dissertation]. University of Guelph; 2012. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3274

University of South Africa

6. Peloakgosi-Shikwambani, Keneilwe. Analysis of Babesia rossi transcriptome in dogs diagnosed with canine babesiosis .

Degree: 2018, University of South Africa

URL: http://hdl.handle.net/10500/24424

► Background: Canine babesiosis is a tick-borne disease causing detrimental health effects on the domestic dogs with huge economic impact on the owners. The most complicated… (more)

▼ Background: Canine babesiosis is a tick-borne disease causing detrimental health effects on the domestic dogs with huge economic impact on the owners. The most complicated form of canine babesiosis is caused by a pathogenic Babesia rossi parasite. Canine babesiosis induced by B. rossi still remains the cause of mortality and morbidity in South African dogs, yet, the transcriptomic and genomic information of this parasite species is still not available. The transcriptomic and genomic information is essential in the disease development and processes for the design of effective disease control strategies. Consequently, our understanding of the mechanisms underlying the pathogenesis of the different genotypes of B. rossi remains limited. A previous study suggested a relationship between the parasite genotype and the disease phenotype. To date, thirteen B. rossi genotypes have been identified and associated with diverse clinical signs in their hosts. Hence the aim of this study was to sequence RNA from samples representing B. rossi genotypes, 19, 29 and 31, in order to have insight on the overall transcriptome of this parasite and to establish if there would be significant differences among the genotypes. Methodology: To screen for B. rossi positive samples, total DNA was extracted from 20 blood samples collected from sick domestic dogs presented at the Onderstepoort Veterinary Academic Hospital (OVAH). Babesia rossi infections were confirmed using the PCR-Reverse Line Blot (RLB) hybridization assay. Further confirmation of infection status was done by amplification of the B. rossi Erythrocyte Membrane Antigen 1 (BrEMA1) gene in all the DNA samples using qualitative PCR (qPCR), followed by sequencing of PCR products. Subsequently, total RNA was extracted from the 20 B. rossi-infected blood samples collected from the same dogs in which DNA was extracted. Three samples representing B. rossi genotypes 19, 29 and 31 were selected for transcriptome analysis. RNA sequencing was performed using the Illumina HiSeq 2000 to allow transcriptome analysis. De novo assembly was performed independently for all three transcriptomes using the Trinity software. The unigenes generated from specific transcriptome assemblies were subjected to global functional annotation using Blast2GO version 2.8.0 software, followed by KEGG database for annotation of biological pathways, and DAVID version 6.7, for COG classification to predict and classify their functions. Results: The sample representing B. rossi genotype 31 was excluded in the transcriptome analysis due to low RNA mass, which usually compromises the quality of the library used in RNA sequencing.Thus, a total of 26 747 238 and 25 709 627 paired-end reads were obtained from B. rossi genotypes 19 and 29, respectively. De novo transcriptome assembly produced a total of 3019 unigenes, with an average length of 419 bp and N50 of 362 bp in B. rossi genotype 19, and 2727 unigenes with an average length of 441 bp and N50 of 362 in B. rossi genotype 29. A total of 1193 unigenes were common… Advisors/Committee Members: Matjila, P.T (advisor), Sibeko, K. P (advisor).

Subjects/Keywords: B. rossi genotypes; De novo analysis; Transcriptome; Canine babesiosis; RNA-sequencing

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APA (6^th Edition):

Peloakgosi-Shikwambani, K. (2018). Analysis of Babesia rossi transcriptome in dogs diagnosed with canine babesiosis . (Masters Thesis). University of South Africa. Retrieved from http://hdl.handle.net/10500/24424

Chicago Manual of Style (16^th Edition):

Peloakgosi-Shikwambani, Keneilwe. “Analysis of Babesia rossi transcriptome in dogs diagnosed with canine babesiosis .” 2018. Masters Thesis, University of South Africa. Accessed March 03, 2021. http://hdl.handle.net/10500/24424.

MLA Handbook (7^th Edition):

Peloakgosi-Shikwambani, Keneilwe. “Analysis of Babesia rossi transcriptome in dogs diagnosed with canine babesiosis .” 2018. Web. 03 Mar 2021.

Vancouver:

Peloakgosi-Shikwambani K. Analysis of Babesia rossi transcriptome in dogs diagnosed with canine babesiosis . [Internet] [Masters thesis]. University of South Africa; 2018. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10500/24424.

Council of Science Editors:

Peloakgosi-Shikwambani K. Analysis of Babesia rossi transcriptome in dogs diagnosed with canine babesiosis . [Masters Thesis]. University of South Africa; 2018. Available from: http://hdl.handle.net/10500/24424

Louisiana State University

7. Francis, Felix. Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae.

Degree: MS, Plant Sciences, 2012, Louisiana State University

URL: etd-06012012-125300 ; https://digitalcommons.lsu.edu/gradschool_theses/1778

► Burkholderia glumae is the primary causal agent of bacterial panicle blight of rice, which is becoming a major threat to global rice production. The genome… (more)

Subjects/Keywords: transcriptome analysis; comparative genomics; bacterial panicle blight; Burkholderia glumae

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APA (6^th Edition):

Francis, F. (2012). Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae. (Masters Thesis). Louisiana State University. Retrieved from etd-06012012-125300 ; https://digitalcommons.lsu.edu/gradschool_theses/1778

Chicago Manual of Style (16^th Edition):

Francis, Felix. “Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae.” 2012. Masters Thesis, Louisiana State University. Accessed March 03, 2021. etd-06012012-125300 ; https://digitalcommons.lsu.edu/gradschool_theses/1778.

MLA Handbook (7^th Edition):

Francis, Felix. “Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae.” 2012. Web. 03 Mar 2021.

Vancouver:

Francis F. Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae. [Internet] [Masters thesis]. Louisiana State University; 2012. [cited 2021 Mar 03]. Available from: etd-06012012-125300 ; https://digitalcommons.lsu.edu/gradschool_theses/1778.

Council of Science Editors:

Francis F. Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae. [Masters Thesis]. Louisiana State University; 2012. Available from: etd-06012012-125300 ; https://digitalcommons.lsu.edu/gradschool_theses/1778

8. 이, 다연. Bidirectional transcriptome analysis of rat bone marrow-derived mesenchymal stem cells and activated microglia in an in vitro coculture system.

Degree: 2020, Ajou University

URL: http://repository.ajou.ac.kr/handle/201003/19283 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000030178

►

Microglia contribute to the pathogenesis of brain diseases by regulating of neuroinflammation. Thus, targeting of neuroinflammation triggered by activated microglia in brain diseases has become… (more)

▼

Microglia contribute to the pathogenesis of brain diseases by regulating of neuroinflammation. Thus, targeting of neuroinflammation triggered by activated microglia in brain diseases has become a promising curative strategy. Bone marrow-derived mesenchymal stem cells (BM-MSCs) have been shown to have therapeutic effects, resulting from the regulation of inflammatory conditions in the brain. In this study, Gene expression pattern in rat BM-MSCs (rBM-MSCs) cocultured with lipopolysaccharide- (LPS-) stimulated primary rat microglia were investigated using microarray analysis and the functional relationships were evaluated through Ingenuity Pathway Analysis (IPA). The effects of rBM-MSC on LPS-stimulated microglia were also assessed using a reverse coculture system and the same transcriptomic analysis. In rBM-MSCs, 67 genes were differentially expressed, which were highly related with migration of cells, compared to control. The gene network was predicted using IPA and LPS-stimulated primary rat microglia increase the migration of rBM-MSCs was validated by experiments. Reversely, expression patterns of the transcriptome in LPS-stimulated primary rat microglia cocultured with rBM-MSCs were changed. Results showed that 64 genes were altered, which were highly related with inflammatory response, compared to absence of rBM-MSCs. In the same procedure with the aforementioned, the prediction of the gene network and experimental validation showed that rBM-MSCs decrease the inflammatory response of LPS-stimulated primary rat microglia. These indicate that LPS-stimulated microglia increase the migration of rBM-MSCs and that rBM-MSCs reduce the inflammatory activity in LPS-stimulated microglia. The results of this study show complex mechanisms underlying the interaction between rBM-MSCs and activated microglia and may be supportive for the advance of stem cell therapy for brain diseases. This study is based on a previously published report

1. Introduction 1 2. Materials and methods 5 2.1. Isolation and maintenance of rat bone marrow-derived mesenchymal stem cells (rBM-MSCs) 5 2.2. Rat microglia primary cultures 7 2.3. Coculture of LPS-stimulated or non-stimulated microglia and rBM-MSCs 9 2.4. Total RNA isolation and microarray analysis 9 2.5. Transcriptomic analysis using Ingenuity Pathway Analysis 10 2.6. Quantitative real-time PCR (qPCR) 14 2.7. Migration assay 17 2.8. Statistical analysis 17 3. Results 18 3.1. Cellular movement-related transcriptomic changes in rBM-MSCs cocultured with LPS-stimulated microglia 18 3.2. Functional prediction of transcriptomic networks in rBM-MSCs cocultured with LPS-stimulated microglia 23 3.3. Increased migratory activity in rBM-MSCs cocultured with LPS-stimulated microglia 28 3.4. Transcriptomic analysis in LPS-stimulated microglia cocultured with rBM-MSCs 30 3.5. Functional prediction of transcriptomic networks and reduced inflammatory response in LPS-stimulated microglia cocultured with rBM-MSCs 34 4. Discussion 41 CONCLUSION 44 REFERENCES 45

Doctor

Advisors/Committee Members: 대학원 의생명과학과, 201624973, 이, 다연.

Subjects/Keywords: bone marrow-derived mesenchymal stem cells; inflammation; microglia; migration; transcriptome analysis

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APA (6^th Edition):

이, �. (2020). Bidirectional transcriptome analysis of rat bone marrow-derived mesenchymal stem cells and activated microglia in an in vitro coculture system. (Thesis). Ajou University. Retrieved from http://repository.ajou.ac.kr/handle/201003/19283 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000030178

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

이, 다연. “Bidirectional transcriptome analysis of rat bone marrow-derived mesenchymal stem cells and activated microglia in an in vitro coculture system.” 2020. Thesis, Ajou University. Accessed March 03, 2021. http://repository.ajou.ac.kr/handle/201003/19283 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000030178.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

이, 다연. “Bidirectional transcriptome analysis of rat bone marrow-derived mesenchymal stem cells and activated microglia in an in vitro coculture system.” 2020. Web. 03 Mar 2021.

Vancouver:

이 �. Bidirectional transcriptome analysis of rat bone marrow-derived mesenchymal stem cells and activated microglia in an in vitro coculture system. [Internet] [Thesis]. Ajou University; 2020. [cited 2021 Mar 03]. Available from: http://repository.ajou.ac.kr/handle/201003/19283 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000030178.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

이 �. Bidirectional transcriptome analysis of rat bone marrow-derived mesenchymal stem cells and activated microglia in an in vitro coculture system. [Thesis]. Ajou University; 2020. Available from: http://repository.ajou.ac.kr/handle/201003/19283 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000030178

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Texas A&M University

9. Aci, Murat. Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans.

Degree: MS, Plant Breeding, 2018, Texas A&M University

URL: http://hdl.handle.net/1969.1/174102

► Soybean is one of the key crops necessary to meet the food requirement of the increasing global population. However, in order to meet this need,… (more)

▼ Soybean is one of the key crops necessary to meet the food requirement of the increasing global population. However, in order to meet this need, the quality and quantity of soybean yield must be greatly enhanced. Soybean yield advancement depends on the presence of favorable genes in the genome pool that have significantly changed during domestication. To make use of those domesticated genes, this study involved seven cultivated, G. max, and four wild-type, G. soja, soybeans. Their genomes were studied from developing pods to decipher the molecular mechanisms underlying crop domestication. Specifically, their transcriptomes were analyzed comparatively to previous related studies, with the intention of contributing further to the literature. For these goals, several bioinformatics applications were utilized, including De novo transcriptome assembly, transcriptome abundance quantification, and discovery of differentially expressed genes (DEGs) and their functional annotations and network visualizations. The results revealed 1,247 DEGs, 916 of which were upregulated in the cultivated soybean in comparison to wild type. Findings were mostly corresponded to literature review results, especially regarding genes affecting two focused, domesticated-related pod-shattering resistance and seed size traits. These traits were shown to be upregulated in cultivated soybeans and down-regulated in wild type. However, the opposite trend was shown in disease-related genes, which were down-regulated or not even present in the cultivated soybean genome. Further, 47 biochemical functions of the identified DEGs at the cellular level were revealed, providing some knowledge about the molecular mechanisms of genes related to the two aforementioned subjected traits. While our findings provide valuable insight about the molecular mechanisms of soybean domestication attributed to annotation of differentially expressed genes and transcripts, these results must be dissected further and/or reprocessed with a higher number of samples in order to advance the field. Advisors/Committee Members: Zhang, Hongbin (advisor), Hague, Steve (committee member), Yuan, Joshua (committee member).

Subjects/Keywords: Molecular Mechanisms; Crop Domestication; Soybean; Transcriptome Analysis; Cultivated Soybean; Wild Soybean; Differentially Expressed Genes; Gene Annotation; Transcriptome Expression

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APA (6^th Edition):

Aci, M. (2018). Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/174102

Chicago Manual of Style (16^th Edition):

Aci, Murat. “Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans.” 2018. Masters Thesis, Texas A&M University. Accessed March 03, 2021. http://hdl.handle.net/1969.1/174102.

MLA Handbook (7^th Edition):

Aci, Murat. “Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans.” 2018. Web. 03 Mar 2021.

Vancouver:

Aci M. Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans. [Internet] [Masters thesis]. Texas A&M University; 2018. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/1969.1/174102.

Council of Science Editors:

Aci M. Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans. [Masters Thesis]. Texas A&M University; 2018. Available from: http://hdl.handle.net/1969.1/174102

Université Paris-Sud – Paris XI

10. Biton, Anne. Analyse en composantes indépendantes du transcriptome de cancers : Independent Component Analysis of Cancer Transcriptome.

Degree: Docteur es, Cancérologie, 2011, Université Paris-Sud – Paris XI

URL: http://www.theses.fr/2011PA11T028

► L'analyse de données d'expression montre qu'il est avantageux d'analyser les processus biologiques en termes de modules plutôt que simplement considérer les gènes un par un.… (more)

▼ L'analyse de données d'expression montre qu'il est avantageux d'analyser les processus biologiques en termes de modules plutôt que simplement considérer les gènes un par un. Dans ce projet nous avons conduit une analyse non supervisée des données d'expression de gènes de plusieurs cohortes de tumeurs urothéliales en appliquant la méthode d'Analyse en Composantes Indépendantes. Plusieurs études ont démontré les meilleures performances de l'ACI par rapport à l'ACP et les méthodes de clustering, pour obtenir une décomposition plus réaliste des données d'expression en patterns d'expression pertinents et associés avec le phénotype d'intérêt.Les tumeurs urothéliales apparaissent et évoluent selon deux voies distinctes dont la probabilité de progression en cancer musculo-invasif diffère radicalement. Excepté la mutation de FGFR3 dans le groupe le moins agressif, les processus moléculaires sous-jacents n'ont pas été complètement identifiés. Le principal objectif de cette thèse était dédié aux interprétations biologiques des différentes composantes indépendantes pour aider à confirmer et étendre la liste des processus biologiques connus pour être impliqués dans le cancer de vessie.Chaque composante indépendante est caractérisée par une liste de projections de gènes et de contributions pondérées d'échantillons tumoraux . En combinant expertise biologique et comparaison des listes de gènes à des voies existantes et en étudiant conjointement l'association des composantes aux annotations cliniques et moléculaires, nous avons pu différencier les CIscausées par des facteurs techniques, tels que le prélèvement chirurgical de celles ayant des interprétations biologiques pertinentes. De plus, parmi les signaux pertinents biologiquement, cette analyse nous a permis de différencier les signaux provenant du stroma, comme la réponse immunitaire médiée par les lymphocytesB&T, de ceux produits par les tumeurs elles-mêmes, comme les signaux reliés à la prolifération ou à la différenciation. La classification des tumeurs selon leurs contributions à certaines CIs a pu être étroitement associée à des annotations anatomo-cliniques, et a mis en évidence de nouveaux sous-types de tumeur spotentiels, qui suggèrent l'existence de voies de progression supplémentaires dans le cancer de vessie. De façon similaire, l'étude des contributions de groupes de tumeurs basés sur des annotations cliniques ou moléculaires a montré différents niveaux de contamination par le stroma entre les tumeurs mutées et nonmutées pour FGFR3. La reproductibilité des composantes a été étudiée en utilisant des graphes de corrélation. La majeure partie des CIs interprétées a été validée sur trois jeux de données indépendants, et plusieurs d'entre elles ont aussi détectées dans un jeu de données de lignées cellulaires.Une deuxième étude sur le rétinoblastome a montré que nous pouvions tirer partie de l'ACI dans des contextes variés. Le rétinoblastome est initié par la perte des deux alléles du gène suppresseur de tumeur RB1. D'autres évènements génomiques non identifiés sont… Advisors/Committee Members: Radvanyi, François (thesis director).

Subjects/Keywords: Analyse en Composantes Indépendantes,; Transcriptome; Cancer de la vessie; Retinoblastome; Bioinformatique; Biostatistiques; Independent Component Analysis,; Transcriptome; Bladder cancer; Retinoblastoma; Bioinformatics; Biostatistics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Biton, A. (2011). Analyse en composantes indépendantes du transcriptome de cancers : Independent Component Analysis of Cancer Transcriptome. (Doctoral Dissertation). Université Paris-Sud – Paris XI. Retrieved from http://www.theses.fr/2011PA11T028

Chicago Manual of Style (16^th Edition):

Biton, Anne. “Analyse en composantes indépendantes du transcriptome de cancers : Independent Component Analysis of Cancer Transcriptome.” 2011. Doctoral Dissertation, Université Paris-Sud – Paris XI. Accessed March 03, 2021. http://www.theses.fr/2011PA11T028.

MLA Handbook (7^th Edition):

Biton, Anne. “Analyse en composantes indépendantes du transcriptome de cancers : Independent Component Analysis of Cancer Transcriptome.” 2011. Web. 03 Mar 2021.

Vancouver:

Biton A. Analyse en composantes indépendantes du transcriptome de cancers : Independent Component Analysis of Cancer Transcriptome. [Internet] [Doctoral dissertation]. Université Paris-Sud – Paris XI; 2011. [cited 2021 Mar 03]. Available from: http://www.theses.fr/2011PA11T028.

Council of Science Editors:

Biton A. Analyse en composantes indépendantes du transcriptome de cancers : Independent Component Analysis of Cancer Transcriptome. [Doctoral Dissertation]. Université Paris-Sud – Paris XI; 2011. Available from: http://www.theses.fr/2011PA11T028

New Jersey Institute of Technology

11. Zhu, Junfei. Comparison of different differential expression analysis tools for rna-seq data.

Degree: MSin Bioinformatics - (M.S.), Computer Science, 2014, New Jersey Institute of Technology

URL: https://digitalcommons.njit.edu/theses/194

► In molecular biology research, RNA-seq is a relatively new method for transcriptome profiling. It utilizes the next generation sequencing technology to provide huge amount… (more)

Subjects/Keywords: Transcriptome profiling; RNA-seq analysis; Differential expression analysis tools; Bioinformatics; Computer Sciences

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APA (6^th Edition):

Zhu, J. (2014). Comparison of different differential expression analysis tools for rna-seq data. (Thesis). New Jersey Institute of Technology. Retrieved from https://digitalcommons.njit.edu/theses/194

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhu, Junfei. “Comparison of different differential expression analysis tools for rna-seq data.” 2014. Thesis, New Jersey Institute of Technology. Accessed March 03, 2021. https://digitalcommons.njit.edu/theses/194.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhu, Junfei. “Comparison of different differential expression analysis tools for rna-seq data.” 2014. Web. 03 Mar 2021.

Vancouver:

Zhu J. Comparison of different differential expression analysis tools for rna-seq data. [Internet] [Thesis]. New Jersey Institute of Technology; 2014. [cited 2021 Mar 03]. Available from: https://digitalcommons.njit.edu/theses/194.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhu J. Comparison of different differential expression analysis tools for rna-seq data. [Thesis]. New Jersey Institute of Technology; 2014. Available from: https://digitalcommons.njit.edu/theses/194

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Pennsylvania

12. Toung, Jonathan M. RNA and DNA Sequence Analysis of the Human Transcriptome.

Degree: 2013, University of Pennsylvania

URL: https://repository.upenn.edu/edissertations/709

► The manifestation of phenotype at the cellular and organismal level is determined in large part by gene expression, or the transcription of DNA into RNA.… (more)

▼ The manifestation of phenotype at the cellular and organismal level is determined in large part by gene expression, or the transcription of DNA into RNA. As such, the study of the transcriptome, or the characterization and quantification of all RNA produced in the cell, is important. Recent advances in sequencing technology have allowed for unprecedented interrogation of the transcriptome at single-nucleotide resolution. In the first part of this thesis, we use RNA-Sequencing (RNA-Seq) to study the human B-cell transcriptome and determine the experimental parameters necessary for sequencing-based studies of gene expression. We discover that deep sequencing is necessary to detect fully and quantify accurately the complexity of human transcriptomes. Furthermore, we find that at high sequencing depths, the vast majority of transcribed elements in human B-cells are detected. In the second part of this thesis, we utilize the sequence information provided by RNA-Seq to analyze systematic differences between DNA and RNA sequence. The transmission of information from DNA to RNA is a critical process and is expected to occur in a one-to-one fashion. By comparing the DNA sequence to RNA sequence of the same individuals, we found all 12 types of RNA-DNA sequence differences (RDDs), the majority of which cannot be explained by known mechanisms such as RNA editing or transcriptional infidelity. We developed computational methods to robustly identify RDDs and control for false positives resulting from genotyping, sequencing, and alignment error. Finally, we explore the genetic basis of RDD levels, or the proportion of reads at a site bearing the sequence difference allele. In particular, we analyzed the levels of RNA editing in unrelated and related individuals and found that a significant portion of individual variation in A-to-G editing levels contains a genetic component. In summary, our results demonstrate that RNA-Seq is a powerful technique for comprehensive and quantitative analysis of gene expression. In addition, the resolution offered by RNA-Seq enables a detailed view of sequence differences between RNA and DNA. Future work will focus on understanding the mechanisms and factors influencing RDDs. Our results suggest that RDD levels may be considered a quantitative and heritable phenotype; as such, a genetic approach may be a sensible method for finding the determinants and mechanism of RDDs.

Subjects/Keywords: Computational biology; Genome analysis; Next-generation sequencing; RNA Editing; RNA-Sequencing; Transcriptome analysis; Bioinformatics; Genetics

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APA (6^th Edition):

Toung, J. M. (2013). RNA and DNA Sequence Analysis of the Human Transcriptome. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/709

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Toung, Jonathan M. “RNA and DNA Sequence Analysis of the Human Transcriptome.” 2013. Thesis, University of Pennsylvania. Accessed March 03, 2021. https://repository.upenn.edu/edissertations/709.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Toung, Jonathan M. “RNA and DNA Sequence Analysis of the Human Transcriptome.” 2013. Web. 03 Mar 2021.

Vancouver:

Toung JM. RNA and DNA Sequence Analysis of the Human Transcriptome. [Internet] [Thesis]. University of Pennsylvania; 2013. [cited 2021 Mar 03]. Available from: https://repository.upenn.edu/edissertations/709.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Toung JM. RNA and DNA Sequence Analysis of the Human Transcriptome. [Thesis]. University of Pennsylvania; 2013. Available from: https://repository.upenn.edu/edissertations/709

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Urbana-Champaign

13. Arro, Jie Alojado. Evolution and domestication of Saccharum using transcriptomic analyses.

Degree: PhD, 0320, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/73074

► Artificial selection during crop domestication has dramatically shaped many wild plant species into high yielding food, fiber, medicinal, and biofuel crops. The trajectory from wild… (more)

▼ Artificial selection during crop domestication has dramatically shaped many wild plant species into high yielding food, fiber, medicinal, and biofuel crops. The trajectory from wild to domesticated is a long and complex process that leaves strong signatures of selection on the genome. Here we use a population genetics approach and transcriptome survey to scan for signatures of selection and domestication in sugarcane (Saccharum), the leading source of global sugar production. The sugarcane genome is highly complex, with ploidy levels ranging from 8n-14n. This complexity has hindered advances in marker assisted breeding and subjects sugarcane to a unique set of evolutionary forces not experienced during the domestication of most diploid crop species. Modern sugarcane is an interspecific hybrid mainly between the cultivated S. officinarum (2n=80) and the wild species S. spontaneum (2n=40-128), with some marginal contribution from S. robustum (2n=60-200) in a few breeding stations. We screened 48 representative accessions of the domesticated S. officinarum and the wild species S. spontaneum and S. robustum to identify genes selected during domestication. 2.8 million single nucleotide polymorphisms (SNPs) were found from 2.2 billion RNA-seq reads generated from leaf and stalk tissue. S. officinarum has twice as much inter-population allelic diversity compared to S. spontaneum and to S. robustum. The stalk transcriptome has more allele diversity than the leaf, reflective of gene expression changes during domestication. The allele diversity in Saccharum is characterized by the prevalence of intermediate-allele frequency typical of a balancing selection and reflective of the high degree of heterozygosity in this species. The population structure of sugarcane does not render to conventional population genetics tests for signals of selection due to the dynamics imposed by fixed heterozygosity. Site frequency spectrum (SFS) pattern describes higher per-site heterozygosity in genes that might be targets of domestication. Around 200 candidate domestication genes were detected in S. officinarum based on the prevalence of balancing selection among ~3000 SNPs. To gain insight into the nature of gene expression divergence in Saccharum, we conducted a comparative transcriptome profiling of leaf and stalk developmental stages in S. officinarum, S. spontaneum and S. robustum. A summary of all the pairwise differential expression tests shows 3,346 genes were differentially expressed between the cultivated and the wild species, most of which were observed in immature stalk and mature leaf tissues. Maturation of stalks and leaves seems to be associated with significant transcript abundance in gene networks related to post-embryonic morphogenesis, lipid localization and perturbation of the phenylpropanoid pathway. This suggests that expression between the cultivated and wild Saccharum are related to differences related to maturation and response to external stimuli, in general, and the biomass accumulation, in particular. In addition,… Advisors/Committee Members: Ming, Ray R. (advisor), Ming, Ray R. (Committee Chair), Downie, Stephen R. (committee member), Brown, Patrick J. (committee member), Sacks, Erik J. (committee member).

Subjects/Keywords: Domestication; Saccharum domestication; Saccharum Transcriptome Analysis; Saccharum Evolution; Saccharum Population Genetics Analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Arro, J. A. (2015). Evolution and domestication of Saccharum using transcriptomic analyses. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/73074

Chicago Manual of Style (16^th Edition):

Arro, Jie Alojado. “Evolution and domestication of Saccharum using transcriptomic analyses.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/73074.

MLA Handbook (7^th Edition):

Arro, Jie Alojado. “Evolution and domestication of Saccharum using transcriptomic analyses.” 2015. Web. 03 Mar 2021.

Vancouver:

Arro JA. Evolution and domestication of Saccharum using transcriptomic analyses. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/73074.

Council of Science Editors:

Arro JA. Evolution and domestication of Saccharum using transcriptomic analyses. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/73074

Penn State University

14. Byrska-bishop, Marta Barbara. Unraveling the mechanism of GATA1s-mediated blood disorders using functional genomics in pluripotent stem cells.

Degree: 2015, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/25936

► GATA1 is a hematopoietic transcription factor important for the development of erythroid, megakaryocytic, and several myeloid lineages. Normally, a human hematopoietic cell expresses both a… (more)

▼ GATA1 is a hematopoietic transcription factor important for the development of erythroid, megakaryocytic, and several myeloid lineages. Normally, a human hematopoietic cell expresses both a full-length form of GATA1 (GATA1fl) and a short form (GATA1s) that lacks the N-terminal transactivation domain (NAD). Germline GATA1 mutations that result in exclusive production of GATA1s (“GATA1s mutations”) have been identified in patients with congenital hypoplastic anemia, Diamond-Blackfan anemia, as well as in individuals with Down syndrome (DS) who suffer from transient myeloproliferative disorder (TMD) and acute megakaryoblastic leukemia. I investigated the function of GATA1s by analyzing genomic data from induced pluripotent stem cells (iPSCs) obtained from somatic tissues of patients with DS-associated TMD and congenital anemia due to a germline GATA1s mutation. Microarray transcriptome profiles of iPSC-derived progenitors revealed that GATA1s upregulated mostly megakaryocytic and myeloid genes, and downregulated predominantly erythroid genes. Single cell expression profiling demonstrated that small changes in expression of many genes contributed to the GATA1s-mediated change in lineage bias from erythroid to myelo-megakaryocytic fate. To provide a mechanistic explanation of the observed phenotype, I integrated genome-wide differential binding profiles of GATA1 isoforms obtained using ChIP-seq with differential transcriptome response to the presence or absence of GATA1fl or GATA1s in murine megakaryocyte-erythroid progenitor cells, G1MEs. I demonstrated that loss of the NAD impairs erythropoiesis and biases cells towards myelo-megakaryopoiesis due to: (i) failure to efficiently bind to a subset of GATA1 erythroid target sites, which prevents the induction of erythroid genes, and (ii) failure to repress a subset of myelo-megakaryocytic genes upon successful binding to DNA. I identified SMAD1 and LMO2 as candidate co-factors that might be involved in NAD-dependent selective chromatin occupancy of GATA1 at erythroid targets and repression of myelo-megakaryocytic genes, respectively. I propose a new model for GATA1 function in hematopoiesis, according to which an imbalance in the relative expression levels of GATA1 isoforms within an individual cell might lead to a bias in cell fate. Specifically, I hypothesize that cells expressing predominantly GATA1fl are more likely to differentiate towards erythroid lineage, while cells expressing predominantly GATA1s are more likely to differentiate towards myeloid and megakaryocytic lineages. Advisors/Committee Members: Ross Cameron Hardison, Dissertation Advisor/Co-Advisor, Ross Cameron Hardison, Committee Chair/Co-Chair, Santhosh Girirajan, Committee Member, Qunhua Li, Committee Member, Marylyn Deriggi Ritchie, Committee Member, Melissa Rolls, Committee Member.

Subjects/Keywords: blood disorders; hematopoiesis; GATA1 transcription factor; transcriptome analysis; induced pluripotent stem cells

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APA (6^th Edition):

Byrska-bishop, M. B. (2015). Unraveling the mechanism of GATA1s-mediated blood disorders using functional genomics in pluripotent stem cells. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/25936

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Byrska-bishop, Marta Barbara. “Unraveling the mechanism of GATA1s-mediated blood disorders using functional genomics in pluripotent stem cells.” 2015. Thesis, Penn State University. Accessed March 03, 2021. https://submit-etda.libraries.psu.edu/catalog/25936.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Byrska-bishop, Marta Barbara. “Unraveling the mechanism of GATA1s-mediated blood disorders using functional genomics in pluripotent stem cells.” 2015. Web. 03 Mar 2021.

Vancouver:

Byrska-bishop MB. Unraveling the mechanism of GATA1s-mediated blood disorders using functional genomics in pluripotent stem cells. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Mar 03]. Available from: https://submit-etda.libraries.psu.edu/catalog/25936.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Byrska-bishop MB. Unraveling the mechanism of GATA1s-mediated blood disorders using functional genomics in pluripotent stem cells. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/25936

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

15. Chow, Anthony. Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer.

Degree: 2012, University of Toronto

URL: http://hdl.handle.net/1807/33381

►

Shortcomings of current methods of prostate cancer detection draw attention to a need for improved biomarkers. The TMPRSS2:ERG gene fusion leads to the overexpression of… (more)

Subjects/Keywords: TMPRSS2:ERG; fusion gene; whole transcriptome analysis; RNA sequencing; prostate cancer; RhoGDIB; 0307

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APA (6^th Edition):

Chow, A. (2012). Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/33381

Chicago Manual of Style (16^th Edition):

Chow, Anthony. “Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer.” 2012. Masters Thesis, University of Toronto. Accessed March 03, 2021. http://hdl.handle.net/1807/33381.

MLA Handbook (7^th Edition):

Chow, Anthony. “Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer.” 2012. Web. 03 Mar 2021.

Vancouver:

Chow A. Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer. [Internet] [Masters thesis]. University of Toronto; 2012. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/1807/33381.

Council of Science Editors:

Chow A. Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer. [Masters Thesis]. University of Toronto; 2012. Available from: http://hdl.handle.net/1807/33381

Northeastern University

16. Torrey, Heather Leah. Characterization of high-persister strains in Mycobacterium tuberculosis.

Degree: PhD, Department of Biology, 2013, Northeastern University

URL: http://hdl.handle.net/2047/d20003140

► Bacterial persister cells are phenotypic variants of the wild-type that are highly tolerant to bactericidal antibiotics. It is thought that persister cells may be responsible… (more)

Subjects/Keywords: high-persister strains; Mycobacterium tuberculosis; whole-genome sequencing; transcriptome analysis; Bacteriology; Biology

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APA (6^th Edition):

Torrey, H. L. (2013). Characterization of high-persister strains in Mycobacterium tuberculosis. (Doctoral Dissertation). Northeastern University. Retrieved from http://hdl.handle.net/2047/d20003140

Chicago Manual of Style (16^th Edition):

Torrey, Heather Leah. “Characterization of high-persister strains in Mycobacterium tuberculosis.” 2013. Doctoral Dissertation, Northeastern University. Accessed March 03, 2021. http://hdl.handle.net/2047/d20003140.

MLA Handbook (7^th Edition):

Torrey, Heather Leah. “Characterization of high-persister strains in Mycobacterium tuberculosis.” 2013. Web. 03 Mar 2021.

Vancouver:

Torrey HL. Characterization of high-persister strains in Mycobacterium tuberculosis. [Internet] [Doctoral dissertation]. Northeastern University; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2047/d20003140.

Council of Science Editors:

Torrey HL. Characterization of high-persister strains in Mycobacterium tuberculosis. [Doctoral Dissertation]. Northeastern University; 2013. Available from: http://hdl.handle.net/2047/d20003140

University of Illinois – Urbana-Champaign

17. Shahzad, Khuram. Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database.

Degree: MS, 4026, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/42472

► To-date bovine liver and adipose tissues have been investigated through several molecular techniques. However, for the most part molecular work in these tissues has been… (more)

▼ To-date bovine liver and adipose tissues have been investigated through several molecular techniques. However, for the most part molecular work in these tissues has been conducted using a reductionist approach discussing the individual genes, proteins or pathways. This approach does not necessarily evaluate the overall biological effect of a particular condition (e.g. treatment, physiological state) on a pathway. In some instances these tissues have been investigated at the transcriptomic and proteomic levels using several bioinformatics techniques such as gene enrichment analysis or over-represented approach (ORA).The ORA analysis is widely-used in scientific community for functional analysis of high-throughput data such as microarray or RNA-sequencing. It is performed to associate gene sets with their relevant biological pathways or functions using statistical methodologies. However, this approach has several limitations including inability to compare time series experiments or multiple treatments within the same experiment. In order to overcome these limitations, the Dynamic Impact Approach (DIA) has been developed by our group. This approach takes the concept of dynamism into consideration using proportion of differentially expressed genes compared to the genes present in array, statistically significant p-values and fold change values. This approach provides a holistic view of dynamic changes along time series experiments by means of impact and flux. The impact and flux take into account the overall biological perturbation and its direction (e.g., either induced or inhibited) to interpret the biological functions. For our time series microarray datasets, we employed both the DIA and enrichment analysis approaches together to infer the biological meanings. The current studies are mainly focused on the systematic evaluation of the tissues during the periparturient period, i.e. the last three weeks through the first three weeks around parturition. The results indicated a significant amount of biological adaptation in the liver and adipose tissue during pregnancy into early lactation. The large amount of data generation and curation needs a way to be systematically stored, retrieved and analyzed using bioinformatics techniques. For this purpose, we have laid the foundation of a ruminant specific microarray database (Ruminant Physiome) for the data mining and representation. The objectives of this research were, 1) to evaluate the metabolic responses in the liver of dairy cows that were overfed or restricted-fed dietary energy prepartum, 2) to evaluate the metabolic changes and physiological adaptations in the bovine adipose tissue occurring during pregnancy into early lactation, and 3) to develop a ruminant specific ‘omics’ website to provide public access to the expression profiling datasets along with their functional results. Advisors/Committee Members: Loor, Juan J. (advisor), Drackley, James K. (committee member), Hurley, Walter L. (committee member).

Subjects/Keywords: Bioinformatics; Systems Biology; Transcriptome profiling; Enrichment analysis; Bovine liver; Bovine adipose tissue; Transition cows

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APA (6^th Edition):

Shahzad, K. (2013). Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/42472

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Shahzad, Khuram. “Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database.” 2013. Thesis, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/42472.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Shahzad, Khuram. “Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database.” 2013. Web. 03 Mar 2021.

Vancouver:

Shahzad K. Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/42472.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Shahzad K. Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database. [Thesis]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/42472

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

RMIT University

18. Vedururu, R. Identification and functional characterisation of Aedes albopictus genes against Chikungunya virus.

Degree: 2019, RMIT University

URL: http://researchbank.rmit.edu.au/view/rmit:162994

► Chikungunya virus (CHIKV) of Alphavirus genus, has caused several outbreaks around the world in the last decade. Once a relatively unknown virus, it now causes… (more)

▼ Chikungunya virus (CHIKV) of Alphavirus genus, has caused several outbreaks around the world in the last decade. Once a relatively unknown virus, it now causes seasonal infections in tropical and some temperate regions. This change in epidemiology is attributed to vector switch from Aedes aegypti to Aedes albopictus, an invasive pest leading to infections in temperate regions. Although recent research has identified mosquito factors influencing infections, our understanding of interaction between CHIKV and its new vector is limited. Using whole transcriptome sequencing of CHIKV infected mosquitoes, we studied differential expression of genes in the midgut and head and thorax, the two critical barrier sites of the mosquito at two time points. We identified several up and down regulated transcripts in the mosquito host genome in response to the viral infection. Two days post-infection, in the midgut tissue of the mosquitoes, 250 differentially expressed transcripts (25 when the next-generation sequencing (NGS) reads were aligned to the published reference genome and 225 when the reads were aligned to a de novo custom transcriptome we generated) were identified. From the head and thorax tissue of the mosquitoes, 8 days post-infection, 159 differentially expressed transcripts (96 when the NGS reads were aligned to the published reference genome and 63 when the reads were aligned to the de novo custom transcriptome) were identified. Twenty-seven of the targets (13 from 2dpi/midgut and 14 from 8dpi/head & thorax) identified to be differentially expressed were validated separately via qRT-PCR. Seven transcripts found to be differentially expressed in midguts of Ae. albopictus two days post-infection were also assessed for changes in expression in midguts of Ae. aegypti two days post-infection. Apart from differential expression in genes, we also identified down regulation of long non-coding RNAs that may also have functional relevance. The comparison between Ae. albopictus and Ae. aegypti also showed that the expression patterns of the same targets are different between the two species of mosquitoes after CHIKV infection. From the targets we validated, two were selected for further functional studies. Niemann-Pick 2 (NPC2) gene homologue was found to be significantly upregulated in the midguts of both Ae. albopictus and Ae. aegypti mosquitoes, two days post-infection with CHIKV. Known cytoplasmic lipid transporters, NPC family proteins had previously been implicated in pathogenesis of several viruses including dengue, Ebola and HIV. In fact, NPC2 protein was found to be essential for successful replication of CHIKV in human fibroblasts. To characterise the role of NPC2 during CHIKV in Ae. albopictus mosquito, the gene was over expressed in C6/36 mosquito cells 24 hours prior infection with the virus. The infectivity titres of extracellular mature virus and intracellular viral RNA levels were compared between wildtype cells and cells over expressing the protein. The expressed NPC2 protein and the virus were also…

Subjects/Keywords: Fields of Research; Chikungunya; Aedes albopictus; host-pathogen interactions; RNASeq; transcriptome analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vedururu, R. (2019). Identification and functional characterisation of Aedes albopictus genes against Chikungunya virus. (Thesis). RMIT University. Retrieved from http://researchbank.rmit.edu.au/view/rmit:162994

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Vedururu, R. “Identification and functional characterisation of Aedes albopictus genes against Chikungunya virus.” 2019. Thesis, RMIT University. Accessed March 03, 2021. http://researchbank.rmit.edu.au/view/rmit:162994.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Vedururu, R. “Identification and functional characterisation of Aedes albopictus genes against Chikungunya virus.” 2019. Web. 03 Mar 2021.

Vancouver:

Vedururu R. Identification and functional characterisation of Aedes albopictus genes against Chikungunya virus. [Internet] [Thesis]. RMIT University; 2019. [cited 2021 Mar 03]. Available from: http://researchbank.rmit.edu.au/view/rmit:162994.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Vedururu R. Identification and functional characterisation of Aedes albopictus genes against Chikungunya virus. [Thesis]. RMIT University; 2019. Available from: http://researchbank.rmit.edu.au/view/rmit:162994

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Adelaide

19. Hin, Nhi. Transcriptome analysis of zebrafish genetic models to reveal early molecular drivers of Alzheimer’s disease.

Degree: 2020, University of Adelaide

URL: http://hdl.handle.net/2440/129610

► Alzheimer’s disease (AD) is a complex neurodegenerative disease that still evades effective treatment. Developing treatments to slow or prevent AD will require a detailed understanding… (more)

▼ Alzheimer’s disease (AD) is a complex neurodegenerative disease that still evades effective treatment. Developing treatments to slow or prevent AD will require a detailed understanding of the early stages of AD at the molecular level. Unfortunately, the pathogenesis of AD progresses silently over decades and, in the case of genetically inherited familial AD, may involve subtle changes starting during young adulthood. The difficulties associated with studying human brains at young ages have meant that transcriptome analyses of accurate animal models are essential. This is the approach taken in the work here, which uses a data-driven, bioinformatics-led approach to analyse brain transcriptomes from knock-in zebrafish models of AD developed to resemble the genetic background of human AD. In the Introduction, the importance of transcriptome analysis in understanding AD at the molecular level is explained. Chapters 2, 3 and 4 describe the first brain transcriptome analyses of two different knock-in zebrafish mutation models (psen1K97fs and psen1Q96_K97del) modelling different aspects of human AD. In both zebrafish models, young adult brains revealed notable transcriptome changes, including changes to immune/stress responses and energy metabolism respectively. Gene network and gene set analysis approaches revealed that some of these gene expression changes were preserved in human AD datasets, suggesting the validity and utility of the approach used. The work in Chapter 4 supported an important role for iron dyshomeostasis in AD across animal models and human AD and demonstrated, for the first time, the viability of detecting iron dyshomeostasis changes relevant to AD at the transcriptional level. This was achieved using a unique computational approach to the definition of gene sets based on predicted Iron Responsive Elements. Lastly, Chapter 5 used an advanced dimension reduction method to integrate zebrafish and mouse AD model datasets with human familial and sporadic AD. This resulted in the first preliminary comparison of human familial and sporadic AD transcriptomes as well as confirmation that the brains of a knock-in familial AD mutation-like zebrafish model (psen1Q96_K97del) and the commonly used 5XFAD mouse model show extensive differences at the molecular level. Overall, analysis of young adult zebrafish brains revealed potential molecular mechanisms relevant to early stages of human AD that were significantly preserved in human familial and sporadic AD datasets. This work demonstrates the value to our understanding of AD of a bioinformatics-led approach involving transcriptome analysis of knock-in zebrafish models. Advisors/Committee Members: Lardelli, Michael (advisor), Pederson, Stephen (advisor), Adelson, David (advisor), School of Biological Sciences (school).

Subjects/Keywords: RNA-seq; transcriptome; transcriptomics; zebrafish; Alzheimer's disesase; data integration; cross-species analysis; familial Alzheimer's disesase

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hin, N. (2020). Transcriptome analysis of zebrafish genetic models to reveal early molecular drivers of Alzheimer’s disease. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/129610

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hin, Nhi. “Transcriptome analysis of zebrafish genetic models to reveal early molecular drivers of Alzheimer’s disease.” 2020. Thesis, University of Adelaide. Accessed March 03, 2021. http://hdl.handle.net/2440/129610.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hin, Nhi. “Transcriptome analysis of zebrafish genetic models to reveal early molecular drivers of Alzheimer’s disease.” 2020. Web. 03 Mar 2021.

Vancouver:

Hin N. Transcriptome analysis of zebrafish genetic models to reveal early molecular drivers of Alzheimer’s disease. [Internet] [Thesis]. University of Adelaide; 2020. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2440/129610.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hin N. Transcriptome analysis of zebrafish genetic models to reveal early molecular drivers of Alzheimer’s disease. [Thesis]. University of Adelaide; 2020. Available from: http://hdl.handle.net/2440/129610

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Ohio University

20. Shen, Kaiyu. Gravitropic Signal Transduction: A Systems Approach to Gene Discovery.

Degree: PhD, Molecular and Cellular Biology (Arts and Sciences), 2014, Ohio University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1387467697

► Gravity is an important stimulus for plants. Gravitropism, the plants' response to gravity, can be divided into three phases: gravity perception, signal transduction and response.… (more)

▼ Gravity is an important stimulus for plants. Gravitropism, the plants' response to gravity, can be divided into three phases: gravity perception, signal transduction and response. Various theories have been proposed to explain the process of gravitropism, yet more genes are needed to elucidate the mechanism of gravitropic signal transduction. A transcriptome analysis, in combination with the Gravity Persistent Signal treatment, was performed to specifically study the genes involved in signal transduction. Analysis generated a list of 318 transcripts that were differentially expressed in plants that were reoriented with respect to gravity as compared to vertical controls. Based on the expression profiles and gene function annotations, five transcription factors, WRKY18, WRKY26, WRKY33, BT2 and ATAIB, were selected for further study. In addition to the standard analysis of differentially expressed genes, a systems approach was adopted to uncover more gravity related genes. A semi-supervised learning method was developed to find additional novel genes. This learning method took a set of 32 known gravity genes from the literature as well as a collection of heterogeneous annotation features, such as existing protein-protein interactions, and co-expression profiles. The learning classifier predicted a list of 50 genes that are functionally related to gravity signal transduction. Based on this list of genes, an interaction network was predicted based two complementary approaches: a dynamic Bayesian network and a time-lagged correlation coefficient. To increase confidence in the predication, genes/interactions that appeared in both networks were selected. This 'intersected' network provided 20 hub and bottleneck genes, fourteen of which had not been previously identified as involved in gravitropism. Such an approach provides a framework to extend current research in a more comprehensive manner, and serves a complementary to the traditional mutant/gene discovery model. Advisors/Committee Members: Wyatt, Sarah (Advisor), Showalter, Allan (Committee Chair).

Subjects/Keywords: Biology; Computer Science; Systems Biology; Semi-supervised machine learning; Gravitropism; Transcriptome analysis; Biological network

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Shen, K. (2014). Gravitropic Signal Transduction: A Systems Approach to Gene Discovery. (Doctoral Dissertation). Ohio University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1387467697

Chicago Manual of Style (16^th Edition):

Shen, Kaiyu. “Gravitropic Signal Transduction: A Systems Approach to Gene Discovery.” 2014. Doctoral Dissertation, Ohio University. Accessed March 03, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1387467697.

MLA Handbook (7^th Edition):

Shen, Kaiyu. “Gravitropic Signal Transduction: A Systems Approach to Gene Discovery.” 2014. Web. 03 Mar 2021.

Vancouver:

Shen K. Gravitropic Signal Transduction: A Systems Approach to Gene Discovery. [Internet] [Doctoral dissertation]. Ohio University; 2014. [cited 2021 Mar 03]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1387467697.

Council of Science Editors:

Shen K. Gravitropic Signal Transduction: A Systems Approach to Gene Discovery. [Doctoral Dissertation]. Ohio University; 2014. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1387467697

21. Rubanova, Natalia. MasterPATH : network analysis of functional genomics screening data : MasterPATH : l'analyse de réseau des données expérimentales de la génomique fonctionnelle.

Degree: Docteur es, Aspects moléculaires et cellulaires de la biologie, 2018, Sorbonne Paris Cité

URL: http://www.theses.fr/2018USPCC109

►

Dans ce travail nous avons élaboré une nouvelle méthode de l'analyse de réseau à définir des membres possibles des voies moléculaires qui sont important pour… (more)

▼

Dans ce travail nous avons élaboré une nouvelle méthode de l'analyse de réseau à définir des membres possibles des voies moléculaires qui sont important pour ce phénotype en utilisant la « hit-liste » des expériences « omics » qui travaille dans le réseau intégré (le réseau comprend des interactions protéine-protéine, de transcription, l’acide ribonucléique micro-l’acide ribonucléique messager et celles métaboliques). La méthode tire des sous-réseaux qui sont construit des voies de quatre types les plus courtes (qui ne se composent des interactions protéine-protéine, ayant au minimum une interaction de transcription, ayant au minimum une interaction l’acide ribonucléique micro-l’acide ribonucléique messager, ayant au minimum une interaction métabolique) entre des hit –gènes et des soi-disant « exécuteurs terminaux » - les composants biologiques qui participent à la réalisation du phénotype finale (s’ils sont connus) ou entre les hit-gènes (si « des exécuteurs terminaux » sont inconnus). La méthode calcule la valeur de la centralité de chaque point culminant et de chaque voie dans le sous-réseau comme la quantité des voies les plus courtes trouvées sur la route précédente et passant à travers le point culminant et la voie. L'importance statistique des valeurs de la centralité est estimée en comparaison avec des valeurs de la centralité dans les sous-réseaux construit des voies les plus courtes pour les hit-listes choisi occasionnellement. Il est supposé que les points culminant et les voies avec les valeurs de la centralité statistiquement signifiantes peuvent être examinés comme les membres possibles des voies moléculaires menant à ce phénotype. S’il y a des valeurs expérimentales et la P-valeur pour un grand nombre des points culminant dans le réseau, la méthode fait possible de calculer les valeurs expérimentales pour les voies (comme le moyen des valeurs expérimentales des points culminant sur la route) et les P-valeurs expérimentales (en utilisant la méthode de Fischer et des transpositions multiples).A l'aide de la méthode masterPATH on a analysé les données de la perte de fonction criblage de l’acide ribonucléique micro et l'analyse de transcription de la différenciation terminal musculaire et les données de la perte de fonction criblage du procès de la réparation de l'ADN. On peut trouver le code initial de la méthode si l’on suit le lien https://github.com/daggoo/masterPATH

In this work we developed a new exploratory network analysis method, that works on an integrated network (the network consists of protein-protein, transcriptional, miRNA-mRNA, metabolic interactions) and aims at uncovering potential members of molecular pathways important for a given phenotype using hit list dataset from “omics” experiments. The method extracts subnetwork built from the shortest paths of 4 different types (with only protein-protein interactions, with at least one transcription interaction, with at least one miRNA-mRNA interaction, with at least one metabolic interaction) between hit genes and so called “final…

Advisors/Committee Members: Morozova, Nadya (thesis director).

Subjects/Keywords: Analyse des réseaux; Perte de fonction сriblage; Profilage du transcriptome; CRISPR/Cas9; Voies moléculaires; Network analysis; Loss-of-function screening; RNA interference; Transcriptome profiling; CRISPR/Cas9; Molecular pathway

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rubanova, N. (2018). MasterPATH : network analysis of functional genomics screening data : MasterPATH : l'analyse de réseau des données expérimentales de la génomique fonctionnelle. (Doctoral Dissertation). Sorbonne Paris Cité. Retrieved from http://www.theses.fr/2018USPCC109

Chicago Manual of Style (16^th Edition):

Rubanova, Natalia. “MasterPATH : network analysis of functional genomics screening data : MasterPATH : l'analyse de réseau des données expérimentales de la génomique fonctionnelle.” 2018. Doctoral Dissertation, Sorbonne Paris Cité. Accessed March 03, 2021. http://www.theses.fr/2018USPCC109.

MLA Handbook (7^th Edition):

Rubanova, Natalia. “MasterPATH : network analysis of functional genomics screening data : MasterPATH : l'analyse de réseau des données expérimentales de la génomique fonctionnelle.” 2018. Web. 03 Mar 2021.

Vancouver:

Rubanova N. MasterPATH : network analysis of functional genomics screening data : MasterPATH : l'analyse de réseau des données expérimentales de la génomique fonctionnelle. [Internet] [Doctoral dissertation]. Sorbonne Paris Cité; 2018. [cited 2021 Mar 03]. Available from: http://www.theses.fr/2018USPCC109.

Council of Science Editors:

Rubanova N. MasterPATH : network analysis of functional genomics screening data : MasterPATH : l'analyse de réseau des données expérimentales de la génomique fonctionnelle. [Doctoral Dissertation]. Sorbonne Paris Cité; 2018. Available from: http://www.theses.fr/2018USPCC109

University of Illinois – Chicago

22. Qin, Wenyi. Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection.

Degree: 2018, University of Illinois – Chicago

URL: http://hdl.handle.net/10027/22613

► High-throughput technology such as microarray and next-generation sequencing (NGS) measure thousands of gene expression in one sample simultaneously. Detecting differentially expressed (DE) genes between disease… (more)

▼ High-throughput technology such as microarray and next-generation sequencing (NGS) measure thousands of gene expression in one sample simultaneously. Detecting differentially expressed (DE) genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. DE genes are potential disease-related genes and are used for generating biological hypothesis of disease mechanism, developing potential clinical diagnosis tools and investigating potential drug targets. Pathway enrichment analysis is another widely accepted expression analysis tool which aims at detecting coordinated expression change within a pre-defined gene sets rather than individual genes. The benefit of gene set analysis over individual gene analysis includes more reproducible and interpretable results and detecting small but consistent change among gene set which could not be detected by DE gene analysis. There have been many successful applications of DE gene detection or gene set analysis in human diseases. However, when the sample size of a study is small, this will lead to lack of power to detect genes/pathways of importance to the disease. Public data integration would alleviate this situation. In this thesis, we first conducted a novel meta-analysis on schizophrenia patients aiming at identifying sex-related genes responsible for gender difference in schizophrenia patients. 46 genes were identified in male group while none were identified in female group due to lack of samples. Motivated by this, we then proposed a novel empirical Bayes based mixture model method to identify DE genes by borrowing shared information across multiple similar disease expression data sets based on the assumption that similar disease tend to share similar DE genes. Through simulation study and real data application, we demonstrated the improved identification power of the proposed method over single data set analysis and other popular meta-analysis methods. We further extended the proposed method to identify the altered gene sets. Simulation test and real data application demonstrated that more enriched pathways could be identified through our proposed methods over single data analysis alone. Overall, we expect that the methods presented in this thesis could provide researchers with a new approach of reusing public data sets when the sample size is limited. Advisors/Committee Members: Lu, Hui (advisor), Dai, Yang (committee member), Royston, Thomas (committee member), Sodhi, Monsheel (committee member), Zhang, Wei (committee member), Lu, Hui (chair).

Subjects/Keywords: data integration; cross disease transcriptome; differentially expressed; Bayesian mixture model; gene set enrichment analysis; schizophrenia; meta-analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Qin, W. (2018). Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/22613

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Qin, Wenyi. “Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection.” 2018. Thesis, University of Illinois – Chicago. Accessed March 03, 2021. http://hdl.handle.net/10027/22613.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Qin, Wenyi. “Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection.” 2018. Web. 03 Mar 2021.

Vancouver:

Qin W. Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection. [Internet] [Thesis]. University of Illinois – Chicago; 2018. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10027/22613.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Qin W. Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection. [Thesis]. University of Illinois – Chicago; 2018. Available from: http://hdl.handle.net/10027/22613

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

UCLA

23. Tian, Yuan. Identification of transcriptional changes associated with syndromic forms of autism.

Degree: Bioinformatics, 2014, UCLA

URL: http://www.escholarship.org/uc/item/7134s59n

► Autism spectrum disorders (ASDs) are highly heritable neuropsychiatric conditions. However, the genetic etiology is greatly heterogeneous. No single genetic cause responsible for the majority of… (more)

▼ Autism spectrum disorders (ASDs) are highly heritable neuropsychiatric conditions. However, the genetic etiology is greatly heterogeneous. No single genetic cause responsible for the majority of ASD cases has been identified so far. Given the genetic heterogeneity, the process through which diverse genetic factors lead to shared phenotypes in ASD remains unclear, and it is critical to understanding the ASD pathophysiology. As previous studies have implied the convergence of pathways in ASD at the transcriptomic level, in this dissertation, we conducted genome-wide expression analysis by using cell lines derived from various syndromic ASD conditions in an attempt to identify potentially common expression alterations in all or a subset of those ASD conditions, and to elucidate the convergent pathway(s) involved in ASD pathogenesis. We analyzed expression profiles of patient-specific neurons derived from induced pluripotent stem cells (iPSCs) from patients with three different monogenic ASD mutations: 22q13.3 deletion, 22q11.2 deletion, and Timothy syndrome (TS). By comparing the ASD mutations with controls, respectively, our analysis revealed substantial gene expression changes in each of these mutations. Some of the identified expression changes could be generalized to neurons and postmortem brains from idiopathic autistic patients. In addition to the iPSC sample cohort, we also analyzed expression profiles of lymphoblast cell line (LCLs) from 5 different syndromic forms of ASD. Significant overlapping expression features were identified among these ASD forms, and a set of them recapitulated the expression features we identified using iPSC-derived neurons. To our knowledge, this is the first time that significant shared transcriptional features have been identified in ASD between brain-related cell types and peripherally derived cell lines, providing strong support for the usefulness of LCLs in exploring ASD pathogenesis. In addition to the similarities, our analysis also highlighted the diversity in gene expression across different ASD mutations, which may explain how each ASD forms are modulated given their phenotypic heterogeneity. Overall, our findings highlight the specificity and convergence of ASD at the transcriptional level, suggesting promising directions for future research.

Subjects/Keywords: Bioinformatics; Neurosciences; Genetics; 22q11.2 deletion syndrome; Autism Spectrum Disorders; gene expression; Syndromic ASD; Timothy syndrome; Transcriptome analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tian, Y. (2014). Identification of transcriptional changes associated with syndromic forms of autism. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/7134s59n

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tian, Yuan. “Identification of transcriptional changes associated with syndromic forms of autism.” 2014. Thesis, UCLA. Accessed March 03, 2021. http://www.escholarship.org/uc/item/7134s59n.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tian, Yuan. “Identification of transcriptional changes associated with syndromic forms of autism.” 2014. Web. 03 Mar 2021.

Vancouver:

Tian Y. Identification of transcriptional changes associated with syndromic forms of autism. [Internet] [Thesis]. UCLA; 2014. [cited 2021 Mar 03]. Available from: http://www.escholarship.org/uc/item/7134s59n.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tian Y. Identification of transcriptional changes associated with syndromic forms of autism. [Thesis]. UCLA; 2014. Available from: http://www.escholarship.org/uc/item/7134s59n

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University

24. Khuansuwan, Sataree. A transcription factor network dictates neuronal cell fate decisions in the zebrafish dorsal diencephalon.

Degree: PhD, Biological Sciences, 2014, Vanderbilt University

URL: http://hdl.handle.net/1803/14223

► The zebrafish epithalamus, which includes the dorsal habenular nuclei and pineal complex, displays robust molecular and anatomical asymmetries. The full elaboration of molecular and anatomical… (more)

Subjects/Keywords: parapineal; left-right asymmetry; Danio rerio; zebrafish; Tbx2b; pineal; pineal complex; transcriptome analysis; Flh; Nr2e3; FACS

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Khuansuwan, S. (2014). A transcription factor network dictates neuronal cell fate decisions in the zebrafish dorsal diencephalon. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14223

Chicago Manual of Style (16^th Edition):

Khuansuwan, Sataree. “A transcription factor network dictates neuronal cell fate decisions in the zebrafish dorsal diencephalon.” 2014. Doctoral Dissertation, Vanderbilt University. Accessed March 03, 2021. http://hdl.handle.net/1803/14223.

MLA Handbook (7^th Edition):

Khuansuwan, Sataree. “A transcription factor network dictates neuronal cell fate decisions in the zebrafish dorsal diencephalon.” 2014. Web. 03 Mar 2021.

Vancouver:

Khuansuwan S. A transcription factor network dictates neuronal cell fate decisions in the zebrafish dorsal diencephalon. [Internet] [Doctoral dissertation]. Vanderbilt University; 2014. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/1803/14223.

Council of Science Editors:

Khuansuwan S. A transcription factor network dictates neuronal cell fate decisions in the zebrafish dorsal diencephalon. [Doctoral Dissertation]. Vanderbilt University; 2014. Available from: http://hdl.handle.net/1803/14223

25. Renata Santos Rodrigues. Análise do perfil de expressão gênica da glândula de peçonha de Bothrops pauloensis (Bothropoides pauloensis).

Degree: 2010, Federal University of Uberlândia

URL: http://www.bdtd.ufu.br//tde_busca/arquivo.php?codArquivo=3979

►

As peçonhas de serpentes do gênero Bothrops consistem em uma fonte de peptídeos e proteínas que apresentam importantes ações farmacológicas ocasionando efeitos locais e sistêmicos… (more)

▼

As peçonhas de serpentes do gênero Bothrops consistem em uma fonte de peptídeos e proteínas que apresentam importantes ações farmacológicas ocasionando efeitos locais e sistêmicos como edema, sangramentos e necrose muscular. Muitas toxinas da peçonha de B. pauloensis têm sido isoladas e caracterizadas através de métodos bioquímicos tradicionais. Com o objetivo de analisar o perfil transcricional da glândula de peçonha de B. pauloensis e desvendar o potencial farmacológico de seus constituintes a nível molecular, foi gerada um biblioteca parcial de cDNA, e as seqüências obtidas foram identificadas por análises de similaridade contra bancos de dados internacionais existentes. Os resultados demonstraram que de um total de 1152 clones seqüenciados, 668 correspondem às seqüências de qualidade (>100pb), havendo um grande predomínio de transcritos que codificam toxinas em relação aos que codificam proteínas envolvidas em funções celulares. Entre as seqüências que codificam toxinas (41,5%), as metaloproteinases (38%) apresentaram maior freqüência, seguidas pelas fosfolipases A2 (27%), peptídeos potencializadores de bradicinina (16,5%) e lectinas tipo-C (8,2%). Outros clones são expressos em menor freqüência como serinoproteinases (5,1%), L-aminoácido oxidases (2,7%), fatores de crescimento neural (NGF) (1,0%), endotelial vascular (VEGF) (0,3%) e hialuronidase (0,3%). Dentre os transcritos que codificam proteínas celulares a maioria consiste em moléculas envolvidas em funções fisiológicas da glândula de peçonha. A maioria desses transcritos celulares está envolvida na expressão gênica e protéica, o que reflete uma alta especialização do tecido para a síntese de toxinas. As análises do transcriptoma da glândula de peçonha de B. pauloensis possibilitaram a identificação de um cluster BP028 contendo 7 sequências correspondentes à L-aminoácido oxidase. A clonagem e amplificação desta svLAAO gerou um fragmento de 1548 pares de bases (pb) que codificam uma proteína madura de 516 resíduos de aminoácidos, com massa molecular de 58 kDa, pI 6,3 e apenas um sítio de glicosilação. Segundo análises filogenéticas, as svLAAOs de serpentes Viperidae e Elapidae apresentaram evidente separação, indicando uma correlação significativa com a especiação, demonstrando que os genes correspondentes a estas sequências são ortólogos.

Bothrops snake venoms are rich sources of peptides and proteins that have important pharmacological actions causing local and systemic effects such as swelling, bleeding and muscle necrosis. Many toxins from the venom of B.pauloensis have been isolated and characterized by classical biochemical methods. Aiming to describe the transcriptional profile of the gland of B. pauloensis and unveil the pharmacological potential of its products at the molecular level a partial cDNA library has generated and the sequences obtained were identified by similarity analysis against existing international databases. The results show that a total of 1152 clones sequenced, 668 correspond to the sequences of quality, with a high prevalence…

Advisors/Committee Members: Maria Inês Homsi Brandeburgo, Veridiana de Melo Rodrigues Ávila, Amélia Hamaguchi, Andreimar Martins Soares, Eliane Candiane Arantes.

Subjects/Keywords: Análise filogenética; Bothropoides pauloensis; L-aminoácido oxidase; Transcriptoma; Modelagem molecular; GENETICA; Serpente peçonhenta - Peçonha; Proteínas; Phylogenetic analysis; Transcriptome; Molecular modeling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rodrigues, R. S. (2010). Análise do perfil de expressão gênica da glândula de peçonha de Bothrops pauloensis (Bothropoides pauloensis). (Thesis). Federal University of Uberlândia. Retrieved from http://www.bdtd.ufu.br//tde_busca/arquivo.php?codArquivo=3979

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Rodrigues, Renata Santos. “Análise do perfil de expressão gênica da glândula de peçonha de Bothrops pauloensis (Bothropoides pauloensis).” 2010. Thesis, Federal University of Uberlândia. Accessed March 03, 2021. http://www.bdtd.ufu.br//tde_busca/arquivo.php?codArquivo=3979.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Rodrigues, Renata Santos. “Análise do perfil de expressão gênica da glândula de peçonha de Bothrops pauloensis (Bothropoides pauloensis).” 2010. Web. 03 Mar 2021.

Vancouver:

Rodrigues RS. Análise do perfil de expressão gênica da glândula de peçonha de Bothrops pauloensis (Bothropoides pauloensis). [Internet] [Thesis]. Federal University of Uberlândia; 2010. [cited 2021 Mar 03]. Available from: http://www.bdtd.ufu.br//tde_busca/arquivo.php?codArquivo=3979.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Rodrigues RS. Análise do perfil de expressão gênica da glândula de peçonha de Bothrops pauloensis (Bothropoides pauloensis). [Thesis]. Federal University of Uberlândia; 2010. Available from: http://www.bdtd.ufu.br//tde_busca/arquivo.php?codArquivo=3979

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of KwaZulu-Natal

26. Dlamini, Mlungisi Thabiso. Whole transcriptome analysis to elucidate the role of mtp in gene regulation of pulmonary epithelial cells infected with Mycobacterium tuberculosis.

Degree: 2016, University of KwaZulu-Natal

URL: http://hdl.handle.net/10413/14772

Abstract available in PDF file. Advisors/Committee Members: Pillay, Manormoney. (advisor).

Subjects/Keywords: Mycrobacterium tuberculosis.; Pulmonary epithelial cell infection model.; Transcriptome analysis.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dlamini, M. T. (2016). Whole transcriptome analysis to elucidate the role of mtp in gene regulation of pulmonary epithelial cells infected with Mycobacterium tuberculosis. (Thesis). University of KwaZulu-Natal. Retrieved from http://hdl.handle.net/10413/14772

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dlamini, Mlungisi Thabiso. “Whole transcriptome analysis to elucidate the role of mtp in gene regulation of pulmonary epithelial cells infected with Mycobacterium tuberculosis.” 2016. Thesis, University of KwaZulu-Natal. Accessed March 03, 2021. http://hdl.handle.net/10413/14772.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dlamini, Mlungisi Thabiso. “Whole transcriptome analysis to elucidate the role of mtp in gene regulation of pulmonary epithelial cells infected with Mycobacterium tuberculosis.” 2016. Web. 03 Mar 2021.

Vancouver:

Dlamini MT. Whole transcriptome analysis to elucidate the role of mtp in gene regulation of pulmonary epithelial cells infected with Mycobacterium tuberculosis. [Internet] [Thesis]. University of KwaZulu-Natal; 2016. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10413/14772.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dlamini MT. Whole transcriptome analysis to elucidate the role of mtp in gene regulation of pulmonary epithelial cells infected with Mycobacterium tuberculosis. [Thesis]. University of KwaZulu-Natal; 2016. Available from: http://hdl.handle.net/10413/14772

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

North Carolina State University

27. Cabrera, Ana Rosa. Advances in resistance monitoring of agricultural pests and in the elucidation of mite reproductive physiology.

Degree: PhD, Entomology, 2010, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/6192

► The work conducted for this dissertation aimed to contribute in our knowledge regarding resistance monitoring of agricultural pests and mite reproduction. Resistance monitoring of lepidopteran… (more)

▼ The work conducted for this dissertation aimed to contribute in our knowledge regarding resistance monitoring of agricultural pests and mite reproduction. Resistance monitoring of lepidopteran pests exposed to transgenic cotton expressing Bacillus thuringiensis (Bt) toxins is necessary and required to prevent the development of insect resistance. A bioassay was developed using Bt cotton plant extracts to rehydrate a heliothine diet and observe feeding disruption of the cotton pest Heliothis virescens. A diagnostic dose was estimated for two different pyramided Bt cotton varieties. The bioassay was evaluated with field H. virescens populations from North Carolina and two Bt resistant, laboratory strains. Ready to use meal pads containing Bt from cotton plants can be stored for up to 5 months. This bioassay is practical, lower cost and can be adapted for other Bt cotton varieties and Bt crops. This work is described in chapter 1. Mites are important medical and agricultural pests. Currently, there is limited information regarding the regulation of female reproduction in mites and few studies have study mite yolk proteins. A review of the literature was conducted regarding the regulation of female reproduction in mites and a new model for the regulation of vitellogenesis in the Acari was proposed. Relevant work on the regulation of vitellogenesis in insects, crustaceans and ticks, as well as observations on the effects of some insect hormones and their analogs on mite reproduction, leads us to conclude that the prevailing assumption that mites regulate vitellogenesis with high levels of juvenile hormone (JH) may not be correct. As a result of this review a new unifying model for the Acari was developed where ecdysteroids, and no JH, regulate vitellogenesis in mites. This review was published in 2009 in the Journal of Insect Physiology and is presented in chapter 2. In chapter 3, the characterization of the major yolk protein vitellin of the twospotted spider mite, Tetranychus urticae, is presented. This work determined T. urticae vitellin is a glycolipoprotein, although the carbohydrate and lipid content appears to be lower than that of the American dog tick, Dermacentor variabilis. It was clear that spider mite vitellin does not carry heme, a fundamental difference with the tick yolk protein. Finally, T. urticae vitellin migrated as a single band under native-PAGE conditions, but five different bands were observed with isoelectric focusing analysis, indicating that multiple Vgs may be expressed. This conclusion is also supported by the recent evidence that T. urticae ovipositing females express at least 4 vitellogenin (Vg) genes. This work was published in the Journal of Insect Physiology in 2009. Finally, the transcriptome analysis of the predatory mite, Phytoseiulus persimilis, is presented in chapter 4. This is the first transcriptome analysis of a mite and as a result of a 454 pyrosequencing project that yielded 12,556 sequences of transcripts. From those, 11 contigs were similar to arthropod Vgs and 6 to… Advisors/Committee Members: Christina Grozinger, Committee Member (advisor), James Harper, Committee Member (advisor), R. Michael Roe, Committee Chair (advisor), Clyde Sorenson, Committee Member (advisor).

Subjects/Keywords: Bt cotton; resistance monitoring; tobacco budworm; Heliothis virescens; mite reproduction; spider mite; Tetranychus urticae; Phytoseiulus persimilis; transcriptome analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cabrera, A. R. (2010). Advances in resistance monitoring of agricultural pests and in the elucidation of mite reproductive physiology. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/6192

Chicago Manual of Style (16^th Edition):

Cabrera, Ana Rosa. “Advances in resistance monitoring of agricultural pests and in the elucidation of mite reproductive physiology.” 2010. Doctoral Dissertation, North Carolina State University. Accessed March 03, 2021. http://www.lib.ncsu.edu/resolver/1840.16/6192.

MLA Handbook (7^th Edition):

Cabrera, Ana Rosa. “Advances in resistance monitoring of agricultural pests and in the elucidation of mite reproductive physiology.” 2010. Web. 03 Mar 2021.

Vancouver:

Cabrera AR. Advances in resistance monitoring of agricultural pests and in the elucidation of mite reproductive physiology. [Internet] [Doctoral dissertation]. North Carolina State University; 2010. [cited 2021 Mar 03]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/6192.

Council of Science Editors:

Cabrera AR. Advances in resistance monitoring of agricultural pests and in the elucidation of mite reproductive physiology. [Doctoral Dissertation]. North Carolina State University; 2010. Available from: http://www.lib.ncsu.edu/resolver/1840.16/6192

28. Chevallier, Lucie. Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste. : Identification of genetic factors involved in the resistance of inbred strains of mice to an experimental infection with Yersinia pestis, the plague agent.

Degree: Docteur es, Génétique, 2012, Paris, AgroParisTech

URL: http://www.theses.fr/2012AGPT0077

► Yersinia pestis, l'agent de la peste, est une bactérie à Gram-négatif classée comme agent pathogène ré-émergent et potentielle arme de bioterrorisme. De plus, l'apparition d'une… (more)

▼ Yersinia pestis, l'agent de la peste, est une bactérie à Gram-négatif classée comme agent pathogène ré-émergent et potentielle arme de bioterrorisme. De plus, l'apparition d'une souche multi-résistance de cette bactérie souligne la nécessité de mieux comprendre comment cette bactérie hyper-virulente interagit avec son hôte. Afin d'identifier des facteurs génétiques de vulnérabilité à la peste, notre laboratoire travaille sur la réponse de souris résistantes versus sensibles à Y. pestis. Notre stratégie pour identifier les facteurs génétiques impliqués dans la résistance/sensibilité à la peste combine une approche de cartographie de QTL (Quantitative Trait Locus) et d'analyse d'expression génique. Nous avons précédemment décrit la lignée SEG/Pas, issue de Mus spretus, comme la première résistante à une souche virulente de Y. pestis, alors que la plupart des lignées murines de laboratoire, telle que la lignée C57BL/6J, sont extrêmement sensible à la bactérie. Des croisements entre SEG/Pas et C57BL/6J nous ont permis d'identifier trois QTL impliqués dans la résistance à Y. pestis, localisés sur les chromosomes 3, 4 et 6. Deux des QTL (situés sur les chromosomes 4 et 6) ont pu être confirmés par l'analyse de lignées congéniques. Plus de 40 % des femelles bi-congéniques hétérozygotes pour ces deux QTL ont survécu à l'infection, alors que tous les témoins C57BL/6J ont succombé. La dissection de ces deux QTL par l'analyse de lignées sous-congéniques, nous a permis d'affiner l'architecture génétique de la résistance à la peste chez SEG/Pas. Nous avons conclu qu'un minimum de quatre facteurs génétiques, au sein de ces deux QTL, sont nécessaires pour augmenter la résistance à Y. pestis chez la Souris. Cependant, la production de plusieurs lignées congéniques portant le QTL situé sur le chromosome 3, dont une lignée triple congénique, ne nous a pas permis de confirmer l'existence de ce QTL. En parallèle de l'analyse génétique, nous avons déterminé que les macrophages de SEG/Pas et de C57BL/6J présentaient des caractéristiques différentes après exposition à Y. pestis. Une analyse différentielle du profil transcriptionnel des macrophages de ces deux lignées a été réalisée à l'aide de puces à ADN. Nos résultats montrent une forte activation de la production cytokinique dans les macrophages de SEG/Pas en réponse à la bactérie, activation qui n'est pas observée dans la lignée C57BL/6J. Ces résultats suggèrent que les souris SEG/Pas sont capables de mettre en place une réponse immune innée plus forte ou peut-être plus précoce que C57BL/6J. Nous avons ensuite étudié par qRT-PCR l'expression en cinétique de 44 gènes dans des macrophages de SEG/Pas, C57BL/6J et des bi-congéniques portant les QTL sur les chromosomes 4 et 6. Cette étude nous a permis de confirmer que les souris SEG/Pas sont capables se mettre en place une forte réponse inflammatoire lors de l'infection. Cependant, aucune différence significative n'a été observée entre la lignée bicongénique et la lignée parentale C57BL/6J. D'autres expériences seront nécessaires afin de… Advisors/Committee Members: Montagutelli, Xavier (thesis director).

Subjects/Keywords: Peste; Souris; Résistance; Yersinia pestis; Lignée congénique; Analyse de transcriptome; Plague; Mouse; Resistance; Yersinia pestis; Congenic strain; Transcriptomic analysis; 616.042

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Chevallier, L. (2012). Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste. : Identification of genetic factors involved in the resistance of inbred strains of mice to an experimental infection with Yersinia pestis, the plague agent. (Doctoral Dissertation). Paris, AgroParisTech. Retrieved from http://www.theses.fr/2012AGPT0077

Chicago Manual of Style (16^th Edition):

Chevallier, Lucie. “Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste. : Identification of genetic factors involved in the resistance of inbred strains of mice to an experimental infection with Yersinia pestis, the plague agent.” 2012. Doctoral Dissertation, Paris, AgroParisTech. Accessed March 03, 2021. http://www.theses.fr/2012AGPT0077.

MLA Handbook (7^th Edition):

Chevallier, Lucie. “Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste. : Identification of genetic factors involved in the resistance of inbred strains of mice to an experimental infection with Yersinia pestis, the plague agent.” 2012. Web. 03 Mar 2021.

Vancouver:

Chevallier L. Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste. : Identification of genetic factors involved in the resistance of inbred strains of mice to an experimental infection with Yersinia pestis, the plague agent. [Internet] [Doctoral dissertation]. Paris, AgroParisTech; 2012. [cited 2021 Mar 03]. Available from: http://www.theses.fr/2012AGPT0077.

Council of Science Editors:

Chevallier L. Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste. : Identification of genetic factors involved in the resistance of inbred strains of mice to an experimental infection with Yersinia pestis, the plague agent. [Doctoral Dissertation]. Paris, AgroParisTech; 2012. Available from: http://www.theses.fr/2012AGPT0077

29. 김, 소민. Transcriptomes of CD27-CD28- and CD27+CD28+ CD8+ T subsets disclose differentially expressed novel genes and signaling pathways in Behçet's disease.

Degree: 2019, Ajou University

URL: http://repository.ajou.ac.kr/handle/201003/17871 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000029178

► BACKGROUND AND OBJECTIVES: Behçet’s disease (BD) is a chronic inflammatory disease characterized by recurrent mucocutaneous ulceration and other complications such as blindness and large vessel… (more)

▼ BACKGROUND AND OBJECTIVES: Behçet’s disease (BD) is a chronic inflammatory disease characterized by recurrent mucocutaneous ulceration and other complications such as blindness and large vessel inflammation. Immunosenescence, aging of immune system, is related to increased susceptibility to infectious diseases, vaccine failure, and chronic low grade systemic inflammation. Our previous study showed increased frequency of senescent CD8+ T cells in the peripheral blood of patients with BD. In this study, to find the global genet-expression characteristics of senescent CD8+ T cells in relation with BD, we examined the transcriptome of CD8+ T lymphocyte subsets (CD27-CD28- senescent and CD27+CD28+ nonsenescent) from BD patients and healthy control (HC) subjects. MATERIAL AND METHODS: Peripheral blood mononuclear cells (PBMCs) were collected from BD patients (n=18) and HCs (n=18). CD8+ T cells were isolated through CD8 microbeads, and those were labelled with conjugated monoclonal antibodies as follows: FITC anti-CD8, allophycocyanin (APC)-H7 anti-CD27 and APC anti-CD28. Using fluorescence-activated cell sorting (FACS), senescent CD8+ T cells (CD8+CD27-CD28-) and non-senescent CD8+ T cells (CD8+CD27+CD28+) were sorted. After sorting, each group of cells were pooled together and cultured in medium (RPMI 1640). Cells were stimulated with anti-CD3 (500ng/ml, clone OKT3) for 72 hours. Total RNA was extracted from anti-CD3-stimulated cells with the RNA isolation kit. Transcriptome analysis was performed. We analyzed the differentially expressed genes from the four different groups (BD patients vs. controls, senescent CD8+ T cells (CD8+ CD27- CD28-) vs. non-senescent CD8+ T cells (CD8+ CD27+ CD28+)). Differentially expressed genes were submitted to Ingenuity Pathway Analysis (IPA) for functional evaluation and identification of significant biological pathways. For the validation of genes that show large fold change value in transcriptome sequencing, additional five BD patients and five HCs were enrolled to collect RNA and perform the real-time PCR on eight genes. RESULTS: Differentially expressed 1103 genes were identified in BD CD27-CD28- subsets compared to HC, while 652 genes were differentially expressed in BD CD27+CD28+ subsets compared to HC. As a result of the real-time PCR, COL5A1, ARHGEF10 showed the same tendency with the transcriptome analysis in the BD CD27-CD28- subsets compared to HCs, among which the statistical significance was shown in COL5A1. Meanwhile, TRPV3, ARHGEF10, UBE2F-SCLY, CD302, and SHANK1 showed the same tendency with the transcriptome analysis in the BD CD27+CD28+ subsets compared to HCs, and the statistical significance was found in TRPV3 and ARHGEF10. Of the significant canonical pathways identified in IPA, 11 pathways showed activity in the opposite direction between CD27+CD28+ and CD27-CD28- subsets, while two pathways tended to be same. The most significant canonical pathway resulted from the IPA was the cAMP-mediated signaling. CONCLUSION: This is the first study for transcriptome analysis of… Advisors/Committee Members: 대학원 의학과, 201624073, 김, 소민.

Subjects/Keywords: Behçet's disease; transcriptome analysis; RNA sequencing; CD8+ T cell; immunosenescence; 베체트병; 전사체 분석; RNA 서열분석; CD8+ T 세포; 면역노화

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

김, �. (2019). Transcriptomes of CD27-CD28- and CD27+CD28+ CD8+ T subsets disclose differentially expressed novel genes and signaling pathways in Behçet's disease. (Thesis). Ajou University. Retrieved from http://repository.ajou.ac.kr/handle/201003/17871 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000029178

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

김, 소민. “Transcriptomes of CD27-CD28- and CD27+CD28+ CD8+ T subsets disclose differentially expressed novel genes and signaling pathways in Behçet's disease.” 2019. Thesis, Ajou University. Accessed March 03, 2021. http://repository.ajou.ac.kr/handle/201003/17871 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000029178.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

김, 소민. “Transcriptomes of CD27-CD28- and CD27+CD28+ CD8+ T subsets disclose differentially expressed novel genes and signaling pathways in Behçet's disease.” 2019. Web. 03 Mar 2021.

Vancouver:

김 �. Transcriptomes of CD27-CD28- and CD27+CD28+ CD8+ T subsets disclose differentially expressed novel genes and signaling pathways in Behçet's disease. [Internet] [Thesis]. Ajou University; 2019. [cited 2021 Mar 03]. Available from: http://repository.ajou.ac.kr/handle/201003/17871 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000029178.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

김 �. Transcriptomes of CD27-CD28- and CD27+CD28+ CD8+ T subsets disclose differentially expressed novel genes and signaling pathways in Behçet's disease. [Thesis]. Ajou University; 2019. Available from: http://repository.ajou.ac.kr/handle/201003/17871 ; http://dcoll.ajou.ac.kr:9080/dcollection/jsp/common/DcLoOrgPer.jsp?sItemId=000000029178

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Freie Universität Berlin

30. Nandy, Constanze. Molekulare Charakterisierung zellulärer Subgruppen in der Schwanzknospe der Maus.

Degree: 2015, Freie Universität Berlin

URL: http://dx.doi.org/10.17169/refubium-4749

► Das kaudale Ende des 9.0 Tage alten Mausembryos besteht aus unterschiedlichen Teilbereichen, welche wichtige Funktionen während der Rumpf- und Schwanzentwicklung inne haben. In dieser Arbeit… (more)

▼ Das kaudale Ende des 9.0 Tage alten Mausembryos besteht aus unterschiedlichen Teilbereichen, welche wichtige Funktionen während der Rumpf- und Schwanzentwicklung inne haben. In dieser Arbeit wurden mehrere Untergruppen des kaudalen Endes von 9 und 10 Tage alten Mausembryonen untersucht. Jede dieser Untergruppen ist durch die spezifische Expression eines Gens charakterisiert. Für diese Arbeit wurden 4 unterschiedliche Markergene, Mixl1, Tlx2, Sct und Pax3 augewählt. Eine Zellstammbaumanalyse, bei welcher eine per Tamoxifen induzierbare Kassette verwendet wurde, ermöglichte Untersuchungen zu ausgewählten Zeitpunkten während der Embryonalentwicklung. Zu diesem Zweck wurden zwei unterschiedliche Reportergene verwendet. Das Venusreportergen, welches vom Promotor des Markergens kontrolliert wurde, sowie ein lacZ-Gen. Das lacZ-Gen, war in den ROSA26R Genlokus integriert und wurde somit nur nach erfolgter Applikation von Tamoxifen durch Rekombinase vermitteltes Ausschneiden einer Stoppkassette exprimiert. Venus exprimierende Zellen wurden zusätzlich mittels fluoreszenzbasierter Durchflusszytometrie sortiert und anschließend für RNA-Sequenzierung verwendet. Die Zellstammbaumanalyse zeigte die Lokalisation der Tochterzellen der unterschiedlichen durch die Markergene charakterisierten Subdomänen. Im lateralen und paraxialen Mesoderm, sowie im Notochord fanden sich Abkömmlinge der Mixl1 exprimierenden Zellen. Tochterzellen von Tlx2 exprimierenden Zellen wurden im Hinterdarm nachgewiesen. Nachkommen von Sct exprimierenden Zellen wurden verstreut im Mesoderm identifiziert. Nachfahren von Pax3 exprimierenden Zellen wurden im Neuralrohr, sowie zu einem späteren Zeitpunkt der Embryonalentwicklung in Nervenknoten gefunden. Die Transkriptomanalyse von sortierten Zellen mit Mixl1 Expression zeigte das Gen Noto in diesen Zellen erhöht exprimiert. Außerdem waren verstärkt exprimierte Gene enthalten, welche in Entwicklungsprozesse involviert sind, die charakteristisch für das Mesoderm sind. Folglich könnten die Mixl1 exprimierenden Zellen aus zwei unterschiedlichen Untergruppen zusammengesetzt sein, oder Vorläufer unterschiedlicher Mesodermdomänen enthalten. Nachkommen Tlx2 exprimierender Zellen wurden im Hinterdarm gefunden. In der Transkriptomanalysi konnten Gene die zu Entwicklung des Endeoderms beitragen und insbesondere für transmembrane Proteine kodierende Gene identifiziert werden. Das Zellen, insbesondere Tlx2 exprimierende Zellen aus dem kaudalen Ende des Mausembryos zur Entwicklung des Hinterdarmes beitragen, ist bisher noch nicht beschrieben worden. Nach bisheriger Auffassung wächst der Hinterdarm vom anterioren in Richtung des Kaudalen Endes. Die Ergebnisse dieser Arbeit legen nahe, dass es zwei Richtungen gibt aus denen Zellen zur Hinterdarmentwicklung beitragen. Bei Zellen aus der Subregion des kaudalen Endes mit Pax3 Expression konnte gezeigt werden, dass diese Zellen Gene exprimieren, die in die Entwicklung von Neuralleistenzellen involviert sind. Diese neuen Ergebnisse zeigen, dass sich auch aus der mesodermalen… Advisors/Committee Members: [email protected] (contact), w (gender), Prof. Dr. Bernhard G. Herrmann (firstReferee), Prof. Dr. Stephan Sigrist (furtherReferee).

Subjects/Keywords: Tlx2; Mixl1; Pax3; Sct; lineage tracing; transcriptome analysis; hindgut development; notochord development; neural crest; 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie

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APA (6^th Edition):

Nandy, C. (2015). Molekulare Charakterisierung zellulärer Subgruppen in der Schwanzknospe der Maus. (Thesis). Freie Universität Berlin. Retrieved from http://dx.doi.org/10.17169/refubium-4749

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nandy, Constanze. “Molekulare Charakterisierung zellulärer Subgruppen in der Schwanzknospe der Maus.” 2015. Thesis, Freie Universität Berlin. Accessed March 03, 2021. http://dx.doi.org/10.17169/refubium-4749.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nandy, Constanze. “Molekulare Charakterisierung zellulärer Subgruppen in der Schwanzknospe der Maus.” 2015. Web. 03 Mar 2021.

Vancouver:

Nandy C. Molekulare Charakterisierung zellulärer Subgruppen in der Schwanzknospe der Maus. [Internet] [Thesis]. Freie Universität Berlin; 2015. [cited 2021 Mar 03]. Available from: http://dx.doi.org/10.17169/refubium-4749.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nandy C. Molekulare Charakterisierung zellulärer Subgruppen in der Schwanzknospe der Maus. [Thesis]. Freie Universität Berlin; 2015. Available from: http://dx.doi.org/10.17169/refubium-4749

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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