The Experts below are selected from a list of 10683 Experts worldwide ranked by ideXlab platform
Kuruvilla, Heather G. - One of the best experts on this subject based on the ideXlab platform.
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Differential Regulation of Drosha and Dicer Homologues by Stress in Tetrahymena thermophila
DigitalCommons@Cedarville, 2021Co-Authors: Carr Tevia, Ward Anna, Gannon Kyle, Powell Jennifer, Rose David, Silveira Nicholas, Vonlehmden Georgia, Wachter Emily, Kuruvilla, Heather G.Abstract:Tetrahymena thermophila are free-living ciliated protozoans that possess two nuclei; a diploid micronucleus used only for mating, and a polyploid macronucleus which governs gene regulation and cellular homeostasis. When environmental conditions are favorable, the micronucleus exists as heterochromatin and the macronucleus is active. However, when conditions are unfavorable, Tetrahymena will attempt to conjugate with another mating type of the same species, in order to obtain new genetic information. During conjugation, the old macronucleus breaks down and a new polyploid macronucleus is regenerated. Macronuclear breakdown in Tetrahymena is governed by small RNAs, similar to miRNAs in multicellular eukaryotes. Our previous research, using the Tetrahymena Genome Database, along with the findings of other scientists, indicates that Tetrahymena possess a number of enzymes homologous to the miRNA processing enzymes, Drosha and Dicer. In our current study, we immunolocalized these enzymes in the presence and absence of cellular stress. Our immunofluorescence data indicate that Dicer-like proteins were expressed at a higher level in stressed cells than in our control cells, while Drosha-like proteins remained at the same level in both cell types
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Immunolocalization of Kinetodesmal Fibers with an Anti-Laminin Antibody in Tetrahymena thermophila
DigitalCommons@Cedarville, 2021Co-Authors: Kuruvilla, Heather G., Ward Anna, Vinczi StephenAbstract:Netrin, a protein in the laminin family, is a pleiotropic signal that guides axonal development as well as angiogenesis in animals. Axonal guidance via netrins is dependent upon the ability of netrin to act both as a chemorepellent and a chemoattractant, depending upon the cell type and the netrin concentration. Tetrahymena thermophila are unicellular eukaryotic protists that can sometimes be used as a model system for neurons, due to the fact that both are excitable cells. Our previous studies have shown that netrin-1-peptide, netrin-3-peptides, and netrin-4 are all chemorepellents in Tetrahymena, and that netrin-like proteins may be isolated from Tetrahymena by Western blotting. Because netrins are part of the laminin family, we used immunofluorescence to investigate whether an anti-laminin antibody would bind to proteins in Tetrahymena. We hypothesized that an anti-laminin antibody should colocalize with an anti-netrin-1 antibody. Instead, we found that our anti-laminin antibody preferentially stained kinetodesmal fibers on the cell membrane, suggesting a structural role for a laminin-like protein in Tetrahymena
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Immunolocalization of a Drosha-Like Protein in Tetrahymena thermophila
DigitalCommons@Cedarville, 2021Co-Authors: Cox Emily, Weidensee, Joanna M., Gibson, Joanna L., Kuruvilla, Heather G.Abstract:Drosha is an enzyme used by animals to process pri-miRNA into pre-miRNA. This processing normally occurs in the nucleus. The partly processed RNA molecule is then exported to the cytosol, where it is fully processed and then used in gene regulation. While much is known about this process in animals, less is known about how unicellular organisms process miRNA. We wanted to compare miRNA processing in the unicellular eukaryote, Tetrahymena thermophila with miRNA processing in the animal kingdom. In our past studies, we have successfully purified miRNA from Tetrahymena thermophila. Our searches of the Tetrahymena Genome Database indicated the presence of multiple genes with very high levels of homology to the miRNA processing enzymes Drosha and Dicer. Because of these data, we postulated that an anti-Drosha antibody would bind to a number of proteins in Tetrahymena. We hypothesized that a Drosha-like protein would immunolocalize to the nucleus of Tetrahymena, as seen in animal systems
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Immunolocalization of a PIGR-like Protein in Tetrahymena thermophila
DigitalCommons@Cedarville, 2021Co-Authors: Fitts, Emily G., Herrera, Fabio M., Vonlehmden Georgia, Kuruvilla, Heather G.Abstract:Netrins are pleiotropic signaling molecules which guide axonal development and help regulate processes such as angiogenesis. Netrins can act as chemorepellents for developing axons, and our previous work has shown that several netrins, including netrin-1, netrin-3, and netrin-4, are chemorepellents in Tetrahymena thermophila. In vertebrates, netrin-1 signals through several receptors, including those in the UNC-5 family. UNC-5 family proteins often signal through the src family of tyrosine kinases. We have previously characterized UNC-5 and src-like proteins in Tetrahymena, by immunolocalization and Western blotting. Sequencing of our src-like proteins gave a number of homologous sequences, including the sequence for polymeric immunoglobulin-like receptor (PIGR). With all of these findings in mind, we hypothesized that Tetrahymena might possess a receptor similar to PIGR, which would localize either to the plasma membrane or cilia of Tetrahymena
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Biochemical Evidence for Netrin-Signaling Homologues in Tetrahymena thermophila
DigitalCommons@Cedarville, 2020Co-Authors: Herrera, Fabio M., Cornelius, Shelby E., Fitts, Emily G., Koenig, Andrew T., Pompo, Kimberly J., Weidensee, Joanna M., Weinhold, Jamie L., Kuruvilla, Heather G.Abstract:Netrins are pleiotropic guidance proteins that are involved in developmental signaling of branched structures within vertebrates. However, like many developmental pathways, dysregulation of the netrin pathway has been implicated in cancer progression and metastasis. Since Tetrahymena respond to guidance proteins, showing chemoattractant and chemorepellent behavior, we hypothesized that we could use these organisms as a model system for cancer signaling. We have previously found that netrin-1-peptided, netrin-3-peptide, and recombinant netrin-4 are all chemorepellents in this organism. Since netrin-1-peptide signals through a tyrosine kinase in Tetrahymena, we hypothesized that Tetrahymena might possess tyrosine kinases as well as a receptor homologous to UNC-5, a netrin receptor which relays signals via tyrosine kinases in vertebrates. Using immunoprecipitation with a polyclonal anti-UNC-5-B antibody, we purified a 250 kD protein from Tetrahymena whole cell extract. Similarly, we immunoprecipitated several proteins, including a 60 kD protein and a 75 kD protein using a polyclonal anti-src-antibody. Our purified samples were sent out for identification by mass spectroscopy. Mass spectroscopy indicated that we have purified a number of novel peptides not currently found in the Tetrahymena Genome Database. Our data indicate that the proteome database in this organism is incomplete, and that there are additional proteins waiting to be discovered in this organism
Jeffrey S Fillingham - One of the best experts on this subject based on the ideXlab platform.
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nucleus specific linker histones hho1 and mlh1 form distinct protein interactions during growth starvation and development in Tetrahymena thermophila
Scientific Reports, 2020Co-Authors: Syed Nabeelshah, Kanwal Ashraf, Alejandro Saettone, Jyoti Garg, Joanna Derynck, Jeanphilippe Lambert, Ronald E Pearlman, Jeffrey S FillinghamAbstract:Chromatin organization influences most aspects of gene expression regulation. The linker histone H1, along with the core histones, is a key component of eukaryotic chromatin. Despite its critical roles in chromatin structure and function and gene regulation, studies regarding the H1 protein-protein interaction networks, particularly outside of Opisthokonts, are limited. The nuclear dimorphic ciliate protozoan Tetrahymena thermophila encodes two distinct nucleus-specific linker histones, macronuclear Hho1 and micronuclear Mlh1. We used a comparative proteomics approach to identify the Hho1 and Mlh1 protein-protein interaction networks in Tetrahymena during growth, starvation, and sexual development. Affinity purification followed by mass spectrometry analysis of the Hho1 and Mlh1 proteins revealed a non-overlapping set of co-purifying proteins suggesting that Tetrahymena nucleus-specific linker histones are subject to distinct regulatory pathways. Furthermore, we found that linker histones interact with distinct proteins under the different stages of the Tetrahymena life cycle. Hho1 and Mlh1 co-purified with several Tetrahymena-specific as well as conserved interacting partners involved in chromatin structure and function and other important cellular pathways. Our results suggest that nucleus-specific linker histones might be subject to nucleus-specific regulatory pathways and are dynamically regulated under different stages of the Tetrahymena life cycle.
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gene network landscape of the ciliate Tetrahymena thermophila
PLOS ONE, 2011Co-Authors: Jie Xiong, Jyoti Garg, Ronald E Pearlman, Jeffrey S Fillingham, Dongxia Yuan, Xingyi Lu, Yue Chang, Chengjie Fu, Wei MiaoAbstract:Background: Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Methodology/Principal Findings: Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. Conclusions/Significance: This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
Syed Nabeelshah - One of the best experts on this subject based on the ideXlab platform.
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nucleus specific linker histones hho1 and mlh1 form distinct protein interactions during growth starvation and development in Tetrahymena thermophila
Scientific Reports, 2020Co-Authors: Syed Nabeelshah, Kanwal Ashraf, Alejandro Saettone, Jyoti Garg, Joanna Derynck, Jeanphilippe Lambert, Ronald E Pearlman, Jeffrey S FillinghamAbstract:Chromatin organization influences most aspects of gene expression regulation. The linker histone H1, along with the core histones, is a key component of eukaryotic chromatin. Despite its critical roles in chromatin structure and function and gene regulation, studies regarding the H1 protein-protein interaction networks, particularly outside of Opisthokonts, are limited. The nuclear dimorphic ciliate protozoan Tetrahymena thermophila encodes two distinct nucleus-specific linker histones, macronuclear Hho1 and micronuclear Mlh1. We used a comparative proteomics approach to identify the Hho1 and Mlh1 protein-protein interaction networks in Tetrahymena during growth, starvation, and sexual development. Affinity purification followed by mass spectrometry analysis of the Hho1 and Mlh1 proteins revealed a non-overlapping set of co-purifying proteins suggesting that Tetrahymena nucleus-specific linker histones are subject to distinct regulatory pathways. Furthermore, we found that linker histones interact with distinct proteins under the different stages of the Tetrahymena life cycle. Hho1 and Mlh1 co-purified with several Tetrahymena-specific as well as conserved interacting partners involved in chromatin structure and function and other important cellular pathways. Our results suggest that nucleus-specific linker histones might be subject to nucleus-specific regulatory pathways and are dynamically regulated under different stages of the Tetrahymena life cycle.
Wei Miao - One of the best experts on this subject based on the ideXlab platform.
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sequencing and characterization of the macronuclear rdna minichromosome of the protozoan Tetrahymena pyriformis
International Journal of Biological Macromolecules, 2020Co-Authors: Wei Miao, Guangying WangAbstract:Abstract Tetrahymena ribosomal DNA (rDNA) is an ideal system for studying eukaryotic DNA replication and gene transcription. In this study, we developed a new method to isolate rDNA from Tetrahymena cells and used it to sequence and annotate the complete 19,670 bp macronuclear rDNA minichromosome of Tetrahymena pyriformis, a species that lacks the germ-line micronucleus and is unable to undergo sexual reproduction. The key features of T. pyriformis and Tetrahymena thermophila rDNA sequences were then compared. Our results showed (i) the short inverted repeats (M repeats) essential for formation of rDNA minichromosome palindromic structure during sexual reproduction in Tetrahymena are highly conserved in T. pyriformis; (ii) in contrast to T. thermophila, which has two tandem domains that coordinately regulate rDNA replication, T. pyriformis has only a single domain; (iii) the 35S pre-rRNA precursor has 80.25% similarity between the two species; and (iv) the G + C content is higher in the transcribed region than the non-transcribed region in both species, but the GC-skew is more stable in T. pyriformis. The new isolation method and annotated information for the T. pyriformis rDNA minichromosome will provide a useful resource for studying DNA replication and chromosome copy number control in Tetrahymena.
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Tetrahymena comparative genomics database tcgd a community resource for Tetrahymena
Database, 2019Co-Authors: Wentao Yang, Wei Miao, Guangying Wang, Chuanqi Jiang, Ying Zhu, Kai Chen, Dongxia Yuan, Jie XiongAbstract:Ciliates are a large and diverse group of unicellular organisms characterized by having the following two distinct type of nuclei within a single cell: micronucleus (MIC) and macronucleus (MAC). Although the genomes of several ciliates in different groups have been sequenced, comparative genomics data for multiple species within a ciliate genus are not yet available. Here we collected the genome information and comparative genomics analysis results for 10 species in the Tetrahymena genus, including the previously sequenced model organism Tetrahymena thermophila and 9 newly sequenced species, and constructed a genus-level comparative analysis platform, the Tetrahymena Comparative Genomics Database (TCGD). Genome sequences, transcriptomic data, gene models, functional annotation, ortholog groups and synteny maps were built into this database and a user-friendly interface was developed for searching, visualizing and analyzing these data. In summary, the TCGD (http://ciliate.ihb.ac.cn) will be an important and useful resource for the ciliate research community.
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nonsense mediated mrna decay in Tetrahymena is ejc independent and requires a protozoa specific nuclease
Nucleic Acids Research, 2017Co-Authors: Wentao Yang, Miao Tian, Jing Zhang, Huai Dang, Wei MiaoAbstract:Nonsense-mediated mRNA decay (NMD) is essential for removing premature termination codon-containing transcripts from cells. Studying the NMD pathway in model organisms can help to elucidate the NMD mechanism in humans and improve our understanding of how this biologically important process has evolved. Ciliates are among the earliest branching eukaryotes; their NMD mechanism is poorly understood and may be primordial. We demonstrate that highly conserved Upf proteins (Upf1a, Upf2 and Upf3) are involved in the NMD pathway of the ciliate, Tetrahymena thermophila. We further show that a novel protozoa-specific nuclease, Smg6L, is responsible for destroying many NMD-targeted transcripts. Transcriptome-wide identification and characterization of NMD-targeted transcripts in vegetative Tetrahymena cells showed that many have exon-exon junctions downstream of the termination codon. However, Tetrahymena may lack a functional exon junction complex (EJC), and the Tetrahymena ortholog of an EJC core component, Mago nashi (Mag1), is dispensable for NMD. Therefore, NMD is EJC independent in this early branching eukaryote.
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gene network landscape of the ciliate Tetrahymena thermophila
PLOS ONE, 2011Co-Authors: Jie Xiong, Jyoti Garg, Ronald E Pearlman, Jeffrey S Fillingham, Dongxia Yuan, Xingyi Lu, Yue Chang, Chengjie Fu, Wei MiaoAbstract:Background: Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Methodology/Principal Findings: Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. Conclusions/Significance: This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
Michael J Cherry - One of the best experts on this subject based on the ideXlab platform.
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Tetrahymena genome database tgd a new genomic resource for Tetrahymena thermophila research
Nucleic Acids Research, 2006Co-Authors: Nicholas A Stover, Cynthia J Krieger, Gail Binkley, Qing Dong, Dianna G Fisk, Robert S Nash, Anand Sethuraman, Shuai Weng, Michael J CherryAbstract:We have developed a web-based resource (available at www.ciliate.org) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the Saccharomyces Genome Database, the Tetrahymena Genome Database (TGD) integrates the wealth of knowledge generated by the Tetrahymena research community about genome structure, genes and gene products with the newly sequenced macronuclear genome determined by The Institute for Genomic Research (TIGR). TGD provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus in our graphical genome browser, gene product annotations utilizing the Gene Ontology, links to published literature about the gene and more. TGD also displays automatic annotations generated for the gene models predicted by TIGR. A variety of tools are available at TGD for searching the Tetrahymena genome, its literature and information about members of the research community.
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Tetrahymena genome database tgd a new genomic resource for Tetrahymena thermophila research
Nucleic Acids Research, 2006Co-Authors: Nicholas A Stover, Cynthia J Krieger, Gail Binkley, Qing Dong, Dianna G Fisk, Robert S Nash, Anand Sethuraman, Shuai Weng, Michael J CherryAbstract:We have developed a web-based resource (available at www.ciliate.org) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the Saccharomyces Genome Database, the Tetrahymena Genome Database (TGD) integrates the wealth of knowledge generated by the Tetrahymena research community about genome structure, genes and gene products with the newly sequenced macronuclear genome determined by The Institute for Genomic Research (TIGR). TGD provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus in our graphical genome browser, gene product annotations utilizing the Gene Ontology, links to published literature about the gene and more. TGD also displays automatic annotations generated for the gene models predicted by TIGR. A variety of tools are available at TGD for searching the Tetrahymena genome, its literature and information about members of the research community.
