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Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle 2017 University of Nebraska - Lincoln

Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle

UCARE Research Products

Possessing some of the largest and most complex genomes of any eukaryotic organelles, plant mitochondria are notorious for their rapidly rearranging genetic framework. In addition to containing a large and complex mitochondrial genome, the mitochondria of several plants in the genus Brassica have also been shown to contain an independent, self-replicating linear plasmid. Interestingly, the plasmid appears to be able to move independently between the cytoplasm and the mitochondria, and it can be paternally inherited, unlike the rest of the mitochondrial genome. The plasmid also has features similar to those of adenoviruses, including terminal inverted repeats and covalently bound proteins ...


The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin 2017 United States Department of Agriculture

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin

Andrew Severin

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and ...


Transcriptomic Responses To Environmental Temperature By Turtles With Temperature-Dependent And Genotypic Sex Determination Assessed By Rnaseq Inform The Genetic Architecture Of Embryonic Gonadal Development, Srihari Radhakrishnan, Robert A. Literman, Jennifer L. Neuwald, Andrew Severin, Nicole Valenzuela 2017 Iowa State University

Transcriptomic Responses To Environmental Temperature By Turtles With Temperature-Dependent And Genotypic Sex Determination Assessed By Rnaseq Inform The Genetic Architecture Of Embryonic Gonadal Development, Srihari Radhakrishnan, Robert A. Literman, Jennifer L. Neuwald, Andrew Severin, Nicole Valenzuela

Andrew Severin

Vertebrate sexual fate is decided primarily by the individual’s genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera—GSD), to test whether TSD’s and GSD’s transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle ...


Transcript Profiles In Longissimus Dorsi Muscle And Subcutaneous Adipose Tissue: A Comparison Of Pigs With Different Postweaning Growth Rates, C. M. Pilcher, C. K. Jones, M. Schroyen, A. J. Severin, J. F. Patience, C. K. Tuggle, J. E. Koltes 2017 Iowa State University

Transcript Profiles In Longissimus Dorsi Muscle And Subcutaneous Adipose Tissue: A Comparison Of Pigs With Different Postweaning Growth Rates, C. M. Pilcher, C. K. Jones, M. Schroyen, A. J. Severin, J. F. Patience, C. K. Tuggle, J. E. Koltes

Andrew Severin

Although most pigs recover rapidly from stresses associated with the transition of weaning, a portion of the population lags behind their contemporaries in growth performance. The underlying biological and molecular mechanisms involved in postweaning differences in growth performance are poorly understood. The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs was reared in commercial conditions and weighed at birth, weaning, and 3 wk postweaning. Transition ADG (tADG) was calculated as the ADG for the ...


Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti 2017 Iowa State University

Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti

Andrew Severin

The Tec family kinase, Itk (interleukin-2 tyrosine kinase), undergoes an in cis autophosphorylation on Y180 within its Src homology 3 (SH3) domain. Autophosphorylation of the Itk SH3 domain by the Itk kinase domain is strictly dependent on the presence of the intervening Src homology 2 (SH2) domain. A direct docking interaction between the Itk kinase and SH2 domains brings the Itk SH3 domain into the active site where Y180 is then phosphorylated. We now identify the residues on the surface of the Itk SH2 domain responsible for substrate docking and show that this SH2 surface mediates autophosphorylation in the full-length ...


The 3-Hydroxyacyl-Acp Dehydratase Component Of The Plant Mitochondrial Fatty Acid Synthase System, Xin Guan, Yozo Okazaki, Andrew Lithio, Ling Li, Xuefeng Zhao, Huanan Jin, Dan Nettleton, Kazuki Saito, Basil J. Nikolau 2017 Iowa State University

The 3-Hydroxyacyl-Acp Dehydratase Component Of The Plant Mitochondrial Fatty Acid Synthase System, Xin Guan, Yozo Okazaki, Andrew Lithio, Ling Li, Xuefeng Zhao, Huanan Jin, Dan Nettleton, Kazuki Saito, Basil J. Nikolau

Ling Li

We report the characterization of the Arabidopsis 3-hydroxyacyl-acyl carrier protein (ACP) dehydratase (mtHD) component of the mitochondrial fatty acid synthase (mtFAS) system, encoded by AT5G60335. The mitochondrial localization and catalytic capability of mtHD were demonstrated with a green fluorescent protein (GFP) transgenesis experiment, and by in vivo complementation and in vitro enzymatic assays. RNAi knockdown lines with reduced mtHD expression exhibit traits typically associated with mtFAS mutants, namely a miniaturized morphological appearance, reduced lipoylation of lipoylated proteins, and altered metabolomes consistent with the reduced catalytic activity of lipoylated enzymes. These alterations are reversed when mthd-rnai mutant plants are grown in ...


Reverse-Genetic Analysis Of The Two Biotin-Containing Subunit Genes Of The Heteromeric Acetyl-Coenzyme A Carboxylase In Arabidopsis Indicates A Unidirectional Functional Redundancy, Xu Li, Hilal Ilarslan, Libuse Brachova, Hui-Rong Qian, Ling Li, Ping Che, Eve Syrkin Wurtele, Basil J. Nikolau 2017 Iowa State University

Reverse-Genetic Analysis Of The Two Biotin-Containing Subunit Genes Of The Heteromeric Acetyl-Coenzyme A Carboxylase In Arabidopsis Indicates A Unidirectional Functional Redundancy, Xu Li, Hilal Ilarslan, Libuse Brachova, Hui-Rong Qian, Ling Li, Ping Che, Eve Syrkin Wurtele, Basil J. Nikolau

Ling Li

The heteromeric acetyl-coenzyme A carboxylase catalyzes the first and committed reaction of de novo fatty acid biosynthesis in plastids. This enzyme is composed of four subunits: biotin carboxyl-carrier protein (BCCP), biotin carboxylase, α-carboxyltransferase, and β-carboxyltransferase. With the exception of BCCP, single-copy genes encode these subunits in Arabidopsis (Arabidopsis thaliana). Reverse-genetic approaches were used to individually investigate the physiological significance of the two paralogous BCCP-coding genes, CAC1A (At5g16390, codes for BCCP1) and CAC1B (At5g15530, codes for BCCP2). Transfer DNA insertional alleles that completely eliminate the accumulation of BCCP2 have no perceptible effect on plant growth, development, and fatty acid accumulation. In ...


Materials And Method For Modifying A Biochemical Component In A Plant, Ling Li, Eve Syrkin Wurtele 2017 Iowa State University

Materials And Method For Modifying A Biochemical Component In A Plant, Ling Li, Eve Syrkin Wurtele

Ling Li

A method of modifying the amount of at least one biochemical component in a plant comprising expressing Qua-Quine Starch (QQS) in the plant, the wild-type of which does not express QQS; a transgenic plant, or part thereof, which comprises and expresses QQS as a transgene and in which the amount of at least one biochemical component is modified; a tissue culture of regenerable cells of the transgenic plant; a vector comprising a nucleotide sequence, which encodes the coding sequence of QQS, operably linked to a non-native promoter, which promotes expression of the nucleotide sequence in a plant, which is other ...


Genome Wide Co-Expression Among The Starch Debranching Enzyme Genes Atisa1, Atisa2, And Atisa3 In Arabidopsis Thaliana, Ling Li, Hilal Ilarslan, Martha G. James, Alan M. Myers, Eve Syrkin Wurtele 2017 Iowa State University

Genome Wide Co-Expression Among The Starch Debranching Enzyme Genes Atisa1, Atisa2, And Atisa3 In Arabidopsis Thaliana, Ling Li, Hilal Ilarslan, Martha G. James, Alan M. Myers, Eve Syrkin Wurtele

Ling Li

Each of four starch debranching enzymes (DBE) is distinct and highly conserved across the plant kingdom; however, the specific functions of these proteins in carbohydrate metabolism are not well understood. DBEs function in both biosynthesis and degradation of starch, and two have been shown to function as multimers in various quarternary structures that can contain one or more DBE proteins, i.e. ISA1 homomultimers and ISA1/ISA2 heteromultimers. This study characterizes potential functional relationships between the three isoamylase-type DBE proteins (ISA) of Arabidopsis using a comprehensive bioinformatics analysis and promoter fusion approach to determine tissue-, subcellular-, and temporal specificity of ...


Comparative Transcriptome Reconstruction Of Four Hypericum Species Focused On Hypericin Biosynthesis, Miroslav Sotak, Odeta Czerankova, Daniel Klein, Zuzana Jurcackova, Ling Li, Eva Cellarova 2017 Pavol Jozef Safarik University in Kosice

Comparative Transcriptome Reconstruction Of Four Hypericum Species Focused On Hypericin Biosynthesis, Miroslav Sotak, Odeta Czerankova, Daniel Klein, Zuzana Jurcackova, Ling Li, Eva Cellarova

Ling Li

Next generation sequencing technology rapidly developed research applications in the field of plant functional genomics. Several Hypericum spp. with an aim to generate and enhance gene annotations especially for genes coding the enzymes supposedly included in biosynthesis of valuable bioactive compounds were analyzed. The first de novo transcriptome profiling of Hypericum annulatum Moris, H. tomentosum L., H. kalmianum L., and H. androsaemum L. leaves cultivated in vitro was accomplished. All four species with only limited genomic information were selected on the basis of differences in ability to synthesize hypericins and presence of dark nodules accumulating these metabolites with purpose to ...


A Screen For Arabidopsis Thalianamutants With Altered Susceptibility To Heterodera Schachtii, T. J. Baum, M. J. E. Wubben II, K. A. Hardy, H. Su, S. R. Rodermel 2017 Iowa State University

A Screen For Arabidopsis Thalianamutants With Altered Susceptibility To Heterodera Schachtii, T. J. Baum, M. J. E. Wubben Ii, K. A. Hardy, H. Su, S. R. Rodermel

Thomas Baum

Genetic approaches are a powerful means to elucidate plant-pathogen interactions. An in vitro screening protocol was developed to identify Arabidopsis thaliana mutants with altered susceptibility to Heterodera schachtii, the sugar beet cyst nematode. In an initial screen of approximately 5,200 ethyl methanesulfonate-generated mutant plants, two stable mutations were identified. Both mutant lines were backcrossed and were found to harbor single recessive mutant alleles. Mutant line 2-4-6 shows an approximately two-fold increase in sedentary and developing nematodes, while mutant line 10-5-2 exhibits a significant decrease in susceptibility that manifests itself only after nematodes become sedentary. Analyses of progeny from crosses ...


Isolation Of Beta-1,4-Endoglucanase Genes From Globodera Tabacumand Their Expression During Parasitism, M. Goellner, G. Smant, J. M. De Boer, T. J. Baum, E. L. Davis 2017 North Carolina State University

Isolation Of Beta-1,4-Endoglucanase Genes From Globodera Tabacumand Their Expression During Parasitism, M. Goellner, G. Smant, J. M. De Boer, T. J. Baum, E. L. Davis

Thomas Baum

Two beta-1,4-endoglucanase (EGase) cDNAs were isolated from Globodera tabacum, the tobacco cyst nematode, and have been designated as GT-eng-1 and GT-eng-2. GT-eng-1 and GT-eng-2 encode precursor proteins with a predicted secretion signal sequence, cellulolytic catalytic domain, and a linker domain. The protein product GT-ENG-1 contains an additional 95 amino acid carboxy terminal sequence with strong similarity to type II cellulose binding domains. Riboprobes and polyclonal antibodies raised to recombinant cyst nematode EGases were used to follow expression patterns of EGase transcripts and proteins throughout the nematode life cycle. EGase transcripts and proteins were specifically detected within the subventral esophageal ...


Cloning Of A Putative Pectate Lyase Gene Expressed In The Subventral Esophageal Glands Of Heterodera Glycines, J. M. de Boer, J. P. McDermott, E. L. Davis, R. S. Hussey, H. Popeijus, G. Smant, T. J. Baum 2017 Iowa State University

Cloning Of A Putative Pectate Lyase Gene Expressed In The Subventral Esophageal Glands Of Heterodera Glycines, J. M. De Boer, J. P. Mcdermott, E. L. Davis, R. S. Hussey, H. Popeijus, G. Smant, T. J. Baum

Thomas Baum

We report the cloning of a Heterodera glycines cDNA that has 72% identity at the amino acid level to a pectate lyase from Globodera rostochiensis. In situ hybridizations showed that the corresponding gene (Hg-pel-1) is expressed in the subventral esophageal gland cells of second-stage juveniles. The deduced amino acid sequence of the H. glycines cDNA shows homology to class III pectate lyases of bacterial and fungal origin.


Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt 2017 University of Texas at Tyler

Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt

Biology Theses

The recent development of DNA-based species classification methods has led to the revision of many morphology-based species designations as genetic data has provided new information for species delineation. Analysis of standardized DNA ‘barcoding’ gene regions has proven particularly effective in resolving the taxonomic status of taxa that display phenotypic and habitat overlap.

Freshwater Unionid and Margaritiferid mussels comprise one of the most diverse aquatic taxa in North America, but are also among the most threatened, with over 70% of the approximately 300 native species considered at-risk or in decline. Although mussels face extensive threats from anthropogenic activity, conservation efforts have ...


Access To Genetics Resources In Indonesia: Need Further Legislation?, Emmy Latifa 2017 University of Oklahoma College of Law

Access To Genetics Resources In Indonesia: Need Further Legislation?, Emmy Latifa

Oklahoma Journal of Law and Technology

No abstract provided.


The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin, Darrell O. Bayles, Daniel J. Nasko, K. Eric Wommack, Adina Howe, Heather K. Allen 2017 United States Department of Agriculture

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin, Darrell O. Bayles, Daniel J. Nasko, K. Eric Wommack, Adina Howe, Heather K. Allen

Agricultural and Biosystems Engineering Publications

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the ...


Tumor Formation In Response To Loss Of Chromatin Remodeler Chd5 In Zebrafish, Taylor R. Sabato, Erin L. Sorlien, Dr. Joseph P. Ogas 2017 Purdue University

Tumor Formation In Response To Loss Of Chromatin Remodeler Chd5 In Zebrafish, Taylor R. Sabato, Erin L. Sorlien, Dr. Joseph P. Ogas

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chromodomain helicase DNA binding protein 5 (CHD5) has been identified as a tumor suppressor in humans. Deletion or mutation of CHD5 has been observed in numerous cancers, including neuroblastoma and melanoma. We hypothesize that chd5 is also a tumor suppressor in zebrafish, a powerful model system to study tumorigenesis. Many genes involved in tumorigenesis are conserved in zebrafish, and they develop fully penetrant tumor phenotypes. We have created chd5 knock-out zebrafish using CRISPR/Cas9 and are monitoring them for tumor development. In addition to the chd5 knock-outs, we are undertaking a double-mutant approach by coupling loss of ...


Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran 2017 Purdue University

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being ...


Production Of A Gonadotropin-Releasing Hormone 2 Receptor Knockdown (Gnrhr2 Kd) Swine Line., Amy T. Desaulniers, Rebecca Cederberg, Ginger A. Mills, Clay A. Lents, Brett R. White 2017 University of Nebraska-Lincoln

Production Of A Gonadotropin-Releasing Hormone 2 Receptor Knockdown (Gnrhr2 Kd) Swine Line., Amy T. Desaulniers, Rebecca Cederberg, Ginger A. Mills, Clay A. Lents, Brett R. White

Faculty Papers and Publications in Animal Science

Swine are the only livestock species that produce both the second mammalian isoform of gonadotropin-releasing hormone (GNRH2) and its receptor (GNRHR2). Previously, we reported that GNRH2 and GNRHR2 mediate LH-independent testosterone secretion from porcine testes. To further explore this ligand-receptor complex, a pig model with reduced GNRHR2 expression was developed. Small hairpin RNA sequences targeting porcine GNRHR2 were subcloned into a lentiviral-based vector, lentiviral particles were generated and microinjected into the perivitelline space of zygotes, and embryos were transferred into a recipient. One GNRHR2 knockdown (KD) female was born that subsequently produced 80 piglets from 6 litters with 46 hemizygous ...


Molecular And Pathological Analyses Of Three New Mouse Mutations That Affect Ear Development And Function, Cong Tian 2017 University of Maine

Molecular And Pathological Analyses Of Three New Mouse Mutations That Affect Ear Development And Function, Cong Tian

Electronic Theses and Dissertations

This dissertation presents three new mouse models that help to study the functions of Enpp1, Atp6v1b1, and Tbx1 for ear development and function. asj (aging with stiffened joints) carries a missense mutation in the mouse Enpp1 gene. Enpp1 encodes the enzyme ENPP1 that regulate soft-tissue calcification and bone mineralization, and is associated with generalized arterial calcification of infancy and hypophosphatemic rickets in human patients. asj mutant mice show severe middle ear infection and tissue calcification, which provide a new mouse model to study otitis media and tympanoscleorosis. Atp6v1b1 encode a protein that is a subunit of the V-ATPase pump, which ...


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