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Altering Oligomerization Of Epha2 Via Mutations In The Intracellular Domain, Ryan W. Lingerak 2018 The University of Akron

Altering Oligomerization Of Epha2 Via Mutations In The Intracellular Domain, Ryan W. Lingerak

Honors Research Projects

Eph receptor tyrosine kinases (RTKs) are activated by membrane-bound ligands called ephrins. Eph RTKs are divided into two subclasses, each activated by a specific classes of the ligand ephrin. The overexpression of Eph receptors is correlated to cancer cell metastasis in several different types of cancers. Studies with the EphA2 extracellular domain (ECD) and ephrinA1 ligand have shown that upon binding of ephrin to the receptor, EphA2 undergoes increased oligomerization and activation. This indicates that oligomerization is intimately connected to kinase activity. High resolution crystal structures of the EphA2 ECD have revealed some details of these ligand bound oligomers, as ...


Tea Induction Of Cyp6a8 Promoter In Drosophila Melanogaster, Fiona Retzer 2017 University of Tennessee, Knoxville

Tea Induction Of Cyp6a8 Promoter In Drosophila Melanogaster, Fiona Retzer

University of Tennessee Honors Thesis Projects

No abstract provided.


Validation Of A Hairy Roots System To Study Soybean-Soybean Aphid Interactions, Stephanie C. Morriss, Matthew E. Studham, Gregory L. Tylka, Gustavo C. Macintosh 2017 Iowa State University

Validation Of A Hairy Roots System To Study Soybean-Soybean Aphid Interactions, Stephanie C. Morriss, Matthew E. Studham, Gregory L. Tylka, Gustavo C. Macintosh

Gregory Tylka

The soybean aphid (Aphis glycines) is one of the main insect pests of soybean (Glycine max) worldwide. Genomics approaches have provided important data on transcriptome changes, both in the insect and in the plant, in response to the plant-aphid interaction. However, the difficulties to transform soybean and to rear soybean aphid on artificial media have hindered our ability to systematically test the function of genes identified by those analyses as mediators of plant resistance to the insect. An efficient approach to produce transgenic soybean material is the production of transformed hairy roots using Agrobacterium rhizogenes; however, soybean aphids colonize leaves ...


Protein Loop Dynamics Are Complex And Depend On The Motions Of The Whole Protein, Michael T. Zimmermann, Robert L. Jernigan 2017 Iowa State University

Protein Loop Dynamics Are Complex And Depend On The Motions Of The Whole Protein, Michael T. Zimmermann, Robert L. Jernigan

Robert Jernigan

We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular ...


Factors Correlating With Significant Differences Between X-Ray Structures Of Myoglobin, Alexander A. Rashin, Marcin J. Domagalski, Michael T. Zimmermann, Wladek Minor, Maksymilian Chruszcz, Robert L. Jernigan 2017 BioChemComp Inc

Factors Correlating With Significant Differences Between X-Ray Structures Of Myoglobin, Alexander A. Rashin, Marcin J. Domagalski, Michael T. Zimmermann, Wladek Minor, Maksymilian Chruszcz, Robert L. Jernigan

Robert Jernigan

Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are ...


Protein Flexibility: Coordinate Uncertainties And Interpretation Of Structural Differences, Alexander A. Rashin, Abraham H. L. Rashin, Robert L. Jernigan 2017 BioChemComp Inc

Protein Flexibility: Coordinate Uncertainties And Interpretation Of Structural Differences, Alexander A. Rashin, Abraham H. L. Rashin, Robert L. Jernigan

Robert Jernigan

Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent `noise', showing that some previous interpretations of protein coordinate changes attributed to external ...


Jennifer Maurer Phd Thesis.Pdf, Jennifer Maurer 2017 University of Massachusetts Medical School

Jennifer Maurer Phd Thesis.Pdf, Jennifer Maurer

Jennifer Maurer


Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation.Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and are ...


Biased Genetic Screen Identifies Novel Genes Involved In Antiviral Defense, Tianyun Long 2017 Louisiana State University and Agricultural and Mechanical College

Biased Genetic Screen Identifies Novel Genes Involved In Antiviral Defense, Tianyun Long

LSU Doctoral Dissertations

ABSTRACT

RNA interference (RNAi) mediates potent antiviral response across kingdoms. In Caenorhabditis elegans nematodes, antiviral RNAi requires a virus sensor that is conserved in mammals and is amplified by secondary small interfering RNAs that are produced in a Dicer-independent manner.

To better understand worm antiviral RNAi, I carried out a biased genetic screen, aiming to identify novel antiviral RNAi genes. To speed up the gene discovery process, the reporter worms used for this genetic screen were engineered to contain extra copies of 4 known antiviral RNAi genes. Therefore, genetic alleles derived from these 4 genes will be automatically rejected during ...


Spatial Mapping And Profiling Of Metabolite Distributions During Germination, Robbyn Anand, Adam D. Feenstra, Liza E. Alexander, Zhihong Song, Andrew R. Korte, Marna Yandeaue-Nelson, Basil J. Nikolau, Young-Jin Lee 2017 Iowa State University

Spatial Mapping And Profiling Of Metabolite Distributions During Germination, Robbyn Anand, Adam D. Feenstra, Liza E. Alexander, Zhihong Song, Andrew R. Korte, Marna Yandeaue-Nelson, Basil J. Nikolau, Young-Jin Lee

Chemistry Publications

Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this paper, we utilize a combination of GC-MS, LC-fluorescence, and mass spectrometry imaging (MSI) approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize seeds, B73 and Mo17. GC and LC analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by GC-MS analysis of polar metabolites also ...


An Organismal Model For Gene Regulatory Networks In The Gut-Associated Immune Response, Katherine M. Buckley, J P. Rast 2017 George Washington University

An Organismal Model For Gene Regulatory Networks In The Gut-Associated Immune Response, Katherine M. Buckley, J P. Rast

Biochemistry and Molecular Medicine Faculty Publications

The gut epithelium is an ancient site of complex communication between the animal immune system and the microbial world. While elements of self-non-self receptors and effector mechanisms differ greatly among animal phyla, some aspects of recognition, regulation, and response are broadly conserved. A gene regulatory network (GRN) approach provides a means to investigate the nature of this conservation and divergence even as more peripheral functional details remain incompletely understood. The sea urchin embryo is an unparalleled experimental model for detangling the GRNs that govern embryonic development. By applying this theoretical framework to the free swimming, feeding larval stage of the ...


Functional Analysis Of Drosophila Integrator Complex In Snrna 3' End Processing, Jiandong Chen 2017 The University of Texas Graduate School of Biomedical Sciences at Houston

Functional Analysis Of Drosophila Integrator Complex In Snrna 3' End Processing, Jiandong Chen

Jiandong Chen

Uridine-rich small nuclear RNAs (U snRNAs) play essential roles in eukaryotic gene expression by facilitating the removal of introns from mRNA precursors and the processing of the replication-dependent histone pre-mRNAs. Formation of the 3’ end of these snRNAs is carried out by a poorly characterized, twelve-membered protein complex named Integrator Complex.

In the effort to understand Integrator Complex function in the formation of the snRNA 3’ end, we performed a functional RNAi screen in Drosophila S2 cells to identify protein factors required for snRNA 3’ end formation. This screen was conducted by using a fluorescence-based reporter that elicits GFP expression ...


Functional Characteristics And Genomic Sequencing Of Antarctic Environmental Isolates, Amanda Kemper, Christina Aigner, Michelle Tigges, Sara Anderson 2017 Minnesota State University Moorhead

Functional Characteristics And Genomic Sequencing Of Antarctic Environmental Isolates, Amanda Kemper, Christina Aigner, Michelle Tigges, Sara Anderson

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Human Rickettsial Pathogen Modulates Arthropod Organic Anion Transporting Polypeptide And Tryptophan Pathway For Its Survival In Ticks, Vikas Taank, Shovan Dutta, Amrita Dasgupta, Durland Fish, John F. Anderson, Hameeda Sultana, Girish Neelakanta 2017 Old Dominion University

Human Rickettsial Pathogen Modulates Arthropod Organic Anion Transporting Polypeptide And Tryptophan Pathway For Its Survival In Ticks, Vikas Taank, Shovan Dutta, Amrita Dasgupta, Durland Fish, John F. Anderson, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

The black-legged tick Ixodes scapularis transmits the human anaplasmosis agent, Anaplasma phagocytophilum. In this study, we show that A. phagocytophilum specifically up-regulates I. scapularis organic anion transporting polypeptide, isoatp4056 and kynurenine amino transferase (kat), a gene involved in the production of tryptophan metabolite xanthurenic acid (XA), for its survival in ticks. RNAi analysis revealed that knockdown of isoatp4056 expression had no effect on A. phagocytophilum acquisition from the murine host but affected the bacterial survival in tick cells. Knockdown of the expression of kat mRNA alone or in combination with isoatp4056 mRNA significantly affected A. phagocytophilum survival and isoatp4056 expression ...


Explore Variable Potential Ion Guide For Mass Spectrometry, Curtiss D. Hanson 2017 University of Northern Iowa

Explore Variable Potential Ion Guide For Mass Spectrometry, Curtiss D. Hanson

Curtiss D. Hanson

A variable potential ion guide for placement within the reflectron of a time-of-flight mass spectrometer includes an elongate resistive electrode placed axially within the reflectron. The electrode may be a non-conductive monofilament coated with a resistive polymer coating, with one end of the electrode coupled to a high potential source, the electrode carrying a potential gradient along its length.


Ion Trap Mass Analyzer Apparatus, Methods, And Systems Utilizing One Or More Multiple Potential Ion Guide (Mpig) Electrodes, Curtiss Dwight Hanson 2017 University of Northern Iowa

Ion Trap Mass Analyzer Apparatus, Methods, And Systems Utilizing One Or More Multiple Potential Ion Guide (Mpig) Electrodes, Curtiss Dwight Hanson

Curtiss D. Hanson

In one aspect of the invention, an ion trap mass analyzer includes a variable- or multi-potential type ion guide (MPIG) assembly which has been pre-configured to produce a parabolic-type potential field. Each MPIG electrode has a resistive coating of designed characteristics. In one example the coating varies in thickness along the length of an underlying uniform substrate. The MPIG assembly can be a single MPIG electrode or an array of a plurality of MPIG electrodes. An array can facilitate delocalization for improved performance. This chemical modification of a uniform underlying substrate promotes cheaper and flexible instruments. The modified MPIG electrodes ...


Multi-Pass Reflectron Time-Of-Flight Mass Spectrometer, Curtiss D. Hanson 2017 University of Northern Iowa

Multi-Pass Reflectron Time-Of-Flight Mass Spectrometer, Curtiss D. Hanson

Curtiss D. Hanson

A novel design for a time-of-flight mass spectrometer capable of tandem mass spectrometry measurements with high resolution and high sensitivity using two variable reflectrons in a co-linear geometry. Variably switched reflectrons are oriented coaxially on opposing ends of the ion flight region allowing multiple passes of the ions along the flight region permitting high resolution, tandem mass spectrometry experiments to be performed. An electrostatic particle guide is incorporated to ensure high ion transmission efficiency in a multi-pass system. In addition to permitting the high transmission efficiency of ions, the EPG can be used in a bipolar pulsed mode to isolate ...


C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl Eggers, Noelle L’Etoile, Laura Miller Conrad, Miri VanHoven 2017 San Jose State University

C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl Eggers, Noelle L’Etoile, Laura Miller Conrad, Miri Vanhoven

Faculty Publications, Chemistry

Predators and prey co-evolve, each maximizing their own fitness, but the effects of predator–prey interactions on cellular and molecular machinery are poorly understood. Here, we study this process using the predator Caenorhabditis elegans and the bacterial prey Streptomyces, which have evolved a powerful defense: the production of nematicides. We demonstrate that upon exposure to Streptomyces at their head or tail, nematodes display an escape response that is mediated by bacterially produced cues. Avoidance requires a predicted G-protein-coupled receptor, SRB-6, which is expressed in five types of amphid and phasmid chemosensory neurons. We establish that species of Streptomyces secrete dodecanoic ...


C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen T. O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Y. Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl K. Eggers, Noelle L’Etoile, Laura C. Miller Conrad, Miri VanHoven 2017 San Jose State University

C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen T. O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Y. Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl K. Eggers, Noelle L’Etoile, Laura C. Miller Conrad, Miri Vanhoven

Miri VanHoven

Predators and prey co-evolve, each maximizing their own fitness, but the effects of predator–prey interactions on cellular and molecular machinery are poorly understood. Here, we study this process using the predator Caenorhabditis elegans and the bacterial prey Streptomyces, which have evolved a powerful defense: the production of nematicides. We demonstrate that upon exposure to Streptomyces at their head or tail, nematodes display an escape response that is mediated by bacterially produced cues. Avoidance requires a predicted G-protein-coupled receptor, SRB-6, which is expressed in five types of amphid and phasmid chemosensory neurons. We establish that species of Streptomyces secrete dodecanoic ...


C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen T. O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Y. Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl K. Eggers, Noelle L’Etoile, Laura C. Miller Conrad, Miri VanHoven 2017 San Jose State University

C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen T. O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Y. Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl K. Eggers, Noelle L’Etoile, Laura C. Miller Conrad, Miri Vanhoven

Daryl K. Eggers

Predators and prey co-evolve, each maximizing their own fitness, but the effects of predator–prey interactions on cellular and molecular machinery are poorly understood. Here, we study this process using the predator Caenorhabditis elegans and the bacterial prey Streptomyces, which have evolved a powerful defense: the production of nematicides. We demonstrate that upon exposure to Streptomyces at their head or tail, nematodes display an escape response that is mediated by bacterially produced cues. Avoidance requires a predicted G-protein-coupled receptor, SRB-6, which is expressed in five types of amphid and phasmid chemosensory neurons. We establish that species of Streptomyces secrete dodecanoic ...


The N-Terminus Of Ift46 Mediates Intraflagellar Transport Of Outer Arm Dynein And Its Cargo-Adaptor Oda16, Yuqing Hou, George B. Witman 2017 University of Massachusetts Medical School

The N-Terminus Of Ift46 Mediates Intraflagellar Transport Of Outer Arm Dynein And Its Cargo-Adaptor Oda16, Yuqing Hou, George B. Witman

Radiology Publications and Presentations

Cilia are assembled via intraflagellar transport (IFT). The IFT machinery is composed of motors and multi-subunit particles, termed IFT-A and IFT-B, that carry cargo into the cilium. Knowledge of how the IFT subunits interact with their cargo is of critical importance for understanding how the unique ciliary domain is established. We previously reported a Chlamydomonas mutant, ift46-1, that fails to express the IFT-B protein IFT46, has greatly reduced levels of other IFT-B proteins, and assembles only very short flagella. A spontaneous suppression of ift46-1 restored IFT-B levels and enabled growth of longer flagella, but the flagella lacked outer dynein arms ...


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