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Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder 2019 Graz University of Technology

Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder

Joan Lin-Cereghino

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (PAOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing a green ...


Transcriptional And Chemical Changes In Soybean Leaves In Response To Long-Term Aphid Colonization, Jessica D. Hohenstein, Matthew Studham, Adam Klein, Nik Kovinich, Kia Barry, Young-Jin Lee, Gustavo C. Macintosh 2019 Iowa State University

Transcriptional And Chemical Changes In Soybean Leaves In Response To Long-Term Aphid Colonization, Jessica D. Hohenstein, Matthew Studham, Adam Klein, Nik Kovinich, Kia Barry, Young-Jin Lee, Gustavo C. Macintosh

Young-Jin Lee

Soybean aphids (Aphis glycines Matsumura) are specialized insects that feed on soybean (Glycine max) phloem sap. Transcriptome analyses have shown that resistant soybean plants mount a fast response that limits aphid feeding and population growth. Conversely, defense responses in susceptible plants are slower and it is hypothesized that aphids block effective defenses in the compatible interaction. Unlike other pests, aphids can colonize plants for long periods of time; yet the effect on the plant transcriptome after long-term aphid feeding has not been analyzed for any plant–aphid interaction. We analyzed the susceptible and resistant (Rag1) transcriptome response to aphid feeding ...


Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf 2019 Utah State University

Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf

Paul G. Wolf

PREMISE OF THE STUDY: In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.

METHODS AND RESULTS: We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.

CONCLUSIONS: Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of ...


An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald 2019 University of Massachusetts Medical School

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

David Grünwald

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. In addition, our method enables state estimation on multivariate Gaussian signals. We validate our approach using simulated data, and benchmark the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We ...


Inferring Processes Of Coevolutionary Diversification In A Community Of Panamanian Strangler Figs And Associated Pollinating Wasps, Jordan D. Satler, Edward Allen Herre, K. Charlotte Jandér, Deren A. R. Eaton, Carlos A. Machado, Tracy A. Heath, John D. Nason 2019 Iowa State University

Inferring Processes Of Coevolutionary Diversification In A Community Of Panamanian Strangler Figs And Associated Pollinating Wasps, Jordan D. Satler, Edward Allen Herre, K. Charlotte Jandér, Deren A. R. Eaton, Carlos A. Machado, Tracy A. Heath, John D. Nason

Tracy Heath

The fig and pollinator wasp obligate mutualism is diverse (~750 described species), ecologically important, and ancient (~80-90 Ma), providing model systems for generating and testing many questions in evolution and ecology. Once thought to be a prime example of strict one-to-one cospeciation, current thinking suggests that genera of pollinator wasps coevolve with corresponding subsections of figs, but the degree to which cospeciation or other processes contributes to the association at finer scales is unclear. Here we use genome-wide sequence data from a community of Panamanian strangler figs (Ficus subgenus Urostigma, section Americana) and associated fig wasp pollinators (Pegoscapus spp.) to ...


A Brief Review Of Non-Avian Reptile Environmental Dna (Edna), With A Case Study Of Painted Turtle (Chrysemys Picta) Edna Under Field Conditions, Clare I. M. Adams, Luke A. Hoekstra, Morgan R. Muell, Fredric J. Janzen 2019 University of Otago

A Brief Review Of Non-Avian Reptile Environmental Dna (Edna), With A Case Study Of Painted Turtle (Chrysemys Picta) Edna Under Field Conditions, Clare I. M. Adams, Luke A. Hoekstra, Morgan R. Muell, Fredric J. Janzen

Fredric Janzen

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 ...


Sequence Assembly, Xiaoqiu Huang 2019 Iowa State University

Sequence Assembly, Xiaoqiu Huang

Xiaoqiu Huang

We describe an efficient method for assembling short reads into long sequences. In this method, a hashing technique is used to compute overlaps between short reads, allowing base mismatches in the overlaps. Then an overlap graph is constructed, with each vertex representing a read and each edge representing an overlap. The overlap graph is explored by graph algorithms to find unique paths of reads representing contigs. The consensus sequence of each contig is constructed by computing alignments of multiple reads without gaps. This strategy has been implemented as a short read assembly program called PCAP.Solexa. We also describe how ...


Meta-Analysis Of Characteristics In Upper Missouri River Fishes: Prediction Of Invasiveness, Steph Purcell 2019 University of Nebraska at Omaha

Meta-Analysis Of Characteristics In Upper Missouri River Fishes: Prediction Of Invasiveness, Steph Purcell

Student Research and Creative Activity Fair

Invasive species are often considered a global threat due to their association with biodiversity loss and novel diseases. The Missouri-Mississippi River Watershed, including the Missouri River Basin, is particularly vulnerable to invasive species because of low species diversity following historic glaciation events. Management of invasive species is imperative in this watershed but continues to be challenging in that there are over 100 invasive species currently present in this region. The goal of this project is to identify characteristics associated with successful invasions that may assist in developing management strategies to reduce the negative outcomes caused by the establishment of invasive ...


Investigating Comt Influence On The Proactive-Reactive Stress Coping Axis In Zebrafish, Sean T. Bresnahan, Ryan Y. Wong 2019 University of Nebraska at Omaha

Investigating Comt Influence On The Proactive-Reactive Stress Coping Axis In Zebrafish, Sean T. Bresnahan, Ryan Y. Wong

Student Research and Creative Activity Fair

Individuals of the same species often display differences in correlated suites of behaviors which are made conspicuous when challenges – stressful, fear-inducing, etc. – are presented. In many species, a specific suite of behaviors (risk-aversion, aggression, exploration, learning, and memory) characterize an alternative set of stress coping styles (proactive and reactive). Such behaviors are regulated in the brain by specific neurotransmitters along with proteins that regulate them. One neurotransmitter regulator protein, catechol-O-methyltransferase (COMT) shows higher baseline whole-brain expression in proactive relative to reactive animals. However, it is not known whether its expression is a cause or a consequence of the stress coping ...


Are Providers Prepared For Genomic Medicine: Interpretation Of Direct-To- Consumer Genetic Testing (Dtc-Gt) Results And Genetic Self-Efficacy By Medical Professionals, Scott McGrath, Dhundy Raj Bastola 2019 University of Nebraska at Omaha

Are Providers Prepared For Genomic Medicine: Interpretation Of Direct-To- Consumer Genetic Testing (Dtc-Gt) Results And Genetic Self-Efficacy By Medical Professionals, Scott Mcgrath, Dhundy Raj Bastola

Student Research and Creative Activity Fair

Purpose:

Precision medicine is set to deliver a rich new data set of genomic information. However, the number of certified specialists in the United States is small, with only 4,244 genetic counselors and 1,302 clinical geneticists. We conducted a national survey of 264 medical professionals to evaluate how they interpret genetic test results, determine their confidence and self-efficacy of interpreting genetic test results with patients, and capture their opinions and experiences with direct-to- consumer genetic tests (DTC-GT).

Methods:

Participants were grouped into two categories, genetic specialists (genetic counselors and clinical geneticists) and medical providers (primary care, internists, physicians ...


How To Build A Human Brain: Evolution, Development, And Education, Aaron P. Blaisdell 2019 University of California, Los Angeles

How To Build A Human Brain: Evolution, Development, And Education, Aaron P. Blaisdell

Journal of Evolution and Health

No abstract provided.


Transcriptional And Chemical Changes In Soybean Leaves In Response To Long-Term Aphid Colonization, Jessica D. Hohenstein, Matthew Studham, Adam Klein, Nik Kovinich, Kia Barry, Young-Jin Lee, Gustavo C. Macintosh 2019 Iowa State University

Transcriptional And Chemical Changes In Soybean Leaves In Response To Long-Term Aphid Colonization, Jessica D. Hohenstein, Matthew Studham, Adam Klein, Nik Kovinich, Kia Barry, Young-Jin Lee, Gustavo C. Macintosh

Chemistry Publications

Soybean aphids (Aphis glycines Matsumura) are specialized insects that feed on soybean (Glycine max) phloem sap. Transcriptome analyses have shown that resistant soybean plants mount a fast response that limits aphid feeding and population growth. Conversely, defense responses in susceptible plants are slower and it is hypothesized that aphids block effective defenses in the compatible interaction. Unlike other pests, aphids can colonize plants for long periods of time; yet the effect on the plant transcriptome after long-term aphid feeding has not been analyzed for any plant–aphid interaction. We analyzed the susceptible and resistant (Rag1) transcriptome response to aphid feeding ...


A Brief Review Of Non-Avian Reptile Environmental Dna (Edna), With A Case Study Of Painted Turtle (Chrysemys Picta) Edna Under Field Conditions, Clare I. M. Adams, Luke A. Hoekstra, Morgan R. Muell, Fredric J. Janzen 2019 University of Otago

A Brief Review Of Non-Avian Reptile Environmental Dna (Edna), With A Case Study Of Painted Turtle (Chrysemys Picta) Edna Under Field Conditions, Clare I. M. Adams, Luke A. Hoekstra, Morgan R. Muell, Fredric J. Janzen

Ecology, Evolution and Organismal Biology Publications

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 ...


Synder: Inferring Genomic Orthologs From Synteny Maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele 2019 Iowa State University

Synder: Inferring Genomic Orthologs From Synteny Maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Ortholog inference is a key step in understanding the evolution and function of a gene or other genomic feature. Yet often no similar sequence can be identified, or the true ortholog is hidden among false positives. A solution is to consider the sequence's genomic context. We present the generic program, synder, for tracing features of interest between genomes based on a synteny map. This approach narrows genomic search-space independently of the sequence of the feature of interest. We illustrate the utility of synder by finding orthologs for the Arabidopsis thaliana 13-member gene family of Nuclear Factor YC transcription factor ...


Using Publicly Available Genbank Data To Teach Plant Phylogeny In High School Classrooms, Madhav P. Nepal, Ethan J. Andersen 2019 South Dakota State University

Using Publicly Available Genbank Data To Teach Plant Phylogeny In High School Classrooms, Madhav P. Nepal, Ethan J. Andersen

iLEARN Teaching Resources

In this teaching module, students will learn about NCBI GenBank, search for DNA/protein sequences from multiple plant species of a gene that encodes Rubisco enzyme, construct and interpret a phylogenetic tree, and discuss traits that allowed plants to adapt their life on land.


Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We studied the biological activity of the Mrub_3018 gene, which we hypothesize is orthologous to E. coli gene B2759. We predicted that Mrub_3018(DNA coordinates 3057916… 3058524) encodes the protein CasB. CasB is a protein in the CRISPR CASCADE that will function as a structural protein. When the rest of the proteins form an “S” formation CasB will connect the front and back of the “S” creating a back bone for the structure. It will help bind ...


Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI ...


Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as ...


Heterodera Glycines Utilizes Promiscuous Spliced Leaders And Demonstrates A Unique Preference For A Species-Specifc Spliced Leader Over C. Elegans Sl1, Stacey N. Barnes, Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Anoop S. Sindhu, Andrew J. Severin, Thomas J. Baum 2019 Iowa State University

Heterodera Glycines Utilizes Promiscuous Spliced Leaders And Demonstrates A Unique Preference For A Species-Specifc Spliced Leader Over C. Elegans Sl1, Stacey N. Barnes, Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Anoop S. Sindhu, Andrew J. Severin, Thomas J. Baum

Office of Biotechnology Publications

Spliced leader trans-splicing (SLTS) plays a part in the maturation of pre-mRNAs in select species across multiple phyla but is particularly prevalent in Nematoda. The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5'-ends of transcripts during RNA-seq library preparation, known as 5'-bias. Existing datasets and ...


Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon 2019 CUNY Hunter College

Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon

School of Arts & Sciences Theses

This study phylogenetically analyzed 30 AMY-related genes from 11 primates. The results show the gradual expansion of the AMY gene family which could have allowed primates to adapt to various ecological landscapes and maximize energy intake from starch-rich foods in periods of food scarcity.


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