Don Paetkau | Saint Mary's College, Notre Dame (original) (raw)

Papers by Don Paetkau

Journal of Microbiology & Biology Education

The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-... more The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org ). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP’s Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled Drosophila genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020–2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning envi...

Genes & Development, 1994

We have used the two-hybrid system to identify proteins that interact with the product of RAD7, a... more We have used the two-hybrid system to identify proteins that interact with the product of RAD7, a gene involved in DNA repair. A screen of a yeast genomic DNA-GAL4 activation domain (GAD) fusion gene library allowed the isolation of plasmids containing sequences corresponding to the 3' end of the SIR3 gene. This gene is known to be involved in the production of transcriptionally silent DNA at the cryptic mating-type cassettes and at telomeres. The cloned sequences coded for amino acids 307-979 of the Sir3 protein. A sir3 deletion allele, constructed in an isogenic rad7-deletion strain, rescued approximately one-quarter of the UV sensitivity associated with the rad7 deletion, indicating that the two genes interact genetically. Radiolabeled fusion proteins, made with the glutathione S-transferase (GST) gene in the vector pGEX-2T, were purified from Escherichia coli and shown to interact in vitro. This evidence suggests that the Sir3 protein interacts with the Rad7 protein to allow...

Journal of Microbiology & Biology Education

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate researc... more The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit.

There is widespread agreement that science, technology, engineering, and mathematics programs sho... more There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a coursebased research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Water, Air, & Soil Pollution, 2021

Microbial contamination of water is a significant burden to public health, particularly in low- a... more Microbial contamination of water is a significant burden to public health, particularly in low- and middle-income countries. To develop an affordable and user-friendly method for detecting microbial water contamination in resource-limited settings, a business card-sized device, named the MicroBioPAD, was developed using filter paper saturated with the chromogenic sugar X-Gal. This device was compared to the standard most probable number (MPN) test and a plate culture-based test to assess fecal pollution of water in Nepal. A total of 120 water samples were collected from the Central (Kathmandu) and Southern (Chitwan) regions; these included 36 samples from three major rivers and 84 samples from various drinking water sources. The MPN and plate culture tests revealed fecal contamination in 93.1 and 27.3% of the samples collected in Kathmandu and Chitwan, respectively, with the levels of E. coli ranging from < 3 to ≥ 1100 CFU/100 ml in the Kathmandu water samples and < 3 to 160 CFU/100 ml in the Chitwan water samples. Compared to the standard culture-based tests, the MicroBioPAD produced positive results within a shorter time (24 h) and showed a 100% accuracy of detection for samples containing ≥ 3 E. coli CFU/ml, suggesting a detection limit of 3 E. coli CFU/ml when using only 100 μl of the sample. The MicroBioPAD will be useful as a relatively faster semi-quantitative device to determine water suitability for bathing, cleaning, and recreational purposes.

The files in this collection consist of the improved genomic sequences, gene annotations, and evi... more The files in this collection consist of the improved genomic sequences, gene annotations, and evidence tracks that were used in the analyses described in the manuscript "Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution" (doi: 10.1534/g3.114.015966). The improved genomic sequences and gene annotations were produced by students participating in the Genomics Education Partnership (GEP; http://gep.wustl.edu) during 2007–2012. This study seeks to understand the evolution of the Muller F element through the comparative analysis of Drosophila melanogaster, Drosophila erecta, Drosophila mojavensis, and Drosophila grimshawi. As part of this analysis, we have improved the genomic scaffolds from the D. mojavensis and D. grimshawi assemblies, and produced manual gene annotations for D. erecta, D. mojavensis, and D. grimshawi. The digital assets include the improved sequences and annotations in GenBank ASN.1 format, and the files required to create the UCSC Genome Browser instances for D. melanogaster, D. erecta, D. mojavensis, and D. grimshawi. The Genome Browser instances include the improved genomic sequences, gene annotations, and the results of the bioinformatics analyses described in the manuscript.

Genetics, 1999

The Drosophila retinal degeneration B protein (RdgB) is a novel integral membrane phosphatidylino... more The Drosophila retinal degeneration B protein (RdgB) is a novel integral membrane phosphatidylinositol transfer protein required for photoreceptor cell viability and light response. We isolated one intragenic suppressor (rdgBsu100) and four autosomal suppressors of the hypomorphic rdgBKS222 retinal degeneration phenotype. The rdgBsu100 suppressor dramatically slowed rdgBKS222's photoreceptor degeneration without significantly improving the electroretinogram (ERG) light response. One autosomal recessive suppressor [su(rdgB)69] significantly slowed rdgBKS222 retinal degeneration and restored the ERG light response near to that of the wild type. Unlike all the previously characterized rdgB suppressors, the four new autosomal suppressors do not affect the ERG light response in rdgB+ flies. Only Su(rdgB)116 exhibited a mutant phenotype in a rdgB+ background, which was smaller R1-6 rhabdomeres. We also examined the extent to which two previously identified visual transduction mutation...

G3 (Bethesda, Md.), Aug 30, 2017

The discordance between genome size and the complexity of eukaryotes can partly be attributed to ... more The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (~5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in Drosophila ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4 Mb region of the D. ananassae F element, and a 1.7 Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F element genes exhibit distinct characteristics compared to D element genes (e.g., larger coding spans, larger introns, more coding exons, lower codon bias), but these differences are exaggerated in ...

CBE—Life Sciences Education, 2014

There is widespread agreement that science, technology, engineering, and mathematics programs sho... more There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or mor...

The Allied Genetic Conference (TAGC) Poster Presentation

Journal of Microbiology & Biology Education

A hallmark of the research experience is encountering difficulty and working through those challe... more A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our “formative frustration” hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned fru...

G3 (Bethesda, Md.), Jan 4, 2015

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila mela... more The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have higher transposon density (25%-50%) than euchromatic reference regions (3%-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% versus 11%-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density ...

CBE life sciences education, 2014

In their 2012 report, the President's Council of Advisors on Science and Technology advocated... more In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a cent...

Journal of Microbiology & Biology Education

Genes & Development, 1994

Journal of Microbiology & Biology Education

Water, Air, & Soil Pollution, 2021

Genetics, 1999

G3 (Bethesda, Md.), Aug 30, 2017

CBE—Life Sciences Education, 2014

There is widespread agreement that science, technology, engineering, and mathematics programs sho... more There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or mor...

The Allied Genetic Conference (TAGC) Poster Presentation

Journal of Microbiology & Biology Education

G3 (Bethesda, Md.), Jan 4, 2015

CBE life sciences education, 2014