David Dunbar

• Ph.D.
• Professor (Associate) at Cabrini University

The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe th...

Phams shared between Arthrobacter phages and phages isolated on other Actinobacteria hosts. (XLSX)

Pairwise alignment of 11 Cluster AK Arthrobacter phages. (PDF)

Pairwise alignment of 6 Cluster AO Arthrobacter phages. (PDF)

Pairwise alignment of 5 Cluster AQ Arthrobacter phages. (PDF)

Pairwise alignment of 2 Cluster AT Arthrobacter phages. (PDF)

Pham data summary. (XLSX)

Pairwise alignment of 2 Cluster AL Arthrobacter phages. (PDF)

Pairwise alignment of 10 Cluster AN Arthrobacter phages. (PDF)

Location of phages on United States map. (PDF)

Pairwise alignment of 2 Cluster AM and 2 Cluster AU Arthrobacter phages. (PDF)

Pairwise alignment of 2 Cluster AP Arthrobacter phages. (PDF)

Relationship between Clusters AM, AU, CC. (PDF)

Location of soil source and permissions. (PDF)

Measurements of head diameter and tail length in electron micrographs. (PDF)

Average nucleotide identity (ANIs) of 48 Arthrobacter phages. (XLSX)

Phams shared between Arthrobacter phage clusters. (PDF)

Gene content analysis data for Fig 18A. (NEX)

Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both Mycobacterium phlei and Mycobacterium smegmatis and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F.

Bacteriophage isolation from environmental samples has been performed for decades using principles set forth by pioneers in microbiology. The isolation of phages infecting Arthrobacter hosts has been limited, perhaps due to the low success rate of many previous isolation techniques, resulting in an underrepresented group of Arthrobacter phages avai...

Mycobacteriophages - viruses of mycobacterial hosts - are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages - Corndog, Catdawg, Dylan, Firecracker, and YungJamal - designated as Cluster O with long flexible tails but...

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. grimsh...

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...

Two community-based research (CBR) courses—Watershed Citizenship and Watershed Ecology—were piloted at Cabrini College in southeastern Pennsylvania. The courses connected service, education, and research using a local Pennsylvania stream, Crabby Creek, as the focal point, while working with several community partners. Course feedback using a qualit...

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 s...

Unlabelled: Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery a...

Unlabelled: Genomic analysis of a large set of phages infecting the common host Mycobacterium smegmatis mc(2)155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate my...

In this work, a method was developed to study the structural proteome of mycobacteriophage Marvin, a recent isolate from soil with 107 predicted coding sequences. This prototype method was applied for semi-quantitative analysis of the composition of this mycobacteriophage virion using ion mobility spectrometry and data-independent acquisition (MS(E...

Undergraduate students at our institution have reported several advantages of early participation in research, includ-ing a stronger desire to continue their education and to gain more research experience (Harrison et al. 2011). A key model of the undergraduate research experience is found in course-based research, in which students are immersed in...

A service-learning project appropriate for a biochemistry or advanced biochemistry course was designed and implemented. The project involved students partnering with a homeless shelter to design informational pamphlets to be displayed at the shelter for the clients’ use. The pamphlet topics were based on diseases studied within the course. Students...

Campus-community partnerships are increasingly recognized as important parts of curricula and have become central to the missions of many colleges. Yet while the notion of service is becoming more prominent at the institutional level, the number of faculty who are actually teaching community-engaged courses is alarmingly low. This paper addresses t...

A growing movement in higher education seeks to integrate authentic research experiences for students in traditional laboratory settings (Lopatto, 2010). These “course-based research” models have been successfully employed at several institutions (Boomer & Dutton, 2002; Brodl, 2005; Caruso, Sandoz, & Kelsey, 2009; Drew & Triplett, 2008; Elwess & La...

Mycobacteriophages represent a genetically diverse group of viruses that infect mycobacterial hosts. Although more than 80 genomes have been sequenced, these still poorly represent the likely diversity of the broader population of phages that can infect the host, Mycobacterium smegmatis mc2155. We describe here a newly discovered phage, Marvin, whi...

Our study, focused on classroom-based research at the introductory level and using the Phage Genomics course as the model, shows evidence that first-year students doing research learn the process of science as well as how scientists practice science. A preliminary but notable outcome of our work, which is based on a small sample, is the change in s...

This article is intended for faculty who are looking for new techniques for teaching a genetics or molecular ecology lab. We have used the bar-coding protocol for both a non-majors watershed ecology lab and a majors-specific genetics lab with equal success. The exercise involves extracting mitochondrial DNA from animal tissue, amplifying a portion...

Undergraduate research has shown that the incorporation of hands-on, inquiry-based activities produces a superior learning environment for all disciplines (Lopatto 2004; Seymour et al. 2004). The majority of undergraduate research takes place outside of the normal classroom laboratory experience, although embedding undergraduate research into cours...

In this article, we identify the steps and strategies that emerged through an interdisciplinary, community-based participatory research (CBPR) project—the Crabby Creek Initiative. The Initiative was undertaken jointly by Cabrini College faculty in biology and psychology, the Valley Creek Restoration Partnership (VCRP), the Stroud Water Research Cen...

O ver the past several years, a number of initiatives have sought to improve the quality of learning in undergraduate science education by relying less on content and more on the process of learning science (Bransford, Brown, and Cocking 2000; NRC 1996; Fox and Hackerman 2003). Perhaps the most significant recommendation for higher education has be...

Species-specific pre-rRNA processing variations may result in fragmented 18S, 5.8S and 28S rRNAs. Some insect 5.8S and 28S rRNAs are further cleaved, creating within a 'hidden break' or 'gap'. We investigated the specificity of the processing mechanism by microinjecting Sciara coprophila (fungus fly) rDNA into Xenopus laevis oocytes to examine inse...

Sequential events in macromolecular biosynthesis are often elegantly coordinated. The small ribosomal subunit (SSU) processome is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome. We have found that a subcomplex of SSU processome proteins, the t-Utps, is also required for optim...

The Saccharomyces cerevisiae Rlp7 protein has extensive identity and similarity to the large ribosomal subunit L7 proteins and shares an RNA-binding domain with them. Rlp7p is not a ribosomal protein; however, it is encoded by an essential gene and therefore must perform a function essential for cell growth. In this report, we show that Rlp7p is a...

Because the organization of snoRNA genes in vertebrates, plants and yeast is diverse, we investigated the organization of snoRNA genes in a distantly related organism, Trypanosoma brucei. We have characterized the second example of a snoRNA gene cluster that is tandemly repeated in the T.brucei genome. The genes encoding the box C/D snoRNAs TBR12,...

We report the identification of 17 box C/D fibrillarin-associated small nucleolar RNAs (snoRNAs) from the ancient eukaryote, Trypanosoma brucei. To systematically isolate and characterize these snoRNAs, the T. brucei cDNA for the box C/D snoRNA common protein, fibrillarin, was cloned and polyclonal antibodies to the recombinant fibrillarin protein...

We report the identification of 17 box C/D fibrillarin-associated small nucleolar RNAs (snoRNAs) from the ancient eukaryote, Trypanosoma brucei. To systematically isolate and characterize these snoRNAs, the T. brucei cDNA for the box C/D snoRNA common protein, fibrillarin, was cloned and polyclonal antibodies to the recombinant fibrillarin protein...

We have studied the role of the U14 small nucleolar RNA (snoRNA) in pre-rRNA methylation and processing in Xenopus oocytes. Depletion of U14 in Xenopus oocytes was achieved by co-injecting two nonoverlapping antisense oligonucleotides. Focusing on the earliest precursor, depletion experiments revealed that the U14 snoRNA is essential for 2'-O-ribos...

We have studied the role of the U14 small nucleolar RNA (snoRNA) in pre-rRNA methylation and processing in Xenopus oocytes. Depletion of U14 in Xenopus oocytes was achieved by co-injecting two nonoverlapping antisense oligonucleotides. Focusing on the earliest precursor, depletion experiments revealed that the U14 snoRNA is essential for 2'-O-ribos...

We have isolated and characterized Mpp10p, a novel protein component of the U3 small nucleolar ribonucleoprotein (snoRNP) from the yeast Saccharomyces cerevisiae. The MPP10 protein was first identified in human cells by its reactivity with an antibody that recognizes specific sites of mitotic phosphorylation. To study the functional role of MPP10 i...

We have used the yeast, Saccharomyces cerevisiae, as a model system to identify a new protein component of the U3 small nucleolar ribonucleoprotein (snoRNP) and to study its role in pre-rRNA processing. Mpp10p, which we have cloned and characterized from humans, mice and yeast, is a 110 kDa protein in yeast. Antibodies to it immunoprecipitate the U...

The U18 small nuclear RNA (snRNA) is one of several newly discovered intron-encoded nucleolar RNAs whose function is unknown. We have studied the accumulation and function of the U18 snRNA in oocytes of the vertebrate, Xenopus laevis. The U18 snRNA contains 13 nt complementary to a highly conserved sequence in 28S ribosomal RNA (rRNA). Three oligon...