an-adapted-optical-density-based-microplate-assay-for-characterizing

An Adapted Optical Density-Based Microplate Assay for Characterizing Actinobacteriophage Infection

Bacteriophages are a key part of natural environments, and they have a powerful ability to shape bacterial populations. To understand how individual ...

Ouachita Baptist University

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 with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange.

Comparative genomics of cluster o mycobacteriophages.

Four bacteriophages infecting  mc155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages.

Genome Sequences of Four Cluster P Mycobacteriophages.

Mass Spectrometry as a Tool to Enhance "-omics" Education.

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Instructional Models for Course-Based Research Experience (CRE) Teaching.

Soil bacteria can be a valuable source of antimicrobial compounds. Here, we report the complete genomes of four soil bacteria that were isolated by undergraduate microbiology students as part of a course-based research experience. These genomes were assembled using a hybrid approach combining paired-end Illumina reads with Oxford Nanopore Technologies MinION reads.

Complete Genome Sequences of Four Putatively Antibiotic-Producing Bacteria Isolated from Soil in Arkansas, USA.

The need for changing how science is taught and the expansion of undergraduate research experiences is essential to foster critical thinking in the Natural Sciences. Most faculty research programs only involve a small number of upper-level undergraduate students each semester. The course-based undergraduate research experience (CURE) model enables more students to take ownership over an independent project and experience authentic research. Further, by creating projects that fit into a curriculum's learning goals and student-oriented outcomes, departments help strengthen critical thinking skills in the classroom. Here, we report on the incorporation of a synthetic biology CURE into a mid-level cellular biology course and two advanced level genetics/molecular biology courses. Synthetic biology involves systematic engineering of novel organisms, such as bacteria and plants, to work as functional devices to solve problems in medicine, agriculture, and manufacturing. The value of synthetic biology and its ultimate utility as a teaching tool relies on reusable, standard genetic parts that can be interchanged using common genetic engineering principles. This Synthetic biology CURE effectively achieves five essential goals: (1) a sense of project ownership; (2) self-efficacy: mastery of a manageable number of techniques; (3) increased tolerance for obstacles through challenging research; (4) increased communication skills; and (5) a sense of belonging in a larger scientific community. Based upon our student assessment data, we demonstrate that this course-based synthetic biology laboratory engages students directly in an authentic research experience and models important elements of collaboration, discovery, iteration, and critical thinking.

From genetics to biotechnology: Synthetic biology as a flexible course-embedded research experience.

Chop, DelRio, and GrandSlam are phage with a  morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.

Article	Year
Comparative genomics of cluster o mycobacteriophages. PloS one\| PubMed ID: 25742016	2015
Genome Sequences of Four Cluster P Mycobacteriophages. Genome announcements\| PubMed ID: 29326199	2018
Mass Spectrometry as a Tool to Enhance "-omics" Education. Journal of microbiology & biology education\| PubMed ID: 29904565	2018
Instructional Models for Course-Based Research Experience (CRE) Teaching. CBE life sciences education\| PubMed ID: 34978921	2022
Complete Genome Sequences of Four Putatively Antibiotic-Producing Bacteria Isolated from Soil in Arkansas, USA. Microbiology resource announcements\| PubMed ID: 34989618	2022
From genetics to biotechnology: Synthetic biology as a flexible course-embedded research experience. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology\| PubMed ID: 36053869	2022
Complete Genome Sequences of Chop, DelRio, and GrandSlam, Three Phages Isolated from Soil in Central Arkansas. Microbiology resource announcements\| PubMed ID: 37036373	2023

Ruth Plymale

Biography

JoVE Journal Publications

Other Publications