Karen Klyczek

Prophage-mediated defence against viral attack and viral counter-defence

Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host–virus dynamics, and counter-defence promotes phage co-evolution.

Exploring Biotechnology Using Case-Based Multimedia

oday, teachers face more challenges than ever, and biology teachers face a special challenge. As technology continues to expand, biology teachers have a responsibility to keep students informed of technological and scientific advances. Biology teachers must also address ethical issues associated with these advances. Here we describe our experiences using case-based molecular biology simulations in high school and introductory college biology classes. This software enables teachers to meet several national science standards, such as connecting science to real-life situations and encouraging students to think about the relationships among science, technology and society. The realistic simulation also encourages students to explore careers in molecular biology and genetics, and gives students experience both in building Web pages and Internet conferencing.

Comparative genomics of Cluster O mycobacteriophages.

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.

Learner-centered methodology for designing and developing multimedia simulation for biology education

Biology students need exposure to modern research techniques relatively early in their educational careers. Computer multimedia simulation tools have been developed to address the challenge of providing all students with hands-on laboratory research experience. This paper presents a learner-centered approach to the design and development of a multimedia simulation for biology education. We present our methodology and a multimedia simulation tool designed and developed using the methodology. Out tool has been widely adopted by biological science educators for teaching molecular biology subjects in a wide range of undergraduate biology courses. We believe that our methodology can be adopted or adapted by learner communities in other disciplines.

Complete Genome Sequences of 38 Gordonia sp. Bacteriophages

ABSTRACT We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity.

Engaging Students in Molecular Biology via Case-Based Learning

Case It!, an IBI prize–winning module, provides computer simulations that enable student analysis of biological materials not usually available in laboratories. Case It! (www.caseitproject.org) originated at the 1995 BioQUEST Summer Workshop (1) and has developed over the years into an effective system for case-based learning useful for both high school and university educators (2, 3). National Science Foundation support has enabled us to distribute all project materials at no cost.

Complete Genome Sequences of 44 Arthrobacter Phages

ABSTRACT We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae, Myoviridae, and Podoviridae) are represented.

Introducing the JMBE Themed Issue on Scientific Citizenship

In this Editorial, the three Guest Editors for JMBEs first standalone themed issue introduce the topic of scientific citizenship and provide an overview of the current ideas and best practices contained within the issue.

Introduction of the H-2Dk gene into a class I-negative tumor cell line confers interferon-γ inducibility upon the silent endogenous H-2Kk gene

Kgv cells do not constitutively express class I mRNA or protein. Interferon (IFN)-gamma, but not IFN-alpha/beta, induces H-2Dk expression. IFN does not induce H-2Kk expression. We examined constitutive and IFN-inducible class I expression on Kgv cells stably transfected with genomic clones of H-2Kk or H-2Dk and on somatic cell hybrid lines constructed between Kgv cells and constitutively class I-positive cells of a distinguishable H-2 haplotype. Our results suggest that both the lack of constitutive class I expression and the inability of IFN-alpha/beta to induce class I expression on Kgv cells are primarily due to cis-regulatory mechanisms. However, stable introduction of the H-2Dk gene into Kgv cells conferred IFN-gamma inducibility upon the silent endogenous H-2Kk gene. Therefore, the failure of IFN-gamma to induce H-2Kk expression on Kgv cells is due, at least in part, to a trans-regulatory mechanism.