2,022 research outputs found
From Petri Dish to Patient: Mycobacteriophages and Their Therapeutic Potential
No full textIn this presentation, Dr. Hatfull describes the origins and planned uses of SEA PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science), a multi-institution research project which IWU students are participating in. SEA-PHAGES is jointly administered by Graham Hatfull\u27s group at the University of Pittsburgh and the Howard Hughes Medical Institute\u27s Science Education division. See details at https://seaphages.org
Fluoromycobacteriophages for drug susceptibility testing (DST) of Mycobacteria
No full textFluoromycobacteriophages are a new class of reporter phages that contain fluorescent reporter genes (gfp, ZsYellow and mCherry) and provide a simple means of revealing the metabolic state of mycobacterial cells and therefore their response to antibiotics. Here we described a simple and rapid method for drug susceptibility testing (DST) of Mycobacterium spp using a fluorescence microscope, a flow cytometer, or a fluorimeter in a convenient multiwell format.Fil: Piuri, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Hatfull, Graham F.. University of Pittsburgh; Estados Unido
A Putative ABC-Transport Operon of Mycobacterium Smegmatis.
No full textWe have recently described the mpr gene of Mycobacterium smegmatis whose product confers resistance to mycobacteriophages L5 and D29 when overproduced (Barsom and Hatfull (1996) Mol. Microbiol. 21, 159-170). We have determined the nt sequence of approximately 3.5 kb immediately adjacent to mpr which appears to encode components of an ATP-binding cassette (ABC) transport system. Four closely-spaced open reading frames (ORF) were identified although two of these may cooperate to produce an integral membrane component of the transport system via a programmed translational frameshift. Another putative protein is also predicted to be an integral membrane protein, while the third is an ABC-transporter protein. We propose that these three putative proteins form a mycobacterial membrane-bound complex involved in protein-dependent transport. This is the first ABC-transport system to be described in mycobacteria.\ud
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Do we need to design course-based undergraduate research experiences for authenticity?
No full textThe recent push for more authentic teaching and learning in science, technology, engineering, and mathematics indicates a shared agreement that undergraduates require greater exposure to professional practices. There is considerable variation, however, in how “authentic” science education is defined. In this paper we present our definition of authenticity as it applies to an “authentic” large-scale undergraduate research experience (ALURE); we also look to the literature and the student voice for alternate perceptions around this concept. A metareview of science education literature confirmed the inconsistency in definitions and application of the notion of authentic science education. An exploration of how authenticity was explained in 604 reflections from ALURE and traditional laboratory students revealed contrasting and surprising notions and experiences of authenticity. We consider the student experience in terms of alignment with 1) the intent of our designed curriculum and 2) the literature definitions of authentic science education. These findings contribute to the conversation surrounding authenticity in science education. They suggest two things: 1) educational experiences can have significant authenticity for the participants, even when there is no purposeful design for authentic practice, and 2) the continuing discussion of and design for authenticity in UREs may be redundant
Generation of affinity-tagged fluoromycobacteriophages by mixed assembly of phage capsids
No full textAddition of affinity tags to bacteriophage particles facilitates a variety of applications, including vaccine construction and diagnosis of bacterial infections. Addition of tags to phage capsids is desirable, as modification of the tails can lead to poor adsorption and loss of infectivity. Although tags can readily be included as fusions to head decoration proteins, many phages do not have decoration proteins as virion components. The addition of a small (10-amino-acid) Strep-tag II (STAG II) to the mycobacteriophage TM4 capsid subunit, gp9, was not tolerated as a genetically homogenous recombinant phage but could be incorporated into the head by growth of wild-type phage on a host expressing the capsid-STAG fusion. Particles with capsids composed of wild-type and STAG-tagged subunit mixtures could be grown to high titers, showed good infectivities, and could be used to isolate phage-bacterium complexes. Preparation of a STAG-labeled fluoromycobacteriophage enabled capture of bacterial complexes and identification of infected bacteria by fluorescence.Fil: Piuri, Mariana. University of Pittsburgh; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Rondon Salazar, Liliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Urdániz, Estefanía. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Hatfull, Graham F.. University of Pittsburgh; Estados Unido
Mycobacteriophage endolysins: Diverse and modular enzymes with multiple catalytic activities
No full textThe mycobacterial cell wall presents significant challenges to mycobacteriophages - viruses that infect mycobacterial hosts - because of its unusual structure containing a mycolic acid-rich mycobacterial outer membrane attached to an arabinogalactan layer that is in turn linked to the peptidoglycan. Although little is known about how mycobacteriophages circumvent these barriers during the process of infection, destroying it for lysis at the end of their lytic cycles requires an unusual set of functions. These include Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, chaperones required for endolysin delivery to peptidoglycan, holins that regulate lysis timing, and the endolysins (Lysin As) that hydrolyze peptidoglycan. Because mycobacterial peptidoglycan contains atypical features including 3→3 interpeptide linkages, it is not surprising that the mycobacteriophage endolysins also have non-canonical features. We present here a bioinformatic dissection of these lysins and show that they are highly diverse and extensively modular, with an impressive number of domain organizations. Most contain three domains with a novel N-terminal predicted peptidase, a centrally located amidase, muramidase, or transglycosylase, and a C-terminal putative cell wall binding domain. © 2012 Payne, Hatfull
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Evolutionary Sweeps of Subviral Parasites and Their Phage Host Bring Unique Parasite Variants and Disappearance of a Phage CRISPR-Cas System
No full textVibrio cholerae is a significant threat to global public health in part due to its propensity for large-scale evolutionary sweeps where lineages emerge and are replaced. These sweeps may originate from the Bay of Bengal, where bacteriophage predation and the evolution of antiphage counterdefenses is a recurring theme. The bacteriophage ICP1 is a key predator of epidemic V. cholerae and is notable for acquiring a CRISPR-Cas system to combat PLE, a defensive subviral parasite encoded by its V. cholerae host. Here, we describe the discovery of four previously unknown PLE variants through a retrospective analysis of >3,000 publicly available sequences as well as one additional variant (PLE10) from recent surveillance of cholera patients in Bangladesh. In recent sampling we also observed a lineage sweep of PLE-negative V. cholerae occurring within the patient population in under a year. This shift coincided with a loss of ICP1's CRISPR-Cas system in favor of a previously prevalent PLE-targeting endonuclease called Odn. Interestingly, PLE10 was resistant to ICP1-encoded Odn, yet it was not found in any recent V. cholerae strains. We also identified isolates from within individual patient samples that revealed both mixed PLE(+)/PLE(-) V. cholerae populations and ICP1 strains possessing CRISPR-Cas or Odn with evidence of in situ recombination. These findings reinforce our understanding of the successive nature of V. cholerae evolution and suggest that ongoing surveillance of V. cholerae, ICP1, and PLE in Bangladesh is important for tracking genetic developments relevant to pandemic cholera that can occur over relatively short timescales. IMPORTANCE With 1 to 4 million estimated cases annually, cholera is a disease of serious global concern in regions where access to safe drinking water is limited by inadequate infrastructure, inequity, or natural disaster. The Global Task Force on Cholera Control (GTFCC.org) considers outbreak surveillance to be a primary pillar in the strategy to reduce mortality from cholera worldwide. Therefore, developing a better understanding of temporal evolutionary changes in the causative agent of cholera, Vibrio cholerae, could help in those efforts. The significance of our research is in tracking the genomic shifts that distinguish V. cholerae outbreaks, with specific attention paid to current and historical trends in the arms race between V. cholerae and a cooccurring viral (bacteriophage) predator. Here, we discover additional diversity of a specific phage defense system in epidemic V. cholerae and document the loss of a phage-encoded CRISPR-Cas system, underscoring the dynamic nature of microbial populations across cholera outbreaks
Diversity of mycobacteriophage genomes displayed as network phylogenies based on shared gene content.
No full text(A) Relationships among representative members of clusters, subclusters, and singleton genomes. One member of each mycobacteriophage cluster and subcluster together with the 7 singletons were compared using Splitstree [39] with a nexus file recording the numbers of shared genes. Clusters are illustrated with colored shading; note that some clusters (e.g., Cluster A) contain several subclusters indicated as nodes, whereas other clusters are not subdivided. Singletons are shown as unlabeled black circles. (B) Diversity of Cluster F mycobacteriophages. All currently sequenced Cluster F mycobacteriophages (n = 188) are displayed as nodes in a network phylogeny using Splitstree. Colored circles show the positions of the Subclusters F2 to F5 genomes; all of the others (n = 177) are grouped in Subcluster F1. This illustrates the substantial intracluster diversity, and pairwise comparisons of Subcluster F1 phages show they may share as few as 40% of their genes.</p
Assessing the George W. Bush Presidency: A Tale of Two Terms
No full textIn one of the first volumes assessing the full two terms of the George W. Bush presidency, Wroe and Herbert have gathered the work of leading American and European scholars. In fifteen succinct and incisive chapters, authorities such as Jim Pfiffner, John Maltese, Graham Wilson and Alan Gitelson offer assessments of the Bush administration's successes and failures. Extensive attention is paid to Bush's foreign policy, including 'The War on Terror' but the focus is broadened to absorb not only the Bush Doctrine and its repercussions, but also his trade and homeland security policies. The president's domestic leadership in economics and social policy is investigated, as are his dealings as president with the other institutions of the U.S. political system. The result is a comprehensive guide to the Bush presidency and its legacy
Mycobacteriophages: Genes and Genomes.
No full textViruses are powerful tools for investigating and manipulating their hosts, but the enormous size and amazing genetic diversity of the bacteriophage population have emerged as something of a surprise. In light of the evident importance of mycobacteria to human health--especially Mycobacterium tuberculosis, which causes tuberculosis--and the difficulties that have plagued their genetic manipulation, mycobacteriophages are especially appealing subjects for discovery, genomic characterization, and manipulation. With more than 70 complete genome sequences available, the mycobacteriophages have provided a wealth of information on the diversity of phages that infect a common bacterial host, revealed the pervasively mosaic nature of phage genome architectures, and identified a huge number of genes of unknown function. Mycobacteriophages have provided key tools for tuberculosis genetics, and new methods for simple construction of mycobacteriophage recombinants will facilitate postgenomic explorations into mycobacteriophage biology.\ud
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