Curation and Characterization of a Collection of Mycobacteriophages

Bacteriophages are the most abundant biological entity on earth, with an estimated number of 1031. Bacteriophages specifically kill bacteria. Phages that infect M.smegmatis could potentially be used as an alternative to antibiotics.https://digitalcommons.mtech.edu/urp_aug_2018/1012/thumbnail.jp

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

Curriculum policy reform in an era of technical accountability: 'fixing' curriculum, teachers and students in English schools

Drawing on a Levinasian ethical perspective, the argument driving this paper is that the technical accountability movement currently dominating the educational system in England is less than adequate because it overlooks educators’ responsibility for ethical relations in responding to difference in respect of the other. Curriculum policy makes a significant contribution to the technical accountability culture through complicity in performativity, high-stakes testing and datafication, at the same time as constituting student and teacher subjectivities. I present two different conceptualizations of subjectivity and education, before engaging these in the analysis of data arising from an empirical study which investigated teachers’ and stakeholders’ experiences of curriculum policy reform in ‘disadvantaged’ English schools. The study’s findings demonstrate how a prescribed programme of technical curriculum regulation attempts to ‘fix’ or mend educational problems by ‘fixing’ or prescribing educational solutions. This not only denies ethical professional relations between students, teachers and parents, but also deflects responsibility for educational success from government to teachers and hastens the move from public to private educational provision. Complying with prescribed curriculum policy requirements shifts attention from broad philosophical and ethical questions about educational purpose as well as conferring a violence by assuming control over student and teacher subjectivities

Annotation of Bacteriophage BigPaolini

Bacteriophages were discovered nearly 100 years ago. With new interest in phages many phages are being analyzed and annotated to understand the diversity within the phage world.https://digitalcommons.mtech.edu/urp_aug_2018/1010/thumbnail.jp

The Amplification and Characterization of Mycobacteriophages MyPhage and SolarFlare

Bacteriophages are viruses that infect and replicate in bacteria and are being researched for medical applications. MyPhage is a Mycobacteriophage discovered in Anaconda, Montana in May of 2009. The student found the phage in soil from a potted plant. The background of SolarFlare is unknown.https://digitalcommons.mtech.edu/urp_aug_2018/1003/thumbnail.jp

Investigation of Genomic Deletion of Mycobacteriophage Moonbeam

Hypothesis: There are two, genomically separate Mycobacteriophages in Moonbeam lysate that was used and sent DNA template to the University of Pittsburgh in 2020. Experimental Aims: Separate and characterize phages with deletion from non-deletion phages in Moonbeam lysate

Digital planning of composite customized veneers using Digital Smile Design: Evaluation of its accuracy and manufacturing

Objectives: This study aimed to evaluate the production of customized composite veneers starting from a two-dimensional (2D) digital preview using the Digital Smile System (DSS). Material and Methods: A photographic examination of 30 patients was performed by taking two digital pictures of the face and a digital preview through the DSS. Moreover, optical scans of the dental arches were obtained and the data were entered into a three-dimensional (3D) software to prepare a virtual preview. The standard tessellation language files were sent for production using CAD-CAM technology. The Friedman test, Bonferroni, and Dunn post hoc tests were used, comparing the linear measurements of the 2D and 3D plans and the final veneers (α =.05). Results: Significant differences emerged between the pictures and digital scans on the mesial–distal widths of the lateral incisors and canine. Linear measurements in the 2D plan were significantly different from those of the 3D plan, except for the height measures of incisors. No significant changes were found on comparing the parameters of the 2D and 3D plans with those of the final pieces. Conclusions: The customized veneers were clinically adequate and similar to 2D and 3D plans, although significant differences emerged between the picture and digital scans as well as between the 2D and 3D plans

Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform

Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three - encoding tape-measure proteins, lysins, and minor tail proteins - are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education. © 2006 Hatfull et al

Facial artery myomucosal flap vs. Islanded facial artery myomucosal flap viability: A systematic review

The aim of this study was to estimate the overall viability of the islanded facial artery myomucosal flap (iFAMM) compared to the facial artery myomucosal flap (FAMM). A systematic review of English articles was performed on PubMed and Cochrane Library electronic databases. Search terms included every nomenclature variant for FAMM flap and iFAMM flap. A total of 373 articles were identified, and 20 articles were considered eligible for inclusion in the review. A total of 486 flaps were evaluated (350 FAMM and 136 i-FAMM flaps). In all studies, the primary outcome assessed was flap viability, collecting the rate of total and partial flap necrosis and then comparing FAMM to i-FAMM. Overall reported partial/total necrosis rate for FAMM flap was 9.7%, 1.4% as total and 8.3% as partial necrosis. Overall partial/total reported necrosis rate for iFAMM flaps was 2.2%, 1.5% as total and 0.7% as partial necrosis. FAMM flaps, both as classical or islanded variants, are an effective option for intraoral small/medium sized defect reconstruction. Outcomes from the present review show a higher partial/total survival rate when this flap is harvested as islanded flap

Repeatability of dental shade by digital spectrophotometry in current, former, and never smokers

Cigarette smoking contributes to poor oral health and dental discoloration. Therefore, stopping smoking may translate into measurable amelioration of dental shade indices. We compared dental shade parameters by digital spectrophotometry among current, former, and never smokers and verified their repeatability at 7 and 30 days. Dental shade parameters (CIE L*a*b* and corresponding whiteness index for dentistry-WID) were measured in current, former, and never smokers with a digital spectrophotometer (Vita Easyshade V) on three separate study visits: at baseline (day 0), at day 7, and day 30. Dental shade parameters were analyzed in 18 current, 18 former, and 20 never smokers. The repeatability of shade parameters was consistent in current, former, and never smokers. L*, a*, b*, and WID show significant short and long-term repeatability (p < 0.0001, by regression analyses). The mean (± SD) WID score of 13.42 (± 4.9) in current smokers was significantly lower compared to the WID score of 20.38 (± 5.3) in never smokers (p = 0.001). No significant differences were observed between current and former smokers and between former smokers and former smokers. Dental shade measurements by digital spectrophotometry were highly reproducible and showed that teeth whiteness of current smokers is substantially inferior compared to never smokers. Objective discrimination of dental shade can be a valuable regulatory science endpoint for investigating oral hygiene and dental aesthetics of consumer care products, smoking cessation medications, and tar-free tobacco products (e-cigarettes, heated tobacco products, oral nicotine products) for cigarette substitution. Clinical trial registration: the study was not registered in ClinicalTrials.gov considering that it is a pilot study, parts of a larger project with ID: NCT04649645