Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater.

Wastewater is discarded from several sources, including industry, livestock, fertilizer application, and municipal waste. If the disposed of wastewater has not been treated and processed before discharge to the environment, pathogenic microorganisms and toxic chemicals are accumulated in the disposal area and transported into the surface waters. The presence of harmful microbes is responsible for thousands of human deaths related to water-born contamination every year. To be able to take the necessary step and quick action against the possible presence of harmful microorganisms and substances, there is a need to improve the effective speed of identification and treatment of these problems. Biosensors are such devices that can give quantitative information within a short period of time. There have been several biosensors developed to measure certain parameters and microorganisms. The discovered biosensors can be utilized for the detection of axenic and mixed microbial strains from the wastewaters. Biosensors can further be developed for specific conditions and environments with an in-depth understanding of microbial organization and interaction within that community. In this regard, bacteriophage-based biosensors have become a possibility to identify specific live bacteria in an infected environment. This paper has investigated the current scenario of microbial community analysis and biosensor development in identifying the presence of pathogenic microorganisms.

A Framework for Evidentiary Reasoning in Biology: Insights from Laboratory Courses Focused on Evolutionary Tree-thinking.

Science educators report that students struggle with understanding, using, and evaluating the evidence underpinning scientific knowledge. However, there are not many studies focused on helping instructors address those difficulties. Here, we report on a laboratory instructor's scaffolding of students' evidentiary reasoning with and about evidence for evolutionary trees with guidance from the Conceptual Analysis of Disciplinary Evidence (CADE) framework, which links biological knowledge with epistemic considerations. To consider both domain-general and discipline-specific aspects of evidence, CADE was implemented to inform scaffolds in two ways: (1) generic evidence scaffolds (GES) reminded students of general epistemic considerations; (2) disciplinary evidence scaffolds (DES) explicitly reminded students of the disciplinary knowledge of relevance for considering biological evidence. An instructor's lab discussions were compared before and after they had a workshop with CADE. CADE helped the lab instructor facilitate students' evidentiary reasoning about evolutionary trees. In comparison to baseline, both GES and DES discussions covered more aspects and relationships among types of evidence for evolutionary tree-thinking and the instructor prompted more kinds of general epistemic considerations and biological knowledge. DES discussions emphasized the importance of disciplinary knowledge for research design. The CADE framework guided planning and implementation of intentional scaffolding aimed at guiding evidentiary reasoning. Supplementary Information: The online version contains supplementary material available at 10.1007/s11191-023-00435-6.

Potency and Powder X-ray Diffraction (PXRD) Evaluation of Levothyroxine Sodium Tablets under Ambient, Accelerated, and Stressed Conditions.

Levothyroxine tablets, although highly prescribed in the United States, have been one of the most frequently recalled products. Because of the importance of the medication, several efforts have been put in place by the United States Food and Drug Administration (US FDA) to control the quality of levothyroxine tablets available to patients using the drug. The choice of excipients used in the formulation has been shown to impact the hygroscopicity and microenvironment, and ultimately the stability of the levothyroxine tablets formulations. Based on information generated from the US FDA Enforcement Report database, one of the main reasons for recalls is the low potency of different batches of the product. The yearly product recall trends for levothyroxine formulations were determined using the FDA Enforcement Report database. Three brands of levothyroxine tablets were selected with excipient lists similar to those products that have been historically recalled. The samples were placed at ambient (~23 °C), accelerated stability (40 °C/75% RH), and stress (50 °C/75% RH) conditions for up to 6 months. Sample potencies were determined at 0, 1.5, 3, and 6 months using the methods for assay and impurities in the United States Pharmacopeia (USP) monograph for levothyroxine tablets. Additional sample monitoring was conducted by overlaying the initial powder X-ray diffractograms (PXRD) of the samples from 0 months with the patterns generated thereafter. There has been a decline in the number of levothyroxine tablets recalled over the years. The highest numbers of recalls were recorded in the years 2013 [33] and 2020 [23]; no recalls occurred in the years 2019 and 2022. All of the brands evaluated met the USP 95.0-105.0% assay requirements at 1.5 months under accelerated conditions; only one of the brands complied at 3 months. Under ambient conditions, two brands were stable at 6 months, with borderline assay results. For stability, levothyroxine was found in microgram quantities in the formulations and PXRD could not detect changes at these low levels. However, we found some distinguishing data for samples under stress conditions.

Determining the solubilities for benzoate, nicotinate, hydrochloride, and malonate salts of bedaquiline.

Determining the solubility of a compound is important for predicting its oral bioavailability, the medium to be used for dissolution, and solvents for cleaning during manufacturing. The solubilities of the newly synthesized benzoate, hydrochloride, nicotinate, and malonate salts of bedaquiline were elucidated, and the plausible reasons for the differences observed in their experimental aqueous solubilities were highlighted. The shake flask method was used to determine the experimental solubilities of the bedaquiline free base and all the salts in water, 0.01 N HCl, and pH 6.8 buffer. The molar and mole fraction solubility estimates of the salts were determined using equations for ideal and non-ideal situations. Furthermore, the relative contribution of the lattice and activity coefficient to the overall aqueous solubility of the salts were predicted graphically. The new salts ranked hydrochloride [0.6437 mg/mL] > malonate [0.0268 mg/ml] > nicotinate [0.0024 mg/mL] > benzoate [0.0004 mg/mL], showed improved aqueous solubility over the free base. The general solubility equation [GSE], fairly predicted the solubilities for the benzoate and malonate salts, but the ideal solubility equations provided poor estimates of their experimental values. Based on the ideal solubility estimates, the crystal lattice contributions of all salts were malonate > nicotinate > HCl > benzoate. However, using the activity coefficient values, the order of hydrophobicity of the bedaquiline salts was: benzoate > nicotinate > malonate > HCl. The salts forms of bedaquiline offered additional solubility as a function of their crystallinity and hydrophobicity.

Continuous improvement of a bioengineering CURE: Preparing students for a changing world.

Based on recent education reform guidelines to prepare professionals who are able to handle new technological, economic, social, and environmental challenges, pedagogical modifications are deemed necessary by the educators. Specifically, in biology, the rapid changes in the content and biological products demand changes in the curriculum. We aim to address this current need by providing an example of a course that was redesigned to meet the current trends of biological engineering education. In this course-based undergraduate research experience (CURE), learning objectives and possible outcomes were developed and assessment mapping was performed to align the course objectives with the Accreditation Board for Engineering and Technology (ABET) recommendations. A description of how one can assess authentic inquiry courses while adhering to the recommendations are discussed. For example, in this particular course, students completed weekly reflection assignments, maintained lab notebooks that were graded every week, presented their research to their peers at the end of the semester, and submitted a final paper to be graded. "Holistic" engineering is crucial for the all-around development of a 21st century engineer. Altering the traditional lecturing with more hands-on learning is crucial for the development of professional and communication skills of students. Such alterations could lead to the production of well-rounded life-long learners to serve the upcoming world.

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

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.

Designing and assessing a data literacy internship program for graduate health sciences students.

This case study presents the results of a data internship and workshop series on data analysis in qualitative biomedical systematic reviews. In a newly developed librarian-led internship program, an intern was trained on data literacy concepts and data analysis tools and, in turn, helped recruit and train other graduate health sciences students. Due to COVID-19 restrictions, a flipped classroom model was applied to develop a completely virtual learning experience for both the intern and workshop attendees. Both the data intern and workshop participants reported improved confidence in data literacy competence at the end of the project. Assessment results suggest that while the workshop series improved participants' data literacy skills, participants might still benefit from additional data literacy instruction. This case also presents a model for student-led instruction that could be particularly useful for informing professional development opportunities for library interns, fellows, and student assistants.

The Identification of Quality Risk Factors for Non-biological Complex Drugs and Epilepsy Drugs Using Statistical Analysis of Formulation-Based Recalls in the USA.

Pharmaceutical companies use the quality by design (QbD) approach to build high-quality drug products. A thorough understanding of risk factors is required to successfully employ QbD. In order to better understand risk factors that potentially impact drug product quality and inform future QbD approaches, we hypothesized root causes of drug product recalls based on publicly available data and a retroactive analysis of drug products recalled by the United States Food and Drug Administration (USFDA) from 2012 to 2018. We focused on two categories of drug products that pose unique regulatory challenges and an increased risk of shortage that could hinder the adequate supply of quality medicine to the patient. Knowing the significant risk factors from previous drug product recalls can help inform QbD and avoid future recalls. Quality recall reasons were studied individually to find risk factors associated with each recall category. Logistical regression statistical tests were done in R using a significance level of 0.05 to find correlations between a recalled product and its manufacturing information such as excipients and manufacturing steps. The results showed significant positive and negative correlations, such as products containing magnesium stearate are more likely to be recalled for impurities and degradation. This information could be used in the future to inform the design and manufacturing of drug products, ensuring consumers receive high-quality products with a low risk of recall.

Salts and Polymorph Screens for Bedaquiline.

Bedaquiline is used to treat multi-resistant tuberculosis in adults. The fumarate salt is commercially available and used in the product Sirturo. To provide open access to bedaquiline molecule once the patent on the chemical substance expires, new salts were screened. This work offers additional information on the bedaquiline system, as new salts may present better pharmacokinetic properties. The current studies focus on the attempted isolation of the acetate, benzoate, benzenesulfonate, hydrobromide, succinate, hydrochloride, tartrate, lactate, maleate, malate, and mesylate salts of bedaquiline. Potential salts were screened using a unique combination of conventional screening, and small-scale experiments supplemented by crystallographic analysis and infrared microspectroscopy. Salts were prepared on a larger scale by dissolving 1:1 ratios of the individual salt formers and bedaquiline base (30 mg, 0.055 mmol) in different solvents and allowing the solutions to evaporate or crystallize. X-ray diffraction (XRD) techniques and spectroscopic and thermal analyses were employed to characterize the salts. The benzoate and maleate salts were selected as lead candidates after reviewing preliminary characterization data. To determine the most stable forms for the leads, a polymorph screen was conducted using solvents of various polarities. These salt screens successfully generated five new salts of bedaquiline, namely, benzoate, maleate, hydrochloride, besylate, and mesylate. The existence of these salts was confirmed by powder XRD, proton NMR, and IR spectroscopies. TGA and DSC thermal analysis along with hot-stage optical microscopy were further used to characterize the salts. The polymorph screen conducted on the salts suggested the absence of additional polymorphs at 1 g scale.

Maleate salts of bedaquiline.

Bedaquiline is one of two important new drugs for the treatment of drug-resistant tuberculosis (TB). It is marketed in the US as its fumarate salt, but only a few salts of bedaquiline have been structurally described so far. We present here five crystal structures of bedaquilinium maleate {systematic name: [4-(6-bromo-2-meth-oxy-quinolin-3-yl)-3-hy-droxy-3-(naphthalen-1-yl)-4-phenyl-but-yl]di-methyl-aza-nium 3-carb-oxy-prop-2-enoate}, C32H32BrN2O2 +·C4H3O4 -, namely, a hemihydrate, a tetra-hydro-furan (THF) solvate, a mixed acetone/hexane solvate, an ethyl acetate solvate, and a solvate-free structure obtained from the acetone/hexane solvate by in situ single-crystal-to-single-crystal desolvation. All salts exhibit a 1:1 cation-to-anion ratio, with the anion present as monoanionic hydro-maleate and a singly protonated bedaquilinium cation. The maleate exhibits the strong intra-molecular hydrogen bond typical for cis-di-carb-oxy-lic acid anions. The conformations of the cations and packing inter-actions in the maleate salts are compared to those of free base bedaquiline and other bedaquilinium salts.

Crystal structures of salts of bedaquiline.

Bedaquiline [systematic name: 1-(6-bromo-2-methoxyquinolin-3-yl)-4-(dimethylamino)-2-(naphthalen-1-yl)-1-phenylbutan-2-ol, C32H31BrN2O2] is one of two important new drugs for the treatment of drug-resistant tuberculosis (TB). It is marketed in the US as its fumarate salt {systematic name: [4-(6-bromo-2-methoxyquinolin-3-yl)-3-hydroxy-3-(naphthalen-1-yl)-4-phenylbutyl]dimethylazanium 3-carboxyprop-2-enoate, C32H32BrN2O2+·C4H3O4-}, and about a dozen other salts of bedaquiline have been described in patent literature, but none have so far been structurally described. In a first communication, we present the crystal structure of bedaquilinium fumarate and of two new benzoate salts, as well as that of a degradation product of the reaction of bedaquilinium fumarate with sodium ethoxide, 3-benzyl-6-bromo-2-methoxyquinoline, C17H14BrNO. The fumarate and benzoate salts both feature cations monoprotonated at the dimethylamino group. The much less basic quinoline N atom remains unprotonated. Both salts feature a 1:1 cation-to-anion ratio, with the fumarate being present as monoanionic hydrofumarate. The conformations of the cations are compared to that of free base bedaquiline and with each other. The flexible backbone of the bedaquiline structure leads to a landscape of conformations with little commonalities between the bedaquiline entities in the various structures. The conformations are distinctively different for the two independent molecules of the free base, the two independent molecules of the hydrofumarate salt, and the one unique cation of the benzoate salt. Packing of the salts is dominated by hydrogen bonding. Hydrogen-bonding motifs, as well as the larger hydrogen-bonded entities within the salts, are quite similar for the salts, despite the vastly differing conformations of the cations, and both the hydrofumarate and the benzoate structure feature chains of hydrogen-bonded anions that are surrounded by and hydrogen bonded to the larger bedaquilinium cations, leading to infinite broad ribbons of anions, cations, and (for the benzoate salt) water molecules. The benzoate salt was isolated in two forms: as a 1.17-hydrate (C32H32BrN2O2+·C7H5O2-·1.166H2O), obtained from acetone or propanol solution, with one fully occupied water molecule tightly integrated into the hydrogen-bonding network of anions and cations, and one partially occupied water molecule [refined occupancy 16.6 (7)%], only loosely hydrogen bonded to the quinoline N atom. The second form is an acetonitrile solvate (C32H32BrN2O2+·C7H5O2-·0.742CH3CN·H2O), in which the partially occupied water molecule is replaced by a 74.2 (7)%-occupied acetonitrile molecule. The partial occupancy induces disorder for the benzoate phenyl ring. The acetonitrile solvate is unstable in atmosphere and converts into a form not distinguishable by powder XRD from the 1.17-hydrate.

Impact of ISO/IEC 17025 laboratory accreditation in sub-Saharan Africa: a case study.

BACKGROUND: The number and severity of nonconformities generated during an audit of a medicine testing laboratory indicates its level of quality compliance. Quality standards are established and maintained to ensure the reliability of laboratory test reports. The National Medicines Regulatory Authority (NMRA) Quality Control laboratories assess the quality of medicines used by the populace as part of their regulatory function. Although countries desire to have reliable medicine testing facilities, accrediting a national laboratory to international standards poses financial and technical challenges for many low-income countries. Sharing the benefits of laboratory accreditation could help more countries within sub-Saharan Africa overcome existing challenges to achieve accreditation and robust quality systems. This study investigated the impact of ISO/IEC 17025 accreditation on the performance of an NMRA Quality Control laboratory to provide evidence of improved quality compliance within a low-resource setting. METHODS: Pre- and post- accreditation audits of nonconformities for management and technical requirements of the ISO/IEC17025:2005 standards were evaluated from a Quality Control laboratory in the National Agency for Food and Drug Administration and Control (NAFDAC), located in Nigeria, West Africa. The following research questions were addressed: "does accreditation impact the adherence to quality standards?" and "does accreditation decrease the severity of nonconformities in Quality Control laboratory audits?" RESULTS: Statistical analysis of the pre- to post- accreditation audits from the years 2013 through 2017 revealed a significant decrease in the total number of nonconformities (χ2 = 74, p-value = 9.99e-05, r = 0.67). Further examination of audits from the years 2013 through 2018 audits also revealed a reduction in the number of nonconformities (χ2 = 53, p-value = 9.99e-05, r = 0.62). A reduction in the number of major observations and a decrease in the severity of nonconformities was also observed. CONCLUSIONS: A higher level of quality compliance was exhibited for the laboratory during the post-accreditation years. Overall, ISO/IEC 17025 accreditation of the NMRA Quality Control laboratory resulted in improved reliability of test reports and enhancement of the laboratory quality system.

An Analytic Investigation of the Drug Formulation-Based Recalls in the USA: See More Beyond the Literal.

High numbers of drug recalls persist despite the tremendous time and effort invested by pharmaceutical organizations and regulatory bodies such as the Food and Drug Administration (FDA) to ensure the quality of safe and effective medicines for the patient. It is imperative to better understand the underlying risk factors of drug formulation-based recalls to best protect the patient from poor quality drugs. Increased knowledge of underlying factors of formulation risk can also help inform the future design and development of drugs. In this study, we used a text mining technique with Python to parse the data and examine drug recalls from the aspect of administration route, dosage form, release mechanism, market type, pharmacologic class, and excipients. Observational analysis of the recalls revealed both high- and low-risk factors for the formulation-based recalls. Higher risk, or an increased probability of a formulation-based recall, was associated with factors such as extended release mechanism, capsule dosage form, oral route of administration, and an increased number of excipients, while lower risk of formulation-based recalls was associated with other factors including the new drug application market type, immediate release mechanism, and solution dosage form. In addition, the factors did not work independently, and we observed interactions among variables. For example, the release mechanism modified the effect of market type, administration route, and dosage form. This study will help inform the future design of quality drug products by pharmaceutical organizations and assist risk-based oversight by regulatory organizations, such as FDA, to ensure patient safety.

Describing teacher conceptions of technology in authentic science inquiry using technological pedagogical content knowledge as a lens.

Technology has become an indispensable component of both modern life science and life science education. However, due to inadequate knowledge and experience, teachers are often unable to include technology essential for practicing science in their teaching. In this regard, professional development workshops for in-service and preservice teachers are beneficial. In this study, we described the role of a professional development workshop in enhancing teachers' technological, pedagogical, and content knowledge through the lens of Technological Pedagogical Content Knowledge framework. Our study is also an example of how teachers can be informed about the current trends in modern research and technology and trained to bring similar research into their classroom. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):380-387, 2019.

An Education Strategy to Respond to Medicine Inequality in Africa.

People living in Africa face a heavy and wide-ranging burden of disease that takes an incalculable toll on social and economic development as well as shortening life expectancy (life expectancy in Tanzania is about 60 vs. about 80 in the United States and Europe. Further, the pharmaceutical market in developing countries is immature and may not support quality medicines. In many cases, a tender system is used, and medicines are bought by the government at the lowest price. In addition to access to medicines, a number of pharmaceutical sciences problems are apparent. The availability of infrastructure and especially standard instruments such as HPLC and X-ray diffraction is minimal. Additionally, there is an important need to increase access to advanced education for men and women in Africa, especially access to state-of-the-art scientific education. Utilizing the mandate of Nelson Mandela, Purdue's conceptual approach has been to utilize education to combat these problems.

A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research.

Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the potential advancement of research and development in complex biomedical systems has created a need for an educated workforce in bioinformatics. However, effectively integrating bioinformatics education through formal and informal educational settings has been a challenge due in part to its cross-disciplinary nature. In this article, we seek to provide an overview of the state of bioinformatics education. This article identifies: 1) current approaches of bioinformatics education at the undergraduate and graduate levels; 2) the most common concepts and skills being taught in bioinformatics education; 3) pedagogical approaches and methods of delivery for conveying bioinformatics concepts and skills; and 4) assessment results on the impact of these programs, approaches, and methods in students' attitudes or learning. Based on these findings, it is our goal to describe the landscape of scholarly work in this area and, as a result, identify opportunities and challenges in bioinformatics education.

A course-based research experience: how benefits change with increased investment in instructional time.

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 schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

A broadly implementable research course in phage discovery and genomics for first-year undergraduate students.

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 and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. IMPORTANCE: Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes.

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 mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode. IMPORTANCE: The bacteriophage population is vast, dynamic, and old and plays a central role in bacterial pathogenicity. We know surprisingly little about the genetic diversity of the phage population, although metagenomic and phage genome sequencing indicates that it is great. Probing the depth of genetic diversity of phages of a common host, Mycobacterium smegmatis, provides a higher resolution of the phage population and how it has evolved. Three new phages constituting a new cluster M further expand the diversity of the mycobacteriophages and introduce novel features. As such, they provide insights into phage genome architecture, virion structure, and gene regulation at the transcriptional and translational levels.

Calibrated peer review for computer-assisted learning of biological research competencies.

Recently, both science and technology faculty have been recognizing biological research competencies that are valued but rarely assessed. Some of these valued learning outcomes include scientific methods and thinking, critical assessment of primary papers, quantitative reasoning, communication, and putting biological research into a historical and broader social context. This article presents examples of Calibrated Peer Review (CPR) assignments that illustrate a computer-assisted method to help students achieve biological research competencies. A new release of CPR is appropriate for engaging students online in reading and writing about investigations. A participant perception inventory was designed for use as a repeated measure to discriminate among beginning, middle, and ending student perceptions. Examples are provided to demonstrate how to assess student perceptions of what they gain from instruction related to science research competencies. Results suggest that students in a large enrollment class consider CPR to be useful for helping them learn about quantitative and categorical research variables; the use of the experimental method to test ideas; the use of controls; analysis, interpretation, and presentation of data; and how to critically read primary papers.