Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature

We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.

Therapeutically useful mycobacteriophages BPs and Muddy require trehalose polyphleates

Mycobacteriophages show promise as therapeutic agents for non-tuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces or mechanisms of phage resistance. We show here that trehalose polyphleates (TPPs)-high-molecular-weight, surface-exposed glycolipids found in some mycobacterial species-are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy. TPP loss leads to defects in adsorption and infection and confers resistance. Transposon mutagenesis shows that TPP disruption is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss by mutation, and some M. abscessus clinical isolates are naturally phage-insensitive due to TPP synthesis gene mutations. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.

Mycobacterium trehalose polyphleates are required for infection by therapeutically useful mycobacteriophages BPs and Muddy

Mycobacteriophages are good model systems for understanding their bacterial hosts and show promise as therapeutic agents for nontuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces, or mechanisms of phage resistance. We show here that surface-exposed trehalose polyphleates (TPPs) are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy, and that TPP loss leads to defects in adsorption, infection, and confers resistance. Transposon mutagenesis indicates that TPP loss is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss, and some M. abscessus clinical isolates are phage-insensitive due to TPP absence. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.

Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection

Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.

Introduction to the special issue on education in acoustics

A substantial fraction of the membership of the Acoustical Society of America are faculty at various types of educational institutions and are actively engaged in educational activities. However, papers focusing on aspects of teaching, pedagogy, demonstrations, student learning, and other education topics are not often published in JASA, even though the Education in Acoustics Committee regularly offers special sessions on these topics at every ASA meeting. This special issue of JASA dedicated to Education in Acoustics includes 41 papers from authors all over the world. This introduction to the special issue briefly describes each of the papers, which have been organized into several broad categories: teaching methods and exercises; project-based learning; use of experiments, demos, and experiential learning; adapting to teaching during COVID-19; circuit models and impedance concepts; software apps and online resources; teaching musical acoustics; and descriptions of acoustics programs at a variety of institutions.

Broadening Access to STEM through the Community College: Investigating the Role of Course-Based Research Experiences (CREs)

Broadening access to science, technology, engineering, and mathematics (STEM) professions through the provision of early-career research experiences for a wide range of demographic groups is important for the diversification of the STEM workforce. The size and diversity of the community college system make it a prime educational site for achieving this aim. However, some evidence shows that women and Black, Latinx, and Native American student groups have been hindered in STEM at the community college level. One option for enhancing persistence in STEM is to incorporate the course-based research experiences (CREs) into the curriculum as a replacement for the prevalent traditional laboratory. This can be achieved through the integration of community colleges within extant, multi-institutional CREs such as the SEA-PHAGES program. Using a propensity score-matching technique, students in a CRE and traditional laboratory were compared on a range of psychosocial variables (project ownership, self-efficacy, science identity, scientific community values, and networking). Results revealed higher ratings for women and persons excluded because of their ethnicity or race (PEERs) in the SEA-PHAGES program on important predictors of persistence such as project ownership and science identity. This suggests that the usage of CREs at community colleges could have positive effects in addressing the gender gap for women and enhance inclusiveness for PEER students in STEM.

Oral 11β-HSD1 inhibitor AZD4017 improves wound healing and skin integrity in adults with type 2 diabetes mellitus: a pilot randomized controlled trial

BACKGROUND

Chronic wounds (e.g. diabetic foot ulcers) reduce the quality of life, yet treatments remain limited. Glucocorticoids (activated by the enzyme 11β-hydroxysteroid dehydrogenase type 1, 11β-HSD1) impair wound healing.

OBJECTIVES

Efficacy, safety, and feasibility of 11β-HSD1 inhibition for skin function and wound healing.

DESIGN

Investigator-initiated, double-blind, randomized, placebo-controlled, parallel-group phase 2b pilot trial.

METHODS

Single-center secondary care setting. Adults with type 2 diabetes mellitus without foot ulcers were administered 400 mg oral 11β-HSD1 inhibitor AZD4017 (n = 14) or placebo (n = 14) bi-daily for 35 days. Participants underwent 3-mm full-thickness punch skin biopsies at baseline and on day 28; wound healing was monitored after 2 and 7 days. Computer-generated 1:1 randomization was pharmacy-administered. Analysis was descriptive and focused on CI estimation. Of the 36 participants screened, 28 were randomized.

RESULTS

Exploratory proof-of-concept efficacy analysis suggested AZD4017 did not inhibit 24-h ex vivoskin 11β-HSD1 activity (primary outcome; difference in percentage conversion per 24 h 1.1% (90% CI: -3.4 to 5.5) but reduced systemic 11β-HSD1 activity by 87% (69-104%). Wound diameter was 34% (7-63%) smaller with AZD4017 at day 2, and 48% (12-85%) smaller after repeat wounding at day 30. AZD4017 improved epidermal integrity but modestly impaired barrier function. Minimal adverse events were comparable to placebo. Recruitment rate, retention, and data completeness were 2.9/month, 27/28, and 95.3%, respectively.

CONCLUSION

A phase 2 trial is feasible, and preliminary proof-of-concept data suggests AZD4017 warrants further investigation in conditions of delayed healing, for example in diabetic foot ulcers.

SIGNIFICANCE STATEMENT

Stress hormone activation by the enzyme 11β-HSD type 1 impairs skin function (e.g. integrity) and delays wound healing in animal models of diabetes, but effects in human skin were previously unknown. Skin function was evaluated in response to treatment with a 11β-HSD type 1 inhibitor (AZD4017), or placebo, in people with type 2 diabetes. Importantly, AZD4017 was safe and well tolerated. This first-in-human randomized, controlled, clinical trial found novel evidence that 11β-HSD type 1 regulates skin function in humans, including improved wound healing, epidermal integrity, and increased water loss. Results warrant further studies in conditions of impaired wound healing, for example, diabetic foot ulcers to evaluate 11β-HSD type 1 as a novel therapeutic target forchronic wounds.

Toward a Phage Cocktail for Tuberculosis: Susceptibility and Tuberculocidal Action of Mycobacteriophages against Diverse Mycobacterium tuberculosis Strains

The global health burden of human tuberculosis (TB) and the widespread antibiotic resistance of its causative agent Mycobacterium tuberculosis warrant new strategies for TB control. The successful use of a bacteriophage cocktail to treat a Mycobacterium abscessus infection suggests that phages could play a role in tuberculosis therapy. To assemble a phage cocktail with optimal therapeutic potential for tuberculosis, we have explored mycobacteriophage diversity to identify phages that demonstrate tuberculocidal activity and determined the phage infection profiles for a diverse set of strains spanning the major lineages of human-adapted strains of the Mycobacterium tuberculosis complex. Using a combination of genome engineering and bacteriophage genetics, we have assembled a five-phage cocktail that minimizes the emergence of phage resistance and cross-resistance to multiple phages, and which efficiently kills the M. tuberculosis strains tested. Furthermore, these phages function without antagonizing antibiotic effectiveness, and infect both isoniazid-resistant and -sensitive strains.IMPORTANCE Tuberculosis kills 1.5 million people each year, and resistance to commonly used antibiotics contributes to treatment failures. The therapeutic potential of bacteriophages against Mycobacterium tuberculosis offers prospects for shortening antibiotic regimens, provides new tools for treating multiple drug-resistant (MDR)-TB and extensively drug-resistant (XDR)-TB infections, and protects newly developed antibiotics against rapidly emerging resistance to them. Identifying a suitable suite of phages active against diverse M. tuberculosis isolates circumvents many of the barriers to initiating clinical evaluation of phages as part of the arsenal of antituberculosis therapeutics.

Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions

Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components, such as bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut's "viral dark matter" and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.

Endovascular management of mycotic aortic aneurysms- A 20-year experience from a single UK centre

AIM

To present the authors' experience of endovascular treatment of confirmed and presumed (microbiology negative) mycotic aortic aneurysms (MAA).

MATERIALS AND METHODS

Patients undergoing endovascular aortic repair were identified retrospectively from 1998 using the radiology information system and an internally kept database until 2018. The primary aim was to assess the technical success and peri-operative morbidity and mortality. The secondary aim was to assess progression of infection, re-interventions, late mortality, and correlation to antibiotic duration pre- and post-procedure.

RESULTS

Thirty-four endovascular aortic procedures were performed for MAA, excluding aorto-enteric fistulas, inflammatory aneurysms, and infected grafts without a new aneurysm. Seventy-six percent of these were thoracic and 24% abdominal. The technical success was 100%. Additional procedures were undertaken in four patients with two requiring a further endovascular procedure. There were two inpatient aneurysm-related mortalities and no inpatient conversions to open repair. The 30-day re-admission and re-intervention rate was 0%. Blood cultures were positive in 45%. There were no secondary graft infections.

CONCLUSION

This is the largest European single-centre study. It supports endovascular management of MAA as a lower-risk alternative to open surgery with the majority of patients presenting acutely, later in life and requiring emergency management.

Genomic diversity of bacteriophages infecting Microbacterium spp

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus

A 15-year-old patient with cystic fibrosis with a disseminated Mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. Effective lytic phage derivatives that efficiently kill the infectious M. abscessus strain were developed by genome engineering and forward genetics. Intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules.

Acoustics of ping-pong: Vibroacoustic analysis of table tennis rackets and balls

The sound resulting from the impact of a table tennis racket and ball can influence a player's perception of equipment quality in addition to providing clues to personal performance. This study explores the vibrational modes of both racket and ball and how those modes contribute to the impact sound. Experimental modal analysis reveals that the racket exhibits a large number of structural vibration modes typical of elliptical plates. Acoustic analysis reveals that two of those structural modes dominate the sound produced by the ball-paddle impact. The rubber padding provides some damping and a significant mass loading to the racket vibrations. The hollow cellulose nitrate balls exhibit vibrational modes typical of a hollow spherical shell, starting with frequencies around 5920 Hz. Experimental frequencies confirm theoretical and computational models. However, the contact time between racket and ball is long enough that the lowest acoustic modes of the ball do not contribute to the radiated sound. Instead, acoustic analysis suggests that the ball appears to radiate sound at a much higher frequency sound (8.5-12 kHz) most likely due to snap-through after buckling common to spherical shells undergoing deformation while impacting a rigid surface at high speeds.

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

BACKGROUND

A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity.

RESULTS

We obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages.

CONCLUSIONS

Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.

PhagesDB: the actinobacteriophage database

The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, characterization and genomics of viruses that infect Actinobacterial hosts. To date, more than 8000 bacteriophages-including over 1600 with sequenced genomes-have been entered into the database. PhagesDB plays a crucial role in organizing the discoveries of phage biologists around the world-including students in the SEA-PHAGES program-and has been cited in over 50 peer-reviewed articles.

Availability and Implementation

http://phagesdb.org/.

Contact

gfh@pitt.edu.

Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes

Next-generation DNA sequencing (NGS) technologies have made generating genomic sequence for organisms of interest affordable and commonplace. However, NGS platforms and analysis software are generally tuned to be used on large and complex genomes or metagenomic samples. Determining the complete genome sequence of a single bacteriophage requires a somewhat different perspective, workflow, and sensitivity to the nature of phages. Because phage genomes consist of mostly coding regions (see Pope/Jacobs-Sera chapter), a very high standard should be adopted when completing these genomes so that the subsequent steps of annotation and analysis are not sabotaged by sequencing errors. While read quality and assembly algorithms have continued to improve, achieving this standard still requires a significant amount of human oversight and expertise. This chapter describes our workflow for sequencing, assembling, and finishing phage genomes to a high standard by the NGS platforms Illumina, Ion Torrent, and 454.

Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages

The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.

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.

Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U

Background

A large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo.

Results

We isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc²155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system.

Conclusions

We predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0734-3) contains supplementary material, which is available to authorized users.

Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems

More than 180 individual phages infecting hosts in the phylum Actinobacteria have been sequenced and grouped into Cluster A because of their similar overall nucleotide sequences and genome architectures. These Cluster A phages are either temperate or derivatives of temperate parents, and most have an integration cassette near the centre of the genome containing an integrase gene and attP. However, about 20% of the phages lack an integration cassette, which is replaced by a 1.4 kbp segment with predicted partitioning functions, including plasmid-like parA and parB genes. Phage RedRock forms stable lysogens in Mycobacterium smegmatis in which the prophage replicates at 2.4 copies/chromosome and the partitioning system confers prophage maintenance. The parAB genes are expressed upon RedRock infection of M. smegmatis, but are downregulated once lysogeny is established by binding of RedRock ParB to parS-L, one of two centromere-like sites flanking the parAB genes. The RedRock parS-L and parS-R sites are composed of eight directly repeated copies of an 8 bp motif that is recognized by ParB. The actinobacteriophage parABS cassettes span considerable sequence diversity and specificity, providing a suite of tools for use in mycobacterial genetics.

OfftargetFinder: a web tool for species-specific RNAi design

MOTIVATION

RNA interference (RNAi) technology is being developed as a weapon for pest insect control. To maximize the specificity that such an approach affords we have developed a bioinformatic web tool that searches the ever-growing arthropod transcriptome databases so that pest-specific RNAi sequences can be identified. This will help technology developers finesse the design of RNAi sequences and suggests which non-target species should be assessed in the risk assessment process.

AVAILABILITY AND IMPLEMENTATION

http://rnai.specifly.org

CONTACT

crobin@unimelb.edu.au.

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

DOI:http://dx.doi.org/10.7554/eLife.06416.001

Viruses are unable to replicate independently. To generate copies of itself, a virus must instead invade a target cell and commandeer that cell's replication machinery. Different viruses are able to invade different types of cell, and a group of viruses known as bacteriophages (or phages for short) replicate within bacteria. The enormous number and diversity of phages in the world means that they play an important role in virtually every ecosystem.

Despite their importance, relatively little is known about how different phage populations are related to each other and how they evolved. Many phages contain their genetic information in the form of strands of DNA. Using genetic sequencing to find out where and how different genes are encoded in the DNA can reveal information about how different viruses are related to each other. These relationships are particularly complicated in phages, as they can exchange genes with other viruses and microbes.

Previous studies comparing the genomes—the complete DNA sequence—of reasonably small numbers of phages that infect the Mycobacterium group of bacteria have found that the phages can be sorted into ‘clusters’ based on similarities in their genes and where these are encoded in their DNA. However, the number of phages investigated so far has been too small to conclude how different clusters are related. Are the clusters separate, or do they form a ‘continuum’ with different genes and DNA sequences shared between different clusters?

Here, Pope, Bowman, Russell et al. compare the individual genomes of 627 bacteriophages that infect the bacterial species Mycobacterium smegmatis. This is by far the largest number of phage genomes analyzed from a single host species. The large number of genomes analyzed allowed a much clearer understanding of the complexity and diversity of these phages to be obtained. The isolation, sequencing and analysis of the hundreds of M. smegmatis bacteriophage genomes was performed by an integrated research and education program, called the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This enabled thousands of undergraduate students from different institutions to contribute to the phage discovery and sequencing project, and co-author the report. SEA-PHAGES therefore shows that it is possible to successfully incorporate genuine scientific research into an undergraduate course, and that doing so can benefit both the students and researchers involved.

The results show that while the genomes could be categorized into 28 clusters, the genomes are not completely unrelated. Instead, a spread of diversity is seen, as genes and groups of genes are shared between different clusters. Pope, Bowman, Russell et al. further reveal that the phage population is in a constant state of change, and continuously acquires genes from other microorganisms and viruses.

DOI:http://dx.doi.org/10.7554/eLife.06416.002

Multiple beam two-plasmon decay: linear threshold to nonlinear saturation in three dimensions

The linear stability of multiple coherent laser beams with respect to two-plasmon-decay instability in an inhomogeneous plasma in three dimensions has been determined. Cooperation between beams leads to absolute instability of long-wavelength decays, while shorter-wavelength shared waves are shown to saturate convectively. The multibeam, in its absolutely unstable form, has the lowest threshold for most cases considered. Nonlinear calculations using a three-dimensional extended Zakharov model show that Langmuir turbulence created by the absolute instability modifies the convective saturation of the shorter-wavelength modes, which are seen to dominate at late times.

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

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 J mycobacteriophages: intron splicing in capsid and tail genes

Bacteriophages isolated on Mycobacterium smegmatis mc²155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution.

Snapshot of haloarchaeal tailed virus genomes

The complete genome sequences of archaeal tailed viruses are currently highly underrepresented in sequence databases. Here, we report the genomic sequences of 10 new tailed viruses infecting different haloarchaeal hosts. Among these, only two viral genomes are closely related to each other and to previously described haloviruses HF1 and HF2. The approximately 760 kb of new genomic sequences in total shows no matches to CRISPR/Cas spacer sequences in haloarchaeal host genomes. Despite their high divergence, we were able to identify virion structural and assembly genes as well as genes coding for DNA and RNA metabolic functions. Interestingly, we identified many genes and genomic features that are shared with tailed bacteriophages, consistent with the hypothesis that haloarchaeal and bacterial tailed viruses share common ancestry, and that a viral lineage containing archaeal viruses, bacteriophages and eukaryotic viruses predates the division of the three major domains of non-viral life. However, as in tailed viruses in general and in haloarchaeal tailed viruses in particular, there are still a considerable number of predicted genes of unknown function.

Acoustic testing and modeling: an advanced undergraduate laboratory

This paper describes an advanced laboratory course in acoustics, specifically targeted for students with an interest in engineering applications at a school with a strongly integrated industrial co-op program. The laboratory course is developed around a three-pronged approach to problem solving that combines and integrates theoretical models, computational models, and experimental data. The course is structured around modules that begin with fundamental concepts and build laboratory skills and expand the knowledge base toward a final project. Students keep a detailed laboratory notebook, write research papers in teams, and must pass laboratory certification exams. This paper describes the course layout and philosophy and shares personal experience from both faculty and student perspectives.

Peripheral arterial disease: a literature review

INTRODUCTION

Peripheral arterial disease (PAD) is a common vascular condition that affects both quality of life and life expectancy with an increased risk of cardiovascular events.

SOURCES OF DATA

A literature search was carried out of Pub-Med, MEDLINE, the Cochrane Library and Google Scholar from the establishment of these databases up to February 2012. The search was performed by using the keywords 'peripheral arterial disease' and one of the following words: 'management', 'investigations', 'risk factors', 'epidemiology', 'revascularization', 'cryoplasty', 'atherectomy' and 'gene therapy'. Studies were limited to those published in English language.

AREAS OF AGREEMENT

Aggressive risk factors modification is needed to reduce cardiovascular-related mortality in PAD patients.

AREAS OF CONTROVERSY

Choice of endovascular or surgical intervention remains controversial in an ever-evolving field.

GROWING POINTS

There is a rapid expansion of endovascular technologies aiming to improve the effectiveness of this modality.

AREAS TIMELY FOR DEVELOPING RESEARCH

The advances in the fields of gene therapy and therapeutic angiogenesis mean these are potential future treatments. Tissue engineering is a developing area and aims to produce grafts with similar patency and infection profiles to those of autologous material. Further elucidation of the pathophysiology of atherosclerosis is required to provide new targets for pharmacotherapy.

Gene therapy in the treatment of peripheral arterial disease

BACKGROUND

Peripheral arterial disease remains a significant global health burden despite revolutionary improvements in endovascular techniques over the past decade. The durability of intervention for critical limb ischaemia is poor, and the condition is associated with high morbidity and mortality rates. To address this deficiency, alternative therapeutic options are being explored. Advances in the fields of gene therapy and therapeutic angiogenesis have led to these being advocated as potential future treatments.

METHODS

Relevant medical literature from PubMed, Embase, the Cochrane Library and Google Scholar from the inception of these databases to June 2011 was reviewed.

RESULTS

Encouraging outcomes in preclinical trials using a variety of proangiogenic growth factors have led to numerous efficacy and safety studies. However, no clinical study has shown significant benefit for gene therapy over placebo.

CONCLUSION

Identifying the optimal site for gene delivery, choice of vector and duration of treatment is needed if gene therapy is to become a credible therapeutic option for peripheral arterial disease.

Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.

Is endovenous laser ablation possible while taking warfarin?

Purpose

The subgroup of patients with venous ulcers requiring anticoagulation for co-morbid conditions has traditionally created a therapeutic dilemma. Perioperative management of anticoagulation can be costly and increase the risk of surgical complications. This group of patients is often elderly and shows poor compliance with compression hosiery. The aim of this study was to investigate the outcome of endovenous laser ablation (EVLA) of the great saphenous vein (GSV) in patients remaining on therapeutic anticoagulation.

Materials and methods

Fifteen consecutive patients (CEAP [clinical, aetiological, anatomical and pathological elements] classification 5 or 6) were treated with standard GSV EVLA using tumescent anaesthesia and a diode 1470-nm radial laser fibre while maintaining international normalized ratio at therapeutic levels. Clinical and duplex follow-up at six weeks and three, six and 12 months were performed.

Results

The GSV was successfully occluded in 14/15 (93%) of patients. The remaining patient had a second successful treatment three months later. No significant complications requiring intervention were encountered.

Conclusion

EVLA using the diode 1470-nm radial fibre is efficacious with minimal complications in patients therapeutically anticoagulated. This treatment should be added to the armamentarium in this problematic patient group.

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size

Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.

Molecular markers to discriminate among four pest species of Helicoverpa (Lepidoptera: Noctuidae)

The four significant pest species in the Helicoverpa genus (H. armigera, H. assulta, H. punctigera and H. zea) are morphologically similar and can only be reliably distinguished through dissection of adult genitalia. Two partial regions of the mitochondrial DNA (mtDNA), the cytochrome oxidase subunit I (COI) and the cytochrome b (Cyt b) genes were amplified by PCR and digested with restriction endonucleases. The restriction patterns, generated by the endonucleases BstZ17I and HphI, demonstrated reliable differentiation of the four Helicoverpa pest species. This technique is fast, reliable and effective at distinguishing specimens irrespective of their life stages and offers support to conventional taxonomic differentiation based on morphological characters.

Vascular endothelial growth factor is associated with histological instability of carotid plaques

Background

Vascular endothelial growth factor (VEGF) promotes events favouring carotid plaque instability: inflammatory chemoattraction, thrombogenesis, and upregulation of matrix metalloproteinases and cell adhesion molecules. The aim of this study was to assess neovascularization, VEGF and its receptors in high-grade stable and unstable carotid plaques.

Methods

Immunohistochemical staining for CD34, VEGF, VEGF receptor (VEGFR) 1 and VEGFR2 was performed in 34 intact carotid endarterectomy specimens, and compared in sections demonstrating maximal histological instability (cap rupture/thinning) or, if stable, maximal stenosis.

Results

VEGF staining was increased in 12 unstable compared with 22 stable plaques (median (interquartile range, i.q.r.) plaque score 4·0 (4·0–4·0) versus 3·0 (2·0–3·0); P = 0·002) with upregulation of VEGFR1 (plaque score 4·0 (2·0–4·0) versus 2·0 (1·0–3·0); P = 0·016). In unstable plaques this was associated with increased microvessel density in the cap (median (i.q.r.) 12·1 (4·0–30·0) versus 1·1 (0·0–7·3) microvessels/mm2; P = 0·017) and shoulder regions (7·7 (3·4–21·4) versus 3·1 (0·4–10·8) microvessels/mm2; P = 0·176).

Conclusion

Increased VEGF and receptor staining were seen in histologically unstable carotid plaques. Although these differences could reflect cytokine-driven inflammatory events accompanying plaque instability, VEGF and VEGFR1 could be key mediators.

Blob dynamics in 3D BOUT simulations of tokamak edge turbulence

Propagating filaments of enhanced plasma density, or blobs, observed in 3D numerical simulations of a diverted, neutral-fueled tokamak are studied. Fluctuations of vorticity, electrical potential phi, temperature Te, and current density J parallel associated with the blobs have a dipole structure perpendicular to the magnetic field and propagate radially with large E x B drift velocities (>1 km/s). The simulation results are consistent with a 3D blob dynamics model that incorporates increased parallel plasma resistivity (from neutral cooling of the X-point region), blob disconnection from the divertor sheath, X-point closure of the current loops, and collisional physics to sustain the phi, Te, J parallel dipoles.

Intracerebral Haemorrhage Following Carotid Endarterectomy

OBJECTIVES

To determine risk factors for the development of hyperperfusion and intra-cerebral haemorrhage following carotid endarterectomy and formulate potential protocols for prevention.

METHODS

MEDLINE database search of the English language literature (1966-2002) was performed using the words 'cerebral haemorrhage', 'intracranial haemorrhage' and 'carotid endarterectomy'. Other articles were cross-referenced by hand.

RESULTS

There are no data from randomised trials confirming the significance of any single risk factor. The evidence suggests that the following may have a role: pre-operative hypertension, recent ipsilateral non-haemorrhagic stroke, previous ischaemic cerebral infarction, surgery for a > 90% ipsilateral internal carotid artery (ICA) stenosis, impaired cerebrovascular reserve, intra-operative haemodynamic or embolic ischaemia, post-operative hypertension, an ipsilateral increase of > or =175% in peak middle cerebral artery velocity (MCAV) and/or a > or =100% increase in pulsatility index.

CONCLUSIONS

A critical ICA stenosis with impaired cerebrovascular reserve resulting in maximal intracerebral vasodilatation and post-operative hyperperfusion (impaired autoregulation) appear to be central to the development of ICH. Appropriate pre-operative screening and post-operative monitoring in high risk patients might identify those who would benefit from manipulation of the haemodynamic events that appear to promote ICH.

Observation of stimulated electron-acoustic-wave scattering

A diffraction-limited laser interacts with a plasma whose conditions are uniform on the scale of the focused laser spot. Two distinct, narrow waves are observed in the backscattered spectrum with phase velocities of v(phi)/v(e) = 1.4+/-0.08 and 4.2+/-0.1, where v(e) is the electron thermal speed. The high-velocity wave is ordinary stimulated Raman scattering (SRS) from a Langmuir wave. The low-velocity wave corresponds to stimulated scattering from an electron-acoustic wave (SEAS), and implies strong electron trapping. Previous SRS data from low-density plasmas are reinterpreted in terms of SEAS.

Risedronate pharmacokinetics and intra- and inter-subject variability upon single-dose intravenous and oral administration

PURPOSE

To determine the pharmacokinetics and absolute bioavailability of risedronate after single-dose oral administration of 30 mg risedronate as a tablet and an aqueous solution, and 0.3 mg risedronate as an intravenous infusion.

METHODS

This study was a randomized, three-treatment, four-period, partial replicate crossover study involving 33 healthy volunteers. Treatments were administered 7 weeks apart, and the third treatment was repeated during the fourth period. Serum and urine were collected over 72 hours and 672 hours, respectively.

RESULTS

Following intravenous administration, renal clearance accounted for 87% of total clearance, with 65% of the dose excreted within 24 hours and 85% of the dose excreted within four weeks. The absolute bioavailability was approximately 0.62% after both oral formulations, and the relative bioavailability of the tablet compared with the oral solution was 104%. The rate and extent of absorption from the two formulations were bioequivalent based on the range proposed for highly variable drugs. Intrasubject variability following oral administration was 50-80%, and was primarily associated with absorption.

CONCLUSION

The majority of the total clearance after intravenous administration of risedronate was renal clearance, indicating that only a small percentage of a systemic dose is potentially incorporated, or "cleared," into bone. The absolute bioavailability of orally administered risedronate is approximately 0.6%, and is independent of formulation. Variability in the pharmacokinetics following oral administration is primarily associated with intrasubject variability in absorption.

Functional, biochemical and genetic diversity of prokaryotic nitrate reductases

Prokaryotic nitrate reduction can serve a number of physiological roles and can be catalysed by a number of biochemically distinct nitrate reductases. Three distinct nitrate reductase classes can be indentified in prokaryotes, NAS, NAR and NAP. NAS is located in the cytoplasmic compartment and participates in nitrogen assimilation. NAR is usually a three-subunit complex anchored to the cytoplasmic face of the membrane with its active site located in the cytoplasmic compartment and is involved in anaerobic nitrate respiration. NAP is a two-subunit complex, located in the periplasmic compartment, that is coupled to quinol oxidation via a membrane anchored tetraheme cytochrome. It shows considerable functional flexibility by participating in anaerobic respiration or redox energy dissipation depending on the organism in which it is found. The members of all three classes of enzymes bind the bis-molybdopterin guanine dinucleotide cofactor at the active site, but they differ markedly in the number and nature of cofactors used to transfer electrons to this site. Analysis of prokaryotic genome sequences available at the time of writing reveals that the different nitrate reductases are phylogenetically widespread.

3/2omega0 radiation from the laser-driven two-plasmon decay instability in an inhomogeneous plasma

We present the results of the first reduced model simulations of the nonlinear development of the two-plasmon decay instability in an inhomogeneous plasma, including properties of the 3/2 harmonic emission. A sharp increase in radiation and Langmuir turbulence fluctuation levels occurs above a threshold laser intensity that depends on initial fluctuation levels. We study the competition between the linear propagation of Langmuir waves in the density gradient and the nonlinear saturation due to the Langmuir decay instability. The secondary decay Langmuir waves can provide the dominant source of the radiation and are essential to explain experiments.

Optical biosensing of nitrite ions using cytochrome cd1 nitrite reductase encapsulated in a sol-gel matrix

Nitrite is an important human health and environmental analyte. As such, the European Union (EU) has imposed a limit for nitrite in potable water of 0.1 mg l-1 (2.18 microM). In order to develop an optical biosensing system for the determination of nitrite ions in environmental waters, cytochrome cd1 nitrite reductase has been extracted and purified from the bacterium Paracoccus pantotrophus. The protein has been spectroscopically characterised in solution and important kinetic parameters of nitrite reduction of the cytochrome cd1 enzyme, i.e., Km, Vmax and kcat have been determined. The influence of pH on the activity of the cytochrome cd1 has been investigated and the results suggest that this enzyme can be used for the determination of nitrite in the pH range 6-9. Biosensing experiments with the cytochrome cd1 in solution suggested that the decrease in intensity of the absorption band associated with the d1 haem (which is the nitrite binding site), at 460 nm, with increasing nitrite concentrations would enable the measurement of this analyte with the optimum limit of detection. The cytochrome cd1 has been encapsulated in a bulk sol-gel monolith with no structural changes observed and retention of enzymatic activity. The detection of nitrite ions in the range 0.075-1.250 microM was achieved, with a limit of detection of 0.075 microM. In order to increase the speed of response, a sol-gel sandwich thin film structure was formulated with the cytochrome cd1. This structure enabled the determination of nitrite concentrations within ca. 5 min. The sol-gel sandwich entrapped cytochrome cd1 enzyme was found to be stable for several months when the films were stored at 4 degrees C.

Development of perfluorocarbon tracer technology for underground leak location

A method has been developed for the atmospheric sampling and analysis of four perfluorocarbon tracer (PFT) compounds simultaneously at the parts per trillion (ppt) level. PFTs were pre-concentrated using adsorbent tube air sampling. Analysis was achieved by thermal desorption (TD) and gas chromatography (GC) with electron capture detection (ECD). Efficient separation of the PFTs from the other sample constituents was achieved by use of a capillary porous layer open tubular (PLOT) GC column without the need to cool the GC oven to sub-ambient temperatures using liquid coolants (M. de Bortoli and E. Pecchio, J. High Resolut. Chromatogr., 1985, 8, 422) or for a catalytic destruction step to remove interferents (T. W. D'Ottavio, R. W. Goodrich and R. N. Dietz, Environ. Sci. Technol., 1986, 20, 100). Results from test field trials with two volatile PFTs that were buried to simulate an underground leaking cable were successful. The PFTs were detected above ground level to pinpoint the leak position. The highest tracer concentrations were detected within 1 m of the simulated leak positions 2 days after tracer burial. The developed technology was applied to an oil leaking high voltage electricity cable. One PFT was added to the cable oil which enabled detection of the oil leak to within 3 m. The reported method has many advantages over currently used leak detection methods and could, in the future, be applied to the detection of underground leaks in a variety of cables and pipes.

Cardiovascular evidence for an intermediate or higher metabolic rate in an ornithischian dinosaur

Computerized tomography scans of a ferruginous concretion within the chest region of an ornithischian dinosaur reveal structures that are suggestive of a four-chambered heart and a single systemic aorta. The apparently derived condition of the cardiovascular system in turn suggests the existence of intermediate-to-high metabolic rates among dinosaurs.

Effect of renal function on risedronate pharmacokinetics after a single oral dose

AIMS

To determine the relationship between risedronate pharmacokinetics and renal function.

METHODS

Risedronate was administered to adult men and women (n=21) with various degrees of renal function (creatinine clearance 15-126 ml min-1 ) as a single oral dose of 30 mg. Serum samples were obtained for 72 h after dosing, and urine samples were collected for 72 h after dosing and then periodically for 6 weeks. Risedronate concentrations were determined using an enzyme-linked immunosorbent assay (ELISA). Risedronate serum concentration-time and urinary excretion rate-time profiles were analysed simultaneously using nonlinear regression.

RESULTS

Renal clearance and volume of distribution were linearly related to creatinine clearance (r2=0.854, P<0.001; and r2=0.317, P<0.01, respectively). Decreases in predicted renal clearance and volume of distribution of 82 and 69%, respectively, were observed when creatinine clearance decreased from 120 to 20 ml min-1. A 64% decrease in predicted oral clearance was observed when creatinine clearance decreased from 120 to 20 ml min-1 (P=0.064). Iohexol clearance, a predictor of renal function, produced similar results to those observed with creatinine clearance. Risedronate was well tolerated by the study population.

CONCLUSIONS

Risedronate renal clearance was significantly related to a decrease in renal function. There was a consistent reduction in oral clearance with a decrease in creatinine clearance. However, based on the regression analysis, generally no dosage adjustment appears to be necessary for most patients with mild or moderate renal impairment (creatinine clearance >20 ml min-1 ).

High-yield production of a human therapeutic protein in tobacco chloroplasts

Transgenic plants have become attractive systems for production of human therapeutic proteins because of the reduced risk of mammalian viral contaminants, the ability to do large scale-up at low cost, and the low maintenance requirements. Here we report a feasibility study for production of a human therapeutic protein through transplastomic transformation technology, which has the additional advantage of increased biological containment by apparent elimination of the transmission of transgenes through pollen. We show that chloroplasts can express a secretory protein, human somatotropin, in a soluble, biologically active, disulfide-bonded form. High concentrations of recombinant protein accumulation are observed (>7% total soluble protein), more than 300-fold higher than a similar gene expressed using a nuclear transgenic approach. The plastid-expressed somatotropin is nearly devoid of complex post-translational modifications, effectively increasing the amount of usable recombinant protein. We also describe approaches to obtain a somatotropin with a non-methionine N terminus, similar to the native human protein. The results indicate that chloroplasts are a highly efficient vehicle for the potential production of pharmaceutical proteins in plants.

Significant differences in estradiol bioavailability from two similarly labelled estradiol matrix transdermal systems

OBJECTIVE

To compare the bioavailabilities of estradiol delivered by two transdermal estradiol matrix systems; Alora and Evorel.

STUDY DESIGN

A single-center, open-label, randomized, two-period cross-over study in 33 postmenopausal women. The subjects received two successive 84-h applications of either Alora or Evorel (each labelled to deliver 50 micrograms/day 17 beta-estradiol) in a randomized sequence. Serial serum samples, collected over the 84-h period following the application of the second patch, were analyzed for estradiol using a validated radioimmunoassay method.

RESULTS

The fluctuation index produced by Evorel was significantly higher than that produced by Alora (Evorel, 135%; Alora, 76%; p < 0.0005). In addition, the estradiol baseline-corrected area under the curve for Evorel was significantly lower than that for Alora (Alora, 2871.8 pg h/ml; Evorel, 1870.6 pg h/ml; p < 0.0005). Both patches were found to be generally well tolerated.

CONCLUSION

Alora delivered a higher, more consistent concentration of estradiol into the systemic circulation over the entire dosing interval than did Everol. Although the full clinical significance of these findings is currently unknown, this study demonstrates that there are significant differences in estradiol delivery from these two products, although they are labelled with the same nominal delivery rate.

The effect of dosing regimen on the pharmacokinetics of risedronate

AIMS

To examine the effect of timing of a risedronate dose relative to food intake on the rate and extent of risedronate absorption following single-dose, oral administration to healthy male and female volunteers.

METHODS

A single-dose, randomized, parallel study design was conducted with volunteers assigned to four treatment groups (31 or 32 subjects per group, 127 subjects total). Each subject was orally administered 30 mg risedronate. Group 1 was fasted for 10 h prior to and 4 h after dosing (fasted group); Groups 2 and 3 were fasted for 10 h and were dosed 1 and 0.5 h, respectively, before a high-fat breakfast; and Group 4 was dosed 2 h after a standard dinner. Blood and urine samples were collected for 168 h after dosing. Pharmacokinetic parameters were estimated by simultaneous analysis of risedronate serum concentration and urinary excretion rate-time data.

RESULTS

Extent of risedronate absorption (AUC and Ae ) was comparable (P=0.4) in subjects dosed 2 h after dinner and 0.5 h before breakfast; however, a significantly greater extent of absorption occurred when risedronate was given 1 or 4 h prior to a meal (1.4- to 2.3-fold greater). Administration 0.5, 1, or 4 h prior to a meal resulted in a significantly greater rate of absorption (Cmax 2.8-, 3.5-, and 4.1-fold greater, respectively) when compared with 2 h after dinner.

CONCLUSIONS

The comparable extent of risedronate absorption when administered either 0.5-1 h before breakfast or 2 h after an evening meal support previous clinical studies where risedronate was found to have similar effectiveness using these dosing regimens. This flexibility in the timing of risedronate administration may provide patients an alternative means to achieve the desired efficacy while maintaining their normal daily routine.

Feasibility of antibody production in plants for human therapeutic use

From the description above, the diversity of antibodies as a class of potential therapeutic agents is weighed against the constraints of developing any therapeutic molecule. Although much of this limit is specific to the antibody design, plant-based production systems have a potential to impact commercialization by making larger volume products manageable, with lower up-front capital requirements. Due to their novel glycosylation pattern (Faye et al. 1989), plants at present may not create antibodies with all the functions of mammalian-glycosylated antibodies (Wright and Morrison 1994). This is not a limit for all current products. Success is dependent on fusing the efficient agriculture infrastructure with the narrow tolerances required for a drug production system. Further validation of plants as a production system will come as more therapeutics from plants follow the corn-produced material through human clinical trials.