Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching.

Organisms have evolved different mechanisms in response to periods of environmental stress, including dormancy - a reversible state of reduced metabolic activity. Transitions to and from dormancy can be random or induced by changes in environmental conditions. Prior theoretical work has shown that stochastic transitioning between active and dormant states at the individual level can maximize fitness at the population level. However, such theories of 'bet-hedging' strategies typically neglect certain physiological features of transitions to dormancy, including time lags to gain protective benefits. Here, we construct and analyze a dynamic model that couples stochastic changes in environmental state with the population dynamics of organisms that can initiate dormancy after an explicit time delay. Stochastic environments are simulated using a multi-state Markov chain through which the mean and variance of environmental residence time can be adjusted. In the absence of time lags (or in the limit of very short lags), we find that bet-hedging strategy transition probabilities scale inversely with the mean environmental residence times, consistent with prior theory. We also find that increasing delays in dormancy decreases optimal transitioning probabilities, an effect that can be influenced by the correlations of environmental noise. When environmental residence times - either good or bad - are uncorrelated, the maximum population level fitness is obtained given low levels of transitioning between active and dormant states. However when environmental residence times are correlated, optimal dormancy initiation and termination probabilities increase insofar as the mean environmental persistent time is longer than the delay to reach dormancy. We also find that bet hedging is no longer advantageous when delays to enter dormancy exceed the mean environmental residence times. Altogether, these results show how physiological limits to dormancy and environmental dynamics shape the evolutionary benefits and even viability of bet hedging strategies at population scales.

Isolation and characterization of a novel Lambda-like phage infecting the bloom-forming cyanobacteria Cylindrospermopsis raciborskii.

Cylindrospermopsis raciborskii is a central bloom-forming cyanobacteria. However, despite its ecological significance, little is known of its interactions with the phages that infect it. Currently, only a single sequenced genome of a Cylindrospermopsis-infecting phage is publicly available. Here we describe the isolation and characterization of Cr-LKS3, a second phage infecting Cylindrospermopsis. Cr-LKS3 is a siphovirus with a higher genome similarity to prophages within heterotrophic bacteria genomes than to any other cyanophage/cyano-prophage, suggesting that it represents a novel cyanophage group. The function, order and orientation of the 72 genes in the Cr-LKS3 genome are highly similar to those of Escherichia virus Lambda (hereafter Lambda), despite the very low sequence similarity between these phages, showing high evolutionary convergence despite the substantial difference in host characteristics. Similarly to Lambda, the genome of Cr-LKS3 contains various genes that are known to be central to lysogeny, suggesting it can enter a lysogenic cycle. Cr-LKS3 has a unique ability to infect a host with a dramatically different GC content, without carrying any tRNA genes to compensate for this difference. This ability, together with its potential lysogenic lifestyle shed light on the complex interactions between C. raciborskii and its phages.

Bovine leukemia virus discovered in human blood.

BACKGROUND: Bovine leukemia virus (BLV) infection is widespread in cattle globally and is present in marketed beef and dairy products. Human infection with BLV has been reported in breast and lung cancer tissues and was significantly associated with breast cancer in 3 case-control studies. The purpose of this current research was to determine if BLV is present in human blood cells and if antibodies to BLV are related to blood cell infection. METHODS: Standard liquid PCR and Sanger DNA sequencing were used to test for BLV in buffy coat cells (leukocytes and platelets) of blood specimens from 95 self-selected female subjects. Enzyme-linked immunosorbent assay (ELISA) for IgG, IgM, and IgA was used to detect antibodies to BLV in the plasma of the corresponding blood samples. RESULTS: BLV DNA was detected in the buffy coat cells of blood in 33/95 (38%) of the subjects by PCR and DNA sequencing. IgG antibodies were detected in 30/95(32%), IgM in 55/95(58%), and IgA in 30/95(32%) of the subjects. There was no significant correlation between presence of the antibodies and presence of BLV DNA. CONCLUSIONS: This first report of BLV in human blood raises the question of whether infection of leukocytes could conceivably lead to leukemia as it does in infected cattle. Also, system wide circulation of infected blood cells could facilitate BLV transit to various internal tissues/organs with potential for their infection and subsequent development of cancer. The most likely route of BLV transmission to humans would be zoonotic, as a foodborne infection. Although eradicated from cattle in some countries, BLV still has a high rate of infection in the Americas, the Middle East, and parts of Europe and Asia. This report of BLV in the blood layer containing human leukocytes/platelets adds important information which could be useful to elucidate possible routes of transmission of BLV to humans and to prevent further human infection.

Classification of traumatic injury to the dural venous sinus using CT venography.

BACKGROUND AND PURPOSE: Cerebral venous sinus thrombosis (CVST) is an underrecognized cause of morbidity in acute traumatic brain injury (TBI). Radiologic diagnosis is challenging in the setting of concurrent extra-axial injury and a lack of standardized diagnostic criteria. The prevalence of traumatic thrombosis versus compression is unknown. Treatment with anticoagulation is often determined by the appropriate classification of the type of traumatic venous injury. METHODS: We developed a two-part radiologic grading method for standardized assessment of traumatic CVST based on (1) the degree of flow limitation through the affected sinus and (2) the location of venous pathology (ie, external compression vs. intrinsic thrombosis) based on computed tomography venography. We applied this grading method to a retrospective cohort of TBI patients presenting to a Level 1 Trauma center. Chart review was performed to identify potential clinical correlates. A senior neuroradiologist graded the entire cohort and a random subsample was selected for blinded rating by two independent neuroradiologists. RESULTS: Seventy-six of 221 patients were identified for inclusion after excluding nontraumatic mechanisms. Seven unique grades were employed to characterize the full extent of venous injuries. The plurality of patients from the cohort (43/76 = 43.4%) suffered compressive injuries. Inter-rater reliability was moderate for the combined grade, kappa = 0.48, p<.05, and substantial for the flow limitation component, kappa = 0.69, p<.05. CONCLUSIONS: We introduce a standardized two-part classification system for traumatic venous sinus injury with moderate-substantial inter-rater reliability. Compressive injuries were more common than thrombotic injuries. Further prospective work is needed to validate the clinical significance of this classification system.

Bacterium secretes chemical inhibitor that sensitizes competitor to bacteriophage infection.

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighboring cells and sequester nutrients. This natural product-mediated competition likely evolved in complex microbial communities that included viral pathogens. From this ecological context, we hypothesized that microbes secrete metabolites that "weaponize" natural pathogens (i.e., bacteriophages) to lyse their competitors. Indeed, we discovered a bacterial secondary metabolite that sensitizes other bacteria to phage infection. We found that this metabolite provides the producer (a Streptomyces sp.) with a fitness advantage over its competitor (Bacillus subtilis) by promoting phage infection. The phage-promoting metabolite, coelichelin, sensitized B. subtilis to a wide panel of lytic phages, and it did so by preventing the early stages of sporulation through iron sequestration. Beyond coelichelin, other natural products may provide phage-mediated competitive advantages to their producers-either by inhibiting sporulation or through yet-unknown mechanisms.

Sputter deposition of PZT piezoelectric films on thin glass substrates for adjustable x-ray optics.

Piezoelectric PbZr(0.52)Ti(0.48)O(3) (PZT) thin films deposited on thin glass substrates have been proposed for adjustable optics in future x-ray telescopes. The light weight of these x-ray optics enables large collecting areas, while the capability to correct mirror figure errors with the PZT thin film will allow much higher imaging resolution than possible with conventional lightweight optics. However, the low strain temperature and flexible nature of the thin glass complicate the use of chemical-solution deposition due to warping of the substrate at typical crystallization temperatures for the PZT. RF magnetron sputtering enabled preparation of PZT films with thicknesses up to 3 µm on Schott D263 glass substrates with much less deformation. X-ray diffraction analysis indicated that the films crystallized with the perovskite phase and showed no indication of secondary phases. Films with 1 cm(2) electrodes exhibited relative permittivity values near 1100 and loss tangents below 0.05. In addition, the remanent polarization was 26 µC/cm(2) with coercive fields of 33 kV/cm. The transverse piezoelectric coefficient was as high as -6.1±0.6 C/m(2). To assess influence functions for the x-ray optics application, the piezoelectrically induced deflection of individual cells was measured and compared with finite-element-analysis calculations. The good agreement between the results suggests that actuation of PZT thin films can control mirror figure errors to a precision of about 5 nm, allowing sub-arcsecond imaging.

Bacteria-phage coevolution with a seed bank.

Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that, by generating a seed bank of protected individuals, dormancy can modify the patterns and processes of antagonistic coevolution. We conducted a factorially designed experiment where we passaged a bacterial host (Bacillus subtilis) and its phage (SPO1) in the presence versus absence of a seed bank consisting of dormant endospores. Owing in part to the inability of phages to attach to spores, seed banks stabilized population dynamics and resulted in minimum host densities that were 30-fold higher compared to bacteria that were unable to engage in dormancy. By supplying a refuge to phage-sensitive strains, we show that seed banks retained phenotypic diversity that was otherwise lost to selection. Dormancy also stored genetic diversity. After characterizing allelic variation with pooled population sequencing, we found that seed banks retained twice as many host genes with mutations, whether phages were present or not. Based on mutational trajectories over the course of the experiment, we demonstrate that seed banks can dampen bacteria-phage coevolution. Not only does dormancy create structure and memory that buffers populations against environmental fluctuations, it also modifies species interactions in ways that can feed back onto the eco-evolutionary dynamics of microbial communities.

Human-Gut Phages Harbor Sporulation Genes.

Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-carried sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially carried by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notably spo0A, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments. IMPORTANCE Phages acquire bacterial genes and use them to alter host metabolism in ways that enhance phage fitness. To date, most auxiliary genes replace or modulate enzymes that are used by the host for nutrition or energy production. However, phage fitness is affected by all aspects of host physiology, including decisions that reduce the metabolic activity of the cell. Here, we focus on endosporulation, a complex and ancient form of dormancy found among the Bacillota that involves hundreds of genes. By coupling homology searches with host classification, we identified 31 phage-carried homologs of sporulation genes that are mostly limited to phages infecting spore-forming bacteria. Nearly one-third of the homologs recovered were regulatory genes, suggesting that phages may manipulate host genetic networks by tapping into their control elements. Our findings also suggest a mechanism by which phages can overcome the defensive strategy of dormancy, which may be involved in coevolutionary dynamics of spore-forming bacteria.

Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages.

Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.

The 21st Century Cures Act and Early Feasibility Studies for Cardiovascular Devices: What Have We Learned, Where Do We Need to Go?

Performance of early feasibility studies in the United States can advance the goal of evaluating the safety and effectiveness of new devices aimed at unmet clinical needs and facilitating earlier access for U.S. patients to new technology. Early feasibility studies are an important component of the 21st Century Cures Act, enacted by Congress in 2016. Although regulatory processes have improved since the introduction of the Early Feasibility Studies Program, impediments at the hospital and clinical site level remain. In this paper, the authors review these issues and outline the structure and function of a clinical site consortium designed to address the problems and improve the U.S. clinical trial ecosystem.

Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them.

Phages and hosts coexist in nature with a high degree of population diversity. This is often explained through coevolutionary models, such as the arms race or density-dependent fluctuating selection, which differ in assumptions regarding the emergence of phage mutants that overcome host resistance. Previously, resistance in the abundant marine cyanobacterium, Prochlorococcus, was found to occur frequently. However, little is known about the ability of phages to overcome this resistance. Here we report that, in some cases, T7-like cyanophage mutants emerge to infect resistant Prochlorococcus strains. These resistance-breaking phages retained the ability to infect the wild-type host. However, fitness of the mutant phages differed on the two hosts. Furthermore, in one case, resistance-breaking was accompanied by costs of decreased fitness on the wild-type host and decreased adsorption specificity, relative to the wild-type phage. In two other cases, fitness on the wild-type host increased. Whole-genome sequencing revealed mutations in probable tail-related genes. These were highly diverse in isolates and natural populations of T7-like cyanophages, suggesting that antagonistic coevolution enhances phage genome diversity. Intriguingly, most interactions did not yield resistance-breaking phages. Thus, resistance mutations raise genetic barriers to continuous arms race cycles and are indicative of an inherent asymmetry in coevolutionary capacity, with hosts having the advantage. Nevertheless, phages coexist with hosts, which we propose relies on combined, parallel action of a limited arms race, fluctuating selection and passive host-switching within diverse communities. Together, these processes generate a constantly changing network of interactions, enabling stable coexistence between hosts and phages in nature.

Occupation and Obstructive Sleep Apnea: A Meta-Analysis.

OBJECTIVE: Obstructive sleep apnea (OSA) remains a prevalent condition, but its occupational burden is unclear. We carried out a systematic review to characterize the consistency and magnitude of occupational associations with OSA. METHODS: We studied OSA within three occupational categories: commercial drivers, organic solvent-exposed workers, other selected occupations. We performed a meta-analysis on the prevalence of OSA among drivers and the risk of OSA associated with solvent exposure. RESULTS: The pooled OSA prevalence in drivers was 41% (95% confidence interval [CI] 26% to 56%) for apnea hypopnea-index (AHI) is greater than 5, and 15% (95% CI 12% to 19%) for AHI is greater than 15. Exposure to solvents was associated with increased but non-statistically significant risk of OSA: summary relative risk, 2.38 (95% CI 0.89 to 6.32). Evidence of occupational association was inconsistent for other factors. CONCLUSIONS: OSA is common among commercial drivers and potentially associated with occupations involving likely solvent exposure.

Bovine leukemia virus linked to breast cancer in Australian women and identified before breast cancer development.

Bovine leukemia virus (BLV), a common virus of cattle globally, was believed for decades not to infect humans. More recent techniques (in situ PCR and DNA sequencing) enabled detection of BLV in human breast tissue, and determination of its significant association with breast cancer in a US population. Using similar techniques to study 96 Australian women, we report here detection of retrotranscribed BLV DNA in breast tissue of 40/50(80%) of women with breast cancer versus 19/46(41%) of women with no history of breast cancer, indicating an age-adjusted odds ratio and confidence interval of 4.72(1.71-13.05). These results corroborate the findings of the previous study of US women with an even higher odds ratio for the Australian population. For 48 of the subjects, paired breast tissue samples, removed 3-10 years apart in two unrelated procedures, were available. For 23/31 (74%) of these, in which the first specimen was diagnosed as nonmalignant (benign or premalignant) and the second as malignant, BLV was already present in benign breast tissue years 3-10 years before the malignancy was diagnosed. This is consistent with the supposition of a causative temporal relationship between BLV infection and subsequent development of cancer.

Invited review article: The Chandra X-ray Observatory.

The Chandra X-ray Observatory is an orbiting x-ray telescope facility. It is one of the National Aeronautics and Space Administration's four "Great Observatories" that collectively have carried out astronomical observations covering the infrared through gamma-ray portion of the electromagnetic spectrum. Chandra is used by astronomers world-wide to acquire imaging and spectroscopic data over a nominal 0.1-10 keV (124-1.24 Å) range. We describe the three major parts of the observatory: the telescope, the spacecraft systems, and the science instruments. This article will emphasize features of the design and development driven by some of the experimental considerations unique to x-ray astronomy. We will update the on-orbit performance and present examples of the scientific highlights.

Virus-host swinging party in the oceans: Incorporating biological complexity into paradigms of antagonistic coexistence.

Bacteria and their viruses (phages) are antagonists, yet have coexisted in nature for billions of years. Models proposed to explain the paradox of antagonistic coexistence generally reach two types of solutions: Arms race-like dynamics that lead to hosts and viruses with increasing resistance and infection ranges; and population fluctuations between diverse host and viral types due to a metabolic cost of resistance. Recently, we found that populations of the marine cyanobacterium, Prochlorococcus, consist of cells with extreme hypervariability in gene sequence and gene content in a viral susceptibility region of the genome. Furthermore, we found a novel cost of resistance where resistance to one set of viruses is accompanied by changes in infection dynamics by other viruses. In this combined mini-review and commentary paper we discuss these findings in the context of existing ecological, evolutionary and genetic models of host-virus coexistence. We suggest that this coexistence is governed mainly by fluctuations between microbial subpopulations with differing viral susceptibility regions and that these fluctuations are driven by both metabolic and enhanced infection costs of resistance. Furthermore, we suggest that enhanced infection leads to passive host-switching by viruses, preventing the development of hosts with universal resistance. These findings highlight the vital importance of community complexity for host-virus coexistence.