Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution

Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace. As more phage genomes are published, new methods are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study by phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. We focus our analyses on virus host range and show how network topology corresponds to host relatedness, how to find groups of genes with the strongest host-specific signatures, and how this perspective can complement phage host prediction tools. We discuss extensions of gene network analysis to predicting the emergence of phages on new hosts, as well as applications to features of phage biology beyond host range

Rephine.r: A pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies

Background. A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools. Methods. We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: (1) indels creating early stop codons and new start codons; (2) interruption by a selfish genetic element; and (3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees. Results. We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g., T4), the Studiervirinae (e.g., T7), and the Pbunaviruses (e.g., PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny. The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single script for automated analysis and with utility functions to assist in building single-copy core genomes and predicting the sources of fragmented genes

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality

Lactobacilli are dominant members of the “healthy” female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction between genomes of the two species. We find eight additional strains of the species L. mulieris among these genomes. Furthermore, one strain, currently classified as L. mulieris UMB7784, is distinct from both L. jensenii and L. mulieris strains. As part of our comparative genomic study, we also investigated the genetic content that distinguishes these two species. Unique to the L. jensenii genomes are several genes related to catabolism of disaccharides. In contrast, L. mulieris genomes encode several cell surface and secreted proteins that are not found within the L. jensenii genomes. These L. jensenii-specific and L. mulieris-specific loci provide insight into phenotypic differences of these two species

Introducing Lu-1, a Novel Lactobacillus jensenii Phage Abundant in the Urogenital Tract

Bacteriophages (phages) play a key role in shaping microbial communities, including those of the human body. Phages are abundant members of the urogenital tract, most often persisting through the lysogenic life cycle as prophages integrated within the genomes of their bacterial hosts. While numerous studies of the urogenital microbiota have focused on the most abundant bacterial member of this niche–Lactobacillus species–very little is known about Lactobacillus phages. Focusing on Lactobacillus jensenii strains from the urinary tract, we identified numerous prophages related to the previously characterized Lv-1 phage from a vaginal L. jensenii strain. Furthermore, we identified a new L. jensenii phage, Lu-1. Evidence suggests that both phages are abundant within the urogenital tract. CRISPR spacer sequences matching to Lv-1 and Lu-1 prophages were identified. While first detected in urinary isolates, the Lu-1 phage was also discovered in L. jensenii isolates from vaginal and perineal swabs, and both phages were found in metagenomic data sets. The prevalence of these phages in the isolates suggests that both phages are active members of the urogenital microbiota

ELFbac: Using the Loader Format for Intent-Level Semantics and Fine-Grained Protection

Adversaries get software to do bad things by rewriting memory and changing control flow. Current approaches to protecting against these attacks leave many exposures; for example, OS-level filesystem protection and OS/architecture support of the userspace/kernelspace distinction fail to protect corrupted userspace code from changing userspace data. In this paper we present a new approach: using the ELF/ABI sections already produced by the standard binary toolchain to define, specify, and enforce fine-grained policy within an application\u27s address space. We experimentally show that enforcement of such policies would stop a large body of current attacks and discuss ways we could extend existing architecture to more efficiently provide such enforcement. Our approach is designed to work with existing ELF executables and the GNU build chain, but it can be extended into the compiler toolchains to support code annotations that take advantage of ELFbac enforcement-while maintaining full compatibility with the existing ELF ABI

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations

Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome

Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species’ evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts

The Impact of Interpixel Capacitance in CMOS Detectors on PSF Shapes and Implications for WFIRST

Unlike optical CCDs, near-infrared detectors, which are based on CMOS hybrid readout technology, typically suffer from electrical crosstalk between the pixels. The interpixel capacitance (IPC) responsible for the crosstalk affects the point-spread function (PSF) of the telescope, increasing the size and modifying the shape of all objects in the images while correlating the Poisson noise. Upcoming weak lensing surveys that use these detectors, such as WFIRST, place stringent requirements on the PSF size and shape (and the level at which these are known), which in turn must be translated into requirements on IPC. To facilitate this process, we present a first study of the effect of IPC on WFIRST PSF sizes and shapes. Realistic PSFs are forward-simulated from physical principles for each WFIRST bandpass. We explore how the PSF size and shape depends on the range of IPC coupling with pixels that are connected along an edge or corner; for the expected level of IPC in WFIRST, IPC increases the PSF sizes by ~5%. We present a linear fitting formula that describes the uncertainty in the PSF size or shape due to uncertainty in the IPC, which could arise for example due to unknown time evolution of IPC as the detectors age or due to spatial variation of IPC across the detector. We also study of the effect of a small anisotropy in the IPC, which further modifies the PSF shapes. Our results are a first, critical step in determining the hardware and characterization requirements for the detectors used in the WFIRST survey

Effect of Levocarnitine vs Placebo as an Adjunctive Treatment for Septic Shock: The Rapid Administration of Carnitine in Sepsis (RACE) Randomized Clinical Trial

Importance: Sepsis induces profound metabolic derangements, while exogenous levocarnitine mitigates metabolic dysfunction by enhancing glucose and lactate oxidation and increasing fatty acid shuttling. Previous trials in sepsis suggest beneficial effects of levocarnitine on patient-centered outcomes. Objectives: To test the hypothesis that levocarnitine reduces cumulative organ failure in patients with septic shock at 48 hours and, if present, to estimate the probability that the most efficacious dose will decrease 28-day mortality in a pivotal phase 3 clinical trial. Design, Setting, and Participants: Multicenter adaptive, randomized, blinded, dose-finding, phase 2 clinical trial (Rapid Administration of Carnitine in Sepsis [RACE]). The setting was 16 urban US medical centers. Participants were patients aged 18 years or older admitted from March 5, 2013, to February 5, 2018, with septic shock and moderate organ dysfunction. Interventions: Within 24 hours of identification, patients were assigned to 1 of the following 4 treatments: low (6 g), medium (12 g), or high (18 g) doses of levocarnitine or an equivalent volume of saline placebo administered as a 12-hour infusion. Main Outcomes and Measures: The primary outcome required, first, a greater than 90% posterior probability that the most promising levocarnitine dose decreases the Sequential Organ Failure Assessment (SOFA) score at 48 hours and, second (given having met the first condition), at least a 30% predictive probability of success in reducing 28-day mortality in a subsequent traditional superiority trial to test efficacy. Results: Of the 250 enrolled participants (mean [SD] age, 61.7 [14.8] years; 56.8% male), 35, 34, and 106 patients were adaptively randomized to the low, medium, and high levocarnitine doses, respectively, while 75 patients were randomized to placebo. In the intent-to-treat analysis, the fitted mean (SD) changes in the SOFA score for the low, medium, and high levocarnitine groups were -1.27 (0.49), -1.66 (0.38), and -1.97 (0.32), respectively, vs -1.63 (0.35) in the placebo group. The posterior probability that the 18-g dose is superior to placebo was 0.78, which did not meet the a priori threshold of 0.90. Mortality at 28 days was 45.9% (34 of 74) in the placebo group compared with 43.3% (45 of 104) for the most promising levocarnitine dose (18 g). Similar findings were noted in the per-protocol analysis. Conclusions and Relevance: In this dose-finding, phase 2 adaptive randomized trial, the most efficacious dose of levocarnitine (18 g) did not meaningfully reduce cumulative organ failure at 48 hours

Error-analysis and comparison to analytical models of numerical waveforms produced by the NRAR Collaboration

The Numerical-Relativity-Analytical-Relativity (NRAR) collaboration is a joint effort between members of the numerical relativity, analytical relativity and gravitational-wave data analysis communities. The goal of the NRAR collaboration is to produce numerical-relativity simulations of compact binaries and use them to develop accurate analytical templates for the LIGO/Virgo Collaboration to use in detecting gravitational-wave signals and extracting astrophysical information from them. We describe the results of the first stage of the NRAR project, which focused on producing an initial set of numerical waveforms from binary black holes with moderate mass ratios and spins, as well as one non-spinning binary configuration which has a mass ratio of 10. All of the numerical waveforms are analysed in a uniform and consistent manner, with numerical errors evaluated using an analysis code created by members of the NRAR collaboration. We compare previously-calibrated, non-precessing analytical waveforms, notably the effective-one-body (EOB) and phenomenological template families, to the newly-produced numerical waveforms. We find that when the binary's total mass is ~100-200 solar masses, current EOB and phenomenological models of spinning, non-precessing binary waveforms have overlaps above 99% (for advanced LIGO) with all of the non-precessing-binary numerical waveforms with mass ratios <= 4, when maximizing over binary parameters. This implies that the loss of event rate due to modelling error is below 3%. Moreover, the non-spinning EOB waveforms previously calibrated to five non-spinning waveforms with mass ratio smaller than 6 have overlaps above 99.7% with the numerical waveform with a mass ratio of 10, without even maximizing on the binary parameters.Comment: 51 pages, 10 figures; published versio