Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

Evidence of syndemic effects influencing older transgender persons' likelihood of contemplating suicide: results from a large national study.

OBJECTIVES: Very little research has examined suicidal ideation or the factors associated with contemplating suicide among older transgender adults. This paper examines whether or not there is evidence of syndemic effects influencing suicidal ideation among transgender persons aged 50 or older. METHODS: Data from the 2015 U.S. National Transgender Survey were used to examine five domains of potentially-syndemic effects (workplace issues, interactions with professionals, using public services, personal safety, and socioeconomic disadvantages) in a sample of 3,724 transgender Americans aged 50 or older. A dichotomous measure of suicidal ideation during the past year was the main outcome measure. RESULTS: The odds of contemplating suicide increased anywhere from 96% to 121% among people experiencing any of the problems under study, and anywhere from 258% to 1,552% (depending upon the syndemic effect domain in question) when they were faced by all of the experiences included in any particular domain. When all items were combined, exposure to any of the domains' problems elevated the risk of contemplating suicide by 276% and exposure to all of the problems examined increased the risk by 861%. The syndemic effects measure remained significant in multivariate analysis controlling for the influence of other potentially-relevant factors. CONCLUSIONS: Considerable evidence for the presence of syndemic effects was found, demonstrating that the more different types of adverse conditions that older transgender person's face, the more likely they are to experience to contemplate suicide. There is evidence that these effects diminish with advancing age.

The Relationship of Anti-Transgender Discrimination, Harassment, and Violence to Binge Drinking among Transgender Adults.

Purpose: Using a minority stress paradigm, this paper examines the relationship between anti-transgender discrimination, harassment, and violence among transgender adults. Methods: Data from the 2015 U.S. National Transgender Survey were used to examine twenty types of anti-transgender experiences/problems (e.g., harassment at work, problems with police officials, verbal and physical assaults) in a sample of 27,715 transgender Americans aged 18 or older. Binge drinking during the previous month was the dependent variable, and eight control measures were examined in the multivariate analysis. Results: Experiencing any of the twenty types of anti-transgender discrimination, harassment, or violence increased the odds of binge drinking by 48%. Experiencing many such problems increased the odds of binge drinking by 104%. Multivariate analysis showed that anti-transgender discrimination, harassment, and violence remains a predictor of binge drinking even when other key measures are taken into account. Younger people, racial minority group members, and persons who were not married or "involved" were at particularly great risk. Conclusions: Consistent with the minority stress paradigm, the more different types of anti-transgender experiences people had, the more likely they were to engage in binge drinking. Targeted intervention needs to help transgender persons to avoid anti-transgender discrimination, harassment, and violence to the greatest extent possible, and to develop resiliency skills whenever they are victimized. This is particularly true for transgender persons who are younger, minority, and not "involved" in a relationship.

Recommendations from Black and Latinx sexual minority males to include pharmacists to increase greater accessibility and OnlyFans stars to promote uptake of injectable PrEP.

BACKGROUND: Pre-exposure Prophylaxis (PrEP) medication is the keystone of preventative measures to curtail the spread of HIV. However, oral PrEP, the pill intended to prevent HIV, has been slow to proliferate among men who have sex with men (MSM). This is of major concern as MSM account for the largest number of new HIV diagnoses in the U.S. More recently, the newest generation of PrEP in the form of a long-acting injectable (LAI) is to be administered every two months as an intramuscular injection and many MSM indicate preferring LAI-PrEP to the oral form of PrEP. However, uptake of PrEP, in all forms, remains low. Research is sparse that focuses on LAI-PrEP uptake among Black/African American and Latinx men who have sex with men (BLMSM). OBJECTIVE: To address this concern, this study explored the willingness to uptake LAI-PrEP, and recommendations for increasing awareness and encouraging uptake of LAI-PrEP among BLMSM. METHODS: Qualitative data were collected between February 2022 to December 2022 through focus groups via Zoom with BLMSM (N=30; Black=14, Latinx=16) aged 18 to 29 (Mean = 23, SD = 3) in Los Angeles County. RESULTS: Findings revealed that while 90% of BLMSM were aware of PrEP in oral form, only 10% were aware of LAI-PrEP. Findings from the qualitative analysis suggested to consider self-administration of LAI-PrEP, allow local community pharmacists to assess and administer it, and promote uptake of LAI-PrEP using high-profile male content creators and stars on OnlyFans social media platform. CONCLUSION: Increasing PrEP uptake, in all forms available, such as promoting awareness through popular social media stars, and engaging community pharmacists in feasible ways, is critical for addressing the disproportionate impact of HIV among the BLMSM community.

Causal Analysis of Physiological Sleep Data Using Granger Causality and Score-Based Structure Learning.

Understanding how the human body works during sleep and how this varies in the population is a task with significant implications for medicine. Polysomnographic studies, or sleep studies, are a common diagnostic method that produces a significant quantity of time-series sensor data. This study seeks to learn the causal structure from data from polysomnographic studies carried out on 600 adult volunteers in the United States. Two methods are used to learn the causal structure of these data: the well-established Granger causality and "DYNOTEARS", a modern approach that uses continuous optimisation to learn dynamic Bayesian networks (DBNs). The results from the two methods are then compared. Both methods produce graphs that have a number of similarities, including the mutual causation between electrooculogram (EOG) and electroencephelogram (EEG) signals and between sleeping position and SpO2 (blood oxygen level). However, DYNOTEARS, unlike Granger causality, frequently finds a causal link to sleeping position from the other variables. Following the creation of these causal graphs, the relationship between the discovered causal structure and the characteristics of the participants is explored. It is found that there is an association between the waist size of a participant and whether a causal link is found between the electrocardiogram (ECG) measurement and the EOG and EEG measurements. It is concluded that a person's body shape appears to impact the relationship between their heart and brain during sleep and that Granger causality and DYNOTEARS can produce differing results on real-world data.

Gold-Mediated Multiple Cysteine Arylation for the Construction of Highly Constrained Bicycle Peptides.

Bicycles are constrained bicyclic peptides formed through reaction of three cysteine residues within a linear sequence with a trivalent, symmetrical small molecule scaffold. Bicycles with high binding affinities to therapeutically important targets can be discovered using screening technologies such as phage display. Increasing the chemical diversity of Bicycles should improve the probability of finding hits to new targets and can be achieved by expanding the toolbox of Bicycle forming chemistries. Gold(III) S-arylation has recently been described as a method for the efficient bioconjugation of cysteine residues under conditions compatible with phage display. Herein, we explore the scope and generality of this methodology for Bicycle construction through the synthesis and evaluation of four novel tris-Gold complexes. These new scaffolds were systematically reacted with a variety of peptide sequences, varying in amino acid loop lengths. All four scaffolds proved to be capable and selective reactive partners for each peptide sequence and afforded the desired Bicycle products in 13-48% isolated yield. This work exemplifies Gold-mediated arylation as a general approach for construction of novel, highly constrained Bicycles.

Uncovering Earth's virome.

Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host­virus interactions.

Review of contaminant levels and effects in shorebirds: Knowledge gaps and conservation priorities.

Environmental pollution has emerged as a major threat to bird populations. Many shorebird populations are declining, although contamination has been documented in some shorebirds, evidence of negative impacts is sparse and this important topic remains understudied. To guide future research and develop effective conservation strategies, we carried out a comprehensive review of environmental pollutants and their consequences on shorebirds. In total, we found 93 relevant articles which examined pollutant contamination in ~37% (79 of 215) of all shorebird species, mostly from the Charadriidae and Scolopacidae families. Studies were geographically biased: the majority were conducted in American flyways, while only 1 was found from Australasia and few were conducted in Asian flyways. The main geographic gap for research includes East Africa, South Asia and Siberian Arctic. The most well-documented pollutants included mercury (Hg, 37 studies), cadmium (33), and lead (Pb, 28); less well studied pollutants were barium (1), calcium (1), strontium (1), dicofols (1), and other newly emerging contaminants, such as plastic debris/microplastics (4) and antibiotics resistance (2). Several pollutants have caused considerable concerns in shorebirds, including embryotoxicity caused by PCBs at non-optimum temperature (laboratory experiments); reduced reproduction performance linked to maternal Hg and paternal Pb (field evidence); and reduced refueling and flight performance related to oil contamination (both field and laboratory evidence). Our results confirm that an in-depth understanding of the local, regional and global factors that influence population trends of shorebirds in light of increasing pollution threats is essential for accurate and effective management and conservation strategies.

A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes.

Media and feed optimization have fueled many-fold improvements in mammalian biopharmaceutical production, but genome editing offers an emerging avenue for further enhancing cell metabolism and bioproduction. However, the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we present a comprehensive pooled CRISPR screen for CHO cell metabolism, including ~16,000 gRNAs against ~2500 metabolic enzymes and regulators. Using this screen, we identified a glutamine response network in CHO cells. Glutamine is particularly important since it is often over-fed to drive increased TCA cycle flux, but toxic ammonia may accumulate. With the screen we found one orphan glutamine-responsive gene with no clear connection to our network. Knockout of this novel and poorly characterized lipase, Abhd11, substantially increased growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait, and elucidate novel regulators of metabolism.

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.

Impact of extremely low-frequency magnetic fields on human postural control.

Studies have found that extremely low-frequency (ELF, < 300 Hz) magnetic fields (MF) can modulate standing balance; however, the acute balance effects of high flux densities in this frequency range have not been systematically investigated yet. This study explores acute human standing balance responses of 22 participants exposed to magnetic induction at 50 and 100 mTrms (MF), and to 1.5 mA alternating currents (AC). The center of pressure displacement (COP) was collected and analyzed to investigate postural modulation. The path length, the area, the velocity, the power spectrum in low (< 0.5 Hz) and medium (0.5-2 Hz) bands have computed and showed the expected effect of the positive control direct current (DC) electric stimulation but failed to show any significant effect of the time-varying stimulations (AC and MF). However, we showed a significant biased stabilization effect on postural data from the custom experimental apparatus employed in this work, which might have neutralized the hypothesized results.

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements.

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. This paper describes the data updates and additional features added during the last two years.

Intracholecystic papillary-tubular neoplasms of the gallbladder - A clinicopathological study of 36 cases.

Intracholecystic papillary-tubular neoplasms (ICPNs) account for <0.5% of all cholecystectomies. There is a lack of significant published data from the Indian subcontinent on ICPN to the best of our knowledge. The objective of the current study was to describe the clinicopathological features of ICPN of gallbladder from the departmental archives during a 5.5-year period. We also aimed to classify them into various histological subtypes and to correlate the clinicopathological parameters of ICPN with invasive adenocarcinoma. This study included 36 cases diagnosed over a period of 5.5 years (2013-2018). Clinical, radiological and histopathological data were analyzed in detail. The incidence of ICPN was 0.8%. The mean age of patients was 45.7 years with a female to male ratio of 1.3:1. Biliary phenotype was associated with invasion (p ≤0.001). Papillary pattern was present in 15 cases (41.6%) and was associated with invasion (p ≤0.001). High grade dysplasia was seen in 34 cases (94.4%), of which invasion was seen in 18 cases (50%). One case in our study also had synchronous common bile duct carcinoma. Majority (92%) of the patients were alive and well at the end of available follow-up (mean of 7 months and 25 days). ICPNs are mass forming neoplasms of the gallbladder with a slight female predominance. Biliary phenotype has an aggressive course, often associated with an invasive adenocarcinoma component. Papillary configuration of the lesion is significantly associated with an invasive component. Diligent follow-up of these lesions is warranted as they can be associated with other malignancies of the biliary system.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.

Human exposure to power frequency magnetic fields up to 7.6 mT: An integrated EEG/fMRI study.

We assessed the effects of power-line frequency (60 Hz in North America) magnetic fields (MF) in humans using simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). Twenty-five participants were enrolled in a pseudo-double-blind experiment involving "real" or "sham" exposure to sinusoidal 60 Hz MF exposures delivered using the gradient coil of an MRI scanner following two conditions: (i) 10 s exposures at 3 mT (10 repetitions); (ii) 2 s exposures at 7.6 mT (100 repetitions). Occipital EEG spectral power was computed in the alpha range (8-12 Hz, reportedly the most sensitive to MF exposure in the literature) with/without exposure. Brain functional activation was studied using fMRI blood oxygen level-dependent (BOLD, inversely correlated with EEG alpha power) maps. No significant effects were detected on occipital EEG alpha power during or post-exposure for any exposure condition. Consistent with EEG results, no effects were observed on fMRI BOLD maps in any brain region. Our results suggest that acute exposure (2-10 s) to 60 Hz MF from 3 to 7.6 mT (30,000 to 76,000 times higher than average public exposure levels for 60 Hz MF) does not induce detectable changes in EEG or BOLD signals. Combined with previous findings in which effects were observed on the BOLD signal after 1 h exposure to 3 mT, 60 Hz MF, this suggests that MF exposure in the low mT range (<10 mT) might require prolonged durations of exposure to induce detectable effects. Bioelectromagnetics. 38:425-435, 2017. © 2017 Wiley Periodicals, Inc.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19,200 studies, 56,000 Biosamples, 56,000 sequencing projects and 39,400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

The Feasibility of Utilizing a Comic for Education in the Emergency Department Setting.

The objective of this study was to determine the feasibility of a comic education module in the Emergency Department setting. A convenience sample of 50 injured children and their caregivers were enrolled. The comic was found to be likeable, easy to read, and provided important information to both children and their caregivers. Total time to read the comic was three minutes (SD 1.4, range 1.4-7.1). Most children (60%) read the comic independently, including all children over age 14 years. At 72-hour phone follow-up, 86% of caregivers had accurate recall of all three comic teaching points. This innovative comic educational module is feasible for use for children ages 4-18 years in the Emergency Department. Though this comic was intended to educate children, caregivers recalled all three teaching points 72 hours after discharge.