YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.

MOTIVATION: In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. Existing tools generally return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low-abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, few tools account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. RESULTS: We present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of ANI, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power and how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. AVAILABILITY AND IMPLEMENTATION: The source code implementing this approach is available via Conda and at https://github.com/KoslickiLab/YACHT. We also provide the code for reproducing experiments at https://github.com/KoslickiLab/YACHT-reproducibles.

Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro.

BACKGROUND: CALCRL (calcitonin receptor-like) protein is an important mediator of the endothelial fluid shear stress response, which is associated with the genetic risk of coronary artery disease. In this study, we functionally characterized the noncoding regulatory elements carrying coronary artery disease that risks single-nucleotide polymorphisms and studied their role in the regulation of CALCRL expression in endothelial cells. METHODS: To functionally characterize the coronary artery disease single-nucleotide polymorphisms harbored around the gene CALCRL, we applied an integrative approach encompassing statistical, transcriptional (RNA-seq), and epigenetic (ATAC-seq [transposase-accessible chromatin with sequencing], chromatin immunoprecipitation assay-quantitative polymerase chain reaction, and electromobility shift assay) analyses, alongside luciferase reporter assays, and targeted gene and enhancer perturbations (siRNA and clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9) in human aortic endothelial cells. RESULTS: We demonstrate that the regulatory element harboring rs880890 exhibits high enhancer activity and shows significant allelic bias. The A allele was favored over the G allele, particularly under shear stress conditions, mediated through alterations in the HSF1 (heat shock factor 1) motif and binding. CRISPR deletion of rs880890 enhancer resulted in downregulation of CALCRL expression, whereas HSF1 knockdown resulted in a significant decrease in rs880890-enhancer activity and CALCRL expression. A significant decrease in HSF1 binding to the enhancer region in endothelial cells was observed under disturbed flow compared with unidirectional flow. CALCRL knockdown and variant perturbation experiments indicated the role of CALCRL in mediating eNOS (endothelial nitric oxide synthase), APLN (apelin), angiopoietin, prostaglandins, and EDN1 (endothelin-1) signaling pathways leading to a decrease in cell proliferation, tube formation, and NO production. CONCLUSIONS: Overall, our results demonstrate the existence of an endothelial-specific HSF (heat shock factor)-regulated transcriptional enhancer that mediates CALCRL expression. A better understanding of CALCRL gene regulation and the role of single-nucleotide polymorphisms in the modulation of CALCRL expression could provide important steps toward understanding the genetic regulation of shear stress signaling responses.

Differential Proteoglycan Expression in Atherosclerosis Alters Platelet Adhesion and Activation.

Proteoglycans are differentially expressed in different atherosclerotic plaque phenotypes, with biglycan and decorin characteristic of ruptured plaques and versican and hyaluronan more prominent in eroded plaques. Following plaque disruption, the exposure of extracellular matrix (ECM) proteins triggers platelet adhesion and thrombus formation. In this study, the impact of differential plaque composition on platelet function and thrombus formation was investigated. Platelet adhesion, activation and thrombus formation under different shear stress conditions were assessed in response to individual proteoglycans and composites representing different plaque phenotypes. The results demonstrated that all the proteoglycans tested mediated platelet adhesion but not platelet activation, and the extent of adhesion observed was significantly lower than that observed with type I and type III collagens. Thrombus formation upon the rupture and erosion ECM composites was significantly reduced (p < 0.05) compared to relevant collagen alone, indicating that proteoglycans negatively regulate platelet collagen responses. This was supported by results demonstrating that the addition of soluble biglycan or decorin to whole blood markedly reduced thrombus formation on type I collagen (p < 0.05). Interestingly, thrombus formation upon the erosion composite displayed aspirin sensitivity, whereas the rupture composite was intensive to aspirin, having implications for current antiplatelet therapy regimes. In conclusion, differential platelet responses and antiplatelet efficacy are observed on ECM composites phenotypic of plaque rupture and erosion. Proteoglycans inhibit thrombus formation and may offer a novel plaque-specific approach to limit arterial thrombosis.

The Business Process Management for Healthcare (BPM+ Health) Consortium: motivation, methodology, and deliverables for enabling clinical knowledge interoperability (CKI).

OBJECTIVES: To enhance the Business Process Management (BPM)+ Healthcare language portfolio by incorporating knowledge types not previously covered and to improve the overall effectiveness and expressiveness of the suite to improve Clinical Knowledge Interoperability. METHODS: We used the BPM+ Health and Object Management Group (OMG) standards development methodology to develop new languages, following a gap analysis between existing BPM+ Health languages and clinical practice guideline knowledge types. Proposal requests were developed based on these requirements, and submission teams were formed to respond to them. The resulting proposals were submitted to OMG for ratification. RESULTS: The BPM+ Health family of languages, which initially consisted of the Business Process Model and Notation, Decision Model and Notation, and Case Model and Notation, was expanded by adding 5 new language standards through the OMG. These include Pedigree and Provenance Model and Notation for expressing epistemic knowledge, Knowledge Package Model and Notation for supporting packaging knowledge, Shared Data Model and Notation for expressing ontic knowledge, Party Model and Notation for representing entities and organizations, and Specification Common Elements, a language providing a standard abstract and reusable library that underpins the 4 new languages. DISCUSSION AND CONCLUSION: In this effort, we adopted a strategy of separation of concerns to promote a portfolio of domain-agnostic, independent, but integrated domain-specific languages for authoring medical knowledge. This strategy is a practical and effective approach to expressing complex medical knowledge. These new domain-specific languages offer various knowledge-type options for clinical knowledge authors to choose from without potentially adding unnecessary overhead or complexity.

Effects of Low and High Maternal Protein Intake on Fetal Skeletal Muscle miRNAome in Sheep.

Prenatal maternal feeding plays an important role in fetal development and has the potential to induce long-lasting epigenetic modifications. MicroRNAs (miRNAs) are non-coding, single-stranded RNAs that serve as one epigenetic mechanism. Though miRNAs have crucial roles in fetal programming, growth, and development, there is limited data regarding the maternal diet and miRNA expression in sheep. Therefore, we analyzed high and low maternal dietary protein for miRNA expression in fetal longissimus dorsi. Pregnant ewes were fed an isoenergetic high-protein (HP, 160-270 g/day), low-protein (LP, 73-112 g/day), or standard-protein diet (SP, 119-198 g/day) during pregnancy. miRNA expression profiles were evaluated using the Affymetrix GeneChip miRNA 4.0 Array. Twelve up-regulated, differentially expressed miRNAs (DE miRNAs) were identified which are targeting 65 genes. The oar-3957-5p miRNA was highly up-regulated in the LP and SP compared to the HP. Previous transcriptome analysis identified that integrin and non-receptor protein tyrosine phosphatase genes targeted by miRNAs were detected in the current experiment. A total of 28 GO terms and 10 pathway-based gene sets were significantly (padj < 0.05) enriched in the target genes. Most genes targeted by the identified miRNAs are involved in immune and muscle disease pathways. Our study demonstrated that dietary protein intake during pregnancy affected fetal skeletal muscle epigenetics via miRNA expression.

Development of Brain Penetrant Pyridazine Pantothenate Kinase Activators.

Conversion of pantothenate to phosphopantothenate in humans is the first dedicated step in the coenzyme A (CoA) biosynthesis pathway and is mediated by four isoforms of pantothenate kinase. These enzymes are allosterically regulated by acyl-CoA levels, which control the rate of CoA biosynthesis. Small molecule activators of the PANK enzymes that overcome feedback suppression increase CoA levels in cultured cells and animals and have shown great potential for the treatment of pantothenate kinase-associated neurodegeneration and propionic acidemias. In this study, we detail the further optimization of PANK pyridazine activators using structure-guided design and focus on the cellular CoA activation potential, metabolic stability, and solubility as the primary drivers of the structure-activity relationship. These studies led to the prioritization of three late-stage preclinical lead PANK modulators with improved pharmacokinetic profiles and the ability to substantially increase brain CoA levels. Compound 22 (BBP-671) eventually advanced into clinical testing for the treatment of PKAN and propionic acidemia.

Gene editing of pigs to control influenza A virus infections.

Proteolytic activation of the hemagglutinin (HA) glycoprotein by host cellular proteases is pivotal for influenza A virus (IAV) infectivity. Highly pathogenic avian influenza viruses possess the multibasic cleavage site of the HA which is cleaved by ubiquitous proteases, such as furin; in contrast, the monobasic HA motif is recognized and activated by trypsin-like proteases, such as the transmembrane serine protease 2 (TMPRSS2). Here, we aimed to determine the effects of TMPRSS2 on the replication of pandemic H1N1 and H3N2 subtype IAVs in the natural host, the pig. The use of the CRISPR/Cas 9 system led to the establishment of homozygous gene edited (GE) TMPRSS2 knockout (KO) pigs. Delayed IAV replication was demonstrated in primary respiratory cells of KO pigs in vitro. IAV infection in vivo resulted in significant reduction of virus shedding in the upper respiratory tract, and lower virus titers and pathological lesions in the lower respiratory tract of TMPRSS2 KO pigs as compared to wild-type pigs. Our findings support the commercial use of GE pigs to mitigate influenza A virus infection in pigs, as an alternative approach to prevent zoonotic influenza A transmissions from pigs to human.

Gene editing of pigs to control influenza A virus infections.

Proteolytic activation of the hemagglutinin (HA) glycoprotein by host cellular proteases is pivotal for influenza A virus (IAV) infectivity. Highly pathogenic avian influenza viruses possess the multibasic cleavage site of the HA which is cleaved by ubiquitous proteases, such as furin; in contrast, the monobasic HA motif is recognized and activated by trypsin-like proteases, such as the transmembrane serine protease 2 (TMPRSS2). Here, we aimed to determine the effects of TMPRSS2 on the replication of pandemic H1N1 and H3N2 subtype IAVs in the natural host, the pig. The use of the CRISPR/Cas 9 system led to the establishment of homozygous gene edited (GE) TMPRSS2 knockout (KO) pigs. Delayed IAV replication was demonstrated in primary respiratory cells of KO pigs in vitro. IAV infection in vivo resulted in significant reduction of virus shedding in the upper respiratory tract, and lower virus titers and pathological lesions in the lower respiratory tract of TMPRSS2 KO pigs as compared to WT pigs. Our findings could support the commercial use of GE pigs to minimize (i) the economic losses caused by IAV infection in pigs, and (ii) the emergence of novel IAVs with pandemic potential through genetic reassortment in the "mixing vessel", the pig.

Science development study for the Atacama Large Aperture Submillimeter Telescope (AtLAST): Solar and stellar observations.

Observations at (sub-)millimeter wavelengths offer a complementary perspective on our Sun and other stars, offering significant insights into both the thermal and magnetic composition of their chromospheres. Despite the fundamental progress in (sub-)millimeter observations of the Sun, some important aspects require diagnostic capabilities that are not offered by existing observatories. In particular, simultaneously observations of the radiation continuum across an extended frequency range would facilitate the mapping of different layers and thus ultimately the 3D structure of the solar atmosphere. Mapping large regions on the Sun or even the whole solar disk at a very high temporal cadence would be crucial for systematically detecting and following the temporal evolution of flares, while synoptic observations, i.e., daily maps, over periods of years would provide an unprecedented view of the solar activity cycle in this wavelength regime. As our Sun is a fundamental reference for studying the atmospheres of active main sequence stars, observing the Sun and other stars with the same instrument would unlock the enormous diagnostic potential for understanding stellar activity and its impact on exoplanets. The Atacama Large Aperture Submillimeter Telescope (AtLAST), a single-dish telescope with 50m aperture proposed to be built in the Atacama desert in Chile, would be able to provide these observational capabilities. Equipped with a large number of detector elements for probing the radiation continuum across a wide frequency range, AtLAST would address a wide range of scientific topics including the thermal structure and heating of the solar chromosphere, flares and prominences, and the solar activity cycle. In this white paper, the key science cases and their technical requirements for AtLAST are discussed.

Observations of our Sun and other stars at wavelengths of around one millimeter, i.e. in the range between infrared and radio waves, present a valuable complementary perspective. Despite significant technological advancements, certain critical aspects necessitate diagnostic capabilities not offered by current observatories. The proposed Atacama Large Aperture Submillimeter Telescope (AtLAST), featuring a 50-meter aperture and slated for construction at a high altitude in Chile's Atacama desert, promises to address these observational needs. Equipped with novel detectors that would cover a wide frequency range, AtLAST could unlock a plethora of scientific studies contributing to a better understanding of our host star. Simultaneous observations over a broad frequency range at rapid succession would enable the imaging of different layers of the Sun, thus elucidating the three-dimensional thermal and magnetic structure of the solar atmosphere and providing important clues for many long-standing central questions such as how the outermost layers of the Sun are heated to very high temperatures, the nature of large-scale structures like prominences, and how flares and coronal mass ejections, i.e. enormous eruptions, are produced. The latter is of particular interest to modern society due to the potentially devastating impact on the technological infrastructure we depend on today. Another unique possibility would be to study the Sun's long-term evolution in this wavelength range, which would yield important insights into its activity cycle. Moreover, the Sun serves as a fundamental reference for other stars as, due to its proximity, it is the only star that can be investigated in such detail. The results for the Sun would therefore have direct implications for understanding other stars and their impact on exoplanets. This article outlines the key scientific objectives and technical requirements for solar observations with AtLAST.

Genome-wide association with footrot in hair and wool sheep.

Ovine footrot is an infectious disease with important contributions from Dichelobacter nodosus and Fusobacterium necrophorum. Footrot is characterized by separation of the hoof from underlying tissue, and this causes severe lameness that negatively impacts animal wellbeing, growth, and profitability. Large economic losses result from lost production as well as treatment costs, and improved genetic tools to address footrot are a valuable long-term goal. Prior genetic studies had examined European wool sheep, but hair sheep breeds such as Katahdin and Blackbelly have been reported to have increased resistance to footrot, as well as to intestinal parasites. Thus, footrot condition scores were collected from 251 U.S. sheep including Katahdin, Blackbelly, and European-influenced crossbred sheep with direct and imputed genotypes at OvineHD array (>500,000 single nucleotide polymorphism) density. Genome-wide association was performed with a mixed model accounting for farm and principal components derived from animal genotypes, as well as a random term for the genomic relationship matrix. We identified three genome-wide significant associations, including SNPs in or near GBP6 and TCHH. We also identified 33 additional associated SNPs with genome-wide suggestive evidence, including a cluster of 6 SNPs in a peak near the genome-wide significance threshold located near the glutamine transporter gene SLC38A1. These findings suggest genetic susceptibility to footrot may be influenced by genes involved in divergent biological processes such as immune responses, nutrient availability, and hoof growth and integrity. This is the first genome-wide study to investigate susceptibility to footrot by including hair sheep and also the first study of any kind to identify multiple genome-wide significant associations with ovine footrot. These results provide a foundation for developing genetic tests for marker-assisted selection to improve resistance to ovine footrot once additional steps like fine mapping and validation are complete.

TGM6, a helminth secretory product, mimics TGF-ß binding to TßRII to antagonize TGF-ß signaling in fibroblasts.

The murine helminth parasite Heligmosomoides polygyrus expresses a family of proteins structurally related to TGF-ß Mimic 1 (TGM1), a secreted five domain protein that activates the TGF-ß pathway and converts naïve T lymphocytes to immunosuppressive Tregs. TGM1 signals through the TGF-ß type I and type II receptors, TßRI and TßRII, with domains 1-2 and 3 binding TßRI and TßRII, respectively, and domains 4-5 binding CD44, a co-receptor abundant on T cells. TGM6 is a homologue of TGM1 that is co-expressed with TGM1, but lacks domains 1 and 2. Herein, we show that TGM6 binds TßRII through domain 3, but does not bind TßRI, or other type I or type II receptors of the TGF-ß family. In TGF-ß reporter assays in fibroblasts, TGM6, but not truncated TGM6 lacking domains 4 and 5, potently inhibits TGF-ß- and TGM1-induced signaling, consistent with its ability to bind TßRII but not TßRI or other receptors of the TGF-ß family. However, TGM6 does not bind CD44 and is unable to inhibit TGF-ß and TGM1 signaling in T cells. To understand how TGM6 binds TßRII, the X-ray crystal structure of the TGM6 domain 3 bound to TßRII was determined at 1.4 Å. This showed that TGM6 domain 3 binds TßRII through an interface remarkably similar to the TGF-ß:TßRII interface. These results suggest that TGM6 has adapted its domain structure and sequence to mimic TGF-ß binding to TßRII and function as a potent TGF-ß and TGM1 antagonist in fibroblasts. The coexpression of TGM6, along with the immunosuppressive TGMs that activate the TGF-ß pathway, may prevent tissue damage caused by the parasite as it progresses through its life cycle from the intestinal lumen to submucosal tissues and back again.