Comprehensive Shielding System Enhances Radiation Protection for Structural Heart Procedures.

Background: This study of radiation exposure (RE) to physicians performing structural heart procedures evaluated the efficacy of a novel comprehensive radiation shield compared to those of traditional shielding methods. A novel comprehensive shielding system (Protego, Image Diagnostics Inc) has been documented to provide superior RE protection during coronary procedures compared to that provided by a standard "drop down" shield. The purpose of this study was to assess the efficacy of this shield in transcatheter aortic valve replacement (TAVR) procedures, which are associated with disproportionate RE to operators. Methods: This single-center, 2-group cohort, observational analysis compared RE to the primary physician operator performing TAVR using the Protego shield (n = 25) with that using a standard drop-down shield with personal leaded apparel (n = 25). RE was measured at both thyroid and waist levels with a real-time dosimetry system (RaySafe i3, RaySafe) and was calculated on a mean per case basis. Data were collected on additional procedural parameters, including access site(s) for device implantation, per case fluoroscopy time, air kerma, and patient factors, including body mass index. Between-group comparisons were conducted to evaluate RE by group and measurement sites. Results: The Protego system reduced operator RE by 99% compared to that using standard protection. RE was significantly lower at both the thyroid level (0.08 ± 0.27 vs 79.2 ± 62.4 µSv; P < .001) and the waist level (0.70 ± 1.50 vs 162.0 ± 91.0 µSv, P < .001). "Zero" total RE was documented by RaySafe in 60% (n = 15) of TAVR cases using Protego. In contrast, standard protection did not achieve zero exposure in a single case. Conclusions: The Protego shield system provides superior operator RE protection during TAVR procedures. This shield allows operators to work without the need for personal lead aprons and has potential to reduce catheterization laboratory occupational health hazards.

SCAI Expert Consensus Statement on the Management of Calcified Coronary Lesions.

The prevalence of calcification in obstructive coronary artery disease is on the rise. Percutaneous coronary intervention of these calcified lesions is associated with increased short-term and long-term risks. To optimize percutaneous coronary intervention results, there is an expanding array of treatment modalities geared toward calcium modification prior to stent implantation. The Society for Cardiovascular Angiography and Interventions, herein, puts forth an expert consensus document regarding methods to identify types of calcified coronary lesions, a central algorithm to help guide use of the various calcium modification strategies, tips for when using each treatment modality, and a look at future studies and trials for treating this challenging lesion subset.

Retrospective Multicenter Analysis of Intravascular Lithotripsy Use During Calcified Left Main Coronary Artery Percutaneous Coronary Interventions.

Background: Intravascular lithotripsy (IVL) safely and effectively modifies calcified coronary lesions during percutaneous coronary interventions (PCI). Data regarding its utility in modifying calcified left main coronary artery (LMCA) disease are limited. This study aimed to evaluate short-term outcomes of IVL-assisted LMCA PCI. Methods: This retrospective multicenter all-comers study analyzed patients who underwent intravascular imaging-guided, IVL-assisted PCI for calcified LMCA disease. Clinical and procedural characteristics were obtained, including intravascular imaging measurements. Technical success was defined as successful stent deployment with <30% residual diameter stenosis. Major adverse cardiac events (MACE) was a composite of all-cause death, myocardial infarction, and target vessel revascularization evaluated immediately postprocedure and at 30-day follow-up. Results: Among 184 patients treated at 7 centers from 2019-2023, IVL-assisted LMCA PCI achieved 99.4% technical success. Calcium fracture was identified in 136/165 cases (82.4%) on post-IVL imaging. Pretreatment minimal luminal area increased significantly compared to post-PCI minimal stent area (MSA) (4.1 ± 1.3 to 9.3 ± 2.5 mm2, respectively; P < .001). There was a direct correlation between IVL balloon size and the final MSA (P = .002). In-hospital MACE was 4.4% and 30-day MACE was 8.8%. In multivariate logistic regression, presentation with troponin-positive myocardial infarction was the sole predictor of 30-day MACE. Conclusions: IVL-assisted PCI for calcified LMCA lesions was safe and resulted in high technical success rates, confirming its utility as an effective treatment in this challenging lesion subset.

Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation.

Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.

Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales.

DNA N6-adenine methylation (6mA) has recently gained importance as an epigenetic modification in eukaryotes. Its function in lineages with high levels, such as early-diverging fungi (EDF), is of particular interest. Here, we investigated the biological significance and evolutionary implications of 6mA in EDF, which exhibit divergent evolutionary patterns in 6mA usage. The analysis of two Mucorales species displaying extreme 6mA usage reveals that species with high 6mA levels show symmetric methylation enriched in highly expressed genes. In contrast, species with low 6mA levels show mostly asymmetric 6mA. Interestingly, transcriptomic regulation throughout development and in response to environmental cues is associated with changes in the 6mA landscape. Furthermore, we identify an EDF-specific methyltransferase, likely originated from endosymbiotic bacteria, as responsible for asymmetric methylation, while an MTA-70 methylation complex performs symmetric methylation. The distinct phenotypes observed in the corresponding mutants reinforced the critical role of both types of 6mA in EDF.

Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces.

The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.

Emergency coronary artery bypass surgery after chronic total occlusion percutaneous coronary intervention: Insights from the PROGRESS-CTO registry.

BACKGROUND: Emergency coronary artery bypass surgery (eCABG) is a serious complication of chronic total occlusion (CTO) percutaneous coronary artery intervention (PCI). METHODS: We examined the incidence and outcomes eCABG among 14,512 CTO PCIs performed between 2012 and 2023 in a large multicenter registry. RESULTS: The incidence of eCABG was 0.12% (n = 17). Mean age was 68 ± 6 years and 69% of the patients were men. The most common reason for eCABG was coronary perforation (70.6%). eCABG patients had larger target vessel diameter (3.36 ± 0.50 vs. 2.90 ± 0.52; p = 0.003), were more likely to have moderate/severe calcification (85.7% vs. 45.8%; p = 0.006), side branch at the proximal cap (91.7% vs. 55.4%; p = 0.025), and balloon undilatable lesions (50% vs. 7.4%; p = 0.001) and to have undergone retrograde crossing (64.7% vs. 30.8%, p = 0.006). eCABG cases had lower technical (35.3% vs. 86.7%; p < 0.001) and procedural (35.3% vs. 86.7%; p < 0.001) success and higher in-hospital mortality (35.3% vs. 0.4%; p < 0.001), coronary perforation (70.6% vs. 4.6%; p < 0.001), pericardiocentesis (47.1% vs. 0.8%; p < 0.001), and major bleeding (11.8% vs. 0.5%; p < 0.001). CONCLUSIONS: The incidence of eCABG after CTO PCI was 0.12% and associated with high in-hospital mortality (35%). Coronary perforation was the most common reason for eCABG.

On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota).

Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.

Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates.

Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.

Impact of Calcium Eccentricity on the Safety and Effectiveness of Coronary Intravascular Lithotripsy: Pooled Analysis From the Disrupt CAD Studies.

BACKGROUND: Coronary intravascular lithotripsy (IVL) safely facilitates successful stent implantation in severely calcified lesions. This analysis sought to determine the relative impact of lesion calcium eccentricity on the safety and effectiveness of IVL using high-resolution optical coherence tomography imaging. METHODS: Individual patient-level data (n=262) were pooled from 4 distinct international prospective studies (Disrupt CAD I, II, III, and IV) and analyzed by an independent optical coherence tomography core laboratory. IVL performance in eccentric versus concentric calcification was analyzed by dividing calcified lesions into quartiles (≤180° [most eccentric], 181°-270°, 271°-359°, and 360° [concentric]) by maximum continuous calcium arc. RESULTS: In the 230 patients with clear imaging field on optical coherence tomography, there were no differences in preprocedure minimum lumen area, diameter stenosis, or maximum calcium thickness. The calcium length and volume index increased progressively with increasing mean and maximum continuous calcium arc (ie, concentricity). Conversely, the minimum calcium thickness decreased progressively with increasing concentricity. Post-procedure, the number of calcium fractures, fracture depth, and fracture width increased with increasing concentricity, with a 4-fold increase in the number of fractures in lesions with 360° of calcium arc compared with ≤180°. This increase in IVL-induced calcium fracture with increasing calcium burden and concentricity facilitated stent expansion and luminal gain such that there were no significant differences across quartiles. CONCLUSIONS: IVL induced calcium fractures proportional to the magnitude of coronary artery calcium, including in eccentric calcium, leading to consistent improvements in stent expansion and luminal gain in both eccentric and concentric calcified coronary lesions.

Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.

Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi.

Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.

Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi.

Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.

Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.

The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.

A standardized quantitative analysis strategy for stable isotope probing metagenomics.

Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.

Terabase-Scale Coassembly of a Tropical Soil Microbiome.

Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.