Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit (Durio zibethinus).

A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076T, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076T potentially represented a novel species within the genus Ligilactobacillus, with the most closely related type strain being Ligilactobacillus agilis DSM 20509T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA-DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076T=DSM 114293T=LMG 32698T).

Genome-wide association study and functional validation implicates JADE1 in tauopathy.

Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-ß (Aß) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aß toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.

Understanding repeat hospitalizations in intermediate-to-high risk aortic stenosis patients following transcatheter aortic valve replacement.

OBJECTIVES: We describe the causes, timing and predictors of readmissions and analyze its impact on clinical outcomes in intermediate-to-high-risk patients with severe symptomatic aortic stenosis (AS) who underwent transcatheter aortic valve replacement (TAVR). BACKGROUND: Intermediate-high risk TAVR patients with severe AS have an increased risk for hospital readmissions due to the high burden of comorbidities. METHODS: Patients who underwent TAVR from 2012 to 2018 at a single tertiary cardiac center were included and followed for 1 year. Readmissions were categorized as noncardiovascular (non-CV) and CV. RESULTS: A total of 611 patients (410 with no readmissions, 201 with ≥1 readmissions) were included. There was a total of 317 readmissions (mean: 1.58 ± 1.09 per readmitted patient) with 65 patients having ≥2 readmissions. 64.0% were non-CV and 36.0% were CV. The top three CV causes were pacemaker/implantable cardioverter-defibrillator placement, bleeding, and stroke. About 23% occurred at 1 m, the majority were CV; 45% occurred between 7 and 12 m, the majority were non-CV. Those with ≥1 readmissions had a higher burden of comorbidities including peripheral arterial disease, diabetes, immunosuppression, prior percutaneous coronary interventions, and dialysis. Readmissions were associated with higher 1-year mortality (adjusted hazard ratio: 2.53, 95% confidence interval: 1.40-4.59; p = 0.002). High-risk patients had higher non-CV readmissions (0.37 ± 0.79 vs. 0.25 ± 0.62; p = 0.044) compared to intermediate-risk patients but similar CV readmissions (p = 0.645). CONCLUSIONS: Understanding readmissions post-TAVR will promote the early identification of at-risk groups and the implementation of preventative measures to improve outcomes and reduce the burden and costs of readmissions.

Loss of LDAH associated with prostate cancer and hearing loss.

Great strides in gene discovery have been made using a multitude of methods to associate phenotypes with genetic variants, but there still remains a substantial gap between observed symptoms and identified genetic defects. Herein, we use the convergence of various genetic and genomic techniques to investigate the underpinnings of a constellation of phenotypes that include prostate cancer (PCa) and sensorineural hearing loss (SNHL) in a human subject. Through interrogation of the subject's de novo, germline, balanced chromosomal translocation, we first identify a correlation between his disorders and a poorly annotated gene known as lipid droplet associated hydrolase (LDAH). Using data repositories of both germline and somatic variants, we identify convergent genomic evidence that substantiates a correlation between loss of LDAH and PCa. This correlation is validated through both in vitro and in vivo models that show loss of LDAH results in increased risk of PCa and, to a lesser extent, SNHL. By leveraging convergent evidence in emerging genomic data, we hypothesize that loss of LDAH is involved in PCa and other phenotypes observed in support of a genotype-phenotype association in an n-of-one human subject.

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.

The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCE The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.

The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera.

In honey bees (Apis mellifera), the epigenetic mark of DNA methylation is central to the developmental regulation of caste differentiation, but may also be involved in additional biological functions. In this study, we examine the whole genome methylation profiles of three stages of the haploid honey bee genome: unfertilised eggs, the adult drones that develop from these eggs and the sperm produced by these drones. These methylomes reveal distinct patterns of methylation. Eggs and sperm show 381 genes with significantly different CpG methylation patterns, with the vast majority being more methylated in eggs. Adult drones show greatly reduced levels of methylation across the genome when compared with both gamete samples. This suggests a dynamic cycle of methylation loss and gain through the development of the drone and during spermatogenesis. Although fluxes in methylation during embryogenesis may account for some of the differentially methylated sites, the distinct methylation patterns at some genes suggest parent-specific epigenetic marking in the gametes. Extensive germ line methylation of some genes possibly explains the lower-than-expected frequency of CpG sites in these genes. We discuss the potential developmental and evolutionary implications of methylation in eggs and sperm in this eusocial insect species.

Transradial and transfemoral coronary angiography and interventions: 1-year outcomes after initiating the transradial approach in a cardiology training program.

BACKGROUND: Limited data are available regarding the safety and feasibility of initiating transradial (TR) diagnostic coronary angiography (CA) and percutaneous coronary intervention (PCI) in cardiology fellowship programs. METHODS: From July 2010 to June 2011, University of California, Davis Medical Center, adopted the TR approach with supervised cardiology fellows as the primary operators. Procedural variables and clinical outcomes of TR and transfemoral (TF) procedures were compared. To minimize confounding variables, ST-elevation myocardial infarction, bypass graft interventions, chronic total occlusions, and procedures with concomitant right heart catheterizations were excluded. To reflect the learning curve of the TR approach, this experience was assessed in 2 sequential 6-month periods. RESULTS: A total of 402 diagnostic CAs and 255 PCIs were included. Transradial access was used in 141 (35%) of the CAs and in 72 (28%) of PCIs. Within the TR-CA and TF-CA (n = 261) groups, there was no difference between fluoroscopy (10.4 ± 6.0 vs 11.0 ± 8.9, P = .63) or procedure (31.8 ± 11.5 vs 33.2 ± 13.8, P = .55) time throughout the academic year with a significant trend toward lower contrast use (128 ± 52 vs 110 vs 50, P = .04) by the second half. In addition, during the second half of the academic year, the TR-CA showed significantly higher fluoroscopy (11.0 ± 8.9 vs 6.7 ± 6.8, P = .001) and procedure (33.2 ± 13.8 vs 27.2 ± 11.6, P = .0015) times when compared with TF-CA. Transfemoral PCI (n = 183) and TR-PCI showed no significant difference between all fluoroscopy and procedure time and contrast use when comparing the 2 halves of the academic year. When comparing TF with TR within each academic half year, there was no difference within the PCI group. Vascular complications were less with the TR approach. Overall procedural success rates were high, and there were low rates of crossover and periprocedural complications in both the TR and the TF groups. CONCLUSION: A TR approach is safe for CA and PCI when performed by supervised operators in training. Although the learning curve for trainees appears slower for TR-CA compared with TF-CA, cardiology fellowship training programs should be encouraged to adopt TR procedures as part of their curriculum.

Environmental challenge rewires functional connections among human genes.

A fundamental question in biology is how a limited number of genes combinatorially govern cellular responses to environmental changes. While the prevailing hypothesis is that relationships between genes, processes, and ontologies could be plastic to achieve this adaptability, quantitatively comparing human gene functional connections between specific environmental conditions at scale is very challenging. Therefore, it remains unclear whether and how human genetic interaction networks are rewired in response to changing environmental conditions. Here, we developed a framework for mapping context-specific genetic interactions, enabling us to measure the plasticity of human genetic architecture upon environmental challenge for ~250,000 interactions, using cell cycle interruption, genotoxic perturbation, and nutrient deprivation as archetypes. We discover large-scale rewiring of human gene relationships across conditions, highlighted by dramatic shifts in the functional connections of epigenetic regulators (TIP60), cell cycle regulators (PP2A), and glycolysis metabolism. Our study demonstrates that upon environmental perturbation, intra-complex genetic rewiring is rare while inter-complex rewiring is common, suggesting a modular and flexible evolutionary genetic strategy that allows a limited number of human genes to enable adaptation to a large number of environmental conditions.

Increasing lysergic acid levels for ergot alkaloid biosynthesis: Directing catalysis via the F-G loop of Clavine oxidases.

Most ergot alkaloid drugs are semi-synthetically derived from the natural product lysergic acid, a valuable precursor for the development of novel ergot alkaloid drugs. Clavine oxidase (CloA) is a putative cytochrome P450, identified in the ergot alkaloid biosynthesis pathway, and a key enzyme that catalyzes the formation of lysergic acid from the precursor alkaloid agroclavine in a two-step oxidation reaction. We demonstrated in this study that Saccharomyces cerevisiae can be used as a viable host for the functional expression of CloA from Claviceps purpurea and its orthologs. We also showed that CloA orthologs differ in their ability to oxidize the substrate agroclavine, with some orthologs only able to perform the first oxidation reaction to produce elymoclavine. Of particular note, we identified a region between the F-G helices of the enzyme that may be involved in directing oxidation of agroclavine by substrate recognition and uptake. Using this knowledge, engineered CloAs were shown to produce lysergic acid at levels exceeding that of wildtype CloA orthologs; a CloA variant, chimeric AT5 9Hypo CloA, increased production levels of lysergic acid to 15 times higher as compared to the wildtype enzyme, demonstrating future utility for the industrial production of ergot alkaloids using biosynthetic routes.

Reconstituting the complete biosynthesis of D-lysergic acid in yeast.

The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments, such as Parkinsonism and dementia. Their synthesis via chemical and biological routes are therefore of industrial relevance, but suffer from several challenges. Current chemical synthesis methods involve long, multi-step reactions with harsh conditions and are not enantioselective; biological methods utilizing ergot fungi, produce an assortment of products that complicate product recovery, and are susceptible to strain degradation. Reconstituting the ergot alkaloid pathway in a strain strongly amenable for liquid fermentation, could potentially resolve these issues. In this work, we report the production of the main ergoline therapeutic precursor, D-lysergic acid, to a titre of 1.7 mg L-1 in a 1 L bioreactor. Our work demonstrates the proof-of-concept for the biological production of ergoline-derived compounds from sugar in an engineered yeast chassis.

Technical Considerations for TAVR in the Treatment of Stentless Bioprosthetic Aortic Valve Insufficiency in LVAD Patients.

An 80-year-old man with a history of bicuspid AV complicated by severe AI presented with progressive NYHA class III symptoms and severe bioprosthetic AV insufficiency. Transcatheter aortic valve replacement was planned via transfemoral approach. We encountered several technical challenges and describe them herein.

Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.

Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of α-synuclein, a dynamic protein linked to Parkinson's disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of α-synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to α-synuclein biology and pathobiology. We found that the conformation of α-synuclein previously shown to drive yeast toxicity-an extended, membrane-bound helix-is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress α-synuclein toxicity. Moreover, we find that sequence determinants of α-synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that α-synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.

Prioritizing Parkinson's disease genes using population-scale transcriptomic data.

Genome-wide association studies (GWAS) have identified over 41 susceptibility loci associated with Parkinson's Disease (PD) but identifying putative causal genes and the underlying mechanisms remains challenging. Here, we leverage large-scale transcriptomic datasets to prioritize genes that are likely to affect PD by using a transcriptome-wide association study (TWAS) approach. Using this approach, we identify 66 gene associations whose predicted expression or splicing levels in dorsolateral prefrontal cortex (DLFPC) and peripheral monocytes are significantly associated with PD risk. We uncover many novel genes associated with PD but also novel mechanisms for known associations such as MAPT, for which we find that variation in exon 3 splicing explains the common genetic association. Genes identified in our analyses belong to the same or related pathways including lysosomal and innate immune function. Overall, our study provides a strong foundation for further mechanistic studies that will elucidate the molecular drivers of PD.

Interstitial lung abnormality is prevalent and associated with worse outcome in patients undergoing transcatheter aortic valve replacement.

BACKGROUND: Interstitial lung abnormality (ILA) is found in 5-10% of the general population and is associated with increased mortality risk. Risk factors for ILA, including advanced age and smoking history also increase the risk for aortic stenosis (AS). Transcatheter aortic valve replacement (TAVR) has become an increasingly utilized intervention for patients with severe AS, and requires a high-resolution computed tomography (HRCT) of the chest to assess aortic valve dimensions. OBJECTIVES: To determine the prevalence and clinical significance of ILA on HRCT performed in patients referred for TAVR. METHODS: Consecutive pre-TAVR HRCTs performed over a 5-year period were reviewed. ILA was defined as bilateral, nondependent reticular opacities. All-cause mortality among TAVR recipients was compared between ILA cases and non-ILA controls matched 2:1 by age and gender using Cox proportional hazards regression and the Kaplan Meier estimator. RESULTS: Of 623 HRCTs screened, ILA was detected in 92 (14.7%), including 62 patients that underwent TAVR. Among ILA cases, 17 (27.4%) had a typical or probable usual interstitial pneumonia pattern, suggesting a diagnosis of idiopathic pulmonary fibrosis. Survival was worse in ILA cases compared to non-ILA controls (p = 0.008) and ILA was an independent predictor of mortality after multivariable adjustment (HR 3.29, 95% CI 1.34-8.08; p = 0.009). CONCLUSIONS: ILA is a common finding among patients with severe AS and is associated with increased mortality in those undergoing TAVR. Further research is needed to elucidate the biology underpinning this observation and determine whether ILA evaluation and risk stratification modulates this mortality risk.

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility.

Here we use deep sequencing to identify sources of variation in mRNA splicing in the dorsolateral prefrontal cortex (DLPFC) of 450 subjects from two aging cohorts. Hundreds of aberrant pre-mRNA splicing events are reproducibly associated with Alzheimer's disease. We also generate a catalog of splicing quantitative trait loci (sQTL) effects: splicing of 3,006 genes is influenced by genetic variation. We report that altered splicing is the mechanism for the effects of the PICALM, CLU and PTK2B susceptibility alleles. Furthermore, we performed a transcriptome-wide association study and identified 21 genes with significant associations with Alzheimer's disease, many of which are found in known loci, whereas 8 are in novel loci. These results highlight the convergence of old and new genes associated with Alzheimer's disease in autophagy-lysosomal-related pathways. Overall, this study of the transcriptome of the aging brain provides evidence that dysregulation of mRNA splicing is a feature of Alzheimer's disease and is, in some cases, genetically driven.

Efficacy and safety of triple antiplatelet therapy with and without concomitant anticoagulation during elective percutaneous coronary intervention (the REMOVE trial).

Adjunctive glycoprotein IIb/IIIa inhibition decreases ischemic events after percutaneous coronary intervention (PCI) but is associated with increased bleeding. We hypothesized that maximal antiplatelet therapy with aspirin, a thienopyridine, and a glycoprotein IIb/IIIa inhibitor without unfractionated heparin (UFH) would result in fewer bleeding complications and maintain efficacy in elective PCI. A total of 159 patients undergoing elective PCI were randomized to intraprocedural eptifibatide alone or eptifibatide plus UFH. Patients received aspirin 325 mg and clopidogrel 300 mg before the procedure. The primary end point was the Landefeld bleeding index. Secondary end points included the composite clinical outcome of in-hospital death, myocardial infarction, urgent target vessel revascularization, and Thrombolysis In Myocardial Infarction major bleeding, and a composite bleeding outcome of major, minor, and nuisance bleeding. The Landefeld bleeding index was significantly lower in the eptifibatide-only group compared with the eptifibatide-plus-UFH group (3.0 vs 3.9, p = 0.03). There was no significant difference in the composite clinical end point between groups (eptifibatide only 17% vs eptifibatide plus UFH 15%, p = 0.7). There was a trend toward a decrease in the composite bleeding end point in the eptifibatide-only compared with the eptifibatide-plus-UFH group (43% vs 56%, p = 0.10). In conclusion, during elective PCI, a strategy of aggressive antiplatelet therapy using aspirin, clopidogrel, and eptifibatide without anticoagulant therapy appears to decrease bleeding complications.

Onset and offset of platelet inhibition after high-dose clopidogrel loading and standard daily therapy measured by a point-of-care assay in healthy volunteers.

An increased loading dose of clopidogrel has been shown to provide more intense and rapid platelet inhibition (PI) than the standard 300-mg dose. However, patient variability in PI and in the timing of platelet recovery may affect efficacy during percutaneous coronary intervention and the bleeding risk of surgery. This study examined the degree of PI after a high-dose load of clopidogrel compared with standard dosing and the time course of functional recovery after the discontinuation of daily therapy. Healthy volunteers (n = 45) were randomized to 3 loading doses of clopidogrel (300, 600, and 900 mg) and continued at 75 mg/day for 6 to 18 days. PI was calculated using a P2Y12-specific point-of-care assay at baseline, hourly for 7 hours after loading, and daily for 5 days after the discontinuation of daily therapy. The groups receiving 600- and 900-mg doses had significantly greater PI than the group receiving the 300-mg dose 2 to 3 hours after loading, but there were no differences between the 600- and 900-mg doses at any time point. Median PI decreased each day after clopidogrel cessation (p < 0.01). On day 5 after discontinuation, the median PI was 12% (interquartile range 0% to 17.4%), but 2 subjects (5%) had persistent PI > 40%. Before day 5, 57% of subjects had recovered platelet function to a PI of < 20%. In conclusion, a 900-mg dose of clopidogrel provides no benefit in terms of magnitude or time to maximal PI compared with a 600-mg dose, but both are superior to a 300-mg dose. A point-of-care assay can identify subjects who may recover platelet function before 5 days after discontinuation or, in contrast, have persistent PI despite discontinuation.

Early- and medium-term outcomes after paclitaxel-eluting stent implantation for sirolimus-eluting stent failure.

The optimal treatment for sirolimus-eluting stent (SES) restenosis is not known. This study evaluated the safety and clinical outcome of paclitaxel-eluting stent (PES) implantation for SES restenosis. From March 2004 to July 2005, PESs were implanted in 125 patients with 140 lesions with SES restenosis. Acute and 6-month clinical outcomes were determined through review of the medical record and/or telephone interview. In-hospital major adverse cardiac events (death, nonfatal myocardial infarction, or repeat revascularization) occurred in 14 patients (11.2%), driven entirely by postprocedure non-Q-wave myocardial infarction. At a mean clinical follow-up of 7.2 +/- 1.8 months, the incidence of target lesion revascularization (TLR) was 14.0%, and the rate of major adverse cardiac events was 17.2%. Subacute thrombosis occurred in 2 patients (1.6%). Length of PES implanted, postprocedure diameter stenosis, and total occlusion of the target lesion were independent predictors of TLR. In patients with de novo SES restenosis, TLR was only 8.7%. In conclusion, at medium-term follow-up, PES implantation for SES failure appears to be safe and effective, although efficacy is decreased in the setting of total occlusions, greater residual diameter stenosis, and longer PESs.