Exploring functionality of the reverse ß-oxidation pathway in Corynebacterium glutamicum for production of adipic acid.

BACKGROUND: Adipic acid, a six-carbon platform chemical mainly used in nylon production, can be produced via reverse ß-oxidation in microbial systems. The advantages posed by Corynebacterium glutamicum as a model cell factory for implementing the pathway include: (1) availability of genetic tools, (2) excretion of succinate and acetate when the TCA cycle becomes overflown, (3) initiation of biosynthesis with succinyl-CoA and acetyl-CoA, and (4) established succinic acid production. Here, we implemented the reverse ß-oxidation pathway in C. glutamicum and assessed its functionality for adipic acid biosynthesis. RESULTS: To obtain a non-decarboxylative condensation product of acetyl-CoA and succinyl-CoA, and to subsequently remove CoA from the condensation product, we introduced heterologous 3-oxoadipyl-CoA thiolase and acyl-CoA thioesterase into C. glutamicum. No 3-oxoadipic acid could be detected in the cultivation broth, possibly due to its endogenous catabolism. To successfully biosynthesize and secrete 3-hydroxyadipic acid, 3-hydroxyadipyl-CoA dehydrogenase was introduced. Addition of 2,3-dehydroadipyl-CoA hydratase led to biosynthesis and excretion of trans-2-hexenedioic acid. Finally, trans-2-enoyl-CoA reductase was inserted to yield 37 µg/L of adipic acid. CONCLUSIONS: In the present study, we engineered the reverse ß-oxidation pathway in C. glutamicum and assessed its potential for producing adipic acid from glucose as starting material. The presence of adipic acid, albeit small amount, in the cultivation broth indicated that the synthetic genes were expressed and functional. Moreover, 2,3-dehydroadipyl-CoA hydratase and ß-ketoadipyl-CoA thiolase were determined as potential target for further improvement of the pathway.

ER stress and distinct outputs of the IRE1α RNase control proliferation and senescence in response to oncogenic Ras.

Oncogenic Ras causes proliferation followed by premature senescence in primary cells, an initial barrier to tumor development. The role of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) in regulating these two cellular outcomes is poorly understood. During ER stress, the inositol requiring enzyme 1α (IRE1α) endoribonuclease (RNase), a key mediator of the UPR, cleaves Xbp1 mRNA to generate a potent transcription factor adaptive toward ER stress. However, IRE1α also promotes cleavage and degradation of ER-localized mRNAs essential for cell death. Here, we show that oncogenic HRas induces ER stress and activation of IRE1α. Reduction of ER stress or Xbp1 splicing using pharmacological, genetic, and RNAi approaches demonstrates that this adaptive response is critical for HRas-induced proliferation. Paradoxically, reduced ER stress or Xbp1 splicing promotes growth arrest and premature senescence through hyperactivation of the IRE1α RNase. Microarray analysis of IRE1α- and XBP1-depleted cells, validation using RNA cleavage assays, and 5' RACE identified the prooncogenic basic helix-loop-helix transcription factor ID1 as an IRE1α RNase target. Further, we demonstrate that Id1 degradation by IRE1α is essential for HRas-induced premature senescence. Together, our studies point to IRE1α as an important node for posttranscriptional regulation of the early Ras phenotype that is dependent on both oncogenic signaling as well as stress signals imparted by the tumor microenvironment and could be an important mechanism driving escape from Ras-induced senescence.

Enhancement of water-window soft x-ray emission from laser-produced Au plasma under low-pressure nitrogen atmosphere.

To generate bright water-window (WW) soft x rays (2.3-4.4 nm), gold slab targets were irradiated with laser pulses (1064 nm, 7 ns, 1 J). Emission spectroscopy showed that the introduction of low-pressure nitrogen enhanced the soft x-ray yield emitted from the laser-produced Au plasma. The intensity of the WW x-ray transported in a 400-Pa N2 atmosphere from the laser-produced plasma increased by 3.8 times over that in vacuum. Considering a strong x-ray absorption, the x-ray yield emitted directly from the Au plasma in the N2 gas was evaluated to be 13 times higher than that in vacuum. Although similar measurements were made for various gases, only N2 gas causes an increase in a soft x-ray yield. The processes leading to this enhancement mechanism were revealed by using hydrodynamic simulation and atomic structure codes.

Using HIV Surveillance Laboratory Data to Identify Out-of-Care Patients.

HIV-associated laboratory tests reported to public health surveillance have been used as a proxy measure of care engagement of HIV+ individuals. As part of a Health Resources and Services Administration (HRSA) Special Projects of National Significance (SPNS) Initiative, the Massachusetts Department of Public Health (MDPH) worked with three pilot clinical facilities to identify HIV+ patients whose last HIV laboratory test occurred at the participating facility but who then appeared to be out of care, defined as an absence of HIV laboratory test results reported to MDPH for at least 6 months. The clinical facilities then reviewed medical records to determine whether these patients were actually not in care, or if there was another reason that they did not have a laboratory test performed, and provided feedback to MDPH on each of the presumed out-of-care patients. In the first year of the pilot project, 37% of patients who appeared to be out of care based on laboratory data were confirmed to be out of care after review of clinical health records. Of those patients who were confirmed to be out of care, 55% had a subsequent laboratory test within 3 months, and 72% had a laboratory test within 6 months, indicating that they had re-engaged with a care provider. MDPH found that it was essential to have clinical staff confirm the care status of patients who were presumed to be out of care based on surveillance data.

GDISC: a web portal for integrative analysis of gene-drug interaction for survival in cancer.

Summary: Survival analysis has been applied to The Cancer Genome Atlas (TCGA) data. Although drug exposure records are available in TCGA, existing survival analyses typically did not consider drug exposure, partly due to naming inconsistencies in the data. We have spent extensive effort to standardize the drug exposure data, which enabled us to perform survival analysis on drug-stratified subpopulations of cancer patients. Using this strategy, we integrated gene copy number data, drug exposure data and patient survival data to infer gene-drug interactions that impact survival. The collection of all analyzed gene-drug interactions in 32 cancer types are organized and presented in a searchable web-portal called gene-drug Interaction for survival in cancer (GDISC). GDISC allows biologists and clinicians to interactively explore the gene-drug interactions identified in the context of TCGA, and discover interactions associated to their favorite cancer, drug and/or gene of interest. In addition, GDISC provides the standardized drug exposure data, which is a valuable resource for developing new methods for drug-specific analysis. Availability and Implementation: GDISC is available at https://gdisc.bme.gatech.edu/. Contact: peng.qiu@bme.gatech.edu.

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline.

The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

Clinical effects of stannous fluoride dentifrice in reducing plaque microbial virulence III: Lipopolysaccharide and TLR2 reporter cell gene activation.

PURPOSE: This study expanded the analysis of subgingival dental plaques from previous research to include the evaluation of cohort, site and treatment effects on chemically measured endotoxin and activation of Toll-like receptor (TLR) based gene expression in two additional reporter cell lines: a TLR2 specific cell line and a THP-1 (multi TLR reporter) cell line. METHODS: Participants from high and low bleeding cohorts were sampled at baseline for both supra and subgingival dental plaque at both healthy as well as clinically diseased sites and then provided with intervention hygiene products including a stabilized SnF2 dentifrice and a new soft bristle manual toothbrush. Following 2 and 4 weeks of assigned dentifrice use, participants returned for a re-evaluation of gingival inflammation and bleeding and repeat samplings of dental plaque. Subgingival sampled plaques were chemically analyzed for endotoxin concentration using a Thermo Scientific Pierce LAL chromogenic endotoxin quantitation kit. Samples were also used for inoculation of two reporter cell assays (an HEK293 TLR2 reporter cell line and a THP-1 monocyte cell line). Reporter cell activation was analyzed via luminescence changes of secreted embryonic alkaline phosphatase. RESULTS: The endotoxin content of subgingival plaque could be measured directly with dye assays and plaque isolates activated gene expression in both TLR reporter cell lines. Higher disease cohorts and sites with gingival inflammation generally showed more endotoxins and higher levels of plaque virulence as compared to low disease cohorts or plaque sampled from clinically healthy sites. SnF2 dentifrice treatment was associated with broad scale reductions in endotoxin content and virulence potentiation properties of dental plaque samples collected subgingivally from patients. CLINICAL SIGNIFICANCE: These results collectively support the use of dye or various reporter cell lines in the characterization of plaque virulence in diseased populations and as a potential route for analysis in clinical evaluations of treatment interventions. Subgingival plaque 'detoxification' including effects on microbial pathogenicity as well as metabolic activity may be considered important mechanisms contributing to clinical benefits of SnF2 dentifrice.

The Use of Degenerate Primers in qPCR Analysis of Functional Genes Can Cause Dramatic Quantification Bias as Revealed by Investigation of nifH Primer Performance.

The measurement of functional gene abundance in diverse microbial communities often employs quantitative PCR (qPCR) with highly degenerate oligonucleotide primers. While degenerate PCR primers have been demonstrated to cause template-specific bias in PCR applications, the effect of such bias on qPCR has been less well explored. We used a set of diverse, full-length nifH gene standards to test the performance of several universal nifH primer sets in qPCR. We found significant template-specific bias in all but the PolF/PolR primer set. Template-specific bias caused more than 1000-fold mis-estimation of nifH gene copy number for three of the primer sets and one primer set resulted in more than 10,000-fold mis-estimation. Furthermore, such template-specific bias will cause qPCR estimates to vary in response to beta-diversity, thereby causing mis-estimation of changes in gene copy number. A reduction in bias was achieved by increasing the primer concentration. We conclude that degenerate primers should be evaluated across a range of templates, annealing temperatures, and primer concentrations to evaluate the potential for template-specific bias prior to their use in qPCR.

HPLC-HRMS Quantification of the Ichthyotoxin Karmitoxin from Karlodinium armiger.

Being able to quantify ichthyotoxic metabolites from microalgae allows for the determination of ecologically-relevant concentrations that can be simulated in laboratory experiments, as well as to investigate bioaccumulation and degradation. Here, the ichthyotoxin karmitoxin, produced by Karlodinium armiger, was quantified in laboratory-grown cultures using high-performance liquid chromatography (HPLC) coupled to electrospray ionisation high-resolution time-of-flight mass spectrometry (HRMS). Prior to the quantification of karmitoxin, a standard of karmitoxin was purified from K. armiger cultures (80 L). The standard was quantified by fluorescent derivatisation using Waters AccQ-Fluor reagent and derivatised fumonisin B1 and fumonisin B2 as standards, as each contain a primary amine. Various sample preparation methods for whole culture samples were assessed, including six different solid phase extraction substrates. During analysis of culture samples, MS source conditions were monitored with chloramphenicol and valinomycin as external standards over prolonged injection sequences (>12 h) and karmitoxin concentrations were determined using the response factor of a closely eluting iturin A2 internal standard. Using this method the limit of quantification was 0.11 µg·mL-1, and the limit of detection was found to be 0.03 µg·mL-1. Matrix effects were determined with the use of K. armiger cultures grown with 13C-labelled bicarbonate as the primary carbon source.

Clinical Effects of Stabilized Stannous Fluoride Dentifrice in Reducing Plaque Microbial Virulence I: Microbiological and Receptor Cell Findings.

OBJECTIVES: Lipopolysaccharides (LPSs) and lipoteichoic acids (LTAs), or bacterial endotoxins, bind with Toll-like receptors (TLRs) that are expressed on host cells of the periodontium, thereby contributing to the periodontal pathogenicity of oral bacteria. Stannous fluoride (SnF2), an antibacterial fluoride that treats and controls gingivitis, has been shown to react with lipophilic domains/anionic charges in LPS and LTA. The effects of bacterial species and dental plaque on toll receptors can be studied using genetically engineered cell lines containing linked toll receptors on their surfaces. This randomized, examiner-blinded study examined the clinical effects of stabilized SnF2 dentifrice intervention on gingivitis and dental plaque virulence in populations exhibiting high and low levels of clinical gingivitis. METHODS: Recruited populations were evaluated for gingival inflammation (MGI) and gingival bleeding (GBI) at baseline and assigned into two cohorts of 20 each, those with high (GBI > 20 sites) and low (GBI < 3 sites) levels of observed bleeding/gingivitis. Participants were sampled at baseline for both supra- and subgingival dental plaque at both healthy (no bleeding, PD = 2 mm), as well as clinically diseased sites (bleeding, PD = 3-4 mm), and then provided with an intervention hygiene product including a stabilized SnF2 dentifrice and a new soft bristle manual toothbrush. Following two and four weeks of assigned dentifrice use, participants returned for a re-evaluation of gingival inflammation and bleeding and repeat samplings of dental plaque. Plaque samples were analyzed by anaerobic culturing of gram negative anaerobes (GNA), as well as by incubation of subgingival sampled plaques with TLR4 transfected HEK293 cells, where gene expression was assessed by measurement of a SEAP alkaline phosphatase reporter as a marker of toll receptor activation. RESULTS: Clinical assessments showed statistically significant reductions in MGI (24-26%) and GBI (42-53%) gingivitis in both diseased and healthy cohorts following four weeks of dentifrice intervention. For all clinical examinations, MGI and bleeding sites were statistically significantly different (lower) in the low bleeding versus the higher bleeding cohort. Supragingival and subgingival GNAs were significantly reduced (p < 0.05) in both high and low disease cohorts at bleeding and healthy sites following four weeks of stabilized SnF2 dentifrice use. TLR activation from subgingival sampled plaque was reduced following four weeks of stabilized SnF2 dentifrice use in both high and low disease cohorts and in both healthy, as well as diseased sites. CONCLUSIONS: Collectively, these results support the potential for stabilized SnF2 dentifrice to provide clinical gingivitis benefits via mechanisms beyond control of plaque mass, potentially directly decreasing the pathogenicity of plaque biofilms by blocking reactivity of LPS and LTA ligands with tissue receptors associated with inflammation. Importantly, benefits could be seen in both diseased sites, as well as sites not yet exhibiting symptoms of inflammation, supporting the activity of SnF2 not just in treating diseased sites, but in preventing disease development. These learnings may influence treatment planning for patients susceptible to gingivitis.

Identification of gene-drug interactions that impact patient survival in TCGA.

BACKGROUND: With the advent of large scale biological data collection for various diseases, data analysis pipelines and workflows need to be established to build frameworks for integrative analysis. Here the authors present a pipeline for identifying disease specific gene-drug interactions using CNV (Copy Number Variation) and clinical data from the TCGA (The Cancer Genome Atlas) project. Two cancer types were selected for analysis, LGG (Brain lower grade glioma) and GBM (Glioblastoma multiforme), due to the possible progression from LGG to GBM in some cases. The copy number and clinical data were then used to preform survival analysis on a gene by gene basis on sub-populations of patients exposed to a given drug. RESULTS: Several gene-drug interactions are identified, where the copy number of a gene is associated to survival of a patient exposed to a certain drug. Both Irinotecan/HAS2 (Hyaluronan synthase 2) and Bevacizumab/PGAM1 (Phosphoglycerate mutase 1) are interactions found in this study with independent confirmation. Independent work in colon, breast cancer and leukemia (Györffy, Breast Cancer Res Treat 123:725-731, 2010; Mueller, Mol Cancer Ther 11:3024-3032, 2010; Hitosugi, Cancer Cell 13:585-600, 2012) showed these two interactions can lead to increased survival. CONCLUSION: While the pipeline produced several possible interactions where increased survival is linked to normal or increased copy number of a given gene for patients treated with a given drug, no instance of low copy number or full deletion was linked to increased survival. The development of this pipeline shows a promising utility to identify possible beneficial gene-drug interactions that could improve patient survival and may illustrate some of the problems inherent in this kind of analysis on these data.

Dynamic Cluster Analysis: An Unbiased Method for Identifying A + 2 Element Containing Compounds in Liquid Chromatographic High-Resolution Time-of-Flight Mass Spectrometric Data.

Dynamic cluster analysis (DCA) is an automated, unbiased technique which can identify Cl, Br, S, and other A + 2 element containing metabolites in liquid chromatographic high-resolution mass spectrometric data. DCA is based on three features, primarily the previously unutilized A + 1 to A + 2 isotope cluster spacing which is a strong classifier in itself but improved with the addition of the monoisotopic mass, and the well-known A:A+2 intensity ratio. Utilizing only the A + 1 to A + 2 isotope cluster spacing and the monoisotopic mass it was possible to filter a chromatogram for metabolites which contain Cl, Br, and S. Screening simulated isotope patterns of the Antibase Natural Products Database it was determined that the A + 1 to A + 2 isotope cluster spacing can be used to correctly classify 97.4% of molecular formulas containing these elements, only misclassifying a few metabolites which were either over 2800 u or metabolites which contained other A + 2 elements, such as Cu, Ni, Mg, and Zn. It was determined that with an interisotopic mass accuracy of 1 ppm, in a fully automated process, using all three parameters, it is possible to specifically filter a chromatogram for S containing metabolites with monoisotopic masses less than 825 u. Furthermore, it was possible to specifically filter a chromatogram for Cl and Br containing metabolites with monoisotopic masses less than 1613 u. Here DCA is applied on (i) simulated isotope patterns of the Antibase natural products databases, (ii) LC-QTOF data of reference standards, and (iii) LC-QTOF data of crude extracts of 10 strains of laboratory grown cultures of the microalga Prymnesium parvum where it identified known metabolites of the prymnesin series as well as over 20 previously undescribed prymnesin-like molecular features.

Chemical Diversity, Origin, and Analysis of Phycotoxins.

Microalgae, particularly those from the lineage Dinoflagellata, are very well-known for their ability to produce phycotoxins that may accumulate in the marine food chain and eventually cause poisoning in humans. This includes toxins accumulating in shellfish, such as saxitoxin, okadaic acid, yessotoxins, azaspiracids, brevetoxins, and pinnatoxins. Other toxins, such as ciguatoxins and maitotoxins, accumulate in fish, where, as is the case for the latter compounds, they can be metabolized to even more toxic metabolites. On the other hand, much less is known about the chemical nature of compounds that are toxic to fish, the so-called ichthyotoxins. Despite numerous reports of algal blooms causing massive fish kills worldwide, only a few types of compounds, such as the karlotoxins, have been proven to be true ichthyotoxins. This review will highlight marine microalgae as the source of some of the most complex natural compounds known to mankind, with chemical structures that show no resemblance to what has been characterized from plants, fungi, or bacteria. In addition, it will summarize algal species known to be related to fish-killing blooms, but from which ichthyotoxins are yet to be characterized.

Quantitation of endotoxin and lipoteichoic acid virulence using toll receptor reporter gene.

PURPOSE: To apply quantitative Toll-like receptors (TLR) cell assays to compare lipopolysaccharides (LPSs) and lipoteichoic acids (LTAs) from different oral bacterial strains for potential pathogenicity in vitro. METHODS: The potency of LPS and LTA from different bacteria on activation of TLR reporter genes in HEK-tlr cell lines was examined. P. gingivalis LPS mix, P. gingivalis 1690 LPS, P. gingivalis 1435/50 LPS, E. coli LPS (E. coli K12), B. subtilis LTA, S. aureus LTA, E. hirae LTA and S. pyogenes LTA were examined in both TLR2 and TLR4 HEK cell line reporter assays. Solutions of LPS and LTA from selected bacteria were applied in a dose response fashion to the TLR reporter cells under standard culture conditions for mammalian cells. Reporter gene secreted-embryonic-alkaline-phosphatase (SEAP) was measured, and half maximal effective concentration (EC50) was determined for each sample. Concentration dependent TLR activation was compared to similar responses to LPS and LTA for commercial BODIPY-TR-Cadaverine and LAL biochemical (non cell based) assays. RESULTS: All LPS from P. gingivalis activated both TLR2 and TLR4 responses. E. coli LPS is a strong activator for TLR4 but not for TLR2 responses. In contrast, both B. subtilis and S. aureus LTA provoked responses only in TLR2, but not in the TLR4 assay. Interestingly, E. hirae LTA and S. pyogenes LTA did not stimulate strong TLR2 responses. Instead, both E. hirae LTA and S. pyogenes LTA mounted a reasonable response in TLR4 reporter gene assay. Both LPS and LTA showed deactivation of fluorescence in BODIPY-TR-Cadaverine while only LPS was active in LAL. As with biochemical assays, an EC50 could be determined for LPS and LTA from various bacterial strains. The EC50 is defined as a concentration of LPS or LTA that provokes a response halfway between the baseline and maximum responses. Lower EC50 means higher potency in promoting TLR responses, and in principle indicates greater toxicity to the host. CLINICAL SIGNIFICANCE: InvivoGen TLR2 and TLR4 assays distinguish specific types of microbial products, such as LPS and LTA from different bacteria. Application of EC50 determinations creates a means for quantitative and comparisons of LPS and LTA virulence in a cellular-based assay and combinations of TLR reporter cell assays along with biochemical evaluation of LPS#47;LTA in BODIPY-TR-Cadaverine and LPS in LAL assays provides a means to quantitate virulence of plaque samples with respect to both LPS and LTA. These learnings have long-term implications for patient care in that understanding the virulence of patients' plaque provides important information to assess risk of oral diseases.

Lipopolysaccharide and lipoteichoic acid binding by antimicrobials used in oral care formulations.

PURPOSE: To study the reactivity of lipopolysaccharide (LPS) and lipoteichoic acid (LTA) with the cationically charged agents cetylpyridinium chloride, stannous fluoride, and the non-cationic agent triclosan. We also assessed the effect of these agents to inhibit LPS and LTA binding to cellular Toll-like Receptors (TLRs) in vitro. METHODS: The ability of these antimicrobials to bind with LPS and/or LTA was assessed in both the Limulus amebocyte lysate and BODIPY-TR-cadaverine dye assays. Mass spectroscopy was then used to confirm that stannous fluoride directly binds with LPS and to determine stoichiometry. Lastly, we looked for possible inhibitory effects of these antimicrobial agents on the ability of fluorescently conjugated LPS to bind to TLR4 expressed on HEK 293 cells. RESULTS: Cetylpyridinium chloride (CPC) and stannous salts including stannous fluoride interfered with LPS and LTA reactivity in both dye assays, while triclosan had no effect. Mass spectroscopy revealed direct binding of stannous fluoride with E. Coli LPS at 1:1 stoichiometric ratios. In the cellular assay, cetylpyridinium chloride and stannous fluoride, but not triclosan, inhibited LPS binding to TLR4. CLINICAL SIGNIFICANCE: These results support a potential mechanism of action for stannous fluoride and CPC formulated in oral products in which these ingredients bind bacterial toxins and potentially render them less toxic to the host. These results may influence home care recommendations for patients at risk for plaque-related diseases.

Pelvic ultrasonography and length of stay in the ED: an observational study.

OBJECTIVES: We compared emergency physician-performed pelvic ultrasonography (EPPU) with radiology department-performed pelvic ultrasonography (RPPU) in emergency department (ED) female patients requiring pelvic ultrasonography and their outcomes in relation to ED length of stay, ED readmission, and alternative diagnosis, within a 14-day follow-up period. METHODS: This was a prospective, observational study of female patients of reproductive age who required either an EPPU or RPPU for their ED evaluation. We hypothesized that patients receiving EPPU would have a length of stay reduction greater than or equal to 60 minutes, as compared with RPPU. Statistical analyses included an independent-samples t test and multivariate regression modeling to control for factors associated with ED LOS. RESULTS: Eighteen resident physicians performed EPPU, with 15 attending physicians supervising. Forty-eight patients received only EPPU, and 84 patients received only RPPU. In univariate analysis, those who received EPPU had an ED LOS 162 minutes less than those who received RPPU (95% confidence interval, 106-209 minutes). In multivariate analysis controlling for gynecologist consultation, disposition, and pregnancy status, patients who received EPPU had an ED LOS reduction of 108 minutes when compared with RPPU (95% confidence interval, 38-166 minutes). Five patients (10%) who had received EPPU and were discharged from the ED returned to the ED within 2 weeks, but none had alternative diagnoses. CONCLUSIONS: Patients with EPPU had statistically and clinically significant reductions in ED LOS, even when controlling for disposition, gynecologist consultation in the ED, and pregnancy status. No patients in the study had an alternative diagnosis within 2 weeks of EPPU.

Mapping and Omics Integration: Towards Precise Rice Disease Resistance Breeding.

Rice (Oryza sativa), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. The integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with a better understanding of their functional roles in disease resistance. The improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because a better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to a more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can result in a transformative impact on rice breeding for enhancing disease resistance.

Pursuit and escape drive fine-scale movement variation during migration in a temperate alpine ungulate.

Climate change reduces snowpack, advances snowmelt phenology, drives summer warming, alters growing season precipitation regimes, and consequently modifies vegetation phenology in mountain systems. Elevational migrants track spatial variation in seasonal plant growth by moving between ranges at different elevations during spring, so climate-driven vegetation change may disrupt historic benefits of migration. Elevational migrants can furthermore cope with short-term environmental variability by undertaking brief vertical movements to refugia when sudden adverse conditions arise. We uncover drivers of fine-scale vertical movement variation during upland migration in an endangered alpine specialist, Sierra Nevada bighorn sheep (Ovis canadensis sierrae) using a 20-year study of GPS collar data collected from 311 unique individuals. We used integrated step-selection analysis to determine factors that promote vertical movements and drive selection of destinations following vertical movements. Our results reveal that relatively high temperatures consistently drive uphill movements, while precipitation likely drives downhill movements. Furthermore, bighorn select destinations at their peak annual biomass and maximal time since snowmelt. These results indicate that although Sierra Nevada bighorn sheep seek out foraging opportunities related to landscape phenology, they compensate for short-term environmental stressors by undertaking brief up- and downslope vertical movements. Migrants may therefore be impacted by future warming and increased storm frequency or intensity, with shifts in annual migration timing, and fine-scale vertical movement responses to environmental variability.