IsoVis - a webserver for visualization and annotation of alternative RNA isoforms.

Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms and how they differ in exonic content, expression levels and potential functions. Here we introduce IsoVis, a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner. IsoVis contains numerous features, including the ability to visualize all RNA isoforms of a gene and their expression levels; the annotation of known isoforms from external databases; mapping of protein domains and features to exons, allowing changes to protein sequence and function between isoforms to be established; and extensive species compatibility. Datasets visualised on IsoVis remain private to the user, allowing analysis of sensitive data. IsoVis visualisations can be downloaded to create publication-ready figures. The IsoVis webserver enables researchers to perform isoform analyses without requiring programming skills, is free to use, and available at https://isomix.org/isovis/.

Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities.

We analyze data from the fall 2020 pandemic response efforts at the University of Colorado Boulder, where more than 72,500 saliva samples were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using qRT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously observed in symptomatic individuals. Regardless of symptomatic status, ∼50% of individuals who test positive for SARS-CoV-2 seem to be in noninfectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral "supercarriers" and possibly also superspreaders.

Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state.

BACKGROUND: Cisplatin (CDDP) is a mainstay treatment for advanced head and neck squamous cell carcinomas (HNSCC) despite a high frequency of innate and acquired resistance. We hypothesised that tumours acquire CDDP resistance through an enhanced reductive state dependent on metabolic rewiring. METHODS: To validate this model and understand how an adaptive metabolic programme might be imprinted, we performed an integrated analysis of CDDP-resistant HNSCC clones from multiple genomic backgrounds by whole-exome sequencing, RNA-seq, mass spectrometry, steady state and flux metabolomics. RESULTS: Inactivating KEAP1 mutations or reductions in KEAP1 RNA correlated with Nrf2 activation in CDDP-resistant cells, which functionally contributed to resistance. Proteomics identified elevation of downstream Nrf2 targets and the enrichment of enzymes involved in generation of biomass and reducing equivalents, metabolism of glucose, glutathione, NAD(P), and oxoacids. This was accompanied by biochemical and metabolic evidence of an enhanced reductive state dependent on coordinated glucose and glutamine catabolism, associated with reduced energy production and proliferation, despite normal mitochondrial structure and function. CONCLUSIONS: Our analysis identified coordinated metabolic changes associated with CDDP resistance that may provide new therapeutic avenues through targeting of these convergent pathways.

Pseudomonas aeruginosa increases the susceptibility of Candida albicans to amphotericin B in dual-species biofilms.

BACKGROUND: Biofilms are the leading cause of nosocomial infections and are hard to eradicate due to their inherent antimicrobial resistance. Candida albicans is the leading cause of nosocomial fungal infections and is frequently co-isolated with the bacterium Pseudomonas aeruginosa from biofilms in the cystic fibrosis lung and severe burn wounds. The presence of C. albicans in multispecies biofilms is associated with enhanced antibacterial resistance, which is largely mediated through fungal extracellular carbohydrates sequestering the antibiotics. However, significantly less is known regarding the impact of polymicrobial biofilms on antifungal resistance. RESULTS: Here we show that, in dual-species biofilms, P. aeruginosa enhances the susceptibility of C. albicans to amphotericin B, an effect that was biofilm specific. Transcriptional analysis combined with gene ontology enrichment analysis identified several C. albicans processes associated with oxidative stress to be differentially regulated in dual-species biofilms, suggesting that P. aeruginosa exerts oxidative stress on C. albicans, likely through the secretion of phenazines. However, the mitochondrial superoxide dismutase SOD2 was significantly down-regulated in the presence of P. aeruginosa. Monospecies biofilms of the sod2Δ mutant were more susceptible to amphotericin B, and the susceptibility of these biofilms was further enhanced by exogenous phenazines. CONCLUSIONS: We propose that in dual-species biofilms, P. aeruginosa simultaneously induces mitochondrial oxidative stress, while down-regulating key detoxification enzymes, which prevents C. albicans mounting an appropriate oxidative stress response to amphotericin B, leading to fungal cell death. This work highlights the importance of understanding the impact of polymicrobial interactions on antimicrobial susceptibility.

Investigation into a Conformationally Locked (Z)-Azidoxime.

High nitrogen compounds find wide use in the development of new propellants and explosives as well as pharmaceutical chemistry as bioisosteres, bacterial stains, and antifungal agents. A class of underexplored high-nitrogen materials includes azidoximes and their 1-hydroxytetrazole isomers. Azidoximes possess an energetic azide group and are quite sensitive to impact, spark, and friction. Therefore, these materials are generated in situ and cyclized under mild acidic conditions to their 1-hydroxytetrazole isomers. Recently, we synthesized a novel 1,2,4-triazine-derived azidoxime; however, upon subjecting this material to established cyclization conditions, no reaction was observed, even after prolonged reaction times with heating. Additional 1,2,4-triazine-derived azidoximes also displayed a similar lack of reactivities. This observation led us to probe the reactivity of these materials with both a DFT investigation and crystallographically based electrostatic potential mapping. In all, the lack of reactivity toward cyclization was found to be due to an inability of 1,2,4-triazine-based azidoximes to isomerize into the reactive (E)-conformation, requiring an activation energy of 26.4 kcal mol-1.

Binding of Nitriles and Isonitriles to V(III) and Mo(III) Complexes: Ligand vs Metal Controlled Mechanism.

The synthesis and structures of nitrile complexes of V(N[tBu]Ar)3, 2 (Ar = 3,5-Me2C6H3), are described. Thermochemical and kinetic data for their formation were determined by variable temperature Fourier transform infrared (FTIR), calorimetry, and stopped-flow techniques. The extent of back-bonding from metal to coordinated nitrile indicates that electron donation from the metal to the nitrile plays a less prominent role for 2 than for the related complex Mo(N[tBu]Ar)3, 1. Kinetic studies reveal similar rate constants for nitrile binding to 2, but the activation parameters depend critically on the nature of R in RCN. Activation enthalpies range from 2.9 to 7.2 kcal·mol-1, and activation entropies from -9 to -28 cal·mol-1·K-1 in an opposing manner. Density functional theory (DFT) calculations provide a plausible explanation supporting the formation of a π-stacking interaction between a pendant arene of the metal anilide of 2 and the arene substituent on the incoming nitrile in favorable cases. Data for ligand binding to 1 do not exhibit this range of activation parameters and are clustered in a small area centered at ΔH‡ = 5.0 kcal·mol-1 and ΔS‡ = -26 cal·mol-1·K-1. Computational studies are in agreement with the experimental data and indicate a stronger dependence on electronic factors associated with the change in spin state upon ligand binding to 1.

Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives.

The drop-weight impact test is an experiment that has been used for nearly 80 years to evaluate handling sensitivity of high explosives. Although the results of this test are known to have large statistical uncertainties, it is one of the most common tests due to its accessibility and modest material requirements. In this paper, we compile a large data set of drop-weight impact sensitivity test results (mainly performed at Los Alamos National Laboratory), along with a compendium of molecular and chemical descriptors for the explosives under test. These data consist of over 500 unique explosives, over 1000 repeat tests, and over 100 descriptors, for a total of about 1500 observations. We use random forest methods to estimate a model of explosive handling sensitivity as a function of chemical and molecular properties of the explosives under test. Our model predicts well across a wide range of explosive types, spanning a broad range of explosive performance and sensitivity. We find that properties related to explosive performance, such as heat of explosion, oxygen balance, and functional group, are highly predictive of explosive handling sensitivity. Yet, models that omit many of these properties still perform well. Our results suggest that there is not one or even several factors that explain explosive handling sensitivity, but that there are many complex, interrelated effects at play.

Higher Viral Load Drives Infrequent Severe Acute Respiratory Syndrome Coronavirus 2 Transmission Between Asymptomatic Residence Hall Roommates.

BACKGROUND: The coronavirus disease 2019 pandemic spread to >200 countries in <6 months. To understand coronavirus spread, determining transmission rate and defining factors that increase transmission risk are essential. Most cases are asymptomatic, but people with asymptomatic infection have viral loads indistinguishable from those in symptomatic people, and they do transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, asymptomatic cases are often undetected. METHODS: Given high residence hall student density, the University of Colorado Boulder established a mandatory weekly screening test program. We analyzed longitudinal data from 6408 students and identified 116 likely transmission events in which a second roommate tested positive within 14 days of the index roommate. RESULTS: Although the infection rate was lower in single-occupancy rooms (10%) than in multiple-occupancy rooms (19%), interroommate transmission occurred only about 20% of the time. Cases were usually asymptomatic at the time of detection. Notably, individuals who likely transmitted had an average viral load approximately 6.5-fold higher than individuals who did not (mean quantification cycle [Cq], 26.2 vs 28.9). Although students with diagnosed SARS-CoV-2 infection moved to isolation rooms, there was no difference in time to isolation between cases with or without interroommate transmission. CONCLUSIONS: This analysis argues that interroommate transmission occurs infrequently in residence halls and provides strong correlative evidence that viral load is proportional to transmission probability.

Allergenicity reduction of the bio-elicited peanut sprout powder (BPSP) and toxicological acceptance of BPSP-supplemented diets assessed with ICR mice.

The allergenic and toxicological acceptances of the bio-elicited peanut sprout powder (BPSP) have not been assessed. BPSP was generated from peanut kernels germinated at 26-28 °C for 72 h (designated as 72 h-NGS). The 72 h-NGS were subsequently sliced, incubated, dried, defatted and pulverized to generate bio-elicited peanut sprout powder (BPSP). Protein solubility of BPSP increased 2.6-fold compared to 72 h-NGS. SDS-PAGE analysis revealed BPSP production triggered extensive degradation of the high-molecular weight peanut allergic proteins, mainly Ara h 1 and Ara h 3. Western blotting detected with peanut allergic patients' IgE indicated decreased in vitro reactivity. Food safety assessment of BPSP was performed with ICR mice fed with basal (control) and three doses of formulated BPSP-supplemented diets containing 0.11 g (normal), 2.5 g (high) and 25 g (super high) BPSP /kg BW. Animals appeared healthy with steady body weight gain in all groups during the entire 35-day dietary intervention. Hematological and serum biochemical analyses revealed no significant difference among groups. Histopathological examination on the tissue sections of primary organs further supported safety with no pathologies. The in vitro allergic reduction and toxicological safety in the BPSP-supplemented dietary intervention in the ICR mice study, support moving forward with BPSP-involved product development. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-022-05537-7.

Mechanistic Pathways for N2O Elimination from trans-R3Sn-O-N═N-O-SnR3 and for Reversible Binding of CO2 to R3Sn-O-SnR3 (R = Ph, Cy).

The rate and mechanism of the elimination of N2O from trans-R3Sn-O-N═N-O-SnR3 (R = Ph (1Ph) and R = Cy (1Cy)) to form R3Sn-O-SnR3 (R = Ph (2Ph) and R = Cy (2Cy)) have been studied using both NMR and IR techniques to monitor the reactions in the temperature range of 39-79 °C in C6D6. Activation parameters for this reaction are ΔH⧧ = 15.8 ± 2.0 kcal·mol-1 and ΔS⧧ = -28.5 ± 5 cal·mol-1·K-1 for 1Ph and ΔH⧧ = 22.7 ± 2.5 kcal·mol-1 and ΔS⧧ = -12.4 ± 6 cal·mol-1·K-1 for 1Cy. Addition of O2, CO2, N2O, or PPh3 to sealed tube NMR experiments did not alter in a detectable way the rate or product distribution of the reactions. Computational DFT studies of elimination of hyponitrite from trans-Me3Sn-O-N═N-O-SnMe3 (1Me) yield a mechanism involving initial migration of the R3Sn group from O to N passing through a marginally stable intermediate product and subsequent N2O elimination. Reactions of 1Ph with protic acids HX are rapid and lead to formation of R3SnX and trans-H2N2O2. Reaction of 1Ph with the metal radical •Cr(CO)3C5Me5 at low concentrations results in rapid evolution of N2O. At higher •Cr(CO)3C5Me5 concentrations, evolution of CO2 rather than N2O is observed. Addition of 1 atm or less CO2 to benzene or toluene solutions of 2Ph and 2Cy resulted in very rapid reaction to form the corresponding carbonates R3Sn-O-C(═O)-O-SnR3 (R = Ph (3Ph) and R = Cy (3Cy)) at room temperature. Evacuation results in fast loss of bound CO2 and regeneration of 2Ph and 2Cy. Variable temperature data for formation of 3Cy yield ΔHo = -8.7 ± 0.6 kcal·mol-1, ΔSo = -17.1 ± 2.0 cal·mol-1·K-1, and ΔGo298K = -3.6 ± 1.2 kcal·mol-1. DFT studies were performed and provide additional insight into the energetics and mechanisms for the reactions.

Global optimization of small bimetallic Pd-Co binary nanoalloy clusters: a genetic algorithm approach at the DFT level.

The global optimisation of small bimetallic PdCo binary nanoalloys are systematically investigated using the Birmingham Cluster Genetic Algorithm (BCGA). The effect of size and composition on the structures, stability, magnetic and electronic properties including the binding energies, second finite difference energies and mixing energies of Pd-Co binary nanoalloys are discussed. A detailed analysis of Pd-Co structural motifs and segregation effects is also presented. The maximal mixing energy corresponds to Pd atom compositions for which the number of mixed Pd-Co bonds is maximised. Global minimum clusters are distinguished from transition states by vibrational frequency analysis. HOMO-LUMO gap, electric dipole moment and vibrational frequency analyses are made to enable correlation with future experiments.

DFT global optimisation of gas-phase and MgO-supported sub-nanometre AuPd clusters.

The Birmingham Parallel Genetic Algorithm (BPGA) has been adopted for the global optimization of free and MgO(100)-supported Pd, Au and AuPd nanocluster structures, over the size range N = 4-10. Structures were evaluated directly using density functional theory, which has allowed the identification of Pd, Au and AuPd global minima. The energetics, structures, and tendency of segregation have been evaluated by different stability criteria such as binding energy, excess energy, second difference in energy, and adsorption energy. The ability of the approach in searching for putative global minimum has been assessed against a systematic homotop search method, which shows a high degree of success.

A comparative study of AumRhn (4 ≤ m + n ≤ 6) clusters in the gas phase versus those deposited on (100) MgO.

A comparative theoretical study has been performed of the gas phase and deposited AumRhn (4 ≤ m + n ≤ 6) clusters. The combined use of a genetic algorithm and Density Functional Theory (DFT) calculations allows us to explore the potential energy surface and, therefore, find efficiently and automatically the global minimum configuration for each composition. Our results show interesting effects on the geometries of the clusters on deposition. This occurs because the rhodium atoms (electronically) prefer to be in contact with the MgO surface, sometimes promoting planar clusters to become three-dimensional when deposited, and three-dimensional clusters in the gas phase to become two-dimensional. Together with the change in geometries, the magnetic moment is reduced from the gas phase, as the electrons rearrange themselves when the cluster interacts with the substrate.

The Effect of Dispersion Correction on the Adsorption of CO on Metallic Nanoparticles.

The effect of dispersion corrections at a range of theory levels on the chemisorption properties of metallic nanoparticles is presented. The site preference for CO on Pt, Au, Pd, and Ir nanoparticles is determined for two geometries, the 38-atom truncated octahedron and the 55-atom icosahedron using density functional theory (DFT). The effects of Grimme's DFT-D2 and DFT-D3 corrections and the optPBE vdW-DF on the site preference of CO is then compared to the "standard" DFT results. Functional behavior is shown to depend not only on the metal but also on the geometry of the nanoparticle with significant effects seen for Pt and Au. There are both qualitative and quantitative differences between the functionals, with significant energetic differences in the chemical ordering of inequivalent sites and adsorption energies varying by up to 1.6 eV.

Outbreak of campylobacteriosis associated with a long-distance obstacle adventure race--Nevada, October 2012.

On October 12, 2012, the Nellis Air Force Base Public Health Flight (Nellis Public Health), near Las Vegas, Nevada, was notified by the Mike O'Callaghan Federal Medical Center (MOFMC) emergency department (ED) of three active-duty military patients who went to the ED during October 10-12 with fever, vomiting, and hemorrhagic diarrhea. Initial interviews by clinical staff members indicated that all three patients had participated October 6-7 in a long-distance obstacle adventure race on a cattle ranch in Beatty, Nevada, in which competitors frequently fell face first into mud or had their heads submerged in surface water. An investigation by Nellis Public Health, coordinated with local and state health officials, identified 22 cases (18 probable and four confirmed) of Campylobacter coli infection among active-duty service members and civilians. A case-control study using data provided by patients and healthy persons who also had participated in the race showed a statistically significant association between inadvertent swallowing of muddy surface water during the race and Campylobacter infection (odds ratio = 19.4; p<0.001). Public health agencies and adventure race organizers should consider informing race attendees of the hazards of inadvertent ingestion of surface water.

Global optimization of 8-10 atom palladium-iridium nanoalloys at the DFT level.

The global optimization of PdnIr(N-n) N = 8-10 clusters has been performed using the Birmingham Cluster Genetic Algorithm (BCGA). Structures were evaluated directly using density functional theory (DFT), which has allowed the identification of Ir and Ir-rich PdIr cubic global minima, displaying a strong tendency to segregate. The ability of the searches to find the putative global minimum has been assessed using a homotop search method, which shows a high degree of success. The role of spin in the system has been considered through a series of spin-restricted reoptimizations of BCGA-DFT minima. The preferred spin of the clusters is found to vary widely with composition, showing no overall trend in lowest-energy multiplicities.

Comparative modelling of chemical ordering in palladium-iridium nanoalloys.

Chemical ordering in "magic-number" palladium-iridium nanoalloys has been studied by means of density functional theory (DFT) computations, and compared to those obtained by the Free Energy Concentration Expansion Method (FCEM) using derived coordination dependent bond energy variations (CBEV), and by the Birmingham Cluster Genetic Algorithm using the Gupta potential. Several compositions have been studied for 38- and 79-atom particles as well as the site preference for a single Ir dopant atom in the 201-atom truncated octahedron (TO). The 79- and 38-atom nanoalloy homotops predicted for the TO by the FCEM/CBEV are shown to be, respectively, the global minima and competitive low energy minima. Significant reordering of minima predicted by the Gupta potential is seen after reoptimisation at the DFT level.

DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.

Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.

Allergenic properties of enzymatically hydrolyzed peanut flour extracts.

BACKGROUND: Peanut flour is a high-protein, low-oil, powdered material prepared from roasted peanut seed. In addition to being a well-established food ingredient, peanut flour is also the active ingredient in peanut oral immunotherapy trials. Enzymatic hydrolysis was evaluated as a processing strategy to generate hydrolysates from peanut flour with reduced allergenicity. METHODS: Soluble fractions of 10% (w/v) light roasted peanut flour dispersions were hydrolyzed with the following proteases: Alcalase (pH 8.0, 60°C), pepsin (pH 2.0, 37°C) or Flavourzyme (pH 7.0, 50°C) for 60 min. Western blotting, inhibition ELISA and basophil activation tests were used to examine IgE reactivity. RESULTS: Western blotting experiments revealed the hydrolysates retained IgE binding reactivity and these IgE-reactive peptides were primarily Ara h 2 fragments regardless of the protease tested. Inhibition ELISA assays demonstrated that each of the hydrolysates had decreased capacity to bind peanut-specific IgE compared with nonhydrolyzed controls. Basophil activation tests revealed that all hydrolysates were comparable (p > 0.05) to nonhydrolyzed controls in IgE cross-linking capacity. CONCLUSIONS: These results indicate that hydrolysis of peanut flour reduced IgE binding capacity; however, IgE cross-linking capacity during hydrolysis was retained, thus suggesting such hydrolysates are not hypoallergenic.