Environmentally relevant concentrations of aqueous atorvastatin produce alterations in cholesterol biosynthesis and gene expression patterns in Xenopus laevis

Numerous studies report active pharmaceutical compounds detected in both wastewater effluent and surface waters. Exposure to statin drugs in general, and atorvastatin in particular, is likely to be a concern. We hypothesized that chronic exposure to low concentrations of atorvastatin in water would result in an adverse effect on production of steroids regulating growth and development of the model amphibian Xenopus laevis. The FETAX assay was used to evaluate the effects of a range of doses of atorvastatin on developing embryos. A 60 day metamorphosis assay assessed the effects of aqueous atorvastatin exposure at environmentally concentrations on metamorphosing tadpoles. A 60 day chronic flow-through exposure evaluated the effects of chronic low concentrations of atorvastatin on adults. The purpose of the FETAX assay was to confirm that atorvastatin can reduce circulating cholesterol in X. laevis with a similar manner to that expected in humans. The results of the 60-day flow-through exposure on metamorphosing tadpoles showed significant evidence of altered cholesterol biosynthesis. The dose-dependent increase in cyp19a1 expression also indicated that the steroidogenesis pathway was affected. The RNAseq analysis confirmed that exposure to environmentally relevant concentrations of atorvastatin does cause significant alterations to global transcriptional profiles in a manner consistent with dysregulation of the cholesterol biosynthesis pathway, both through the downregulation of many genes involved in that pathway, but also in the impacts to other, related pathways. The qPCR data for both adult males and adult females indicated only slight changes in expression with the exception that hmgcr was significantly downregulated in males, and cyp3a4 expression was significantly downregulated in females. The data we present here indicated that chronic exposure to environmentally relevant concentrations of atorvastatin does have the potential to impact early life stage frogs, particularly by altering expression of genes involved in critical molecular pathways.

Solution-processable polytriazoles from spirocyclic monomers for membrane-based hydrocarbon separations

The thermal distillation of crude oil mixtures is an energy-intensive process, accounting for nearly 1% of global energy consumption. Membrane-based separations are an appealing alternative or tandem process to distillation due to intrinsic energy efficiency advantages. We developed a family of spirocyclic polytriazoles from structurally diverse monomers for membrane applications. The resulting polymers were prepared by a convenient step-growth method using copper-catalysed azide-alkyne cycloaddition, providing very fast reaction rates, high molecular weights and solubilities in common organic solvents and non-interconnected microporosity. Fractionation of whole Arabian light crude oil and atmospheric tower bottom feeds using these materials enriched the low-boiling-point components and removed trace heteroatom and metal impurities (comparable performance with the lighter feed as the commercial polyimide, Matrimid), demonstrating opportunities to reduce the energy cost of crude oil distillation with tandem membrane processes. Membrane-based molecular separation under these demanding conditions is made possible by high thermal stability and a moderate level of dynamic chain mobility, leading to transient interconnections between micropores, as revealed by the calculations of static and swollen pore structures.

Data-driven predictions of complex organic mixture permeation in polymer membranes

Membrane-based organic solvent separations are rapidly emerging as a promising class of technologies for enhancing the energy efficiency of existing separation and purification systems. Polymeric membranes have shown promise in the fractionation or splitting of complex mixtures of organic molecules such as crude oil. Determining the separation performance of a polymer membrane when challenged with a complex mixture has thus far occurred in an ad hoc manner, and methods to predict the performance based on mixture composition and polymer chemistry are unavailable. Here, we combine physics-informed machine learning algorithms (ML) and mass transport simulations to create an integrated predictive model for the separation of complex mixtures containing up to 400 components via any arbitrary linear polymer membrane. We experimentally demonstrate the effectiveness of the model by predicting the separation of two crude oils within 6-7% of the measurements. Integration of ML predictors of diffusion and sorption properties of molecules with transport simulators enables for the rapid screening of polymer membranes prior to physical experimentation for the separation of complex liquid mixtures.

Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens

Macrophages employ an array of pattern recognition receptors to detect and eliminate intracellular pathogens that access the cytosol. The cytosolic carbohydrate sensors Galectin-3, -8, and -9 (Gal-3, Gal-8, and Gal-9) recognize damaged pathogen-containing phagosomes, and Gal-3 and Gal-8 are reported to restrict bacterial growth via autophagy in cultured cells. However, the contribution of these galectins to host resistance during bacterial infection in vivo remains unclear. We found that Gal-9 binds directly to Mycobacterium tuberculosis (Mtb) and Salmonella enterica serovar Typhimurium (Stm) and localizes to Mtb in macrophages. To determine the combined contribution of membrane damage-sensing galectins to immunity, we generated Gal-3, -8, and -9 triple knockout (TKO) mice. Mtb infection of primary macrophages from TKO mice resulted in defective autophagic flux but normal bacterial replication. Surprisingly, these mice had no discernable defect in resistance to acute infection with Mtb, Stm or Listeria monocytogenes, and had only modest impairments in bacterial growth restriction and CD4 T cell activation during chronic Mtb infection. Collectively, these findings indicate that while Gal-3, -8, and -9 respond to an array of intracellular pathogens, together these membrane damage-sensing galectins play a limited role in host resistance to bacterial infection.

Seasonal and diurnal variations of Kelvin-Helmholtz Instability at terrestrial magnetopause

Kelvin-Helmholtz Instability is ubiquitous at Earth's magnetopause and plays an important role in plasma entry into the magnetosphere during northward interplanetary magnetic fields. Here, using one solar cycle of data from NASA THEMIS (Time History of Events and Macro scale Interactions during Substorms) and MMS (Magnetospheric Multiscale) missions, we found that KHI occurrence rates show seasonal and diurnal variations with the rate being high near the equinoxes and low near the solstices. The instability depends directly on the Earth's dipole tilt angle. The tilt toward or away from the Sun explains most of the seasonal and diurnal variations, while the tilt in the plane perpendicular to the Earth-Sun line explains the difference between the equinoxes. The results reveal the critical role of dipole tilt in modulating KHI across the magnetopause as a function of time, highlighting the importance of Sun-Earth geometry for solar wind-magnetosphere interaction and for space weather.

Hydrophobic polyamide nanofilms provide rapid transport for crude oil separation

Hydrocarbon separation relies on energy-intensive distillation. Membrane technology can offer an energy-efficient alternative but requires selective differentiation of crude oil molecules with rapid liquid transport. We synthesized multiblock oligomer amines, which comprised a central amine segment with two hydrophobic oligomer blocks, and used them to fabricate hydrophobic polyamide nanofilms by interfacial polymerization from self-assembled vesicles. These polyamide nanofilms provide transport of hydrophobic liquids more than 100 times faster than that of conventional hydrophilic counterparts. In the fractionation of light crude oil, manipulation of the film thickness down to ~10 nanometers achieves permeance one order of magnitude higher than that of current state-of-the-art hydrophobic membranes while retaining comparable size- and class-based separation. This high permeance can markedly reduce plant footprint, which expands the potential for using membranes made of ultrathin nanofilms in crude oil fractionation.

Aqueously altered igneous rocks sampled on the floor of Jezero crater, Mars

The Perseverance rover landed in Jezero crater, Mars, to investigate ancient lake and river deposits. We report observations of the crater floor, below the crater's sedimentary delta, finding the floor consists of igneous rocks altered by water. The lowest exposed unit, informally named Séítah, is a coarsely crystalline olivine-rich rock, which accumulated at the base of a magma body. Fe-Mg carbonates along grain boundaries indicate reactions with CO₂-rich water, under water-poor conditions. Overlying Séítah is a unit informally named Máaz, which we interpret as lava flows or the chemical complement to Séítah in a layered igneous body. Voids in these rocks contain sulfates and perchlorates, likely introduced by later near-surface brine evaporation. Core samples of these rocks were stored aboard Perseverance for potential return to Earth.

An olivine cumulate outcrop on the floor of Jezero crater, Mars

The geological units on the floor of Jezero crater, Mars, are part of a wider regional stratigraphy of olivine-rich rocks, which extends well beyond the crater. We investigate the petrology of olivine and carbonate-bearing rocks of the Séítah formation in the floor of Jezero. Using multispectral images and x-ray fluorescence data, acquired by the Perseverance rover, we performed a petrographic analysis of the Bastide and Brac outcrops within this unit. We find that these outcrops are composed of igneous rock, moderately altered by aqueous fluid. The igneous rocks are mainly made of coarse-grained olivine, similar to some Martian meteorites. We interpret them as an olivine cumulate, formed by settling and enrichment of olivine through multi-stage cooling of a thick magma body.

Obesity and Pregnancy

The worldwide rates of obesity have increased significantly in recent decades. In the United States, more than 50% of pregnant women are overweight or obese. Obese gravid women are more prone to adverse pregnancy outcomes, including gestational diabetes, hypertensive disorders, and cardiovascular diseases. The adverse outcomes extend beyond the pregnant obese woman; offspring of obese women are themselves at increased risk of prematurity, fetal death, injury during birth, and transient respiratory problems and metabolic effects (ie, neonatal hypoglycemia). Furthermore, maternal obesity can predispose their offspring to long-term health problems, potentially generating an intergenerational cycle of obesity and insulin resistance.

N-Aryl-linked spirocyclic polymers for membrane separations of complex hydrocarbon mixtures

The fractionation of crude-oil mixtures through distillation is a large-scale, energy-intensive process. Membrane materials can avoid phase changes in such mixtures and thereby reduce the energy intensity of these thermal separations. With this application in mind, we created spirocyclic polymers with N-aryl bonds that demonstrated noninterconnected microporosity in the absence of ladder linkages. The resulting glassy polymer membranes demonstrated nonthermal membrane fractionation of light crude oil through a combination of class- and size-based "sorting" of molecules. We observed an enrichment of molecules lighter than 170 daltons corresponding to a carbon number of 12 or a boiling point less than 200°C in the permeate. Such scalable, selective membranes offer potential for the hybridization of energy-efficient technology with conventional processes such as distillation.

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.

Psychosocial and functional contributors to personal recovery in serious mental illness

Background: Although recovery-oriented services have been conceptualized to improve personal recovery, related research often focuses on measures of clinical recovery. Identifying the relationships between personal recovery, clinical recovery, and psychosocial variables will inform service components and outcome measurement in recovery-oriented services. Aims: This study sought to determine the connection between personal recovery and two sets of potential contributors: psychosocial variables (i.e., empowerment, resilience, and consumer involvement) and functional indicators of clinical recovery. Method: These relationships were examined by analyzing survey data collected from 266 consumers who are receiving public mental health services in the United States. Results: Empowerment, resilience and psychological involvement were associated with personal recovery. Clinical recovery did not uniquely contribute to personal recovery once psychosocial factors were accounted for. Interactions revealed that the relationship between psychological involvement and personal recovery was stronger for those who had been recently hospitalized, and for those with relatively greater resilience. Conclusions: Results indicate that personal recovery is an essential outcome measure for recovery-oriented services that cannot be replaced by clinical recovery outcome measurement. Additionally, empowerment, resilience, and consumer involvement are key components of recovery, which suggests that services and outcome measures should prioritize incorporation of these constructs.

Give me a SINE: how Selective Inhibitors of Nuclear Export modulate autophagy and aging

Autophagy is a cellular recycling process leading to lysosomal degradation of damaged macromolecules, which can protect cells against aging. The transcription factor EB (TFEB), a major transcriptional regulator of genes involved in autophagy and lysosomal function, is emerging as an attractive target for pharmacological modulation. Recently, we demonstrated that inhibiting the function of nuclear export protein exportin 1 (XPO1 or CRM1) with RNAi or with selective inhibitors of nuclear export (SINE) results in the nuclear enrichment of TFEB and enhancement of autophagy in model organisms and human cells. In addition to current efforts to validate the use of SINE in cancer therapies, our work highlights the potential benefits of these drugs toward improving outcomes in neurodegenerative diseases and aging.

Escherichia coli: an old friend with new tidings

Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.

Chemistry, mineralogy, and grain properties at Namib and High dunes, Bagnold dune field, Gale crater, Mars: A synthesis of Curiosity rover observations

The Mars Science Laboratory Curiosity rover performed coordinated measurements to examine the textures and compositions of aeolian sands in the active Bagnold dune field. The Bagnold sands are rounded to subrounded, very fine to medium sized (~45-500 μm) with ≥6 distinct grain colors. In contrast to sands examined by Curiosity in a dust-covered, inactive bedform called Rocknest and soils at other landing sites, Bagnold sands are darker, less red, better sorted, have fewer silt-sized or smaller grains, and show no evidence for cohesion. Nevertheless, Bagnold mineralogy and Rocknest mineralogy are similar with plagioclase, olivine, and pyroxenes in similar proportions comprising >90% of crystalline phases, along with a substantial amorphous component (35% ± 15%). Yet Bagnold and Rocknest bulk chemistry differ. Bagnold sands are Si enriched relative to other soils at Gale crater, and H₂O, S, and Cl are lower relative to all previously measured Martian soils and most Gale crater rocks. Mg, Ni, Fe, and Mn are enriched in the coarse-sieved fraction of Bagnold sands, corroborated by visible/near-infrared spectra that suggest enrichment of olivine. Collectively, patterns in major element chemistry and volatile release data indicate two distinctive volatile reservoirs in Martian soils: (1) amorphous components in the sand-sized fraction (represented by Bagnold) that are Si-enriched, hydroxylated alteration products and/or H₂O- or OH-bearing impact or volcanic glasses and (2) amorphous components in the fine fraction (<40 μm; represented by Rocknest and other bright soils) that are Fe, S, and Cl enriched with low Si and adsorbed and structural H₂O.

Application of fecal near-infrared reflectance spectroscopy profiling for the prediction of diet nutritional characteristics and voluntary intake in beef cattle

The objective of this study was to evaluate the use of fecal near-infrared reflectance spectroscopy (NIRS) profiling to predict diet nutritional characteristics and voluntary DMI in beef cattle. Fecal samples were collected for growing cattle across 11 experiments in which individual animal performance and DMI was measured. Dried and ground fecal composite samples collected from each animal were subjected to fecal NIRS analysis by a Foss NIRS 6500 scanning monochromator (Foss, Eden Prairie, MN) at the Grazingland Animal Nutrition Laboratory (Temple, TX). Fecal spectra were then used to develop equations to predict diet composition (trials 1 to 11; = 408), digestibility (trials 1 to 5; = 155), and DMI (trials 1 to 11; = 408). Coefficients of determination for calibration () and cross-validation () for prediction of diet nutritional characteristics were lower for NDF ( = 0.85; = 0.82) than for CP ( = 0.90; = 0.88). For the prediction of DMI, and ranged from 0.69 and 0.67 for the prediction of trial-average DMI to 0.76 and 0.73 for the prediction of fecal-collection-period DMI. While the and obtained for the prediction of DMI were lower than those obtained for the prediction of diet composition or digestibility, fecal NIRS prediction equations for DMI were successful in predicting the mean DMI of groups, as no differences were found for the prediction of fecal-collection-period DMI (Diff. = 1.10; = 0.72) or trial DMI (Diff. = -0.47; = 0.86).

The Virus–Host Interactome

While viruses encode a limited repertoire of factors, their influence on host proteins is substantial. Various high-throughput technologies have been employed to gain a global understanding of how viruses rewire cellular machinery to promote replication and evade immune responses. These approaches can elucidate the interplay that occurs between virus and host by identifying host factors that directly associate with viral proteins, determining what cellular factors impact the viral lifecycle and what viral countermeasures circumvent immune surveillance. This chapter will discuss system-level technologies that are used to identify host proteins, pathways, and biochemical complexes that govern viral pathogenesis. We will examine the information that can be gained from genome- and proteome-level analyses of host–pathogen interactions, the advantages and pitfalls of various methods and provide examples of significant breakthroughs that have been facilitated using OMICs-based technologies.

Long-term efficacy of sitagliptin as either monotherapy or add-on therapy to metformin: improvement in glycemic control over 2 years in patients with type 2 diabetes

OBJECTIVE

To evaluate the efficacy of once daily sitagliptin 100 mg as monotherapy or as add-on to metformin in patients with type 2 diabetes mellitus (T2DM) over 2 years of treatment.

RESEARCH DESIGN AND METHODS

The monotherapy analysis used pooled 104 week data from 64 patients in two randomized, double-blind trials evaluating the safety and efficacy of sitagliptin monotherapy. Data used were from patients who were randomized to sitagliptin 100 mg/day, were not on an antihyperglycemic agent at the screening visit, had baseline A1C of 7.0%-10.0%, and had Week 104 A1C measurements. The add-on to metformin analysis used pooled data from 347 patients in two randomized double-blind trials evaluating the safety and efficacy of sitagliptin + metformin combination therapy. Data used were from patients who were randomized to sitagliptin 100 mg/day + metformin ≥1500 mg/day, had baseline A1C of 7%-10%, and had Week 104 A1C measurements. Excluded from either analysis were patients who discontinued prior to 2 years (e.g., due to lack of efficacy, a need for rescue medications, or adverse experiences). Analysis endpoints were A1C, fasting plasma glucose (FPG), HOMA-β, proinsulin/insulin (P/I) ratio, and for monotherapy, 2 hour post-meal plasma glucose (PMG).

RESULTS

For the pooled monotherapy cohort, after 2 years of treatment, mean A1C, FPG, and 2 hour PMG decreased from baseline values of 7.9%, 156 mg/dL, and 223 mg/dL to 6.9%, 143 mg/dL, and 191 mg/dL, respectively, while HOMA-β increased from 67% to 85% and P/I ratio improved from 0.57 to 0.28. For the pooled add-on to metformin cohort, after 2 years of treatment, mean A1C and FPG decreased from baseline values of 7.7% and 160 mg/dL to 6.9% and 140 mg/dL, respectively, while HOMA-β increased from 50% to 62% and P/I ratio improved from 0.33 to 0.28. These analyses are limited in that only patients who were able to complete 104 weeks of study were included.

CONCLUSION

In the subset of patients with T2DM who maintained and completed treatment for 2 years with sitagliptin as monotherapy or as add-on to metformin, improvements in glycemic control and measures of β-cell function were observed over the course of treatment.

An integrated data analysis tool for improving measurements on the MST RFP

Many plasma diagnostics contain complementary information. For example, the double-foil soft x-ray system (SXR) and the Thomson Scattering diagnostic (TS) on the Madison Symmetric Torus both measure electron temperature. The complementary information from these diagnostics can be combined using a systematic method based on integrated data analysis techniques, leading to more accurate and sensitive results. An integrated data analysis tool based on Bayesian probability theory was able to estimate electron temperatures that are consistent with both the SXR and TS diagnostics and more precise than either. A Markov Chain Monte Carlo analysis to increase the flexibility of the tool was implemented and benchmarked against a grid search method.

Separation membranes. Interfacial microfluidic processing of metal-organic framework hollow fiber membranes

Molecular sieving metal-organic framework (MOF) membranes have great potential for energy-efficient chemical separations, but a major hurdle is the lack of a scalable and inexpensive membrane fabrication mechanism. We describe a route for processing MOF membranes in polymeric hollow fibers, combining a two-solvent interfacial approach for positional control over membrane formation (at inner and outer surfaces, or in the bulk, of the fibers), a microfluidic approach to replenishment or recycling of reactants, and an in situ module for membrane fabrication and permeation. We fabricated continuous molecular sieving ZIF-8 membranes in single and multiple poly(amide-imide) hollow fibers, with H2/C3H8 and C3H6/C3H8 separation factors as high as 370 and 12, respectively. We also demonstrate positional control of the ZIF-8 films and characterize the contributions of membrane defects and lumen bypass.

Effect of topical corticosteroids on allergic airway inflammation and disease severity in obstructive sleep apnoea

BACKGROUND

The incidence of sleep-related breathing disorders is correlated with lower and upper airway inflammatory diseases, such as asthma and allergic rhinitis. We hypothesized that corticosteroids treatment would lead to a greater reduction in disease severity in obstructive sleep apnoea syndrome (OSAS) patients with concomitant allergic rhinitis vs. non-allergic OSAS patients by reducing the level of inflammation in upper airway tissues.

OBJECTIVE

This study was performed to determine whether treatment with intranasal corticosteroids could reduce upper airway inflammation and improve sleep parameters in obstructive sleep apnoea syndrome patients with or without concomitant allergic rhinitis.

METHODS

Obstructive sleep apnoea syndrome patients with (n = 34) or without (n = 21) documented allergic rhinitis voluntarily enrolled in the study and were assessed at baseline and after corticosteroids treatment for 10-12 weeks. Sleep studies were performed and biopsies were obtained from the inferior turbinate, nasopharynx, and uvula. The apnoea-hypopnoea index, sleep quality, and level of daytime alertness were determined, and immunocytochemistry was used to phenotype tissue inflammation.

RESULTS

Standard sleep indices improved following treatment in the entire cohort of obstructive sleep apnoea syndrome patients, with greater improvement seen in the allergic rhinitis group. Allergic rhinitis patients demonstrated significantly improved O2 saturation and a lower supine apnoea-hypopnoea index score after corticosteroid treatment; similar improvements were not seen in the non-allergic rhinitis group. Eosinophilia was detected at all three sites in the allergic rhinitis group, but not in the non-allergic rhinitis group. Following treatment, fewer eosinophils and CD4 lymphocytes were documented at all three biopsy sites in the allergic group; the reduction in inflammation was less apparent in the non-allergic rhinitis group.

CONCLUSION

This study has provided important molecular and clinical evidence regarding the ability of corticosteroids to reduce upper airway inflammation and improve obstructive sleep apnoea syndrome morbidity patients with concomitant allergic rhinitis.

Relationships between postweaning residual feed intake in heifers and forage use, body composition, feeding behavior, physical activity, and heart rate of pregnant beef females

The objectives of this study were to determine if residual feed intake (RFI) classification of beef heifers affected efficiency of forage utilization, body composition, feeding behavior, heart rate, and physical activity of pregnant females. Residual feed intake was measured in growing Bonsmara heifers for 2 yr (n=62 and 53/yr), and heifers with the lowest (n=12/yr) and highest (n=12/yr) RFI were retained for breeding. Of the 48 heifers identified as having divergent RFI, 19 second-parity and 23 first-parity females were used in the subsequent pregnant-female trial. Pregnant females were fed a chopped hay diet (ME=2.11 Mcal kg(-1) DM) in separate pens equipped with GrowSafe bunks to measure individual intake and feeding behavior. Body weights were measured at 7-d intervals and BCS and ultrasound measurements of 12th-rib fat depth, rump fat depth, and LM area obtained on d 0 and 77. Heart rate and physical activity were measured for 7 consecutive d. First-parity females had lower (P<0.05) initial BW, BW gain, and initial hip height and tended (P=0.07) to have lower DMI compared to second-parity females. Females with low RFI as heifers consumed 17% less (P<0.01) forage compared to females with high RFI as heifers but maintained the same BW, BW gain, and body composition. Likewise, RFI classification did not affect calving date. An interaction (P=0.04) between heifer RFI classification and parity was found for calf birth weight. Calves from first-parity low-RFI females were lighter at birth (P<0.01) than calves from high-RFI females, but RFI classification did not affect BW of calves born to second-parity females. Residual feed intake classification did not affect bunk visit frequency, but low-RFI females spent 26% less time (P<0.01) at the bunk compared to high-RFI females. First-parity females had more (P<0.05) daily step counts and greater lying-bout frequencies compared to second-parity females, but physical activity was not affected by RFI classification. Heart rates of females classified as low RFI were 7% lower (P=0.03) compared to high-RFI females. Heifer postweaning RFI but not G:F or residual gain were positively correlated with forage intake (r=0.38) and RFI (r=0.42) of pregnant females. Results indicate that heifers identified as having low postweaning RFI have greater efficiency of forage utilization as pregnant females, with minimal impacts on growth, body composition, calving date, and calf birth BW, compared to their high-RFI counterparts.

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

OBJECTIVES

Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae.

METHODS

Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes were predicted from genomic sequences using BLASTn-based comparisons of de novo-assembled contigs with a study database of >100 known resistance-associated loci, including plasmid-associated and chromosomal genes. Predictions were made for seven commonly used antimicrobials: amoxicillin, co-amoxiclav, ceftriaxone, ceftazidime, ciprofloxacin, gentamicin and meropenem. Comparisons were made with phenotypic results obtained in duplicate by broth dilution (BD Phoenix). Discrepancies, either between duplicate BD Phoenix results or between genotype and phenotype, were resolved with gradient diffusion analyses.

RESULTS

A wide variety of antimicrobial resistance genes were identified, including blaCTX-M, blaLEN, blaOKP, blaOXA, blaSHV, blaTEM, aac(3')-Ia, aac-(3')-IId, aac-(3')-IIe, aac(6')-Ib-cr, aadA1a, aadA4, aadA5, aadA16, aph(6')-Id, aph(3')-Ia, qnrB and qnrS, as well as resistance-associated mutations in chromosomal gyrA and parC genes. The sensitivity of genome-based resistance prediction across all antibiotics for both species was 0.96 (95% CI: 0.94-0.98) and the specificity was 0.97 (95% CI: 0.95-0.98). Very major and major error rates were 1.2% and 2.1%, respectively.

CONCLUSIONS

Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.

Distribution of phylogenetic groups, sequence type ST131, and virulence-associated traits among Escherichia coli isolates from men with pyelonephritis or cystitis and healthy controls

Urinary tract infections (UTI), which are mostly caused by Escherichia coli, are an important public health problem worldwide. Although men experience diverse UTI syndromes, there have been relatively few molecular-epidemiological studies of UTI pathogenesis in men. We studied the distribution of 22 E. coli virulence factor (VF) genes, major phylogenetic groups, sequence type ST131, and UTI-associated O antigens among 101 pyelonephritis, 153 cystitis and 135 fecal healthy control E. coli isolates from men aged 30-70 years in a regional area of NSW, Australia. Overall, the studied traits exhibited a prevalence gradient across these groups, highest in pyelonephritis, intermediate in cystitis, and lowest among fecal isolates. Differences in virulence gene prevalence between cystitis and pyelonephritis isolates were limited to eight genes. The UTI-associated O antigens were also distributed widely, but types O6, O25 and O75 were significantly associated with pyelonephritis. The ST131 clonal group, which accounted for 13% of isolates overall (22% of group B2 isolates), likewise exhibited a significant descending prevalence gradient from pyelonephritis (36%), through cystitis (8%), to fecal (0%) isolates. These findings contribute to better understanding of the pathogenesis of UTIs in men and identify specific VF genes and O types, and a prominent clonal group (ST131), as being important in UTI pathogenesis in this population.

Tigecycline treatment for urinary tract infections: case report and literature review

Antimicrobial resistance among Gram-negatives is increasing; treatment options are limited. Although tigecycline is used infrequently for urinary tract infection (UTI), greater use is likely as resistance increases. We report successful treatment of an episode of febrile UTI and probable prostatitis with tigecycline, and summarize the relevant literature.

Detecting 2009 pandemic influenza A (H1N1) virus infection: availability of diagnostic testing led to rapid pandemic response

Diagnostic tests for detecting emerging influenza virus strains with pandemic potential are critical for directing global influenza prevention and control activities. In 2008, the Centers for Disease Control and Prevention received US Food and Drug Administration approval for a highly sensitive influenza polymerase chain reaction (PCR) assay. Devices were deployed to public health laboratories in the United States and globally. Within 2 weeks of the first recognition of 2009 pandemic influenza H1N1, the Centers for Disease Control and Prevention developed and began distributing a new approved pandemic influenza H1N1 PCR assay, which used the previously deployed device platform to meet a >8-fold increase in specimen submissions. Rapid antigen tests were widely used by clinicians at the point of care; however, test sensitivity was low (40%-69%). Many clinical laboratories developed their own pandemic influenza H1N1 PCR assays to meet clinician demand. Future planning efforts should identify ways to improve availability of reliable testing to manage patient care and approaches for optimal use of molecular testing for detecting and controlling emerging influenza virus strains.

Molecular epidemiology of Escherichia coli bacteremia in liver transplant recipients

The characteristics of Escherichia coli strains causing bacteremia in profoundly immunosuppressed patients such as transplant recipients are undefined. The phylogenetic group and the virulence genotype of 57 distinct E. coli strains that caused bacteremia in 53 liver transplant recipients were investigated, and the association of these characteristics with host factors and in-hospital mortality was examined. Phylogenetic groups A, B1, B2, and D accounted for 39%, 10%, 25%, and 26% of the isolates, respectively. The most prevalent virulence genes were fyuA (yersiniabactin system: 70%) and iutA (aerobactin system: 63%), whereas hlyA (alpha-hemolysin) and cnf1 (cytotoxic necrotizing factor 1) occurred in only 14% and 12% of isolates, respectively. Most virulence genes were significantly more prevalent among group B2 and D isolates, vs. group A and B1 isolates. The overall rate of in-hospital mortality after E. coli bacteremia was 20%. Predictors of mortality included onset of bacteremia within 30 days of transplantation or during the intensive care unit stay, and non-urinary source and cutaneous source, but not E. coli phylogenetic group or virulence profile. Compared with historical E. coli bloodstream isolates from non-transplant patients, those from liver transplant recipients are characterized by a higher prevalence of groups A and B1 isolates and reduced virulence gene content. This finding can be explained by the severely immunocompromised status of the patients and the predominance of abdominal-source bacteremic episodes. Time of onset and source of bacteremia, not bacterial characteristics, predict mortality.

Stability and bioavailability of a flucytosine suspension

The stability and bioavailability of a suspension of flucytosine was evaluated. There was found to be no change in the flucytosine content of the suspension over a three month period. A shelf life of at least three months could be given to suspensions made by large scale dispensing.

The bioavailability of the suspension was compared with that of commercially available tablets in eight healthy male volunteers. A single dose (2g) of tablets was administered to each volunteer and urine samples were collected over a 24 hour period. After a washout period of one week, the procedure was repeated using the suspension (2g/20ml). The bioavailability of the suspension relative to commercially available tablets was 80.7 per cent. The high performance liquid chromatography (HPLC) method used was found to give consistent results for tablet and suspension assays and for urine analysis (relative standard deviation 1.8 per cent, correlation coefficient r = 0.996).

Where patients have impaired swallowing reflexes or few accessible sites for venepuncture, flucytosine suspension may have several advantages when large doses (10–15g/day) need to be administered.

Factors influencing community pharmacist participation in clinical audit: a qualitative study of barriers and drivers of change

Focal points

A quantitative method for assessing stages of the rat estrous cycle

The impact of gender and/or hormone variations on a wide variety of neural functions makes the choice between studying males or females (or both) of a given species difficult. Although female rats are widely used experimentally, few studies control for the stage of estrus. More detailed information about how to distinguish the various stages of the estrous cycle is needed. For the present study, vaginal smears were obtained once a day and stained using an adaptation of the Papanicolaou (PAP) procedure. Images are provided of unstained "wet" samples and the corresponding PAP stained smears illustrating the cellular profile for each stage of the cycle as well as post-ovariectomy. The different cell populations across the cycle were quantified and ratios determined to show trends between the predominant and other cell types in each stage of the estrous cycle. Both stained and unstained images and cell quantification data provide valuable guidelines for distinguishing the stages of the estrous cycle.

The Anopheles gambiae adult midgut peritrophic matrix proteome

Malaria is a devastating disease. For transmission to occur, Plasmodium, the causative agent of malaria, must complete a complex developmental cycle in its mosquito vector. Thus, the mosquito is a potential target for disease control. Plasmodium ookinetes, which develop within the mosquito midgut, must first cross the midgut's peritrophic matrix (PM), a thick extracellular sheath that completely surrounds the blood meal. The PM poses a partial, natural barrier against parasite invasion of the midgut and it is speculated that modifications to the PM may lead to a complete barrier to infection. However, such strategies require thorough characterization of the structure of the PM. Here, we describe for the first time, the complete PM proteome of the main malaria vector, Anopheles gambiae. Altogether, 209 proteins were identified by mass spectrometry. Among them were nine new chitin-binding peritrophic matrix proteins, expanding the list from three to twelve peritrophins. Lastly, we provide a model for the putative interactions among the proteins identified in this study.

Evaluation of allergic lung inflammation by computed tomography in a rat model in vivo

The ability of micro-computed tomography (CT) to noninvasively evaluate allergic pulmonary inflammation in an experimental model was investigated. In addition, two image segmentation methods and the value of respiratory gating were investigated in the context of this model. Brown Norway rats were exposed to one of four doses of house dust mite (HDM) extract (0, 0.15, 15 or 150 microg) delivered intratracheally every 24 h for 10 days. CT scanning was performed at baseline and after several longitudinal HDM exposures. Both thoracic- and lung-segmentation methods yielded similar results when standardisation practices were employed. While tissue histology correlated well with CT images, cell counts from bronchoalveolar lavage depicted greater inflammation than did density measures from CT images. Evidence from representative CT slices and transaxial density distribution indicated that inflammation was primarily associated with major airways and extended into the periphery from these focal points. Respiratory gating demonstrated that images of the inspiratory state provided greater contrast of inflammatory processes. Lastly, decreases in tidal volumes indicated significant mechanical respiratory changes in animals exposed to both 15 and 150 microg. In summary, CT image segmentation can extract pertinent data on in vivo allergic airway/lung inflammation. Furthermore, respiratory gating provides additional contrast and insight into these quantification practices.

Kinetic Alfvén Wave Turbulence and Transport through a Reconnection Diffusion Region

We demonstrate from observations that kinetic Alfvén waves may play an important role in facilitating magnetic reconnection. These waves radiate outwards from the diffusion region oblique to the magnetic field in a conelike pattern delimited by the X line separatrices with outward energy fluxes equivalent to that contained in the outstreaming ions. It is shown that the wave vectors reverse across the X and symmetry lines and have a large out of plane component. We estimate that these waves drive significant transport through the diffusion region.

Escherichia coli colonizing the neurogenic bladder are similar to widespread clones causing disease in patients with normal bladder function

STUDY DESIGN

Clonal typing of neurogenic clones.

OBJECTIVE

To determine whether neurogenic clones carried over weeks in the urine of asymptomatic children with neurogenic bladder were similar to known uropathogenic clones associated with disease.

SETTING

Michigan State University; VA Medical Center, Minneapolis, MN, USA.

METHODS

Escherichia coli isolates from the urine of 15 children previously followed were typed by multilocus sequence typing and compared to 2 human pyelonephritis genome strains, 29 pediatric or adult symptomatic urinary tract infection strains, 15 pediatric asymptomatic bacteriuria strains, 6 animal urinary tract infection strains and a neonatal meningitis-septicemia prototype K1 strain. Phylotypes and virulence genotypes were determined using PCR.

RESULTS

Twenty-nine E. coli isolates were classified into 15 clones. Six of 15 clones were the same sequence type or a close relative to a clone that caused disease in a human or animal. These clones were considered uropathogens. The remaining nine clones were not closely related to a clone that caused disease and were considered commensal clones. Uropathogens were predominantly group B2, exhibited more virulence genes and were carried for more weeks in the neurogenic bladder compared to commensal clones. Nine of 15 children carried one or more uropathogenic clones; 4 children carried one or more commensal clones and 2 children carried both uropathogenic and commensal clones.

CONCLUSION

Children with neurogenic bladder most commonly carried commensal clones. Uropathogenic clones were associated with prolonged carriage, however, carriage was not associated with symptomatic disease or deterioration of the upper urinary tract.

In silico discovery of transcription regulatory elements in Plasmodium falciparum

BACKGROUND

With the sequence of the Plasmodium falciparum genome and several global mRNA and protein life cycle expression profiling projects now completed, elucidating the underlying networks of transcriptional control important for the progression of the parasite life cycle is highly pertinent to the development of new anti-malarials. To date, relatively little is known regarding the specific mechanisms the parasite employs to regulate gene expression at the mRNA level, with studies of the P. falciparum genome sequence having revealed few cis-regulatory elements and associated transcription factors. Although it is possible the parasite may evoke mechanisms of transcriptional control drastically different from those used by other eukaryotic organisms, the extreme AT-rich nature of P. falciparum intergenic regions (approximately 90% AT) presents significant challenges to in silico cis-regulatory element discovery.

RESULTS

We have developed an algorithm called Gene Enrichment Motif Searching (GEMS) that uses a hypergeometric-based scoring function and a position-weight matrix optimization routine to identify with high-confidence regulatory elements in the nucleotide-biased and repeat sequence-rich P. falciparum genome. When applied to promoter regions of genes contained within 21 co-expression gene clusters generated from P. falciparum life cycle microarray data using the semi-supervised clustering algorithm Ontology-based Pattern Identification, GEMS identified 34 putative cis-regulatory elements associated with a variety of parasite processes including sexual development, cell invasion, antigenic variation and protein biosynthesis. Among these candidates were novel motifs, as well as many of the elements for which biological experimental evidence already exists in the Plasmodium literature. To provide evidence for the biological relevance of a cell invasion-related element predicted by GEMS, reporter gene and electrophoretic mobility shift assays were conducted.

CONCLUSION

This GEMS analysis demonstrates that in silico regulatory element discovery can be successfully applied to challenging repeat-sequence-rich, base-biased genomes such as that of P. falciparum. The fact that regulatory elements were predicted from a diverse range of functional gene clusters supports the hypothesis that cis-regulatory elements play a role in the transcriptional control of many P. falciparum biological processes. The putative regulatory elements described represent promising candidates for future biological investigation into the underlying transcriptional control mechanisms of gene regulation in malaria parasites.

Measurement of branching fractions and mass spectra of B-->Kpipigamma

We present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B-->Kpipigamma in the range m(Kpipi)<1.8 GeV/c(2). We reconstruct four final states: K(+)pi(-)pi(+)gamma, K(+)pi(-)pi(0)gamma, K(S)(0)pi(-)pi(+)gamma, and K(S)(0)pi(+)pi(0)gamma, where K(S)(0)-->pi(+)pi(-). Using 232 x 10(6) e(+)e(-)-->BB events recorded by the BABAR experiment at the SLAC PEP-II asymmetric-energy storage ring, we measure the branching fractions B(B(+)-->K(+)pi(-)pi(+)gamma)=[2.95+/-0.13(stat)+/-0.20(syst)] x 10(-5), B(B(0)-->K(+)pi(-)pi(0)gamma)=[4.07+/-0.22(stat)+/-0.31(syst)] x 10(-5), B(B(0)-->K(0)pi(+)pi(-)gamma)=[1.85+/-0.21(stat)+/-0.12(syst)] x 10(-5), and B(B(+)-->K(0)pi(+)pi(0)gamma)=[4.56+/-0.42(stat)+/-0.31(syst)] x 10(-5).

Pyroclastic activity at Home Plate in Gusev Crater, Mars

Home Plate is a layered plateau in Gusev crater on Mars. It is composed of clastic rocks of moderately altered alkali basalt composition, enriched in some highly volatile elements. A coarsegrained lower unit lies under a finer-grained upper unit. Textural observations indicate that the lower strata were emplaced in an explosive event, and geochemical considerations favor an explosive volcanic origin over an impact origin. The lower unit likely represents accumulation of pyroclastic materials, whereas the upper unit may represent eolian reworking of the same pyroclastic materials.

Measurement of the pseudoscalar decay constant fDs using charm-tagged events in e+e- collisions at square root s=10.58 GeV

Using 230.2 fb-1 of e+e- annihilation data collected with the BABAR detector at and near the peak of the Upsilon(4S) resonance, 489+/-55 events containing the pure leptonic decay Ds+-->micro;+numicro have been isolated in charm-tagged events. The ratio of partial widths Gamma(D+-->micro+numicro)/Gamma(Ds+-->phipi+) is measured to be 0.143+/-0.018+/-0.006 allowing a determination of the pseudoscalar decay constant fDs=(283+/-17+/-7+/-14) MeV. The errors are statistical, systematic, and from the Ds+-->phipi+ branching ratio, respectively.

Observation of a Charmed Baryon Decaying to D;{0}p at a Mass Near 2.94 GeV/c;{2}

A search for charmed baryons decaying to D(0)p reveals two states: the Lambdac(2880)+ baryon and a previously unobserved state at a mass of [2939.8+/-1.3(stat)+/-1.0(syst)] MeV/c2 and with an intrinsic width of [17.5+/-5.2(stat)+/-5.9(syst)] MeV. Consistent and significant signals are observed for the K(-)pi(+) and K(-)pi(+)pi(-)pi(+) decay modes of the D0 in 287 fb(-1) annihilation data recorded by the BABAR detector at a center-of-mass energy of 10.58 GeV. There is no evidence in the D+p spectrum of doubly charged partners. The mass and intrinsic width of the Lambdac(2880)+ baryon and relative yield of the two baryons are also measured.

Planetary science: bedrock formation at Meridiani Planum

The Mars Exploration Rover Opportunity discovered sulphate-rich sedimentary rocks at Meridiani Planum on Mars, which are interpreted by McCollom and Hynek as altered volcanic rocks. However, their conclusions are derived from an incorrect representation of our depositional model, which is upheld by more recent Rover data. We contend that all the available data still support an aeolian and aqueous sedimentary origin for Meridiani bedrock.