Urine Complement Proteins and the Risk of Kidney Disease Progression and Mortality in Type 2 Diabetes.

ObjectiveWe examined the association of urine complement proteins with progression to end-stage renal disease (ESRD) or death in people with type 2 diabetes and proteinuric diabetic kidney disease (DKD).Research design and methodsUsing targeted mass spectrometry, we quantified urinary abundance of 12 complement proteins in a predominantly Mexican American cohort with type 2 diabetes and proteinuric DKD (n = 141). The association of urine complement proteins with progression to ESRD or death was evaluated using time-to-event analyses.ResultsAt baseline, median estimated glomerular filtration rate (eGFR) was 54 mL/min/1.73 m2 and urine protein-to-creatinine ratio 2.6 g/g. Sixty-seven participants developed ESRD or died, of whom 39 progressed to ESRD over a median of 3.1 years and 40 died over a median 3.6 years. Higher urine CD59, an inhibitor of terminal complement complex formation, was associated with a lower risk of ESRD (hazard ratio [HR] [95% CI per doubling] 0.50 [0.29-0.87]) and death (HR [95% CI] 0.56 [0.34-0.93]), after adjustment for demographic and clinical covariates, including baseline eGFR and proteinuria. Higher urine complement components 4 and 8 were associated with lower risk of death (HR [95% CI] 0.57 [0.41-0.79] and 0.66 [0.44-0.97], respectively); higher urine factor H-related protein 2, a positive regulator of the alternative complement pathway, was associated with greater risk of death (HR [95% CI] 1.61 [1.05-2.48]) in fully adjusted models.ConclusionsIn a largely Mexican American cohort with type 2 diabetes and proteinuric DKD, urine abundance of several complement and complement regulatory proteins was strongly associated with progression to ESRD and death

Erroneously old radiocarbon ages from terrestrial pollen concentrates in Yellowstone Lake, Wyoming, USA

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in [Schiller, C. M., Whitlock, C., Elder, K. L., Iverson, N. A., & Abbott, M. B. Erroneously old radiocarbon ages from terrestrial pollen concentrates in Yellowstone Lake, Wyoming, USA. Radiocarbon, 63(1), (2021): 321-342, https://doi.org/10.1017/RDC.2020.118.Accelerator mass spectrometry (AMS) dating of pollen concentrates is often used in lake sediment records where large, terrestrial plant remains are unavailable. Ages produced from chemically concentrated pollen as well as manually picked Pinaceae grains in Yellowstone Lake (Wyoming) sediments were consistently 1700–4300 cal years older than ages established by terrestrial plant remains, tephrochronology, and the age of the sediment-water interface. Previous studies have successfully utilized the same laboratory space and methods, suggesting the source of old-carbon contamination is specific to these samples. Manually picking pollen grains precludes admixture of non-pollen materials. Furthermore, no clear source of old pollen grains occurs on the deglaciated landscape, making reworking of old pollen grains unlikely. High volumes of CO2 are degassed in the Yellowstone Caldera, potentially introducing old carbon to pollen. While uptake of old CO2 through photosynthesis is minor (F14C approximately 0.99), old-carbon contamination may still take place in the water column or in surficial lake sediments. It remains unclear, however, what mechanism allows for the erroneous ages of highly refractory pollen grains while terrestrial plant remains were unaffected. In the absence of a satisfactory explanation for erroneously old radiocarbon ages from pollen concentrates, we propose steps for further study.This research was supported by NSF Grant No. 1515353 to C. Whitlock and sampling in Yellowstone National Park was conducted under permits YELL-SCI-0009 and YELL-SCI-5054

A refined, controlled 16S rRNA gene sequencing approach reveals limited detection of cerebrospinal fluid microbiota in children with bacterial meningitis

Advances in both laboratory and computational components of high-throughput 16S amplicon sequencing (16S HTS) have markedly increased its sensitivity and specificity. Additionally, these refinements have better delineated the limits of sensitivity, and contributions of contamination to these limits, for 16S HTS that are particularly relevant for samples with low bacterial loads, such as human cerebrospinal fluid (CSF). The objectives of this work were to (i) optimize the performance of 16S HTS in CSF samples with low bacterial loads by defining and addressing potential sources of error, and (ii) perform refined 16S HTS on CSF samples from children diagnosed with bacterial meningitis and compare results with those from microbiological cultures. Several bench and computational approaches were taken to address potential sources of error for low bacterial load samples. We compared DNA yields and sequencing results after applying three different DNA extraction approaches to an artificially constructed mock-bacterial community. We also compared two postsequencing computational contaminant removal strategies, decontam R and full contaminant sequence removal. All three extraction techniques followed by decontam R yielded similar results for the mock community. We then applied these methods to 22 CSF samples from children diagnosed with meningitis, which has low bacterial loads relative to other clinical infection samples. The refined 16S HTS pipelines identified the cultured bacterial genus as the dominant organism for only 3 of these samples. We found that all three DNA extraction techniques followed by decontam R generated similar DNA yields for mock communities at the low bacterial loads representative of CSF samples. However, the limits of detection imposed by reagent contaminants and methodologic bias precluded the accurate detection of bacteria in CSF from children with culture-confirmed meningitis using these approaches, despite rigorous controls and sophisticated computational approaches. Although we did not find current DNA-based diagnostics to be useful for pediatric meningitis samples, the utility of these methods for CSF shunt infection remains undefined. Future advances in sample processing methods to minimize or eliminate contamination will be required to improve the sensitivity and specificity of these methods for pediatric meningitis

Environmentally relevant exposure to an antidepressant alters courtship behaviours in a songbird

Pharmaceuticals in the environment are a recently identified global threat to wildlife, including birds. Like other human pharmaceuticals, the antidepressant fluoxetine (Prozac) enters the environment via sewage and has been detected at wastewater treatment plants. Birds foraging on invertebrates at these sites can be exposed to pharmaceuticals, although the implications of exposure are poorly understood. We conducted experiments to test whether chronic exposure to a maximally environmentally relevant concentration of fluoxetine (2.7 μg day-1) altered courtship behaviour and female reproductive physiology in wild-caught starlings (Sturnus vulgaris), a species commonly found foraging on invertebrates at wastewater treatment plants. When paired with a female over two days, males sang less and were more aggressive towards fluoxetine-treated females than controls. Fluoxetine-treated females were initially aggressive towards males, becoming significantly less aggressive by the second day. In contrast, control females expressed intermediate levels of aggression throughout. We found no effect of female treatment on female courtship behaviour. Female body condition, circulating testosterone and circulating oestradiol were unaffected by treatment and did not account for male preference. Our findings suggest that exposure to an antidepressant reduced female attractiveness, adding to growing evidence that environmental concentrations of pharmaceuticals can alter important traits related to individual fitness and population dynamics

Molecular characterization of microbiota in cerebrospinal fluid from patients with CSF shunt infections using whole genome amplification followed by shotgun sequencing

Understanding the etiology of cerebrospinal fluid (CSF) shunt infections and reinfections requires detailed characterization of associated microorganisms. Traditionally, identification of bacteria present in the CSF has relied on culture methods, but recent studies have used high throughput sequencing of 16S rRNA genes. Here we evaluated the method of shotgun DNA sequencing for its potential to provide additional genomic information. CSF samples were collected from 3 patients near the beginning and end of each of 2 infection episodes. Extracted total DNA was sequenced by: (1) whole genome amplification followed by shotgun sequencing (WGA) and (2) high-throughput sequencing of the 16S rRNA V4 region (16S). Taxonomic assignments of sequences from WGA and 16S were compared with one another and with conventional microbiological cultures. While classification of bacteria was consistent among the 3 approaches, WGA provided additional insights into sample microbiological composition, such as showing relative abundances of microbial versus human DNA, identifying samples of questionable quality, and detecting significant viral load in some samples. One sample yielded sufficient non-human reads to allow assembly of a high-qualit

Detecting fluoxetine and norfluoxetine in wild bird tissues and feathers

The contamination of the environment with human pharmaceuticals is widespread and demand for such products is mounting globally. Wild vertebrates may be at particular risk from any effects from pharmaceuticals, because of the evolutionary conservation of drug targets. However, exposure of wildlife to pharmaceuticals is poorly characterised, partly due to challenges associated with detecting rapidly metabolised compounds. As part of a wider study on the behavioural effects of fluoxetine (Prozac) on Eurasian starlings (Sturnus vulgaris), we investigated which avian samples are best suited for detecting exposure to fluoxetine in free-living birds. We analysed plasma, various tissues and tail feathers (grown both in the wild and in captivity during the dosing period) from fluoxetine-treated birds (dosed daily with 0.035 mg kg-1 bodyweight for 28 weeks), and liver tissue and tail feathers from sham-dosed birds. We detected fluoxetine in only two of twelve plasma samples from dosed birds. In dosed birds, median concentrations of free fluoxetine/norfluoxetine in tissues (two hour post-final dose) were: 111.2/67.6 ng g-1 in liver, 29.6/5.7 ng g-1 in kidney, 14.2/4.0 ng g-1 in lung, 15.1/1.6 ng g-1 in brain. We estimated that fluoxetine would remain detectable in liver and kidney approximately 4.5 times longer (90 h) than in brain (20h). In dosed birds, fluoxetine was detected in feathers regrown during the dosing period (median concentration = 11.4 ng g-1) at concentrations significantly higher than in regrown feathers from control birds. Fluoxetine residues were detected in wild-grown feathers (grown before the birds were brought into captivity) at concentrations up to 27.0 ng g-1, providing some evidence of likely exposure in the wild. Our results show liver and kidney can be used for detecting fluoxetine in avian carcasses and provide a first indication that feathers may be useful for assessing exposure to fluoxetine, and possibly other pharmaceuticals

Protective Antigens Against Glanders Identified by Expression Library Immunization

Burkholderia are highly evolved Gram-negative bacteria that primarily infect solipeds but are transmitted to humans by ingestion and cutaneous or aerosol exposures. Heightened concern over human infections of Burkholderia mallei and the very closely related species B. pseudomallei is due to the pathogens’ proven effectiveness as bioweapons, and to the increased potential for natural opportunistic infections in the growing diabetic and immuno-compromised populations. These Burkholderia species are nearly impervious to antibiotic treatments and no vaccine exists. In this study, the genome of the highly virulent B. mallei ATCC23344 strain was examined by expression library immunization for gene-encoded protective antigens. This protocol for genomic-scale functional screening was customized to accommodate the unusually large complexity of Burkholderia, and yielded 12 new putative vaccine candidates. Five of the candidates were individually tested as protein immunogens and three were found to confer significant partial protection against a lethal pulmonary infection in a murine model of disease. Determinations of peripheral blood cytokine and chemokine profiles following individual protein immunizations show that interleukin-2 (IL-2) and IL-4 are elicited by the three confirmed candidates, but unexpectedly interferon-γ and tumor necrosis factor-α are not. We suggest that these pathogen components, discovered using genetic immunization and confirmed in a conventional protein format, will be useful toward the development of a safe and effective glanders vaccine

Characterization of cerebrospinal fluid (CSF) microbiota at the time of initial surgical intervention for children with hydrocephalus

OBJECTIVE: To characterize the microbiota of the cerebrospinal fluid (CSF) from children with hydrocephalus at the time of initial surgical intervention. STUDY DESIGN: CSF was obtained at initial surgical intervention. One aliquot was stored in skim milk-tryptone-glucose-glycerol (STGG) medium and the second was unprocessed; both were then stored at -70°C. Bacterial growth for CSF samples stored in STGG were subsequently characterized using aerobic and anaerobic culture on blood agar and MALDI-TOF sequencing. All unprocessed CSF samples underwent 16S quantitative polymerase chain reaction (qPCR) sequencing, and a subset underwent standard clinical microbiological culture. CSF with culture growth (either after storage in STGG or standard clinical) were further analyzed using whole-genome amplification sequencing (WGAS). RESULTS: 11/66 (17%) samples stored in STGG and 1/36 (3%) that underwent standard clinical microbiological culture demonstrated bacterial growth. Of the organisms present, 8 were common skin flora and 4 were potential pathogens; only 1 was also qPCR positive. WGAS findings and STGG culture findings were concordant for only 1 sample, identifying Staphylococcus epidermidis. No significant difference in time to second surgical intervention was observed between the STGG culture-positive and negative groups. CONCLUSION(S): Using high sensitivity methods, we detected the presence of bacteria in a subset of CSF samples at the time of first surgery. Therefore, the true presence of bacteria in CSF of children with hydrocephalus cannot be ruled out, though our findings may suggest these bacteria are contaminants or false positives of the detection methods. Regardless of origin, the detection of microbiota in the CSF of these children may not have any clinical significance

Risk Factors for First Cerebrospinal Fluid Shunt Infection: Findings from a Multi-Center Prospective Cohort Study

ObjectiveTo quantify the extent to which cerebrospinal fluid (CSF) shunt revisions are associated with increased risk of CSF shunt infection, after adjusting for patient factors that may contribute to infection risk.Study designWe used the Hydrocephalus Clinical Research Network registry to assemble a large prospective 6-center cohort of 1036 children undergoing initial CSF shunt placement between April 2008 and January 2012. The primary outcome of interest was first CSF shunt infection. Data for initial CSF shunt placement and all subsequent CSF shunt revisions prior to first CSF shunt infection, where applicable, were obtained. The risk of first infection was estimated using a multivariable Cox proportional hazard model accounting for patient characteristics and CSF shunt revisions, and is reported using hazard ratios (HRs) with 95% CI.ResultsOf the 102 children who developed first infection within 12 months of placement, 33 (32%) followed one or more CSF shunt revisions. Baseline factors independently associated with risk of first infection included: gastrostomy tube (HR 2.0, 95% CI, 1.1, 3.3), age 6-12 months (HR 0.3, 95% CI, 0.1, 0.8), and prior neurosurgery (HR 0.4, 95% CI, 0.2, 0.9). After controlling for baseline factors, infection risk was most significantly associated with the need for revision (1 revision vs none, HR 3.9, 95% CI, 2.2, 6.5; ≥2 revisions, HR 13.0, 95% CI, 6.5, 24.9).ConclusionsThis study quantifies the elevated risk of infection associated with shunt revisions observed in clinical practice. To reduce risk of infection risk, further work should optimize revision procedures

Clinical impairment in premanifest and early Huntington's disease is associated with regionally specific atrophy.

TRACK-HD is a multicentre longitudinal observational study investigating the use of clinical assessments and 3-Tesla magnetic resonance imaging as potential biomarkers for future therapeutic trials in Huntington's disease (HD). The cross-sectional data from this large well-characterized dataset provide the opportunity to improve our knowledge of how the underlying neuropathology of HD may contribute to the clinical manifestations of the disease across the spectrum of premanifest (PreHD) and early HD. Two hundred and thirty nine gene-positive subjects (120 PreHD and 119 early HD) from the TRACK-HD study were included. Using voxel-based morphometry (VBM), grey and white matter volumes were correlated with performance in four domains: quantitative motor (tongue force, metronome tapping, and gait); oculomotor [anti-saccade error rate (ASE)]; cognition (negative emotion recognition, spot the change and the University of Pennsylvania smell identification test) and neuropsychiatric measures (apathy, affect and irritability). After adjusting for estimated disease severity, regionally specific associations between structural loss and task performance were found (familywise error corrected, P < 0.05); impairment in tongue force, metronome tapping and ASE were all associated with striatal loss. Additionally, tongue force deficits and ASE were associated with volume reduction in the occipital lobe. Impaired recognition of negative emotions was associated with volumetric reductions in the precuneus and cuneus. Our study reveals specific associations between atrophy and decline in a range of clinical modalities, demonstrating the utility of VBM correlation analysis for investigating these relationships in HD