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Apolipoprotein E (APOE) and Galectin-3 (Gal-3) are markers of activated microglia in neurodegenerative diseases of the central nervous system, whose targeting is protective in mouse models of glaucoma. In this study, we examined levels of APOE and Gal-3 in human aqueous humor (AH) and serum samples. Single-center, cross-sectional study. A total of 100 glaucoma and 110 control patients at Massachusetts Eye and Ear. We enrolled patients with various types and stages of glaucoma undergoing planned ophthalmic surgery as part of their routine care and compared them with patients without glaucoma undergoing phacoemulsification for age-related cataract. At the start of ophthalmic surgery, we collected AH and serum from 100 glaucoma and 110 control patients. APOE and Gal-3 levels were quantified by enzyme-linked immunosorbent assays. APOE and Gal-3 levels in AH and serum. APOE and Gal-3 levels were significantly elevated in the AH of glaucoma patients compared to controls (2.72 vs. 0.85 µg/ml, P  < 0.0001 for APOE, and 2.89 vs. 1.45 ng/ml, P  < 0.001 for Gal-3). A positive correlation was observed between AH APOE and Gal-3 levels in the glaucoma cohort ( R  = 0.44, P  < 0.0001). While serum Gal-3 levels were similar between groups (25.5 vs. 25.7 ng/ml, P  = 0.92), APOE levels were significantly elevated in the serum of glaucoma patients compared to controls (58.7 vs. 30.2 µg/ml, P  < 0.0001). Serum APOE levels were not correlated with AH APOE levels in either the glaucoma or the control groups (both R  ~ 0, P  > 0.05) or dependent on APOE genotype. Our findings demonstrate that AH Gal-3 and APOE are elevated in patients with glaucoma. In contrast, only serum APOE was elevated in our glaucoma cohort, possibly reflecting the known dysregulation of lipid metabolism that occurs in this disease.

Neurofilament light chain (NfL) is a neuronal cytoskeletal protein that has been identified as a marker of neurodegeneration in diseases of the central nervous system. In this study, we investigated whether NfL in the aqueous humor (AH) can serve as a marker of neurodegeneration in glaucoma in a racially diverse North American population. Single-center, case-control study. We enrolled patients with various types and stages of glaucoma undergoing planned ophthalmic surgery as part of their routine care and compared them with patients without glaucoma undergoing phacoemulsification for age-related cataract. We collected AH from 39 glaucoma patients and 10 patients without glaucoma. AH NfL was quantified using the Single-Molecule Array (Simoa) NF-light assay (Quanterix). Demographic information, such as age, body mass index, sex, and self-reported race, as well as clinical information, such as pre-operative intraocular pressure (IOP), maximum IOP, and number of pre-operative glaucoma medications, was obtained by reviewing the medical record. Levels of AH NfL. In a model controlling for age and body mass index (BMI), NfL was significantly elevated in AH from glaucoma patients (mean: 429 pg/mL; standard deviation [SD]: 1136 pg/mL) compared to AH from patients without glaucoma (mean: 3.1 pg/mL; SD: 1.9 pg/mg): P = 0.002. Higher AH NfL was associated with higher maximum IOP (R = 0.44, P = 0.005), higher pre-operative IOP (R = 0.46, P = 0.003), and more pre-operative glaucoma medications (R = 0.61, P < 0.001). There was no association between AH NfL and Humphrey visual field mean deviation (R = -0.20, P = 0.220), retinal nerve fiber layer thickness as measured with optical coherence tomography (R = 0.07, P = 0.694), or glaucoma stage (R = 0.015, P = 0.935). Our findings suggest that AH NfL may have clinical utility as a marker of glaucomatous neurodegeneration.

Background/aimsTo review the long-term results of treatment of optic nerve sheath meningiomas (ONSMs) with conformal radiotherapy.MethodsEleven patients with presumed ONSM were treated with fractionated conformal radiotherapy using 45–54 Gy in 25–30 fractions and followed for more than 5 years. Affected eye visual acuity in logMAR notation, colour vision, threshold perimetry, mean deviation (dB) and imaging were studied before and after treatment.AnalysisIncluded adverse effects of treatment and the frequency of affected eye maintained or improved vision.ResultsThere were nine women and two men with a mean age of 45.3. Vision or field loss was the most common presentation. All had abnormal MR imaging. The follow-up period after radiotherapy was 61–156 months (mean 89.6). Visual acuity was unchanged or improved in 10 patients (91%). The average difference between pretreatment and final logMAR visual acuity was 0.08, while the average difference in visual-field mean deviation was −4.63 dB. The radiographic appearance of the tumours was stable in size in nine patients and decreased in two. No major side effects from radiation were seen.ConclusionsVision, MRI and complication outcomes are favourable for using fractionated conformal radiotherapy for ONSM.

NRC publication: Yes

Currently, the complete chemical characterization of nanoparticles (< 100 nm) represents an analytical challenge, since these particles are abundant in number but have negligible mass. Several methods for particle-phase characterization have been recently developed to better detect and infer more accurately the sources and fates of sub-100 nm particles, but a detailed comparison of different approaches is missing. Here we report on the chemical composition of secondary organic aerosol (SOA) nanoparticles from experimental studies of α-pinene ozonolysis at −50, −30, and −10 ∘C and intercompare the results measured by different techniques. The experiments were performed at the Cosmics Leaving OUtdoor Droplets (CLOUD) chamber at the European Organization for Nuclear Research (CERN). The chemical composition was measured simultaneously by four different techniques: (1) thermal desorption–differential mobility analyzer (TD–DMA) coupled to a NO3- chemical ionization–atmospheric-pressure-interface–time-of-flight (CI–APi–TOF) mass spectrometer, (2) filter inlet for gases and aerosols (FIGAERO) coupled to an I− high-resolution time-of-flight chemical ionization mass spectrometer (HRToF-CIMS), (3) extractive electrospray Na+ ionization time-of-flight mass spectrometer (EESI-TOF), and (4) offline analysis of filters (FILTER) using ultra-high-performance liquid chromatography (UHPLC) and heated electrospray ionization (HESI) coupled to an Orbitrap high-resolution mass spectrometer (HRMS). Intercomparison was performed by contrasting the observed chemical composition as a function of oxidation state and carbon number, by estimating the volatility and comparing the fraction of volatility classes, and by comparing the thermal desorption behavior (for the thermal desorption techniques: TD–DMA and FIGAERO) and performing positive matrix factorization (PMF) analysis for the thermograms. We found that the methods generally agree on the most important compounds that are found in the nanoparticles. However, they do see different parts of the organic spectrum. We suggest potential explanations for these differences: thermal decomposition, aging, sampling artifacts, etc. We applied PMF analysis and found insights of thermal decomposition in the TD–DMA and the FIGAERO.

New particle formation in the upper free troposphere is a major global source of cloud condensation nuclei (CCN) 1 – 4 . However, the precursor vapours that drive the process are not well understood. With experiments performed under upper tropospheric conditions in the CERN CLOUD chamber, we show that nitric acid, sulfuric acid and ammonia form particles synergistically, at rates that are orders of magnitude faster than those from any two of the three components. The importance of this mechanism depends on the availability of ammonia, which was previously thought to be efficiently scavenged by cloud droplets during convection. However, surprisingly high concentrations of ammonia and ammonium nitrate have recently been observed in the upper troposphere over the Asian monsoon region 5 , 6 . Once particles have formed, co-condensation of ammonia and abundant nitric acid alone is sufficient to drive rapid growth to CCN sizes with only trace sulfate. Moreover, our measurements show that these CCN are also highly efficient ice nucleating particles—comparable to desert dust. Our model simulations confirm that ammonia is efficiently convected aloft during the Asian monsoon, driving rapid, multi-acid HNO 3 –H 2 SO 4 –NH 3 nucleation in the upper troposphere and producing ice nucleating particles that spread across the mid-latitude Northern Hemisphere. By performing experiments under upper tropospheric conditions, nitric acid, sulfuric acid and ammonia can form particles synergistically, at rates orders of magnitude faster than any two of the three components.

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium— Arthrospira platensis . Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic. While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.

Background Inflammation is more common among African Americans (AAs), and it is associated with frailty, poor physical performance, and mortality in community-dwelling older adults. Given the elevated inflammation levels among end-stage renal disease (ESRD) patients, inflammation may be associated with adverse health outcomes such as frailty, physical impairment, and poor health-related quality of life (HRQOL), and these associations may differ between AA and non-AA ESRD patients. Methods One thousand three ESRD participants were recruited at kidney transplant evaluation (4/2014–5/2017), and inflammatory markers (interleukin-6 [IL-6], tumor necrosis factor-a receptor-1 [TNFR1], C-reactive protein [CRP]) were measured. We quantified the association with frailty (Fried phenotype), physical impairment (Short Physical Performance Battery [SPPB]), and fair/poor HRQOL at evaluation using adjusted modified Poisson regression and tested whether these associations differed by race (AA vs. non-AA). Results Non-AAs had lower levels of TNFR1 (9.7 ng/ml vs 14.0 ng/ml, p  < 0.001) and inflammatory index (6.7 vs 6.8, p  < 0.001) compared to AAs, but similar levels of IL-6 (4.5 pg/ml vs 4.3 pg/ml, p  > 0.9) and CRP (4.7 μg/ml vs 4.9 μg/ml, p  = 0.4). Non-AAs had an increased risk of frailty with elevated IL-6 (RR = 1.58, 95% CI:1.27–1.96, p  < 0.001), TNFR1 (RR = 1.60, 95% CI:1.25–2.05, p  < 0.001), CRP (RR = 1.41, 95% CI:1.10–1.82, p  < 0.01), and inflammatory index (RR = 1.82, 95% CI:1.44–2.31, p  < 0.001). The associations between elevated inflammatory markers and frailty were not present among AAs. Similar results were seen with SPPB impairment and poor/fair HRQOL. Conclusions Non-AAs with elevated inflammatory markers may need closer follow-up and may benefit from prehabilitation to improve physical function, reduce frailty burden, and improve quality of life prior to transplant.

Recent advances in computational methods have made realistic large-scale simulations of animal locomotion possible. This has resulted in numerous mathematical and computational studies of animal movement through fluids and over substrates with the purpose of better understanding organisms' performance and improving the design of vehicles moving through air and water and on land. This work has also motivated the development of improved numerical methods and modeling techniques for animal locomotion that is characterized by the interactions of fluids, substrates, and structures. Despite the large body of recent work in this area, the application of mathematical and numerical methods to improve our understanding of organisms in the context of their environment and physiology has remained relatively unexplored. Nature has evolved a wide variety of fascinating mechanisms of locomotion that exploit the properties of complex materials and fluids, but only recently are the mathematical, computational, and robotic tools available to rigorously compare the relative advantages and disadvantages of different methods of locomotion in variable environments. Similarly, advances in computational physiology have only recently allowed investigators to explore how changes at the molecular, cellular, and tissue levels might lead to changes in performance at the organismal level. In this article, we highlight recent examples of how computational, mathematical, and experimental tools can be combined to ultimately answer the questions posed in one of the grand challenges in organismal biology: \"Integrating living and physical systems.\"

During summer, ammonia emissions in Southeast Asia influence air pollution and cloud formation. Convective transport by the South Asian monsoon carries these pollutant air masses into the upper troposphere and lower stratosphere (UTLS), where they accumulate under anticyclonic flow conditions. This air mass accumulation is thought to contribute to particle formation and the development of the Asian Tropopause Aerosol Layer (ATAL). Despite the known influence of ammonia and particulate ammonium on air pollution, a comprehensive understanding of the ATAL is lacking. In this modelling study, the influence of ammonia on particle formation is assessed with emphasis on the ATAL. We use the EMAC chemistry-climate model, incorporating new particle formation parameterisations derived from experiments at the CERN CLOUD chamber. Our diurnal cycle analysis confirms that new particle formation mainly occurs during daylight, with a 10-fold enhancement in rate. This increase is prominent in the South Asian monsoon UTLS, where deep convection introduces high ammonia levels from the boundary layer, compared to a baseline scenario without ammonia. Our model simulations reveal that this ammonia-driven particle formation and growth contributes to an increase of up to 80% in cloud condensation nuclei (CCN) concentrations at cloud-forming heights in the South Asian monsoon region. We find that ammonia profoundly influences the aerosol mass and composition in the ATAL through particle growth, as indicated by an order of magnitude increase in nitrate levels linked to ammonia emissions. However, the effect of ammonia-driven new particle formation on aerosol mass in the ATAL is relatively small. Ammonia emissions enhance the regional aerosol optical depth (AOD) for shortwave solar radiation by up to 70%. We conclude that ammonia has a pronounced effect on the ATAL development, composition, the regional AOD, and CCN concentrations.