Sequencing of the onion (Allium cepa) genome is challenging because it has one of the largest nuclear genomes among cultivated plants. We undertook pilot sequencing of onion genomic DNA to estimate ...gene densities and investigate the nature and distribution of repetitive DNAs. Complete sequences from two onion BACs were AT rich (64.8%) and revealed long tracts of degenerated retroviral elements and transposons, similar to other larger plant genomes. Random BACs were end sequenced and only 3 of 460 ends showed significant (e < -25) non-organellar hits to the protein databases. The BAC-end sequences were AT rich (63.4%), similar to the completely sequenced BACs. A total of 499,997 bp of onion genomic DNA yielded an estimated mean density of one gene per 168 kb, among the lowest reported to date. Methyl filtration was highly effective relative to random shotgun reads in reducing frequencies of anonymous sequences from 82 to 55% and increasing non-organellar protein hits from 4 to 42%. Our results revealed no evidence for gene-dense regions and indicated that sequencing of methyl-filtered genomic fragments should be an efficient approach to reveal genic sequences in the onion genome.
SOMAscan™ is a complex proteomic platform created by SomaLogic. Experimental data resulting from the assay is provided by SomaLogic in a proprietary text-based format called ADAT. This manuscript ...describes a user-friendly point and click open source, platform-independent software tool designed to be used for navigating and plotting data from an ADAT file. This tool was used either alone or in conjunction with other tools as a first pass analysis of the data on several different on-going research projects. We have seen a need from our experience for a web interface to the ADAT file so that users can navigate, generate plots, perform QC and conduct statistical analysis on their own data in a point and click manner. After several rounds of interacting with biologists and their requirements with respect to data analysis, we present an online interactive Shiny Web Tool for Navigating and Plotting data contained within the ADAT file. Extensive video tutorials, example data, the tool and the source code are available online.
This paper investigates the chemical durability of a fluoroindate (IZSBGC) glass (developed by our previous research for low-loss fluoroindate fiber production) compared to the widely studied ...fluorozirconate (ZBLAN) system via leaching of glass samples in deionized water. The chemical stability of both glass systems is probed using a series of analytical techniques such as FTIR, XPS and SEM to study the sample surfaces (before and after leaching) and hydrated layer products, both of which reflected the nature of the leaching process. Our experimental results suggest that IZSBGC glass presented better chemical stability in water than ZBLAN. The absorption due to both OH super(-) stretching and HOH bending vibrations for both glass types increased with increasing amounts of hydrated layers formed during the leaching. The investigation of hydrated layers using SEM suggests that the NaF content in fluoride glass accelerated the leaching significantly. XPS analyses suggest that (hydr)oxyfluorides and hydroxides formed on both fluorozirconate and fluoroindate glass surfaces after leaching, respectively. The degradation of fiber breaking strain in NaF-free IZSBGC glass is less than that of NaF-containing ZBLAN glass.
Active and passive variants of La-containing tellurite glasses have been developed with matched refractive indices. The consequences of adding lanthanum to the glass was studied through measurements ...of the crystallization stability, glass viscosity and the loss of unstructured fibers. Doping the glass with erbium allowed for any spectroscopic changes to be observed through measurements of the absorption and energy level lifetimes. The fluorescence emission spectra were measured at 1.5 microm and, to the best of our knowledge, for the first time in tellurite glass at 2.7 microm.
We combine suspended-core microstructured optical fibers with the photoinduced electron transfer (PET) effect to demonstrate a new type of fluorescent optical fiber-dip sensing platform for small ...volume ion detection. A sensor design based on a simple model PET-fluoroionophore system and small core microstructured optical fiber capable of detecting sodium ions is demonstrated. The performance of the dip sensor operating in a high sodium concentration regime (925 ppm Na(+)) and for lower sodium concentration environments (18.4 ppm Na(+)) is explored and future approaches to improving the sensor's signal stability, sensitivity and selectivity are discussed.
Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors of immune responses and their ...biological basis is of broad interest, given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in patients with systemic lupus erythematosus with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell-type I IFN-T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activity.
COVID-19 exhibits extensive patient-to-patient heterogeneity. To link immune response variation to disease severity and outcome over time, we longitudinally assessed circulating proteins as well as ...188 surface protein markers, transcriptome, and T cell receptor sequence simultaneously in single peripheral immune cells from COVID-19 patients. Conditional-independence network analysis revealed primary correlates of disease severity, including gene expression signatures of apoptosis in plasmacytoid dendritic cells and attenuated inflammation but increased fatty acid metabolism in CD56dimCD16hi NK cells linked positively to circulating interleukin (IL)-15. CD8+ T cell activation was apparent without signs of exhaustion. Although cellular inflammation was depressed in severe patients early after hospitalization, it became elevated by days 17–23 post symptom onset, suggestive of a late wave of inflammatory responses. Furthermore, circulating protein trajectories at this time were divergent between and predictive of recovery versus fatal outcomes. Our findings stress the importance of timing in the analysis, clinical monitoring, and therapeutic intervention of COVID-19.
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•Multiparameter metric captures finer shades of disease severity to empower analyses•Network analysis reveals primary disease severity correlates in pDCs and NK cells•Analysis of timing effects suggests a late immune response juncture•Inflammatory divergence at the late juncture predicts fatal-recovery outcomes
A quantitative disease severity metric is developed by integrating clinical data and circulating cytokines to capture finer shades of disease severity. Multimodal single-cell profiling and immune cell analyses of COVID-19 patients over time reveal a late wave of diverging inflammatory and host immune responses that predicts recovery versus fatality.
We demonstrate the first fluorozirconate microstructured fiber for use in the mid-infrared. The fiber preform was manufactured via extrusion of a 200 g billet through a complex graphite die. The ...fiber exhibits large mode area of 6,600 microm(2), loss of 3 dB/m at 4 microm and only marginal excess loss relative to a corresponding unstructured fiber.
Abstract
Background
Growth and differentiation factor 15 (GDF-15) has been associated with obesity, muscle wasting, and cachexia. The receptor for GDF-15 was recently identified in the brainstem and ...regulates food intake and metabolism. The relationship of plasma GDF-15 with the age-associated decline of muscle mass and strength, gait speed, and physical performance in adults has not been well characterized.
Methods
Plasma GDF-15, grip strength, 6-m gait speed, 400-m walking test time, lower extremity physical performance score, appendicular lean mass, and fat mass were measured in 194 healthy adult participants, aged 22–93 years, of the Baltimore Longitudinal Study of Aging.
Results
Plasma GDF-15 concentrations increased with age (p < .001) and were higher in whites compared with blacks and Asians (p = .04). Adults with higher plasma GDF-15 had slower 6-m gait speed, longer 400-m walking time, and lower physical performance score in multivariable analyses adjusting for age and race. Plasma GDF-15 was not associated with grip strength, appendicular lean mass, or fat mass.
Conclusions
Elevated plasma GDF-15 is associated with slower gait speed, higher 400-m walking time, and lower physical performance in very healthy community-dwelling adults. The relationship between plasma GDF-15 and sarcopenia-related outcomes may be stronger in the population not selected to be healthy, and this hypothesis should be tested in a representative population.
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