Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma.

BACKGROUND: The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived. RESULTS: Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin. In addition, extremely abundant small RNAs derived from human Y RNAs were detected. CONCLUSIONS: A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

Reticular pseudodrusen in age-related macular degeneration.

Historically, drusen, which are recognized as the hallmark of age-related macular degeneration (AMD), have been described in terms of size, margins, and texture, and several studies have emphasized the importance of large soft drusen particularly when combined with focal pigmentary irregularities in determining the risk of progression to neovascular AMD. However, recent developments in imaging over the past decade have revealed a further distinct phenotype strongly associated with the development of late AMD, namely, reticular pseudodrusen (RPD) or reticular drusen. Reticular pseudodrusen appear as yellowish interlacing networks in the fundus and, although visible on color photography, are better visualized using infrared imaging or spectral domain optical coherence tomography. Studies correlating spectral domain optical coherence tomography and confocal scanning laser ophthalmoscopy have shown that RPD are subretinal deposits located internal to the retinal pigment epithelium in contrast to traditional drusen, which are located external to the retinal pigment epithelium. As multiple longitudinal studies have revealed RPD are strong predictors for progression to both neovascular AMD and geographic atrophy, the interest in understanding the role that RPD play in the pathogenesis of AMD has grown. This review focuses on the current literature concerning RPD and considers what is currently known regarding their epidemiology, risk factors, appearance in both retinal imaging and histology, impact on visual function, relationship to other AMD lesions, and association with the development of late AMD.

Subscapular skinfold thickness, not other anthropometric and dual-energy X-ray absorptiometry-measured adiposity, is positively associated with the presence of age-related macular degeneration: a cross-sectional study from National Health and Nutrition Examination Survey 2005-2006.

OBJECTIVE: Current literature reveals an association between anthropometric measures of adiposity (AnthM) and age-related macular degeneration (AMD), but few have explored the disease association with imaging methods. This study aimed to explore the relationship between AMD status and dual-energy X-ray absorptiometry measures (DEXAMs) among a representative sample of the US population, and compare the association with AnthM. METHOD: Using a representative sample in the National Health and Nutrition Examination Study 2005-2006 (n=1632), DEXAMs across the whole body and waist (ie, android), and relative fat distributions (eg, percentage fat, android-to-total body ratio) were analysed between no AMD (baseline) and any AMD. Bivariate analyses across AMD status were similarly performed for AnthM (ie, body mass index, waist circumference and skinfold thicknesses) and potential confounders (ie, demographics and health-related variables). Significant adiposity measures were analysed using logistic regression, adjusting for confounders. RESULTS: The participants in the sample were aged 40-69 years, were majority female (52%) and mainly Caucasian (76.5%). Bivariate analysis revealed having any AMD had positive significant associations with android-to-total fat ratio and subscapular skinfold thickness (SSFT). Other AnthM and DEXAMs were not significant. After adjusting age, gender and prescription of cholesterol-lowering medicine, only SSFT remained significantly associated. CONCLUSION: SSFT represents an independent risk factor for AMD presence compared with other AnthM and DEXAMs. SSFT is an established method of measuring fat under the skin (ie, subcutaneous fat). Hence, subcutaneous fat may be more relevant in explaining the adiposity-AMD link due to physiological properties specific to the tissue. Limitations include the restricted age range and low numbers of participants with late AMD.

Rapid quantification of microRNAs in plasma using a fast real-time PCR system.

The ability to rapidly detect circulating small RNAs, in particular microRNAs (miRNAs), would further increase their already established potential as biomarkers for a range of conditions. One rate-limiting factor in miRNA detection is the time taken to perform quantitative real-time PCR (qPCR) amplification. We therefore evaluated the ability of a novel thermal cycler to perform this step in less than 10 minutes. Quantitative PCR was performed on an xxpress thermal cycler (BJS Biotechnologies), which employs a resistive heating system and forced air cooling to achieve thermal ramp rates of 10°C/s, and a conventional Peltier-controlled LightCycler 480 system (Roche) ramping at 4.8°C/s. The quantification cycle (Cq) for detection of 18S rDNA from a standard genomic DNA sample was significantly more variable across the block (F-test, P = 2.4 × 10(-25)) for the xxpress (20.01 ± 0.47 sd) than for the LightCycler (19.87 ± 0.04 sd). RNA was extracted from human plasma, reverse transcribed, and a panel of miRNAs was amplified and detected using SYBR Green. The sensitivities of the two systems were broadly comparable-both detected a panel of miRNAs reliably, and both indicated similar relative abundances. The xxpress thermal cycler facilitates rapid qPCR detection of small RNAs and brings point-of-care diagnostics based upon detection of circulating miRNAs a step closer to reality.

Appearance of the frequency-doubling stimulus at threshold.

PURPOSE: It has been argued that the threshold for detecting frequency-doubling (FD) technology perimeter stimuli differs from the threshold for perceiving spatial structure (pattern) in the same targets. Thresholds for perceiving spatial structure have typically been assessed using orientation-identification experiments. The authors investigated the influence of orientation, edge profile, and psychophysical method on the origin of the reported differences in detection and orientation-identification thresholds for FD gratings. METHODS: Detection and orientation-identification thresholds were determined in 12 observers with the use of FD stimuli (0.25 cyc/deg, 25 Hz) presented centrally and at 15 degrees eccentricity. Edge profile (square- and Gaussian-windowed) and orientation (horizontal, vertical, and oblique) were independently modified. Detection thresholds were also measured for spatially uniform flickering targets (25 Hz). Orientation-identification thresholds using a two-alternative forced choice (2-AFC) and a two-interval forced choice (2-IFC) method were also compared in five experienced observers. RESULTS: Orientation-identification and detection thresholds did not significantly differ under any condition tested. Orientation-identification thresholds obtained with 2-AFC were not significantly different from those obtained with 2-IFC. Thresholds for spatially uniform flicker were significantly lower than for FD stimuli. CONCLUSIONS: The authors found that orientation-identification and detection thresholds for FD gratings did not differ and argue that recent findings to the contrary arise from the inappropriate use of spatially uniform flicker targets as alternatives in 2-IFC experiments.