Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO.

dsRNA is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. DMSO has been used to denature dsRNA prior to the reverse-transcription stage to improve reverse transcriptase PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve the sequencing yield of a dsRNA virus (Φ6) in a short-read next-generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a ssRNA viral genome (influenza A/California/07/2009). We suggest that up to 50 % DMSO treatment be used prior to cDNA synthesis when samples of interest are composed of or may contain dsRNA

The equatorial rotation velocity of the photosphere is measured to be the same as sunspots

The equatorial rotation rate of the photosphere was measured at effect data. It was found that scattered light has a large influence and must be taken into account properly. When this was done it was found that the rotation rate from Doppler shifts agreed very well with the rate found for sunspots. Short-term fluctuations in rotation rate (i.e. from day to day) were less than plus or minus 15 m/s and were thus within observational errors

A physical mechanism for the prediction of the sunspot number during solar cycle 21

On physical grounds it is suggested that the sun's polar field strength near a solar minimum is closely related to the following cycle's solar activity. Four methods of estimating the sun's polar magnetic field strength near solar minimum are employed to provide an estimate of cycle 21's yearly mean sunspot number at solar maximum of 140 plus or minus 20. This estimate is considered to be a first order attempt to predict the cycle's activity using one parameter of physical importance

The sun's magnetic sector structure

The synoptic appearance of solar magnetic sectors is studied using 454 sector boundaries observed at earth during 1959-1973. The sectors are clearly visible in the photospheric magnetic field. Sector boundaries can be clearly identified as north-south running demarcation lines between regions of persistent magnetic polarity imbalances. These regions extend up to about 35 deg of latitude on both sides of the equator. They generally do not extend into the polar caps. The polar cap boundary can be identified as an east-west demarcation line marking the poleward limit of the sectors. The typical flux imbalance for a magnetic sector is about 4 x 10 to the 21st power Maxwells

The mean magnetic field of the sun: Observations at Stanford

A solar telescope was built at Stanford University to study the organization and evolution of large-scale solar magnetic fields and velocities. The observations are made using a Babcock-type magnetograph which is connected to a 22.9 m vertical Littrow spectrograph. Sun-as-a-star integrated light measurements of the mean solar magnetic field were made daily since May 1975. The typical mean field magnitude is about 0.15 gauss with typical measurement error less than 0.05 gauss. The mean field polarity pattern is essentially identical to the interplanetary magnetic field sector structure (seen near the earth with a 4 day lag). The differences in the observed structures can be understood in terms of a warped current sheet model

Comparison of H alpha synoptic charts with the large-scale solar magnetic field as observed at Stanford

Two methods of observing the neutral line of the large-scale photospheric magnetic field are compared: (1) neutral line positions inferred from H alpha photographs and (2) observations of the photospheric magnetic field made with low spatial resolution (3 arc min.) and high sensitivity using the Stanford magnetograph. The comparison is found to be very favorable

Development and validation of a chemostat gut model to study both planktonic and biofilm modes of growth of Clostridium difficile and human microbiota

Copyright: 2014 Crowther et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The human gastrointestinal tract harbours a complex microbial community which exist in planktonic and sessile form. The degree to which composition and function of faecal and mucosal microbiota differ remains unclear. We describe the development and characterisation of an in vitro human gut model, which can be used to facilitate the formation and longitudinal analysis of mature mixed species biofilms. This enables the investigation of the role of biofilms in Clostridium difficile infection (CDI). A well established and validated human gut model of simulated CDI was adapted to incorporate glass rods that create a solid-gaseous-liquid interface for biofilm formation. The continuous chemostat model was inoculated with a pooled human faecal emulsion and controlled to mimic colonic conditions in vivo. Planktonic and sessile bacterial populations were enumerated for up to 46 days. Biofilm consistently formed macroscopic structures on all glass rods over extended periods of time, providing a framework to sample and analyse biofilm structures independently. Whilst variation in biofilm biomass is evident between rods, populations of sessile bacterial groups (log10 cfu/g of biofilm) remain relatively consistent between rods at each sampling point. All bacterial groups enumerated within the planktonic communities were also present within biofilm structures. The planktonic mode of growth of C. difficile and gut microbiota closely reflected observations within the original gut model. However, distinct differences were observed in the behaviour of sessile and planktonic C. difficile populations, with C. difficile spores preferentially persisting within biofilm structures. The redesigned biofilm chemostat model has been validated for reproducible and consistent formation of mixed species intestinal biofilms. This model can be utilised for the analysis of sessile mixed species communities longitudinally, potentially providing information of the role of biofilms in CDI.Peer reviewe

Criminal self-efficacy and perceptions of risk and reward among women methamphetamine manufacturers

People consider potential risks and rewards while deciding whether to engage in crime. Such perceptions and their impact on behavior can vary according to individual differences like criminal self-efficacy, or one’s perception of criminal competency. We examine perceptions of skill, risk, and reward using semi-structured interviews with 46 women “shake and bake” meth cooks currently residing in a halfway house in Alabama. Those who expressed cooking self-efficacy identified many tangible and intangible rewards in meth cooking, which motivated them to persist. They believed the risks were lower and surmountable, employing various risk management strategies. Those who did not express cooking self-efficacy saw cooking as anxiety-inducing, rather than rewarding. They saw the risks as inevitable and made little effort to prevent them but continued cooking to maintain access to meth. Findings indicate that individual levels of criminal self-efficacy should be considered in studies of decision-making and in intervention and treatment strategies