Design and cloning strategies for constructing shRNA expression vectors

BACKGROUND: Short hairpin RNA (shRNA) encoded within an expression vector has proven an effective means of harnessing the RNA interference (RNAi) pathway in mammalian cells. A survey of the literature revealed that shRNA vector construction can be hindered by high mutation rates and the ensuing sequencing is often problematic. Current options for constructing shRNA vectors include the use of annealed complementary oligonucleotides (74 % of surveyed studies), a PCR approach using hairpin containing primers (22 %) and primer extension of hairpin templates (4 %). RESULTS: We considered primer extension the most attractive method in terms of cost. However, in initial experiments we encountered a mutation frequency of 50 % compared to a reported 20 – 40 % for other strategies. By modifying the technique to be an isothermal reaction using the DNA polymerase Phi29, we reduced the error rate to 10 %, making primer extension the most efficient and cost-effective approach tested. We also found that inclusion of a restriction site in the loop could be exploited for confirming construct integrity by automated sequencing, while maintaining intended gene suppression. CONCLUSION: In this study we detail simple improvements for constructing and sequencing shRNA that overcome current limitations. We also compare the advantages of our solutions against proposed alternatives. Our technical modifications will be of tangible benefit to researchers looking for a more efficient and reliable shRNA construction process

The effects of stem length and core placement on shRNA activity

<p>Abstract</p> <p>Background</p> <p>Expressed short hairpin RNAs (shRNA) used in mammalian RNA interference (RNAi) are often designed around a specific short interfering RNA (siRNA) core. Whilst there are algorithms to aid siRNA design, hairpin-specific characteristics such as stem-length and siRNA core placement within the stem are not well defined.</p> <p>Results</p> <p>Using more than 91 hairpins designed against HIV-1 Tat and Vpu, we investigated the influence of both of these factors on suppressive activity, and found that stem length does not correspond with predictable changes in suppressive activity. We also detected multiple processed products for all stem lengths tested. However, the entire length of the hairpin stem was not equally processed into active products. As such, the placement of the siRNA core at the base terminus was critical for activity.</p> <p>Conclusion</p> <p>We conclude that there is no fixed correlation between stem length and suppressive activity. Instead, core selection and placement likely have a greater influence on the effectiveness of shRNA-based silencing.</p

A comparison of multiple shRNA expression methods for combinatorial RNAi

RNAi gene therapies for HIV-1 will likely need to employ multiple shRNAs to counter resistant strains. We evaluated 3 shRNA co-expression methods to determine their suitability for present use; multiple expression vectors, multiple expression cassettes and single transcripts comprised of several dsRNA units (aka domains) with each being designed to a different target. Though the multiple vector strategy was effective with 2 shRNAs, the increasing number of vectors required is a major shortcoming. With single transcript configurations we only saw adequate activity from 1 of 10 variants tested, the variants being comprised of 2 - 3 different target domains. Whilst single transcript configurations have the most advantages on paper, these configurations can not yet be rapidly and reliably re-configured for new targets. However, our multiple cassette combinations of 2, 3 and 4 (29 bp) shRNAs were all successful, with suitable activity maintained in all positions and net activities comparable to that of the corresponding single shRNAs. We conclude that the multiple cassette strategy is the most suitably developed for present use as it is easy to design, assemble, is directly compatible with pre-existing shRNA and can be easily expanded

Influence of age on respiratory modulation of muscle sympathetic nerve activity, blood pressure and baroreflex function in humans

New Findings What is the central question of this study? Does ageing influence the respiratory‐related bursting of muscle sympathetic nerve activity (MSNA) and the association between the rhythmic fluctuations in MSNA and blood pressure (Traube–Hering waves) that occur with respiration? What is the main finding and its importance? Despite the age‐related elevation in MSNA, the cyclical inhibition of MSNA during respiration is similar between young and older individuals. Furthermore, central respiratory–sympathetic coupling plays a role in the generation of Traube–Hering waves in both young and older humans. Healthy ageing and alterations in respiratory–sympathetic coupling have been independently linked with heightened sympathetic neural vasoconstrictor activity. We investigated how age influences the respiratory‐related modulation of muscle sympathetic nerve activity (MSNA) and the association between the rhythmic fluctuations in MSNA and blood pressure that occur with respiration (Traube–Hering waves; THW). Ten young (22 ± 2 years; mean ± SD) and 10 older healthy men (58 ± 6 years) were studied while resting supine and breathing spontaneously. MSNA, blood pressure and respiration were recorded simultaneously. Resting values were ascertained and respiratory cycle‐triggered averaging of MSNA and blood pressure measurements performed. The MSNA burst incidence was higher in older individuals [22.7 ± 9.2 versus 42.2 ± 13.7 bursts (100 heart beats)−1, P < 0.05], and was reduced to a similar extent in the inspiratory to postinspiratory period in young and older subjects (by ∼25% compared with mid‐ to late expiration). A similar attenuation of MSNA burst frequency (in bursts per minute), amplitude and total activity (burst frequency × mean burst amplitude) was also observed in the inspiratory to postinspiratory period in both groups. A significant positive correlation between respiratory‐related MSNA and the magnitude of Traube–Hering waves was observed in all young (100%) and most older subjects (80%). These data suggest that the strength of the cyclical inhibition of MSNA during respiration is similar between young and older individuals; thus, alterations in respiratory–sympathetic coupling appear not to contribute to the age‐related elevation in MSNA. Furthermore, central respiratory–sympathetic coupling plays a role in the generation of Traube–Hering waves in both healthy young and older humans

Tools for characterizing biomembranes : final LDRD report.

A suite of experimental nuclear magnetic resonance (NMR) spectroscopy tools were developed to investigate lipid structure and dynamics in model membrane systems. By utilizing both multinuclear and multidimensional NMR experiments a range of different intra- and inter-molecular contacts were probed within the membranes. Examples on pure single component lipid membranes and on the canonical raft forming mixture of DOPC/SM/Chol are presented. A unique gel phase pretransition in SM was also identified and characterized using these NMR techniques. In addition molecular dynamics into the hydrogen bonding network unique to sphingomyelin containing membranes were evaluated as a function of temperature, and are discussed

Joint analysis of stressors and ecosystem services to enhance restoration effectiveness

With increasing pressure placed on natural systems by growing human populations, both scientists and resource managers need a better understanding of the relationships between cumulative stress from human activities and valued ecosystem services. Societies often seek to mitigate threats to these services through large-scale, costly restoration projects, such as the over one billion dollar Great Lakes Restoration Initiative currently underway. To help inform these efforts, we merged high-resolution spatial analyses of environmental stressors with mapping of ecosystem services for all five Great Lakes. Cumulative ecosystem stress is highest in near-shore habitats, but also extends offshore in Lakes Erie, Ontario, and Michigan. Variation in cumulative stress is driven largely by spatial concordance among multiple stressors, indicating the importance of considering all stressors when planning restoration activities. In addition, highly stressed areas reflect numerous different combinations of stressors rather than a single suite of problems, suggesting that a detailed understanding of the stressors needing alleviation could improve restoration planning. We also find that many important areas for fisheries and recreation are subject to high stress, indicating that ecosystem degradation could be threatening key services. Current restoration efforts have targeted high-stress sites almost exclusively, but generally without knowledge of the full range of stressors affecting these locations or differences among sites in service provisioning. Our results demonstrate that joint spatial analysis of stressors and ecosystem services can provide a critical foundation for maximizing social and ecological benefits from restoration investments. www.pnas.org/lookup/suppl/doi:10.1073/pnas.1213841110/-/DCSupplementa

Amplitude enhancements in Antarctic MF radar echoes

Enhancements in the amplitude of returns from a medium-frequency (MF) radar at Davis, Antarctica, have been identified and their potential use as a measure of polar mesosphere summer echoes (PMSE) has been explored. A method for finding these enhancements has been applied to data spanning the period from mid-1995 to the end of 1997. The character of these enhancements on short and long timescales has been studied, and factors that may affect their detection have been considered. It has been found that they are short-lived (2 min or less being most common) and largely limited to the months around summer. Apart from describing the character of these amplitude enhancements, this study illustrates the potential pitfalls associated with identifying a proxy measure of PMSE.D. J. Murphy, R. A. Vincenthttp://cat.inist.fr/?aModele=afficheN&cpsidt=85383

A Radio Survey of Seven Southern X-ray Luminous Clusters of Galaxies

The Australia Telescope Compact Array (ATCA) has been used at 1.38 and 2.38 GHz to survey seven southern Abell clusters of galaxies with high X-ray luminosities: A2746, A2837, A3126, A3216, A3230, A3827 and A3836. The clusters have also been surveyed at 0.843 GHz with the Molonglo Observatory Synthesis Telescope (MOST). We have listed a complete 1.38-GHz sample of 149 radio sources within the Abell circles centred on their X-ray centroids. We compare their identification fractions, emitted 1.38-GHz and optical powers, radio spectral indices and radial variation in projected source density with those of the radio-selected samples of Slee et al. (1998). We compare our fractional radio luminosity function with that of the radio-selected samples of Ledlow and Owen (1996) and Slee et al. (1998). Three significant differences are noted between X-ray and radio-selected samples of clusters; (1) the X-ray sample has an excess of flat-spectrum radio sources; (2) the fractional radio luminosity function for the FR I sources in the X-ray selected sample is much steeper, implying that fewer of their cluster galaxies become hosts for the stronger FR I radio galaxies; (3) a complete absence of FR II radio galaxies in the X-ray selected sample. The average excess projected density of radio sources near our cluster centres is approx. 5 times the background source density.Comment: 24 pages, 8 figures, plus 6 figures to be published online only; accepted to appear in MNRA

Superconducting nanowire photon number resolving detector at telecom wavelength

The optical-to-electrical conversion, which is the basis of optical detectors, can be linear or nonlinear. When high sensitivities are needed single-photon detectors (SPDs) are used, which operate in a strongly nonlinear mode, their response being independent of the photon number. Nevertheless, photon-number resolving (PNR) detectors are needed, particularly in quantum optics, where n-photon states are routinely produced. In quantum communication, the PNR functionality is key to many protocols for establishing, swapping and measuring entanglement, and can be used to detect photon-number-splitting attacks. A linear detector with single-photon sensitivity can also be used for measuring a temporal waveform at extremely low light levels, e.g. in long-distance optical communications, fluorescence spectroscopy, optical time-domain reflectometry. We demonstrate here a PNR detector based on parallel superconducting nanowires and capable of counting up to 4 photons at telecommunication wavelengths, with ultralow dark count rate and high counting frequency