Recovery of Small DNA Fragments from Serum Using Compaction Precipitation

Background: While most nucleic acids are intracellular, trace amounts of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), including micro RNAs, can also be found in peripheral blood. Many studies have suggested the potential utility of these circulating nucleic acids in prenatal diagnosis, early cancer detection, and the diagnosis of infectious diseases. However, DNA circulating in blood is usually present at very low concentrations (ng/ml), and is in the form of relatively small fragments (,1,000 bp), making its isolation challenging. Methods: Here we report an improved method for the isolation of small DNA fragments from serum using selective precipitation by quaternary ammonium compaction agents. A 151 bp fragment of double-stranded DNA from the Escherichia coli bacteriophage lambda served as the model DNA in our experiments. DNA was serially diluted in serum until undetectable by conventional polymerase chain reaction (PCR), before being enriched by compaction precipitation. Results: Starting with concentrations two to three orders of magnitude lower than the PCR-detectable level (0.01 ng/ml), we were able to enrich the DNA to a detectable level using a novel compaction precipitation protocol. The isolated DNA product after compaction precipitation was largely free of serum contaminants and was suitable for downstream applications. Conclusions: Using compaction precipitation, we were able to isolate and concentrate small DNA from serum, and increase the sensitivity of detection by more than four orders of magnitude. We were able to recover and detect very low levels (0.01 ng/ml) of a small DNA fragment in serum. In addition to being very sensitive, the method is fast, simple, inexpensive, and avoids the use of toxic chemicals

Increasing Binding Efficiency via Reporter Shape and Flux in a Viral Nanoparticle Lateral-Flow Assay

To identify factors controlling the performance of reporter particles in a sensitive lateral-flow assay (LFA), we investigated the effect of the flux and shape of filamentous bacteriophage (phage) on the performance of phage LFAs. Phage of three different lengths and diameters were modified with biotin and AlexaFluor 555 as binding and read-out elements, respectively. The binding efficiencies of the functionalized phage were tested in a fibrous glass LFA membrane modified with avidin. The total binding rate, quantified using real-time particle counting and particle image velocimetry, decreased monotonically with the average bulk flux of phage through the membrane. At the pore scale, more phage bound in regions with faster local flow, confirming that both average and local flux increased binding. The number of bound phage increased with the aspect ratio of the phage and scaled with the phage surface area, consistent with a binding interaction controlled by the number of recognition elements on the surface. Together, these results indicate that increasing the likelihood that recognition elements on the surface of phage encounter the fibers enhances the assay binding efficiency and suggests one origin for the improved performance of nonspherical phage reporters

A Systematic Review: Light Therapy for Individuals with Dementia and Implications for Practice

This systematic review seeks to answer the question: is light therapy an effective intervention for sundowning symptoms experienced by individuals who have dementia

A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies.

Primary cilia organize Hedgehog signaling and shape embryonic development, and their dysregulation is the unifying cause of ciliopathies. We conducted a functional genomic screen for Hedgehog signaling by engineering antibiotic-based selection of Hedgehog-responsive cells and applying genome-wide CRISPR-mediated gene disruption. The screen can robustly identify factors required for ciliary signaling with few false positives or false negatives. Characterization of hit genes uncovered novel components of several ciliary structures, including a protein complex that contains δ-tubulin and ε-tubulin and is required for centriole maintenance. The screen also provides an unbiased tool for classifying ciliopathies and showed that many congenital heart disorders are caused by loss of ciliary signaling. Collectively, our study enables a systematic analysis of ciliary function and of ciliopathies, and also defines a versatile platform for dissecting signaling pathways through CRISPR-based screening

Commensurate and Incommensurate Vortex States in Superconductors with Periodic Pinning Arrays

As a function of applied field, we find a rich variety of ordered and partially-ordered vortex lattice configurations in systems with square or triangular arrays of pinning sites. We present formulas that predict the matching fields at which commensurate vortex configurations occur and the vortex lattice orientation with respect to the pinning lattice. Our results are in excellent agreement with recent imaging experiments on square pinning arrays [K. Harada et al., Science 274, 1167 (1996)].Comment: 9 pages, 3 figures. Accepted to Physical Review

Gravitation: Global Formulation and Quantum Effects

A nonintegrable phase-factor global approach to gravitation is developed by using the similarity of teleparallel gravity with electromagnetism. The phase shifts of both the COW and the gravitational Aharonov-Bohm effects are obtained. It is then shown, by considering a simple slit experiment, that in the classical limit the global approach yields the same result as the gravitational Lorentz force equation of teleparallel gravity. It represents, therefore, the quantum mechanical version of the classical description provided by the gravitational Lorentz force equation. As teleparallel gravity can be formulated independently of the equivalence principle, it will consequently require no generalization of this principle at the quantum level.Comment: Latex (IOP style), 14 pages, 3 figures. To appear in Classical and Quantum Gravit

Circular strings in Kerr-AdS5AdS_5 black holes

The quest for extension of holographic correspondence to the case of finite temperature naturally includes Kerr-AdS black holes and their field theory duals. We probe the five-dimensional Kerr-AdS space time by pulsating strings. First we find particular pulsating string solutions and then semi-classically quantize the theory. For the string with large values of energy, we use the Bohr-Sommerfeld analysis to find the energy of the string as a function of a large quantum number. We obtain the wave function of the problem and thoroughly study the corrections to the energy, which according to the holographic dictionary are related to anomalous dimensions of certain operators in the dual gauge theory. The interpretation of results from holographic point of view is not straightforward since the dual theory is at finite temperature. Nevertheless, near or at conformal point the expressions can be thought of as the dispersion relations of stationary states.Comment: 32 pp, 1 figure; v2: Sec.3 improved, Sec.4 recalculated for a general case, typos corrected, Appendix B included; v3: Sec.3 corrected, new figure of an effective potential added, typos correcte

A tele-assessment system for monitoring treatment effects in subjects with spinal cord injury.

We developed a method for remote measurement of balance and leg force in patients with spinal cord injury (SCI). In a group of 21 patients, both telemedicine and conventional clinical assessments were conducted at baseline and six months later. Telemedicine assessments were successfully acquired and transmitted at first attempt. The time required to set up the telemedicine equipment, position the subject, perform the measurements, and then send the data to the university laboratory was approximately 30 minutes. After six months, several motor and sensory functions showed significant changes. There were significant correlations between changes in remotely-measured leg force and changes in several of the American Spinal Injury Association (ASIA) sensory and motor scores. Changes in balance did not show any significant correlations with changes in the ASIA scores. Intra-rater reliability was better than inter-rater reliability. Use of telemedicine to remotely monitor changes in patients with SCI appears promising