Specific and complete human genome amplification with improved yield achieved by phi29 DNA polymerase and a novel primer at elevated temperature

<p>Abstract</p> <p>Backgrounds</p> <p>Whole genome amplification (WGA) is a practical solution to eliminate molecular analysis limitations associated with genomic DNA (gDNA) quantity. Different methods have been developed to amplify the whole genome, including primer extension preamplification (PEP), degenerate oligonucleotide primed PCR (DOP-PCR), and multiple displacement amplification (MDA). Each of these methods has its own merits and limitations.</p> <p>Findings</p> <p>Effects of primer length and composition on amplification quality and quantity were explored in this study at two different temperatures (30°C & 40°C). New primer designs combined with elevated amplification temperature has significantly improved MDA as measured by amplification yield, genome coverage, and allele drop out (ADO) analysis. A remarkable finding was the comprehensive amplification, at 30°C & 40°C, of the human whole genome via the use of GGGCAGGA*N*G hotspot recombination consensus primer. Amplification was characterized by Affymetrix 10K SNP chip analysis. Finally, the use of new primer designs has suppressed the template-independent DNA amplification (TIDA) both at 30°C and 40°C.</p> <p>Conclusion</p> <p>The use of new primers in this study combined with elevated incubation temperatures in MDA has remarkably improved the specificity, amplification yield, and suppressed TIDA.</p

Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study

BACKGROUND: Hereditary Hemochromatosis (HH) is an autosomal recessive disorder highlighted byiron-overload. Two popular mutations in HFE, p.C282Y and p.H63D, have been discovered and found to associate with HH in different ethnic backgrounds. p.C282Y and p.H63D diagnosis is usually made byrestriction enzyme analysis. However, the use of this technique is largelylimited to research laboratories because they are relativelyexpensive, time-consuming, and difficult to transform into a high throughput format. METHODS: Single nucleotide variations in target DNA sequences can be readily identified using molecular beacon fluorescent probes. These are quenched probes with loop and hairpin structure, and they become fluorescent upon specific target recognition. We developed high throughput homogeneous real-time PCR assays using molecular beacon technology, to genotype p.C282Y and p.H63D variants. Representative samples of different genotypes for these variants were assayed by restriction enzyme analysis and direct sequencing as bench mark methods for comparison with the newly developed molecular beacon-based real-time PCR assay. RESULTS: Complete concordance was achieved by all three assay formats. Homozygotes (mutant and wildtype) and heterozygotes were readily differentiated by the allele specific molecular beacons as reported by the associated fluorophore in the real-time assay developed in this study. Additionally, these assays were used in a high throughput format to establish the allele frequency of C282Y and H63D in Saudis for the first time. CONCLUSION: These assays may be reliably applied as a diagnostic test or large scale method for population screening

Speckle Observations of Binary Stars with the WIYN Telescope. III. A Partial Survey of A, F, and G Dwarfs

Two hundred thirty nearby main-sequence stars with spectral types in the range of A to G have been observed by way of speckle interferometry using the WIYN 3.5 m telescope at Kitt Peak, Arizona. The stars had no previous mention of duplicity in the literature. Of those observed, 14 showed clear evidence of a companion, and 63 were classified as suspected nonsingle based on a power spectrum analysis. The remaining stars discussed show no evidence of duplicity to the limit of the detection system in high-quality observations

FAPRI 2000 U.S. Agricultural Outlook

Crop Production/Industries, Livestock Production/Industries,

Early twentieth-century Vogue, George Wolfe Plank and the "Freaks of Mayfair"

Vogue was one of the most influential fashion magazines of the twentieth century. In the 1920s its British edition, launched in 1916, became a focus for various forms of queer visual and cultural expression. The origins of the related ‘amusing style’, which delighted in camp display, can be traced to the romantic and artistic collaboration between the American artist George Wolfe Plank and the British writer E. F. Benson during World War One. The illustrations that Plank produced for Benson’s book of satirical sketches of life in London’s high society, The Freaks of Mayfair (1916), shed light on the camp images that Plank designed for the covers of both the American and British editions of the magazine. Therefore, Plank can be understood to have played a key role in the development of queer visual culture during the early twentieth century

FAPRI 2001 U.S. and World Agricultural Outlook

Crop Production/Industries, Livestock Production/Industries,

FAPRI 2000 World Agricultural Outlook

The Food and Agricultural Policy Research Institute (FAPRI) prepares a preliminary agricultural outlook on world agricultural production, consumption, and trade every fall. This is followed by an outside review, re-evaluation of projections, and completion of the final baseline in January. The FAPRI 2000 World Agricultural Outlook presents these final projections for world agricultural markets. A companion volume, the FAPRI 2000 U.S. Agricultural Outlook, presents the U.S. component of the baseline. FAPRI projections assume average weather patterns worldwide, existing policy, and policy commitments under current trade agreements. FAPRI projections do not include conjectures on potential policy changes, such as those resulting from the likely eastward enlargement of the European Union (EU). The baseline predicts recovery of world agricultural production, consumption, and trade, but with remaining price weakness for crops. Stock-to-use ratios in world crop markets remain high despite the strong recovery of Asian and Latin American economies. Above-average yields kept world production high relative to demand in 1999. In contrast, pork and beef prices are increasing significantly above their 1999 level. The physical volume of U.S. agricultural exports is projected to reverse the downward trend of fiscal year (FY) 1999, whereas the value of agricultural exports continue to decline for one more year before recovering because of low crop prices in 2000/01. World crop trade is projected to increase by 55 million metric tons (mmt) in the coming decade, with the United States capturing 49 percent of the expanded market, but still unable to increase its market share by a large percentage. Following this expansion of the market, grain prices increase by 35 percent in the projection period, but still stay well below the peak of 1995/96. The increase in world crop trade reflects the increasing specialization occurring in world agriculture. Increased market access and land scarcity in many Asian economies induce them to import grains and oilseeds to meet their feed demand. Developing Asia remains the fastest growing market for corn in the next decade. With implementation of Agenda 2000 reforms, the EU will reduce its wheat domestic price relative to the world price and will export wheat without subsidies after 2004, constraining gains in market shares for the United States. EU barley exports will expand significantly in the coming years but are likely to be constrained by General Agreement on Tariffs and Trade (GATT) commitments on export subsidies after 2004. World meat trade will increase by 31 percent over the next decade. The United States has become a competitive producer and exporter of meat products. In the coming decade, the United States will experience the largest meat export growth rates among major exporters of beef, pork, and broilers. U.S. exporters capture more than 70 percent of the growth in trade, increasing their share of the combined meat markets from 23 percent in 1999 to 37 percent in 2009. Meat imports are recovering and expanding rapidly in Japan, South Korea, and Taiwan. In Japan, the share of imports in consumption increases from 38 percent in the 1990s to 49 percent at the end of the next decade. Taiwan meat imports will triple from 1990-1999 levels to 2000-2009 levels, driven by imports of beef, non muscle pork products, and the opening of the poultry market. Recovery of Asian food demand will prompt dairy prices to grow by about 1 percent per year over the next decade. Total milk production is projected to increase, with particularly strong growth in the United States, Mexico, Argentina, and Brazil. Most of the growth occurs through yield increases. Per capita cheese consumption is expected to grow by 1 to 2 percent a year in most countries.Crop Production/Industries, Livestock Production/Industries,

STM Spectroscopy of ultra-flat graphene on hexagonal boron nitride

Graphene has demonstrated great promise for future electronics technology as well as fundamental physics applications because of its linear energy-momentum dispersion relations which cross at the Dirac point. However, accessing the physics of the low density region at the Dirac point has been difficult because of the presence of disorder which leaves the graphene with local microscopic electron and hole puddles, resulting in a finite density of carriers even at the charge neutrality point. Efforts have been made to reduce the disorder by suspending graphene, leading to fabrication challenges and delicate devices which make local spectroscopic measurements difficult. Recently, it has been shown that placing graphene on hexagonal boron nitride (hBN) yields improved device performance. In this letter, we use scanning tunneling microscopy to show that graphene conforms to hBN, as evidenced by the presence of Moire patterns in the topographic images. However, contrary to recent predictions, this conformation does not lead to a sizable band gap due to the misalignment of the lattices. Moreover, local spectroscopy measurements demonstrate that the electron-hole charge fluctuations are reduced by two orders of magnitude as compared to those on silicon oxide. This leads to charge fluctuations which are as small as in suspended graphene, opening up Dirac point physics to more diverse experiments than are possible on freestanding devices.Comment: Nature Materials advance online publication 13/02/201

Sensory Electrical Stimulation Improves Foot Placement during Targeted Stepping Post-Stroke

Proper foot placement is vital for maintaining balance during walking, requiring the integration of multiple sensory signals with motor commands. Disruption of brain structures post-stroke likely alters the processing of sensory information by motor centers, interfering with precision control of foot placement and walking function for stroke survivors. In this study, we examined whether somatosensory stimulation, which improves functional movements of the paretic hand, could be used to improve foot placement of the paretic limb. Foot placement was evaluated before, during, and after application of somatosensory electrical stimulation to the paretic foot during a targeted stepping task. Starting from standing, twelve chronic stroke participants initiated movement with the non-paretic limb and stepped to one of five target locations projected onto the floor with distances normalized to the paretic stride length. Targeting error and lower extremity kinematics were used to assess changes in foot placement and limb control due to somatosensory stimulation. Significant reductions in placement error in the medial–lateral direction (p = 0.008) were observed during the stimulation and post-stimulation blocks. Seven participants, presenting with a hip circumduction walking pattern, had reductions (p = 0.008) in the magnitude and duration of hip abduction during swing with somatosensory stimulation. Reductions in circumduction correlated with both functional and clinical measures, with larger improvements observed in participants with greater impairment. The results of this study suggest that somatosensory stimulation of the paretic foot applied during movement can improve the precision control of foot placement