MPprimer: a program for reliable multiplex PCR primer design

<p>Abstract</p> <p>Background</p> <p>Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in diagnostic applications of clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons with similar electrophoretic mobility.</p> <p>Results</p> <p>A program named MPprimer was developed to help users for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR assay. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. The experimental validation from 2× to 5× plex PCR demonstrates the reliability of MPprimer. As another example, MPprimer is able to design the multiplex PCR primers for DMD (dystrophin gene which caused Duchenne Muscular Dystrophy), which has 79 exons, for 20×, 20×, 20×, 14×, and 5× plex PCR reactions in five tubes to detect underlying exon deletions.</p> <p>Conclusions</p> <p>MPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays.</p

A Demographic Profile of Independently Incorporated Native American Foundations and Selected Funds in the United States

This report gives basic demographic information on 60 grantmaking entities grouped into three categories: 1) Native foundations that are independently incorporated; 2) 501c3 Native organizations; and 3) tribal funds. These categories capture the variety of Native controlled approaches currently at work in the field

Wireless, battery-free optoelectronic systems as subdermal implants for local tissue oximetry

Monitoring regional tissue oxygenation in animal models and potentially in human subjects can yield insights into the underlying mechanisms of local O2-mediated physiological processes and provide diagnostic and therapeutic guidance for relevant disease states. Existing technologies for tissue oxygenation assessments involve some combination of disadvantages in requirements for physical tethers, anesthetics, and special apparatus, often with confounding effects on the natural behaviors of test subjects. This work introduces an entirely wireless and fully implantable platform incorporating (i) microscale optoelectronics for continuous sensing of local hemoglobin dynamics and (ii) advanced designs in continuous, wireless power delivery and data output for tether-free operation. These features support in vivo, highly localized tissue oximetry at sites of interest, including deep brain regions of mice, on untethered, awake animal models. The results create many opportunities for studying various O2-mediated processes in naturally behaving subjects, with implications in biomedical research and clinical practice.Center for Bio-Integrated Electronics at Northwestern University; Soft and Hybrid Nanotechnology Experimental (SHyNE) Resource (NSF) [ECCS-1542205]; Materials Research Science and Engineering Center [DMR-1720139]; State of Illinois; Northwestern University; Developmental Therapeutics Core at Northwestern University; Robert H. Lurie Comprehensive Cancer Center [NCI CA060553]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Reliability analysis of the Ahringer Caenorhabditis elegans RNAi feeding library: a guide for genome-wide screens

<p>Abstract</p> <p>Background</p> <p>The Ahringer <it>C. elegans </it>RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by direct sequencing, and there are potential errors, including: 1) mis-annotation (the clone with the retired gene name should be remapped to the actual target gene); 2) nonspecific PCR amplification; 3) cross-RNAi; 4) mis-operation such as sample loading error, <it>etc</it>.</p> <p>Results</p> <p>Here we performed a reliability analysis on the Ahringer <it>C. elegans </it>RNAi feeding library, which contains 16,256 bacterial strains, using a bioinformatics approach. Results demonstrated that most (98.3%) of the bacterial strains in the library are reliable. However, we also found that 2,851 (17.54%) bacterial strains need to be re-annotated even they are reliable. Most of these bacterial strains are the clones having the retired gene names. Besides, 28 strains are grouped into unreliable category and 226 strains are marginal because of probably expressing unrelated double-stranded RNAs (dsRNAs). The accuracy of the prediction was further confirmed by direct sequencing analysis of 496 bacterial strains. Finally, a freely accessible database named CelRNAi (<url>http://biocompute.bmi.ac.cn/CelRNAi/</url>) was developed as a valuable complement resource for the feeding RNAi library by providing the predicted information on all bacterial strains. Moreover, submission of the direct sequencing result or any other annotations for the bacterial strains to the database are allowed and will be integrated into the CelRNAi database to improve the accuracy of the library. In addition, we provide five candidate primer sets for each of the unreliable and marginal bacterial strains for users to construct an alternative vector for their own RNAi studies.</p> <p>Conclusions</p> <p>Because of the potential unreliability of the Ahringer <it>C. elegans </it>RNAi feeding library, we strongly suggest the user examine the reliability information of the bacterial strains in the CelRNAi database before performing RNAi experiments, as well as the post-RNAi experiment analysis.</p

Complex 3D microfluidic architectures formed by mechanically guided compressive buckling.

Microfluidic technologies have wide-ranging applications in chemical analysis systems, drug delivery platforms, and artificial vascular networks. This latter area is particularly relevant to 3D cell cultures, engineered tissues, and artificial organs, where volumetric capabilities in fluid distribution are essential. Existing schemes for fabricating 3D microfluidic structures are constrained in realizing desired layout designs, producing physiologically relevant microvascular structures, and/or integrating active electronic/optoelectronic/microelectromechanical components for sensing and actuation. This paper presents a guided assembly approach that bypasses these limitations to yield complex 3D microvascular structures from 2D precursors that exploit the full sophistication of 2D fabrication methods. The capabilities extend to feature sizes <5 μm, in extended arrays and with various embedded sensors and actuators, across wide ranges of overall dimensions, in a parallel, high-throughput process. Examples include 3D microvascular networks with sophisticated layouts, deterministically designed and constructed to expand the geometries and operating features of artificial vascular networks

Study on the Heat of Hydration and Strength Development of Cast-In-Situ Foamed Concrete

This study aims to investigate the relationship between the heat of hydration and the strength development of cast-in-situ foamed concrete. First, indoor model tests are conducted to determine the effects of the casting density and the fly ash content on the hydration heat of foamed concrete in semiadiabatic conditions. Second, compression tests are carried out to evaluate the development of the compressive strength with the curing time under standard curing conditions and temperature matched curing conditions. Third, the hydration heat development of the foamed concrete is tested in four projects. The results showed that the peak temperature, the maximum temperature change rate, and the maximum temperature difference increased with the increase in the casting density at different positions in the foamed concrete. For the same casting density of the foamed concrete, the peak temperature, the maximum temperature change rate, and the maximum temperature difference decreased with the increase in the fly ash content. For the foamed concrete without the admixture, the early strength was significantly higher under temperature matched curing conditions than under standard curing conditions, but the temperature matched curing conditions had a clear inhibitory effect on the strength of the foamed concrete. The strengths during the early stage and the later stage were both improved under temperature matched curing conditions after adding the fly ash, and the greater the fly ash content, the larger the effect. The maximum temperature increments were higher in the indoor model test than in the field tests for the same casting density. Reasonable cooling measures and the addition of fly ash decreased the maximum temperature increments and increased the corresponding casting times

Execution Optimization for Composite Services Through Multiple Engines

Abstract. Web services are rapidly emerging as a popular standard for sharing data and functionality among heterogeneous systems. We propose a general purpose Web Service Management System (WSMSME ) that enables executing composite services through multiple engines. This paper tackles a first basic WSMSME problem: execution optimization for composite services through multiple engines. Our main result comprises two dynamic programming algorithms. One helps minimizes the number of engines required to complete a composite service when computational capability of each engine is relatively changeless; the other optimally minimizes the heaviest load of engines by segmenting a pipelined execution plan into sub-sequences before they are dispatched and executed; Both of the two can obtain optimal solutions in polynomial time. Experiments with an initial prototype indicate that our algorithms can lead to significant performance improvement over more straightforward techniques

Multi-stage Cu remobilization of the Huping metamorphic-hydrothermal deposit in the southern North China Craton

The Zhongtiao region is a well-endowed Cu metallogenic province in the southern North China Craton and contains a large number of early Precambrian Cu deposits of different styles, most of which have been subjected to the ca. 1.85 Ga regional metamorphism. However, whether there was any role for the Proterozoic metamorphism on the extensive Cu mineralization is yet to be well understood. This paper presents an integrated investigation on the field geology, mineral chemistry, fluid inclusion and C-H-O-S isotopes of the Huping metamorphic-hydrothermal deposit in the Neoarchean-Paleoproterozoic Zhongtiao metamorphic terranes, and reveals multi-stage Cu remobilization that formed and upgraded the Cu deposits in the region. We identified three stages of syn- to post-metamorphic Cu remobilization/transportation in the Huping Cu deposit, including (I) early mechanical transport, (II) intermediate metamorphic-hydrothermal remobilization and (III) late meteoric fluid incursion. In stage I, sulfides were remobilized and transported internally under lower-greenschist facies metamorphism, forming the veinlet-disseminated ores and chalcopyrite (avg. delta S-34 = 2.1 parts per thousand, similar to the chlorite-amphibole schist wall rocks). In stage II, the immiscibility of metamorphic fluids (avg. delta O-18 = 4.6 parts per thousand and SD = -56.6 parts per thousand) from the metamorphic terranes triggered the precipitation of higher delta S-34 chalcopyrite (avg. 8.0 parts per thousand), led by the incorporation of extra sulfur during the fluid migration. In stage III, incursion of meteoric fluids into the waning metamorphic-hydrothermal system formed the barren quartz-calcite veins (avg. delta O-18 = 0.09 parts per thousand and delta C-13 = -0.88 parts per thousand). During these Cu remobilization processes, the earlier-formed sulfides were chemically stable during the mechanical transfer by regional metamorphism and deformation. Subsequently, the immiscibility of metamorphic fluids induced significant Cu remobilization and precipitation in the metamorphic-hydrothermal system. We thus propose a model of multi-stage mechanical and chemical Cu remobilization for the Huping Cu deposit, which highlights the crucial impacts of metamorphic-remobilization processes on the regional Cu mineralization in the Zhongtiao region