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Sample records for rapid molecular resource

  1. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics.

    PubMed

    James, Ameh; Macdonald, Joanne

    2015-01-01

    Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.

  2. Rapid Molecular Assays for the Detection of Yellow Fever Virus in Low-Resource Settings

    PubMed Central

    Escadafal, Camille; Faye, Oumar; Sall, Amadou Alpha; Faye, Ousmane; Weidmann, Manfred; Strohmeier, Oliver; von Stetten, Felix; Drexler, Josef; Eberhard, Michael; Niedrig, Matthias; Patel, Pranav

    2014-01-01

    Background Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by Aedes mosquitoes. The causative agent, the yellow fever virus (YFV), is found in tropical and subtropical areas of South America and Africa. Although a vaccine is available since the 1930s, YF still causes thousands of deaths and several outbreaks have recently occurred in Africa. Therefore, rapid and reliable diagnostic methods easy to perform in low-resources settings could have a major impact on early detection of outbreaks and implementation of appropriate response strategies such as vaccination and/or vector control. Methodology The aim of this study was to develop a YFV nucleic acid detection method applicable in outbreak investigations and surveillance studies in low-resource and field settings. The method should be simple, robust, rapid and reliable. Therefore, we adopted an isothermal approach and developed a recombinase polymerase amplification (RPA) assay which can be performed with a small portable instrument and easy-to-use lyophilized reagents. The assay was developed in three different formats (real-time with or without microfluidic semi-automated system and lateral-flow assay) to evaluate their application for different purposes. Analytical specificity and sensitivity were evaluated with a wide panel of viruses and serial dilutions of YFV RNA. Mosquito pools and spiked human plasma samples were also tested for assay validation. Finally, real-time RPA in portable format was tested under field conditions in Senegal. Conclusion/Significance The assay was able to detect 20 different YFV strains and demonstrated no cross-reactions with closely related viruses. The RPA assay proved to be a robust, portable method with a low detection limit (<21 genome equivalent copies per reaction) and rapid processing time (<20 min). Results from real-time RPA field testing were comparable to results obtained in the laboratory, thus confirming our method is suitable for YFV detection in

  3. Rapid molecular screening for multidrug-resistant tuberculosis in a resource-limited region of China.

    PubMed

    Zhang, Dan; Liu, Beizhong; Wang, Yufeng; Pang, Yu

    2014-10-01

    To investigate the molecular characteristics of MDR and XDR strains circulating in Chongqing, China. The drug target genes conferring for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), ofloxacin (OFLX) and kanamycin (KAN) resistance were screened by DNA sequencing to determine the mutation frequencies in this area. Drug susceptibility of 208 MDR isolates revealed that 132 (63.46%) were resistant to streptomycin (SM), 96 (46.15%) to ethambutol (EMB), 51 (24.52%) to ofloxacin (OFLX), and 26 (12.50%) to kanamycin (KAN); six (2.88%) isolates had XDR profiles. In comparison with the drug susceptibility phenotype, the sensitivity of drug resistance by DNA sequencing was 91.83% for RIF, 87.50% for INH, 66.67% for EMB, 74.51% for OFLX and 53.85% for KAN resistance. 12.50% of EMB- and 1.27% of OFLX-susceptible isolates were harboured genetic mutations in embB and gyrA, respectively. Our findings demonstrate that the hot-spot regions localised in rpoB, katG and inhA genes serve as excellent markers for the corresponding drug resistance, while EMB, OFLX or KAN drug-resistant TB cases may not be identifiable by scanning embB, gyrA, rrs and eis promoter in Chongqing, indicating that further studies on the drug resistance mechanisms of EMB, OFLX and KAN are urgently needed to elucidate the low sensitivity between genomic substitutions and drug-resistant phenotype. © 2014 John Wiley & Sons Ltd.

  4. Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

    PubMed Central

    Bai, Xiaodong; Zhang, Wei; Orantes, Lucia; Jun, Tae-Hwan; Mittapalli, Omprakash; Mian, M. A. Rouf; Michel, Andrew P.

    2010-01-01

    Background Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, the invasive soybean aphid, Aphis glycines, lacks in any significant molecular resources. Methodology/Principal Findings Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to develop both transcriptomic and genomic resources, including expressed genes and molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 transcripts and 56,688 genomic sequences. From this data set, 635 SNPs and 1,382 microsatellite markers were identified. For each sequencing method, different soybean aphid biotypes were used which revealed potential biotype specific markers. In addition, we uncovered 39,822 bp of sequence that were related to the obligatory endosymbiont, Buchnera aphidicola, as well as sequences that suggest the presence of Hamiltonella defensa, a facultative endosymbiont. Conclusions and Significance Molecular resources for an invasive, non-model aphid species were generated. Additionally, the power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and help provide novel targets for soybean aphid control. PMID:20614011

  5. Water Resources of Rapides Parish

    USGS Publications Warehouse

    Griffith, J.M.

    2009-01-01

    Rapides Parish, located in central Louisiana, contains fresh groundwater and surface-water resources. In 2005, about 443 million gallons per day (Mgal/d) were withdrawn from water sources in Rapides Parish. About 92 percent (409 Mgal/d) was withdrawn from surface water, and 8 percent (34 Mgal/d) was withdrawn from groundwater. Withdrawals for power generation accounted for 91 percent (403 Mgal/d) of the total water withdrawn. Withdrawals for other uses included public supply (27 Mgal/d), irrigation (9 Mgal/d), and aquaculture (3 Mgal/d). Water withdrawals in the parish generally increased from 1960 to 1995 and decreased from 1995 to 2005. This fact sheet summarizes basic information on the water resources of Rapides Parish, La. Information on groundwater and surface-water availability, quality, development, use, and trends is based on previously published reports listed in the references section.

  6. Challenges for rapid molecular HIV diagnostics.

    PubMed

    Schito, Marco L; D'Souza, M Patricia; Owen, S Michele; Busch, Michael P

    2010-04-15

    The introduction of serological point-of-care assays 10 years ago dramatically changed the way that human immunodeficiency virus (HIV) infection was identified and diagnosed. Testing at the point of care has lead to a dramatic increase in the number of individuals who are screened and, most importantly, receive their HIV test result. As the AIDS epidemic continues to mature and scientific advances in prevention and treatment are evaluated and implemented, there is a need to identify acute (viremic preseroconversion) infections and to discriminate "window phase" infections from those that are serologically positive, especially in resource-limited settings, where the majority of vulnerable populations reside and where the incidence of HIV infection is highest. Rapid testing methods are now at a crossroads. There is opportunity to implement and evaluate the incremental diagnostic usefulness of new test modalities that are based on sophisticated molecular diagnostic technologies and that can be performed in settings where laboratory infrastructure is minimal. The way forward requires sound scientific judgment and an ability to further develop and implement these tests despite a variety of technical, social, and operational hurdles, to declare success.

  7. A rapid molecular approach for chromosomal phasing.

    PubMed

    Regan, John F; Kamitaki, Nolan; Legler, Tina; Cooper, Samantha; Klitgord, Niels; Karlin-Neumann, George; Wong, Catherine; Hodges, Shawn; Koehler, Ryan; Tzonev, Svilen; McCarroll, Steven A

    2015-01-01

    Determining the chromosomal phase of pairs of sequence variants - the arrangement of specific alleles as haplotypes - is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ascertaining the phase of pairs of DNA sequence variants (separated by 1-200 kb) without cloning or manual single-molecule dilution. In each Drop-Phase reaction, genomic DNA segments are isolated in tens of thousands of nanoliter-sized droplets together with allele-specific fluorescence probes, in a single reaction well. Physically linked alleles partition into the same droplets, revealing their chromosomal phase in the co-distribution of fluorophores across droplets. We demonstrated the accuracy of this method by phasing members of trios (revealing 100% concordance with inheritance information), and demonstrate a common clinical application by phasing CFTR alleles at genomic distances of 11-116 kb in the genomes of cystic fibrosis patients. Drop-Phase is rapid (requiring less than 4 hours), scalable (to hundreds of samples), and effective at long genomic distances (200 kb).

  8. Molecular oncology testing in resource-limited settings.

    PubMed

    Gulley, Margaret L; Morgan, Douglas R

    2014-11-01

    Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship by detecting pertinent pathogen genomes and human gene variants to identify those at highest risk for progression to cancer, to classify lesions, to predict effective therapy, and to monitor tumor burden over time. Prime examples are human papillomavirus in cervical neoplasia, Helicobacter pylori and Epstein-Barr virus in gastric adenocarcinoma and lymphoma, and hepatitis B or C virus in hepatocellular cancer. Research is underway to engineer devices that overcome social, economic, and technical barriers limiting effective laboratory support. Additional challenges include an educated workforce, infrastructure for quality metrics and record keeping, and funds to sustain molecular test services. The combination of well-designed interfaces, novel and robust electrochemical technology, and telemedicine tools will promote adoption by frontline providers. Fast turnaround is crucial for surmounting loss to follow-up, although increased use of cell phones, even in rural areas, enhances options for patient education and engagement. Links to a broadband network facilitate consultation and centralized storage of medical data. Molecular technology shows promise to address gaps in health care through rapid, user-friendly, and cost-effective devices reflecting clinical priorities in resource-poor areas.

  9. Molecular Oncology Testing in Resource-Limited Settings

    PubMed Central

    Gulley, Margaret L.; Morgan, Douglas R.

    2015-01-01

    Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship by detecting pertinent pathogen genomes and human gene variants to identify those at highest risk for progression to cancer, to classify lesions, to predict effective therapy, and to monitor tumor burden over time. Prime examples are human papillomavirus in cervical neoplasia, Helicobacter pylori and Epstein-Barr virus in gastric adenocarcinoma and lymphoma, and hepatitis B or C virus in hepatocellular cancer. Research is underway to engineer devices that overcome social, economic, and technical barriers limiting effective laboratory support. Additional challenges include an educated workforce, infrastructure for quality metrics and record keeping, and funds to sustain molecular test services. The combination of well-designed interfaces, novel and robust electrochemical technology, and telemedicine tools will promote adoption by frontline providers. Fast turnaround is crucial for surmounting loss to follow-up, although increased use of cell phones, even in rural areas, enhances options for patient education and engagement. Links to a broadband network facilitate consultation and centralized storage of medical data. Molecular technology shows promise to address gaps in health care through rapid, user-friendly, and cost-effective devices reflecting clinical priorities in resource-poor areas. PMID:25242061

  10. Molecular Adaptation during a Rapid Adaptive Radiation

    PubMed Central

    Kapralov, Maxim V.; Votintseva, Antonina A.; Filatov, Dmitry A.

    2013-01-01

    “Explosive” adaptive radiations on islands remain one of the most puzzling evolutionary phenomena and the evolutionary genetic processes behind such radiations remain unclear. Rapid morphological and ecological evolution during island radiations suggests that many genes may be under fairly strong selection, although this remains untested. Here, we report that during a rapid recent diversification in the Hawaiian endemic plant genus Schiedea (Caryophyllaceae), 5 in 36 studied genes evolved under positive selection. Positively selected genes are involved in defence mechanisms, photosynthesis, and reproduction. Comparison with eight mainland plant groups demonstrates both the relaxation of purifying selection and more widespread positive selection in Hawaiian Schiedea. This provides compelling evidence that adaptive evolution of protein-coding genes may play a significant role during island adaptive radiations. PMID:23355532

  11. Implementation of Rapid Molecular Infectious Disease Diagnostics: the Role of Diagnostic and Antimicrobial Stewardship.

    PubMed

    Messacar, Kevin; Parker, Sarah K; Todd, James K; Dominguez, Samuel R

    2017-03-01

    New rapid molecular diagnostic technologies for infectious diseases enable expedited accurate microbiological diagnoses. However, diagnostic stewardship and antimicrobial stewardship are necessary to ensure that these technologies conserve, rather than consume, additional health care resources and optimally affect patient care. Diagnostic stewardship is needed to implement appropriate tests for the clinical setting and to direct testing toward appropriate patients. Antimicrobial stewardship is needed to ensure prompt appropriate clinical action to translate faster diagnostic test results in the laboratory into improved outcomes at the bedside. This minireview outlines the roles of diagnostic stewardship and antimicrobial stewardship in the implementation of rapid molecular infectious disease diagnostics.

  12. Molecular diagnostics for low resource settings

    NASA Astrophysics Data System (ADS)

    Weigl, Bernhard H.

    2010-03-01

    As traditional high quality diagnostic laboratories are not widely available or affordable in developing country health care settings, microfluidics-based point-of-care diagnostics may be able to address the need to perform complex assays in under-resourced areas. Many instrument-based as well as non-instrumented microfluidic prototype diagnostics are currently being developed. In addition to various engineering challenges, the greatest remaining issue is the search for truly low-cost disposable manufacturing methods. Diagnostics for global health, and specifically microfluidics and molecular-based low resource diagnostics, have become a very active research area over the last five years, thanks in part to new funding that became available from the Bill and Melinda Gates Foundation, the National Institutes of Health, and other sources. This has led to a number of interesting prototype devices that are now in advanced development or clinical validation. These devices include disposables and instruments that perform multiplexed PCR-based lab-on-a-chips for enteric, febrile, and vaginal diseases, as well as immunoassays for diseases such as malaria, HIV, and various sexually transmitted diseases. More recently, instrument-free diagnostic disposables based on isothermal nucleic acid amplification have been developed as well. Regardless of platform, however, the search for truly low-cost manufacturing methods that would result in cost of goods per disposable of around US1/unit at volume remains a big challenge. This talk will give an overview over existing platform development efforts as well as present some original research in this area at PATH.

  13. National uranium resource evaluation, Rapid City Quadrangle, South Dakota

    SciTech Connect

    Nanna, R.F.; Milton, E.J.

    1982-04-01

    The Rapid City (1/sup 0/ x 2/sup 0/) Quadrangle, South Dakota, was evaluated for environments favorble for uranium deposits to a depth of 1500 m. Criteria used were those of the National Uranium Resource Evaluation. Field reconnaissance involved the use of hand-held scintillometers to investigate uranium occurrences reported in the literature and anomalies in aerial radiometric surveys, and geochemical samples of stream sediments and well waters. Gamma-ray logs were used to define the favorable environments in the subsurface. Environments favorable for sandstone-type uranium deposits occur in the Inyan Kara Group, the Fox Hills Sandstone, and the Hell Creek Formation. Environments considered unfavorable for uranium deposits include all Precambrian, Paleozoic, Mesozoic, and Tertiary rocks other than those identified as favorable.

  14. Rapid Response Team composition, resourcing and calling criteria in Australia.

    PubMed

    Jones, Daryl; Drennan, Kelly; Hart, Graeme K; Bellomo, Rinaldo; Web, Steven A R

    2012-05-01

    Rapid Response Teams (RRTs) have been introduced into at least 60% of Intensive Care Unit (ICU) - equipped Australian hospitals to review deteriorating ward patients. Most studies have assessed their impact on patient outcome and less information exists on team composition or aspects of their calling criteria. We obtained information on team composition, resourcing and details of activation criteria from 39 of 108 (36.1%) RRT-equipped Australian hospitals. We found that all 39 teams operated 24/7 (h/days), but only 10 (25.6%) had received additional funding for the service. Although 38/39 teams, were physician-led medical emergency teams, in 7 (17.9%) sites the most senior member would be unlikely to have advanced airway skills. Three quarters of calling criteria were structured into "ABCD", and approximately 40% included cardiac and/or respiratory arrest as a calling criterion. Thresholds for calling criteria varied widely (particularly for respiratory rate and heart rate), as did the wording of the worried/concerned criterion. There was also wide variation in the number and nature of additional activation criteria. Our findings imply the likelihood of significant practice variation in relation to RRT composition, staff skill set and activation criteria between hospitals. We recommend improved resourcing of RRTs, training of the team members, and consideration for improved standardisation of calling criteria across institutions. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  15. Rapid topography mapping of scalar fields: Large molecular clusters

    NASA Astrophysics Data System (ADS)

    Yeole, Sachin D.; López, Rafael; Gadre, Shridhar R.

    2012-08-01

    An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CP's) of small systems. It is further applied to large molecular clusters viz. (H2O)25, (C6H6)8 and also to a unit cell of valine crystal at MP2/6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincaré-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.

  16. Nanoscale tailor-made membranes for precise and rapid molecular sieve separation.

    PubMed

    Wang, Jing; Zhu, Junyong; Zhang, Yatao; Liu, Jindun; Van der Bruggen, Bart

    2017-03-02

    The precise and rapid separation of different molecules from aqueous, organic solutions and gas mixtures is critical to many technologies in the context of resource-saving and sustainable development. The strength of membrane-based technologies is well recognized and they are extensively applied as cost-effective, highly efficient separation techniques. Currently, empirical-based approaches, lacking an accurate nanoscale control, are used to prepare the most advanced membranes. In contrast, nanoscale control renders the membrane molecular specificity (sub-2 nm) necessary for efficient and rapid molecular separation. Therefore, as a growing trend in membrane technology, the field of nanoscale tailor-made membranes is highlighted in this review. An in-depth analysis of the latest advances in tailor-made membranes for precise and rapid molecule sieving is given, along with an outlook to future perspectives of such membranes. Special attention is paid to the established processing strategies, as well as the application of molecular dynamics (MD) simulation in nanoporous membrane design. This review will provide useful guidelines for future research in the development of nanoscale tailor-made membranes with a precise and rapid molecular sieve separation property.

  17. Resource Paper: Molecular Excited State Relaxation Processes.

    ERIC Educational Resources Information Center

    Rhodes, William

    1979-01-01

    Develops the concept of oscillatory v dissipative limits as it applies to electronic excited state processes in molecular systems. Main emphasis is placed on the radiative and nonradiative dynamics of the excited state of a molecule prepared by interaction with light or some other excitation source. (BT)

  18. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009–31 January 2010

    USDA-ARS?s Scientific Manuscript database

    This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primiti...

  19. Rapid formation of molecular clouds from turbulent atomic gas

    NASA Astrophysics Data System (ADS)

    Glover, S. C. O.; Mac Low, M.-M.

    The characteristic lifetimes of molecular clouds remain uncertain and a topic of frequent debate, with arguments having recently been advanced both in support of short-lived clouds, with lifetimes of a few Myr or less (see e.g. Elmegreen 2000; Hartmann et al. 2001) and in support of much longer-lived clouds, with lifetimes of the order of 10 Myr or more (see e.g. Tassis & Mouschovias, 2004; Goldsmith & Li, 2005). An argument that has previously been advanced in favour of longer lived clouds is the apparent difficulty involved in converting sufficient atomic hydrogen to molecular hydrogen within the short timescale required by the rapid cloud formation scenario. However, previous estimates of the time required for this conversion to occur have not taken into account the effects of the supersonic turbulence which is inferred to be present in the atomic gas. In this contribution, we present results from a set of high resolution three-dimensional simulations of turbulence in gravitationally unstable atomic gas. These simulations were performed using a modified version of the ZEUS-MP hydrodynamical code (Norman 2000), and include a detailed treatment of the thermal balance of the gas and of the formation of molecular hydrogen. The effects of photodissociation of H2 by the Galactic UV field are also included, with a simple local approximation used to compute the effects of H2 self-shielding. The results of our simulations demonstrate that H2 formation occurs rapidly in turbulent atomic gas. Starting from purely atomic gas, large quantities of molecular gas can be produced on timescales of less than a Myr, given turbulent velocity dispersions and magnetic field strengths consistent with observations. Moreover, as our simulations underestimate the effectiveness of H2 self-shielding and dust absorption, we can be confident that the molecular fractions which we compute are strong lower limits on the true values. The formation of large quantities of molecular gas on the

  20. A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings.

    PubMed

    Wong, Grace; Wong, Isaac; Chan, Kamfai; Hsieh, Yicheng; Wong, Season

    2015-01-01

    Many modern molecular diagnostic assays targeting nucleic acids are typically confined to developed countries or to the national reference laboratories of developing-world countries. The ability to make technologies for the rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a revolutionary step forward in global health. Many molecular assays are also developed based on polymerase chain reactions (PCR), which require thermal cyclers that are relatively heavy (>20 pounds) and need continuous electrical power. The temperature ramping speed of most economical thermal cyclers are relatively slow (2 to 3 °C/s) so a polymerase chain reaction can take 1 to 2 hours. Most of all, these thermal cyclers are still too expensive ($2k to $4k) for low-resource setting uses. In this article, we demonstrate the development of a low-cost and rapid water bath based thermal cycler that does not require active temperature control or continuous power supply during PCR. This unit costs $130 to build using commercial off-the-shelf items. The use of two or three vacuum-insulated stainless-steel Thermos food jars containing heated water (for denaturation and annealing/extension steps) and a layer of oil on top of the water allow for significantly stabilized temperatures for PCR to take place. Using an Arduino-based microcontroller, we automate the "archaic" method of hand-transferring PCR tubes between water baths. We demonstrate that this innovative unit can deliver high speed PCR (17 s per PCR cycle) with the potential to go beyond the 1,522 bp long amplicons tested in this study and can amplify from templates down to at least 20 copies per reaction. The unit also accepts regular PCR tubes and glass capillary tubes. The PCR efficiency of our thermal cycler is not different from other commercial thermal cyclers. When combined with a rapid nucleic acid detection approach, the thermos thermal cycler (TTC) can enable on-site molecular

  1. A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings

    PubMed Central

    Wong, Grace; Wong, Isaac; Chan, Kamfai; Hsieh, Yicheng; Wong, Season

    2015-01-01

    Background Many modern molecular diagnostic assays targeting nucleic acids are typically confined to developed countries or to the national reference laboratories of developing-world countries. The ability to make technologies for the rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a revolutionary step forward in global health. Many molecular assays are also developed based on polymerase chain reactions (PCR), which require thermal cyclers that are relatively heavy (>20 pounds) and need continuous electrical power. The temperature ramping speed of most economical thermal cyclers are relatively slow (2 to 3°C/s) so a polymerase chain reaction can take 1 to 2 hours. Most of all, these thermal cyclers are still too expensive ($2k to $4k) for low-resource setting uses. Methodology/Principal Findings In this article, we demonstrate the development of a low-cost and rapid water bath based thermal cycler that does not require active temperature control or continuous power supply during PCR. This unit costs $130 to build using commercial off-the-shelf items. The use of two or three vacuum-insulated stainless-steel Thermos food jars containing heated water (for denaturation and annealing/extension steps) and a layer of oil on top of the water allow for significantly stabilized temperatures for PCR to take place. Using an Arduino-based microcontroller, we automate the “archaic” method of hand-transferring PCR tubes between water baths. Conclusions/Significance We demonstrate that this innovative unit can deliver high speed PCR (17 s per PCR cycle) with the potential to go beyond the 1,522 bp long amplicons tested in this study and can amplify from templates down to at least 20 copies per reaction. The unit also accepts regular PCR tubes and glass capillary tubes. The PCR efficiency of our thermal cycler is not different from other commercial thermal cyclers. When combined with a rapid nucleic acid detection approach

  2. Water resources of the Grand Rapids area, Michigan

    USGS Publications Warehouse

    Stramel, G.J.; Wisler, C.O.; Laird, L.B.

    1954-01-01

    The Grand Rapids area, Michigan, has three sources from which to obtain its water supply: Lake Michigan, the Grand River and its tributaries, and ground water. Each of the first two and possibly the third is capable of supplying the entire needs of the area.This area is now obtaining a part of its supply from each of these sources. Of the average use of 50 mgd (million gallons per day) during 1951, Lake Michigan supplied 29 mgd; the Grand River and its tributaries supplied 1 mgd; and ground water supplied 20 mgd.Lake Michigan offers a practically unlimited source of potable water. However, the cost of delivery to the Grand Rapids area presents an economic problem in the further development of this source. Even without storage the Grand River can provide an adequate supply for the city of Grand Rapids. The present average use of the city of Grand Rapids is about 30 mgd and the maximum use is about 60 mgd, while the average flow of the Grand River is 2, 495 mgd or 3, 860 cfs (cubic feet per second) and the minimum daily flow recorded is 246 mgd. The quality and temperature of water in the Grand River is less desirable than Lake Michigan water. However, with proper treatment its chemical quality can be made entirely satisfactory.The city of Grand Rapids is actively engaged in a study that will lead to the expansion of its present water-supply facilities to meet the expected growth in population in Grand Rapids and its environs.Ground-water aquifers in the area are a large potential source of supply. The Grand Rapids area is underlain by glacial material containing a moderately hard to very hard water of varying chemical composition but suitable for most uses. The glacial outwash and lacustrine deposits bordering principal streams afford the greatest potential for the development of large supplies of potable ground water. Below the glacial drift, bedrock formations contain water that is extremely hard and moderately to highly mineralized. Thus the major sources of

  3. Rapid molecular identification of human taeniid cestodes by pyrosequencing approach.

    PubMed

    Thanchomnang, Tongjit; Tantrawatpan, Chairat; Intapan, Pewpan M; Sanpool, Oranuch; Janwan, Penchom; Lulitanond, Viraphong; Tourtip, Somjintana; Yamasaki, Hiroshi; Maleewong, Wanchai

    2014-01-01

    Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse.

  4. Rapid Molecular Identification of Human Taeniid Cestodes by Pyrosequencing Approach

    PubMed Central

    Thanchomnang, Tongjit; Tantrawatpan, Chairat; Intapan, Pewpan M.; Sanpool, Oranuch; Janwan, Penchom; Lulitanond, Viraphong; Tourtip, Somjintana; Yamasaki, Hiroshi; Maleewong, Wanchai

    2014-01-01

    Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse. PMID:24945530

  5. Molecular markers: a potential resource for ginger genetic diversity studies.

    PubMed

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  6. Rapid extraction and purification of environmental DNA for molecular cloning applications and molecular diversity studies.

    PubMed

    Santosa, D A

    2001-01-01

    A rapid method for the extraction and purification of DNA from environmental samples for molecular cloning applications was developed. The indigenous cells from plant debris, organic materials, sediments, and soils were lysed directly by using DAS-IZ solution and the nucleic acids were precipitated with isopropanol. A simple purification step using DAS-IIZ solution without binding matrix produced highly pure, colorless and undegraded DNA with molecular weight of more than 20 kb. The superiority of this method was tested for wide applications in molecular cloning, i.e., construction of genomic library by using Lambda DASHII Vector and GigapackIII XL, plasmid library, cloning of gene encoding protease, and molecular microbial diversity analysis. An additional advantage of this method is that only 0.1 g of sample is required, if analysis of many samples in short time should be done. To extract large amounts of environmental DNA for molecular cloning lasts only 30 min and to purify it less than 1 h.

  7. Rapid genetic adaptation during the first four months of survival under resource exhaustion.

    PubMed

    Avrani, Sarit; Bolotin, Evgeni; Katz, Sophia; Hershberg, Ruth

    2017-03-28

    Many bacteria, including the model bacterium Escherichia coli can survive for years within spent media, following resource exhaustion. We carried out evolutionary experiments, followed by full genome sequencing of hundreds of evolved clones to study the dynamics by which E. coli adapts during the first four months of survival under resource exhaustion. Our results reveal that bacteria evolving under resource exhaustion are subject to intense selection, manifesting in rapid mutation accumulation, enrichment in functional mutation categories and extremely convergent adaptation. In the most striking example of convergent adaptation, we found that across five independent populations adaptation to conditions of resource exhaustion occurs through mutations to the three same specific positions of the RNA polymerase core enzyme. Mutations to these three sites are strongly antagonistically pleiotropic, in that they sharply reduce exponential growth rates in fresh media. Such antagonistically pleiotropic mutations, combined with the accumulation of additional mutations, severely reduce the ability of bacteria surviving under resource exhaustion to grow exponentially in fresh media. We further demonstrate that the three positions at which these resource exhaustion mutations occur are conserved for the ancestral E. coli allele, across bacterial phyla, with the exception of non-culturable bacteria that carry the resource exhaustion allele at one of these positions, at very high frequencies. Finally, our results demonstrate that adaptation to resource exhaustion is not limited by mutational input and that bacteria are able to rapidly adapt under resource exhaustion in a temporally precise manner through allele frequency fluctuations.

  8. Rapid Molecular Detection of Multidrug-Resistant Tuberculosis by PCR-Nucleic Acid Lateral Flow Immunoassay.

    PubMed

    Kamphee, Hatairat; Chaiprasert, Angkana; Prammananan, Therdsak; Wiriyachaiporn, Natpapas; Kanchanatavee, Airin; Dharakul, Tararaj

    2015-01-01

    Several existing molecular tests for multidrug-resistant tuberculosis (MDR-TB) are limited by complexity and cost, hindering their widespread application. The objective of this proof of concept study was to develop a simple Nucleic Acid Lateral Flow (NALF) immunoassay as a potential diagnostic alternative, to complement conventional PCR, for the rapid molecular detection of MDR-TB. The NALF device was designed using antibodies for the indirect detection of labeled PCR amplification products. Multiplex PCR was optimized to permit the simultaneous detection of the drug resistant determining mutations in the 81-bp hot spot region of the rpoB gene (rifampicin resistance), while semi-nested PCR was optimized for the S315T mutation detection in the katG gene (isoniazid resistance). The amplification process additionally targeted a conserved region of the genes as Mycobacterium tuberculosis (Mtb) DNA control. The optimized conditions were validated with the H37Rv wild-type (WT) Mtb isolate and Mtb isolates with known mutations (MT) within the rpoB and katG genes. Results indicate the correct identification of WT (drug susceptible) and MT (drug resistant) Mtb isolates, with the least limit of detection (LOD) being 104 genomic copies per PCR reaction. NALF is a simple, rapid and low-cost device suitable for low resource settings where conventional PCR is already employed on a regular basis. Moreover, the use of antibody-based NALF to target primer-labels, without the requirement for DNA hybridization, renders the device generic, which could easily be adapted for the molecular diagnosis of other infectious and non-infectious diseases requiring nucleic acid detection.

  9. Novel techniques and future directions in molecular diagnosis of malaria in resource-limited settings.

    PubMed

    Oriero, Eniyou Cheryll; Van Geertruyden, Jean-Pierre; Nwakanma, Davis C; D'Alessandro, Umberto; Jacobs, Jan

    2015-01-01

    Despite being preventable and treatable, malaria remains a global health concern with approximately 1.2 billion people at high risk of being infected, 90% of whom are in the resource-limited settings of sub-Saharan Africa. The continued decline in malaria cases globally has rekindled the possibility of elimination in certain regions. As humans constitute the main reservoir of malaria, prompt and accurate diagnosis by microscopy or rapid diagnostic tests is part not only of effective disease management but also of control measures. However, for malaria elimination, more sensitive diagnostic tools are needed to detect asymptomatic and sub-microscopic infections that contribute to transmission. Molecular techniques, which involve amplification of nucleic acids, are being developed and modified to suit this purpose. This report provides a summary of the nucleic acid amplification tests that are currently available for diagnosis of malaria, with current improvements and adaptations for use in resource-limited settings.

  10. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010.

    PubMed

    Anderson, Cynthia M; Aparicio, Gallego J; Atangana, Alain R; Beaulieu, Jean; Bruford, M W; Cain, Forrest; Campos, T; Cariani, A; Carvalho, M A; Chen, Nan; Chen, P P; Clamens, A-L; Clark, Ann M; Coeur D'Acier, A; Connolly, Paul; Cordero-Rivera, Adolfo; Coughlan, James P; Cross, Thomas S; David, Bruno; DE Bruyn, Colin; DE Meyer, M; DE Ridder, Chantal; Delatte, H; Dettori, M T; Downer, S J; Dubreuil, Christine; Evans, K J; Fan, Bin; Ferrara, G; Gagné, André; Gaillard, Maria; Gigliarelli, L; Giovinazzi, J; Gomez, D R; Grünwald, N J; Hansson, Bengt; Huotari, T; Jank, L; Jousselin, E; Jungmann, L; Kaczmarek, M E; Khasa, Damase P; Kneebone, Jeff; Korpelainen, H; Kostamo, K; Lanfaloni, L; Lin, Haoran; Liu, Xiaochun; Lucentini, L; Maes, G E; Mahaffee, W F; Meng, Zining; Micali, S; Milano, I; Mok, H F; Morin, L; Neill, T M; Newton, Craig H; Gigi Ostrow, D; Palomba, A; Panara, F; Puletti, M E; Quarta, R; Quilici, S; Ramos, A K B; Rigaud, Thierry; Risterucci, A M; Salomon, Matthew P; Sánchez-Guillén, Rosa A; Sarver, Shane K; Sequeira, A S; Sforça, D A; Simiand, C; Smith, Brian; Sousa, A C B; Souza, A P; Stepien, C C; Stuckert, A J; Sulikowski, James; Tayeh, A; Tinti, F; Tsang, Paul C W; VAN Houdt, J K J; Vendramin, E; Verde, I; Virgilio, M; Wang, Huan L; Wang, L E; Wattier, Rémi A; Wellenreuther, Maren; Xie, Cong X; Zane, L; Zhang, Xiu J; Zhang, Yong; Zhuang, Zhimeng; Zucchi, M I

    2010-05-01

    This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.

  11. Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013.

    PubMed

    Arias, M C; Atteke, Christiane; Augusto, S C; Bailey, J; Bazaga, Pilar; Beheregaray, Luciano B; Benoit, Laure; Blatrix, Rumsaïs; Born, Céline; Brito, R M; Chen, Hai-kui; Covarrubias, Sara; de Vega, Clara; Djiéto-Lordon, Champlain; Dubois, Marie-Pierre; Francisco, F O; García, Cristina; Gonçalves, P H P; González, Clementina; Gutiérrez-Rodríguez, Carla; Hammer, Michael P; Herrera, Carlos M; Itoh, H; Kamimura, S; Karaoglu, H; Kojima, S; Li, Shou-Li; Ling, Hannah J; Matos-Maraví, Pável F; McKey, Doyle; Mezui-M'Eko, Judicaël; Ornelas, Juan Francisco; Park, R F; Pozo, María I; Ramula, Satu; Rigueiro, Cristina; Sandoval-Castillo, Jonathan; Santiago, L R; Seino, Miyuki M; Song, Chang-Bing; Takeshima, H; Vasemägi, Anti; Wellings, C R; Yan, Ji; Yu-Zhou, Du; Zhang, Chang-Rong; Zhang, Tian-Yun

    2013-07-01

    This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross-tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii. © 2013 John Wiley & Sons Ltd.

  12. Molecular identification of the turf grass rapid blight pathogen.

    PubMed

    Craven, K D; Peterson, P D; Windham, D E; Mitchell, T K; Martin, S B

    2005-01-01

    Rapid blight is a newly described disease on turf grasses, primarily found on golf courses using suboptimal water for irrigation purposes. On the basis of shared morphological characteristics, it has been proposed that the rapid blight pathogen belongs to a genus of stramenopiles, Labyrinthula, which had been known to cause disease of marine plants only. We have collected 10 isolates from four species of turf grass in five states and sequenced portions of the SSU (18S) rDNA gene from each to provide a definitive taxonomic placement for rapid blight pathogens. We also included sequences from Labyrinthuloides yorkensis, Schizochytrium aggregatum, Aplanochytrium sp., Thraustochytrium striatum, Achlya bisexualis and several nonturf-grass isolates of Labyrinthula. We found that rapid blight isolates indeed are placed firmly within the genus Labyrinthula and that they lack detectable genetic diversity in the 18S rDNA region. We propose that the rapid blight pathogens share a recent common ancestor and might have originated from a single, infected population.

  13. Rapid, Affordable and Portable Medium-Throughput Molecular Device for Zika Virus

    PubMed Central

    Chan, Kamfai; Weaver, Scott C.; Wong, Pui-Yan; Lie, Sherly; Wang, Eryu; Guerbois, Mathilde; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Zika virus (ZIKV) has gained global attention as an etiologic agent of fetal microcephaly and Guillain-Barré syndrome. Existing immuno-based rapid tests often fail to distinguish between Zika and related flaviviruses that are common in affected regions of Central and South Americas and the Caribbean. The US CDC and qualified state health department laboratories can perform the reverse transcription polymerase chain reaction (RT-PCR) ZIKV test using highly sophisticated instruments with long turnaround times. The preliminary results of a portable and low-cost molecular diagnostics system for ZIKV infection are reported here. In less than 15 minutes, this low-cost platform can automatically perform high quality RNA extraction from up to 12 ZIKV-spiked urine samples simultaneously. It can also perform reverse transcription recombinase polymerase amplification reaction (RT-RPA) in ≤15 minutes. The fluorescent signal produced from probe-based RT-RPA or RT-PCR assays can be monitored using LEDs and a smartphone camera. In addition, the RT-RPA and RT-PCR assays do not cross-react with dengue and chikungunya viral RNA. This low-cost system lacks complicated, sensitive and high cost components, making it suitable for resource-limited settings. It has the potential to offer simple sample-to-answer molecular diagnostics and can inform healthcare workers of patients’ diagnosis promptly. PMID:27934884

  14. Rapid, Affordable and Portable Medium-Throughput Molecular Device for Zika Virus.

    PubMed

    Chan, Kamfai; Weaver, Scott C; Wong, Pui-Yan; Lie, Sherly; Wang, Eryu; Guerbois, Mathilde; Vayugundla, Siva Praneeth; Wong, Season

    2016-12-09

    Zika virus (ZIKV) has gained global attention as an etiologic agent of fetal microcephaly and Guillain-Barré syndrome. Existing immuno-based rapid tests often fail to distinguish between Zika and related flaviviruses that are common in affected regions of Central and South Americas and the Caribbean. The US CDC and qualified state health department laboratories can perform the reverse transcription polymerase chain reaction (RT-PCR) ZIKV test using highly sophisticated instruments with long turnaround times. The preliminary results of a portable and low-cost molecular diagnostics system for ZIKV infection are reported here. In less than 15 minutes, this low-cost platform can automatically perform high quality RNA extraction from up to 12 ZIKV-spiked urine samples simultaneously. It can also perform reverse transcription recombinase polymerase amplification reaction (RT-RPA) in ≤15 minutes. The fluorescent signal produced from probe-based RT-RPA or RT-PCR assays can be monitored using LEDs and a smartphone camera. In addition, the RT-RPA and RT-PCR assays do not cross-react with dengue and chikungunya viral RNA. This low-cost system lacks complicated, sensitive and high cost components, making it suitable for resource-limited settings. It has the potential to offer simple sample-to-answer molecular diagnostics and can inform healthcare workers of patients' diagnosis promptly.

  15. Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

    PubMed

    Zheng, Wenwei; Rohrdanz, Mary A; Clementi, Cecilia

    2013-10-24

    The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

  16. Discordant rapid HIV tests: lessons from a low-resource community.

    PubMed

    Adetunji, A A; Kuti, M A; Audu, R A; Muyibi, S A; Imhansoloeva, M; Mosuro, O A; Solanke, E A; Akpa, O M; Irabor, A E; Ladipo, Mma; Berzins, B; Robertson, K; Ogunniyi, A; Adewole, I F; Taiwo, B O

    2017-07-31

    HIV rapid antibody tests are widely used in Africa, but dual testing sometimes produces discordant results. It is not clear if discordant rapid HIV tests should always heighten suspicion by frontline health workers that early HIV infection is present. Some studies have reported that discordant rapid tests have value for identifying early HIV infection in high HIV prevalence populations. It is not known if rapid test performance influenced this conclusion, or if this observation will hold true for low HIV prevalence populations. We therefore explored the occurrence of discordant rapid HIV tests in a low-resource community. A cross-sectional sample of HIV status-unaware adults with recent exposure to unsafe sex was assessed using a validated risk-based tool (University of North Carolina (UNC)-Malawi Risk Screening Score) for acute HIV infection. Participants received rapid testing with Determine™ HIV 1/2 and Uni-Gold™ HIV assays, plus plasma HIV-1 antigen testing with the COBAS(®) Ampliprep/COBAS(®) Taqman(®) HIV-1 assay, followed by western blot in those with detected HIV-1 antigen. Of 408 participants, 1.0% were confirmed to have established HIV infection. The discordance between rapid tests at initial screening was 2.45 and 2.94% when the two assays were used sequentially and simultaneously, respectively. Discordant rapid tests were strongly associated with risk scores > 2 [odds ratio (OR) 10.88; 95% confidence interval (CI) 2.35-50.43], and with detected HIV-1 RNA (OR 26.06; 95% CI 3.91-173.60). When the sample occurrence of discordance between the first and second tests is below 5%, discordant rapid tests in an adult with sexual risk behaviour should trigger strong suspicion of early HIV infection in low HIV prevalence populations. © 2017 British HIV Association.

  17. Rapid detection and simultaneous molecular profile characterization of Acanthamoeba infections.

    PubMed

    Goldschmidt, Pablo; Degorge, Sandrine; Benallaoua, Djida; Batellier, Laurence; Di Cave, David; Chaumeil, Christine

    2012-10-01

    Diagnosis of Acanthamoeba by microscopic examination, culture, and polymerase chain reactions (PCRs) has several limitations (sensitivity, specificity, lack of detection of several strains, cost of testing for discrimination among strains). We developed a new high-resolution melting real-time PCR (HRM) to detect and characterize Acanthamoeba infections. HRM performances were evaluated with strains from the American Type Culture Collection (ATCC) and with 20 corneal scrapings. The DNA extracted from specimens were amplified, detected, and characterized in 1 run using 2 original primers diluted in a solution containing an intercalating dye. Detection and molecular characterization of Acanthamoeba infections could be achieved in less than 2.5 h with a dramatic reduction in cost of reactants (postamplification procedures and radioactive or fluorescent-labeled molecular probes were unnecessary). HRM detection limits were 0.1 cyst/μL or less (including genotypes T5 and T11), and its sensitivity and specificity were higher than other molecular tests. For the tested strains from the ATCC, the HRM drafted 4 different profiles: Type I (genotypes T2 and T4), Type II (T5 and T7), Type III (T8), and Type IV (T1, T3, T6, T9, T11, T12, and T13).

  18. Utilization of rapid response resources and outcomes in a comprehensive cancer center*.

    PubMed

    Austin, Charles A; Hanzaker, Chris; Stafford, Renae; Mayer, Celeste; Culp, Loc; Lin, Feng-Chang; Chang, Lydia

    2014-04-01

    To compare the differences in characteristics and outcomes of cancer center patients with other subspecialty medical patients reviewed by rapid response teams. A retrospective cohort study of hospitalized general medicine patients, subspecialty medicine patients, and oncology patients requiring rapid response team activation over a 2-year period from September 2009 to August 2011. Five hundred fifty-seven subspecialty medical patients required rapid response team intervention. A single academic medical center in the southeastern United States (800+ bed) with a dedicated 50-bed inpatient comprehensive cancer care center. Data abstraction from computerized medical records and a hospital quality improvement rapid response database. Of the 557 patients, 135 were cancer center patients. Cancer center patients had a significantly higher Charlson Comorbidity Score (4.4 vs 2.9, < 0.001). Cancer center patients had a significantly longer hospitalization period prior to rapid response team activation (11.4 vs 6.1 d, p < 0.001). There was no significant difference between proportions of patients requiring ICU transfer between the two groups (odds ratio, 1.2; 95% CI, 0.8-1.8). Cancer center patients had a significantly higher in-hospital mortality compared with the other subspecialty medical patients (33% vs 18%; odds ratio, 2.2; 95% CI, 1.50-3.5). If the rapid response team event required an ICU transfer, this finding was more pronounced (56% vs 23%; odds ratio, 4.0; 95% CI, 2.0-7.8). The utilization of rapid response team resources during the 2-year period studied was also much higher for the oncology patients with 37.34 activations per 1,000 patient discharges compared with 20.86 per 1,000 patient discharges for the general medical patients. Oncology patients requiring rapid response team activation have a significantly higher in-hospital mortality rate, particularly if the rapid response team requires ICU transfer. Oncology patients also utilize rapid response team

  19. Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2010-30 November 2010.

    PubMed

    Agostini, Cecilia; Agudelo, P A; Bâ, K; Barber, P A; Bisol, Paolo Maria; Brouat, C; Burgess, Treena I; Calves, I; Carrillo Avila, Mauricio; Chow, S; Cordes, Lisa; Da Silva, D; Dalecky, A; De Meester, L; Doadrio, Ignacio; Dobigny, G; Duplantier, J M; Evison, Sophie E F; Ford, Rebecca; Fresneau, Dominique; Galetti, Pedro M; Gauthier, P; Geldof, S; Granjon, L; Guérin, F; St J Hardy, Giles E; Hernandez Escobar, Carlos; Hima, K; Hu, Juan; Huang, Luqi; Humeau, L; Jansen, B; Jaquemet, S; Jiang, Zhi-Qiang; Jung, Sung-Ju; Kim, Bong-Seok; Kim, Cheol-Hee; Kim, Jong-Oh; Lai, Choay-Hoong; Laroche, J; Lavergne, E; Lawton-Rauh, A; Le Corre, M; Leach, M M; Lee, Jehee; Leo, Audrey E; Lichtenzveig, Judith; Lin, Lin; Linde, Celeste C; Liu, Shu-Fang; Marino, Ilaria A M; McKeown, Niall J; Nohara, K; Oh, Myung-Joo; Okamoto, H; Oliver, Richard; Olivera Angel, Martha; Ornelas-García, Claudia Patricia; Orsini, L; Ostos Alfonso, Henry; Othman, A S; Papetti, Chiara; Patarnello, Tomaso; Pedraza-Lara, Carlos; Piller, Kyle R; Poteaux, Chantal; Requier, J-B; Roziana, M K; Semba, Y; Sembene, M; Shah, Ramisah M; Shahril, A R; Shao, Aijuan; Shaw, Paul W; Song, Liangke; Souza Ferreira, Ronara; Su, Yong-Quan; Suzuki, N; Tatard, C; Taylor, Katherine M; Taylor, Paul W J; Thiam, M; Valbuena, Ruben; Wang, He; Yang, Byung-Gyoo; Yuan, Qingjun; Zajonz, U; Zane, Lorenzo; Zhu, Ling; Zhuang, Zhi-Meng; Zulaiha, A R

    2011-03-01

    This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.

  20. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2010 - 31 May 2010.

    PubMed

    Andree, K; Axtner, Jan; Bagley, M J; Barlow, E J; Beebee, T J C; Bennetzen, Jeffrey L; Bermingham, Eldredge; Boisselier-Dubayle, M C; Bozarth, Christine A; Brooks, Christopher P; Brown, R P; Catanese, Gaetano; Cavers, S; Ceron-Souza, Ivania; Chak, Solomon T C; Chan, M N; Charles-Dominique, P; Chen, C Y; Chen, J D; Chinchilla, Leah; DA Silva, D; Dafreville, S; Daunt, F; Delatte, H; Dorge, T; Duncan, N; Durand, J D; Duvernell, D; Estep, Matt; Fan, Sigang; Fattahi, R; Villela, Oscar Flores; Fong, Yokking; Fréville, H; Funes, Victoria; Gallardo-Escarate, C; Ganeshaiah, K N; Ghaffari, M R; Girod, C; Gomez-Moliner, B J; Gonzalez-Porter, Gracia P; Gosa, A; Govers, F; Guérin, F; Guindo, Diarah; Hailer, Frank; Haye, P A; Hoelmer, Kim A; Hofmann, S; Hong, Yan; Hu, Chaoqun; Huang, S W; Humeau, L; Infante, Carlos; Jackson, S A; Jacobsen, E; Jowkar, A; Kafi, M; Kermani, M J; Kim, Hyojoong; Kim, Kyung Seok; Kim, Min-Young; Knibb, W; Koita, Ousmane A; Korpelainen, H; Lambourdiere, J; Lasso, Eloisa; Leblois, R; Lee, Hang; Lee, Seunghwan; Leung, F C C; Leung, Kenneth M Y; Li, Chunhong; Li, Y; Lieckfeldt, Dietmar; Lizana, M; Loughry, W J; Luo, Peng; Madeira, M J; Mahmoodi, P; Maldonado, Jesús E; Mardi, M; Mendes, O; Miehe, G; Muth, Peter; Nacci, D; Naveen Kumar, L; Ng, Wai-Chuen; Pailler, T; Parzies, Heiko K; Perez, Laura; Pfunder, M; Pietiläinen, M; Pirseyedi, S M; Porta, D; Porta, J; Porta, J M; Quilici, S; Rakotoarivelo, F P; Ramesha, B T; Ravikanth, G; Riéra, B; Risterucci, A M; Roberts, D A; Samadi, S; Sarasola-Puente, V; Sarrazin, E; Sarthou, C; Schmidt, Anke; Segovia, N I; Shen, K N; Simiand, C; Sman, Muhammad Hidayat Bin; Solhoy, T; Sommer, Simone; Sumangala, R C; Taubert, Ramona; Tejangkura, T; Telford, A; Testa, A; Tollon-Cordet, C; Tzeng, W N; Uma Shaanker, R; Van Der Lee, T A J; VAN Mourik, Thomas A; Vasudeva, R; Wai, T C; Wang, R L; Welch, Mark E; Weltzien, Eva; Whitehead, A; Woodard, Anastasia; Xia, Jianjun; Zeinolabedini, M; Zhang, Lvping

    2010-11-01

    This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross-tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii.

  1. Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2010-31 January 2011.

    PubMed

    Agata, Kiyokazu; Alasaad, Samer; Almeida-Val, Vera Maria Fonseca; Alvarez-Dios, J A; Barbisan, F; Beadell, Jon S; Beltrán, J F; Benítez, M; Bino, G; Bleay, Colin; Bloor, P; Bohlmann, Jörg; Booth, Warren; Boscari, E; Caccone, Adalgisa; Campos, Tatiana; Carvalho, B M; Climaco, Gisele Torres; Clobert, Jean; Congiu, L; Cowger, Christina; Dias, G; Doadrio, I; Farias, Izeni Pires; Ferrand, N; Freitas, Patrícia D; Fusco, G; Galetti, Pedro M; Gallardo-Escárate, Cristian; Gaunt, Michael W; Ocampo, Zaneli Gomez; Gonçalves, H; Gonzalez, E G; Haye, Pilar; Honnay, O; Hyseni, Chaz; Jacquemyn, H; Jowers, Michael J; Kakezawa, Akihiro; Kawaguchi, Eri; Keeling, Christopher I; Kwan, Ye-Seul; La Spina, Michelangelo; Lee, Wan-Ok; Leśniewska, M; Li, Yang; Liu, Haixia; Liu, Xiaolin; Lopes, S; Martínez, P; Meeus, S; Murray, Brent W; Nunes, Aline G; Okedi, Loyce M; Ouma, Johnson O; Pardo, B G; Parks, Ryan; Paula-Silva, Maria Nazaré; Pedraza-Lara, C; Perera, Omaththage P; Pino-Querido, A; Richard, Murielle; Rossini, Bruno C; Samarasekera, N Gayathri; Sánchez, Antonio; Sanchez, Juan A; Santos, Carlos Henrique Dos Anjos; Shinohara, Wataru; Soriguer, Ramón C; Sousa, Adna Cristina Barbosa; Sousa, Carolina Fernandes Da Silva; Stevens, Virginie M; Tejedo, M; Valenzuela-Bustamante, Myriam; Van de Vliet, M S; Vandepitte, K; Vera, M; Wandeler, Peter; Wang, Weimin; Won, Yong-Jin; Yamashiro, A; Yamashiro, T; Zhu, Changcheng

    2011-05-01

    This article documents the addition of 238 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alytes dickhilleni, Arapaima gigas, Austropotamobius italicus, Blumeria graminis f. sp. tritici, Cobitis lutheri, Dendroctonus ponderosae, Glossina morsitans morsitans, Haplophilus subterraneus, Kirengeshoma palmata, Lysimachia japonica, Macrolophus pygmaeus, Microtus cabrerae, Mytilus galloprovincialis, Pallisentis (Neosentis) celatus, Pulmonaria officinalis, Salminus franciscanus, Thais chocolata and Zootoca vivipara. These loci were cross-tested on the following species: Acanthina monodon, Alytes cisternasii, Alytes maurus, Alytes muletensis, Alytes obstetricans almogavarii, Alytes obstetricans boscai, Alytes obstetricans obstetricans, Alytes obstetricans pertinax, Cambarellus montezumae, Cambarellus zempoalensis, Chorus giganteus, Cobitis tetralineata, Glossina fuscipes fuscipes, Glossina pallidipes, Lysimachia japonica var. japonica, Lysimachia japonica var. minutissima, Orconectes virilis, Pacifastacus leniusculus, Procambarus clarkii, Salminus brasiliensis and Salminus hilarii. © 2011 Blackwell Publishing Ltd.

  2. Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2012 - 31 March 2012.

    PubMed

    Andris, Malvina; Arias, M C; Barthel, Brandon L; Bluhm, Burton H; Bried, Joël; Canal, D; Chen, X M; Cheng, P; Chiappero, Marina B; Coelho, Manuela M; Collins, Angela B; Dash, M; Davis, Michelle C; Duarte, Margarida; Dubois, Marie-Pierre; Françoso, E; Galmes, M A; Gopal, Keshni; Jarne, Philippe; Kalbe, Martin; Karczmarski, Leszek; Kim, Hun; Martella, Mónica B; McBride, Richard S; Negri, Valeria; Negro, J J; Newell, Annakay D; Piedade, Ana F; Puchulutegui, Cecilia; Raggi, Lorenzo; Samonte, Irene E; Sarasola, J H; See, D R; Seyoum, Seifu; Silva, Mónica C; Solaro, C; Tolley, Krystal A; Tringali, Michael D; Vasemägi, A; Xu, L S; Zanón-Martínez, J I

    2012-07-01

    This article documents the addition of 171 microsatellite marker loci and 27 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bombus pauloensis, Cephalorhynchus heavisidii, Cercospora sojina, Harpyhaliaetus coronatus, Hordeum vulgare, Lachnolaimus maximus, Oceanodroma monteiroi, Puccinia striiformis f. sp. tritici, Rhea americana, Salmo salar, Salmo trutta, Schistocephalus solidus, Sousa plumbea and Tursiops aduncus. These loci were cross-tested on the following species: Aquila heliaca, Bulweria bulwerii, Buteo buteo, Buteo swainsoni, Falco rusticolus, Haliaeetus albicilla, Halobaena caerulea, Hieraaetus fasciatus, Oceanodroma castro, Puccinia graminis f. sp. Tritici, Puccinia triticina, Rhea pennata and Schistocephalus pungitii. This article also documents the addition of 27 sequencing primer pairs for Puffinus baroli and Bulweria bulwerii and cross-testing of these loci in Oceanodroma castro, Pelagodroma marina, Pelecanoides georgicus, Pelecanoides urinatrix, Thalassarche chrysostoma and Thalassarche melanophrys.

  3. Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010.

    PubMed

    Aggarwal, Ramesh K; Allainguillaume, Joel; Bajay, M M; Barthwal, Santan; Bertolino, P; Chauhan, Priti; Consuegra, Sofia; Croxford, Adam; Dalton, Desiré L; den Belder, E; Díaz-Ferguson, E; Douglas, M R; Drees, Michael; Elderson, J; Esselink, G D; Fernández-Manjarrés, J F; Frascaria-Lacoste, N; Gäbler-Schwarz, Steffi; Garcia de Leaniz, Carlos; Ginwal, H S; Goodisman, Michael A D; Guo, Baoling; Hamilton, M B; Hayes, Paul K; Hong, Yan; Kajita, Tadashi; Kalinowski, Steven T; Keller, Laurent; Koop, Ben F; Kotzé, Antoinette; Lalremruata, Albert; Leese, Florian; Li, Chunhong; Liew, W Y; Martinelli, S; Matthews, Emily A; Medlin, Linda K; Messmer, Amber M; Meyer, Elisabeth I; Monteiro, M; Moyer, G R; Nelson, R John; Nguyen, Thuy T T; Omoto, C; Ono, Junya; Pavinato, V A C; Pearcy, Morgan; Pinheiro, J B; Power, L D; Rawat, Anita; Reusch, Thorsten B H; Sanderson, Dan; Sannier, J; Sathe, Santosh; Sheridan, C K; Smulders, M J M; Sukganah, A; Takayama, Koji; Tamura, Mariko; Tateishi, Yoichi; Vanhaecke, Delphine; Vu, Ninh V; Wickneswari, R; Williams, A S; Wimp, G M; Witte, Volker; Zucchi, M I

    2011-01-01

    This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia. © 2010 Blackwell Publishing Ltd.

  4. Permanent genetic resources added to molecular ecology resources database 1 December 2012-31 January 2013.

    PubMed

    Arranz, Silvia E; Avarre, Jean-Christophe; Balasundaram, Chellam; Bouza, Carmen; Calcaterra, Nora B; Cezilly, Frank; Chen, Shi-long; Cipriani, Guido; Cruz, V P; D'Esposito, D; Daniel, Carla; Dejean, Alain; Dharaneedharan, Subramanian; Díaz, Juan; Du, Man; Durand, Jean-Dominique; Dziadek, Jarosław; Foresti, F; Peng-cheng, Fu; Gao, Qing-bo; García, Graciela; Gauffre-Autelin, Pauline; Giovino, Antonio; Goswami, Mukunda; Guarino, Carmine; Guerra-Varela, Jorge; Gutiérrez, Verónica; Harris, D J; Heo, Moon-Soo; Khan, Gulzar; Kim, Mija; Lakra, Wazir S; Lauth, Jérémie; Leclercq, Pierre; Lee, Jeonghwa; Lee, Seung-Ho; Lee, Soohyung; Lee, Theresa; Li, Yin-hu; Liu, Hongbo; Liu, Shufang; Malé, Pierre-Jean G; Mandhan, Rishi Pal; Martinez, Paulino; Mayer, Veronika E; Mendel, Jan; Mendes, N J; Mendonça, F F; Minias, Alina; Minias, Piotr; Oh, Kyeong-Suk; Oliveira, C; Orivel, Jérôme; Orsini, L; Pardo, Belén G; Perera, A; Procaccini, G; Rato, C; Ríos, Néstor; Scibetta, Silvia; Sharma, Bhagwati S; Sierens, Tim; Singh, Akhilesh; Terer, Taita; Triest, Ludwig; Urbánková, Soňa; Vera, Manuel; Villanova, Gabriela V; Voglmayr, Hermann; Vyskočilová, Martina; Wang, Hongying; Wang, Jiu-li; Wattier, Rémi A; Xing, Rui; Yadav, Kamalendra; Yin, Guibo; Yuan, Yanjiao; Yun, Jong-Chul; Zhang, Fa-qi; Zhang, Jing-hua; Zhuang, Zhimeng

    2013-05-01

    This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba. © 2013 Blackwell Publishing Ltd.

  5. Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012.

    PubMed

    Arias, M C; Arnoux, E; Bell, James J; Bernadou, Abel; Bino, Giorgia; Blatrix, R; Bourguet, Denis; Carrea, Cecilia; Clamens, Anne-Laure; Cunha, Haydée A; d'Alençon, E; Ding, Yi; Djieto-Lordon, C; Dubois, M P; Dumas, P; Eraud, C; Faivre, B; Francisco, F O; Françoso, E; Garcia, M; Gardner, Jonathan P A; Garnier, S; Gimenez, S; Gold, John R; Harris, D J; He, Guangcun; Hellemans, B; Hollenbeck, Christopher M; Jing, Shengli; Kergoat, G J; Liu, Bingfang; McDowell, Jan R; McKey, D; Miller, Terrence L; Newton, Erica; Pagenkopp Lohan, Katrina M; Papetti, Chiara; Paterson, Ian; Peccoud, J; Peng, Xinxin; Piatscheck, F; Ponsard, Sergine; Reece, Kimberly S; Reisser, Céline M O; Renshaw, Mark A; Ruzzante, Daniel E; Sauve, M; Shields, Jeffrey D; Solé-Cava, Antonio; Souche, E L; Van Houdt, J K J; Vasconcellos, Anderson; Volckaert, F A M; Wang, Shuzhen; Xiao, Jie; Yu, Hangjin; Zane, Lorenzo; Zannato, Barbara; Zemlak, Tyler S; Zhang, Chunxiao; Zhao, Yan; Zhou, Xi; Zhu, Lili

    2012-05-01

    This article documents the addition of 473 microsatellite marker loci and 71 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross-tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax. © 2012 Blackwell Publishing Ltd.

  6. The Water-Energy-Food Nexus in a Rapidly Developing Resource Sector

    NASA Astrophysics Data System (ADS)

    Allen, D. M.; Kirste, D. M.

    2014-12-01

    Technological advances and access to global markets have changed the rate at which resource exploitation takes place. The environmental impact of the rapid development and distribution of resources such as minerals and hydrocarbons has led to a greater potential for significant stress on water resources both in terms of quality and quantity. How and where those impacts manifest is crucial to determining appropriate risk management strategies. North East British Columbia has an abundance of shale gas reserves that are anticipated to be exploited at a large scale in coming years, primarily for export as liquefied natural gas (LNG). However, there is growing concern that fracking and other activities related to shale gas development pose risks to water quality and quantity in the region. Water lies at the center of the water-energy-food nexus, with an accelerating water demand for fracking and industrial operations as well as for domestic, environmental and agricultural uses. Climate change is also anticipated to alter the hydrologic regime, posing added stress to the water resource. This case study examines the water-energy-food nexus in the context of a region that is impacted by a rapidly developing resource sector, encompassing water demand/supply, climate change, interaction between deep aquifers and shallow aquifers/surface waters, water quality concerns related to fracking, land use disturbance, and community impacts. Due to the rapid rate of development, there are significant knowledge gaps in our understanding of the water resource. Currently agencies are undertaking water resource assessments and establishing monitoring sites. This research aims to assess water security in North East British Columbia in a coordinated fashion through various partnerships. In addition to collecting baseline knowledge and data, the study will evaluate risk and resilience indicators in relation to water security. A risk assessment framework specific to the shale gas development

  7. Rapid methods for the extraction and archiving of molecular grade fungal genomic DNA.

    PubMed

    Borman, Andrew M; Palmer, Michael; Johnson, Elizabeth M

    2013-01-01

    The rapid and inexpensive extraction of fungal genomic DNA that is of sufficient quality for molecular approaches is central to the molecular identification, epidemiological analysis, taxonomy, and strain typing of pathogenic fungi. Although many commercially available and in-house extraction procedures do eliminate the majority of contaminants that commonly inhibit molecular approaches, the inherent difficulties in breaking fungal cell walls lead to protocols that are labor intensive and that routinely take several hours to complete. Here we describe several methods that we have developed in our laboratory that allow the extremely rapid and inexpensive preparation of fungal genomic DNA.

  8. Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

    PubMed Central

    Cazanave, Charles; Greenwood-Quaintance, Kerryl E.; Hanssen, Arlen D.; Karau, Melissa J.; Schmidt, Suzannah M.; Gomez Urena, Eric O.; Mandrekar, Jayawant N.; Osmon, Douglas R.; Lough, Lindsay E.; Pritt, Bobbi S.; Steckelberg, James M.

    2013-01-01

    We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (n = 272) or hip (n = 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P = 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure. PMID:23658273

  9. Rapid molecular microbiologic diagnosis of prosthetic joint infection.

    PubMed

    Cazanave, Charles; Greenwood-Quaintance, Kerryl E; Hanssen, Arlen D; Karau, Melissa J; Schmidt, Suzannah M; Gomez Urena, Eric O; Mandrekar, Jayawant N; Osmon, Douglas R; Lough, Lindsay E; Pritt, Bobbi S; Steckelberg, James M; Patel, Robin

    2013-07-01

    We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (n = 272) or hip (n = 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P = 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure.

  10. The rapid evolution of molecular genetic diagnostics in neuromuscular diseases.

    PubMed

    Volk, Alexander E; Kubisch, Christian

    2017-10-01

    The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.

  11. Molecular origins of rapid and continuous morphological evolution.

    PubMed

    Fondon, John W; Garner, Harold R

    2004-12-28

    Mutations in cis-regulatory sequences have been implicated as being the predominant source of variation in morphological evolution. We offer a hypothesis that gene-associated tandem repeat expansions and contractions are a major source of phenotypic variation in evolution. Here, we describe a comparative genomic study of repetitive elements in developmental genes of 92 breeds of dogs. We find evidence for selection for divergence at coding repeat loci in the form of both elevated purity and extensive length polymorphism among different breeds. Variations in the number of repeats in the coding regions of the Alx-4 (aristaless-like 4) and Runx-2 (runt-related transcription factor 2) genes were quantitatively associated with significant differences in limb and skull morphology. We identified similar repeat length variation in the coding repeats of Runx-2, Twist, and Dlx-2 in several other species. The high frequency and incremental effects of repeat length mutations provide molecular explanations for swift, yet topologically conservative morphological evolution.

  12. A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

    PubMed Central

    Danley, Patrick D; Mullen, Sean P; Liu, Fenglong; Nene, Vishvanath; Quackenbush, John; Shaw, Kerry L

    2007-01-01

    Background As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models in other biological fields. Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution. Results We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket Laupala kohalensis. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web page Conclusion Orthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus Laupala have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic

  13. Resources

    MedlinePlus

    ... Gastrointestinal disorders - resources Hearing impairment - resources Hearing or speech impairment - resources Heart disease - resources Hemophilia - resources Herpes - resources Incest - resources Incontinence - ...

  14. Permanent Genetic Resources added to Molecular Ecology Resources database 1 January 2009-30 April 2009.

    PubMed

    Abercrombie, L G; Anderson, C M; Baldwin, B G; Bang, I C; Beldade, R; Bernardi, G; Boubou, A; Branca, A; Bretagnolle, F; Bruford, M W; Buonamici, A; Burnett, R K; Canal, D; Cárdenas, H; Caullet, C; Chen, S Y; Chun, Y J; Cossu, C; Crane, C F; Cros-Arteil, S; Cudney-Bueno, R; Danti, R; Dávila, J A; Della Rocca, G; Dobata, S; Dunkle, L D; Dupas, S; Faure, N; Ferrero, M E; Fumanal, B; Gigot, G; González, I; Goodwin, S B; Groth, D; Hardesty, B D; Hasegawa, E; Hoffman, E A; Hou, M L; Jamsari, A F J; Ji, H J; Johnson, D H; Joseph, L; Justy, F; Kang, E J; Kaufmann, B; Kim, K S; Kim, W J; Koehler, A V; Laitung, B; Latch, P; Liu, Y D; Manjerovic, M B; Martel, E; Metcalfe, S S; Miller, J N; Midgley, J J; Migeon, A; Moore, A J; Moore, W L; Morris, V R F; Navajas, M; Navia, D; Neel, M C; De Nova, P J G; Olivieri, I; Omura, T; Othman, A S; Oudot-Canaff, J; Panthee, D R; Parkinson, C L; Patimah, I; Pérez-Galindo, C A; Pettengill, J B; Pfautsch, S; Piola, F; Potti, J; Poulin, R; Raimondi, P T; Rinehart, T A; Ruzainah, A; Sarver, S K; Scheffler, B E; Schneider, A R R; Silvain, J F; Siti Azizah, M N; Springer, Y P; Stewart, C N; Sun, W; Tiedemann, R; Tsuji, K; Trigiano, R N; Vendramin, G G; Wadl, P A; Wang, L; Wang, X; Watanabe, K; Waterman, J M; Weisser, W W; Westcott, D A; Wiesner, K R; Xu, X F; Yaegashi, S; Yuan, J S

    2009-09-01

    This article documents the addition of 283 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Agalinis acuta; Ambrosia artemisiifolia; Berula erecta; Casuarius casuarius; Cercospora zeae-maydis; Chorthippus parallelus; Conyza canadensis; Cotesia sesamiae; Epinephelus acanthistius; Ficedula hypoleuca; Grindelia hirsutula; Guadua angustifolia; Leucadendron rubrum; Maritrema novaezealandensis; Meretrix meretrix; Nilaparvata lugens; Oxyeleotris marmoratus; Phoxinus neogaeus; Pristomyrmex punctatus; Pseudobagrus brevicorpus; Seiridium cardinale; Stenopsyche marmorata; Tetranychus evansi and Xerus inauris. These loci were cross-tested on the following species: Agalinis decemloba; Agalinis tenella; Agalinis obtusifolia; Agalinis setacea; Agalinis skinneriana; Cercospora zeina; Cercospora kikuchii; Cercospora sorghi; Mycosphaerella graminicola; Setosphaeria turcica; Magnaporthe oryzae; Cotesia flavipes; Cotesia marginiventris; Grindelia Xpaludosa; Grindelia chiloensis; Grindelia fastigiata; Grindelia lanceolata; Grindelia squarrosa; Leucadendron coniferum; Leucadendron salicifolium; Leucadendron tinctum; Leucadendron meridianum; Laodelphax striatellus; Sogatella furcifera; Phoxinus eos; Phoxinus rigidus; Phoxinus brevispinosus; Phoxinus bicolor; Tetranychus urticae; Tetranychus turkestani; Tetranychus ludeni; Tetranychus neocaledonicus; Tetranychus amicus; Amphitetranychus viennensis; Eotetranychus rubiphilus; Eotetranychus tiliarium; Oligonychus perseae; Panonychus citri; Bryobia rubrioculus; Schizonobia bundi; Petrobia harti; Xerus princeps; Spermophilus tridecemlineatus and Sciurus carolinensis.

  15. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009.

    PubMed

    Abdoullaye, Doukary; Acevedo, I; Adebayo, Abisola A; Behrmann-Godel, Jasminca; Benjamin, R C; Bock, Dan G; Born, Céline; Brouat, Carine; Caccone, Adalgisa; Cao, Ling-Zhen; Casado-Amezúa, P; Catanéo, J; Correa-Ramirez, M M; Cristescu, Melania E; Dobigny, Gauthier; Egbosimba, Emmanuel E; Etchberger, Lianna K; Fan, Bin; Fields, Peter D; Forcioli, D; Furla, P; Garcia de Leon, F J; García-Jiménez, R; Gauthier, Philippe; Gergs, René; González, Clementina; Granjon, Laurent; Gutiérrez-Rodríguez, Carla; Havill, Nathan P; Helsen, P; Hether, Tyler D; Hoffman, Eric A; Hu, Xiangyang; Ingvarsson, Pär K; Ishizaki, S; Ji, Heyi; Ji, X S; Jimenez, M L; Kapil, R; Karban, R; Keller, Stephen R; Kubota, S; Li, Shuzhen; Li, Wansha; Lim, Douglas D; Lin, Haoran; Liu, Xiaochun; Luo, Yayan; Machordom, A; Martin, Andrew P; Matthysen, E; Mazzella, Maxwell N; McGeoch, Mélodie A; Meng, Zining; Nishizawa, M; O'Brien, Patricia; Ohara, M; Ornelas, Juan Francisco; Ortu, M F; Pedersen, Amy B; Preston, L; Ren, Qin; Rothhaupt, Karl-Otto; Sackett, Loren C; Sang, Qing; Sawyer, G M; Shiojiri, K; Taylor, Douglas R; Van Dongen, S; Van Vuuren, Bettine Jansen; Vandewoestijne, S; Wang, H; Wang, J T; Wang, L E; Xu, Xiang-Li; Yang, Guang; Yang, Yongping; Zeng, Y Q; Zhang, Qing-Wen; Zhang, Yongping; Zhao, Y; Zhou, Yan

    2010-01-01

    This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides. © 2009 Blackwell Publishing Ltd.

  16. Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2011-30 September 2011.

    PubMed

    A'Hara, S W; Amouroux, P; Argo, Emily E; Avand-Faghih, A; Barat, Ashoktaru; Barbieri, Luiz; Bert, Theresa M; Blatrix, R; Blin, Aurélie; Bouktila, D; Broome, A; Burban, C; Capdevielle-Dulac, C; Casse, N; Chandra, Suresh; Cho, Kyung Jin; Cottrell, J E; Crawford, Charles R; Davis, Michelle C; Delatte, H; Desneux, Nicolas; Djieto-Lordon, C; Dubois, M P; El-Mergawy, R A A M; Gallardo-Escárate, C; Garcia, M; Gardiner, Mary M; Guillemaud, Thomas; Haye, P A; Hellemans, B; Hinrichsen, P; Jeon, Ji Hyun; Kerdelhué, C; Kharrat, I; Kim, Ki Hwan; Kim, Yong Yul; Kwan, Ye-Seul; Labbe, Ellen M; LaHood, Eric; Lee, Kyung Mi; Lee, Wan-Ok; Lee, Yat-Hung; Legoff, Isabelle; Li, H; Lin, Chung-Ping; Liu, S S; Liu, Y G; Long, D; Maes, G E; Magnoux, E; Mahanta, Prabin Chandra; Makni, H; Makni, M; Malausa, Thibaut; Matura, Rakesh; McKey, D; McMillen-Jackson, Anne L; Méndez, M A; Mezghani-Khemakhem, M; Michel, Andy P; Paul, Moran; Muriel-Cunha, Janice; Nibouche, S; Normand, F; Palkovacs, Eric P; Pande, Veena; Parmentier, K; Peccoud, J; Piatscheck, F; Puchulutegui, Cecilia; Ramos, R; Ravest, G; Richner, Heinz; Robbens, J; Rochat, D; Rousselet, J; Saladin, Verena; Sauve, M; Schlei, Ora; Schultz, Thomas F; Scobie, A R; Segovia, N I; Seyoum, Seifu; Silvain, J-F; Tabone, Elisabeth; Van Houdt, J K J; Vandamme, S G; Volckaert, F A M; Wenburg, John; Willis, Theodore V; Won, Yong-Jin; Ye, N H; Zhang, W; Zhang, Y X

    2012-01-01

    This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra gotyla, Hippodamia convergens, Linnaea borealis, Menippe mercenaria, Menippe adina, Parus major, Pinus densiflora, Portunus trituberculatus, Procontarinia mangiferae, Rhynchophorus ferrugineus, Schizothorax richardsonii, Scophthalmus rhombus, Tetraponera aethiops, Thaumetopoea pityocampa, Tuta absoluta and Ugni molinae. These loci were cross-tested on the following species: Barilius bendelisis, Chiromantes haematocheir, Eriocheir sinensis, Eucalyptus camaldulensis, Eucalyptus cladocalix, Eucalyptus globulus, Garra litaninsis vishwanath, Garra para lissorhynchus, Guindilla trinervis, Hemigrapsus sanguineus, Luma chequen. Guayaba, Myrceugenia colchagüensis, Myrceugenia correifolia, Myrceugenia exsucca, Parasesarma plicatum, Parus major, Portunus pelagicus, Psidium guayaba, Schizothorax richardsonii, Scophthalmus maximus, Tetraponera latifrons, Thaumetopoea bonjeani, Thaumetopoea ispartensis, Thaumetopoea libanotica, Thaumetopoea pinivora, Thaumetopoea pityocampa ena clade, Thaumetopoea solitaria, Thaumetopoea wilkinsoni and Tor putitora. This article also documents the addition of nine EPIC primer pairs for Euphaea decorata, Euphaea formosa, Euphaea ornata and Euphaea yayeyamana.

  17. Clinical librarian support for rapid review of clinical utility of cancer molecular biomarkers.

    PubMed

    Geng, Yimin; Fowler, Clara S; Fulton, Stephanie

    2015-01-01

    The clinical librarian used a restricted literature searching and quality-filtering approach to provide relevant clinical evidence for the use of cancer molecular biomarkers by institutional policy makers and clinicians in the rapid review process. The librarian-provided evidence was compared with the cited references in the institutional molecular biomarker algorithm. The overall incorporation rate of the librarian-provided references into the algorithm was above 80%. This study suggests the usefulness of clinical librarian expertise for clinical practice. The searching and filtering methods for high-level evidence can be adopted by information professionals who are involved in the rapid literature review.

  18. The Role of Temporal Context and Expectancy in Resource Allocation to and Perception of Rapid Serial Events

    ERIC Educational Resources Information Center

    Kranczioch, Cornelia; Dhinakaran, Janani

    2013-01-01

    The perception of target events presented in a rapid stream of non-targets is impaired for early target positions, but then gradually improves, a phenomenon known as attentional awakening. This phenomenon has been associated with better resource allocation. It is unclear though whether improved resource allocation and attentional awakening are a…

  19. Pruning and Prioritising: A Case Study of a Pragmatic Method for Managing a Rapid Systematic Review with Limited Resources

    ERIC Educational Resources Information Center

    Harnan, Sue Elizabeth; Cooper, Katy; Jones, Sarah Lynne; Jones, Elaine

    2015-01-01

    Full systematic reviews are time and resource heavy. We describe a method successfully used to produce a rapid review of yoga for health and wellbeing, with limited resources, using mapping methods. Inclusion and exclusion criteria were developed a priori and refined "post hoc," with the review team blind to the study results to minimise…

  20. The Role of Temporal Context and Expectancy in Resource Allocation to and Perception of Rapid Serial Events

    ERIC Educational Resources Information Center

    Kranczioch, Cornelia; Dhinakaran, Janani

    2013-01-01

    The perception of target events presented in a rapid stream of non-targets is impaired for early target positions, but then gradually improves, a phenomenon known as attentional awakening. This phenomenon has been associated with better resource allocation. It is unclear though whether improved resource allocation and attentional awakening are a…

  1. Perspective: Rapid synthesis of complex oxides by combinatorial molecular beam epitaxy

    SciTech Connect

    A. T. Bollinger; Wu, J.; Bozovic, I.

    2016-03-15

    In this study, the molecular beam epitaxy(MBE) technique is well known for producing atomically smooth thin films as well as impeccable interfaces in multilayers of many different materials. In particular, molecular beam epitaxy is well suited to the growth of complex oxides, materials that hold promise for many applications. Rapid synthesis and high throughput characterization techniques are needed to tap into that potential most efficiently. We discuss our approach to doing that, leaving behind the traditional one-growth-one-compound scheme and instead implementing combinatorial oxide molecular beam epitaxy in a custom built system.

  2. Perspective: Rapid synthesis of complex oxides by combinatorial molecular beam epitaxy

    DOE PAGES

    A. T. Bollinger; Wu, J.; Bozovic, I.

    2016-03-15

    In this study, the molecular beam epitaxy(MBE) technique is well known for producing atomically smooth thin films as well as impeccable interfaces in multilayers of many different materials. In particular, molecular beam epitaxy is well suited to the growth of complex oxides, materials that hold promise for many applications. Rapid synthesis and high throughput characterization techniques are needed to tap into that potential most efficiently. We discuss our approach to doing that, leaving behind the traditional one-growth-one-compound scheme and instead implementing combinatorial oxide molecular beam epitaxy in a custom built system.

  3. African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

    PubMed Central

    Mwai, Okeyo; Hanotte, Olivier; Kwon, Young-Jun; Cho, Seoae

    2015-01-01

    At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers. PMID:26104394

  4. Rapid warming in Tibet, China: public perception, response and coping resources in urban Lhasa

    PubMed Central

    2013-01-01

    Background Tibet, average altitude more than 4,000 meters, is warming faster than anywhere else in China. The increase in temperatures may aggravate existing health problems and lead to the emergence of new risks. However, there are no actions being taken at present to protect population health due to limited understanding about the range and magnitude of health effects of climate change. Methods The study was a cross-sectional survey of 619 respondents from urban Lhasa, Tibet in August 2012 with the aim to investigate public perceptions of risk, heat experiences, and coping resources. Results Respondents are aware of the warming that has occurred in Lhasa in recent years. Over 78% reported that rising temperature is either a “very” or “somewhat” serious threat to their own health, and nearly 40% reported they had experienced heat-related symptoms. Sex, age, education and income influenced perceived risks, health status, and heat experience. The vast majority of respondents reported that they had altered their behaviour on hot summer days. Bakuo, a sub-district at the city center, is considered especially vulnerable to heat because of sparse vegetation, high population density, poor dwelling conditions and a high proportion of low-income population. However, neighborhood social ties were stronger in Bakuo than other study locations. Conclusions The study suggests that actions are needed now to minimize downside effects of rapid warming in Tibet, because of increasing human exposure to high temperatures and uneven distribution of the resources needed to cope. PMID:24103412

  5. Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes

    PubMed Central

    Moskalev, Alexey; Zhikrivetskaya, Svetlana; Shaposhnikov, Mikhail; Dobrovolskaya, Evgenia; Gurinovich, Roman; Kuryan, Oleg; Pashuk, Aleksandr; Jellen, Leslie C.; Aliper, Alex; Peregudov, Alex; Zhavoronkov, Alex

    2016-01-01

    Aging research is a multi-disciplinary field encompassing knowledge from many areas of basic, applied and clinical research. Age-related processes occur on molecular, cellular, tissue, organ, system, organismal and even psychological levels, trigger the onset of multiple debilitating diseases and lead to a loss of function, and there is a need for a unified knowledge repository designed to track, analyze and visualize the cause and effect relationships and interactions between the many elements and processes on all levels. Aging Chart (http://agingchart.org/) is a new, community-curated collection of aging pathways and knowledge that provides a platform for rapid exploratory analysis. Building on an initial content base constructed by a team of experts from peer-reviewed literature, users can integrate new data into biological pathway diagrams for a visible, intuitive, top-down framework of aging processes that fosters knowledge-building and collaboration. As the body of knowledge in aging research is rapidly increasing, an open visual encyclopedia of aging processes will be useful to both the new entrants and experts in the field. PMID:26602690

  6. The NIH-NIAID Schistosomiasis Resource Center at the Biomedical Research Institute: Molecular Redux

    PubMed Central

    Cody, James J.; Ittiprasert, Wannaporn; Miller, André N.; Henein, Lucie; Mentink-Kane, Margaret M.; Hsieh, Michael H.

    2016-01-01

    Schistosomiasis remains a health burden in many parts of the world. The complex life cycle of Schistosoma parasites and the economic and societal conditions present in endemic areas make the prospect of eradication unlikely in the foreseeable future. Continued and vigorous research efforts must therefore be directed at this disease, particularly since only a single World Health Organization (WHO)-approved drug is available for treatment. The National Institutes of Health (NIH)–National Institute of Allergy and Infectious Diseases (NIAID) Schistosomiasis Resource Center (SRC) at the Biomedical Research Institute provides investigators with the critical raw materials needed to carry out this important research. The SRC makes available, free of charge (including international shipping costs), not only infected host organisms but also a wide array of molecular reagents derived from all life stages of each of the three main human schistosome parasites. As the field of schistosomiasis research rapidly advances, it is likely to become increasingly reliant on omics, transgenics, epigenetics, and microbiome-related research approaches. The SRC has and will continue to monitor and contribute to advances in the field in order to support these research efforts with an expanding array of molecular reagents. In addition to providing investigators with source materials, the SRC has expanded its educational mission by offering a molecular techniques training course and has recently organized an international schistosomiasis-focused meeting. This review provides an overview of the materials and services that are available at the SRC for schistosomiasis researchers, with a focus on updates that have occurred since the original overview in 2008. PMID:27764112

  7. Expansion of the USDA-ARS Germplasm Resources Information Network (GRIN) database to accommodate molecular data

    USDA-ARS?s Scientific Manuscript database

    The USDA-ARS National Plant Germplasm System (NPGS) provides both germplasm and data on genetic resources to researchers and breeders world wide. New tables and codes that hold data relating to molecular markers and multi-locus genotypes have been added to the Germplasm Resources Information Networ...

  8. Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

    PubMed

    Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

    2014-07-15

    Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Rapid multiplexed molecular phenotyping of ex vivo and in vivo tissues with targeted SERS NPs

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Khan, Altaz; Som, Madhura; Leigh, Steven Y.; Wang, Danni; Chen, Ye; McVeigh, Patrick; Wilson, Brian C.; Liu, Jonathan T. C.

    2014-05-01

    We are developing a miniature fiber-optic spectral-detection device and topical-staining protocol to rapidly detect multiplexed surface-enhanced Raman scattering (SERS) nanoparticles (NPs) targeted to cell-surface biomarkers in fresh tissues. Ex vivo and in vivo experiments were performed to optimize our strategy for the rapid detection of multiple cell-surface biomarkers following a brief (5 min) topical application of SERS NPs on tissues. The simultaneous detection and ratiometric quantification of targeted and nontargeted NPs allows for an unambiguous assessment of molecular expression that is insensitive to nonspecific variations in NP concentrations, potentially enabling point-of-care surgical guidance or early disease detection.

  10. Ensuring the quality of HIV rapid testing in resource-poor countries using a systematic approach to training.

    PubMed

    Yao, Katy; Wafula, Winnie; Bile, Ebi Celestin; Cheignsong, Rachanee; Howard, Stacy; Demby, Austin; Nkengasong, John

    2010-10-01

    HIV rapid testing is a key tool in the fight against the HIV/AIDS epidemic; it enables the rapid expansion of prevention and treatment programs in resource-limited countries. Meeting the goals of these programs means that millions of people will need testing annually. Accuracy and reliability of these tests are critical to the success of these programs. Given the enormous number of rapid tests that are performed each year, even a low error rate of 0.5% applied to 100 million people will result in 500,000 erroneous results. Ensuring the quality of HIV rapid testing presents unique challenges in that testing is often performed in various settings by personnel without formal laboratory training. This article describes the development and implementation of a generic HIV rapid test training package using a systems approach in an effort to standardize training and ensure the quality of rapid tests. It also highlights achievements from Uganda, Haiti, and Botswana.

  11. Improving Pediatric Rapid Response Team Performance Through Crew Resource Management Training of Team Leaders.

    PubMed

    Siems, Ashley; Cartron, Alexander; Watson, Anne; McCarter, Robert; Levin, Amanda

    2017-02-01

    Rapid response teams (RRTs) improve the detection of and response to deteriorating patients. Professional hierarchies and the multidisciplinary nature of RRTs hinder team performance. This study assessed whether an intervention involving crew resource management training of team leaders could improve team performance. In situ observations of RRT activations were performed pre- and post-training intervention. Team performance and dynamics were measured by observed adherence to an ideal task list and by the Team Emergency Assessment Measure tool, respectively. Multiple quartile (median) and logistic regression models were developed to evaluate change in performance scores or completion of specific tasks. Team leader and team introductions (40% to 90%, P = .004; 7% to 45%, P = .03), floor team presentations in Situation Background Assessment Recommendation format (20% to 65%, P = .01), and confirmation of the plan (7% to 70%, P = .002) improved after training in patients transferred to the ICU (n = 35). The Team Emergency Assessment Measure metric was improved in all 4 categories: leadership (2.5 to 3.5, P < .001), teamwork (2.7 to 3.7, P < .001), task management (2.9 to 3.8, P < .001), and global scores (6.0 to 9.0, P < .001) for teams caring for patients who required transfer to the ICU. Targeted crew resource management training of the team leader resulted in improved team performance and dynamics for patients requiring transfer to the ICU. The intervention demonstrated that training the team leader improved behavior in RRT members who were not trained. Copyright © 2017 by the American Academy of Pediatrics.

  12. The rapid distraction of attentional resources toward the source of incongruent stimulus input during multisensory conflict

    PubMed Central

    Donohue, Sarah E.; Todisco, Alexandra E.; Woldorff, Marty G.

    2013-01-01

    Neuroimaging work on multisensory conflict suggests that the relevant modality receives enhanced processing in the face of incongruency. However, the degree of stimulus processing in the irrelevant modality and the temporal cascade of the attentional modulations in either the relevant or irrelevant modalities are unknown. Here, we employed an audiovisual conflict paradigm with a sensory probe in the task-irrelevant modality (vision) to gauge the attentional allocation to that modality. Event-related potentials (ERPs) were recorded as subjects attended to and discriminated spoken auditory letters while ignoring simultaneous bilateral visual letter stimuli that were either fully congruent, fully incongruent, or partially incongruent (one side incongruent, one congruent) with the auditory stimulation. Half of the audiovisual letter stimuli were followed 500-700 ms later by a bilateral visual probe stimulus. As expected, ERPs to the audiovisual stimuli showed an incongruency ERP effect (fully incongruent versus fully congruent) of an enhanced, centrally distributed, negative-polarity wave starting ~250 ms. More critically here, the sensory ERP components to the visual probes were larger when they followed fully incongruent versus fully congruent multisensory stimuli, with these enhancements greatest on fully incongruent trials with the slowest response times. In addition, on the slowest-response partially incongruent trials, the P2 sensory component to the visual probes was larger contralateral to the preceding incongruent visual stimulus. These data suggest that, in response to conflicting multisensory stimulus input, the initial cognitive effect is a capture of attention by the incongruent irrelevant-modality input, pulling neural processing resources toward that modality, resulting in rapid enhancement, rather than rapid suppression, of that input. PMID:23249355

  13. Multiple scavengers respond rapidly to pulsed carrion resources at the land-ocean interface

    NASA Astrophysics Data System (ADS)

    Schlacher, Thomas A.; Strydom, Simone; Connolly, Rod M.

    2013-04-01

    Sandy beaches are the globe's longest interface region between the oceans and the continents, forming highly permeable boundaries across which matter flows readily. Stranded marine carrion supplies a high-quality food source to scavengers, but the role of animal carcasses is generally under-reported in sandy-beach food webs. We examined the response of scavengers to pulsed subsidies in the form of experimental additions of fish carcasses to the dune-beach interface in eastern Australia. Ghost crabs (Ocypode spp.) are the dominant invertebrate scavengers in these habitats and they responded strongly and consistently to changed resource availability: densities increased significantly within days of carrion augmentations. Carcasses added experimentally also formed local nuclei for a diversity of vertebrate scavengers that aggregated at food falls; these included large lizards, several species of birds (including raptors), and foxes. Consumption of fish carrion by the vertebrate scavengers was rapid and often complete. There is also evidence for higher-order interactions, where responses of invertebrate scavengers became depressed in plots where vertebrate scavenger activity was intense. Our findings emphasize that carrion can be a pivotal component of beach food webs.

  14. Rapid identification of Candida dubliniensis using a species-specific molecular beacon.

    PubMed

    Park, S; Wong, M; Marras, S A; Cross, E W; Kiehn, T E; Chaturvedi, V; Tyagi, S; Perlin, D S

    2000-08-01

    Candida dubliniensis is an opportunistic fungal pathogen that has been linked to oral candidiasis in AIDS patients, although it has recently been isolated from other body sites. DNA sequence analysis of the internal transcribed spacer 2 (ITS2) region of rRNA genes from reference Candida strains was used to develop molecular beacon probes for rapid, high-fidelity identification of C. dubliniensis as well as C. albicans. Molecular beacons are small nucleic acid hairpin probes that brightly fluoresce when they are bound to their targets and have a significant advantage over conventional nucleic acid probes because they exhibit a higher degree of specificity with better signal-to-noise ratios. When applied to an unknown collection of 23 strains that largely contained C. albicans and a smaller amount of C. dubliniensis, the species-specific probes were 100% accurate in identifying both species following PCR amplification of the ITS2 region. The results obtained with the molecular beacons were independently verified by random amplified polymorphic DNA analysis-based genotyping and by restriction enzyme analysis with enzymes BsmAI and NspBII, which cleave recognition sequences within the ITS2 regions of C. dubliniensis and C. albicans, respectively. Molecular beacons are promising new probes for the rapid detection of Candida species.

  15. Investigating molecular structures: Rapidly examining molecular fingerprints through fast passage broadband fourier transform microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Grubbs, Garry Smith Smitty, II

    Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation off, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 mus) than the molecular relaxation (≈100 mus). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and

  16. Quantum state specific reactant preparation in a molecular beam by rapid adiabatic passage

    NASA Astrophysics Data System (ADS)

    Chadwick, Helen; Hundt, P. Morten; van Reijzen, Maarten E.; Yoder, Bruce L.; Beck, Rainer D.

    2014-01-01

    Highly efficient preparation of molecules in a specific rovibrationally excited state for gas/surface reactivity measurements is achieved in a molecular beam using tunable infrared (IR) radiation from a single mode continuous wave optical parametric oscillator (cw-OPO). We demonstrate that with appropriate focusing of the IR radiation, molecules in the molecular beam crossing the fixed frequency IR field experience a Doppler tuning that can be adjusted to achieve complete population inversion of a two-level system by rapid adiabatic passage (RAP). A room temperature pyroelectric detector is used to monitor the excited fraction in the molecular beam and the population inversion is detected and quantified using IR bleaching by a second IR-OPO. The second OPO is also used for complete population transfer to an overtone or combination vibration via double resonance excitation using two spatially separated RAP processes.

  17. Quantum state specific reactant preparation in a molecular beam by rapid adiabatic passage

    SciTech Connect

    Chadwick, Helen Hundt, P. Morten; Reijzen, Maarten E. van; Yoder, Bruce L.; Beck, Rainer D.

    2014-01-21

    Highly efficient preparation of molecules in a specific rovibrationally excited state for gas/surface reactivity measurements is achieved in a molecular beam using tunable infrared (IR) radiation from a single mode continuous wave optical parametric oscillator (cw-OPO). We demonstrate that with appropriate focusing of the IR radiation, molecules in the molecular beam crossing the fixed frequency IR field experience a Doppler tuning that can be adjusted to achieve complete population inversion of a two-level system by rapid adiabatic passage (RAP). A room temperature pyroelectric detector is used to monitor the excited fraction in the molecular beam and the population inversion is detected and quantified using IR bleaching by a second IR-OPO. The second OPO is also used for complete population transfer to an overtone or combination vibration via double resonance excitation using two spatially separated RAP processes.

  18. Rapid analysis of acylglycerols in low molecular weight milk fat fractions.

    PubMed

    Craven, R J; Lencki, R W

    2007-05-01

    A suitable analytical method was required to facilitate development of an industrial-scale short-path distillation (SPD) process. Short-path distillation produces milk fat distillates (MFD) enriched in low molecular weight milk fat components-viz. free fatty acids, monoacylglycerols, diacylglycerols, cholesterol and low molecular weight triacylglycerols. In this case, solid-phase extraction (SPE) was considered a better alternative than thin-layer chromatography for separating polar and apolar lipid components in MFD samples due to its speed and near-complete recoveries. Solid-phase extraction of MFDs yielded two fractions, both of which are sufficiently pure for subsequent analysis by gas chromatography. This procedure provided rapid and complete chemical characterization (including mass balances) of low-molecular weight milk-fat fractions.

  19. Molecular imprinted photonic crystal hydrogels for the rapid and label-free detection of imidacloprid.

    PubMed

    Wang, Xuan; Mu, Zhongde; Liu, Ran; Pu, Yuepu; Yin, Lihong

    2013-12-15

    A novel sensor for the rapid and label-free detection of imidacloprid was developed based on the combination of a colloidal crystal templating method and a molecular imprinting technique. The molecular imprinted photonic hydrogel film was prepared with methacrylic acid as monomers, ethylene glycol dimethylacrylate as cross-linkers and imidacloprid as imprinting template molecules. When the colloidal crystal template and the molecularly imprinted template was removed, the resulted MIPH film possessed a highly ordered three-dimensional macroporous structure with nanocavities. The response of the MIPH film to imidacloprid in aqueous solution can be detected through a readable Bragg diffraction red shift. When the concentration of imidacloprid increased from 10(-13) to 10(-7) g/mL, the Bragg diffraction peak shifted from 551 to 589 nm, while there were no obvious peak shifts for thiamethoxam and acetamiprid. This sensor which comprises of no label techniques and expensive instruments has potential application for the detection of trace imidacloprid.

  20. Acanthamoeba keratitis: improving the Scottish diagnostic service for the rapid molecular detection of Acanthamoeba species.

    PubMed

    Alexander, Claire Low; Coyne, Michael; Jones, Brian; Anijeet, Deepa

    2015-07-01

    Acanthamoeba species are responsible for causing the potentially sight-threatening condition, Acanthamoeba keratitis, which is commonly associated with contact lens use. In this report, we highlight the challenges faced using conventional laboratory identification methods to identify this often under-reported pathogen, and discuss the reasons for introducing the first national service in Scotland for the rapid and sensitive molecular identification of Acanthamoeba species. By comparing culture and molecular testing data from a total of 63 patients (n = 80 samples) throughout Scotland presenting with ocular eye disease, we describe the improvement in detection rates where an additional four positive cases were identified using a molecular assay versus culture. The testing of a further ten patients by confocal imaging is also presented. This report emphasizes the importance of continuing to improve clinical laboratory services to ensure a prompt, correct diagnosis and better prognosis, in addition to raising awareness of this potentially debilitating opportunistic pathogen.

  1. CBMAR: a comprehensive β-lactamase molecular annotation resource

    PubMed Central

    Srivastava, Abhishikha; Singhal, Neelja; Goel, Manisha; Virdi, Jugsharan Singh; Kumar, Manish

    2014-01-01

    β-Lactam antibiotics are among the most widely used antibiotics against microbial pathogens. However, enzymatic hydrolysis of these antibiotics by bacterial β-lactamases is increasingly compromising their efficiency. Although new generation β-lactam antibiotics have been developed to combat antibiotic resistance, β-lactamases have also evolved along with the new variants of the substrate. A strong selection pressure from the newer generation of β-lactam antibiotics has resulted in evolution of different families within each class of β-lactamase. To facilitate detailed characterization of different families of β-lactamases, we have created a database, CBMAR, which facilitates comprehensive molecular annotation and discovery of novel β-lactamases. As against the limited scope of other existing similar databases, CBMAR provides information useful for molecular and biochemical characterization of each family of β-lactamase. The basic architecture of CBMAR is based on Ambler classification, which divides β-lactamases as serine (Classes A, C and D) and metallo-β-lactamases (Class B). Each class is further divided into several families on the basis of their hydrolytic character. In CBMAR, each family is annotated with (i) sequence variability, (ii) antibiotic resistance profile, (iii) inhibitor susceptibility, (iv) active site, (v) family fingerprints, (vi) mutational profile, (vii) variants, (viii) gene location, (ix) phylogenetic tree and several other features. Each entry also has external links to the relevant protein/nucleotide sequence and structure databases. The database also supports sequence similarity searches using BLAST and assigns a new β-lactamase protein to its respective family on the basis of family-specific fingerprint. Database URL: http://14.139.227.92/mkumar/lactamasedb PMID:25475113

  2. Molecularly imprinted photonic hydrogels as colorimetric sensors for rapid and label-free detection of vanillin.

    PubMed

    Peng, Hailong; Wang, Shenqi; Zhang, Zhong; Xiong, Hua; Li, Jinhua; Chen, Lingxin; Li, Yanbin

    2012-02-29

    A novel colorimetric sensor for the rapid and label-free detection of vanillin, based on the combination of photonic crystal and molecular imprinting technique, was developed. The sensing platform of molecularly imprinted photonic hydrogel (MIPH) was prepared by a noncovalent and self-assembly approach using vanillin as a template molecule. Morphology characterization by scanning electron microscope (SEM) showed that the MIPH possessed a highly ordered three-dimensional (3D) macroporous structure with nanocavities. The vanillin recognition events of the created nonocavities could be directly transferred into readable optical signals through a change in Bragg diffraction of the ordered macropores array of MIPH. The Bragg diffraction peak shifted from 451 to 486 nm when the concentration of the vanillin was increased from 10⁻¹² to 10⁻³ mol L⁻¹ within 60 s, whereas there were no obvious peak shifts for methyl and ethyl vanillin, indicating that the MIPH had high selectivity and rapid response for vanillin. The adsorption results showed that the hierarchical porous structure and homogeneous layers were formed in the MIPH with higher adsorption capacity. The application of such a label-free sensor with high selectivity, high sensitivity, high stability, and easy operation might offer a potential method for rapid real-time detection of trace vanillin.

  3. Competition for Cognitive Resources During Rapid Serial Processing: Changes Across Childhood

    PubMed Central

    Heim, Sabine; Wirth, Nadine; Keil, Andreas

    2011-01-01

    The ability to direct cognitive resources to target objects despite distraction by competing information plays an important role for the development of mental aptitudes and skills. We examined developmental changes of this ability in a cross-sectional design, using the “attentional blink” (AB) paradigm. The AB is a pronounced impairment of T2 report, which occurs when a first (T1) and second target (T2) embedded in a rapid stimulus sequence are separated by at least one distractor and occur within 500 ms of each other. Two groups of children (6- to 7-year-olds and 10- to 11-year-olds; ns = 21 and 24, respectively) were asked to identify green targets in two AB tasks: one using non-linguistic symbols and the other letters or words. The temporal distance or stimulus-onset asynchrony (SOA) between T1 and T2 varied between no intervening distractor (Lag 1, 116-ms SOA) and up to 7 intervening distractors (Lag 8, 928-ms SOA). In the symbol task, younger children linearly increased T2 identification with increasing lag. Older children, however, displayed a hook-shaped pattern as typically seen in adults, with lowest identification reports in T2 symbols at the critical blink interval (Lag 2, 232-ms SOA), and a slight performance gain for the Lag 1 condition. In the verbal task, the older group again exhibited a prominent drop in T2 identification at Lag 2, whereas the younger group showed a more alleviated and temporally diffuse AB impairment. Taken together, this pattern of results suggests that the control of attention allocation and/or working memory consolidation of targets among distractors represents a cognitive skill that emerges during primary school age. PMID:21713183

  4. The SUCCESS model for laboratory performance and execution of rapid molecular diagnostics in patients with sepsis.

    PubMed

    Dekmezian, Mhair; Beal, Stacy G; Damashek, Mary Jane; Benavides, Raul; Dhiman, Neelam

    2015-04-01

    Successful performance and execution of rapid diagnostics in a clinical laboratory hinges heavily on careful validation, accurate and timely communication of results, and real-time quality monitoring. Laboratories must develop strategies to integrate diagnostics with stewardship and evidence-based clinical practice guidelines. We present a collaborative SUCCESS model for execution and monitoring of rapid sepsis diagnostics to facilitate timely treatment. Six months after execution of the Verigene Gram-Positive Blood Culture (BC-GP) and the AdvanDx PNA-FISH assays, data were collected on 579 and 28 episodes of bacteremia and fungemia, respectively. Clinical testing was executed using a SUCCESS model comprising the following components: stewardship, utilization of resources, core strategies, concierge services, education, support, and surveillance. Stewardship needs were identified by evaluating the specialty services benefiting from new testing. Utilization of resources was optimized by reviewing current treatment strategies and antibiogram and formulary options. Core strategies consisted of input from infectious disease leadership, pharmacy, and laboratory staff. Concierge services included automated Micro-eUpdate and physician-friendly actionable reports. Education modules were user-specific, and support was provided through a dedicated 24/7 microbiology hotline. Surveillance was performed by daily audit by the director. Using the SUCCESS model, the turnaround time for the detailed report with actionable guidelines to the physician was ∼3 hours from the time of culture positivity. The overall correlation between rapid methods and culture was 94% (546/579). Discrepant results were predominantly contaminants such as a coagulase-negative staphylococci or viridans streptococci in mixed cultures. SUCCESS is a cost-effective and easily adaptable model for clinical laboratories with limited stewardship resources.

  5. Simulating the Formation of Molecular Clouds. II. Rapid Formation from Turbulent Initial Conditions

    NASA Astrophysics Data System (ADS)

    Glover, Simon C. O.; Mac Low, Mordecai-Mark

    2007-04-01

    In this paper we present results from a large set of numerical simulations that demonstrate that H2 formation occurs rapidly in turbulent gas. Starting with purely atomic hydrogen, large quantities of molecular hydrogen can be produced on timescales of 1-2 Myr, given turbulent velocity dispersions and magnetic field strengths consistent with observations. Moreover, as our simulations underestimate the effectiveness of H2 self-shielding and dust absorption, we can be confident that the molecular fractions that we compute are strong lower limits on the true values. The formation of large quantities of molecular gas on the timescale required by rapid cloud formation models therefore appears to be entirely plausible. We also investigate the density and temperature distributions of gas in our model clouds. We show that the density probability distribution function is approximately lognormal, with a dispersion that agrees well with the prediction of Padoan and coworkers. The temperature distribution is similar to that of a polytrope, with an effective polytropic index γeff~=0.8, although at low gas densities, the scatter of the actual gas temperature around this mean value is considerable, and the polytropic approximation does not capture the full range of behavior of the gas.

  6. Molecular diversity analysis of eggplant (Solanum melongena) genetic resources.

    PubMed

    Ali, Z; Xu, Z L; Zhang, D Y; He, X L; Bahadur, S; Yi, J X

    2011-06-14

    Eggplant (Solanum melongena), a vegetable that is cultivated worldwide, is of considerable importance to agriculture in China. We analyzed the diversity of this plant using inter-simple sequence repeat (ISSR) and RAPD procedures to subdivide 143 Chinese-cultivated eggplants based on coefficient of parentage, genetic diversity index (GDI) and canonical discriminant analysis. ISSR markers were more effective than RAPD markers for detecting genetic diversity, which ranged from 0.10-0.51, slightly lower than what is known from other crops. Our ISSR/RAPD data provide molecular evidence that coincides with morphological-based classification into three varieties and further subdivision into eight groups, except for two groups. Intensive use of elite parents and extensive crossing within groups have resulted in increased coefficient of parentage and proportional contribution but decreased GDI during the past decades. The mean coefficient of parentage and proportional contribution increased from 0.05 to 0.10% and from 3.22 to 6.46% during 1980-1991 and 1992-2003, respectively. The GDI of landraces was 0.21, higher than the 0.09 and 0.08 calculated for the hybrid cultivars released during the two periods. The recent introduction of alien genotypes into eggplant breeding programs may broaden the genetic base.

  7. Tuberculosis drug resistance testing by molecular methods: opportunities and challenges in resource limited settings.

    PubMed

    Abebe, Gemeda; Paasch, Fabienne; Apers, Ludwig; Rigouts, Leen; Colebunders, Robert

    2011-02-01

    One of the greatest threats to global tuberculosis (TB) control is the growing prevalence of drug-resistant bacilli. Correctly diagnosing drug-resistant TB patients is more problematic in resource-limited settings as there is no or limited infrastructure for drug susceptibility testing (DST) of TB bacilli. The conventional phenotypic DST method for TB takes weeks before declaring the results and initiating proper anti-TB treatment. Molecular DST offers advantages over the phenotypic methods mainly because of the short turnaround time. This review summarizes the different molecular DST methods for TB and discusses challenges and opportunities in implementing them in resource-limited settings.

  8. Development of a novel, simple and rapid molecular identification system for clinical Candida species.

    PubMed

    Deák, R; Bodai, L; Aarts, H J M; Maráz, A

    2004-08-01

    Identification of clinical yeast isolates causing candidiasis is routinely performed by commercial yeast identification systems based on biochemical, morphological and physiological tests. These systems require 3-5 days and the proportion of identifications that are incorrect is high. Our novel and rapid molecular identification system for clinical Candida species is based on the analysis of restriction patterns obtained from PCR-generated ribosomal DNA sequences using five restriction enzymes. A software package (CandID) was designed to include a database of restriction fragment length polymorphism (RFLP) patterns for 29 Candida species. For 'in-house' validation, 122 clinical isolates that had previously identified in clinical laboratories were typed by this system. These clinical isolates were also independently re-identified by the API 20C AUX system. The ribosomal DNA RFLP database in the context of supporting analytical software allowed simple and rapid (1 work day) identification.

  9. Molecular and Cellular Mechanisms of Rapid-Acting Antidepressants Ketamine and Scopolamine

    PubMed Central

    Wohleb, Eric S.; Gerhard, Danielle; Thomas, Alex; Duman, Ronald S.

    2017-01-01

    Major depressive disorder (MDD) is a prevalent neuropsychiatric disease that causes profound social and economic burdens. The impact of MDD is compounded by the limited therapeutic efficacy and delay of weeks to months of currently available medications. These issues highlight the need for more efficacious and faster-acting treatments to alleviate the burdens of MDD. Recent breakthroughs demonstrate that certain drugs, including ketamine and scopolamine, produce rapid and long-lasting antidepressant effects in MDD patients. Moreover, preclinical work has shown that the antidepressant actions of ketamine and scopolamine in rodent models are caused by an increase of extracellular glutamate, elevated BDNF, activation of the mammalian target of rapamycin complex 1 (mTORC1) cascade, and increased number and function of spine synapses in the prefrontal cortex (PFC). Here we review studies showing that both ketamine and scopolamine elicit rapid antidepressant effects through converging molecular and cellular mechanisms in the PFC. In addition, we discuss evidence that selective antagonists of NMDA and muscarinic acetylcholine (mACh) receptor subtypes (i.e., NR2B and M1-AChR) in the PFC produce comparable antidepressant responses. Furthermore, we discuss evidence that ketamine and scopolamine antagonize inhibitory interneurons in the PFC leading to disinhibition of pyramidal neurons and increased extracellular glutamate that promotes the rapid antidepressant responses to these agents. Collectively, these studies indicate that specific NMDA and mACh receptor subtypes on GABAergic interneurons are promising targets for novel rapid-acting antidepressant therapies. PMID:26955968

  10. Molecular and Cellular Mechanisms of Rapid-Acting Antidepressants Ketamine and Scopolamine.

    PubMed

    Wohleb, Eric S; Gerhard, Danielle; Thomas, Alex; Duman, Ronald S

    2017-01-01

    Major depressive disorder (MDD) is a prevalent neuropsychiatric disease that causes profound social and economic burdens. The impact of MDD is compounded by the limited therapeutic efficacy and delay of weeks to months of currently available medications. These issues highlight the need for more efficacious and faster-acting treatments to alleviate the burdens of MDD. Recent breakthroughs demonstrate that certain drugs, including ketamine and scopolamine, produce rapid and long-lasting antidepressant effects in MDD patients. Moreover, preclinical work has shown that the antidepressant actions of ketamine and scopolamine in rodent models are caused by an increase of extracellular glutamate, elevated BDNF, activation of the mammalian target of rapamycin complex 1 (mTORC1) cascade, and increased number and function of spine synapses in the prefrontal cortex (PFC). Here we review studies showing that both ketamine and scopolamine elicit rapid antidepressant effects through converging molecular and cellular mechanisms in the PFC. In addition, we discuss evidence that selective antagonists of NMDA and muscarinic acetylcholine (mACh) receptor subtypes (i.e., NR2B and M1-AChR) in the PFC produce comparable antidepressant responses. Furthermore, we discuss evidence that ketamine and scopolamine antagonize inhibitory interneurons in the PFC leading to disinhibition of pyramidal neurons and increased extracellular glutamate that promotes the rapid antidepressant responses to these agents. Collectively, these studies indicate that specific NMDA and mACh receptor subtypes on GABAergic interneurons are promising targets for novel rapid-acting antidepressant therapies.

  11. Molecular-orientation-induced rapid roughening and morphology transition in organic semiconductor thin-film growth.

    PubMed

    Yang, Junliang; Yim, Sanggyu; Jones, Tim S

    2015-03-24

    We study the roughening process and morphology transition of organic semiconductor thin film induced by molecular orientation in the model of molecular semiconductor copper hexadecafluorophthalocyanine (F16CuPc) using both experiment and simulation. The growth behaviour of F16CuPc thin film with the thickness, D, on SiO2 substrate takes on two processes divided by a critical thickness: (1) D ≤ 40 nm, F16CuPc thin films are composed of uniform caterpillar-like crystals. The kinetic roughening is confirmed during this growth, which is successfully analyzed by Kardar-Parisi-Zhang (KPZ) model with scaling exponents α = 0.71 ± 0.12, β = 0.36 ± 0.03, and 1/z = 0.39 ± 0.12; (2) D > 40 nm, nanobelt crystals are formed gradually on the caterpillar-like crystal surface and the film growth shows anomalous growth behaviour. These new growth behaviours with two processes result from the gradual change of molecular orientation and the formation of grain boundaries, which conversely induce new molecular orientation, rapid roughening process, and the formation of nanobelt crystals.

  12. Molecular-Orientation-Induced Rapid Roughening and Morphology Transition in Organic Semiconductor Thin-Film Growth

    PubMed Central

    Yang, Junliang; Yim, Sanggyu; Jones, Tim S.

    2015-01-01

    We study the roughening process and morphology transition of organic semiconductor thin film induced by molecular orientation in the model of molecular semiconductor copper hexadecafluorophthalocyanine (F16CuPc) using both experiment and simulation. The growth behaviour of F16CuPc thin film with the thickness, D, on SiO2 substrate takes on two processes divided by a critical thickness: (1) D ≤ 40 nm, F16CuPc thin films are composed of uniform caterpillar-like crystals. The kinetic roughening is confirmed during this growth, which is successfully analyzed by Kardar-Parisi-Zhang (KPZ) model with scaling exponents α = 0.71 ± 0.12, β = 0.36 ± 0.03, and 1/z = 0.39 ± 0.12; (2) D > 40 nm, nanobelt crystals are formed gradually on the caterpillar-like crystal surface and the film growth shows anomalous growth behaviour. These new growth behaviours with two processes result from the gradual change of molecular orientation and the formation of grain boundaries, which conversely induce new molecular orientation, rapid roughening process, and the formation of nanobelt crystals. PMID:25801646

  13. Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010-31 March 2010.

    PubMed

    Aurelle, D; Baker, A J; Bottin, L; Brouat, C; Caccone, A; Chaix, A; Dhakal, P; Ding, Y; Duplantier, J M; Fiedler, W; Fietz, J; Fong, Y; Forcioli, D; Freitas, T R O; Gunnarsson, G H; Haddrath, O; Hadziabdic, D; Hauksdottir, S; Havill, N P; Heinrich, M; Heinz, T; Hjorleifsdottir, S; Hong, Y; Hreggvidsson, G O; Huchette, S; Hurst, J; Kane, M; Kane, N C; Kawakami, T; Ke, W; Keith, R A; Klauke, N; Klein, J L; Kun, J F J; Li, C; Li, G-Q; Li, J-J; Loiseau, A; Lu, L-Z; Lucas, M; Martins-Ferreira, C; Mokhtar-Jamaï, K; Olafsson, K; Pampoulie, C; Pan, L; Pooler, M R; Ren, J-D; Rinehart, T A; Roussel, V; Santos, M O; Schaefer, H M; Scheffler, B E; Schmidt, A; Segelbacher, G; Shen, J-D; Skirnisdottir, S; Sommer, S; Tao, Z-R; Taubert, R; Tian, Y; Tomiuk, J; Trigiano, R N; Ungerer, M C; Van Wormhoudt, A; Wadl, P A; Wang, D-Q; Weis-Dootz, T; Xia, Q; Yuan, Q-Y

    2010-07-01

    This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described). © 2010 Blackwell Publishing Ltd.

  14. Does Rapid and Sustained Economic Growth Lead to Convergence in Health Resources: The Case of China From 1980 to 2010.

    PubMed

    Liang, Di; Zhang, Donglan; Huang, Jiayan; Schweitzer, Stuart

    2016-01-01

    China's rapid and sustained economic growth offers an opportunity to ask whether the advantages of growth diffuse throughout an economy, or remain localized in areas where the growth has been the greatest. A critical policy area in China has been the health system, and health inequality has become an issue that has led the government to broaden national health insurance programs. This study investigates whether health system resources and performance have converged over the past 30 years across China's 31 provinces. To examine geographic variation of health system resources and performance at the provincial level, we measure the degree of sigma convergence and beta convergence in indicators of health system resources (structure), health services utilization (process), and outcome. All data are from officially published sources: the China Health Statistics Year Book and the China Statistics Year Book. Sigma convergence is found for resource indicators, whereas it is not observed for either process or outcome indicators, indicating that disparities only narrowed in health system resources. Beta convergence is found in most indicators, except for 2 procedure indicators, reflecting that provinces with poorer resources were catching up. Convergence found in this study probably reflects the mixed outcome of government input, and market forces. Thus, left alone, the equitable distribution of health care resources may not occur naturally during a period of economic growth. Governmental and societal efforts are needed to reduce geographic health variation and promote health equity. © The Author(s) 2016.

  15. Fabrication of Polymerase Chain Reaction Plastic Lab-on-a-Chip Device for Rapid Molecular Diagnoses.

    PubMed

    Trinh, Kieu The Loan; Zhang, Hainan; Kang, Dong-Jin; Kahng, Sung-Hyun; Tall, Ben D; Lee, Nae Yoon

    2016-05-01

    We aim to fabricate a thermoplastic poly(methylmethacrylate) (PMMA) Lab-on-a-Chip device to perform continuous- flow polymerase chain reactions (PCRs) for rapid molecular detection of foodborne pathogen bacteria. A miniaturized plastic device was fabricated by utilizing PMMA substrates mediated by poly(dimethylsiloxane) interfacial coating, enabling bonding under mild conditions, and thus avoiding the deformation or collapse of microchannels. Surface characterizations were carried out and bond strength was measured. The feasibility of the Lab-on-a-Chip device for performing on-chip PCR utilizing a lab-made, portable dual heater was evaluated. The results were compared with those obtained using a commercially available thermal cycler. A PMMA Lab-on-a-Chip device was designed and fabricated for conducting PCR using foodborne pathogens as sample targets. A robust bond was established between the PMMA substrates, which is essential for performing miniaturized PCR on plastic. The feasibility of on-chip PCR was evaluated using Escherichia coli O157:H7 and Cronobacter condimenti, two worldwide foodborne pathogens, and the target amplicons were successfully amplified within 25 minutes. In this study, we present a novel design of a low-cost and high-throughput thermoplastic PMMA Lab-on-a-Chip device for conducting microscale PCR, and we enable rapid molecular diagnoses of two important foodborne pathogens in minute resolution using this device. In this regard, the introduced highly portable system design has the potential to enable PCR investigations of many diseases quickly and accurately.

  16. Rapid characterization of lignocellulosic feedstocks for fuels and chemicals: Molecular beam mass spectrometric approach

    SciTech Connect

    Agblevor, F.A.; Davis, M.F.; Evans, R.J.

    1995-03-01

    Rapid characterization of biomass feedstocks has a pivotal role in the development of biomass energy because of the large number of samples that must be analyzed due to the diversity of biomass feedstocks and the significant differences in the chemical and physical properties of these feedstocks. Conventional chemical analysis of biomass feedstocks, although very useful, is time-consuming and not very practical for large scale screening experiments, hence the need for rapid characterization techniques. The molecular beam mass spectrometer and pyrolysis gas chromatography, which can analyze biomass pyrolysis vapors in real time, are unique tools for rapid qualitative and quantitative analyses of biomass feedstocks. Several biomass feedstocks (herbaceous, woody, and agricultural residues) were screened for the effects of storage, season of harvest, geographic location, clonal, and species variation on the pyrolysis products of the feedstocks. For herbaceous species such as sericea lespedeza, the season of harvest had a significant effect on the pyrolysis products. Effects of clonal variation on the composition of hybrid poplar feedstocks was easily discerned with the molecular beam mass spectrometric analysis. The effect of geographic location on the poplar clones pyrolysis products was minimal. However, in the case of switchgrass, varietal influence on the pyrolysis products was minimal, but where the plant was grown had a strong influence on the pyrolysis products of the feedstock. Significant differences because of species variation could also be shown from the pyrolysis products of various biomass feedstocks. The influence of storage time on biomass samples stored outside in the open could also be discerned from the pyrolysis products of the feedstocks. The differences noted in the pyrolysis products of the feedstocks were noted for samples which were significantly degraded during storage either through the action of microflora or weathering.

  17. Molecular genetics research in ADHD: ethical considerations concerning patients' benefit and resource allocation.

    PubMed

    Rothenberger, Lillian Geza

    2012-12-01

    Immense resource allocations have led to great data output in genetic research. Concerning ADHD resources spent on genetic research are less than those spent on clinical research. But there are successful efforts made to increase support for molecular genetics research in ADHD. Concerning genetics no evidence based conclusive results have significant impact on prevention, diagnosis or treatment yet. With regard to ethical aspects like the patients' benefit and limited resources the question arises if it is indicated to think about a new balance of resource allocation between molecular genetics and non-genetics research in ADHD. An ethical reflection was performed focusing on recent genetic studies and reviews based on a selective literature search. There are plausible reasons why genetic research results in ADHD are somehow disappointing for clinical practice so far. Researchers try to overcome these gaps systematically, without knowing what the potential future benefits for the patients might be. Non-genetic diagnostic/therapeutic research may lead to clinically relevant findings within a shorter period of time. On the other hand, non-genetic research in ADHD may be nurtured by genetic approaches. But, with the latter there exist significant risks of harm like stigmatization and concerns regarding data protection. Isolated speeding up resources of genetic research in ADHD seems questionable from an ethical point of view. There is a need to find a new balance of resource allocation between genetic and non-genetic research in ADHD, probably by integrating genetics more systematically into clinical research. A transdisciplinary debate is recommended.

  18. Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples.

    PubMed

    Northcott, Paul A; Shih, David J H; Remke, Marc; Cho, Yoon-Jae; Kool, Marcel; Hawkins, Cynthia; Eberhart, Charles G; Dubuc, Adrian; Guettouche, Toumy; Cardentey, Yoslayma; Bouffet, Eric; Pomeroy, Scott L; Marra, Marco; Malkin, David; Rutka, James T; Korshunov, Andrey; Pfister, Stefan; Taylor, Michael D

    2012-04-01

    The diagnosis of medulloblastoma likely encompasses several distinct entities, with recent evidence for the existence of at least four unique molecular subgroups that exhibit distinct genetic, transcriptional, demographic, and clinical features. Assignment of molecular subgroup through routine profiling of high-quality RNA on expression microarrays is likely impractical in the clinical setting. The planning and execution of medulloblastoma clinical trials that stratify by subgroup, or which are targeted to a specific subgroup requires technologies that can be economically, rapidly, reliably, and reproducibly applied to formalin-fixed paraffin embedded (FFPE) specimens. In the current study, we have developed an assay that accurately measures the expression level of 22 medulloblastoma subgroup-specific signature genes (CodeSet) using nanoString nCounter Technology. Comparison of the nanoString assay with Affymetrix expression array data on a training series of 101 medulloblastomas of known subgroup demonstrated a high concordance (Pearson correlation r = 0.86). The assay was validated on a second set of 130 non-overlapping medulloblastomas of known subgroup, correctly assigning 98% (127/130) of tumors to the appropriate subgroup. Reproducibility was demonstrated by repeating the assay in three independent laboratories in Canada, the United States, and Switzerland. Finally, the nanoString assay could confidently predict subgroup in 88% of recent FFPE cases, of which 100% had accurate subgroup assignment. We present an assay based on nanoString technology that is capable of rapidly, reliably, and reproducibly assigning clinical FFPE medulloblastoma samples to their molecular subgroup, and which is highly suited for future medulloblastoma clinical trials.

  19. Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

    PubMed

    Yang, Qing; Sun, Fanyue; Yang, Zhi; Li, Hongjun

    2014-01-01

    Calanus sinicus Brodsky (Copepoda, Crustacea) is a dominant zooplanktonic species widely distributed in the margin seas of the Northwest Pacific Ocean. In this study, we utilized an RNA-Seq-based approach to develop molecular resources for C. sinicus. Adult samples were sequenced using the Illumina HiSeq 2000 platform. The sequencing data generated 69,751 contigs from 58.9 million filtered reads. The assembled contigs had an average length of 928.8 bp. Gene annotation allowed the identification of 43,417 unigene hits against the NCBI database. Gene ontology (GO) and KEGG pathway mapping analysis revealed various functional genes related to diverse biological functions and processes. Transcripts potentially involved in stress response and lipid metabolism were identified among these genes. Furthermore, 4,871 microsatellites and 110,137 single nucleotide polymorphisms (SNPs) were identified in the C. sinicus transcriptome sequences. SNP validation by the melting temperature (T m )-shift method suggested that 16 primer pairs amplified target products and showed biallelic polymorphism among 30 individuals. The present work demonstrates the power of Illumina-based RNA-Seq for the rapid development of molecular resources in nonmodel species. The validated SNP set from our study is currently being utilized in an ongoing ecological analysis to support a future study of C. sinicus population genetics.

  20. Comprehensive Transcriptome Study to Develop Molecular Resources of the Copepod Calanus sinicus for Their Potential Ecological Applications

    PubMed Central

    Yang, Qing; Sun, Fanyue; Yang, Zhi; Li, Hongjun

    2014-01-01

    Calanus sinicus Brodsky (Copepoda, Crustacea) is a dominant zooplanktonic species widely distributed in the margin seas of the Northwest Pacific Ocean. In this study, we utilized an RNA-Seq-based approach to develop molecular resources for C. sinicus. Adult samples were sequenced using the Illumina HiSeq 2000 platform. The sequencing data generated 69,751 contigs from 58.9 million filtered reads. The assembled contigs had an average length of 928.8 bp. Gene annotation allowed the identification of 43,417 unigene hits against the NCBI database. Gene ontology (GO) and KEGG pathway mapping analysis revealed various functional genes related to diverse biological functions and processes. Transcripts potentially involved in stress response and lipid metabolism were identified among these genes. Furthermore, 4,871 microsatellites and 110,137 single nucleotide polymorphisms (SNPs) were identified in the C. sinicus transcriptome sequences. SNP validation by the melting temperature (T m)-shift method suggested that 16 primer pairs amplified target products and showed biallelic polymorphism among 30 individuals. The present work demonstrates the power of Illumina-based RNA-Seq for the rapid development of molecular resources in nonmodel species. The validated SNP set from our study is currently being utilized in an ongoing ecological analysis to support a future study of C. sinicus population genetics. PMID:24982883

  1. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    PubMed

    Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

    2016-06-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  2. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

    PubMed Central

    Waagmeester, Andra; Pico, Alexander R.

    2016-01-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

  3. An integrated microfluidic platform for rapid tumor cell isolation, counting and molecular diagnosis.

    PubMed

    Hung, Lien-Yu; Chuang, Ying-Hsin; Kuo, Hsin-Tzu; Wang, Chih-Hung; Hsu, Keng-Fu; Chou, Cheng-Yang; Lee, Gwo-Bin

    2013-04-01

    Ovarian cancer is the second most common of the gynecological cancers in Taiwan. It is challenging to diagnose at an early stage when proper treatment is the most effective. It is well recognized that the detection of tumor cells (TCs) is critical for determining cancer growth stages and may provide important information for accurate diagnosis and even prognosis. In this study, a new microfluidic platform integrated with a moving-wall micro-incubator, a micro flow cytometer and a molecular diagnosis module performed automated identification of ovarian cancer cells. By efficiently mixing the cells and immunomagnetic beads coated with specific antibodies, the target TCs were successfully isolated from the clinical samples. Then counting of the target cells was achieved by a combination of the micro flow cytometer and an optical detection module and showed a counting accuracy as high as 92.5 %. Finally, cancer-associated genes were amplified and detected by the downstream molecular diagnosis module. The fluorescence intensity of specific genes (CD24 and HE4) associated with ovarian cancer was amplified by the molecular diagnosis module and the results were comparable to traditional slab-gel electrophoresis analysis, with a limit of detection around 10 TCs. This integrated microfluidic platform realized the concept of a "lab-on-a-chip" and had advantages which included automation, disposability, lower cost and rapid diagnosis and, therefore, may provide a promising approach for the fast and accurate detection of cancer cells.

  4. Rapid molecular prenatal diagnosis of spondyloepiphyseal dysplasia congenita by PCR-SSP assay.

    PubMed

    Cui, Ying-Xia; Xia, Xin-Yi; Bu, Ying; Zhou, Guo-Hua; Yang, Bin; Lu, Hong-Yong; Shi, Yi-Chao; Pan, Lian-Jun; Huang, Yu-Feng; Li, Xiao-Jun

    2008-12-01

    Heterozygous mutations of COL2A1 gene are responsible for type II collagenopathies. The common skeletal phenotypes include achondrogenesis type II, hypochondrogenesis, Stickler dysplasia, Kniest dysplasia, late onset spondyloepiphyseal dysplasia, and spondyloepiphyseal dysplasia congenita (SEDC). Prevention of SEDC can be achieved by prenatal diagnosis. This study reports the first rapid molecular prenatal diagnosis of SEDC performed in China by polymerase chain reaction sequence-specific primer (PCR-SSP) analysis. The pregnant woman we previously reported with SEDC carried the G to A substitution at nucleotide 1510 in exon 23 of COL2A1 gene, which caused a change from glycine to serine at codon 504 (G504S). By the time the woman got pregnant again, she had terminated two pregnancies and still had no child. In the first pregnancy, the molecular mutation of the family was not yet identified, and therefore prenatal diagnosis was unable to be performed by DNA analysis. In the second pregnancy, G504S mutation was found from fetal DNA. At the time of her third pregnancy, the woman and her husband became extremely worried about the potential SEDC for the fetus. For this reason, a quick and reliable molecular prenatal diagnosis of SEDC was performed by a PCR-SSP on an amniocyte sample collected at the 14th week of pregnancy. No mutation of the fetal DNA was identified. The result was obtained within 24 h after the sample was collected. The technique could be applied in confirmatory diagnosis and prenatal diagnosis for the affected family.

  5. Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

    PubMed

    Sun, Zhonglou; Pan, Tao; Hu, Chaochao; Sun, Lu; Ding, Hengwu; Wang, Hui; Zhang, Chenling; Jin, Hong; Chang, Qing; Kan, Xianzhao; Zhang, Baowei

    2017-01-01

    The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

  6. Emerging technologies in point-of-care molecular diagnostics for resource-limited settings.

    PubMed

    Peeling, Rosanna W; McNerney, Ruth

    2014-06-01

    Emerging molecular technologies to diagnose infectious diseases at the point at which care is delivered have the potential to save many lives in developing countries where access to laboratories is poor. Molecular tests are needed to improve the specificity of syndromic management, monitor progress towards disease elimination and screen for asymptomatic infections with the goal of interrupting disease transmission and preventing long-term sequelae. In simplifying laboratory-based molecular assays for use at point-of-care, there are inevitable compromises between cost, ease of use and test performance. Despite significant technological advances, many challenges remain for the development of molecular diagnostics for resource-limited settings. There needs to be more advocacy for these technologies to be applied to infectious diseases, increased efforts to lower the barriers to market entry through streamlined and harmonized regulatory approaches, faster policy development for adoption of new technologies and novel financing mechanisms to enable countries to scale up implementation.

  7. Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis

    PubMed Central

    Ferguson, Tanya M.; Weigel, Kris M.; Lakey Becker, Annie; Ontengco, Delia; Narita, Masahiro; Tolstorukov, Ilya; Doebler, Robert; Cangelosi, Gerard A.; Niemz, Angelika

    2016-01-01

    Nucleic acid amplification testing (NAAT) enables rapid and sensitive diagnosis of tuberculosis (TB), which facilitates treatment and mitigates transmission. Nucleic acid extraction from sputum constitutes the greatest technical challenge in TB NAAT for near-patient settings. This report presents preliminary data for a semi-automated sample processing method, wherein sputum is disinfected and liquefied, followed by PureLyse® mechanical lysis and solid-phase nucleic acid extraction in a miniaturized, battery-operated bead blender. Sputum liquefaction and disinfection enabled a >104 fold reduction in viable load of cultured Mycobacterium tuberculosis (M.tb) spiked into human sputum, which mitigates biohazard concerns. Sample preparation via the PureLyse® method and a clinically validated manual method enabled positive PCR-based detection for sputum spiked with 104 and 105 colony forming units (cfu)/mL M.tb. At 103 cfu/mL sputum, four of six and two of six samples amplified using the comparator and PureLyse® method, respectively. For clinical specimens from TB cases and controls, the two methods provided 100% concordant results for samples with 1 mL input volume (N = 41). The semi-automated PureLyse® method therefore performed similarly to a validated manual comparator method, but is faster, minimally instrumented, and can be integrated into TB molecular diagnostic platforms designed for near-patient low-resource settings. PMID:26785769

  8. Rapid Molecular Detection Methods for Arboviruses of Livestock of Importance to Northern Europe

    PubMed Central

    Johnson, Nicholas; Voller, Katja; Phipps, L. Paul; Mansfield, Karen; Fooks, Anthony R.

    2012-01-01

    Arthropod-borne viruses (arboviruses) have been responsible for some of the most explosive epidemics of emerging infectious diseases over the past decade. Their impact on both human and livestock populations has been dramatic. The early detection either through surveillance or diagnosis of virus will be a critical feature in responding and resolving the emergence of such epidemics in the future. Although some of the most important emerging arboviruses are human pathogens, this paper aims to highlight those diseases that primarily affect livestock, although many are zoonotic and some occasionally cause human mortality. This paper also highlights the molecular detection methods specific to each virus and identifies those emerging diseases for which a rapid detection methods are not yet developed. PMID:22219660

  9. Identification and Molecular Mechanisms of the Rapid Tonicity-induced Relocalization of the Aquaporin 4 Channel.

    PubMed

    Kitchen, Philip; Day, Rebecca E; Taylor, Luke H J; Salman, Mootaz M; Bill, Roslyn M; Conner, Matthew T; Conner, Alex C

    2015-07-03

    The aquaporin family of integral membrane proteins is composed of channels that mediate cellular water flow. Aquaporin 4 (AQP4) is highly expressed in the glial cells of the central nervous system and facilitates the osmotically driven pathological brain swelling associated with stroke and traumatic brain injury. Here we show that AQP4 cell surface expression can be rapidly and reversibly regulated in response to changes of tonicity in primary cortical rat astrocytes and in transfected HEK293 cells. The translocation mechanism involves PKA activation, influx of extracellular calcium, and activation of calmodulin. We identify five putative PKA phosphorylation sites and use site-directed mutagenesis to show that only phosphorylation at one of these sites, serine 276, is necessary for the translocation response. We discuss our findings in the context of the identification of new therapeutic approaches to treating brain edema. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. A rapid, one step molecular identification of Trichoderma citrinoviride and Trichoderma reesei.

    PubMed

    Saroj, Dina B; Dengeti, Shrinivas N; Aher, Supriya; Gupta, Anil K

    2015-06-01

    Trichoderma species are widely used as production hosts for industrial enzymes. Identification of Trichoderma species requires a complex molecular biology based identification involving amplification and sequencing of multiple genes. Industrial laboratories are required to run identification tests repeatedly in cell banking procedures and also to prove absence of production host in the product. Such demands can be fulfilled by a brief method which enables confirmation of strain identity. This communication describes one step identification method for two common Trichoderma species; T. citrinoviride and T. reesei, based on identification of polymorphic region in the nucleotide sequence of translation elongation factor 1 alpha. A unique forward primer and common reverse primer resulted in 153 and 139 bp amplicon for T. citrinoviride and T. reesei, respectively. Simplification was further introduced by using mycelium as template for PCR amplification. Method described in this communication allows rapid, one step identification of two Trichoderma species.

  11. Molecular identification of rapidly adapting mechanoreceptors and their developmental dependence on ret signaling.

    PubMed

    Luo, Wenqin; Enomoto, Hideki; Rice, Frank L; Milbrandt, Jeffrey; Ginty, David D

    2009-12-24

    In mammals, the first step in the perception of form and texture is the activation of trigeminal or dorsal root ganglion (DRG) mechanosensory neurons, which are classified as either rapidly (RA) or slowly adapting (SA) according to their rates of adaptation to sustained stimuli. The molecular identities and mechanisms of development of RA and SA mechanoreceptors are largely unknown. We found that the "early Ret(+)" DRG neurons are RA mechanoreceptors, which form Meissner corpuscles, Pacinian corpuscles, and longitudinal lanceolate endings. The central projections of these RA mechanoreceptors innervate layers III through V of the spinal cord and terminate within discrete subdomains of the dorsal column nuclei. Moreover, mice lacking Ret signaling components are devoid of Pacinian corpuscles and exhibit a dramatic disruption of RA mechanoreceptor projections to both the spinal cord and medulla. Thus, the early Ret(+) neurons are RA mechanoreceptors and Ret signaling is required for the assembly of neural circuits underlying touch perception.

  12. Preparation and rapid thermal annealing of AlN thin films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Liu, B.; Gao, J.; Wu, K. M.; Liu, C.

    2009-05-01

    AlN films were grown at 785 ∘C on (0001) sapphire substrates by radio-frequency assisted molecular beam epitaxy. Post-growth rapid thermal annealing (RTA) was carried out from 900 to 1200 ∘C for 10 s in flowing N 2. The morphological and structural properties of the AlN epilayers before and after the RTA were studied by atomic force microscopy, x-ray diffraction and transmission electron microscopy. It is found that the threading dislocations can be decreased to an order of magnitude by using an interlayer growth method. The surface roughness (RMS) of the AlN thin films becomes larger with the increase of annealing temperature. The full width at half maximum of AlN (0002) rocking curve reaches its minimum after the RTA at 1000 ∘C.

  13. Fabrication of Polymerase Chain Reaction Plastic Lab-on-a-Chip Device for Rapid Molecular Diagnoses

    PubMed Central

    2016-01-01

    Purpose: We aim to fabricate a thermoplastic poly(methylmethacrylate) (PMMA) Lab-on-a-Chip device to perform continuous- flow polymerase chain reactions (PCRs) for rapid molecular detection of foodborne pathogen bacteria. Methods: A miniaturized plastic device was fabricated by utilizing PMMA substrates mediated by poly(dimethylsiloxane) interfacial coating, enabling bonding under mild conditions, and thus avoiding the deformation or collapse of microchannels. Surface characterizations were carried out and bond strength was measured. The feasibility of the Lab-on-a-Chip device for performing on-chip PCR utilizing a lab-made, portable dual heater was evaluated. The results were compared with those obtained using a commercially available thermal cycler. Results: A PMMA Lab-on-a-Chip device was designed and fabricated for conducting PCR using foodborne pathogens as sample targets. A robust bond was established between the PMMA substrates, which is essential for performing miniaturized PCR on plastic. The feasibility of on-chip PCR was evaluated using Escherichia coli O157:H7 and Cronobacter condimenti, two worldwide foodborne pathogens, and the target amplicons were successfully amplified within 25 minutes. Conclusions: In this study, we present a novel design of a low-cost and high-throughput thermoplastic PMMA Lab-on-a-Chip device for conducting microscale PCR, and we enable rapid molecular diagnoses of two important foodborne pathogens in minute resolution using this device. In this regard, the introduced highly portable system design has the potential to enable PCR investigations of many diseases quickly and accurately. PMID:27230459

  14. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology.

    PubMed

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10(-3) for bcr1 and bcr3 and 10(-)2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL.

  15. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology

    PubMed Central

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10−3 for bcr1 and bcr3 and 10−2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362

  16. Nanotools and molecular techniques to rapidly identify and fight bacterial infections.

    PubMed

    Dinarelli, S; Girasole, M; Kasas, S; Longo, G

    2016-01-20

    Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

  17. A rapid manual processing technique for resource-limited small laboratories

    PubMed Central

    Jali, Pramod K; Donoghue, Mandana; Gadiwan, Mohsin

    2015-01-01

    Background: Surgical pathology is an integral part of diagnosis and management planning in patient care. In the absence of widespread automation, many small laboratories are unable to provide this service due to lack of time. Currently, the shortest processing schedule for formalin-fixed paraffin-embedded tissues is 16 working hours; most small laboratories cannot complete the rapid schedules within the average 8–9 working hours. Thus, the availability of an 8–9 h processing schedule that provide satisfactory results can help many small laboratories in routinely providing surgical pathology services. Objectives: To evaluate the effectiveness of a new rapid processing schedule and compare it with two existing rapid processing schedules. Materials and Methods: This animal study tested a new rapid processing schedule suggested by authors with overnight preprocessing in 60% isopropyl alcohol followed by an 8 h processing schedule. This was tested and compared with the rapid processing schedules described by Godkar's (11 h) and Bancroft's (2 working days). A routinely used automatic tissue processor long cycle (17 h) was the control. Each schedule was used on 20 tongue specimens. The prepared slides were evaluated for surface area and linear tissue shrinkage, ease of sectioning, quality of hematoxylin and eosin staining, histological appearance and artifacts. Results: No statistical differences were found between schedules. Overall total average performance ranking placed Bancroft's schedule as the best with only 27.9% of the sections processed and stained showing any shortcomings, followed closely by the test schedule suggested by authors (28.7%), Godkar's (31.8%) and the automatic processor schedule/control (33.3%). Conclusion: The test results indicated that the schedule devised by authors is an effective rapid processing cycle that produces diagnostic quality histological results when compared with other conventional processing schedules for small tissue blocks

  18. Ancient low–molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw

    USGS Publications Warehouse

    Drake, Travis W.; Wickland, Kimberly P.; Spencer, Robert G. M.; McKnight, Diane M.; Striegl, Robert G.

    2015-01-01

    Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high–temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low–molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters.

  19. Ancient low–molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw

    PubMed Central

    Drake, Travis W.; Wickland, Kimberly P.; Spencer, Robert G. M.; McKnight, Diane M.; Striegl, Robert G.

    2015-01-01

    Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high–temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low–molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters. PMID:26504243

  20. A method to rapidly induce organelle-specific molecular activities and membrane tethering.

    PubMed

    Komatsu, Toru; Inoue, Takanari

    2014-01-01

    In this chapter we describe a technique for rapid protein targeting to individual intracellular organelles. This method enables a real-time imaging-based study of cellular behavior in response to controlled induction of signaling events in a specifically targeted cellular compartment. We provide rationales and a step-by-step protocol for probe design and imaging of protein targeting along with two different applications of this technique. One application involves organelle-specific activation of small GTPases, while the other application involves membrane tethering of two different organelles. In the former case, we activate Rac1 and Ras at distinct intracellular locations in order to study compartmentalization of their signaling pathways, and in the latter example, we induce membrane tethering of the endoplasmic reticulum and mitochondria in order to study organelle-organelle communication. The described technique allows to rapidly perturb molecular activities and organelle-organelle communications at precise locations with specified timing and represents a powerful strategy to dissect spatiotemporally complex biological processes.

  1. [Present and future perspectives for the rapid molecular diagnosis of TB and MDR-TB].

    PubMed

    Tanasescu, Mihaela; Didilescu, Cristian; Marica, Constantin

    2013-01-01

    Tuberculosis is still one of the diseases with a major medical and social impact, and in terms of early diagnosis (which would imply a fair treatment and established at the time), difficulties related to the delay bacilli isolation in culture, decreased susceptibility testing methods to antituberculosis drugs, lack of methods for differentiation of M. Tuberculosis complex germs of non-TB Mycobacteria, may have important clinical implications. Traditional testing of anti-TB drug susceptibility on solid Löwenstein-Jensen medium (gold standard) or liquid media can only be performed using grown samples. Determining the time it takes up to 42 days on solid media and 12 days for liquid media. For MDR/XDR TB cases itis absolutely essential to reduce the detection time. In these cases rapid diagnostic methods prove their usefulness. Automatic testing in liquid medium, molecular hybridization methods are currently recommended by the current WHO guidelines. Rapid diagnosis of MDR-TBis extremely useful for the early establishment of an effective treatment tailored more accurately on the spectrum of sensitivity of the resistant strain (thus reducing the risk of developing additional resistance to other drugs) and control the spread of these strains. Genetic diagnostic methods, approved and recommended by the WHO, can reduce the time of diagnosis of TB case and, importantly, the case of MDR-TB. They do not replace the current standard diagnostic methods and resistance profile, but complete them in selected cases.

  2. Ancient low-molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw.

    PubMed

    Drake, Travis W; Wickland, Kimberly P; Spencer, Robert G M; McKnight, Diane M; Striegl, Robert G

    2015-11-10

    Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high-temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low-molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters.

  3. A new rapid molecular point-of-care assay for Trichomonas vaginalis: preliminary performance data.

    PubMed

    Pearce, David M; Styles, David N; Hardick, Justin P; Gaydos, Charlotte A

    2013-09-01

    Trichomonas vaginalis infection is the most prevalent treatable sexually transmitted infection (STI) in the world. An accurate point-of-care (PoC) molecular test would enable patients to be tested and treated for T vaginalis in a single visit to the genitourinary medicine clinic, community STI clinic, pharmacy or doctor's office. In this report, we describe a rapid prototype assay for T vaginalis designed for use in conjunction with the Atlas io PoC platform, and initial verification of its performance using 90 clinical samples. A rapid prototype T vaginalis assay was designed. The test, featuring novel electrochemical end-point detection, used a multi-copy region of the T vaginalis genome as the assay target. Ninety clinical vaginal swab samples were used to verify the performance of the prototype assay. The assay demonstrated a sensitivity and specificity of 95.5% (42/44) and 95.7% (44/46), respectively, when tested using clinical samples. Assay inclusivity was demonstrated for a number of geographically diverse T vaginalis isolates, and the test showed no cross-reactivity with either human DNA or a panel of DNAs isolated from common cross-reactants. The sensitivity and specificity achieved using this prototype assay is comparable with that achieved for existing central laboratory nucleic acid amplification tests used for screening patients for T vaginalis.

  4. A new rapid molecular point-of-care assay for Trichomonas vaginalis: preliminary performance data

    PubMed Central

    Pearce, David M; Styles, David N; Hardick, Justin P; Gaydos, Charlotte A

    2013-01-01

    Objective Trichomonas vaginalis infection is the most prevalent treatable sexually transmitted infection (STI) in the world. An accurate point-of-care (PoC) molecular test would enable patients to be tested and treated for T vaginalis in a single visit to the genitourinary medicine clinic, community STI clinic, pharmacy or doctor’s office. In this report, we describe a rapid prototype assay for T vaginalis designed for use in conjunction with the Atlas io PoC platform, and initial verification of its performance using 90 clinical samples. Methods A rapid prototype T vaginalis assay was designed. The test, featuring novel electrochemical endpoint detection, used a multi-copy region of the T vaginalis genome as the assay target. Ninety clinical vaginal swab samples were used to verify the performance of the prototype assay. Results The assay demonstrated a sensitivity and specificity of 95.5% (42/44) and 95.7% (44/46), respectively, when tested using clinical samples. Assay inclusivity was demonstrated for a number of geographically diverse T vaginalis isolates, and the test showed no cross-reactivity with either human DNA or a panel of DNAs isolated from common cross-reactants. Conclusions The sensitivity and specificity achieved using this prototype assay is comparable with that achieved for existing central laboratory nucleic acid amplification tests used for screening patients for T vaginalis. PMID:23605852

  5. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.

    PubMed

    Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K

    2016-07-03

    Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods.

  6. Optical molecular imaging approach for rapid assessment of response of individual cancer cells to chemotherapy

    NASA Astrophysics Data System (ADS)

    Luo, Zhen; Tikekar, Rohan Vijay; Samadzadeh, Kiana Michelle; Nitin, Nitin

    2012-10-01

    Predicting the response of individual patients to cytotoxic chemotherapy drugs is critical for developing individualized therapies. With this motivation, an optical molecular imaging approach was developed to detect cisplatin induced changes in the uptake and intracellular retention of choline. Intracellular uptake of choline was characterized using a click chemistry reaction between propargyl choline and Alexa-488 azide. Cisplatin induced changes in the uptake of propargyl choline in cells and tumor spheroids were compared with similar measurements using a fluorescent analogue of deoxyglucose and conventional cell viability assays. Uptake and intracellular retention of propargyl choline decreased with an increase in concentration of cisplatin. Intracellular uptake of propargyl choline was significantly reduced within 3 h of incubation with a sub-lethal dose of cisplatin. Results demonstrate that the imaging approach based on propargyl choline was more sensitive in detecting the early response of cancer cells to cisplatin as compared to the imaging based on fluorescent analogue of deoxyglucose and cell viability assays. Imaging measurements in tumor spheroids show a significant decrease in the uptake of propargyl choline following treatment with cisplatin. Overall, the results demonstrate a novel optical molecular imaging approach for rapid measurement of the response of individual cancer cells to cisplatin treatment.

  7. Rapid Characterization of Molecular Chemistry, Nutrient Make-Up and Microlocation of Internal Seed Tissue

    SciTech Connect

    Yu,P.; Block, H.; Niu, Z.; Doiron, K.

    2007-01-01

    Wheat differs from corn in biodegradation kinetics and fermentation characteristics. Wheat exhibits a relatively high rate (23% h{sup 01}) and extent (78% DM) of biodegradation, which can lead to metabolic problems such as acidosis and bloat in ruminants. The objective of this study was to rapidly characterize the molecular chemistry of the internal structure of wheat (cv. AC Barrie) and reveal both its structural chemical make-up and nutrient component matrix by analyzing the intensity and spatial distribution of molecular functional groups within the intact seed using advanced synchrotron-powered Fourier transform infrared (FTIR) microspectroscopy. The experiment was performed at the U2B station of the National Synchrotron Light Source at Brookhaven National Laboratory, New York, USA. The wheat tissue was imaged systematically from the pericarp, seed coat, aleurone layer and endosperm under the peaks at {approx}1732 (carbonyl C{double_bond}O ester), 1515 (aromatic compound of lignin), 1650 (amide I), 1025 (non-structural CHO), 1550 (amide II), 1246 (cellulosic material), 1160, 1150, 1080, 930, 860 (all CHO), 3350 (OH and NH stretching), 2928 (CH{sub 2} stretching band) and 2885 cm{sup -1} (CH{sub 3} stretching band). Hierarchical cluster analysis and principal component analysis were applied to analyze the molecular FTIR spectra obtained from the different inherent structures within the intact wheat tissues. The results showed that, with synchrotron-powered FTIR microspectroscopy, images of the molecular chemistry of wheat could be generated at an ultra-spatial resolution. The features of aromatic lignin, structural and non-structural carbohydrates, as well as nutrient make-up and interactions in the seeds, could be revealed. Both principal component analysis and hierarchical cluster analysis methods are conclusive in showing that they can discriminate and classify the different inherent structures within the seed tissue. The wheat exhibited distinguishable

  8. Resource Guide in Economic Education for Sauk Rapids Public Schools, Grades K-3.

    ERIC Educational Resources Information Center

    Saint Cloud State Coll., Minn. Center for Economic Education.

    This five-part resource guide, giving teachers clear identification of and access to economic concepts and activities, provides examples of how basic economic concepts and practices can be meaningfully and systematically incorporated in K-3 social studies. Part I lists major economic generalizations for grades K-3 to provide teachers with a…

  9. Extended Services in Schools: Developing Resources to Prepare Student Teachers for a Rapidly Changing Working Environment

    ERIC Educational Resources Information Center

    Griffiths, Sue; Smith, Andy

    2011-01-01

    The role of schools in providing extended services to their communities continues to undergo change and development. This has raised issues regarding the training of student teachers who are increasingly likely to take up appointments in schools offering extended services. This research project investigated the development of resources to prepare…

  10. Geology and ground-water resources of the Grand Rapids area, north-central Minnesota

    USGS Publications Warehouse

    Oakes, Edward L.

    1970-01-01

    This report is one of a series of studies of geology and ground-water availability conducted in and near selected communities on the Mesabi Iron Range, north-central and northeastern Minnesota. This report describes the geology and ground-water conditions in the 303 square-mile Grand Rapids area.

  11. Molecularly imprinted fluorescent hollow nanoparticles as sensors for rapid and efficient detection λ-cyhalothrin in environmental water.

    PubMed

    Wang, Jixiang; Qiu, Hao; Shen, Hongqiang; Pan, Jianming; Dai, Xiaohui; Yan, Yongsheng; Pan, Guoqing; Sellergren, Börje

    2016-11-15

    Molecularly imprinted fluorescent polymers have shown great promise in biological or chemical separations and detections, due to their high stability, selectivity and sensitivity. In this work, molecularly imprinted fluorescent hollow nanoparticles, which could rapidly and efficiently detect λ-cyhalothrin (a toxic insecticide) in water samples, was reported. The molecularly imprinted fluorescent sensor showed excellent sensitivity (the limit of detection low to 10.26nM), rapid detection rate (quantitative detection of λ-cyhalothrin within 8min), regeneration ability (maintaining good fluorescence properties after 8 cycling operation) and appreciable selectivity over several structural analogs. Moreover, the fluorescent sensor was further used to detect λ-cyhalothrin in real samples form the Beijing-Hangzhou Grand Canal Water. Despite the relatively complex components of the environmental water, the molecularly imprinted fluorescent hollow nanosensor still showed good recovery, clearly demonstrating the potential value of this smart sensor nanomaterial in environmental monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Designing and Developing Open Education Resources in Higher Education: A Molecular Biology Project

    PubMed Central

    Parisky, Alex; Boulay, Rachel

    2014-01-01

    Recent advances in internet technology have transformed how we gather and share information in today's world and have provided us with a platform to access educational resources and related information on the Internet. Every day, new technologies are developed that are changing the when and where we access that information. The capabilities of new technologies have allowed society to access information and learn virtually anywhere. As technical ingenuity continues to generate new technologies and paths of communication, we must look for opportunities to collaborate, share and extend our educational resources in higher education. Distributing Open Educational Resources (OER) in the form of freely licensed materials is necessary in order to laterally influence current advances in learning technologies. Online resources are being used in a variety of contexts to supplement instruction and training at higher education institutions. The aim of this Open Educational Resource project was to design and develop a blended learning instructional program to assist online users in developing familiarity with laboratory techniques prior to conducting molecular biology research in an authentic laboratory setting. This paper will look at the background of OER, describe the online materials that the Center for Cardiovascular Research (CCR) developed for open use, and discuss the outcomes and implications for use. PMID:25126132

  13. Designing and Developing Open Education Resources in Higher Education: A Molecular Biology Project.

    PubMed

    Parisky, Alex; Boulay, Rachel

    2013-01-01

    Recent advances in internet technology have transformed how we gather and share information in today's world and have provided us with a platform to access educational resources and related information on the Internet. Every day, new technologies are developed that are changing the when and where we access that information. The capabilities of new technologies have allowed society to access information and learn virtually anywhere. As technical ingenuity continues to generate new technologies and paths of communication, we must look for opportunities to collaborate, share and extend our educational resources in higher education. Distributing Open Educational Resources (OER) in the form of freely licensed materials is necessary in order to laterally influence current advances in learning technologies. Online resources are being used in a variety of contexts to supplement instruction and training at higher education institutions. The aim of this Open Educational Resource project was to design and develop a blended learning instructional program to assist online users in developing familiarity with laboratory techniques prior to conducting molecular biology research in an authentic laboratory setting. This paper will look at the background of OER, describe the online materials that the Center for Cardiovascular Research (CCR) developed for open use, and discuss the outcomes and implications for use.

  14. Water resources in a rapidly growing region-Oakland County, Michigan

    USGS Publications Warehouse

    Aichele, Stephen S.

    2005-01-01

    Despite considerable expansion of urban areas, streamflow characteristics at most sites have not been affected. However, at several sites in areas of the county that are both supplied by ground water and sewered, statistically significant downward trends in low-flow stream discharges have been noted between 1970 and 2003. Stream chemistry, compared to a previous study of county water resources prepared in 1972, has generally improved, with marked decreases in concentrations of nitrogen, phosphorus, and sulfate. Chloride concentrations, however, have increased dramatically in river and lake water across the county. Detectable concentrations of personal-care products, flame retardants, and petroleum fuel compounds were identified at all river sites sampled. 

  15. Mass disasters: rapid molecular screening of human remains by means of short tandem repeats typing.

    PubMed

    Corach, D; Sala, A; Penacino, G; Sotelo, A

    1995-09-01

    Human remains identification represents a challenging situation and constitutes a difficult task associated with mass disasters. The only highly efficient means for individual and family group reconstruction is that based on DNA typing. On July 18, 1994 an explosion destroyed the A.M.I.A. (Argentine Israeli Association). Over 100 people died; however, the exact number of victims is still being investigated. Our Service received over 70 remains to be characterized by DNA typing in order to determine the number of victims and to try to reconstruct the family groups to which they belonged. DNA was extracted by a cetyltrimethylammonium bromide (CTAB) based protocol, a rapid molecular screening of all samples was carried out by multiplex STR amplifications including HUMTH01, HUMFABP, HUMHPRTB, HUMRENA4, HUMVWA, HUMFES/FPS and Y27H39LR. Samples with identical genotypes were HaeIII-digested. Southern blotted and probed with YNH-24 (D2S44). PH-30 (D4S139). LH-1 (D5S110) and MS-1 (D1S7) for variable number of tandem repeats (VNTR) evaluation. The minisatellite variant repeat (MVR) approach was used in those cases in which band or profile shift were detected in Southern blot assays. Kinship between victims and putative relatives was initially evaluated by comparison of short tandem repeat (STR) profiles and then confirmed by VNTR with the above probes. The high identification efficiency attained in this case is, in part, supported by a previous experience, the DNA-based molecular characterization of human remains caused by the explosion of the Israeli Embassy in Buenos Aires, March 1992.

  16. Neolithic agriculture, freshwater resources and rapid environmental changes on the lower Yangtze, China

    NASA Astrophysics Data System (ADS)

    Qin, Jungan; Taylor, David; Atahan, Pia; Zhang, Xinrong; Wu, Guoxuan; Dodson, John; Zheng, Hongbo; Itzstein-Davey, Freea

    2011-01-01

    Analyses of sedimentary evidence in the form of spores, pollen, freshwater algae, dinoflagellate cysts, phytoliths and charcoal from AMS 14C-dated, Holocene-aged sequences provide an excellent opportunity to examine the responses of Neolithic agriculturalists in the lower Yangtze to changing environments. Evidence from two sites close to the southern margin of the Yangtze delta and separated by what is now Hangzhou Bay attests the critical importance to early attempts at food production of access to freshwater resources. More readily, if episodically, available freshwater resources during the early to mid-Holocene on the Hangjiahu plain may have encouraged an early reliance on rice-based agriculture, which in turn facilitated the accumulation of agricultural surpluses and cultural diversification. Cultural change was relatively attenuated and human population pressures possibly lower on the Ningshao plain, seemingly because of much more profound environmental impacts of variations in local hydrological conditions, and because predominantly saline conditions, associated with rising relative sea level, hampered the early development of irrigated agriculture. The evidence, although largely dating to the early and middle parts of the Holocene, provides a timely warning of the complexity of vulnerability to climate change-induced processes of agriculture, and indeed human activities more generally, on megadeltas in Asia.

  17. Rapid Molecular Detection of Zika Virus in Acute-Phase Urine Samples Using the Recombinase Polymerase Amplification Assay.

    PubMed

    Abd El Wahed, Ahmed; Sanabani, Sabri Saeed; Faye, Oumar; Pessôa, Rodrigo; Patriota, João Veras; Giorgi, Ricardo Rodrigues; Patel, Pranav; Böhlken-Fascher, Susanne; Landt, Olfert; Niedrig, Matthias; Zanotto, Paolo Marinho de Andrade; Czerny, Claus Peter; Sall, Amadou A; Weidmann, Manfred

    2017-01-25

    Currently the detection of Zika virus (ZIKV) in patient samples is done by real-time RT-PCR. Samples collected from rural area are sent to highly equipped laboratories for screening. A rapid point-of-care test is needed to detect the virus, especially at low resource settings. In this report, we describe the development of a reverse transcription isothermal recombinase polymerase amplification (RT-RPA) assay for the identification of ZIKV. RT-RPA assay was portable, sensitive (21 RNA molecules), and rapid (3-15 minutes). No cross-reactivity was detected to other flaviviruses, alphaviruses and arboviruses. Compared to real-time RT-PCR, the diagnostic sensitivity was 92%, while the specificity was 100%. The developed assay is a promising platform for rapid point of need detection of ZIKV in low resource settings and elsewhere (e.g. during mass gathering).

  18. Rapid Molecular Detection of Zika Virus in Acute-Phase Urine Samples Using the Recombinase Polymerase Amplification Assay

    PubMed Central

    Abd El Wahed, Ahmed; Sanabani, Sabri Saeed; Faye, Oumar; Pessôa, Rodrigo; Patriota, João Veras; Giorgi, Ricardo Rodrigues; Patel, Pranav; Böhlken-Fascher, Susanne; Landt, Olfert; Niedrig, Matthias; Zanotto, Paolo Marinho de Andrade; Czerny, Claus Peter; Sall, Amadou A.; Weidmann, Manfred

    2017-01-01

    Background: Currently the detection of Zika virus (ZIKV) in patient samples is done by real-time RT-PCR. Samples collected from rural area are sent to highly equipped laboratories for screening. A rapid point-of-care test is needed to detect the virus, especially at low resource settings. Methodology/Principal Findings: In this report, we describe the development of a reverse transcription isothermal recombinase polymerase amplification (RT-RPA) assay for the identification of ZIKV. RT-RPA assay was portable, sensitive (21 RNA molecules), and rapid (3-15 minutes). No cross-reactivity was detected to other flaviviruses, alphaviruses and arboviruses. Compared to real-time RT-PCR, the diagnostic sensitivity was 92%, while the specificity was 100%. Conclusions/Significance: The developed assay is a promising platform for rapid point of need detection of ZIKV in low resource settings and elsewhere (e.g. during mass gathering). PMID:28239513

  19. Evaluation of two rapid screening assays for detecting hepatitis C antibodies in resource-constrained settings.

    PubMed

    Kosack, Cara S; Nick, Sigrid

    2016-05-01

    To evaluate the diagnostic accuracy of the OraQuick HCV rapid antibody test from OraSure and the Multisure HCV antibody assay from MP Biomedicals. Five seropanels from patients, intravenous drug users and blood donors with and without HCV infection were used on the two rapid immunochromatographic tests. Sensitivity, specificity and predictive values were calculated. In addition, seropanels from 10 seroconverters were used to assess early identification of HCV infection. The study was undertaken in a laboratory at Paul Ehrlich Institute in Germany. Panel 1 contained of 55 positive and 25 negative samples. The OraQuick HCV test had a sensitivity of 100% (95% CI: 93.5-100) and a specificity of 100% (95% CI: 86.3-100). The Multisure HCV test had a sensitivity of 100% (95% CI: 93.5-100) and a specificity of 96% (95% CI: 79.6-99.9). Panel 2 consisted of 193 pre-characterised anti-HCV-positive patient samples. The OraQuick HCV test identified 191 samples correctly and the Multisure HCV 192. The sensitivity was 99.0% (95% CI: 96.3-99.9) for the OraQuick HCV test and 99.5% (95% CI: 97.1-100) for the Multisure HCV test. Panel 3 was composed of seroconversion samples of 10 patients. The OraQuick HCV test detected all of these 10 infections while the Multisure HCV test detected six and was indeterminate on 2. Panel 4 included 53 anti-HCV negative blood samples from blood donors. Both tests correctly identified all 53. Panel 5 consisted of 26 samples of HCV/HIV co-infected patients. The sensitivity of the OraQuick HCV test was 65.2% (95% CI: 42.8-82.8) after 20 min and 73.9% (95% CI: 51.3-88.9) after 40 min of incubation. The Multisure HCV test had a sensitivity of 96.2% (95% CI: 80.4-99.9). This evaluation revealed good sensitivity for both rapid screening assays. The detection of seroconverters, however, was lower in the MutiSure HCV test. Therefore the MultiSure test should be used with hesitation in high incidence settings. The OraQuick gave HCV false-negative results in

  20. Rapid Evaporation of Water on Graphene/Graphene-Oxide: A Molecular Dynamics Study.

    PubMed

    Li, Qibin; Xiao, Yitian; Shi, Xiaoyang; Song, Shufeng

    2017-09-07

    To reveal the mechanism of energy storage in the water/graphene system and water/grapheme-oxide system, the processes of rapid evaporation of water molecules on the sheets of graphene and graphene-oxide are investigated by molecular dynamics simulations. The results show that both the water/graphene and water/grapheme-oxide systems can store more energy than the pure water system during evaporation. The hydroxyl groups on the surface of graphene-oxide are able to reduce the attractive interactions between water molecules and the sheet of graphene-oxide. Also, the radial distribution function of the oxygen atom indicates that the hydroxyl groups affect the arrangement of water molecules at the water/graphene-oxide interface. Therefore, the capacity of thermal energy storage of the water/graphene-oxide system is lower than that of the water/graphene system, because of less desorption energy at the water/graphene-oxide interface. Also, the evaporation rate of water molecules on the graphene-oxide sheet is slower than that on the graphene sheet. The Leidenfrost phenomenon can be observed during the evaporation process in the water/grapheme-oxide system.

  1. Rapid Evaporation of Water on Graphene/Graphene-Oxide: A Molecular Dynamics Study

    PubMed Central

    Li, Qibin; Xiao, Yitian; Shi, Xiaoyang; Song, Shufeng

    2017-01-01

    To reveal the mechanism of energy storage in the water/graphene system and water/grapheme-oxide system, the processes of rapid evaporation of water molecules on the sheets of graphene and graphene-oxide are investigated by molecular dynamics simulations. The results show that both the water/graphene and water/grapheme-oxide systems can store more energy than the pure water system during evaporation. The hydroxyl groups on the surface of graphene-oxide are able to reduce the attractive interactions between water molecules and the sheet of graphene-oxide. Also, the radial distribution function of the oxygen atom indicates that the hydroxyl groups affect the arrangement of water molecules at the water/graphene-oxide interface. Therefore, the capacity of thermal energy storage of the water/graphene-oxide system is lower than that of the water/graphene system, because of less desorption energy at the water/graphene-oxide interface. Also, the evaporation rate of water molecules on the graphene-oxide sheet is slower than that on the graphene sheet. The Leidenfrost phenomenon can be observed during the evaporation process in the water/grapheme-oxide system. PMID:28880207

  2. Rapid measurement of molecular transport and interaction inside living cells using single plane illumination.

    PubMed

    Hedde, Per Niklas; Stakic, Milka; Gratton, Enrico

    2014-11-14

    The ability to measure biomolecular dynamics within cells and tissues is very important to understand fundamental physiological processes including cell adhesion, signalling, movement, division or metabolism. Usually, such information is obtained using particle tracking methods or single point fluctuation spectroscopy. We show that image mean square displacement analysis, applied to single plane illumination microscopy data, is a faster and more efficient way of unravelling rapid, three-dimensional molecular transport and interaction within living cells. From a stack of camera images recorded in seconds, the type of dynamics such as free diffusion, flow or binding can be identified and quantified without being limited by current camera frame rates. Also, light exposure levels are very low and the image mean square displacement method does not require calibration of the microscope point spread function. To demonstrate the advantages of our approach, we quantified the dynamics of several different proteins in the cyto- and nucleoplasm of living cells. For example, from a single measurement, we were able to determine the diffusion coefficient of free clathrin molecules as well as the transport velocity of clathrin-coated vesicles involved in endocytosis. Used in conjunction with dual view detection, we further show how protein-protein interactions can be quantified.

  3. Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation.

    PubMed

    Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

    2016-12-14

    NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

  4. Rapid screening for citrus canker resistance employing pathogen-associated molecular pattern-triggered immunity responses

    PubMed Central

    Pitino, Marco; Armstrong, Cheryl M; Duan, Yongping

    2015-01-01

    Citrus canker, caused by the bacterial pathogen Xanthomonas citri ssp. citri (Xcc), has been attributed to millions of dollars in loss or damage to commercial citrus crops in subtropical production areas of the world. Since identification of resistant plants is one of the most effective methods of disease management, the ability to screen for resistant seedlings plays a key role in the production of a long-term solution to canker. Here, an inverse correlation between reactive oxygen species (ROS) production by the plant and the ability of Xcc to grow and form lesions on infected plants is reported. Based on this information, a novel screening method that can rapidly identify citrus seedlings that are less susceptible to early infection by Xcc was devised by measuring ROS accumulation triggered by a 22-amino acid sequence of the conserved N-terminal part of flagellin (flg22) from X. citri ssp. citri (Xcc-flg22). In addition to limiting disease symptoms, ROS production was also correlated with the expression of basal defense-related genes such as the pattern recognition receptors LRR8 and FLS2, the leucine-rich repeat receptor-like protein RLP12, and the defense-related gene PR1, indicating an important role for pathogen-associated molecular pattern-triggered immunity (PTI) in determining resistance to citrus canker. Moreover, the differential expression patterns observed amongst the citrus seedlings demonstrated the existence of genetic variations in the PTI response among citrus species/varieties. PMID:26504581

  5. Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination

    PubMed Central

    Hedde, Per Niklas; Stakic, Milka; Gratton, Enrico

    2014-01-01

    The ability to measure biomolecular dynamics within cells and tissues is very important to understand fundamental physiological processes including cell adhesion, signalling, movement, division or metabolism. Usually, such information is obtained using particle tracking methods or single point fluctuation spectroscopy. We show that image mean square displacement analysis, applied to single plane illumination microscopy data, is a faster and more efficient way of unravelling rapid, three-dimensional molecular transport and interaction within living cells. From a stack of camera images recorded in seconds, the type of dynamics such as free diffusion, flow or binding can be identified and quantified without being limited by current camera frame rates. Also, light exposure levels are very low and the image mean square displacement method does not require calibration of the microscope point spread function. To demonstrate the advantages of our approach, we quantified the dynamics of several different proteins in the cyto- and nucleoplasm of living cells. For example, from a single measurement, we were able to determine the diffusion coefficient of free clathrin molecules as well as the transport velocity of clathrin-coated vesicles involved in endocytosis. Used in conjunction with dual view detection, we further show how protein-protein interactions can be quantified. PMID:25394360

  6. Detection of shigella in lettuce by the use of a rapid molecular assay with increased sensitivity

    PubMed Central

    Jiménez, Kenia Barrantes; McCoy², Clyde B.; Achí, Rosario

    2010-01-01

    A Multiplex Polymerase Chain Reaction (PCR) assay to be used as an alternative to the conventional culture method in detecting Shigella and enteroinvasive Escherichia coli (EIEC) virulence genes ipaH and ial in lettuce was developed. Efficacy and rapidity of the molecular method were determined as compared to the conventional culture. Lettuce samples were inoculated with different Shigella flexneri concentrations (from 10 CFU/ml to 107 CFU/ml). DNA was extracted directly from lettuce after inoculation (direct-PCR) and after an enrichment step (enrichment PCR). Multiplex PCR detection limit was 104CFU/ml, diagnostic sensitivity and specificity were 100% accurate. An internal amplification control (IAC) of 100 bp was used in order to avoid false negative results. This method produced results in 1 to 2 days while the conventional culture method required 5 to 6 days. Also, the culture method detection limit was 106 CFU/ml, diagnostic sensitivity was 53% and diagnostic specificity was 100%. In this study a Multiplex PCR method for detection of virulence genes in Shigella and EIEC was shown to be effective in terms of diagnostic sensitivity, detection limit and amount of time as compared to Shigella conventional culture. PMID:24031579

  7. Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

    2016-12-01

    NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

  8. Detection of shigella in lettuce by the use of a rapid molecular assay with increased sensitivity.

    PubMed

    Jiménez, Kenia Barrantes; McCoy, Clyde B; Achí, Rosario

    2010-10-01

    A Multiplex Polymerase Chain Reaction (PCR) assay to be used as an alternative to the conventional culture method in detecting Shigella and enteroinvasive Escherichia coli (EIEC) virulence genes ipaH and ial in lettuce was developed. Efficacy and rapidity of the molecular method were determined as compared to the conventional culture. Lettuce samples were inoculated with different Shigella flexneri concentrations (from 10 CFU/ml to 10(7) CFU/ml). DNA was extracted directly from lettuce after inoculation (direct-PCR) and after an enrichment step (enrichment PCR). Multiplex PCR detection limit was 10(4)CFU/ml, diagnostic sensitivity and specificity were 100% accurate. An internal amplification control (IAC) of 100 bp was used in order to avoid false negative results. This method produced results in 1 to 2 days while the conventional culture method required 5 to 6 days. Also, the culture method detection limit was 10(6) CFU/ml, diagnostic sensitivity was 53% and diagnostic specificity was 100%. In this study a Multiplex PCR method for detection of virulence genes in Shigella and EIEC was shown to be effective in terms of diagnostic sensitivity, detection limit and amount of time as compared to Shigella conventional culture.

  9. Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation

    PubMed Central

    Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

    2016-01-01

    NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process. PMID:27966594

  10. SalmoBase: an integrated molecular data resource for Salmonid species.

    PubMed

    Samy, Jeevan Karloss Antony; Mulugeta, Teshome Dagne; Nome, Torfinn; Sandve, Simen Rød; Grammes, Fabian; Kent, Matthew Peter; Lien, Sigbjørn; Våge, Dag Inge

    2017-06-26

    Salmonids are ray-finned fishes which constitute 11 genera and at least 70 species including Atlantic salmon, whitefishes, graylings, rainbow trout, and char. The common ancestor of all Salmonidae experienced a whole genome duplication (WGD) ~80 million years ago, resulting in an autotetraploid genome. Genomic rediplodization is still going on in salmonid species, providing an unique system for studying evolutionary consequences of whole genome duplication. In recent years, high quality genome sequences of Atlantic salmon and Rainbow trout has been established, due to their scientific and commercial values. In this paper we introduce SalmoBase ( http://www.salmobase.org/ ), a tool for making molecular resources for salmonids public available in a framework of visualizations and analytic tools. SalmoBase has been developed as a part of the ELIXIR.NO project. Currently, SalmoBase contains molecular resources for Atlantic salmon and Rainbow trout. Data can be accessed through BLAST, Genome Browser (GBrowse), Genetic Variation Browser (GVBrowse) and Gene Expression Browser (GEBrowse). To the best of our knowledge, SalmoBase is the first database which integrates salmonids data and allow users to study salmonids in an integrated framework. The database and its tools (e.g., comparative genomics tools, synteny browsers) will be expanded as additional public resources describing other Salmonidae genomes become available.

  11. Pd0-mediated rapid cross-coupling reactions, the rapid C-[11C]methylations, revolutionarily advancing the syntheses of short-lived PET molecular probes.

    PubMed

    Suzuki, Masaaki; Doi, Hisashi; Koyama, Hiroko; Zhang, Zhouen; Hosoya, Takamitsu; Onoe, Hirotaka; Watanabe, Yasuyoshi

    2014-06-01

    Positron emission tomography is a noninvasive method for monitoring drug (or diagnostic) behavior and its localization on the target molecules in the living systems, including the human body, using a short-lived positron-emitting radionuclide. New methodologies for introducing representative short-lived radionuclides, (11)C and (18)F, into the carbon frameworks of biologically active organic compounds have been established by developing rapid C-[(11)C]methylations and C-[(18)F]fluoromethylations using rapid Pd(0)-mediated cross-coupling reactions between [(11)C]methyl iodide (sp(3)-hybridized carbon) and an excess amount of organotributylstannane or organoboronic acid ester having sp(2) (phenyl, heteroaromatic, or alkenyl), sp(alkynyl), or sp(3) (benzyl and cinnamyl)-hybridized carbons; and [(18)F]fluoromethyl halide (iodide or bromide) and an organoboronic acid ester, respectively. These rapid reactions provide a firm foundation for an efficient and general synthesis of short-lived (11)C- or (18)F-labeled PET molecular probes to promote in vivo molecular imaging studies. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Rapid, Machine-learned Resource Allocation: Application to High-redshift Gamma-Ray Burst Follow-up

    NASA Astrophysics Data System (ADS)

    Morgan, A. N.; Long, James; Richards, Joseph W.; Broderick, Tamara; Butler, Nathaniel R.; Bloom, Joshua S.

    2012-02-01

    As the number of observed gamma-ray bursts (GRBs) continues to grow, follow-up resources need to be used more efficiently in order to maximize science output from limited telescope time. As such, it is becoming increasingly important to rapidly identify bursts of interest as soon as possible after the event, before the afterglows fade beyond detectability. Studying the most distant (highest redshift) events, for instance, remains a primary goal for many in the field. Here, we present our Random Forest Automated Triage Estimator for GRB redshifts (RATE GRB-z ) for rapid identification of high-redshift candidates using early-time metrics from the three telescopes onboard Swift. While the basic RATE methodology is generalizable to a number of resource allocation problems, here we demonstrate its utility for telescope-constrained follow-up efforts with the primary goal to identify and study high-z GRBs. For each new GRB, RATE GRB-z provides a recommendation—based on the available telescope time—of whether the event warrants additional follow-up resources. We train RATE GRB-z using a set consisting of 135 Swift bursts with known redshifts, only 18 of which are z > 4. Cross-validated performance metrics on these training data suggest that ~56% of high-z bursts can be captured from following up the top 20% of the ranked candidates, and ~84% of high-z bursts are identified after following up the top ~40% of candidates. We further use the method to rank 200 + Swift bursts with unknown redshifts according to their likelihood of being high-z.

  13. ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data.

    PubMed

    Lavender, Christopher A; Shapiro, Andrew J; Burkholder, Adam B; Bennett, Brian D; Adelman, Karen; Fargo, David C

    2017-04-11

    Established and emerging next generation sequencing (NGS)-based technologies allow for genome-wide interrogation of diverse biological processes. However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques. Here, we present Online Resource for Integrative Omics (ORIO; https://orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data. To use ORIO, the user specifies NGS data of interest along with a list of genomic coordinates. Genomic coordinates may be biologically relevant features from a variety of sources, such as ChIP-seq peaks for a given protein or transcription start sites from known gene models. ORIO first iteratively finds read coverage values at each genomic feature for each NGS dataset. Data are then integrated using clustering-based approaches, giving hierarchical relationships across NGS datasets and separating individual genomic features into groups. In focusing its analysis on read coverage, ORIO makes limited assumptions about the analyzed data; this allows the tool to be applied across data from a variety of experiments and techniques. Results from analysis are presented in dynamic displays alongside user-controlled statistical tests, supporting rapid statistical validation of observed results. We emphasize the versatility of ORIO through diverse examples, ranging from NGS data quality control to characterization of enhancer regions and integration of gene expression information. Easily accessible on a public web server, we anticipate wide use of ORIO in genome-wide investigations by life scientists.

  14. RAPID, MACHINE-LEARNED RESOURCE ALLOCATION: APPLICATION TO HIGH-REDSHIFT GAMMA-RAY BURST FOLLOW-UP

    SciTech Connect

    Morgan, A. N.; Richards, Joseph W.; Butler, Nathaniel R.; Bloom, Joshua S.; Long, James; Broderick, Tamara

    2012-02-20

    As the number of observed gamma-ray bursts (GRBs) continues to grow, follow-up resources need to be used more efficiently in order to maximize science output from limited telescope time. As such, it is becoming increasingly important to rapidly identify bursts of interest as soon as possible after the event, before the afterglows fade beyond detectability. Studying the most distant (highest redshift) events, for instance, remains a primary goal for many in the field. Here, we present our Random Forest Automated Triage Estimator for GRB redshifts (RATE GRB-z ) for rapid identification of high-redshift candidates using early-time metrics from the three telescopes onboard Swift. While the basic RATE methodology is generalizable to a number of resource allocation problems, here we demonstrate its utility for telescope-constrained follow-up efforts with the primary goal to identify and study high-z GRBs. For each new GRB, RATE GRB-z provides a recommendation-based on the available telescope time-of whether the event warrants additional follow-up resources. We train RATE GRB-z using a set consisting of 135 Swift bursts with known redshifts, only 18 of which are z > 4. Cross-validated performance metrics on these training data suggest that {approx}56% of high-z bursts can be captured from following up the top 20% of the ranked candidates, and {approx}84% of high-z bursts are identified after following up the top {approx}40% of candidates. We further use the method to rank 200 + Swift bursts with unknown redshifts according to their likelihood of being high-z.

  15. Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

    USDA-ARS?s Scientific Manuscript database

    In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

  16. Rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

    PubMed

    Mulholland, Claire V; Ruthe, Ali; Cursons, Ray T; Durrant, Robert; Karalus, Noel; Coley, Kathryn; Bower, James; Permina, Elizabeth; Coleman, Megan J; Roberts, Sally A; Arcus, Vickery L; Cook, Gregory M; Aung, Htin Lin

    2017-03-23

    Despite New Zealand being a low-tuberculosis (TB) burden country, there are disproportionately high rates of TB in particular populations. Here, we report a rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

  17. Use of molecular beacons for the rapid analysis of DNA damage induced by exposure to an atmospheric pressure plasma jet

    SciTech Connect

    Kurita, Hirofumi E-mail: mizuno@ens.tut.ac.jp; Miyachika, Saki; Yasuda, Hachiro; Takashima, Kazunori; Mizuno, Akira E-mail: mizuno@ens.tut.ac.jp

    2015-12-28

    A rapid method for evaluating the damage caused to DNA molecules upon exposure to plasma is demonstrated. Here, we propose the use of a molecular beacon for rapid detection of DNA strand breaks induced by atmospheric pressure plasma jet (APPJ) irradiation. Scission of the molecular beacon by APPJ irradiation leads to separation of the fluorophore-quencher pair, resulting in an increase in fluorescence that directly correlates with the DNA strand breaks. The results show that the increase in fluorescence intensity is proportional to the exposure time and the rate of fluorescence increase is proportional to the discharge power. This simple and rapid method allows the estimation of DNA damage induced by exposure to a non-thermal plasma.

  18. Model-Driven Methodology for Rapid Deployment of Smart Spaces Based on Resource-Oriented Architectures

    PubMed Central

    Corredor, Iván; Bernardos, Ana M.; Iglesias, Josué; Casar, José R.

    2012-01-01

    Advances in electronics nowadays facilitate the design of smart spaces based on physical mash-ups of sensor and actuator devices. At the same time, software paradigms such as Internet of Things (IoT) and Web of Things (WoT) are motivating the creation of technology to support the development and deployment of web-enabled embedded sensor and actuator devices with two major objectives: (i) to integrate sensing and actuating functionalities into everyday objects, and (ii) to easily allow a diversity of devices to plug into the Internet. Currently, developers who are applying this Internet-oriented approach need to have solid understanding about specific platforms and web technologies. In order to alleviate this development process, this research proposes a Resource-Oriented and Ontology-Driven Development (ROOD) methodology based on the Model Driven Architecture (MDA). This methodology aims at enabling the development of smart spaces through a set of modeling tools and semantic technologies that support the definition of the smart space and the automatic generation of code at hardware level. ROOD feasibility is demonstrated by building an adaptive health monitoring service for a Smart Gym. PMID:23012544

  19. Rapid, Quantitative Assessment of Submerged Cultural Resource Degradation Using Repeat Video Surveys and Structure from Motion

    NASA Astrophysics Data System (ADS)

    Mertes, J. R.; Zant, C. N.; Gulley, J. D.; Thomsen, T. L.

    2017-08-01

    Monitoring, managing and preserving submerged cultural resources (SCR) such as shipwrecks can involve time consuming detailed physical surveys, expensive side-scan sonar surveys, the study of photomosaics and even photogrammetric analysis. In some cases, surveys of SCR have produced 3D models, though these models have not typically been used to document patterns of site degradation over time. In this study, we report a novel approach for quantifying degradation and changes to SCR that relies on diver-acquired video surveys, generation of 3D models from data acquired at different points in time using structure from motion, and differencing of these models. We focus our study on the shipwreck S.S. Wisconsin, which is located roughly 10.2 km southeast of Kenosha, Wisconsin, in Lake Michigan. We created two digital elevation models of the shipwreck using surveys performed during the summers of 2006 and 2015 and differenced these models to map spatial changes within the wreck. Using orthomosaics and difference map data, we identified a change in degradation patterns. Degradation was anecdotally believed to be caused by inward collapse, but maps indicated a pattern of outward collapse of the hull structure, which has resulted in large scale shifting of material in the central upper deck. In addition, comparison of the orthomosaics with the difference map clearly shows movement of objects, degradation of smaller pieces and in some locations, an increase in colonization of mussels.

  20. Model-driven methodology for rapid deployment of smart spaces based on resource-oriented architectures.

    PubMed

    Corredor, Iván; Bernardos, Ana M; Iglesias, Josué; Casar, José R

    2012-01-01

    Advances in electronics nowadays facilitate the design of smart spaces based on physical mash-ups of sensor and actuator devices. At the same time, software paradigms such as Internet of Things (IoT) and Web of Things (WoT) are motivating the creation of technology to support the development and deployment of web-enabled embedded sensor and actuator devices with two major objectives: (i) to integrate sensing and actuating functionalities into everyday objects, and (ii) to easily allow a diversity of devices to plug into the Internet. Currently, developers who are applying this Internet-oriented approach need to have solid understanding about specific platforms and web technologies. In order to alleviate this development process, this research proposes a Resource-Oriented and Ontology-Driven Development (ROOD) methodology based on the Model Driven Architecture (MDA). This methodology aims at enabling the development of smart spaces through a set of modeling tools and semantic technologies that support the definition of the smart space and the automatic generation of code at hardware level. ROOD feasibility is demonstrated by building an adaptive health monitoring service for a Smart Gym.

  1. Heat-mediated, ultra-rapid electrophoretic transfer of high and low molecular weight proteins to nitrocellulose membranes.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2002-08-01

    Here, we report an ultra-rapid method for the transfer of high and low molecular weight proteins to nitrocellulose membranes following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In this procedure, the electro-transfer was performed with heated (70-75 degrees C) normal transfer buffer from which methanol had been omitted. Complete transfer of high and low molecular weight proteins (a purified protein, molecular weight protein standards and proteins from a human tissue extract) could be carried out in 10 min for a 0.75-mm, 7% SDS-PAGE gel. For 10% and 12.5% gels (0.75 mm), the corresponding time was 15 min. In the case of 1.5-mm gels, a complete transfer could be carried out in 20 min for 7%, 10% and 12.5% gels. The permeability of the gel is increased by heat, such that the proteins trapped in the polyacrylamide gel matrix can be easily transferred to the membrane. When the heat-mediated transfer method was compared with a conventional transfer protocol, under similar conditions, we found that the latter method transferred minimal low molecular weight proteins while retaining most of the high molecular weight proteins in the gel. In summary, this procedure is very rapid, avoids the use of methanol and is particularly useful for the transfer of high molecular weight proteins.

  2. Rapid molecular evolution across amniotes of the IIS/TOR network.

    PubMed

    McGaugh, Suzanne E; Bronikowski, Anne M; Kuo, Chih-Horng; Reding, Dawn M; Addis, Elizabeth A; Flagel, Lex E; Janzen, Fredric J; Schwartz, Tonia S

    2015-06-02

    The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.

  3. Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis.

    PubMed

    Howell, Kate J; Peters, Sarah E; Wang, Jinhong; Hernandez-Garcia, Juan; Weinert, Lucy A; Luan, Shi-Lu; Chaudhuri, Roy R; Angen, Øystein; Aragon, Virginia; Williamson, Susanna M; Parkhill, Julian; Langford, Paul R; Rycroft, Andrew N; Wren, Brendan W; Maskell, Duncan J; Tucker, Alexander W

    2015-12-01

    Haemophilus parasuis causes Glässer's disease and pneumonia in pigs. Indirect hemagglutination (IHA) is typically used to serotype this bacterium, distinguishing 15 serovars with some nontypeable isolates. The capsule loci of the 15 reference strains have been annotated, and significant genetic variation was identified between serovars, with the exception of serovars 5 and 12. A capsule locus and in silico serovar were identified for all but two nontypeable isolates in our collection of >200 isolates. Here, we describe the development of a multiplex PCR, based on variation within the capsule loci of the 15 serovars of H. parasuis, for rapid molecular serotyping. The multiplex PCR (mPCR) distinguished between all previously described serovars except 5 and 12, which were detected by the same pair of primers. The detection limit of the mPCR was 4.29 × 10(5) ng/μl bacterial genomic DNA, and high specificity was indicated by the absence of reactivity against closely related commensal Pasteurellaceae and other bacterial pathogens of pigs. A subset of 150 isolates from a previously sequenced H. parasuis collection was used to validate the mPCR with 100% accuracy compared to the in silico results. In addition, the two in silico-nontypeable isolates were typeable using the mPCR. A further 84 isolates were analyzed by mPCR and compared to the IHA serotyping results with 90% concordance (excluding those that were nontypeable by IHA). The mPCR was faster, more sensitive, and more specific than IHA, enabling the differentiation of 14 of the 15 serovars of H. parasuis.

  4. Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis

    PubMed Central

    Peters, Sarah E.; Wang, Jinhong; Hernandez-Garcia, Juan; Weinert, Lucy A.; Luan, Shi-Lu; Chaudhuri, Roy R.; Angen, Øystein; Aragon, Virginia; Williamson, Susanna M.; Langford, Paul R.; Rycroft, Andrew N.; Wren, Brendan W.; Maskell, Duncan J.; Tucker, Alexander W.

    2015-01-01

    Haemophilus parasuis causes Glässer's disease and pneumonia in pigs. Indirect hemagglutination (IHA) is typically used to serotype this bacterium, distinguishing 15 serovars with some nontypeable isolates. The capsule loci of the 15 reference strains have been annotated, and significant genetic variation was identified between serovars, with the exception of serovars 5 and 12. A capsule locus and in silico serovar were identified for all but two nontypeable isolates in our collection of >200 isolates. Here, we describe the development of a multiplex PCR, based on variation within the capsule loci of the 15 serovars of H. parasuis, for rapid molecular serotyping. The multiplex PCR (mPCR) distinguished between all previously described serovars except 5 and 12, which were detected by the same pair of primers. The detection limit of the mPCR was 4.29 × 105 ng/μl bacterial genomic DNA, and high specificity was indicated by the absence of reactivity against closely related commensal Pasteurellaceae and other bacterial pathogens of pigs. A subset of 150 isolates from a previously sequenced H. parasuis collection was used to validate the mPCR with 100% accuracy compared to the in silico results. In addition, the two in silico-nontypeable isolates were typeable using the mPCR. A further 84 isolates were analyzed by mPCR and compared to the IHA serotyping results with 90% concordance (excluding those that were nontypeable by IHA). The mPCR was faster, more sensitive, and more specific than IHA, enabling the differentiation of 14 of the 15 serovars of H. parasuis. PMID:26424843

  5. Rapid molecular evolution across amniotes of the IIS/TOR network

    PubMed Central

    McGaugh, Suzanne E.; Bronikowski, Anne M.; Kuo, Chih-Horng; Reding, Dawn M.; Addis, Elizabeth A.; Flagel, Lex E.; Janzen, Fredric J.

    2015-01-01

    The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades. PMID:25991861

  6. Use of Flow Cytometry for Rapid, Quantitative Detection of Poliovirus-Infected Cells via TAT Peptide-Delivered Molecular Beacons

    PubMed Central

    Sivaraman, Divya; Yeh, Hsiao-Yun; Mulchandani, Ashok; Yates, Marylynn V.

    2013-01-01

    Rapid and efficient detection of viral infection is crucial for the prevention of disease spread during an outbreak and for timely clinical management. In this paper, the utility of Tat peptide-modified molecular beacons (MBs) as a rapid diagnostic tool for the detection of virus-infected cells was demonstrated. The rapid intracellular delivery mediated by the Tat peptide enabled the detection of infected cells within 30 s, reaching saturation in signal in 30 min. This rapid detection scheme was coupled with flow cytometry (FC), resulting in an automated, high-throughput method for the identification of virus-infected cells. Because of the 2-order-of-magnitude difference in fluorescence intensity between infected and uninfected cells, as few as 1% infected cells could be detected. Because of its speed and sensitivity, this approach may be adapted for the practical diagnosis of multiple viral infections. PMID:23160127

  7. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

    PubMed Central

    Laing, Chad R.; Lingohr, Erika J.; Gannon, Victor P. J.; Nash, John H. E.; Taboada, Eduardo N.

    2016-01-01

    For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub

  8. Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.

    SciTech Connect

    Wullschleger, Stan D; Weston, David; Davis, John M

    2009-01-01

    The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefitted greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which tree biologists can now explore the genome-wide effects of temperature, water and nutrient limitations on processes that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a number of examples whereby a systems approach, one that focuses on transcriptomic, proteomic, and metabolomic analyses is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment.

  9. Effect of nanostructure on rapid boiling of water on a hot copper plate: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Fu, Ting; Mao, Yijin; Tang, Yong; Zhang, Yuwen; Yuan, Wei

    2016-08-01

    Molecular dynamic simulations are performed to study the effects of nanostructure on rapid boiling of water that is suddenly heated by a hot copper plate. The results show that the nanostructure has significant effects on energy transfer from solid copper plate to liquid water and phase change process from liquid water to vapor. The liquid water on the solid surface rapidly boil after contacting with an extremely hot copper plate and consequently a cluster of liquid water moves upward during phase change. The temperature of the water film when it separates from solid surface and its final temperature when the system is at equilibrium strongly depend on the size of the nanostructure. These temperatures increase with increasing size of nanostructure. Furthermore, a non-vaporized molecular layer is formed on the surface of the copper plate even continuous heat flux is passing into water domain through the plate.

  10. Resource use, governance and case load of rapid response teams in Australia and New Zealand in 2014.

    PubMed

    2016-12-01

    Rapid response teams (RRTs) are a mandatory element of Australian national health care policy. However, the uptake, resourcing, case load and funding of RRTs in Australian and New Zealand hospitals remain unknown. To assess the clinical activity, funding, staffing and governance of RRTs in Australian and New Zealand hospitals. Survey of Australian and New Zealand hospitals as part of a biannual audit of intensive care resources and capacity. Of 207 hospitals surveyed, 165 (79.7%) participated, including 22 (13.3%) from New Zealand. RRTs were present in 138/143 (95.5%) Australian and 11/22 (50%) New Zealand hospitals equipped with intensive care units (P < 0.001). Additional funding was provided in 43/146 hospitals (29.4%) but was more likely in tertiary ICUs (P < 0.001) and in New Zealand (P = 0.012). ICU staff participated in 147/148 RRTs (99.3%), which involved medical staff only (10.2%), nursing staff only (6.8%), and both medical and nursing staff (76.2%). Isolated ICU nursing involvement was more common in smaller ICUs (P = 0.005), in rural/regional and metropolitan hospitals (P = 0.04), and in New Zealand (P = 0.006). Dedicated ICU outreach registrars and consultants were present in 19/146 hospitals (13.0%) and 14/145 hospitals (9.7%), respectively. The ICU provided oversight for 122/147 RRTs (83%). In the 2013-14 financial year, there were more than 104 000 RRT calls. In cases where data were known, ICU staff provided staff for most RRTs, and oversight for more than 80% of RRTs. However, additional funding for ICU RRT staff and dedicated doctors was relatively uncommon.

  11. Rapid molecular detection of tuberculosis and rifampicin drug resistance: retrospective analysis of a national U.K. molecular service over the last decade.

    PubMed

    Seoudi, N; Mitchell, S L; Brown, T J; Dashti, F; Amin, A K; Drobniewski, F A

    2012-04-01

    Fast and reliable detection of Mycobacterium tuberculosis complex (MTBC) and drug resistance is crucial in establishing effective treatment and enforcing timely public health measures. The authors analysed the performance of a national U.K. molecular diagnostic service over a decade, based on the use of a line probe assay (Innolipa, LiPA) compared with conventional liquid and solid cultures with rapid molecular identification and culture-based drug resistance testing. Data were available for 7836 consecutive patient samples using LiPA and the reference microbiological technique (conventional liquid and solid cultures with rapid molecular identification and culture-based drug resistance testing). For all sputum specimens (n=3382) the sensitivity, specificity, positive predictive value, negative predictive value and accuracy for MTBC detection were 93.4%, 85.6%, 92.7%, 86.9% and 90.7%; the equivalent values for smear-positive sputum specimens (n=2606) were 94.7%, 80.9%, 93.9%, 83.3% and 91.3%. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy for detection of rifampicin resistance in all sputum samples (n=1667) were 92.1%, 99.3%, 89.4%, 99.5% and 98.9%, respectively; the equivalent values for smear-positive sputum specimens (n=1477) were 93.3%, 99.3%, 87.5%, 99.6% and 99%. Between January 2006 and December 2008, LiPA saved 25.3 and 32.2 days for TB diagnosis and rifampicin resistance of smear-positive samples, respectively. A molecular diagnostic service, using a non-automated line probe assay approach, provides a rapid and reliable national service for diagnosing MTBC and rifampicin resistance.

  12. Physical heterogeneity increases biofilm resource use and its molecular diversity in stream mesocosms.

    PubMed

    Singer, Gabriel; Besemer, Katharina; Schmitt-Kopplin, Philippe; Hödl, Iris; Battin, Tom J

    2010-04-01

    Evidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC), a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood. Using six 40-m-long streamside flumes, we created a gradient of streambed landscapes with increasing spatial flow heterogeneity to assess how physical heterogeneity, inherent to streams, affects biofilm diversity and DOC use. We determined bacterial biodiversity in all six landscapes using 16S-rRNA fingerprinting and measured carbon uptake from glucose and DOC experimentally injected to all six flumes. The diversity of DOC molecules removed from the water was determined from ultrahigh-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS). Bacterial beta diversity, glucose and DOC uptake, and the molecular diversity of DOC use all increased with increasing flow heterogeneity. Causal modeling and path analyses of the experimental data revealed that the uptake of glucose was largely driven by physical processes related to flow heterogeneity, whereas biodiversity effects, such as complementarity, most likely contributed to the enhanced uptake of putatively recalcitrant DOC compounds in the streambeds with higher flow heterogeneity. Our results suggest biophysical mechanisms, including hydrodynamics and microbial complementarity effects, through which physical heterogeneity induces changes of resource use and carbon fluxes in streams. These findings highlight the importance of fine-scale streambed heterogeneity for microbial biodiversity and ecosystem functioning in streams, where homogenization and loss of habitats increasingly reduce biodiversity.

  13. Physical Heterogeneity Increases Biofilm Resource Use and Its Molecular Diversity in Stream Mesocosms

    PubMed Central

    Singer, Gabriel; Besemer, Katharina; Schmitt-Kopplin, Philippe; Hödl, Iris; Battin, Tom J.

    2010-01-01

    Background Evidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC), a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood. Methodology/Principal Findings Using six 40-m-long streamside flumes, we created a gradient of streambed landscapes with increasing spatial flow heterogeneity to assess how physical heterogeneity, inherent to streams, affects biofilm diversity and DOC use. We determined bacterial biodiversity in all six landscapes using 16S-rRNA fingerprinting and measured carbon uptake from glucose and DOC experimentally injected to all six flumes. The diversity of DOC molecules removed from the water was determined from ultrahigh-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS). Bacterial beta diversity, glucose and DOC uptake, and the molecular diversity of DOC use all increased with increasing flow heterogeneity. Causal modeling and path analyses of the experimental data revealed that the uptake of glucose was largely driven by physical processes related to flow heterogeneity, whereas biodiversity effects, such as complementarity, most likely contributed to the enhanced uptake of putatively recalcitrant DOC compounds in the streambeds with higher flow heterogeneity. Conclusions/Significance Our results suggest biophysical mechanisms, including hydrodynamics and microbial complementarity effects, through which physical heterogeneity induces changes of resource use and carbon fluxes in streams. These findings highlight the importance of fine-scale streambed heterogeneity for microbial biodiversity and ecosystem functioning in streams, where homogenization and loss of habitats increasingly reduce biodiversity. PMID:20376323

  14. Ground-water resources of the Rapid Valley unit, Cheyenne Division, South Dakota, with a section on the surface waters of Rapid Valley

    USGS Publications Warehouse

    Rosier, Arthur J.; Snell, L.J.

    1953-01-01

    The flow of Rapid Creek is affected by a variety of conditions. A few miles west of Rapid City, where Rapid Creek flows over the Englewood and Pahasapa limestones and the Minnelusa sandstone, there is a loss of about 8 cfs of water in a distance of a few miles. In the 3-mile reach of Rapid Creek between the Canyon Lake stream-gaging station and the Rapid City stream-gaging station there is a gain of about 20 cfs; much of this gain in flow may be attributed to the inflow from Cleghorn and Jackson springs and to the addition of water from the State-owned cement plant. In the Rapid Valley unit, the flow of the creek during the irrigation season is affected largely by the amount of water diverted for irrigation. The irrigation canals act as bypass channels, much of the water being returned to Rapid Creek by way of spillage into normally dry tributary creek channels and by movement through ground-water bodies that discharge into Rapid Creek.

  15. Evaluation of a Rapid Molecular Drug-Susceptibility Test for Tuberculosis.

    PubMed

    Xie, Yingda L; Chakravorty, Soumitesh; Armstrong, Derek T; Hall, Sandra L; Via, Laura E; Song, Taeksun; Yuan, Xing; Mo, Xiaoying; Zhu, Hong; Xu, Peng; Gao, Qian; Lee, Myungsun; Lee, Jongseok; Smith, Laura E; Chen, Ray Y; Joh, Joon Sung; Cho, YoungSoo; Liu, Xin; Ruan, Xianglin; Liang, Lili; Dharan, Nila; Cho, Sang-Nae; Barry, Clifton E; Ellner, Jerrold J; Dorman, Susan E; Alland, David

    2017-09-14

    Fluoroquinolones and second-line injectable drugs are the backbone of treatment regimens for multidrug-resistant tuberculosis, and resistance to these drugs defines extensively drug-resistant tuberculosis. We assessed the accuracy of an automated, cartridge-based molecular assay for the detection, directly from sputum specimens, of Mycobacterium tuberculosis with resistance to fluoroquinolones, aminoglycosides, and isoniazid. We conducted a prospective diagnostic accuracy study to compare the investigational assay against phenotypic drug-susceptibility testing and DNA sequencing among adults in China and South Korea who had symptoms of tuberculosis. The Xpert MTB/RIF assay and sputum culture were performed. M. tuberculosis isolates underwent phenotypic drug-susceptibility testing and DNA sequencing of the genes katG, gyrA, gyrB, and rrs and of the eis and inhA promoter regions. Among the 308 participants who were culture-positive for M. tuberculosis, when phenotypic drug-susceptibility testing was used as the reference standard, the sensitivities of the investigational assay for detecting resistance were 83.3% for isoniazid (95% confidence interval [CI], 77.1 to 88.5), 88.4% for ofloxacin (95% CI, 80.2 to 94.1), 87.6% for moxifloxacin at a critical concentration of 0.5 μg per milliliter (95% CI, 79.0 to 93.7), 96.2% for moxifloxacin at a critical concentration of 2.0 μg per milliliter (95% CI, 87.0 to 99.5), 71.4% for kanamycin (95% CI, 56.7 to 83.4), and 70.7% for amikacin (95% CI, 54.5 to 83.9). The specificity of the assay for the detection of phenotypic resistance was 94.3% or greater for all drugs except moxifloxacin at a critical concentration of 2.0 μg per milliliter (specificity, 84.0% [95% CI, 78.9 to 88.3]). When DNA sequencing was used as the reference standard, the sensitivities of the investigational assay for detecting mutations associated with resistance were 98.1% for isoniazid (95% CI, 94.4 to 99.6), 95.8% for fluoroquinolones (95% CI, 89.6 to

  16. Resources.

    ERIC Educational Resources Information Center

    Aviation/Space, 1980

    1980-01-01

    The resources listed different types of materials related to the aerospace science under specified categories: free materials and inexpensive, selected government publication, audiovisual (government, nongovernment), aviation books, and space books. The list includes the publisher's name and the price for each publication. (SK)

  17. Resources.

    ERIC Educational Resources Information Center

    Stewart, John; MacDonald, Ian

    1980-01-01

    Presents a guide to resources on television drama available to teachers for classroom use in television curriculum. Lists American and British television drama videorecordings of both series and individual presentations and offers a bibliography of "one-off" single fiction plays produced for British television. (JMF)

  18. Resources.

    ERIC Educational Resources Information Center

    Aviation/Space, 1980

    1980-01-01

    The resources listed different types of materials related to the aerospace science under specified categories: free materials and inexpensive, selected government publication, audiovisual (government, nongovernment), aviation books, and space books. The list includes the publisher's name and the price for each publication. (SK)

  19. Rapid evolution of hyaluronan synthase to improve hyaluronan production and molecular mass in Bacillus subtilis.

    PubMed

    Zhang, Linpei; Huang, Hao; Wang, Hao; Chen, Jian; Du, Guocheng; Kang, Zhen

    2016-12-01

    To improve the production and molecular mass of the glycosaminoglycan hyaluronan (HA) in Bacillus subtilis by engineering hyaluronan synthase (HAS) from Streptococcus zooepidemicus. By mutating regions within HAS intracellular domains, five positive variants exhibiting higher HA production (from 1.22 to 2.24 g l(-1)) and molecular mass values (from 1.20 to 1.36 × 10(6) Da) were constructed and characterized. Overexpression of the V5 variant and the genes tuaD and glmU increased HA production and molecular mass to 2.8 g l(-1) and 2.4 × 10(6) Da, respectively. This study provides a novel strategy for improving HA production and its molecular mass.

  20. Rapid effects of estrogens on behavior: environmental modulation and molecular mechanisms.

    PubMed

    Laredo, Sarah A; Villalon Landeros, Rosalina; Trainor, Brian C

    2014-10-01

    Estradiol can modulate neural activity and behavior via both genomic and nongenomic mechanisms. Environmental cues have a major impact on the relative importance of these signaling pathways with significant consequences for behavior. First we consider how photoperiod modulates nongenomic estrogen signaling on behavior. Intriguingly, short days permit rapid effects of estrogens on aggression in both rodents and song sparrows. This highlights the importance of considering photoperiod as a variable in laboratory research. Next we review evidence for rapid effects of estradiol on ecologically-relevant behaviors including aggression, copulation, communication, and learning. We also address the impact of endocrine disruptors on estrogen signaling, such as those found in corncob bedding used in rodent research. Finally, we examine the biochemical mechanisms that may mediate rapid estrogen action on behavior in males and females. A common theme across these topics is that the effects of estrogens on social behaviors vary across different environmental conditions.

  1. Rapid effects of estrogens on behavior: environmental modulation and molecular mechanisms

    PubMed Central

    Laredo, Sarah A.; Landeros, Rosalina Villalon; Trainor, Brian C.

    2014-01-01

    Estradiol can modulate neural activity and behavior via both genomic and nongenomic mechanisms. Environmental cues have a major impact on the relative importance of these signaling pathways with significant consequences for behavior. First we consider how photoperiod modulates nongenomic estrogen signaling on behavior. Intriguingly, short days permit rapid effects of estrogens on aggression in both rodents and song sparrows. This highlights the importance of considering photoperiod as a variable in laboratory research. Next we review evidence for rapid effects of estradiol on ecologically-relevant behaviors including aggression, copulation, communication, and learning. We also address the impact of endocrine disruptors on estrogen signaling, such as those found in corncob bedding used in rodent research. Finally, we examine the biochemical mechanisms that may mediate rapid estrogen action on behavior in males and females. A common theme across these topics is that the effects of estrogens on social behaviors vary across different environmental conditions. PMID:24685383

  2. Combine-ARMS: a rapid and cost-effective protocol for molecular characterization of beta-thalassemia in Malaysia.

    PubMed

    Tan, K L; Tan, J A; Wong, Y C; Wee, Y C; Thong, M K; Yap, S F

    2001-01-01

    Beta-thalassemia major patients have chronic anemia and are dependent on blood transfusions to sustain life. Molecular characterization and prenatal diagnosis of beta3-thalassemia is essential in Malaysia because about 4.5% of the population are heterozygous carriers for beta-thalassemia. The high percentage of compound heterozygosity (47.62%) found in beta-thalassemia major patients in the Thalassaemia Registry, University of Malaya Medical Centre (UMMC), Malaysia, also supports a need for rapid, economical, and sensitive protocols for the detection of beta-thalassemia mutations. Molecular characterization of beta-thalassemia mutations in Malaysia is currently carried out using ARMS, which detects a single beta-thalassemia mutation per PCR reaction. We developed and evaluated Combine amplification refractory mutation system (C-ARMS) techniques for efficient molecular detection of two to three beta-thalassemia mutations in a single PCR reaction. Three C-ARMS protocols were evaluated and established for molecular characterization of common beta-thalassemia mutations in the Malay and Chinese ethnic groups in Malaysia. Two C-ARMS protocols (cd 41-42/IVSII #654 and -29/cd 71-72) detected the beta-thalassemia mutations in 74.98% of the Chinese patients studied. The CARMS for cd 41-42/IVSII #654 detected beta-thalassemia mutations in 72% of the Chinese families. C-ARMS for cd 41-42/IVSI #5/cd 17 allowed detection of beta-thalassemia mutations in 36.53% of beta-thalassemia in the Malay patients. C-ARMS for cd 41-42/IVSI #5/cd 17 detected beta-thalassemia in 45.54% of the Chinese patients. We conclude that C-ARMS with the ability to detect two to three mutations in a single reaction provides more rapid and cost-effective protocols for beta-thalassemia prenatal diagnosis and molecular analysis programs in Malaysia.

  3. Synthesis of multi-core-shell magnetic molecularly imprinted microspheres for rapid recognition of dicofol in tea.

    PubMed

    Yan, Hongyuan; Cheng, Xiaoling; Sun, Ning

    2013-03-20

    Magnetic multi-core-shell molecularly imprinted microspheres (Fe3O4@MIMs) based on multi-Fe3O4 nanoparticles as core structures and dummy imprinted materials as shell structures have been synthesized by a surface-imprinted technique using dichlorodiphenyltrichloroethane as the dummy template and were successfully used as a specific adsorbent for rapid isolation of trace levels of dicofol from teas. The resulting Fe3O4@MIMs were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, vibrating sample magnetometer, and thermogravimetric analysis. In comparison to the imprinted polymers prepared by the traditional polymerizations, the obtained Fe3O4@MIMs showed regularly spherical shape, porous morphologies, high saturation magnetization [56.8 electromagnetic units (emu)/g], and rapid response time (15 s). The as-synthesized Fe3O4@MIMs, which incorporated the excellent molecular recognition and magnetic separation properties, were successfully used as special adsorbents for rapid isolation and extraction of trace levels of dicofol and its analogues from a complicated tea matrix.

  4. Ligand Replacement Approach to Raman-Responded Molecularly Imprinted Monolayer for Rapid Determination of Penicilloic Acid in Penicillin.

    PubMed

    Zhang, Liying; Jin, Yang; Huang, Xiaoyan; Zhou, Yujie; Du, Shuhu; Zhang, Zhongping

    2015-12-01

    Penicilloic acid (PA) is a degraded byproduct of penicillin and often causes fatal allergies to humans, but its rapid detection in penicillin drugs remains a challenge due to its similarity to the mother structure of penicillin. Here, we reported a ligand-replaced molecularly imprinted monolayer strategy on a surface-enhanced Raman scattering (SERS) substrate for the specific recognition and rapid detection of Raman-inactive PA in penicillin. The bis(phenylenediamine)-Cu(2+)-PA complex was first synthesized and stabilized onto the surface of silver nanoparticle film that was fabricated by a bromide ion-added silver mirror reaction. A molecularly imprinted monolayer was formed by the further modification of alkanethiol around the stabilized complex on the Ag film substrate, and the imprinted recognition site was then created by the replacement of the complex template with Raman-active probe molecule p-aminothiophenol. When PA rebound into the imprinted site in the alkanethiol monolayer, the SERS signal of p-aminothiophenol exhibited remarkable enhancement with a detection limit of 0.10 nM. The imprinted monolayer can efficiently exclude the interference of penicillin and thus provides a selective determination of 0.10‰ (w/w) PA in penicillin, which is about 1 order of magnitude lower than the prescribed residual amount of 1.0‰. The strategy reported here is simple, rapid and inexpensive compared to the traditional chromatography-based methods.

  5. Rapid and amplification-free detection of fish pathogens by utilizing a molecular beacon-based microfluidic system.

    PubMed

    Su, Yi-Chih; Wang, Chih-Hung; Chang, Wen-Hsin; Chen, Tzong-Yueh; Lee, Gwo-Bin

    2015-01-15

    Nervous necrosis virus (NNV) and iridovirus are highly infectious pathogens that can cause lethal diseases in various species of fish. These infectious diseases have no effective treatments and the mortality rate is over 80%, which could cause dramatic economic losses in the aquaculture industry. Conventional diagnostic methods of NNV or iridovirus infected fishes, such as virus culture, enzyme-linked immunosorbent assays and nucleic acid assays usually require time-consuming and complex procedures performed by specialized technicians with delicate laboratory facilities. Rapid, simple, accurate and on-site detection of NNV and iridovirus infections would enable timely preventive measures such as immediate sacrifice of infected fishes, and is therefore critically needed for the aquaculture industry. In this study, a microfluidic-based assay that employ magnetic beads conjugated with viral deoxyribonucleic acid (DNA) capturing probes and fluorescent DNA molecular beacons were developed to rapidly detect NNV and iridovirus. Importantly, this new assay was realized in an integrated microfluidic system with a custom-made control system. With this approach, direct and automated NNV and iridovirus detection from infected fishes can be achieved in less than 30 min. Therefore, this molecular-beacon based microfluidic system presents a potentially promising tool for rapid diagnosis of fish pathogens in the field in the future.

  6. Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions.

    PubMed

    Bakker, Theo C M; Giger, Thomas; Frommen, Joachim G; Largiadèr, Carlo R

    2017-08-01

    There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences. Three molecular PCR-based sex tests were developed, in which the first, the second or both insertions were covered. In five European populations (from DE, CH, NL, GB) of three-spined sticklebacks, tests with both insertions combined showed two clearly separated bands on agarose minigels in males and one band in females. The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods.

  7. Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection.

    PubMed

    Barreda-García, Susana; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Lobo-Castañón, María Jesús

    2017-09-20

    Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed. Graphical Abstract Expanding the analytical toolbox for the detection of DNA sequences specific of pathogens with isothermal helicase dependent amplification (HDA).

  8. Molecularly chemisorbed intermediate state to oxygen adsorption on Pd{110} [rapid communication

    NASA Astrophysics Data System (ADS)

    Junell, P.; Honkala, K.; Hirsimäki, M.; Valden, M.; Laasonen, K.

    2003-12-01

    Translational energy ( ET) dependence of oxygen (O 2) adsorption on Pd{1 1 0} has been investigated with molecular beam surface scattering (MBSS) experiments. The initial sticking probability ( S0) and adsorption kinetics of oxygen are shown to depend strongly on ET of the incident molecule. An inverse surface temperature dependence of S0 is also observed at low translational energies. Using density-functional theory calculations several O 2 adsorption potential energy curves (PECs) on Pd{1 1 0} were determined. Direct adsorption PECs with an activation barrier and two PECs with a molecular chemisorption state were found. Both experimental and theoretical results indicate a twofold adsorption mechanism. At low ET molecules end up in a very attractive molecularly chemisorbed precursor state from which they eventually dissociate. At higher ET more molecules begin to dissociate via a direct activated adsorption channel.

  9. Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules.

    PubMed

    Wang, Baojun; Buck, Martin

    2014-10-11

    We designed and constructed versatile modular genetic logic gates in bacterial cells. These function as digital logic 1-input Buffer gate, 2-input and 3-input AND gates with one inverted input and integrate multiple chemical input signals in customised logic manners. Such rapidly engineered devices serve to achieve increased sensing signal selectivity.

  10. Rapid determination of the molecular weight distribution of total cellular fatty acids using chemical ionization mass spectrometry.

    PubMed

    Schwarzenbach, R P; Fisher, N S

    1978-01-01

    A new method for the qualitative and quantitative determination of the molecular weight distribution of total cellular fatty acids is described. The method includes a simple extraction-saponification followed by chemical ionization-mass spectrometric analysis of the saponifiable matter. This technique requires small quantities of cell material which, combined with the rapidity and precision of the analysis, makes it attractive to the biologist interested in changes in the fatty acid composition of growing cells. As an example, an application of this method to the fatty acid determination of marine diatoms at different growth stages is presented.

  11. The VA Point-of-Care Precision Oncology Program: Balancing Access with Rapid Learning in Molecular Cancer Medicine

    PubMed Central

    Fiore, Louis D.; Brophy, Mary T.; Turek, Sara; Kudesia, Valmeek; Ramnath, Nithya; Shannon, Colleen; Ferguson, Ryan; Pyarajan, Saiju; Fiore, Melissa A.; Hornberger, John; Lavori, Philip

    2016-01-01

    The Department of Veterans Affairs (VA) recognized the need to balance patient-centered care with responsible creation of generalizable knowledge on the effectiveness of molecular medicine tools. Embracing the principles of the rapid learning health-care system, a new clinical program called the Precision Oncology Program (POP) was created in New England. The POP integrates generalized knowledge about molecular medicine in cancer with a database of observations from previously treated veterans. The program assures access to modern genomic oncology practice in the veterans affairs (VA), removes disparities of access across the VA network of clinical centers, disseminates the products of learning that are generalizable to non-VA settings, and systematically presents opportunities for patients to participate in clinical trials of targeted therapeutics. PMID:26949343

  12. Rapid Detection of Rifampin Resistance in Mycobacterium tuberculosis Isolates from India and Mexico by a Molecular Beacon Assay

    PubMed Central

    Varma-Basil, Mandira; El-Hajj, Hiyam; Colangeli, Roberto; Hazbón, Manzour Hernando; Kumar, Sujeet; Bose, Mridula; Bobadilla-del-Valle, Miriam; García, Lourdes García; Hernández, Araceli; Kramer, Fred Russell; Osornio, Jose Sifuentes; Ponce-de-León, Alfredo; Alland, David

    2004-01-01

    We assessed the performance of a rapid, single-well, real-time PCR assay for the detection of rifampin-resistant Mycobacterium tuberculosis by using clinical isolates from north India and Mexico, regions with a high incidence of tuberculosis. The assay uses five differently colored molecular beacons to determine if a short region of the M. tuberculosis rpoB gene contains mutations that predict rifampin resistance in most isolates. Until now, the assay had not been sufficiently tested on samples from countries with a high incidence of tuberculosis. In the present study, the assay detected mutations in 16 out of 16 rifampin-resistant isolates from north India (100%) and in 55 of 64 rifampin-resistant isolates from Mexico (86%) compared to results with standard susceptibility testing. The assay did not detect mutations (a finding predictive of rifampin susceptibility) in 37 out of 37 rifampin-susceptible isolates from India (100%) and 125 out of 126 rifampin-susceptible isolates from Mexico (99%). DNA sequencing revealed that none of the nine rifampin-resistant isolates from Mexico, which were misidentified as rifampin susceptible by the molecular beacon assay, contained a mutation in the region targeted by the molecular beacons. The one rifampin-susceptible isolate from Mexico that appeared to be rifampin resistant by the molecular beacon assay contained an S531W mutation, which is usually associated with rifampin resistance. Of the rifampin-resistant isolates that were correctly identified in the molecular beacon assay, one contained a novel L530A mutation and another contained a novel deletion between codons 511 and 514. Overall, the molecular beacon assay appears to have sufficient sensitivity (89%) and specificity (99%) for use in countries with a high prevalence of tuberculosis. PMID:15583274

  13. Rapid PCR real-time genotyping of M-Malton alpha1-antitrypsin deficiency alleles by molecular beacons.

    PubMed

    Orrù, Germano; Faa, Gavino; Pillai, Sara; Pilloni, Luca; Montaldo, Caterina; Pusceddu, Gesuina; Piras, Vincenzo; Coni, Pierpaolo

    2005-12-01

    Alpha1-Antitrypsin deficiency is an autosomal codominant inherited disorder, with increased risk of developing lung and liver disease. The large majority of subjects affected by alpha1-antitrypsin deficiency carry the PIZZ or PISZ genotypes, which can be easily detected using several molecular methods. Another pathologic allele, the M-Malton variant (also known as Mnichinan and Mcagliari), can mimic the Pi Z clinical phenotype, but this alpha1-antitrypsin deficiency variant is not easily recognizable and, therefore, seems to be more under-recognized than the Z or S alleles. We report the development of a rapid qualitative fluorescent real-time PCR assay designed for the detection of the M-Malton alpha1-antitrypsin deficiency alleles using 2 specific molecular beacons. The assay is able to detect in a single tube the homozygous as well the heterozygous genotypes. The procedure combines the great sensitivity of the polymerase chain reaction, the specificity provided by allele-specific molecular beacons, and the throughput of a multi-color fluorescence detection procedure. This technique will be useful for research and molecular diagnostic laboratories involved in the study of alpha1-antitrypsin deficiency-related diseases.

  14. Rapid molecular diagnostic test for Zika virus with low demands on sample preparation and instrumentation.

    PubMed

    Eboigbodin, Kevin E; Brummer, Mirko; Ojalehto, Tuomas; Hoser, Mark

    2016-12-01

    Zika virus has only recently gained attention due to recent large outbreaks worldwide. An easy to use nucleic acid amplification test could play an important role in the early detection of the infection and patient management. Here, we report a rapid and robust isothermal nucleic acid amplification assay for the detection of Zika virus. The method is cost-effective and compatible with portable instrumentation, enabling near patient testing and field use.

  15. Rapid detection of IHNV by molecular padlock recognition and surface-associated isothermal amplification

    NASA Astrophysics Data System (ADS)

    McCarthy, Erik L.; Egeler, Teressa J.; Bickerstaff, Lee E.; Pereira da Cunha, Mauricio; Millard, Paul J.

    2005-11-01

    RNA sequences derived from infectious hematopoeitic necrosis virus (IHNV) could be detected using a combination of surface-associated molecular padlock DNA probes (MPP) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV were recognized by MPP. Circularized MPP were then captured on the inner surface of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA gave rise to DNA concatamers, which were in turn bound by the fluorescent reporter SYBR Green II nucleic acid stain, and measured by microfluorimetry. Surface-associated molecular padlock technology, combined with isothermal RCA, exhibited high selectivity and sensitivity without thermal cycling. This technology is applicable to direct RNA and DNA detection, permitting detection of a variety of viral or bacterial pathogens.

  16. Geological dates and molecular rates: rapid divergence of rivers and their biotas.

    PubMed

    Waters, Jonathan M; Rowe, Diane L; Apte, Smita; King, Tania M; Wallis, Graham P; Anderson, Leigh; Norris, Richard J; Craw, Dave; Burridge, Christopher P

    2007-04-01

    We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

  17. Development of Molecular Resources for an Intertidal Clam, Sinonovacula constricta, Using 454 Transcriptome Sequencing

    PubMed Central

    Niu, Donghong; Wang, Lie; Sun, Fanyue; Liu, Zhanjiang; Li, Jiale

    2013-01-01

    Background The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait. Results Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated. Conclusion De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta. PMID:23935831

  18. Rapid Molecular Identification of Pathogenic Yeasts by Pyrosequencing Analysis of 35 Nucleotides of Internal Transcribed Spacer 2 ▿

    PubMed Central

    Borman, Andrew M.; Linton, Christopher J.; Oliver, Debra; Palmer, Michael D.; Szekely, Adrien; Johnson, Elizabeth M.

    2010-01-01

    Rapid identification of yeast species isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. Here, we have evaluated the utility of pyrosequencing analysis of a portion of the internal transcribed spacer 2 region (ITS2) for identification of pathogenic yeasts. A total of 477 clinical isolates encompassing 43 different fungal species were subjected to pyrosequencing analysis in a strictly blinded study. The molecular identifications produced by pyrosequencing were compared with those obtained using conventional biochemical tests (AUXACOLOR2) and following PCR amplification and sequencing of the D1-D2 portion of the nuclear 28S large rRNA gene. More than 98% (469/477) of isolates encompassing 40 of the 43 fungal species tested were correctly identified by pyrosequencing of only 35 bp of ITS2. Moreover, BLAST searches of the public synchronized databases with the ITS2 pyrosequencing signature sequences revealed that there was only minimal sequence redundancy in the ITS2 under analysis. In all cases, the pyrosequencing signature sequences were unique to the yeast species (or species complex) under investigation. Finally, when pyrosequencing was combined with the Whatman FTA paper technology for the rapid extraction of fungal genomic DNA, molecular identification could be accomplished within 6 h from the time of starting from pure cultures. PMID:20702674

  19. Rapid microwave-assisted synthesis of molecularly imprinted polymers on carbon quantum dots for fluorescent sensing of tetracycline in milk.

    PubMed

    Hou, Juan; Li, Huiyu; Wang, Long; Zhang, Ping; Zhou, Tianyu; Ding, Hong; Ding, Lan

    2016-01-01

    In this paper, a novel, selective and eco-friendly sensor for the detection of tetracycline was developed by grafting imprinted polymers onto the surface of carbon quantum dots. A simple microwave-assisted approach was utilized to fabricate the fluorescent imprinted composites rapidly for the first time, which could shorten the polymerization time and simplify the experimental procedure dramatically. The novel composites not only demonstrated excellent fluorescence stability and special binding sites, but also could selectively accumulate target analytes. Under optimal conditions, the relative fluorescence intensity of the composites decreased linearly with increasing the concentration of tetracycline from 20 nM to 14 µM. The detection limit of tetracycline was 5.48 nM. The precision and reproducibility of the proposed sensor were also acceptable. Significantly, the practicality of this ultrasensitive sensor for tetracycline detection in milk was further validated, revealing the advantages of simplicity, sensitivity, selectivity and low cost. This approach combines the high selective adsorption property of molecular imprinted polymers and the sensitivity of fluorescence detection. It is envisioned that the development of fluorescent molecularly imprinted composites will offer a new way of thinking for rapid analysis in complex samples.

  20. Rapid molecular haemagglutinin subtyping of avian influenza isolates by specific real-time RT-PCR tests.

    PubMed

    Elizalde, Maia; Agüero, Montserrat; Buitrago, Dolores; Yuste, María; Arias, María Luisa; Muñoz, María Jesús; Lelli, Davide; Pérez-Ramírez, Elisa; Moreno-Martin, Ana María; Fernández-Pinero, Jovita

    2014-02-01

    Sixteen haemagglutinin (HA) subtypes of avian influenza viruses (AIV) have been described to date. Rapid subtype identification of any AIV is of major interest because of the possible serious consequences for the poultry industry and even public health. Molecular techniques currently allow immediate accurate subtype characterisation prior to virus isolation. In this study, a set of fourteen specific real-time RT-PCR methods were developed and evaluated for AIV HA subtyping (H1-H4, H6-H8, H10-H16), H5 and H9 being excluded on the basis of the current validity of the European Union (EU) recommended specific assays. Specific primers and probes sets for each HA-subtype were designed to hybridise the largest isolates range within each single subtype, considering the Eurasian lineage as a major target. The robustness and general application of the 14 HA-subtype methods were verified by the analysis of 110 AIV isolates belonging to all 16 HA-subtypes, performed in different laboratories. The developed real-time RT-PCR assays proved to be highly specific and revealed suitable sensitivity, allowing direct HA-subtyping of clinical material. In summary, this study provides for the first time a panel of molecular tests using specific hydrolysis probes for rapid and complete AIV HA-subtype identification.

  1. Rapid Identification and Characterization of Francisella by Molecular Biology and Other Techniques

    PubMed Central

    Lai, Xin-He; Zhao, Long-Fei; Chen, Xiao-Ming; Ren, Yi

    2016-01-01

    Francisella tularensis is the causative pathogen of tularemia and a Tier 1 bioterror agent on the CDC list. Considering the fact that some subpopulation of the F. tularensis strains is more virulent, more significantly associated with mortality, and therefore poses more threat to humans, rapid identification and characterization of this subpopulation strains is of invaluable importance. This review summarizes the up-to-date developments of assays for mainly detecting and characterizing F. tularensis and a touch of caveats of some of the assays. PMID:27335619

  2. Rapid DNA extraction protocol from stool, suitable for molecular genetic diagnosis of colon cancer.

    PubMed

    Abbaszadegan, Mohammad Reza; Velayati, Arash; Tavasoli, Alireza; Dadkhah, Ezzat

    2007-07-01

    Colorectal cancer (CRC) is one of the most common forms of cancers in the world and is curable if diagnosed at the early stage. Analysis of DNA extracted from stool specimens is a recent advantage to cancer diagnostics. Many protocols have been recommended for DNA extraction from stool, and almost all of them are difficult and time consuming, dealing with high amount of toxic materials like phenol. Their results vary due to sample collection method and further purification treatment. In this study, an easy and rapid method was optimized for isolating the human DNA with reduced PCR inhibitors present in stool. Fecal samples were collected from 10 colonoscopy-negative adult volunteers and 10 patients with CRC. Stool (1 g) was extracted using phenol/chloroform based protocol. The amplification of P53 exon 9 was examined to evaluate the extraction efficiency for human genomic targets and also compared its efficiency with Machiels et al. and Ito et al. protocols. The amplification of exon 9 of P53 from isolated fecal DNA was possible in most cases in 35 rounds of PCR using no additional purification procedure for elimination of the remaining inhibitors.inhibitors. A useful, rapid and easy protocol for routine extraction of DNA from stool was introduced and compared with two previous protocols.

  3. Simple and rapid molecular techniques for identification of amylose levels in rice varieties.

    PubMed

    Cheng, Acga; Ismail, Ismanizan; Osman, Mohamad; Hashim, Habibuddin

    2012-01-01

    The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)(10), (CT)(11), (CT)(16), (CT)(17), and (CT)(18) were identified. Of these, (CT)(11) and (CT)(17) were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)(10) and (CT)(11), while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5'-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE.

  4. Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection - a new frontier?

    PubMed Central

    2012-01-01

    Among critically ill patients, the diagnosis of bloodstream infection poses a major challenge. Current standard bacterial identification based on blood culture platforms is intrinsically time-consuming and slow. The continuous evolvement of molecular techniques has the potential of providing a faster, more sensitive and direct identification of causative pathogens without prior need for cultivation. This may ultimately impact clinical decision-making and antimicrobial treatment. This review summarises the currently available technologies, their strengths and limitations and the obstacles that have to be overcome in order to develop a satisfactory bedside point-of-care diagnostic tool for detection of bloodstream infection. PMID:22647543

  5. A Rapid Molecular Test for Determining Yersinia pestis Susceptibility to Ciprofloxacin by the Quantification of Differentially Expressed Marker Genes

    PubMed Central

    Steinberger-Levy, Ida; Shifman, Ohad; Zvi, Anat; Ariel, Naomi; Beth-Din, Adi; Israeli, Ofir; Gur, David; Aftalion, Moshe; Maoz, Sharon; Ber, Raphael

    2016-01-01

    Standard antimicrobial susceptibility tests used to determine bacterial susceptibility to antibiotics are growth dependent and time consuming. The long incubation time required for standard tests may render susceptibility results irrelevant, particularly for patients infected with lethal bacteria that are slow growing on agar but progress rapidly in vivo, such as Yersinia pestis. Here, we present an alternative approach for the rapid determination of antimicrobial susceptibility, based on the quantification of the changes in the expression levels of specific marker genes following exposure to growth-inhibiting concentrations of the antibiotic, using Y. pestis and ciprofloxacin as a model. The marker genes were identified by transcriptomic DNA microarray analysis of the virulent Y. pestis Kimberley53 strain after exposure to specific concentrations of ciprofloxacin for various time periods. We identified several marker genes that were induced following exposure to growth-inhibitory concentrations of ciprofloxacin, and we confirmed the marker expression profiles at additional ciprofloxacin concentrations using quantitative RT-PCR. Eleven candidate marker transcripts were identified, of which four mRNA markers were selected for a rapid quantitative RT-PCR susceptibility test that correctly determined the Minimal Inhibitory Concentration (MIC) values and the categories of susceptibility of several Y. pestis strains and isolates harboring various ciprofloxacin MIC values. The novel molecular susceptibility test requires just 2 h of antibiotic exposure in a 7-h overall test time, in contrast to the 24 h of antibiotic exposure required for a standard microdilution test. PMID:27242774

  6. Rapid and molecular selective electrochemical sensing of phthalates in aqueous solution.

    PubMed

    Zia, Asif I; Mukhopadhyay, Subhas Chandra; Yu, Pak-Lam; Al-Bahadly, I H; Gooneratne, Chinthaka P; Kosel, J Rgen

    2015-05-15

    Reported research work presents real time non-invasive detection of phthalates in spiked aqueous samples by employing electrochemical impedance spectroscopy (EIS) technique incorporating a novel interdigital capacitive sensor with multiple sensing thin film gold micro-electrodes fabricated on native silicon dioxide layer grown on semiconducting single crystal silicon wafer. The sensing surface was functionalized by a self-assembled monolayer of 3-aminopropyltrietoxysilane (APTES) with embedded molecular imprinted polymer (MIP) to introduce selectivity for the di(2-ethylhexyl) phthalate (DEHP) molecule. Various concentrations (1-100 ppm) of DEHP in deionized MilliQ water were tested using the functionalized sensing surface to capture the analyte. Frequency response analyzer (FRA) algorithm was used to obtain impedance spectra so as to determine sample conductance and capacitance for evaluation of phthalate concentration in the sample solution. Spectrum analysis algorithm interpreted the experimentally obtained impedance spectra by applying complex nonlinear least square (CNLS) curve fitting in order to obtain electrochemical equivalent circuit and corresponding circuit parameters describing the kinetics of the electrochemical cell. Principal component analysis was applied to deduce the effects of surface immobilized molecular imprinted polymer layer on the evaluated circuit parameters and its electrical response. The results obtained by the testing system were validated using commercially available high performance liquid chromatography diode array detector system.

  7. Molecular phylogeny of the small carpenter bees (Hymenoptera: Apidae: Ceratinini) indicates early and rapid global dispersal.

    PubMed

    Rehan, Sandra M; Chapman, Tom W; Craigie, Andrew I; Richards, Miriam H; Cooper, Steven J B; Schwarz, Michael P

    2010-06-01

    The small carpenter bees (tribe Ceratinini, family Apidae) are recorded from all continents except Antarctica. The Ceratinini have a near-global distribution which contrasts strongly with their sister tribe, the Allodapini which has a largely southern Old World distribution. The Ceratinini therefore provides an excellent group to understand the factors that help determine the biogeography and radiation of the bees. This is the first molecular study of ceratinine bees covering representatives from both northern and southern hemisphere Old and New World regions. We use two mitochondrial and one nuclear marker (totalling 2807 nucleotides) to examine the age, cladogenesis and historical biogeography of this tribe. Tree topology and molecular dating support an African origin at about 47 Mya with subsequent dispersal into Eurasia 44 Mya, and followed by an American invasion 32 Mya. Concentrated African and Malagasy sampling revealed there were two or three dispersals events into Madagascar ranging from 25 to 9 Mya. Lineage through time analyses suggest higher rates of cladogenesis close to the origin of the tribe, and this corresponds to both major dispersal events and divergences of lineages leading to extant subgenera. Ceratinini have potentially great importance for future studies to understand the relative roles of dispersal ability and time of origin in determining bee biogeography.

  8. Preparation of molecularly imprinted polymer with double templates for rapid simultaneous determination of melamine and dicyandiamide in dairy products.

    PubMed

    Liu, Jiang; Song, Han; Liu, Jie; Liu, Yuan; Li, Le; Tang, Hui; Li, Yingchun

    2015-03-01

    In this study, a rapid and accurate determination strategy was established for simultaneous measurement of melamine (MLM) and dicyandiamide (DCD) directly in powdered milk by coupling molecularly imprinted solid-phase extraction (MISPE) with high performance liquid chromatography (HPLC). A novel double-template technique was adopted for preparing SPE packing agent and the obtained double-templated (MLM and DCD) molecularly imprinted polymers (MD-MIPs) was characterized by Fourier-transform infrared spectroscopy and scanning electron microscope (SEM). The molecular recognition ability and the binding capability of the as-prepared polymers towards MLM and DCD were evaluated via static and dynamic binding tests, and it was found that the MD-MIPs showed better affinity and selectivity for both templates compared with single-templated MIPs and non-imprinted polymers (NIPs). An approach based on MISPE and HPLC was then developed and optimized to detect MLM and DCD in powdered milk. The detection limit of the method (S/N=3) were 0.13 μg/g for MLM and 0.07 μg/g for DCD, and the relative standard deviation (RSD) of intra-day and inter-day determination for MLM was 3.3% and 4.7%, and 3.5% and 5.9% for DCD. The recoveries in MLM and DCD analysis at three spiked levels were 93.1-100.1% and 75.7-82.5%, respectively, with all RSD less than 5.2%.

  9. Identification and Molecular Mechanisms of the Rapid Tonicity-induced Relocalization of the Aquaporin 4 Channel*

    PubMed Central

    Kitchen, Philip; Day, Rebecca E.; Taylor, Luke H. J.; Salman, Mootaz M.; Bill, Roslyn M.; Conner, Matthew T.; Conner, Alex C.

    2015-01-01

    The aquaporin family of integral membrane proteins is composed of channels that mediate cellular water flow. Aquaporin 4 (AQP4) is highly expressed in the glial cells of the central nervous system and facilitates the osmotically driven pathological brain swelling associated with stroke and traumatic brain injury. Here we show that AQP4 cell surface expression can be rapidly and reversibly regulated in response to changes of tonicity in primary cortical rat astrocytes and in transfected HEK293 cells. The translocation mechanism involves PKA activation, influx of extracellular calcium, and activation of calmodulin. We identify five putative PKA phosphorylation sites and use site-directed mutagenesis to show that only phosphorylation at one of these sites, serine 276, is necessary for the translocation response. We discuss our findings in the context of the identification of new therapeutic approaches to treating brain edema. PMID:26013827

  10. A molecular bar-coded DNA repair resource for pooled toxicogenomic screens.

    PubMed

    Rooney, John P; Patil, Ashish; Zappala, Maria R; Conklin, Douglas S; Cunningham, Richard P; Begley, Thomas J

    2008-11-01

    DNA damage from exogenous and endogenous sources can promote mutations and cell death. Fortunately, cells contain DNA repair and damage signaling pathways to reduce the mutagenic and cytotoxic effects of DNA damage. The identification of specific DNA repair proteins and the coordination of DNA repair pathways after damage has been a central theme to the field of genetic toxicology and we have developed a tool for use in this area. We have produced 99 molecular bar-coded Escherichia coli gene-deletion mutants specific to DNA repair and damage signaling pathways, and each bar-coded mutant can be tracked in pooled format using bar-code specific microarrays. Our design adapted bar-codes developed for the Saccharomyces cerevisiae gene-deletion project, which allowed us to utilize an available microarray product for pooled gene-exposure studies. Microarray-based screens were used for en masse identification of individual mutants sensitive to methyl methanesulfonate (MMS). As expected, gene-deletion mutants specific to direct, base excision, and recombinational DNA repair pathways were identified as MMS-sensitive in our pooled assay, thus validating our resource. We have demonstrated that molecular bar-codes designed for S. cerevisiae are transferable to E. coli, and that they can be used with pre-existing microarrays to perform competitive growth experiments. Further, when comparing microarray to traditional plate-based screens both overlapping and distinct results were obtained, which is a novel technical finding, with discrepancies between the two approaches explained by differences in output measurements (DNA content versus cell mass). The microarray-based classification of Deltatag and DeltadinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Deltatag and DeltadinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy. A novel biological finding is the observation that while

  11. Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): Evidence for rapid diversification and host shifts in spider wasps.

    PubMed

    Rodriguez, Juanita; Pitts, James P; Florez, Jaime A; Bond, Jason E; von Dohlen, Carol D

    2016-01-01

    Pompilinae is one of the largest subfamilies of spider wasps (Pompilidae). Most pompilines are generalist spider predators at the family level, but some taxa exhibit ecological specificity (i.e., to spider-host guild). Here we present the first molecular phylogenetic analysis of Pompilinae, toward the aim of evaluating the monophyly of tribes and genera. We further test whether changes in the rate of diversification are associated with host-guild shifts. Molecular data were collected from five nuclear loci (28S, EF1-F2, LWRh, Wg, Pol2) for 76 taxa in 39 genera. Data were analyzed using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results were compared with previous hypotheses of subfamilial and tribal classification, as well as generic relationships in the subfamily. The classification of Pompilus and Agenioideus is also discussed. A Bayesian relaxed molecular clock analysis was used to examine divergence times. Diversification rate-shift tests accounted for taxon-sampling bias using ML and BI approaches. Ancestral host family and host guild were reconstructed using MP and ML methods. Ancestral host guild for all Pompilinae, for the ancestor at the node where a diversification rate-shift was detected, and two more nodes back in time was inferred using BI. In the resulting phylogenies, Aporini was the only previously proposed monophyletic tribe. Several genera (e.g., Pompilus, Microphadnus and Schistonyx) are also not monophyletic. Dating analyses produced a well-supported chronogram consistent with topologies from BI and ML results. The BI ancestral host-use reconstruction inferred the use of spiders belonging to the guild "other hunters" (frequenting the ground and vegetation) as the ancestral state for Pompilinae. This guild had the highest probability for the ML reconstruction and was equivocal for the MP reconstruction; various switching events to other guilds occurred throughout the evolution of the group. The diversification of

  12. Rapid and Accurate Molecular Identification of the Emerging Multidrug-Resistant Pathogen Candida auris.

    PubMed

    Kordalewska, Milena; Zhao, Yanan; Lockhart, Shawn R; Chowdhary, Anuradha; Berrio, Indira; Perlin, David S

    2017-08-01

    Candida auris is an emerging multidrug-resistant fungal pathogen causing nosocomial and invasive infections associated with high mortality. C. auris is commonly misidentified as several different yeast species by commercially available phenotypic identification platforms. Thus, there is an urgent need for a reliable diagnostic method. In this paper, we present fast, robust, easy-to-perform and interpret PCR and real-time PCR assays to identify C. auris and related species: Candida duobushaemulonii, Candida haemulonii, and Candida lusitaniae Targeting rDNA region nucleotide sequences, primers specific for C. auris only or C. auris and related species were designed. A panel of 140 clinical fungal isolates was used in both PCR and real-time PCR assays followed by electrophoresis or melting temperature analysis, respectively. The identification results from the assays were 100% concordant with DNA sequencing results. These molecular assays overcome the deficiencies of existing phenotypic tests to identify C. auris and related species. Copyright © 2017 Kordalewska et al.

  13. Molecular Diffusion of Volatiles in Lunar Regolith during the Resource Prospector Mission Sample Acquisition

    NASA Astrophysics Data System (ADS)

    Teodoro, L. A.; Colaprete, A.; Roush, T. L.; Elphic, R. C.; Cook, A.; Kleinhenz, J.; Fritzler, E.; Smith, J. T.; Zacny, K.

    2016-12-01

    In the context of NASA's Resource Prospector (RP) mission to the high latitudes and permanently shadowed regions of the Moon, we study 3D models of volatile transport in the lunar regolith. This mission's goal is to extract and identify volatile species in the top meter of the lunar regolith layer. Roughly, RP consists of 5 elements: i) the Neutron Spectrometer System will search for high hydrogen concentrations and in turn select optimum drilling locations; ii) The Near Infrared Volatile Spectrometer System (NIRVSS) will characterize the nature of the surficial water ice; iii) The Drill Sub-system will extract samples from the top meter of the lunar surface and deliver them to the Oxygen and Volatile Extraction Node (OVEN); iv) OVEN will heat up the sample and extract the volatiles therein, that will be v) transferred to the Lunar Advanced Volatiles Analysis system for chemical composition analysis. A series of vacuum cryogenic experiments have been carried out at Glenn Research Center with the aim of quantifying the volatile losses during the drilling/sample acquisition phase and sample delivery to crucibles steps. These experiments' outputs include: i) Pressure measurements of several chemical species (e.g. H2O, Ar); ii) Temperature measurements within and at the surface of the lunar simulant using thermocouples; and iii) Surficial temperature NIRVSS measurements. Here, we report on the numerical modeling we are carrying out to understand the physics underpinning these experiments. The models include 2 main parts: i) reliable computation of temperature variation throughout the lunar soil container during the experiment as constrained by temperature measurements; and ii) molecular diffusion of volatiles. The latter includes both Fick's (flight of the molecules in the porous) and Knudsen's (sublimation of volatile molecules at the grain surface) laws. We also mimic the soil porosity by randomly allocating 75 microns particles in the simulation volume. Our

  14. Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level.

    PubMed

    Jarocki, Piotr; Podleśny, Marcin; Komoń-Janczara, Elwira; Kucharska, Jagoda; Glibowska, Agnieszka; Targoński, Zdzisław

    2016-07-22

    Members of the genus Bifidobacterium are anaerobic Gram-positive Actinobacteria, which are natural inhabitants of human and animal gastrointestinal tract. Certain bifidobacteria are frequently used as food additives and probiotic pharmaceuticals, because of their various health-promoting properties. Due to the enormous demand on probiotic bacteria, manufacture of high-quality products containing living microorganisms requires rapid and accurate identification of specific bacteria. Additionally, isolation of new industrial bacteria from various environments may lead to multiple isolations of the same strain, therefore, it is important to apply rapid, low-cost and effective procedures differentiating bifidobacteria at the intra-species level. The identification of new isolates using microbiological and biochemical methods is difficult, but the accurate characterization of isolated strains may be achieved using a polyphasic approach that includes classical phenotypic methods and molecular procedures. However, some of these procedures are time-consuming and cumbersome, particularly when a large group of new isolates is typed, while some other approaches may have too low discriminatory power to distinguish closely related isolates obtained from similar sources. This work presents the evaluation of the discriminatory power of four molecular methods (ARDRA, RAPD-PCR, rep-PCR and SDS-PAGE fingerprinting) that are extensively used for fast differentiation of bifidobacteria up to the strain level. Our experiments included 17 reference strains and showed that in comparison to ARDRA, genotypic fingerprinting procedures (RAPD and rep-PCR) seemed to be less reproducible, however, they allowed to differentiate the tested microorganisms even at the intra-species level. In general, RAPD and rep-PCR have similar discriminatory power, though, in some instances more than one oligonucleotide needs to be used in random amplified polymorphic DNA analysis. Moreover, the results also

  15. The importance of brain banks for molecular neuropathological research: The New South Wales Tissue Resource Centre experience.

    PubMed

    Dedova, Irina; Harding, Antony; Sheedy, Donna; Garrick, Therese; Sundqvist, Nina; Hunt, Clare; Gillies, Juliette; Harper, Clive G

    2009-01-01

    New developments in molecular neuropathology have evoked increased demands for postmortem human brain tissue. The New South Wales Tissue Resource Centre (TRC) at The University of Sydney has grown from a small tissue collection into one of the leading international brain banking facilities, which operates with best practice and quality control protocols. The focus of this tissue collection is on schizophrenia and allied disorders, alcohol use disorders and controls. This review highlights changes in TRC operational procedures dictated by modern neuroscience, and provides examples of applications of modern molecular techniques to study the neuropathogenesis of many different brain disorders.

  16. Does genetic conflict drive rapid molecular evolution of nuclear transport genes in Drosophila?

    PubMed

    Presgraves, Daven C

    2007-04-01

    The Segregation Distorter (SD) system of Drosophila melanogaster is one the best-characterized meiotic drive complexes known. SD gains an unfair transmission advantage through heterozygous SD/SD(+) males by incapacitating SD(+)-bearing spermatids so that virtually all progeny inherit SD. Segregation distorter (Sd), the primary distorting locus in the SD complex, is a truncated duplication of the RanGAP gene, a major regulator of the small GTPase Ran, which has several functions including the maintenance of the nucleocytoplasmic RanGTP concentration gradient that mediates nuclear transport. The truncated Sd-RanGAP protein is enzymatically active but mislocalizes to the nucleus where it somehow causes distortion. Here I present data consistent with the idea that wild-type RanGAP, and possibly other loci able to influence the RanGTP gradient, has been caught up in an ancient genetic conflict that predates the SD complex. The legacy of this conflict could include the unexpectedly rapid evolution of nuclear transport-related proteins, the accumulation of chromosomal inversions, the recruitment of gene duplications, and the turnover of repetitive sequences in the centric heterochromatin. (c) 2007 Wiley Periodicals, Inc.

  17. Determination of very rapid molecular rotation by using the central electron paramagnetic resonance line.

    PubMed

    Kurban, Mark R

    2013-02-21

    Picosecond rotational correlation times of perdeuterated tempone (PDT) are found in alkane and aromatic liquids by directly using the spectral width of the central electron paramagnetic resonance line. This is done by mathematically eliminating the nonsecular spectral density from the spectral parameter equations, thereby removing the need to assume a particular form for it. This is preferable to fitting a constant correction factor to the spectral density, because such a factor does not fit well in the low picosecond range. The electron-nuclear spin dipolar interaction between the probe and solvent is shown to be negligible for the very rapid rotation of PDT in these liquids at the temperatures of the study. The rotational correlation times obtained with the proposed method generally agree to within experimental uncertainty with those determined by using the traditional parameters. Using the middle line width offers greater precision and smoother trends. Previous work with the central line width is discussed, and past discrepancies are explained as possibly resulting from residual inhomogeneous broadening. The rotational correlation time almost forms a common curve across all of the solvents when plotted with respect to isothermal compressibility, which shows the high dependence of rotation on liquid free volume.

  18. Major intercontinentally distributed sequence types of Kingella kingae and development of a rapid molecular typing tool.

    PubMed

    Basmaci, Romain; Bidet, Philippe; Yagupsky, Pablo; Muñoz-Almagro, Carmen; Balashova, Nataliya V; Doit, Catherine; Bonacorsi, Stéphane

    2014-11-01

    Although Kingella kingae is the most common etiology of osteoarticular infections in young children, is a frequent cause of bacteremia in those younger than 4 years, and has been involved in clusters of invasive infections among daycare center attendees, the population structure of the species has not been systematically studied. Using multilocus sequence typing, we investigated the genetic diversity of the largest intercontinental collection of K. kingae strains to date. To facilitate typing of bacterial isolates, we developed a novel genotyping tool that targets the DNA uptake sequence (DUS). Among 324 strains isolated from asymptomatic carriers and patients from Israel, Europe, North America, and Australia with various invasive forms of the disease from 1960 to 2013, we identified 64 sequence types (STs) and 12 ST complexes (STcs). Five predominant STcs, comprising 72.2% of all strains, were distributed intercontinentally. ST-6 was the most frequent, showing a worldwide distribution, and appeared genotypically isolated by exhibiting few neighboring STs, suggesting an optimal fitness. ST-14 and ST-23 appeared to be the oldest groups of bacteria, while ST-25 probably emerged more recently from the highly evolutive ST-23. Using the DUS typing method, randomly chosen isolates were correctly classified to one of the major STcs. The comprehensive description of K. kingae evolution would help to detect new emerging clones and decipher virulence and fitness mechanisms. The rapid and reproducible DUS typing method may serve in the initial investigation of K. kingae outbreaks.

  19. Major Intercontinentally Distributed Sequence Types of Kingella kingae and Development of a Rapid Molecular Typing Tool

    PubMed Central

    Basmaci, Romain; Bidet, Philippe; Yagupsky, Pablo; Muñoz-Almagro, Carmen; Balashova, Nataliya V.; Doit, Catherine

    2014-01-01

    Although Kingella kingae is the most common etiology of osteoarticular infections in young children, is a frequent cause of bacteremia in those younger than 4 years, and has been involved in clusters of invasive infections among daycare center attendees, the population structure of the species has not been systematically studied. Using multilocus sequence typing, we investigated the genetic diversity of the largest intercontinental collection of K. kingae strains to date. To facilitate typing of bacterial isolates, we developed a novel genotyping tool that targets the DNA uptake sequence (DUS). Among 324 strains isolated from asymptomatic carriers and patients from Israel, Europe, North America, and Australia with various invasive forms of the disease from 1960 to 2013, we identified 64 sequence types (STs) and 12 ST complexes (STcs). Five predominant STcs, comprising 72.2% of all strains, were distributed intercontinentally. ST-6 was the most frequent, showing a worldwide distribution, and appeared genotypically isolated by exhibiting few neighboring STs, suggesting an optimal fitness. ST-14 and ST-23 appeared to be the oldest groups of bacteria, while ST-25 probably emerged more recently from the highly evolutive ST-23. Using the DUS typing method, randomly chosen isolates were correctly classified to one of the major STcs. The comprehensive description of K. kingae evolution would help to detect new emerging clones and decipher virulence and fitness mechanisms. The rapid and reproducible DUS typing method may serve in the initial investigation of K. kingae outbreaks. PMID:25143574

  20. Rapid Molecular Assays for Specific Detection and Quantitation of Loa loa Microfilaremia

    PubMed Central

    Fink, Doran L.; Kamgno, Joseph; Nutman, Thomas B.

    2011-01-01

    Background Accurate diagnosis of Loa loa infection is essential to the success of mass drug administration efforts to eliminate onchocerciasis and lymphatic filariasis, due to the risk of fatal encephalopathic reactions to ivermectin occurring among highly microfilaremic Loa-infected individuals living in areas co-endemic for multiple filarial species. Methodology/Principal Findings From a pool of over 1,800 L. loa microfilaria (mf) expressed sequence tags, 18 candidate L. loa mf-specific PCR targets were identified. Real-time PCR (qPCR) assays were developed for two targets (LLMF72 and LLMF269). The qPCR assays were highly specific for L. loa compared with related filariae and also highly sensitive, with detection limits of 0.1 pg genomic DNA, or 1% of DNA extracted from normal blood spiked with a single L. loa microfilaria. Using various DNA extraction methods with dried blood spots obtained from Cameroonian subjects with parasitologically proven loiasis, the LLMF72 qPCR assay successfully estimated mf burden in 65 of 68 samples (50–96,000 mf/mL by microscopy), including all 12 samples subjected to a simple 10-minute boiling extraction. Additionally, the assay detected low-level microfilaremia among 5 of 16 samples from patients thought to be amicrofilaremic by microscopy. Conclusions/Significance This novel, rapid, highly sensitive and specific qPCR assay is an important step forward in the laboratory diagnosis of L. loa infection. PMID:21912716

  1. Whole-exome sequencing enables rapid determination of xeroderma pigmentosum molecular etiology.

    PubMed

    Ortega-Recalde, Oscar; Vergara, Jéssica Inés; Fonseca, Dora Janeth; Ríos, Xiomara; Mosquera, Hernando; Bermúdez, Olga María; Medina, Claudia Liliana; Vargas, Clara Inés; Pallares, Argemiro Enrique; Restrepo, Carlos Martín; Laissue, Paul

    2014-01-01

    Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by extreme sensitivity to actinic pigmentation changes in the skin and increased incidence of skin cancer. In some cases, patients are affected by neurological alterations. XP is caused by mutations in 8 distinct genes (XPA through XPG and XPV). The XP-V (variant) subtype of the disease results from mutations in a gene (XPV, also named POLH) which encodes for Polη, a member of the Y-DNA polymerase family. Although the presence and severity of skin and neurological dysfunctions differ between XP subtypes, there are overlapping clinical features among subtypes such that the sub-type cannot be deduced from the clinical features. In this study, in order to overcome this drawback, we undertook whole-exome sequencing in two XP sibs and their father. We identified a novel homozygous nonsense mutation (c.897T>G, p.Y299X) in POLH which causes the disease. Our results demonstrate that next generation sequencing is a powerful approach to rapid determination of XP genetic etiology.

  2. Rapid Classification of Imaged Objects Using Molecular Factor and Multivariate Optical Computing

    NASA Astrophysics Data System (ADS)

    Pearl, Megan Renee

    Unique algorithm development is vital for the success of novel instrumentation. Our lab has focused on the design of imaging systems based on molecular factor and multivariate optical computing. A simulation-driven design approach was utilized to develop a multimode infrared imaging system for chemical contrast enhancement. This infrared thermal imaging system is based on molecular factor (MFC) and lockin computing methods. MFC was accomplished with filter elements made of thin organic films deposited on IR-transparent substrates and allows a system response to be tuned to a specific analyte. Unique algorithms were written in-house using MatLabRTM (The Mathworks, Natick, MA). The algorithms used a lock-in computing technique to amplify the diffuse re ectance signal, which is only a few percent of the total signal. Intensive thin film studies were conducted to understand the effects of films on fabric to improve our simulation-driven design approach. A prototype instrument has been validated through the production of a real setup. We have shown that it is able to detect trace amounts of blood diluted in water (as small as 1:100) on fabric as well as differentiate blood from common false positives of other blood detection methods (i.e., luminol). The second imaging system was designed for the differentiation of phytoplankton species in the ocean. Multivariate optical computing (MOC) was applied to the uorescence excitation spectra of individual phytoplankton cells to design multivariate optical elements (MOEs). MOEs are filters fabricated to mimic linear discriminants analysis (LDA) results based on plankton spectroscopy. The imaging system uses these MOEs housed in a filter wheel to produce "streak" images of phytoplankton as they flow past a CCD camera, with each streak having the appearance of a barcode whose intensities are related to scores of the plankton spectra on linear discriminant functions. Algorithms for this system have been designed to automatically

  3. Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains.

    PubMed Central

    Hoe, N.; Nakashima, K.; Grigsby, D.; Pan, X.; Dou, S. J.; Naidich, S.; Garcia, M.; Kahn, E.; Bergmire-Sweat, D.; Musser, J. M.

    1999-01-01

    Serotype M1 group A Streptococcus, the most common cause of invasive disease in many case series, generally have resisted extensive molecular subtyping by standard techniques (e.g., multilocus enzyme electrophoresis, pulsed-field gel electrophoresis). We used automated sequencing of the sic gene encoding streptococcal inhibitor of complement and of a region of the chromosome with direct repeat sequences to unambiguously differentiate 30 M1 isolates recovered from 28 patients in Texas with invasive disease episodes temporally clustered and thought to represent an outbreak. Sequencing of the emm gene was less useful for M1 strain differentiation, and restriction fragment length polymorphism analysis with IS1548 or IS1562 as Southern hybridization probes did not provide epidemiologically useful subtyping information. Sequence polymorphism in the direct repeat region of the chromosome and IS1548 profiling data support the hypothesis that M1 organisms have two main evolutionary lineages marked by the presence or absence of the speA2 allele encoding streptococcal pyrogenic exotoxin A2. PMID:10221878

  4. Direct molecular diffusion and micro-mixing for rapid dewatering of LiBr solution

    SciTech Connect

    Bigham, S; Isfahani, RN; Moghaddam, S

    2014-03-01

    A slow molecular diffusion rate often limits the desorption process of an absorbate molecule from a liquid absorbent. To enhance the desorption rate, the absorbent is often boiled to increase the liquid vapor interfacial area. However, the growth of bubbles generated during the nucleate boiling process still remains mass-diffusion limited. Here, it is shown that a desorption rate higher than that of boiling can be achieved, if the vapor absorbent interface is continuously replenished with the absorbate-rich solution to limit the concentration boundary layer growth. The study is conducted in a LiBr-water-solution, in which the water molecules' diffusion rate is quite slow. The manipulation of the vapor solution interface concentration distribution is enabled by the mechanical confinement of the solution flow within microchannels, using a hydrophobic vapor-venting membrane and the implementation of microstructures on the flow channel's bottom wall. The microstructures stretch and fold the laminar streamlines within the solution film and produce vortices. The vortices continuously replace the concentrated solution at the vapor solution interface with the water-rich solution brought from the bottom and middle of the flow channel. The physics of the process is described using a combination of experimental and numerical studies. Published by Elsevier Ltd.

  5. Distinct molecular processes associated with isometric force generation and rapid tension recovery after quick release.

    PubMed Central

    Brenner, B; Chalovich, J M; Yu, L C

    1995-01-01

    It was proposed by Huxley and Simmons (Nature 1971, 233:533-538) that force-generating cross-bridges are attached to actin in several stable positions. In this concept, isometric force is generated by the same mechanism as the quick tension recovery after an abrupt release of length; i.e., when crossbridges proceed from the first postulated stable position to the second and/or subsequent positions, resulting in straining of the elastic elements within the cross-bridges. Therefore, isometric force is generated by cross-bridges in the second or even subsequent stable positions. However, through mechanical measurements of skinned rabbit psoas muscle fibers, we found that during isometric contraction only the first stable state is significantly occupied; i.e., isometric force is generated by cross-bridges in the first of the stable states. Thus, isometric force and the quick tension recovery appear to result from two distinctly different molecular processes. We propose that isometric force results from a structural change in the actomyosin complex associated with the transition from a weakly bound configuration to a strongly bound configuration before the reaction steps in the Huxley-Simmons model, whereas a major component of quick tension recovery originates from transitions among the subsequent strongly bound states. Mechanical, biochemical, and structural evidence for the two distinct processes is summarized and reviewed. PMID:7787051

  6. [Comparison of different molecular assays for the rapid detection of enterovirus 71 (EV71)].

    PubMed

    Wei, Hai-Yan; Huang, Xue-Yong; Xu, Yu-Ling; Ma, Hong; Chen, Hao-Min; Xu, Bian-Li

    2012-11-01

    Molecular detection of enterovirus (EV)71 RNA based on PCR methods is a quick and sensitive approach. At present, different PCR-based methods for EV71 RNA detection are available, but comparisons of results obtained using different approaches are limited. This study is to compare the analytical sensitivity and specificity of different real-time reverse transcription-polymerase chain reaction (rRT-PCR) and conventional reverse transcription-polymerase chain reaction (cRT-PCR) assays for enterovirus and EV71 detection, Altogether, three rRT-PCR assays and one cRT-PCR assay targeting the 5'UTR gene for universal detection of enterovirus; two rRT-PCR assays andone cRT-PCR assay targeting the VP1 gene for specific detection of EV 71 were examined. All assays showed good specificity. The detection sensitivity ranged from 8.19 x 10 to 8.19 x 10(5) copy equivalents. In general, rRT-PCR assays were more sensitive than cRT-PCR assays. All rRT-PCR assays showed 100% sensitivity for clinical specimens.

  7. Distinct molecular processes associated with isometric force generation and rapid tension recovery after quick release.

    PubMed

    Brenner, B; Chalovich, J M; Yu, L C

    1995-04-01

    It was proposed by Huxley and Simmons (Nature 1971, 233:533-538) that force-generating cross-bridges are attached to actin in several stable positions. In this concept, isometric force is generated by the same mechanism as the quick tension recovery after an abrupt release of length; i.e., when crossbridges proceed from the first postulated stable position to the second and/or subsequent positions, resulting in straining of the elastic elements within the cross-bridges. Therefore, isometric force is generated by cross-bridges in the second or even subsequent stable positions. However, through mechanical measurements of skinned rabbit psoas muscle fibers, we found that during isometric contraction only the first stable state is significantly occupied; i.e., isometric force is generated by cross-bridges in the first of the stable states. Thus, isometric force and the quick tension recovery appear to result from two distinctly different molecular processes. We propose that isometric force results from a structural change in the actomyosin complex associated with the transition from a weakly bound configuration to a strongly bound configuration before the reaction steps in the Huxley-Simmons model, whereas a major component of quick tension recovery originates from transitions among the subsequent strongly bound states. Mechanical, biochemical, and structural evidence for the two distinct processes is summarized and reviewed.

  8. Xpert® MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance.

    PubMed

    Lawn, Stephen D; Nicol, Mark P

    2011-09-01

    Global TB control efforts have been severely hampered by the lack of diagnostic tests that are accurate, simple to use and can be applied at the point of clinical care. This has been further compounded by the widespread inability to test for drug resistance. The Xpert(®) MTB/RIF assay is a rapid molecular assay that can be used close to the point of care by operators with minimal technical expertise, enabling diagnosis of TB and simultaneous assessment of rifampicin resistance to be completed within 2 h. Moreover, this can be accomplished using unprocessed sputum samples as well as clinical specimens from extrapulmonary sites. We review in detail the development of this assay, its evaluation within the laboratory, its utility among adult and pediatric TB suspects, its use as a screening tool for HIV-associated TB and studies of its implementation at the district and sub-district levels in resource-limited settings. Following endorsement by the WHO in 2010, we consider the next steps in the implementation of the assay and its potential impact in high burden settings.

  9. Xpert® MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance

    PubMed Central

    Lawn, Stephen D; Nicol, Mark P

    2011-01-01

    Global TB control efforts have been severely hampered by the lack of diagnostic tests that are accurate, simple to use and can be applied at the point of clinical care. This has been further compounded by the widespread inability to test for drug resistance. The Xpert® MTB/RIF assay is a rapid molecular assay that can be used close to the point of care by operators with minimal technical expertise, enabling diagnosis of TB and simultaneous assessment of rifampicin resistance to be completed within 2 h. Moreover, this can be accomplished using unprocessed sputum samples as well as clinical specimens from extrapulmonary sites. We review in detail the development of this assay, its evaluation within the laboratory, its utility among adult and pediatric TB suspects, its use as a screening tool for HIV-associated TB and studies of its implementation at the district and sub-district levels in resource-limited settings. Following endorsement by the WHO in 2010, we consider the next steps in the implementation of the assay and its potential impact in high burden settings. PMID:21958145

  10. Rapid and high throughput molecular identification of diverse mosquito species by high resolution melting analysis

    PubMed Central

    Ajamma, Yvonne Ukamaka; Mararo, Enock; Omondi, David; Onchuru, Thomas; Muigai, Anne W. T.; Masiga, Daniel; Villinger, Jandouwe

    2016-01-01

    -species. This approach can be employed for rapid identification of mosquitoes. PMID:27703667

  11. Rapid and high throughput molecular identification of diverse mosquito species by high resolution melting analysis.

    PubMed

    Ajamma, Yvonne Ukamaka; Mararo, Enock; Omondi, David; Onchuru, Thomas; Muigai, Anne W T; Masiga, Daniel; Villinger, Jandouwe

    2016-01-01

    -species. This approach can be employed for rapid identification of mosquitoes.

  12. Familial dysalbuminemic hyperthyroxinemia: a rare example of albumin polymorphism and its rapid molecular diagnosis.

    PubMed

    AvRuskin, Theodore W; Juan, Christina S; Weiss, Roy E

    2002-06-01

    Familial dysalbuminemic hyperthyroxinemia (FDH) is the most common cause of euthyroid hyperthyroxinemia, although a rare example of albumin polymorphism. FDH is inherited in an autosomal dominant manner and is characterized by enhanced binding of thyroxine to a mutant form of albumin, probably at Site 1, subdomain 11A. Previous laboratory tests of FDH have been cumbersome, rarely available, and required demonstration of anti-albumin precipitable T4, isoelectric focusing of serum for albumin in presence of labeled T4 and, occasionally, comparison of the concentrations of metabolites of T4 that have different binding affinities to the abnormal albumin. Recent studies have shown that the same mutation in the albumin gene that results in FDH has been found in 13 unrelated families. A G-->A transition in codon 218 of the albumin gene resulted in the replacement of arginine with histidine. An intragenic Sac-1 polymorphic site was found in association with the specific FDH mutation, suggesting a founder effect. FDH in our Hispanic family was confirmed by isoelectric focusing of serum. Results of thyroid function tests in our affected patients were typical for the phenotype: high total T4 and normal total T3. Genomic DNA was amplified by PCR using a mismatched oligonucleotide primer that produced a unique restriction site (Dra III) only if the DNA sample contained the mutation in codon 218: CGC (Arg) to CAC (His). In affected individuals of this family expression of the FDH phenotype was associated with the presence of His218 in one of the two alleles. Analysis linking the FDH mutation to the Sac-1 polymorphism in this family was not informative. DNA analysis is a rapid and simple method to diagnose FDH in individuals with euthyroid hyperthyroxinemia.

  13. Use of Electrochemical DNA Biosensors for Rapid Molecular Identification of Uropathogens in Clinical Urine Specimens

    PubMed Central

    Liao, Joseph C.; Mastali, Mitra; Gau, Vincent; Suchard, Marc A.; Møller, Annette K.; Bruckner, David A.; Babbitt, Jane T.; Li, Yang; Gornbein, Jeffrey; Landaw, Elliot M.; McCabe, Edward R. B.; Churchill, Bernard M.; Haake, David A.

    2006-01-01

    We describe the first species-specific detection of bacterial pathogens in human clinical fluid samples using a microfabricated electrochemical sensor array. Each of the 16 sensors in the array consisted of three single-layer gold electrodes—working, reference, and auxiliary. Each of the working electrodes contained one representative from a library of capture probes, each specific for a clinically relevant bacterial urinary pathogen. The library included probes for Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Enterocococcus spp., and the Klebsiella-Enterobacter group. A bacterial 16S rRNA target derived from single-step bacterial lysis was hybridized both to the biotin-modified capture probe on the sensor surface and to a second, fluorescein-modified detector probe. Detection of the target-probe hybrids was achieved through binding of a horseradish peroxidase (HRP)-conjugated anti-fluorescein antibody to the detector probe. Amperometric measurement of the catalyzed HRP reaction was obtained at a fixed potential of −200 mV between the working and reference electrodes. Species-specific detection of as few as 2,600 uropathogenic bacteria in culture, inoculated urine, and clinical urine samples was achieved within 45 min from the beginning of sample processing. In a feasibility study of this amperometric detection system using blinded clinical urine specimens, the sensor array had 100% sensitivity for direct detection of gram-negative bacteria without nucleic acid purification or amplification. Identification was demonstrated for 98% of gram-negative bacteria for which species-specific probes were available. When combined with a microfluidics-based sample preparation module, the integrated system could serve as a point-of-care device for rapid diagnosis of urinary tract infections. PMID:16455913

  14. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system

    PubMed Central

    Huang, Helen J.; Falchook, Gerald S.; Devogelaere, Benoit; Kockx, Mark; Bempt, Isabelle Vanden; Reijans, Martin; Naing, Aung; Fu, Siqing; Piha-Paul, Sarina A.; Hong, David S.; Holley, Veronica R.; Tsimberidou, Apostolia M.; Stepanek, Vanda M.; Patel, Sapna P.; Kopetz, E. Scott; Subbiah, Vivek; Wheler, Jennifer J.; Zinner, Ralph G.; Karp, Daniel D.; Luthra, Rajyalakshmi; Roy-Chowdhuri, Sinchita; Sablon, Erwin; Meric-Bernstam, Funda; Maertens, Geert; Kurzrock, Razelle

    2015-01-01

    Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTM BRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction–based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTM BRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation–detecting tests. PMID:26330075

  15. Rapid preparation of molecularly imprinted polymers by microwave-assisted emulsion polymerization for the extraction of florfenicol in milk.

    PubMed

    Chen, Haiyan; Son, Sunil; Zhang, Fengshuang; Yan, Jin; Li, Yi; Ding, Hong; Ding, Lan

    2015-03-01

    In this study, we proposed a rapid and simple method for the preparation of molecularly imprinted polymers (MIPs) by emulsion polymerization. The polymerization process was accelerated by microwave heating, and the reaction time was greatly shortened. The obtained MIPs were spherical in shape and exhibited a uniform morphology. The MIPs with selectivity and high affinity to florfenicol were successfully applied as solid-phase extraction materials to extract and clean up the florfenicol in milk, followed by liquid chromatography-tandem mass spectrometry (LC-MS) analysis. The parameters affecting the performance of extraction and LC-MS analysis were evaluated. The detection limit of the method was 4.1ngmL(-1). The relative standard deviations of intra- and inter-day were in the range of 3.5-4.7% and 3.9-7.5%, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Accessible Surfaces of Beta Proteins Increase with Increasing Protein Molecular Mass More Rapidly than Those of Other Proteins

    PubMed Central

    Glyakina, Anna V.; Bogatyreva, Natalya S.; Galzitskaya, Oxana V.

    2011-01-01

    Here we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-α, all-β, α/β and α+β proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular mass more rapidly than in other classes, and what structural peculiarities are responsible for this effect. The beta structural class of proteins was found to be the leader, with the following possible explanations of this fact. First, in beta structural proteins, the fraction of residues not included in the regular secondary structure is the largest, and second, the accessible surface area of packaged elements of the beta-structure increases more rapidly with increasing molecular mass in comparison with the alpha-structure. Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of α+β proteins (the average probability is 0.73±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without proline) and α/β proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.70±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without the proline residue). There is a linear relationship between the number of hydrogen bonds and the number of amino acid residues in the protein (). PMID:22145047

  17. Aptamer contained triple-helix molecular switch for rapid fluorescent sensing of acetamiprid.

    PubMed

    Liu, Xin; Li, Ying; Liang, Jing; Zhu, Wenyue; Xu, Jingyue; Su, Ruifang; Yuan, Lei; Sun, Chunyan

    2016-11-01

    In this study, an aptamer-based fluorescent sensing platform using triple-helix molecular switch (THMS) was developed for the pesticide screening represented by acetamiprid. The THMS was composed of two tailored DNA probes: a label-free central target specific aptamer sequence flanked by two arm segments acting as a recognition probe; a hairpin-shaped structure oligonucleotide serving as a signal transduction probe (STP), labeled with a fluorophore and a quencher at the 3' and 5'-end, respectively. In the absence of acetamiprid, complementary bindings of two arm segments of the aptamers with the loop sequence of STP enforce the formation of THMS with the "open" configuration of STP, and the fluorescence of THMS is on. In the presence of target acetamiprid, the aptamer-target binding results in the formation of a structured aptamer/target complex, which disassembles the THMS and releases the STP. The free STP is folded to a stem loop structure, and the fluorescence is quenched. The quenched fluorescence intensity was proportional to the concentration of acetamiprid in the range from 100 to 1200nM, with the limit of detection (LOD) as low as 9.12nM. In addition, this THMS-based method has been successfully used to test and quantify acetamiprid in Chinese cabbage with satisfactory recoveries, and the results were in full agreement with those from LC-MS. The aptamer-based THMS presents distinct advantages, including high stability, remarkable sensitivity, and preservation of the affinity and specificity of the original aptamer. Most importantly, this strategy is convenient and generalizable by virtue of altering the aptamer sequence without changing the triple-helix structure. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection.

  18. Development of a one-step probe based molecular assay for rapid immunodiagnosis of infection with M. tuberculosis using dried blood spots.

    PubMed

    Blauenfeldt, Thomas; Heyckendorf, Jan; Graff Jensen, Sidse; Lange, Christoph; Drabe, Camilla; Hermansen, Thomas S; de Thurah, Lena; Lillebaek, Troels; Eugen-Olsen, Jesper; Seersholm, Niels; Hoff, Søren; Bonde, Jesper; Ruhwald, Morten

    2014-01-01

    Antigen specific release of IP-10 is the most promising alternative marker to IFN-γ for infection with M. tuberculosis. Compared to Interferon-γ release assays (IGRA), IP-10 is released in high levels enabling novel approaches such as field friendly dried blood spots (DBS) and molecular detection. To develop a robust IP-10 based molecular assay for the diagnosis of infection with M. tubercuolsis from whole blood and DBS. We developed a one-step probe based multiplex RT-qPCR assay for detecting IP-10 and IFN-γ mRNA expression from whole blood and DBS samples. The assay was validated and applied for the diagnosis of M. tuberculosis infection in DBS samples from 43 patients with confirmed TB, 13 patients with latent TB and 96 presumed uninfected controls. In parallel, IP-10 and INF-γ levels were measured in Quantiferon (QFT-TB) plasma supernatants. IP-10 mRNA upregulation was detectable at 4 hours after stimulation (6 fold upregulation) peaking at 8 hours (108 fold upregulation). IFN-γ expression occurred in concert but levels were lower (peak 6.7 fold upregulation). IP-10 gene expression level was significantly higher in patients with tuberculosis (median 31.2, IQR 10.7-67.0) and persons with latent tuberculosis infection (LTBI) (41.2, IQR 9.8-64.9) compared to healthy controls (1.6, IQR 1.1-2.4; p<0.0001). The IP-10 mRNA and protein based tests had comparable diagnostic accuracy to QFT-TB, sensitivity (85% and 88% vs 85%) and specificity (96% and 96% vs 97%, p = ns.). We developed a rapid, robust and accurate molecular immunodiagnostic test for M. tuberculosis infection. By combining DBS based sample acquisition, mail or currier based sample transport with centralized molecular detection, this immunodiagnostic test concept can reduce the local technological requirements everywhere and make it possible to offer highly accurate immunodiagnostic tests in low resource settings.

  19. Designing a critical care nurse-led rapid response team using only available resources: 6 years later.

    PubMed

    Mitchell, Anne; Schatz, Marilyn; Francis, Heather

    2014-06-01

    Rapid response teams have been introduced to intervene in the care of patients whose condition deteriorates unexpectedly by bringing clinical experts quickly to the patient's bedside. Evidence supporting the need to overcome failure to deliver optimal care in hospitals is robust; whether rapid response teams demonstrate benefit by improving patient safety and reducing the occurrence of adverse events remains controversial. Despite inconsistent evidence regarding the effectiveness of rapid response teams, concerns regarding care and costly consequences of unaddressed deterioration in patients' condition have prompted many hospitals to implement rapid response teams as a patient safety strategy. A cost-neutral structure for a rapid response team led by a nurse from the intensive care unit was implemented with the goal of reducing cardiopulmonary arrests occurring outside the intensive care unit. The results of 6 years' experience indicate that a sustainable and effective rapid response team response can be put into practice without increasing costs or adding positions and can decrease the percentage of cardiopulmonary arrests occurring outside the intensive care unit.

  20. Rapid molecular identification of Listeria species by use of real-time PCR and high-resolution melting analysis.

    PubMed

    Jin, Dazhi; Luo, Yun; Zhang, Zheng; Fang, Weijia; Ye, Julian; Wu, Fang; Ding, Gangqiang

    2012-05-01

    Identification of Listeria species via a molecular method is critical for food safety and clinical diagnosis. In this study, an assay integrating real-time quantitative PCR (Q-PCR) with high-resolution melting (HRM) curve analysis was developed and assessed for rapid identification of six Listeria species. The ssrA gene, which encodes a transfer-messenger RNA (tmRNA) is conserved and common to all bacterial phyla, contains a variable domain in Listeria spp. Therefore, Q-PCR and a HRM profile were applied to characterize this gene. Fifty-three Listeria species and 45 non-Listeria species were detected using one primer set, with an accuracy of 100% in reference to conventional methods. There was a 93.3% correction rate to 30 artificially contaminated samples. Thus, Q-PCR with melting profiling analysis proved able to identify Listeria species accurately. Consequently, this study demonstrates that the assay we developed is a functional tool for rapidly identifying six Listeria species, and has the potential for discriminating novel species food safety and epidemiological research.

  1. [The present and future prospects in rapid molecular diagnosis of tuberculosis and MDR-TB (First Part)].

    PubMed

    Tănăsescu, Mihaela; Didilescu, Cristian; Marica, Constantin

    2013-01-01

    Tuberculosis is still one of the diseases with a major medical and social impact, and in terms of early diagnosis (which would imply a fair treatment and established at the time), difficulties related to the delay bacilli isolation in culture, decreased susceptibility testing methods to antituberculosis drugs, lack of methods for differentiation of M. Tuberculosis complex germs of non TB Mycobacteria, may have important clinical implications. Traditional testing of anti-TB drug susceptibility on solid Löwenstein-Jensen medium (gold standard) or liquid media can only be performed using grown samples. Determining the time it takes up to 42 days on solid media and 12 days for liquid media. For MDR/XDR TB cases is absolutely essential to reduce the detection time. In these cases prove their usefulness rapid diagnostic methods. Automatic testing in liquid medium, molecular hybridization methods are currently recommended by the current WHO guidelines. Rapid diagnosis of MDR-TB is extremely useful for the early establishment of an effective treatment tailored more accurately on the spectrum of sensitivity of the resistant strain (thus reducing the risk of developing additional resistance to other drugs) and control the spread of these strains. Genetic diagnostic methods, approved and recommended by the WHO, can reduce the time of diagnosis of TB case and, importantly, the case of MDR TB. They do not replace the current standard diagnostic methods and resistance profile, but complete them in selected cases.

  2. Comparison of rapid immunodiagnosis assay kit with molecular and immunopathological approaches for diagnosis of rabies in cattle

    PubMed Central

    Ahmad, Ajaz; Singh, C. K.

    2016-01-01

    Aim: Presently, diagnosis of rabies is primarily based on, conventional fluorescent antibody technique (FAT), immunopathological and molecular techniques. Recently, rapid immunodiagnostic assay (RIDA) - A monoclonal antibody-based technique has been introduced for rapid diagnosis of rabies. The present investigation is envisaged to study the efficacy of RIDA kit for the diagnosis of rabies in cattle. Materials and Methods: About 11 brain samples from cattle, clinically suspected for rabies, were screened by the FAT, Heminested reverse transcriptase polymerase chain reaction (HnRT-PCR), Immunohistochemistry (IHC), and RIDA. Results: The sensitivity for detection of rabies from brain tissue by RIDA was 85.7% as compared to 100% by IHC as well as HnRT-PCR. The accuracy of detection of rabies by RIDA was 91.6% as compared to 100% that of IHC and HnRT-PCR, whereas specificity of RIDA was 100% like that of the IHC and HnRT-PCR. Conclusion: Despite a comparatively low-sensitivity and accuracy of RIDA, latter can still be useful in screening a large number of field samples promptly. However, it is recommended that negative results with RIDA in cattle need to be authenticated by suitable alternative diagnostic approaches. PMID:27051193

  3. A simple capillary electrophoresis method for the rapid separation and determination of intact low molecular weight and unfractionated heparins.

    PubMed

    Patel, Rahul P; Narkowicz, Christian; Hutchinson, Joseph P; Hilder, Emily F; Jacobson, Glenn A

    2008-01-07

    A simple, selective and accurate capillary electrophoresis (CE) method has been developed for the rapid separation and identification of various low molecular weight heparins (LMWHs) and unfractionated heparin. Separation and operational parameters were investigated using dalteparin sodium as the test LMWH. The developed method used a 70 cm fused silica capillary (50 microm i.d.) with a detection window 8.5 cm from the distal end. Phosphate electrolyte (pH 3.5; 50 mM), an applied voltage of -30 k V, UV detection at 230 nm and sample injection at 20 mbar for 5s were used. The method performance was assessed in terms of linearity, selectivity, intra- and inter-day precision and accuracy. The method was successfully applied to the European Pharmacopeia LMWH standard, dalteparin sodium, enoxaparin sodium and heparin sodium with a significant reduction in the run time and increased resolution compared with previously reported CE methods. Different CE separation profiles were obtained for various LMWHs and unfractionated heparin showing significant structural diversity. The current methodology was sensitive enough to reveal minor constituent differences between two different batches of enoxaparin sodium. This CE method also clearly showed chemical changes that occurred to LMWHs under different stress conditions. The sensitivity, selectivity and simplicity of the developed method allow its application in research or manufacturing for the identification, stability analysis, characterization and monitoring of batch-to-batch consistency of different low molecular weight and unfractionated heparins.

  4. Apta-nanosensor preparation and in vitro assay for rapid Diazinon detection using a computational molecular approach.

    PubMed

    Jokar, Mahmoud; Safaralizadeh, Mohammad Hassan; Hadizadeh, Farzin; Rahmani, Fatemeh; Kalani, Mohamad Reza

    2017-02-01

    Aptamers (ss-DNA or ss-RNA), also known as artificial antibodies, have been selected in vitro median to bind target molecules with high affinity and selectivity. Diazinon is one of the most widely used organophosphorus insecticides in developing and underdeveloped countries as insecticide and acaricide. Diazinon is readily absorbed from the gastrointestinal system and rapidly distributed throughout the body. Thus, the design of clinical and laboratory diagnostics using nanobiosensors is necessary. A computational approach allows us to screen or rank receptor structure and predict interaction outcomes with a deeper understanding, and it is much more cost effective than laboratory attempts. In this research, the best sequence (high affinity bind Diazinon-ssDNA) was ranked among 12 aptamers isolated from SELEX experimentation. Docking results, as the first virtual screening stage and static technique, selected frequent conformation of each aptamer. Then, the quantity and quality of aptamer-Diazinon interaction were simulated using molecular dynamics as a mobility technique. RMSD, RMSF, radius of gyration, and the number of hydrogen bonds formed between Diazinon-aptamer were monitored to assess the quantity and quality of interactions. G-quadruplex DNA aptamer (DF20) showed to be a reliable candidate for Diazinon biosensing. The apta-nanosensor designed using simulation results allowed with linearity detection in the range of .141-.65 nM and a LOD of 17.903 nM, and it was validated using a computational molecular approach.

  5. Operational feasibility of using whole blood in the rapid HIV testing algorithm of a resource-limited settings like Bangladesh

    PubMed Central

    Munshi, Saif U.; Oyewale, Tajudeen O.; Begum, Shahnaz; Uddin, Ziya; Tabassum, Shahina

    2016-01-01

    Background Serum-based rapid HIV testing algorithm in Bangladesh constitutes operational challenge to scaleup HIV testing and counselling (HTC) in the country. This study explored the operational feasibility of using whole blood as alternative to serum for rapid HIV testing in Bangladesh. Methods Whole blood specimens were collected from two study groups. The groups included HIV-positive patients (n = 200) and HIV-negative individuals (n = 200) presenting at the reference laboratory in Dhaka, Bangladesh. The specimens were subjected to rapid HIV tests using the national algorithm with A1 = Alere Determine (United States), A2 = Uni-Gold (Ireland), and A3 = First Response (India). The sensitivity and specificity of the test results, and the operational cost were compared with current serum-based testing. Results The sensitivities [95% of confidence interval (CI)] for A1, A2, and A3 tests using whole blood were 100% (CI: 99.1–100%), 100% (CI: 99.1–100%), and 97% (CI: 96.4–98.2%), respectively, and specificities of all test kits were 100% (CI: 99.1–100%). Significant (P < 0.05) reduction in the cost of establishing HTC centre and consumables by 94 and 61%, respectively, were observed. The cost of administration and external quality assurance reduced by 39 and 43%, respectively. Overall, there was a 36% cost reduction in total operational cost of rapid HIV testing with blood when compared with serum. Conclusion Considering the similar sensitivity and specificity of the two specimens, and significant cost reduction, rapid HIV testing with whole blood is feasible. A review of the national HIV rapid testing algorithm with whole blood will contribute toward improving HTC coverage in Bangladesh. PMID:26945143

  6. Operational feasibility of using whole blood in the rapid HIV testing algorithm of a resource-limited settings like Bangladesh.

    PubMed

    Munshi, Saif U; Oyewale, Tajudeen O; Begum, Shahnaz; Uddin, Ziya; Tabassum, Shahina

    2016-03-01

    Serum-based rapid HIV testing algorithm in Bangladesh constitutes operational challenge to scaleup HIV testing and counselling (HTC) in the country. This study explored the operational feasibility of using whole blood as alternative to serum for rapid HIV testing in Bangladesh. Whole blood specimens were collected from two study groups. The groups included HIV-positive patients (n = 200) and HIV-negative individuals (n = 200) presenting at the reference laboratory in Dhaka, Bangladesh. The specimens were subjected to rapid HIV tests using the national algorithm with A1 = Alere Determine (United States), A2 = Uni-Gold (Ireland), and A3 = First Response (India). The sensitivity and specificity of the test results, and the operational cost were compared with current serum-based testing. The sensitivities [95% of confidence interval (CI)] for A1, A2, and A3 tests using whole blood were 100% (CI: 99.1-100%), 100% (CI: 99.1-100%), and 97% (CI: 96.4-98.2%), respectively, and specificities of all test kits were 100% (CI: 99.1-100%). Significant (P < 0.05) reduction in the cost of establishing HTC centre and consumables by 94 and 61%, respectively, were observed. The cost of administration and external quality assurance reduced by 39 and 43%, respectively. Overall, there was a 36% cost reduction in total operational cost of rapid HIV testing with blood when compared with serum. Considering the similar sensitivity and specificity of the two specimens, and significant cost reduction, rapid HIV testing with whole blood is feasible. A review of the national HIV rapid testing algorithm with whole blood will contribute toward improving HTC coverage in Bangladesh.

  7. The human resource information system: a rapid appraisal of Pakistan’s capacity to employ the tool

    PubMed Central

    2013-01-01

    Background Human resources are an important building block of the health system. During the last decade, enormous investment has gone into the information systems to manage human resources, but due to the lack of a clear vision, policy, and strategy, the results of these efforts have not been very visible. No reliable information portal captures the actual state of human resources in Pakistan’s health sector. The World Health Organization (WHO) has provided technical support for the assessment of the existing system and development of a comprehensive Human Resource Information System (HRIS) in Pakistan. Methods The questions in the WHO-HRIS Assessment tool were distributed into five thematic groups. Purposively selected (n=65) representatives from the government, private sector, and development partners participated in this cross sectional study, based on their programmatic affiliations. Results Fifty-five percent of organizations and departments have an independent Human Resources (HR) section managed by an establishment branch and are fully equipped with functional computers. Forty-five organizations (70%) had HR rules, regulations and coordination mechanisms, yet these are not implemented. Data reporting is mainly in paper form, on prescribed forms (51%), registers (3%) or even plain papers (20%). Data analysis does not give inputs to the decision making process and dissemination of information is quite erratic. Most of the organizations had no feedback mechanism for cross checking the HR data, rendering it unreliable. Conclusion Pakistan is lacking appropriate HRIS management. The current HRIS indeed has a multitude of problems. In the wake of 2011 reforms within the health sector, provinces are even in a greater need for planning their respective health department services and must work on the deficiencies and inefficiencies of their HRIS so that the gaps and HR needs are better aligned for reaching the 2015 UN Millennium Development Goals (MDGs) targets

  8. MOLECULAR GENETIC TOOLS FOR ASSESSING THE STATUS AND VULNERABILITY OF AQUATIC RESOURCES

    EPA Science Inventory

    Development of ecological indicators that efficiently capture the present condition and project future vulnerabilities of biological resources is critical to sound environmental management. For this reason, the ORD's Ecological Research Program is developing genetic methodologies...

  9. MOLECULAR GENETIC TOOLS FOR ASSESSING THE STATUS AND VULNERABILITY OF AQUATIC RESOURCES

    EPA Science Inventory

    Development of ecological indicators that efficiently capture the present condition and project future vulnerabilities of biological resources is critical to sound environmental management. For this reason, the ORD's Ecological Research Program is developing genetic methodologies...

  10. A Randomized Clinical Trial Comparing Use of Rapid Molecular Testing for Staphylococcus aureus for Patients With Cutaneous Abscesses in the Emergency Department With Standard of Care.

    PubMed

    May, Larissa S; Rothman, Richard E; Miller, Loren G; Brooks, Gillian; Zocchi, Mark; Zatorski, Catherine; Dugas, Andrea F; Ware, Chelsea E; Jordan, Jeanne A

    2015-12-01

    To determine whether real-time availability of rapid molecular results of Staphylococcus aureus would impact emergency department clinician antimicrobial selection for adults with cutaneous abscesses. We performed a prospective, randomized controlled trial comparing a rapid molecular test with standard of care culture-based testing. Follow-up telephone calls were made at between 2 and 7 days, 1 month, and 3 months after discharge. Two urban, academic emergency departments. Patients at least 18 years old presenting with a chief complaint of abscess, cellulitis, or insect bite and receiving incision and drainage were eligible. Seven hundred seventy-eight people were assessed for eligibility and 252 met eligibility criteria. Clinician antibiotic selection and clinical outcomes were evaluated. An ad hoc outcome of test performance was performed. We enrolled 252 patients and 126 were randomized to receive the rapid test. Methicillin-susceptible S. aureus-positive patients receiving rapid test results were prescribed beta-lactams more often than controls (absolute difference, 14.5% [95% CI, 1.1%-30.1%]) whereas methicillin-resistant S. aureus-positive patients receiving rapid test results were more often prescribed anti-methicillin-resistant S. aureus antibiotics (absolute difference, 21.5% [95% CI, 10.1%-33.0%]). There were no significant differences between the 2 groups in 1-week or 3-month clinical outcomes. Availability of rapid molecular test results after incision and drainage was associated with more-targeted antibiotic selection. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01523899.

  11. Rapid PCR-Based Molecular Pathotyping of H5 and H7 Avian Influenza Viruses ▿ †

    PubMed Central

    Leijon, Mikael; Ullman, Karin; Thyselius, Susanna; Zohari, Siamak; Pedersen, Janice C.; Hanna, Amanda; Mahmood, Sahar; Banks, Jill; Slomka, Marek J.; Belák, Sándor

    2011-01-01

    While the majority of avian influenza virus (AIV) subtypes are classified as low-pathogenicity avian influenza viruses (LPAIV), the H5 and H7 subtypes have the ability to mutate to highly pathogenic avian influenza viruses (HPAIV) in poultry and therefore are the etiological agents of notifiable AIV (NAIV). It is of great importance to distinguish HPAIV from LPAIV variants during H5/H7 outbreaks and surveillance. To this end, a novel and fast strategy for the molecular pathotyping of H5/H7 AIVs is presented. The differentiation of the characteristic hemagglutinin (HA) protein cleavage sites (CSs) of HPAIVs and LPAIVs is achieved by a novel PCR method where the samples are interrogated for all existing CSs with a 484-plex primer mixture directly targeting the CS region. CSs characteristic for HP or LP H5/H7 viruses are distinguished in a seminested duplex real-time PCR format using plexor fluorogenic primers. Eighty-six laboratory isolates and 60 characterized NAIV-positive clinical specimens from poultry infected with H5/H7 both experimentally and in the field were successfully pathotyped in the validation. The method has the potential to substitute CS sequencing in the HA gene for the determination of the molecular pathotype, thereby providing a rapid means to acquire additional information concerning NAIV outbreaks, which may be critical to their management. The new assay may be extended to the LP/HP differentiation of previously unknown H5/H7 isolates. It may be considered for integration into surveillance and control programs in both domestic and wild bird populations. PMID:21900520

  12. Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

    PubMed

    Wordley, Claire; Slate, Jon; Stapley, Jessica

    2011-01-01

    Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage.

  13. Rapid diagnostic tests for molecular surveillance of Plasmodium falciparum malaria -assessment of DNA extraction methods and field applicability.

    PubMed

    Morris, Ulrika; Aydin-Schmidt, Berit; Shakely, Delér; Mårtensson, Andreas; Jörnhagen, Louise; Ali, Abdullah S; Msellem, Mwinyi I; Petzold, Max; Gil, José P; Ferreira, Pedro E; Björkman, Anders

    2013-03-19

    The need for new malaria surveillance tools and strategies is critical, given improved global malaria control and regional elimination efforts. High quality Plasmodium falciparum DNA can reliably be extracted from malaria rapid diagnostic tests (RDTs). Together with highly sensitive molecular assays, wide scale collection of used RDTs may serve as a modern tool for improved malaria case detection and drug resistance surveillance. However, comparative studies of DNA extraction efficiency from RDTs and the field applicability are lacking. The aim of this study was to compare and evaluate different methods of DNA extraction from RDTs and to test the field applicability for the purpose of molecular epidemiological investigations. DNA was extracted from two RDT devices (Paracheck-Pf® and SD Bioline Malaria Pf/Pan®), seeded in vitro with 10-fold dilutions of cultured 3D7 P. falciparum parasites diluted in malaria negative whole blood. The level of P. falciparum detection was determined for each extraction method and RDT device with multiple nested-PCR and real-time PCR assays. The field applicability was tested on 855 paired RDT (Paracheck-Pf) and filter paper (Whatman® 3MM) blood samples (734 RDT negative and 121 RDT positive samples) collected from febrile patients in Zanzibar 2010. RDT positive samples were genotyped at four key single nucleotide polymorphisms (SNPs) in pfmdr1 and pfcrt as well as for pfmdr1 copy number, all associated with anti-malarial drug resistance. The P. falciparum DNA detection limit varied with RDT device and extraction method. Chelex-100 extraction performed best for all extraction matrixes. There was no statistically significant difference in PCR detection rates in DNA extracted from RDTs and filter paper field samples. Similarly there were no significant differences in the PCR success rates and genotyping outcomes for the respective SNPs in the 121 RDT positive samples. The results support RDTs as a valuable source of parasite DNA and

  14. Use of Molecular Methods for the Rapid Mass Detection of Schistosoma mansoni (Platyhelminthes: Trematoda) in Biomphalaria spp. (Gastropoda: Planorbidae)

    PubMed Central

    Jannotti-Passos, Liana Konovaloffi; Dos Santos Carvalho, Omar

    2017-01-01

    The low stringency-polymerase chain reaction (LS-PCR) and loop-mediated isothermal amplification (LAMP) assays were used to detect the presence of S. mansoni DNA in (1) Brazilian intermediate hosts (Biomphalaria glabrata, B. straminea, and B. tenagophila) with patent S. mansoni infections, (2) B. glabrata snails with prepatent S. mansoni infections, (3) various mixtures of infected and noninfected snails; and (4) snails infected with other trematode species. The assays showed high sensitivity and specificity and could detect S. mansoni DNA when one positive snail was included in a pool of 1,000 negative specimens of Biomphalaria. These molecular approaches can provide a low-cost, effective, and rapid method for detecting the presence of S. mansoni in pooled samples of field-collected Biomphalaria. These assays should aid mapping of transmission sites in endemic areas, especially in low prevalence regions and improve schistosomiasis surveillance. It will be a useful tool to monitor low infection rates of snails in areas where control interventions are leading towards the elimination of schistosomiasis. PMID:28246533

  15. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: Fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

    SciTech Connect

    Worley, K.C.; Lindsay, E.A.; McCabe, E.R.B.

    1995-07-17

    Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosome deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available. 17 refs., 2 figs.

  16. Lake secondary production fueled by rapid transfer of low molecular weight organic carbon from terrestrial sources to aquatic consumers.

    PubMed

    Berggren, M; Ström, L; Laudon, H; Karlsson, J; Jonsson, A; Giesler, R; Bergström, A-K; Jansson, M

    2010-07-01

    Carbon of terrestrial origin often makes up a significant share of consumer biomass in unproductive lake ecosystems. However, the mechanisms for terrestrial support of lake secondary production are largely unclear. By using a modelling approach, we show that terrestrial export of dissolved labile low molecular weight carbon (LMWC) compounds supported 80% (34-95%), 54% (19-90%) and 23% (7-45%) of the secondary production by bacteria, protozoa and metazoa, respectively, in a 7-km(2) boreal lake (conservative to liberal estimates in brackets). Bacterial growth on LMWC was of similar magnitude as that of primary production (PP), and grazing on bacteria effectively channelled the LMWC carbon to higher trophic levels. We suggest that rapid turnover of forest LMWC pools enables continuous export of fresh photosynthates and other labile metabolites to aquatic systems, and that substantial transfer of LMWC from terrestrial sources to lake consumers can occur within a few days. Sequestration of LMWC of terrestrial origin, thus, helps explain high shares of terrestrial carbon in lake organisms and implies that lake food webs can be closely dependent on recent terrestrial PP.

  17. A molecular dynamics study on thin film liquid boiling characteristics under rapid linear boundary heating: Effect of liquid film thickness

    NASA Astrophysics Data System (ADS)

    Rabbi, Kazi Fazle; Tamim, Saiful Islam; Faisal, A. H. M.; Mukut, K. M.; Hasan, Mohammad Nasim

    2017-06-01

    This study is a molecular dynamics investigation of phase change phenomena i.e. boiling of thin liquid films subjected to rapid linear heating at the boundary. The purpose of this study is to understand the phase change heat transfer phenomena at nano scale level. In the simulation, a thin film of liquid argon over a platinum surface has been considered. The simulation domain herein is a three-phase system consisting of liquid and vapor argon atoms placed over a platinum wall. Initially the whole system is brought to an equilibrium state at 90 K and then the temperature of the bottom wall is increased to a higher temperature (250K) within a finite time interval. Four different liquid argon film thicknesses have been considered (3 nm, 4 nm, 5 nm and 6 nm) in this study. The boundary heating rate (40×109 K/s) is kept constant in all these cases. Variation in system temperature, pressure, net evaporation number, spatial number density of the argon region with time for different film thickness have been demonstrated and analyzed. The present study indicates that the pattern of phase transition may be significantly different (i.e. evaporation or explosive boiling) depending on the liquid film thickness. Among the four cases considered in the present study, explosive boiling has been observed only for the liquid films of 5nm and 6nm thickness, while for the other cases, evaporation take place.

  18. Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat.

    PubMed

    Wicker, Thomas; Yahiaoui, Nabila; Guyot, Romain; Schlagenhauf, Edith; Liu, Zhong-Da; Dubcovsky, Jorge; Keller, Beat

    2003-05-01

    To study genome evolution in wheat, we have sequenced and compared two large physical contigs of 285 and 142 kb covering orthologous low molecular weight (LMW) glutenin loci on chromosome 1AS of a diploid wheat species (Triticum monococcum subsp monococcum) and a tetraploid wheat species (Triticum turgidum subsp durum). Sequence conservation between the two species was restricted to small regions containing the orthologous LMW glutenin genes, whereas >90% of the compared sequences were not conserved. Dramatic sequence rearrangements occurred in the regions rich in repetitive elements. Dating of long terminal repeat retrotransposon insertions revealed different insertion events occurring during the last 5.5 million years in both species. These insertions are partially responsible for the lack of homology between the intergenic regions. In addition, the gene space was conserved only partially, because different predicted genes were identified on both contigs. Duplications and deletions of large fragments that might be attributable to illegitimate recombination also have contributed to the differentiation of this region in both species. The striking differences in the intergenic landscape between the A and A(m) genomes that diverged 1 to 3 million years ago provide evidence for a dynamic and rapid genome evolution in wheat species.

  19. Rapidly Increasing Prevalence of Penicillin-Resistant Streptococcus pneumoniae in Middle Tennessee: a 10-Year Clinical and Molecular Analysis

    PubMed Central

    Tang, Yi-Wei; Li, Haijing; Griffin, Jane P.; Haas, David W.; D'Agata, Erika M. C.

    2002-01-01

    The clinical and molecular epidemiology of penicillin-resistant Streptococcus pneumoniae and the diagnostic accuracy of a six-primer PCR assay in identifying penicillin resistance were analyzed by using clinical isolates recovered over a 10-year period in middle Tennessee. The prevalence of non-penicillin-susceptible S. pneumoniae isolates (MIC, ≥0.1 μg/ml) increased from 10% in 1990 to 70% in 1999 (P < 0.001). Among S. pneumoniae isolates for which the penicillin MIC was ≥2 μg/ml (highly penicillin-resistant S. pneumoniae [PRSP]), 23 and 5% were resistant to at least three and at least five other antimicrobial classes, respectively. Pulsed-field gel electrophoresis identified 13 unique strain types, with type B accounting for 33% of PRSP isolates. The sensitivity, specificity, and negative and positive predictive values of the PCR assay in detecting PRSP were 99, 100, 99, and 100%, respectively. Penicillin resistance is rapidly increasing among S. pneumoniae isolates in Tennessee. The simultaneous detection of S. pneumoniae and high-level penicillin resistance can be accurately performed with the six-primer PCR assay. PMID:11825948

  20. Use of Molecular Methods for the Rapid Mass Detection of Schistosoma mansoni (Platyhelminthes: Trematoda) in Biomphalaria spp. (Gastropoda: Planorbidae).

    PubMed

    Caldeira, Roberta Lima; Jannotti-Passos, Liana Konovaloffi; Dos Santos Carvalho, Omar

    2017-01-01

    The low stringency-polymerase chain reaction (LS-PCR) and loop-mediated isothermal amplification (LAMP) assays were used to detect the presence of S. mansoni DNA in (1) Brazilian intermediate hosts (Biomphalaria glabrata, B. straminea, and B. tenagophila) with patent S. mansoni infections, (2) B. glabrata snails with prepatent S. mansoni infections, (3) various mixtures of infected and noninfected snails; and (4) snails infected with other trematode species. The assays showed high sensitivity and specificity and could detect S. mansoni DNA when one positive snail was included in a pool of 1,000 negative specimens of Biomphalaria. These molecular approaches can provide a low-cost, effective, and rapid method for detecting the presence of S. mansoni in pooled samples of field-collected Biomphalaria. These assays should aid mapping of transmission sites in endemic areas, especially in low prevalence regions and improve schistosomiasis surveillance. It will be a useful tool to monitor low infection rates of snails in areas where control interventions are leading towards the elimination of schistosomiasis.

  1. eSnail: a transcriptome-based molecular resource of the central nervous system for terrestrial gastropods.

    PubMed

    Zhao, Min; Wang, Tianfang; Stewart, Michael J; Bose, Utpal; Suwansa-Ard, Saowaros; Storey, Kenneth B; Cummins, Scott F

    2017-09-28

    To expand on emerging terrestrial gastropod molecular resources, we have undertaken transcriptome-based sequencing of the central nervous system (CNS) from six ecologically invasive terrestrial gastropods. Focusing on snail species Cochlicella acuta and Helix aspersa, and reticulated slugs Deroceras invadens, Deroceras reticulatum, Lehmannia nyctelia, and Milax gagates, we obtained a total of 367,869,636 high quality reads and compared them with existing CNS transcript resources for the invasive Mediterranean snail, Theba pisana. In total we obtained, 419,289 unique transcripts (unigenes) from 1,410,569 assembled contigs, with BLAST search analysis of multiple protein databases leading to the annotation of 124,268 unigenes, of which 92,544 mapped to NCBI non-redundant protein databases. We found that these transcriptomes have representatives in most biological functions, based on comparison of gene ontology, KEGG pathway, and protein family contents, demonstrating a high range of transcripts responsible for regulating metabolic activities and molecular functions occurring within the CNS. To provide an accessible genetic resource, we also demonstrate the presence of 66,687 microsatellites and 304,693 single nucleotide variants, which can be used for the design of potentially thousands of unique primers for functional screening. An online 'eSnail' database with a user-friendly web interface was implemented to query all the information obtained herein (http://soft.bioinfo-minzhao.org/esnail). We demonstrate the usefulness of the database through the mining of molluscan neuropeptides. As the most comprehensive CNS transcriptome resource for terrestrial gastropods, eSnail may serve as a useful gateway for researchers to explore gastropod CNS function for multiple purposes, including for the development of biocontrol approaches. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  2. Development of a molecular assay system for the rapid detection and identification of Ug99 and related races of Puccinia graminis

    USDA-ARS?s Scientific Manuscript database

    In the last decade the complexity and distribution of the Ug99 race group of Puccinia graminis f. sp. tritici has dramatically expanded. In order to provide rapid tools, a two-stage molecular assay system has been developed using real-time polymerase chain reaction methodologies and TaqMan probes. S...

  3. Molecular fingerprinting of cacao (Theobroma cacao L.) genetic resources in the Dominican Republic

    USDA-ARS?s Scientific Manuscript database

    Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic ranking 11th in the world and number one in organic cacao exports. Dominican cacao genetic resources are maintained, propagated and distributed nationally out of the IDIAF’s Mata Larga research stations. T...

  4. Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

    USDA-ARS?s Scientific Manuscript database

    Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded mole...

  5. Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis Glycines Matsumura

    USDA-ARS?s Scientific Manuscript database

    Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded mole...

  6. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

    PubMed Central

    Wyffels, Jennifer; L. King, Benjamin; Vincent, James; Chen, Chuming; Wu, Cathy H.; Polson, Shawn W.

    2014-01-01

    Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase ( http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources. PMID:25309735

  7. Resource management and operations in southwest South Dakota: Climate change scenario planning workshop summary January 20-21, 2016, Rapid City, SD

    USGS Publications Warehouse

    Fisichelli, Nicholas A.; Schuurman, Gregor W; Symstad, Amy; Ray, Andrea; Miller, Brian; Cross, Molly; Rowland, Erika

    2016-01-01

    The Scaling Climate Change Adaptation in the Northern Great Plains through Regional Climate Summaries and Local Qualitative-Quantitative Scenario Planning Workshops project synthesizes climate data into 3-5 distinct but plausible climate summaries for the northern Great Plains region; crafts quantitative summaries of these climate futures for two focal areas; and applies these local summaries by developing climate-resource-management scenarios through participatory workshops and, where possible, simulation models. The two focal areas are central North Dakota and southwest South Dakota (Figure 1). The primary objective of this project is to help resource managers and scientists in a focal area use scenario planning to make management and planning decisions based on assessments of critical future uncertainties.This report summarizes project work for public and tribal lands in the southwest South Dakota grasslands focal area, with an emphasis on Badlands National Park and Buffalo Gap National Grassland. The report explains scenario planning as an adaptation tool in general, then describes how it was applied to the focal area in three phases. Priority resource management and climate uncertainties were identified in the orientation phase. Local climate summaries for relevant, divergent, and challenging climate scenarios were developed in the second phase. In the final phase, a two-day scenario planning workshop held January 20-21, 2016 in Rapid City, South Dakota, featured scenario development and implications, testing management decisions, and methods for operationalizing scenario planning outcomes.

  8. MALDI-TOF MS Enables the Rapid Identification of the Major Molecular Types within the Cryptococcus neoformans/C. gattii Species Complex

    PubMed Central

    Firacative, Carolina; Trilles, Luciana; Meyer, Wieland

    2012-01-01

    Background The Cryptococcus neoformans/C. gattii species complex comprises two sibling species that are divided into eight major molecular types, C. neoformans VNI to VNIV and C. gattii VGI to VGIV. These genotypes differ in host range, epidemiology, virulence, antifungal susceptibility and geographic distribution. The currently used phenotypic and molecular identification methods for the species/molecular types are time consuming and expensive. As Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) offers an effective alternative for the rapid identification of microorganisms, the objective of this study was to examine its potential for the identification of C. neoformans and C. gattii strains at the intra- and inter-species level. Methodology Protein extracts obtained via the formic acid extraction method of 164 C. neoformans/C. gattii isolates, including four inter-species hybrids, were studied. Results The obtained mass spectra correctly identified 100% of all studied isolates, grouped each isolate according to the currently recognized species, C. neoformans and C. gattii, and detected potential hybrids. In addition, all isolates were clearly separated according to their major molecular type, generating greater spectral differences among the C. neoformans molecular types than the C. gattii molecular types, most likely reflecting a closer phylogenetic relationship between the latter. The number of colonies used and the incubation length did not affect the results. No spectra were obtained from intact yeast cells. An extended validated spectral library containing spectra of all eight major molecular types was established. Conclusions MALDI-TOF MS is a rapid identification tool for the correct recognition of the two currently recognized human pathogenic Cryptococcus species and offers a simple method for the separation of the eight major molecular types and the detection of hybrid strains within this species complex in the

  9. Evaluation of 3M Molecular Detection System and ANSR Pathogen Detection System for rapid detection of Salmonella from egg products.

    PubMed

    Hu, L; Ma, L M; Zheng, S; He, X; Wang, H; Brown, E W; Hammack, T S; Zhang, G

    2017-05-01

    Isothermal amplification assay is a novel simple detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was to evaluate the effectiveness of the 3M Molecular Detection System (MDS) and ANSR Pathogen Detection System (PDS) for the detection of Salmonella in egg products as compared to the Food and Drug Administration's Bacteriological Analytical Manual (BAM) culture method and a modified culture method (3M MDS and ANSR PDS preferred method). Two Salmonella ser. Enteritidis (18579, PT4; CDC_2010K_1441, PT8), one Salmonella ser. Heidelberg (607310-1), and one Salmonella ser. Typhimurium (0723) isolates were used in this study. Seven wet egg products and 13 dry egg products were inoculated with these strains individually at 1 to 5 CFU/25 g. One set of test portions was prepared following FDA BAM procedures [with lactose broth (LB) as pre-enrichment broth]. Another set of test portions was prepared using buffered peptone water (BPW) as pre-enrichment broth, as instructed by the 2 detection systems. Results from 3M MDS and ANSR PDS were 100% in agreement with their BPW-based culture method results. When LB was used as pre-enrichment broth, the number of Salmonella positive test portions (80 tested), identified with the BAM, 3M MDS, and ANSR PDS, were 63, 61, and 60, respectively. In conclusion, both 3M MDS and ANSR PDS Salmonella assays were as effective as their BPW based culture methods and were equivalent to the BAM culture method for the detection of Salmonella in egg products. These sensitive isothermal assays can be used as rapid detection tools for Salmonella in egg products provided that BPW is used as pre-enrichment broth. Published by Oxford University Press on behalf of Poultry Science Association 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  10. Molecular phylogeny and divergence dates for Australasian elapids and sea snakes (hydrophiinae): evidence from seven genes for rapid evolutionary radiations.

    PubMed

    Sanders, K L; Lee, M S Y; Leys, R; Foster, R; Keogh, J Scott

    2008-05-01

    One of the most prolific radiations of venomous snakes, the Australo-Melanesian Hydrophiinae includes approximately 100 species of Australasian terrestrial elapids plus all approximately 60 species of viviparous sea snakes. Here, we estimate hydrophiine relationships based on a large data set comprising 5800 bp drawn from seven genes (mitochondrial: ND4, cytb, 12S, 16S; nuclear: rag1, cmos, myh). These data were analysed using parsimony, likelihood and Bayesian methods to better resolve hydrophiine phylogeny and provide a timescale for the terrestrial and marine radiations. Among oviparous forms, Cacophis, Furina and Demansia are basal to other Australian elapids (core oxyuranines). The Melanesian Toxicocalamus and Aspidomorphus group with Demansia, indicating multiple dispersal events between New Guinea and Australia. Oxyuranus and Pseudonaja form a robust clade. The small burrowing taxa form two separate clades, one consisting of Vermicella and Neelaps calanotus, and the other including Simoselaps, Brachyurophis and Neelaps bimaculatus. The viviparous terrestrial elapids form three separate groups: Acanthophis, the Rhinoplocephalus group and the Notechis-Hemiaspis group. True sea snakes (Hydrophiini) are robustly united with the Notechis-Hemiaspis group. Many of the retrieved groupings are consistent with previous molecular and morphological analyses, but the polyphyly of the viviparous and burrowing groups, and of Neelaps, are novel results. Bayesian relaxed clock analyses indicate very recent divergences: the approximately 160 species of the core Australian radiation (including sea snakes) arose within the last 10 Myr, with most inter-generic splits dating to between 10 and 6 Ma. The Hydrophis sea snake lineage is an exceptionally rapid radiation, with > 40 species evolving within the last 5 Myr.

  11. CD19-targeted T cells rapidly induce molecular remissions in adults with chemotherapy-refractory acute lymphoblastic leukemia

    PubMed Central

    Brentjens, Renier; Davila, Marco L; Riviere, Isabelle; Park, Jae; Wang, Xiuyan; Cowell, Lindsay G; Bartido, Shirley; Stefanski, Jolanta; Taylor, Clare; Olszewska, Malgorzata; Borquez-Ojeda, Oriana; Qu, Jinrong; Wasielewska, Teresa; He, Qing; Bernal, Yvette; Rijo, Ivelise V; Hedvat, Cyrus; Kobos, Rachel; Curran, Kevin; Steinherz, Peter; Jurcic, Joseph; Rosenblat, Todd; Maslak, Peter; Frattini, Mark; Sadelain, Michel

    2013-01-01

    Adults with relapsed B-acute lymphoblastic leukemia (ALL) have a dismal prognosis. Only those patients able to achieve a second remission with no minimal residual disease (MRD−) have a hope for long-term survival in the context of a subsequent allogeneic hematopoietic stem cell transplantation (allo-HSCT). We have treated 5 relapsed B-ALL subjects with autologous T cells expressing a CD19-specific CD28/CD3ζ second generation dual-signaling chimeric antigen receptor (CAR) termed 19-28z. All patients with persistent morphological disease or MRD+ disease upon T cell infusion demonstrated rapid tumor eradication and achieved MRD-negative complete remissions as assessed by deep sequencing PCR. Therapy was well tolerated although significant cytokine elevations, specifically observed in those patients with morphologic evidence of disease at the time of treatment, required lymphotoxic steroid therapy to ameliorate cytokine-mediated toxicities. Significantly, cytokine elevations directly correlated to tumor burden at the time of CAR modified T cell infusions. Tumor cells from one patient with relapsed disease after CAR modified T cell therapy, ineligible for additional allo-HSCT therapy, exhibited persistent expression of CD19 and sensitivity to autologous 19-28z T cell mediated cytotoxicity suggesting potential clinical benefit of additional CAR modified T cell infusions. These results demonstrate the marked anti-tumor efficacy of 19-28z CAR modified T cells in patients with relapsed/refractory B-ALL and the reliability of this novel therapy to induce profound molecular remissions, an ideal bridge to potentially curative therapy with subsequent allo-HSCT. PMID:23515080

  12. Development of rapid phenotypic system for the identification of Gram-negative oxidase-positive bacilli in resource-limited settings.

    PubMed

    Kazmi, Mahmooda; Khan, Adnan; Kazmi, Shahana Urooj

    2013-06-01

    Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology. The diagnosis and surveillance of diseases is dependent, to a great extent, on laboratory services, which cannot function without effective reliable reagents and diagnostics. Despite the advancement in microbiology diagnosis globally, resourcelimited countries still struggle to provide an acceptable diagnosis quality which helps in clinical disease management and improve their mortality and morbidity data. During this study an indigenous product, Quick Test Strip (QTS) NE, was developed for the rapid identification of biochemically slower group of Gram-negative oxidase-positive bacilli that covers 19 different bacterial genera. Some of the members belonging to these groups are well-established human pathogens, e.g. various species of Vibrio, Pseudomonas, Burkholderia, Aeromonas, Achromobacter and Stenotrophomonas. This study also evaluates the performance of QTS-NE by comparing with genotypic characterization methods. A total of 232 clinical and reference bacterial isolates were tested by three different methods. QTSNE provides 100 percent concordant results with other rapid identification and molecular characterization methods and confirms the potential to be used in clinical diagnosis.

  13. Impact of rapid molecular diagnostic tests on time to treatment initiation and outcomes in patients with multidrug-resistant tuberculosis, Tamil Nadu, India.

    PubMed

    Nair, Dina; Navneethapandian, Pooranaganga D; Tripathy, Jaya Prasad; Harries, Anthony D; Klinton, Joel S; Watson, Basilea; Sivaramakrishnan, Gomathi N; Reddy, Devarajulu S; Murali, Lakshmi; Natrajan, Mohan; Swaminathan, Soumya

    2016-09-01

    India is replacing culture and drug sensitivity testing (CDST) with rapid molecular tests for diagnosing MDR-TB. We assessed the impact of rapid tests on time to initiation of treatment and outcomes in patients with MDR-TB compared with CDST. A retrospective cohort study involving MDR-TB patients from six districts in Tamil Nadu state, who underwent CDST (2010-2011) and rapid tests (2012-2013). There were 135 patients in the CDST group and 389 in the rapid diagnostic test group. Median time from sputum receipt at the laboratory to initiation of MDR-TB treatment was 130 days (IQR 75-213) in the CDST group and 22 days (IQR 14-38) in the rapid diagnostic test group (p<0.001). Overall treatment success was 30% with CDST and 41% with rapid tests (p<0.05), but there was high loss to follow-up >30% in both groups and missing data were higher in CDST (13%) compared with rapid tests (3%). There were significantly higher risks of unfavourable treatment outcomes in males (aRR 1.3, 95% CI 1.1-1.5) and those with treatment initiation delays >30 days (aRR 1.3, 95% CI 1.0-1.6). Rapid molecular diagnostic tests shortened the time to initiate treatment which was associated with reduced unfavourable outcomes in MDR-TB patients. This supports the policy to scale up these tests in India. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Rapid, low-cost and instrument-free CD4+ cell counting for HIV diagnostics in resource-poor settings.

    PubMed

    Glynn, Macdara T; Kinahan, David J; Ducrée, Jens

    2014-08-07

    We present a novel, user-friendly and widely autonomous point-of-care diagnostic to enable HIV monitoring in resource-poor regions where the current pandemic is most prevalent. To specifically isolate magnetically tagged CD4+ cells directly from patient blood, the low-cost and disposable microfluidic chip operates by dual-force CD4+ cell magnetophoresis; whereby the interplay of flow and magnetic fields governs the trajectory of target cells depending on whether the cell binds to a magnetic microbead. Instrument-free pumping is implemented by a finger-actuated elastic membrane; tagged beads are laterally deflected by a small and re-useable permanent magnet. The single-depth and monolithic microfluidic structure can easily be fabricated in a single casting step. After their magnetophoretic isolation from whole blood, estimation of CD4+ cell concentrations is then measured by bright-field inspection of the capture chamber. In addition, an optional fluorescence measurement can be used for confirmation of the bright-field result if required. On-chip CD4+ estimation produces a linear response over the full range of medically relevant CD4+ cell concentrations. Our technology combines high-efficiency capture (93.0 ± 3.3%) and cell enumeration.

  15. Evolution on the move: specialization on widespread resources associated with rapid range expansion in response to climate change.

    PubMed

    Bridle, Jon R; Buckley, James; Bodsworth, Edward J; Thomas, Chris D

    2014-02-07

    Generalist species and phenotypes are expected to perform best under rapid environmental change. In contrast to this view that generalists will inherit the Earth, we find that increased use of a single host plant is associated with the recent climate-driven range expansion of the UK brown argus butterfly. Field assays of female host plant preference across the UK reveal a diversity of adaptations to host plants in long-established parts of the range, whereas butterflies in recently colonized areas are more specialized, consistently preferring to lay eggs on one host plant species that is geographically widespread throughout the region of expansion, despite being locally rare. By common-garden rearing of females' offspring, we also show an increase in dispersal propensity associated with the colonization of new sites. Range expansion is therefore associated with an increase in the spatial scale of adaptation as dispersive specialists selectively spread into new regions. Major restructuring of patterns of local adaptation is likely to occur across many taxa with climate change, as lineages suited to regional colonization rather than local success emerge and expand.

  16. Integrating molecular design resources within modern drug discovery research: the Roche experience.

    PubMed

    Stahl, Martin; Guba, Wolfgang; Kansy, Manfred

    2006-04-01

    Various computational disciplines, such as cheminformatics, ADME modeling, virtual screening, chemogenomics search strategies and classic structure-based design, should be seen as one multifaceted discipline contributing to the early drug discovery process. Although significant resources enabling these activities have been established, their true integration into daily research should not be taken for granted. This article reviews value-adding activities from target assessment to lead optimization, and highlights the technical and process-related aspects that can be considered essential for performance and alignment within the research organization.

  17. A Randomized Clinical Trial Comparing Use of Rapid Molecular Testing for Staphylococcus aureus for Patients With Cutaneous Abscesses in the Emergency Department With Standard of Care

    PubMed Central

    May, Larissa S.; Rothman, Richard E.; Miller, Loren G.; Brooks, Gillian; Zocchi, Mark; Zatorski, Catherine; Dugas, Andrea F.; Ware, Chelsea E.; Jordan, Jeanne A.

    2017-01-01

    OBJECTIVE To determine whether real-time availability of rapid molecular results of Staphylococcus aureus would impact emergency department clinician antimicrobial selection for adults with cutaneous abscesses. DESIGN We performed a prospective, randomized controlled trial comparing a rapid molecular test with standard of care culture-based testing. Follow-up telephone calls were made at between 2 and 7 days, 1 month, and 3 months after discharge. SETTING Two urban, academic emergency departments. PATIENTS Patients at least 18 years old presenting with a chief complaint of abscess, cellulitis, or insect bite and receiving incision and drainage were eligible. Seven hundred seventy-eight people were assessed for eligibility and 252 met eligibility criteria. METHODS Clinician antibiotic selection and clinical outcomes were evaluated. An ad hoc outcome of test performance was performed. RESULTS We enrolled 252 patients and 126 were randomized to receive the rapid test. Methicillin-susceptible S. aureus–positive patients receiving rapid test results were prescribed beta-lactams more often than controls (absolute difference, 14.5% [95% CI, 1.1%–30.1%]) whereas methicillin-resistant S. aureus–positive patients receiving rapid test results were more often prescribed anti–methicillin-resistant S. aureus antibiotics (absolute difference, 21.5% [95% CI, 10.1%–33.0%]). There were no significant differences between the 2 groups in 1-week or 3-month clinical outcomes. CONCLUSION Availability of rapid molecular test results after incision and drainage was associated with more-targeted antibiotic selection. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01523899 PMID:26306996

  18. Green Is the New Black: The Need for a New Currency That Values Water Resources in Rapidly Developing Landscapes

    NASA Astrophysics Data System (ADS)

    Creed, I. F.; Webster, K. L.; Kreutzweiser, D. P.; Beall, F.

    2014-12-01

    Canada's boreal forest supports many aquatic ecosystem services (AES) due to the intimate linkage between aquatic systems and their surrounding terrestrial watersheds in forested landscapes. There is an increasing risk to AES because natural development activities (forest management, mining, energy) have resulted in disruptions that deteriorate aquatic ecosystems at local (10s of km2) to regional (100s of km2) scales. These activities are intensifying and expanding, placing at risk the healthy aquatic ecosystems that provide AES and may threaten the continued development of the energy, forest, and mining sectors. Remarkably, we know little about the consequences of these activities on AES. The idea that AES should be explicitly integrated into modern natural resource management regulations is gaining broad acceptance. A major need is the ability to measure cumulative effects and determine thresholds (the points where aquatic ecosystems and their services cannot recover to a desired state within a reasonable time frame) in these cumulative effects. However, there is no single conceptual approach to assessing cumulative effects that is widely accepted by both scientists and managers. We present an integrated science-policy framework that enables the integration of AES into forest management risk assessment and prevention/mitigation strategies. We use this framework to explore the risk of further deterioration of AES by (1) setting risk criteria; (2) using emerging technologies to map process-based indicators representing causes and consequences of risk events to the deterioration of AES; (3) assessing existing prevention and mitigation policies in place to avoid risk events; and (4) identifying priorities for policy change needed to reduce risk event. Ultimately, the success of this framework requires that higher value be placed on AES, and in turn to improve the science and management of the boreal forest.

  19. Are Treponema pallidum Specific Rapid and Point-of-Care Tests for Syphilis Accurate Enough for Screening in Resource Limited Settings? Evidence from a Meta-Analysis

    PubMed Central

    Jafari, Yalda; Peeling, Rosanna W.; Shivkumar, Sushmita; Claessens, Christiane; Joseph, Lawrence; Pai, Nitika Pant

    2013-01-01

    Background Rapid and point-of-care (POC) tests for syphilis are an invaluable screening tool, yet inadequate evaluation of their diagnostic accuracy against best reference standards limits their widespread global uptake. To fill this gap, a systematic review and meta-analysis was conducted to evaluate the sensitivity and specificity of rapid and POC tests in blood and serum samples against Treponema pallidum (TP) specific reference standards. Methods Five electronic databases (1980–2012) were searched, data was extracted from 33 articles, and Bayesian hierarchical models were fit. Results In serum samples, against a TP specific reference standard point estimates with 95% credible intervals (CrI) for the sensitivities of popular tests were: i) Determine, 90.04% (80.45, 95.21), ii) SD Bioline, 87.06% (75.67, 94.50), iii) VisiTect, 85.13% (72.83, 92.57), and iv) Syphicheck, 74.48% (56.85, 88.44), while specificities were: i) Syphicheck, 99.14% (96.37, 100), ii) Visitect, 96.45% (91.92, 99.29), iii) SD Bioline, 95.85% (89.89, 99.53), and iv) Determine, 94.15% (89.26, 97.66). In whole blood samples, sensitivities were: i) Determine, 86.32% (77.26, 91.70), ii) SD Bioline, 84.50% (78.81, 92.61), iii) Syphicheck, 74.47% (63.94, 82.13), and iv) VisiTect, 74.26% (53.62, 83.68), while specificities were: i) Syphicheck, 99.58% (98.91, 99.96), ii) VisiTect, 99.43% (98.22, 99.98), iii) SD Bioline, 97.95%(92.54, 99.33), and iv) Determine, 95.85% (92.42, 97.74). Conclusions Rapid and POC treponemal tests reported sensitivity and specificity estimates comparable to laboratory-based treponemal tests. In resource limited settings, where access to screening is limited and where risk of patients lost to follow up is high, the introduction of these tests has already been shown to improve access to screening and treatment to prevent stillbirths and neonatal mortality due to congenital syphilis. Based on the evidence, it is concluded that rapid and POC tests are useful in resource

  20. Are Treponema pallidum specific rapid and point-of-care tests for syphilis accurate enough for screening in resource limited settings? Evidence from a meta-analysis.

    PubMed

    Jafari, Yalda; Peeling, Rosanna W; Shivkumar, Sushmita; Claessens, Christiane; Joseph, Lawrence; Pai, Nitika Pant

    2013-01-01

    Rapid and point-of-care (POC) tests for syphilis are an invaluable screening tool, yet inadequate evaluation of their diagnostic accuracy against best reference standards limits their widespread global uptake. To fill this gap, a systematic review and meta-analysis was conducted to evaluate the sensitivity and specificity of rapid and POC tests in blood and serum samples against Treponema pallidum (TP) specific reference standards. Five electronic databases (1980-2012) were searched, data was extracted from 33 articles, and Bayesian hierarchical models were fit. In serum samples, against a TP specific reference standard point estimates with 95% credible intervals (CrI) for the sensitivities of popular tests were: i) Determine, 90.04% (80.45, 95.21), ii) SD Bioline, 87.06% (75.67, 94.50), iii) VisiTect, 85.13% (72.83, 92.57), and iv) Syphicheck, 74.48% (56.85, 88.44), while specificities were: i) Syphicheck, 99.14% (96.37, 100), ii) Visitect, 96.45% (91.92, 99.29), iii) SD Bioline, 95.85% (89.89, 99.53), and iv) Determine, 94.15% (89.26, 97.66). In whole blood samples, sensitivities were: i) Determine, 86.32% (77.26, 91.70), ii) SD Bioline, 84.50% (78.81, 92.61), iii) Syphicheck, 74.47% (63.94, 82.13), and iv) VisiTect, 74.26% (53.62, 83.68), while specificities were: i) Syphicheck, 99.58% (98.91, 99.96), ii) VisiTect, 99.43% (98.22, 99.98), iii) SD Bioline, 97.95%(92.54, 99.33), and iv) Determine, 95.85% (92.42, 97.74). Rapid and POC treponemal tests reported sensitivity and specificity estimates comparable to laboratory-based treponemal tests. In resource limited settings, where access to screening is limited and where risk of patients lost to follow up is high, the introduction of these tests has already been shown to improve access to screening and treatment to prevent stillbirths and neonatal mortality due to congenital syphilis. Based on the evidence, it is concluded that rapid and POC tests are useful in resource limited settings with poor access to

  1. Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

    PubMed

    Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

    2015-06-19

    The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and

  2. A Rapid Protoyping Approach for the Evaluation of Potential GPM-Era Precipitation Products for Water Resources Management Applications

    NASA Astrophysics Data System (ADS)

    Anantharaj, V. G.; Houser, P. R.; Turk, F. J.; Peterson, C. A.; Hossain, F.; Moorhead, R. J.; Toll, D. L.; Mostovoy, G.

    2009-04-01

    In order to facilitate the operational transition of satellite data, research products and advances in numerical modeling, the NASA Applied Sciences Program (ASP) had adopted a systems engineering approach to help identify and advanced and basic research capabilities that may be further developed for operational applications. This novel approach was envisioned to accelerate the harvesting of NASA's investment in research for societal benefits. International programs such as the Global Earth Observing System of Systems (GEOSS) could benefit from such systematic and integrated approaches to identify and extend the results of earth and environmental sciences for the benefits of global society. This new approach by the ASP was based on three phases of implementation, namely: (a) "Solutions Networks" for systematically examining data products, capabilities, and results from NASA Earth science research in order to find identify and prioritize candidate research activities that have the potential for societal benefits; (b) "Rapid Prototyping Capability (RPC)" experiments to further develop and tailor basic research and further evaluate and quantify their potential impacts for applications and decision support; and (c) "Integrated System Solutions (ISS)" to fully execute the transition the research to operational implementation and benchmark the performance resulting from integrating NASA Earth observations and science results. The RPC science experiments can be rapidly prototyped in order to evaluate the suitability of data, algorithms and models. They are designed to characterize uncertainties involved in the data, models, and decision making process while maintaining scientific rigor through the entire process. This approach helps identify scientific and logistical risks earlier in the process so that they can be appropriately addressed in a timely manner to minimize risk. GPM is promoted as "a science mission with broad societal applications," that will address

  3. Rapid enterovirus molecular testing in cerebrospinal fluid reduces length of hospitalization and duration of antibiotic therapy in children with aseptic meningitis.

    PubMed

    Huizing, Kirsten M N; Swanink, Caroline M A; Landstra, Anneke M; van Zwet, Anton A; van Setten, Petra A

    2011-12-01

    We studied the potential benefits of introducing a rapid enterovirus molecular test in children with enterovirus meningitis. The 2 groups of pediatric patients were comparable with respect to clinical and laboratory data, but differed in availability of enterovirus test results. In the control group, the results were available within 3 to 7 days, whereas in the study group, rapid enterovirus molecular test results were available within 3 to 24 hours. The median duration of hospitalization and the duration of antibiotics were significantly reduced to, respectively, 2 days and 1 day in the study group when compared with the control group (P < 0.001). Mean costs per patient calculation showed an average reduction of more than US $1450 (P < 0.001).

  4. Improved laboratory resource utilization and patient care with the use of rapid on-site evaluation for endobronchial ultrasound fine-needle aspiration biopsy.

    PubMed

    Collins, Brian T; Chen, Alexander C; Wang, Jeff F; Bernadt, Cory T; Sanati, Souzan

    2013-10-01

    Endobronchial ultrasound guided (EBUS) fine-needle aspiration (FNA) biopsy has become widely used to evaluate patients with thoracic abnormalities. Rapid on-site evaluation (ROSE) can provide the bronchoscopist with immediate evaluation findings during the procedure. This study examines EBUS FNA biopsy procedures with and without ROSE, and investigates the impact of ROSE service on the EBUS procedure and laboratory resource utilization. The cytopathology database at Washington University Medical Center, St. Louis, Missouri, was searched for EBUS FNA biopsy cases before and after introduction of ROSE service, and a matched cohort was collected. Reports were reviewed and pertinent data was collected, such as sites biopsied, ROSE performance, slide smears, cell blocks, and diagnostic categories. Statistical analysis of the results was performed. A matched case-controlled EBUS FNA cohort of 340 patients (680 total) for each category of non-ROSE and ROSE service were identified. There was a 33% reduction in the number of sites biopsied with ROSE. A total of 68% of patients with ROSE had just one biopsy site compared to only 36% of non-ROSE patients. There was a 30% decrease in total slides (mean, 5.27 slides) after the introduction of ROSE. All of these improvements were statistically significant. EBUS FNA biopsy ROSE service benefits patients by contributing to significantly fewer biopsies and improved utilization of health care resources. ROSE service results in substantially fewer total slides, which has a significant impact on the cytopathology laboratory work effort. The use of ROSE for EBUS FNA biopsy provides significant improvements in patient care and laboratory resource utilization. © 2013 American Cancer Society.

  5. Prevalence of Chlamydia trachomatis Infection among Low- and High-Risk Filipino Women and Performance of Chlamydia Rapid Tests in Resource-Limited Settings▿

    PubMed Central

    Saison, Francis; Mahilum-Tapay, Lourdes; Michel, Claude-Edouard E.; Buttress, Nigel D.; Nadala, Elpidio Cesar B.; Magbanua, Jose Paolo V.; Harding-Esch, Emma M.; Villaruel, M. Odeta; Canong, Lorna; Celis, Rey L.; Lee, Helen H.

    2007-01-01

    The prevalence of urogenital Chlamydia trachomatis infection was determined with a PCR-based test of women from low- and high-risk populations in Iloilo City, Philippines, between August 2002 and March 2006. Two rapid tests for C. trachomatis, Clearview Chlamydia MF and the Chlamydia Rapid Test (CRT), were also evaluated in these resource-limited settings. Specimens were obtained from female sex workers (FSWs; n = 1,484) attending a social hygiene clinic (SHC) and from women (n = 838) attending an obstetrics-gynecology (OB-GYN) clinic. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the rapid tests were determined, with PCR as the gold standard. The PCR positivity rate for SHC participants (72% asymptomatic) ranged from 17.9 to 32.0% during the study period. Compared with those of PCR, the sensitivities and specificities of the Clearview test were 53.5 and 99.1%, respectively, with endocervical swab specimens (CS; n = 822) from the FSWs and 31.1 and 95.2%, respectively, with vaginal swab specimens (VS; n = 333) from these women. The sensitivity, specificity, PPV, and NPV of the CRT with VS from the FSWs were 71.0, 99.0, 97.1, and 87.9%, respectively. At the OB-GYN site, the PCR positivity rate with VS was 6.3%. The sensitivity, specificity, PPV, and NPV of the CRT with these specimens were 86.8, 99.6, 93.9, and 99.1%, respectively. The performance of the Clearview test at the SHC was thus markedly lower with VS than with CS, whereas the CRT performed well with VS from both populations. PMID:17942659

  6. Rapid and direct quantitative detection of viable bifidobacteria in probiotic yogurt by combination of ethidium monoazide and real-time PCR using a molecular beacon approach.

    PubMed

    Meng, X C; Pang, R; Wang, C; Wang, L Q

    2010-11-01

    The potential of ethidium monoazide (EMA) real-time PCR method based on molecular beacon probe for rapid detection of viable bifidobacteria present in probiotic yogurt was evaluated in this work. A real-time PCR with molecular beacon assay was developed to determine genus Bifidobacterium quantitatively in order to increase the sensitivity and specificity of assay. EMA was used to treat probiotic yogurt prior to DNA extraction and real-time PCR detection to allow detection of only viable bacteria. The primer set of Bif-F/Bif-R which is genus-specific for Bifid. was designed. The specificity of the probes ensures that no signal is generated by non-target amplicons. Linear regression analysis demonstrated a good correlation (R² = 0·9948) between the EMA real-time PCR results and the plate counting, and real-time quantitative PCR results correlated adequately with enumeration of bifidobacteria by culture for commercial probiotic yogurt. This culture-independent approach is promising for the direct and rapid detection of viable bifidobacteria in commercial probiotic yogurt, and the detection can be carried out within 4 h. The detection limit for this method is about 10⁴ cell/ml. In conclusion, the direct quantitative EMA real-time PCR assay based on molecular beacon described in this research is a rapid and quantitative method.

  7. Methicillin-resistant Staphylococcus aureus infection rate after implementation of an antibiotic care bundle based on results of rapid molecular screening.

    PubMed

    Stano, Paola; Avolio, Manuela; De Rosa, Rita; Modolo, Maria Luisa; Camporese, Alessandro

    2013-01-01

    Colonization with methicillin-resistant Staphylococcus aureus (MRSA) is a risk factor for subsequent invasive MRSA infection, particularly in patients admitted to critical areas. We conducted a surveillance among patients admitted to our Intensive Care Unit (ICU) to determine whether the implementation of a specific MRSA antibiotic care bundle (ACB) based on rapid molecular screening for MRSA and de-colonization, reduced the total MRSA infection rate. A total of 431 and 577 nasal swabs were obtained from ICU patients at admission from April 2009 through December 2010 (pre-ACB period) and, after the bundle implementation, from January 2011 through December 2012 (post-ACB period), respectively. Nasal swabs were analyzed by the rapid molecular test Xpert MRSA. All patients were followed-up during their whole ICU stay to determine whether they developed MRSA infection. Overall, 31 out of 431 (7.1%) patients were colonized with MRSA at admission during the pre-ACB period and 49 out of 577 (8.4%) were colonized with MRSA during the post-ACB period. The rate of MRSA infection in ICU significantly declined from 2% in pre-ACB to 0.3% in post-ACB, with a total decrease of 100% in two consecutive semesters between July 2011 and July 2012 (p<0.001). The analysis demonstrated a significant decline in MRSA infections following the introduction of active rapid molecular surveillance and the specific ACB at our ICU and in the risk associated with MRSA bacteremia.

  8. Dilution testing using rapid diagnostic tests in a HIV diagnostic algorithm: a novel alternative for confirmation testing in resource limited settings.

    PubMed

    Shanks, Leslie; Siddiqui, M Ruby; Abebe, Almaz; Piriou, Erwan; Pearce, Neil; Ariti, Cono; Masiga, Johnson; Muluneh, Libsework; Wazome, Joseph; Ritmeijer, Koert; Klarkowski, Derryck

    2015-05-14

    Current WHO testing guidelines for resource limited settings diagnose HIV on the basis of screening tests without a confirmation test due to cost constraints. This leads to a potential risk of false positive HIV diagnosis. In this paper, we evaluate the dilution test, a novel method for confirmation testing, which is simple, rapid, and low cost. The principle of the dilution test is to alter the sensitivity of a rapid diagnostic test (RDT) by dilution of the sample, in order to screen out the cross reacting antibodies responsible for falsely positive RDT results. Participants were recruited from two testing centres in Ethiopia where a tiebreaker algorithm using 3 different RDTs in series is used to diagnose HIV. All samples positive on the initial screening RDT and every 10th negative sample underwent testing with the gold standard and dilution test. Dilution testing was performed using Determine™ rapid diagnostic test at 6 different dilutions. Results were compared to the gold standard of Western Blot; where Western Blot was indeterminate, PCR testing determined the final result. 2895 samples were recruited to the study. 247 were positive for a prevalence of 8.5 % (247/2895). A total of 495 samples underwent dilution testing. The RDT diagnostic algorithm misclassified 18 samples as positive. Dilution at the level of 1/160 was able to correctly identify all these 18 false positives, but at a cost of a single false negative result (sensitivity 99.6 %, 95 % CI 97.8-100; specificity 100 %, 95 % CI: 98.5-100). Concordance between the gold standard and the 1/160 dilution strength was 99.8 %. This study provides proof of concept for a new, low cost method of confirming HIV diagnosis in resource-limited settings. It has potential for use as a supplementary test in a confirmatory algorithm, whereby double positive RDT results undergo dilution testing, with positive results confirming HIV infection. Negative results require nucleic acid testing to rule out false

  9. The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery.

    PubMed

    Stroehlein, Andreas J; Young, Neil D; Korhonen, Pasi K; Jabbar, Abdul; Hofmann, Andreas; Sternberg, Paul W; Gasser, Robin B

    2015-12-08

    Protein kinases regulate a plethora of essential signalling and other biological pathways in all eukaryotic organisms, but very little is known about them in most parasitic nematodes. Here, we defined, for the first time, the entire complement of protein kinases (kinome) encoded in the barber's pole worm (Haemonchus contortus) through an integrated analysis of transcriptomic and genomic datasets using an advanced bioinformatic workflow. We identified, curated and classified 432 kinases representing ten groups, 103 distinct families and 98 subfamilies. A comparison of the kinomes of H. contortus and Caenorhabditis elegans (a related, free-living nematode) revealed considerable variation in the numbers of casein kinases, tyrosine kinases and Ca(2+)/calmodulin-dependent protein kinases, which likely relate to differences in biology, habitat and life cycle between these worms. Moreover, a suite of kinase genes was selectively transcribed in particular developmental stages of H. contortus, indicating central roles in developmental and reproductive processes. In addition, using a ranking system, drug targets (n = 13) and associated small-molecule effectors (n = 1517) were inferred. The H. contortus kinome will provide a useful resource for fundamental investigations of kinases and signalling pathways in this nematode, and should assist future anthelmintic discovery efforts; this is particularly important, given current drug resistance problems in parasitic nematodes.

  10. A molecular marker for in situ genetic resource conservation of Capsicum annuum var. acuminatum (Solanaceae).

    PubMed

    Kaewdoungdee, N; Tanee, T

    2013-02-28

    The Thailand cultivar pepper 'phrik man bangchang' (Capsicum annuum var. acuminatum, Solanaceae) was originally cultivated in the Bangchang Subdistrict, Amphawa District in Samut Songkhram Province. The cultivated areas are limited; we verified its distribution in Thailand for in situ 'phrik man bangchang' genetic resource conservation. Samples were collected from the original cultivation area of Bangchang Subdistrict (Or) and were randomly explored in Ratchaburi Province (RB), Khon Kaen Province (KK), and Sakon Nakhon Province (SN). A pure line from The Tropical Vegetable Research Center at Kasetsart University was used as the standard indicator. Two more Capsicum species, C. chinensis and C. frutescens, and a species from another genus in the family, Solanum melongena, were included. A dendrogram constructed from random amplified polymorphic DNA fingerprints indicated that the Or, RB, KK, and SN samples were C. annuum var. acuminatum with supportive similarity coefficients of 0.79 to 0.98. Finally, DNA barcodes, from psbA-trnH spacer region, were provided for the 3 wild species, C. annuum var. acuminatum, C. chinensis, and C. frutescens under GenBank accession Nos. JQ087869-JQ087871. The nucleotide variations between species were 0.23 to 0.26. In summary, 'phrik man bangchang' is still being planted in Bangchang Subdistrict, but only in small areas. The distribution of planting areas is expected to be throughout Thailand.

  11. Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

    PubMed

    Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

    2016-02-01

    The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

  12. Rapid Determination of Six Low Molecular Carbonyl Compounds in Tobacco Smoke by the APCI-MS/MS Coupled to Data Mining.

    PubMed

    Zhao, Wuduo; Zhang, Qidong; Lu, Binbin; Sun, Shihao; Zhang, Shusheng; Zhang, Jianxun

    2017-01-01

    A simple method was established for the rapid determination of low molecular carbonyl compounds by the combination of atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS/MS) and data mining. The ionization was carried out in positive mode, and six low molecular carbonyl compounds of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde were analyzed by both full scan mode and daughter scan mode. To overcome the quantitative difficulties from isomer of acetone/propionaldehyde and butanone/butyraldehyde, the quantitation procedure was performed with the characteristic ion of [CH3O](+) under CID energy of 5 and 15 eV. Subsequently, the established method was successfully applied to analysis of six low molecular carbonyl compounds in tobacco smoke with analytical period less than four minutes. The contents of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde for a cigarette were about 63 ± 5.8, 325 ± 82, 55 ± 9.7, 11 ± 1.4, 67 ± 5.9, and 12 ± 1.8 μg/cig, respectively. The experimental results indicated that the established method had the potential application in rapid determination of low molecular carbonyl compounds.

  13. Molecular characterization of Wilms tumor from a resource-constrained region of sub-Saharan Africa

    PubMed Central

    Murphy, Andrew J.; Axt, Jason R.; de Caestecker, Christian; Pierce, Janene; Correa, Hernan; Seeley, Erin H.; Caprioli, Richard M.; Newton, Mark W.; de Caestecker, Mark P.; Lovvorn, Harold N.

    2012-01-01

    Sub-Saharan African children have an increased incidence of Wilms tumor (WT) and experience alarmingly poor outcomes. Although these outcomes are largely due to inadequate therapy, we hypothesized that WT from this region exhibit features of biologic aggressiveness that may warrant broader implementation of high-risk therapeutic protocols. We evaluated 15 Kenyan WT (KWT) for features of aggressive disease (blastemal predominance, Ki67/cellular proliferation) and treatment resistance (anaplasia, p53 immunopositivity). To explore additional biologic features of KWT, we determined the mutational status of the CTNNB1/β-catenin and WT1 genes and performed immunostaining for markers of Wnt pathway activation (β-catenin) and nephronic progenitor cell self-renewal (WT1, CITED1, SIX2). We characterized the proteome of KWT using imaging mass spectrometry (IMS). Results were compared to histology and age-matched North American WT (NAWT) controls. For KWT patients, blastemal predominance was noted in 53.3% and anaplasia in 13%. We detected increased loss to follow up (p=0.028), disease relapse (p=0.044), mortality (p=0.001), and nuclear unrest (p=0.001) in KWT patients compared to controls. KWT and NAWT showed similar Ki67/cellular proliferation. We detected an increased proportion of epithelial nuclear β-catenin in KWT (p=0.013). All 15 KWT were found to harbor wild-type β-catenin, and 1 contained a WT1 nonsense mutation. WT1 was detected by immunostaining in 100% of KWT, CITED1 in 80%, and SIX2 in 80%. IMS revealed a molecular signature unique to KWT that was distinct from NAWT. African WTs appear to express markers of adverse clinical behavior and treatment resistance and may require alternative therapies or implementation of high-risk treatment protocols. PMID:22437966

  14. Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery

    PubMed Central

    Bocanegra, Melanie; Choi, Yoon-La; Girard, Luc; Gandhi, Jeet; Kwei, Kevin A.; Hernandez-Boussard, Tina; Wang, Pei; Gazdar, Adi F.; Minna, John D.; Pollack, Jonathan R.

    2009-01-01

    candidate breast cancer genes. Conclusions Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, cancer stem cell biology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes. PMID:19582160

  15. High Molecular Weight Typing with MALDI-TOF MS - A Novel Method for Rapid Typing of Clostridium difficile.

    PubMed

    Rizzardi, Kristina; Åkerlund, Thomas

    2015-01-01

    Clostridium difficile strains were typed by a newly developed MALDI-TOF method, high molecular weight typing, and compared to PCR ribotyping. Among 500 isolates representing 59 PCR ribotypes a total of 35 high molecular weight types could be resolved. Although less discriminatory than PCR ribotyping, the method is extremely fast and simple, and supports for cost-effective screening of isolates during outbreak situations.

  16. Rapid-Antigen Test Negative Malaria in a Traveler Returning From Thailand, Molecularly Diagnosed as Plasmodium knowlesi.

    PubMed

    Mackroth, Maria S; Tappe, Dennis; Tannich, Egbert; Addo, Marylyn; Rothe, Camilla

    2016-01-01

    Plasmodium knowlesi has been identified in the last decade as a fifth species causing malaria in areas of South East Asia. Due to its short erythrocytic cycle, rapid development of high parasitemia and severe manifestations are frequently observed. Therefore, prompt diagnosis of infection is essential to prevent complications, but the low sensitivity of rapid diagnostic tests for P knowlesi pose a diagnostic challenge in acute settings. In this study, we report the case of a German traveler to Thailand, who was treated for P knowlesi malaria after returning to Germany. Rapid antigen test for malaria was negative on presentation. Diagnosis of a nonfalciparum malaria was made based on microscopy, and species definition was determined using polymerase chain reaction technique.

  17. Rapid-Antigen Test Negative Malaria in a Traveler Returning From Thailand, Molecularly Diagnosed as Plasmodium knowlesi

    PubMed Central

    Mackroth, Maria S.; Tappe, Dennis; Tannich, Egbert; Addo, Marylyn; Rothe, Camilla

    2016-01-01

    Plasmodium knowlesi has been identified in the last decade as a fifth species causing malaria in areas of South East Asia. Due to its short erythrocytic cycle, rapid development of high parasitemia and severe manifestations are frequently observed. Therefore, prompt diagnosis of infection is essential to prevent complications, but the low sensitivity of rapid diagnostic tests for P knowlesi pose a diagnostic challenge in acute settings. In this study, we report the case of a German traveler to Thailand, who was treated for P knowlesi malaria after returning to Germany. Rapid antigen test for malaria was negative on presentation. Diagnosis of a nonfalciparum malaria was made based on microscopy, and species definition was determined using polymerase chain reaction technique. PMID:27006963

  18. Comparison of laboratory costs of rapid molecular tests and conventional diagnostics for detection of tuberculosis and drug-resistant tuberculosis in South Africa.

    PubMed

    Shah, Maunank; Chihota, Violet; Coetzee, Gerrit; Churchyard, Gavin; Dorman, Susan E

    2013-07-29

    The World Health Organization has endorsed the use of molecular methods for the detection of TB and drug-resistant TB as a rapid alternative to culture-based systems. In South Africa, the Xpert MTB/Rif assay and the GenoType MTBDRplus have been implemented into reference laboratories for diagnosis of TB and drug-resistance, but their costs have not been fully elucidated. We conducted a detailed reference laboratory cost analysis of new rapid molecular assays (Xpert and MTBDRplus) for tuberculosis testing and drug-resistance testing in South Africa, and compared with the costs of conventional approaches involving sputum microscopy, liquid mycobacterial culture, and phenotypic drug sensitivity testing. From a laboratory perspective, Xpert MTB/RIF cost $14.93/sample and the MTBDRplus line probe assay cost $23.46/sample, compared to $16.88/sample using conventional automated liquid culture-based methods. Laboratory costs of Xpert and MTBDRplus were most influenced by cost of consumables (60-80%). At current public sector pricing, Xpert MTB/RIF and MTBDRplus are comparable in cost to mycobacterial culture and conventional drug sensitivity testing. Overall, reference laboratories must balance costs with performance characteristics and the need for rapid results.

  19. Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights.

    PubMed

    Khudyakov, Jane I; Preeyanon, Likit; Champagne, Cory D; Ortiz, Rudy M; Crocker, Daniel E

    2015-02-08

    The northern elephant seal, Mirounga angustirostris, is a valuable animal model of fasting adaptation and hypoxic stress tolerance. However, no reference sequence is currently available for this and many other marine mammal study systems, hindering molecular understanding of marine adaptations and unique physiology. We sequenced a transcriptome of M. angustirostris derived from muscle sampled during an acute stress challenge experiment to identify species-specific markers of stress axis activation and recovery. De novo assembly generated 164,966 contigs and a total of 522,699 transcripts, of which 68.70% were annotated using mouse, human, and domestic dog reference protein sequences. To reduce transcript redundancy, we removed highly similar isoforms in large gene families and produced a filtered assembly containing 336,657 transcripts. We found that a large number of annotated genes are associated with metabolic signaling, immune and stress responses, and muscle function. Preliminary differential expression analysis suggests a limited transcriptional response to acute stress involving alterations in metabolic and immune pathways and muscle tissue maintenance, potentially driven by early response transcription factors such as Cebpd. We present the first reference sequence for Mirounga angustirostris produced by RNA sequencing of muscle tissue and cloud-based de novo transcriptome assembly. We annotated 395,102 transcripts, some of which may be novel isoforms, and have identified thousands of genes involved in key physiological processes. This resource provides elephant seal-specific gene sequences, complementing existing metabolite and protein expression studies and enabling future work on molecular pathways regulating adaptations such as fasting, hypoxia, and environmental stress responses in marine mammals.

  20. Rapid Formation of Molecular Bromine from Deliquesced NaBr Aerosol in the Presence of Ozone and UV Light

    EPA Science Inventory

    The formation of gas-phase bromine from aqueous sodium bromide aerosols is investigated through a combination of chamber experiments and chemical kinetics modeling. Experiments show that Br2(g) is produced rapidly from deliquesced NaBr aerosols in the presence of OH radicals prod...

  1. Rapid Formation of Molecular Bromine from Deliquesced NaBr Aerosol in the Presence of Ozone and UV Light

    EPA Science Inventory

    The formation of gas-phase bromine from aqueous sodium bromide aerosols is investigated through a combination of chamber experiments and chemical kinetics modeling. Experiments show that Br2(g) is produced rapidly from deliquesced NaBr aerosols in the presence of OH radicals prod...

  2. Rapid analysis of the chemical composition of agricultural fibers using near infrared spectroscopy and pyrolysis molecular beam mass spectrometry

    Treesearch

    Stephen S. Kelley; Roger M. Rowell; Mark Davis; Cheryl K. Jurich; Rebecca Ibach

    2004-01-01

    The chemical composition of a variety of agricultural biomass samples was analyzed with near infrared spectroscopy and pyrolysis molecular beam mass spectroscopy. These samples were selected from a wide array of agricultural residue samples and included residues that had been subjected to a variety of di2erent treatments including solvent extractions and chemical...

  3. Evaluation of 3M molecular detection system and ANSR pathogen detection system for rapid detection of salmonella from egg products

    USDA-ARS?s Scientific Manuscript database

    Loop-mediated isothermal amplification (LAMP) is a novel simple detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was to evaluate the effectiveness of 3M Molecular Detection System (MDS) and ANSR Pathogen Det...

  4. [THE SENSITIVITY AND SPECIFICITY OF THE MOLECULAR GENOTYPE MTBDRPL US ASSAY (HAIN LIFESCIENCE GMBH, GERMANY) FOR RAPID DIAGNOSIS OF DRUG SUSCEPTIBILITY IN MYCOBACTERIUM TUBERCULOSIS ON SPUTUM SPECIMENS].

    PubMed

    2010-01-01

    The efficiency of the molecular GenoType MTBDRplus (Hain Lifescience GmbH, Germany) assay was evaluated for the rapid diagnosis of rifampicin and isoniazid susceptibility in Mycobacterium tuberculosis (MBT) on 168 sputum specimens from patients with pulmonary tuberculosis in the Samara Region. The interpretable results from the molecular genetic assay were obtained for 91.7% of the specimens with the rates significantly higher in the sputum specimens graded 2+ and 3+ than in those graded 1+. The sensitivity and specificity of the assay for the detection of rifampicin, isoniazid, and multidrug resistance were 96.2%, 97.4%; 97.1% and 90.7%; 83.3%; 88.9%, respectively. Mutations in codon 531 of the rpoB gene and codon 315 of the katG gene were most common in rifampicin- and isoniazid-resistant strains, respectively. The high sensitivity, rapidness-to-use, and the simultaneous treatment of a large number of sputum specimens permit the authors to recommend the GenoType MTBDRplus assay as a major screening tool for the detection of drug resistance in MBT.

  5. Effect of rapid thermal annealing on InP1-xBix grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Wu, X. Y.; Wang, K.; Pan, W. W.; Wang, P.; Li, Y. Y.; Song, Y. X.; Gu, Y.; Yue, L.; Xu, H.; Zhang, Z. P.; Cui, J.; Gong, Q.; Wang, S. M.

    2015-09-01

    The effect of post-growth rapid thermal annealing on structural and optical properties of InP1-xBix thin films was investigated. InPBi shows good thermal stability up to 500 °C and a modest improvement in photoluminescence (PL) intensity with an unchanged PL spectral feature. Bismuth outdiffusion from InPBi and strain relaxation are observed at about 600 °C. The InPBi sample annealed at 800 °C shows an unexpected PL spectrum with different energy transitions.

  6. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    PubMed

    Yang, Huaan; Tao, Ye; Zheng, Zequn; Li, Chengdao; Sweetingham, Mark W; Howieson, John G

    2012-07-17

    In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker

  7. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    PubMed Central

    2012-01-01

    Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for

  8. A randomised controlled trial of high vs low volume initiation and rapid vs slow advancement of milk feeds in infants with birthweights ≤ 1000 g in a resource-limited setting.

    PubMed

    Raban, Shukri; Santhakumaran, Shalini; Keraan, Quanitah; Joolay, Yaseen; Uthaya, Sabita; Horn, Alan; Modi, Neena; Harrison, Michael

    2016-11-01

    Optimal feeding regimens for infants ≤ 1000 g have not been established and are a global healthcare concern. A controlled trial to establish the safety and efficacy of high vs low volume initiation and rapid vs slow advancement of milk feeds in a resource-limited setting was undertaken. Infants ≤ 1000 g birthweight were randomised to one of four arms, either low (4 ml/kg/day) or high (24 ml/kg/day) initiation and either slow (24 ml/kg/day) or rapid (36 ml/kg/day) advancement of exclusive feeds of human milk (mother's or donor) until a weight of 1200 g was reached. After this point, formula was used to supplement insufficient mother's milk. The primary outcome was time to reach 1500 g. infants were recruited (51: low/slow; 47: low/rapid; 52: high/slow; 50: high/rapid). Infants on rapid advancement regimens reached 1500 g most rapidly (hazard ratio 1.48, 95% CI 1.05-2.09, P=0.03). The rapid advancement groups also regained birthweight more rapidly (hazard ratio 1.77, 95% CI 1.26-2.50, P=0.001). There was no apparent effect of high vs low initiation volumes but there was some evidence of interaction between interventions. There were no significant differences in other secondary outcomes, including necrotising enterocolitis, feed intolerance and late-onset sepsis. In this small pilot study, higher initiation feed volumes and larger daily increments appeared to be well tolerated and resulted in more rapid early weight gain. These data provide justification for a larger study in resource-limited settings to address mortality, necrotising enterocolitis and other important outcomes.

  9. Preparation of hybrid molecularly imprinted polymer with double-templates for rapid simultaneous purification of theophylline and chlorogenic acid in green tea.

    PubMed

    Tang, Weiyang; Li, Guizhen; Row, Kyung Ho; Zhu, Tao

    2016-05-15

    A novel double-templates technique was adopted for solid-phase extraction packing agent, and the obtained hybrid molecularly imprinted polymers with double-templates (theophylline and chlorogenic acid) were characterized by fourier transform infrared and field emission scanning electron microscope. The molecular recognition ability and binding capability for theophylline and chlorogenic acid of polymers was evaluated by static absorption and dynamic adsorption curves. A rapid and accurate approach was established for simultaneous purification of theophylline and chlorogenic acid in green tea by coupling hybrid molecularly imprinted solid-phase extraction with high performance liquid chromatography. With optimization of SPE procedure, a reliable analytical method was developed for highly recognition towards theophylline and chlorogenic acid in green tea with satisfactory extraction recoveries (theophylline: 96.7% and chlorogenic acid: 95.8%). The limit of detection and limit of quantity of the method were 0.01 μg/mL and 0.03 μg/mL for theophylline, 0.05 μg/mL and 0.17 μg/mL for chlorogenic acid, respectively. The recoveries of proposed method at three spiked levels analysis were 98.7-100.8% and 98.3-100.2%, respectively, with the relative standard deviation less than 1.9%. Hybrid molecularly imprinted polymers with double-templates showed good performance for two kinds of targets, and the proposed approach with high affinity of hybrid molecularly imprinted polymers might offer a novel method for the purification of complex samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy.

    PubMed

    Egan, Scott P; Grey, Erin; Olds, Brett; Feder, Jeffery L; Ruggiero, Steven T; Tanner, Carol E; Lodge, David M

    2015-04-07

    Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.

  11. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae.

    PubMed

    Mao, Yunrui; Zhang, Yonghua; Xu, Chuan; Qiu, Yingxiong

    2016-01-01

    Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.

  12. An EST dataset for Metasequoia glyptostroboides buds: the first EST resource for molecular genomics studies in Metasequoia.

    PubMed

    Zhao, Ying; Thammannagowda, Shivegowda; Staton, Margaret; Tang, Sha; Xia, Xinli; Yin, Weilun; Liang, Haiying

    2013-03-01

    The "living fossil" Metasequoia glyptostroboides Hu et Cheng, commonly known as dawn redwood or Chinese redwood, is the only living species in the genus and is valued for its essential oil and crude extracts that have great potential for anti-fungal activity. Despite its paleontological significance and economical value as a rare relict species, genomic resources of Metasequoia are very limited. In order to gain insight into the molecular mechanisms behind the formation of reproductive buds and the transition from vegetative phase to reproductive phase in Metasequoia, we performed sequencing of expressed sequence tags from Metasequoia vegetative buds and female buds. By using the 454 pyrosequencing technology, a total of 1,571,764 high-quality reads were generated, among which 733,128 were from vegetative buds and 775,636 were from female buds. These EST reads were clustered and assembled into 114,124 putative unique transcripts (PUTs) with an average length of 536 bp. The 97,565 PUTs that were at least 100 bp in length were functionally annotated by a similarity search against public databases and assigned with Gene Ontology (GO) terms. A total of 59 known floral gene families and 190 isotigs involved in hormone regulation were captured in the dataset. Furthermore, a set of PUTs differentially expressed in vegetative and reproductive buds, as well as SSR motifs and high confidence SNPs, were identified. This is the first large-scale expressed sequence tags ever generated in Metasequoia and the first evidence for floral genes in this critically endangered deciduous conifer species.

  13. Rapid Molecular Testing for TB to Guide Respiratory Isolation in the U.S.: A Cost-Benefit Analysis

    PubMed Central

    Millman, Alexander J.; Dowdy, David W.; Miller, Cecily R.; Brownell, Robert; Metcalfe, John Z.; Cattamanchi, Adithya; Davis, J. Lucian

    2013-01-01

    Background Respiratory isolation of inpatients during evaluation for TB is a slow and costly process in low-burden settings. Xpert MTB/RIF (Xpert) is a novel molecular test for tuberculosis (TB) that is faster and more sensitive but substantially more expensive than smear microscopy. No previous studies have examined the costs of molecular testing as a replacement for smear microscopy in this setting. Methods We conducted an incremental cost–benefit analysis comparing the use of a single negative Xpert versus two negative sputum smears to release consecutive adult inpatients with presumed TB from respiratory isolation at an urban public hospital in the United States. We estimated all health-system costs and patient outcomes related to Xpert implementation, diagnostic evaluation, isolation, hospitalization, and treatment. We performed sensitivity and probabilistic uncertainty analyses to determine at what threshold the Xpert strategy would become cost-saving. Results Among a hypothetical cohort of 234 individuals undergoing evaluation for presumed active TB annually, 6.4% had culture-positive TB. Compared to smear microscopy, Xpert reduced isolation bed utilization from an average of 2.7 to 1.4 days per patient, leading to a 48% reduction in total annual isolation bed usage from 632 to 328 bed-days. Xpert saved an average of $2,278 (95% uncertainty range $1582–4570) per admission, or $533,520 per year, compared with smear microscopy. Conclusions Molecular testing for TB could provide substantial savings to hospitals in high-income countries by reducing respiratory isolation usage and overall length of stay. PMID:24278155

  14. A Novel Monte Carlo Scheme for the Rapid Equilibration of Atomistic Model Polymer Systems of Precisely Defined Molecular Architecture

    NASA Astrophysics Data System (ADS)

    Karayiannis, Nikos Ch.; Mavrantzas, Vlasis G.; Theodorou, Doros N.

    2002-03-01

    Two novel connectivity-altering atomistic Monte Carlo moves are presented for the fast equilibration of condensed phases of long-chain systems with a variety of chain architectures. With the new moves, isotropic or oriented melts of linear or long-chain branched polymers, dense brushes of terminally grafted macromolecules, and cyclic peptides can be simulated. Results concerning the structural, conformational, and volumetric properties of linear, monodisperse polyethylene melts, simulated with a new united-atom molecular model, are in excellent agreement with experimental data.

  15. [Development of modified molecular beacon based real-time PCR assay for the rapid detection of Salmonella choleraesuis and Salmonella paratyphi C].

    PubMed

    Lin, Yiman; Shi, Xiaolu; Zhu, Yumei; Qiu, Yaqun; Li, Yinhui; Lv, Dongyue; Hu, Qinghua

    2011-07-01

    To develop real-time PCR assay based on modified molecular beacon for simultaneous detection of S. choleraesuis and S. paratyphi C. The established method was applied to the rapid detection of S. choleraesuis in food and stool samples of food poisoning, and then was applied to the identification of Salmonella C. Based on the sequences (CP000857.1) published in GenBank, Two sets of primers and modified molecular beacon were designed. The Real-time PCR assay for the simultaneous detection of S. paratyphi C and S. choleraesuis was developed with optimized PCR procedures and PCR components, while other 11 different bacterial species were as the control. Then the sensitivity and specificity of the assay were tested using 77 Samonella strains. The assay was applied to the detection of 70 food samples. The limit of detection achieved was 10 fg/reaction or 20 CUF/reaction, Only Salmonella paratyphi C and Salmonella choleraesuis strains generated fluorescent signals. No cross-reaction was observed with other 11 bacterium, the sensitivity and specificity were both 100%. No samples among 70 food samples were found Salmonella positive by both real-time PCR assay and traditional culture method. It could be finished within 2 hours from template preparation to detection and the overall test would be finished within one day. The real-time PCR assay was rapid, sensitive and specific. It could be applied to the rapid diagnosis of S. paratyphi C and S. choleraesuis in food and stool samples of food poisoning and the identification of Salmonella C to guarantee food safety.

  16. Rapid Restoration of Thrombus Formation and High-Molecular-Weight von Willebrand Factor Multimers in Patients with Severe Aortic Stenosis After Valve Replacement.

    PubMed

    Yamashita, Keigo; Yagi, Hideo; Hayakawa, Masaki; Abe, Takehisa; Hayata, Yoshihiro; Yamaguchi, Naoko; Sugimoto, Mitsuhiko; Fujimura, Yoshihiro; Matsumoto, Masanori; Taniguchi, Shigeki

    2016-10-01

    Patients with severe aortic stenosis (AS) may have bleeding episodes due to the loss of high-molecular-weight (HMW) von Willebrand factor multimers (VWFMs). The absence of HMW-VWFMs and bleeding tendency are usually corrected after aortic valve replacement (AVR). To investigate the process of VWFM recovery and symptoms in patients with severe AS, we analyzed changes in VWF antigen (VWF:Ag), ADAMTS13 activity (ADAMTS13:AC), and platelet thrombus formation under high shear stress conditions. Nine patients with severe AS undergoing AVR were analyzed. Evident deficiency of HMW-VWFMs was observed in six patients before surgery, which was rapidly restored within 8 days after AVR. Median levels of VWF:Ag before surgery, on postoperative days (PODs) 1, 8, 15, and 22, and one year after AVR were 78.1%, 130%, 224%, 155%, 134%, and 142%, respectively. In contrast, ADAMTS13:AC was 50.5%, 35.5%, 25.5%, 25.1%, 30.3%, and 84.6%, respectively. Preoperative thrombus formation but not surface coverage was significantly lower than that on POD 22, which was considered as normal level in each patient. Compared with preoperative levels, thrombus volume was significantly lower on POD 1, but rapidly increased by POD 8. Bleeding tendency and loss of HMW-VWFMs observed in patients with severe AS before surgery was rapidly corrected after AVR. Instead, patients were in a VWF-predominant state between POD 8 and 22.

  17. Rapid Restoration of Thrombus Formation and High-Molecular-Weight von Willebrand Factor Multimers in Patients with Severe Aortic Stenosis After Valve Replacement

    PubMed Central

    Yamashita, Keigo; Yagi, Hideo; Hayakawa, Masaki; Abe, Takehisa; Hayata, Yoshihiro; Yamaguchi, Naoko; Sugimoto, Mitsuhiko; Fujimura, Yoshihiro; Taniguchi, Shigeki

    2016-01-01

    Aim: Patients with severe aortic stenosis (AS) may have bleeding episodes due to the loss of high-molecular-weight (HMW) von Willebrand factor multimers (VWFMs). The absence of HMW-VWFMs and bleeding tendency are usually corrected after aortic valve replacement (AVR). To investigate the process of VWFM recovery and symptoms in patients with severe AS, we analyzed changes in VWF antigen (VWF:Ag), ADAMTS13 activity (ADAMTS13:AC), and platelet thrombus formation under high shear stress conditions. Methods: Nine patients with severe AS undergoing AVR were analyzed. Results: Evident deficiency of HMW-VWFMs was observed in six patients before surgery, which was rapidly restored within 8 days after AVR. Median levels of VWF:Ag before surgery, on postoperative days (PODs) 1, 8, 15, and 22, and one year after AVR were 78.1%, 130%, 224%, 155%, 134%, and 142%, respectively. In contrast, ADAMTS13:AC was 50.5%, 35.5%, 25.5%, 25.1%, 30.3%, and 84.6%, respectively. Preoperative thrombus formation but not surface coverage was significantly lower than that on POD 22, which was considered as normal level in each patient. Compared with preoperative levels, thrombus volume was significantly lower on POD 1, but rapidly increased by POD 8. Conclusion: Bleeding tendency and loss of HMW-VWFMs observed in patients with severe AS before surgery was rapidly corrected after AVR. Instead, patients were in a VWF-predominant state between POD 8 and 22. PMID:27052664

  18. Rapid renaturation of complementary DNA strands mediated by cationic detergents: a role for high-probability binding domains in enhancing the kinetics of molecular assembly processes.

    PubMed Central

    Pontius, B W; Berg, P

    1991-01-01

    The rate of renaturation for complementary DNA strands can be enhanced greater than 10(4)-fold by the addition of simple cationic detergents, and the reaction is qualitatively and quantitatively very similar to that found with purified heterogeneous nuclear ribonucleoprotein A1 protein. Under optimal conditions, renaturation rates are greater than 2000-fold faster than reactions run in 1 M NaCl at 68 degrees C. The reaction is second-order with respect to DNA concentration, and reaction rates approach or equal the rate with which complementary strands are expected to encounter each other in solution. Renaturation can even be observed well above the expected melting temperature of the duplex DNA, demonstrating that some cationic detergents have DNA double-helix-stabilizing properties. The reaction is also extremely rapid in the presence of up to a 10(6)-fold excess of noncomplementary sequences, establishing that renaturation is specific and relatively independent of heterologous DNA. This finding also implies that up to several thousand potential target sequences can be sampled per strand per second. Such reagents may be useful for procedures that require rapid nucleic acid renaturation, and these results suggest ways to identify and design other compounds that increase the kinetics of association reactions. Moreover, this work provides further support for a model relating the existence of flexible, weakly interacting, repeating domains to their function in rapid molecular assembly processes in vitro and in vivo. PMID:1896475

  19. Leishmania OligoC-TesT as a Simple, Rapid, and Standardized Tool for Molecular Diagnosis of Cutaneous Leishmaniasis in Peru▿

    PubMed Central

    Espinosa, Diego; Boggild, Andrea K.; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

    2009-01-01

    Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru. PMID:19553579

  20. Leishmania OligoC-TesT as a simple, rapid, and standardized tool for molecular diagnosis of cutaneous leishmaniasis in Peru.

    PubMed

    Espinosa, Diego; Boggild, Andrea K; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

    2009-08-01

    Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru.

  1. Rapid molecular determination of methicillin resistance in staphylococcal bacteraemia improves early targeted antibiotic prescribing: a randomized clinical trial.

    PubMed

    Emonet, S; Charles, P G; Harbarth, S; Stewardson, A J; Renzi, G; Uckay, I; Cherkaoui, A; Rougemont, M; Schrenzel, J

    2016-11-01

    Empiric therapy of methicillin-susceptible Staphylococcus aureus (MSSA) infections with vancomycin is associated with poorer outcome than targeted therapy with β-lactams. Our objective was to evaluate whether rapid determination of methicillin resistance shortens the time from Gram stain to targeted antimicrobial therapy in staphylococcal bacteraemia, thereby reducing vancomycin overuse. This was a single-centre open parallel RCT. Gram-positive cocci in clusters in positive blood culture underwent real-time PCR for rapid species and methicillin resistance determination parallel to conventional microbiology. Patients were randomized 1:1 so that clinicians would be informed of PCR results (intervention group) or not (control group). Eighty-nine patients (intervention 48, control 41) were analysed. MRSA was identified in seven patients, MSSA in 46, and CoNS in 36. PCR results were highly concordant (87/89) with standard microbiology. Median time (hours) from Gram stain to transmission of methicillin-susceptibility was 3.9 (2.8-4.3) vs. 25.4 (24.4-26-7) in intervention vs. control groups (p <0.001). Median time (hours) from Gram stain to targeted treatment was similar for 'all staphylococci' [6 (3.8-10) vs. 8 (1-36) p 0.13] but shorter in the intervention group when considering S. aureus only [5 (3-7) vs. 25.5 (3.8-54) p <0.001]. When standard susceptibility testing was complete, 41/48 (85.4%) patients in the intervention group were already receiving targeted therapy compared with 23/41 (56.1%) in the control group (p 0.004). There was no significant effect on clinical outcomes. Rapid determination of methicillin resistance in staphylococcal bacteraemia is accurate and reduces significantly the time to targeted antibiotic therapy in the subgroup of S. aureus, thereby avoiding unnecessary exposure to vancomycin. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  2. Molecularly imprinted polymer cartridges coupled on-line with high performance liquid chromatography for simple and rapid analysis of dextromethorphan in human plasma samples.

    PubMed

    Moein, Mohammad Mahdi; Javanbakht, Mehran; Akbari-Adergani, Behrouz

    2011-04-01

    In this paper, a novel method is described for automated determination of dextromethorphan in biological fluids using molecularly imprinted solid-phase extraction (MISPE) as a sample clean-up technique combined with high performance liquid chromatography (HPLC). The water-compatible molecularly imprinted polymers (MIPs) were prepared using methacrylic acid as functional monomer, ethylene glycol dimethacrylate as cross-linker, chloroform as porogen and dextromethorphan as template molecule. These imprinted polymers were used as solid-phase extraction sorbent for the extraction of dextromethorphan from human plasma samples. Various parameters affecting the extraction efficiency of the MIP cartridges were evaluated. The high selectivity of the sorbent coupled to the high performance liquid chromatographic system permitted a simple and rapid analysis of this drug in plasma samples with limits of detection (LOD) and quantification (LOQ) of 0.12 ng/mL and 0.35 ng/mL, respectively. The MIP selectivity was evaluated by analyzing of the dextromethorphan in presence of several substances with similar molecular structures and properties. Results from the HPLC analyses showed that the recoveries of dextromethorphan using MIP cartridges from human plasma samples in the range of 1-50 ng/mL were higher than 87%. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Rapid screening of low-molecular-weight phenols from persimmon (Diospyros kaki) pulp using liquid chromatography/UV-visible/electrospray mass spectrometry analysis.

    PubMed

    Sentandreu, Enrique; Cerdán-Calero, Manuela; Halket, John M; Navarro, José L

    2015-06-01

    Persimmon fruits have been widely used in traditional medicine owing to their phenolic composition. This research aims to perform a rapid, detailed and affordable study of the profile of low-molecular-weight phenols from persimmon pulp. Two different HPLC-DAD/ESI-MS(n) analyses were performed using a routine three-dimensional ion trap mass spectrometer to analyze the ethanolic extract of persimmon pulp: (1) an untargeted data-dependent analysis to identify the majority of small phenols that included full MS and MS(2) scan events; (2) a targeted data-dependent analysis to identify polymerized phenols (dimers and formic acid adducts) through a source-induced dissociation analysis that included full MS and MS(2) scan events. Thirty-two low-molecular-weight phenols were detected, comprising gallic acid and its glycoside and acyl derivatives, glycosides of p-coumaric, vanillic and cinnamic acids and different flavone di-C-hexosides, most of them reported for the first time in persimmon. The use of a straightforward and affordable methodology of analysis led to obtain an up-to-date profiling of low-molecular-weight phenols in persimmon. The results can help future actions aimed to expand the understanding of the phenolic metabolome of persimmon cultivars. © 2014 Society of Chemical Industry.

  4. Chromosomes for molecular hybridization. Assignment of repetitive and single copy genes using a rapid filter-fixation method.

    PubMed

    Langer, G; Blin, N; Stoehr, M

    1984-01-01

    Specific recombinant DNA sequences (5S rRNA, B1, albumin) were assigned to flow sorted chromosomes of the Chinese hamster cell line CHV79. For this purpose, a rapid protocol was developed using filterbound chromosomal DNA and probing with various nucleic acids, that allows sequence identification in chromosomes. A flow histogram and a flow karyogram of the CHV79 cell line were established by flow analysis in order to calculate the amount of DNA per CHV79 cell and their chromosomes. Subsequently, metaphase chromosomes or chromosomal groups were fractionated by electronic sorting and a defined number of chromosomes was directly bound to nitrocellulose filters for sequence homology analysis by a dot blot hybridization procedure. This procedure not only allows the assigning of specific DNA sequences to particular chromosomes, it is also applicable to studies of changes in karyotypes, for example translocations of given sequences.

  5. Flow cytometry in environmental microbiology: a rapid approach for the isolation of single cells for advanced molecular biology analysis.

    PubMed

    Ferrari, Belinda C; Winsley, Tristrom J; Bergquist, Peter L; Van Dorst, Josie

    2012-01-01

    The isolation and subsequent characterization of microbial cells from within environmental samples is a difficult process. Flow cytometry and cell sorting, when combined with the application of fluorescent probes, have the capability for the detection and separation of diverse microbial populations from within complex mixtures. The isolation of single cells allows for downstream investigations towards system-level characterization of unknown Bacterial Phyla to occur. We describe here the combination of fluorescent in situ hybridization and cell sorting for the detection and isolation of Candidate Division TM7 bacteria from an enriched soil sample. The result is the isolation of rare cells suitable for advanced molecular analysis including whole genome amplification and high-throughput pyrosequencing.

  6. Screening and Rapid Molecular Diagnosis of Tuberculosis in Prisons in Russia and Eastern Europe: A Cost-Effectiveness Analysis

    PubMed Central

    Winetsky, Daniel E.; Negoescu, Diana M.; DeMarchis, Emilia H.; Almukhamedova, Olga; Dooronbekova, Aizhan; Pulatov, Dilshod; Vezhnina, Natalia; Owens, Douglas K.; Goldhaber-Fiebert, Jeremy D.

    2012-01-01

    Background Prisons of the former Soviet Union (FSU) have high rates of multidrug-resistant tuberculosis (MDR-TB) and are thought to drive general population tuberculosis (TB) epidemics. Effective prison case detection, though employing more expensive technologies, may reduce long-term treatment costs and slow MDR-TB transmission. Methods and Findings We developed a dynamic transmission model of TB and drug resistance matched to the epidemiology and costs in FSU prisons. We evaluated eight strategies for TB screening and diagnosis involving, alone or in combination, self-referral, symptom screening, mass miniature radiography (MMR), and sputum PCR with probes for rifampin resistance (Xpert MTB/RIF). Over a 10-y horizon, we projected costs, quality-adjusted life years (QALYs), and TB and MDR-TB prevalence. Using sputum PCR as an annual primary screening tool among the general prison population most effectively reduced overall TB prevalence (from 2.78% to 2.31%) and MDR-TB prevalence (from 0.74% to 0.63%), and cost US$543/QALY for additional QALYs gained compared to MMR screening with sputum PCR reserved for rapid detection of MDR-TB. Adding sputum PCR to the currently used strategy of annual MMR screening was cost-saving over 10 y compared to MMR screening alone, but produced only a modest reduction in MDR-TB prevalence (from 0.74% to 0.69%) and had minimal effect on overall TB prevalence (from 2.78% to 2.74%). Strategies based on symptom screening alone were less effective and more expensive than MMR-based strategies. Study limitations included scarce primary TB time-series data in FSU prisons and uncertainties regarding screening test characteristics. Conclusions In prisons of the FSU, annual screening of the general inmate population with sputum PCR most effectively reduces TB and MDR-TB prevalence, doing so cost-effectively. If this approach is not feasible, the current strategy of annual MMR is both more effective and less expensive than strategies using self

  7. A novel technique for detecting antibiotic-resistant typhoid from rapid diagnostic tests.

    PubMed

    Nic Fhogartaigh, Caoimhe; Dance, David A B; Davong, Viengmon; Tann, Pisey; Phetsouvanh, Rattanaphone; Turner, Paul; Dittrich, Sabine; Newton, Paul N

    2015-05-01

    Fluoroquinolone-resistant typhoid is increasing. An antigen-detecting rapid diagnostic test (RDT) can rapidly diagnose typhoid from blood cultures. A simple, inexpensive molecular technique performed with DNA from positive RDTs accurately identified gyrA mutations consistent with phenotypic susceptibility testing results. Field diagnosis combined with centralized molecular resistance testing could improve typhoid management and surveillance in low-resource settings. Copyright © 2015, Nic Fhogartaigh et al.

  8. Rapid community identification, pain and distress associated with lymphoedema and adenolymphangitis due to lymphatic filariasis in resource-limited communities of North-eastern Nigeria.

    PubMed

    Akogun, O B; Akogun, M K; Apake, E; Kale, O O

    2011-09-01

    Identification of communities with people that could benefit from adenolymphangitis (ADL) and lymphoedema morbidity management within Lymphatic Filariasis Elimination Programmes (NLFEP) in many African countries is a major challenge to programme managers. Another challenge is advocating for proportionate allocation of funds to alleviating the suffering that afflicted people bear. In this study we developed a rapid qualitative technique of identifying communities where morbidity management programme could be situated and documenting the pain and distress that afflicted persons endure. Estimates given by health personnel and by community resource persons were compared with systematic household surveys for the number of persons with lymphoedema of the lower limb. Communities in Northeastern Nigeria, with the largest number of lymphoedema cases were selected and a study of local knowledge, physical, psychosocial burden and intervention-seeking activities associated with the disease documented using an array of techniques (including household surveys, key informant interviews, group discussions and informal conversations). Health personnel gave a more accurate estimate of the number of lymphoedema patients in their communities than either the community leader or the community directed ivermectin distributor (CDD). Community members with lymphoedema preferred to confide in health personnel from other communities. The people had a well developed local vocabulary for lymphoedema and are well aware of the indigenous transmission theories. Although the people associated the episodic ADL attacks with the rains which were more frequent at that period they did not associate the episodes with gross lymphoedema. There were diverse theories about lymphoedema causation with heredity, accidental stepping on charmed objects and organisms, breaking taboos. The most popular belief about causation, however, is witchcraft (60.9%). The episodic attacks are dreaded by the afflicted, since

  9. Redundancy and Molecular Evolution: The Rapid Induction of Bone Formation by the Mammalian Transforming Growth Factor-β3 Isoform

    PubMed Central

    Ripamonti, Ugo; Duarte, Raquel; Parak, Ruqayya; Dickens, Caroline; Dix-Peek, Therese; Klar, Roland M.

    2016-01-01

    The soluble osteogenic molecular signals of the transforming growth factor-β (TGF-β) supergene family are the molecular bases of the induction of bone formation and postnatal bone tissue morphogenesis with translation into clinical contexts. The mammalian TGF-β3 isoform, a pleiotropic member of the family, controls a vast array of biological processes including the induction of bone formation. Recombinant hTGF-β3 induces substantial bone formation when implanted with either collagenous bone matrices or coral-derived macroporous bioreactors in the rectus abdominis muscle of the non-human primate Papio ursinus. In marked contrast, the three mammalian TGF-βs do not initiate the induction of bone formation in rodents and lagomorphs. The induction of bone by hTGF-β3/preloaded bioreactors is orchestrated by inducing fibrin-fibronectin rings that structurally organize tissue patterning and morphogenesis within the macroporous spaces. Induced advancing extracellular matrix rings provide the structural anchorage for hyper chromatic cells, interpreted as differentiating osteoblasts re-programmed by hTGF-β3 from invading myoblastic and/or pericytic differentiated cells. Runx2 and Osteocalcin expression are significantly up-regulated correlating to multiple invading cells differentiating into the osteoblastic phenotype. Bioreactors pre-loaded with recombinant human Noggin (hNoggin), a BMPs antagonist, show down-regulation of BMP-2 and other profiled osteogenic proteins' genes resulting in minimal bone formation. Coral-derived macroporous constructs preloaded with binary applications of hTGF-β3 and hNoggin also show down-regulation of BMP-2 with the induction of limited bone formation. The induction of bone formation by hTGF-β3 is via the BMPs pathway and it is thus blocked by hNoggin. Our systematic studies in P. ursinus with translational hTGF-β3 in large cranio-mandibulo-facial defects in humans are now requesting the re-evaluation of “Bone: formation by

  10. Redundancy and Molecular Evolution: The Rapid Induction of Bone Formation by the Mammalian Transforming Growth Factor-β3 Isoform.

    PubMed

    Ripamonti, Ugo; Duarte, Raquel; Parak, Ruqayya; Dickens, Caroline; Dix-Peek, Therese; Klar, Roland M

    2016-01-01

    The soluble osteogenic molecular signals of the transforming growth factor-β (TGF-β) supergene family are the molecular bases of the induction of bone formation and postnatal bone tissue morphogenesis with translation into clinical contexts. The mammalian TGF-β3 isoform, a pleiotropic member of the family, controls a vast array of biological processes including the induction of bone formation. Recombinant hTGF-β3 induces substantial bone formation when implanted with either collagenous bone matrices or coral-derived macroporous bioreactors in the rectus abdominis muscle of the non-human primate Papio ursinus. In marked contrast, the three mammalian TGF-βs do not initiate the induction of bone formation in rodents and lagomorphs. The induction of bone by hTGF-β3/preloaded bioreactors is orchestrated by inducing fibrin-fibronectin rings that structurally organize tissue patterning and morphogenesis within the macroporous spaces. Induced advancing extracellular matrix rings provide the structural anchorage for hyper chromatic cells, interpreted as differentiating osteoblasts re-programmed by hTGF-β3 from invading myoblastic and/or pericytic differentiated cells. Runx2 and Osteocalcin expression are significantly up-regulated correlating to multiple invading cells differentiating into the osteoblastic phenotype. Bioreactors pre-loaded with recombinant human Noggin (hNoggin), a BMPs antagonist, show down-regulation of BMP-2 and other profiled osteogenic proteins' genes resulting in minimal bone formation. Coral-derived macroporous constructs preloaded with binary applications of hTGF-β3 and hNoggin also show down-regulation of BMP-2 with the induction of limited bone formation. The induction of bone formation by hTGF-β3 is via the BMPs pathway and it is thus blocked by hNoggin. Our systematic studies in P. ursinus with translational hTGF-β3 in large cranio-mandibulo-facial defects in humans are now requesting the re-evaluation of "Bone: formation by

  11. The gene search system. A method for efficient detection and rapid molecular identification of genes in Drosophila melanogaster.

    PubMed Central

    Toba, G; Ohsako, T; Miyata, N; Ohtsuka, T; Seong, K H; Aigaki, T

    1999-01-01

    We have constructed a P-element-based gene search vector for efficient detection of genes in Drosophila melanogaster. The vector contains two copies of the upstream activating sequence (UAS) enhancer adjacent to a core promoter, one copy near the terminal inverted repeats at each end of the vector, and oriented to direct transcription outward. Genes were detected on the basis of phenotypic changes caused by GAL4-dependent forced expression of vector-flanking DNA, and the transcripts were identified with reverse transcriptase PCR (RT-PCR) using the vector-specific primer and followed by direct sequencing. The system had a greater sensitivity than those already in use for gain-of-function screening: 64% of the vector insertion lines (394/613) showed phenotypes with forced expression of vector-flanking DNA, such as lethality or defects in adult structure. Molecular analysis of 170 randomly selected insertions with forced expression phenotypes revealed that 21% matched the sequences of cloned genes, and 18% matched reported expressed sequence tags (ESTs). Of the insertions in cloned genes, 83% were upstream of the protein-coding region. We discovered two new genes that showed sequence similarity to human genes, Ras-related protein 2 and microsomal glutathione S-transferase. The system can be useful as a tool for the functional mapping of the Drosophila genome. PMID:9927464

  12. Method for the rapid detection and molecular characterization of DNA alkylating agents by MALDI-TOF mass spectrometry.

    PubMed

    Garaguso, Ignazio; Halter, Roman; Krzeminski, Jacek; Amin, Shantu; Borlak, Jürgen

    2010-10-15

    Metabolic activation of polycyclic aromatic hydrocarbons (PAH) may cause DNA adduct formation. While these are commonly detected by the ³²P-postlabeling assay, this method is not informative on the chemical nature of the alkylating agent. Here we report a simple and reliable method that employs MALDI-TOF-MS with 2,5-dihydroxybenzoic acid (DHB) matrix layer (ML) sample preparations for the detection and structural characterization of PAH-DNA adducts. The method involves the enzymatic digestion of DNA to 2'-deoxynucleotides followed by solid phase extraction to remove salt and other contaminants prior to MALDI-MS analysis. By collision induced dissociation (CID) structurally relevant fragments are obtained to permit characterization of the alkylating molecules and the adducted nucleotide. Next to guanosine, adenosine and cytidine adducts formed from reactions with (±)-anti-benzo[a]pyrene-7,8-diol-9,10-epoxide (B[a]PDE) are identified at a sensitivity of <100 fmol and a mass accuracy of <10 ppm. Studies with (±)-anti-benzo[c]-chrysene-9,10-diol-11,12-epoxide (B[c]ChDE) further document the versatility and usefulness of the method. When compared with the ³²P-postlabeling assay MALDIMS only indentified deoxycytidine as well nucleoside and dinucleotides adducts. Therefore, this sensitive method enables molecular specification and characterization of adducted nucleotides and of the alkylating agent, and thus, provides comprehensive information that is beyond the ³²P-postlabeling assay.

  13. A Molecular Toolbox for Rapid Generation of Viral Vectors to Up- or Down-Regulate Neuronal Gene Expression in vivo

    PubMed Central

    White, Melanie D.; Milne, Ruth V. J.; Nolan, Matthew F.

    2011-01-01

    We introduce a molecular toolbox for manipulation of neuronal gene expression in vivo. The toolbox includes promoters, ion channels, optogenetic tools, fluorescent proteins, and intronic artificial microRNAs. The components are easily assembled into adeno-associated virus (AAV) or lentivirus vectors using recombination cloning. We demonstrate assembly of toolbox components into lentivirus and AAV vectors and use these vectors for in vivo expression of inwardly rectifying potassium channels (Kir2.1, Kir3.1, and Kir3.2) and an artificial microRNA targeted against the ion channel HCN1 (HCN1 miRNA). We show that AAV assembled to express HCN1 miRNA produces efficacious and specific in vivo knockdown of HCN1 channels. Comparison of in vivo viral transduction using HCN1 miRNA with mice containing a germ line deletion of HCN1 reveals similar physiological phenotypes in cerebellar Purkinje cells. The easy assembly and re-usability of the toolbox components, together with the ability to up- or down-regulate neuronal gene expression in vivo, may be useful for applications in many areas of neuroscience. PMID:21772812

  14. Rapid visual identification of PCR amplified nucleic acids by centrifugal gel separation: Potential use for molecular point-of-care tests.

    PubMed

    Hwang, Sang-Hyun; Kim, Dong-Eun; Im, Ji-Hyun; Kang, Su-Jin; Lee, Do-Hoon; Son, Sang Jun

    2016-05-15

    Recently, nucleic acid amplification and detection techniques have progressed based on advances in in microfluidics, microelectronics, and optical systems. Nucleic acids amplification based point-of-care test (POCT) in resource-limited settings requires simple visual detection methods. Several biosensing methods including lateral flow immunoassays (LFIA) were previously used to visually detect nucleic acids. However, prolonged assay time, several washing steps, and a need for specific antibodies limited their use. Here we developed a novel, rapid method to visualize amplified nucleic acids with naked eyes in clinical samples. First, we optimized conditions based on separation using very low centrifugal force and a density medium to detect human papillomavirus (HPV)-16 DNA in cervical specimens. After DNA extraction, HPV16 PCR was performed with biotin-labeled forward primer and Cy3-labeled reverse primer. PCR amplicon was mixed with streptavidin-magnetic beads, introduced into the density medium. After two-minute centrifugation, the result was visually identified. This system showed identical results with commercial HPV real-time PCR for 30 clinical samples and could detect up to 10(2)copies/mL of HPV DNA without any optical instruments. This robust and sensitive visual detection system is suitable for non-specialist personnel and point-of-care diagnosis in low-resource settings. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Impact of Rapid Molecular Screening at Hospital Admission on Nosocomial Transmission of Methicillin-Resistant Staphylococcus aureus: Cluster Randomised Trial

    PubMed Central

    Roisin, Sandrine; Laurent, Christine; Denis, Olivier; Dramaix, Michèle; Nonhoff, Claire; Hallin, Marie; Byl, Baudouin; Struelens, Marc J.

    2014-01-01

    Design Cluster randomised crossover trial with seven wards randomly allocated to intervention or control arm. Setting Medical and surgical wards of a university hospital with active MRSA control programme. Participants All patients hospitalized >48 h in study wards and screened for MRSA on admission and discharge Intervention: Rapid PCR-based screening test for MRSA compared with control screening test by enrichment culture using chromogenic agar. Objective We determined the benefit of PCR-detection versus culture-based detection of MRSA colonisation upon patient admission on early implementation of isolation precautions and reduction of hospital transmission of MRSA. Main outcome Cumulative rate of MRSA hospital acquisition of in patients screened negative on admission. Randomization The sequential order of inclusion of study wards in each arm was randomised by assigning a number to each ward and using a computer generated list of random numbers. Findings Of 3704 eligible patients, 67.8% were evaluable for the study. Compared with culture, PCR-screening reduced the median test reporting time from admission from 88 to 11 hours (p<0.001) and the median time from admission to isolation from 96 to 25 hours (p<0.001). MRSA acquisition was detected in 36 patients (3.2%) in the control arm and 34 (3.2%) in the intervention arm. The incidence density rate of hospital acquired MRSA was 2.82 and 2.57/1,000 exposed patient-days in the control and intervention arm, respectively (risk ratio 0.91 (95% confidence interval, 0.60–1.39). Poisson regression model adjusted for colonisation pressure, compliance with hand hygiene and antibiotic use indicated a RR 0.99 (95% CI, 0.69 to 1.44). Interpretation Universal PCR screening for MRSA on admission to medical and surgical wards in an endemic setting shortened the time to implement isolation precautions but did not reduce nosocomial acquisition of MRSA. Trial registration clinicaltrials.gov NCT00846105 PMID:24836438

  16. Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting.

    PubMed

    Laing, Chad; Pegg, Crystal; Yawney, Davis; Ziebell, Kim; Steele, Marina; Johnson, Roger; Thomas, James E; Taboada, Eduardo N; Zhang, Yongxiang; Gannon, Victor P J

    2008-11-01

    In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprint Escherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79 E. coli O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major E. coli O157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other E. coli O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related E. coli O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.

  17. Evaluation of a new rapid molecular diagnostic system for Plasmodium falciparum combined with DNA filter paper, loop-mediated isothermal amplification, and melting curve analysis.

    PubMed

    Yamamura, Mariko; Makimura, Koichi; Ota, Yasuo

    2009-01-01

    Falciparum malaria is a fatal infection without immediate diagnosability or treatment. There are shortages of clinicians and examiners skilled in the treatment of malaria in non-endemic countries, including Japan. This study was performed to evaluate a novel rapid molecular diagnostic system consisting of loop-mediated isothermal amplification (LAMP) combined with DNA filter paper (FTA card) and melting curve analysis. Combining LAMP with melting curve analysis enabled diagnosis of Plasmodium falciparum more accurately with relative ease. FTA cards could be used to clarify problems regarding storage, infectivity, and transportation. The LAMP assay was carried out at a constant temperature of 63 degrees C for 90 min. The diagnostic system (malaria-LAMP) accurately diagnosed malaria (47 samples from Thailand and 50 from Zimbabwe) with 97.8% sensitivity and 85.7% specificity as compared with microscopic methods, indicating the usefulness of this combined system.

  18. Rapid detection of Acinetobacter baumannii and molecular epidemiology of carbapenem-resistant A. baumannii in two comprehensive hospitals of Beijing, China.

    PubMed

    Li, Puyuan; Niu, Wenkai; Li, Huan; Lei, Hong; Liu, Wei; Zhao, Xiangna; Guo, Leijing; Zou, Dayang; Yuan, Xin; Liu, Huiying; Yuan, Jing; Bai, Changqing

    2015-01-01

    Acinetobacter baumannii is an important opportunistic pathogen associated with a variety of nosocomial infections. A rapid and sensitive molecular detection in clinical isolates is quite needed for the appropriate therapy and outbreak control of A. baumannii. Group 2 carbapenems have been considered the agents of choice for the treatment of multiple drug-resistant A. baumannii. But the prevalence of carbapenem-resistant A. baumannii (CRAB) has been steadily increasing in recent years. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of A. baumannii in clinical samples by using high-specificity primers of the bla OXA-51 gene. Then we investigated the OXA-carbapenemases molecular epidemiology of A. baumannii isolates in two comprehensive hospitals in Beijing. The results showed that the LAMP assay could detect target DNA within 60 min at 65°C. The detection limit was 50 pg/μl, which was about 10-fold greater than that of PCR. Furthermore, this method could distinguish A. baumannii from the homologous A. nosocomialis and A. pittii. A total of 228 positive isolates were identified by this LAMP-based method for A. baumannii from 335 intensive care unit patients with clinically suspected multi-resistant infections in two hospitals in Beijing. The rates of CRAB are on the rise and are slowly becoming a routine phenotype for A. baumannii. Among the CRABs, 92.3% harbored both the bla OXA-23 and bla OXA-51 genes. Thirty-three pulsotypes were identified by pulsed-field gel electrophoresis, and the majority belonged to clone C. In conclusion, the LAMP method developed for detecting A. baumannii was faster and simpler than conventional PCR and has great potential for both point-of-care testing and basic research. We further demonstrated a high distribution of class D carbapenemase-encoding genes, mainly OXA-23, which presents an emerging threat in hospitals in China.

  19. Rapid detection of Acinetobacter baumannii and molecular epidemiology of carbapenem-resistant A. baumannii in two comprehensive hospitals of Beijing, China

    PubMed Central

    Li, Puyuan; Niu, Wenkai; Li, Huan; Lei, Hong; Liu, Wei; Zhao, Xiangna; Guo, Leijing; Zou, Dayang; Yuan, Xin; Liu, Huiying; Yuan, Jing; Bai, Changqing

    2015-01-01

    Acinetobacter baumannii is an important opportunistic pathogen associated with a variety of nosocomial infections. A rapid and sensitive molecular detection in clinical isolates is quite needed for the appropriate therapy and outbreak control of A. baumannii. Group 2 carbapenems have been considered the agents of choice for the treatment of multiple drug-resistant A. baumannii. But the prevalence of carbapenem-resistant A. baumannii (CRAB) has been steadily increasing in recent years. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of A. baumannii in clinical samples by using high-specificity primers of the blaOXA-51 gene. Then we investigated the OXA-carbapenemases molecular epidemiology of A. baumannii isolates in two comprehensive hospitals in Beijing. The results showed that the LAMP assay could detect target DNA within 60 min at 65°C. The detection limit was 50 pg/μl, which was about 10-fold greater than that of PCR. Furthermore, this method could distinguish A. baumannii from the homologous A. nosocomialis and A. pittii. A total of 228 positive isolates were identified by this LAMP-based method for A. baumannii from 335 intensive care unit patients with clinically suspected multi-resistant infections in two hospitals in Beijing. The rates of CRAB are on the rise and are slowly becoming a routine phenotype for A. baumannii. Among the CRABs, 92.3% harbored both the blaOXA-23 and blaOXA-51 genes. Thirty-three pulsotypes were identified by pulsed-field gel electrophoresis, and the majority belonged to clone C. In conclusion, the LAMP method developed for detecting A. baumannii was faster and simpler than conventional PCR and has great potential for both point-of-care testing and basic research. We further demonstrated a high distribution of class D carbapenemase-encoding genes, mainly OXA-23, which presents an emerging threat in hospitals in China. PMID:26441924

  20. Rapid visible color change and physical swelling during water exposure in triethanolamine-metalcone films formed by molecular layer deposition

    SciTech Connect

    Lemaire, Paul C.; Oldham, Christopher J.; Parsons, Gregory N.

    2016-01-15

    Molecular layer deposition (MLD) of “metalcones,” including alucone, zincone, titanicone, and others, involves self-limiting half-reactions between organic and organometallic (or metal-halide) reactants. Studies have typically focused on metal precursors reacting with ethylene glycol or glycerol to form the films' polymeric O-M-O-(CH{sub x}){sub y}-O-M-O repeat units. The authors report new MLD materials that incorporate tertiary amine groups into the organic linkage. Specifically, reacting triethanolamine (TEA) with either trimethylaluminum or titanium tetrachloride produces TEA-alucone (Al-TEA) and TEA-titanicone (Ti-TEA), respectively, and the amine group leads to unique physical and optical properties. Fourier-transform infrared (FTIR) analysis confirms that the films have prominent C-H, C-N, and M-O-C peaks, consistent with the expected bond structure. When exposed to vapors, including water, alcohol, or ammonia, the Ti-TEA films changed their visible color within minutes and increased physical thickness by >35%. The Al-TEA showed significantly less response. X-ray photoelectron spectroscopy and FTIR suggest that HCl generated during MLD coordinates to the amine forming a quaternary ammonium salt that readily binds adsorbates via hydrogen bonding. The visible color change is reversible, and ellipsometry confirms that the color change results from vapor absorption. The unique absorptive and color-changing properties of the TEA-metalcone films point to new possible applications for MLD materials in filtration, chemical absorption, and multifunctional chemical separations/sensing device systems.

  1. Evaluation of Two Molecular Assays for Rapid Detection of Mycobacterium tuberculosis Resistance to Fluoroquinolones in High-Tuberculosis and -Multidrug-Resistance Settings ▿

    PubMed Central

    Kontsevaya, I.; Mironova, S.; Nikolayevskyy, V.; Balabanova, Y.; Mitchell, S.; Drobniewski, F.

    2011-01-01

    The Russian Federation is a high-tuberculosis (TB)-burden country with high rates of drug resistance, including multidrug and extensive drug resistance to TB (M/XDRTB). Rapid diagnosis of resistance to fluoroquinolones (FQs) using molecular assays is essential for the implementation of appropriate drug regimens and prevention of the transmission of XDR strains. A total of 51 individual MDRTB strains were tested by pyrosequencing of the quinolone resistance determining region of the gyrA gene and the GenoType MTBDRsl assay (Hain Lifescience, GmbH, Nehren, Germany), and the results were evaluated against those obtained by phenotypic drug susceptibility testing (DST). Mutations were detected in 25 (78.1%) FQ-resistant strains, with the majority of mutations (n = 19 [73.0%]) found in codon 94 of the gyrA gene; the novel mutation 1457 C→Τ was found in the gyrB gene. Three mixed allelic variants were detected, which is a well-known phenomenon in areas with high TB and drug-resistant TB rates. The sensitivity and specificity of pyrosequencing (86.2 and 100%, respectively) and MTBDRsl (86.2 and 100%, respectively) were high; however, the results for 5.9% of the analyzed strains were unreadable when MTBDRsl was used. The MTBDRsl and pyrosequencing assays offer a rapid and accurate means for diagnosing resistance to FQs in high-TB-burden areas. PMID:21632897

  2. Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae)

    PubMed Central

    Kingston, Sarah E; Adams, Lara D; Rosel, Patricia E

    2009-01-01

    Background Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference. PMID:19811651

  3. Rapid degradation of Congo red by molecularly imprinted polypyrrole-coated magnetic TiO2 nanoparticles in dark at ambient conditions.

    PubMed

    Wei, Shoutai; Hu, Xiaolei; Liu, Hualong; Wang, Qiang; He, Chiyang

    2015-08-30

    A novel molecularly imprinted polymer (MIP)-coated magnetic TiO2 nanocomposite was prepared, using methyl orange (MO) as the dummy template and pyrrole as functional monomer, for degradation of Congo red (CR). The nanocomposite was characterized by Fourier transform infrared spectroscopy, thermo-gravimetric analysis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer. The imprinting efficiency of the imprinted nanoparticles was investigated by static binding test, and their degradation ability toward CR was also studied. Moreover, the effects of pH, temperature, dissolved oxygen and oscillation rate on degradation rate of CR were investigated. Results showed that the imprinted nanocomposite had higher adsorption ability for MO compared with the non-imprinted one. Moreover, it could degrade CR rapidly in dark at room temperature and atmospheric pressure and could be recycled easily by a magnet with a good reusability. A degradation mechanism was proposed according to LC-MS analysis of degradation products of CR. The new imprinted nanoparticles showed high catalytic activity at ambient conditions without light illumination and additional chemicals, and therefore, it can be potentially applied to the rapid, "green" and low-cost degradation of CR in industrial printing and dyeing wastewater.

  4. Evaluation of two molecular assays for rapid detection of mycobacterium tuberculosis resistance to fluoroquinolones in high-tuberculosis and -multidrug-resistance Settings.

    PubMed

    Kontsevaya, I; Mironova, S; Nikolayevskyy, V; Balabanova, Y; Mitchell, S; Drobniewski, F

    2011-08-01

    The Russian Federation is a high-tuberculosis (TB)-burden country with high rates of drug resistance, including multidrug and extensive drug resistance to TB (M/XDRTB). Rapid diagnosis of resistance to fluoroquinolones (FQs) using molecular assays is essential for the implementation of appropriate drug regimens and prevention of the transmission of XDR strains. A total of 51 individual MDRTB strains were tested by pyrosequencing of the quinolone resistance determining region of the gyrA gene and the GenoType MTBDRsl assay (Hain Lifescience, GmbH, Nehren, Germany), and the results were evaluated against those obtained by phenotypic drug susceptibility testing (DST). Mutations were detected in 25 (78.1%) FQ-resistant strains, with the majority of mutations (n = 19 [73.0%]) found in codon 94 of the gyrA gene; the novel mutation 1457 C→Τ was found in the gyrB gene. Three mixed allelic variants were detected, which is a well-known phenomenon in areas with high TB and drug-resistant TB rates. The sensitivity and specificity of pyrosequencing (86.2 and 100%, respectively) and MTBDRsl (86.2 and 100%, respectively) were high; however, the results for 5.9% of the analyzed strains were unreadable when MTBDRsl was used. The MTBDRsl and pyrosequencing assays offer a rapid and accurate means for diagnosing resistance to FQs in high-TB-burden areas.

  5. Dummy-surface molecularly imprinted polymers on magnetic graphene oxide for rapid and selective quantification of acrylamide in heat-processed (including fried) foods.

    PubMed

    Ning, Fangjian; Qiu, Tingting; Wang, Qi; Peng, Hailong; Li, Yanbin; Wu, Xiaqing; Zhang, Zhong; Chen, Linxin; Xiong, Hua

    2017-04-15

    Novel nano-sized dummy-surface molecularly imprinted polymers (DSMIPs) on a magnetic graphene oxide (GO-Fe3O4) surface were developed as substrates, using propionamide as a dummy template molecule for the selective recognition and rapid pre-concentration and removal of acrylamide (AM) from food samples. These products showed rapid kinetics, high binding capacity (adsorption at 3.68mg·g(-1)), and selectivity (imprinting factor α 2.83); the adsorption processes followed the Langmuir-Freundlich isotherm and pseudo-second-order kinetic models. Excellent recognition selectivity toward acrylamide was achieved compared to structural analogs, such as propionic and acrylic acids (selectivity factor β 2.33, and 2.20, respectively). Moreover, DSMIPs-GO-Fe3O4 was used to quantify acrylamide in food samples, yielding satisfactory recovery (86.7-94.3%) and low relative standard deviation (<4.85%). Thus, our DSMIPs-GO-Fe3O4-based procedure was demonstrated to be a convenient and practical method for the separation, enrichment, and removal of acrylamide from food samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

    PubMed

    Paz, Andrea; Crawford, Andrew J

    2012-11-01

    Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

  7. Ionic liquid molecularly imprinted polymers for application in pipette-tip solid-phase extraction coupled with gas chromatography for rapid screening of dicofol in celery.

    PubMed

    Yan, Hongyuan; Yang, Chen; Sun, Yunyun; Row, Kyung Ho

    2014-09-26

    A new type of ionic liquid molecularly imprinted polymers (IL-MIPs) synthesized by precipitation polymerization using 1-allyl-3-methylimidazolium bromide as an auxiliary solvent and α-chloro-dichlorodiphenyltrichloroethane (α-chloro-DDT) as the template was applied as a selective sorbent of minimized pipette tip-solid-phase extraction (PT-SPE) for rapid isolation and extraction of dicofol (DCF) from celery samples. The pretreatment procedure of celery samples involved only 2.0mg of IL-MIPs, 0.8 mL of acetonitrile-water (ACN-H2O; 1:1, v/v) (washing solvent), and 1.0 mL of acetone-10% acetic acid (HOAc) (elution solvent). Compared with molecularly imprinted polymers (MIPs), ionic liquid-non-imprinted polymers (IL-NIPs) and conventional sorbents such as C18, Si, NH2, and Al2O3-N, IL-MIPs showed higher adsorption and purification capacity to DCF in aqueous solution. Good linearity for DCF was observed in the range from 2.3 to 232.5 ng g(-1) (r(2)=0.9995). The average recoveries at three spiking levels ranged from 86.6% to 101.9% with relative standard deviations (RSDs) of ≤ 6.5% (n=3). The presented IL-MIPs-PT-SPE-GC/ECD method combines the advantages of MIPs, IL, and PT-SPE, and can be used in aqueous conditions with high affinity and selectivity to analytes of complex samples.

  8. Rapid three-dimensional microfluidic mixer for high viscosity solutions to unravel earlier folding kinetics of G-quadruplex under molecular crowding conditions.

    PubMed

    Liu, Chao; Li, Ying; Li, Yiwei; Chen, Peng; Feng, Xiaojun; Du, Wei; Liu, Bi-Feng

    2016-01-01

    Rapid mixing of highly viscous solutions is a great challenge, which helps to analyze the reaction kinetics in viscous liquid phase, particularly to discover the folding kinetics of macromolecules under molecular crowding conditions mimicking the conditions inside cells. Here, we demonstrated a novel microfluidic mixer based on Dean flows with three-dimensional (3D) microchannel configuration for fast mixing of high-viscosity fluids. The main structure contained three consecutive subunits, each consisting of a "U"-type channel followed by a chamber with different width and height. Thus, the two solutions injected from the two inlets would undergo a mixing in the first "U"-type channel due to the Dean flow effect, and simultaneous vortices expansions in both horizontal and vertical directions in the following chamber. Numerical simulations and experimental characterizations confirmed that the micromixer could achieve a mixing time of 122.4μs for solutions with viscosities about 33.6 times that of pure water. It was the fastest micromixer for high viscosity solutions compared with previous reports. With this highly efficient 3D microfluidic mixer, we further characterized the early folding kinetics of human telomere G-quadruplex under molecular crowding conditions, and unravelled a new folding process within 550μs.

  9. High-risk Long QT Syndrome Mutations in the Kv7.1 (KCNQ1) Pore Disrupt the Molecular Basis for Rapid K+ Permeation

    PubMed Central

    Burgess, Don E.; Bartos, Daniel C.; Reloj, Allison R.; Campbell, Kenneth S.; Johnson, Jonathan N.; Tester, David J.; Ackerman, Michael J.; Fressart, Véronique; Denjoy, Isabelle; Guicheney, Pascale; Moss, Arthur J.; Ohno, Seiko; Horie, Minoru; Delisle, Brian P.

    2012-01-01

    Type 1 long QT syndrome (LQT1) syndrome is caused by loss-of-function mutations in the KCNQ1, which encodes the K+ channel (Kv7.1) that underlies the slowly activating delayed rectifier K+ current in the heart. Intragenic risk stratification suggests LQT1 mutations that disrupt conserved amino acid residues in the pore are an independent risk factor for LQT1-related cardiac events. The purpose of this study is to determine possible molecular mechanisms that underlie the loss-of-function for these high-risk mutations. Extensive genotype-phenotype analyses of LQT1 patients showed that T322M-, T322A-, or G325R-Kv7.1 confer a high risk for LQT1-related cardiac events. Heterologous expression of these mutations with KCNE1 revealed they generated non-functional channels and caused dominant negative suppression of WT-Kv7.1 current. Molecular dynamic simulations (MDS) of analogous mutations in KcsA (T85M-, T85A-, and G88R-KcsA) demonstrated that they disrupted the symmetrical distribution of the carbonyl oxygen atoms in the selectivity filter, which upset the balance between the strong attractive and K+-K+ repulsive forces required for rapid K+ permeation. We conclude high-risk LQT1 mutations in the pore likely disrupt the architectural and physical properties of the K+ channel selectivity filter. PMID:23092362

  10. Combined molecular gram typing and high-resolution melting analysis for rapid identification of a syndromic panel of bacteria responsible for sepsis-associated bloodstream infection.

    PubMed

    Ozbak, Hani; Dark, Paul; Maddi, Satyanarayana; Chadwick, Paul; Warhurst, Geoffrey

    2012-01-01

    Effective diagnosis and treatment of bloodstream infections are often hampered by a lack of time-critical information from blood cultures. Molecular techniques aimed at the detection of circulating pathogen DNA have the potential to dramatically improve the timeliness of infection diagnosis. Our aim in this study was to establish a rapid, low-cost PCR approach using high-resolution melting analysis to identify a syndromic panel of 21 pathogens responsible for most bloodstream bacterial infections encountered in critical care environments. A broad-range, real-time PCR technique that combines primers for molecular Gram classification and high-resolution melting analysis in a single run was established. The differentiation of bacterial species was achieved using a multiparameter, decision-tree approach that was based on Gram type, grouping according to melting temperature, and sequential comparisons of melting profiles against multiple reference organisms. A preliminary validation study was undertaken by blinded analysis of 53 consecutive bloodstream isolates from a clinical microbiology laboratory. Fifty isolates contained organisms that were present in the panel, and 96% of these were identified correctly at the genus or species level. A correct Gram classification was reported for all 53 isolates. This technique shows promise as a cost-effective tool for the timely identification of bloodstream pathogens, allowing clinicians to make informed decisions on appropriate antibiotic therapies at an earlier stage.

  11. Molecularly imprinted polymer cartridges coupled on-line with high performance liquid chromatography for simple and rapid analysis of human insulin in plasma and pharmaceutical formulations.

    PubMed

    Moein, Mohammad Mahdi; Javanbakht, Mehran; Akbari-adergani, Behrouz

    2014-04-01

    In this paper, a novel method is described for automated determination of human insulin in biological fluids using principle of sequential injection on a molecularly imprinted solid-phase extraction (MISPE) cartridge as a sample clean-up technique combined with high performance liquid chromatography (HPLC). The water-compatible molecularly imprinted polymers (MIPs) were prepared using methacrylic acid as a functional monomer, ethylene glycol dimethacrylate as a cross-linker, chloroform as a porogen and insulin as a template molecule. The imprinted polymers were then employed as the solid-phase extraction sorbent for on-line extraction of insulin from human plasma samples. To achieve the best condition, influential parameters on the extraction efficiency were thoroughly investigated. Rapid and simple analysis of the hormone was successfully accomplished through the good selectivity of the prepared sorbent coupled with HPLC. Limits of detection (LOD) and quantification (LOQ) of 0.2 ng mL(-1), 0.7 ng mL(-1), and 0.03 ng mL(-1), 0.1 ng mL(-1) were obtained in plasma and urine respectively. The obtained data exhibited the great recoveries for extraction of insulin from human plasma and pharmaceutical samples, higher than 87%.

  12. Rapid and Delayed Effects of Pulsed Radiofrequency on Neuropathic Pain: Electrophysiological, Molecular, and Behavioral Evidence Supporting Long-Term Depression.

    PubMed

    Huang, Ren-Yu; Liao, Chia-Chi; Tsai, Shih-Ying; Yen, Chen-Tung; Lin, Chii-Wann; Chen, Tsung-Chi; Lin, Wei-Tso; Chang, Chi-Heng; Wen, Yeong-Ray

    2017-02-01

    Pulsed radiofrequency (PRF) has been widely employed for ameliorating clinical neuropathic pain. How PRF alters electrophysiological transmission and modulates biomolecular functions in neural tissues has yet to be clarified. We previously demonstrated that an early application of low-voltage bipolar PRF adjacent to the dorsal root ganglion (DRG) reduced acute neuropathic pain in animals. By contrast, the present study investigated how PRF alters postsynaptic sensitization to produce early and delayed effects on neuropathic pain. Our objective was to test the hypothesis that a 5-minute session of PRF could rapidly produce selective long-term depression (LTD) on C-fiber-mediated spinal sensitization and sustain the effect through the long-lasting inhibition of injury-induced ERK-MAPK activation. This may explain the prolonged analgesic effect of PRF on chronic neuropathic pain. Experiments were conducted on both normal rats and neuropathic pain rats that received spinal nerve ligation (SNL) 8 days prior. An animal laboratory in a medical center of a university in Taiwan. We first compared changes in field potentials in the L5 superficial spinal dorsal horn (SDH) that were evoked by conditioning electrical stimuli in the sciatic nerve in male adult rats before (as the baseline) and after PRF stimulation for at least 2 hours. Bipolar PRF was applied adjacent to the L5 DRG at an intensity of 5 V for 5 minutes, whereas the control rats were treated with sham applications. The electrophysiological findings were tested for any correlation with induction of spinal phospho-ERK (p-ERK) in normal and neuropathic pain rats. We then investigated the delayed effect of PRF on SNL-maintained pain behaviors for 2 weeks as well as p-ERK in SDH among the control, SNL, and PRF groups. Finally, potential injury in the DRGs after PRF stimulation was evaluated through behavioral observations and ATF-3, a neuronal stress marker. In the evoked field-potential study, the recordings mediated

  13. Molecular identification of adenovirus sequences: a rapid scheme for early typing of human adenoviruses in diagnostic samples of immunocompetent and immunodeficient patients.

    PubMed

    Madisch, Ijad; Wölfel, Roman; Harste, Gabi; Pommer, Heidi; Heim, Albert

    2006-09-01

    Precise typing of human adenoviruses (HAdV) is fundamental for epidemiology and the detection of infection chains. As only few of the 51 adenovirus types are associated with life- threatening disseminated diseases in immunodeficient patients, detection of one of these types may have prognostic value and lead to immediate therapeutic intervention. A recently published molecular typing scheme consisting of two steps (sequencing of a generic PCR product closely adjacent to loop 1 of the main neutralization determinant epsilon, and for species HAdV-B, -C, and -D the sequencing of loop 2 [Madisch et al., 2005]) was applied to 119 clinical samples. HAdV DNA was typed unequivocally even in cases of culture negative samples, for example in immunodeficient patients before HAdV causes high virus loads and disseminated disease. Direct typing results demonstrated the predominance of HAdV-1, -2, -5, and -31 in immunodeficient patients suggesting the significance of the persistence of these viruses for the pathogenesis of disseminated disease. In contrast, HAdV-3 predominated in immunocompetent patients and cocirculation of four subtypes was demonstrated. Typing of samples from a conjunctivitis outbreak in multiple military barracks demonstrated various HAdV types (2, 4, 8, 19) and not the suspected unique adenovirus etiology. This suggests that our molecular typing scheme will be also useful for epidemiological investigations. In conclusion, our two-step molecular typing system will permit the precise and rapid typing of clinical HAdV isolates and even of HAdV DNA in clinical samples without the need of time-consuming virus isolation prior to typing.

  14. Development of magnetic molecularly imprinted polymers with double templates for the rapid and selective determination of amphenicol antibiotics in water, blood, and egg samples.

    PubMed

    Wei, Shoulian; Li, Jianwen; Liu, Yong; Ma, Jinkui

    2016-11-18

    A magnetic mesoporous dual-template molecularly imprinted polymer (Fe3O4@mSiO2 @DMIP) with a specific recognition capability for chloramphenicol (CAP) and florfenicol (FF) was synthesised. CAP and FF were used as dual-template molecules, α-methacrylic acid and Fe3O4@mSiO2@-CHCH2 as dual functional monomers, and ethylene glycol dimethyl methacrylate as a crosslinking agent. For comparison, a magnetic mesoporous non-molecularly imprinted polymer (Fe3O4@mSiO2@NIP) was also prepared using the same synthesis procedure, but without the dual templates. The prepared polymers were characterised using scanning electron microscopy, Fourier-transform infrared spectroscopy and adsorption experiments. Results indicated that both the Fe3O4@mSiO2@DMIP and the Fe3O4@mSiO2 @NIP were microspherical nanoparticles, and the surface of the Fe3O4@mSiO2@DMIP was rougher than that of the Fe3O4@mSiO2@NIP. In addition, the prepared Fe3O4@mSiO2@DMIP possessed a higher adsorption capacity and better selectivity for CAP and FF than the Fe3O4@mSiO2@NIP. The maximum static adsorption capacities of the Fe3O4@mSiO2@ DMIP for CAP and FF were 146.5 and 190.1mgg(-1), respectively, whereas those of the Fe3O4@mSiO2 @NIP were 50.0 and 44.0mgg(-1), respectively. The obtained Fe3O4@mSiO2@DMIP particles were applied as a magnetic solid-phase extraction sorbent for the rapid and selective extraction of CAP, FF, and thiamphenicol (TAP) in water, chicken blood and egg samples. The method of magnetic molecularly imprinted solid-phase extraction (M-MISPE) coupled to high-performance liquid chromatography with UV detection (HPLC-UV) was conducted to detect CAP, FF, and TAP. The limits of detection for CAP, FF, and TAP were 0.16, 0.08, and 0.08μgkg(-1), respectively. The average recovery and precision values for the spiked water, chicken blood, and egg samples ranged from 88.3% to 99.1% and 2.7% to 7.9%, respectively. Given its rapidity, selectivity, and sensitivity, the developed method of M-MISPE coupled to

  15. Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress.

    PubMed

    Bouétard, Anthony; Noirot, Céline; Besnard, Anne-Laure; Bouchez, Olivier; Choisne, Damien; Robe, Eugénie; Klopp, Christophe; Lagadic, Laurent; Coutellec, Marie-Agnès

    2012-11-01

    Due to their ability to explore whole genome response to drugs and stressors, omics-based approaches are widely used in toxicology and ecotoxicology, and identified as powerful tools for future ecological risk assessment and environmental monitoring programs. Understanding the long-term effects of contaminants may indeed benefit from the coupling of genomics and eco-evolutionary hypotheses. Next-generation sequencing provides a new way to investigate pollutants impact, by targeting early responses, screening chemicals, and directly quantifying gene expression, even in organisms without reference genome. Lymnaea stagnalis is a freshwater mollusk in which access to genomic resources is critical for many scientific issues, especially in ecotoxicology. We used 454-pyrosequencing to obtain new transcriptomic resources in L. stagnalis and to preliminarily explore gene expression response to a redox-cycling pesticide, diquat. We obtained 151,967 and 128,945 high-quality reads from control and diquat-exposed individuals, respectively. Sequence assembly provided 141,999 contigs, of which 124,387 were singletons. BlastX search revealed significant match for 34.6 % of the contigs (21.2 % protein hits). KEGG annotation showed a predominance of hits with genes involved in energy metabolism and circulatory system, and revealed more than 400 putative genes involved in oxidative stress, cellular/molecular stress and signaling pathways, apoptosis, and metabolism of xenobiotics. Results also suggest that diquat may have a great diversity of molecular effects. Moreover, new genetic markers (putative SNPs) were discovered. We also created a Ensembl-like web-tool for data-mining ( http://genotoul-contigbrowser.toulouse.inra.fr:9095/Lymnaea_stagnalis/index.html ). This resource is expected to be relevant for any genomic approach aimed at understanding the molecular basis of physiological and evolutionary responses to environmental stress in L. stagnalis.

  16. Napalm as an energy resource: a study of the molecular weight distribution of polystyrene in napalm and its use in middle distillate fuels.

    PubMed

    Mushrush; Beal; Hardy; Hughes

    1999-09-01

    The large quantity of napalm that is currently being treated as hazardous waste represents a viable energy resource that is too valuable to waste. However, there are significant problems to be overcome before this material can be used as an energy source. The scientific and environmental problems include: the broad molecular weight distribution of polystyrene, solubility and compatibility in a fuel matrix, methods to ensure complete combustion, high benzene concentration, low flash point due to the presence of gasoline, and safety in transportation and handling. In this paper, we present data on the molecular weight distribution of the polystyrene present in the napalm mixture, extraction of the gasoline and benzene from napalm, solubility of napalm in middle distillate fuels, simulated burner characteristics of napalm fuel mixtures, and accelerated storage stability studies of napalm fuel mixtures.

  17. Preparation of molecularly imprinted polymers on the surface of magnetic carbon nanotubes with a pseudo template for rapid simultaneous extraction of four fluoroquinolones in egg samples.

    PubMed

    Xiao, Deli; Dramou, Pierre; Xiong, Nanqian; He, Hua; Yuan, Danhua; Dai, Hao; Li, Hui; He, Xiaomei; Peng, Jun; Li, Nan

    2013-06-07

    Fluoroquinolones (FQs) have emerged as one of the most important class of antibiotics. Due to their low concentration in bio-matrix samples which contain a lot of interfering substances, the efficient solid phase extraction and accurate determination of FQs remain a challenge. In this paper, a new strategy for the isolation and enrichment of FQs from egg samples was obtained by molecularly imprinted polymers on the surface of magnetic carbon nanotubes (MCNTs@MIP), which not only can be collected and separated rapidly by an external magnetic field, but also have a high specific surface area, outstanding mechanical properties and specific recognition for FQs. MCNTs@MIP were prepared using ofloxacin as a pseudo template, methacrylic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linker. The characteristics of the MCNTs@MIP were assessed by transmission electron microscopy (TEM), multipoint Brunauer-Emmett-Teller (BET) analysis, vibrating sample magnetometry (VSM), X-ray diffraction (XRD) and Fourier transform infrared (FT-IR) spectroscopy. The results of the adsorption experiments not only demonstrated rapid dynamic adsorption but also showed a high selectivity toward FQs. An extraction method using MCNTs@MIP coupled with high performance liquid chromatography (HPLC) was developed for the determination of four FQs in egg samples. The recovery of four FQs ranged from 95.2% ± 3.2% to 100.7% ± 3.1% and the detection limits ranged from 0.25-0.40 ng g(-1). The results demonstrate that the proposed method based on pseudo template MCNTs@MIP is a promising approach for the preconcentration, purification, and simultaneous analysis of four FQs in bio-matrix samples.

  18. Molecular approach for the rapid detection of Bacillus and Pseudomonas genera--dominant antagonistic groups--from diverse ecological niches using colony multiplex PCR.

    PubMed

    Nair, Anusree V; Pradeep, M A; Vijayan, K K

    2014-07-01

    Bacillus and Pseudomonas are the dominant groups of bacteria known for their antagonistic potential against many plant and animal pathogens. Presently, exploration of these genera with antagonistic property for disease management of aquaculture system is gaining more importance to overcome the use of antibiotics and related resistance issues. Rapid screening and identification of these genera from diverse bacterial populations by conventional methods is laborious, cost-intensive, and time-consuming. To overcome these limiting factors, in the present study, a colony multiplex PCR (cmPCR) method was developed and evaluated for the rapid detection of Bacillus and Pseudomonas. The technique amplifies the partial 16S rRNA gene of Bacillus and Pseudomonas with a product size of ~1,100 and ~375 bp, respectively, using single forward (BSF2) and two reverse primers (PAGSR and BK1R). Reliability of the cmPCR method was confirmed by screening 472 isolates obtained from ten different eco-stations, of which 133 isolates belonged to Bacillus and 32 to Pseudomonas. The cmPCR method also helped to identify six different Pseudomonas spp. and 14 different Bacillus spp. from environmental samples. Of the total 472 isolates studied, 46 showed antagonistic activity, among which 63 % were Bacillus and 17.4 % were Pseudomonas. Thus, the newly developed molecular approach provides a quick, sensitive, and potential screening tool to detect novel, antagonistically important Bacillus and Pseudomonas genera for their use in aquaculture. Further, it can also act as a taxonomic tool to understand the distribution of these genera from wide ecological niches and their exploitation for diverse biotechnological applications.

  19. An antibiotic care bundle approach based on results of rapid molecular screening for nasal carriage of methicillin-resistant Staphylococcus aureus in the intensive care unit.

    PubMed

    Stano, Paola; Avolio, Manuela; De Rosa, Rita; Modolo, Maria Luisa; Basso, Stefano M M; Lumachi, Franco; Camporese, Alessandro

    2012-01-01

    The potential role of active methicillin-resistant Staphylococcus aureus (MRSA) surveillance in the intensive care unit (ICU), has been recently proposed as a guide for antibiotic treatment in patients suspected of being infected with MRSA by using an antibiotic care bundle (ACB) approach. A group of 376 consecutive ICU patients were prospectively screened for nasal carriage of MRSA using a real-time polymerase chain reaction test. The study group consisted of 244 (64.9%) males and (35.1%) females, with a median age of 64 (range 17-95 years). Overall, 26 (6.9%) patients were positive for MRSA, while 350 (93.1%) were MRSA-negative. No difference was observed in gender and age between groups. During ICU stay, 9 (2.4%) patients developed generalized MRSA infection, of whom 8 out of 26 (30.8%) were MRSA-carriers and one out of the 350 (0.3%) was MRSA-negative. Thus, a strong relationship between MRSA infection and MRSA carriage (relative risk=107.7, 95% confidence interval=14.0-828.5, p<0.0001) was found. Subsequently, in our ICU, we developed and introduced a new ACB approach based on rapid nasal screening results for improving the management of critically ill patients. The use of anti-MRSA agents should be re-evaluated daily on the basis of clinical and laboratory features, with positive cultures from sterile site or signs of active infection supporting prolongation of empirical treatment. On the contrary, MRSA-negative clinical cultures support a de-escalation strategy. In conclusion, the early identification of MRSA-carriers using a rapid molecular screening is safe and accurate, allowing MRSA-positive patients, who will more likely develop MRSA infections, to be detected.

  20. Rapid identification of ascomycetous yeasts from clinical specimens by a molecular method based on flow cytometry and comparison with identifications from phenotypic assays.

    PubMed

    Page, Brent T; Shields, Christine E; Merz, William G; Kurtzman, Cletus P

    2006-09-01

    This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

  1. Rapid Detection of Melamine in Tap Water and Milk Using Conjugated "One-Step" Molecularly Imprinted Polymers-Surface Enhanced Raman Spectroscopic Sensor.

    PubMed

    Hu, Yaxi; Lu, Xiaonan

    2016-05-01

    An innovative "one-step" sensor conjugating molecularly imprinted polymers and surface enhanced Raman spectroscopic-active substrate (MIPs-SERS) was investigated for simultaneous extraction and determination of melamine in tap water and milk. This sensor was fabricated by integrating silver nanoparticles (AgNPs) with MIPs synthesized by bulk polymerization of melamine (template), methacrylic acid (functional monomer), ethylene glycol dimethacrylate (cross-linking agent), and 2,2'-azobisisobutyronitrile (initiator). Static and kinetic adsorption tests validated the specific affinity of MIPs-AgNPs to melamine and the rapid adsorption equilibration rate. Principal component analysis segregated SERS spectral features of tap water and milk samples with different melamine concentrations. Partial least squares regression models correlated melamine concentrations in tap water and skim milk with SERS spectral features. The limit of detection (LOD) and limit of quantification (LOQ) of melamine in tap water were determined as 0.0019 and 0.0064 mmol/L, while the LOD and LOQ were 0.0165 and 0.055 mmol/L for the determination of melamine in skim milk. However, this sensor is not ideal to quantify melamine in tap water and skim milk. By conjugating MIPs with SERS-active substrate (that is, AgNPs), reproducibility of SERS spectral features was increased, resulting in more accurate detection. The time required to determine melamine in tap water and milk were 6 and 25 min, respectively. The low LOD, LOQ, and rapid detection confirm the potential of applying this sensor for accurate and high-throughput detection of melamine in tap water and milk.

  2. Rapid Molecular Fingerprinting of Pathogens

    DTIC Science & Technology

    2006-08-31

    establishing appropriate biotinylation conditions and the availability of sufficient quantities of purified virus for library screening . Additionally...the level of peptide display on the cell surface was found to be lower than desired for optimal library screening . This problem was corrected by...remaining virus sample with the green fluroescent probe Alexa 488. However, Alexa labeling resulted in insufficient fluorescent signals for library

  3. Molecular pharmacognosy: a new borderline discipline.

    PubMed

    Huang, Lu-Qi; Yuan, Yuan; Cui, Guang-Hong; Dai, Zhu-Bo; Xiao, Pei-Gen

    2009-11-01

    Pharmacognosy has developed rapidly in recent years and now represents a highly interdisciplinary science. At the boundary between pharmacognosy and molecular biology, molecular pharmacognosy has developed as a new borderline discipline. Using the method and technology of molecular biology, molecular pharmacognosy focuses on resolving a wide range of challenging problems, such as distinguishing herbal and animal drug populations by molecular marker assay, conserving and utilizing wild resources on the basis of knowledge of genetic diversity, investigating the mechanism of active compound accumulation and obtaining new resources with higher quality through genetic engineering. Recent research results show that molecular pharmacognosy has extended the scope of pharmacognostical science and plays an important role in the safe and efficient usage of crude drugs.

  4. Rational molecular engineering of cyclopentadithiophene-bridged D-A-π-A sensitizers combining high photovoltaic efficiency with rapid dye adsorption

    NASA Astrophysics Data System (ADS)

    Chai, Qipeng; Li, Wenqin; Liu, Jingchuan; Geng, Zhiyuan; Tian, He; Zhu, Wei-Hong

    2015-06-01

    Dye-sensitized solar cell (DSSC) is considered as a feasible route to the clean and renewable energy conversion technique. The commercial application requires further enhancements on photovoltaic efficiency and simplification on the device fabrication. For avoiding the unpreferable trade-off between photocurrent (JSC) and photovoltage (VOC), here we report the molecular engineering and comprehensive photovoltaic characterization of three cyclopentadithiophene-bridged D-A-π-A motif sensitizers with a change in donor group. We make a careful choice on the donor and conjugation bridge for synergistically increasing JSC and VOC. Comparing with the reference dye WS-2, the photovoltaic efficiency with the single component dye of WS-51 increases by 18%, among one of the rare examples in pure metal-free organic dyes exceeding 10% in combination with traditional iodine redox couples. Moreover, WS-51 exhibits several prominent merits on potentially scale-up industrial application: i) facile synthetic route to target molecule, ii) simple dipping procedure without requirement of co-sensitization, and iii) rapid dye adsorption capability.

  5. Rational molecular engineering of cyclopentadithiophene-bridged D-A-π-A sensitizers combining high photovoltaic efficiency with rapid dye adsorption

    PubMed Central

    Chai, Qipeng; Li, Wenqin; Liu, Jingchuan; Geng, Zhiyuan; Tian, He; Zhu, Wei-hong

    2015-01-01

    Dye-sensitized solar cell (DSSC) is considered as a feasible route to the clean and renewable energy conversion technique. The commercial application requires further enhancements on photovoltaic efficiency and simplification on the device fabrication. For avoiding the unpreferable trade-off between photocurrent (JSC) and photovoltage (VOC), here we report the molecular engineering and comprehensive photovoltaic characterization of three cyclopentadithiophene-bridged D-A-π-A motif sensitizers with a change in donor group. We make a careful choice on the donor and conjugation bridge for synergistically increasing JSC and VOC. Comparing with the reference dye WS-2, the photovoltaic efficiency with the single component dye of WS-51 increases by 18%, among one of the rare examples in pure metal-free organic dyes exceeding 10% in combination with traditional iodine redox couples. Moreover, WS-51 exhibits several prominent merits on potentially scale-up industrial application: i) facile synthetic route to target molecule, ii) simple dipping procedure without requirement of co-sensitization, and iii) rapid dye adsorption capability. PMID:26066974

  6. Ionic liquid-mediated molecularly imprinted solid-phase extraction coupled with gas chromatography-electron capture detector for rapid screening of dicofol in vegetables.

    PubMed

    Yan, Hongyuan; Sun, Ning; Han, Yehong; Yang, Chen; Wang, Mingyu; Wu, Ruijun

    2013-09-13

    New ionic liquid-mediated molecularly imprinted polymers (IL-MIPs) were prepared by precipitation polymerization using 1-butyl-3-methylimidazolium hexafluorophosphate (BMIM(+)PF6(-)) as the auxiliary solvent, α-chloro-DDT as the dummy template, and they were successfully applied as the sorbents of solid-phase extraction (SPE) for rapid screening of dicofol from cabbage, tomato, and carrot samples. The IL-MIPs were characterized by FTIR, FE-SEM, static adsorption and chromatographic evaluation, and the results revealed that the IL-MIPs had higher adsorption capacity and selectivity to dicofol in aqueous solution than that of ionic liquid-mediated non-imprinted polymers (IL-NIPs) and non-imprinted polymers (NIPs). Under the optimized conditions, the IL-MIPs-SPE-GC method offered good linearity (0.4-40.0ngg(-1), r(2)=0.9995) and the average recoveries of dicofol at three spiked levels were in a range of 84.6-104.1% (n=3) with RSD≤7.6%. The proposed method obviously improved the selectivity and purification effect, and eliminated the effect of template leakage on dicofol quantitative analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Rational molecular engineering of cyclopentadithiophene-bridged D-A-π-A sensitizers combining high photovoltaic efficiency with rapid dye adsorption.

    PubMed

    Chai, Qipeng; Li, Wenqin; Liu, Jingchuan; Geng, Zhiyuan; Tian, He; Zhu, Wei-Hong

    2015-06-11

    Dye-sensitized solar cell (DSSC) is considered as a feasible route to the clean and renewable energy conversion technique. The commercial application requires further enhancements on photovoltaic efficiency and simplification on the device fabrication. For avoiding the unpreferable trade-off between photocurrent (JSC) and photovoltage (VOC), here we report the molecular engineering and comprehensive photovoltaic characterization of three cyclopentadithiophene-bridged D-A-π-A motif sensitizers with a change in donor group. We make a careful choice on the donor and conjugation bridge for synergistically increasing JSC and VOC. Comparing with the reference dye WS-2, the photovoltaic efficiency with the single component dye of WS-51 increases by 18%, among one of the rare examples in pure metal-free organic dyes exceeding 10% in combination with traditional iodine redox couples. Moreover, WS-51 exhibits several prominent merits on potentially scale-up industrial application: i) facile synthetic route to target molecule, ii) simple dipping procedure without requirement of co-sensitization, and iii) rapid dye adsorption capability.

  8. Development and application of a novel fluorescent nanosensor based on FeSe quantum dots embedded silica molecularly imprinted polymer for the rapid optosensing of cyfluthrin.

    PubMed

    Li, Xunjia; Jiao, Hai-Feng; Shi, Xi-Zhi; Sun, Aili; Wang, Xiujuan; Chai, Jiye; Li, De-Xiang; Chen, Jiong

    2018-01-15

    A novel molecularly imprinted silica layer appended to FeSe quantum dots (MIP-FeSe-QDs) was fabricated and utilized as a recognition element to develop a selective and sensitive fluorescent nanosensor for cyfluthrin (CYF) determination. The MIP-FeSe-QDs were characterized by fluorescence spectrometry, scanning electron microscopy, transmission electron microscopy, and Fourier transform infrared spectroscopy. Excellent selectivity and high sensitivity of MIP-FeSe-QDs to CYF molecules were observed based on the fluorescence quenching of FeSe-QDs. Under optimal conditions, a good linear relationship was found between fluorescence quenching effect and increased CYF concentration within 0.010-0.20mg/L, with a correlation coefficient of 0.9911. The practicality of the developed sensor method for CYF detection in fish and sediment samples was further validated. Good recoveries ranging from 88.0% to 113.9% with<6.8% relative standard deviations were obtained. The detection limits of CYF in sediment and fish samples were 1.3 and 1.0µg/kg, respectively. This study established a novel, rapid fluorescent nanosensor detection method based on MIP-QDs for successfully analyzing CYF in fish and sediment samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Trifunctional molecular beacon-mediated quadratic amplification for highly sensitive and rapid detection of mercury(II) ion with tunable dynamic range.

    PubMed

    Zhao, Yue; Liu, Huaqing; Chen, Feng; Bai, Min; Zhao, Junwu; Zhao, Yongxi

    2016-12-15

    Analyses of target with low abundance or concentration varying over many orders of magnitude are severe challenges faced by numerous assay methods due to their modest sensitivity and limited dynamic range. Here, we introduce a homogeneous and rapid quadratic polynomial amplification strategy through rational design of a trifunctional molecular beacon, which serves as not only a reporter molecule but also a bridge to couple two stage amplification modules without adding any reaction components or process other than basic linear amplification. As a test bed for our studies, we took mercury(II) ion as an example and obtained a high sensitivity with detection limit down to 200 pM within 30min. In order to create a tunable dynamic range, homotropic allostery is employed to modulate the target specific binding. When the number of metal binding site varies from 1 to 3, signal response is programmed accordingly with useful dynamic range spanning 50, 25 and 10 folds, respectively. Furthermore, the applicability of the proposed method in river water and biological samples are successfully verified with good recovery and reproducibility, indicating considerable potential for its practicality in complex real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. A novel molecularly imprinted material based on magnetic halloysite nanotubes for rapid enrichment of 2,4-dichlorophenoxyacetic acid in water.

    PubMed

    Zhong, Shian; Zhou, Chengyun; Zhang, Xiaona; Zhou, Hui; Li, Hui; Zhu, Xiaohong; Wang, Yan

    2014-07-15

    A new type of magnetic halloysite nanotubes molecularly imprinted polymer (MHNTs@MIP) based on halloysite nanotubes (HNTs) with embedded magnetic nanoparticles was introduced in this study. MHNTs@MIP was prepared through surface imprinting technology, using 2,4-dichlorophenoxyacetic acid (2,4-D) as a template, 4-vinylpyridine as the monomer, divinylbenzene as cross-linking agents, and 2,2-azodiisobutyronitrile as initiator. MHNTs@MIP was characterized by Fourier Transform Infrared Spectrometer, transmission electron microscopy, X-ray diffraction, and vibrating sample magnetometer. MHNTs@MIP exhibited rapid and reliable analysis with supermagnetic properties, as well as repeated use and template-specific recognition. The adsorption capacity of magnetic halloysite nanotubes non-imprinted polymer (MHNTs@NIP) and MHNTs@MIP was 10.3mg/g and 35.2mg/g, respectively. In the detailed discussion on specific selectivity, MHNTs@MIP can be applied as an adsorbent for sample pretreatment extraction and obtain high recoveries of about 85-94%. After extraction, high-performance liquid chromatography was used to detect 2,4-D residue in water.

  11. Graphitized Porous Carbon for Rapid Screening of Angiotensin-Converting Enzyme Inhibitory Peptide GAMVVH from Silkworm Pupa Protein and Molecular Insight into Inhibition Mechanism.

    PubMed

    Tao, Mengliang; Sun, Huaju; Liu, Long; Luo, Xuan; Lin, Guoyou; Li, Renbo; Zhao, Zhenxia; Zhao, Zhongxing

    2017-10-04

    A novel hydrophobic hexapeptide with high angiotensin-converting enzyme (ACE) inhibitory activity was screened from silkworm pupa protein (SPP) hydrolysate via graphitized porous carbon and reverse-phase high-performance liquid chromatography methods. Graphitized porous carbon derived from dopamine, possessing high surface area and high graphitic carbon, was used to rapidly screen and enrich hydrophobic peptides from SPP hydrolysate. The ACE inhibition pattern and mechanism of the purified peptide were also systematically studied by the classic Lineweaver-Burk model and by molecular docking/dynamic simulation. The novel hydrophobic hexapeptide was identified as Gly-Ala-Met-Val-Val-His (GAMVVH, IC50 = 19.39 ± 0.21 μM) with good thermal/antidigestive stabilities. Lineweaver-Burk plots revealed that GAMVVH behaved as a competitive ACE inhibitor. It formed hydrogen bonds with S1 and S2 pockets of ACE and established competitive coordination with Zn(II) of ACE. The synergy of hydrogen bonds with active pockets and Zn(II) coordination efficiently changed the three-dimensional structure of ACE and thus inhibited bioactivity of ACE.

  12. Molecular and pedigree analysis applied to conservation of animal genetic resources: the case of Brazilian Somali hair sheep.

    PubMed

    Paiva, Samuel R; Facó, Olivardo; Faria, Danielle A; Lacerda, Thaísa; Barretto, Gabriel B; Carneiro, Paulo L S; Lobo, Raimundo N B; McManus, Concepta

    2011-10-01

    The first registers of Somali sheep in Brazil are from the beginning of the 1900s. This breed, adapted to the dry climate and scarce food supply, is restricted in the northeast region of the country. Molecular marker technologies, especially those based on genotyping microsatellite and mtDNA loci, can be used in conjunction with breeding (pedigree analysis) and consequently the maintenance of genetic variation in herds. Animals from the Brazilian Somali Conservation Nuclei from Embrapa Sheep and Goats in Ceará State were used to validate genetic monitoring by traditional pedigree methods and molecular markers. Nineteen microsatellite markers and 404 base pairs from the control region of mtDNA were used. For total herd diversity, an average 5.32 alleles were found, with expected heterozygosity of 0.5896, observed heterozygosity of 0.6451, 0.4126 for molecular coancestrality, and coefficient of inbreeding (F (IS)) was -0.095. Comparing molecular coancestrality means over the years, there was a consistent increase in this parameter within the herd, increasing from 0.4157 to 0.4769 in 2 years (approx. 12% variation). Sixteen mtDNA haplotypes were identified. Inbreeding and other estimates from genealogical analyses confirm the results from molecular markers. From these results, it is possible to state that microsatellites are useful tools in genetic management of herds, especially when routine herd recording is not carried out, or there were gaps in recent generations. As well as pedigree control, genetic diversity can be optimized. Based on the results, and despite herd recording in the herd of Brazilian Somali of Embrapa Sheep and Goats, additional management measures need to be carried out in this herd to reduce inbreeding and optimize genetic variation.

  13. Molecular genomics resource for the parasitic nematode Spirocerca lupi: Identification of 149 microsatellite loci using FIASCO and next generation sequencing.

    PubMed

    Reid, Kerry; Mitha, Janishtha R; Greeff, Jaco M; de Waal, Pamela J

    2015-01-01

    Understanding genetic diversity and movement patterns in parasitic organisms is paramount to establish control and management strategies. In this study we developed a microsatellite resource as well as a diagnostic multiplex for the cosmopolitan parasitic nematode Spirocerca lupi, known to cause spirocercosis in canids. A combination of microsatellite enrichment and 454 sequencing was used to identify 149 unique microsatellite loci in S. lupi. Twenty loci were characterized further in two sampling sites in South Africa, with 10 loci identified as polymorphic (allele ranges from 4 to 17). These loci were designed into a single diagnostic multiplex suitable for species identification and population genetics studies. The markers were also successful in cross-species amplification in Cylicospirura felineus, Philonema oncorhynchi and Gongylonema pulchrum. Our resource provides a large set of candidate loci for a number of nematode studies as well as loci suitable for diversity and population genetics studies of S. lupi within the South African context as well as globally.

  14. The Resilience Activation Framework: A conceptual model of how access to social resources promotes adaptation and rapid recovery in post-disaster settings

    PubMed Central

    Abramson, David M.; Grattan, Lynn M.; Mayer, Brian; Colten, Craig E.; Arosemena, Farah A.; Rung, Ariane; Lichtveld, Maureen

    2014-01-01

    A number of governmental agencies have called for enhancing citizen’s resilience as a means of preparing populations in advance of disasters, and as a counter-balance to social and individual vulnerabilities. This increasing scholarly, policy and programmatic interest in promoting individual and communal resilience presents a challenge to the research and practice communities: to develop a translational framework that can accommodate multi-disciplinary scientific perspectives into a single, applied model. The Resilience Activation Framework provides a basis for testing how access to social resources, such as formal and informal social support and help, promotes positive adaptation or reduced psychopathology among individuals and communities exposed to the acute collective stressors associated with disasters, whether manmade, natural, or technological in origin. Articulating the mechanisms by which access to social resources activate and sustain resilience capacities for optimal mental health outcomes post-disaster can lead to the development of effective preventive and early intervention programs. PMID:24870399

  15. The resilience activation framework: a conceptual model of how access to social resources promotes adaptation and rapid recovery in post-disaster settings.

    PubMed

    Abramson, David M; Grattan, Lynn M; Mayer, Brian; Colten, Craig E; Arosemena, Farah A; Bedimo-Rung, Ariane; Lichtveld, Maureen

    2015-01-01

    A number of governmental agencies have called for enhancing citizens' resilience as a means of preparing populations in advance of disasters, and as a counterbalance to social and individual vulnerabilities. This increasing scholarly, policy, and programmatic interest in promoting individual and communal resilience presents a challenge to the research and practice communities: to develop a translational framework that can accommodate multidisciplinary scientific perspectives into a single, applied model. The Resilience Activation Framework provides a basis for testing how access to social resources, such as formal and informal social support and help, promotes positive adaptation or reduced psychopathology among individuals and communities exposed to the acute collective stressors associated with disasters, whether human-made, natural, or technological in origin. Articulating the mechanisms by which access to social resources activate and sustain resilience capacities for optimal mental health outcomes post-disaster can lead to the development of effective preventive and early intervention programs.

  16. Indirect rapid prototyping of sol-gel hybrid glass scaffolds for bone regeneration - Effects of organic crosslinker valence, content and molecular weight on mechanical properties.

    PubMed

    Hendrikx, Stephan; Kascholke, Christian; Flath, Tobias; Schumann, Dirk; Gressenbuch, Mathias; Schulze, F Peter; Hacker, Michael C; Schulz-Siegmund, Michaela

    2016-04-15

    We present a series of organic/inorganic hybrid sol-gel derived glasses, made from a tetraethoxysilane-derived silica sol (100% SiO2) and oligovalent organic crosslinkers functionalized with 3-isocyanatopropyltriethoxysilane. The material was susceptible to heat sterilization. The hybrids were processed into pore-interconnected scaffolds by an indirect rapid prototyping method, described here for the first time for sol-gel glass materials. A large panel of polyethylene oxide-derived 2- to 4-armed crosslinkers of molecular weights ranging between 170 and 8000Da were incorporated and their effect on scaffold mechanical properties was investigated. By multiple linear regression, 'organic content' and the 'content of ethylene oxide units in the hybrid' were identified as the main factors that determined compressive strength and modulus, respectively. In general, 3- and 4-armed crosslinkers performed better than linear molecules. Compression tests and cell culture experiments with osteoblast-like SaOS-2 cells showed that macroporous scaffolds can be produced with compressive strengths of up to 33±2MPa and with a pore structure that allows cells to grow deep into the scaffolds and form mineral deposits. Compressive moduli between 27±7MPa and 568±98MPa were obtained depending on the hybrid composition and problems associated with the inherent brittleness of sol-gel glass materials could be overcome. SaOS-2 cells showed cytocompatibility on hybrid glass scaffolds and mineral accumulation started as early as day 7. On day 14, we also found mineral accumulation on control hybrid glass scaffolds without cells, indicating a positive effect of the hybrid glass on mineral accumulation. We produced a hybrid sol-gel glass material with significantly improved mechanical properties towards an application in bone regeneration and processed the material into macroporous scaffolds of controlled architecture by indirect rapid prototyping. We were able to produce macroporous materials

  17. Development of a reverse transcription-loop-mediated isothermal amplification assay for detection of pandemic (H1N1) 2009 virus as a novel molecular method for diagnosis of pandemic influenza in resource-limited settings.

    PubMed

    Kubo, Toru; Agoh, Masanobu; Mai, Le Q; Fukushima, Kiyoyasu; Nishimura, Hidekazu; Yamaguchi, Akinori; Hirano, Manabu; Yoshikawa, Akira; Hasebe, Futoshi; Kohno, Shigeru; Morita, Kouichi

    2010-03-01

    This paper reports on the development of a one-step, real-time reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the hemagglutinin (HA) gene for the rapid molecular-based detection of pandemic (H1N1) 2009 virus. The detection limit of the pandemic (H1N1) 2009 virus HA-specific RT-LAMP assay was same as that of the currently used real-time reverse transcription-PCR method. The assay detected the pandemic (H1N1) 2009 virus HA gene in 136 RNA samples extracted from nasopharyngeal swab specimens from Japanese and Vietnamese patients. No cross-reactive amplification with the RNA of other seasonal influenza viruses was observed, and the detection of specific viral genome targets in clinical specimens was achieved in less than 40 min. The sensitivity and specificity of the pandemic (H1N1) 2009 virus HA-specific RT-LAMP assay obtained in this study were 97.8% and 100%, respectively. Use of the (H1N1) 2009 virus HA-specific RT-LAMP assay will enable the faster and easier diagnosis of pandemic (H1N1) 2009 virus infection, especially in resource-limited situations in developing countries.

  18. Development of a Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Detection of Pandemic (H1N1) 2009 Virus as a Novel Molecular Method for Diagnosis of Pandemic Influenza in Resource-Limited Settings▿

    PubMed Central

    Kubo, Toru; Agoh, Masanobu; Mai, Le Q.; Fukushima, Kiyoyasu; Nishimura, Hidekazu; Yamaguchi, Akinori; Hirano, Manabu; Yoshikawa, Akira; Hasebe, Futoshi; Kohno, Shigeru; Morita, Kouichi

    2010-01-01

    This paper reports on the development of a one-step, real-time reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the hemagglutinin (HA) gene for the rapid molecular-based detection of pandemic (H1N1) 2009 virus. The detection limit of the pandemic (H1N1) 2009 virus HA-specific RT-LAMP assay was same as that of the currently used real-time reverse transcription-PCR method. The assay detected the pandemic (H1N1) 2009 virus HA gene in 136 RNA samples extracted from nasopharyngeal swab specimens from Japanese and Vietnamese patients. No cross-reactive amplification with the RNA of other seasonal influenza viruses was observed, and the detection of specific viral genome targets in clinical specimens was achieved in less than 40 min. The sensitivity and specificity of the pandemic (H1N1) 2009 virus HA-specific RT-LAMP assay obtained in this study were 97.8% and 100%, respectively. Use of the (H1N1) 2009 virus HA-specific RT-LAMP assay will enable the faster and easier diagnosis of pandemic (H1N1) 2009 virus infection, especially in resource-limited situations in developing countries. PMID:20071551

  19. Molecular 14-C analyses on lipid biomarkers in the water column and surface sediments reveal rapid aging of remobilized terrestrial organic carbon in a sub-Arctic basin

    NASA Astrophysics Data System (ADS)

    Vonk, J.; Gustafsson, Ö.; van Dongen, B.

    2009-04-01

    Riverine export of terrestrial organic carbon (terrOC) plays an important role in the global carbon cycle. Molecular composition, phase associations, transport and remineralization processes determine the fate of terrOC in the world's shelf areas, thereby potentially influencing climate through various carbon-climate feedback links. The vast sub-Arctic and Arctic terrestrial carbon pools, freeze-locked in northern peatlands, could be of particular interest in a warming climate scenario. The Kalix River, flowing into the Bothnian Bay in the northernmost Baltic Sea is one of Europe's largest unregulated rivers, draining sub-Arctic peatland prone to climate-warming effects. The Kalix is believed to resemble the great western Siberian-Arctic rivers that are far less accessible but draining similar, still partly frozen, high carbon content areas. Here we present compound-specific radiocarbon analysis (CSRA) on terrestrial lipid biomarkers in surface water particulate OC (POC) from the Kalix - Bothnian Bay system. In combination with bulk 14-C and CSRA on surface sediments from the same off-river transect this shows (1) a rapid apparent aging of long-chain n-alkanoic acids from water column to surface sediments and (2) long-chain n-alkane 14-C ages in surface sediments that are similar and even older than catchment peat basal ages. This combines with mass balance modelling results for this system to suggest a higher reactivity of remobilized recalcitrant terrOC than previously thought. We hypothesize that the terrOC is released from two different pools. Soil surface layers release humic-rich, easily degrading OC that mostly stays in suspension whereas OC that is coated to heavier mineral particles from deeper soil layers degrades slower and settles faster. Fraction modern 14-C signals in the range 0.18 - 0.47 of presumably mineral-bound terrestrial OC in surface sediments may indicate ongoing remobilization of ancient carbon reservoirs.

  20. Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources.

    PubMed

    Boettcher, P J; Tixier-Boichard, M; Toro, M A; Simianer, H; Eding, H; Gandini, G; Joost, S; Garcia, D; Colli, L; Ajmone-Marsan, P

    2010-05-01

    The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.

  1. Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits.

    PubMed

    Mangin, Brigitte; Pouilly, Nicolas; Boniface, Marie-Claude; Langlade, Nicolas B; Vincourt, Patrick; Vear, Felicity; Muños, Stéphane

    2017-06-01

    SNP genotyping of 114 cultivated sunflower populations showed that the multiplication process and the main traits selected during breeding of sunflower cultivars drove molecular diversity of the populations. The molecular diversity in a set of 114 cultivated sunflower populations was studied by single-nucleotide polymorphism genotyping. These populations were chosen as representative of the 400 entries in the INRA collection received or developed between 1962 and 2011 and made up of land races, open-pollinated varieties, and breeding pools. Mean allele number varied from 1.07 to 1.90. Intra-population variability was slightly reduced according to the number of multiplications since entry but some entries were probably largely homozygous when received. A principal component analysis was used to study inter-population variability. The first 3 axes accounted for 17% of total intra-population variability. The first axis was significantly correlated with seed oil content, more closely than just the distinction between oil and confectionary types. The second axis was related to the presence or absence of restorer genes and the third axis to flowering date and possibly to adaptation to different climates. Our results provide arguments highlighting the effect of the maintenance process on the within population genetic variability as well as on the impact of breeding for major agronomic traits on the between population variability of the collection. Propositions are made to improve sunflower population maintenance procedures to keep maximum genetic variability for future breeding.

  2. Water resources

    NASA Technical Reports Server (NTRS)

    Salomonson, V. V.; Rango, A.

    1973-01-01

    The application of ERTS-1 imagery to the conservation and control of water resources is discussed. The effects of exisiting geology and land use in the water shed area on the hydrologic cycle and the general characteristics of runoff are described. The effects of floods, snowcover, and glaciers are analyzed. The use of ERTS-1 imagery to map surface water and wetland areas to provide rapid inventorying over large regions of water bodies is reported.

  3. Rapid Direct Testing of Susceptibility of Mycobacterium tuberculosis to Isoniazid and Rifampin on Nutrient and Blood Agar in Resource-Starved Settings

    PubMed Central

    Ikram, Aamer; Coban, Ahmet Yilmaz; Martin, Anandi

    2012-01-01

    In this study, we evaluated the performance of blood agar (by macroscopic growth) and nutrient agar (by a microcolony detection method) for drug susceptibility testing of Mycobacterium tuberculosis against rifampin (RIF) and isoniazid (INH), using 67 smear-positive sputum specimens. The direct proportion method on Lowenstein-Jensen (LJ) medium was used as the “gold standard.” Compared with LJ medium, results for both media were in 100% agreement for RIF, while for INH the agreement levels for blood agar and nutrient agar were 98% and 95%, respectively. Within 2 weeks, 100% of specimens yielded results on blood agar, while 96.8% of specimens yielded results on nutrient agar. Our study showed that blood agar and nutrient agar can be used as alternative media for direct susceptibility testing of RIF and INH, especially in resource-poor settings. PMID:22357498

  4. HPV genotyping linear assay test comparison in cervical cancer patients: implications for HPV prevalence and molecular epidemiology in a limited-resource area in Bandung, Indonesia.

    PubMed

    Panigoro, Ramdan; Susanto, Herman; Novel, Sinta Sasika; Hartini, Sri; Sahiratmadja, Edhyana

    2013-01-01

    Persistent infection with high risk human papillomavirus (hrHPV) is strongly associated with cervical cancer. Normal cervical cells may also harbor hrHPV, and detection of early hrHPV infection may minimize risk of cervical cancer development. This study aimed to compare two commercial HPV genotyping assays that may affordable for early screening in a limited-resource setting in Bandung, Indonesia. DNA from cervical biopsies with histologically confirmed as squamous cell cervical cacinoma were HPV genotyped by Linear Assay 1 (Roche Diagnostics, Mannheim, Germany) or Linear Assay 2 (Digene HPV Genotyping RH Test, Qiagen Gaithersburg, MD). In a subset of samples of each group, HPV genotype results were then compared. Of 28 samples genotyped by linear assay 1, 22 (78.6%) demonstrated multiple infections with HPV-16 and other hrHPV types 18, 45 and/or 52. In another set of 38 samples genotyped by linear assay 2, 28 (68.4%) were mostly single infections by hrHPV type 16 or 18. Interestingly, 4 samples that had been tested by both kits showed discordant results. In a limited-resource area such as in Indonesia, country with a high prevalence of HPV infection a reliable cervical screening test in general population for early hrHPV detection is needed. Geographical variation in HPV genotyping result might have impacts for HPV prevalence and molecular epidemiology as the distribution in HPV genotypes should give clear information to assess the impact of HPV prophylactic vaccines.

  5. Fresh-frozen, optimal cutting temperature (OCT) compound-embedded bone marrow aspirates: a reliable resource for morphological, immunohistochemical and molecular examinations.

    PubMed

    Lim, J; Kim, Y; Lee, W; Kim, M; Lee, E J; Kang, C S; Han, K

    2010-02-01

    The usefulness of fresh-frozen, optimal cutting temperature (OCT) compound-embedded (FFOE) bone marrow (BM) aspirates was evaluated as a reliable resource for morphological, immunohistochemical and molecular examinations. One hundred BM aspirates were collected in polypropylene tubes and immediately frozen for 2 h in a deep freezer. Frozen BM was transferred to a cryomold filled with OCT compound and the prepared samples were stored in a deep freezer. Histological examination and immunohistochemical staining, polymerase chain reaction (PCR), sequencing and reverse transcription (RT)-PCR were performed to evaluate the quality of the FFOE BM sections in 10% of randomly selected samples. FFOE BM sections revealed better morphologies than paraffin-embedded clot sections in haematoxylin and eosin staining because mature erythrocytes were removed during the staining process in frozen BM sections. Immunohistochemical staining for CD34 revealed excellent staining quality and oil red O staining showed that fat vacuoles in cells were well preserved. The quality of genomic DNA in FFOE BM sections was suitable for obtaining about 2000 bp PCR product for the human leucocyte antigen-A locus followed by direct sequencing of the sample, and the quality of total RNA was suitable for detection of BCR-ABL fusion transcript. FFOE BM aspirates are a reliable resource for various laboratory tests of diagnostic and research arenas.

  6. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

    PubMed Central

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-01-01

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program. PMID:26540077

  7. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement.

    PubMed

    Kim, Tae-Sung; Raveendar, Sebastin; Suresh, Sundan; Lee, Gi-An; Lee, Jung-Ro; Cho, Joon-Hyeong; Lee, Sok-Young; Ma, Kyung-Ho; Cho, Gyu-Taek; Chung, Jong-Wook

    2015-11-02

    The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.

  8. Non-instrumented nucleic acid amplification (NINA): instrument-free molecular malaria diagnostics for low-resource settings.

    PubMed

    Labarre, Paul; Gerlach, Jay; Wilmoth, Jared; Beddoe, Andrew; Singleton, Jered; Weigl, Bernhard

    2010-01-01

    We have achieved the first complete, non-instrumented nucleic acid amplification test (NAAT) using a calcium oxide heat source thermally linked to an engineered phase change material. These two components alone maintain a thermal profile suitable for the loop-mediated isothermal amplification assay. Starting with computational fluid dynamics analysis, we identified nominal geometry for the exothermic reaction chamber, phase change material chamber, thermal insulation, and packaging. Using this model, we designed and fabricated an alpha prototype assay platform. We have verified the function of this multi-pathogen-capable platform with both fluorescent and visual turbidity indications using samples spiked with malaria DNA. Both the exothermically heated platform samples and samples heated on a Perkin-Elmer GeneAmp9600 thermocycler were first incubated at 62°C for 45 minutes, then heated to 95°C to terminate enzyme activity, then analyzed. Results from the exothermically heated, non-instrumented platform were comparable to those from the thermocycler. These developments will enable point-of-care diagnostics using accurate NAATs which until now have required a well-equipped laboratory. The aim of this research is to provide pathogen detection with NAAT-level sensitivity in low-resource settings where assays such as immunochromatographic strip tests are successfully used but where there is no access to the infrastructure and logistics required to operate and maintain instrument-based diagnostics.

  9. The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center: a unique resource for defining the "molecular histology" of the breast.

    PubMed

    Sherman, Mark E; Figueroa, Jonine D; Henry, Jill E; Clare, Susan E; Rufenbarger, Connie; Storniolo, Anna Maria

    2012-04-01

    "Molecular histology" of the breast may be conceptualized as encompassing the normative ranges of histologic structure and marker expression in normal breast tissues in relation to a woman's age and life experiences. Studies of molecular histology can aid our understanding of early events in breast carcinogenesis and provide data for comparison with diseased breast tissues. Until recently, lack of epidemiologically annotated, optimally prepared normal breast tissues obtained from healthy women presented a barrier to breast cancer research. The Komen Tissue Bank at Indiana University (Indianapolis, IN) is a unique biorepository that was developed to overcome this limitation. The Bank enrolls healthy donors who provide questionnaire data, blood, and up to four breast biopsies, which are prepared as both formalin-fixed, paraffin-embedded and frozen tissues. The resource is accessible to researchers worldwide through a proposal submission, review, and approval process. As of November 2010, the Bank had collected specimens and information from 1,174 donors. In this review, we discuss the importance of studying normal breast tissues, assess the strengths and limitations of studying normal tissues obtained from different sources, and summarize the features of the Komen Tissue Bank. As research projects are completed, results will be posted on the Bank's website. 2012 AACR

  10. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    PubMed Central

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  11. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

    PubMed

    Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

    2011-08-10

    Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation

  12. Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings

    PubMed Central

    Debes, Amanda K.; Ateudjieu, Jerome; Guenou, Etiene; Lopez, Anna Lena; Bugayong, Mark Philip; Retiban, Pearl Joy; Garrine, Marcelino; Mandomando, Inacio; Li, Shan; Stine, O. Colin; Sack, David A.

    2016-01-01

    Background Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving this understanding is not only the lack of regular cholera disease surveillance, but also the lack of laboratory capabilities in endemic countries to preserve, store and ship isolates in a timely manner. We evaluated the use of simplified sample preservation methods for molecular characterization using multi-locus variable-number tandem-repeat analysis (MLVA) for differentiation of Vibrio cholerae genotypes. Methods and Findings Forty-seven V. cholerae isolates and 18 enriched clinical specimens (e.g. stool specimens after enrichment in broth) from cholera outbreaks in Cameroon were preserved on Whatman filter paper for DNA extraction. The samples were collected from two geographically distinct outbreaks in the Far North of Cameroon (FNC) in June 2014 and October 2014. In addition, a convenience sample of 14 isolates from the Philippines and 8 from Mozambique were analyzed. All 87 DNAs were successfully analyzed including 16 paired samples, one a cultured isolate and the other the enriched specimen from which the isolate was collected. Genotypic results were identical between 15 enriched specimens and their culture isolates and the other pair differed at single locus. Two closely related, but distinct clonal complexes were identified among the Cameroonian specimens from 2014. Conclusions Collecting V. cholerae using simplified laboratory methods in remote and low-resource settings allows for subsequent advanced molecular characterization of V. cholerae O1. These simplified DNA preservation methods identify V. cholerae and make possible timely information regarding the genetic diversity of V. cholerae; our results set the stage for continued molecular

  13. Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings.

    PubMed

    Debes, Amanda K; Ateudjieu, Jerome; Guenou, Etienne; Guenou, Etiene; Lopez, Anna Lena; Bugayong, Mark Philip; Retiban, Pearl Joy; Garrine, Marcelino; Mandomando, Inacio; Li, Shan; Stine, O Colin; Sack, David A

    2016-01-01

    Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving this understanding is not only the lack of regular cholera disease surveillance, but also the lack of laboratory capabilities in endemic countries to preserve, store and ship isolates in a timely manner. We evaluated the use of simplified sample preservation methods for molecular characterization using multi-locus variable-number tandem-repeat analysis (MLVA) for differentiation of Vibrio cholerae genotypes. Forty-seven V. cholerae isolates and 18 enriched clinical specimens (e.g. stool specimens after enrichment in broth) from cholera outbreaks in Cameroon were preserved on Whatman filter paper for DNA extraction. The samples were collected from two geographically distinct outbreaks in the Far North of Cameroon (FNC) in June 2014 and October 2014. In addition, a convenience sample of 14 isolates from the Philippines and 8 from Mozambique were analyzed. All 87 DNAs were successfully analyzed including 16 paired samples, one a cultured isolate and the other the enriched specimen from which the isolate was collected. Genotypic results were identical between 15 enriched specimens and their culture isolates and the other pair differed at single locus. Two closely related, but distinct clonal complexes were identified among the Cameroonian specimens from 2014. Collecting V. cholerae using simplified laboratory methods in remote and low-resource settings allows for subsequent advanced molecular characterization of V. cholerae O1. These simplified DNA preservation methods identify V. cholerae and make possible timely information regarding the genetic diversity of V. cholerae; our results set the stage for continued molecular epidemiological research to better understand the

  14. Psychrobacter arcticus 273-4 Uses Resource Efficiency and Molecular Motion Adaptations for Subzero Temperature Growth▿ †

    PubMed Central

    Bergholz, Peter W.; Bakermans , Corien; Tiedje, James M.

    2009-01-01

    Permafrost soils are extreme environments that exert low-temperature, desiccation, and starvation stress on bacteria over thousands to millions of years. To understand how Psychrobacter arcticus 273-4 survived for >20,000 years in permafrost, transcriptome analysis was performed during growth at 22°C, 17°C, 0°C, and −6°C using a mixed-effects analysis of variance model. Genes for transcription, translation, energy production, and most biosynthetic pathways were downregulated at low temperatures. Evidence of isozyme exchange was detected over temperature for d-alanyl-d-alanine carboxypeptidases (dac1 and dac2), DEAD-box RNA helicases (csdA and Psyc_0943), and energy-efficient substrate incorporation pathways for ammonium and acetate. Specific functions were compensated by upregulation of genes at low temperature, including genes for the biosynthesis of proline, tryptophan, and methionine. RNases and peptidases were generally upregulated at low temperatures. Changes in energy metabolism, amino acid metabolism, and RNase gene expression were consistent with induction of a resource efficiency response. In contrast to results observed for other psychrophiles and mesophiles, only clpB and hsp33 were upregulated at low temperature, and there was no upregulation of other chaperones and peptidyl-prolyl isomerases. relA, csdA, and dac2 knockout mutants grew more slowly at low temperature, but a dac1 mutant grew more slowly at 17°C. The combined data suggest that the basal biological machinery, including translation, transcription, and energy metabolism, is well adapted to function across the growth range of P. arcticus from −6°C to 22°C, and temperature compensation by gene expression was employed to address specific challenges to low-temperature growth. PMID:19168616

  15. Optimizing end-to-end system performance for millimeter and submillimeter spectroscopy of protostars : wideband heterodyne receivers and sideband-deconvolution techniques for rapid molecular-line surveys

    NASA Astrophysics Data System (ADS)

    Sumner, Matthew Casey

    This thesis describes the construction, integration, and use of a new 230-GHz ultra-wideband heterodyne receiver, as well as the development and testing of a new sideband-deconvolution algorithm, both designed to enable rapid, sensitive molecular-line surveys. The 230-GHz receiver, known as Z-Rex, is the first of a new generation of wideband receivers to be installed at the Caltech Submillimeter Observatory (CSO). Intended as a proof-of-concept device, it boasts an ultra-wide IF output range of sim 6 - 18 GHz, offering as much as a twelvefold increase in the spectral coverage that can be achieved with a single LO setting. A similarly wideband IF system has been designed to couple this receiver to an array of WASP2 spectrometers, allowing the full bandwidth of the receiver to be observed at low resolution, ideal for extra-galactic redshift surveys. A separate IF system feeds a high-resolution 4-GHz AOS array frequently used for performing unbiased line surveys of galactic objects, particularly star-forming regions. The design and construction of the wideband IF system are presented, as is the work done to integrate the receiver and the high-resolution spectrometers into a working system. The receiver is currently installed at the CSO where it is available for astronomers' use. In addition to demonstrating wideband design principles, the receiver also serves as a testbed for a synthesizer-driven, active LO chain that is under consideration for future receiver designs. Several lessons have been learned, including the importance of driving the final amplifier of the LO chain into saturation and the absolute necessity of including a high-Q filter to remove spurious signals from the synthesizer output. The on-telescope performance of the synthesizer-driven LO chain is compared to that of the Gunn-oscillator units currently in use at the CSO. Although the frequency agility of the synthesized LO chain gives it a significant advantage for unbiased line surveys, the cleaner

  16. A Simple, Inexpensive Device for Nucleic Acid Amplification without Electricity—Toward Instrument-Free Molecular Diagnostics in Low-Resource Settings

    PubMed Central

    LaBarre, Paul; Hawkins, Kenneth R.; Gerlach, Jay; Wilmoth, Jared; Beddoe, Andrew; Singleton, Jered; Boyle, David; Weigl, Bernhard

    2011-01-01

    Background Molecular assays targeted to nucleic acid (NA) markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS) where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR) instrumentation (another is sample preparation). Methodology/Principal Findings In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented. Conclusions/Significance We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA) heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes. PMID:21573065

  17. Occurrence and molecular characterization of free-living amoeba species (Acanthamoeba, Hartmannella, and Saccamoeba limax) in various surface water resources of Iran.

    PubMed

    Mahmoudi, Mohammad Reza; Rahmati, Behnaz; Seyedpour, Seyed Hosssen; Karanis, Panagiotis

    2015-12-01

    This study was conducted to determine the presence and molecular identity of Acanthamoeba species in the surface water resources of four provinces in Iran, namely Guilan, Mazandaran (North of Iran), Alborz, and Tehran (capital city), using culture- and molecular-based methods. During March to November 2014, 49 surface water samples were collected from environmental water sources-the distinct surface waters of Guilan, Mazandaran, Alborz, and Tehran provinces, in Iran. For the isolation of Acanthamoeba species, approximately 500 ml of the water samples were filtered through a cellulose nitrate membrane with a pore size of 0.45 μ. The filter was transferred onto non-nutrient agar plates seeded with Gram-negative bacteria (Escherichia coli) as a food source. The presence of Acanthamoeba was confirmed by the genus-specific primer pair JDP1 and 2, and/or NA primers were used to identify Acanthamoeba and certain other free-living amoebae. In total, 38 out of 49 samples were positive by culture and/or PCR for Acanthamoeba and other free-living amoebae from all three provinces. By sequencing the positive isolates, the strains were shown to belong to Acanthamoeba (16 isolates belonged to T4 and 2 isolates belonged to T5), Hartmannella vermiformis (3/24), and Saccamoeba limax (2/24). The T4 and T5 genotypes were detected in Guilan and Mazandaran provinces. Two isolates from Guilan and Tehran provinces belonged to S. limax, and H. vermiformis was detected in Guilan province. The results of this study highlight the need to pay more attention to free-living amoebae, as human activity was observed in all of the localities from which these samples were taken. These surface waters can be potential sources for the distribution and transmission of pathogenic Acanthamoeba in the study areas, and free-living amoebas (FLA) (particularly the Acanthamoeba species) can serve as hosts for and vehicles of various microorganisms.

  18. A study of the efficacy and cost-effectiveness of MRSA screening and monitoring on surgical wards using a new, rapid molecular test (EMMS)

    PubMed Central

    Hardy, Katherine J; Szczepura, Ala; Davies, Ruth; Bradbury, Andrew; Stallard, Nigel; Gossain, Savita; Walley, Paul; Hawkey, Peter M

    2007-01-01

    Background MRSA is a significant contributor to prolonged hospital stay, poor clinical outcome and increased healthcare costs amongst surgical patients. A PCR test has been developed for rapid detection of MRSA in nasal swabs. The aims of this study are (1) to estimate the effectiveness of screening using this rapid PCR tests vs culture in reducing MRSA cross-infection rates; (2) to compare the cost of each testing strategy, including subsequent health care costs; and (3) to model different policies for the early identification and control of MRSA infection in surgical patients. Methods/Design The study is a prospective two-period cross-over study set in 7 surgical wards covering different surgical specialities. A total of 10,000 patients > 18 years will be tested over 16 months. The only difference between the two study periods is the method used for the detection of MRSA in each ward (rapid v conventional culture), with all other infection control practices remaining consistent between the arms. The study has been designed to complement routine practice in the NHS. Outcomes are MRSA cross-infection rates (primary outcome) and need for antibiotic therapy and MRSA-related morbidity. Parallel economic and modelling studies are being conducted to aid in the interpretation of the results and to evaluate the cost-effectiveness of the rapid PCR screening strategy. Discussion This paper highlights the design, methods and operational aspects of a study evaluating rapid MRSA screening in the surgical ward setting. PMID:17915008

  19. Molecular pharmacognosy.

    PubMed

    Huang, LuQi; Xiao, PeiGen; Guo, LanPing; Gao, WenYuan

    2010-06-01

    This article analyzes the background and significance of molecular pharmacognosy, including the molecular identification of medicinal raw materials, phylogenetic evolution of medicinal plants and animals, evaluation and preservation of germplasm resources for medicinal plants and animals, etiology of endangerment and protection of endangered medicinal plants and animals, biosynthesis and bioregulation of active components in medicinal plants, and characteristics and the molecular bases of top-geoherbs.

  20. Isolation and molecular characterization of potentially pathogenic Acanthamoeba genotypes from diverse water resources including household drinking water from Khyber Pakhtunkhwa, Pakistan.

    PubMed

    Tanveer, Tania; Hameed, Abdul; Muazzam, Ambreen Gul; Jung, Suk-Yul; Gul, Asma; Matin, Abdul

    2013-08-01

    Acanthamoeba, an opportunistic protozoan pathogen, is ubiquitous in nature, and therefore plays a predatory role and helps control microbial communities in the ecosystem. These Acanthamoeba species are recognized as opportunistic human pathogens that may cause blinding keratitis and rare but fatal granulomatous encephalitis. To date, there is not a single report demonstrating Acanthamoeba isolation and identification from environmental sources in Pakistan, and that is the aim of this study. Acanthamoeba were identified by morphological characteristics of their cysts on non-nutrient agar plates seeded with Escherichia coli. Additionally, the polymerase chain reaction (PCR) was performed with genus-specific primers followed by direct sequencing of the PCR product for molecular identification. Furthermore, our PCR and sequencing results confirmed seven different pathogenic and nonpathogenic genotypes, including T2-T10, T4, T5, T7, T15, T16, and T17. To the best of our knowledge, we have identified and isolated Acanthamoeba sp., for the first time, from water resources of Khyber Pakhtunkhwa, Pakistan. There is an urgent need to address (1) the pathogenic potential of the identified genotypes and (2) explore other environmental sources from the country to examine the water quality and the current status of Acanthamoeba species in Pakistan, which may be a potential threat for public health across the country.

  1. A rapid method for preparation of nucleic acid extracts from potato psyllids for detection of 'Candidatus Liberibacter solancearum' and molecular analysis

    USDA-ARS?s Scientific Manuscript database

    A rapid method has been developed and validated for PCR analysis of potato psyllids for Candidatus Liberibacter solanacearum (Lso), the causal agent of zebra chip disease of potatoes. The method is also suitable for PCR amplification and high resolution melting analysis of the cytochrome oxidase I ...

  2. Molecular Identification of Helicoverpa armigera (Lepidoptera: Noctuidae: Heliothinae) in Argentina and Development of a Novel PCR-RFLP Method for its Rapid Differentiation From H. zea and H. gelotopoeon.

    PubMed

    Arneodo, Joel D; Balbi, Emilia I; Flores, Fernando M; Sciocco-Cap, Alicia

    2015-12-01

    Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae: Heliothinae) is among the most voracious global pests of agriculture. Adults of this species were identified recently in northern Argentina by dissection of male genitalia. In this work, a rapid and simple molecular tool was designed to distinguish H. armigera from the morphologically similar indigenous bollworms Helicoverpa zea (Boddie) and Helicoverpa gelotopoeon (Dyar), regardless of the life stage. Amplification of partial COI gene with a new primer pair, and subsequent digestion with endonuclease HinfI, yielded different RFLP profiles for the three main Helicoverpa pests currently present in South America. The method was validated in Helicoverpa specimens collected across Argentina, whose identity was further corroborated by COI sequencing and phylogenetic analysis. The data reported here constitute the first molecular confirmation of this pest in the country. The survey revealed the occurrence of H. armigera in northern and central Argentina, including the main soybean- and maize-producing area.

  3. Rapid reduction of BCR-ABL1 transcript predicts deep molecular response in dasatinib-treated chronic-phase chronic myeloid leukaemia patients.

    PubMed

    Murai, Kazunori; Yamaguchi, Kohei; Ito, Shigeki; Miyagishima, Takuto; Shindo, Motohiro; Wakasa, Kentaro; Inomata, Mitsue; Nagashima, Takahiro; Kondo, Takeshi; Fujimoto, Nozomu; Yamamoto, Satoshi; Yonezumi, Masakatsu; Oyake, Tatsuo; Shugo, Kowata; Tsukushi, Yasuhiko; Mine, Takahiro; Meguro, Kuniaki; Ikeda, Kazuhiko; Watanabe, Reiko; Saito, Souichi; Sato, Shinji; Tajima, Katsushi; Chou, Takaaki; Kubo, Kohmei; Oba, Koji; Sakamoto, Junichi; Ishida, Yoji

    2017-09-12

    We conducted a phase-II study to evaluate the efficacy and safety of dasatinib in patients newly diagnosed with chronic-phase chronic myeloid leukaemia (CML-CP) in Japan (IMIDAS PART 2 study). Seventy-nine patients were administered 100 mg dasatinib once daily. We examined pre-treatment and post-treatment influences of various factors. The BCR-ABL1 international scale (IS), halving time (HT), and reduction rate of BCR-ABL1 transcript within the initial 1 or 3 months of therapy (RR-BCR-ABL11m,3m ) were the post-treatment factors investigated to predict the molecular response. The estimated major molecular response (MMR), molecular response 4.0 (MR4.0), and molecular response 4.5 (MR4.5) rates were 77.2%, 49.4%, and 35.4%, respectively, at 12 months. Grade 3/4 non-haematologic adverse events were infrequent. Multivariate analysis showed that age >65 years was significantly correlated with MR4.0 and MR4.5 (deep molecular response: DMR) at 12 months. All post-treatment factors at 3 months predicted DMR by univariate analysis. However, RR-BCR-ABL13m was the only significant landmark for predicting DMR by multivariate analysis. Primary treatment of CML-CP with dasatinib enabled early achievement of MMR and DMR, particularly in elderly patients, with high safety. Furthermore, RR-BCR-ABL13m was found to be a more useful predictor of DMR than HT-BCR-ABL1 and BCR-ABL1 IS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  4. A rapid molecular diagnosis of cutaneous leishmaniasis by colorimetric malachite green-loop-mediated isothermal amplification (LAMP) combined with an FTA card as a direct sampling tool.

    PubMed

    Nzelu, Chukwunonso O; Cáceres, Abraham G; Guerrero-Quincho, Silvia; Tineo-Villafuerte, Edwin; Rodriquez-Delfin, Luis; Mimori, Tatsuyuki; Uezato, Hiroshi; Katakura, Ken; Gomez, Eduardo A; Guevara, Angel G; Hashiguchi, Yoshihisa; Kato, Hirotomo

    2016-01-01

    Leishmaniasis remains one of the world's most neglected diseases, and early detection of the infectious agent, especially in developing countries, will require a simple and rapid test. In this study, we established a quick, one-step, single-tube, highly sensitive loop-mediated isothermal amplification (LAMP) assay for rapid detection of Leishmania DNA from tissue materials spotted on an FTA card. An FTA-LAMP with pre-added malachite green was performed at 64°C for 60min using a heating block and/or water bath and DNA amplification was detected immediately after incubation. The LAMP assay had high detection sensitivity down to a level of 0.01 parasites per μl. The field- and clinic-applicability of the colorimetric FTA-LAMP assay was demonstrated with 122 clinical samples collected from patients suspected of having cutaneous leishmaniasis in Peru, from which 71 positives were detected. The LAMP assay in combination with an FTA card described here is rapid and sensitive, as well as simple to perform, and has great potential usefulness for diagnosis and surveillance of leishmaniasis in endemic areas. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Integration of Novel Low-Cost Colorimetric, Laser Photometric, and Visual Fluorescent Techniques for Rapid Identification of Falsified Medicines in Resource-Poor Areas: Application to Artemether–Lumefantrine

    PubMed Central

    Green, Michael D.; Hostetler, Dana M.; Nettey, Henry; Swamidoss, Isabel; Ranieri, Nicola; Newton, Paul N.

    2015-01-01

    The availability of falsified antimalarial drugs can be reduced with effective drug regulatory agencies and proper enforcement. Fundamental to these agencies taking action, rapid identification must be made as soon as they appear in the market place. Since falsified antimalarials occur mostly in developing countries, performing drug analysis presents itself with unique challenges. A fundamental factor in choosing a useful technique is affordability and simplicity. Therefore, we suggest a three-tiered drug evaluation strategy for identifying a falsified drug in resource-poor areas. Tier I is a simple comparison of a tablet's weight and dimensions with official specifications. Tier II uses inexpensive photometric devices (laser and fluorescence) to evaluate a tablet. Suspicious samples from Tier I and II assessments are then subjected to a colorimetric assay for active ingredients identification and quantification. In this article, we evaluate a novel colorimetric assay for the simultaneous assessment of both lumefantrine and artemether in co-formulated Coartem™ tablets, and integrate the method with two novel, low-cost, fluorescence and laser photometric devices. Image analysis software is used for the assessments. Although artemether–lumefantrine is used as an example, the strategy may be adapted to other medicines. PMID:25897066

  6. Development of Xenopus Resource Centers: the National Xenopus Resource and the European Xenopus Resource Center

    PubMed Central

    Pearl, Esther J.; Grainger, Robert M.; Guille, Matthew; Horb, Marko E.

    2013-01-01

    Xenopus is an essential vertebrate model system for biomedical research that has contributed to important discoveries in many disciplines, including cell biology, molecular biology, physiology, developmental biology and neurobiology. However, unlike other model systems no central repository/stock center for Xenopus had been established until recently. Similar to mouse, zebrafish and fly communities, which have established stock centers, Xenopus researchers need to maintain and distribute rapidly growing numbers of inbred, mutant and transgenic frog strains, along with DNA and protein resources, and individual laboratories struggle to accomplish this efficiently. In the last five years two resource centers were founded to address this need: the European Xenopus Resource Center (EXRC) at the University of Portsmouth in England, and the National Xenopus Resource (NXR) at the Marine Biological Laboratory (MBL) in Woods Hole, MA, USA. These two centers work together to provide resources and support to the Xenopus research community. The EXRC and NXR serve as stock centers and acquire, produce, maintain and distribute mutant, inbred and transgenic X. laevis and X. tropicalis lines. Independently, the EXRC is a repository for Xenopus cDNAs, fosmids and antibodies; it also provides oocytes and wild type frogs within the UK. The NXR will complement these services by providing research training and promoting intellectual interchange through hosting minicourses and workshops and offering space for researchers to perform short-term projects at the MBL. Together the EXRC and NXR will enable researchers to improve productivity by providing resources and expertise to all levels, from graduate students to experienced PIs. These two centers will also enable investigators that use other animal systems to take advantage of Xenopus’ unique experimental features to complement their studies. PMID:22253050

  7. Preparation of a magnetic molecularly imprinted polymer with pseudo template for rapid simultaneous determination of cyromazine and melamine in bio-matrix samples.

    PubMed

    Wang, Xianhua; Fang, Qiuxue; Liu, Shipeng; Chen, Lei

    2012-09-01

    A magnetic molecularly imprinted polymer (M-MIP) for cyromazine and melamine was prepared by simple suspension polymerization using a pseudo template, 2-(4,6-diamino-1,3,5-triazin-2-ylamino)ethanethiol disulfide. The M-MIP was characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, and vibrating sample magnetometry. Molecular recognition properties and binding capability to cyromazine and melamine were evaluated by adsorption testing, which showed the M-MIP had better affinity and selectivity than the magnetic non-imprinted polymer (M-NIP) for cyromazine and melamine. A method based on molecularly imprinted solid-phase extraction assisted by magnetic separation was developed for extraction of cyromazine and melamine from bio-matrix samples. Various conditions, for example desorption conditions, amount of M-MIP, extraction time, and sample pH were optimized. High-performance liquid chromatography with UV detection was used to determine cyromazine and melamine after extraction. The proposed method was successfully applied to determination of cyromazine and melamine in egg and milk samples. Recovery of standard spiked cyromazine and melamine from these samples was between 71.86 and 80.57%, with intraday and interday relative standard deviation ranging from 3.45 to 6.39% and from 3.95 to 7.84%, respectively. The results indicate that the pseudo template M-MIP can be used for preconcentration, purification, and analysis of cyromazine and melamine in bio-matrix samples.

  8. Rapid screening, separation, and detection of hydroxyl radical scavengers from total flavonoids of Ginkgo biloba leaves by chromatography combined with molecular devices.

    PubMed

    Wang, Jing; Zheng, Meizhu; Chen, Lina; Liu, Zhiqiang; Zhang, Yuchi; Liu, Chun-Ming; Liu, Shu

    2016-11-01

    Hydroxyl radicals are the most reactive free radical of human body, a strong contributor to tissue damage. In this study, liquid chromatography coupled to electrospray ionization mass spectrometry was applied to screen and identify hydroxyl radical scavengers from the total flavonoids of Ginkgo biloba leaves, and high-performance counter current chromatography was used to separate and isolate the active compounds. Furthermore, molecular devices were used to determine hydroxyl radical scavenging activities of the obtained hydroxyl radical scavengers and other flavonoids from G. biloba leaves. As a result, six compounds were screened as hydroxyl radical scavengers, but only three flavonoids, namely, rutin, cosmos glycosides and apigenin-7-O-Glu-4'-O-Rha, were isolated successfully from total flavonoids by high-performance counter current chromatography. The purities of the three obtained compounds were over 90%, respectively, as determined by liquid chromatography. Molecular devices with 96-well microplates evaluation indicated that the 50% scavenging concentration values of screened compounds were lower than that of other flavonoids, they performed greater hydroxyl radical scavenging activity, and the evaluation effects were consistent with the liquid chromatography with mass spectrometry screening results. Therefore, chromatography combined with molecular devices is a feasible and an efficient method for systematic screening, identification, isolation, and evaluation of bioactive components in mixture of botanical medicines. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)

    PubMed Central

    Gor, Mian Chee; Mantri, Nitin; Pang, Edwin

    2016-01-01

    A Fragaria Discovery Panel (FDP; strawberry-specific SDA) containing 287 features was constructed by subtracting the pooled gDNA of nine non-angiosperm species from the pooled gDNA of five strawberry genotypes. This FDP was used for Bulk Segregant Analysis (BSA) to enable identification of molecular markers associated with day-neutrality. Analysis of hybridisation patterns of a short day (SD) DNA bulk and three day-neutral (DN) DNA bulks varying in flowering strength allowed identification of a novel feature, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. The signal intensities of FaP2E11 feature obtained from the strong DN bulk (DN1) is three fold higher than the short day bulk (SD), indicating that the putative marker may linked to a CKX1 variant allele with lower enzyme activity. We propose a model for flowering regulation based on the hypothesis that flowering strength may be regulated by the copy number of FaP2E11-linked CKX1 alleles. This study demonstrates the feasibility of the SDA-based BSA approach for the identification of molecular markers associated with day-neutrality in strawberry. This innovative strategy is an efficient and cost-effective approach for molecular marker discovery. PMID:27586242

  10. Rapid determination of theophylline in serum by selective extraction using a heated molecularly imprinted polymer micro-column with differential pulsed elution.

    PubMed

    Mullett, W M; Lai, E P

    1999-12-01

    Molecular imprinting of theophylline in poly(methacrylic acid ethylene dimethacrylate) form binding sites with complementary size, shape and chemical functionalities to theophylline. This molecularly imprinted polymer (MIP) can be packed into a micro-column for selective solid phase extraction (SPE) of theophylline from 20 microl of sample solution. Its chemical inertness and thermal stability allow the use of various organic solvents and elevated column temperatures for effective binding of theophylline. Non-specific adsorption of interfering drugs on the MIP surface is eliminated by an intermediate wash with 20 microl of acetonitrile, prior to quantitative desorption of the bound theophylline by 20 microl of methanol for in-line UV spectrophotometric determination. In this differential pulsed elution (DPE) technique, both the column temperature and solvent flow rate can be optimized to enhance selectivity. Application of this micro-analytical method, molecularly imprinted solid phase extraction DPE (MISPE-DPE), is demonstrated for accurate determination of theophylline in human blood serum. The method is validated over a linear range from 2 microg/ml to at least 20 microg/ml.

  11. [Molecular mechanism of the acquisition of new-quinolone resistance in Mycobacterium leprae and M. tuberculosis and rapid differentiation methods for resistant bacilli].

    PubMed

    Kim, Hyun; Suzuki, Haruka; Matsuoka, Masanori; Matsuba, Takashi; Yokoyama, Kazumasa; Nakajima, Chie; Suzuki, Yasuhiko

    2011-02-01

    Drugs included in new-quinolone are used for the treatment of leprosy with single lesion. These drugs are also known to be effective drugs for the treatment of multi-drug resistant M. tuberculosis. Recent emergence of new-quinolone resistant M. leprae and M. tuberculosis enforced the urgent elucidation of the mode of emergence of new-quinolone resistant strains. In this review, new-quinolone drugs, their mode of action and mechanism of acquisition of resistance by M. leprae and M. tuberculosis were explained. And rapid differentiation methods for resistant bacilli were also introduced.

  12. Molecular cloning of growth hormone encoding cDNA of Indian major carps by a modified rapid amplification of cDNA ends strategy.

    PubMed

    Venugopal, T; Mathavan, S; Pandian, T J

    2002-06-01

    A modified rapid amplification of cDNA ends (RACE) strategy has been developed for cloning highly conserved cDNA sequences. Using this modified method, the growth hormone (GH) encoding cDNA sequences of Labeo rohita, Cirrhina mrigala and Catla catla have been cloned, characterized and overexpressed in Escherichia coli. These sequences show 96-98% homology to each other and are about 85% homologous to that of common carp. Besides, an attempt has been made for the first time to describe a 3-D model of the fish GH protein.

  13. Utility of Serological Tests in the Era of Molecular Testing for Diagnosis of Human Brucellosis in Endemic Area with Limited Resources

    PubMed Central

    Metgud, Sharada C.; Mutnal, Manohar B; Nagamoti, Mahantesh B; Patil, Chidanand S.

    2016-01-01

    . The SAT was upheld as very good quick, easy to perform and economical screening test for human brucellosis. SAT as rapid screening test and STAT as more definitive test can be very well adopted by laboratories working in resource scarce settings for diagnosis of human brucellosis in absence of PCR even for population with normally elevated antibodies levels due to residing in Brucella endemic areas. PMID:27042465

  14. Ultrahigh Molecular Weight Linear Block Copolymers: Rapid Access by Reversible-Deactivation Radical Polymerization and Self- Assembly into Large Domain Nanostructures

    SciTech Connect

    Mapas, Jose Kenneth D.; Thomay, Tim; Cartwright, Alexander N.; Ilavsky, Jan; Rzayev, Javid

    2016-05-05

    Block copolymer (BCP) derived periodic nanostructures with domain sizes larger than 150 nm present a versatile platform for the fabrication of photonic materials. So far, the access to such materials has been limited to highly synthetically involved protocols. Herein, we report a simple, “user-friendly” method for the preparation of ultrahigh molecular weight linear poly(solketal methacrylate-b-styrene) block copolymers by a combination of Cu-wire-mediated ATRP and RAFT polymerizations. The synthesized copolymers with molecular weights up to 1.6 million g/mol and moderate dispersities readily assemble into highly ordered cylindrical or lamella microstructures with domain sizes as large as 292 nm, as determined by ultra-small-angle x-ray scattering and scanning electron microscopy analyses. Solvent cast films of the synthesized block copolymers exhibit stop bands in the visible spectrum correlated to their domain spacings. The described method opens new avenues for facilitated fabrication and the advancement of fundamental understanding of BCP-derived photonic nanomaterials for a variety of applications.

  15. Validation of the 16S rDNA and COI DNA barcoding technique for rapid molecular identification of stored product psocids (Insecta: Psocodea: Liposcelididae).

    PubMed

    Yang, Qianqian; Zhao, Shuo; Kucerová, Zuzana; Stejskal, Václav; Opit, George; Qin, Meng; Cao, Yang; Li, Fujun; Li, Zhihong

    2013-02-01

    Psocids are serious storage pests, and their control is hampered by the fact that different species respond differently to insecticides used for the control of stored-product insect pests. Additionally, psocids of genus Liposcelis that are commonly associated with stored-products are difficult to identify using morphological characteristics. The goal of this study was to validate molecular identification of stored-product psocids of genus Liposcelis based on 16S rDNA and cytochrome oxidase I (COI) DNA barcoding. Unidentified liposcelids (Liposcelis DK) imported from Denmark to China were compared with 14 population samples of seven common species (L. bostrychophila, L. brunnea, L. corrodens, L. decolor, L. entomophila, L. mendax, and L. paeta). The explored species (DK) liposcelids shared >98% sequence similarity for both the 16S rDNA and COI genes with the reference L. corrodens samples (98.32 and 98.94% for 16S rDNA and COI, respectively). A neighbor-joining tree revealed that the explored DK sample and the reference L. corrodens samples belong to the same clade. These molecular results were verified by morphological identification of DK specimens, facilitated by SEM microphotography. The DNA barcoding method and the neighbor-joining phylogenetic analyses indicated that both the 16S rDNA and COI genes were suitable for Liposcelis species identification. DNA barcoding has great potential for use in fast and accurate liposcelid identification.

  16. Bacillus anthracis-like bacteria and other B. cereus group members in a microbial community within the International Space Station: a challenge for rapid and easy molecular detection of virulent B. anthracis.

    PubMed

    van Tongeren, Sandra P; Roest, Hendrik I J; Degener, John E; Harmsen, Hermie J M

    2014-01-01

    For some microbial species, such as Bacillus anthracis, the etiologic agent of the disease anthrax, correct detection and identification by molecular methods can be problematic. The detection of virulent B. anthracis is challenging due to multiple virulence markers that need to be present in order for B. anthracis to be virulent and its close relationship to Bacillus cereus and other members of the B. cereus group. This is especially the case in environments where build-up of Bacillus spores can occur and several representatives of the B. cereus group may be present, which increases the chance for false-positives. In this study we show the presence of B. anthracis-like bacteria and other members of the B. cereus group in a microbial community within the human environment of the International Space Station and their preliminary identification by using conventional culturing as well as molecular techniques including 16S rDNA sequencing, PCR and real-time PCR. Our study shows that when monitoring the microbial hygiene in a given human environment, health risk assessment is troublesome in the case of virulent B. anthracis, especially if this should be done with rapid, easy to apply and on-site molecular methods.

  17. Bacillus anthracis-Like Bacteria and Other B. cereus Group Members in a Microbial Community Within the International Space Station: A Challenge for Rapid and Easy Molecular Detection of Virulent B. anthracis

    PubMed Central

    van Tongeren, Sandra P.; Roest, Hendrik I. J.; Degener, John E.; Harmsen, Hermie J. M.

    2014-01-01

    For some microbial species, such as Bacillus anthracis, the etiologic agent of the disease anthrax, correct detection and identification by molecular methods can be problematic. The detection of virulent B. anthracis is challenging due to multiple virulence markers that need to be present in order for B. anthracis to be virulent and its close relationship to Bacillus cereus and other members of the B. cereus group. This is especially the case in environments where build-up of Bacillus spores can occur and several representatives of the B. cereus group may be present, which increases the chance for false-positives. In this study we show the presence of B. anthracis-like bacteria and other members of the B. cereus group in a microbial community within the human environment of the International Space Station and their preliminary identification by using conventional culturing as well as molecular techniques including 16S rDNA sequencing, PCR and real-time PCR. Our study shows that when monitoring the microbial hygiene in a given human environment, health risk assessment is troublesome in the case of virulent B. anthracis, especially if this should be done with rapid, easy to apply and on-site molecular methods. PMID:24945323

  18. Rapid Detection of Pathogens

    SciTech Connect

    David Perlin

    2005-08-14

    Pathogen identification is a crucial first defense against bioterrorism. A major emphasis of our national biodefense strategy is to establish fast, accurate and sensitive assays for diagnosis of infectious diseases agents. Such assays will ensure early and appropriate treatment of infected patients. Rapid diagnostics can also support infection control measures, which monitor and limit the spread of infectious diseases agents. Many select agents are highly transmissible in the early stages of disease, and it is critical to identify infected patients and limit the risk to the remainder of the population and to stem potential panic in the general population. Nucleic acid-based molecular approaches for identification overcome many of the deficiencies associated with conventional culture methods by exploiting both large- and small-scale genomic differences between organisms. PCR-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for bacterial, fungal and many viral pathogenic agents. When combined with fluorescence-based oligonucleotide detection systems, this approach provides real-time, quantitative, high fidelity analysis capable of single nucleotide allelic discrimination (4). These probe systems offer rapid turn around time (<2 h) and are suitable for high throughput, automated multiplex operations that are critical for clinical diagnostic laboratories. In this pilot program, we have used molecular beacon technology invented at the Public health Research Institute to develop a new generation of molecular probes to rapidly detect important agents of infectious diseases. We have also developed protocols to rapidly extract nucleic acids from a variety of clinical specimen including and blood and tissue to for detection in the molecular assays. This work represented a cooperative research development program between the Kramer-Tyagi/Perlin labs on probe development

  19. Development and application of quartz crystal microbalance sensor based on novel molecularly imprinted sol-gel polymer for rapid detection of histamine in foods.

    PubMed

    Dai, Jie; Zhang, Yan; Pan, Mingfei; Kong, Lingjie; Wang, Shuo

    2014-06-11

    To rapidly detect histamine (HA) in foods, a novel material for HA-specific recognition was synthesized by a sol-gel process and coated on a quartz crystal microbalance (QCM) sensor. The Scatchard model was used to evaluate the adsorption performance of the material; high affinity for HA was demonstrated. Based on QCM frequency change, the sensor exhibited linear behavior for HA concentrations of 0.11 × 10(-2) to 4.45 × 10(-2) mg L(-1), a detection limit of 7.49 × 10(-4) mg kg(-1) (S/N = 3), high selectivity for HA (selectivity coefficient >4) compared with structural analogues, good reproducibility, and long-term stability. The sensor was used to determine the concentration of HA in spiked fish products; the recovery values were satisfactory (93.2-100.4%) and compared well with those obtained by high-performance liquid chromatography (correlation coefficient, r(2) = 0.9965).

  20. The impact of the roll-out of rapid molecular diagnostic testing for tuberculosis on empirical treatment in Cape Town, South Africa

    PubMed Central

    Caldwell, Judy; Kaplan, Richard; Cobelens, Frank; Wood, Robin

    2017-01-01

    Abstract Objective To investigate the impact of introducing a rapid test as the first-line diagnostic test for drug-sensitive tuberculosis in Cape Town, South Africa. Methods Xpert® MTB/RIF (Xpert®), an automated polymerase-chain-reaction-based assay, was rolled out between 2011 and 2013. Data were available on 102 007 adults treated for pulmonary tuberculosis between 2010 and 2014. Tuberculosis notification rates per 100 000 population were calculated for each calendar year and for each year relative to the test roll-out locally, overall and by bacteriological confirmation. Empirical treatment was defined as treatment given without bacteriological confirmation by Xpert®, sputum smear microscopy or sputum culture. Findings Between 2010 and 2014, the proportion of human immunodeficiency virus (HIV)-negative patients treated empirically for tuberculosis declined from 23% (2445/10 643) to 11% (1149/10 089); in HIV-positive patients, it declined from 42% (4229/9985) to 27% (2364/8823). The overall tuberculosis notification rate decreased by 12% and 19% among HIV-negative and HIV-positive patients, respectively; the rate of bacteriologically confirmed cases increased by 1% and 3%, respectively; and the rate of empirical treatment decreased by 56% and 49%, respectively. These changes occurred gradually following the test’s introduction and stabilized after 3 years. Conclusion Roll-out of the rapid test in a setting with a high prevalence of pulmonary tuberculosis and HIV infection was associated with a halving of empirical treatment that occurred gradually after the test’s introduction, possibly reflecting the time needed for full implementation. More than a quarter of HIV-positive patients with tuberculosis were still treated empirically, highlighting the diagnostic challenge in these patients. PMID:28804167

  1. Evaluation of Rapid Molecular Detection Assays for Salmonella in Challenging Food Matrices at Low Inoculation Levels and Using Difficult-to-Detect Strains.

    PubMed

    Ryan, Gina; Roof, Sherry; Post, Laurie; Wiedmann, Martin

    2015-09-01

    Assays for detection of foodborne pathogens are generally initially evaluated for performance in validation studies carried out according to guidelines provided by validation schemes (e.g., AOAC International or the International Organization for Standardization). End users often perform additional validation studies to evaluate the performance of assays in specific matrices (e.g., specific foods or raw material streams of interest) and with specific pathogen strains. However, these types of end-user validations are typically not well defined. This study was conducted to evaluate a secondary end user validation of four AOAC-validated commercial rapid detection assays (an isothermal nucleic acid amplification, an immunoassay, and two PCR-based assays) for their ability to detect Salmonella in two challenging matrices (dry pet food and dark chocolate). Inclusivity was evaluated with 68 diverse Salmonella strains at low population levels representing the limit of detection (LOD) for each assay. One assay detected all strains at the LOD, two assays detected multiple strains only at 10 times the LOD, and the fourth assay failed to detect two strains (Salmonella bongori and S. enterica subsp. houtenae) even at 1,000 times the LOD; this assay was not further evaluated. The three remaining assays were subsequently evaluated for their ability to detect five selected Salmonella strains in food samples contaminated at fractional levels. Unpaired comparisons revealed no significant difference between the results for each given assay and the results obtained with the reference assay. However, analysis of paired culture-confirmed results revealed assay false-negative rates of 4 to 26% for dry pet food and 12 to 16% for dark chocolate. Overall, our data indicate that rapid assays may have high false-negative rates when performance is evaluated under challenging conditions, including low-moisture matrices, strains that are difficult to detect, injured cells, and low inoculum

  2. Potential of Cupriavidus metallidurans CH34 for in situ resource utilization from basalt by determining the molecular micro-mineral interactions

    NASA Astrophysics Data System (ADS)

    Byloos, Bo; Van Houdt, Rob; Boon, Nico; Leys, Natalie

    In order to maintain a persistent human presence in space, materials must either be provided from Earth or generated from material already present in space, in a process referred to as 'in situ resource utilization (ISRU)'. Microorganisms can biomine useful elements from extra-terrestrial materials for use as nutrients in a life support system or to aid in the creation of soil. To effectively use bacteria in an ISRU process more needs to be known about the molecular mechanisms behind microbe-mineral interaction and the influence of microgravity and radiation that affect bioleaching. The aim of this research project is to define the microbe-mineral interactions on basalt, which is a major constituent of Lunar or Martian regolith, the mechanisms that are important in bioleaching and how this process will be altered by space flight conditions. In particular, the research will be focussed on the determination of the genes and proteins involved in the biosynthesis of metallophores and exopolysaccharides (EPS), and biofilm formation. Iron, copper and phosphate uptake mechanisms are investigated in detail because these have been shown to be essential for life and bacteria are faced with limitation of these nutrients in the environment. In this study the bacterium Cupriavidus metallidurans CH34 is used to study these interactions. C. metallidurans CH34 is a soil bacterium which is resistant to up to 20 different heavy metal ions. Its behaviour in space has already been determined with earlier flight experiments to the ISS. It was recently discovered that C. metallidurans forms a biofilm and is capable of leaching calcium, magnesium and iron from basalt to sustain its growth First, C. metallidurans was grown in conditions with and without basalt, iron, copper and phosphate and the production of EPS and metallophores was examined. The iron, copper and phosphate concentrations which are limiting and optimal to allow C. metallidurans cell proliferation could be determined as

  3. The Enigma ML FluAB-RSV assay: a fully automated molecular test for the rapid detection of influenza A, B and respiratory syncytial viruses in respiratory specimens.

    PubMed

    Goldenberg, Simon D; Edgeworth, Jonathan D

    2015-01-01

    The Enigma(®) ML FluAB-RSV assay (Enigma Diagnostics, Porton Down, Salisbury, UK) is a CE-IVD marked multiplex molecular panel for the detection of influenza A, B and respiratory syncytial viruses in nasopharyngeal swabs. The assay runs on the fully automated Enigma ML platform without further specimen manipulation and provides a sample-to-answer result within 95 min. The reported sensitivity and specificity for influenza A are 100% (95% CI: 98.2-100) and 98.3% (95% CI: 95.5-99.4), respectively, for influenza B are 100% (95% CI: 98.2-100) and 98.7% (95% CI: 96-99.6), respectively, and for respiratory syncytial virus are 100% (95% CI: 98.2-100) and 99.4% (95% CI: 97.2-99.9), respectively.

  4. Discovering novel interactions at the nuclear pore complex using bead halo: a rapid method for detecting molecular interactions of high and low affinity at equilibrium.

    PubMed

    Patel, Samir S; Rexach, Michael F

    2008-01-01

    A highly sensitive, equilibrium-based binding assay termed "Bead Halo" was used here to identify and characterize interactions involving components of the nucleocytoplasmic transport machinery in eukaryotes. Bead Halo uncovered novel interactions between the importin Kap95 and the nucleoporins (nups) Nic96, Pom34, Gle1, Ndc1, Nup84, and Seh1, which likely occur during nuclear pore complex biogenesis. Bead Halo was also used to characterize the molecular determinants for binding between Kap95 and the family of nups that feature multiple phenylalanine-glycine motifs (FG nups). Binding was sensitive to the number of FG motifs present and to amino acid (AA) residues immediately flanking the FG motifs. Also, binding was reduced but not abolished when phenylalanine residues in all FG motifs were replaced by tyrosine or tryptophan. These results suggest flexibility in the binding pockets of Kap95 and synergism in binding FG motifs. The hypothesis that Nup53 and Nup59 bind directly to membranes through a C-terminal amphipathic alpha helix and to DNA via an RNA recognition motif domain was also tested and validated using Bead Halo. The results support a role for these nups in nuclear pore membrane biogenesis and in gene expression. Finally, Bead Halo detected binding of the nups Gle1, Nup60, and Nsp1 to phospholipid bilayers. This may reflect the known interaction between Gle1 and phosphoinositides and suggests similar interactions for Nup60 and Nsp1. As the Bead Halo assay detected molecular interactions in cell lysates, as well as between purified components, it can be adapted for large-scale proteomic studies using automated robotics and microscopy.

  5. A conveniently prepared and hypersensitized small molecular fluorescent probe: Rapidly detecting free zinc ion in HepG2 cells and Arabidopsis.

    PubMed

    Gan, Xiaoping; Sun, Ping; Li, Hong; Tian, Xiaohe; Zhang, Baowei; Wu, Jieying; Tian, Yupeng; Zhou, Hongping

    2016-12-15

    In this paper, we reported a conveniently prepared fluorescent probe for zinc ions detection, which constructed by the condensation reaction between p-(benzothiazolyl)aniline with 4, 4- diethylaminesalicylaldehyde. The sensing ability of the probe toward zinc ions in vitro was tested by a series of UV-Vis and fluorescence spectroscopy studies, which showed that the probe possessed high sensitivity with a detection limit of 5.8nM and a rapid response time of 10s. We also carried out fluorescent bio-imaging of the probe for zinc ions in human liver hepatocellular carcinoma cells (HepG2), which showed that the probe could be utilized to detect the intracellular endogenous zinc ions visually without introducing external zinc sources. Meanwhile, co-staining experiment with organelle selective trackers was performed to illustrate that the probe could locate at endoplasmic reticulum. Finally, we successfully used it as a zinc ion developer in plant tissue, which clearly demonstrated the distribution of zinc ions in the growth stage of plant tissue. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Molecular Cloning and Sequencing of the aroA Gene from Actinobacillus pleuropneumoniae and Its Use in a PCR Assay for Rapid Identification

    PubMed Central

    Moral, Carmen Hernanz; Soriano, Alberto Cascón; Salazar, María Sánchez; Marcos, Javier Yugueros; Ramos, Susana Suárez; Carrasco, German Naharro

    1999-01-01

    The gene (aroA) of Actinobacillus pleuropneumoniae, serotype 2, encoding 5-enolpyruvylshikimate-3-phosphate synthase was cloned by complementation of the aroA mutation in Escherichia coli K-12 strain AB2829, and the nucleotide sequence was determined. A pair of primers from the 5′ and 3′ termini were selected to be the basis for development of a specific PCR assay. A DNA fragment of 1,025 bp was amplified from lysed A. pleuropneumoniae serotypes 1 to 12 of biovar 1 or from isolated DNA. No PCR products were detected when chromosomal DNAs from other genera were used as target DNAs; however, a 1,025-bp DNA fragment was amplified when Actinobacillus equuli chromosomal DNA was used as a target, which could be easily differentiated by its NAD independence. The PCR assay developed was very sensitive, with lower detection limits of 12 CFU with A. pleuropneumoniae cells and 0.8 pg with extracted DNA. Specificity and sensitivity make this PCR assay a useful method for the rapid identification and diagnosis of A. pleuropneumoniae infections. PMID:10203526

  7. Comparison of Molecular Detection Method (Nested Polymerase Chain Reaction) with Blood Culture and Paired Widal test for the Rapid Diagnosis of Typhoid Fever.

    PubMed

    Khan, S; Miah, R A; Pal, S; Khatun, S; Fatema, N; Roy, R R; Naheen, C R

    2017-01-01

    Typhoid fever is a major health problem in developing countries in spite of the use of antibiotics and the development of newer antibacterial drugs. Blood culture & serological tests (specially Widal test) which are invariably done in Bangladesh for typhoid fever diagnosis give unacceptable levels of false negative & false positive results respectively. This cross sectional study was done at Bangabandhu Sheikh Mujib Medical University from March 2013 to February 2014. In this study, a polymerase chain reaction-based technique (which has 100% specificity for Salmonella Typhi) was compared with blood culture and widal test among 80 clinically suspected cases of typhoid fever. PCR showed maximum positivity rate (70%) followed by widal test (43.75%) and blood culture (16.25%). PCR showed positive results for 17(48.6%) of 35 typhoid patients with negative results with blood culture and widal test. The results of the study revealed that PCR is rapid and reliable diagnostic technique for detection of S. Typhi in clinically suspected typhoid fever cases, as compared to most commonly done methods such as conventional blood culture, widal test applied.

  8. Molecular cloning of a cysteine proteinase cDNA from adult Ancylostoma ceylanicum by the method of rapid amplification of cDNA ends using polymerase chain reaction.

    PubMed

    Mieszczanek, J; Kofta, W; Wedrychowicz, H

    2000-12-01

    The hookworm Ancylostoma ceylanicum is a parasite of great importance in human and veterinary medicine. The most promising vaccination trials against hookworm infections are based on antigens belonging to the proteinase family. The aim of the present research was to isolate a cysteine proteinase gene from A. ceylanicum. This was achieved by rapid amplification of cDNA ends using polymerase chain reaction (RACE-PCR). A set of consensus oligonucleotide primers was designed to anneal to the conserved coding regions of cysteine proteinase. The PCR products were cloned and sequenced. The novel sequence displayed a high degree of homology with genes of cysteine proteinases known from other hookworm species. In the coding region the nucleotide identity with accp-1, the cysteine proteinase gene of A. caninum, reaches 84.3%. Analysis of the expression of acey-1. the cysteine proteinase gene of A. ceylanicum, suggests that it is produced exclusively in the gland cells of either adult worms or blood-feeding stages of A. ceylanicum.

  9. Rapid and highly sensitive determination of low-molecular-weight carbonyl compounds in drinking water and natural water by preconcentration HPLC with 2,4-dinitrophenylhydrazine.

    PubMed

    Takeda, Kazuhiko; Katoh, Shinya; Nakatani, Nobutake; Sakugawa, Hiroshi

    2006-12-01

    The aim of this research was to develop a simple procedure for a highly sensitive determination of low-molecular-weight (LMW) carbonyl compounds in drinking water and natural water. We employed a preconcentration HPLC system with 2,4-dinitrophenylhydrazine (DNPH) for the determination of LMW carbonyl compounds. A C-18 reverse-phase preconcentration column was used instead of a sample loop at the sample injection valve. A 0.1 - 5.0 mL portion of the derivatized sample solution was injected with a gas-tight syringe, and a 15% acetonitrile aqueous solution was pushed through the preconcentration column to remove the unreacted excess DNPH, which caused serious interference in the determination of formaldehyde. The detection limits were 1 - 3 nM with a relative standard deviation of 2 - 5% for 20 nM standard solutions (n = 5). The calibration curves were essentially unaffected by coexisting sea salts. Applications to commercial mineral water, tap water, river water, pond water and seawater are presented.

  10. A Novel Molecular Microbiologic Technique for the Rapid Diagnosis of Microbial Invasion of the Amniotic Cavity and Intra-Amniotic Infection in Preterm Labor with Intact Membranes

    PubMed Central

    Romero, Roberto; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Chaemsaithong, Piya; Gotsch, Francesca; Dong, Zhong; Ahmed, Ahmed I.; Yoon, Bo Hyun; Hassan, Sonia; Kim, Chong J.; Korzeniewski, Steven J.; Yeo, Lami

    2014-01-01

    in these factors between patients with positive PCR/ESI-MS (≥17 GE/well) who had negative AF cultures compared to those with positive AF cultures; and 6) PCR/ESI-MS detected genomic material from viruses in two patients (1.4%). Conclusion 1) Rapid diagnosis of intra-amniotic infection is possible using PCR/ESI-MS, which can provide results within 8 hours; 2) the combined use of biomarkers of inflammation and PCR/ESI-MS allows for the rapid identification of specific bacteria and viruses in women with preterm labor and intra-amniotic infection; and 3) this approach may allow for administration of timely and specific interventions to reduce morbidity attributed to infection-induced preterm birth. PMID:24417618

  11. Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections*

    PubMed Central

    Brealey, David; Libert, Nicolas; Abidi, Nour Elhouda; O’Dwyer, Michael; Zacharowski, Kai; Mikaszewska-Sokolewicz, Malgorzata; Schrenzel, Jacques; Simon, François; Wilks, Mark; Picard-Maureau, Marcus; Chalfin, Donald B.; Ecker, David J.; Sampath, Rangarajan; Singer, Mervyn

    2015-01-01

    to 57% of patients. Conclusions: Polymerase chain reaction/electrospray ionization-mass spectrometry provides rapid pathogen identification in critically ill patients. The ability to rule out infection within 6 hours has potential clinical and economic benefits. PMID:26327198

  12. Astrocyte Structural and Molecular Response to Elevated Intraocular Pressure Occurs Rapidly and Precedes Axonal Tubulin Rearrangement within the Optic Nerve Head in a Rat Model

    PubMed Central

    Tehrani, Shandiz; Davis, Lauren; Cepurna, William O.; Choe, Tiffany E.; Lozano, Diana C.; Monfared, Ashley; Cooper, Lauren; Cheng, Joshua; Johnson, Elaine C.; Morrison, John C.

    2016-01-01

    Glaucomatous axon injury occurs at the level of the optic nerve head (ONH) in response to uncontrolled intraocular pressure (IOP). The temporal response of ONH astrocytes (glial cells responsible for axonal support) to elevated IOP remains unknown. Here, we evaluate the response of actin-based astrocyte extensions and integrin-based signaling within the ONH to 8 hours of IOP elevation in a rat model. IOP elevation of 60 mm Hg was achieved under isoflurane anesthesia using anterior chamber cannulation connected to a saline reservoir. ONH astrocytic extension orientation was significantly and regionally rearranged immediately after IOP elevation (inferior ONH, 43.2° ± 13.3° with respect to the anterior-posterior axis versus 84.1° ± 1.3° in controls, p<0.05), and re-orientated back to baseline orientation 1 day post IOP normalization. ONH axonal microtubule filament label intensity was significantly reduced 1 and 3 days post IOP normalization, and returned to control levels on day 5. Phosphorylated focal adhesion kinase (FAK) levels steadily decreased after IOP normalization, while levels of phosphorylated paxillin (a downstream target of FAK involved in focal adhesion dynamics) were significantly elevated 5 days post IOP normalization. The levels of phosphorylated cortactin (a downstream target of Src kinase involved in actin polymerization) were significantly elevated 1 and 3 days post IOP normalization and returned to control levels by day 5. No significant axon degeneration was noted by morphologic assessment up to 5 days post IOP normalization. Actin-based astrocyte structure and signaling within the ONH are significantly altered within hours after IOP elevation and prior to axonal cytoskeletal rearrangement, producing some responses that recover rapidly and others that persist for days despite IOP normalization. PMID:27893827

  13. Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections.

    PubMed

    Vincent, Jean-Louis; Brealey, David; Libert, Nicolas; Abidi, Nour Elhouda; O'Dwyer, Michael; Zacharowski, Kai; Mikaszewska-Sokolewicz, Malgorzata; Schrenzel, Jacques; Simon, François; Wilks, Mark; Picard-Maureau, Marcus; Chalfin, Donald B; Ecker, David J; Sampath, Rangarajan; Singer, Mervyn

    2015-11-01

    -mass spectrometry provides rapid pathogen identification in critically ill patients. The ability to rule out infection within 6 hours has potential clinical and economic benefits.

  14. Single drop microextraction as a concentrating probe for rapid screening of low molecular weight drugs from human urine in atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry.

    PubMed

    Shrivas, Kamlesh; Wu, Hui-Fen

    2007-01-01

    The present work reports the development of a new analytical procedure for simple and rapid screening of low molecular weight drugs (<500 Da) from human urine samples by atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS) combined with single drop microextraction (SDME). The success of the proposed method is due to the use of methyltrioctylammonium chloride (MTOAC) as additive to avoid the noise arising from the matrix ions (alpha-cyano-4-hydroxycinnamic acid (CHCA)). SDME also aided in alleviating the interferences arising from other matrix ions present in the urine samples prior to AP-MALDI-MS analysis. Factors affecting the extraction efficiency of drugs, such as selection of solvent, stirring speed, extraction time, exposure volume of extraction phase and salt addition, have been optimized. The optimum molar ratio of CHCA/MTOAC that gave the minimum background noise of CHCA ions was 700:1. The limit of detection (LOD) and relative standard deviation (RSD) of the method were in the ranges 0.3-1.6 microM and 7.8-11.4%, respectively. The SDME method was compared with liquid-liquid extraction (LLE) and hollow fiber liquid-phase microextraction (HF-LPME) to evaluate the compatibility of the present method in the extraction of drugs from urine samples. The role of MTOAC as matrix ion signal suppressor and SDME as analyte-separating device in the rapid screening of low molecular weight drugs from human urine samples using AP-MALDI/MS has been reported. Copyright (c) 2007 John Wiley & Sons, Ltd.

  15. Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples

    PubMed Central

    Pinchbeck, G. L.; Loughnane, P.; Aklilu, N.; Ashine, T.; Stringer, A. P.; Gordon, L.; Marshall, M.; Christley, R. M.

    2016-01-01

    Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum. This molecular diagnostic method now permits investigation of the epidemiology of EZL. PMID:27707938

  16. Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples.

    PubMed

    Scantlebury, C E; Pinchbeck, G L; Loughnane, P; Aklilu, N; Ashine, T; Stringer, A P; Gordon, L; Marshall, M; Christley, R M; McCarthy, A J

    2016-12-01

    Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum This molecular diagnostic method now permits investigation of the epidemiology of EZL.

  17. Fiber resources

    Treesearch

    P. J. Ince

    2004-01-01

    In economics, primary inputs or factors of production define the term ‘resources.’ Resources include land resources (plants, animals, and minerals), labor, capital, and entrepreneurship. Almost all pulp and paper fiber resources are plant materials obtained from trees or agricultural crops. These resources encompass plant materials harvested directly from the land (...

  18. Development of a molecular-beacon-based multi-allelic real-time RT-PCR assay for the detection of human coronavirus causing severe acute respiratory syndrome (SARS-CoV): a general methodology for detecting rapidly mutating viruses.

    PubMed

    Hadjinicolaou, Andreas V; Farcas, Gabriella A; Demetriou, Victoria L; Mazzulli, Tony; Poutanen, Susan M; Willey, Barbara M; Low, Donald E; Butany, Jagdish; Asa, Sylvia L; Kain, Kevin C; Kostrikis, Leondios G

    2011-04-01

    Emerging infectious diseases have caused a global effort for development of fast and accurate detection techniques. The rapidly mutating nature of viruses presents a major difficulty, highlighting the need for specific detection of genetically diverse strains. One such infectious agent is SARS-associated coronavirus (SARS-CoV), which emerged in 2003. This study aimed to develop a real-time RT-PCR detection assay specific for SARS-CoV, taking into account its intrinsic polymorphic nature due to genetic drift and recombination and the possibility of continuous and multiple introductions of genetically non-identical strains into the human population, by using mismatch-tolerant molecular beacons designed to specifically detect the SARS-CoV S, E, M and N genes. These were applied in simple, reproducible duplex and multiplex real-time PCR assays on 25 post-mortem samples and constructed RNA controls, and they demonstrated high target detection ability and specificity. This assay can readily be adapted for detection of other emerging and rapidly mutating pathogens.

  19. A novel molecular microbiologic technique for the rapid diagnosis of microbial invasion of the amniotic cavity and intra-amniotic infection in preterm labor with intact membranes.

    PubMed

    Romero, Roberto; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Chaemsaithong, Piya; Gotsch, Francesca; Dong, Zhong; Ahmed, Ahmed I; Yoon, Bo Hyun; Hassan, Sonia S; Kim, Chong Jai; Korzeniewski, Steven J; Yeo, Lami

    2014-04-01

    AF cultures and those with positive AF cultures; and (v) PCR/ESI-MS detected genomic material from viruses in two patients (1.4%). (i) Rapid diagnosis of intra-amniotic infection is possible using PCR/ESI-MS; (ii) the combined use of biomarkers of inflammation and PCR/ESI-MS allows for the identification of specific bacteria and viruses in women with preterm labor and intra-amniotic infection; and (iii) this approach may allow for administration of timely and specific interventions to reduce morbidity attributed to infection-induced preterm birth. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  20. Herpes - resources

    MedlinePlus

    Genital herpes - resources; Resources - genital herpes ... The following organizations are good resources for information on genital herpes : March of Dimes -- www.marchofdimes.com/pregnancy/complications-herpes The American College of Obstetricians and Gynecologists -- ...

  1. Rapid Prototyping

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Javelin, a Lone Peak Engineering Inc. Company has introduced the SteamRoller(TM) System as a commercial product. The system was designed by Javelin during a Phase II NASA funded small commercial product. The purpose of the invention was to allow automated-feed of flexible ceramic tapes to the Laminated Object Manufacturing rapid prototyping equipment. The ceramic material that Javelin was working with during the Phase II project is silicon nitride. This engineered ceramic material is of interest for space-based component.

  2. High Resolution Melting as a rapid, reliable, accurate and cost-effective emerging tool for genotyping pathogenic bacteria and enhancing molecular epidemiological surveillance: a comprehensive review of the literature.

    PubMed

    Tamburro, M; Ripabelli, G

    2017-01-01

    Rapid, reliable and accurate molecular typing methods are essential for outbreaks detection and infectious diseases control, for monitoring the evolution and dynamics of microbial populations, and for effective epidemiological surveillance. The introduction of a novel method based on the analysis of melting temperature of amplified products, known as High Resolution Melting (HRM) since 2002, has found applications in epidemiological studies, either for identification of bacterial species or molecular typing, as well as an extensive and increasing use in many research fields. HRM method is based on the use of saturating third generation dyes, advanced real-time PCR platforms, and bioinformatics tools. To describe, by a comphrehensive review of the literature, the use, application and usefulness of HRM for the genotyping of bacterial pathogens in the context of epidemiological surveillance and public health. A literature search was carried out during July-August 2016, by consulting the biomedical databases PubMed/Medline, Scopus, EMBASE, and ISI Web of Science without limits. The search strategy was performed according to the following keywords: high resolution melting analysis and bacteria and genotyping or molecular typing. All the articles evaluating the application of HRM for bacterial pathogen genotyping were selected and reviewed, taking into account the objective of each study, the rationale explaining the use of this technology, and the main results obtained in comparison with gold standards and/or alternative methods, when available. HRM method was extensively used for molecular typing of both Gram-positive and Gram-negative bacterial pathogens, representing a versatile genetic tool: a) to evaluate genetic diversity and subtype at species/subspecies level, based also on allele discrimination/identification and mutation screening; b) to recognize phylogenetic groupings (lineage, sublineage, subgroups); c) to identify antimicrobial resistance; d) to detect and

  3. Pakistan RAPID III.

    PubMed

    Bhatti, M U

    1990-01-01

    The author describes the software called RAPID (Resources for the Awareness of Population Impact on Development), which was developed by the Futures Group, a U.S. company. The software is designed for IBM-PCs and compatibles, with a configuration that includes 640K RAM, a fixed disk drive, and DOS 2.0 or higher. The application in Pakistan of this software in an information, education, and communication program sponsored by the National Institute of Population Studies, including the translation of the software into Urdu, is briefly outlined.

  4. Rapid wetting dynamics

    NASA Astrophysics Data System (ADS)

    Carlson, Andreas; Bellani, Gabriele; Amberg, Gustav

    2010-11-01

    Contact lines between solids and liquid or gas interfaces appear in very many instances of fluid flows. This could be coffee stains, water-oil mixtures in oil recovery, hydrophobic feet of insects or leaves in nature. In the present work we elucidate some of the wetting physics governing the very rapid wetting. Experimental and numerical results of spontaneously spreading droplets are presented, where focus is directed towards understanding the very rapid flow regime and highly dynamic initial wetting phase, where the contact line speed is limited by dissipative processes on a molecular scale occurring at the contact line. In particular we show the influence of the surface wettability and the liquid viscosity on the spreading dynamics, such as the contact line motion and dynamic contact angle in time.

  5. A More Rapid, Rapid Response.

    PubMed

    Robison, Justin; Slamon, Nicholas B

    2016-09-01

    Critical care physicians' standard for arrival to a rapid response team activation is 10 minutes or less at this institution. This study proposes that a FaceTime (Apple, Cupertino, CA) video call between the staff at the bedside and the critical care physician will allow the implementation of potentially life-saving therapies earlier than the current average response (4.5 min). Prospective cohort study. Freestanding, tertiary-care children's hospital. Pediatric patients ages 0-17. Six units were chosen as matched pairs. In the telemedicine units, after notification of an rapid response team, the critical care intensivist established a FaceTime video call with the nurse at the bedside and gathered history, visually assessed the patient, and suggested interventions. Simultaneously, the rapid response nurse, respiratory therapist, and fellow were dispatched to respond to the bedside. After the video call, the intensivist also reported to the bedside. The control units followed the standard rapid response team protocol: the intensivist physically responded to the bedside. Differences in response time, number of interventions, Pediatric Early Warning System scores, and disposition were measured, and the PICU course of those transferred was evaluated. The telemedicine group's average time to establish FaceTime interface was 2.6 minutes and arrival at bedside was 3.7 minutes. The control group average arrival time was 3.6 minutes. The difference between FaceTime interface and physical arrival in the control group was statistically significant (p = 0.012). Physical arrival times between the telemedicine and control groups remained consistent. Fifty-eight percent of the telemedicine patients and 73% of the control patients were admitted to the PICU (p = 0.13). Of patients transferred to the PICU, there was no difference in rate of intubation, initiation of bilevel positive airway pressure, central line placement, or vasopressors. The study group averaged 1.4 interventions

  6. Models of Rapid Solidification

    NASA Technical Reports Server (NTRS)

    Gilmer, G. H.; Broughton, J. Q.

    1984-01-01

    Laser annealing studies provide much information on various consequences of rapid solidification, including the trapping of impurities in the crystal, the generation of vacancies and twins, and on the fundamental limits to the speed of the crystal-melt interface. Some results obtained by molecular dynamics methods of the solidification of a Lennard-Jones liquid are reviewed. An indication of the relationship of interface speed to undercooling for certain materials can be derived from this model. Ising model simulations of impurity trapping in silicon are compared with some of the laser annealing results. The consequences of interface segregation and atomic strain are discussed.

  7. Models of Rapid Solidification

    NASA Technical Reports Server (NTRS)

    Gilmer, G. H.; Broughton, J. Q.

    1984-01-01

    Laser annealing studies provide much information on various consequences of rapid solidification, including the trapping of impurities in the crystal, the generation of vacancies and twins, and on the fundamental limits to the speed of the crystal-melt interface. Some results obtained by molecular dynamics methods of the solidification of a Lennard-Jones liquid are reviewed. An indication of the relationship of interface speed to undercooling for certain materials can be derived from this model. Ising model simulations of impurity trapping in silicon are compared with some of the laser annealing results. The consequences of interface segregation and atomic strain are discussed.

  8. Health Care Resource Utilization and Costs in Patients with Chronic Myeloid Leukemia with Better Adherence to Tyrosine Kinase Inhibitors and Increased Molecular Monitoring Frequency.

    PubMed

    Latremouille-Viau, Dominick; Guerin, Annie; Gagnon-Sanschagrin, Patrick; Dea, Katherine; Cohen, Benjamin G; Joseph, George J

    2017-02-01

    Frequent molecular monitoring (qPCR tests), as recommended by evidence-based monitoring guidelines, is associated with higher adherence to tyrosine kinase inhibitors (TKIs) in the management of chronic myeloid leukemia (CML); both factors have been associated with better clinical and economic outcomes. To (a) estimate the effect of more frequent qPCR tests on health care resource utilization (HRU) and associated costs, including direct (effect of qPCR test frequency on HRU) and indirect (through TKI adherence) effects, and (b) develop an economic model applicable to multiple clinical practice scenarios. Adult patients newly diagnosed with CML who started TKI firstline therapy were identified from U.S. administrative claims data (2010-2015). TKI adherence (medication possession ratio [MPR]), number of inpatient days, emergency room (ER) visits, outpatient service days, and mean costs per HRU event were measured during the first year of CML treatment. Direct and indirect effects of qPCR test frequency were estimated using multivariate regression models. Subsequently, an economic model was developed to assess the overall effect of varying qPCR test frequency on HRU and associated costs during the first year of CML treatment under different clinical practice scenarios; the scenario reported is the increase from 1 to 2 qPCR tests. Of the 1,431 patients included, 36% had no qPCR tests, the average qPCR test frequency was 1.6, and the average MPR was 0.86 during the first year of CML treatment. The direct effect of increasing qPCR test frequency by 1 was associated with 13.0% fewer inpatient days (adjusted incidence rate ratio [adjusted IRR] = 0.87; P = 0.010); 8.3% fewer ER visits (adjusted IRR = 0.92; P = 0.043); and 3.0% more outpatient service days (adjusted IRR = 1.03; P = 0.002). Each increase of 1 test was associated with an increase in TKI adherence by 2.2 percentage points (adjusted MPR difference = 0.022; P < 0.001). When considering the indirect effect of q

  9. Unresolved molecular phylogenies of gibbons and siamangs (Family: Hylobatidae) based on mitochondrial, Y-linked, and X-linked loci indicate a rapid Miocene radiation or sudden vicariance event.

    PubMed

    Israfil, H; Zehr, S M; Mootnick, A R; Ruvolo, M; Steiper, M E

    2011-03-01

    According to recent taxonomic reclassification, the primate family Hylobatidae contains four genera (Hoolock, Nomascus, Symphalangus, and Hylobates) and between 14 and 18 species, making it by far the most species-rich group of extant hominoids. Known as the "small apes", these small arboreal primates are distributed throughout Southeast, South and East Asia. Considerable uncertainty surrounds the phylogeny of extant hylobatids, particularly the relationships among the genera and the species within the Hylobates genus. In this paper we use parsimony, likelihood, and Bayesian methods to analyze a dataset containing nearly 14 kilobase pairs, which includes newly collected sequences from X-linked, Y-linked, and mitochondrial loci together with data from previous mitochondrial studies. Parsimony, likelihood, and Bayesian analyses largely failed to find a significant difference among phylogenies with any of the four genera as the most basal taxon. All analyses, however, support a tree with Hylobates and Symphalangus as most closely related genera. One strongly supported phylogenetic result within the Hylobates genus is that Hylobates pileatus is the most basal taxon. Multiple analyses failed to find significant support for any singular genus-level phylogeny. While it is natural to suspect that there might not be sufficient data for phylogenetic resolution (whenever that situation occurs), an alternative hypothesis relating to the nature of gibbon speciation exists. This lack of resolution may be the result of a rapid radiation or a sudden vicariance event of the hylobatid genera, and it is likely that a similarly rapid radiation occurred within the Hylobates genus. Additional molecular and paleontological evidence are necessary to better test among these, and other, hypotheses of hylobatid evolution. Copyright © 2010 Elsevier Inc. All rights reserved.

  10. Unresolved molecular phylogenies of gibbons and siamangs (Family: Hylobatidae) based on mitochondrial, Y-linked, and X-linked loci indicate a rapid Miocene radiation or sudden vicariance event

    PubMed Central

    Israfil, H.; Zehr, S. M.; Mootnick, A. R.; Ruvolo, M.; Steiper, M. E.

    2010-01-01

    According to recent taxonomic reclassification, the primate family Hylobatidae contains four genera (Hoolock, Nomascus, Symphalangus, and Hylobates) and between 14-18 species, making it by far the most species-rich group of extant hominoids. Known as the “small apes”, these small arboreal primates are distributed throughout Southeast, South and East Asia. Considerable uncertainty surrounds the phylogeny of extant hylobatids, particularly the relationships among the genera and the species within the Hylobates genus. In this paper we use parsimony, likelihood, and Bayesian methods to analyze a dataset containing nearly 14 kilobase pairs, which includes newly collected sequences from X-linked, Y-linked, and mitochondrial loci together with data from previous mitochondrial studies. Parsimony, likelihood, and Bayesian analyses largely failed to find a significant difference among phylogenies with any of the four genera as the most basal taxon. All analyses, however, support a tree with Hylobates and Symphalangus as most closely related genera. One strongly supported phylogenetic result within the Hylobates genus is that H. pileatus is the most basal taxon. Multiple analyses failed to find significant support for any singlular genus-level phylogeny. While it is natural to suspect that there might not be sufficient data for phylogenetic resolution (whenever that situation occurs), an alternative hypothesis relating to the nature of gibbon speciation exists. This lack of resolution may be the result of a rapid radiation or a sudden vicariance event of the hylobatid genera, and it is likely that a similarly rapid radiation occurred within the Hylobates genus. Additional molecular and paleontological evidence are necessary to better test among these, and other, hypotheses of hylobatid evolution. PMID:21074627

  11. Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Wright, John D.

    1995-02-01

    This book describes the chemical and physical structure of molecular crystals, their optical and electronic properties, and the reactions between neighboring molecules in crystals. In the second edition, the author has taken into account research that has undergone extremely rapid development since the first edition was published in 1987. For instance, he gives extensive coverage to the applications of molecular materials in high-technology devices (e.g. optical communications, laser printers, photocopiers, liquid crystal displays, solar cells, and more). There is also an entirely new chapter on the recently discovered Buckminsterfullerene carbon molecule (C60) and organic non-linear optic materials.

  12. Acyclic diene metathesis with a monomer from renewable resources: control of molecular weight and one-step preparation of block copolymers.

    PubMed

    Rybak, Anastasiya; Meier, Michael A R

    2008-01-01

    The preparation of a long-chain aliphatic alpha,omega-diene from plant oil derivatives and its subsequent polymerization through acyclic diene metathesis (ADMET) is described. The ADMET bulk polymerization of the thus-obtained monomer, undecyl undecenoate, was investigated and optimized by applying ruthenium-based metathesis catalysts from Grubbs and Hoveyda-Grubbs, leading to high-molecular-weight polyesters. Moreover, by applying different amounts of methyl 10-undecenoate as a chain stopper in this ADMET step growth polymerization, the molecular weight of the resulting polyester could be tuned in a range from approximately 10 to 45 kDa. Finally, the application of a poly(ethylene glycol) methyl ether acrylate as the chain stopper led to the preparation of ABA triblock copolymers in a one-step, one-pot procedure.

  13. The treasury of the commons: making use of public gene expression resources to better characterize the molecular diversity of inhibitory interneurons in the cerebellar cortex.

    PubMed

    Schilling, Karl; Oberdick, John

    2009-12-01

    We mined the Allen Mouse Brain Atlas for genes expressed in cerebellar cortical inhibitory interneurons that would allow identification and possibly distinction of these cells. We identified some 90 genes that are highly expressed in specific subsets of cerebellar cortical inhibitory interneurons or various combinations thereof. Four genes are exclusively expressed, within the cerebellar cortex, in molecular layer interneurons, and ten genes label exclusively inhibitory interneurons in the granule cell layer or subsets thereof. Differential expression of many of these genes in cells residing in the lower versus the upper molecular layer provides evidence that these cells, traditionally referred to as basket and stellate cells, are indeed molecularly distinct. Two genes could be identified as novel markers for unipolar brush cells. Intersection of these data with embryonic expression patterns as documented in the genepaint repository does not support a hierarchical model of cerebellar interneuron development, but may be more easily reconciled with the view that cerebellar inhibitory interneurons derive from a common precursor pool from which they are specified only late into their development. The novel markers identified here should prove useful for probing the timing and mechanisms supporting cerebellar cortical interneuron specification and diversification.

  14. Highly Stereoselective Synthesis of 1,6-Ketoesters Mediated by Ionic Liquids: A Three-component Reaction Enabling Rapid Access to a New Class of Low Molecular Weight Gelators.

    PubMed

    Sundén, Henrik; Ta, Linda; Axelsson, Anton

    2015-11-27

    In organic chemistry ionic liquids (ILs) have emerged as safe and recyclable reaction solvents. In the presence of a base ILs can be deprotonated to form catalytically active N-Heterocyclic Carbenes (NHCs). Here we have used ILs as precatalysts in the addition of α,β-unsaturated aldehydes to chalcones to form 1,6-ketoesters, incorporating an anti-diphenyl moiety in a highly stereoselective fashion. The reaction has a broad substrate scope and several functional groups and heteroaromatics can be integrated into the ketoester backbone in generally good yields with maintained stereoselectivity. The reaction protocol is robust and scalable. The starting materials are inexpensive and the products can be obtained after simple filtration, avoiding solvent-demanding chromatography. Furthermore, the IL can be recycled up to 5 times without any loss of reactivity. Moreover, the 1,6-ketoester end product is a potent gelator in several hydrocarbon based solvents. The method enables rapid access to and evaluation of a new class of low molecular weight gelators (LMWGs) from recyclable and inexpensive starting materials.

  15. Selective removal of ATP degradation products from food matrices II: Rapid screening of hypoxanthine and inosine by molecularly imprinted matrix solid-phase dispersion for evaluation of fish freshness.

    PubMed

    Cela-Pérez, M C; Barbosa-Pereira, L; Vecino, X; Pérez-Ameneiro, M; Lasagabaster Latorre, Aurora; López-Vilariño, J M; González Rodríguez, M V; Moldes, A B; Cruz, J M

    2015-04-01

    A water compatible molecularly imprinted polymer (MIP), synthesized using theophylline (TPH) as dummy-template and acrylamide (AM) as functional monomer, has been employed as supporting material in matrix solid-phase dispersion combined with ultra performance liquid chromatography-photodiode array detection (MSPD-UPLC-PDA) for selective determination of adenosine triphosphate (ATP) derivatives in fish samples. ATP degradation products are used as freshness index for assessment of fish quality. The solid sample was directly blended with MIP in MSPD procedure resulting in sample disruption and subsequent adsorption of the compounds on the MIP. By using n-hexane and ammonium hydroxide aqueous solution at pH 9 as the washing and elution solvent, respectively, satisfactory recoveries and clean chromatograms have been obtained. Good linearity for hypoxanthine (HYP) and inosine (INO) has been observed with correlation coefficients (R(2)) of 0.9987 and 0.9986, respectively. The recoveries of the two ATP derivatives at three different spiked levels ranged from 106.5% to 113.4% for HYP and from 103.1% to 111.2% for INO, with average relative standard deviations lower than 4.2% in both cases. This new method, which is rapid, simple and sensitive, can be used as an alternative tool to conventional tedious methods. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Earth Resources

    ERIC Educational Resources Information Center

    Brewer, Tom

    1970-01-01

    Reviews some of the more concerted, large-scale efforts in the earth resources areas" in order to help the computer community obtain insights into the activities it can jointly particpate in withthe earth resources community." (Author)

  17. Alzheimer - resources

    MedlinePlus

    Resources - Alzheimer ... The following organizations are good resources for information on Alzheimer disease : Alzheimer's Association -- www.alz.org Alzheimer's Disease Education and Referral Center -- www.nia.nih.gov/alzheimers ...

  18. Ostomy - resources

    MedlinePlus

    Resources - ostomy ... The following organizations are good resources for information on ostomies: American Society of Colon and Rectal Surgeons -- www.fascrs.org/patients/disease-condition/ostomy-expanded-version United ...

  19. Psoriasis - resources

    MedlinePlus

    Resources - psoriasis ... The following organizations are good resources for information about psoriasis : American Academy of Dermatology -- www.aad.org/skin-conditions/dermatology-a-to-z/psoriasis National Institute of ...

  20. SIDS - resources

    MedlinePlus

    Resources - SIDS ... The following organizations are good resources for information on SIDS (Sudden Infant Death Syndrome) : American SIDS Institute -- sids.org Centers for Disease Control and Prevention -- www.cdc. ...

  1. Cancer - resources

    MedlinePlus

    Resources - cancer ... The following organizations are good resources for information on cancer : American Cancer Society -- www.cancer.org Cancer Care -- www.cancercare.org Cancer.Net -- www.cancer.net/coping- ...

  2. Scoliosis - resources

    MedlinePlus

    Resources - scoliosis ... The following organizations are good resources for information on scoliosis : American Academy of Orthopedic Surgeons -- orthoinfo.aaos.org/topic.cfm?topic=A00626 National Institute of Arthritis and ...

  3. Scleroderma - resources

    MedlinePlus

    Resources - scleroderma ... The following organizations are good resources for information on scleroderma : American College of Rheumatology -- www.rheumatology.org/practice/clinical/patients/diseases_and_conditions/scleroderma.asp National Institute ...

  4. Blindness - resources

    MedlinePlus

    Resources - blindness ... The following organizations are good resources for information on blindness : American Foundation for the Blind -- www.afb.org Foundation Fighting Blindness -- www.blindness.org National Eye Institute -- ...