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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. PMID:26517245

  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. 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

  4. A Rapid Molecular Approach for Chromosomal Phasing

    PubMed Central

    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). PMID:25739099

  5. Rapid diagnosis of medulloblastoma molecular subgroups

    PubMed Central

    Schwalbe, Ed C.; Lindsey, Janet C.; Straughton, Debbie; Hogg, Twala L.; Cole, Michael; Megahed, Hisham; Ryan, Sarra L.; Lusher, Meryl E.; Taylor, Michael D.; Gilbertson, Richard J.; Ellison, David W.; Bailey, Simon; Clifford, Steven C.

    2011-01-01

    PURPOSE Microarray studies indicate medulloblastoma comprises distinct molecular disease subgroups, which offer potential for improved clinical management. EXPERIMENTAL DESIGN Minimal mRNA expression signatures diagnostic for the Wnt/Wingless (WNT) and Sonic Hedgehog (SHH) subgroups were developed, validated and used to assign subgroup affiliation in 173 tumours from four independent cohorts, alongside a systematic investigation of subgroup clinical and molecular characteristics. RESULTS WNT tumours (12% (21/173)) were diagnosed >5 years of age (peak, 10 years), displayed classic histology, CTNNB1 mutation (19/20), associated chromosome 6 loss and have previously been associated with favourable prognosis. SHH cases (24% (42/173)) predominated in infants (<3 years) and showed an age-dependent relationship to desmoplastic/nodular pathology; all infant desmoplastic/nodular cases (previously associated with a good outcome) were SHH-positive, but these relationships broke down in non-infants. PTCH1 mutations were common (34%; 11/32), but PTCH1 exon1c hypermethylation, chromosome 9q and REN (KCTD11) genetic loss were not SHH-associated, and SMO or SUFU mutation, PTCH1 exon1a or SUFU hypermethylation did not play a role, indicating novel activating mechanisms in the majority of SHH cases. SHH tumours were associated with an absence of COL1A2 methylation. WNT/SHH-independent medulloblastomas (64% (110/173)) showed all histologies, peaked at 3-6 years, and were exclusively associated with chromosome 17p loss. CONCLUSIONS Medulloblastoma subgroups are characterised by distinct genomic, epigenomic and clinico-pathological features, and clinical outcomes. Validated array-independent gene expression assays for the rapid assessment of subgroup affiliation in small biopsies, provide a basis for their routine clinical application, in strategies including molecular disease-risk stratification and delivery of targeted therapeutics. PMID:21325292

  6. Rapid molecular diagnostic tools for avian influenza

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An accurate and early diagnosis of a foreign animal disease is crucial for rapid control and eradication of an outbreak in a country previously free of the disease. Historically many animal diseases have been controlled based solely on clinical signs of disease. However with avian influenza virus ...

  7. Review of rapid molecular diagnostic tools for avian influenza

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular diagnostics tests are commonly used to diagnose avian influenza virus (AIV) because they are sensitive, can be performed rapidly, with high throughput, and at a moderate cost. Molecular diagnostic tests have recently proven themselves to be invaluable in controlling disease outbreaks arou...

  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. PMID:25242061

  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. Rapid Intraoperative Molecular Characterization of Glioma

    PubMed Central

    Shankar, Ganesh M.; Francis, Joshua M.; Rinne, Mikael L.; Ramkissoon, Shakti H.; Huang, Franklin W.; Venteicher, Andrew S.; Akama-Garren, Elliot H.; Kang, Yun Jee; Lelic, Nina; Kim, James C.; Brown, Loreal E.; Charbonneau, Sarah K.; Golby, Alexandra J.; Pedamallu, Chandra Sekhar; Hoang, Mai P.; Sullivan, Ryan J.; Cherniack, Andrew D.; Garraway, Levi A.; Stemmer-Rachamimov, Anat; Reardon, David A.; Wen, Patrick Y.; Brastianos, Priscilla K.; Curry, William T.; Barker, Fred G.; Hahn, William C.; Nahed, Brian V.; Ligon, Keith L.; Louis, David N.; Cahill, Daniel P.; Meyerson, Matthew

    2016-01-01

    IMPORTANCE Conclusive intraoperative pathologic confirmation of diffuse infiltrative glioma guides the decision to pursue definitive neurosurgical resection. Establishing the intraoperative diagnosis by histologic analysis can be difficult in low-cellularity infiltrative gliomas. Therefore, we developed a rapid and sensitive genotyping assay to detect somatic single-nucleotide variants in the telomerase reverse transcriptase (TERT) promoter and isocitrate dehydrogenase 1 (IDH1). OBSERVATIONS This assay was applied to tissue samples from 190 patients with diffuse gliomas, including archived fixed and frozen specimens and tissue obtained intraoperatively. Results demonstrated 96% sensitivity (95% CI, 90%–99%) and 100% specificity (95% CI, 95%–100%) for World Health Organization grades II and III gliomas. In a series of live cases, glioma-defining mutations could be identified within 60 minutes, which could facilitate the diagnosis in an intraoperative timeframe. CONCLUSIONS AND RELEVANCE The genotyping method described herein can establish the diagnosis of low-cellularity tumors like glioma and could be adapted to the point-of-care diagnosis of other lesions that are similarly defined by highly recurrent somatic mutations. PMID:26181761

  11. 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.

  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. 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)

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  16. 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

  17. 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. PMID:24945530

  18. 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

  19. Remote and rapid pathological diagnosis in a resource challenged unit.

    PubMed

    Carey, P; Fudzulani, R; Scholfield, D; Chagaluka, G; Tomoka, T; Liombe, G; Banda, K; Wadehra, V; Samarasinghe, S; Molyneux, E M; Bailey, S

    2014-06-01

    Malawi is one of the world's poorest countries, but despite this, has a dedicated paediatric oncology service. The service has been hampered by the inability to make a timely cytological diagnosis in the majority of patients. A telemedicine programme was commenced to help overcome this problem, and the results for the first 197 consecutive patients are described. The results are compared with the local reports where available. Most samples were fine needle aspirates (104/197-53%), but others included bone marrow aspirates, peripheral blood films and other fluid collections. A diagnosis was arrived at in 52% of the samples; there were 46 discordant results, 38 were when one or other of the local or distant teams were unable to make a diagnosis, and only 8 where the diagnoses of the 2 teams differed. Diagnoses were made and reports were compiled by the 'distant' team within 24 h and sent to the centre in Malawi. This simple telepathology initiative has had a positive impact on clinical management, and could be used in other less resourced centres twinned with better resourced ones. PMID:24561316

  20. Permanent genetic resources added to Molecular Ecology Resources Database 1 June 2012-31 July 2012.

    PubMed

    Barat, Ashoktaru; Bravo, S P; Chandra, Suresh; Corrêa, A S; Giombini, M I; Guedes, R N C; Huailei, Ma; Lal, Kuldeep K; Liang, Lu; Matura, Rakesh; Mohindra, Vindhya; Oliveira, L O; Patangia, Ruchi; Qiyong, Liu; Sah, Rama Shankar; Singh, Akanksha; Singh, Birender Kumar; Singh, Rajeev K; Tosto, D S; Tripathi, Ratnesh K; Vinson, C C

    2012-11-01

    This article documents the addition of 96 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Clarias batrachus, Marmota himalayana, Schizothorax richardsonii, Sitophilus zeamais and Syagrus romanzoffiana. These loci were cross-tested on the following species: Clarias dussumeri, Clarias gariepinus, Heteropneustus fossilis, Sitophilus granarius and Sitophilus oryzae. PMID:23006415

  1. Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics

    PubMed Central

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

    2013-01-01

    The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes 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 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 300K 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. PMID:23865517

  2. Rapid characterization of molecular diffusion by NMR spectroscopy.

    PubMed

    Pudakalakatti, Shivanand M; Chandra, Kousik; Thirupathi, Ravula; Atreya, Hanudatta S

    2014-11-24

    An NMR-based approach for rapid characterization of translational diffusion of molecules has been developed. Unlike the conventional method of acquiring a series of 2D (13)C and (1)H spectra, the proposed approach involves a single 2D NMR spectrum, which can be acquired in minutes. Using this method, it was possible to detect the presence of intermediate oligomeric species of diphenylalanine in solution during the process of its self-assembly to form nanotubular structures. PMID:25331210

  3. Rapid Prototyping of Chemical Microsensors Based on Molecularly Imprinted Polymers Synthesized by Two-Photon Stereolithography.

    PubMed

    Gomez, Laura Piedad Chia; Spangenberg, Arnaud; Ton, Xuan-Anh; Fuchs, Yannick; Bokeloh, Frank; Malval, Jean-Pierre; Tse Sum Bui, Bernadette; Thuau, Damien; Ayela, Cédric; Haupt, Karsten; Soppera, Olivier

    2016-07-01

    Two-photon stereolithography is used for rapid prototyping of submicrometre molecularly imprinted polymer-based 3D structures. The structures are evaluated as chemical sensing elements and their specific recognition properties for target molecules are confirmed. The 3D design capability is exploited and highlighted through the fabrication of an all-organic molecularly imprinted polymeric microelectromechanical sensor. PMID:27145145

  4. Rapid preparation of molecularly imprinted polymer by frontal polymerization.

    PubMed

    Zhong, Dan-Dan; Liu, Xin; Pang, Qian-Qian; Huang, Yan-Ping; Liu, Zhao-Sheng

    2013-04-01

    Frontal polymerization was successfully applied, for the first time, to obtain molecularly imprinted polymers (MIPs). The method provides a solvent-free polymerization mode, and the reaction can be completed in 30 min. By this approach, MIPs were synthesized using a mixture of levofloxacin (template), methacrylic acid, and divinylbenzene. The effect of template concentration and the amount of comonomer on the imprinting effect of the resulting MIPs was investigated. The textural and morphological parameters of the MIP particles were also characterized by mercury intrusion porosimetry, nitrogen adsorption isotherms, and scanning electron microscopy, providing evidence concerning median pore diameter, pore volumes, and pore size distributions. The levofloxacin-imprinted polymer formed in frontal polymerization mode showed high selectivity, with an imprinting factor of 5.78. The results suggest that frontal polymerization provides an alternative means to prepare MIPs that are difficult to synthesize and may open up new perspectives in the field of MIPs. PMID:23392405

  5. 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

  6. 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. PMID:21429127

  7. 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. PMID:23693143

  8. 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. PMID:21565062

  9. Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2011-30 November 2011.

    PubMed

    Abreu, Aluana G; Albaina, A; Alpermann, Tilman J; Apkenas, Vanessa E; Bankhead-Dronnet, S; Bergek, Sara; Berumen, Michael L; Cho, Chang-Hung; Clobert, Jean; Coulon, Aurélie; DE Feraudy, D; Estonba, A; Hankeln, Thomas; Hochkirch, Axel; Hsu, Tsai-Wen; Huang, Tsurng-Juhn; Irigoien, X; Iriondo, M; Kay, Kathleen M; Kinitz, Tim; Kothera, Linda; LE Hénanff, Maxime; Lieutier, F; Lourdais, Olivier; Macrini, Camila M T; Manzano, C; Martin, C; Morris, Veronica R F; Nanninga, Gerrit; Pardo, M A; Plieske, Jörg; Pointeau, S; Prestegaard, Tore; Quack, Markus; Richard, Murielle; Savage, Harry M; Schwarcz, Kaiser D; Shade, Jessica; Simms, Ellen L; Solferini, Vera N; Stevens, Virginie M; Veith, Michael; Wen, Mei-Juan; Wicker, Florian; Yost, Jennifer M; Zarraonaindia, I

    2012-03-01

    This article documents the addition of 139 microsatellite marker loci and 90 pairs of single-nucleotide polymorphism sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Aglaoctenus lagotis, Costus pulverulentus, Costus scaber, Culex pipiens, Dascyllus marginatus, Lupinus nanus Benth, Phloeomyzus passerini, Podarcis muralis, Rhododendron rubropilosum Hayata var. taiwanalpinum and Zoarces viviparus. These loci were cross-tested on the following species: Culex quinquefasciatus, Rhododendron pseudochrysanthum Hay. ssp. morii (Hay.) Yamazaki and R. pseudochrysanthum Hayata. This article also documents the addition of 48 sequencing primer pairs and 90 allele-specific primers for Engraulis encrasicolus. PMID:22296658

  10. Permanent genetic resources added to molecular ecology resources database 1 April 2012 - 31 May 2012.

    PubMed

    Abelló, P; Ai, Weiming; Altmann, Carolin; Bernardi, Giacomo; Bonato, Olivier; Burchhardt, Kathleen M; Chen, Xiao; Chen, Zhijian; Cížková, Dagmar; Clouet, Cécile; Cubeta, Marc A; Garcia-Merchan, V H; Gauthier, Nathalie; Gibson, Shane; Halačka, Karel; Hamdi, Faten; Hankeln, Thomas; Hochkirch, Axel; Hrbek, Tomas; Jackson, Alexis M; Lin, Chongwen; Lin, Si-Min; Macpherson, E; Macrander, Jason; Marešová, Eva; Mendel, Jan; Nowak, Michał; Orti, Guillermo; Palero, F; Papoušek, Ivo; Pascual, M; Schmitt, Thomas; Semmens, Brice X; Streito, Jean-Claude; Tian, En-Wei; Tseng, Shu-Ping; Veith, Michael; Vetešník, Lukáš; Wang, Hurng-Yi; Weyer, Jessica; Willis, Stuart; Yu, Hui; Zhou, Zhiming

    2012-09-01

    This article documents the addition of 123 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brenthis ino, Cichla orinocensis, Cichla temensis, Epinephelus striatus, Gobio gobio, Liocarcinus depurator, Macrolophus pygmaeus, Monilinia vaccinii-corymbosi, Pelochelys cantorii, Philotrypesis josephi, Romanogobio vladykovi, Takydromus luyeanus and Takydromus viridipunctatus. These loci were cross-tested on the following species: Cichla intermedia, Cichla ocellaris, Cichla pinima, Epinephelus acanthistius, Gobio carpathicus, Gobio obtusirostris, Gobio sp. 1, Gobio volgensis, Macrolophus costalis, Macrolophus melanotoma, Macrolophus pygmaeus, Romanogobio albipinnatus, Romanogobio banaticus, Romanogobio belingi, Romanogobio kesslerii, Romanogobio parvus, Romanogobio pentatrichus, Romanogobio uranoscopus, Takydromus formosanus, Takydromus hsuehshanesis and Takydromus stejnegeri. PMID:22898144

  11. RAPADAPTE for rapid guideline development: high-quality clinical guidelines can be rapidly developed with limited resources.

    PubMed

    Alper, Brian S; Tristan, Mario; Ramirez-Morera, Anggie; Vreugdenhil, Maria M T; Van Zuuren, Esther J; Fedorowicz, Zbys

    2016-06-01

    Guideline development is challenging, expensive and labor-intensive. A high-quality guideline with 90 recommendations for breast cancer treatment was developed within 6 months with limited resources in Costa Rica. We describe the experience and propose a process others can use and adapt.The ADAPTE method (using existing guidelines to minimize repeating work that has been done) was used but existing guidelines were not current. The method was extended to use databases that systematically identify, appraise and synthesize evidence for clinical application (DynaMed, EBM Guidelines) to provide current evidence searches and critical appraisal of evidence. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to rate the quality of evidence and the strength of recommendations. Draft recommendations with supporting evidence were provided to panel members for facilitated voting to target panel discussion to areas necessary for reaching consensus.Training panelists in guideline development methodology facilitated rapid consensus development. Extending 'guideline adaptation' to 'evidence database adaptation' was highly effective and efficient. Methods were created to simplify mapping DynaMed evidence ratings to GRADE ratings. Twelve steps are presented to facilitate rapid guideline development and enable further adaptation by others.This is a case report and the RAPADAPTE method was retrospectively derived. Prospective replication and validation will support advances for the guideline development community. If guideline development can be accelerated without compromising validity and relevance of the resulting recommendations this would greatly improve our ability to impact clinical care. PMID:27097885

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.

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

    DOE PAGESBeta

    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.

  15. 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. PMID:22642264

  16. 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. PMID:22448966

  17. 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. PMID:21429157

  18. Use of quality rapid diagnostic testing for safe blood transfusion in resource-limited settings.

    PubMed

    Mbanya, D

    2013-05-01

    Blood safety in sub-Saharan Africa is jeopardized by multiple and diverse factors, including the predominance of high-risk family/replacement donors and the high prevalence of transfusion-transmissible infections (TTIs). Thus, stringent diagnostic strategies are vital. Western blotting is costly and technically demanding, and nucleic acid testing technologies, which have been reported to reliably reduce the rate of TTI, are not available in resource-limited settings. Therefore, there is a need for reliable and affordable testing alternatives in these settings. Rapid diagnostic testing has been widely adopted in developing countries, but, for effectiveness in blood safety, highly sensitive tests and the strict selection of low-risk blood donors are indispensable. Although the pre-serological window period remains a source of residual risk for transmission of TTIs during blood transfusion, the combination antigen-antibody rapid tests could contribute significantly to shortening the window period. Thus, despite its limitations, rapid diagnostic testing continues to contribute significantly to blood safety, as a cost-effective means of enhancing screening for TTIs and reducing their transmission in resource-limited rural settings. PMID:23464853

  19. Resources

    MedlinePlus

    ... palate - resources Colon cancer - resources Cystic fibrosis - resources Depression - resources Diabetes - resources Digestive disease - resources Drug abuse - resources Eating disorders - resources Elder care - resources Epilepsy - resources Family troubles - ...

  20. Resources

    MedlinePlus

    ... Diabetes - resources Digestive disease - resources Drug abuse - resources Eating disorders - resources Elder care - resources Epilepsy - resources Family troubles - resources Gastrointestinal disorders - resources Hearing impairment - resources ...

  1. 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. PMID:21564911

  2. 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. PMID:22136175

  3. Negative scaling relationship between molecular diversity and resource abundances

    NASA Astrophysics Data System (ADS)

    Kamimura, Atsushi; Kaneko, Kunihiko

    2016-06-01

    Cell reproduction involves replication of diverse molecule species, in contrast to a simple replication system with fewer components. To address this question of diversity, we study theoretically a cell system with catalytic reaction dynamics that grows by uptake of environmental resources. It is shown that limited resources lead to increased diversity of components within the system, and the number of coexisting species increases with a negative power of the resource uptake. The relationship is explained from the optimum growth speed of the cell, determined by a tradeoff between the utility of diverse resources and the concentration onto fewer components to increase the reaction rate.

  4. 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…

  5. Molecular Mechanisms Underlying the Rapid Arrhythmogenic Action of Bisphenol A in Female Rat Hearts

    PubMed Central

    Gao, Xiaoqian; Liang, Qian; Chen, Yamei

    2013-01-01

    Previously we showed that bisphenol A (BPA), an environmental estrogenic endocrine disruptor, rapidly altered Ca2+ handling and promoted arrhythmias in female rat hearts. The underlying molecular mechanism was not known. Here we examined the cardiac-specific signaling mechanism mediating the rapid impact of low-dose BPA in female rat ventricular myocytes. We showed that protein kinase A (PKA) and Ca2+/CaM-dependent protein kinase II (CAMKII) signaling pathways are the two major pathways activated by BPA. Exposure to 1 nM BPA rapidly increased production of cAMP and rapidly but transiently increased the phosphorylation of the ryanodine receptors by PKA but not by CAMKII. BPA also rapidly increased the phosphorylation of phospholamban (PLN), a key regulator protein of sarcoplasmic reticulum Ca2+ reuptake, by CAMKII but not PKA. The increase in CAMKII phosphorylation of PLN was mediated by phospholipase C and inositol trisphosphate receptor-mediated Ca2+ release, likely from the endoplasmic reticulum Ca2+ storage. These two pathways are likely localized, impacting only their respective target proteins. The rapid impacts of BPA on ryanodine receptors and PLN phosphorylation were mediated by estrogen receptor-β but not estrogen receptor-α. BPA's rapid signaling in cardiac myocytes did not involve activation of ERK1/2. Functional analysis showed that PKA but not CAMKII activation contributed to BPA-induced sarcoplasmic reticulum Ca2+ leak, and both PKA and CAMKII were necessary contributors to the stimulatory effect of BPA on arrhythmogenesis. These results provide mechanistic insight into BPA's rapid proarrhythmic actions in female cardiac myocytes and contribute to the assessment of the consequence and potential cardiac toxicity of BPA exposure. PMID:24140712

  6. Rapid molecular characterization of Clostridium difficile and assessment of populations of C. difficile in stool specimens.

    PubMed

    Wroblewski, Danielle; Hannett, George E; Bopp, Dianna J; Dumyati, Ghinwa K; Halse, Tanya A; Dumas, Nellie B; Musser, Kimberlee A

    2009-07-01

    Our laboratory has developed testing methods that use real-time PCR and pyrosequencing analysis to enable the rapid identification of potential hypervirulent Clostridium difficile strains. We describe a real-time PCR assay that detects four C. difficile genes encoding toxins A (tcdA) and B (tcdB) and the binary toxin genes (cdtA and cdtB), as well as a pyrosequencing assay that detects common deletions in the tcdC gene in less than 4 h. A subset of historical and recent C. difficile isolates (n = 31) was also analyzed by pulsed-field gel electrophoresis to determine the circulating North American pulsed-field (NAP) types that have been isolated in New York State. Thirteen different NAP types were found among the 31 isolates tested, 13 of which were NAP type 1 strains. To further assess the best approach to utilizing our conventional and molecular methods, we studied the populations of C. difficile in patient stool specimens (n = 23). Our results indicated that 13% of individual stool specimens had heterogeneous populations of C. difficile when we compared the molecular characterization results for multiple bacterial isolates (n = 10). Direct molecular analysis of stool specimens gave results that correlated well with the results obtained with cultured stool specimens; the direct molecular analysis was rapid, informative, and less costly than the testing of multiple patient stool isolates. PMID:19403775

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

    PubMed

    Chadwick, Helen; Hundt, P Morten; van Reijzen, Maarten E; 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. PMID:25669393

  8. 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.

  9. 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.

  10. 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

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

    PubMed

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

    2015-07-01

    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

  12. 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

  13. 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

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

    PubMed

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  16. New and rapid procedure for the isolation of ultra-high molecular weight eukaryotic DNA

    SciTech Connect

    Longmire, J.L.; Lewis, A.; Meincke, L.J.; Hildebrand, C.E.

    1986-05-01

    The authors have developed a novel procedure that permits the rapid extraction and isolation of ultra-high molecular weight DNA from avian or mammalian cells using dialysis against a solution of polyethylene glycol (PEG). Cells harvested by centrifugation and washed twice in ice-cold Ca/sup + +/- and Mg/sup + +/-free phosphate buffered saline were resuspended in 5 ml 0.01 M Tris-Cl (pH 8.0); 0.001 M EDTA (TE); sodium dodecyl sulfate and proteinase K were added to final concentrations of 0.1% and 0.1 mg/ml, respectively. After incubation at 37/sup 0/C overnight, the viscous solution was transferred to a mini-collodian bag and concentrated by dialysis against 4-5 changes of 20% PEG in TE over a period of 5 hours at RT. Concentrated samples were desalted by dialysis against fresh TE for two 15 minute intervals. DNA obtained using this procedure gives A/sub 260//A/sub 280/ consistently >1.8. Analysis of DNA size using pulsed field gel electrophoresis revealed a distribution of fragments >500 Kb in length. Further measurements examined were (1) restriction enzyme digestibility, (2) ligation efficiency of restricted DNA, and (3) cloning efficiency using the lambda vector Ch21A. This novel methodology offers a valuable alternative protocol for rapid purification of ultrahigh molecular weight DNA for various applications in molecular biology.

  17. Rapid environmental degradation in a subarctic ecosystem influences resource use of a keystone avian herbivore.

    PubMed

    Winiarski, Kristopher J; McWilliams, Scott R; Rockwell, Robert F

    2012-09-01

    1. Environmental degradation can change resource use strategies of animals and thereby affect survival and fitness. Arctic herbivores may be especially susceptible to the effects of such environmental change because their rapid growth rates demand high-quality forage, which may be limited as environmental conditions deteriorate. We studied the consequences of a trophic cascade, driven by Lesser Snow Goose (Chen caerulescens caerulescens) overgrazing on the south-west coast of Hudson Bay, Canada, which has caused tidal marsh (TM) degradation and the reduction in high-quality forage plants, on gosling growth and resource use. 2. We compared resource use and body size of goslings that inhabited tidal and freshwater marsh (FM) to determine how current foraging strategies influence growth and to test the hypothesis that during early growth goslings require and so consume high-quality TM plants, but that during later growth they may switch to foraging in lower-quality FM. 3. To investigate gosling resource use throughout growth, we measured once a week for 28 days the body size of goslings as well as stable isotope ratios (δ(34) S, δ(15) N and δ(13) C) in multiple tissues of goslings that were collected from both TM and nearby FM. We also measured the stable isotope ratios in forage plants sampled along transects and from gosling foreguts. We used an isotope-mixing model to determine the contribution of FM plants to gosling tissues. 4. Contrary to the proposed hypothesis, goslings inhabiting FM or TM primarily consumed FM plants during early growth. Furthermore, goslings that foraged extensively in FM had similar growth rates and grew to a similar size and body mass, as goslings that foraged in the degraded TM. However, goslings that currently inhabit freshwater or TM were significantly smaller than goslings that inhabited TM in the 1980s prior to habitat degradation. 5. Consequences of smaller overall body size include decreased survival and fecundity for arctic

  18. 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. PMID:25829640

  19. 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

  20. 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.

  1. Evaluating Developed Rule Sets Transferability For Extracting Forest Resources From Rapid Eye Data

    NASA Astrophysics Data System (ADS)

    Kindu, Mengistie; Elatawneh, Alata; Corti, Nicolas; Wallner, Adelheid; Felbermeier, Bernhard; Cabra, Ricardo A.; Schneider, Thomas; Knoke, Thomas

    2013-12-01

    This study examined transferability of developed rule sets in an Alpine test site of Germany (Oberammergau) on classifying forest/non-forest at level 1 and forest types (coniferous, deciduous and mixed) at level 2 from RapidEye satellite image. It was evaluated in test sites of three environmental settings; Ethiopia (Munessa), Ecuador (San Francisco) and China (Shangnan) with similar land use/cover types and topography. The same pre-processing steps were applied in each image of all test sites. Object-based image analysis was used to evaluate the rule sets transferability. Comparisons of direct transferability were conducted using accuracies of the classified images. The forest/non-forest classification at level 1 result reveals the direct transferability. However, accuracies decline steeply along with a disturbed nature of the forest resources. The results of forest type classification at level 2 also show the need of further refinement of the already developed rule sets. Adding more rules or adapting to each of the environmental setting is recommended for higher accuracy.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Past research efforts on genetic mapping in Brassica oleracea and Brassica rapa have been disconnected, utilizing separate mapping populations and different sets of molecular markers. Here we present public immortal mapping populations, molecular markers and linkage maps for rapid cycling B. rapa a...

  3. [Rapid fabrication of molecularly imprinted polymer fibers for solid phase microextraction of bisphenol A].

    PubMed

    Hu, Mei; Zhang, Yijun; Yang, Jinghua; Zhou, Xiaomao; Wei, Zhuqing; Ding, Xiaoqing; Zhang, Yuping

    2015-02-01

    The rapid preparation of molecularly imprinted polymer (MIP) fibers was reported using bisphenol A (BPA) as the template molecular, acetonitrile (ACN) as the porogenic solvent, α-methacrylic acid (MAA) as the functional monomer, ethylene dimethacrylate (EDMA) as the crosslinker, and azodiisobutyronitrile (AIBN) as the thermal initiator. It was carried out within a capillary of 530 µm inner diameter (I. D.) by microwave irradiation in 7 min. The resulted BPA-MIP fibers were pushed out from the capillary, eluted in a vial and inserted in the capillary again followed by the application of the solid phase microextraction (SPME) procedure. The extraction performance was investigated in detail by varying the molar ratios between the template and the monomer (BPA/MAA), the concentration of NaCl, the extraction and desorption time, the pH value and the desorption solvents. The selectivity of the prepared MIP and non-molecularly imprinted polymer (NIP) fibers was comparatively evaluated by selecting two structurally-related compounds, phenol (P) and 4-phenylphenol (PP), and non-analogue dicyandiamide (DCD). The established method was successfully applied for the pretreatment and determination of BPA from beverage samples coupled to high performance liquid chromatography (HPLC). Under the optimal conditions, the linear range of BPA was 10-400 µg/L; the detection limit (LOD) was 0.45 µg/L and the recoveries spiked in the mineral water were 88.4%-102. 8%. The results demonstrated that the developed method can determine BPA in real samples with some advantages of simple pretreatment, rapid analysis, low limit of detection and low consumption of materials. PMID:25989683

  4. 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. PMID:23993570

  5. Competition for cognitive resources during rapid serial processing: changes across childhood.

    PubMed

    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

  6. Molecular dynamics simulation studies of structural and dynamical properties of rapidly quenched Al

    SciTech Connect

    Shen, B.; Liu, C. Y.; Jia, Y.; Yue, G. Q.; Ke, F. S.; Zhao, H. B.; Chen, L. Y.; Wang, S. Y.; Wang, Cai-Zhuang; Ho, Kai-Ming

    2013-06-11

    The structural and dynamical properties of rapidly quenched Al are studied by molecular dynamics simulations. The pair-correlation function of high temperature liquid Al agrees well with the experimental results. Different cooling rates are applied with high cooling rates leading to glass formation, while low cooling rates leading to crystallization. The local structures are characterized by Honeycutt–Andersen indices and Voronoi tessellation analysis. The results show that for high cooling rates, the local structures of the liquid and glassy Al are predominated by icosahedral clusters, together with considerable amount of face-centered cubic and hexagonal close packed short-range orders. These short-range order results are further confirmed using the recently developed atomic cluster alignment method. Moreover, the atomic cluster alignment clearly shows the crystal nucleation process in supercooled liquid of Al. Finally, the mean square displacement for the liquid is also analyzed, and the corresponding diffusion coefficient as a function of temperature is calculated.

  7. 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

  8. 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

  9. 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

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

    PubMed

    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 >10(4) 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 10(4) and 10(5) colony forming units (cfu)/mL M.tb. At 10(3) 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

  11. 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

  12. An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli

    PubMed Central

    Nehring, Ralf B.; Gu, Franklin; Lin, Hsin-Yu; Gibson, Janet L.; Blythe, Martin J.; Wilson, Ray; Bravo Núñez, María Angélica; Hastings, P. J.; Louis, Edward J.; Frisch, Ryan L.; Hu, James C.; Rosenberg, Susan M.

    2016-01-01

    With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter—ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing (‘forward genomics’) demonstrates a strategy that could similarly enable rapid screens in many other microbes. PMID:26578563

  13. 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. PMID:26504243

  14. 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

  15. 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.

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

    PubMed

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

    2016-07-01

    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. PMID:25830555

  17. A rapid assay for affinity and kinetics of molecular interactions with nucleic acids.

    PubMed

    Donaldson, Gregory P; Roelofs, Kevin G; Luo, Yiling; Sintim, Herman O; Lee, Vincent T

    2012-04-01

    The Differential Radial Capillary Action of Ligand Assay (DRaCALA) allows detection of protein interactions with low-molecular weight ligands based on separation of the protein-ligand complex by differential capillary action. Here, we present an application of DRaCALA to the study of nucleic acid-protein interactions using the Escherichia coli cyclic AMP receptor protein (CRP). CRP bound in DRaCALA specifically to (32)P-labeled oligonucleotides containing the consensus CRP binding site, but not to oligonucleotides with point mutations known to abrogate binding. Affinity and kinetic studies using DRaCALA yielded a dissociation constant and dissociation rate similar to previously reported values. Because DRaCALA is not subject to ligand size restrictions, whole plasmids with a single CRP-binding site were used as probes, yielding similar results. DNA can also function as an easily labeled carrier molecule for a conjugated ligand. Sequestration of biotinylated nucleic acids by streptavidin allowed nucleic acids to take the place of the protein as the immobile binding partner. Therefore, any molecular interactions involving nucleic acids can be tested. We demonstrate this principle utilizing a bacterial riboswitch that binds cyclic-di-guanosine monophosphate. DRaCALA is a flexible and complementary approach to other biochemical methods for rapid and accurate measurements of affinity and kinetics at near-equilibrium conditions. PMID:22210888

  18. [Rapidly labelled low molecular weight components in nucleic acid preparations from plant cells].

    PubMed

    Richter, G; Grotha, R

    1974-09-01

    After pulse-labelling with [(3)H]nucleosides and [(3)H]orotic acid of freely suspended callus cells of Petroselinum sativum and tissue fragments of the liverwort Riella helicophylla, rapidly labelled low molecular weight components were detected among the total nucleic acids when these were extracted in the presence of Mg(2+) and finally precipitated with alcohol. These highly labelled species could clearly be distinguished from the 5 S- and 4 S-RNA on the basis of their migration in agarose-polyacrylamide gels (2.4%) and their elution from Sephadex G-150 columns. No degradation was obtained with DNase and RNase. By using [(14)C]ATP as a marker it was found that the low molecular components consisted mainly of nucleoside triphosphates. Only small amounts of nucleoside diphosphates were detected, which were obviously formed by degradation of the former. Nucleic acid preparations free of nucleoside phosphates were obtained by using Mg-free extraction buffers containing EDTA. PMID:24458196

  19. A Molecular Imaging Paradigm to Rapidly Profile Response to Angiogenesis-directed Therapy in Small Animals

    PubMed Central

    Virostko, John; Xie, Jingping; Hallahan, Dennis E.; Arteaga, Carlos L.; Gore, John C.; Manning, H. Charles

    2009-01-01

    Purpose The development of novel angiogenesis-directed therapeutics is hampered by the lack of non-invasive imaging metrics capable of assessing treatment response. We report the development and validation of a novel molecular imaging paradigm to rapidly assess response to angiogenesis-directed therapeutics in preclinical animal models. Procedures A monoclonal antibody-based optical imaging probe targeting vascular endothelial growth factor receptor-2 (VEGFR2) expression was synthesized and evaluated in vitro and in vivo via multispectral fluorescence imaging. Results The optical imaging agent demonstrated specificity for the target receptor in cultured endothelial cells and in vivo. The agent exhibited significant accumulation within 4T1 xenograft tumors. Mice bearing 4T1 xenografts and treated with sunitinib exhibited both tumor growth arrest and decreased accumulation of NIR800-αVEGFR2ab compared to untreated cohorts (p=0.0021). Conclusions Molecular imaging of VEGFR2 expression is a promising non-invasive biomarker for assessing angiogenesis and evaluating the efficacy of angiogenesis-directed therapies. PMID:19130143

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

    PubMed Central

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

    2012-01-01

    Abstract. 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. PMID:23224005

  1. Rapid detection of infectious rotavirus group A using a molecular beacon assay.

    PubMed

    Bertol, Jéssica Wildgrube; Gatti, Maria Silvia Viccari

    2016-08-01

    Rapid, sensitive and specific methods are necessary to detect and quantify infectious viruses. Cultivating and detecting enteric viruses in cell culture are difficult, thus impairing the advancement of knowledge regarding virus-induced diarrhea. Rotavirus (RV) detection has been conducted by serological or molecular biology methods, which do not provide information regarding viral infectivity. Molecular beacons (MBs) have demonstrated efficacy for viral detection in cell culture. We propose a MB assay to detect human rotavirus group A (HuRVA) in cell culture. MA104 cells were mock-infected or infected with HuRVA strains (RotaTeq(®) vaccine and K8 strains), and a specific MB for the HuRVA VP6 gene was used for virus detection. Mock-infected cells showed basal fluorescence, while infected cells exhibited increased fluorescence emission. MB hybridization to the viral mRNA target of HuRVA was confirmed. Fluorescence increased according to the increase in the number of infectious viral particles per cell (MOI 0.5-MOI 1). This technique provides quick and efficient HuRVA detection in cell culture without a need for viral culture for several days or many times until cytopathic effects are visualized. This methodology could be applied in the selection of samples for developing RV vaccines. PMID:27131514

  2. 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

  3. 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. PMID:19072565

  4. Molecular mechanism of lysosomal sialidase deficiency in galactosialidosis involves its rapid degradation.

    PubMed Central

    Vinogradova, M V; Michaud, L; Mezentsev, A V; Lukong, K E; El-Alfy, M; Morales, C R; Potier, M; Pshezhetsky, A V

    1998-01-01

    Galactosialidosis is an inherited lysosomal storage disease caused by the combined deficiency of lysosomal sialidase and beta-galactosidase secondary to the deficiency of cathepsin A/protective protein, which is associated with sialidase and beta-galactosidase in a high-molecular weight (1.27MDa) complex. Clinical phenotypes of patients as well as the composition of compounds which are stored in patient's tissues implicate sialidase deficiency as the underlying pathogenic defect. The recent cloning and sequencing of lysosomal sialidase [Pshezhetsky, Richard, Michaud, Igdoura, Wang, Elsliger, Qu, Leclerc, Gravel, Dallaire and Potier (1997), Nature Genet. 15, 316-320] allowed us to study the molecular mechanism of sialidase deficiency in galactosialidosis. By Western blotting, using antibodies against the recombinant human enzyme, and by NH2-terminal sequencing, we showed that sialidase is synthesized as a 45.5 kDa precursor and after the cleavage of the 47-amino acid signal peptide and glycosylation becomes a 48.3 kDa mature active enzyme present in the 1.27 kDa complex. Transgenic expression of sialidase in cultured skin fibroblasts from normal controls and from galactosialidosis patients, followed by immunofluorescent and immunoelectron microscopy showed that in both normal and affected cells the expressed sialidase was localized on lysosomal and plasma membranes, but the amount of sialidase found in galactosialidosis cells was approximately 5-fold reduced. Metabolic labelling studies demonstrated that the 48.3 kDa mature active form of sialidase was stable in normal fibroblasts (half-life approximately 2.7 h), whereas in galactosialidosis fibroblasts the enzyme was rapidly converted (half-life approximately 30 min) into 38.7 and 24 kDa catalytically inactive forms. Altogether our data provide evidence that the molecular mechanism of sialidase deficiency in galactosialidosis is associated with abnormal proteolytic cleavage and fast degradation. PMID:9480870

  5. A low complexity rapid molecular method for detection of Clostridium difficile in stool.

    PubMed

    McElgunn, Cathal J; Pereira, Clint R; Parham, Nicholas J; Smythe, James E; Wigglesworth, Michael J; Smielewska, Anna; Parmar, Surendra A; Gandelman, Olga A; Brown, Nicholas M; Tisi, Laurence C; Curran, Martin D

    2014-01-01

    Here we describe a method for the detection of Clostridium difficile from stool using a novel low-complexity and rapid extraction process called Heat Elution (HE). The HE method is two-step and takes just 10 minutes, no specialist instruments are required and there is minimal hands-on time. A test method using HE was developed in conjunction with Loop-mediated Isothermal Amplification (LAMP) combined with the real-time bioluminescent reporter system known as BART targeting the toxin B gene (tcdB). The HE-LAMP-BART method was evaluated in a pilot study on clinical fecal samples (tcdB(+), n = 111; tcdB(-), n= 107). The HE-LAMP-BART method showed 95.5% sensitivity and 100% specificity against a gold standard reference method using cytotoxigenic culture and also a silica-based robotic extraction followed by tcdB PCR to control for storage. From sample to result, the HE-LAMP-BART method typically took 50 minutes, whereas the PCR method took >2.5 hours. In a further study (tcdB(+), n = 47; tcdB(-), n= 28) HE-LAMP-BART was compared to an alternative commercially available LAMP-based method, Illumigene (Meridian Bioscience, OH), and yielded 87.2% sensitivity and 100% specificity for the HE-LAMP-BART method compared to 76.6% and 100%, respectively, for Illumigene against the reference method. A subset of 27 samples (tcdB(+), n = 25; tcdB(-), n= 2) were further compared between HE-LAMP-BART, Illumigene, GeneXpert (Cepheid, Sunnyvale, CA) and RIDA®QUICK C. difficile Toxin A/B lateral flow rapid test (R-Biopharm, Darmstadt, Germany) resulting in sensitivities of HE-LAMP-BART 92%, Illumigene 72% GeneXpert 96% and RIDAQuick 76% against the reference method. The HE-LAMP-BART method offers the advantages of molecular based approaches without the cost and complexity usually associated with molecular tests. Further, the rapid time-to-result and simple protocol means the method can be applied away from the centralized laboratory settings. PMID:24416173

  6. A Low Complexity Rapid Molecular Method for Detection of Clostridium difficile in Stool

    PubMed Central

    McElgunn, Cathal J.; Pereira, Clint R.; Parham, Nicholas J.; Smythe, James E.; Wigglesworth, Michael J.; Smielewska, Anna; Parmar, Surendra A.; Gandelman, Olga A.; Brown, Nicholas M.; Tisi, Laurence C.; Curran, Martin D.

    2014-01-01

    Here we describe a method for the detection of Clostridium difficile from stool using a novel low-complexity and rapid extraction process called Heat Elution (HE). The HE method is two-step and takes just 10 minutes, no specialist instruments are required and there is minimal hands-on time. A test method using HE was developed in conjunction with Loop-mediated Isothermal Amplification (LAMP) combined with the real-time bioluminescent reporter system known as BART targeting the toxin B gene (tcdB). The HE-LAMP-BART method was evaluated in a pilot study on clinical fecal samples (tcdB+, n =  111; tcdB−, n  = 107). The HE-LAMP-BART method showed 95.5% sensitivity and 100% specificity against a gold standard reference method using cytotoxigenic culture and also a silica-based robotic extraction followed by tcdB PCR to control for storage. From sample to result, the HE-LAMP-BART method typically took 50 minutes, whereas the PCR method took >2.5 hours. In a further study (tcdB+, n =  47; tcdB−, n  = 28) HE-LAMP-BART was compared to an alternative commercially available LAMP-based method, Illumigene (Meridian Bioscience, OH), and yielded 87.2% sensitivity and 100% specificity for the HE-LAMP-BART method compared to 76.6% and 100%, respectively, for Illumigene against the reference method. A subset of 27 samples (tcdB+, n =  25; tcdB−, n  = 2) were further compared between HE-LAMP-BART, Illumigene, GeneXpert (Cepheid, Sunnyvale, CA) and RIDA®QUICK C. difficile Toxin A/B lateral flow rapid test (R-Biopharm, Darmstadt, Germany) resulting in sensitivities of HE-LAMP-BART 92%, Illumigene 72% GeneXpert 96% and RIDAQuick 76% against the reference method. The HE-LAMP-BART method offers the advantages of molecular based approaches without the cost and complexity usually associated with molecular tests. Further, the rapid time-to-result and simple protocol means the method can be applied away from the centralized laboratory settings. PMID:24416173

  7. 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. PMID:26895881

  8. 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. PMID:27208472

  9. 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. PMID:27336457

  10. 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

  11. Developmental and molecular physiological evidence for the role of phosphoenolpyruvate carboxylase in rapid cotton fibre elongation.

    PubMed

    Li, Xiao-Rong; Wang, Lu; Ruan, Yong-Ling

    2010-01-01

    Cotton fibres are hair-like single-cells that elongate to several centimetres long after their initiation from the ovule epidermis at anthesis. The accumulation of malate, along with K+ and sugars, is thought to play an important role in fibre elongation through osmotic regulation and charge balance. However, there is a lack of evidence for or against such an hypothesis. Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme responsible for the synthesis of malate. The potential role of PEPC in cotton fibre elongation is examined here. Developmentally, PEPC activity was higher at the rapid elongation phase than that at the slow elongation stage. Genotypically, PEPC activity correlated positively with the rate of fibre elongation and the final fibre length attained. Importantly, suppression of PEPC activity by LiCl that reduces its phosphorylation status decreased fibre length. To examine the molecular basis underlying PEPC activity, two cDNAs encoding PEPC, GhPEPC1 and 2, were cloned, which represents the major PEPC genes expressed in cotton fibre. RT-PCR analyses revealed that GhPEPC1 and 2 were highly expressed at the rapid elongation phase but weakly at the slow-to-terminal elongation period. In situ hybridization detected mRNA of GhPEPC1 and 2 in 1 d young fibres but not in the ovule epidermis prior to fibre initiation. Collectively, the data indicate that cotton fibre elongation requires high activity of PEPC, probably through the expression of the GhPEPC1 and 2 genes. PMID:19815688

  12. The Concept of 'Peak Water' for Managing Water Resources in a Rapidly Changing World (Invited)

    NASA Astrophysics Data System (ADS)

    Gleick, P. H.

    2010-12-01

    Managing water resources, and new threats to those resources, will require new thinking, strategies, and tools. Part of the inability to successfully address water problems is the result of traditional approaches to water management that fail to integrate economic, social, and political considerations into technology- and science-based strategies. In particular, human uses of water have consistently come at the expense of ecosystems because of, initially, a lack of knowledge of the links between human and environmental water needs, and later, an inability to integrate the two. This talk will introduce the concept of "Peak Water," recently defined in three ways: peak renewable water resources, peak non-renewable water resources, and peak ecological water. Each of these terms offers the opportunity to help reshape water management decisions in particular regions in ways that can reduce risks to water systems and help managers develop adaptation strategies that meet multiple objectives.

  13. 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

  14. 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

  15. Pulsed molecular-beam, diode-laser spectrometry using rapid scanning techniques

    NASA Astrophysics Data System (ADS)

    De Piante, A.; Campbell, E. J.; Buelow, S. J.

    1989-05-01

    We describe a diode-laser spectrometer for obtaining direct absorption, rovibrational spectra of monomers and/or weakly bound, molecular complexes which are found in supersonic expansions. The spectrometer incorporates a tunable, semiconductor diode-laser source and a pulsed-gas slit nozzle. White cell optics are used in the vacuum chamber to increase effective path length, and a Fabry-Perot etalon is used for relative frequency calibration. Stabilization of the source output is accomplished by locking onto a zero crossing of the etalon fringe-spacing pattern with a gated integrator. The diode laser is scanned rapidly (˜0.2 cm-1/ms) to modulate absorption signals at frequencies which can be electronically filtered from source noise. For 2000 scans, absorbances as small as 1.3×10-5 (0.003% absorption) can be detected. Amplitude fluctuations in the detected signal due to interference effects in the optics and gain variations in the diode laser are eliminated by recording data with and without gas flow from the nozzle, then performing the appropriate subtractions. Because source drift and multiple crossing-angle effects contribute ≤0.0005 cm-1, observed linewidths (0.003 cm-1) were determined to be laser limited. Data obtained on the van der Waals molecule (ArṡCo) are presented and discussed.

  16. Molecularly imprinted ionic liquid magnetic microspheres for the rapid isolation of organochlorine pesticides in environmental water.

    PubMed

    Qiao, Fengxia; Gao, Mengmeng; Yan, Hongyuan

    2016-04-01

    A new type of molecularly imprinted ionic liquid magnetic microspheres was synthesized by aqueous suspension polymerization, using 4,4'-dichlorobenzhydrol as a dummy template, and 1-allyl-3-ethylimidazolium hexafluorophosphate and methacrylic acid as co-functional monomers. The results of morphology and magnetic property evaluation of the obtained microspheres demonstrated that it was monodispersed spherical, possessed a rough surface, and an outstanding magnetic properties. Binding experiments revealed that it had a substantial adsorption capacity and strong recognition ability to organochlorine pesticides (OCPs) in aqueous solution. Then the microspheres were applied as an adsorbent of magnetic dispersive solid-phase extraction for the selective recognition and rapid determination of OCPs in environmental water. Under the optimum conditions, good linearity of the three types of OCPs (dicofol, tetradifon, and p,p'-dichlorodiphenyldichloroethane) was achieved in the range of 1.0-100 ng/mL (r ≥ 0.9994). The recoveries at three spiking levels ranged from 82.6 to 100.4% with the RSDs less than 6.9%. PMID:26791136

  17. Molecular Diagnosis of Long-QT syndrome at 10 Days of Life by Rapid Whole Genome Sequencing

    PubMed Central

    Priest, James R.; Ceresnak, Scott R.; Dewey, Frederick E.; Malloy-Walton, Lindsey E.; Dunn, Kyla; Grove, Megan E.; Perez, Marco V.; Maeda, Katsuhide; Dubin, Anne M.; Ashley, Euan A.

    2014-01-01

    Background The advent of clinical next generation sequencing is rapidly changing the landscape of rare disease medicine. Molecular diagnosis of long QT syndrome (LQTS) can impact clinical management, including risk stratification and selection of pharmacotherapy based on the type of ion channel affected, but results from current gene panel testing requires 4 to 16 weeks before return to clinicians. Objective A term female infant presented with 2:1 atrioventricular block and ventricular arrhythmias consistent with perinatal LQTS, requiring aggressive treatment including epicardial pacemaker, and cardioverter-defibrillator implantation and sympathectomy on day of life two. We sought to provide a rapid molecular diagnosis for optimization of treatment strategies. Methods We performed CLIA-certified rapid whole genome sequencing (WGS) with a speed-optimized bioinformatics platform to achieve molecular diagnosis at 10 days of life. Results We detected a known pathogenic variant in KCNH2 that was demonstrated to be paternally inherited by followup genotyping. The unbiased assessment of the entire catalog of human genes provided by whole genome sequencing revealed a maternally inherited variant of unknown significance in a novel gene. Conclusions Rapid clinical WGS provides faster and more comprehensive diagnostic information by 10 days of life than standard gene-panel testing. In selected clinical scenarios such as perinatal LQTS, rapid WGS may be able to provide more timely and clinically actionable information than a standard commercial test. PMID:24973560

  18. Resource redistribution patterns induced by rapid vegetation shifts and their impacts on land degradation at the desert margins

    NASA Astrophysics Data System (ADS)

    Ravi, S.; Huxman, T. E.; D'Odorico, P.; Collins, S. L.

    2008-12-01

    A common form of land degradation at the desert margins involves the rapid interconversion of vegetation between grasses and woody plants, with ecohydrological and biogeochemical consequences. Here we show, using a combination of field experiments and a spatially explicit model, that the process of degradation can be facilitated both by an increase in heterogeneity (shrub encroachment in to grasslands) and in homogeneity (exotic annual grass invasion into desert shrublands) of soil resources, depending on the plant functional type inducing the change in soil resource distribution. The changes in resource distribution affect patterns of plant productivity and degradation potential. The distribution of soil resources (nutrients and soil moisture), in turn, are controlled by the feedbacks between aeolian/hydrologic transport processes, vegetation and disturbance. Disturbances like fire and grazing greatly affect the rates and patterns of resource redistribution in these systems. Thus, the feedbacks among ecological-hydrological and geomorphic processes acting at patch scale affect the emerging vegetation patterns in these arid landscapes with impacts on regional climate and desertification.

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

    NASA Astrophysics Data System (ADS)

    Kurita, Hirofumi; Miyachika, Saki; Yasuda, Hachiro; Takashima, Kazunori; Mizuno, Akira

    2015-12-01

    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.

  20. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  2. 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.

  3. 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

  4. 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

    2015-06-01

    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

  5. 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

  6. 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

  7. 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. PMID:25126132

  8. 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.

  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. 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.

  11. 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.

  12. [Isolation and characterization of rapidly labelled high molecular RNA from freely suspended callus cells of parsley (Petroselinum sativum)].

    PubMed

    Seitz, U; Richter, G

    1970-12-01

    By culturing of callus tissue originating from root explants of Petroselinum sativum in a synthetic liquid medium under aeration, freely suspended single cells and small clusters consisting of mostly five cells were obtained. The rapidly dividing cells did not exhibit any morphogenesis. Their nucleic acid metabolism was investigated by pulse experiments with (32)P-orthophosphate. Rapidly labelled RNA was prominently found associated with high molecular RNA. During the fractionation of the total nucleic acids on MAK columns it was eluted after the ribosomal RNA components. Its base ratio, however, differed from the latter in that the AMP content was higher than the GMP content. Sucrose gradient centrifugation and polyacrylamide gel electrophoresis resulted in the separation of the ribosomal RNA from the rapidly labelled RNA, thus proving the higher molecular weight of the latter. Based upon the migration in the gel a sedimentation coefficient of approximately 32S was calculated. The possible function of the heavy rapidly labelled RNA component as precursor of ribosomal RNA is discussed. PMID:24500301

  13. The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes

    PubMed Central

    Xie, Yuan; Bergström, Tobias; Jiang, Yiwen; Johansson, Patrik; Marinescu, Voichita Dana; Lindberg, Nanna; Segerman, Anna; Wicher, Grzegorz; Niklasson, Mia; Baskaran, Sathishkumar; Sreedharan, Smitha; Everlien, Isabelle; Kastemar, Marianne; Hermansson, Annika; Elfineh, Lioudmila; Libard, Sylwia; Holland, Eric Charles; Hesselager, Göran; Alafuzoff, Irina; Westermark, Bengt; Nelander, Sven; Forsberg-Nilsson, Karin; Uhrbom, Lene

    2015-01-01

    Glioblastoma (GBM) is the most frequent and malignant form of primary brain tumor. GBM is essentially incurable and its resistance to therapy is attributed to a subpopulation of cells called glioma stem cells (GSCs). To meet the present shortage of relevant GBM cell (GC) lines we developed a library of annotated and validated cell lines derived from surgical samples of GBM patients, maintained under conditions to preserve GSC characteristics. This collection, which we call the Human Glioblastoma Cell Culture (HGCC) resource, consists of a biobank of 48 GC lines and an associated database containing high-resolution molecular data. We demonstrate that the HGCC lines are tumorigenic, harbor genomic lesions characteristic of GBMs, and represent all four transcriptional subtypes. The HGCC panel provides an open resource for in vitro and in vivo modeling of a large part of GBM diversity useful to both basic and translational GBM research. PMID:26629530

  14. 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

  15. 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. PMID:23012544

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

    PubMed

    Yoshida, Catherine E; Kruczkiewicz, Peter; 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

  17. 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

  18. 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.

  19. 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. PMID:11336396

  20. 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. PMID:26545037

  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. Direct Detection of Nocardia spp. in Clinical Samples by a Rapid Molecular Method

    PubMed Central

    Couble, Andrée; Rodríguez-Nava, Verónica; de Montclos, Michèle Pérouse; Boiron, Patrick; Laurent, Frédéric

    2005-01-01

    We developed a 16S PCR-based assay for the rapid detection of Nocardia spp. directly from human clinical samples. The applicability of the assay was confirmed by using 18 samples from patients with nocardiosis as diagnosed by conventional cultures and 20 clinical samples from patients with confirmed tuberculosis used as negative controls. PMID:15815019

  3. 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

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

    PubMed

    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

  5. UCLA's Molecular Screening Shared Resource: enhancing small molecule discovery with functional genomics and new technology.

    PubMed

    Damoiseaux, Robert

    2014-05-01

    The Molecular Screening Shared Resource (MSSR) offers a comprehensive range of leading-edge high throughput screening (HTS) services including drug discovery, chemical and functional genomics, and novel methods for nano and environmental toxicology. The MSSR is an open access environment with investigators from UCLA as well as from the entire globe. Industrial clients are equally welcome as are non-profit entities. The MSSR is a fee-for-service entity and does not retain intellectual property. In conjunction with the Center for Environmental Implications of Nanotechnology, the MSSR is unique in its dedicated and ongoing efforts towards high throughput toxicity testing of nanomaterials. In addition, the MSSR engages in technology development eliminating bottlenecks from the HTS workflow and enabling novel assays and readouts currently not available. PMID:24661210

  6. 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. PMID:17464882

  7. 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. PMID:26695231

  8. 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

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

    PubMed

    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

  10. 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

  11. Rapid investigation of cases and clusters of Legionnaires' disease in England and Wales using direct molecular typing.

    PubMed

    Mentasti, Massimo; Afshar, Baharak; Collins, Samuel; Walker, Jimmy; Harrison, Timothy G; Chalker, Vicki

    2016-06-01

    Legionella pneumophila is the leading cause of Legionnaires' disease, a severe pneumonia that can occur as sporadic cases or point-source outbreaks affecting multiple patients. The infection is acquired by inhalation of aerosols from contaminated water systems. In order to identify the probable source and prevent further cases, clinical and environmental isolates are compared using phenotypic and genotypic methods. Typically up to 10 days are required to isolate L. pneumophila prior to the application of standard typing protocols. A rapid protocol using a real-time PCR specific for L. pneumophila and serogroup 1, combined with nested direct molecular typing, was adopted by Public Health England in 2012 to reduce reporting time for preliminary typing results. This rapid protocol was first used to investigate an outbreak that occurred in July/August 2012 and due to the positive feedback from that investigation, it was subsequently applied to other incidents in England and Wales where faster typing results would have aided incident investigation. We present here results from seven incidents that occurred between July 2012 and June 2015 where the use of this rapid approach provided preliminary characterization of the infecting strain in an average 1.58 days (SD 1.01) after sample receipt in contrast to 9.53 days (SD 3.73) when standard protocols were applied. PMID:27046155

  12. 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. PMID:25218198

  13. MIRG Survey 2011: snapshot of rapidly evolving label-free technologies used for characterizing molecular interactions.

    PubMed

    Yadav, Satya P; Bergqvist, Simon; Doyle, Michael L; Neubert, Thomas A; Yamniuk, Aaron P

    2012-09-01

    The field of label-free biophysical technologies used to quantitatively characterize macromolecular interactions with each other and with small molecules has grown enormously in the last 10 years. The most widely used analytical technologies for characterizing biomolecular interactions are surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), biolayer interferometry (BLI), and analytical ultracentrifugation (AUC). Measuring interaction parameters accurately and quantitatively is challenging, as it requires specialized expertise, training, and instrumentation. The Molecular Interaction Research Group (MIRG) conducted an online survey designed to capture the current profile of label-free technologies, including ITC, SPR, and other biosensors used in academia and the pharmaceutical industry sector. The main goal of the survey was to take a snapshot of laboratory, instrumentation, applications for measuring various biophysical parameters, confidence in data interpretation, data validation and acceptability, and limitations of using various technologies. Through this survey, we anticipate that the participating laboratories will be able to gauge their own capabilities and gain insights into the relative success of the different technologies that they use for characterizing molecular interactions. PMID:22942789

  14. Use of the Agilent 2100 bioanalyzer for rapid and reproducible molecular typing of Streptococcus pneumoniae.

    PubMed

    Hathaway, Lucy J; Brugger, Silvio; Martynova, Alina; Aebi, Suzanne; Mühlemann, Kathrin

    2007-03-01

    Restriction fragment length polymorphism (RFLP) analysis is an economic and fast technique for molecular typing but has the drawback of difficulties in accurately sizing DNA fragments and comparing banding patterns on agarose gels. We aimed to improve RFLP for typing of the important human pathogen Streptococcus pneumoniae and to compare the results with the commonly used typing techniques of pulsed-field gel electrophoresis and multilocus sequence typing. We designed primers to amplify a noncoding region adjacent to the pneumolysin gene. The PCR product was digested separately with six restriction endonucleases, and the DNA fragments were analyzed using an Agilent 2100 bioanalyzer for accurate sizing. The combined RFLP results for all enzymes allowed us to assign each of the 47 clinical isolates of S. pneumoniae tested to one of 33 RFLP types. RFLP analyzed using the bioanalyzer allowed discrimination between strains similar to that obtained by the more commonly used techniques of pulsed-field gel electrophoresis, which discriminated between 34 types, and multilocus sequence typing, which discriminated between 35 types, but more quickly and with less expense. RFLP of a noncoding region using the Agilent 2100 bioanalyzer could be a useful addition to the molecular typing techniques in current use for S. pneumoniae, especially as a first screen of a local population. PMID:17202282

  15. A simple and rapid strategy for the molecular cloning and monitoring of mouse HtrA2 serine protease.

    PubMed

    Kim, Goo-Young; Nam, Min-Kyung; Kim, Sang-Soo; Kim, Ho-Young; Lee, Sang-Kyu; Rhim, Hyangshuk

    2008-03-01

    A simple and rapid strategy for molecular cloning using a gel-free and antibiotic selection method is described which allows for the complete elimination of DNA extraction by gel electrophoresis, and thus has several advantages over gel-based cloning methods, including: (i) a cloning efficiency that is approximately 10-times higher due to the prevention of ethidium bromide ultraviolet-induced DNA damage and contamination with ligase inhibitors; (ii) the amount of plasmid DNA required is approximately five times less; and (iii) the cloning time is several hours less. Once the target gene, such as mouse HtrA2 serine protease, was cloned into the pEGFP-N3 plasmid, the integrity of the kanamycin-resistant molecular clone encoding the GFP fusion protein was verified by immunoblot and immunofluorescence assays. In addition, the integrity of the ampicillin-resistant molecular clone was directly evaluated by analyzing the expression and affinity purification of the GST fusion protein and by measuring its enzymatic activity. Therefore, this method is suitable for the routine construction of a plasmid expressing the gene of interest, and the usefulness of this strategy can be demonstrated by monitoring the expression of the target gene in E. coli and mammalian cells. PMID:17939055

  16. 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

    2015-07-01

    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

  17. 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

  18. Pyrosequencing for rapid molecular identification of Schistosoma japonicum and S. mekongi eggs and cercariae.

    PubMed

    Thanchomnang, Tongjit; Tantrawatpan, Chairat; Intapan, Pewpan M; Sri-Aroon, Pusadee; Limpanont, Yanin; Lulitanond, Viraphong; Janwan, Penchom; Sanpool, Oranuch; Tourtip, Somjintana; Maleewong, Wanchai

    2013-09-01

    Schistosomiasis, which is caused by Schistosoma japonicum and S. mekongi, is a chronic and dangerous widespread disease affecting several countries in Asia. Differentiation between S. japonicum and S. mekongi eggs and/or cercariae via microscopic examination is difficult due to morphological similarities. It is important to identify these etiological agents isolated from animals and humans at the species or genotype level. In this study, a pyrosequencing assay designed to detect S. japonicum and S. mekongi DNA in fecal samples and infected snails was developed and evaluated as an alternative tool to diagnose schistosomiasis. New primers targeting the 18S ribosomal RNA gene were designated for specific amplification. S. japonicum and S. mekongi were identified using a 43-nucleotide pattern of the 18S ribosomal RNA gene and were differentiated using 7 nucleotides within this region. S. japonicum and S. mekongi-infected snails and fecal samples derived from infected mice and rats were differentially detected within a short period of time. The analytical sensitivity of the method enabled the identification of as little as a single cercaria artificially introduced into a pool of 10 non-infected snails and 2 eggs inoculated in 100mg of non-infected fecal sample. To evaluate the comparative efficacy of the assay, identical samples were also analyzed via microscopy and Sanger sequencing. The pyrosequencing technique was found to be superior to the microscopy method and more rapid than the Sanger sequencing method. These results suggest that the pyrosequencing assay is rapid, simple, sensitive and accurate in identifying S. japonicum and S. mekongi in intermediate hosts and fecal samples of the final host. PMID:23831037

  19. A rapid and accurate method for calculation of stratospheric photolysis rates with molecular scattering

    NASA Technical Reports Server (NTRS)

    Boughner, Robert E.

    1986-01-01

    A method for calculating the photodissociation rates needed for photochemical modeling of the stratosphere, which includes the effects of molecular scattering, is described. The procedure is based on Sokolov's method of averaging functional correction. The radiation model and approximations used to calculate the radiation field are examined. The approximated diffuse fields and photolysis rates are compared with exact data. It is observed that the approximate solutions differ from the exact result by 10 percent or less at altitudes above 15 km; the photolysis rates differ from the exact rates by less than 5 percent for altitudes above 10 km and all zenith angles, and by less than 1 percent for altitudes above 15 km.

  20. Rapid and Sensitive Detection of Rotavirus Molecular Signatures Using Surface Enhanced Raman Spectroscopy

    PubMed Central

    Driskell, Jeremy D.; Zhu, Yu; Kirkwood, Carl D.; Zhao, Yiping; Dluhy, Richard A.; Tripp, Ralph A.

    2010-01-01

    Human enteric virus infections range from gastroenteritis to life threatening diseases such as myocarditis and aseptic meningitis. Rotavirus is one of the most common enteric agents and mortality associated with infection can be very significant in developing countries. Most enteric viruses produce diseases that are not distinct from other pathogens, and current diagnostics is limited in breadth and sensitivity required to advance virus detection schemes for disease intervention strategies. A spectroscopic assay based on surface enhanced Raman scattering (SERS) has been developed for rapid and sensitive detection of rotavirus. The SERS method relies on the fabrication of silver nanorod array substrates that are extremely SERS-active allowing for direct structural characterization of viruses. SERS spectra for eight rotavirus strains were analyzed to qualitatively identify rotaviruses and to classify each according to G and P genotype and strain with >96% accuracy, and a quantitative model based on partial least squares regression analysis was evaluated. This novel SERS-based virus detection method shows that SERS can be used to identify spectral fingerprints of human rotaviruses, and suggests that this detection method can be used for pathogen detection central to human health care. PMID:20419101

  1. 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. PMID:23320940

  2. Determination of Very Rapid Molecular Rotation by Using the Central EPR Line

    PubMed Central

    Kurban, Mark R.

    2014-01-01

    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 non-secular 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. PMID:23320940

  3. Whole-Exome Sequencing Enables Rapid Determination of Xeroderma Pigmentosum Molecular Etiology

    PubMed Central

    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

    2013-01-01

    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. PMID:23755135

  4. Rapid molecular TB diagnosis: evidence, policy making and global implementation of Xpert MTB/RIF.

    PubMed

    Weyer, Karin; Mirzayev, Fuad; Migliori, Giovanni Battista; Van Gemert, Wayne; D'Ambrosio, Lia; Zignol, Matteo; Floyd, Katherine; Centis, Rosella; Cirillo, Daniela M; Tortoli, Enrico; Gilpin, Chris; de Dieu Iragena, Jean; Falzon, Dennis; Raviglione, Mario

    2013-07-01

    If tuberculosis (TB) is to be eliminated as a global health problem in the foreseeable future, improved detection of patients, earlier diagnosis and timely identification of rifampicin resistance will be critical. New diagnostics released in recent years have improved this perspective but they require investments in laboratory infrastructure, biosafety and staff specialisation beyond the means of many resource-constrained settings where most patients live. Xpert MTB/RIF, a new assay employing automated nucleic acid amplification to detect Mycobacterium tuberculosis, as well as mutations that confer rifampicin resistance, holds the promise to largely overcome these operational challenges. In this article we position Xpert MTB/RIF in today's TB diagnostic landscape and describe its additional potential as an adjunct to surveillance and surveys, taking into account considerations of pricing and ethics. In what could serve as a model for the future formulation of new policy on diagnostics, we trace the unique process by which the World Health Organization consulted international expertise and systematically assessed published evidence and freshly emerging experience from the field ahead of its endorsement of the Xpert MTB/RIF technology in 2010, summarise subsequent research findings and guidance on who to test and how, and provide perspectives on scaling up the new technology. PMID:23180585

  5. 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.

  6. Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon.

    PubMed

    Lim, Eun-Kyung; Guk, Kyeonghye; Kim, Hyeran; Chung, Bong-Hyun; Jung, Juyeon

    2016-01-01

    A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies. PMID:26509476

  7. 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. PMID:25614968

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

    PubMed

    Janku, Filip; Claes, Bart; 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

    2015-09-29

    Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTMBRAF 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 IdyllaTMBRAF 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

  9. 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

  10. Rapid molecular diagnosis of the Gilbert's syndrome-associated exon 1 mutation within the UGT1A1 gene.

    PubMed

    Hsieh, T-Y; Shiu, T-Y; Chu, N-F; Chao, T-Y; Chu, H-C; Chang, W-K; Chao, Y-C; Huang, H-H

    2014-01-01

    Gilbert's syndrome is suspected in patients with unconjugated hyperbilirubinemia caused by decreased activity of the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene in the absence of abnormal liver function and hemolysis. The major genetic variants underlying Gilbert's syndrome are TATA-box repeats of the promoter region and exon 1 G211A of the coding region, particularly in Asians. The efficacy of DNA melting curve analysis, however, has not been established for the G211A mutation. For rapid and accurate molecular diagnosis of Gilbert's syndrome, DNA melting curve analysis was evaluated for its genotyping capability not only for TATA-box repeats of the UGT1A1 promoter, but also for G211A of UGT1A1 exon 1. TA repeats within the TATA-box sequence and the exon 1 G211A mutation of the UGT1A1 gene were analyzed by DNA melting curve analysis. To evaluate the assay reliability, direct sequencing or polyacrylamide gel electrophoresis was used as a comparative method. All homozygous and heterozygous polymorphisms of A(TA)7TAA within the TATA-box allele and of exon 1 G211A mutants of the UGT1A1 gene were successfully identified with DNA melting curve analysis. DNA melting curve analysis is, therefore, an effective molecular method for the rapid diagnosis of Gilbert's syndrome, as it detects not only TATA-box polymorphisms but also the exon 1 G211A mutation located within the UGT1A1 gene. PMID:24615032

  11. Rapid Concentration and Molecular Enrichment Approach for Sensitive Detection of Escherichia coli and Shigella Species in Potable Water Samples ▿

    PubMed Central

    Maheux, Andrée F.; Bissonnette, Luc; Boissinot, Maurice; Bernier, Jean-Luc T.; Huppé, Vicky; Picard, François J.; Bérubé, Ève; Bergeron, Michel G.

    2011-01-01

    In this work, we used a rapid, simple, and efficient concentration-and-recovery procedure combined with a DNA enrichment method (dubbed CRENAME [concentration and recovery of microbial particles, extraction of nucleic acids, and molecular enrichment]), that we coupled to an Escherichia coli/Shigella-specific real-time PCR (rtPCR) assay targeting the tuf gene, to sensitively detect E. coli/Shigella in water. This integrated method was compared to U.S. Environmental Protection Agency (EPA) culture-based Method 1604 on MI agar in terms of analytical specificity, ubiquity, detection limit, and rapidity. None of the 179 non-E. coli/Shigella strains tested was detected by both methods, with the exception of Escherichia fergusonii, which was detected by the CRENAME procedure combined with the E. coli/Shigella-specific rtPCR assay (CRENAME + E. coli rtPCR). DNA from all 90 E. coli/Shigella strains tested was amplified by the CRENAME + E. coli rtPCR, whereas the MI agar method had limited ubiquity and detected only 65 (72.2%) of the 90 strains tested. In less than 5 h, the CRENAME + E. coli rtPCR method detected 1.8 E. coli/Shigella CFU whereas the MI agar method detected 1.2 CFU/100 ml of water in 24 h (95% confidence). Consequently, the CRENAME method provides an easy and efficient approach to detect as little as one Gram-negative E. coli/Shigella cell present in a 100-ml potable water sample. Coupled with an E. coli/Shigella-specific rtPCR assay, the entire molecular procedure is comparable to U.S. EPA Method 1604 on MI agar in terms of analytical specificity and detection limit but provides significant advantages in terms of speed and ubiquity. PMID:21764965

  12. Improved rapid molecular diagnosis of multidrug-resistant tuberculosis using a new reverse hybridization assay, REBA MTB-MDR

    PubMed Central

    Bang, Hyeeun; Park, Sangjung; Hwang, Joohwan; Jin, Hyunwoo; Cho, Eunjin; Kim, Dae Yoon; Song, Taeksun; Shamputa, Isdore Chola; Via, Laura E.; Barry, Clifton E.; Cho, Sang-Nae

    2011-01-01

    Rapid diagnosis of multidrug-resistant tuberculosis (MDR-TB) is essential for the prompt initiation of effective second-line therapy to improve treatment outcome and limit transmission of this obstinate disease. A variety of molecular methods that enable the rapid detection of mutations implicated in MDR-TB have been developed. The sensitivity of the methods is dependent, in principle, on the repertoire of mutations being detected, which is typically limited to mutations in the genes rpoB, katG and the promoter region of inhA. In this study, a new reverse hybridization assay, REBA MTB-MDR (M&D), that probes mutations in the oxyR–ahpC intergenic region, in addition to those in rpoB, katG and the inhA promoter region, was evaluated. A set of 240 Mycobacterium tuberculosis clinical isolates from patients receiving retreatment regimens was subjected to conventional phenotypic drug-susceptibility testing (DST) and the REBA MTB-MDR assay. The nucleotide sequences of the loci known to be involved in drug resistance were determined for comparison. In brief, the results showed that the REBA MTB-MDR assay efficiently recognized nucleotide changes in the oxyR–ahpC intergenic region as well as those in rpoB, katG and the inhA promoter region with higher sensitivity, resulting in an 81.0 % detection rate for isoniazid resistance. Inclusion of the oxyR–ahpC intergenic region in the REBA MTB-MDR assay improved the overall sensitivity of molecular DST for MDR-TB from 73.1 to 79.9 %. PMID:21596910

  13. Application of Molecular and Serological Methods for Rapid Detection of Mycoplasma gallisepticum Infection (Avian mycoplasmosis).

    PubMed

    Qasem, Jafar A; Al-Mouqati, Salwa A; Al-Ali, Ebtesam M; Ben-Haji, Ahmad

    2015-02-01

    Mycoplasma infection is a major problem in veterinary medicine and in poultry production. The pathogen has many strains, so that diagnosis of the disease using culture method is not effective. The objective of this work was to evaluate the prevalence of Mycoplasma gallisepticum (MG) in Kuwait poultry farms using serology and molecular methods in comparison to the culture under specific conditions. A total of 50 swab samples from choanal cleft and tracheal samples and blood samples were obtained from three different local farms, the blood samples were processed for an Enzyme Linked Immunosorbent Assay (ELISA) detection and the swab samples for Polymerase Chain Reaction (PCR) and culture methods detection. A PCR diagnostic kit (VenoMGs) and ELISA diagnostic kit (ProFLOK), were used in comparison to the traditional culture method, to study the spread of this disease in samples from broiler and layer flocks. Fifty chicken samples were tested for mycoplasmosis, samples tested with ELISA gave 24 positive (48%) and 29 were positive by PCR (58%) and only seven (14%) were positive with culture methods. Swab samples obtained from the choanal cleft gave more positive (60%) with PCR than tracheal samples (56.6%). The culture gave 20 and 5% positive, respectively for tracheal and choanal samples. The methods reported here are of high sensitivity and specificity for Mycoplasma. Both the PCR and ELISA methods are superior to culture method for detection of avian mycoplasmosis. This study showed that MG infection is prevalent in commercial broiler and layer chickens in Kuwait poultry farms. The use of these methods for surveillance of the disease will establish data concerning the predominant Mycoplasmosis diseases in Kuwait if done on a large scale. PMID:26364358

  14. 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. PMID:27591592

  15. 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

  16. 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

  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. Development of a One-Step Probe Based Molecular Assay for Rapid Immunodiagnosis of Infection with M. tuberculosis Using Dried Blood Spots

    PubMed Central

    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

    Background 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. Aim To develop a robust IP-10 based molecular assay for the diagnosis of infection with M. tubercuolsis from whole blood and DBS. Method 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. Results 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.). Conclusion 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. PMID:25184553

  19. A Rapid, Fully Automated, Molecular-Based Assay Accurately Analyzes Sentinel Lymph Nodes for the Presence of Metastatic Breast Cancer

    PubMed Central

    Hughes, Steven J.; Xi, Liqiang; Raja, Siva; Gooding, William; Cole, David J.; Gillanders, William E.; Mikhitarian, Keidi; McCarty, Kenneth; Silver, Susan; Ching, Jesus; McMillan, William; Luketich, James D.; Godfrey, Tony E.

    2006-01-01

    Objective: To develop a fully automated, rapid, molecular-based assay that accurately and objectively evaluates sentinel lymph nodes (SLN) from breast cancer patients. Summary Background Data: Intraoperative analysis for the presence of metastatic cancer in SLNs from breast cancer patients lacks sensitivity. Even with immunohistochemical staining (IHC) and time-consuming review, alarming discordance in the interpretation of SLN has been observed. Methods: A total of 43 potential markers were evaluated for the ability to accurately characterize lymph node specimens from breast cancer patients as compared with complete histologic analysis including IHC. Selected markers then underwent external validation on 90 independent SLN specimens using rapid, multiplex quantitative reverse transcription-polymerase chain reaction (QRT-PCR) assays. Finally, 18 SLNs were analyzed using a completely automated RNA isolation, reverse transcription, and quantitative PCR instrument (GeneXpert). Results: Following analysis of potential markers, promising markers were evaluated to establish relative level of expression cutoff values that maximized classification accuracy. A validation set of 90 SLNs from breast cancer patients was prospectively characterized using 4 markers individually or in combinations, and the results compared with histologic analysis. A 2-marker assay was found to be 97.8% accurate (94% sensitive, 100% specific) compared with histologic analysis. The fully automated GeneXpert instrument produced comparable and reproducible results in less than 35 minutes. Conclusions: A rapid, fully automated QRT-PCR assay definitively characterizes breast cancer SLN with accuracy equal to conventional pathology. This approach is superior to intraoperative SLN analysis and can provide standardized, objective results to assist in pathologic diagnosis. PMID:16495705

  20. Clinical versus Rapid Molecular HIV Diagnosis in Hospitalized African Infants: A Randomized Controlled Trial Simulating Point-of-Care Infant Testing

    PubMed Central

    McCollum, Eric D.; Preidis, Geoffrey A.; Maliwichi, Madalitso; Olson, Dan; McCrary, L. Madeline; Kazembe, Peter N.; van der Horst, Charles; Hoffman, Irving; Hosseinipour, Mina C.

    2014-01-01

    Objective Many African infants fail to receive their diagnostic HIV molecular test results and subsequently, antiretroviral therapy (ART). To determine whether a point-of-care molecular HIV test increases ART access for hospitalized Malawian infants, we simulated a point-of-care test using rapid HIV RNA polymerase chain reaction (Rapid PCR) and compared patient outcomes to an optimized standard care that included assessment with the World Health Organization (WHO) clinical algorithm for HIV infection plus a DNA PCR with a turnaround time of several weeks (standard care). Design Randomized controlled trial. Methods Hospitalized HIV-exposed Malawian infants <12 months old were randomized into Rapid PCR or standard care. Rapid PCR infants obtained molecular test results within 48 hours to facilitate immediate ART, similar to a point-of-care test. Standard care infants meeting clinical criteria were also offered inpatient ART. The primary outcome was appropriate in-hospital ART for DNA or RNA PCR-confirmed HIV-infected infants. Results 300 infants were enrolled. A greater proportion of HIV-infected infants receiving Rapid PCR, versus standard care, started inpatient ART (72.3% vs 47.8%, p=0.016). Among molecular test-negative infants, 26.9% receiving standard care unnecessarily initiated inpatient ART, versus 0.0% receiving Rapid PCR (p<0.001). Rapid PCR modestly reduced the median days to ART (3.0 vs 6.5, p=0.001) but did not influence outpatient follow-up for HIV-infected infants (78.1% vs 82.4%, P = 0.418). Conclusions Rapid PCR, versus an optimized standard care, increased the proportion of hospitalized HIV-infected infants initiating ART and reduced ART exposure in molecular test-negative infants, without meaningfully impacting time to ART initiation or follow-up rates. PMID:24326604

  1. A novel adenosine-based molecular beacon probe for room temperature nucleic acid rapid detection in cotton thread device.

    PubMed

    Du, Ting-E; Wang, Yiyun; Zhang, Yi; Zhang, Tian; Mao, Xun

    2015-02-25

    We used cotton thread as substrate to develop a novel room temperature DNA detection device for low-cost, sensitive and rapid detection of a human genetic disease, hereditary tyrosinemia type I related DNA sequences. A novel adenosine based molecular beacon (ABMB) probe modified on gold nanoparticle was used as reporter probe. In the presence of coralyne, a small molecule which can react with adenosines, the ABMB would form a hairpin structure just like traditional molecular beacon used extensively. In the presence of target DNA sequences, the hairpin structure of ABMB modified on gold nanoparticles will be opened and the biotin group modified at one end of the DNA probes will be released and react with the streptavidin immobilized on the test zone of the cotton thread. The response of the thread based DNA test device is linear over the range of 2.5-100 nM complementary DNA. The ability of our developed device for discriminating the single base mismatched DNA related to a human genetic disease, hereditary tyrosinemia type I, was improved comparing with previous report. It is worth mentioning that the whole assay procedure for DNA test is performed under room temperature which simplified the assay procedures greatly. PMID:25702276

  2. Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing.

    PubMed

    Piatek, A S; Telenti, A; Murray, M R; El-Hajj, H; Jacobs, W R; Kramer, F R; Alland, D

    2000-01-01

    Past genotypic studies of Mycobacterium tuberculosis may have incorrectly estimated the importance of specific drug resistance mutations due to a number of sampling biases including an overrepresentation of multidrug-resistant (MDR) isolates. An accurate assessment of resistance mutations is crucial for understanding basic resistance mechanisms and designing genotypic drug resistance assays. We developed a rapid closed-tube PCR assay using fluorogenic reporter molecules called molecular beacons to detect reportedly common M. tuberculosis mutations associated with resistance to isoniazid and rifampin. The assay was used in a comparative genotypic investigation of two different study populations to determine whether these known mutations account for most cases of clinical drug resistance. We analyzed samples from a reference laboratory in Madrid, Spain, which receives an overrepresentation of MDR isolates similar to prior studies and from a community medical center in New York where almost all of the resistant isolates and an equal number of susceptible controls were available. The ability of the molecular beacon assay to predict resistance to isoniazid and rifampin was also assessed. The overall sensitivity and specificity of the assay for isoniazid resistance were 85 and 100%, respectively, and those for rifampin resistance were 98 and 100%, respectively. Rifampin resistance mutations were detected equally well in isolates from both study populations; however, isoniazid resistance mutations were detected in 94% of the isolates from Madrid but in only 76% of the isolates from New York (P = 0.02). In New York, isoniazid resistance mutations were significantly more common in the MDR isolates (94%) than in single-drug-resistant isolates (44%; P < 0.001). No association between previously described mutations in the kasA gene and isoniazid resistance was found. The first mutations that cause isoniazid resistance may often occur in sequences that have not been commonly

  3. 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)

  4. A Molecular Bar-Coded DNA Repair Resource for Pooled Toxicogenomic Screens

    PubMed Central

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

    2008-01-01

    DNA damage from exogenous and endogenous sources can promote mutations and cell death. Fortunately, cells contain DNA repair and damage signalling 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 signalling 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 over-lapping 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 verse cell mass). The microarray-based classification of Δtag and ΔdinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Δtag and ΔdinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy. A novel biological finding is the observation that while ΔdinG cells

  5. 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

  6. Rapid Molecular Detection of Metastatic Head and Neck Squamous Cell Carcinoma as an Intraoperative Adjunct to Sentinel Lymph Node Biopsy

    PubMed Central

    Ferris, Robert L.; Stefanika, Patrick; Xi, Liqiang; Gooding, William; Seethala, Raja R.; Godfrey, Tony E.

    2012-01-01

    (n=62) nodes in a validation subset. Summary Detection of metastatic SCCHN using multiplexed qRT-PCR can be rapid, accurate, and automated, and may enable SNB to be used for intraoperative decision-making. PCR amplification of tumor marker genes is an effective method of intraoperative molecular staging of SCCHN, and could more appropriately guide application of neck dissection in pN+ SCCHN patients, sparing 60–70% of pN0 patients from unnecessary neck dissection. This technique may also be used for identifying residual neck disease post-treatment, using outpatient fine needle aspiration (FNA) biopsy specimens. PMID:22447185

  7. Molecular Dynamics Simulation of Microstructure Transitions in a Large-Scale Liquid Metal Al System During Rapid Cooling Processes

    NASA Astrophysics Data System (ADS)

    Liu, Rang-Su; Dong, Ke-Jun; Li, Ji-Yong; Yu, Ai-Bing; Zou, Rui-Ping

    2002-08-01

    We perform a molecular dynamics simulation of microstructure transitions in a large-scale system consisting of 400 000 atoms of liquid metal Al by the Clare supercomputer. A cluster-type index method is proposed to describe the structures of various short-range-order clusters in the liquid system. It is demonstrated that the icosahedron cluster (12 0 12 0) plays the most important role in the microstructure transition and that some larger clusters (containing more than 130 atoms) are formed in the system during the rapid cooling processes. It is obvious that the larger clusters are formed by means of combining some middle clusters, and that the middle clusters are formed with several smaller clusters. However, the larger clusters are not formed to be the multi-shell configuration as shown in the mass spectrum analysis of the cluster configurations of Al obtained by gaseous deposition, ionic spray methods and so on. This result can be used to explain the essential distinction between the cluster configurations of Al formed in two different ways.

  8. Optimization of Molecularly Imprinted Polymer Method for Rapid Screening of 17β-Estradiol in Water by Fluorescence Quenching

    PubMed Central

    Yang, Yu; Lai, Edward P. C.

    2011-01-01

    A new method was optimized for rapid screening of 17β-estradiol (E2) in water under 10 min. Molecularly imprinted polymer (MIP) particles (325 ± 25 nm) were added in a water sample at pH 5.5 and 20°C to form a suspension. Fluorescence emission from E2 nonspecifically bound onto the MIP particles was first quenched by large gold nanoparticles (43 ± 5 nm). The Stern-Volmer plot was linear, with dynamic quenching constants (Ksv) of 2.9 ×104 M−1. Fluorescence emission from E2 specifically bound inside the MIP particles was next quenched by small nitrite anions that easily penetrated the imprinted cavities. The Stern-Volmer plot became nonlinear, with Ksv = 2.1 × 102 M−1 and static quenching constant (V) below 1.0 M−1. The difference between these two emission intensities varied as the initial E2 concentration in water, generating a Scatchard calibration curve with R2 > 0.97 from 0.1 to 10 ppb. PMID:21826142

  9. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus

    PubMed Central

    Bhullar, Navreet K.; Street, Kenneth; Mackay, Michael; Yahiaoui, Nabila; Keller, Beat

    2009-01-01

    The continuous improvement of crop plants is essential for agriculture in the coming decades and relies on the use of genetic variability through breeding. However, domestication and modern breeding have reduced diversity in the crop germplasm. Global gene banks conserve diversity, but these resources remain underexplored owing to a lack of efficient strategies to isolate important alleles. Here we describe a large-scale allele-mining project at the molecular level. We first selected a set of 1,320 bread wheat landraces from a database of 16,089 accessions, using the focused identification of germplasm strategy. On the basis of a hierarchical selection procedure on this set, we then isolated 7 resistance alleles of the powdery mildew resistance gene Pm3, doubling the known functional allelic diversity at this locus. This targeted approach for molecular utilization of gene bank accessions reveals landraces as a rich resource of new functional alleles. This strategy can be implemented for other studies on the molecular diversity of agriculturally important genes, as well as for molecular breeding. PMID:19470492

  12. Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus.

    PubMed

    Bhullar, Navreet K; Street, Kenneth; Mackay, Michael; Yahiaoui, Nabila; Keller, Beat

    2009-06-01

    The continuous improvement of crop plants is essential for agriculture in the coming decades and relies on the use of genetic variability through breeding. However, domestication and modern breeding have reduced diversity in the crop germplasm. Global gene banks conserve diversity, but these resources remain underexplored owing to a lack of efficient strategies to isolate important alleles. Here we describe a large-scale allele-mining project at the molecular level. We first selected a set of 1,320 bread wheat landraces from a database of 16,089 accessions, using the focused identification of germplasm strategy. On the basis of a hierarchical selection procedure on this set, we then isolated 7 resistance alleles of the powdery mildew resistance gene Pm3, doubling the known functional allelic diversity at this locus. This targeted approach for molecular utilization of gene bank accessions reveals landraces as a rich resource of new functional alleles. This strategy can be implemented for other studies on the molecular diversity of agriculturally important genes, as well as for molecular breeding. PMID:19470492

  13. 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

  14. Field and laboratory comparative evaluation of rapid malaria diagnostic tests versus traditional and molecular techniques in India

    PubMed Central

    2010-01-01

    Background Malaria presents a diagnostic challenge in most tropical countries. Microscopy remains the gold standard for diagnosing malaria infections in clinical practice and research. However, microscopy is labour intensive, requires significant skills and time, which causes therapeutic delays. The objective of obtaining result quickly from the examination of blood samples from patients with suspected malaria is now made possible with the introduction of rapid malaria diagnostic tests (RDTs). Several RDTs are available, which are fast, reliable and simple to use and can detect Plasmodium falciparum and non-falciparum infections or both. A study was conducted in tribal areas of central India to measure the overall performance of several RDTs for diagnosis of P. falciparum and non-falciparum infections in comparison with traditional and molecular techniques. Such data will be used to guide procurement decisions of policy makers and programme managers. Methods Five commercially available RDTs were tested simultaneously in field in parallel with peripheral blood smears in outbreak-affected areas. The evaluation is designed to provide comparative data on the performance of each RDT. In addition, molecular method i.e. polymerase chain reaction (PCR) was also carried out to compare all three methods. Results A total of 372 patients with a clinical suspicion of malaria from Bajag Primary Health Centre (PHC) of district Dindori and Satanwada PHC of district Shivpuri attending the field clinics of Regional Medical Research Centre were included in the study. The analysis revealed that the First Response Malaria Antigen pLDH/HRP2 combo test was 94.7% sensitive (95% CI 89.5-97.7) and 69.9% specific (95% CI 63.6-75.6) for P. falciparum. However, for non-falciparum infections (Plasmodium vivax) the test was 84.2% sensitive (95% CI 72.1-92.5) and 96.5% specific (95% CI 93.8-98.2). The Parascreen represented a good alternative. All other RDTs were relatively less sensitive for

  15. 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...

  16. 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. PMID:21429109

  17. Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding.

    PubMed

    Joshi, Trupti; Fitzpatrick, Michael R; Chen, Shiyuan; Liu, Yang; Zhang, Hongxin; Endacott, Ryan Z; Gaudiello, Eric C; Stacey, Gary; Nguyen, Henry T; Xu, Dong

    2014-01-01

    Soybean Knowledge Base (http://soykb.org) is a comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja. PMID:24136998

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. A molecular based strategy for rapid diagnosis of toxigenic Fusarium species associated to cereal grains from Argentina.

    PubMed

    Sampietro, D A; Marín, P; Iglesias, J; Presello, D A; Vattuone, M A; Catalan, C A N; Gonzalez Jaen, M T

    2010-01-01

    Fusarium species are worldwide causal agents of ear rot in cereals. Their toxigenic potential is a health risk for both humans and animals. In Argentina, most identification of these fungi has been based on morphological and cross-fertility criteria which are time consuming and require considerable expertise in Fusarium taxonomy and physiology. DNA based approaches have been reported as rapid, sensitive and specific alternatives to identify the main fumonisin and trichothecene-producing Fusarium species. In this work, we used PCR assays and the partial sequence of TEF1-alpha gene (Translation Elongation Factor-1 alpha) to identify the fumonisin and trichothecene-producing species in Fusarium isolates from diverse regions of Argentina. The relative efficiency and reliability of those methods to improve mycotoxin risk prediction in this country were also assessed. Species-specific PCR assays were targeted toward multicopy IGS (Intergenic Spacer of rDNA units) and on the toxin biosynthetic genes FUM1 (fumonisins) and TRI13 and TRI7 genes (trichothecenes). PCR assays based on FUM1 gene and IGS sequences allowed detection and discrimination of the fumonisin producers Fusarium proliferatum and Fusarium verticillioides. Molecular identification of nonfumonisin producers from Gibberella fujikuroi species complex was possible after determination of TEF1-alplha gene sequences, which indicated the presence of Fusarium subglutinans, Fusarium andiyazi and Fusarium thapsinum. TEF-1 alpha gene sequences also allowed discrimination of the different species of the Fusarium graminearum complex (F. graminearum sensu lato) as F. graminearum sensu stricto, Fusarium meridionale and Fusarium boothii. The last two species belonged to NIV chemotype and were detected for the first time in the subtropical region of Argentina while F. graminearum sensu stricto was DON producer only, which was also confirmed by specific PCR assays based on TRI137/TRI7 genes. Our results indicated that the PCR

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  2. 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. PMID:26392185

  3. Rapid Training and Implementation of the Pollock Technique, a Safe, Effective Newborn Circumcision Procedure, in a Low-Resource Setting

    PubMed Central

    Bristow, Claire C.; Pollock, Neil; Crouse, Pierre; Theodore, Harry; Bonhomme, Jerry; Gaston, Claire F. Stéphanie; Dévieux, Jessy G.; Pape, Jean William; Klausner, Jeffrey D.

    2015-01-01

    Male circumcision is highly protective against urinary tract infections, inflammatory conditions of the penis, sexually transmitted infections, and urogenital cancers. We aimed to reintroduce newborn male circumcision through the creation of a training program in Port-au-Prince, Haiti—an area with a considerable burden of preventable urogenital infections, sexually transmitted infections, and low circumcision rate—after an earlier study reported that a majority of Haitian medical providers were in need of and wanted newborn circumcision training. The program was conducted at the GHESKIO Health Centers, a large, non-governmental clinic offering comprehensive pediatric and adult health services. Two Haitian obstetricians and seven nurses learned circumcision procedures. On training completion, one of two obstetricians achieved surgical competence. Introduction of a newborn male circumcision training program was feasible, achieving an acceptable rate of procedural competency and high-quality services. Permanent resources now exist in Haiti to train additional providers to perform newborn male circumcisions. PMID:27335959

  4. 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.

  5. 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

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

    PubMed

    Wyffels, Jennifer; King, Benjamin L; 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. Use of a Rapid Test for Diagnosis of Dengue during Suspected Dengue Outbreaks in Resource-Limited Regions.

    PubMed

    Hunsperger, Elizabeth A; Sharp, Tyler M; Lalita, Paul; Tikomaidraubuta, Kini; Cardoso, Yolanda Rebello; Naivalu, Taina; Khan, Aalisha Sahu; Marfel, Maria; Hancock, W Thane; Tomashek, Kay M; Margolis, Harold S

    2016-08-01

    Dengue is major public health problem, globally. Timely verification of suspected dengue outbreaks allows for public health response, leading to the initiation of appropriate clinical care. Because the clinical presentation of dengue is nonspecific, dengue diagnosis would benefit from a sensitive rapid diagnostic test (RDT). We evaluated the diagnostic performance of an RDT that detects dengue virus (DENV) nonstructural protein 1 (NS1) and anti-DENV IgM during suspected acute febrile illness (AFI) outbreaks in four countries. Real-time reverse transcription-PCR and anti-DENV IgM enzyme-linked immunosorbent assay were used to verify RDT results. Anti-DENV IgM RDT sensitivity and specificity ranged from 55.3 to 91.7% and 85.3 to 98.5%, respectively, and NS1 sensitivity and specificity ranged from 49.7 to 92.9% and 22.2 to 89.0%, respectively. Sensitivity varied by timing of specimen collection and DENV serotype. Combined test results moderately improved the sensitivity. The use of RDTs identified dengue as the cause of AFI outbreaks where reference diagnostic testing was limited or unavailable. PMID:27225409

  8. 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

    2014-02-01

    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. PMID:24335979

  9. 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

    2014-08-01

    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. PMID:24911165

  10. High Molecular Weight Typing with MALDI-TOF MS - A Novel Method for Rapid Typing of Clostridium difficile

    PubMed Central

    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. PMID:25923527

  11. 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

  12. 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.

  13. Rapid detection of live methicillin-resistant Staphylococcus aureus by using an integrated microfluidic system capable of ethidium monoazide pre-treatment and molecular diagnosis

    PubMed Central

    Liu, Yu-Hsin; Wang, Chih-Hung; Wu, Jiunn-Jong; Lee, Gwo-Bin

    2012-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium resistant to all existing penicillin and lactam-based antimicrobial drugs and, therefore, has become one of the most prevalent antibiotic-resistant pathogens found in hospitals. The multi-drug resistant characteristics of MRSA make it challenging to clinically treat infected patients. Therefore, early diagnosis of MRSA has become a public-health priority worldwide. Conventionally, cell-culture based methodology and microscopic identification are commonly used for MRSA detection. However, they are relatively time-consuming and labor-intensive. Recently, molecular diagnosis based on nucleic acid amplification techniques, such as polymerase chain reaction (PCR), has been widely investigated for the rapid detection of MRSA. However, genomic DNA of both live and dead pathogens can be distinguished by conventional PCR. These results thus could not provide sufficient confirmation of an active infection for clinicians. In this study, live MRSA was rapidly detected by using a new integrated microfluidic system. The microfluidic system has been demonstrated to have 100% specificity to detect live MRSA with S. aureus and other pathogens commonly found in hospitals. The experimental results showed that the limit of detection for live MRSA from biosamples was approximately 102 CFU/μl. In addition, the entire diagnostic protocol, from sample pre-treatment to fluorescence observation, can be automatically completed within 2.5 h. Consequently, this microfluidic system may be a powerful tool for the rapid molecular diagnosis of live MRSA. PMID:24019858

  14. Comparison of laboratory costs of rapid molecular tests and conventional diagnostics for detection of tuberculosis and drug-resistant tuberculosis in South Africa

    PubMed Central

    2013-01-01

    Background 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. Methods 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. Results 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%). Conclusions 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. PMID:23895665

  15. 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

  16. Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling.

    PubMed

    Killian, J Keith; Walker, Robert L; Suuriniemi, Miia; Jones, Laura; Scurci, Stephanie; Singh, Parvati; Cornelison, Robert; Harmon, Shannon; Boisvert, Nichole; Zhu, Jack; Wang, Yonghong; Bilke, Sven; Davis, Sean; Giaccone, Giuseppe; Smith, William I; Meltzer, Paul S

    2010-11-01

    Microarray technologies provide high-resolution maps of chromosome imbalances and epigenomic aberrations in the cancer cell genome. Such assays are often sensitive to sample DNA integrity, voiding the utility of many archival pathology specimens and necessitating the special handling of prospective clinical specimens. We have identified the remarkable preservation of higher-molecular weight DNA in archival fine-needle aspiration cytopathology specimens from patients greater than 10 years of age. We further demonstrate the outstanding technical performance of 57 fine-needle aspiration cytopathology samples for aberration detection on high-resolution comparative genomic hybridization array, DNA methylation, and single nucleotide polymorphism genotyping platforms. Forty-four of 46 malignant aspirates in this study manifested unequivocal genomic aberrations. Importantly, matched Papanicolaou and Diff-Quik fine-needle aspiration cytopathology samples showed critical differences in DNA preservation and DNA integrity. Overall, this study identifies a largely untapped reserve of human pathology specimens for molecular profiling studies, with ramifications for the prospective collection of clinical biospecimens. PMID:20959611

  17. High-Dose Imatinib in Newly Diagnosed Chronic-Phase Chronic Myeloid Leukemia: High Rates of Rapid Cytogenetic and Molecular Responses

    PubMed Central

    Cortes, Jorge E.; Kantarjian, Hagop M.; Goldberg, Stuart L.; Powell, Bayard L.; Giles, Francis J.; Wetzler, Meir; Akard, Luke; Burke, John M.; Kerr, Robert; Saleh, Mansoor; Salvado, August; McDougall, Karen; Albitar, Maher; Radich, Jerald

    2009-01-01

    Purpose Long-term clinical outcome data have established imatinib 400 mg/d as standard front-line treatment for newly diagnosed patients with chronic myeloid leukemia (CML). Patients and Methods The Rationale and Insight for Gleevec High-Dose Therapy (RIGHT) trial is a multicenter study of imatinib 400 mg twice a day as initial therapy in 115 patients (70% Sokal low risk) with newly diagnosed CML in chronic phase who were observed for both molecular and cytogenetic responses for up to 18 months. Eighty-three patients (72%) completed the study, 10 patients (9%) discontinued the study because of adverse events, and six patients (5%) discontinued because of unsatisfactory therapeutic effect. Results Polymerase chain reaction analysis demonstrated rapid kinetics of major molecular response (MMR), with 48% of patients achieving MMR by 6 months, 54% by 12 months, and 63% by 18 months. Corresponding complete molecular response rates were 39%, 44%, and 55%, respectively. Median dose-intensity was 98%. Overall, 79% of patients who received at least 90% dose-intensity achieved MMR. The most frequent adverse events included myelosuppression, rash, fatigue, and musculoskeletal symptoms. Conclusion This study suggests that imatinib 400 mg twice a day results in more rapid reduction in tumor burden than imatinib 400 mg/d with minimal added toxicity. PMID:19720924

  18. 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

  19. 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...

  20. Molecular Analysis Among MCA13-reactive Isolates Reveals a Strategy for Rapid Assessment of Citrus tristeza Virus Severity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus tristeza virus (CTV) genotypes vary in disease severity ranging from symptomless to virulent (stem pitting) in commercial citrus plantings. Because CTV is spread by propagation and by aphid vectors, rapid identification and virulence typing are critical for control and interdiction activitie...

  1. Molecular analysis among MCA13-reactive isolates reveals a rapid strategy for assessment of Citrus tristeza virus severity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus tristeza virus (CTV) usually occurs as a complex of strains that vary greatly in severity and aphid transmissibility. A rapid assay, therefore, is needed to distinguish potentially mild vs. severe strains of CTV for disease mitigation. An economical and practical strategy to screen for poten...

  2. Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resource.

    PubMed

    Eichler, Evan E; DeJong, Pieter J

    2002-05-01

    The anticipated completion of two of the most biomedically relevant genomes, mouse and human, within the next three years provides an unparalleled opportunity for the large-scale exploration of genome evolution. Targeted sequencing of genomic regions in a panel of primate species and comparison to reference genomes will provide critical insight into the nature of single-base pair variation, mechanisms of chromosomal rearrangement, patterns of selection, and species adaptation. Although not recognized as model "genetic organisms" because of their longevity and low fecundity, 30 of the approximately 300 primate species are targets of biomedical research. The existence of a human reference sequence and genomic primate BAC libraries greatly facilitates the recovery of genes/genomic regions of high biological interest because of an estimated maximum neutral nucleotide sequence divergence of 25%. Primate species, therefore, may be regarded as the ideal model "genomic organisms". Based on existing BAC library resources, we propose the construction of a panel of primate BAC libraries from phylogenetic anchor species for the purpose of comparative medicine as well as studies of genome evolution. PMID:11997334

  3. Molecular epidemiology of Pseudomonas aeruginosa from cystic fibrosis in Sicily: genome macrorestriction analysis and rapid PCR-ribotyping.

    PubMed

    Agodi, A; Sciacca, A; Campanile, F; Messina, C; Barchitta, M; Sciacca, S; Stefani, S

    2000-07-01

    This study addresses the epidemiologic relatedness of a collection of Pseudomonas aeruginosa isolates from cystic fibrosis patients attending the Pediatric Clinic, Catania, Sicily. Genome macrorestriction analysis after pulsed field gel electrophoresis (PFGE) was used to characterise all strains. Furthermore, a rapid typing procedure, developed in this study, based on polymerase chain reaction amplified ribosomal DNA spacer polymorphisms (PCR-ribotyping), straight from bacterial cultures, was used. On the basis of macrorestriction analysis after PFGE, persistence of infection was shown in all patients; two cross-transmission episodes were identified in the nosocomial as well as in the familiar environment. PCR-ribotyping proved to be useful for a DNA-based identification test, suitable for screening purposes. The rapid amplification protocol here tested is proposed to evaluate the discriminatory power of other specific target sequences in PCR-based typing assays, for epidemiologic purposes. PMID:10939047

  4. New renewable resource amphiphilic molecular design for size-controlled and highly ordered polyaniline nanofibers.

    PubMed

    Anilkumar, P; Jayakannan, M

    2006-06-20

    We demonstrate here, for the first time, a unique strategy for conducting polyaniline nanofibers based on renewable resources. Naturally available cardanol, which is an industrial waste and main pollutant from the cashew nut industry, is utilized for producing well-defined polyaniline nanofibers. A new amphiphilic molecule is designed and developed from cardanol, which forms a stable emulsion with aniline for a wide composition range in water (1:1 to 1:100 dopant/aniline mole ratio) to produce polyaniline nanofibers. The scanning electron microscopy and transmission electron microscopy analysis of the nanofibers reveals that the dopant/aniline ratio plays a major role in determining the shape and size of polyaniline nanofibers. The nanofiber length increases with the increase in the dopant/aniline ratio, and perfectly linear, well-defined nanofibers of lengths as long as 7-8 muM were produced. The amphiphilic dopant has a built-in head-to-tail geometry and effectively penetrates into the polyaniline chains to form highly organized nanofibers. Wide-angle X-ray diffraction (WXRD) spectra of the nanofibers showed a new peak at 2theta = 6.3 (d spacing = 13.9 A) corresponding to the three-dimensional solid-state ordering of polyaniline-dopant chains, and this peak intensity increases with increase in the nanofiber length. The comparison of morphology and WXRD reveals that high ordering in polyaniline chains results in the formation of long, well-defined nanofibers, and this direct correlation for the polyaniline nanofibers with solid-state ordering has been established. The conductivity of the polyaniline nanofibers also increases with increase in the solid-state ordering rather than increasing with the extent of doping. The polyaniline nanofibers are freely soluble in water and possess high environmental and thermal stability up to 300 degrees C for various applications. PMID:16768535

  5. 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 0.01μg/mL and 0.03μg/mL for theophylline, 0.05μg/mL and 0.17μg/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. PMID:26992488

  6. Rapid molecular subtyping by reverse transcription polymerase chain reaction of the neuraminidase gene of avian influenza A viruses.

    PubMed

    Fereidouni, S R; Starick, E; Grund, C; Globig, A; Mettenleiter, T C; Beer, M; Harder, T

    2009-03-30

    Accurate identification of hemagglutinin (HA) and neuraminidase (NA) subtypes of influenza A viruses is an integral part of monitoring programs targeting avian influenza viruses (AIV). Use of highly sensitive molecular screening methods such as pan influenza-specific real-time RT-PCR (rRT-PCR) yields an increasing number of samples which are positive for AIV RNA but negative by virus isolation and, therefore, require molecular, instead of serological, subtyping. We developed specific RT-PCR assays for all known nine AIV NA subtypes. Validation using 43 reference isolates from different animal species revealed good performance characteristics regarding sensitivity and specificity. On basis of serial tenfold dilution series of reference isolates a benchmark value of C(t) 32 in an M gene-specific rRT-PCR became evident below which all nine NA subtypes were readily detectable by the subtype-specific RT-PCRs. For subtypes N1, N2, N4 and N6 detection was extended to dilutions with C(t) values of up to 35. Diagnostic applicability of the whole set of conventional NA-specific RT-PCRs was evaluated by analysis of 119 different diagnostic samples from wild birds which proved to be positive for AIV by M gene-specific rRT-PCR. Diagnostic sensitivity and specificity was confirmed by sequencing NA amplicons from 41 field isolates generated from this set and by NA inhibition assays. A universal molecular HA/NA subtyping algorithm for rRT-PCR positive avian influenza virus monitoring samples is proposed which may complement classical serological subtyping of influenza A virus isolates. PMID:19028027

  7. 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

    2015-04-01

    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. PMID:25686279

  8. Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Sterile or Nonsterile Clinical Samples by a New Molecular Assay

    PubMed Central

    Francois, Patrice; Pittet, Didier; Bento, Manuela; Pepey, Béatrice; Vaudaux, Pierre; Lew, Daniel; Schrenzel, Jacques

    2003-01-01

    A rapid procedure was developed for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) directly from sterile sites or mixed flora samples (e.g., nose or inguinal swabs). After a rapid conditioning of samples, the method consists of two main steps: (i) immunomagnetic enrichment in S. aureus and (ii) amplification-detection profile on DNA extracts using multiplex quantitative PCR (5′-exonuclease qPCR, TaqMan). The triplex qPCR assay measures simultaneously the following targets: (i) mecA gene, conferring methicillin resistance, common to both S. aureus and Staphylococcus epidermidis; (ii) femA gene from S. aureus; and (iii) femA gene from S. epidermidis. This quantitative approach allows discrimination of the origin of the measured mecA signal. qPCR data were calibrated using two reference strains (MRSA and methicillin-resistant S. epidermidis) processed in parallel to clinical samples. This 96-well format assay allowed analysis of 30 swab samples per run and detection of the presence of MRSA with exquisite sensitivity compared to optimal culture-based techniques. The complete protocol may provide results in less than 6 h (while standard procedure needs 2 to 3 days), thus allowing prompt and cost-effective implementation of contact precautions. PMID:12517857

  9. The manual mycobacteria growth indicator tube and the nitrate reductase assay for the rapid detection of rifampicin resistance of M. Tuberculosis in low resource settings

    PubMed Central

    2012-01-01

    Background Tuberculosis (TB) is a disease of poverty that contributes significantly to ill-health in developing countries. Drug resistant TB is a major challenge to disease control. Early diagnosis and rapid determination of drug sensitivity is of paramount importance in eradication of TB. Although automated liquid culture based methods are available for rapid detection of drug resistance, the high cost of these tests prevent them from being used routinely in low resource settings. This study compares two phenotypic methods, the manual Mycobacteria Growth Indicator Tube (MGIT) and the Nitrate Reductase Assay (NRA) in liquid medium, with the agar proportion method (APM), the gold standard for susceptibility testing of Mycobacterium tuberculosis. Methodology Fourteen day old M. tuberculosis strains (n=373) grown on solid media were used for drug susceptibility testing by APM, NRA and the manual MGIT method. Rifampicin free and rifampicin incorporated (final concentration, 1 μg/ml) media were inoculated with the recommended concentrations of mycobacterial suspensions and incubated at 37°C in 5% CO2. In the APM, the proportion of colonies in the drug containing medium was determined. In the NRA, the colour change in the medium was compared with a standard colour series after day 6 and day 12 of incubation. Growth in the MGIT was detected using the manual MGIT reader from day 2 onwards. The 2 methods were compared with the gold standard, APM to determine sensitivity and specificity and agreement between the methods was calculated using kappa statistics. Results Thirty one (31) rifampicin resistant isolates were identified. When compared with the APM, the sensitivity of detection of rifampicin resistance was 85% for the NRA and 93% for the manual MGIT and the specificity was 99% and 100% respectively. Both assays, NRA (κ=0.86) and manual MGIT method (κ= 0.94) were in excellent agreement with the APM. The mean turnaround time for manual MGIT method and NRA were 08

  10. Ni(II)NTA AuNPs as a low-resource malarial diagnostic platform for the rapid colorimetric detection of Plasmodium falciparum Histidine-Rich Protein-2.

    PubMed

    Gulka, Christopher P; Swartz, Joshua D; Wright, David W

    2015-04-01

    Diagnosing infectious diseases remains a challenge in the developing world where there is a lack of dependable electricity, running water, and skilled technicians. Although rapid immunochromatographic tests (RDTs) have been deployed to diagnose diseases such as malaria, the extreme climate conditions encountered in these regions compounded with the discrepancies in test manufacturing have yielded varying results, so that more innovative and robust technologies are sought. Devoid of antibodies and thermally sensitive materials, we present a robust, colorimetric diagnostic platform for the detection of a malarial biomarker, Plasmodium falciparum Histidine-Rich Protein 2 (PfHRP-II). The assay exploits the optical properties of gold nanoparticles, covalently coupling them to a Ni(II)NTA recognition element specific for PfHRP-II. In the presence of the recombinant malarial biomarker (rcHRP-II), the Ni(II)NTA AuNPs begin to crosslink and aggregate in as little as one minute, triggering a red-to-purple color change in solution. To increase assay sensitivity and platform stability suitable for low-resource regions, the Ni(II)NTA AuNPs were assembled with varying spacer ligands in a mixed monolayer presentation. When assembled with a negatively charged Peg4-thiol ligand, the Ni(II)NTA AuNPs demonstrate low nanomolar limits of rcHRP-II detection in physiological concentrations of human serum albumin and maintain excellent stability at 37°C when stored for four weeks. Detection of the malaria biomarker is also measured by capturing and processing images of aggregated gold nanoparticles with a smartphone camera. By utilizing a smartphone camera and image processing application, there is no significant difference in assay sensitivity and rcHRP-II limit of detection in comparison to a spectrophotometer, further making this diagnostic platform applicable for use in low-resource regions. PMID:25640131

  11. Variegated clonality and rapid emergence of new molecular lesions in xenografts of acute lymphoblastic leukemia are associated with drug resistance.

    PubMed

    Nowak, Daniel; Liem, Natalia L M; Mossner, Maximilian; Klaumünzer, Marion; Papa, Rachael A; Nowak, Verena; Jann, Johann C; Akagi, Tadayuki; Kawamata, Norihiko; Okamoto, Ryoko; Thoennissen, Nils H; Kato, Motohiro; Sanada, Masashi; Hofmann, Wolf-Karsten; Ogawa, Seishi; Marshall, Glenn M; Lock, Richard B; Koeffler, H Phillip

    2015-01-01

    The use of genome-wide copy-number analysis and massive parallel sequencing has revolutionized the understanding of the clonal architecture of pediatric acute lymphoblastic leukemia (ALL) by demonstrating that this disease is composed of highly variable clonal ancestries following the rules of Darwinian selection. The current study aimed to analyze the molecular composition of childhood ALL biopsies and patient-derived xenografts with particular emphasis on mechanisms associated with acquired chemoresistance. Genomic DNA from seven primary pediatric ALL patient samples, 29 serially passaged xenografts, and six in vivo selected chemoresistant xenografts were analyzed with 250K single-nucleotide polymorphism arrays. Copy-number analysis of non-drug-selected xenografts confirmed a highly variable molecular pattern of variegated subclones. Whereas primary patient samples from initial diagnosis displayed a mean of 5.7 copy-number alterations per sample, serially passaged xenografts contained a mean of 8.2 and chemoresistant xenografts a mean of 10.5 copy-number alterations per sample, respectively. Resistance to cytarabine was explained by a new homozygous deletion of the DCK gene, whereas methotrexate resistance was associated with monoallelic deletion of FPGS and mutation of the remaining allele. This study demonstrates that selecting for chemoresistance in xenografted human ALL cells can reveal novel mechanisms associated with drug resistance. PMID:25450514

  12. Rapid identification of molecular changes in tulsi (Ocimum sanctum Linn) upon ageing using leaf spray ionization mass spectrometry.

    PubMed

    Sarkar, Depanjan; Srimany, Amitava; Pradeep, T

    2012-10-01

    Tulsi or Holy Basil (Ocimum sanctum Linn) is a medicinally important plant. Ursolic acid (UA) and oleanolic acid (OA) are among its major constituents which account for many medicinal activities of the plant. In the present work, we deployed a new ambient ionization method, leaf spray ionization, for rapid detection of UA, OA and their oxidation products from tulsi leaves. Tandem electrospray ionization mass spectrometry (ESI-MS) has been performed on tulsi leaf extracts in methanol to establish the identity of the compounds. We probed changes occurring in the relative amounts of the parent compounds (UA and OA) with their oxidized products and the latter show an increasing trend upon ageing. The findings are verified by ESI-MS analysis of tulsi leaf extracts, which shows the same trend proving the reliability of the leaf spray method. PMID:22900261

  13. 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

  14. 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

  15. 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

  16. Rapid and Specific Detection, Molecular Epidemiology, and Experimental Virulence of the O16 Subgroup within Escherichia coli Sequence Type 131

    PubMed Central

    Clermont, Olivier; Johnston, Brian; Clabots, Connie; Tchesnokova, Veronika; Sokurenko, Evgeni; Junka, Adam F.; Maczynska, Beata; Denamur, Erick

    2014-01-01

    Escherichia coli sequence type 131 (ST131), a widely disseminated multidrug-resistant extraintestinal pathogen, typically exhibits serotype O25b:H4. However, certain ST131 isolates exhibit serotype O16:H5 and derive from a phylogenetic clade that is distinct from the classic O25b:H4 ST131 clade. Both clades are assigned to ST131 by the Achtman multilocus sequence typing (MLST) system and a screening PCR assay that targets ST131-specific sequence polymorphisms in the mdh and gyrB genes. However, they are classified as separate STs by the Pasteur Institute MLST system, and an ST131 PCR method that targets the O25b rfb region and an ST131-specific polymorphism in pabB detects only the O25b-associated clade. Here, we describe a novel PCR-based method that allows for rapid and specific detection of the O16-associated ST131 clade. The clade members uniformly contained allele 41 of fimH (type 1 fimbrial adhesin) and a narrow range of alleles of gyrA and parC (fluoroquinolone target genes). The virulence genotypes of the clade members resembled those of classic O25b:H4 ST131 isolates; representative isolates were variably lethal in a mouse subcutaneous sepsis model. Several pulsotypes spanned multiple sources (adults, children, pets, and human fecal samples) and locales. An analysis of recent clinical E. coli collections showed that the O16 ST131 clade is globally distributed, accounts for 1 to 5% of E. coli isolates overall, and, when compared with other ST131 isolates, it is associated with resistance to ampicillin, gentamicin, and trimethoprim-sulfamethoxazole and with susceptibility to fluoroquinolones and extended-spectrum cephalosporins. Attention to this O16-associated ST131 clade, which is facilitated by our novel PCR-based assay, is warranted in future epidemiological studies of ST131 and, conceivably, in clinical applications. PMID:24501035

  17. 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. PMID:25762768

  18. 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

  19. Molecular evolution of GH in primates: characterisation of the GH genes from slow loris and marmoset defines an episode of rapid evolutionary change.

    PubMed

    Wallis, O C; Zhang, Y P; Wallis, M

    2001-06-01

    Pituitary growth hormone (GH), like several other protein hormones, shows an unusual episodic pattern of molecular evolution in which sustained bursts of rapid change are imposed on long periods of very slow evolution (near-stasis). A marked period of rapid change occurred in the evolution of GH in primates or a primate ancestor, and gave rise to the species specificity that is characteristic of human GH. We have defined more precisely the position of this burst by cloning and sequencing the GH genes for a prosimian, the slow loris (Nycticebus pygmaeus) and a New World monkey, marmoset (Callithrix jacchus). Slow loris GH is very similar in sequence to pig GH, demonstrating that the period of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. The putative marmoset GH is similar in sequence to human GH, demonstrating that the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence for mature GH, and is not marked in other components of the gene sequence including signal peptide, 5' upstream region and introns. A number of factors support the idea that this episode of rapid change was due to positive adaptive selection. Thus (1) there is no apparent loss of function of GH in man compared with non-primates, (2) after the episode of rapid change the rate of evolution fell towards the slow basal level that is seen for most mammalian GHs, (3) the accelerated rate of substitution for the exons of the GH gene significantly exceeds that for introns, and (4) the amino acids contributing to the hydrophobic core of GH are strongly conserved when higher primate and other GH sequences are compared, and for coding sequences other than that coding for hydrophobic core residues the rate of substitution for non-synonymous sites (K(A)) is significantly greater than that for synonymous sites (K(S)). In slow loris, as

  20. 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. PMID:26774997

  1. 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. PMID:25867589

  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 silicon outdiffusion from SiC substrates during molecular-beam epitaxial growth of AlGaN/GaN/AlN transistor structures

    SciTech Connect

    Hoke, W.E.; Torabi, A.; Mosca, J.J.; Hallock, R.B.; Kennedy, T.D.

    2005-10-15

    AlGaN/GaN/AlN transistor structures were grown onto SiC substrates by molecular-beam epitaxy. Under aluminum-rich growth conditions for the AlN nucleation layer, undesirable n-type conduction is observed near the GaN/AlN interface for even thick (>1000 A) AlN layers. Silicon is identified as the unwanted dopant from secondary-ion mass spectroscopy measurements. Atomic force microscopy surface maps reveal free aluminum metal on AlN surfaces grown under modest aluminum-rich conditions. It is proposed that rapid silicon migration is caused by molten aluminum reacting with the SiC substrate resulting in dissolved silicon that rapidly migrates through the growing AlN layer. This behavior is significantly reduced using a growth flux ratio of aluminum to reactive nitrogen close to unity. The resulting buffer leakage current of the GaN high electron mobility transistor structure is reduced by more than four orders of magnitude.

  4. 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

    2016-03-01

    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. PMID:26717836

  5. Rapid Molecular Profiling of Myeloproliferative Neoplasms Using Targeted Exon Resequencing of 86 Genes Involved in JAK-STAT Signaling and Epigenetic Regulation.

    PubMed

    Magor, Graham W; Tallack, Michael R; Klose, Nathan M; Taylor, Debra; Korbie, Darren; Mollee, Peter; Trau, Matt; Perkins, Andrew C

    2016-09-01

    Myeloproliferative neoplasms (MPNs) are a heterogeneous group of blood disorders characterized by excess production of mature blood cells and an increased risk of late transformation to acute myeloid leukemia or primary myelofibrosis. Approximately 15% of MPN cases do not carry mutations in JAK2, CALR, or MPL and are thus often referred to as triple-negative cases. These are caused by a diverse set of rare mutations in cytokine receptors, JAK-STAT signaling pathway components, or epigenetic modifiers. In addition, some cases diagnosed as MPN are reactive rather than clonal disorders, so a negative result from a genetic screen can be informative. To obtain a comprehensive rapid molecular diagnosis for most MPNs, we developed an assay to detect genetic mutations (single nucleotide variants and/or small insertions/deletions) in 86 genes using targeted exon resequencing (AmpliSeq) and a bench-top semiconductor machine (Ion Torrent Personal Genome Machine). Our assay reliably detects well characterized mutations in JAK2, CALR, and MPL, but also rarer mutations in ASXL1, TET2, SH2B3, and other genes. Some of these mutations are novel. We find multiple mutations in advanced cases, suggesting co-operation between Janus kinase-STAT pathway mutations and epigenetic mutations in disease progression. This assay can be used to follow molecular progression, clonal heterogeneity, and drug resistance in MPNs. PMID:27449473

  6. 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%. PMID:24607106

  7. Resources, resources, resources....

    PubMed

    1997-01-01

    Several resources provided by different types of organizations are available to transgender people in the New York area. Some of these organizations include the Gender Identity Project, Harlem United Community AIDS Center, Hetrick Martin Institute, SafeSpace and Youth Enrichment Services (YES). Organization telephone numbers, addresses, and their targeted audiences are provided. PMID:11364801

  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. 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. PMID:27061315

  10. A handheld flow genetic analysis system (FGAS): towards rapid, sensitive, quantitative and multiplex molecular diagnosis at the point-of-care level.

    PubMed

    Shu, Bowen; Zhang, Chunsun; Xing, Da

    2015-06-21

    A handheld flow genetic analysis system (FGAS) is proposed for rapid, sensitive, multiplex and real-time quantification of nucleic acids at the point-of-care (POC) level. The FGAS includes a helical thermal-gradient microreactor and a microflow actuator, as well as control circuitry for temperature, fluid and power management, and smartphone fluorescence imaging. All of these features are integrated into a field-portable and easy-to-use molecular diagnostic platform powered by lithium batteries. Due to the unique design of the microreactor, not only steady temperatures for denaturation and annealing/extension but also a linear thermal gradient for spatial high-resolution melting can be achieved through simply maintaining a single heater at constant temperature. The smartphone fluorescence imaging system has a wide field of view that captures all PCR channels of the microreactor in a single snapshot without the need for any mechanical scanning. By these designs, the FGAS enables real-time monitoring of the temporal and spatial fluorescence signatures of amplicons during continuous-flow amplification. On the current FGAS, visual detection of as little as 10 copies per μL of genomic DNA of Salmonella enterica was achieved in 15 min, with real-time quantitative detection of the DNA over 6 orders of magnitude concentration from 10(6) to 10(1) copies per μL also completed in 7.5-15 min. In addition, multiple pathogenic DNA targets could be simultaneously discriminated with direct bar-chart readout or multiplex spatial melting in serial flow. We anticipate that the FGAS has great potential to become a next-generation gene analyzer for POC molecular diagnostics. PMID:25953325

  11. Internal transcribed spacer sequence-based rapid molecular identification of Prototheca zopfii and Prototheca blaschkeae directly from milk of infected cows.

    PubMed

    Marques, S; Huss, V A R; Pfisterer, K; Grosse, C; Thompson, G

    2015-05-01

    The increasing incidence of rare mastitis-causing pathogens has urged the implementation of fast and efficient diagnostic and control measures. Prototheca algae are known to be associated with diseases in humans and animals. In the latter, the most prevalent form of protothecosis is bovine mastitis with Prototheca zopfii and Prototheca blaschkeae representing the most common pathogenic species. These nonphotosynthetic and colorless green algae are ubiquitous in different environments and are widely resistant against harmful conditions and antimicrobials. Hence, the association of Prototheca with bovine mastitis represents a herd problem, requiring fast and easy identification of the infectious agent. The purpose of this study was to develop a reliable and rapid method, based on the internal transcribed spacer (ITS) sequences of ribosomal DNA, for molecular identification and discrimination between P. zopfii and P. blaschkeae in bovine mastitic milk. The complete ITS sequences of 32 Prototheca isolates showed substantial interspecies but moderate intraspecies variability facilitating the design of species-specific PCR amplification primers. The species-specific PCR was successfully applied to the identification of P. zopfii and P. blaschkeae directly from milk samples. The intraspecific ITS phylogeny was compared for each species with the geographical distribution of the respective Prototheca isolates, but no significant correlation was found. PMID:25726118

  12. Development of the molecular methods for rapid detection and differentiation of Fusarium oxysporum and F. oxysporum f. sp. niveum in Taiwan.

    PubMed

    Lin, Ying-Hong; Chen, Kan-Shu; Chang, Jing-Yi; Wan, Yu-Ling; Hsu, Ching-Chi; Huang, Jenn-Wen; Chang, Pi-Fang Linda

    2010-09-30

    Fusarium wilt, caused by Fusarium oxysporum (Fo), is one of the most important fungal diseases worldwide. Like other plant pathogens, Fo displays specialized forms in association with its hosts. For example, F. oxysporum f. sp. niveum (Fon) is the damaging pathogen causing Fusarium wilt disease on watermelon, whereas F. oxysporum f. sp. cubense is the pathogen that infects banana. A rapid and reliable pathogen identification or disease diagnosis is essential for the integrated disease management practices in many crops. In this study, two new primer sets, Fon-1/Fon-2 and FnSc-1/FnSc-2, were developed to differentiate Fon and Fo, respectively. The PCR method using the novel primer sets has high sensitivity to detect Fon when the DNA concentration was as low as 0.01 pg or when the conidia number was as few as 5. In comparison with the published primer set, the Fon-1/Fon-2 primer set, derived from the sequence of OP-M12 random primer-amplified fragment, produced a 174 bp DNA fragment, and was more specific to Fon in Taiwan. In addition, with optimized PCR parameters, the molecular method using the Fon-1/Fon-2 primer set could directly detect Fon even when watermelon samples were collected in its early stage of disease development. PMID:20471505

  13. 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.

  14. A rapid drug release system with a NIR light-activated molecular switch for dual-modality photothermal/antibiotic treatments of subcutaneous abscesses.

    PubMed

    Chiang, Wei-Lun; Lin, Tzu-Tsen; Sureshbabu, Radhakrishnan; Chia, Wei-Tso; Hsiao, Hsu-Chan; Liu, Hung-Yi; Yang, Chih-Man; Sung, Hsing-Wen

    2015-02-10

    Eradicating subcutaneous bacterial infections remains a significant challenge. This work reports an injectable system of hollow microspheres (HMs) that can rapidly produce localized heat activated by near-infrared (NIR) light and control the release of an antibiotic via a "molecular switch" in their polymer shells, as a combination strategy for treating subcutaneous abscesses. The HMs have a shell of poly(d,l-lactic-co-glycolic acid) (PLGA) and an aqueous core that is comprised of vancomycin (Van) and polypyrrole nanoparticles (PPy NPs), which are photothermal agents. Experimental results demonstrate that the micro-HMs ensure efficiently the spatial stabilization of their encapsulated Van and PPy NPs at the injection site in mice with subcutaneous abscesses. Without NIR irradiation, the HMs elute a negligible drug concentration, but release substantially more when exposed to NIR light, suggesting that this system is suitable as a photothermally-responsive drug delivery system. The combination of photothermally-induced hyperthermia and antibiotic therapy with HMs increases cytotoxicity for bacteria in abscesses, to an extent that is greater than the sum of the two treatments alone, demonstrating a synergistic effect. This treatment platform may find other clinical applications, especially for localized hyperthermia-based cancer therapy. PMID:25499553

  15. Efficient determination of protocatechuic acid in fruit juices by selective and rapid magnetic molecular imprinted solid phase extraction coupled with HPLC.

    PubMed

    Xie, Lianwu; Guo, Junfang; Zhang, Yuping; Shi, Shuyun

    2014-08-13

    Magnetic molecular imprinted polymers (MMIPs) have been prepared as solid phase material to selectively extract protocatechuic acid (PCA) from fruit juices with high capacity and fast binding kinetics. The resulting MMIPs were characterized by TEM, FT-IR, TGA, and VSM. The adsorption process between PCA and MMIPs followed Langumuir adsorption isotherm with maximum adsorption capacity at 7.5 mg/g and pseudo-second-order reaction kinetics with fast binding kinetics (equilibrium time at 40 min). In addition, the prepared MMIPs showed rapid magnetic separation (10 s) and reusability (retained 94.9% after six cycles). Subsequently, MMIPs were successfully applied for selective enrichment and determination of PCA from fruit juices (0.45 μg/mL in grape juice but not detected in apple juice, pineapple juice, orange juice, and peach juice) with satisfactory recoveries (92-107%). The results indicated that synthesized MMIPs can be used for efficient and selective extraction of PCA from complex matrices. PMID:25075753

  16. 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

  17. Novel molecular diagnostic tools for malaria elimination: a review of options from the point of view of high-throughput and applicability in resource limited settings.

    PubMed

    Britton, Sumudu; Cheng, Qin; McCarthy, James S

    2016-01-01

    As malaria transmission continues to decrease, an increasing number of countries will enter pre-elimination and elimination. To interrupt transmission, changes in control strategies are likely to require more accurate identification of all carriers of Plasmodium parasites, both symptomatic and asymptomatic, using diagnostic tools that are highly sensitive, high throughput and with fast turnaround times preferably performed in local health service settings. Currently available immunochromatographic lateral flow rapid diagnostic tests and field microscopy are unlikely to consistently detect infections at parasite densities less than 100 parasites/µL making them insufficiently sensitive for detecting all carriers. Molecular diagnostic platforms, such as PCR and LAMP, are currently available in reference laboratories, but at a cost both financially and in turnaround time. This review describes the recent progress in developing molecular diagnostic tools in terms of their capacity for high throughput and potential for performance in non-reference laboratories for malaria elimination. PMID:26879936

  18. Non-local competition drives both rapid divergence and prolonged stasis in a model of speciation in populations with degenerate resource consumption.

    PubMed

    Atamas, Nicholas; Atamas, Michael S; Atamas, Faina; Atamas, Sergei P

    2012-01-01

    The theory of speciation is dominated by adaptationist thinking, with less attention to mechanisms that do not affect species adaptation. Degeneracy--the imperfect specificity of interactions between diverse elements of biological systems and their environments--is key to the adaptability of populations. A mathematical model was explored in which population and resource were distributed one-dimensionally according to trait value. Resource consumption was degenerate--neither strictly location-specific nor location-independent. As a result, the competition for resources among the elements of the population was non-local. Two modeling approaches, a modified differential-integral Verhulstian equation and a cellular automata model, showed similar results: narrower degeneracy led to divergent dynamics with suppression of intermediate forms, whereas broader degeneracy led to suppression of diversifying forms, resulting in population stasis with increasing phenotypic homogeneity. Such behaviors did not increase overall adaptation because they continued after the model populations achieved maximal resource consumption rates, suggesting that degeneracy-driven distributed competition for resources rather than selective pressure toward more efficient resource exploitation was the driving force. The solutions were stable in the presence of limited environmental stochastic variability or heritable phenotypic variability. A conclusion was made that both dynamic diversification and static homogeneity of populations may be outcomes of the same process--distributed competition for resource not affecting the overall adaptation--with the difference between them defined by the spread of trait degeneracy in a given environment. Thus, biological degeneracy is a driving force of both speciation and stasis in biology, which, by themselves, are not necessarily adaptive in nature. PMID:23268831

  19. Rapid rise and fall of selfish sex-ratio X chromosomes in Drosophila simulans: spatiotemporal analysis of phenotypic and molecular data.

    PubMed

    Bastide, Héloïse; Cazemajor, Michel; Ogereau, David; Derome, Nicolas; Hospital, Frédéric; Montchamp-Moreau, Catherine

    2011-09-01

    Sex-ratio drive, which has been documented in several Drosophila species, is induced by X-linked segregation distorters. Contrary to Mendel's law of independent assortment, the sex-ratio chromosome (X(SR)) is inherited by more than half the offspring of carrier males, resulting in a female-biased sex ratio. This segregation advantage allows X(SR) to spread in populations, even if it is not beneficial for the carriers. In the cosmopolitan species D. simulans, the Paris sex-ratio is caused by recently emerged selfish X(SR) chromosomes. These chromosomes have triggered an intragenomic conflict, and their propagation has been halted over a large area by the evolution of complete drive suppression. Previous molecular population genetics analyses revealed a selective sweep indicating that the invasion of X(SR) chromosomes was very recent in Madagascar (likely less than 100 years ago). Here, we show that X(SR) chromosomes are now declining at this location as well as in Mayotte and Kenya. Drive suppression is complete in the three populations, which display little genetic differentiation and share swept haplotypes, attesting to a common and very recent ancestry of the X(SR) chromosomes. Patterns of DNA sequence variation also indicate a fitness cost of the segmental duplication involved in drive. The data suggest that X(SR) chromosomes started declining first on the African continent, then in Mayotte, and finally in Madagascar and strongly support a scenario of rapid cycling of X chromosomes. Once drive suppression has evolved, standard X(ST) chromosomes locally replace costly X(SR) chromosomes in a few decades. PMID:21498605

  20. 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. PMID:10502603

  1. 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

  2. eyeGENE®: a vision community resource facilitating patient care and paving the path for research through molecular diagnostic testing

    PubMed Central

    Blain, D; Goetz, KE; Ayyagari, R; Tumminia, SJ

    2013-01-01

    Molecular genetics and genomics are revolutionizing the study and treatment of inherited eye diseases. In recognition of the impact of molecular genetics on vision and ophthalmology, the National Eye Institute established the National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE®) as a multidirectional research initiative whereby a clinical component for patients diagnosed with inherited eye disease fosters research into the causes and mechanisms of these ophthalmic diseases. This is accomplished by broadening access to genetic diagnostic testing and maintaining a repository of DNA samples from clinically characterized individuals and their families to allow investigations of the causes, interventions, and management of genetic eye disorders. The eyeGENE® Network currently includes Clinical Laboratory Improvement Amendments (CLIA)-certified diagnostic laboratory partners, over 270 registered clinical organizations with 500 registered users from around the United States and Canada, and is now testing approximately 100 genes representing 35 inherited eye diseases. To date, the Network has received 4400 samples from individuals with rare inherited eye diseases, which are available for access by the vision research community. eyeGENE® is a model partnership between the U.S. federal government, eye health care providers, CLIA-approved molecular diagnostic laboratories, private industry, and scientists who represent a broad research constituency. PMID:23662816

  3. 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

  4. 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. PMID:20500756

  5. 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

  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

    2015-01-01

    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

  8. 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

  9. A rapid method for preparation of nucleic acid extracts from potato psyllids for detection of 'Candidatus Liberibacter solancearum' and molecular analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  10. 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.