WorldWideScience

Sample records for simultaneous multiple species

  1. Acoustic classification of multiple simultaneous bird species: a multi-instance multi-label approach

    Science.gov (United States)

    F. Briggs; B. Lakshminarayanan; L. Neal; X.Z. Fern; R. Raich; S.F. Hadley; A.S. Hadley; M.G. Betts

    2012-01-01

    Although field-collected recordings typically contain multiple simultaneously vocalizing birds of different species, acoustic species classification in this setting has received little study so far. This work formulates the problem of classifying the set of species present in an audio recording using the multi-instance multi-label (MIML) framework for machine learning...

  2. Sequential and simultaneous multiple explanation

    Directory of Open Access Journals (Sweden)

    Robert Litchfield

    2007-02-01

    Full Text Available This paper reports two experiments comparing variants of multiple explanation applied in the early stages of a judgment task (a case involving employee theft where participants are not given a menu of response options. Because prior research has focused on situations where response options are provided to judges, we identify relevant dependent variables that an intervention might affect when such options are not given. We use these variables to build a causal model of intervention that illustrates both the intended effects of multiple explanation and some potentially competing processes that it may trigger. Although multiple explanation clearly conveys some benefits (e.g., willingness to delay action to engage in information search, increased detail, quality and confidence in alternative explanations in the present experiments, we also found evidence that it may initiate or enhance processes that attenuate its advantages (e.g., feelings that one does not need more data if one has multiple good explanations.

  3. Simultaneous gene finding in multiple genomes.

    Science.gov (United States)

    König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

    2016-11-15

    As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Simultaneous assembly of multiple test forms

    NARCIS (Netherlands)

    van der Linden, Willem J.; Adema, J.J.; Adema, Jos J.

    1998-01-01

    An algorithm for the assembly of multiple test forms is proposed in which the multiple-form problem is reduced to a series of computationally less intensive two-form problems. At each step, one form is assembled to its true specifications; the other form is a dummy assembled only to maintain a

  5. Simultaneous assembly of multiple test forms

    NARCIS (Netherlands)

    van der Linden, Willem J.; Adema, Jos J.

    1997-01-01

    An algorithm for the assembly of multiple test forms is proposed in which the multiple-form problem is reduced to a series of computationally less intensive two-form problems. At each step one form is assembled to its true specifications; the other form is a dummy assembled only to maintain a

  6. Simultaneous assembly of multiple test forms

    OpenAIRE

    van der Linden, Willem J.; Adema, Jos J.

    1997-01-01

    An algorithm for the assembly of multiple test forms is proposed in which the multiple-form problem is reduced to a series of computationally less intensive two-form problems. At each step one form is assembled to its true specifications; the other form is a dummy assembled only to maintain a balance between the quality of the current form and the remaining forms. It is shown how the method can be implemented using the technique of 0-1 linear programming. Two empirical examples using a former...

  7. Simultaneous assembly of multiple test forms

    OpenAIRE

    van der Linden, Willem J.; Adema, J.J.; Adema, Jos J.

    1998-01-01

    An algorithm for the assembly of multiple test forms is proposed in which the multiple-form problem is reduced to a series of computationally less intensive two-form problems. At each step, one form is assembled to its true specifications; the other form is a dummy assembled only to maintain a balance between the quality of the current form and the remaining forms. It is shown how the method can be implemented using the technique of O-1 linear programming. Two empirical examples using a forme...

  8. Multiple Primary Cancers: Simultaneously Occurring Prostate ...

    African Journals Online (AJOL)

    2016-05-20

    May 20, 2016 ... Original Article. How to cite this article: Popoola AA, Abiola OO, Buhari T, Ushie AF,. Olanipekun HB, Arogundade AK. Multiple primary cancers: .... documented in literature as due to scattering of radiation effect.[29] and chemotherapy for the thyroid cancer. Two of the patients died of complications of the ...

  9. Simultaneous estimation of QTL parameters for mapping multiple traits

    Indian Academy of Sciences (India)

    Z

    proposed a strategy of simultaneously estimating all QTL parameters in the multiple-trait multiple. -interval mapping. ... (A201207), the Science and Technology Innovation Team in Higher Education Institutions of. Heilongjiang Province (No. 2014TD005), and the Innovation Project for University Students of. Heilongjiang ...

  10. Simultaneous comparisons of treatments at multiple time points

    DEFF Research Database (Denmark)

    Pallmann, Philip; Pretorius, Mias; Ritz, Christian

    2017-01-01

    hypotheses as well as a global test decision. We compare via simulation the powers of multiple contrast tests based on a joint model and multiple marginal models, respectively, and quantify the benefit of incorporating longitudinal correlation, i.e. the advantage over Bonferroni. Practical application.......e. occasion-specific models. Upon parameter and covariance estimation with either modeling approach, we employ a variant of multiple contrast tests that acknowledges correlation between time points and test statistics. This method provides simultaneous confidence intervals and adjusted p-values for elementary......We discuss several aspects of multiple inference in longitudinal settings, focusing on many-to-one and all-pairwise comparisons of (a) treatment groups simultaneously at several points in time, or (b) time points simultaneously for several treatments. We assume a continuous endpoint...

  11. The Physiologic Effects of Multiple Simultaneous Electronic Control Device Discharges

    Science.gov (United States)

    Dawes, Donald M.; Ho, Jeffrey D.; Reardon, Robert F.; Sweeney, James D.; Miner, James R.

    2010-01-01

    Objectives: Law enforcement and military personnel use electronic control devices to control non-compliant and actively resistive subjects. The TASER® Shockwave is a new electronic control device designed specifically as an area denial device capable of delivering multiple simultaneous discharges. This is the first study to examine the effects of multiple simultaneous device discharges in humans. Methods: Volunteers were exposed to multiple (two to three), simultaneous 5-second discharges from the Shockwave device to the chest, back, chest to abdomen, or thighs. Blood was analyzed before and after discharge for pH, lactate, potassium, creatine kinase (CK), and troponin. Continuous spirometry was performed before, during, and after the discharge. In addition, electrocardiograms (ECGs) before and after discharge were recorded, and echocardiography was used to determine the rhythm during discharge. Results: Small elevations of lactate occurred. Moderate increases in CK at 24 hours occurred and appeared to be related to the number of simultaneous discharges. There was a trend to a decrease in minute ventilation in the volunteers exposed to two simultaneous discharges, but it did not reach statistical significance. ECG changes only reflected an increase in vagal tone, and there was no evidence of capture by echocardiography. Five-second, simultaneous, multiple exposures to the TASER Shockwave device were reasonably tolerated by our human volunteers. Conclusion: Our study suggests that this device may have a reasonable risk/benefit ratio when used to protect an area from a threat. PMID:20411076

  12. The Physiologic Effects of Multiple Simultaneous Electronic Control Device Discharges

    Directory of Open Access Journals (Sweden)

    Dawes, Donald M

    2010-02-01

    Full Text Available Objectives: Law enforcement and military personnel use electronic control devices to control non-compliant and actively resistive subjects. The TASER® Shockwave is a new electronic control device designed specifically as an area denial device capable of delivering multiple simultaneous discharges. This is the first study to examine the effects of multiple simultaneous device discharges in humans.Methods: Volunteers were exposed to multiple (two to three, simultaneous 5-second discharges from the Shockwave device to the chest, back, chest to abdomen, or thighs. Blood was analyzed before and after discharge for pH, lactate, potassium, creatine kinase (CK, and troponin. Continuous spirometry was performed before, during, and after the discharge. In addition, electrocardiograms (ECGs before and after discharge were recorded, and echocardiography was used to determine the rhythm during discharge.Results: Small elevations of lactate occurred. Moderate increases in CK at 24 hours occurred and appeared to be related to the number of simultaneous discharges. There was a trend to a decrease in minute ventilation in the volunteers exposed to two simultaneous discharges, but it did not reach statistical significance. ECG changes only reflected an increase in vagal tone, and there was no evidence of capture by echocardiography. Five-second, simultaneous, multiple exposures to the TASER Shockwave device were reasonably tolerated by our human volunteers.Conclusion: Our study suggests that this device may have a reasonable risk/benefit ratio when used to protect an area from a threat. [West J Emerg Med. 2010; 11(1:49-56].

  13. Simultaneous detection of Legionella species and L. anisa, L. bozemanii, L. longbeachae and L. micdadei using conserved primers and multiple probes in a multiplex real-time PCR assay.

    Science.gov (United States)

    Cross, Kristen E; Mercante, Jeffrey W; Benitez, Alvaro J; Brown, Ellen W; Diaz, Maureen H; Winchell, Jonas M

    2016-07-01

    Legionnaires' disease is a severe respiratory disease that is estimated to cause between 8,000 and 18,000 hospitalizations each year, though the exact burden is unknown due to under-utilization of diagnostic testing. Although Legionella pneumophila is the most common species detected in clinical cases (80-90%), other species have also been reported to cause disease. However, little is known about Legionnaires' disease caused by these non-pneumophila species. We designed a multiplex real-time PCR assay for detection of all Legionella spp. and simultaneous specific identification of four clinically-relevant Legionella species, L. anisa, L. bozemanii, L. longbeachae, and L. micdadei, using 5'-hydrolysis probe real-time PCR. The analytical sensitivity for detection of nucleic acid from each target species was ≤50fg per reaction. We demonstrated the utility of this assay in spiked human sputum specimens. This assay could serve as a tool for understanding the scope and impact of non-pneumophila Legionella species in human disease. Published by Elsevier Inc.

  14. Observations of simultaneous upward lightning leaders from multiple tall structures

    Science.gov (United States)

    Warner, Tom A.

    2012-11-01

    We present high-speed camera observations (up to 7200 images per second) and correlated electric field measurements of upward lightning leaders initiated simultaneously from multiple tall towers. Four towers spanning a horizontal distance of 2.9 km and ranging in height from 121 to 191 m, developed upward leaders following a nearby positive cloud-to-ground (+ CG) flash on 7/16/09 UT in Rapid City, South Dakota, USA during the summer thunderstorm season. The optical and electric field observations suggest that all four upward propagating leaders were positive polarity (i.e., upward negative lightning) and initiated simultaneously approximately 2 ms following the + CG return stroke. There was significant intracloud flash activity prior to the return stroke, and upward leader initiation coincided with the passage of horizontally extensive in-cloud negative breakdown following the + CG return stroke. This observation supports the idea that downward positive cloud-to-ground lightning can trigger upward negative lightning from multiple tall objects. Specifically, the triggering component is an area of horizontally propagating negative breakdown following the + CG return stroke that influences a broad area resulting in simultaneous or near-simultaneous, positive polarity upward leader initiation from multiple tall objects.

  15. Structured plant metabolomics for the simultaneous exploration of multiple factors

    Science.gov (United States)

    Vasilev, Nikolay; Boccard, Julien; Lang, Gerhard; Grömping, Ulrike; Fischer, Rainer; Goepfert, Simon; Rudaz, Serge; Schillberg, Stefan

    2016-01-01

    Multiple factors act simultaneously on plants to establish complex interaction networks involving nutrients, elicitors and metabolites. Metabolomics offers a better understanding of complex biological systems, but evaluating the simultaneous impact of different parameters on metabolic pathways that have many components is a challenging task. We therefore developed a novel approach that combines experimental design, untargeted metabolic profiling based on multiple chromatography systems and ionization modes, and multiblock data analysis, facilitating the systematic analysis of metabolic changes in plants caused by different factors acting at the same time. Using this method, target geraniol compounds produced in transgenic tobacco cell cultures were grouped into clusters based on their response to different factors. We hypothesized that our novel approach may provide more robust data for process optimization in plant cell cultures producing any target secondary metabolite, based on the simultaneous exploration of multiple factors rather than varying one factor each time. The suitability of our approach was verified by confirming several previously reported examples of elicitor–metabolite crosstalk. However, unravelling all factor–metabolite networks remains challenging because it requires the identification of all biochemically significant metabolites in the metabolomics dataset. PMID:27853298

  16. Interaction and coalescence of multiple simultaneous and non-simultaneous blast waves

    Science.gov (United States)

    Qiu, S.; Eliasson, V.

    2016-05-01

    Interaction of multiple blast waves can be used to direct energy toward a target while simultaneously reducing collateral damage away from the target area. In this paper, simulations of multiple point source explosives were performed and the resulting shock interaction and coalescence behavior were explored. Three to ten munitions were placed concentrically around the target, and conditions at the target area were monitored and compared to those obtained using a single munition. For each simulation, the energy summed over all munitions was kept constant, while the radial distances between target and munitions and the munition initiation times were varied. Each munition was modeled as a point source explosion. The resulting blast wave propagation and shock front coalescence were solved using the inviscid Euler equations of gas dynamics on overlapping grids employing a finite difference scheme. Results show that multiple munitions can be beneficial for creating extreme conditions at the intended target area; over 20 times higher peak pressure is obtained for ten simultaneous munitions compared to a single munition. Moreover, peak pressure at a point away from the target area is reduced by more than a factor of three.

  17. Successful endovascular treatment for simultaneous multiple thromboemboli following myocardial infarction.

    Science.gov (United States)

    Sakai, Akiko; Hara, Hidehiko; Nakamura, Masato

    2013-06-01

    An 81-year-old female was referred for myocardial infarction with heart failure. She was successfully treated with percutaneous coronary intervention (PCI), and left ventriculogram revealed an apical thrombus 20 mm in diameter. Multiple simultaneous thromboemboli occurred in her right renal artery, supramesenteric artery (SMA), and right popliteal artery on the fifth day after PCI despite anticoagulant therapy. Emergency endovascular therapy (EVT) with an aspiration catheter and ballooning were performed to the popliteal and renal artery, in addition to additional stenting of the SMA because of an intramural hematoma. This one session of emergency EVT was sufficient to save this patient, and no sequelae were observed after this treatment.

  18. Negotiating for more: the multiple equivalent simultaneous offer.

    Science.gov (United States)

    Heller, Richard E

    2014-02-01

    Whether a doctor, professional baseball manager, or a politician, having successful negotiation skills is a critical part of being a leader. Building upon prior journal articles on negotiation strategy, the author presents the concept of the multiple equivalent simultaneous offer (MESO). The concept of a MESO is straightforward: as opposed to making a single offer, make multiple offers with several variables. Each offer alters the different variables, such that the end result of each offer is equivalent from the perspective of the party making the offer. Research has found several advantages to the use of MESOs. For example, using MESOs, an offer was more likely to be accepted, and the counterparty was more likely to be satisfied with the negotiated deal. Additional benefits have been documented as well, underscoring why a prepared radiology business leader should understand the theory and practice of MESO. Copyright © 2014 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  19. Measuring multiple nano-textured areas simultaneously with imaging scatterometry

    DEFF Research Database (Denmark)

    Madsen, Jonas Skovlund; Hansen, Poul Erik; Bilenberg, Brian

    2017-01-01

    the full illumination spot, scatterometry analysis can be made pixel by pixel. An area of interest much smaller than the spot size can therefore be characterized and the user first has to select the area of interest in the post-processing. Furthermore, a specific area on the sample can easily be found...... and areas with defects can be avoided. These advantages make imaging scatterometry a very effective and user-friendly characterization method and allow us to determine the homogeneity of a nano- Textured surface by performing pixel-wise analyses. In the analysis an inverse modelling approach is used, where...... measured diffraction efficiencies are compared to simulated diffraction efficiencies using a least-square fitting approach. We demonstrate an imaging scatterometry setup built into an optical microscope. The setup is capable of measuring multiple 2D gratings with pitches of 200 nm simultaneously...

  20. Simultaneous identification of multiple driver pathways in cancer.

    Directory of Open Access Journals (Sweden)

    Mark D M Leiserson

    Full Text Available Distinguishing the somatic mutations responsible for cancer (driver mutations from random, passenger mutations is a key challenge in cancer genomics. Driver mutations generally target cellular signaling and regulatory pathways consisting of multiple genes. This heterogeneity complicates the identification of driver mutations by their recurrence across samples, as different combinations of mutations in driver pathways are observed in different samples. We introduce the Multi-Dendrix algorithm for the simultaneous identification of multiple driver pathways de novo in somatic mutation data from a cohort of cancer samples. The algorithm relies on two combinatorial properties of mutations in a driver pathway: high coverage and mutual exclusivity. We derive an integer linear program that finds set of mutations exhibiting these properties. We apply Multi-Dendrix to somatic mutations from glioblastoma, breast cancer, and lung cancer samples. Multi-Dendrix identifies sets of mutations in genes that overlap with known pathways - including Rb, p53, PI(3K, and cell cycle pathways - and also novel sets of mutually exclusive mutations, including mutations in several transcription factors or other genes involved in transcriptional regulation. These sets are discovered directly from mutation data with no prior knowledge of pathways or gene interactions. We show that Multi-Dendrix outperforms other algorithms for identifying combinations of mutations and is also orders of magnitude faster on genome-scale data. Software available at: http://compbio.cs.brown.edu/software.

  1. Isolation of multiple nontuberculous mycobacteria species in the same patients.

    Science.gov (United States)

    Lim, Hyo-Jeong; Park, Chang Min; Park, Young Sik; Lee, Jinwoo; Lee, Sang-Min; Yang, Seok-Chul; Yoo, Chul-Gyu; Kim, Young Whan; Han, Sung Koo; Yim, Jae-Joon

    2011-11-01

    During the observation of many patients with nontuberculous mycobacteria (NTM) infections, we have often isolated different NTM species in the same patient. In this study we elucidated the patterns of multiple NTM species isolation. The analysis included all patients from whom more than one species of mycobacteria were cultured from a respiratory specimen at Seoul National University Hospital, a tertiary referral hospital in South Korea, between January 2002 and December 2008. The demographic characteristics and clinical and radiographic findings were reviewed retrospectively. Multiple NTM species were isolated from 37 patients. Four patients with Mycobacterium gordonae, Mycobacterium terrae, or Mycobacterium lentiflavum were excluded due to the possibility of contamination. Transition to another NTM species was observed in 23 patients (69.7%), while alternating isolation of two or three NTM species was seen in nine patients. Two species were isolated simultaneously from different sputum samples collected from one patient on the same day. Different NTM species were isolated from the same patients. Copyright © 2011 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  2. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    . aeruginosa were found to be significantly larger than ulcers without the presence of P. aeruginosa (P wound is colonised by multiple bacterial species and that once they are established many of them persist in the wound. Our results suggest that the presence...

  3. Doses of Nearby Nature Simultaneously Associated with Multiple Health Benefits

    Directory of Open Access Journals (Sweden)

    Daniel T. C. Cox

    2017-02-01

    Full Text Available Exposure to nature provides a wide range of health benefits. A significant proportion of these are delivered close to home, because this offers an immediate and easily accessible opportunity for people to experience nature. However, there is limited information to guide recommendations on its management and appropriate use. We apply a nature dose-response framework to quantify the simultaneous association between exposure to nearby nature and multiple health benefits. We surveyed ca. 1000 respondents in Southern England, UK, to determine relationships between (a nature dose type, that is the frequency and duration (time spent in private green space and intensity (quantity of neighbourhood vegetation cover of nature exposure and (b health outcomes, including mental, physical and social health, physical behaviour and nature orientation. We then modelled dose-response relationships between dose type and self-reported depression. We demonstrate positive relationships between nature dose and mental and social health, increased physical activity and nature orientation. Dose-response analysis showed that lower levels of depression were associated with minimum thresholds of weekly nature dose. Nearby nature is associated with quantifiable health benefits, with potential for lowering the human and financial costs of ill health. Dose-response analysis has the potential to guide minimum and optimum recommendations on the management and use of nearby nature for preventative healthcare.

  4. Doses of Nearby Nature Simultaneously Associated with Multiple Health Benefits.

    Science.gov (United States)

    Cox, Daniel T C; Shanahan, Danielle F; Hudson, Hannah L; Fuller, Richard A; Anderson, Karen; Hancock, Steven; Gaston, Kevin J

    2017-02-09

    Exposure to nature provides a wide range of health benefits. A significant proportion of these are delivered close to home, because this offers an immediate and easily accessible opportunity for people to experience nature. However, there is limited information to guide recommendations on its management and appropriate use. We apply a nature dose-response framework to quantify the simultaneous association between exposure to nearby nature and multiple health benefits. We surveyed ca. 1000 respondents in Southern England, UK, to determine relationships between (a) nature dose type, that is the frequency and duration (time spent in private green space) and intensity (quantity of neighbourhood vegetation cover) of nature exposure and (b) health outcomes, including mental, physical and social health, physical behaviour and nature orientation. We then modelled dose-response relationships between dose type and self-reported depression. We demonstrate positive relationships between nature dose and mental and social health, increased physical activity and nature orientation. Dose-response analysis showed that lower levels of depression were associated with minimum thresholds of weekly nature dose. Nearby nature is associated with quantifiable health benefits, with potential for lowering the human and financial costs of ill health. Dose-response analysis has the potential to guide minimum and optimum recommendations on the management and use of nearby nature for preventative healthcare.

  5. [Simultaneous screening method for Bordetella species by conventional PCR assay].

    Science.gov (United States)

    Akiyama, Yumi; Saito, Etsuko; Enomoto, Miki; Tsuji, Hidetaka; Chikahira, Masatsugu; Yoshida, Masashi

    2013-11-01

    A simultaneous screening method using conventional PCR was developed for the detection and discrimination of Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii. A formulated multiprex method employing 4 kinds of paired primers on amplification of 4 corresponding different insertion sequences (IS481, IS1001, IS1002 and hIS1001) enabled rapid screening and identification. The detection limits of each DNA extracted from 3 kinds of Bordetella species were 5fg/microL for each. Obscure existences of B. pertussis and B. holmesii at low levels were confirmed with the LAMP method. This multiplex assay was applied to the clinical specimens obtained from patients with pertussis-like symptoms at sentinel clinics under the epidemiological surveillance of infectious diseases of Hyogo prefecture in FY2012. Among 42 nasopharyngeal swabs, B. pertussis was detected from 12 samples including 8 samples collected at outbreak in nursery school. The use of this method for the surveillance of infectious agents enabled us to search for 3 kinds of Bordetella species at once with low costs.

  6. Simultaneous mapping of multiple gene loci with pooled segregants.

    Directory of Open Access Journals (Sweden)

    Jürgen Claesen

    Full Text Available The analysis of polygenic, phenotypic characteristics such as quantitative traits or inheritable diseases remains an important challenge. It requires reliable scoring of many genetic markers covering the entire genome. The advent of high-throughput sequencing technologies provides a new way to evaluate large numbers of single nucleotide polymorphisms (SNPs as genetic markers. Combining the technologies with pooling of segregants, as performed in bulked segregant analysis (BSA, should, in principle, allow the simultaneous mapping of multiple genetic loci present throughout the genome. The gene mapping process, applied here, consists of three steps: First, a controlled crossing of parents with and without a trait. Second, selection based on phenotypic screening of the offspring, followed by the mapping of short offspring sequences against the parental reference. The final step aims at detecting genetic markers such as SNPs, insertions and deletions with next generation sequencing (NGS. Markers in close proximity of genomic loci that are associated to the trait have a higher probability to be inherited together. Hence, these markers are very useful for discovering the loci and the genetic mechanism underlying the characteristic of interest. Within this context, NGS produces binomial counts along the genome, i.e., the number of sequenced reads that matches with the SNP of the parental reference strain, which is a proxy for the number of individuals in the offspring that share the SNP with the parent. Genomic loci associated with the trait can thus be discovered by analyzing trends in the counts along the genome. We exploit the link between smoothing splines and generalized mixed models for estimating the underlying structure present in the SNP scatterplots.

  7. Quantification of multiple simultaneously occurring nitrogen flows in the euphotic ocean

    Science.gov (United States)

    Xu, Min Nina; Wu, Yanhua; Zheng, Li Wei; Zheng, Zhenzhen; Zhao, Huade; Laws, Edward A.; Kao, Shuh-Ji

    2017-03-01

    The general features of the N cycle in the sunlit region of the ocean are well known, but methodological difficulties have previously confounded simultaneous quantification of transformation rates among the many different forms of N, e.g., ammonium (NH4+), nitrite (NO2-), nitrate (NO3-), and particulate/dissolved organic nitrogen (PN/DON). However, recent advances in analytical methodology have made it possible to employ a convenient isotope labeling technique to quantify in situ fluxes among oft-measured nitrogen species within the euphotic zone. Addition of a single 15N-labeled NH4+ tracer and monitoring of the changes in the concentrations and isotopic compositions of the total dissolved nitrogen (TDN), PN, NH4+, NO2-, and NO3- pools allowed us to quantify the 15N and 14N fluxes simultaneously. Constraints expressing the balance of 15N and 14N fluxes between the different N pools were expressed in the form of simultaneous equations, the unique solution of which via matrix inversion yielded the relevant N fluxes, including rates of NH4+, NO2-, and NO3- uptake; ammonia oxidation; nitrite oxidation; DON release; and NH4+ uptake by bacteria. The matrix inversion methodology that we used was designed specifically to analyze the results of incubations under simulated in situ conditions in the euphotic zone. By taking into consideration simultaneous fluxes among multiple N pools, we minimized potential artifacts caused by non-targeted processes in traditional source-product methods. The proposed isotope matrix method facilitates post hoc analysis of data from on-deck incubation experiments and can be used to probe effects of environmental factors (e.g., pH, temperature, and light) on multiple processes under controlled conditions.

  8. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun

    2012-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between

  9. Managing multiple international risks simultaneously with an optimal hedging model

    OpenAIRE

    Gboroton F. Sarassoro; Raymond M. Leuthold

    1991-01-01

    A risk management model based on portfolio theory which accounts jointly for price, quantity, interest rate and exchange rate risks is developed and applied to cocoa and coffee production and exports in the Ivory Coast. Utilizing commodity and financial futures markets jointly, the results show that a government export agency can reduce risks from 27% to 89% by following a multicommodity hedging program which manages several risks simultaneously. The model and technique developed are applicab...

  10. Optimized simultaneous inversion of primary and multiple reflections; Inversion linearisee simultanee des reflexions primaires et des reflexions multiples

    Energy Technology Data Exchange (ETDEWEB)

    Pelle, L.

    2003-12-01

    The removal of multiple reflections remains a real problem in seismic imaging. Many preprocessing methods have been developed to attenuate multiples in seismic data but none of them is satisfactory in 3D. The objective of this thesis is to develop a new method to remove multiples, extensible in 3D. Contrary to the existing methods, our approach is not a preprocessing step: we directly include the multiple removal in the imaging process by means of a simultaneous inversion of primaries and multiples. We then propose to improve the standard linearized inversion so as to make it insensitive to the presence of multiples in the data. We exploit kinematics differences between primaries and multiples. We propose to pick in the data the kinematics of the multiples we want to remove. The wave field is decomposed into primaries and multiples. Primaries are modeled by the Ray+Born operator from perturbations of the logarithm of impedance, given the velocity field. Multiples are modeled by the Transport operator from an initial trace, given the picking. The inverse problem simultaneously fits primaries and multiples to the data. To solve this problem with two unknowns, we take advantage of the isometric nature of the Transport operator, which allows to drastically reduce the CPU time: this simultaneous inversion is this almost as fast as the standard linearized inversion. This gain of time opens the way to different applications to multiple removal and in particular, allows to foresee the straightforward 3D extension. (author)

  11. Modeling Simultaneous Multiple Fracturing Using the Combined Finite-Discrete Element Method

    Directory of Open Access Journals (Sweden)

    Quansheng Liu

    2018-01-01

    Full Text Available Simultaneous multiple fracturing is a key technology to facilitate the production of shale oil/gas. When multiple hydraulic fractures propagate simultaneously, there is an interaction effect among these propagating hydraulic fractures, known as the stress-shadow effect, which has a significant impact on the fracture geometry. Understanding and controlling the propagation of simultaneous multiple hydraulic fractures and the interaction effects between multiple fractures are critical to optimizing oil/gas production. In this paper, the FDEM simulator and a fluid simulator are linked, named FDEM-Fluid, to handle hydromechanical-fracture coupling problems and investigate the simultaneous multiple hydraulic fracturing mechanism. The fractures propagation and the deformation of solid phase are solved by FDEM; meanwhile the fluid flow in the fractures is modeled using the principle of parallel-plate flow model. Several tests are carried out to validate the application of FDEM-Fluid in hydraulic fracturing simulation. Then, this FDEM-Fluid is used to investigate simultaneous multiple fractures treatment. Fractures repel each other when multiple fractures propagate from a single horizontal well, while the nearby fractures in different horizontal wells attract each other when multiple fractures propagate from multiple parallel horizontal wells. The in situ stress also has a significant impact on the fracture geometry.

  12. A PDP model of the simultaneous perception of multiple objects

    Science.gov (United States)

    Henderson, Cynthia M.; McClelland, James L.

    2011-06-01

    Illusory conjunctions in normal and simultanagnosic subjects are two instances where the visual features of multiple objects are incorrectly 'bound' together. A connectionist model explores how multiple objects could be perceived correctly in normal subjects given sufficient time, but could give rise to illusory conjunctions with damage or time pressure. In this model, perception of two objects benefits from lateral connections between hidden layers modelling aspects of the ventral and dorsal visual pathways. As with simultanagnosia, simulations of dorsal lesions impair multi-object recognition. In contrast, a large ventral lesion has minimal effect on dorsal functioning, akin to dissociations between simple object manipulation (retained in visual form agnosia and semantic dementia) and object discrimination (impaired in these disorders) [Hodges, J.R., Bozeat, S., Lambon Ralph, M.A., Patterson, K., and Spatt, J. (2000), 'The Role of Conceptual Knowledge: Evidence from Semantic Dementia', Brain, 123, 1913-1925; Milner, A.D., and Goodale, M.A. (2006), The Visual Brain in Action (2nd ed.), New York: Oxford]. It is hoped that the functioning of this model might suggest potential processes underlying dorsal and ventral contributions to the correct perception of multiple objects.

  13. Delivering multiple independent RIB simultaneously: Technical and operational challenges

    Energy Technology Data Exchange (ETDEWEB)

    Morton, A.C.

    2016-06-01

    ISAC is an ISOL-type facility at which RIB are produced by direct reactions of 480 MeV protons from TRIUMFs main cyclotron on thick targets. Like other ISOL-type facilities, ISAC is limited to the production and delivery of a single RIB at any given time. ARIEL, the Advanced Rare-IsotopE Laboratory, will provide for the production and delivery of, ultimately, two additional RIB, the first produced by photofission on actinide targets using electrons from a new superconducting electron linac and the second by direct and indirect reactions with protons from TRIUMFs main cyclotron. This will allow for the simultaneous delivery of three independent RIB to experimental areas at ARIEL and ISAC. The shift from single-user to multi-user operation will introduce significant technical and operational challenges that RIB facilities have not yet had to address. Almost all aspects of facility operation will become more complex as the first RIB from ARIEL targets become available.

  14. Learning multiple rules simultaneously: Affixes are more salient than reduplications.

    Science.gov (United States)

    Gervain, Judit; Endress, Ansgar D

    2017-04-01

    Language learners encounter numerous opportunities to learn regularities, but need to decide which of these regularities to learn, because some are not productive in their native language. Here, we present an account of rule learning based on perceptual and memory primitives (Endress, Dehaene-Lambertz, & Mehler, Cognition, 105(3), 577-614, 2007; Endress, Nespor, & Mehler, Trends in Cognitive Sciences, 13(8), 348-353, 2009), suggesting that learners preferentially learn regularities that are more salient to them, and that the pattern of salience reflects the frequency of language features across languages. We contrast this view with previous artificial grammar learning research, which suggests that infants "choose" the regularities they learn based on rational, Bayesian criteria (Frank & Tenenbaum, Cognition, 120(3), 360-371, 2013; Gerken, Cognition, 98(3)B67-B74, 2006, Cognition, 115(2), 362-366, 2010). In our experiments, adult participants listened to syllable strings starting with a syllable reduplication and always ending with the same "affix" syllable, or to syllable strings starting with this "affix" syllable and ending with the "reduplication". Both affixation and reduplication are frequently used for morphological marking across languages. We find three crucial results. First, participants learned both regularities simultaneously. Second, affixation regularities seemed easier to learn than reduplication regularities. Third, regularities in sequence offsets were easier to learn than regularities at sequence onsets. We show that these results are inconsistent with previous Bayesian rule learning models, but mesh well with the perceptual or memory primitives view. Further, we show that the pattern of salience revealed in our experiments reflects the distribution of regularities across languages. Ease of acquisition might thus be one determinant of the frequency of regularities across languages.

  15. Novel microarrays for simultaneous serodiagnosis of multiple antiviral antibodies.

    Directory of Open Access Journals (Sweden)

    Ponnurengam Malliappan Sivakumar

    Full Text Available We developed an automated diagnostic system for the detection of virus-specific immunoglobulin Gs (IgGs that was based on a microarray platform. We compared efficacies of our automated system with conventional enzyme immunoassays (EIAs. Viruses were immobilized to microarrays using a radical cross-linking reaction that was induced by photo-irradiation. A new photoreactive polymer containing perfluorophenyl azide (PFPA and poly(ethylene glycol methacrylate was prepared and coated on plates. Inactivated measles, rubella, mumps, Varicella-Zoster and recombinant Epstein-Barr viruse antigen were added to coated plates, and irradiated with ultraviolet light to facilitate immobilization. Virus-specific IgGs in healthy human sera were assayed using these prepared microarrays and the results obtained compared with those from conventional EIAs. We observed high correlation (0.79-0.96 in the results between the automated microarray technique and EIAs. The microarray-based assay was more rapid, involved less reagents and sample, and was easier to conduct compared with conventional EIA techniques. The automated microarray system was further improved by introducing reagent storage reservoirs inside the chamber, thereby conserving the use of expensive reagents and antibodies. We considered the microarray format to be suitable for rapid and multiple serological diagnoses of viral diseases that could be developed further for clinical applications.

  16. Evidence for simultaneous syntactic processing of multiple words during reading.

    Science.gov (United States)

    Snell, Joshua; Meeter, Martijn; Grainger, Jonathan

    2017-01-01

    A hotly debated issue in reading research concerns the extent to which readers process parafoveal words, and how parafoveal information might influence foveal word recognition. We investigated syntactic word processing both in sentence reading and in reading isolated foveal words when these were flanked by parafoveal words. In Experiment 1 we found a syntactic parafoveal preview benefit in sentence reading, meaning that fixation durations on target words were decreased when there was a syntactically congruent preview word at the target location (n) during the fixation on the pre-target (n-1). In Experiment 2 we used a flanker paradigm in which participants had to classify foveal target words as either noun or verb, when those targets were flanked by syntactically congruent or incongruent words (stimulus on-time 170 ms). Lower response times and error rates in the congruent condition suggested that higher-order (syntactic) information can be integrated across foveal and parafoveal words. Although higher-order parafoveal-on-foveal effects have been elusive in sentence reading, results from our flanker paradigm show that the reading system can extract higher-order information from multiple words in a single glance. We propose a model of reading to account for the present findings.

  17. Simultaneity, Sequentiality, and Speed: Organizational Messages about Multiple-Task Completion

    Science.gov (United States)

    Stephens, Keri K.; Cho, Jaehee K.; Ballard, Dawna I.

    2012-01-01

    Workplace norms for task completion increasingly value speed and the ability to accomplish multiple tasks at once. This study situates this popularized issue of multitasking within the context of chronemics scholarship by addressing related issues of simultaneity, sequentiality, and speed. Ultimately, we consider 2 multiple-task completion…

  18. Dissolution Model of Multiple Species: Leaching of Highly Soluble Minerals

    Science.gov (United States)

    Moreno, Luis; Ordóñez, Javier I.; Cisternas, Luis A.

    2017-06-01

    Dissolution of multi-species from a solid matrix is widely extended in different processes such as leaching of minerals; however, its modeling is often focused on a single species. A model for the simultaneous dissolution of soluble species was developed, which considers different solubilities and dissolution rates and considers that particle collapses when the rapidly soluble species is depleted. The collapsed matter is formed by inert material and a fraction of the soluble species with lower dissolution rate that has not dissolved yet. The model is applied to the leaching of a water-soluble mineral (caliche) with two soluble species dissolving simultaneously with different rates. Measured outlet concentrations of nitrate and magnesium were used to validate the model. Results showed that the model reproduced adequately the leaching of species with rapid and intermediate dissolution rate. Effect of the operating and kinetic parameters on the leaching process is also shown using the actual conditions of heap leaching for caliche mineral.

  19. Method of analyzing multiple sample simultaneously by detecting absorption and systems for use in such a method

    Science.gov (United States)

    Yeung, Edward S.; Gong, Xiaoyi

    2004-09-07

    The present invention provides a method of analyzing multiple samples simultaneously by absorption detection. The method comprises: (i) providing a planar array of multiple containers, each of which contains a sample comprising at least one absorbing species, (ii) irradiating the planar array of multiple containers with a light source and (iii) detecting absorption of light with a detetion means that is in line with the light source at a distance of at leaat about 10 times a cross-sectional distance of a container in the planar array of multiple containers. The absorption of light by a sample indicates the presence of an absorbing species in it. The method can further comprise: (iv) measuring the amount of absorption of light detected in (iii) indicating the amount of the absorbing species in the sample. Also provided by the present invention is a system for use in the abov metho.The system comprises; (i) a light source comrnpising or consisting essentially of at leaat one wavelength of light, the absorption of which is to be detected, (ii) a planar array of multiple containers, and (iii) a detection means that is in line with the light source and is positioned in line with and parallel to the planar array of multiple contiainers at a distance of at least about 10 times a cross-sectional distance of a container.

  20. Multi-compound polarization by DNP allows simultaneous assessment of multiple enzymatic activities in vivo.

    Science.gov (United States)

    Wilson, David M; Keshari, Kayvan R; Larson, Peder E Z; Chen, Albert P; Hu, Simon; Van Criekinge, Mark; Bok, Robert; Nelson, Sarah J; Macdonald, Jeffrey M; Vigneron, Daniel B; Kurhanewicz, John

    2010-07-01

    recorded for the individual metabolites. These studies demonstrated the feasibility of simultaneously measuring in vivo pH and tumor metabolism using nontoxic, endogenous species, and the potential to extend the multi-polarization approach to include up to four hyperpolarized probes providing multiple metabolic and physiologic measures in a single MR acquisition. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  1. Using Simultaneous Prompting Procedure to Promote Recall of Multiplication Facts by Middle School Students with Cognitive Impairment

    Science.gov (United States)

    Rao, Shaila; Mallow, Lynette

    2009-01-01

    This study examined effectiveness of simultaneous prompting system in teaching students with cognitive impairment to automate recall of multiplication facts. A multiple probes design with multiple sets of math facts and replicated across multiple subjects was used to assess effectiveness of simultaneous prompting on recall of basic multiplication…

  2. Universal Multiplex PCR: a novel method of simultaneous amplification of multiple DNA fragments

    Directory of Open Access Journals (Sweden)

    Wen Daxing

    2012-08-01

    Full Text Available Abstract Background Multiplex PCR has been successfully applied in many areas since it was first reported in 1988; however, it suffers from poor universality. Results A novel method called Universal Multiplex PCR (UM-PCR was created, which simultaneously amplifies multiple target fragments from genomic DNA. The method has two steps. First, the universal adapter-F and universal adapter-R are connected to the forward primers and the reverse primers, respectively. Hairpin structures and cross dimers of five pairs of adapter-primers are detected. Second, UM-PCR amplification is implemented using a novel PCR procedure termed “Two Rounds Mode” (three and 28–32 cycles. The first round (the first three cycles is named the “One by One Annealing Round”. The second round (28–32 cycles combines annealing with extension. In the first two cycles of the first round, primers only amplify the specific templates; there are no templates for the universal adapters. The templates of universal adapters begin to be synthesized from the second cycle of the first round, and universal adapters and primers commence full amplification from the third cycle of the first round. Conclusions UM-PCR greatly improves the universality of multiplex PCR. UM-PCR could rapidly detect the genetic purity of maize seeds. In addition, it could be applied in other areas, such as analysis of polymorphisms, quantitative assays and identifications of species.

  3. Multiple-fluorophore-specie detection with a tapered Fabry-Perot fluorescence spectrometer.

    Science.gov (United States)

    Wahl, Jeremy A; Van Delden, Jay S; Tiwari, Sandip

    2005-09-01

    A novel fluorescence spectrometer and method for the simultaneous detection of multiple-fluorophore species in a no-moving-parts, instantaneous manner is described. In the reported embodiment of the instrument, a tapered Fabry-Perot filter is used to spatially encode the fluorescence spectrum from a multiple-dye-containing test sample. Using a pseudoinverse reconstruction algorithm, we spectrally decode the particle concentration for each dye specie in the test sample. Experimental results are reported along with a theoretical treatment of the method.

  4. The simultaneous occurrence of multiple myeloma and JAK2 positive myeloproliferative neoplasms - Report on two cases

    OpenAIRE

    Badelita, S; Dobrea, C.; Colita, A; Dogaru, M; Dragomir, M; Jardan, C; Coriu, D.

    2015-01-01

    Multiple myeloma and JAK2 positive chronic myeloproliferative neoplasms are hematologic malignancies with a completely different cellular origin. Two cases of simultaneous occurrence of multiple myeloma, one with primary myelofibrosis and another one with essential thrombocythemia are reported in this article. In such cases, an accurate diagnosis requires a molecular testing, including gene sequencing and differential diagnosis of pancytosis associated with splenic amyloidosis. In general, in...

  5. A light-switchable bidirectional expression module allowing simultaneous regulation of multiple genes.

    Science.gov (United States)

    Chen, Xianjun; Li, Ting; Wang, Xue; Yang, Yi

    2015-10-02

    Several light-regulated genetic circuits have been applied to spatiotemporally control transgene expression in mammalian cells. However, simultaneous regulation of multiple genes using one genetic device by light has not yet been reported. In this study, we engineered a bidirectional expression module based on LightOn system. Our data showed that both reporter genes could be regulated at defined and quantitative levels. Simultaneous regulation of four genes was further achieved in cultured cells and mice. Additionally, we successfully utilized the bidirectional expression module to monitor the expression of a suicide gene, showing potential for photodynamic gene therapy. Collectively, we provide a robust and useful tool to simultaneously control multiple genes expression by light, which will be widely used in biomedical research and biotechnology. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Predicting Final GPA of Graduate School Students: Comparing Artificial Neural Networking and Simultaneous Multiple Regression

    Science.gov (United States)

    Anderson, Joan L.

    2006-01-01

    Data from graduate student applications at a large Western university were used to determine which factors were the best predictors of success in graduate school, as defined by cumulative graduate grade point average. Two statistical models were employed and compared: artificial neural networking and simultaneous multiple regression. Both models…

  7. Tracking Multiple Statistics: Simultaneous Learning of Object Names and Categories in English and Mandarin Speakers

    Science.gov (United States)

    Chen, Chi-hsin; Gershkoff-Stowe, Lisa; Wu, Chih-Yi; Cheung, Hintat; Yu, Chen

    2017-01-01

    Two experiments were conducted to examine adult learners' ability to extract multiple statistics in simultaneously presented visual and auditory input. Experiment 1 used a cross-situational learning paradigm to test whether English speakers were able to use co-occurrences to learn word-to-object mappings and concurrently form object categories…

  8. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    The aim of the study was to investigate the bacterial profile of chronic venous leg ulcers and the importance of the profile to ulcer development. Patients with persisting venous leg ulcers were included and followed for 8 weeks. Every second week, ulcer samples were collected and the bacterial...... of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing....... species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  9. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

    Science.gov (United States)

    Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

    2015-09-15

    There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

  10. Strong neutral spatial effects shape tree species distributions across life stages at multiple scales.

    Directory of Open Access Journals (Sweden)

    Yue-Hua Hu

    Full Text Available Traditionally, ecologists use lattice (regional summary count data to simulate tree species distributions to explore species coexistence. However, no previous study has explicitly compared the difference between using lattice count and basal area data and analyzed species distributions at both individual species and community levels while simultaneously considering the combined scenarios of life stage and scale. In this study, we hypothesized that basal area data are more closely related to environmental variables than are count data because of strong environmental filtering effects. We also address the contribution of niche and the neutral (i.e., solely dependent on distance factors to species distributions. Specifically, we separately modeled count data and basal area data while considering life stage and scale effects at the two levels with simultaneous autoregressive models and variation partitioning. A principal coordinates of neighbor matrix (PCNM was used to model neutral spatial effects at the community level. The explained variations of species distribution data did not differ significantly between the two types of data at either the individual species level or the community level, indicating that the two types of data can be used nearly identically to model species distributions. Neutral spatial effects represented by spatial autoregressive parameters and the PCNM eigenfunctions drove species distributions on multiple scales, different life stages and individual species and community levels in this plot. We concluded that strong neutral spatial effects are the principal mechanisms underlying the species distributions and thus shape biodiversity spatial patterns.

  11. VORICONAZOLE TOXICITY IN MULTIPLE PENGUIN SPECIES.

    Science.gov (United States)

    Hyatt, Michael W; Georoff, Timothy A; Nollens, Hendrik H; Wells, Rebecca L; Clauss, Tonya M; Ialeggio, Donna M; Harms, Craig A; Wack, Allison N

    2015-12-01

    Aspergillosis is a common respiratory fungal disease in penguins managed under human care. Triazole antifungal drugs, including itraconazole, are most commonly used for treatment; however, itraconazole treatment failures from drug resistance are becoming more common, requiring newer treatment options. Voriconazole, a newer triazole, is being used more often. Until recently, no voriconazole pharmacokinetic studies had been performed in penguins, leading to empiric dosing based on other avian studies. This has led to increased anecdotal reporting of apparent voriconazole toxicity in penguins. This report describes 18 probable and 6 suspected cases of voriconazole toxicity in six penguin species from nine institutions: 12 African penguins (Spheniscus demersus), 5 Humboldt penguins (Spheniscus humboldti), 3 Magellanic penguins (Spheniscus magellanicus), 2 gentoo penguins (Pygoscelis papua papua), 1 macaroni penguin (Eudyptes chrysolophus), and 1 emperor penguin (Aptenodytes forsteri). Observed clinical signs of toxicity included anorexia, lethargy, weakness, ataxia, paresis, apparent vision changes, seizure-like activity, and generalized seizures. Similar signs of toxicity have also been reported in humans, in whom voriconazole therapeutic plasma concentration for Aspergillus spp. infections is 2-6 μg/ml. Plasma voriconazole concentrations were measured in 18 samples from penguins showing clinical signs suggestive of voriconazole toxicity. The concentrations ranged from 8.12 to 64.17 μg/ml, with penguins having plasma concentrations above 30 μg/ml exhibiting moderate to severe neurologic signs, including ataxia, paresis, and seizures. These concentrations were well above those known to result in central nervous system toxicity, including encephalopathy, in humans. This case series highlights the importance of species-specific dosing of voriconazole in penguins and plasma therapeutic drug monitoring. Further investigation, including pharmacokinetic studies, is

  12. Acute Simultaneous Thrombotic Occlusion of Multiple Coronary Arteries in Acute Myocardial Infarction: A Case Report

    Directory of Open Access Journals (Sweden)

    Mohammad Mahdi Daei

    2017-05-01

    Full Text Available Introduction Simultaneous multiple coronary artery thrombosis is a rare finding in ST segment elevation myocardial infarction (STEMI, and has a high mortality rate. Case Presentation We report a case of myocardial infarction with cardiogenic shock, left bundle branch block, and multiple ST segment elevation on the electrocardiogram and thrombotic occlusion of the left circumflex, optus marginal, and left anterior descending arteries on emergency coronary angiography. Thrombus aspiration was performed at left circumflex, optus marginal, and left anterior descending arteries. Conclusions In patients with STEMI, multiple coronary thrombosis is unusual and associated with high patient mortality.

  13. Fully coupled simulation of multiple hydraulic fractures to propagate simultaneously from a perforated horizontal wellbore

    Science.gov (United States)

    Zeng, Qinglei; Liu, Zhanli; Wang, Tao; Gao, Yue; Zhuang, Zhuo

    2017-05-01

    In hydraulic fracturing process in shale rock, multiple fractures perpendicular to a horizontal wellbore are usually driven to propagate simultaneously by the pumping operation. In this paper, a numerical method is developed for the propagation of multiple hydraulic fractures (HFs) by fully coupling the deformation and fracturing of solid formation, fluid flow in fractures, fluid partitioning through a horizontal wellbore and perforation entry loss effect. The extended finite element method (XFEM) is adopted to model arbitrary growth of the fractures. Newton's iteration is proposed to solve these fully coupled nonlinear equations, which is more efficient comparing to the widely adopted fixed-point iteration in the literatures and avoids the need to impose fluid pressure boundary condition when solving flow equations. A secant iterative method based on the stress intensity factor (SIF) is proposed to capture different propagation velocities of multiple fractures. The numerical results are compared with theoretical solutions in literatures to verify the accuracy of the method. The simultaneous propagation of multiple HFs is simulated by the newly proposed algorithm. The coupled influences of propagation regime, stress interaction, wellbore pressure loss and perforation entry loss on simultaneous propagation of multiple HFs are investigated.

  14. Simultaneous detection of randomly arranged multiple barcodes using time division multiplexing technique

    Science.gov (United States)

    Haider, Saad Md. Jaglul; Islam, Md. Kafiul

    2010-02-01

    A method of detecting multiple barcodes simultaneously using time division multiplexing technique has been proposed in this paper to minimize the effective time needed for handling multiple tags of barcodes and to lessen the overall workload. Available barcode detection systems can handle multiple types of barcode but a single barcode at a time. This is not so efficient and can create large queue and chaos in places like mega shopping malls or large warehouses where we need to scan huge number of barcodes daily. Our proposed system is expected to improve the real time identification of goods or products on production lines and in automated warehouses or in mega shopping malls in a much more convenient and efficient way. For identifying of multiple barcodes simultaneously, a particular arrangement and orientation of LASER scanner and reflector have been used with a special curve shaped basement where the barcodes are placed. An effective and novel algorithm is developed to extract information from multiple barcodes which introduces starting pattern and ending pattern in barcodes with bit stuffing technique for the convenience of multiple detections. CRC technique is also used for trustworthiness of detection. The overall system enhances the existing single barcode detection system by a great amount although it is easy to implement and use.

  15. Simultaneous measurement of the species concentration, flow velocity, and temperature in a gas jet

    Science.gov (United States)

    He, Q.; Glosemeyer, D.; Bennis, G. L.; Soltanolkotabi, M.; Gupta, R.

    1999-03-01

    Photothermal deflection spectroscopy has the potential of serving as an important diagnostic technique in combustion environments for measurements of species concentration, temperature, and flow velocity. We demonstrate, by application to a jet of N2 seeded with 0.5% NO2, that these three important parameters can be measured simultaneously, that is, in a single pulse.

  16. Simultaneously measuring multiple protein interactions and their correlations in a cell by Protein-interactome Footprinting.

    Science.gov (United States)

    Luo, Si-Wei; Liang, Zhi; Wu, Jia-Rui

    2017-03-24

    Quantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers. Using PiF, we quantitatively reveal dynamic patterns of PPIs and their correlation network in E. coli two-component systems.

  17. Effect of Multiple Simultaneous Vaccines on Polio Seroresponse and Associated Health Outcomes

    Science.gov (United States)

    2015-01-01

    Haemophilus influenzae type b vaccine given concurrently with meningococcal group C conjugate vaccine at 2, 3 and 4 months of age. Arch Dis Child 2007;92:11–6...responses to biological warfare vaccines in human vaccinees . Clin Infect Dis 2006;43:1–7. 20] Butler D. Admission on Gulf War vaccines spurs debate on...Naval Health Research Center Effect of Multiple, Simultaneous Vaccines on Polio Seroresponse and Associated Health Outcomes Michael P

  18. Simultaneous X-ray diffraction from multiple single crystals of macromolecules

    DEFF Research Database (Denmark)

    Paithankar, Karthik S.; Sørensen, Henning Osholm; Wright, Jonathan P.

    2011-01-01

    The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedu...... could be useful both in relation to diffraction data obtained from intergrown crystals and to alleviate the problem of rapid diffraction decay arising from the effects of radiation damage....

  19. Plasmonic nanosensors for simultaneous quantification of multiple protein-protein binding affinities.

    Science.gov (United States)

    Ahijado-Guzmán, Rubén; Prasad, Janak; Rosman, Christina; Henkel, Andreas; Tome, Lydia; Schneider, Dirk; Rivas, Germán; Sönnichsen, Carsten

    2014-10-08

    Most of current techniques used for the quantification of protein-protein interactions require the analysis of one pair of binding partners at a time. Herein we present a label-free, simple, fast, and cost-effective route to characterize binding affinities between multiple macromolecular partners simultaneously, using optical dark-field spectroscopy and individual protein-functionalized gold nanorods as sensing elements. Our NanoSPR method could easily become a simple and standard tool in biological, biochemical, and medical laboratories.

  20. Bilateral Simultaneous Central Retinal Vein Occlusion Presenting as Initial Manifestation of Multiple Myeloma

    Directory of Open Access Journals (Sweden)

    Kamath SJ

    2014-08-01

    Full Text Available A fifty years old male with a medical history of diabetes mellitus presented with complaints of sudden painless bilateral vision loss since 2 weeks. Ophthalmic examination showed visual acuity in both eyes were counting finger 2 meters. Intraocular pressure and anterior segment examination findings in both eyes were normal. Funduscopy revealed bilateral central retinal vein occlusion (CRVO. Haematological and radiological investigations confirmed diagnosis of multiple myeloma and ocular manifestation in the form of bilateral simultaneous CRVO was the first presentation of multiple myeloma. This patient had a double hyper viscosity insult with severe diabetes mellitus and multiple myeloma. Since abnormal blood viscosity plays a role in the causation of bilateral CRVO, systemic investigation for underlying hyperviscosity syndromes including blood dyscrasias such as multiple myeloma is warranted.

  1. Simultaneous determination of butyltin and phenyltin species in sediments using ultrasound-assisted leaching

    Energy Technology Data Exchange (ETDEWEB)

    Carpinteiro, J.; Rodriguez, I.; Cela, R. [Dpto. Quimica Analitica, Nutricion y Bromatologia, Universidad de Santiago de Compostela (Spain)

    2001-08-01

    A fast and simple procedure is presented for the simultaneous leaching of butyl (mono, di and tributyl) and phenyl organotin species from sediment samples. Leached compounds are further ethylated with sodium tetraethylborate in aqueous medium, and analyzed by gas chromatography. After testing the stability of triphenyltin under different extraction conditions, ultrasound-assisted leaching at room temperature in the presence of acetic acid was been proposed as an extraction procedure compatible with the simultaneous determination of phenyl- and butyltin compounds in sediments. Recoveries between 70 and 90% were obtained for phenyl species in spiked samples prepared in the laboratory. Results for butyltin species were validated by use of the reference material PACS-2. Quantification limits, using GC-MIP-AES as measurement technique, were approximately 5-10 ng g{sup -1}. Precision in the consecutive analysis of three sediment samples varied between 3 and 10%. (orig.)

  2. Tumor suppressor miR-1 inhibits tumor growth and metastasis by simultaneously targeting multiple genes

    Science.gov (United States)

    Liu, Cuilian; Zhang, Song; Wang, Qizhi; Zhang, Xiaobo

    2017-01-01

    Cancer progression depends on tumor growth and metastasis, which are activated or suppressed by multiple genes. An individual microRNA may target multiple genes, suggesting that a miRNA may suppress tumor growth and metastasis via simultaneously targeting different genes. However, thus far, this issue has not been explored. In the present study, the findings showed that miR-1 could simultaneously inhibit tumor growth and metastasis of gastric and breast cancers by targeting multiple genes. The results indicated that miR-1 was significantly downregulated in cancer tissues compared with normal tissues. The miR-1 overexpression led to cell cycle arrest in the G1 phase in gastric and breast cancer cells but not in normal cells. Furthermore, the miR-1 overexpression significantly inhibited the metastasis of gastric and breast cancer cells. An analysis of the underlying mechanism revealed that the simultaneous inhibition of tumor growth and metastasis mediated by miR-1 was due to the synchronous targeting of 6 miR-1 target genes encoding cyclin dependent kinase 4, twinfilin actin binding protein 1, calponin 3, coronin 1C, WAS protein family member 2 and thymosin beta 4, X-linked. In vivo assays demonstrated that miR-1 efficiently inhibited tumor growth and metastasis of gastric and breast cancers in nude mice. Therefore, our study contributed novel insights into the miR-1′s roles in tumorigenesis of gastric and breast cancers. PMID:28159933

  3. Multiple peaks of species abundance distributions induced by sparse interactions

    CERN Document Server

    Obuchi, Tomoyuki; Tokita, Kei

    2016-01-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self interaction $u$, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of $u$ below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all spe...

  4. Multiple modes in a coral species abundance distribution.

    Science.gov (United States)

    Dornelas, Maria; Connolly, Sean R

    2008-10-01

    Species abundance distributions are an important measure of biodiversity and community structure. These distributions are affected by sampling, and alternative species-abundance models often make similar predictions for small sample sizes. Very large samples reveal the relative abundances of rare species, and thus provide information about species relative abundances that small samples cannot. Here, we present the species-abundance distribution for a sample of > 40,000 coral colonies at a single site, exceeding existing samples of coral local assemblages by over an order of magnitude. This abundance distribution is multimodal when examined on a logarithmic scale. Four different model selection procedures all indicate that the underlying community abundance distribution has at least three modes. We show that the multiple modes are not caused by mixtures of species with different habitat preferences. However, spatial aggregation partially explains our results. We inspect published work on species abundance distributions, and suggest that multimodality may be a common feature of large samples.

  5. Simultaneous and spatially separated detection of multiple orbital angular momentum states

    Science.gov (United States)

    Tudor, R.; Mihailescu, M.; Kusko, C.; Paun, I. A.; Nan, A. E.; Kusko, M.

    2016-06-01

    We present a method for spatially separated detection of multiple orbital angular momentum (OAM) states, simultaneous. The starting point is the generation of axially superposed Laguerre-Gauss beams, carrying multiple OAM states using a single computer generated hologram. The information contained in the OAM superposition is transferred to the first diffraction order and is detected at the receiver with a reading mask, which contains two perpendicular superposed fork-like holograms, ensuring the spatial separation of the OAM states. The dynamic of the process is studied in terms of the number of generated OAM states and the constructive parameters values. The experimental investigations use an optical arrangement based on a spatial light modulator in the transmitter unit and an amplitude mask in the receiver unit. This proof of concept experiment demonstrates the possibility of simultaneously detection of multiple OAM states in points located at different coordinates, controlled through the design of the holograms and shows the capability of our proposed method to increase the capacity of free-space optical communication channels.

  6. Lasiodiplodia species fungal osteomyelitis in a multiple myeloma patient.

    Science.gov (United States)

    Mohan, M; Shalin, S C; Kothari, A; Rico, J C C; Caradine, K; Burgess, M

    2016-10-01

    Lasiodiplodia species are environmental fungi that have been reported as a cause of infection in both immunocompetent and immunocompromised patients. We present a case of fungal osteomyelitis caused by Lasiodiplodia species in a patient with multiple myeloma after autologous stem cell transplant. The patient was successfully treated with a combination of surgery and oral voriconzole. To the best of our knowledge, this is the first reported case of fungal osteomyelitis caused by Lasiodiplodia species. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Intracellular Microreactors as Artificial Organelles to Conduct Multiple Enzymatic Reactions Simultaneously

    DEFF Research Database (Denmark)

    Gallardo, Maria Godoy; Labay, Cédric Pierre; Jansman, Michelle M. T.

    2017-01-01

    The creation of artificial organelles is a new paradigm in medical therapy that aims to substitute for missing cellular function by replenishing a specific cellular task. Artificial organelles tackle the challenge of mimicking metabolism, which is the set of chemical reactions that occur within...... and Amplex Red substrates, which are specific for TRP and HRP, respectively. Conversion of the substrates into the respective fluorescent products is observed. This report on the first microreactor conducting multiple enzymatic reactions simultaneously inside a cell is a considerable step in the field...

  8. A shape identification problem in estimating simultaneously two interfacial configurations in a multiple region domain

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Cheng-Hung; Shih, Chen-Chung [National Cheng Kung University, Tainan (Taiwan). Department of Systems and Naval Mechatronic Engineering

    2006-01-15

    A two-dimensional shape identification problem, i.e. inverse geometry problem, of estimating simultaneously two interfacial configurations in a multiple (three) region domain is solved in this study by using the Conjugate Gradient Method (CGM) and Boundary Element Method (BEM)-based inverse algorithm. Two over-utilized conditions should be applied in determining two gradient equations; this differs from our previous relevant studies. Numerical experiments using different measurement errors and number of sensors were performed to justify the validity of the conjugate gradient method in solving this shape identification problem. Finally it is concluded that the present algorithm can estimate the accurate interfacial configurations. (author)

  9. Simultaneous measurement of spectra at multiple ranges using a single spectrometer.

    Science.gov (United States)

    Lienert, Barry; Porter, John; Sharma, Shiv K

    2009-08-20

    We have designed and built an instrument having the capability to measure and display spectra at multiple ranges near simultaneously in real time. An excitation laser beam is oriented parallel to and offset from the axis of the light collection optics. The image of the laser beam is then displaced with range. Multiple optical fibers collect the displaced images at different ranges. The output ends of these fibers are positioned vertically along the input slit of a spectrometer that disperses the light from each fiber along different rows of the spectrometer's two-dimensional detector array. The detector array rows then give an immediate visual comparison of spectra at different ranges. A small prototype of this system covering a range from 3 to 13 m has been built. It has been successfully tested using containers holding two distinct fluorescent dyes. Numerical simulations indicate that the technique can be extended to longer-range systems.

  10. A pulse coding and decoding strategy to perform Lamb wave inspections using simultaneously multiple actuators

    Science.gov (United States)

    De Marchi, Luca; Marzani, Alessandro; Moll, Jochen; Kudela, Paweł; Radzieński, Maciej; Ostachowicz, Wiesław

    2017-07-01

    The performance of Lamb wave based monitoring systems, both in terms of diagnosis time and data complexity, can be enhanced by increasing the number of transducers used to actuate simultaneously the guided waves in the inspected medium. However, in case of multiple simultaneously-operated actuators the interference among the excited wave modes within the acquired signals has to be considered for the further processing. To this aim, in this work a code division strategy based on the Warped Frequency Transform is presented. At first, the proposed procedure encodes actuation pulses using Gold sequences. Next, for each considered actuator the acquired signals are compensated from dispersion by cross correlating the warped version of the actuated and received signals. Compensated signals form the base for a final wavenumber imaging meant at emphasizing defects and or anomalies by removing incident wavefield and edge reflections. The proposed strategy is tested numerically, and validated through an experiment in which guided waves are actuated in a plate by four piezoelectric transducers operating simultaneously.

  11. Simultaneous two-axis shearographic interferometer using multiple wavelengths and a color camera

    Science.gov (United States)

    Richoz, Guillaume L.; Schajer, Gary S.

    2016-02-01

    Multi-component measurements in shearography and other applications of Electronic Speckle Pattern Interferometry (ESPI) are typically achieved using multiple optical configurations that are activated sequentially to measure each desired quantity separately. A novel optical setup is introduced here where orthogonal shearography measurements are simultaneously made using a single color-camera imaging multiple monochromatic light sources of different wavelengths. The Red-Green-Blue (RGB) sensors of a conventional Bayer type camera are read separately, thereby providing three independent color signals and independent ESPI phase maps. Orthogonal axis shearography is achieved using a modified shearography interferometer where a dichroic filter is added to provide a second wavelength-dependent measurement. The availability of the two surface slopes gives the opportunity for the data to be summed numerically to give the surface displacement shape. This application is of significant practical interest because the surface displacement measurement can be made under field conditions by taking advantage of the well-known optical stability of shearography measurements. The two simultaneously measured surface slopes also offer the possibility to mathematically compensate for non-uniformity and non-orthogonality in the image shear caused by mirror non-flatness and/or mirror misalignments.

  12. Simultaneous Second Harmonic Generation of Multiple Wavelength Laser Outputs for Medical Sensing

    Directory of Open Access Journals (Sweden)

    Chang-Seok Kim

    2011-06-01

    Full Text Available Multiple wavelength light sources in the medical spectral window region are useful for various medical sensing applications in tissue by distinguishing the absorption and scattering coefficients optically. We propose a simultaneous second harmonic generation of multiple wavelength fiber laser output using parallel channels of periodically-poled lithium niobate (PPLN waveguides. High intensity dual wavelength lasing output is experimentally realized with two tunable fiber Bragg gratings of 1,547.20 nm and 1,554.48 nm for the efficient conversion to the half wavelengths, 773.60 nm and 777.24 nm, by using two parallel PPLN channels. Compared with a conventional dual second harmonic generation (SHG configuration based on two different input wavelengths from each independent light source, this method has a relatively higher efficiency to align the input light beam into the adjacent parallel PPLN channels simultaneously. The use of fiber lasers offers several advantages since they are relatively inexpensive, provide high power in excess of tens of watts, are widely tunable, and can produce pulses from milliseconds to femtoseconds.

  13. Simultaneous Second Harmonic Generation of Multiple Wavelength Laser Outputs for Medical Sensing

    Science.gov (United States)

    Son, Seung Nam; Song, Jae-Jin; Kang, Jin U.; Kim, Chang-Seok

    2011-01-01

    Multiple wavelength light sources in the medical spectral window region are useful for various medical sensing applications in tissue by distinguishing the absorption and scattering coefficients optically. We propose a simultaneous second harmonic generation of multiple wavelength fiber laser output using parallel channels of periodically-poled lithium niobate (PPLN) waveguides. High intensity dual wavelength lasing output is experimentally realized with two tunable fiber Bragg gratings of 1,547.20 nm and 1,554.48 nm for the efficient conversion to the half wavelengths, 773.60 nm and 777.24 nm, by using two parallel PPLN channels. Compared with a conventional dual second harmonic generation (SHG) configuration based on two different input wavelengths from each independent light source, this method has a relatively higher efficiency to align the input light beam into the adjacent parallel PPLN channels simultaneously. The use of fiber lasers offers several advantages since they are relatively inexpensive, provide high power in excess of tens of watts, are widely tunable, and can produce pulses from milliseconds to femtoseconds. PMID:22163945

  14. Simultaneous entanglement swapping of multiple orbital angular momentum states of light.

    Science.gov (United States)

    Zhang, Yingwen; Agnew, Megan; Roger, Thomas; Roux, Filippus S; Konrad, Thomas; Faccio, Daniele; Leach, Jonathan; Forbes, Andrew

    2017-09-21

    High-bit-rate long-distance quantum communication is a proposed technology for future communication networks and relies on high-dimensional quantum entanglement as a core resource. While it is known that spatial modes of light provide an avenue for high-dimensional entanglement, the ability to transport such quantum states robustly over long distances remains challenging. To overcome this, entanglement swapping may be used to generate remote quantum correlations between particles that have not interacted; this is the core ingredient of a quantum repeater, akin to repeaters in optical fibre networks. Here we demonstrate entanglement swapping of multiple orbital angular momentum states of light. Our approach does not distinguish between different anti-symmetric states, and thus entanglement swapping occurs for several thousand pairs of spatial light modes simultaneously. This work represents the first step towards a quantum network for high-dimensional entangled states and provides a test bed for fundamental tests of quantum science.Entanglement swapping in high dimensions requires large numbers of entangled photons and consequently suffers from low photon flux. Here the authors demonstrate entanglement swapping of multiple spatial modes of light simultaneously, without the need for increasing the photon numbers with dimension.

  15. Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

    Science.gov (United States)

    Afonin, Kirill A.; Desai, Ravi; Viard, Mathias; Kireeva, Maria L.; Bindewald, Eckart; Case, Christopher L.; Maciag, Anna E.; Kasprzak, Wojciech K.; Kim, Taejin; Sappe, Alison; Stepler, Marissa; KewalRamani, Vineet N.; Kashlev, Mikhail; Blumenthal, Robert; Shapiro, Bruce A.

    2014-01-01

    Control over the simultaneous delivery of different functionalities and their synchronized intracellular activation can greatly benefit the fields of RNA and DNA biomedical nanotechnologies and allow for the production of nanoparticles and various switching devices with controllable functions. We present a system of multiple split functionalities embedded in the cognate pairs of RNA–DNA hybrids which are programmed to recognize each other, re-associate and form a DNA duplex while also releasing the split RNA fragments which upon association regain their original functions. Simultaneous activation of three different functionalities (RNAi, Förster resonance energy transfer and RNA aptamer) confirmed by multiple in vitro and cell culture experiments prove the concept. To automate the design process, a novel computational tool that differentiates between the thermodynamic stabilities of RNA–RNA, RNA–DNA and DNA–DNA duplexes was developed. Moreover, here we demonstrate that besides being easily produced by annealing synthetic RNAs and DNAs, the individual hybrids carrying longer RNAs can be produced by RNA polymerase II-dependent transcription of single-stranded DNA templates. PMID:24194608

  16. Simultaneous Determination of Arsenic and Selenium Species in Sediment Extracts Utilizing Coupled Techniques with Mass Spectrometric Detection

    Science.gov (United States)

    Yoon, H.; Yoon, C.

    2009-12-01

    Arsenic has been recognized as one of the major problems of toxicity in several parts of the world. It is well known that the toxicity of arsenic depends on its chemical form. Selenium is one of the minor but plays an important biological role in human health. The multiple roles of selenium, deficiency and toxicity, depend on its chemical form and concentration. The multielement detection capability of ICP-MS makes it an ideal detector for multielement chromatographic separation. Most of multielement separation analyses by LC-ICP-MS are applied to standard or to water samples. Only very few reports deal with solid matrices. A procedure for the simultaneous determination of arsenic and selenium species in phosphoric acid extracts of sediment samples by liquid chromatography coupled to ICP-MS has been developing. Arsenic species, arsenite [As(III)], arsenate [As(V)], dimethylarsinic acid (DMA), monomethylarsonic acid (MMA), and selenium species, selenite [Se(IV)], selenate [Se(VI)] were separated on anion exchange column by a mobile phase of ammonium dihydrogen phosphate. The total analysis took less than 10 min with gradient elution at flow rate of 1.0 mL/min. The sonication extraction was used with dry sediment and phosphoric acid. Reaction gases such as methane and oxygen was used to remove spectral interferences on arsenic and selenium measurement. The estimated detection limits in the sediment ranged between 1 and 25 ng/g for the arsenic and selenium species. The repeatability was less than 15% (RSD) for 1 µg/L arsenic species and 5 µg/L selenium species. Accuracy of the method was assessed through the recovery of the spiked sediment. Recoveries ranged between 82 and 115 % for all the species.

  17. Assessing Neurocognition via Gamified Experimental Logic: A Novel Approach to Simultaneous Acquisition of Multiple ERPs.

    Science.gov (United States)

    Nair, Ajay K; Sasidharan, Arun; John, John P; Mehrotra, Seema; Kutty, Bindu M

    2016-01-01

    The present study describes the development of a neurocognitive paradigm: "Assessing Neurocognition via Gamified Experimental Logic" (ANGEL), for performing the parametric evaluation of multiple neurocognitive functions simultaneously. ANGEL employs an audiovisual sensory motor design for the acquisition of multiple event related potentials (ERPs)-the C1, P50, MMN, N1, N170, P2, N2pc, LRP, P300, and ERN. The ANGEL paradigm allows assessment of 10 neurocognitive variables over the course of three "game" levels of increasing complexity ranging from simple passive observation to complex discrimination and response in the presence of multiple distractors. The paradigm allows assessment of several levels of rapid decision making: speeded up response vs. response-inhibition; responses to easy vs. difficult tasks; responses based on gestalt perception of clear vs. ambiguous stimuli; and finally, responses with set shifting during challenging tasks. The paradigm has been tested using 18 healthy participants from both sexes and the possibilities of varied data analyses have been presented in this paper. The ANGEL approach provides an ecologically valid assessment (as compared to existing tools) that quickly yields a very rich dataset and helps to assess multiple ERPs that can be studied extensively to assess cognitive functions in health and disease conditions.

  18. Assessing Neurocognition via Gamified Experimental Logic: A novel approach to simultaneous acquisition of multiple ERPs

    Directory of Open Access Journals (Sweden)

    Ajay Kumar eNair

    2016-01-01

    Full Text Available The present study describes the development of a neurocognitive paradigm: ‘Assessing Neurocognition via Gamified Experimental Logic’ (ANGEL, for performing the parametric evaluation of multiple neurocognitive functions simultaneously. ANGEL employs an audiovisual sensory motor design for the acquisition of multiple event related potentials (ERPs - the C1, P50, MMN, N1, N170, P2, N2pc, LRP, P300 and ERN. The ANGEL paradigm allows assessment of ten neurocognitive variables over the course of three ‘game’ levels of increasing complexity ranging from simple passive observation to complex discrimination and response in the presence of multiple distractors. The paradigm allows assessment of several levels of rapid decision making: speeded up response vs response-inhibition; responses to easy vs difficult tasks; responses based on gestalt perception of clear vs ambiguous stimuli; and finally, responses with set shifting during challenging tasks. The paradigm has been tested using 18 healthy participants from both sexes and the possibilities of varied data analyses have been presented in this paper. The ANGEL approach provides an ecologically valid assessment (as compared to existing tools that quickly yields a very rich dataset and helps to assess multiple ERPs that can be studied extensively to assess cognitive functions in health and disease conditions.

  19. Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes

    Directory of Open Access Journals (Sweden)

    Tavaré Simon

    2009-04-01

    Full Text Available Abstract Background Fluorescent proteins such as GFP (Green Fluorescent Protein and DsRED (Discosoma sp.Red Fluorescent Protein are often used as reporter molecules for transgene expression in Drosophila and other species. We have recently reported methods that allow simultaneous tracking of animal movement and GFP expression in real time, however the assay was limited to single animals and a single transgene. Numerous studies would be facilitated by methods that allow for assay of multiple animals and multiple transgenes. Findings Here we report an improved fly video tracking system that allows multiple transgenic flies to be tracked simultaneously using visible light, GFP fluorescence and DsRED fluorescence. The movement of multiple flies could be accurately tracked at real time rates, while simultaneously assaying the expression level of two different transgenes marked with GFP and DsRED. The individual flies could be accurately tracked and distinguished even during periods when transgene fluorescence was undetected. For example, characteristic patterns of hsp70 and hsp22 transgene induction could be simultaneously quantified and correlated with animal movement in aging flies, and as groups of flies died due to dessication/starvation. Conclusion The improved methods allow for more efficient assay of the correlation between gene expression, behavior, aging and mortality: multiple animals can be assayed with simultaneous quantification of multiple transgenes using GFP and DsRED fluorescence. These methods should allow for increased flexibility in experimental designs. For example, in the future it should be possible to use gene expression levels to predict remaining life span more accurately, and to quantify gene expression changes caused by interactions between animals in real time.

  20. Multiple factors and thresholds explaining fish species distributions in lowland streams

    Directory of Open Access Journals (Sweden)

    Cristina Trigal

    2015-07-01

    Full Text Available Appropriate restoration and conservation measures require a good understanding of the factors limiting the distribution of species, the presence of steep changes in the distribution along environmental gradients and the effect of environmental interactions on species distribution. We used 12 environmental variables describing connectivity, hydrology, climate and stream morphology, to model the distributions of 17 fish species from 2005 Swedish stream sites that were sampled between 2000 and 2011. Modeling was performed using boosted regression trees and random forest, two machine learning techniques to assess the relationship between species distributions and their environment. Temperature, width and connectivity (minimum distance to lake or the sea and water discharge, were the most important variables explaining changes in species distribution at large spatial scales. Response curves of fitted occurrence probabilities along predictors often showed abrupt changes, however, clear threshold effects were difficult to detect. Our results show also differences across species and even in the outcomes of the two algorithms, implying that a simultaneous assessment of multiple species may provide a better signal of ecosystem change than the use of surrogate species.

  1. Simultaneous quantification of multiple food- and waterborne pathogens by use of microfluidic quantitative PCR.

    Science.gov (United States)

    Ishii, Satoshi; Segawa, Takahiro; Okabe, Satoshi

    2013-05-01

    The direct quantification of multiple pathogens has been desired for diagnostic and public health purposes for a long time. In this study, we applied microfluidic quantitative PCR (qPCR) technology to the simultaneous detection and quantification of multiple food- and waterborne pathogens. In this system, multiple singleplex qPCR assays were run under identical detection conditions in nanoliter-volume chambers that are present in high densities on a chip. First, we developed 18 TaqMan qPCR assays that could be run in the same PCR conditions by using prevalidated TaqMan probes. Specific and sensitive quantification was achieved by using these qPCR assays. With the addition of two previously validated TaqMan qPCR assays, we used 20 qPCR assays targeting 10 enteric pathogens, a fecal indicator bacterium (general Escherichia coli), and a process control strain in the microfluidic qPCR system. We preamplified the template DNA to increase the sensitivity of the qPCR assays. Our results suggested that preamplification was effective for quantifying small amounts of the template DNA without any major impact on the sensitivity, efficiency, and quantitative performance of qPCR. This microfluidic qPCR system allowed us to detect and quantify multiple pathogens from fecal samples and environmental water samples spiked with pathogens at levels as low as 100 cells/liter. These results suggest that the routine monitoring of multiple pathogens in food and water samples is now technically feasible. This method may provide more reliable information for risk assessment than the current fecal contamination indicator approach.

  2. Simultaneous Segmentation of Prostatic Zones Using Active Appearance Models With Multiple Coupled Levelsets.

    Science.gov (United States)

    Toth, Robert; Ribault, Justin; Gentile, John; Sperling, Dan; Madabhushi, Anant

    2013-09-01

    In this work we present an improvement to the popular Active Appearance Model (AAM) algorithm, that we call the Multiple-Levelset AAM (MLA). The MLA can simultaneously segment multiple objects, and makes use of multiple levelsets, rather than anatomical landmarks, to define the shapes. AAMs traditionally define the shape of each object using a set of anatomical landmarks. However, landmarks can be difficult to identify, and AAMs traditionally only allow for segmentation of a single object of interest. The MLA, which is a landmark independent AAM, allows for levelsets of multiple objects to be determined and allows for them to be coupled with image intensities. This gives the MLA the flexibility to simulataneously segmentation multiple objects of interest in a new image. In this work we apply the MLA to segment the prostate capsule, the prostate peripheral zone (PZ), and the prostate central gland (CG), from a set of 40 endorectal, T2-weighted MRI images. The MLA system we employ in this work leverages a hierarchical segmentation framework, so constructed as to exploit domain specific attributes, by utilizing a given prostate segmentation to help drive the segmentations of the CG and PZ, which are embedded within the prostate. Our coupled MLA scheme yielded mean Dice accuracy values of .81, .79 and .68 for the prostate, CG, and PZ, respectively using a leave-one-out cross validation scheme over 40 patient studies. When only considering the midgland of the prostate, the mean DSC values were .89, .84, and .76 for the prostate, CG, and PZ respectively.

  3. Energetics of multiple-ion species hohlraum plasmasa)

    Science.gov (United States)

    Neumayer, P.; Berger, R. L.; Callahan, D.; Divol, L.; Froula, D. H.; London, R. A.; MacGowan, B. J.; Meezan, N. B.; Michel, P. A.; Ross, J. S.; Sorce, C.; Widmann, K.; Suter, L. J.; Glenzer, S. H.

    2008-05-01

    A study of the laser-plasma interaction processes has been performed in multiple-ion species hohlraum plasmas at conditions similar to those expected in indirect drive inertial confinement fusion targets. Gas-filled hohlraums with electron densities of 5.5×1020 and 9×1020cm-3 are heated by 14.3kJ of laser energy (wavelength 351nm) to electron temperatures of 3keV and backscattered laser light is measured. Landau damping of the ion acoustic waves is increased by adding hydrogen to a CO2 or CF4 gas. Stimulated Brillouin backscattering of a 351nm probe beam is found to decrease monotonically with increasing Landau damping, accompanied by a comparable increase in the transmission. More efficient energy coupling into the hohlraum by suppression of backscatter from the heater beams results in an increased hohlraum radiation temperature, showing that multiple-ion species plasmas improve the overall hohlraum energetics. The reduction in backscatter is reproduced by linear gain calculations as well as detailed full-scale three-dimensional laser-plasma interaction simulations, demonstrating that Landau damping is the controlling damping mechanism in inertial confinement fusion relevant high-electron temperature plasmas. These findings have led to the inclusion of multiple-ion species plasmas in the hohlraum point design for upcoming ignition campaigns at the National Ignition Facility.

  4. Multiple species of noninteracting molecules adsorbed on a Bethe lattice.

    Science.gov (United States)

    Cohen, Michael; Harris, A B

    2008-10-01

    A simple method, previously used to calculate the equilibrium concentration of dimers adsorbed on a Bethe lattice as a function of the dimer activity, is generalized to solve the problem of a Bethe lattice in contact with a reservoir containing a mixture of molecules. The molecules may have arbitrary sizes and shapes consistent with the geometry of the lattice and the molecules do not interact with one another except for the hard-core restriction that two molecules cannot touch the same site. We obtain a set of simultaneous nonlinear equations, one equation for each species of molecule, which determines the equilibrium concentration of each type of molecule as a function of the (arbitrary) activities of the various species. Surprisingly, regardless of the number of species, the equilibrium concentrations are given explicitly in terms of the solution of a single equation in one unknown which can be solved numerically, if need be. Some numerical examples show that increasing the activity of one species need not necessarily decrease the equilibrium concentration of all other species. We also calculate the adsorption isotherm of an "annealed" Bethe lattice consisting of two types of sites which differently influence the activity of an adsorbed molecule. We prove that if the reservoir contains a finite number of molecular species, regions of two different polymer densities cannot simultaneously exist on the lattice. The widely used Guggenheim theory of mixtures, which can also be construed as a theory of adsorption, assumes for simplicity that the molecules in the mixture are composed of elementary units, which occupy sites of a lattice of coordination number q . Guggenheim's analysis relies on approximate combinatorial formulas which become exact on a Bethe lattice of the same coordination number, as we show in an appendix. Our analysis involves no combinatorics and relies only on recognizing the statistical independence of certain quantities. Despite the nominal

  5. Dual Band Electrodes in Generator-Collector Mode: Simultaneous Measurement of Two Species

    CERN Document Server

    Barnes, Edward O; Dale, Sara E C; Marken, Frank; Compton, Richard G

    2013-01-01

    A computational model for the simulation of a double band collector-generator experiment is applied to the situation where two electrochemical reactions occur concurrently. It is shown that chronoamperometric measurements can be used to take advantage of differences in diffusion coefficients to measure the concentrations of both electroactive species simultaneously, by measuring the time at which the collection efficiency reaches a specific value. The separation of the electrodes is shown to not affect the sensitivity of the method (in terms of percentage changes in the measured time to reach the specified collection efficiency), but wider gaps can provide a greater range of (larger) absolute values of this characteristic time. It is also shown that measuring the time taken to reach smaller collection efficiencies can allow for the detection of smaller amounts of whichever species diffuses faster. The case of a system containing both ascorbic acid and opamine in water is used to exemplify the method, and it i...

  6. Planning, implementing, and monitoring multiple-species habitat conservation plans.

    Science.gov (United States)

    Franklin, Janet; Regan, Helen M; Hierl, Lauren A; Deutschman, Douglas H; Johnson, Brenda S; Winchell, Clark S

    2011-03-01

    Despite numerous recommendations for various aspects of the design and monitoring of habitat conservation plans, there remains a need to synthesize existing guidelines into a comprehensive scheme and apply it to real-world conservation programs. We review tools for systematic conservation planning and elements for designing and implementing ecological monitoring in an adaptive management context. We apply principles of monitoring design to the San Diego Multiple Species Conservation Program (MSCP) in California, USA--one of the first multispecies habitat conservation plans, located in a landscape where high biodiversity and urban development converge. Tools for spatial conservation planning are aimed to conserve biodiversity, often in the context of a limited budget. In practice, these methods may not accommodate legislative mandates, budgetary uncertainties, and the range of implementation mechanisms available across consortia of stakeholders. Once a reserve is implemented, the question becomes whether it is effective at conserving biodiversity, and if not, what actions are required to make it effective. In monitoring plan development, status and threats should be used to prioritize species and communities that require management action to ensure their persistence. Conceptual models documenting the state of knowledge of the system should highlight the main drivers affecting status and trends of species or communities. Monitoring strategies require scientifically justified decisions based on sampling, response, and data design. Because the framework illustrated here tackles multiple species, communities, and threats at the urban-wildland interface, it will have utility for ecosystem managers struggling to design monitoring programs.

  7. CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

    Science.gov (United States)

    Cutler, Andrew D.; Magnotti, Gaetano

    2010-01-01

    The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

  8. Simultaneously extracting multiple parameters via fitting one single autocorrelation function curve in diffuse correlation spectroscopy.

    Science.gov (United States)

    Dong, Lixin; He, Lian; Lin, Yu; Shang, Yu; Yu, Guoqiang

    2013-02-01

    Near-infrared diffuse correlation spectroscopy (DCS) has recently been employed for noninvasive acquisition of blood flow information in deep tissues. Based on the established correlation diffusion equation, the light intensity autocorrelation function detected by DCS is determined by a blood flow index αD(B), tissue absorption coefficient μ(a), reduced scattering coefficient μ'(s), and a coherence factor β. This study is designed to investigate the possibility of extracting multiple parameters such as μ(a), μ'(s), β, and αD(B) through fitting one single autocorrelation function curve and evaluate the performance of different fitting methods. For this purpose, computer simulations, tissue-like phantom experiments, and in vivo tissue measurements were utilized. The results suggest that it is impractical to simultaneously fit αD(B) and μ(a) or αD(B) and μ'(s) from one single autocorrelation function curve due to the large crosstalk between these paired parameters. However, simultaneously fitting β and αD(B) is feasible and generates more accurate estimation with smaller standard deviation compared to the conventional two-step fitting method (i.e., first calculating β and then fitting αD(B)). The outcomes from this study provide a crucial guidance for DCS data analysis.

  9. Simultaneous Measurement of Multiple Mechanical Properties of Single Cells Using AFM by Indentation and Vibration.

    Science.gov (United States)

    Zhang, Chuang; Shi, Jialin; Wang, Wenxue; Xi, Ning; Wang, Yuechao; Liu, Lianqing

    2017-12-01

    The mechanical properties of cells, which are the main characteristics determining their physical performance and physiological functions, have been actively studied in the fields of cytobiology and biomedical engineering and for the development of medicines. In this study, an indentation-vibration-based method is proposed to simultaneously measure the mechanical properties of cells in situ, including cellular mass (m), elasticity (k), and viscosity (c). The proposed measurement method is implemented based on the principle of forced vibration stimulated by simple harmonic force using an atomic force microscope (AFM) system integrated with a piezoelectric transducer as the substrate vibrator. The corresponding theoretical model containing the three mechanical properties is derived and used to perform simulations and calculations. Living and fixed human embryonic kidney 293 (HEK 293) cells were subjected to indentation and vibration to measure and compare their mechanical parameters and verify the proposed approach. The results that the fixed sample cells are more viscous and elastic than the living sample cells and the measured mechanical properties of cell are consistent within, but not outside of the central region of the cell, are in accordance with the previous studies. This work provides an approach to simultaneous measurement of the multiple mechanical properties of single cells using an integrated AFM system based on the principle force vibration and thickness-corrected Hertz model. This study should contribute to progress in biomedical engineering, cytobiology, medicine, early diagnosis, specific therapy and cell-powered robots.

  10. Aptamer- and nucleic acid enzyme-based systems for simultaneous detection of multiple analytes

    Science.gov (United States)

    Lu, Yi [Champaign, IL; Liu, Juewen [Albuquerque, NM

    2011-11-15

    The present invention provides aptamer- and nucleic acid enzyme-based systems for simultaneously determining the presence and optionally the concentration of multiple analytes in a sample. Methods of utilizing the system and kits that include the sensor components are also provided. The system includes a first reactive polynucleotide that reacts to a first analyte; a second reactive polynucleotide that reacts to a second analyte; a third polynucleotide; a fourth polynucleotide; a first particle, coupled to the third polynucleotide; a second particle, coupled to the fourth polynucleotide; and at least one quencher, for quenching emissions of the first and second quantum dots, coupled to the first and second reactive polynucleotides. The first particle includes a quantum dot having a first emission wavelength. The second particle includes a second quantum dot having a second emission wavelength different from the first emission wavelength. The third polynucleotide and the fourth polynucleotide are different.

  11. Simultaneous synthesis of anatase colloidal and multiple-branched rutile TiO{sub 2} nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Trong Tung; Duong, Ngoc Huyen [School of Engineering Physics, Hanoi University of Science and Technology, Hanoi (Viet Nam); Mai, Xuan Dung [Dept. of Chemistry, Hanoi Pedagogical University No2, Vinh Phuc (Viet Nam)

    2017-03-15

    Facile synthesis of titanium dioxide (TiO{sub 2} ) nanostructures with controllability over their cystallinity, dimensions, and shape is in demand for diverse optoelectronic applications. Anatase colloidal particles and precipitates of rutile bundles were synthesized simultaneously using HCl catalyzed sol–gel process with titanium tetrachloride as Ti precursor. The crystallinity and the morphology of these two separable TiO{sub 2} phases were studied by X-ray diffraction, Raman spectroscopy, and transmission electron microscopy. The results show that by varying HCl concentration during synthesis, dimensions of colloidal anatase can be tuned from spherical particles with a diameter of 2–5 nm to nanorods of dimension of 4 nm (width) × 14 nm (length). The rutile bundles whose size increased with aging time consisted of multiple branches with elongation along c-axis. Both anatase nanorods and rutile bundles can be applied as highly efficient photocatalysts or electron conduits.

  12. Development and validation of a universal primer pair for the simultaneous detection of eight animal species.

    Science.gov (United States)

    Xue, Chaobo; Wang, Pingya; Zhao, Jin; Xu, Aichun; Guan, Feng

    2017-04-15

    In the present study, we developed a novel simplex PCR assay for the simultaneous detection of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig and camel. A unique pair of universal primers was designed to target mitochondrial DNA variable regions in the eight animal species, generating, 787, 763, 563, 512, 507, 491, 455 and 385bp long fragments for goat, sheep, deer, buffalo, cattle, yak, pig and camel, respectively. The assay showed no cross-reactivity with other common domestic animals, and was validated by sequencing and enzyme digestion. Detection limit for DNA samples from the eight animal species varied between 6 and 20pg in a 20μl PCR mixture. Interestingly, the newly developed method successfully identified 170 commercial meat products, and is simple, fast, sensitive, specific, and cost-effective. Therefore, it could be used for the detection of goat, sheep, deer, buffalo, cattle, yak, pig, and camel species in foodstuffs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Diffusion of multiple species with excluded-volume effects

    KAUST Repository

    Bruna, Maria

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. © 2012 American Institute of Physics.

  14. Towards Omni-Tomography—Grand Fusion of Multiple Modalities for Simultaneous Interior Tomography

    Science.gov (United States)

    Wang, Ge; Zhang, Jie; Gao, Hao; Weir, Victor; Yu, Hengyong; Cong, Wenxiang; Xu, Xiaochen; Shen, Haiou; Bennett, James; Furth, Mark; Wang, Yue; Vannier, Michael

    2012-01-01

    We recently elevated interior tomography from its origin in computed tomography (CT) to a general tomographic principle, and proved its validity for other tomographic modalities including SPECT, MRI, and others. Here we propose “omni-tomography”, a novel concept for the grand fusion of multiple tomographic modalities for simultaneous data acquisition in a region of interest (ROI). Omni-tomography can be instrumental when physiological processes under investigation are multi-dimensional, multi-scale, multi-temporal and multi-parametric. Both preclinical and clinical studies now depend on in vivo tomography, often requiring separate evaluations by different imaging modalities. Over the past decade, two approaches have been used for multimodality fusion: Software based image registration and hybrid scanners such as PET-CT, PET-MRI, and SPECT-CT among others. While there are intrinsic limitations with both approaches, the main obstacle to the seamless fusion of multiple imaging modalities has been the bulkiness of each individual imager and the conflict of their physical (especially spatial) requirements. To address this challenge, omni-tomography is now unveiled as an emerging direction for biomedical imaging and systems biomedicine. PMID:22768108

  15. Simultaneous Analysis of Multiple Allergens in Food Products by LC-MS/MS.

    Science.gov (United States)

    New, Lee Sun; Schreiber, Andre; Stahl-Zeng, Jianru; Liu, Hua-Fen

    2017-12-05

    There is currently no cure for food allergies, and sufferers can only rely on the correct labeling of foods toavoid allergens. Hence, it is important that analytical methods are sensitive and accurate enough to screen for the presence of multiple allergens in food products. In this study, we developed an LC-tandem MS method that is able to simultaneously screen or quantify the signature tryptic peptides of multiple allergen commodities. This method is capable of screening and identifying egg white, skim milk, peanut, soy, and tree nuts (almond, Brazil nut, cashew, hazelnut, pecan, pine nut, pistachio, and walnut) at a detection limit of 10 ppm in incurred bread and cookies. It was further tested for the quantitative analysis of whole-egg, whole-milk, peanut butter, and hazelnut commodities, which are incurred or spiked into selected food matrixes as defined in AOAC INTERNATIONAL Standard Method Performance Requirement (SMPR®) 2016.002. The method demonstrated excellent sensitivity with a Method quantitative limit of 3 ppm for whole egg and 10 ppm for the remaining three allergen commodities. It also demonstrated good recovery (60‒119%) and repeatability (RSDr allergen commodity and was able to meet the minimum performance requirements of the SMPR.

  16. Energetics of Multiple-Ion Species Hohlraum Plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Neumayer, P; Berger, R; Callahan, D; Divol, L; Froula, D; London, R; MacGowan, B J; Meezan, N; Michel, P; Ross, J S; Sorce, C; Widmann, K; Suter, L; Glenzer, S H

    2007-11-05

    A study of the laser-plasma interaction processes in multiple-ion species plasmas has been performed in plasmas that are created to emulate the plasma conditions in indirect drive inertial confinement fusion targets. Gas-filled hohlraums with densities of xe22/cc are heated to Te=3keV and backscattered laser light is measured by a suite of absolutely calibrated backscatter diagnostics. Ion Landau damping is increased by adding hydrogen to the CO2/CF4 gas fill. We find that the backscatter from stimulated Brillouin scattering is reduced is monotonically reduced with increasing damping, demonstrating that Landau damping is the controlling damping mechanism in ICF relevant high-electron temperature plasmas. The reduction in backscatter is accompanied by a comparable increase in both transmission of a probe beam and an increased hohlraum radiation temperature, showing that multiple-ion species plasmas improve the overall hohlraum energetics/performance. Comparison of the experimental data to linear gain calculations as well as detailed full-scale 3D laser-plasma interaction simulations show quantitative agreement. Our findings confirm the importance of Landau damping in controlling backscatter from high-electron temperature hohlraum plasmas and have lead to the inclusion of multi-ion species plasmas in the hohlraum point design for upcoming ignition campaigns at the National Ignition Facility.

  17. New multiplex PCR method for the simultaneous diagnosis of the three known species of equine tapeworm.

    Science.gov (United States)

    Bohórquez, G Alejandro; Luzón, Mónica; Martín-Hernández, Raquel; Meana, Aránzazu

    2015-01-15

    Although several techniques exist for the detection of equine tapeworms in serum and feces, the differential diagnosis of tapeworm infection is usually based on postmortem findings and the morphological identification of eggs in feces. In this study, a multiplex polymerase chain reaction (PCR)-based method for the simultaneuos detection of Anoplocephala magna, Anoplocephala perfoliata and Anoplocephaloides mamillana has been developed and validated. The method simultaneously amplifies hypervariable SSUrRNA gene regions in the three tapeworm species in a single reaction using three pairs of primers, which exclusively amplify the internal transcribed spacer 2 (ITS-2) in each target gene. The method was tested on three types of sample: (a) 1/10, 1/100, 1/500, 1/1000, 1/2000 and 1/5000 dilutions of 70 ng of genomic DNA of the three tapeworm species, (b) DNA extracted from negative aliquots of sediments of negative control fecal samples spiked with 500, 200, 100, 50 and 10 eggs (only for A. magna and A. perfoliata; no A. mamillana eggs available) and (c) DNA extracted from 80, 50, 40, 30, 10 and 1 egg per 2 μl of PCR reaction mix (only for A. magna and A. perfoliata; no A. mamillana eggs available). No amplification was observed against the DNA of Gasterophilus intestinalis, Parascaris equorum and Strongylus vulgaris. The multiplex PCR method emerged as specific for the three tapeworms and was able to identify as few as 50 eggs per fecal sample and as little as 0.7 ng of control genomic DNA obtained from the three species. The method proposed is able to differentiate infections caused by the two most frequent species A. magna or A. perfoliata when the eggs are present in feces and is also able to detect mixed infections by the three cestode species. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Simultaneous analysis of glycolipids and phospholids molecular species in avocado (Persea americana Mill) fruit.

    Science.gov (United States)

    Pacetti, Deborah; Boselli, Emanuele; Lucci, Paolo; Frega, Natale G

    2007-05-25

    The molecular species of phospholipids (PLs) and glycolipids (GLs) were simultaneously characterized in the pulp and almond of the avocado fruit (Persea americana Mill) of four varieties by means of high performance liquid chromatography-electrospray ionisation ion-trap tandem mass spectrometry. In the pulp, the predominant species of monoglycosyldiglycerides (MGD) were m/z 796.6 (oleic/linolenic and linoleic/linoleic acids) and m/z 800.4 (stearic/linoleic and oleic/oleic acids). One of the main diglycosyldiglycerides (DGD) both in the pulp and almond was m/z 958.5 (oleic/linolenic); however, the pulp was also rich of m/z 962.4 (oleic/oleic), whereas in the almond, m/z 934.5 (palmitic/linoleic and palmitoleic/oleic) and m/z 960.5 (oleic/linoleic and stearic/linolenic) were more abundant. In the almond, the main PL classes (phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI)) contained always palmitic/linoleic acids. Alpha-linolenic acid was contained as MGD (linolenic/linolenic) and DGD (linolenic/linolenic), more present in the pulp than in the almond. The major molecular species of glycocerebrosides (GCer) in the pulp and almond carried hydroxy-palmitic acid (C(16h:0))/4,8-sphyngadienine (d(18:2)).

  19. Isotope fractionation associated with the simultaneous biodegradation of multiple nitrophenol isomers by Pseudomonas putida B2.

    Science.gov (United States)

    Wijker, Reto S; Zeyer, Josef; Hofstetter, Thomas B

    2017-05-24

    Quantifying the extent of biodegradation of nitroaromatic compounds (NACs) in contaminated soils and sediments is challenging because of competing oxidative and reductive reaction pathways. We have previously shown that the stable isotope fractionation of NACs reveals the routes of degradation even if it is simultaneously caused by different bacteria. However, it is unclear whether compound-specific isotope analysis (CSIA) can be applied in situations where multiple pollutants are biodegraded by only one microorganism under multi-substrate conditions. Here we examined the C and N isotope fractionation of 2-nitrophenol (2-NP) and 3-nitrophenol (3-NP) during biodegradation by Pseudomonas putida B2 through monooxygenation and partial reductive pathways, respectively, in the presence of single substrates vs. binary substrate mixtures. Laboratory experiments showed that the reduction of 3-NP by Pseudomonas putida B2 is associated with large N and minor C isotope fractionation with C and N isotope enrichment factors, εC and εN, of -0.3 ± 0.1‰ and -22 ± 0.2‰, respectively. The opposite isotope fractionation trends were found for 2-NP monooxygenation. In the simultaneous presence of 2-NP and 3-NP, 2-NP is biodegraded at identical rate constants and εC and εN values (-1.0 ± 0.1‰ and -1.3 ± 0.2‰) to those found for the monooxygenation of 2-NP in single substrate experiments. While the pathway and N isotope fractionation of 3-NP reduction (εN = -24 ± 1.1‰) are independent of the presence of 2-NP, intermediates of 2-NP monooxygenation interfere with 3-NP reduction. Because neither pH, substrate uptake, nor aromatic substituents affected the kinetic isotope effects of nitrophenol biodegradation, our study illustrates that CSIA provides robust scientific evidence for the assessment of natural attenuation processes.

  20. Atomic species identification at the (101) anatase surface by simultaneous scanning tunnelling and atomic force microscopy

    Science.gov (United States)

    Stetsovych, Oleksandr; Todorović, Milica; Shimizu, Tomoko K.; Moreno, César; Ryan, James William; León, Carmen Pérez; Sagisaka, Keisuke; Palomares, Emilio; Matolín, Vladimír; Fujita, Daisuke; Perez, Ruben; Custance, Oscar

    2015-01-01

    Anatase is a pivotal material in devices for energy-harvesting applications and catalysis. Methods for the accurate characterization of this reducible oxide at the atomic scale are critical in the exploration of outstanding properties for technological developments. Here we combine atomic force microscopy (AFM) and scanning tunnelling microscopy (STM), supported by first-principles calculations, for the simultaneous imaging and unambiguous identification of atomic species at the (101) anatase surface. We demonstrate that dynamic AFM-STM operation allows atomic resolution imaging within the material's band gap. Based on key distinguishing features extracted from calculations and experiments, we identify candidates for the most common surface defects. Our results pave the way for the understanding of surface processes, like adsorption of metal dopants and photoactive molecules, that are fundamental for the catalytic and photovoltaic applications of anatase, and demonstrate the potential of dynamic AFM-STM for the characterization of wide band gap materials. PMID:26118408

  1. Herbivores, tidal elevation, and species richness simultaneously mediate nitrate uptake by seaweed assemblages.

    Science.gov (United States)

    Bracken, Matthew E S; Jones, Emily; Williams, Susan L

    2011-05-01

    In order for research into the consequences of biodiversity changes to be more applicable to real-world ecosystems, experiments must be conducted in the field, where a variety of factors other than diversity can affect the rates of key biogeochemical and physiological processes. Here, we experimentally evaluate the effects of two factors known to affect the diversity and composition of intertidal seaweed assemblages--tidal elevation and herbivory--on nitrate uptake by those assemblages. Based on surveys of community composition at the end of a 1.5-year press experiment, we found that both tide height and herbivores affected seaweed community structure. Not surprisingly, seaweed species richness was greater at lower tidal elevations. Herbivores did not affect richness, but they altered the types of species that were present; seaweed species characterized by higher rates of nitrate uptake were more abundant in herbivore-removal plots. Both tide height and herbivores affected nitrate uptake by seaweed assemblages. Individual seaweed species, as well as entire seaweed assemblages, living higher on the shore had greater rates of biomass-specific nitrate uptake, particularly at high ambient nitrate concentrations. Grazed seaweed assemblages exhibited reduced nitrate uptake, but only at low nitrate concentrations. We evaluated the effect of seaweed richness on nitrate uptake, both alone and after accounting for effects of tidal elevation and herbivores. When only richness was considered, we found no effect on uptake. However, when simultaneous effects of richness, tide height, and herbivores on uptake were evaluated, we found that all three had relatively large and comparable effects on nitrate uptake coefficients and that there was a negative relationship between seaweed richness and nitrate uptake. Particularly because effects of richness on uptake were not apparent unless the effects of tide height and herbivory were also considered, these results highlight the

  2. Breeding approaches in simultaneous selection for multiple stress tolerance of maize in tropical environments

    Directory of Open Access Journals (Sweden)

    Denić M.

    2007-01-01

    Full Text Available Maize is the principal crop and major staple food in the most countries of Sub-Saharan Africa. However, due to the influence of abiotic and biotic stress factors, maize production faces serious constraints. Among the agro-ecological conditions, the main constraints are: lack and poor distribution of rainfall; low soil fertility; diseases (maize streak virus, downy mildew, leaf blights, rusts, gray leaf spot, stem/cob rots and pests (borers and storage pests. Among the socio-economic production constraints are: poor economy, serious shortage of trained manpower; insufficient management expertise, lack of use of improved varieties and poor cultivation practices. To develop desirable varieties, and thus consequently alleviate some of these constraints, appropriate breeding approaches and field-based methodologies in selection for multiple stress tolerance, were implemented. These approaches are mainly based on: a Crossing selected genotypes with more desirable stress tolerant and other agronomic traits; b Using the disease/pest spreader row method, combined with testing and selection of created progenies under strong to intermediate pressure of drought and low soil fertility in nurseries; and c Evaluation of the varieties developed in multi-location trials under low and "normal" inputs. These approaches provide testing and selection of large number of progenies, which is required for simultaneous selection for multiple stress tolerance. Data obtained revealed that remarkable improvement of the traits under selection was achieved. Biggest progress was obtained in selection for maize streak virus and downy mildew resistance, flintiness and earliness. In the case of drought stress, statistical analyses revealed significant negative correlation between yield and anthesis-silking interval, and between yield and days to silk, but positive correlation between yield and grain weight per ear.

  3. DEP-On-Go for Simultaneous Sensing of Multiple Heavy Metals Pollutants in Environmental Samples

    Directory of Open Access Journals (Sweden)

    Madhu Biyani

    2016-12-01

    Full Text Available We describe a simple and affordable “Disposable electrode printed (DEP-On-Go” sensing platform for the rapid on-site monitoring of trace heavy metal pollutants in environmental samples for early warning by developing a mobile electrochemical device composed of palm-sized potentiostat and disposable unmodified screen-printed electrode chips. We present the analytical performance of our device for the sensitive detection of major heavy metal ions, namely, mercury, cadmium, lead, arsenic, zinc, and copper with detection limits of 1.5, 2.6, 4.0, 5.0, 14.4, and, 15.5 μg·L−1, respectively. Importantly, the utility of this device is extended to detect multiple heavy metals simultaneously with well-defined voltammograms and similar sensitivity. Finally, “DEP-On-Go” was successfully applied to detect heavy metals in real environmental samples from groundwater, tap water, house dust, soil, and industry-processed rice and noodle foods. We evaluated the efficiency of this system with a linear correlation through inductively coupled plasma mass spectrometry, and the results suggested that this system can be reliable for on-site screening purposes. On-field applications using real samples of groundwater for drinking in the northern parts of India support the easy-to-detect, low-cost (<1 USD, rapid (within 5 min, and reliable detection limit (ppb levels performance of our device for the on-site detection and monitoring of multiple heavy metals in resource-limited settings.

  4. Molecular characterization of Blastocystis species in Oregon identifies multiple subtypes.

    Science.gov (United States)

    Whipps, Christopher M; Boorom, Ken; Bermudez, Luiz E; Kent, Michael L

    2010-03-01

    The association of Blastocystis species infections with gastrointestinal symptoms in humans is clouded by the variable presentation of disease and multiple lineages of the parasite that can infect humans and other animals. It has long been suspected that certain subtypes of Blastocystis may be more or less pathogenic, be restricted to certain hosts, or have limits to their geographic distribution. In the state of Oregon, USA, Blastocystis spp. are the most commonly encountered parasites in fecal specimens submitted for diagnostic evaluation, yet the diversity of subtypes is unknown. In this study, fecal samples were collected from individuals experiencing symptoms associated with blastocystosis and analyzed by polymerase chain reaction for presence of the parasite and DNA sequenced for subtyping. Five of 19 individuals tested positive for the parasite, all of which were also positive by previous ova and parasitology examination. DNA sequencing of the small subunit ribosomal DNA and elongation factor 1 alpha gene followed by phylogenetic subtyping identified five unique subtypes, representing Blastocystis subtypes 1, 2, 3, 4, and 8. No symptoms were consistently associated with presence or absence of infection, although abdominal pain and fatigue were reported by all infected individuals. Multiple subtypes are indicative of multiple sources of infection, suggesting more extensive surveys are required to understand the transmission of this parasite.

  5. Simultaneous quantitative live cell imaging of multiple FRET-based biosensors.

    Directory of Open Access Journals (Sweden)

    Andrew Woehler

    Full Text Available We have developed a novel method for multi-color spectral FRET analysis which is used to study a system of three independent FRET-based molecular sensors composed of the combinations of only three fluorescent proteins. This method is made possible by a novel routine for computing the 3-D excitation/emission spectral fingerprint of FRET from reference measurements of the donor and acceptor alone. By unmixing the 3D spectrum of the FRET sample, the total relative concentrations of the fluorophores and their scaled FRET efficiencies are directly measured, from which apparent FRET efficiencies can be computed. If the FRET sample is composed of intramolecular FRET sensors it is possible to determine the total relative concentration of the sensors and then estimate absolute FRET efficiency of each sensor. Using multiple tandem constructs with fixed FRET efficiency as well as FRET-based calcium sensors with novel fluorescent protein combinations we demonstrate that the computed FRET efficiencies are accurate and changes in these quantities occur without crosstalk. We provide an example of this method's potential by demonstrating simultaneous imaging of spatially colocalized changes in [Ca(2+], [cAMP], and PKA activity.

  6. A new parameter to simultaneously assess antioxidant activity for multiple phenolic compounds present in food products.

    Science.gov (United States)

    Yang, Hong; Xue, Xuejia; Li, Huan; Tay-Chan, Su Chin; Ong, Seng Poon; Tian, Edmund Feng

    2017-08-15

    In this work, we established a new methodology to simultaneously assess the relative reaction rates of multiple antioxidant compounds in one experimental set-up. This new methodology hypothesizes that the competition among antioxidant compounds towards limiting amount of free radical (in this article, DPPH) would reflect their relative reaction rates. In contrast with the conventional detection of DPPH decrease at 515nm on a spectrophotometer, depletion of antioxidant compounds treated by a series of DPPH concentrations was monitored instead using liquid chromatography coupled with quadrupole time-of-flight (LC-QTOF). A new parameter, namely relative antioxidant activity (RAA), has been proposed to rank these antioxidants according to their reaction rate constants. We have investigated the applicability of RAA using pre-mixed standard phenolic compounds, and also extended this application to two food products, i.e. red wine and green tea. It has been found that RAA correlates well with the reported k values. This new parameter, RAA, provides a new perspective in evaluating antioxidant compounds present in food and herbal matrices. It not only realistically reflects the antioxidant activity of compounds when co-existing with competitive constituents; and it could also quicken up the discovery process in the search for potent yet rare antioxidants from many herbs of food/medicinal origins. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Aptamer/quantum dot-based simultaneous electrochemical detection of multiple small molecules

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Haixia [Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Jiang Bingying [School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400040 (China); Xiang Yun, E-mail: yunatswu@swu.edu.cn [Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Zhang Yuyong; Chai Yaqin [Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Yuan Ruo, E-mail: yuanruo@swu.edu.cn [Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China)

    2011-03-04

    A novel strategy for 'signal on' and sensitive one-spot simultaneous detection of multiple small molecular analytes based on electrochemically encoded barcode quantum dot (QD) tags is described. The target analytes, adenosine triphosphate (ATP) and cocaine, respectively, are sandwiched between the corresponding set of surface-immobilized primary binding aptamers and the secondary binding aptamer/QD bioconjugates. The captured QDs yield distinct electrochemical signatures after acid dissolution, whose position and size reflect the identity and level, respectively, of the corresponding target analytes. Due to the inherent amplification feature of the QD labels and the 'signal on' detection scheme, as well as the sensitive monitoring of the metal ions released upon acid dissolution of the QD labels, low detection limits of 30 nM and 50 nM were obtained for ATP and cocaine, respectively, in our assays. Our multi-analyte sensing system also shows high specificity to target analytes and promising applicability to complex sample matrix, which makes the proposed assay protocol an attractive route for screening of small molecules in clinical diagnosis.

  8. Simultaneous detection of multiple gas concentrations with multi-frequency wavelength modulation spectroscopy

    Science.gov (United States)

    Zhang, Zhirong; Xia, Hua; Dong, Fengzhong; Pang, Tao; Wu, Bian; Sun, Pengshuai; Wang, Gaoxuan; Wang, Yu

    2013-11-01

    A multi-frequency wavelength modulation spectroscopy (MF-WMS) method for simultaneous monitoring multiple gas concentrations is reported. Two wavelength lasers are selected and scanned at the same sawtooth waveform and different sinusoidal modulation frequencies. Also, a 2-in-1 coupler is used to collect laser beams into a single-mode fiber to deliver the combined beams to a same optical path. The outputs from the same InGaAs detector are demodulated by a set of homemade digital lock-in-amplifiers to obtain the harmonic signals, accordingly. The new multi-pass cell was designed and filled with five different concentrations of H2S and HCl gas mixtures for further analysis. In addition, an \\alpha\\text{-}\\beta\\text{-}\\gamma digital filter and a data running means method were used to further improve the stability. The results show that the signal-to-noise ratio and the anti-interference ability had been improved and the MF-WMS system gives a good performance in terms of reproducibility and feasibility.

  9. Simultaneous and sequential hemorrhage of multiple cerebral cavernous malformations: a case report.

    Science.gov (United States)

    Louis, Nundia; Marsh, Robert

    2016-02-09

    The etiology of cerebral cavernous malformation hemorrhage is not well understood. Causative physiologic parameters preceding hemorrhagic cavernous malformation events are often not reported. We present a case of an individual with sequential simultaneous hemorrhages in multiple cerebral cavernous malformations with a new onset diagnosis of hypertension. A 42-year-old white man was admitted to our facility with worsening headache, left facial and tongue numbness, dizziness, diplopia, and elevated blood pressure. His past medical history was significant for new onset diagnosis of hypertension and chronic seasonal allergies. Serial imaging over the ensuing 8 days revealed sequential hemorrhagic lesions. He underwent suboccipital craniotomy for resection of the lesions located in the fourth ventricle and right cerebellum. One month after surgery, he had near complete resolution of his symptoms with mild residual vertigo but symptomatic chronic hypertension. Many studies have focused on genetic and inflammatory mechanisms contributing to cerebral cavernous malformation rupture, but few have reported on the potential of hemodynamic changes contributing to cerebral cavernous malformation rupture. Systemic blood pressure changes clearly have an effect on angioma pressures. When considering the histopathological features of cerebral cavernous malformation architecture, changes in arterial pressure could cause meaningful alterations in hemorrhage propensity and patterns.

  10. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species

    Directory of Open Access Journals (Sweden)

    M. Radhika

    2014-06-01

    Full Text Available Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC. The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.

  11. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species.

    Science.gov (United States)

    Radhika, M; Saugata, Majumder; Murali, H S; Batra, H V

    2014-01-01

    Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC). The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.

  12. Simultaneous detection of multiple DNA targets by integrating dual-color graphene quantum dot nanoprobes and carbon nanotubes.

    Science.gov (United States)

    Qian, Zhaosheng; Shan, Xiaoyue; Chai, Lujing; Chen, Jianrong; Feng, Hui

    2014-12-01

    Simultaneous detection of multiple DNA targets was achieved based on a biocompatible graphene quantum dots (GQDs) and carbon nanotubes (CNTs) platform through spontaneous assembly between dual-color GQD-based probes and CNTs and subsequently self-recognition between DNA probes and targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. A Platform for Rapid, Quantitative Assessment of Multiple Drug Combinations Simultaneously in Solid Tumors In Vivo.

    Directory of Open Access Journals (Sweden)

    Joyoti Dey

    Full Text Available While advances in high-throughput screening have resulted in increased ability to identify synergistic anti-cancer drug combinations, validation of drug synergy in the in vivo setting and prioritization of combinations for clinical development remain low-throughput and resource intensive. Furthermore, there is currently no viable method for prospectively assessing drug synergy directly in human patients in order to potentially tailor therapies. To address these issues we have employed the previously described CIVO platform and developed a quantitative approach for investigating multiple combination hypotheses simultaneously in single living tumors. This platform provides a rapid, quantitative and cost effective approach to compare and prioritize drug combinations based on evidence of synergistic tumor cell killing in the live tumor context. Using a gemcitabine resistant model of pancreatic cancer, we efficiently investigated nine rationally selected Abraxane-based combinations employing only 19 xenografted mice. Among the drugs tested, the BCL2/BCLxL inhibitor ABT-263 was identified as the one agent that synergized with Abraxane® to enhance acute induction of localized apoptosis in this model of human pancreatic cancer. Importantly, results obtained with CIVO accurately predicted the outcome of systemic dosing studies in the same model where superior tumor regression induced by the Abraxane/ABT-263 combination was observed compared to that induced by either single agent. This supports expanded use of CIVO as an in vivo platform for expedited in vivo drug combination validation and sets the stage for performing toxicity-sparing drug combination studies directly in cancer patients with solid malignancies.

  14. Hierarchical pictorial structures for simultaneously localizing multiple organs in volumetric pre-scan CT

    Science.gov (United States)

    Montillo, Albert; Song, Qi; Das, Bipul; Yin, Zhye

    2015-03-01

    Parsing volumetric computed tomography (CT) into 10 or more salient organs simultaneously is a challenging task with many applications such as personalized scan planning and dose reporting. In the clinic, pre-scan data can come in the form of very low dose volumes acquired just prior to the primary scan or from an existing primary scan. To localize organs in such diverse data, we propose a new learning based framework that we call hierarchical pictorial structures (HPS) which builds multiple levels of models in a tree-like hierarchy that mirrors the natural decomposition of human anatomy from gross structures to finer structures. Each node of our hierarchical model learns (1) the local appearance and shape of structures, and (2) a generative global model that learns probabilistic, structural arrangement. Our main contribution is twofold. First we embed the pictorial structures approach in a hierarchical framework which reduces test time image interpretation and allows for the incorporation of additional geometric constraints that robustly guide model fitting in the presence of noise. Second we guide our HPS framework with the probabilistic cost maps extracted using random decision forests using volumetric 3D HOG features which makes our model fast to train and fast to apply to novel test data and posses a high degree of invariance to shape distortion and imaging artifacts. All steps require approximate 3 mins to compute and all organs are located with suitably high accuracy for our clinical applications such as personalized scan planning for radiation dose reduction. We assess our method using a database of volumetric CT scans from 81 subjects with widely varying age and pathology and with simulated ultra-low dose cadaver pre-scan data.

  15. Modeling species occurrence dynamics with multiple states and imperfect detection

    Science.gov (United States)

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics. ?? 2009 by the Ecological Society of America.

  16. Dynamic models for problems of species occurrence with multiple states

    Science.gov (United States)

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture?recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.

  17. Improvement on simultaneous determination of chromium species in aqueous solution by ion chromatography and chemiluminescence detection

    DEFF Research Database (Denmark)

    Gammelgaard, Bente; Liao, Y.P.; Jons, O.

    1997-01-01

    A sensitive method for the simultaneous determination of chromium(III) and chromium(VI) was chromatography and chemiluminescence detection. Two Dionex ion-exchange guard columns in series, CG5 and AG7, were used to separate chromium(III) from chromium(VI). Chromium(VI) was reduced by potassium...... sulphite, whereupon both species were detected by use of the luminol-hydrogen peroxide chemiluminescence system. Parameters affecting retention times and resolution of the separator columns, such as eluent pH, eluent composition, reductant pH and concentration, and flow rates were optimized. Furthermore...... was 1.4% for chromium(III) and 2.5% for chromium(VI), respectively. The accuracy of the chromium(III) determination was determined by analysis of the NIST standard reference material 1643c, Trace elements in water with the result 19.1 +/- 1.0 mu g Cr(III) l(-1) (certified value 19.0 +/- 0.6 mu g Cr...

  18. Multi-color femtosecond source for simultaneous excitation of multiple fluorescent proteins in two-photon fluorescence microscopy

    Science.gov (United States)

    Wang, Ke; Liu, Tzu-Ming; Wu, Juwell; Horton, Nicholas G.; Lin, Charles P.; Xu, Chris

    2013-02-01

    Simultaneous imaging of cells expressing multiple fluorescent proteins (FPs) is of particular interest in applications such as mapping neural circuits, tracking multiple immune cell populations, etc. To visualize both in vivo and ex vivo tissue morphology and physiology at a cellular level deep within scattering tissues, two-photon fluorescence microscopy (2PM) is a powerful tool that has found wide applications. However, simultaneous imaging of multiple FPs with 2PM is greatly hampered by the lack of proper ultrafast lasers offering multi-color femtosecond pulses, each targeting the two-photon absorption peak of a different FP. Here we demonstrate simultaneous two-photon fluorescence excitation of RFP, YFP, and CFP in human melanoma cells engineered to express a "rainbow" pallet of colors, using a novel fiber-based source with energetic, three-color femtosecond pulses. The three-color pulses, centered at 775 nm, 864 nm and 950 nm, are obtained through second harmonic generation of the 1550 nm pump laser and SHG of the solitons at 1728 nm and 1900 nm generated through soliton self-frequency shift (SSFS) of the pump laser in a large-mode-area (LMA) fiber. The resulting wavelengths are well matched to the two-photon absorption peaks of the three FPs for efficient excitation. Our results demonstrate that multi-color femtosecond pulse generation using SSFS and a turn-key, fiber-based femtosecond laser can fulfill the requirements for simultaneous imaging of multiple FPs in 2PM, opening new opportunities for a wide range of biological applications where non-invasive, high-resolution imaging of multiple fluorescent indicators is required.

  19. Trace element diffusion in minerals: the role of multiple diffusion mechanisms operating simultaneously

    Science.gov (United States)

    Dohmen, R.; Marschall, H.; Wiedenbeck, M.; Polednia, J.; Chakraborty, S.

    2016-12-01

    Diffusion of trace elements, often with ionic charge that differs from those of ions in the regular structural sites of a mineral, controls a number of important processes in rocks, such as: (i) Closure of radiogenic isotopic systems, (e.g. Pb diffusion in rutile; REE diffusion in garnet); (ii) Closure of trace element thermometers (e.g., Zr in rutile, Mg in plagioclase, Al in olivine); (iii) Closure of element exchange between melt inclusions and host minerals (e.g., H, REE in olivine). In addition, preserved trace element zoning profiles in minerals can be used for diffusion chronometry (e.g. Nb in rutile, Mg in plagioclase). However, experimentally determined diffusion coefficients of these trace elements are in many cases controversial (e.g., REE in olivine: [1] vs. [2]; Mg in plagioclase: [3] vs. [4]). We have carried out experiments to study the diffusion behavior in olivine, rutile, and plagioclase, and are able to show that two mechanisms of diffusion, differing in rates by up to four orders of magnitude, may operate simultaneously in a given crystal. The two mechanisms result in complex diffusion profile shapes. As a general rule, the incorporation of heterovalent substituting elements in relatively high concentrations is necessary to activate two diffusion mechanisms. This behavior is produced by the control of these elements on the point defect chemistry of a mineral - these impurities become a majority point defect when a threshold concentration limit is exceeded. In certain cases, e.g., for Li in olivine, the trace element can also be incorporated in different sites, resulting in interaction of the different species with other point defects (vacancies) during diffusion. Thus, depending on the diffusion couple used in the experiment, the associated concentration gradients within the mineral, and the analytical techniques used to measure the diffusion profile, only one diffusion mechanism may be activated or detected. These studies allow us to explain

  20. The spatial distribution of the reactive iodine species IO from simultaneous active and passive DOAS observations

    Directory of Open Access Journals (Sweden)

    K. Seitz

    2010-03-01

    Full Text Available We present investigations of the reactive iodine species (RIS IO, OIO and I2 in a coastal region from a field campaign simultaneously employing active long path differential optical absorption spectroscopy (LP-DOAS as well as passive multi-axis differential optical absorption spectroscopy (MAX-DOAS. The campaign took place at the Martin Ryan Institute (MRI in Carna, County Galway at the Irish West Coast about 6 km south-east of the atmospheric research station Mace Head in summer 2007. In order to study the horizontal distribution of the trace gases of interest, we established two almost parallel active LP-DOAS light paths, the shorter of 1034 m length just crossing the intertidal area, whereas the longer one of 3946 m length also crossed open water during periods of low tide. In addition we operated two passive Mini-MAX-DOAS instruments with the same viewing direction. While neither OIO nor I2 could be unambiguously identified with any of the instruments, IO could be detected with active as well as passive DOAS. The IO column densities seen at both active LP-DOAS light paths are almost the same. Thus it can be concluded that coastal IO is almost exclusively located in the intertidal area, where we detected mixing ratios of up to 29±8.8 ppt (equivalent to pmol/mol. Nucleation events with particle concentrations of 106 cm−3 particles were observed each day correlating with high IO mixing ratios. Therefore we feel that our detected IO concentrations confirm the results of model studies, which state that in order to explain such particle bursts, IO mixing ratios of 50 to 100 ppt in so called "hot-spots" are required.

  1. Simultaneous Targeting of Multiple Gene Homeologs to Alter Seed Oil Production in Camelina sativa.

    Science.gov (United States)

    Aznar-Moreno, J A; Durrett, T P

    2017-07-01

    The ability to transform Camelina sativa easily with biosynthetic enzymes derived from other plants has made this oil seed crop an ideal platform for the production of unusual lipids valuable for different applications. However, in addition to expressing transgenic enzymes, the suppression of endogenous enzyme activity to reduce competition for common substrates or cofactors is also required to enhance the production of target compounds. As camelina possesses a relatively undifferentiated hexaploid genome, up to three gene homeologs can code for any particular enzymatic activity, complicating efforts to alter endogenous biosynthetic pathways. New genome editing technologies, such as that offered by the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system, offer the capability to introduce mutations into specifically targeted genomic sites. Here, by using a carefully designed guide RNA identical to all three homeologs, we demonstrate the ability of the CRISPR/Cas genome editing system to introduce mutations in all three CsDGAT1 or CsPDAT1 homeologous genes important for triacylglycerol (TAG) synthesis in developing seeds. Sequence analysis from transgenic T1 plants revealed that each CsDGAT1 or each CsPDAT1 homeolog was altered by multiple mutations, resulting in a genetic mosaic in the plants. Interestingly, seed harvested from both CsDGAT1- and CsPDAT1-targeted lines was often shrunken and wrinkled. Further, lipid analysis revealed that many lines produced seed with reduced oil content and altered fatty acid composition, consistent with the role of the targeted genes in seed oil biosynthesis. The CRISPR/Cas system therefore represents a useful method to alter endogenous biosynthetic pathways efficiently in polyploid species such as camelina. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  2. Optimal timing of harvest of two fish species with multiple gear types

    NARCIS (Netherlands)

    Hagendoorn, J.; Kruitwagen, S.; Heijman, W.J.M.

    2000-01-01

    In this paper a bioeconomic model is developed for a commercial fishery with multiple gear types in the case of two independent fish species. Where most bioeconomic fishery models focus on either multiple gear types or multiple species (mostly predator-prey relationships) this model combines both

  3. A novel GMO biosensor for rapid ultrasensitive and simultaneous detection of multiple DNA components in GMO products.

    Science.gov (United States)

    Huang, Lin; Zheng, Lei; Chen, Yinji; Xue, Feng; Cheng, Lin; Adeloju, Samuel B; Chen, Wei

    2015-04-15

    Since the introduction of genetically modified organisms (GMOs), there has been on-going and continuous concern and debates on the commercialization of products derived from GMOs. There is an urgent need for development of highly efficient analytical methods for rapid and high throughput screening of GMOs components, as required for appropriate labeling of GMO-derived foods, as well as for on-site inspection and import/export quarantine. In this study, we describe, for the first time, a multi-labeling based electrochemical biosensor for simultaneous detection of multiple DNA components of GMO products on the same sensing interface. Two-round signal amplification was applied by using both an exonuclease enzyme catalytic reaction and gold nanoparticle-based bio-barcode related strategies, respectively. Simultaneous multiple detections of different DNA components of GMOs were successfully achieved with satisfied sensitivity using this electrochemical biosensor. Furthermore, the robustness and effectiveness of the proposed approach was successfully demonstrated by application to various GMO products, including locally obtained and confirmed commercial GMO seeds and transgenetic plants. The proposed electrochemical biosensor demonstrated unique merits that promise to gain more interest in its use for rapid and on-site simultaneous multiple screening of different components of GMO products. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Simultaneous Detection and Prevalence of Allergens in Anisakis Species Isolated from Marine Fishes.

    Science.gov (United States)

    Lee, Woo Joo; Seo, Dong Joo; Oh, Hyejin; Jeon, Su Been; Jung, Day; Choi, Changsun

    2016-05-01

    This study was conducted to develop a multiplex reverse transcription (RT) PCR for the detection of Anisakis allergens and to investigate the relationship between allergen profiles and anisakid larvae isolated from Scomber japonicus, Trichiurus lepturus, and Conger myriaster in Korea. The species of Anisakis was determined using Anisakis pegreffii-specific PCR and restriction fragment length polymorphism analysis. The prevalence and profiles of five Ani s allergens were examined by multiplex RTPCR. A. pegreffii and Anisakis typica accounted for 97.1 and 2.9%, respectively, of the 140 larvae examined. In A. pegreffii, allergen prevalence was 41.2% for Ani s 1, 72.1% for Ani s 2, 69.9% for Ani s 3, 86.7% for Ani s 4, and 93.4% for Ani s 5. Most A. pegreffii larvae had multiple allergen profiles, and 80.7% of A. pegreffii carried both Ani s 4 and Ani s 5, which are heat-resistant allergens. Fifty-two to 65% of A. pegreffii isolated from S. japonicus and C. myriaster carried all five Ani s allergens.

  5. Multiple mating in natural populations of a simultaneous hermaphrodite, Lymnaea stagnalis

    NARCIS (Netherlands)

    Nakadera, Yumi; Mariën, Janine; Van Straalen, Nico M.; Koene, Joris M.

    2017-01-01

    In field populations, it is largely unknown how many mating partners simultaneous hermaphrodites have, although their promiscuous mating is often observed in captivity. Documenting the number of mates in natural populations can expand the understanding of postcopulatory sexual selection and the

  6. Everyday multiscreening : How the simultaneous usage of multiple screens affects information processing and advertising effectiveness

    NARCIS (Netherlands)

    Segijn, C.M.

    2017-01-01

    Today, people have access to a variety of screens, such as a television, laptop, smartphone, and tablet. Screen saturation and the convergence of these technologies have led to an increase in combining different screens simultaneously, also known as multiscreening. With so many new devices and

  7. Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus cichla) using multi-locus data.

    Science.gov (United States)

    Willis, Stuart C; Macrander, Jason; Farias, Izeni P; Ortí, Guillermo

    2012-06-22

    Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an

  8. Do siblings always form and evolve simultaneously? Testing the coevality of multiple protostellar systems through SEDs

    Science.gov (United States)

    Murillo, N. M.; van Dishoeck, E. F.; Tobin, J. J.; Fedele, D.

    2016-07-01

    Context. Multiplicity is common in field stars and among protostellar systems. Models suggest two paths of formation: turbulent fragmentation and protostellar disk fragmentation. Aims: We attempt to find whether or not the coevality frequency of multiple protostellar systems can help to better understand their formation mechanism. The coevality frequency is determined by constraining the relative evolutionary stages of the components in a multiple system. Methods: Spectral energy distributions (SEDs) for known multiple protostars in Perseus were constructed from literature data. Herschel PACS photometric maps were used to sample the peak of the SED for systems with separations ≥7″, a crucial aspect in determining the evolutionary stage of a protostellar system. Inclination effects and the surrounding envelope and outflows were considered to decouple source geometry from evolution. This together with the shape and derived properties from the SED was used to determine each system's coevality as accurately as possible. SED models were used to examine the frequency of non-coevality that is due to geometry. Results: We find a non-coevality frequency of 33 ± 10% from the comparison of SED shapes of resolved multiple systems. Other source parameters suggest a somewhat lower frequency of non-coevality. The frequency of apparent non-coevality that is due to random inclination angle pairings of model SEDs is 17 ± 0.5%. Observations of the outflow of resolved multiple systems do not suggest significant misalignments within multiple systems. Effects of unresolved multiples on the SED shape are also investigated. Conclusions: We find that one-third of the multiple protostellar systems sampled here are non-coeval, which is more than expected from random geometric orientations. The other two-thirds are found to be coeval. Higher order multiples show a tendency to be non-coeval. The frequency of non-coevality found here is most likely due to formation and enhanced by

  9. Spatially controlled simultaneous patterning of multiple growth factors in three-dimensional hydrogels

    Science.gov (United States)

    Wylie, Ryan G.; Ahsan, Shoeb; Aizawa, Yukie; Maxwell, Karen L.; Morshead, Cindi M.; Shoichet, Molly S.

    2011-10-01

    Three-dimensional (3D) protein-patterned scaffolds provide a more biomimetic environment for cell culture than traditional two-dimensional surfaces, but simultaneous 3D protein patterning has proved difficult. We developed a method to spatially control the immobilization of different growth factors in distinct volumes in 3D hydrogels, and to specifically guide differentiation of stem/progenitor cells therein. Stem-cell differentiation factors sonic hedgehog (SHH) and ciliary neurotrophic factor (CNTF) were simultaneously immobilized using orthogonal physical binding pairs, barnase-barstar and streptavidin-biotin, respectively. Barnase and streptavidin were sequentially immobilized using two-photon chemistry for subsequent concurrent complexation with fusion proteins barstar-SHH and biotin-CNTF, resulting in bioactive 3D patterned hydrogels. The technique should be broadly applicable to the patterning of a wide range of proteins.

  10. Quantification of multiple simultaneously occurring nitrogen flows in the euphotic ocean

    OpenAIRE

    Xu, Min Nina; Wu,Yanhua; Zheng, Li Wei; Zheng, Zhenzhen; Zhao, Huade; Laws, Edward A.; Kao, Shuh-Ji

    2017-01-01

    The general features of the N cycle in the sunlit region of the ocean are well known, but methodological difficulties have previously confounded simultaneous quantification of transformation rates among the many different forms of N, e.g., ammonium (NH4+), nitrite (NO2−), nitrate (NO3−), and particulate/dissolved organic nitrogen (PN/DON). However, recent advances in analytical methodology have made it possible to employ a convenient isotope labeling technique to quantify ...

  11. Simultaneous initiation and growth of multiple radial hydraulic fractures from a horizontal wellbore

    Science.gov (United States)

    Lecampion, Brice; Desroches, Jean

    2015-09-01

    Multi-stage fracturing is the current preferred method of completion of horizontal wells in unconventional hydrocarbon reservoirs. Its core component consists in simultaneously initiating and propagating an array of hydraulic fractures. We develop a numerical model for the initiation and growth of an array of parallel radial hydraulic fractures. The solution accounts for fracture growth, coupling between elastic deformation and fluid flow in the fractures, elastic stress interactions between fractures and fluid flow in the wellbore. We also take into account the presence of a local pressure drop (function of the entering flow rate) at the connection between the well and the fracture, i.e., a choke-like effect due to current well completion practices, also referred to as entry friction. The partitioning of the fluid into the different fractures at any given time is part of the solution and is a critical indicator of simultaneous (balanced fluid partitioning) versus preferential growth. We validate our numerical model against reference solutions and a laboratory experiment for the initiation and growth of a single radial hydraulic fracture. We then investigate the impact of stress interaction on preferential growth of a subset of fractures in the array. Our results show that a sufficiently large local entry friction provides a strong feedback in the system and thus can counteract elastic stress interaction between fractures, thereby ensuring simultaneous growth. We propose a dimensionless number capturing the competition between stress interaction and local entry friction. This dimensionless number is a function of rock properties, fracture spacing and injection parameters. We verify that it captures the transition from the case of simultaneous growth (entry friction larger than interaction stress) to the case of preferential growth of some fractures (interaction stress larger than entry friction). We also discuss the implication of these results for multi

  12. All set, indeed! N2pc components reveal simultaneous attentional control settings for multiple target colors.

    OpenAIRE

    Grubert, Anna; Eimer, Martin

    2016-01-01

    To study whether top-down attentional control processes can be set simultaneously for different visual features, we employed a spatial cueing procedure to measure behavioural and electrophysiological markers of task-set contingent attentional capture during search for one or two possible colour-defined targets (One Colour and Two Colour tasks). Search arrays were preceded by spatially non-predictive colour singleton cues. Behavioural spatial cueing effects indicative of attentional capture we...

  13. Simultaneous priming along multiple feature dimensions in a visual search task.

    Science.gov (United States)

    Kristjánsson, Arni

    2006-08-01

    What we have recently seen generally has a large effect on how we consequently perceive our visual environment. Such priming effects play a surprisingly large role in visual search tasks, for example. It is unclear, however, whether different features of an object show independent but simultaneous priming. For example, if the color and orientation of a target item are the same as on a previous trial, is performance better than if only one of those features is repeated? In other words this paper presents an attempt at assessing the capacity of priming for different feature dimensions. Observers searched for a three featured object (a gabor patch that was either redscale or greenscale, oriented either to the left or right of vertical and of high or low spatial frequency) among distractors with different values along these feature dimensions. Which feature was the target defining feature; which was the response defining feature and which was the irrelevant feature, was varied between the different experiments. Task relevant features (target defining, or response defining) always resulted in priming effects, while when spatial frequency or orientation were task irrelevant neither resulted in priming, but color always did, even when task irrelevant. Further experiments showed that priming from spatial frequency and orientation could occur when they were task irrelevant but only when the other feature of the two was kept constant across all display items. The results show that simultaneous priming for different features can occur simultaneously, but also that task relevance has a strong modulatory effect on the priming.

  14. Characteristics of 263K Scrapie Agent in Multiple Hamster Species

    Science.gov (United States)

    Barbian, Kent D.; Race, Brent; Favara, Cynthia; Gardner, Don; Taubner, Lara; Porcella, Stephen; Race, Richard

    2009-01-01

    Transmissible spongiform encephalopathy (TSE) diseases are known to cross species barriers, but the pathologic and biochemical changes that occur during transmission are not well understood. To better understand these changes, we infected 6 hamster species with 263K hamster scrapie strain and, after each of 3 successive passages in the new species, analyzed abnormal proteinase K (PK)–resistant prion protein (PrPres) glycoform ratios, PrPres PK sensitivity, incubation periods, and lesion profiles. Unique 263K molecular and biochemical profiles evolved in each of the infected hamster species. Characteristics of 263K in the new hamster species seemed to correlate best with host factors rather than agent strain. Furthermore, 2 polymorphic regions of the prion protein amino acid sequence correlated with profile differences in these TSE-infected hamster species. PMID:19193264

  15. An improved approach to align and embed multiple brain samples in a gelatin-based matrix for simultaneous histological processing.

    Science.gov (United States)

    Nagamoto-Combs, Kumi; Manocha, Gunjan D; Puig, Kendra; Combs, Colin K

    2016-03-01

    Preparation and processing of free-floating histological sections involve a series of steps. The amount of labor, particularly sectioning and mounting, quickly multiplies as the number of samples increases. Embedding tissue samples in a flexible matrix allows simultaneous handling of multiple samples and preserves the integrity of the tissue during histological processing. However, aligning multiple asymmetrical samples, for example small-animal brains, in a particular orientation requires skillful arrangement and securing of the samples by pinning onto a solid surface. Consequently, costly technical services offered by contract research organizations are often sought. An improved approach to align and embed multiple whole or half rodent brain samples into a gelatin-based matrix is described. Using a template specifically designed to form arrayed mouse brain-shaped cavities, a "receiving matrix" is prepared. Inserting brain samples directly into the cavities allows the samples to be effortlessly positioned into a uniform orientation and embedded in a block of matrix. Multiple mouse brains were arrayed in a uniform orientation in a gelatin matrix block with ease using the receiving matrix. The gelatin-embedded brains were simultaneously sectioned and stained, and effortlessly mounted onto glass slides. The improved approach allowed multiple whole or half mouse brains to be easily arrayed without pinning the samples onto a solid surface and prevented damages or shifting of the samples during embedding. The new approach to array multiple brain samples provides a simple way to prepare gelatin-embedded whole or half brain arrays of commercial quality. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Simultaneous navigation of multiple Pareto surfaces, with an application to multicriteria IMRT planning with multiple beam angle configurations.

    Science.gov (United States)

    Craft, David; Monz, Michael

    2010-02-01

    To introduce a method to simultaneously explore a collection of Pareto surfaces. The method will allow radiotherapy treatment planners to interactively explore treatment plans for different beam angle configurations as well as different treatment modalities. The authors assume a convex optimization setting and represent the Pareto surface for each modality or given beam set by a set of discrete points on the surface. Weighted averages of these discrete points produce a continuous representation of each Pareto surface. The authors calculate a set of Pareto surfaces and use linear programming to navigate across the individual surfaces, allowing switches between surfaces. The switches are organized such that the plan profits in the requested way, while trying to keep the change in dose as small as possible. The system is demonstrated on a phantom pancreas IMRT case using 100 different five beam configurations and a multicriteria formulation with six objectives. The system has intuitive behavior and is easy to control. Also, because the underlying linear programs are small, the system is fast enough to offer real-time exploration for the Pareto surfaces of the given beam configurations. The system presented offers a sound starting point for building clinical systems for multicriteria exploration of different modalities and offers a controllable way to explore hundreds of beam angle configurations in IMRT planning, allowing the users to focus their attention on the dose distribution and treatment planning objectives instead of spending excessive time on the technicalities of delivery.

  17. Multi-color quantum dot-based fluorescence immunoassay array for simultaneous visual detection of multiple antibiotic residues in milk.

    Science.gov (United States)

    Song, Erqun; Yu, Mengqun; Wang, Yunyun; Hu, Weihua; Cheng, Dan; Swihart, Mark T; Song, Yang

    2015-10-15

    Antibiotic residues, which are among the most common contaminants in animal-based food products such as milk, have become a significant public health concern. Here, we combine a multicolor quantum dot (QD)-based immunofluorescence assay and an array analysis method to achieve simultaneous, sensitive and visual detection of streptomycin (SM), tetracycline (TC), and penicillin G (PC-G) in milk. Antibodies (Abs) for SM, TC and PC-G were conjugated to QDs with different emission wavelengths (QD 520 nm, QD 565 nm and QD 610 nm) to serve as detection probes (QD-Ab). Then a direct competitive fluorescent immunoassay was performed in antigen-coated microtiter plate wells for simultaneous qualitative and quantitative detection of SM, TC, and PC-G residues, based on fluorescence of the QD-Ab probes. The linear ranges for SM, TC and PC-G were 0.01-25 ng/mL, 0.01-25 ng/mL and 0.01-10 ng/mL, respectively, with detection limit of 5 pg/mL for each of them. Based on fluorescence of the QD-Ab probes, residues of the three antibiotics were determined visually and simultaneously. Compared with a commercial enzyme-linked immunosorbent assay kit, our method could achieve simultaneous analysis of multiple target antibiotics in multiple samples in a single run (high-throughput analysis) and improved accuracy and sensitivity for analysis of residues of the three antibiotics in authentic milk samples. This new analytical tool can play an important role in ameliorating the negative impact of the residual antibiotics on human health and the ecosystem. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Electrochemical genosensor array for the simultaneous detection of multiple high-risk human papillomavirus sequences in clinical samples

    Energy Technology Data Exchange (ETDEWEB)

    Civit, Laia [Nanobiotechnology and Bioanalysis Group, Departament d' Enginyeria Quimica, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Fragoso, Alex, E-mail: alex.fragoso@urv.cat [Nanobiotechnology and Bioanalysis Group, Departament d' Enginyeria Quimica, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Hoelters, Sebastian; Duerst, Matthias [Department for Gynecology, Jena University Hospital, Friedrich-Schiller-University Jena, D-07743 Jena (Germany); O' Sullivan, Ciara K., E-mail: ciara.osullivan@urv.cat [Nanobiotechnology and Bioanalysis Group, Departament d' Enginyeria Quimica, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Institucio Catalana de Recerca i Estudis Avancats, Passeig Lluis Companys 23, 08010 Barcelona (Spain)

    2012-02-17

    Highlights: Black-Right-Pointing-Pointer High-risk human papillomavirus is detected in virtually all-invasive cervical cancers. Black-Right-Pointing-Pointer Electrochemical genosensor for simultaneous detection of multiple high-risk HPV applied to cervical scrape samples. Black-Right-Pointing-Pointer Excellent correlation with HPV genotyping carried out within a hospital laboratory. - Abstract: An electrochemical genosensor array for the simultaneous detection of three high-risk human papillomavirus (HPV) DNA sequences, HPV16, 18 and 45, exhibiting high sensitivity and selectivity is presented. The electrodes of a 4 Multiplication-Sign 4 array were modified via co-immobilization of a 1:100 (mol/mol) mixture of a thiolated probe and an oligoethyleneglycol-terminated bipodal thiol. Detection of synthetic and PCR products was carried out in a sandwich type format, with the target hybridized between a surface immobilized probe and a horseradish peroxidase-labelled secondary reporter probe. The detection limits obtained in the detection of each individual target were in the pM range, allowing the application of this sensor for the detection of samples obtained from PCR amplification of cervical scrape samples. The results obtained exhibited an excellent correlation with the HPV genotyping carried out within a hospital laboratory. Multiplexing and cross-reactivity studies demonstrated high selectivity over potential interfering sequences, facilitating application of the developed platform for the high-throughput screening of multiple high-risk DNA sequences.

  19. Generating multiple wavelengths, simultaneously, in a Ti:sapphire ring laser with a ramp-hold-fire seeding technique

    Science.gov (United States)

    Moore, Thomas Z.; Anderson, F. Scott

    2012-03-01

    The ability to simultaneously produce pulsed laser output over multiple discrete wavelengths can mitigate many of the timing and jitter issues associated with the use of multiple laser systems. In addition, Fourier-transform limited laser output on every pulse is required for many applications such as with pump-probe detection, non-linear frequency mixing, differential absorption lidar (DIAL), and resonance ionization. As a matter of practice, such lasers need to be capable of operating within uncontrolled or noisy environments. We report on a novel Ti:sapphire ring laser that has been developed to produce Fourier-transform limited 20-ns laser pulses at multiple discrete wavelengths, simultaneously, utilizing a Ramp-Hold-Fire (RHF) seeding technique. Resonance of the seed light is achieved by using a KD*P crystal to modify the phase of the light circulating within the slave oscillator cavity where the fast response of the crystal results in a seeding technique that is immune to noise throughout the acoustic regime.

  20. A convenient method for simultaneous quantification of multiple phytohormones and metabolites: application in study of rice-bacterium interaction

    Directory of Open Access Journals (Sweden)

    Liu Hongbo

    2012-01-01

    Full Text Available Abstract Background Simultaneous analysis of multiple functional-related phytohormones and their metabolites will improve our understanding of interactions among different hormones in the same biologic process. Results A method was developed for simultaneous quantification of multiple phytohormones, abscisic acid, indole-3-acetic acid (IAA, jasmonic acid (JA, and salicylic acid, hormone conjugates, IAA-aspartic acid, JA-isoleucine, and methyl JA, and phytoalexins, momilactone A, naringenin, and sakuranetin. This method combines a convenient procedure for preparing filtrated crude extracted samples and a sensitive quantification assay using ultra fast liquid chromatography-electrospray ionization tandem mass spectrometry (UFLC-ESI-MS. With this method, we determined the dynamic profiles of defense-related phytohormones, hormone metabolites, and phytoalexins in the interaction of rice with Xanthomonas oryzae pv. oryzae (Xoo, which causes bacterial blight, one of the most devastating diseases of rice worldwide. Conclusion This UFLC-ESI-MS method is convenient, sensitive, reliable, and inexpensive for quantification of multiple phytohormones and metabolites compared to current methods. The results obtained by application of this method in studying rice-bacterial interaction provide a basis for understanding the molecular mechanisms of rice defense responses.

  1. Gateway Vectors for Simultaneous Detection of Multiple Protein−Protein Interactions in Plant Cells Using Bimolecular Fluorescence Complementation

    Science.gov (United States)

    Hikino, Kazumi; Goto-Yamada, Shino; Nishimura, Mikio; Nakagawa, Tsuyoshi; Mano, Shoji

    2016-01-01

    Bimolecular fluorescence complementation (BiFC) is widely used to detect protein—protein interactions, because it is technically simple, convenient, and can be adapted for use with conventional fluorescence microscopy. We previously constructed enhanced yellow fluorescent protein (EYFP)-based Gateway cloning technology-compatible vectors. In the current study, we generated new Gateway cloning technology-compatible vectors to detect BiFC-based multiple protein—protein interactions using N- and C-terminal fragments of enhanced cyan fluorescent protein (ECFP), enhanced green fluorescent protein (EGFP), and monomeric red fluorescent protein (mRFP1). Using a combination of N- and C-terminal fragments from ECFP, EGFP and EYFP, we observed a shift in the emission wavelength, enabling the simultaneous detection of multiple protein—protein interactions. Moreover, we developed these vectors as binary vectors for use in Agrobacterium infiltration and for the generate transgenic plants. We verified that the binary vectors functioned well in tobacco cells. The results demonstrate that the BiFC vectors facilitate the design of various constructions and are convenient for the detection of multiple protein—protein interactions simultaneously in plant cells. PMID:27490375

  2. Gateway Vectors for Simultaneous Detection of Multiple Protein-Protein Interactions in Plant Cells Using Bimolecular Fluorescence Complementation.

    Science.gov (United States)

    Kamigaki, Akane; Nito, Kazumasa; Hikino, Kazumi; Goto-Yamada, Shino; Nishimura, Mikio; Nakagawa, Tsuyoshi; Mano, Shoji

    2016-01-01

    Bimolecular fluorescence complementation (BiFC) is widely used to detect protein-protein interactions, because it is technically simple, convenient, and can be adapted for use with conventional fluorescence microscopy. We previously constructed enhanced yellow fluorescent protein (EYFP)-based Gateway cloning technology-compatible vectors. In the current study, we generated new Gateway cloning technology-compatible vectors to detect BiFC-based multiple protein-protein interactions using N- and C-terminal fragments of enhanced cyan fluorescent protein (ECFP), enhanced green fluorescent protein (EGFP), and monomeric red fluorescent protein (mRFP1). Using a combination of N- and C-terminal fragments from ECFP, EGFP and EYFP, we observed a shift in the emission wavelength, enabling the simultaneous detection of multiple protein-protein interactions. Moreover, we developed these vectors as binary vectors for use in Agrobacterium infiltration and for the generate transgenic plants. We verified that the binary vectors functioned well in tobacco cells. The results demonstrate that the BiFC vectors facilitate the design of various constructions and are convenient for the detection of multiple protein-protein interactions simultaneously in plant cells.

  3. Simultaneous Determination of Binding Constants for Multiple Carbohydrate Hosts in Complex Mixtures

    DEFF Research Database (Denmark)

    Meier, Sebastian; Beeren, Sophie

    2014-01-01

    We describe a simple method for the simultaneous determination of association constants for a guest binding to seven different hosts in a mixture of more than 20 different oligosaccharides. If the binding parameters are known for one component in the mixture, a single NMR titration suffices...... to determine binding constants for all other detectable and resolvable hosts. With the use of high-resolution 1H−13C HSQC experiments, complexes of amphiphiles with more than 10 different maltooligosaccharides can be resolved. Hereby, the binding capabilities of a set of structurally related hosts can...

  4. Multiple causes of high extinction risk in large mammal species.

    Science.gov (United States)

    Cardillo, Marcel; Mace, Georgina M; Jones, Kate E; Bielby, Jon; Bininda-Emonds, Olaf R P; Sechrest, Wes; Orme, C David L; Purvis, Andy

    2005-08-19

    Many large animal species have a high risk of extinction. This is usually thought to result simply from the way that species traits associated with vulnerability, such as low reproductive rates, scale with body size. In a broad-scale analysis of extinction risk in mammals, we find two additional patterns in the size selectivity of extinction risk. First, impacts of both intrinsic and environmental factors increase sharply above a threshold body mass around 3 kilograms. Second, whereas extinction risk in smaller species is driven by environmental factors, in larger species it is driven by a combination of environmental factors and intrinsic traits. Thus, the disadvantages of large size are greater than generally recognized, and future loss of large mammal biodiversity could be far more rapid than expected.

  5. Genetically engineered Mengo virus vaccination of multiple captive wildlife species.

    Science.gov (United States)

    Backues, K A; Hill, M; Palmenberg, A C; Miller, C; Soike, K F; Aguilar, R

    1999-04-01

    Encephalomyocarditis virus (EMCV), has caused the deaths of many species of animals in zoological parks and research institutions. The Audubon Park Zoo, (New Orleans, Louisiana, USA) attempted vaccination of several species with a killed EMCV vaccine with mixed results. This paper reports an attempt at vaccination against EMCV using a genetically engineered, live attenuated Mengo virus (vMC0) at the Audubon Park Zoo and Miami Metro Zoo, (Miami, Florida, USA) from December 1996 to June 1997. Several species of animals were vaccinated with vMC0, which is serologically indistinguishable from the field strain of EMCV. Serum samples were taken at the time of vaccination and again 21 days later, then submitted for serum neutralization titers against EMCV. The vaccinate species included red capped mangebey (Cercocebus torquatus), colobus (Colobus guereza), angolan colobus (Colobus angolensis), ruffed lemur (Lemur variegatus ruber and Lemur variegatus variegatus), back lemur (Lemur macaco), ring-tailed lemur (Lemur catta), siamang (Hylobates syndactylus), diana guenon (Cercopithicus diana), spider monkey (Ateles geoffroyi), common marmoset (Callithrix jacchus), talapoin monkey (Cercopithecus talapoin), Brazilian tapir (Tapirus terrestris), Baird's tapir (Tapirus bairdii), Malayan tapir (Tapirus indicus), dromedary camel (Camelus dromedarius), bactrian camel (Camelus bactrianus), gerenuk (Litocranius walleri), guanaco (Lama glama guanicoe), black duiker (Cephalophus niger), Vietnamese potbellied pig (Sus scrofa), babirusa (Babyrousa babyrussa), collard peccary (Tayass tajacu), and African crested porcupine (Hystrix africaeaustralis). The vaccine response was variable, with high virus neutralizing antibody titer responses in some primate species and mixed to poor responses for other species. No ill effects were seen with vaccination.

  6. Simultaneous small-sample comparisons in longitudinal or multi-endpoint trials using multiple marginal models

    DEFF Research Database (Denmark)

    Pallmann, Philip; Ritz, Christian; Hothorn, Ludwig A

    2018-01-01

    simplifies the modelling process: the core idea is to "marginalise" the problem and fit multiple small models to different portions of the data, and then estimate the overall covariance matrix in a subsequent, separate step. Using these estimates guarantees strong control of the family-wise error rate...

  7. MEG evidence that the central auditory system simultaneously encodes multiple temporal cues

    NARCIS (Netherlands)

    Simpson, M.I.G.; Barnes, G.R.; Johnson, S.R.; Hillebrand, A.; Singh, K.D.; Green, G.G.R.

    2009-01-01

    Speech contains complex amplitude modulations that have envelopes with multiple temporal cues. The processing of these complex envelopes is not well explained by the classical models of amplitude modulation processing. This may be because the evidence for the models typically comes from the use of

  8. All Set! Evidence of Simultaneous Attentional Control Settings for Multiple Target Colors

    Science.gov (United States)

    Irons, Jessica L.; Folk, Charles L.; Remington, Roger W.

    2012-01-01

    Although models of visual search have often assumed that attention can only be set for a single feature or property at a time, recent studies have suggested that it may be possible to maintain more than one attentional control setting. The aim of the present study was to investigate whether spatial attention could be guided by multiple attentional…

  9. Novel method of simultaneous multiple immunogold localization on resin sections in high resolution scanning electron microscopy

    Czech Academy of Sciences Publication Activity Database

    Nebesářová, Jana; Wandrol, P.; Vancová, Marie

    2016-01-01

    Roč. 12, č. 1 (2016), s. 105-517 ISSN 1549-9634 R&D Projects: GA TA ČR(CZ) TE01020118 Institutional support: RVO:60077344 Keywords : multiple immunolabeling * gold nanoparticles * high resolution SEM * STEM imaging * BSE imaging Subject RIV: EA - Cell Biology Impact factor: 5.720, year: 2016

  10. Simultaneous and rapid determination of multiple component concentrations in a Kraft liquor process stream

    Science.gov (United States)

    Li, Jian [Marietta, GA; Chai, Xin Sheng [Atlanta, GA; Zhu, Junyoung [Marietta, GA

    2008-06-24

    The present invention is a rapid method of determining the concentration of the major components in a chemical stream. The present invention is also a simple, low cost, device of determining the in-situ concentration of the major components in a chemical stream. In particular, the present invention provides a useful method for simultaneously determining the concentrations of sodium hydroxide, sodium sulfide and sodium carbonate in aqueous kraft pulping liquors through use of an attenuated total reflectance (ATR) tunnel flow cell or optical probe capable of producing a ultraviolet absorbency spectrum over a wavelength of 190 to 300 nm. In addition, the present invention eliminates the need for manual sampling and dilution previously required to generate analyzable samples. The inventive method can be used in Kraft pulping operations to control white liquor causticizing efficiency, sulfate reduction efficiency in green liquor, oxidation efficiency for oxidized white liquor and the active and effective alkali charge to kraft pulping operations.

  11. Simultaneous Online Monitoring of Multiple Reactions Using a Miniature Mass Spectrometer.

    Science.gov (United States)

    Pulliam, Christopher J; Bain, Ryan M; Osswald, Heather L; Snyder, Dalton T; Fedick, Patrick W; Ayrton, Stephen T; Flick, Tawnya G; Cooks, R Graham

    2017-07-05

    Advances in chemical sampling using miniature mass spectrometer technology are used to monitor slow reactions at a frequency of ca. 180 h-1 (on the Mini 12) with no sample carryover and with inline derivatization in the case of poorly ionizing compounds. Moreover, we demonstrate high reproducibility with a relative error of less than 10% for major components. Monitoring is enabled using a continuous-flow nanoelectrospray (CF-nESI) probe contained in a custom-built 3D-printed rotary holder. The holder position is automatically set using a stepper motor controlled by a microcontroller. Reaction progress of up to six reactions, including hydrazone formation and Katritzky transamination, can be monitored simultaneously without carryover for several hours.

  12. Characterisation of a cryostat using simultaneous, single-beam multiple-surface laser vibrometry

    Energy Technology Data Exchange (ETDEWEB)

    Kissinger, Thomas; Charrett, Thomas O. H.; James, Stephen W.; Tatam, Ralph P., E-mail: r.p.tatam@cranfield.ac.uk [Engineering Photonics, Cranfield University, Cranfield, MK43 0AL (United Kingdom); Adams, Alvin; Twin, Andrew [Oxford Instruments Nanoscience, Tubney Woods, Abingdon, Oxon, OX13 5QX (United Kingdom)

    2016-06-28

    A novel range-resolved interferometric signal processing technique that uses sinusoidal optical frequency modulation is applied to multi-surface vibrometry, demonstrating simultaneous optical measurements of vibrations on two surfaces using a single, collimated laser beam, with a minimum permissible distance of 3.5 cm between surfaces. The current system, using a cost-effective laser diode and a fibre-coupled, downlead insensitive setup, allows an interferometric fringe rate of up to 180 kHz to be resolved with typical displacement noise levels of 8 pm · Hz{sup −05}. In this paper, the system is applied to vibrometry measurements of a table-top cryostat, with concurrent measurements of the optical widow and the sample holder target inside. This allows the separation of common-mode vibrations of the whole cryostat from differential vibrations between the window and the target, allowing any resonances to be identified.

  13. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Maury, Jerome; Germann, Susanne Manuela; Jacobsen, Simo Abdessamad

    2016-01-01

    of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci......Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred...... option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set...

  14. Relevance of simultaneous mono-ubiquitinations of multiple units of PCNA homo-trimers in DNA damage tolerance.

    Directory of Open Access Journals (Sweden)

    Rie Kanao

    Full Text Available DNA damage tolerance (DDT pathways, including translesion synthesis (TLS and additional unknown mechanisms, enable recovery from replication arrest at DNA lesions. DDT pathways are regulated by post-translational modifications of proliferating cell nuclear antigen (PCNA at its K164 residue. In particular, mono-ubiquitination by the ubiquitin ligase RAD18 is crucial for Polη-mediated TLS. Although the importance of modifications of PCNA to DDT pathways is well known, the relevance of its homo-trimer form, in which three K164 residues are present in a single ring, remains to be elucidated. Here, we show that multiple units of a PCNA homo-trimer are simultaneously mono-ubiquitinated in vitro and in vivo. RAD18 catalyzed sequential mono-ubiquitinations of multiple units of a PCNA homo-trimer in a reconstituted system. Exogenous PCNA formed hetero-trimers with endogenous PCNA in WI38VA13 cell transformants. When K164R-mutated PCNA was expressed in these cells at levels that depleted endogenous PCNA homo-trimers, multiple modifications of PCNA complexes were reduced and the cells showed defects in DDT after UV irradiation. Notably, ectopic expression of mutant PCNA increased the UV sensitivities of Polη-proficient, Polη-deficient, and REV1-depleted cells, suggesting the disruption of a DDT pathway distinct from the Polη- and REV1-mediated pathways. These results suggest that simultaneous modifications of multiple units of a PCNA homo-trimer are required for a certain DDT pathway in human cells.

  15. Relevance of simultaneous mono-ubiquitinations of multiple units of PCNA homo-trimers in DNA damage tolerance.

    Science.gov (United States)

    Kanao, Rie; Masuda, Yuji; Deguchi, Saori; Yumoto-Sugimoto, Mayumi; Hanaoka, Fumio; Masutani, Chikahide

    2015-01-01

    DNA damage tolerance (DDT) pathways, including translesion synthesis (TLS) and additional unknown mechanisms, enable recovery from replication arrest at DNA lesions. DDT pathways are regulated by post-translational modifications of proliferating cell nuclear antigen (PCNA) at its K164 residue. In particular, mono-ubiquitination by the ubiquitin ligase RAD18 is crucial for Polη-mediated TLS. Although the importance of modifications of PCNA to DDT pathways is well known, the relevance of its homo-trimer form, in which three K164 residues are present in a single ring, remains to be elucidated. Here, we show that multiple units of a PCNA homo-trimer are simultaneously mono-ubiquitinated in vitro and in vivo. RAD18 catalyzed sequential mono-ubiquitinations of multiple units of a PCNA homo-trimer in a reconstituted system. Exogenous PCNA formed hetero-trimers with endogenous PCNA in WI38VA13 cell transformants. When K164R-mutated PCNA was expressed in these cells at levels that depleted endogenous PCNA homo-trimers, multiple modifications of PCNA complexes were reduced and the cells showed defects in DDT after UV irradiation. Notably, ectopic expression of mutant PCNA increased the UV sensitivities of Polη-proficient, Polη-deficient, and REV1-depleted cells, suggesting the disruption of a DDT pathway distinct from the Polη- and REV1-mediated pathways. These results suggest that simultaneous modifications of multiple units of a PCNA homo-trimer are required for a certain DDT pathway in human cells.

  16. Rapid Screening for Flavone C-Glycosides in the Leaves of Different Species of Bamboo and Simultaneous Quantitation of Four Marker Compounds by HPLC-UV/DAD

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2012-01-01

    Full Text Available A strategy for analyzing flavone C-glucosides in the leaves of different species of bamboo was developed. Firstly, the flavone C-glycosides were extracted from the bamboo leaves (51 species in 17 genera with methanol and chromatographed on silica gel 60 plates in automatic developing chamber (ADC2, and a qualitative survey using simple derivatization steps with the NP reagent was carried out. The flavone C-glycosides were found in 40 of 51 species of bamboo examined. Secondly, an HPLC method with photodiode array and multiple wavelength detector was optimized and validated for the simultaneous determination of flavone C-glycosides, including isoorientin, isovitexin, orientin, and vitexin in the leaves of three species of bamboo and the flavone C-glycosides were confirmed by LC/MS. The optimized HPLC method proved to be linear in the concentration range tested (0.2–100 μg/mL, r2≥0.9997, precise (RSD≤1.56%, and accurate (88–106%. The concentration ranges of isoorientin, isovitexin, orientin, and vitexin in three bamboo leaves samples were 1.00–2.78, 0–0.31, 0–0.07, and 0.20–0.68 mg/g, respectively. The proposed method was validated to be simple and reliable and can be a tool for quality control of bamboo leaf extract or its commercial products.

  17. Bilateral Simultaneous Central Retinal Vein Occlusion Presenting as Initial Manifestation of Multiple Myeloma

    OpenAIRE

    Kamath SJ; Kamath GM; Roopashree

    2014-01-01

    A fifty years old male with a medical history of diabetes mellitus presented with complaints of sudden painless bilateral vision loss since 2 weeks. Ophthalmic examination showed visual acuity in both eyes were counting finger 2 meters. Intraocular pressure and anterior segment examination findings in both eyes were normal. Funduscopy revealed bilateral central retinal vein occlusion (CRVO). Haematological and radiological investigations confirmed diagnosis of multiple myeloma and ocular mani...

  18. Epidemiology of single and multiple species of helminth infections ...

    African Journals Online (AJOL)

    Objective: To describe the patterns of single and multiple helminth infection in school children from Busia District, Kenya. Design: A cross-sectional school survey using a randomly selected sample, forming part of an evaluation study of an ongoing deworming project. Setting: Budalangi and Funyula divisions of Busia District ...

  19. A versatile size-coded flow cytometric bead assay for simultaneous detection of multiple microRNAs coupled with a two-step cascading signal amplification.

    Science.gov (United States)

    Qiu, Liying; Zhang, Yuecheng; Liu, Chenghui; Li, Zhengping

    2017-03-07

    A versatile flow cytometric bead assay is developed for the sensitive and simultaneous detection of multiple microRNAs that combines an elegant enzyme-mediated cascading signal amplification on magnetic beads with a novel bead size-encoding mechanism.

  20. Comparison and clinical utility evaluation of four multiple allergen simultaneous tests including two newly introduced fully automated analyzers

    Directory of Open Access Journals (Sweden)

    John Hoon Rim

    2016-04-01

    Full Text Available Background: We compared the diagnostic performances of two newly introduced fully automated multiple allergen simultaneous tests (MAST analyzers with two conventional MAST assays. Methods: The serum samples from a total of 53 and 104 patients were tested for food panels and inhalant panels, respectively, in four analyzers including AdvanSure AlloScreen (LG Life Science, Korea, AdvanSure Allostation Smart II (LG Life Science, PROTIA Allergy-Q (ProteomeTech, Korea, and RIDA Allergy Screen (R-Biopharm, Germany. We compared not only the total agreement percentages but also positive propensities among four analyzers. Results: Evaluation of AdvanSure Allostation Smart II as upgraded version of AdvanSure AlloScreen revealed good concordance with total agreement percentages of 93.0% and 92.2% in food and inhalant panel, respectively. Comparisons of AdvanSure Allostation Smart II or PROTIA Allergy-Q with RIDA Allergy Screen also showed good concordance performance with positive propensities of two new analyzers for common allergens (Dermatophagoides farina and Dermatophagoides pteronyssinus. The changes of cut-off level resulted in various total agreement percentage fluctuations among allergens by different analyzers, although current cut-off level of class 2 appeared to be generally suitable. Conclusions: AdvanSure Allostation Smart II and PROTIA Allergy-Q presented favorable agreement performances with RIDA Allergy Screen, although positive propensities were noticed in common allergens. Keywords: Multiple allergen simultaneous test, Automated analyzer

  1. Multiple molecular mechanisms cause reproductive isolation between three yeast species.

    Directory of Open Access Journals (Sweden)

    Jui-Yu Chou

    Full Text Available Nuclear-mitochondrial conflict (cytonuclear incompatibility is a specific form of Dobzhansky-Muller incompatibility previously shown to cause reproductive isolation in two yeast species. Here, we identified two new incompatible genes, MRS1 and AIM22, through a systematic study of F2 hybrid sterility caused by cytonuclear incompatibility in three closely related Saccharomyces species (S. cerevisiae, S. paradoxus, and S. bayanus. Mrs1 is a nuclear gene product required for splicing specific introns in the mitochondrial COX1, and Aim22 is a ligase encoded in the nucleus that is required for mitochondrial protein lipoylation. By comparing different species, our result suggests that the functional changes in MRS1 are a result of coevolution with changes in the COX1 introns. Further molecular analyses demonstrate that three nonsynonymous mutations are responsible for the functional differences of Mrs1 between these species. Functional complementation assays to determine when these incompatible genes altered their functions show a strong correlation between the sequence-based phylogeny and the evolution of cytonuclear incompatibility. Our results suggest that nuclear-mitochondrial incompatibility may represent a general mechanism of reproductive isolation during yeast evolution.

  2. As multiple fish species in large marine ecosystems are harvested ...

    African Journals Online (AJOL)

    CMPTMAC10

    agement even in cases where human demand is con- trolled by current “best” fisheries management prac- tice: the questions have led on the one hand to public calls for specific set-asides of marine forage species for top predators (e.g. Greenpeace vs National Marine. Fisheries Service 80 F. Supp. 2d 1137 WD. Wash.,.

  3. Simultaneous Detection of Multiple Fish Pathogens Using a Naked-Eye Readable DNA Microarray

    Directory of Open Access Journals (Sweden)

    King-Jung Lin

    2012-02-01

    Full Text Available We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3′-indolylphosphate, p-toluidine salt (NBT/BCIP, resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 103 CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens.

  4. Simultaneous imaging of multiple focal planes in scanning two-photon absorption microscope by photon counting

    Science.gov (United States)

    Carriles, Ramón; Hoover, Erich E.; Amir, Wafa; Squier, Jeffery A.

    2007-09-01

    We demonstrate a two-photon absorption scanning microscope capable of imaging two focal planes simultaneously. The 23MHz fundamental laser is split in two, one part delayed in time while the other is focused with a deformable mirror to change its divergence. Both parts are then recombined to form a 46MHz pulse train consisting of two interlaced trains with different divergences that after the objective are focused at different sample depths. At the detection path, photon counting techniques allow photons coming from each depth to be separated based on their relative timing with respect to the 46MHz train. The separation is accomplished using a field-programmable gate array that has been programmed to switch back and forth between two counters at a rate provided by a master clock generated by the 46MHz pulse train. The computer that controls the scanners reads and resets the counters before moving to a new pixel. The scheme is demonstrated for two depths but can be extended to a larger number, the ultimate limit being the fluorescence lifetime. This technique could also be implemented for second or third harmonic generation microscopy, in this case the ultimate achievable number of focal planes would be determined by the electronics speed.

  5. Simultaneous analysis of multiple neurotransmitters by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry.

    Science.gov (United States)

    Tufi, Sara; Lamoree, Marja; de Boer, Jacob; Leonards, Pim

    2015-05-22

    Neurotransmitters are endogenous metabolites that allow the signal transmission across neuronal synapses. Their biological role is crucial for many physiological functions and their levels can be changed by several diseases. Because of their high polarity, hydrophilic interaction liquid chromatography (HILIC) is a promising tool for neurotransmitter analysis. Due to the large number of HILIC stationary phases available, an evaluation of the column performances and retention behaviors has been performed on five different commercial HILIC packing materials (silica, amino, amide and two zwitterionic stationary phases). Several parameters like the linear correlation between retention and the distribution coefficient (logD), the separation factor k and the column resolution Rs have been investigated and the column performances have been visualized with a heat map and hierarchical clustering analysis. An optimized and validated HILIC-MS/MS method based on the ZIC-cHILIC column is proposed for the simultaneous detection and quantification of twenty compounds consisting of neurotransmitters, precursors and metabolites: 3-methoxytyramine (3-MT), 5-hydroxyindoleacetic acid (5-HIAA), 5-hydroxy-L-tripthophan, acetylcholine, choline, L-3,4-dihydroxyphenylalanine (L-DOPA), dopamine, epinephrine, γ-aminobutyric acid (GABA), glutamate, glutamine, histamine, histidine, L-tryptophan, L-tyrosine, norepinephrine, normetanephrine, phenylalanine, serotonin and tyramine. The method was applied to neuronal metabolite profiling of the central nervous system of the freshwater snail Lymnaea stagnalis. This method is suitable to explore neuronal metabolism and its alteration in different biological matrices. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Simultaneous Multi-Species Tracking in Live Cells with Quantum Dot Conjugates

    DEFF Research Database (Denmark)

    Clausen, M. P.; Christensen, Eva Arnspang; Ballou, B.

    2014-01-01

    Quantum dots are available in a range of spectrally separated emission colors and with a range of water-stabilizing surface coatings that offers great flexibility for enabling bio-specificity. In this study, we have taken advantage of this flexibility to demonstrate that it is possible to perform...... a simultaneous investigation of the lateral dynamics in the plasma membrane of i) the transmembrane epidermal growth factor receptor, ii) the glucosylphospatidylinositol-anchored protein CD59, and iii) ganglioside G(M1)-cholera toxin subunit B clusters in a single cell. We show that a large number...... that the heterogeneity is decreased upon treating the cells with methyl-beta-cyclodextrin....

  7. Representation of Students in Solving Simultaneous Linear Equation Problems Based on Multiple Intelligence

    Science.gov (United States)

    Yanti, Y. R.; Amin, S. M.; Sulaiman, R.

    2018-01-01

    This study described representation of students who have musical, logical-mathematic and naturalist intelligence in solving a problem. Subjects were selected on the basis of multiple intelligence tests (TPM) consists of 108 statements, with 102 statements adopted from Chislet and Chapman and 6 statements equal to eksistensial intelligences. Data were analyzed based on problem-solving tests (TPM) and interviewing. See the validity of the data then problem-solving tests (TPM) and interviewing is given twice with an analyzed using the representation indikator and the problem solving step. The results showed that: the stage of presenting information known, stage of devising a plan, and stage of carrying out the plan those three subjects were using same form of representation. While he stage of presenting information asked and stage of looking back, subject of logical-mathematic was using different forms of representation with subjects of musical and naturalist intelligence. From this research is expected to provide input to the teacher in determining the learning strategy that will be used by considering the representation of students with the basis of multiple intelligences.

  8. Cultivar mixtures for the simultaneous management of multiple diseases: tan spot and leaf rust of wheat.

    Science.gov (United States)

    Cox, C M; Garrett, K A; Bowden, R L; Fritz, A K; Dendy, S P; Heer, W F

    2004-09-01

    ABSTRACT Because of differences in life histories between Puccinia triticina, a highly specialized, polycyclic, windborne pathogen with a shallow dispersal gradient, and Pyrenophora tritici-repentis, a residue-borne pathogen with a steep dispersal gradient, wheat mixtures are expected to be more effective at controlling leaf rust than tan spot. The objectives of this research were to determine the effect of two-cultivar mixtures with varying proportions and different pathogen resistance profiles on the severity of tan spot and leaf rust, to evaluate yield of the mixtures in the presence or absence of disease, and to directly compare the relative effectiveness of cultivar mixing for tan spot versus leaf rust. In a field experiment at two sites in Kansas over two growing seasons, winter wheat cvs. Jagger and 2145, which have differential resistance reactions to leaf rust and tan spot, each were planted in proportions of 0.25, 0.50, 0.75, and 1.00. Plots were inoculated with each pathogen alone, both pathogens, treated with a fungicide, or exposed to ambient conditions. For both diseases for all siteyears, severity decreased substantially on the susceptible cultivar as the proportion of that cultivar decreased in mixture. Mixtures were significantly more effective at reducing leaf rust than tan spot in three of four site-years. Mixtures generally yielded the same as the weighted mean of components in monoculture although, in two of three site-years, at least one fungicide-treated and one diseased mixture each yielded higher than expected values. Although this particular mixture produced only modest yield benefits, the potential for simultaneous reductions in tan spot and leaf rust was demonstrated.

  9. Simultaneous Targeting of Multiple Hemagglutinins to APCs for Induction of Broad Immunity against Influenza.

    Science.gov (United States)

    Anderson, Ane Marie; Baranowska-Hustad, Marta; Braathen, Ranveig; Grodeland, Gunnveig; Bogen, Bjarne

    2018-02-02

    There is a need for vaccines that can confer broad immunity against highly diverse pathogens, such as influenza. The efficacy of conventional influenza vaccines is dependent on accurate matching of vaccines to circulating strains, but slow and limited production capacities increase the probability of vaccine mismatches. In contrast, DNA vaccination allows for rapid production of vaccines encoding novel influenza Ags. The efficacy of DNA vaccination is greatly improved if the DNA-encoded vaccine proteins target APCs. In this study, we have used hemagglutinin (HA) genes from each of six group 1 influenza viruses (H5, H6, H8, H9, H11, and H13), and inserted these into a DNA vaccine format that induces delivery of the HA protein Ags to MHC class II molecules on APCs. Each of the targeted DNA vaccines induced high titers of strain-specific anti-HA Abs. Importantly, when the six HA vaccines were mixed and injected simultaneously, the strain-specific Ab titers were maintained. In addition, the vaccine mixture induced Abs that cross-reacted with strains not included in the vaccine mixture (H1) and could protect mice against a heterosubtypic challenge with the H1 viruses A/Puerto Rico/8/1934 (H1N1) and A/California/07/2009 (H1N1). The data suggest that vaccination with a mixture of HAs could be useful for induction of strain-specific immunity against strains represented in the mixture and, in addition, confer some degree of cross-protection against unrelated influenza strains. Copyright © 2018 by The American Association of Immunologists, Inc.

  10. Visual cortex responses to single- and simultaneous multiple-electrode stimulation of the retina: implications for retinal prostheses.

    Science.gov (United States)

    Shivdasani, Mohit N; Fallon, James B; Luu, Chi D; Cicione, Rosemary; Allen, Penny J; Morley, John W; Williams, Chris E

    2012-09-19

    The aim of this study was to compare simultaneous stimulation of multiple electrodes to single-electrode stimulation in a retinal prosthesis. A platinum electrode array was implanted into the suprachoroidal space in six normally sighted anesthetized cats. Multiunit activity from the primary visual cortex in response to retinal stimulation was recorded. Cortical thresholds, yield of responses, dynamic ranges, and the spread of retinal activation were measured for three modes of stimulation: single electrode, half-row (six-electrode horizontal line), and column (seven-electrode vertical line). Stimulation of the best half-rows and columns was found to elicit activity with higher yield and lower charge thresholds per electrode compared to the best single electrodes. Dynamic ranges between the three modes were similar. As expected, peak voltages measured for columns and half-rows were lower than those measured for single electrodes. Spread of retinal activation, determined by the increase in threshold with distance in the retina from the best site, was found to be similar between single- and multiple-electrode stimulation but dependent on orientation. The lower thresholds, higher yield, equivalent dynamic ranges, and equivalent spread of retinal activation observed from simultaneous stimulation of multiple electrodes may be due to current and/or neural summation within the retina. Such stimulation techniques could be useful for the presentation of lines and edges of objects using a suprachoroidal retinal stimulator with low voltage compliance. Furthermore, the results suggest that more complex visual processing strategies in addition to sequential stimulation of individual electrodes should be considered for retinal prostheses.

  11. Optimal design of compact and connected nature reserves for multiple species.

    Science.gov (United States)

    Wang, Yicheng; Önal, Hayri

    2016-04-01

    When designing a conservation reserve system for multiple species, spatial attributes of the reserves must be taken into account at species level. The existing optimal reserve design literature considers either one spatial attribute or when multiple attributes are considered the analysis is restricted only to one species. We built a linear integer programing model that incorporates compactness and connectivity of the landscape reserved for multiple species. The model identifies multiple reserves that each serve a subset of target species with a specified coverage probability threshold to ensure the species' long-term survival in the reserve, and each target species is covered (protected) with another probability threshold at the reserve system level. We modeled compactness by minimizing the total distance between selected sites and central sites, and we modeled connectivity of a selected site to its designated central site by selecting at least one of its adjacent sites that has a nearer distance to the central site. We considered structural distance and functional distances that incorporated site quality between sites. We tested the model using randomly generated data on 2 species, one ground species that required structural connectivity and the other an avian species that required functional connectivity. We applied the model to 10 bird species listed as endangered by the state of Illinois (U.S.A.). Spatial coherence and selection cost of the reserves differed substantially depending on the weights assigned to these 2 criteria. The model can be used to design a reserve system for multiple species, especially species whose habitats are far apart in which case multiple disjunct but compact and connected reserves are advantageous. The model can be modified to increase or decrease the distance between reserves to reduce or promote population connectivity. © 2015 Society for Conservation Biology.

  12. Microfluidic assay for simultaneous culture of multiple cell types on surfaces or within hydrogels.

    Science.gov (United States)

    Shin, Yoojin; Han, Sewoon; Jeon, Jessie S; Yamamoto, Kyoko; Zervantonakis, Ioannis K; Sudo, Ryo; Kamm, Roger D; Chung, Seok

    2012-06-07

    This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel-incorporating chambers between surface-accessible microchannels. By using this platform, well-defined biochemical and biophysical stimuli can be applied to multiple cell types interacting over distances of type assays can be used to study cell survival, proliferation, migration, morphogenesis and differentiation under controlled conditions. Applications include the study of previously unexplored cellular interactions, and they have already provided new insights into how biochemical and biophysical factors regulate interactions between populations of different cell types. It takes 3 d to fabricate the system and experiments can run for up to several weeks.

  13. Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems

    Science.gov (United States)

    Chen, Yuhan; Wang, Shengjun; Hilgetag, Claus C.; Zhou, Changsong

    2013-01-01

    The formation of the complex network architecture of neural systems is subject to multiple structural and functional constraints. Two obvious but apparently contradictory constraints are low wiring cost and high processing efficiency, characterized by short overall wiring length and a small average number of processing steps, respectively. Growing evidence shows that neural networks are results from a trade-off between physical cost and functional value of the topology. However, the relationship between these competing constraints and complex topology is not well understood quantitatively. We explored this relationship systematically by reconstructing two known neural networks, Macaque cortical connectivity and C. elegans neuronal connections, from combinatory optimization of wiring cost and processing efficiency constraints, using a control parameter , and comparing the reconstructed networks to the real networks. We found that in both neural systems, the reconstructed networks derived from the two constraints can reveal some important relations between the spatial layout of nodes and the topological connectivity, and match several properties of the real networks. The reconstructed and real networks had a similar modular organization in a broad range of , resulting from spatial clustering of network nodes. Hubs emerged due to the competition of the two constraints, and their positions were close to, and partly coincided, with the real hubs in a range of values. The degree of nodes was correlated with the density of nodes in their spatial neighborhood in both reconstructed and real networks. Generally, the rebuilt network matched a significant portion of real links, especially short-distant ones. These findings provide clear evidence to support the hypothesis of trade-off between multiple constraints on brain networks. The two constraints of wiring cost and processing efficiency, however, cannot explain all salient features in the real networks. The discrepancy

  14. Trade-off between multiple constraints enables simultaneous formation of modules and hubs in neural systems.

    Directory of Open Access Journals (Sweden)

    Yuhan Chen

    Full Text Available The formation of the complex network architecture of neural systems is subject to multiple structural and functional constraints. Two obvious but apparently contradictory constraints are low wiring cost and high processing efficiency, characterized by short overall wiring length and a small average number of processing steps, respectively. Growing evidence shows that neural networks are results from a trade-off between physical cost and functional value of the topology. However, the relationship between these competing constraints and complex topology is not well understood quantitatively. We explored this relationship systematically by reconstructing two known neural networks, Macaque cortical connectivity and C. elegans neuronal connections, from combinatory optimization of wiring cost and processing efficiency constraints, using a control parameter α, and comparing the reconstructed networks to the real networks. We found that in both neural systems, the reconstructed networks derived from the two constraints can reveal some important relations between the spatial layout of nodes and the topological connectivity, and match several properties of the real networks. The reconstructed and real networks had a similar modular organization in a broad range of α, resulting from spatial clustering of network nodes. Hubs emerged due to the competition of the two constraints, and their positions were close to, and partly coincided, with the real hubs in a range of α values. The degree of nodes was correlated with the density of nodes in their spatial neighborhood in both reconstructed and real networks. Generally, the rebuilt network matched a significant portion of real links, especially short-distant ones. These findings provide clear evidence to support the hypothesis of trade-off between multiple constraints on brain networks. The two constraints of wiring cost and processing efficiency, however, cannot explain all salient features in the real

  15. A method for simultaneous quantification of phospholipid species by routine 31P NMR

    DEFF Research Database (Denmark)

    Brinkmann-Trettenes, Ulla; Stein, Paul C.; Klösgen, Beate Maria

    2012-01-01

    are equal within experimental error. Changing the pH of the buffer enables peak separation for different phospholipid species. This is an advantage compared to the commercial enzyme assay based on phospholipase D and choline oxidase. The reported method, using routine 31P NMR equipment, is suitable when...

  16. Spontaneous motor entrainment to music in multiple vocal mimicking species.

    Science.gov (United States)

    Schachner, Adena; Brady, Timothy F; Pepperberg, Irene M; Hauser, Marc D

    2009-05-26

    The human capacity for music consists of certain core phenomena, including the tendency to entrain, or align movement, to an external auditory pulse [1-3]. This ability, fundamental both for music production and for coordinated dance, has been repeatedly highlighted as uniquely human [4-11]. However, it has recently been hypothesized that entrainment evolved as a by-product of vocal mimicry, generating the strong prediction that only vocal mimicking animals may be able to entrain [12, 13]. Here we provide comparative data demonstrating the existence of two proficient vocal mimicking nonhuman animals (parrots) that entrain to music, spontaneously producing synchronized movements resembling human dance. We also provide an extensive comparative data set from a global video database systematically analyzed for evidence of entrainment in hundreds of species both capable and incapable of vocal mimicry. Despite the higher representation of vocal nonmimics in the database and comparable exposure of mimics and nonmimics to humans and music, only vocal mimics showed evidence of entrainment. We conclude that entrainment is not unique to humans and that the distribution of entrainment across species supports the hypothesis that entrainment evolved as a by-product of selection for vocal mimicry.

  17. Implementing Digital Feedback Controls for the Multiple Simultaneous Ring Cavities in the FASOR-X System

    Science.gov (United States)

    Baker, J.; Gallant, D.; Lucero, A.; Miller, H.; Stohs, J.

    2011-09-01

    Precision tuned high power (~50W) 589nm generation for use in laser sodium guidestar generation is a key capability in today’s modern adaptive optical systems. The approached used is Sum-Frequency Generation (SFG) of 1319nm and 1064nm lines of Nd:YAG in an LBO crystal. High power narrow line sources are not commercially available, so low power narrow-band NPRO sources are mated with resonantly tuned high power ring lasers to achieve high power pumps. Efficient conversion of 589nm requires high pump intensities within the LBO crystal, therefore a doubly-resonant ring cavity is used. Four implementations of the Pound-Drever-Hall method are applied to achieve these. Finally, precision wavelength tuning is required to generate the correct wavelength as measured by a Wavemeter and verified by a low pressure Na-cell. These multiple control loops are all interconnected, to some degree, with various physical requirements, constraints, and caveats. Like any worthwhile project, the systems integration of the control systems has been an educational endeavor.

  18. Simultaneous Optimization of Multiple Response Variables for the Gelatin-chitosan Microcapsules Containing Angelica Essential Oil.

    Science.gov (United States)

    Li, Qiang; Sun, Li-Jian; Gong, Xian-Feng; Wang, Yang; Zhao, Xue-Ling

    2017-01-01

    Angelica essential oil (AO), a major pharmacologically active component of Angelica sinensis (Oliv.) Diels, possesses hemogenesis, analgesic activities, and sedative effect. The application of AO in pharmaceutical systems had been limited because of its low oxidative stability. The AO-loaded gelatin-chitosan microcapsules with prevention from oxidation were developed and optimized using response surface methodology. The effects of formulation variables (pH at complex coacervation, gelatin concentration, and core/wall ratio) on multiple response variables (yield, encapsulation efficiency, antioxidation rate, percent of drug released in 1 h, and time to 85% drug release) were systemically investigated. A desirability function that combined these five response variables was constructed. All response variables investigated were found to be highly dependent on the formulation variables, with strong interactions observed between the formulation variables. It was found that optimum overall desirability of AO microcapsules could be obtained at pH 6.20, gelatin concentration 25.00%, and core/wall ratio 40.40%. The experimental values of the response variables highly agreed with the predicted values. The antioxidation rate of optimum formulation was approximately 8 times higher than that of AO. The in-vitro drug release from microcapsules was followed Higuchi model with super case-II transport mechanism.

  19. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    Science.gov (United States)

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

  20. Simultaneous inversion of multiple land surface parameters from MODIS optical-thermal observations

    Science.gov (United States)

    Ma, Han; Liang, Shunlin; Xiao, Zhiqiang; Shi, Hanyu

    2017-06-01

    Land surface parameters from remote sensing observations are critical in monitoring and modeling of global climate change and biogeochemical cycles. Current methods for estimating land surface variables usually focus on individual parameters separately even from the same satellite observations, resulting in inconsistent products. Moreover, no efforts have been made to generate global products from integrated observations from the optical to Thermal InfraRed (TIR) spectrum. Particularly, Middle InfraRed (MIR) observations have received little attention due to the complexity of the radiometric signal, which contains both reflected and emitted radiation. In this paper, we propose a unified algorithm for simultaneously retrieving six land surface parameters - Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), land surface albedo, Land Surface Emissivity (LSE), Land Surface Temperature (LST), and Upwelling Longwave radiation (LWUP) by exploiting MODIS visible-to-TIR observations. We incorporate a unified physical radiative transfer model into a data assimilation framework. The MODIS visible-to-TIR time series datasets include the daily surface reflectance product and MIR-to-TIR surface radiance, which are atmospherically corrected from the MODIS data using the Moderate Resolution Transmittance program (MODTRAN, ver. 5.0). LAI was first estimated using a data assimilation method that combines MODIS daily reflectance data and a LAI phenology model, and then the LAI was input to the unified radiative transfer model to simulate spectral surface reflectance and surface emissivity for calculating surface broadband albedo and emissivity, and FAPAR. LST was estimated from the MIR-TIR surface radiance data and the simulated emissivity, using an iterative optimization procedure. Lastly, LWUP was estimated using the LST and surface emissivity. The retrieved six parameters were extensively validated across six representative sites with

  1. Fungal species and multiple mycotoxin contamination of cultivated forage crops

    Directory of Open Access Journals (Sweden)

    Galina Kononenko

    2015-12-01

    Full Text Available The quality of grass samples used for animal feed by combining mycotoxin measures and mycological determination of mycobiota were explored. The samples of the plant material were collected in 2014 in two stages: before the first mowing (May–June and before the second one (July–August from the fields of stock-farms located in northwestern part of the Russia. All samples were divided into three types: grasses, mixture of different grasses and clover, alfalfa mixed with timothy. The occurrence of aflatoxin B1, alternariol, citrinin, cyclopiazonic acid, deoxynivalenol, diacetoxyscirpenol, emodin, ergot alkaloids, fumonisins, mycophenolic acid, ochratoxin A, PR-toxin, roridin A, sterigmatocystin, T-2 toxin, and zearalenone were determined using ELISA. The multiple fungal and mycotoxin contaminations are already formed in plant tissues by the moment of first mowing. The complexes of mycotoxins including up to 14–16 components and the combined character of plant contamination quite correspond to the taxonomic variety of mycobiota.

  2. Simultaneous imaging of multiple contrast agents using full-spectrum micro-CT

    Science.gov (United States)

    Clark, D. P.; Touch, M.; Barber, W.; Badea, C. T.

    2015-03-01

    One of the major challenges for in vivo, micro-computed tomography (CT) imaging is poor soft tissue contrast. To increase contrast, exogenous contrast agents can be used as imaging probes. Combining these probes with a photon counting x-ray detector (PCXD) allows energy-sensitive CT and probe material decomposition from a series of images associated with different x-ray energies. We have implemented full-spectrum micro-CT using a PCXD and 2 keV energy sampling. We then decomposed multiple k-edge contrast materials present in an object (iodine, barium, and gadolinium) from water. Since the energy bins were quite narrow, the projection data was very noisy. This noise and further spectral distortions amplify errors in post-reconstruction material decompositions. Here, we propose and demonstrate a novel post-reconstruction denoising scheme which jointly enforces local and global gradient sparsity constraints, improving the contrast-to-noise ratio in full-spectrum micro-CT data and resultant material decompositions. We performed experiments using both calibration phantoms and ex vivo mouse data. Denoising increased the material contrast-to-noise ratio by an average of 13 times relative to filtered backprojection reconstructions. The relative decomposition error after denoising was 21%. To further improve material decomposition accuracy in future work, we also developed a model of the spectral distortions caused by PCXD imaging using known spectra from radioactive isotopes (109Cd, 133Ba). In future work, we plan to combine this model with the proposed denoising algorithm, enabling material decomposition with higher sensitivity and accuracy.

  3. Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species.

    Science.gov (United States)

    Colabella, Claudia; Corte, Laura; Roscini, Luca; Shapaval, Volha; Kohler, Achim; Tafintseva, Valeria; Tascini, Carlo; Cardinali, Gianluigi

    2017-01-01

    The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance

  4. Mini-SNaPshot multiplex assays authenticate elephant ivory and simultaneously identify the species origin.

    Science.gov (United States)

    Kitpipit, Thitika; Thongjued, Kantima; Penchart, Kitichaya; Ouithavon, Kanita; Chotigeat, Wilaiwan

    2017-03-01

    Illegal trading of ivory is mainly responsible for the dramatic decline in elephant populations. Thailand is one of the largest laundering hotspots for African ivory, as the domestic Asian elephant ivory can be legally traded. So, to help combat ivory poaching and smuggling, an efficient method is needed to identify the elephant species from its ivory and ivory products. In this study, a mini-SNaPshot® multiplex assay was developed and fully validated for the identification of confiscated ivory and low DNA template ivory products. Elephantid- and elephant species-specific mitochondrial single nucleotide polymorphisms (SNPs) were identified from 207 mammalian and 1705 elephant/mammoth cytochrome b sequence alignments. Seven informative SNPs were used for assay development. The assay unambiguously and accurately identified authentic elephant ivory and its species of origin on the basis of peak size and color observed in the haplotype profile. The assay was highly efficient for analysis of confiscated ivory and low-template ivory products with a 99.29% success rate (N=140). It was highly reproducible, exhibited no cross-reaction with eight other mammalian DNA; and had 100% identification accuracy. In addition, nested and direct PCR amplification were also compatible with the developed assay. This efficient assay should benefit wildlife forensic laboratories and aid in the prosecution of elephant-related crimes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  5. A method for simultaneously delineating multiple targets in 3D-FISH using limited channels, lasers, and fluorochromes.

    Science.gov (United States)

    Zhao, F Y; Yang, X; Chen, D Y; Ma, W Y; Zheng, J G; Zhang, X M

    2014-01-01

    Many studies have suggested a link between the spatial organization of genomes and fundamental biological processes such as genome reprogramming, gene expression, and differentiation. Multicolor fluorescence in situ hybridization on three-dimensionally preserved nuclei (3D-FISH), in combination with confocal microscopy, has become an effective technique for analyzing 3D genome structure and spatial patterns of defined nucleus targets including entire chromosome territories and single gene loci. This technique usually requires the simultaneous visualization of numerous targets labeled with different colored fluorochromes. Thus, the number of channels and lasers must be sufficient for the commonly used labeling scheme of 3D-FISH, "one probe-one target". However, these channels and lasers are usually restricted by a given microscope system. This paper presents a method for simultaneously delineating multiple targets in 3D-FISH using limited channels, lasers, and fluorochromes. In contrast to other labeling schemes, this method is convenient and simple for multicolor 3D-FISH studies, which may result in widespread adoption of the technique. Lastly, as an application of the method, the nucleus locations of chromosome territory 18/21 and centromere 18/21/13 in normal human lymphocytes were analyzed, which might present evidence of a radial higher order chromatin arrangement.

  6. A new multiple-stage electrocoagulation process on anaerobic digestion effluent to simultaneously reclaim water and clean up biogas.

    Science.gov (United States)

    Liu, Zhiguo; Stromberg, David; Liu, Xuming; Liao, Wei; Liu, Yan

    2015-03-21

    A new multiple-stage treatment process was developed via integrating electrocoagulation with biogas pumping to simultaneously reclaim anaerobic digestion effluent and clean up biogas. The 1st stage of electrocoagulation treatment under the preferred reaction condition led to removal efficiencies of 30%, 81%, 37% and >99.9% for total solids, chemical oxygen demand, total nitrogen and total phosphorus, respectively. Raw biogas was then used as a reactant and pumped into the effluent to simultaneously neutralize pH of the effluent and remove H2S in the biogas. The 2nd stage of electrocoagulation treatment on the neutralized effluent showed that under the selected reaction condition, additional 60% and 10% of turbidity and chemical oxygen demand were further removed. The study concluded a dual-purpose approach for the first time to synergistically combine biogas purification and water reclamation for anaerobic digestion system, which well addresses the downstream challenges of anaerobic digestion technology. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Cocktail-Dosing Microdialysis Study to Simultaneously Assess Delivery of Multiple Organic-Cationic Drugs to the Brain.

    Science.gov (United States)

    Kitamura, Atsushi; Okura, Takashi; Higuchi, Kei; Deguchi, Yoshiharu

    2016-02-01

    Brain microdialysis is a powerful tool to estimate brain-to-plasma unbound concentration ratio at the steady state (Kp,uu) of compounds by direct measurement of the unbound concentration in brain interstitial fluid. Here, we evaluated a method to estimate Kp,uu values of multiple organic-cationic drugs simultaneously, by means of brain microdialysis combined with cocktail dosing. Five cationic drugs (diphenhydramine, memantine, oxycodone, pyrilamine, and tramadol), substrates of the proton-coupled organic cation antiport system, were selected as model drugs, and compared under single-dosing and cocktail-dosing conditions. We selected doses of the drugs at which no significant drug-drug interaction occurs at the proton-coupled organic cation antiport system in the blood-brain barrier (BBB). This was confirmed by uptake studies in hCMEC/D3 cells, an in vitro BBB model. The Kp,uu values after cocktail administration were in the range of 1.8-5.2, and were in good agreement with those after single administration. These results suggest that the microdialysis method with cocktail dosing is suitable to estimate Kp,uu values of several cationic drugs simultaneously, if there is no drug-drug interaction during BBB transport. The method could be useful for evaluating drug candidates with high Kp,uu values at an early stage in the development of central nervous system-acting drugs. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  8. Simultaneous quantification of Myelin Basic Protein and Tau proteins in cerebrospinal fluid and serum of Multiple Sclerosis patients using nanoimmunosensor.

    Science.gov (United States)

    Derkus, Burak; Acar Bozkurt, Pinar; Tulu, Metin; Emregul, Kaan C; Yucesan, Canan; Emregul, Emel

    2017-03-15

    This study was aimed at the development of an immunosensor for the simultaneous quantification of Myelin Basic Protein (MBP) and Tau proteins in cerebrospinal fluid (CSF) and serum, obtained from Multiple Sclerosis (MS) patients. The newly developed GO/pPG/anti-MBP/anti-Tau nanoimmunosensor has been established by immobilization of MBP and Tau antibodies. The newly developed nanoimmunosensor was tested, optimized and characterized using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The developed nanoimmunosensor was seen to have detection limits of 0.30nM for MBP and 0.15nM for Tau proteins which were sufficient for the levels to be analysed in neuro-clinic. The clinical study performed using CSF and serum of MS patients showed that the designed nanoimmunosensor was capable of detecting the proteins properly, that were essentially proven by ELISA. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Ca analysis: An Excel based program for the analysis of intracellular calcium transients including multiple, simultaneous regression analysis☆

    Science.gov (United States)

    Greensmith, David J.

    2014-01-01

    Here I present an Excel based program for the analysis of intracellular Ca transients recorded using fluorescent indicators. The program can perform all the necessary steps which convert recorded raw voltage changes into meaningful physiological information. The program performs two fundamental processes. (1) It can prepare the raw signal by several methods. (2) It can then be used to analyze the prepared data to provide information such as absolute intracellular Ca levels. Also, the rates of change of Ca can be measured using multiple, simultaneous regression analysis. I demonstrate that this program performs equally well as commercially available software, but has numerous advantages, namely creating a simplified, self-contained analysis workflow. PMID:24125908

  10. Ca analysis: an Excel based program for the analysis of intracellular calcium transients including multiple, simultaneous regression analysis.

    Science.gov (United States)

    Greensmith, David J

    2014-01-01

    Here I present an Excel based program for the analysis of intracellular Ca transients recorded using fluorescent indicators. The program can perform all the necessary steps which convert recorded raw voltage changes into meaningful physiological information. The program performs two fundamental processes. (1) It can prepare the raw signal by several methods. (2) It can then be used to analyze the prepared data to provide information such as absolute intracellular Ca levels. Also, the rates of change of Ca can be measured using multiple, simultaneous regression analysis. I demonstrate that this program performs equally well as commercially available software, but has numerous advantages, namely creating a simplified, self-contained analysis workflow. Copyright © 2013 The Author. Published by Elsevier Ireland Ltd.. All rights reserved.

  11. Exploiting off-targeting in guide-RNAs for CRISPR systems for simultaneous editing of multiple genes.

    Science.gov (United States)

    Ferreira, Raphael; Gatto, Francesco; Nielsen, Jens

    2017-10-01

    Bioinformatics tools to design guide-RNAs (gRNAs) in Clustered Regularly Interspaced Short Palindromic Repeats systems mostly focused on minimizing off-targeting to enhance efficacy of genome editing. However, there are circumstances in which off-targeting might be desirable to target multiple genes simultaneously with a single gRNA. We termed these gRNAs as promiscuous gRNAs. Here, we present a computational workflow to identify promiscuous gRNAs that putatively bind to the region of interest for a defined list of genes in a genome. We experimentally validated two promiscuous gRNA for gene deletion, one targeting FAA1 and FAA4 and one targeting PLB1 and PLB2, thus demonstrating that multiplexed genome editing through design of promiscuous gRNA can be performed in a time and cost-effective manner. © 2017 Federation of European Biochemical Societies.

  12. Rapid Simultaneous Mapping of Total and Myelin Water Content, T1 and T2* in Multiple Sclerosis

    CERN Document Server

    Arhelger, Volker; Gliedstein, Detlef; Lafontaine, Marie-Sofie; Tonkova, Vyara; Holz, Dietrich; Böer, Andreas; Schenk, Jochen; Neeb, Heiko; (,; Koblenz, University of Applied Sciences; Koblenz, Radiologisches Institut Hohenzollernstrasse; Engineering, Institute for Medical; Koblenz, Information Processing; Boeer, Neurologie Dr; Koblenz,

    2010-01-01

    Quantitative magnetic resonance imaging might provide a more specific insight into disease process, progression and therapeutic response of multiple sclerosis. We present an extension of a previously published approach for the simultaneous mapping of brain T1, T2* and total water content. In addition to those three parameters, the method presented in the current work allows for the measurement of myelin bound water content, a surrogate marker of tissue myelination. Myelin water was measured based on its distinct relaxation with reduced T2*, resulting in a multiexponential decay signal. However, only 10 points could be acquired on the relaxation curve within a maximum echo time of <40ms as the quantitative protocol has been adapted previously for fast acquisitions with whole brain coverage. The sparse sampling required an adaption of the optimisation approach with additional constraints necessary in order to obtain reliable results. Therefore, the corresponding pool fractions were determined using linear op...

  13. Eight-Color Multiplex Immunohistochemistry for Simultaneous Detection of Multiple Immune Checkpoint Molecules within the Tumor Microenvironment.

    Science.gov (United States)

    Gorris, Mark A J; Halilovic, Altuna; Rabold, Katrin; van Duffelen, Anne; Wickramasinghe, Iresha N; Verweij, Dagmar; Wortel, Inge M N; Textor, Johannes C; de Vries, I Jolanda M; Figdor, Carl G

    2018-01-01

    Therapies targeting immune checkpoint molecules CTLA-4 and PD-1/PD-L1 have advanced the field of cancer immunotherapy. New mAbs targeting different immune checkpoint molecules, such as TIM3, CD27, and OX40, are being developed and tested in clinical trials. To make educated decisions and design new combination treatment strategies, it is vital to learn more about coexpression of both inhibitory and stimulatory immune checkpoints on individual cells within the tumor microenvironment. Recent advances in multiple immunolabeling and multispectral imaging have enabled simultaneous analysis of more than three markers within a single formalin-fixed paraffin-embedded tissue section, with accurate cell discrimination and spatial information. However, multiplex immunohistochemistry with a maximized number of markers presents multiple difficulties. These include the primary Ab concentrations and order within the multiplex panel, which are of major importance for the staining result. In this article, we report on the development, optimization, and application of an eight-color multiplex immunohistochemistry panel, consisting of PD-1, PD-L1, OX40, CD27, TIM3, CD3, a tumor marker, and DAPI. This multiplex panel allows for simultaneous quantification of five different immune checkpoint molecules on individual cells within different tumor types. This analysis revealed major differences in the immune checkpoint expression patterns across tumor types and individual tumor samples. This method could ultimately, by characterizing the tumor microenvironment of patients who have been treated with different immune checkpoint modulators, form the rationale for the design of immune checkpoint-based immunotherapy in the future. Copyright © 2017 by The American Association of Immunologists, Inc.

  14. A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model

    Science.gov (United States)

    Stojowska, Karolina; Krawczyk, Beata

    2014-01-01

    We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s), while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR), whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR). The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal “band-based” results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb) complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3′ recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5′ rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided. PMID:25522278

  15. Conflicting Role of Mycobacterium Species in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Davide Cossu

    2017-05-01

    Full Text Available Mycobacterium is a genus of aerobic and acid-fast bacteria, which include several pathogenic organisms that cause serious diseases in mammals. Previous studies have associated the immune response against mycobacteria with multiple sclerosis (MS, a chronic demyelinating disease of the central nervous system with unknown etiology. The role of mycobacteria in the pathological process has been controversial and often conflicting. We provide a detailed review of the mycobacteria that have been linked to MS over the last three decades, with a focus on Mycobacterium bovis bacille Calmette–Guérin vaccine for human and oral exposure to Mycobacterium avium subsp. paratuberculosis. We will also discuss the exposure and genetic susceptibility to mycobacterial infection, the protective role of vaccination, as well as the possible mechanisms involved in initiating or worsening MS symptoms, with particular emphasis on the molecular mimicry between mycobacterial and human proteins. Finally, we will introduce topics such as heat shock proteins and recognition by innate immunity, and toll-like receptor signaling-mediated responses to Mycobacterium exposure.

  16. Conflicting Role of Mycobacterium Species in Multiple Sclerosis.

    Science.gov (United States)

    Cossu, Davide; Yokoyama, Kazumasa; Hattori, Nobutaka

    2017-01-01

    Mycobacterium is a genus of aerobic and acid-fast bacteria, which include several pathogenic organisms that cause serious diseases in mammals. Previous studies have associated the immune response against mycobacteria with multiple sclerosis (MS), a chronic demyelinating disease of the central nervous system with unknown etiology. The role of mycobacteria in the pathological process has been controversial and often conflicting. We provide a detailed review of the mycobacteria that have been linked to MS over the last three decades, with a focus on Mycobacterium bovis bacille Calmette-Guérin vaccine for human and oral exposure to Mycobacterium avium subsp. paratuberculosis. We will also discuss the exposure and genetic susceptibility to mycobacterial infection, the protective role of vaccination, as well as the possible mechanisms involved in initiating or worsening MS symptoms, with particular emphasis on the molecular mimicry between mycobacterial and human proteins. Finally, we will introduce topics such as heat shock proteins and recognition by innate immunity, and toll-like receptor signaling-mediated responses to Mycobacterium exposure.

  17. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions

    Energy Technology Data Exchange (ETDEWEB)

    Sala, Davide; Giachetti, Andrea; Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it; Rosato, Antonio, E-mail: rosato@cerm.unifi.it [University of Florence, Magnetic Resonance Center (CERM) (Italy)

    2016-11-15

    The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.

  18. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions.

    Science.gov (United States)

    Sala, Davide; Giachetti, Andrea; Luchinat, Claudio; Rosato, Antonio

    2016-11-01

    The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.

  19. Large roads reduce bat activity across multiple species.

    Science.gov (United States)

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.

  20. Large roads reduce bat activity across multiple species.

    Directory of Open Access Journals (Sweden)

    Justin Kitzes

    Full Text Available Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis, big brown bat (Eptesicus fuscus, hoary bat (Lasiurus cinereus, and silver-haired bat (Lasionycteris noctivagans. The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.

  1. Where and how to manage: optimal selection of conservation actions for multiple species

    NARCIS (Netherlands)

    Teeffelen, van A.J.A.; Moilanen, A.

    2008-01-01

    Multiple alternative options are frequently available for the protection, maintenance or restoration of conservation areas. The choice of a particular management action can have large effects on the species occurring in the area, because different actions have different effects on different species.

  2. Simultaneous multiple DWDM channel NRZ-to-RZ regenerative format conversion at 10 and 20 Gb/s.

    Science.gov (United States)

    Yu, Yu; Zhang, Xinliang; Rosas-Fernández, Jose B; Huang, Dexiu; Penty, Richard V; White, Ian H

    2009-03-02

    We propose and demonstrate simultaneous optoelectronic NRZ-to-RZ regenerative format conversion for multiple DWDM channels using a single phase modulator (PM) and a fibre delay-interferometer (DI). In order to accommodate multiple DWDM channels, the DI is designed to have a free spectral range (FSR) equal to the channel spacing. This thus extracts the chirp induced by the phase modulation for all the channels at the same time. Since the original carriers are suppressed to some extent, the NRZ-to-RZ conversions can be achieved with regeneration. Multi-channel format conversion is successfully demonstrated for 16 channels at 10 Gb/s and 8 channels at 20 Gb/s, with a channel spacing of 100 GHz. Bit error ratio (BER) measurements at 10 Gb/s show 3.5 and 4.2 dB penalty improvements for 50 and 75 km transmission without dispersion compensation, respectively. Significant extinction ratio (ER) improvement and timing jitter reduction is observed for the converted channels.

  3. Simultaneous detection of both nitric oxide and reactive oxygen species in guinea pig vestibular sensory cells.

    Science.gov (United States)

    Takumida, Masaya; Anniko, Matti

    2002-01-01

    Gentamicin-induced production of reactive oxygen species (ROS) and of nitric oxide (NO) in the vestibular end organs of the guinea pig was investigated by applying two new fluorescence indicators, 4,5-diaminofluorescein diacetate for direct detection of NO and dihydrotetramethylrosamine for ROS. The vestibular sensory cells produced both NO and ROS after exposure to gentamicin. A nonspecific inhibitor of NO synthase, L-NAME, inhibited the production of NO but did not appear to affect the production of ROS following exposure to gentamicin. In contrast, a radical scavenger, D-methionine, or the neurotrophin BDNF suppressed the production of ROS, in turn stimulating NO production. These findings could indicate that both NO and ROS play an important role in aminoglycoside ototoxicity. Copyright 2002 S. Karger AG, Basel

  4. A PCR-RFLP method for the simultaneous differentiation of three Entamoeba species.

    Science.gov (United States)

    Fontecha, Gustavo A; García, Kimberly; Rueda, María Mercedes; Sosa-Ochoa, Wilfredo; Sánchez, Ana Lourdes; Leiva, Byron

    2015-01-01

    Amoebiasis caused by Entamoeba histolytica continues to be one of the most common parasitic diseases in the developing world. Despite its relevance, due to the lack of accurate diagnostic methods, the true clinical and public health importance of this parasite remains uncertain. The aim of this study was to develop a new diagnostic tool to differentiate E.histolytica from the morphologically undistinguishable E.dispar and E.moshkovskii. We developed a specific, fast and simple PCR-RFLP method that was able to accurately differentiate experimentally-obtained restriction patterns from the three Entamoeba species. This new method could prove useful for clinical and epidemiological purposes. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Molecular evidence for high frequency of multiple paternity in a freshwater shrimp species Caridina ensifera.

    Science.gov (United States)

    Yue, Gen Hua; Chang, Alex

    2010-09-14

    Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve. In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers. Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species.

  6. Integrated optic chemical sensor for the simultaneous detection and quantification of multiple ions. Final report, March--September 1995

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza, E.

    1995-09-01

    This final report summarizes the work performed by Physical Optics Corporation (POC) on the DOE contract entitled {open_quotes}Integrated Optic Chemical Sensor for the Simultaneous Detection and Quantification of Multiple Metal Ions{close_quotes}. This project successfully demonstrated a multi-element integrated optic chemical sensor (IOCS) system capable of simultaneous detection and quantification of metal ions in a water flow stream. POC`s innovative integrated optic chemical sensor technology uses an array of chemically active optical waveguides integrated in parallel in a single small IOCS chip. The IOCS technique uses commonly available materials and straightforward processing to produce channel waveguides in porous glass, each channel treated with a chemical indicator that responds optically to heavy metal ions in a water flow stream. The porosity of the glass allows metal ions present in the water to diffuse into the glass and interact with the immobilized indicators, producing a measurable optical chance. For the {open_quotes}proof-of-concept{close_quotes} demonstration, POC designed and fabricated two types of IOCS chips. Type I uses an array of four straight channel waveguides, three of which are doped with a metal sensitive indicator, an ionophore. The undoped fourth channel is used as the reference channel. Type II uses a 1 x 4 star coupler structure with three sensing channels and a reference channel. Successful implementation of the IOCS technology is expected to have a broad impact on water quality control as well as in the commercial environmental monitoring market. Because of the self-referenced, multidetection capability of the IOCS technique, POC`s water quality sensors are expected to find markets in environmental monitoring and protection, ground water monitoring, and in-line process control. Specific applications include monitoring of chromium, copper, and iron ions in water discharged by the metal plating industry.

  7. Evaluation of Potential Fungal Species for the in situ Simultaneous Saccharification and Fermentation (SSF of Cellulosic Material

    Directory of Open Access Journals (Sweden)

    Leeuwen, J.

    2011-01-01

    Full Text Available Three fungal species were evaluated for their abilities to saccharify pure cellulose. The three species chosen represented three major wood-rot molds; brown rot (Gloeophyllum trabeum, white rot (Phanerochaete chrysosporium and soft rot (Trichoderma reesei. After solid state fermentation of the fungi on the filter paper for four days, the saccharified cellulose was then fermented to ethanol by using Saccharomyces cerevisiae. The efficiency of the fungal species in saccharifying the filter paper was compared against a low dose (25 FPU/g cellulose of a commercial cellulase. Total sugar, cellobiose and glucose were monitored during the fermentation period, along with ethanol, acetic acid and lactic acid. Results indicated that the most efficient fungal species in saccharifying the filter paper was T. reesei with 5.13 g/100 g filter paper of ethanol being produced at days 5, followed by P. chrysosporium at 1.79 g/100 g filter paper. No ethanol was detected for the filter paper treated with G. trabeum throughout the five day fermentation stage. Acetic acid was only produced in the sample treated with T. reesei and the commercial enzyme, with concentration 0.95 and 2.57 g/100 g filter paper, respectively at day 5. Lactic acid production was not detected for all the fungal treated filter paper after day 5. Our study indicated that there is potential in utilizing in situ enzymatic saccharification of biomass by using T. reesei and P. chrysosporium that may lead to an economical simultaneous saccharification and fermentation process for the production of fuel ethanol.

  8. LC-MS method for the simultaneous quantitation of the anti-inflammatory constituents in oregano (Origanum species).

    Science.gov (United States)

    Shen, Diandian; Pan, Min-Hsiung; Wu, Qing-Li; Park, Chung-Heon; Juliani, H Rodolfo; Ho, Chi-Tang; Simon, James E

    2010-06-23

    Oregano (Origanum spp.), a popular herb in western and Middle Eastern cuisine, was reported to show anti-inflammatory activities in vitro and in vivo but without any information as to the compounds responsible, whether the plants were authenticated or only contained true Origanum spp. Using a wide range of botanically authenticated oregano, we were able to show that oregano had anti-inflammatory activity and then using biodirected-guided fractionation, identified the anti-inflammatory agents in oregano as rosmarinic acid, oleanolic acid, and ursolic acid. In this study, we successfully developed an LC-MS (SIM mode) method to achieve coquantitation of these three organic acids with the application of a unique tandem column system. The detection of rosmarinic acid was optimal under negative ion mode of SIM, whereas oleanolic acid and ursolic acid were sensitive to positive ion mode. The simultaneous quantitation was attained by setting two time segments in one run to facilitate the ESI polarity switch. For the investigated analytes romarinic acid, oleanolic acid, and ursolic acid, good linearities (r(2) > 0.999) were obtained for each calibration curve. Validation for this method showed a precision (relative standard deviation) ranging from 4.84 to 6.41%, and the recoveries varied from 92.2 to 100.8% for the three analytes. A quantitative survey of these anti-inflammatory constituents in different oregano species (O. vulgare ssp. hirtum, O. vulgare, and O. syriacum) and chemotypes within the species varied significantly in their accumulation of rosmarinic, oleanolic, and ursolic acids. Significant variation in chemical composition between species and within a species was found.

  9. Simultaneous Determination of Multiple Sesquiterpenes in Curcuma wenyujin Herbal Medicines and Related Products with One Single Reference Standard

    Directory of Open Access Journals (Sweden)

    Zhi-Min Wang

    2013-02-01

    Full Text Available Some Curcuma species are widely used as herbal medicines. Sesquiterpenes are their important bioactive compounds and their quantitative analysis is generally accomplished by gas chromatography (GC or high performance liquid chromatography (HPLC, but the instability and high cost of some sesquiterpene reference standards have limited their application. It is necessary to find a practicable means to control the quality of herbal medicines. Using one stable component contained in Curcuma species to determine multiple analogues should be a practical option. In this study, a simple HPLC method for determination of sesquiterpenes using relative response factors (RRFs has been developed. The easily available and stable active component curdione was selected as the reference compound for calculating the RRFs of the other eight sesquiterpenes, including zedoarondiol (Zedo, isozedoarondiol (Isoz, aerugidiol (Aeru, (4S,5S-(+-germacrone-4,5-epoxide (Epox, curcumenone (Curc, neocurdione (Neoc, germacrone (Germ and furanodiene (Fura. Their RRFs against curdione were between 0.131–1.301, with a good reproducibility. By using the RRFs, the quantification of sesquiterpenes in Curcuma wenyujin herbal medicines and related products was carried out. The method is especially useful for the determination of (4S,5S-(+-germacrone-4,5-epoxide, curcumenone, germacrone and furanodiene, which often are regarded as the principle components in Curcuma species, but unstable when were purified. It is an ideal means to analyze the components for which reference standards are not readily available.

  10. Simultaneous determination of multiple sesquiterpenes in Curcuma wenyujin herbal medicines and related products with one single reference standard.

    Science.gov (United States)

    Zhu, Jing-Jing; An, Yue-Wei; Hu, Guang; Yin, Guo-Ping; Zhang, Qi-Wei; Wang, Zhi-Min

    2013-02-06

    Some Curcuma species are widely used as herbal medicines. Sesquiterpenes are their important bioactive compounds and their quantitative analysis is generally accomplished by gas chromatography (GC) or high performance liquid chromatography (HPLC), but the instability and high cost of some sesquiterpene reference standards have limited their application. It is necessary to find a practicable means to control the quality of herbal medicines. Using one stable component contained in Curcuma species to determine multiple analogues should be a practical option. In this study, a simple HPLC method for determination of sesquiterpenes using relative response factors (RRFs) has been developed. The easily available and stable active component curdione was selected as the reference compound for calculating the RRFs of the other eight sesquiterpenes, including zedoarondiol (Zedo), isozedoarondiol (Isoz), aerugidiol (Aeru), (4S,5S)-(+)-germacrone-4,5-epoxide (Epox), curcumenone (Curc), neocurdione (Neoc), germacrone (Germ) and furanodiene (Fura). Their RRFs against curdione were between 0.131-1.301, with a good reproducibility. By using the RRFs, the quantification of sesquiterpenes in Curcuma wenyujin herbal medicines and related products was carried out. The method is especially useful for the determination of (4S,5S)-(+)-germacrone-4,5-epoxide, curcumenone, germacrone and furanodiene, which often are regarded as the principle components in Curcuma species, but unstable when were purified. It is an ideal means to analyze the components for which reference standards are not readily available.

  11. Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Duchoslav, Eva; Sampaio, Julio

    2006-01-01

    We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragme...... of glycerophospholipids. The automated analysis of total lipid extracts was powered by a robotic nanoflow ion source and produced currently the most detailed description of the glycerophospholipidome....

  12. Simultaneous detection of cow and buffalo species in milk from China, India, and Pakistan using multiplex real-time PCR.

    Science.gov (United States)

    Cottenet, G; Blancpain, C; Golay, P-A

    2011-08-01

    Asian countries are major producers of cow and buffalo milk. For quality and authenticity purposes, a multiplex real-time PCR assay was developed to specifically and simultaneously detect DNA from these 2 bovine species. Targeting the cytochrome b gene of mitochondrial DNA, common PCR primers amplified a 105-bp fragment, and 2 fluorescent probes specific to either cow or buffalo were designed for their identification. Specificity was successfully tested on 6 other species, including sheep and goat, and sensitivity reached 1% of cow DNA in buffalo DNA and vice versa. As an evaluation, the method was tested using 119 freeze-dried Asian milk samples from regional industrial milk facilities. Although these samples did not cover the entire Asian zone, the multiplex assay indicated that approximately 20% of the samples (mainly from India) showed high levels of cross-contamination of cow milk by buffalo milk, and vice versa. Fast, sensitive, and straightforward, this method is fit-for-purpose for the authenticity control of Asian milk. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  13. Three-dimensional reconstruction of tumor microvasculature: simultaneous visualization of multiple components in paraffin-embedded tissue.

    Science.gov (United States)

    Gijtenbeek, J M M; Wesseling, P; Maass, C; Burgers, L; van der Laak, J A W M

    2005-01-01

    Three-dimensional (3D) visualization of microscopic structures may provide useful information about the exact 3D configuration, and offers a useful tool to examine the spatial relationship between different components in tissues. A promising field for 3D investigation is the microvascular architecture in normal and pathological tissue, especially because pathological angiogenesis plays a key role in tumor growth and metastasis formation. This paper describes an improved method for 3D reconstruction of microvessels and other microscopic structures in transmitted light microscopy. Serial tissue sections were stained for the endothelial marker CD34 to highlight microvessels and corresponding images were selected and aligned. Alignment of stored images was further improved by automated non-rigid image registration, and automated segmentation of microvessels was performed. Using this technique, 3D reconstructions were produced of the vasculature of the normal brain. Also, to illustrate the complexity of tumor vasculature, 3D reconstructions of two brain tumors were performed: a hemangioblastoma and a glioblastoma multiforme. The possibility of multiple component visualization was shown in a 3D reconstruction of endothelium and pericytes of normal cerebellar cortex and a hemangioblastoma using alternate staining for CD34 and alpha-smooth muscle actin in serial sections, and of a GBM using immunohistochemical double staining. In conclusion, the described 3D reconstruction procedure provides a promising tool for simultaneous visualization of microscopic structures.

  14. Simultaneous dual-functioning InGaN/GaN multiple-quantum-well diode for transferrable optoelectronics

    Science.gov (United States)

    Shi, Zheng; Yuan, Jialei; Zhang, Shuai; Liu, Yuhuai; Wang, Yongjin

    2017-10-01

    We propose a wafer-level procedure for the fabrication of 1.5-mm-diameter dual functioning InGaN/GaN multiple-quantum-well (MQW) diodes on a GaN-on-silicon platform for transferrable optoelectronics. Nitride semiconductor materials are grown on (111) silicon substrates with intermediate Al-composition step-graded buffer layers, and membrane-type MQW-diode architectures are obtained by a combination of silicon removal and III-nitride film backside thinning. Suspended MQW-diodes are directly transferred from silicon to foreign substrates such as metal, glass and polyethylene terephthalate by mechanically breaking the support beams. The transferred MQW-diodes display strong electroluminescence under current injection and photodetection under light irradiation. Interestingly, they demonstrate a simultaneous light-emitting light-detecting function, endowing the 1.5-mm-diameter MQW-diode with the capability of producing transferrable optoelectronics for adjustable displays, wearable optical sensors, multifunctional energy harvesting, flexible light communication and monolithic photonic circuit.

  15. Polymer nanopillar-gold arrays as surface-enhanced Raman spectroscopy substrate for the simultaneous detection of multiple genes.

    Science.gov (United States)

    Picciolini, Silvia; Mehn, Dora; Morasso, Carlo; Vanna, Renzo; Bedoni, Marzia; Pellacani, Paola; Marchesini, Gerardo; Valsesia, Andrea; Prosperi, Davide; Tresoldi, Cristina; Ciceri, Fabio; Gramatica, Furio

    2014-10-28

    In our study, 2D nanopillar arrays with plasmonic crystal properties are optimized for surface-enhanced Raman spectroscopy (SERS) application and tested in a biochemical assay for the simultaneous detection of multiple genetic leukemia biomarkers. The special fabrication process combining soft lithography and plasma deposition techniques allows tailoring of the structural and chemical parameters of the crystal surfaces. In this way, it has been possible to tune the plasmonic resonance spectral position close to the excitation wavelength of the monochromatic laser light source in order to maximize the enhancing properties of the substrate. Samples are characterized by scanning electron microscopy and reflectance measurements and tested for SERS activity using malachite green. Besides, as the developed substrate had been prepared on a simple glass slide, SERS detection from the support side is also demonstrated. The optimized substrate is functionalized with thiol-modified capture oligonucleotides, and concentration-dependent signal of the target nucleotide is detected in a sandwich assay with labeled gold nanoparticles. Gold nanoparticles functionalized with different DNA and various Raman reporters are applied in a microarray-based assay recognizing a disease biomarker (Wilms tumor gene) and housekeeping gene expressions in the same time on spatially separated microspots. The multiplexing performance of the SERS-based bioassay is illustrated by distinguishing Raman dyes based on their complex spectral fingerprints.

  16. Simultaneous ammonium and nitrate removal by a modified intermittently aerated sequencing batch reactor (SBR with multiple filling events

    Directory of Open Access Journals (Sweden)

    Hajsardar Mehdi

    2016-09-01

    Full Text Available Optimized methods for simultaneous removal of nitrate, nitrite and ammonium are important features of nutrient removal. Nitrogen removal efficiency in an intermittently aerated sequencing batch reactor (IA-SBR with multiple filling events was studied. No external carbon source was added and three filling events were considered. Oxidationreduction potential (ORP and pH curve at solids retention time (SRT of 20 d were analyzed. Effects of three organic loading rates (OLR, 0.67, 1.0 and 1.5 kgCOD/m3d, and three nitrogen loading rates (NLR, 0.054, 0.1 and 0.15 kgN/m3d, on nitrogen removal were studied. Nitrate Apex in pH curve and Nitrate Knee in ORP profile indicated that the end of denitrification would be achieved sooner. The kinetic coefficients of endogenous decay (kd and yield (Y were identified to evaluate heterotrophic specific denitrification rate (SDNRb. In period 2 at NLR of 0.054 kgN/m3d and considering 2 anoxic and 3 aerobic phases, nitrogen removal efficiency was 91.43%.

  17. Simultaneous screening of multiple mutations by invader assay improves molecular diagnosis of hereditary hearing loss: a multicenter study.

    Directory of Open Access Journals (Sweden)

    Shin-ichi Usami

    Full Text Available Although etiological studies have shown genetic disorders to be a common cause of congenital/early-onset sensorineural hearing loss, there have been no detailed multicenter studies based on genetic testing. In the present report, 264 Japanese patients with bilateral sensorineural hearing loss from 33 ENT departments nationwide participated. For these patients, we first applied the Invader assay for screening 47 known mutations of 13 known deafness genes, followed by direct sequencing as necessary. A total of 78 (29.5% subjects had at least one deafness gene mutation. Mutations were more frequently found in the patients with congenital or early-onset hearing loss, i.e., in those with an awareness age of 0-6 years, mutations were significantly higher (41.8% than in patients with an older age of awareness (16.0%. Among the 13 genes, mutations in GJB2 and SLC26A4 were mainly found in congenital or early-onset patients, in contrast with mitochondrial mutations (12S rRNA m.1555A>G, tRNA(Leu(UUR m.3243A>G, which were predominantly found in older-onset patients. The present method of simultaneous screening of multiple deafness mutations by Invader assay followed by direct sequencing will enable us to detect deafness mutations in an efficient and practical manner for clinical use.

  18. Novel set of real-time PCR primers for simultaneous detection of Liberibacter species associated with citrus Huanglongbing

    Directory of Open Access Journals (Sweden)

    Ingrid Georgina Orce

    2015-06-01

    Full Text Available Huanglongbing (HLB, a devastating citrus disease caused by the bacterium “Candidatus Liberibacter spp.”, is now responsible for significant economic losses worldwide. Yet, no effective disease control has been found, and the non-cultivability of the bacterium has severely hampered studies on the pathogen. The 16S rDNA gene is a well-characterized sequence, essential for cell survival, and is used for bacterial identification or assignment of close relationships at the genus and species levels. Quantitative Real-Time PCR (qPCR assays based on 16S rDNA genes are widely used in the detection of “Ca. Liberibacter spp.” in multiplex reactions. We have developed for the first time a set of qPCR primers based on the conserved 16S rDNA gene, which specifically and simultaneously detects in a singleplex reaction, all three bacterial species associated with HLB, and can differentiateCa.Liberibacter asiaticus or africanus from americanus by their characteristic melting curves. The assay is very sensitive, and it was possible to amplify expected DNA fragments with an efficiency of 98 % using the Syber Green system and a Ct value lower than tested methods for HLB diagnosis. The application of this fast, simple and efficient detection methodology could also be important in the detection of all species of HLB-associated Liberibacters and could contribute to early pathogen detection, a crucial step in the development of preventive strategies aimed at avoiding the dissemination of this devastating disease in HLB-free areas.

  19. Simultaneous determination of vasicine and vasicinone by High-performance liquid chromatography in roots of eight Sida species.

    Science.gov (United States)

    Subramanya, M D; Pai, Sandeep R; Ankad, Gireesh M; Hegde, Harsha V; Roy, Subarna; Hoti, S L

    2016-01-01

    Sida L. is a medicinally important genus widely used in conventional systems of medicine in India. The present study aims toward simultaneous determination of two bioactive compounds vasicine and vasicinone in root extracts of eight Sida spp. from Western Ghats, India. Determination of vasicine and vasicinone was undertaken in methanolic root extracts (10% w/v) of Sida acuta, Sida cordata, Sida cordifolia, Sida rhombifolia, Sida spinosa, Sida indica, Sida retusa and Sida mysorensis by high performance liquid chromatography (HPLC) method. The standards were prepared with the concentration of mg/mL. Data were expressed as mean values of three reading and relative standard deviations. The separation was achieved on a Waters, Nova-Pack, C18 (250 mm × 4.6 mm, 5 μ) column, with acetonitrile - 0.1 M phosphate buffer-glacial acetic acid (15: 85: 1, v/v/v) as solvent system at a flow-rate of 1.0 mL/min. The effluent was monitored using ultraviolet detection at a wavelength of 300 nm. Both calibration curves of standard showed good linear regression (R2 > 0.994). The limit of detection and the limit of quantification for vasicine was 0.110 and 0.333 μg/mL and for vasicinone was 0.059 and 0.179 μg/mL respectively. The vasicine content was highest in S. cordifolia (9.891 ± 0.495 μg/100 mg) and vasicinone content was rich in S. cordata (33.013 ± 1.651 μg/100 mg.) The content of vasicinone was higher than vasicine. HPLC method provides simple, accurate, and reproducible quantitative analysis for simultaneous determination of vasicine and vasicinone. Among the selected Sida species, S. cordifolia and S. cordata were found to be rich in the vasicine and vasicinone contents, respectively.

  20. Identification and Management of Multiple Threats to Rare and Endangered Plant Species

    Science.gov (United States)

    2013-07-30

    Benefits: Biodiversity conservation projects should critically consider effects of multiple stressors; however, our results emphasize the...increased invasion of nonnative plant species, and shifts in soil invertebrate and microbial communities (Bohlen et. al., 2004b; Hale et. al., 2005a...native plant invasions Invasion of non-native plants is considered a major threat to native biodiversity ; non-native plants can displace native species

  1. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    Directory of Open Access Journals (Sweden)

    McLeish Michael J

    2012-01-01

    Full Text Available Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

  2. Molecular evidence for high frequency of multiple paternity in a freshwater shrimp species Caridina ensifera.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    Full Text Available BACKGROUND: Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers. CONCLUSIONS/SIGNIFICANCE: Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species.

  3. Simultaneous measurement at multiple depths of in situ rates of denitrification in the bed of a groundwater-fed river

    Science.gov (United States)

    Lansdown, Katrina; Trimmer, Mark; Heppell, Kate

    2010-05-01

    Typically characterised by steep chemical gradients and variable redox conditions, the hyporheic zone is considered a 'hotpot' or site of enhanced biogeochemical activity in the aquatic environment. As such the importance of the hyporheic zone for the attenuation of nutrients such as nitrate in a fluvial network has long been recognised. Controls on nitrogen transformations, however, especially at depths greater than 10cm below the sediment-water interface, remain comparatively less understood. Most work aimed at quantifying denitrification in the hyporheic zone has involved laboratory incubation of recovered sediments which is likely to affect the estimate of the true in situ rate. Results of such studies are usually cited as 'potential' rates of denitrification and have undoubtedly improved the understanding of nitrogen cycling in the aquatic environment. There is, however, a need for in situ measurement to improve our knowledge of nitrogen cycling in the river bed. Here, rates of denitrification in the hyporheic zone have been measured at multiple depths, simultaneously using 'push-pull' methodology (e.g. Snodgrass and Kitanidis 1998). The 'push-pull' technique involves injection of a solution containing reactant(s) (e.g. nitrate) and a conservative tracer (e.g. chloride) into the sediment and extraction of pore water samples over time. Recovered samples are screened for the removal of reactant(s) and/or the accumulation of products(s). Temporal changes in the conservative tracer are used to correct the concentration of the reactant(s) and product(s) for dispersion and advection. The disadvantage of the 'traditional' 'push-pull' methodology is that rates of nitrate removal are measured rather than rates of denitrification. In this research, comparison of measured and 'corrected' nitrate concentrations allowed the rate of nitrate removal (or production) to be quantified. In order to determine in situ rates of denitrification we used 15N-enriched nitrate as the

  4. Multiple approaches for enhancing all-organic electronics photoluminescent sensors: simultaneous oxygen and pH monitoring.

    Science.gov (United States)

    Liu, Rui; Xiao, Teng; Cui, Weipan; Shinar, Joseph; Shinar, Ruth

    2013-05-17

    Key issues in using organic light emitting diodes (OLEDs) as excitation sources in structurally integrated photoluminescence (PL)-based sensors are the low forward light outcoupling, the OLEDs' broad electroluminescence (EL) bands, and the long-lived remnant EL that follows an EL pulse. The outcoupling issue limits the detection sensitivity (S) as only ~20% of the light generated within standard OLEDs can be forward outcoupled and used for sensor probe excitation. The EL broad band interferes with the analyte-sensitive PL, leading to a background that reduces S and dynamic range. In particular, these issues hinder designing compact sensors, potentially miniaturizable, that are devoid of optical filters and couplers. We address these shortcomings by introducing easy-to-employ multiple approaches for outcoupling improvement, PL enhancement, and background EL reduction leading to novel, compact all-organic device architectures demonstrated for simultaneous monitoring of oxygen and pH. The sensor comprises simply-fabricated, directionally-emitting, narrower-band, multicolor microcavity OLED excitation and small molecule- and polymer-based organic photodetectors (OPDs) with a more selective spectral response. Additionally, S and PL intensity for oxygen are enhanced by using polystyrene (PS):polyethylene glycol (PEG) blends as the sensing film matrix. By utilizing higher molecular weight PS, the ratio τ0/τ100 (PL decay time τ at 0% O2/τ at 100% O2) that is often used to express S increases ×1.9 to 20.7 relative to the lower molecular weight PS, where this ratio is 11.0. This increase reduces to ×1.7 when the PEG is added (τ0/τ100=18.2), but the latter results in an increase ×2.7 in the PL intensity. The sensor's response time is <10s in all cases. The microporous structure of these blended films, with PEG decorating PS pores, serves a dual purpose. It results in light scattering that reduces the EL that is waveguided in the substrate of the OLEDs and

  5. A multiplex nanoparticle-based bio-barcoded DNA sensor for the simultaneous detection of multiple pathogens.

    Science.gov (United States)

    Zhang, Deng; Huarng, Michael C; Alocilja, Evangelyn C

    2010-12-15

    A highly amplified, nanoparticle-based, bio-barcoded electrochemical biosensor for the simultaneous multiple detection of the protective antigen A (pagA) gene (accession number, M22589) of Bacillus anthracis and the insertion element (Iel) gene (accession number, Z83734) of Salmonella enteritidis is reported in this paper. The biosensor system is mainly composed of three nanoparticles: gold nanoparticles (AuNPs), magnetic nanoparticles (MNPs), and nanoparticle tracers (NTs, such as PbS and CdS). The AuNPs are coated with the first target-specific DNA probe (1pDNA), which can recognize one end of the target DNA sequence (tDNA), and many NT-terminated bio-barcode ssDNA (bDNA-NT), which act as signal reporter and amplifier. The MNPs are coated with the second target-specific DNA probe (2pDNA) that can recognize the other end of the target gene. After binding the nanoparticles with the target DNA, the following sandwich structure is formed: MNP-2pDNA/tDNA/1pDNA-AuNP-bDNA-NTs. A magnetic field is applied to separate the sandwich structure from the unreacted materials. Because the AuNPs have a large number of nanoparticle tracers per DNA probe binding event, there is substantial amplification. After the nanoparticle tracer is dissolved in 1M nitric acid, the NT(2+) ions are detected by square wave anodic stripping voltammetry (SWASV) on screen-printed carbon electrode (SPCE) chips. The results show that the detection limit of this multiplex bio-barcoded DNA sensor are 0.5 ng/mL of the insertion element (Iel) gene of S. enteritidis using CdS, and 50 pg/mL of the pagA gene of B. anthracis using PbS NTs. The nanoparticle-based bio-barcoded DNA sensor has potential application in rapid detection of multiple pathogenic agents in the same sample. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Genetic components to caste allocation in a multiple-queen ant species

    NARCIS (Netherlands)

    Libbrecht, Romain; Schwander, Tanja; Keller, Laurent

    2011-01-01

    Reproductive division of labor and the coexistence of distinct castes are hallmarks of insect societies. In social insect species with multiple queens per colony, the fitness of nestmate queens directly depends on the process of caste allocation (i.e., the relative investment in queen, sterile

  7. Where and how to manage: Optimal selection of conservation actions for multiple species.

    Directory of Open Access Journals (Sweden)

    Astrid van Teeffelen

    2008-01-01

    Full Text Available Multiple alternative options are frequently available for the protection, maintenance or restoration of conservation areas. The choice of a particular management action can have large effects on the species occurring in the area, because different actions have different effects on different species. Together with the fact that conservation funds are limited and particular management actions are costly, it would be desirable to be able to identify where, and what kind of management should be applied to maximize conservation benefits. Currently available site-selection algorithms can identify the optimal set of sites for a reserve network. However, these algorithms have not been designed to answer what kind of action would be most beneficial at these sites when multiple alternative actions are available. We describe an algorithm capable of solving multi-species planning problems with multiple management options per site. The algorithm is based on benefit functions, which translate the effect of a management action on species representation levels into a value, in order to identify the most beneficial option. We test the performance of this algorithm with simulated data for different types of benefit functions and show that the algorithm’s solutions are optimal, or very near globally optimal, partially depending on the type of benefit function used. The good performance of the proposed algorithm suggests that it could be profitably used for large multi-action multi-species conservation planning problems.

  8. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

    Directory of Open Access Journals (Sweden)

    Rasoloarison Rodin M

    2009-02-01

    Full Text Available Abstract Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2 and three nuclear markers (adora3, fiba and vWF. Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results.

  9. Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe.

    Science.gov (United States)

    Hagenblad, Jenny; Hülskötter, Jennifer; Acharya, Kamal Prasad; Brunet, Jörg; Chabrerie, Olivier; Cousins, Sara A O; Dar, Pervaiz A; Diekmann, Martin; De Frenne, Pieter; Hermy, Martin; Jamoneau, Aurélien; Kolb, Annette; Lemke, Isgard; Plue, Jan; Reshi, Zafar A; Graae, Bente Jessen

    2015-08-20

    Invasive species can be a major threat to native biodiversity and the number of invasive plant species is increasing across the globe. Population genetic studies of invasive species can provide key insights into their invasion history and ensuing evolution, but also for their control. Here we genetically characterise populations of Impatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. We compared populations from the species' native range in Kashmir, India, to those in its invaded range, along a latitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasive species were collated. Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an area outside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations of I. glandulifera is unusually low compared to native populations, in particular when compared to other invasive species. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. We find evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in the native range. I. glandulifera populations with significant inbreeding were only found in the species' native range and invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe we detect cases of migration between distantly located populations. Human activities therefore seem to, at least partially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe. Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges, widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypic plasticity may therefore be an important component of the

  10. Multiple factors contribute to reproductive isolation between two co-existing Habenaria species (Orchidaceae).

    Science.gov (United States)

    Zhang, Wenliu; Gao, Jiangyun

    2017-01-01

    Reproductive isolation is a key feature that forms barriers to gene flow between distinct plants. In orchids, prezygotic reproductive isolation has been considered to be strong, because their associations with highly specific pollinators. In this study, the reproductive ecology and reproductive isolation of two sympatric Habenaria species, H. davidii and H. fordii, was investigated by floral phenology and morphology, hand-pollination experiments and visitor observation in southwest China. The two species were dependent on insects for pollination and completely self-compatible. A number of factors have been identified to limit gene flow between the two species and achieved full reproductive isolation. Ecogeographic isolation was a weak barrier. H. fordii and H. davidii had completely overlapped flowering periods, and floral morphology plays an important role in floral isolation. The two species shared the same hawkmoth pollinator, Cechenena lineosa, but the pollinaria of the two orchids were attached on different body parts of pollinators. Prezygotic isolation was not complete, but the interspecific pollination treatments of each species resulted in no seed sets, indicating that unlike many other orchid species, in which the postzygotic reproductive isolation is very weak or complete absence, the post-zygotic isolation strongly acted in the stage of seed production between two species. The results illustrate the reproductive isolation between two species involves multiple plant life-history stages and a variety of reproductive barriers can contribute to overall isolation.

  11. Multiple factors contribute to reproductive isolation between two co-existing Habenaria species (Orchidaceae.

    Directory of Open Access Journals (Sweden)

    Wenliu Zhang

    Full Text Available Reproductive isolation is a key feature that forms barriers to gene flow between distinct plants. In orchids, prezygotic reproductive isolation has been considered to be strong, because their associations with highly specific pollinators. In this study, the reproductive ecology and reproductive isolation of two sympatric Habenaria species, H. davidii and H. fordii, was investigated by floral phenology and morphology, hand-pollination experiments and visitor observation in southwest China. The two species were dependent on insects for pollination and completely self-compatible. A number of factors have been identified to limit gene flow between the two species and achieved full reproductive isolation. Ecogeographic isolation was a weak barrier. H. fordii and H. davidii had completely overlapped flowering periods, and floral morphology plays an important role in floral isolation. The two species shared the same hawkmoth pollinator, Cechenena lineosa, but the pollinaria of the two orchids were attached on different body parts of pollinators. Prezygotic isolation was not complete, but the interspecific pollination treatments of each species resulted in no seed sets, indicating that unlike many other orchid species, in which the postzygotic reproductive isolation is very weak or complete absence, the post-zygotic isolation strongly acted in the stage of seed production between two species. The results illustrate the reproductive isolation between two species involves multiple plant life-history stages and a variety of reproductive barriers can contribute to overall isolation.

  12. The Sri Lankan torrent toads (Bufonidae: Adenominae: Adenomus): species boundaries assessed using multiple criteria.

    Science.gov (United States)

    Meegaskumbura, Madhava; Senevirathne, Gayani; Wijayathilaka, Nayana; Jayawardena, Beneeta; Bandara, Champika; Manamendra-Arachchi, Kelum; Pethiyagoda, Rohan

    2015-01-19

    The bufonid genus Adenomus, an endemic of the montane and lowland rainforests of central and south-western Sri Lanka, has been considered to comprise of three species, viz. A. kelaartii, A. dasi and A. kandianus, the last of which has been recently highlighted as "the world's rarest toad". We conducted a survey across the known range of Adenomus and used multiple criteria to delineate species boundaries within the genus. These include: a molecular phylogeny based on a 16S ribosomal RNA gene fragment; an examination of the external morphology of adults and larvae, and the skeletal morphology of adults; a bioacoustic analysis; and ecological niche modelling. We show that Adenomus is monophyletic and that it comprises only two species: A. kelaartii and A. kandianus, with A. dasi being a junior synonym of the latter. For the two valid species of Adenomus, we provide detailed osteological descriptions; clarify the distribution patterns; and provide genetic data to facilitate their scientific conservation management. 

  13. Liquid metal ion source and alloy for ion emission of multiple ionic species

    Science.gov (United States)

    Clark, Jr., William M.; Utlaut, Mark W.; Wysocki, Joseph A.; Storms, Edmund K.; Szklarz, Eugene G.; Behrens, Robert G.; Swanson, Lynwood W.; Bell, Anthony E.

    1987-06-02

    A liquid metal ion source and alloy for the simultaneous ion evaporation of arsenic and boron, arsenic and phosphorus, or arsenic, boron and phosphorus. The ionic species to be evaporated are contained in palladium-arsenic-boron and palladium-arsenic-boron-phosphorus alloys. The ion source, including an emitter means such as a needle emitter and a source means such as U-shaped heater element, is preferably constructed of rhenium and tungsten, both of which are readily fabricated. The ion sources emit continuous beams of ions having sufficiently high currents of the desired species to be useful in ion implantation of semiconductor wafers for preparing integrated circuit devices. The sources are stable in operation, experience little corrosion during operation, and have long operating lifetimes.

  14. Primary Multiple Simultaneous Intracerebral Hemorrhages between 1950 and 2013: Analysis of Data on Age, Sex and Outcome

    Directory of Open Access Journals (Sweden)

    Denchai Laiwattana

    2014-05-01

    Full Text Available Background: Primary multiple simultaneous intracerebral hemorrhages (MSICHs are quite rare. Although occasional reports have been found, there have been no systematic reviews. The published case reports and case series contain overlapping data, leading to erroneous information about MSICHs. This is the first extensive review of accessible studies published in English on MSICHs. Our primary objective was to analyze the demographic data on age, sex, outcome and prognosis with regard to primary MSICHs. Summary: A PubMed search without language restriction for articles with results from human studies and registered between January 1950 and September 2013 yielded 677 articles. The following inclusion criteria were applied: (1 reported case(s or case series on primary MSICHs; (2 text partly or fully in English, and (3 text contains identifiable data on age, sex and outcome of patients. A total of 24 articles met all the inclusion criteria. The reference lists of these 24 articles were inspected for additional relevant articles, which yielded another 20 articles. In all, 248 cases were identified; 143 cases were excluded for various reasons: 52 duplicate cases, 18 cases of multiple nonsimultaneous intracerebral hemorrhages, 25 cases of secondary MSICHs, and 48 cases with incomplete data on age, sex and outcome. The remaining 105 cases were analyzed. MSICHs were found to be more common in bilateral cases (53.33%: there were bilateral basal ganglia hemorrhages (33.33%, bilateral thalamic hemorrhages (18.10%, bilateral lobar hemorrhages (0.95% and bilateral cerebellar hemorrhages (0.95%. Nonbilateral MSICHs were found in 46.67% of the cases. The hematomas were commonly distributed in the basal ganglia (45.83%, thalamus (30.56% and cerebellum (10.19%. MSICHs were more frequently encountered in males (60.95%; average age: 59.13 ± 12.49 years. The average age of the female patients was higher (63.89 ± 13.11 years. Patients with primary MSICHs had a

  15. Assessing multiple paternity in three commercially exploited shark species: Mustelus mustelus, Carcharhinus obscurus and Sphyrna lewini.

    Science.gov (United States)

    Rossouw, C; Wintner, S P; Bester-Van Der Merwe, A E

    2016-08-01

    In this study, multiple paternity (MP) was investigated in three commercially important shark species, common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and scalloped hammerhead Sphyrna lewini occurring in southern Africa. Reduced marker panels of between five and six microsatellite loci were constructed for each species and used to genotype and assess the presence of MP in a total of 60 M. mustelus individuals from six litters, 90 C. obscurus individuals from 14 litters and 54 S. lewini individuals from 13 litters. Analysis in GERUD and COLONY revealed the presence of MP in all three species. Multiple paternities were observed in 67, 35 and 46% of the litters of M. mustelus, C. obscurus and S. lewini, with corresponding average sire size of 1·6, 1·4 and 2·0, respectively. The variation in the rate of MP among the three species is in accordance with previous studies whilst the comparatively high frequency of MP observed for M. mustelus, matches what has previously been reported for shark species demonstrating aggregation behaviour. © 2016 The Fisheries Society of the British Isles.

  16. Novel evidence for within-species leaf economics spectrum at multiple spatial scales

    Directory of Open Access Journals (Sweden)

    Yu-Kun eHu

    2015-10-01

    Full Text Available Leaf economics spectrum (LES, characterizing covariation among a suite of leaf traits relevant to carbon and nutrient economics, has been examined largely among species but hardly within species. In addition, very little attempt has been made to examine whether the existence of LES depends on spatial scales. To address these questions, we quantified the variation and covariation of four leaf economic traits (specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus contents in a cosmopolitan wetland species (Phragmites australis at three spatial (inter-regional, regional and site scales across most of the species range in China. The species expressed large intraspecific variation in the leaf economic traits at all of the three spatial scales. It also showed strong covariation among the four leaf economic traits across the species range. The coordination among leaf economic traits resulted in LES at all three scales and the environmental variables determining variation in leaf economic traits were different among the spatial scales. Our results provide novel evidence for within-species LES at multiple spatial scales, indicating that resource trade-off could also constrain intraspecific trait variation mainly driven by climatic and/or edaphic differences.

  17. Influence of multiple ion species on low-frequency electromagnetic wave instabilities. [in solar wind

    Science.gov (United States)

    Brinca, Armando L.; Tsurutani, Bruce T.

    1989-01-01

    The effect of multiple (singly ionized) coexisting newborn ion species on the stability of low-frequency electromagnetic waves was investigated using a plasma model in which solar wind magnetoplasma is made up of isotropic Maxwellian electron and proton populations with a common number density of 4.95/cu cm and temperatures equal to 17.2 eV and 6.9 eV, respectively. It is shown that the effect of multiple ions on wave growth, for given background magnetoplasma conditions and relative densities, depends not only on their mass but also on the physical nature of the wave modes. If the ion masses are disparate, each one of the coexisting ion beams tends to stimulate instabilities without undue influence from the other species. If the masses of newborn ions are similar, they can strongly catalyze wave growth of fluidlike nonresonant modes, but bring about weak growth enhancements in cyclotron resonant instabilities.

  18. Informing Species Conservation at Multiple Scales Using Data Collected for Marine Mammal Stock Assessments

    OpenAIRE

    Alana Grech; James Sheppard; Helene Marsh

    2011-01-01

    BACKGROUND: Conservation planning and the design of marine protected areas (MPAs) requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys con...

  19. Effects of multiple heteroatom species and topographic defects on electrocatalytic and capacitive performances of graphene

    Science.gov (United States)

    Fan, Mengmeng; Huang, Yang; Yuan, Fanshu; Hao, Qingli; Yang, Jiazhi; Sun, Dongping

    2017-10-01

    N-doped graphene has been widely researched as metal-free electrocatalyst and electrode material of energy storage devices but the effect of heteroatom species and topographic defects on these applications was rarely reported. We successfully prepared dual (N, S) or ternary heteroatoms (N, S, P)-doped graphene by simple hydrothermal and then carbonization treatment. Compared to singly N doping, multiple heteroatom species dopant is beneficial to positively move onset potential, approach four electron catalytic pathway in oxygen reduction reaction (ORR) due to the synergistic effect. The emerging topographic defects induced by removing heteroatoms and oxygen at high temperature also act as efficient active sites for positively shifting onset potential. Meanwhile, the porous ternary heteroatoms-doped graphene possesses a good capacitive performance such as high gravimetric capacitance (196.4 Fg-1 at 1 Ag-1), high retained rate (92.7%), 98% retention over 2000 recycling. The excellent capacitive properties derive from large specific surface area (943.5 m2 g-1), mesoporous structure, particularly the important role of abundant dopants of multiple heteroatom species. Therefore, we demonstrated the effect of heteroatom species and topographic defects on electrocatalyzing ORR and capacitive performance.

  20. Multiple species of scuttle flies (Diptera: Phoridae) as contaminants in forensic entomology laboratory insect colony.

    Science.gov (United States)

    Zuha, R M; Jenarthanan, L X Q; Disney, R H L; Omar, B

    2015-09-01

    In forensic entomology, larval rearing usually includes the presence of biological contaminants including scuttle flies (Diptera: Phoridae). Scuttle flies are recognized as forensically important insects and have been reported causing nuisance and contamination in laboratory environments. This paper reports for the first time the finding of multiple scuttle fly species affecting colonies of third instar larvae of the Oriental latrine blowfly, Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae), reared indoors at the Forensic Science Simulation Site, Universiti Kebangsaan Malaysia. Adult scuttle flies were discovered inside a rearing container after the emergence of adult C. megacephala., The scuttle fly species are Megaselia scalaris (Loew), M. spiracularis Schmitz and Puliciphora borinquenensis (Wheeler). Notes on the life history and biology of these species are discussed herein.

  1. Characters with multiple usages- phenotypic variability analysis at Echinacea purpurea (L. Moench species

    Directory of Open Access Journals (Sweden)

    Mihai Radu POP

    2010-11-01

    Full Text Available Merging aesthetics with utility, some medicinal plants can benefit both of a high production and decoration potential. This calls for diversification of improvement directions of the species. Through this article we suggest one of these species, Echinacea purpurea (L. Moench. This is considered to be important at this time, acquisition of new biological forms - varieties in this species, which show multiple attributes utility based on key biological characteristics, agronomic, physiological, biochemical and agrochemical (medicinal, decorative, culinary etc.. To achieve this goal, studies were undertaken, given in this article, which is the starting point for selecting characters representative for our targets.The results presented in this study reveal a pronounced genetic polymorphism showing the selection operation can use the original material for a quantitative and qualitative differentiation of valuable genotypes that could be approved.

  2. Parallel Propagation of Electromagnetic Waves in a Partially Ionized Plasma with Multiple Species

    Science.gov (United States)

    Huang, Y.; Song, P.; Tu, J.

    2016-12-01

    When waves propagate along the magnetic field in a partially ionized plasma with two or more ion species e.g. H+ and O+, such as in the Earth's ionosphere, because of the differences in mass and density, each species responds to the perturbations of electromagnetic fields differently. Furthermore, collisions among the different ions species, between ions and electrons, and between ions and neutrals also affect the wave propagation. With the linear analysis and the assumption of cold plasma, the general dispersion relation of propagation covering all frequencies, from MHD waves to the light propagation, in a medium with arbitrary species of ions, anions and neutrals is derived from the multiple fluids treatment, in combination with Faraday's Law and Ampere's Law including the displacement current. There are several stop bands and characteristic frequencies. For each ion or anion species, there is a resonant frequency at its cyclotron frequency and a cutoff frequency which depends on the mass density of the speciesand and the magnetic field. The waves are strongly damped at the resonant frequencies and become reflective at the cutoff frequencies. With the collisions, the wave propagates slower than the Alfven speed with the frequency below the ion-neutral collision frequency because of an inertia loading process by neutrals. When the collisions are stronger, the resonance is weaker as the cyclotron motion of the ions is disrupted frequently by the collisions. The roles of the collisions played in wave propagation in the stop bands and in wave damping will be discussed.

  3. Improvements and Variants of the Multiple Antigen Blot Assay-MABA: An Immunoenzymatic Technique for Simultaneous Antigen and Antibody Screening.

    Science.gov (United States)

    Noya, Oscar; Losada, Sandra; Toledo, Marilyan; Gauna, Adriana; Lorenzo, María Angelita; Bermúdez, Henry; de Noya, Belkisyolé Alarcón

    2015-01-01

    This simple, versatile, reliable, reproducible, multipurpose, and inexpensive technique is based on the adhesion of different antigens to a single nitrocellulose strip using, as template, an acrylic device containing 28 parallel channels. The inclusion of channels containing normal human serum improves the quality control of this assay. Antigen-sensitized nitrocellulose strips are cut perpendicularly to the antigen-rows, exposed to immune sera followed by the appropriate conjugate. Positive signals are recorded using chemiluminescent or precipitable colorimetric substrates. This assay allows the simultaneous qualitative demonstration of antigenicity and immunogenicity of antigens obtained as synthetic peptides, recombinant molecules, or crude preparations, with high sensitivity and specificity. Its major value is based on the rapid and simultaneous comparative evaluation of various antigenic preparations allowing the diagnosis of a variety of infectious, allergic, and autoimmune diseases. It can in general be used to detect any type of antibody or circulating antigen. Some improvements and variants of the original technique are included.

  4. Multiple vs. single phytoplankton species alter stoichiometry of trophic interaction with zooplankton.

    Science.gov (United States)

    Plum, Christoph; Hüsener, Matthias; Hillebrand, Helmut

    2015-11-01

    Despite the progress made in explaining trophic interactions through the stoichiometric interplay between consumers and resources, it remains unclear how the number of species in a trophic group influences the effects of elemental imbalances in food webs. Therefore, we conducted a laboratory experiment to test the hypothesis that multispecies producer assemblages alter the nutrient dynamics in a pelagic community. Four algal species were reared in mono- and polycultures under a 2 x 2 factorial combination of light and nutrient supply, thereby contrasting the stoichiometry of trophic interactions involving single vs. multiple producer species. After 9 d, these cultures were fed to the calanoid copepod Acartia tonsa, and we monitored biomass, resource use, and C:N:P stoichiometry in both phyto- and zooplankton. According to our expectations, light and N supply resulted in gradients of phytoplankton biomass and nutrient composition (C:N:P). Significant net diversity effects for algal biomass and C:N:P ratios reflected the greater responsiveness of the phytoplankton polyculture to altered resource supply compared to monocultures. These alterations of elemental ratios were common, and were partly triggered by changes in species frequency in the mixtures and partly by diversity-related changes in resource use. Copepod individual biomass increased under high light (HL) and N-reduced (-N) conditions, when food was high in C:N but low in C:P and N:P, whereas copepod growth was obviously P limited, and copepod stoichiometry was not affected by phytoplankton elemental composition. Correspondingly, copepod individual biomass reflected significant net diversity effects: compared to expectations- derived from monocultures, copepod individuals feeding on algal polycultures remained smaller than predicted under HL and N-sufficient (+N) conditions but grew larger than predicted under HL, -N and low light +N conditions. In conclusion, multiple producer species altered the

  5. Simultaneous saccharification and fermentation of hydrothermal pretreated lignocellulosic biomass: evaluation of process performance under multiple stress conditions

    OpenAIRE

    Kelbert, M.; Romaní, Aloia; Coelho, Eduardo; Pereira, L; Teixeira, J. A.; Domingues, Lucília

    2016-01-01

    Industrial lignocellulosic bioethanol processes are exposed to different environmental stresses (such as inhibitor compounds, high temperature, and high solid loadings). In this study, a systematic approach was followed where the liquid and solid fractions were mixed to evaluate the influence of varied solid loadings, and different percentages of liquor were used as liquid fraction to determine inhibitor effect. Ethanol production by simultaneous saccharification and fermentation (SSF) of hyd...

  6. Simultaneous spectrophotometric determination of synthetic dyes in food samples after cloud point extraction using multiple response optimizations.

    Science.gov (United States)

    Heidarizadi, Elham; Tabaraki, Reza

    2016-01-01

    A sensitive cloud point extraction method for simultaneous determination of trace amounts of sunset yellow (SY), allura red (AR) and brilliant blue (BB) by spectrophotometry was developed. Experimental parameters such as Triton X-100 concentration, KCl concentration and initial pH on extraction efficiency of dyes were optimized using response surface methodology (RSM) with a Doehlert design. Experimental data were evaluated by applying RSM integrating a desirability function approach. The optimum condition for extraction efficiency of SY, AR and BB simultaneously were: Triton X-100 concentration 0.0635 mol L(-1), KCl concentration 0.11 mol L(-1) and pH 4 with maximum overall desirability D of 0.95. Correspondingly, the maximum extraction efficiency of SY, AR and BB were 100%, 92.23% and 95.69%, respectively. At optimal conditions, extraction efficiencies were 99.8%, 92.48% and 95.96% for SY, AR and BB, respectively. These values were only 0.2%, 0.25% and 0.27% different from the predicted values, suggesting that the desirability function approach with RSM was a useful technique for simultaneously dye extraction. Linear calibration curves were obtained in the range of 0.02-4 for SY, 0.025-2.5 for AR and 0.02-4 μg mL(-1) for BB under optimum condition. Detection limit based on three times the standard deviation of the blank (3Sb) was 0.009, 0.01 and 0.007 μg mL(-1) (n=10) for SY, AR and BB, respectively. The method was successfully used for the simultaneous determination of the dyes in different food samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. The Application of Multiobjective Genetic Algorithm to the Parameter Optimization of Single-Well Potential Stochastic Resonance Algorithm Aimed at Simultaneous Determination of Multiple Weak Chromatographic Peaks

    Directory of Open Access Journals (Sweden)

    Haishan Deng

    2014-01-01

    Full Text Available Simultaneous determination of multiple weak chromatographic peaks via stochastic resonance algorithm attracts much attention in recent years. However, the optimization of the parameters is complicated and time consuming, although the single-well potential stochastic resonance algorithm (SSRA has already reduced the number of parameters to only one and simplified the process significantly. Even worse, it is often difficult to keep amplified peaks with beautiful peak shape. Therefore, multiobjective genetic algorithm was employed to optimize the parameter of SSRA for multiple optimization objectives (i.e., S/N and peak shape and multiple chromatographic peaks. The applicability of the proposed method was evaluated with an experimental data set of Sudan dyes, and the results showed an excellent quantitative relationship between different concentrations and responses.

  8. The application of multiobjective genetic algorithm to the parameter optimization of single-well potential stochastic resonance algorithm aimed at simultaneous determination of multiple weak chromatographic peaks.

    Science.gov (United States)

    Deng, Haishan; Xie, Shaofei; Xiang, Bingren; Zhan, Ying; Li, Wei; Li, Xiaohua; Jiang, Caiyun; Wu, Xiaohong; Liu, Dan

    2014-01-01

    Simultaneous determination of multiple weak chromatographic peaks via stochastic resonance algorithm attracts much attention in recent years. However, the optimization of the parameters is complicated and time consuming, although the single-well potential stochastic resonance algorithm (SSRA) has already reduced the number of parameters to only one and simplified the process significantly. Even worse, it is often difficult to keep amplified peaks with beautiful peak shape. Therefore, multiobjective genetic algorithm was employed to optimize the parameter of SSRA for multiple optimization objectives (i.e., S/N and peak shape) and multiple chromatographic peaks. The applicability of the proposed method was evaluated with an experimental data set of Sudan dyes, and the results showed an excellent quantitative relationship between different concentrations and responses.

  9. New highland distribution records of multiple Anopheles species in the Ecuadorian Andes

    Directory of Open Access Journals (Sweden)

    Hunter Fiona F

    2011-08-01

    Full Text Available Abstract Background Several recent climate change reviews have stressed the possibility of some malaria vectors occupying regions of higher altitudes than previously recorded. Indeed, highland malaria has been observed in several African nations, possibly attributable to changes in land use, vector control and local climate. This study attempts to expand the current knowledge of the distribution of common Anopheles species in Ecuador, with particular attention to highland regions (> 500 m of the Andes. Methods Extensive field collections of larvae were undertaken in 2008, 2009 and 2010 throughout all regions of Ecuador (except the lower-altitude Amazonian plain and compared to historical distribution maps reproduced from the 1940s. Larvae were identified using both a morphological key and sequencing of the 800 bp region of the CO1 mitochondrial gene. In addition, spatial statistics (Getis-Ord Hotspot Analysis: Gi* were used to determine high and low-density clusters of each species in Ecuador. Results Distributions have been updated for five species of Anopheles in Ecuador: Anopheles albimanus, Anopheles pseudopunctipennis, Anopheles punctimacula, Anopheles eiseni and Anopheles oswaldoi s.l.. Historical maps indicate that An. pseudopunctipennis used to be widespread in highland Andean valleys, while other species were completely restricted to lowland areas. By comparison, updated maps for the other four collected species show higher maximum elevations and/or more widespread distributions in highland regions than previously recorded. Gi* analysis determined some highland hot spots for An. albimanus, but only cold spots for all other species. Conclusions This study documents the establishment of multiple anopheline species in high altitude regions of Ecuador, often in areas where malaria eradication programs are not focused.

  10. A novel system for simultaneous or sequential integration of multiple gene-loading vectors into a defined site of a human artificial chromosome.

    Directory of Open Access Journals (Sweden)

    Teruhiko Suzuki

    Full Text Available Human artificial chromosomes (HACs are gene-delivery vectors suitable for introducing large DNA fragments into mammalian cells. Although a HAC theoretically incorporates multiple gene expression cassettes of unlimited DNA size, its application has been limited because the conventional gene-loading system accepts only one gene-loading vector (GLV into a HAC. We report a novel method for the simultaneous or sequential integration of multiple GLVs into a HAC vector (designated as the SIM system via combined usage of Cre, FLP, Bxb1, and φC31 recombinase/integrase. As a proof of principle, we first attempted simultaneous integration of three GLVs encoding EGFP, Venus, and TdTomato into a gene-loading site of a HAC in CHO cells. These cells successfully expressed all three fluorescent proteins. Furthermore, microcell-mediated transfer of HACs enabled the expression of those fluorescent proteins in recipient cells. We next demonstrated that GLVs could be introduced into a HAC one-by-one via reciprocal usage of recombinase/integrase. Lastly, we introduced a fourth GLV into a HAC after simultaneous integration of three GLVs by FLP-mediated DNA recombination. The SIM system expands the applicability of HAC vectors and is useful for various biomedical studies, including cell reprogramming.

  11. Simultaneous excitation of selective multiple Raman Stokes wavelengths (green-yellow-red) using shaped multi-step pulses from an all-fiber MOPA system

    Science.gov (United States)

    Lin, Dejiao; Alam, Shaif-ul; Teh, Peh Siong; Chen, Kang Kang; Richardson, David J.

    2011-02-01

    We report the simultaneous excitation of multiple Raman Stokes lines in a 250 m long fiber using multi-step pump pulses. The frequency doubled output of a single polarization all-fiber Yb-doped MOPA operating at 1060 nm was used as the pump source. By adjusting the pump power and the pulse profiles we achieved the simultaneous excitation of green (1st Stokes), yellow (4th Stokes) and red light (6th Stokes) using 3-step pulses or the combination of any two using 2-step pulses. Through the use of pulse shaping we generate sequences of colored pulses with the flexibility of providing dynamic, agile frequency tuning between well-defined wavelengths.

  12. Extension of the Viscous Collision Limiting Direct Simulation Monte Carlo Technique to Multiple Species

    Science.gov (United States)

    Liechty, Derek S.; Burt, Jonathan M.

    2016-01-01

    There are many flows fields that span a wide range of length scales where regions of both rarefied and continuum flow exist and neither direct simulation Monte Carlo (DSMC) nor computational fluid dynamics (CFD) provide the appropriate solution everywhere. Recently, a new viscous collision limited (VCL) DSMC technique was proposed to incorporate effects of physical diffusion into collision limiter calculations to make the low Knudsen number regime normally limited to CFD more tractable for an all-particle technique. This original work had been derived for a single species gas. The current work extends the VCL-DSMC technique to gases with multiple species. Similar derivations were performed to equate numerical and physical transport coefficients. However, a more rigorous treatment of determining the mixture viscosity is applied. In the original work, consideration was given to internal energy non-equilibrium, and this is also extended in the current work to chemical non-equilibrium.

  13. Forelimb preferences in human beings and other species: multiple models for testing hypotheses on lateralization

    Directory of Open Access Journals (Sweden)

    Elisabetta eVersace

    2015-03-01

    Full Text Available Consistent preferences in the use of right/left forelimbs are not exclusively present in humans. Functional asymmetries in forelimb use have been widely documented in a variety of vertebrate and invertebrate species. A matter of debate is whether non-human species exhibit a degree and consistency of functional forelimb asymmetries comparable to human handedness. The comparison is made difficult by the variability in hand use in humans and the few comparable studies conducted on other species. In spite of this, interesting continuities appear in functions such as feeding, object manipulation and communicative gestures. Studies on invertebrates show how widespread forelimb preferences are among animals, and the importance of experience for the development of forelimb asymmetries. Vertebrate species have been extensively investigated to clarify the origins of forelimb functional asymmetries: comparative evidence shows that selective pressures for different functions have likely driven the evolution of human handedness. Evidence of a complex genetic architecture of human handedness is in line with the idea of multiple evolutionary origins of this trait.

  14. A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

    Science.gov (United States)

    Matsushita, Tadashi; Arakawa, Etsuo; Voegeli, Wolfgang; Yano, Yohko F.

    2013-01-01

    An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed. PMID:23254659

  15. Simultaneous determination of arsenic and mercury species in rice by ion-pairing reversed phase chromatography with inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Fang, Yong; Pan, Yushi; Li, Peng; Xue, Mei; Pei, Fei; Yang, Wenjian; Ma, Ning; Hu, Qiuhui

    2016-12-15

    An analytical method using reversed phase chromatography-inductively coupled plasma mass spectrometry for arsenic and mercury speciation analysis was described. The effect of ion-pairing reagent on simultaneous separation of four arsenic (arsenite, arsenate, monomethlyarsonate and dimethylarsinate) and three mercury species (inorganic mercury (Hg(II)), methylmecury and ethylmercury) was investigated. Parameters including concentrations and pH of the mobile phase were optimized. The separation and re-equilibration time was attained within 20min. Meanwhile, a sequential extraction method for arsenic and mercury in rice was tested. Subsequently, 1% HNO3 microwave-assisted extraction was chosen. Calibration curves based on peak area measurements were linear with correlation coefficient greater than 0.9958 for each species in the range studied. The detection limits of the species were in the range of 0.84-2.41μg/L for arsenic and 0.01-0.04μg/L for mercury, respectively. The proposed method was then successfully applied for the simultaneous determination of arsenic and mercury species in rice flour standard material and two kinds of rice from local markets. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. CRISPR/Cas9 : A molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Mans, R.; Van Rossum, H.M.; Wijsman, M.; Backx, A.; Kuijpers, N.G.A.; van den Broek, M.; Daran-Lapujade, P.A.S.; Pronk, J.T.; Van Maris, A.J.A.; Daran, J.G.

    2015-01-01

    A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast

  17. Exploiting off-targeting in guide-RNAs for CRISPR systems for simultaneous editing of multiple genes

    DEFF Research Database (Denmark)

    Ferreira, Raphael; Gatto, Francesco; Nielsen, Jens

    2017-01-01

    Bioinformatics tools to design guide-RNAs (gRNAs) in Clustered Regularly Interspaced Short Palindromic Repeats systems mostly focused on minimizing off-targeting to enhance efficacy of genome editing. However, there are circumstances in which off-targeting might be desirable to target multiple ge...

  18. Interactions among invaders: community and ecosystem effects of multiple invasive species in an experimental aquatic system.

    Science.gov (United States)

    Johnson, Pieter T J; Olden, Julian D; Solomon, Christopher T; Vander Zanden, M Jake

    2009-02-01

    With ecosystems increasingly supporting multiple invasive species, interactions among invaders could magnify or ameliorate the undesired consequences for native communities and ecosystems. We evaluated the individual and combined effects of rusty crayfish (Orconectes rusticus) and Chinese mystery snails [Bellamya (=Cipangopaludina) chinensis] on native snail communities (Physa, Helisoma and Lymnaea sp.) and ecosystem attributes (algal chlorophyll a and nutrient concentrations). Both invaders are widespread in the USA and commonly co-occur within northern temperate lakes, underscoring the importance of understanding their singular and joint effects. An outdoor mesocosm experiment revealed that while the two invaders had only weakly negative effects upon one another, both negatively affected the abundance and biomass of native snails, and their combined presence drove one native species to extinction and reduced a second by >95%. Owing to its larger size and thicker shell, adult Bellamya were protected from crayfish attack relative to native species (especially Physa and Lymnaea), suggesting the co-occurrence of these invaders in nature could have elevated consequences for native communities. The per capita impacts of Orconectes (a snail predator) on native snails were substantially greater than those of Bellamya (a snail competitor). Crayfish predation also had a cascading effect by reducing native snail biomass, leading to increased periphyton growth. Bellamya, in contrast, reduced periphyton biomass, likely causing a reduction in growth by native lymnaeid snails. Bellamya also increased water column N:P ratio, possibly because of a low P excretion rate relative to native snail species. Together, these findings highlight the importance of understanding interactions among invasive species, which can have significant community- and ecosystem-level effects.

  19. Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions.

    Directory of Open Access Journals (Sweden)

    Mohamed B F Hawash

    Full Text Available The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found in primates.We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes of Trichuris recovered from a human and a porcine host in China and from a françois' leaf-monkey (China were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from Trichuris from françois' leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related.Our results indicate that Trichuris species infecting humans and pigs are phylogenetically distinct across geographical regions, which might have important implications for the implementation of suitable and effective control strategies in different regions. Moreover, we provide support for the hypothesis that Trichuris infecting primates represents a complex of cryptic species with some species being able to infect both humans and non-human primates.

  20. Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

    Directory of Open Access Journals (Sweden)

    Bruce Warburton

    Full Text Available Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula, stoats (Mustela ermine, and ship rats (Rattus rattus are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha, 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several

  1. Multiple Alternaria species groups are associated with leaf blotch and fruit spot diseases of apple in Australia

    National Research Council Canada - National Science Library

    Harteveld, D. O. C; Akinsanmi, O. A; Drenth, A

    2013-01-01

    ... blotch and fruit spot of apples were identified. Sequences of Alternaria allergen a1 and endopolygalacturonase gene regions revealed that multiple Alternaria species groups are associated with both diseases...

  2. Multiple dispersal vectors drive range expansion in an invasive marine species.

    Science.gov (United States)

    Richardson, Mark F; Sherman, Craig D H; Lee, Randall S; Bott, Nathan J; Hirst, Alastair J

    2016-10-01

    The establishment and subsequent spread of invasive species is widely recognized as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, environmental DNA (eDNA) plankton sampling and hydrodynamic modelling, we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow, a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast, hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems. © 2016 John Wiley & Sons Ltd.

  3. Basic relationships in electronegative plasmas with a multiplicity of negative and positive ion species

    CERN Document Server

    Franklin, R N

    2003-01-01

    Recent simulations by So et al (2002 J. Phys. D 35 2978-87) have shown inter alia that in CF sub 4 where there are two negative ions of comparable density, the plasma is structured, in that there are essentially three regions so far as the negative ions are concerned. In the inner region one negative ion species is concentrated, in the outer region electrons dominate over negative ions, while the intermediate has only one species of negative ion. This confirms earlier work (Franklin R N 2002a J. Phys. D: Appl. Phys. 35 536-42; 2002b J. Phys. D: Appl. Phys. 35 747-50) and justifies extending that work to cover situations where there is a multiplicity of both positive and negative ions. In this paper we give explicit results for the central electronegativities and electropositivities for the case of two species of ion of each sign, and also determine the relative sizes of the regions occupied by the negative ions. By effectively varying the electron temperature through the ionization rate, we indicate how these...

  4. A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini).

    Science.gov (United States)

    Hendrich, Lars; Balke, Michael

    2011-02-03

    Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species' taxonomy and biology. The diving beetle Neobidessodes darwiniensissp. n. (Coleoptera: Dytiscidae, Bidessini) is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea.

  5. A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini

    Directory of Open Access Journals (Sweden)

    Lars Hendrich

    2011-02-01

    Full Text Available Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species'  taxonomy and biology. The diving beetle Neobidessodes darwiniensis sp. n. (Coleoptera, Dytiscidae, Bidessini is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea.

  6. Development of a multiple detection technique for fungi by DNA microarray with the simultaneous use of internal transcribed spacer region of ribosomal RNA gene and β-tubulin gene probes.

    Science.gov (United States)

    Isshiki, Atsunori; Takeharu, Hitoshi; Aoki, Shunsuke; Kokaji, Mami; Tanabe, Suguru; Kasetani, Taisuke; Yoshida, Mitsuhiro

    2014-01-01

    We offer the first description of the development of a multiple detection technique for fungi by DNA microarray with the simultaneous use of internal transcribed spacer region (ITS) of ribosomal RNA gene and β-tubulin gene probes. The assay uses 12 oligonucleotide probes and multiplex amplification to detect fungal species belonging to various sections of Aspergillus, the Eurotium genus, and the Penicillium genus. The specificity of each probe was tested using 231 reference fungal strains, including 79 target and 152 non-target strains in 102 species of 24 genera. We determined the optimum concentration of the primer pairs for multiplex PCR to be 0.5 μM for the β-tubulin gene and 0.125 μM for the ITS region. In the field trial using 76 specimens containing 323 fungi (up to five fungal strains were included in one specimen), the concordance rate between the DNA microarray and the DNA sequencing results was 97.4% at the species or genus levels.

  7. Multiple resource limitation: Non-equilibrium coexistence of species in a competition model using a synthesizing unit.

    NARCIS (Netherlands)

    Dutta, P.S.; Kooi, B.W.; Feudel, U.

    2014-01-01

    During the last two decades, the simple view of resource limitation by a single resource has been changed due to the realization that co-limitation by multiple resources is often an important determinant of species growth. Hence, the multiple resource limitation hypothesis needs to be taken into

  8. Optimization of Micellar Electrokinetic Chromatography Method for the Simultaneous Determination of Seven Hydrophilic and Four Lipophilic Bioactive Components in Three Salvia Species.

    Science.gov (United States)

    Cao, Jiliang; Hu, Ji; Wei, Jinchao; Li, Baocai; Zhang, Mi; Xiang, Cheng; Li, Peng

    2015-08-21

    A micellar electrokinetic chromatography (MEKC) method was developed for the simultaneous determination of seven hydrophilic phenolic acids and four lipophilic tanshinones in three Salvia species. In normal MEKC mode using SDS as surfactant, the investigated 11 compounds could not be well separated. Therefore, several buffer modifiers including β-cyclodextrins (β-CD), ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]BF4) and organic solvents have been added to the buffer solution to improve the separation selectivity. Under the optimized conditions (BGE, 15 mM sodium tetraborate with 10 mM SDS, 5 mM β-CD, 10 mM [bmim]BF4 and 15% ACN (v/v) as additives; buffer pH, 9.8; voltage, 20 kV; temperature, 25 °C), the 11 investigated analytes could achieve baseline separation in 34 min. The proposed MEKC was additionally validated by evaluating the linearity (R(2) ≥ 0.9965), LODs (0.27-1.39 μg·mL(-1)), and recovery (94.26%-105.17%), demonstrating this method was reproducible, accurate and reliable. Moreover, the contents of the 11 compounds in three Salvia species, including S. miltiorrhiza, S. przewalskii and S. castanea were analyzed. The result showed that the established MEKC method was simple and practical for the simultaneous determination of the hydrophilic and lipophilic bioactive components in Salvia species, which could be used to effectively evaluate the quality of these valued medicinal plants.

  9. Simultaneous application of multiple platforms (Glider, Scanfish, profiling mooring, CTD) to improve detection and quantification of temporal ocean dynamics

    Science.gov (United States)

    Meyer, D.; Prien, R. D.; Lips, U.; Naumann, M.; Liblik, T.; Schulz-Bull, D. E.

    2016-02-01

    Ocean dynamics are difficult to observe given the broad spectrum of temporal and spatial scales. Robotic technology can be used to address this issue, and help to investigate the variability of physical and biogeochemical processes. This work focuses on ocean robots and in particular on glider technology which seems to be one of the most promising oceanographic tools for future marine research. In this context, we present the results of an observational program conducted in the Baltic Sea combining a profiling mooring (GODESS - Gotland Deep Environmental Sampling Station) and glider technology (Slocum). The temporal variability is captured by the mooring, while the spatial variability is obtained from the glider sampling the surrounding area. Furthermore, classical CTD-measurements and an underwater vehicle (Scanfish) are used simultaneously by two different research vessels to validate and complement the observing network. The main aim of the study is to identify possible synergies between the different platforms and to get a better understanding of maximizing the information content of the data collected by this network. The value and the quality of the data of each individual platform is analyzed and their contribution to the performance of the network itself evaluated.

  10. A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

    Science.gov (United States)

    Chen, Jing; Xu, Huimin; He, Ping-An; Dai, Qi; Yao, Yuhua

    2016-01-01

    Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based. The original and consensus sequences were combined with physicochemical properties. And elements information of different rows and columns in position-specific scoring matrix were taken into consideration simultaneously for more core and essence information. Computational methods based on gene ontology (GO) have been demonstrated to be superior to methods based on other features. Then principal component analysis (PCA) is applied for feature selection and reduced vectors are input to a support vector machine (SVM) to predict protein subcellular localization. The proposed method can achieve a prediction accuracy of 98.28% and 97.87% on a stringent Gram-positive (Gpos) and Gram-negative (Gneg) dataset with Jackknife test, respectively. At last, we calculate "absolute true overall accuracy (ATOA)", which is stricter than overall accuracy. The ATOA obtained from the proposed method is also up to 97.32% and 93.06% for Gpos and Gneg. From both the rationality of testing procedure and the success rates of test results, the current method can improve the prediction quality of protein subcellular localization. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  11. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

    Directory of Open Access Journals (Sweden)

    Aron J Fazekas

    Full Text Available A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s. We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples. The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA to 59% (trnH-psbA of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci, with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs. Several loci (matK, psbK-psbI, trnH-psbA were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations. This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the

  12. Comparison of grouper infection with two different iridoviruses using transcriptome sequencing and multiple reference species selection.

    Science.gov (United States)

    Liu, Chun-Cheng; Ho, Li-Ping; Yang, Cin-Hang; Kao, Tsung-Yu; Chou, Hsin-Yiu; Pai, Tun-Wen

    2017-12-01

    Due to high-density aquafarming in Taiwan, groupers are commonly infected with two different iridoviruses: Megalocytivirus (grouper iridovirus of Taiwan, TGIV) and Ranavirus (grouper iridovirus, GIV). Iridoviral diseases cause mass mortality, and surviving fish retain these pathogens, which can then be horizontally transferred. These viruses have therefore become a major challenge for grouper aquaculture. In this study, comparisons of the biological responses of groupers to infection with these two different iridoviruses were performed. A novel approach for transcriptomic analysis was proposed to enhance the discovery of differentially expressed genes and associated biological pathways. In this method, suitable and available reference species are selected from the NCBI taxonomy tree and the Ensembl and KEGG databases instead of either choosing only one model species or adopting the NCBI non-redundant dataset as references. Our results show that selection of multiple appropriate model species as references increases the efficiency and performance of analyses compared to those of traditional approaches. Using this method, 17 shared pathways and 5 specific pathways were found to be significantly differentially expressed following infection with the two iridoviruses, among which 11 pathways were additionally identified based on the proposed method of multiple reference species selection. Among the pathways responsive to infection with a specific iridovirus, the spliceosomal pathway (ko03040; p-value = 0.0011) was exclusively associated with TGIV infection, while the glycolysis/gluconeogenesis pathway (ko00010; p-value = 0.0032) was associated with GIV infection. These findings and designed corresponding biological experiments may facilitate a deeper understanding of the mechanisms by which both TGIV and GIV cause fatal infections, as well as the ways in which they induce different pathologies and symptoms. We believe that the proposed novel mechanism for de novo

  13. Reconstructing Water Column Hydrography Using Individual Shell Stable Isotope Data From Multiple Planktic Foraminifera Species

    Science.gov (United States)

    Spero, H. J.; Fehrenbacher, J. S.; Davis, K. V.; Griffin, J. M.; Grimm, B. L.; Kercher, P.; Kostlan, M.; Menicucci, A. J.; Santare, L.; Starnes, J.; Vetter, L.; Wilbanks, E.; Wildgoose, M.

    2012-12-01

    Oxygen and carbon isotope data from planktic foraminifera play an important role in reconstructing past ocean temperatures, salinity and nutrient content since they first appeared in a publication by Cesare Emiliani in 1955. For most of the next 5 decades, research focused on analyses of foraminifera shells from a few mixed layer and thermocline species. Such analyses have typically been conducted on multiple shell samples from an assemblage of foraminifera, pooled into a single analysis. It has long been recognized that significant depth-specific and seasonal information is contained within populations of shells and that analyses of single specimens and some underutilized species could provide novel information about water column processes and hydrography. Nevertheless, it has only been in the past decade that researchers have begun to explore this individual-shell multispecies paleoenvironmental archive for paleoceanographic applications. As a result of experiments with living foraminifera, our understanding of the mechanisms that contribute to the vital effect black box that governs inter- and intraspecific geochemical variability in foraminifera has attained a level of maturity that now allows us to reconcile foraminifera biology and ecology with the geochemical signals obtained from marine sediments. Within this context, we present individual shell carbon and oxygen isotope data from 11 species of planktonic foraminifera (G. ruber (pink & white var.), G. sacculifer, O. universa, G. siphonifera, S. dehiscens, G. conglobatus, G. menardii, N. dutertrei, P. obliquiloculata, G. truncatulinoides and G. tumida). We use these data to reconstruct late Holocene water column hydrography from cores in the Caribbean (ODP 999A; 12°45'N, 78°25'W; 2,827 m) and eastern equatorial Pacific (TR163-19; 2°16'N, 90°57'W, 2348 m). We show that interpretation of such complex data sets requires consideration of biological and environmental controls such as symbiont photosynthesis

  14. A simplified and versatile system for the simultaneous expression of multiple siRNAs in mammalian cells using Gibson DNA Assembly.

    Science.gov (United States)

    Deng, Fang; Chen, Xiang; Liao, Zhan; Yan, Zhengjian; Wang, Zhongliang; Deng, Youlin; Zhang, Qian; Zhang, Zhonglin; Ye, Jixing; Qiao, Min; Li, Ruifang; Denduluri, Sahitya; Wang, Jing; Wei, Qiang; Li, Melissa; Geng, Nisha; Zhao, Lianggong; Zhou, Guolin; Zhang, Penghui; Luu, Hue H; Haydon, Rex C; Reid, Russell R; Yang, Tian; He, Tong-Chuan

    2014-01-01

    RNA interference (RNAi) denotes sequence-specific mRNA degradation induced by short interfering double-stranded RNA (siRNA) and has become a revolutionary tool for functional annotation of mammalian genes, as well as for development of novel therapeutics. The practical applications of RNAi are usually achieved by expressing short hairpin RNAs (shRNAs) or siRNAs in cells. However, a major technical challenge is to simultaneously express multiple siRNAs to silence one or more genes. We previously developed pSOS system, in which siRNA duplexes are made from oligo templates driven by opposing U6 and H1 promoters. While effective, it is not equipped to express multiple siRNAs in a single vector. Gibson DNA Assembly (GDA) is an in vitro recombination system that has the capacity to assemble multiple overlapping DNA molecules in a single isothermal step. Here, we developed a GDA-based pSOK assembly system for constructing single vectors that express multiple siRNA sites. The assembly fragments were generated by PCR amplifications from the U6-H1 template vector pB2B. GDA assembly specificity was conferred by the overlapping unique siRNA sequences of insert fragments. To prove the technical feasibility, we constructed pSOK vectors that contain four siRNA sites and three siRNA sites targeting human and mouse β-catenin, respectively. The assembly reactions were efficient, and candidate clones were readily identified by PCR screening. Multiple β-catenin siRNAs effectively silenced endogenous β-catenin expression, inhibited Wnt3A-induced β-catenin/Tcf4 reporter activity and expression of Wnt/β-catenin downstream genes. Silencing β-catenin in mesenchymal stem cells inhibited Wnt3A-induced early osteogenic differentiation and significantly diminished synergistic osteogenic activity between BMP9 and Wnt3A in vitro and in vivo. These findings demonstrate that the GDA-based pSOK system has been proven simplistic, effective and versatile for simultaneous expression of multiple

  15. Micropatterned superhydrophobic structures for the simultaneous culture of multiple cell types and the study of cell-cell communication.

    Science.gov (United States)

    Efremov, Alexander N; Stanganello, Eliana; Welle, Alexander; Scholpp, Steffen; Levkin, Pavel A

    2013-02-01

    The ability to control spatial arrangement and geometry of different cell types while keeping them separated and in close proximity for a long time is crucial to mimic and study variety of biological processes in vitro. Although the existing cell patterning technologies allow co-culturing of different cell types, they are usually limited to relatively simple geometry. The methods used for obtaining complex geometries are usually applicable for patterning only one or two cell types. Here we introduce a convenient method for creating patterns of multiple (up to twenty) different cell types on one substrate. The method virtually allows any complexity of cell pattern geometry. Cell positioning on the substrate is realized by a parallel formation of multiple cell-containing microreservoirs confined to the geometry of highly hydrophilic regions surrounded by superhydrophobic borders built-in a fine nanoporous polymer film. As a case study we showed the cross-talk between two cell populations via Wnt signaling molecules propagation during co-culture in a mutual culture medium. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Multiplexed continuous-wave diode-laser cavity ringdown measurements of multiple species

    Science.gov (United States)

    Totschnig, Gerhard; Baer, Douglas S.; Wang, Jian; Winter, Franz; Hofbauer, Hermann; Hanson, Ronald K.

    2000-04-01

    Rapid cavity ringdown measurements of multiple broadband absorbing species (methanol and isopropanol) in gas mixtures have been recorded with two multiplexed continuous-wave distributed-feedback diode lasers operating near 1.4 m. A measurement sensitivity of 2.4 10 9 cm 1 for a 4.3-s averaging time was achieved in a 39.5-cm-long static cell with 99.94% reflectivity mirrors. This corresponds to a water-vapor detection limit of less than 2 ppb (parts in 10 9 ) for the strong H 2 O lines near 1.4 m. The shot-to-shot noise of the decay time constant was approximately 0.3 0.7%, and ringdown acquisition rates as great as 900 Hz were achieved.

  17. Informing species conservation at multiple scales using data collected for marine mammal stock assessments.

    Directory of Open Access Journals (Sweden)

    Alana Grech

    Full Text Available BACKGROUND: Conservation planning and the design of marine protected areas (MPAs requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys conducted to inform mandatory stock assessments. METHODOLOGY AND RESULTS: We use a 20-year time series of systematic aerial surveys of dugong (Dugong dugong abundance to create spatially-explicit models of dugong distribution and relative density at the scale of the coastal waters of northeast Australia (∼136,000 km(2. We interpolated the corrected data at the scale of 2 km * 2 km planning units using geostatistics. Planning units were classified as low, medium, high and very high dugong density on the basis of the relative density of dugongs estimated from the models and a frequency analysis. Torres Strait was identified as the most significant dugong habitat in northeast Australia and the most globally significant habitat known for any member of the Order Sirenia. The models are used by local, State and Federal agencies to inform management decisions related to the Indigenous harvest of dugongs, gill-net fisheries and Australia's National Representative System of Marine Protected Areas. CONCLUSION/SIGNIFICANCE: In this paper we demonstrate that spatially-explicit population models add value to data collected for stock assessments, provide a robust alternative to predictive habitat distribution models, and inform species conservation at multiple scales.

  18. Informing species conservation at multiple scales using data collected for marine mammal stock assessments.

    Science.gov (United States)

    Grech, Alana; Sheppard, James; Marsh, Helene

    2011-03-28

    Conservation planning and the design of marine protected areas (MPAs) requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys conducted to inform mandatory stock assessments. We use a 20-year time series of systematic aerial surveys of dugong (Dugong dugong) abundance to create spatially-explicit models of dugong distribution and relative density at the scale of the coastal waters of northeast Australia (∼136,000 km(2)). We interpolated the corrected data at the scale of 2 km * 2 km planning units using geostatistics. Planning units were classified as low, medium, high and very high dugong density on the basis of the relative density of dugongs estimated from the models and a frequency analysis. Torres Strait was identified as the most significant dugong habitat in northeast Australia and the most globally significant habitat known for any member of the Order Sirenia. The models are used by local, State and Federal agencies to inform management decisions related to the Indigenous harvest of dugongs, gill-net fisheries and Australia's National Representative System of Marine Protected Areas. In this paper we demonstrate that spatially-explicit population models add value to data collected for stock assessments, provide a robust alternative to predictive habitat distribution models, and inform species conservation at multiple scales.

  19. Invasive species information networks: Collaboration at multiple scales for prevention, early detection, and rapid response to invasive alien species

    Science.gov (United States)

    Simpson, Annie; Jarnevich, Catherine S.; Madsen, John; Westbrooks, Randy G.; Fournier, Christine; Mehrhoff, Les; Browne, Michael; Graham, Jim; Sellers, Elizabeth A.

    2009-01-01

    Accurate analysis of present distributions and effective modeling of future distributions of invasive alien species (IAS) are both highly dependent on the availability and accessibility of occurrence data and natural history information about the species. Invasive alien species monitoring and detection networks (such as the Invasive Plant Atlas of New England and the Invasive Plant Atlas of the MidSouth) generate occurrence data at local and regional levels within the United States, which are shared through the US National Institute of Invasive Species Science. The Inter-American Biodiversity Information Network's Invasives Information Network (I3N), facilitates cooperation on sharing invasive species occurrence data throughout the Western Hemisphere. The I3N and other national and regional networks expose their data globally via the Global Invasive Species Information Network (GISIN). International and interdisciplinary cooperation on data sharing strengthens cooperation on strategies and responses to invasions. However, limitations to effective collaboration among invasive species networks leading to successful early detection and rapid response to invasive species include: lack of interoperability; data accessibility; funding; and technical expertise. This paper proposes various solutions to these obstacles at different geographic levels and briefly describes success stories from the invasive species information networks mentioned above. Using biological informatics to facilitate global information sharing is especially critical in invasive species science, as research has shown that one of the best indicators of the invasiveness of a species is whether it has been invasive elsewhere. Data must also be shared across disciplines because natural history information (e.g. diet, predators, habitat requirements, etc.) about a species in its native range is vital for effective prevention, detection, and rapid response to an invasion. Finally, it has been our

  20. Simultaneous and intercontinental tests show synchronism between the local gravimetric tide and the ultra-weak photon emission in seedlings of different plant species.

    Science.gov (United States)

    Gallep, Cristiano M; Barlow, Peter W; Burgos, Rosilene C R; van Wijk, Eduard P A

    2017-01-01

    In order to corroborate the hypothesis that variations in the rate of spontaneous ultra-weak photon emission (UPE) from germinating seedlings are related to local variations of the lunisolar tidal force, a series of simultaneous tests was performed using the time courses of UPE collected from three plant species-corn, wheat and sunflower-and also from wheat samples whose grains were transported between continents, from Brazil to The Netherlands and vice versa. All tests which were run in parallel showed coincident inflections within the UPE time courses not only between seedlings of the same species but also between the different species. In most cases, the UPE inflections were synchronised with the turning points in the local gravimetric tidal variation. Statistical tests using the local Pearson correlation verified these coincidences in the two time series. The results therefore support the hypothesis of a relationship between UPE emissions and, in the oscillations, the local gravimetric tide. This applies to both the emissions from seedlings of different species and to the seedlings raised from transported grain samples of the same species.

  1. Rapid identification and simultaneous analysis of multiple constituents from Rheum tanguticum Maxim. ex Balf. by UPLC/Q-TOF-MS.

    Science.gov (United States)

    Gao, Liang-Liang; Guo, Tao; Xu, Xu-Dong; Yang, Jun-Shan

    2017-07-01

    Rhubarb contains biologically active compounds such as anthraquinones, anthrones, stilbenes and tannins. A rapid and efficient UPLC/Q-TOF-MS/MS method was developed and applied towards identifying the constituents of Rheum tanguticum Maxim. ex Balf. for the first time. Chemical constituents were separated and investigated by UPLC/Q-TOF-MS/MS in the negative ion mode. The ESI-MS(2) fragmentation pathways of four types of compounds were interpreted, providing a very useful guidance for the characterisation of different types of compounds. Based on the exact mass information, fragmentation characteristic and LC retention time of 7 reference standards, 30 constituents were tentatively identified from the methanol extract of R. tanguticum. Among them, seven compounds were described for the first time from R. tanguticum and two from the genus Rheum were described for the first time. The analytical tool used here is valuable for the rapid separation and identification of multiple and minor constituents in methanol extracts of R. tanguticum.

  2. Combination of Multiple Resistance Traits from Wild Relative Species in Chrysanthemum via Trigeneric Hybridization

    Science.gov (United States)

    Deng, Yanming; Jiang, Jiafu; Chen, Sumei; Teng, Nianjun; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Chen, Fadi

    2012-01-01

    Background With the objective of combining multiple resistant traits from wild relative species in florist’s chrysanthemums, trigeneric hybridization was conducted by crossing two intergeneric F1 hybrids Chrysanthemum grandiflorum × Artemisia vulgaris and Chrysanthemum crassum × Crossostephium chinense. Methodology/Principal Findings To assess post-pollination phenomena, we investigated pollen germination on the stigma and embryo development, using fluorescence and scanning electron microscopy and paraffin-embedded sections, respectively. We selected eight putative trigeneric hybrid lines that showed the greatest morphological differences from the parents from among the progeny derived via embryo rescue. The hybridity of one trigeneric hybrid was further confirmed by fluorescent genomic in situ hybridization; in addition, the aphid resistance and salt tolerance of this hybrid were higher than those of the chrysanthemum parent and the C. grandiflorum × A. vulgaris F1 hybrid, respectively. Conclusions/Significance The enhanced aphid resistance of the hybrid line reflects the inheritance of chromosomes from A. vulgaris, which carries genes that encode bioactive components. The enhanced salt tolerance of the trigeneric hybrid is attributable to inheritance of genetic materials from Chrysanthemum crassum and Crossostephium chinense, which act to maintain the compartmentation of Na+ and K+ ions and their selective transportation among different organs to avert deleterious effects and protect the photosynthetic apparatus. The results indicate that trigeneric hybridization between different bigeneric hybrids is a promising method for combination of multiple stress-resistance traits for improvement of chrysanthemum. PMID:22952958

  3. Combination of multiple resistance traits from wild relative species in Chrysanthemum via trigeneric hybridization.

    Science.gov (United States)

    Deng, Yanming; Jiang, Jiafu; Chen, Sumei; Teng, Nianjun; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Chen, Fadi

    2012-01-01

    With the objective of combining multiple resistant traits from wild relative species in florist's chrysanthemums, trigeneric hybridization was conducted by crossing two intergeneric F(1) hybrids Chrysanthemum grandiflorum × Artemisia vulgaris and Chrysanthemum crassum × Crossostephium chinense. To assess post-pollination phenomena, we investigated pollen germination on the stigma and embryo development, using fluorescence and scanning electron microscopy and paraffin-embedded sections, respectively. We selected eight putative trigeneric hybrid lines that showed the greatest morphological differences from the parents from among the progeny derived via embryo rescue. The hybridity of one trigeneric hybrid was further confirmed by fluorescent genomic in situ hybridization; in addition, the aphid resistance and salt tolerance of this hybrid were higher than those of the chrysanthemum parent and the C. grandiflorum × A. vulgaris F(1) hybrid, respectively. The enhanced aphid resistance of the hybrid line reflects the inheritance of chromosomes from A. vulgaris, which carries genes that encode bioactive components. The enhanced salt tolerance of the trigeneric hybrid is attributable to inheritance of genetic materials from Chrysanthemum crassum and Crossostephium chinense, which act to maintain the compartmentation of Na(+) and K(+) ions and their selective transportation among different organs to avert deleterious effects and protect the photosynthetic apparatus. The results indicate that trigeneric hybridization between different bigeneric hybrids is a promising method for combination of multiple stress-resistance traits for improvement of chrysanthemum.

  4. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    Energy Technology Data Exchange (ETDEWEB)

    Spill, Fabian, E-mail: fspill@bu.edu [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Alarcon, Tomas [Centre de Recerca Matematica, Campus de Bellaterra, Edifici C, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Atonòma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Maini, Philip K. [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Byrne, Helen [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Computational Biology Group, Department of Computer Science, University of Oxford, Oxford OX1 3QD (United Kingdom)

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  5. Femtosecond, fully resonant electronically enhanced CARS (FREE-CARS) for simultaneous single-shot thermometry and detection of minor combustion species

    Science.gov (United States)

    Stauffer, Hans U.; Schmidt, Jacob B.; Richardson, Daniel R.; Roy, Sukesh; Wrzesinski, Paul J.; Gord, James R.

    2017-02-01

    Femtosecond time-resolved, fully resonant electronically enhanced coherent anti-Stokes Raman scattering (FREECARS) spectroscopy, incorporating a two-color ultraviolet excitation scheme, is used to demonstrate chemically selective and sensitive detection of gas-phase species, including nitric oxide (NO) and the hydroxyl (OH) radical. The observed time-dependent, spectrally resolved CARS signal contains rich structure that depends both on the rovibronic states accessed within the bandwidth of the initial (pump) excitation pulse and the Raman-active rovibrational levels within the vibrationally excited ground electronic state that are accessed following interaction with the second (Stokes) excitation pulse. By comparing experimental spectra to computational simulations, therefore, this approach also allows simultaneous determination of local temperature associated with the thermal distribution of initial states under singlelaser- shot conditions. For OH radical detected in a reacting flow, spectral resolution of the emitted FREE-CARS signal allows simultaneous single-shot detection of relative OH mole fraction and temperature in a laminar ethylene-air flame at 1-kHz repetition rates. By comparison to previously reported OH concentration and temperature measurements, we demonstrate excellent single-shot temperature accuracies ( 2% deviation from adiabatic flame temperature) and precisions ( 2% standard deviation), with simultaneous relative OH concentration measurements that demonstrate high detection sensitivity (100-300 ppm).

  6. Simultaneous identification and quantification of anthraquinones, polydatin, and resveratrol in Polygonum multiflorum, various Polygonum species, and dietary supplements by liquid chromatography and microscopic study of Polygonum species.

    Science.gov (United States)

    Avula, Bharathi; Joshi, Vaishali C; Wang, Yan-Hong; Khan, Ikhlas A

    2007-01-01

    A high-performance liquid chromatographic (HPLC) method with ultraviolet absorption detection was developed to determine the presence of anthraquinones, polydatin, and resveratrol in Polygonum multiflorum Thunb. as well as other medicinal Polygonum species, viz., P. cuspidatum, P. oriental, P. aviculare, and P. vulgare, as well as commercial products that claim to contain P. multiflorum. The best results were obtained with a Phenomenex Gemini C18 column using gradient mobile phase composed of water (0.1% acetic acid) and acetonitrile (0.1% acetic acid). Elution was at a flow rate of 1.0 mL/min. The detection wavelength was 280 nm for anthraquinones and 320 nm for polydatin and resveratrol. The main anthraquinones identified were emodin and physcion. The HPLC pattern of P. multiflorum was also compared with 5 other species of Polygonum. The method was validated for precision, repeatability, and accuracy. The relative standard deviation was between 0.9 and 1.6%. The method was sensitive, quick, and accurate for determination of anthraquinones, polydatin, and resveratrol in 6 different species of Polygonum and can be used for quality control of P. multiflorum. The commercial samples and the 6 Polygonum species were compared microscopically, and a detailed description is provided for P. multiflorum.

  7. Towards simultaneous calibration-free and ultra-fast sensing of temperature and species in the intrapulse mode

    KAUST Repository

    Chrystie, Robin S.M.

    2014-07-02

    We report on exploiting the down-chirp phenomenon seen in quantum cascade lasers (QCLs), when modulated with long pulses, for the purpose of performing calibration-free and temporally resolved measurements. Intrapulse spectra of a native species (e.g., H2O), common to combustion environments, were generated near λ = 7.62 μm at repetition rates as high as 3.125 MHz. Two-line absorption spectroscopy was employed to infer calibration-free temperature from the chirp-induced intrapulse spectra. In this study, such temperature measurements were limited to rates of 250 kHz due to spectral distortion at higher repetition rates. We demonstrate the ease at which accurate temperatures and H2O compositions can be achieved using simple and compact QCLs operated in the intrapulse mode. The sensor is also applicable to other species, and has the potential to be integrated into commercial technologies. © 2014 The Combustion Institute.

  8. Ultra-Performance Liquid Chromatography for the Simultaneous Quantification of Rutin and Chlorogenic Acid in Leaves of Ribes L. Species by Conventional and Chemometric Calibration Approaches.

    Science.gov (United States)

    Kendir, Gülsen; Dinç, Erdal; Güvenç, Ayşegül Köroǧlu

    2015-10-01

    A new ultra-performance liquid chromatography (UPLC) using conventional and chemometric calibrations was improved for the simultaneous estimation of chlorogenic acid (CA) and rutin (RUT) in leaves of Ribes L. species (R. rubrum, R. biebersteinii, R. nigrum, R. uva-crispa, R. alpinum, R. orientale, R. multiflorum and R. anatolica). The UPLC separation for CA and RUT in samples were performed on a Waters UPLC BEH phenyl column (100 mm × 1.0 mm i.d., 1.7 μm) and mobile phase consisting of acetonitrile and 0.1 M formic acid buffer, pH = 3.77 (15:85, v/v) containing 1.0 mL triethylamine in 1,000 mL mobile phase. Multi-wavelength UPLC chromatograms of CA and RUT in calibration and plant samples were obtained by the photodiode array (PDA) detection at the wavelength set from 290 to 360 nm with the interval of Δλ = 10 nm. Conventional UPLC-single and chemometric calibrations were subjected to the analysis of the related compounds. By using UPLC data, conventional and chemometric calibrations in the linear concentration range between 2.5 and 40.0 μg/mL for all compounds were applied for the simultaneous quantitative analysis of CA and RUT in plant samples of seven different Ribes species. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Towards an integration of biodiversity-ecosystem functioning and food web theory to evaluate relationships between multiple ecosystem services

    NARCIS (Netherlands)

    Hines, Jes; van der Putten, W.H.; De Deyn, G.B.; Wagg, Cameron; Voigt, Winfried; Mulder, Christian; Weisser, Wolfgang W.; Engel, Jan; Melian, Carlos; Scheu, Stefan; Birkhofer, Klaus; Ebeling, Anne; Scherber, Christoph; Eisenhauer, Nico

    2015-01-01

    Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that

  10. Giant increase in piezoelectric coefficient of AlN by Mg-Nb simultaneous addition and multiple chemical states of Nb

    Science.gov (United States)

    Uehara, Masato; Shigemoto, Hokuto; Fujio, Yuki; Nagase, Toshimi; Aida, Yasuhiro; Umeda, Keiichi; Akiyama, Morito

    2017-09-01

    Aluminum nitride (AlN) is one of piezoelectric materials, which are eagerly anticipated for use in microelectromechanical systems (MEMS) applications such as communication resonators, sensors, and energy harvesters. AlN is particularly excellent in generated voltage characteristics for the MEMS rather than oxide piezoelectric materials such as lead zirconium titanate Pb(Zr, Ti)O3. However, it is necessary to improve the piezoelectric properties of AlN in order to advance the performance of the MEMS. We dramatically increased the piezoelectric coefficient d33 of AlN films by simultaneously adding magnesium (Mg) and niobium (Nb). The d33 of Mg39.3Nb25.0Al35.7N is 22 pC/N, which is about four times that of AlN. The d33 is increased by Mg and Nb simultaneous addition, and is not increased by Mg or Nb single addition. Interestingly, the Nb has multiple chemical states, and which are influenced by the Mg concentration.

  11. Selective and simultaneous determination of indigo carmine and allura red in candy samples at the nano-concentration range by flow injection analysis with multiple pulse amperometric detection.

    Science.gov (United States)

    Deroco, Patrícia B; Medeiros, Roberta A; Rocha-Filho, Romeu C; Fatibello-Filho, Orlando

    2018-05-01

    A novel, unique electroanalytical method was developed for the simultaneous quantification of the dyes indigo carmine (IC) and allura red (AR) in candies by coupling flow injection analysis and multiple pulse amperometry with a cathodically pretreated boron-doped diamond electrode, using 0.30 mol L-1 H2SO4 as supporting electrolyte. A dual-potential waveform was employed, causing the electrooxidation of either IC solely or IC and AR simultaneously. Thence, subtraction of current signals was used to quantify IC and AR in the concentration ranges of 70.0-1000 nmol L-1 and 40.0-770 nmol L-1, with limits of detection of 40.0 nmol L-1 and 7.0 nmol L-1, respectively. The proposed method, which permits up to 153 determinations per hour with good precision, was successfully applied in the quantification of these dyes in samples of commercial candies; their obtained contents were similar (at a 95% confidence level) to those from a comparative HPLC method. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Simultaneous determination of bioactive compounds in Piper nigrum L. and a species comparison study using HPLC-PDA.

    Science.gov (United States)

    Rao, Vidadala Rama Subba; Raju, Sagi Satyanarayana; Sarma, Vanka Umamaheswara; Sabine, Fouriner; Babu, Kothapalli Hari; Babu, Katragadda Suresh; Rao, Janaswamy Madhusudana

    2011-08-01

    Piper nigrum L. is a traditional medicine widely used in India for illnesses such as constipation, diarrhoea, earache, gangrene, heart disease, hernia, hoarseness, indigestion, insect bites, insomnia, joint pain, liver problems, lung disease, oral abscesses, sunburn, tooth decay and toothaches. In this study, six bioactive compounds, namely piperine (1), pellitorine (2), guineensine (3), pipnoohine (4), trichostachine (5) and piperonal (6) were quantified in different extracts of P. nigrum L. and compared with those of P. longum L. and P. chaba Hunter. To evaluate the quality of P. nigrum, a simple, accurate and precise HPLC-PDA method was developed for the simultaneous determination of the above-mentioned six compounds. The separation was achieved by Phenomenex Luna RP C(18) column (150 × 4.6 mm, 5 µm, Phenomenex Inc, CA, USA) with a binary gradient solvent system of water-acetonitrile, at a flow rate of 1.0 mL min(-1) and detected at 210, 232, 262 and 343 nm. All six calibration curves showed good linearity (R (2) > 0.9966). The method was reproducible with intra- and inter-day variations of less than 2% and 5%, respectively. The results demonstrated that this method is simple, reliable and suitable for the quality control of these plants.

  13. Optimization of Micellar Electrokinetic Chromatography Method for the Simultaneous Determination of Seven Hydrophilic and Four Lipophilic Bioactive Components in Three Salvia Species

    Directory of Open Access Journals (Sweden)

    Jiliang Cao

    2015-08-01

    Full Text Available A micellar electrokinetic chromatography (MEKC method was developed for the simultaneous determination of seven hydrophilic phenolic acids and four lipophilic tanshinones in three Salvia species. In normal MEKC mode using SDS as surfactant, the investigated 11 compounds could not be well separated. Therefore, several buffer modifiers including β-cyclodextrins (β-CD, ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]BF4 and organic solvents have been added to the buffer solution to improve the separation selectivity. Under the optimized conditions (BGE, 15 mM sodium tetraborate with 10 mM SDS, 5 mM β-CD, 10 mM [bmim]BF4 and 15% ACN (v/v as additives; buffer pH, 9.8; voltage, 20 kV; temperature, 25 °C, the 11 investigated analytes could achieve baseline separation in 34 min. The proposed MEKC was additionally validated by evaluating the linearity (R2 ≥ 0.9965, LODs (0.27–1.39 μg·mL–1, and recovery (94.26%–105.17%, demonstrating this method was reproducible, accurate and reliable. Moreover, the contents of the 11 compounds in three Salvia species, including S. miltiorrhiza, S. przewalskii and S. castanea were analyzed. The result showed that the established MEKC method was simple and practical for the simultaneous determination of the hydrophilic and lipophilic bioactive components in Salvia species, which could be used to effectively evaluate the quality of these valued medicinal plants.

  14. Additive effects of climate and fisheries drive ongoing declines in multiple albatross species.

    Science.gov (United States)

    Pardo, Deborah; Forcada, Jaume; Wood, Andrew G; Tuck, Geoff N; Ireland, Louise; Pradel, Roger; Croxall, John P; Phillips, Richard A

    2017-12-12

    Environmental and anthropogenic factors often drive population declines in top predators, but how their influences may combine remains unclear. Albatrosses are particularly threatened. They breed in fast-changing environments, and their extensive foraging ranges expose them to incidental mortality (bycatch) in multiple fisheries. The albatross community at South Georgia includes globally important populations of three species that have declined by 40-60% over the last 35 years. We used three steps to deeply understand the drivers of such dramatic changes: (i) describe fundamental demographic rates using multievent models, (ii) determine demographic drivers of population growth using matrix models, and (iii) identify environmental and anthropogenic drivers using ANOVAs. Each species was affected by different processes and threats in their foraging areas during the breeding and nonbreeding seasons. There was evidence for two kinds of combined environmental and anthropogenic effects. The first was sequential; in wandering and black-browed albatrosses, high levels of bycatch have reduced juvenile and adult survival, then increased temperature, reduced sea-ice cover, and stronger winds are affecting the population recovery potential. The second was additive; in gray-headed albatrosses, not only did bycatch impact adult survival but also this impact was exacerbated by lower food availability in years following El Niño events. This emphasizes the need for much improved implementation of mitigation measures in fisheries and better enforcement of compliance. We hope our results not only help focus future management actions for these populations but also demonstrate the power of the modelling approach for assessing impacts of environmental and anthropogenic drivers in wild animal populations.

  15. Simultaneous temperature and multi-species measurements in opposed jet flames of nitrogen-diluted hydrogen and air

    Science.gov (United States)

    Wehrmeyer, J. A.; Cheng, T. S.; Pitz, R. W.; Nandula, S.; Wilson, L. G.; Pellett, G. L.

    1991-01-01

    A narrowband UV Raman scattering system is used to obtain measurement profiles of major and minor species concentrations, temperature, and mixture fraction in opposed jet diffusion flames. The measurement profiles can be compared to previously obtained temperature and concentration profiles (Pellett et al., 1989), obtained using CARS, and they can also be qualitatively compared to the predicted concentration and temperature profiles in pure hydrogen/air flames (Gutheil and Williams, 1990) and in diluted hydrogen/air flames (Dixon-Lewis and Missaghi, 1988; Ho and Isaac, 1991). The applied stress-rates for the two flame conditions studied are 240/s and 340/s, with respective hydrogen concentrations in the fuel jet of 0.67 and 0.83, on a mole fraction basis (0.13 and 0.26 hydrogen mass fractions, respectively).

  16. Tunable multiple emissions in manganese-concentrated sulfide through simultaneous tailoring of Mn-site coordination and Mn-Mn pair geometry

    Science.gov (United States)

    Chen, Zitao; Song, Enhai; Ye, Shi; Zhang, Qinyuan

    2017-12-01

    In contrast to generally single-band visible emission feature from Mn2+, simultaneous visible (VIS) and near-infrared (NIR) multiple emissions are demonstrated in Mn2+ concentrated sulfide (MnS) by only involving a single crystallographic site. Upon varying the Mn2+-site coordination and/or Mn-Mn pairs geometry in different structural MnS, the multiple emissions from divalent manganese can be easily tuned from 575 to 720 nm (VIS) or from 880 to 900 or 1380 nm (NIR), respectively. The excitation spectroscopy and the luminescent decay, together with crystal structural analyses, are employed to investigate the electronic transition and the excited state dynamics of these Mn2+ concentrated systems. It is found that the VIS and NIR emissions can be ascribed to the isolated Mn2+ ion and exchange coupled Mn-Mn pair center, respectively. The effect of crystal field and bridging geometry, as well as temperature on the exchange coupled Mn2+ pairs NIR emissive center, is also investigated in detail. This work not only provides keen insights into the de-excitation pathway of Mn2+-concentrated material, but also offers the possibilities of designing a novel NIR emitting source for various photonic applications.

  17. Small molecule CP-31398 induces reactive oxygen species-dependent apoptosis in human multiple myeloma.

    Science.gov (United States)

    Arihara, Yohei; Takada, Kohichi; Kamihara, Yusuke; Hayasaka, Naotaka; Nakamura, Hajime; Murase, Kazuyuki; Ikeda, Hiroshi; Iyama, Satoshi; Sato, Tsutomu; Miyanishi, Koji; Kobune, Masayoshi; Kato, Junji

    2017-09-12

    Reactive oxygen species (ROS) are normal byproducts of a wide variety of cellular processes. ROS have dual functional roles in cancer cell pathophysiology. At low to moderate levels, ROS act as signaling transducers to activate cell proliferation, migration, invasion, and angiogenesis. In contrast, high levels of ROS induce cell death. In multiple myeloma (MM), ROS overproduction is the trigger for apoptosis induced by several anticancer compounds, including proteasome inhibitors. However, no drugs for which oxidative stress is the main mechanism of action are currently used for treatment of MM in clinical situations. In this study, we demonstrate that the p53-activating small molecule CP-31398 (CP) effectively inhibits the growth of MM cell lines and primary MM isolates from patients. CP also suppresses the growth of MM xenografts in mice. Mechanistically, CP was found to induce intrinsic apoptosis in MM cells via increasing ROS production. Interestingly, CP-induced apoptosis occurs regardless of the p53 status, suggesting that CP has additional mechanisms of action. Our findings thus indicate that CP could be an attractive candidate for treatment of MM patients harboring p53 abnormalities; this satisfies an unmet clinical need, as such individuals currently have a poor prognosis.

  18. Image-based red blood cell counter for multiple species of wild and domestic animals

    Directory of Open Access Journals (Sweden)

    C.R.M. Mauricio

    Full Text Available ABSTRACT RBC count plays an important role in animal diagnosis. Despite the many technologies available in different automated hematology analyzers, when it comes to the blood of wild animals it is still difficult to find an easy and affordable solution for multiple species. This study aims to evaluate the proposed automatic red blood cell counter. Blood samples (1 ocelot - Leopardus pardalis, 1 monkey - Cebus apella, 1 coati - Nasua nasua, 62 dogs - Canis familiaris, and 5 horses - Equus caballus were analyzed using three methods: 1-manual count, 2-automatic count by image, and 3-semi-automatic count by image; blood from dogs and horses were also analyzed by a fourth method: 4-automatic count by impedance. The counts in methods 2 and 3 were produced by the proposed red blood cell counter. Results were compared using Pearson's correlation and plots with different methods as the criterion standard. RBC counts in methods 1, 2, and 3 correlated very well with those in the method 4 (r ≥ 0.94. RBC counts produced by method 2 were highly correlated with method 3 (r = 0.998. The results indicate that the proposed method can be used as an automatic or semi-automatic counting method in clinics that are currently using the manual method for RBC assessment.

  19. Lepidopteran larva consumption of soybean foliage: basis for developing multiple-species economic thresholds for pest management decisions.

    Science.gov (United States)

    Bueno, Regiane Cristina Oliveira de Freitas; Bueno, Adeney de Freitas; Moscardi, Flávio; Parra, José Roberto Postali; Hoffmann-Campo, Clara Beatriz

    2011-02-01

    Defoliation by Anticarsia gemmatalis (Hübner), Pseudoplusia includens (Walker), Spodoptera eridania (Cramer), S. cosmioides (Walker) and S. frugiperda (JE Smith) (Lepidoptera: Noctuidae) was evaluated in four soybean genotypes. A multiple-species economic threshold (ET), based upon the species' feeding capacity, is proposed with the aim of improving growers' management decisions on when to initiate control measures for the species complex. Consumption by A. gemmatalis, S. cosmioides or S. eridania on different genotypes was similar. The highest consumption of P. includens was 92.7 cm(2) on Codetec 219RR; that of S. frugiperda was 118 cm(2) on Codetec 219RR and 115.1 cm(2) on MSoy 8787RR. The insect injury equivalent for S. cosmoides, calculated on the basis of insect consumption, was double the standard consumption by A. gemmatalis, and statistically different from the other species tested, which were similar to each other. As S. cosmioides always defoliated nearly twice the leaf area of the other species, the injury equivalent would be 2 for this lepidopteran species and 1 for the other species. The recommended multiple-species ET to trigger the beginning of insect control would then be 20 insect equivalents per linear metre. Copyright © 2010 Society of Chemical Industry.

  20. Simultaneous analysis of free and humic acid complexed europium and gadolinium species by CE-ICP-MS

    Energy Technology Data Exchange (ETDEWEB)

    Kautenburger, R.; Nowotka, K.; Beck, H.P. [Institut fuer Anorganische und Analytische Chemie und Radiochemie, Universitaet des Saarlandes, P.O. Box 151150, 66041 Saarbruecken (Germany)

    2005-07-01

    -ICP-MS coupling-system it was possible to quantify metal concentrations from the detection limit up to approximately 1 ppm on a linear scale. This setup was used to separate metal / humic acid-species in a 10 mM acetic acid / 1 mM acetate buffer system. With humic acid as complexing ligand, free metal species could be separated from the metal-humate-complexes on a time resolved scale. The ratios of free metal ions and metal-humate- complexes are change with different experimental conditions like pH values or metal concentrations. This research is financially supported by the 'Bundesministerium fuer Wirtschaft und Arbeit' (BMWA, project 02E9683). (authors)

  1. Metasurfaces: Simultaneous Stokes parameters

    Science.gov (United States)

    Lepetit, Thomas; Kanté, Boubacar

    2015-11-01

    Techniques for determining Stokes parameters, which fully define the polarization state of a wave, require multiple measurements, thus potentially leading to inaccuracies. Researchers now show how to simultaneously determine the parameters for visible light using periodic metal structures.

  2. δ15N values of atmospheric N species simultaneously collected using sector-based samplers distant from sources - Isotopic inheritance and fractionation

    Science.gov (United States)

    Savard, Martine M.; Cole, Amanda; Smirnoff, Anna; Vet, Robert

    2017-08-01

    The nitrogen isotope ratios (δ15N) of atmospheric N species are commonly suggested as indicators of N emission sources. Therefore, numerous research studies have developed analytical methodologies and characterized primary (gases) and secondary emission products (mostly precipitation and aerosols) from various emitters. These previous studies have generally collected either reduced or oxidized N forms, and sampled them separately prior to determining their δ15N values. Distinctive isotopic signals have been reported for emissions from various sources, and seasonality of the δ15N values has been frequently attributed to shifts in relative contributions from sources with different isotopic signals. However, theoretical concepts suggest that temperature effects on isotopic fractionation may also affect the δ15N values of atmospheric reaction products. Here we use a sector-based multi-stage filter system to simultaneously collect seven reduced and oxidized N species downwind from five different source types in Alberta, Canada. We report δ15N values obtained with a state-of-the-art gold-furnace pre-concentrator online with an isotope ratio mass spectrometer (IRMS) to provide representative results even for oxidized-N forms. We find that equilibrium isotope effects and their temperature dependence play significant roles in determining the δ15N values of the secondary emission products. In the end, seasonal δ15N changes here are mainly caused by temperature effects on fractionation, and the δ15N values of only two N species from one source type can be retained as potential fingerprints of emissions.

  3. Development of a simultaneous identification method for 13 animal species using two multiplex real-time PCR assays and melting curve analysis.

    Science.gov (United States)

    Ishida, Natsumi; Sakurada, Makoto; Kusunoki, Hiroshi; Ueno, Yasuhiro

    2017-11-26

    We developed a simple and rapid method for animal species identification in the forensic science field based on mitochondrial DNA using two multiplex real-time PCRs and analysis of the resultant SYBR Green I melting curves. This method was designed to identify nine domestic animals simultaneously (dog, cat, rabbit, cattle, pig, chicken, goat, sheep and horse) and four wild animals (deer, raccoon-dog, monkey and bear) by comparing the different melting temperatures of the amplicons produced from samples originating from each species. For this analysis, we targeted various mitochondrial genes, including those encoding cytochrome b (cytb), NADH dehydrogenase 5 (ND5), cytochrome c oxidase 3 (COX3), tRNA-ND5, and tRNA-ATP synthase 8 (ATP8). For practical applications, this study presents a validation of this assay including its specificity, sensitivity and robustness. The limits of detection in the multiplex reactions were 10 pg for eight of the nine animals, excluding horse (1 pg for horse). The method was able to correctly identify the animal species from artificial forensic samples including blood stains, saliva, hair and bone, and samples digested in artificial gastric fluid, and for 17 forensic casework samples. The data from the multiplex real-time PCR assays are obtainable only 30 min after DNA extraction of the samples, making the assays useful for screening samples containing DNA from unknown animal origin in the forensic field. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. San Diego Multiple Species Conservation Program (MSCP) Rare Plant Monitoring Review and Revision

    Science.gov (United States)

    McEachern, Kathryn; Pavlik, Bruce M.; Rebman, Jon; Sutter, Rob

    2007-01-01

    Introduction The San Diego Multiple Species Conservation Program (MSCP) was developed for the conservation of plants and animals in the south part of San Diego County, under the California Natural Community Conservation Planning Act of 1991 (California Department of Fish and Game) and the Federal Endangered Species Act of 1973, as amended (16 U.S. Code 1531-1544.) The Program is on the leading edge of conservation, as it seeks to both guide development and conserve at-risk species with the oversight of both State and Federal agencies. Lands were identified for inclusion in the MSCP based on their value as habitat for at-risk plants or plant communities (Natural Community Conservation Planning, 2005). Since its inception in the mid-1990s the Program has protected over 100,000 acres, involving 15 jurisdictions and the U.S. Fish and Wildlife Service (USFWS) and California Department of Fish and Game (CDFG) in the conservation of 87 taxa. Surveys for covered species have been conducted, and management and monitoring have been implemented at some high priority sites. Each jurisdiction or agency manages and monitors their conservation areas independently, while collaborating regionally for long-term protection. The San Diego MSCP is on the forefront of conservation, in one of the most rapidly growing urban areas of the country. The planning effort that developed the MSCP was state-of-the-art, using expert knowledge, spatial habitat modeling, and principles of preserve design to identify and prioritize areas for protection. Land acquisition and protection are ahead of schedule for most jurisdictions. Surveys have verified the locations of many rare plant populations known from earlier collections, and they provide general information on population size and health useful for further conservation planning. Management plans have been written or are in development for most MSCP parcels under jurisdictional control. Several agencies are developing databases for implementation

  5. Development of a thermostabilized, one-step, nested, tetraplex PCR assay for simultaneous identification and differentiation of Entamoeba species, Entamoeba histolytica and Entamoeba dispar from stool samples.

    Science.gov (United States)

    Foo, Phiaw Chong; Chan, Yean Yean; See Too, Wei Cun; Tan, Zi Ning; Wong, Weng Kin; Lalitha, Pattabhiraman; Lim, Boon Huat

    2012-09-01

    Entamoeba histolytica is the only Entamoeba species that causes amoebiasis in humans. Approximately 50 million people are infected, with 100, 000 deaths annually in endemic countries. Molecular diagnosis of Entamoeba histolytica is important to differentiate it from the morphologically identical Entamoeba dispar to avoid unnecessary medication. Conventional molecular diagnostic tests require trained personnel, cold-chain transportation and/or are storage-dependent, which make them user-unfriendly. The aim of this study was to develop a thermostabilized, one-step, nested, tetraplex PCR assay for the detection of Entamoeba histolytica, Entamoeba dispar and Entamoeba species in cold-chain-free and ready-to-use form. The PCR test was designed based on the Entamoeba small subunit rRNA (SSU-rRNA) gene, which detects the presence of any Entamoeba species, and simultaneously can be used to differentiate Entamoeba histolytica from Entamoeba dispar. In addition, a pair of primers was designed to serve as an internal amplification control to help identify inhibitors in the samples. All PCR reagents together with the designed primers were thermostabilized by lyophilization and were stable at 24 °C for at least 6 months. The limit of detection of the tetraplex PCR was found to be 39 pg DNA or 1000 cells for Entamoeba histolytica and 78 pg DNA or 1000 cells for Entamoeba dispar, and the specificity was 100 %. In conclusion, this cold-chain-free, thermostabilized, one-step, nested, multiplex PCR assay was found to be efficacious in differentiating Entamoeba histolytica from other non-pathogenic Entamoeba species.

  6. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Science.gov (United States)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  7. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  8. Genetic complexity and multiple infections with more Parvovirus species in naturally infected cats

    Directory of Open Access Journals (Sweden)

    Battilani Mara

    2011-03-01

    Full Text Available Abstract Parvoviruses of carnivores include three closely related autonomous parvoviruses: canine parvovirus (CPV, feline panleukopenia virus (FPV and mink enteritis virus (MEV. These viruses cause a variety of serious diseases, especially in young patients, since they have a remarkable predilection for replication in rapidly dividing cells. FPV is not the only parvovirus species which infects cats; in addition to MEV, the new variants of canine parvovirus, CPV-2a, 2b and 2c have also penetrated the feline host-range, and they are able to infect and replicate in cats, causing diseases indistinguishable from feline panleukopenia. Furthermore, as cats are susceptible to both CPV-2 and FPV viruses, superinfection and co-infection with multiple parvovirus strains may occur, potentially facilitating recombination and high genetic heterogeneity. In the light of the importance of cats as a potential source of genetic diversity for parvoviruses and, since feline panleukopenia virus has re-emerged as a major cause of mortality in felines, the present study has explored the molecular characteristics of parvovirus strains circulating in cat populations. The most significant findings reported in this study were (a the detection of mixed infection FPV/CPV with the presence of one parvovirus variant which is a true intermediate between FPV/CPV and (b the quasispecies cloud size of one CPV sample variant 2c. In conclusion, this study provides new important results about the evolutionary dynamics of CPV infections in cats, showing that CPV has presumably started a new process of readaptation in feline hosts.

  9. Estimating the species tree for Hawaiian Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution.

    Science.gov (United States)

    Willyard, Ann; Wallace, Lisa E; Wagner, Warren L; Weller, Stephen G; Sakai, Ann K; Nepokroeff, Molly

    2011-07-01

    Schiedea (Caryophyllaceae) is a monophyletic genus of 34 species, all endemic to the Hawaiian Islands, that arose from a single colonization, providing one of the best examples of adaptive radiation in Hawai'i. Species utilize a range of habitats and exhibit a variety of growth forms and transitions in breeding systems from hermaphroditism toward dimorphism or autogamy. Our study included the most thorough sampling to date: 2-5 individuals per species and 4 independent genetic partitions: eight plastid and three low-copy nuclear loci (9217bps), allowing a three-locus BEST species tree. Despite incomplete resolution at the tips, our results support monophyly for each extant species. Gene trees revealed several clear cases of cytonuclear incongruence, likely created by interspecific introgression. Conflict occurs at the divergence of section Alphaschiedea as well as at the tips. Ages inferred from a BEAST analysis allow an original colonization onto either Nihoa or Kauaì and inform some aspects of inter-island migrations. We suggest that several hard polytomies on the species tree are biologically realistic, signifying either nearly simultaneous speciation or historical introgressive hybridization. Based on inferred node ages that exceed expected coalescent times, we propose that undetected nuclear introgression may play a larger role than incomplete lineage sorting in sections Schiedea and Mononeura. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Analysis of multiple tsetse fly populations in Uganda reveals limited diversity and species-specific gut microbiota.

    Science.gov (United States)

    Aksoy, Emre; Telleria, Erich L; Echodu, Richard; Wu, Yineng; Okedi, Loyce M; Weiss, Brian L; Aksoy, Serap; Caccone, Adalgisa

    2014-07-01

    The invertebrate microbiome contributes to multiple aspects of host physiology, including nutrient supplementation and immune maturation processes. We identified and compared gut microbial abundance and diversity in natural tsetse flies from Uganda using five genetically distinct populations of Glossina fuscipes fuscipes and multiple tsetse species (Glossina morsitans morsitans, G. f. fuscipes, and Glossina pallidipes) that occur in sympatry in one location. We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals. Our results show extremely limited diversity in field flies of different tsetse species. The obligate endosymbiont Wigglesworthia dominated all samples (>99%), but we also observed wide prevalence of low-density Sodalis (tsetse's commensal endosymbiont) infections (microbiota composition among the genetically distinct G. f. fuscipes flies and between different sympatric species. Interestingly, Wigglesworthia density varied in different species (10(4) to 10(6) normalized genomes), with G. f. fuscipes having the highest levels. We describe the factors that may be responsible for the reduced diversity of tsetse's gut microbiota compared to those of other insects. Additionally, we discuss the implications of Wigglesworthia and Sodalis density variations as they relate to trypanosome transmission dynamics and vector competence variations associated with different tsetse species. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  11. Metals and organotins in multiple bivalve species in a one-off global survey

    DEFF Research Database (Denmark)

    Larsen, Martin Mørk; Strand, Jakob; Christensen, Jan H.

    2011-01-01

    contamination levels on a global scale. Metal concentrations in nine bivalve species were normalised to the Mytilidae family using conversion factors based on cosampled species and literature bioconcentration factors. The lowest metal and tributyltin concentrations were below background assessment...

  12. Impacts of multiple stressors on biodiversity and ecosystem functioning: the role of species co-tolerance

    NARCIS (Netherlands)

    Vinebrooke, R.D.; Cottingham, K.L.; Norberg, J.; Scheffer, M.; Dodson, S.I.; Maberly, S.C.; Sommer, U.

    2004-01-01

    Ecosystem resistance to a single stressor relies on tolerant species that can compensate for sensitive competitors and maintain ecosystem processes, such as primary production. We hypothesize that resistance to additional stressors depends increasingly on species tolerances being positively

  13. Three in One?Multiple Faunal Elements within an Endangered European Butterfly Species

    OpenAIRE

    Marius Junker; Marie Zimmermann; Ramos, Ana A.; Patrick Gros; Martin Konvička; Gabriel Nève; László Rákosy; Toomas Tammaru; Rita Castilho; Thomas Schmitt

    2015-01-01

    Ice ages within Europe forced many species to retreat to refugia, of which three major biogeographic basic types can be distinguished: "Mediterranean", "Continental" and "Alpine / Arctic" species. However, this classification often fails to explain the complex phylogeography of European species with a wide range of latitudinal and altitudinal distribution. Hence, we tested for the possibility that all three mentioned faunal elements are represented within one species. Our data was obtained by...

  14. Characterization of blue mold Penicillium species isolated from stored fruits using multiple highly conserved loci

    Science.gov (United States)

    Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locatio...

  15. Determinants of species richness patterns in the Netherlands across multiple taxonomic groups

    NARCIS (Netherlands)

    Schouten, M.A.; Verweij, P.A.; Barendregt, Arie; Kleukers, R.J.M.C.; Kalkman, V.J.; Ruiter, P.C. de

    2009-01-01

    We examined the species richness patterns of five different species groups (mosses, reptiles and amphibians, grasshoppers and crickets, dragonflies, and hoverflies) in the Netherlands (41,500 km2) using sampling units of 5 × 5 km. We compared the spatial patterns of species richness of the five

  16. Chapter Four : Towards an Integration of Biodiversity–Ecosystem Functioning and Food Web Theory to Evaluate Relationships between Multiple Ecosystem Services

    NARCIS (Netherlands)

    Hines, J.; Putten, van der W.H.; Deyn, de G.B.; Wagg, C.; Voigt, W.; Mulder, C.; Weisser, W.W.; Engel, J.; Melian, C.; Scheu, S.; Birkhofer, K.; Ebeling, A.; Scherber, C.; Eisenhauer, N.

    2015-01-01

    Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that

  17. Simultaneous species-specific PCR detection and viability testing of poly(vinyl alcohol) cryogel-entrapped Rhodococcus spp. after their exposure to petroleum hydrocarbons.

    Science.gov (United States)

    Kuyukina, Maria S; Ivshina, Irena B; Serebrennikova, Marina K; Rubtsova, Ekaterina V; Krivoruchko, Anastasiya V

    2013-08-01

    A method of simultaneous species-specific PCR detection and viability testing of poly(vinyl alcohol) cryogel-entrapped Rhodococcus spp. was developed that allowed the estimation of immobilized Rhodococcus opacus and Rhodococcus ruber survival after their exposure to petroleum hydrocarbon mixture. Spectrophotometric INT assay revealed high tolerance of gel-immobilized rhodococci to petroleum hydrocarbons, while among two Rhodococcus strains studied, R. ruber tolerated better to hydrocarbons compared to R. opacus. These findings were confirmed by respirometry results that showed increased respiratory activity of gel-immobilized Rhodococcus strains after 10-day incubation with 3% (v/v) petroleum hydrocarbon mixture. Moreover, jointly incubated rhodococcal strains demonstrated higher oxidative activities toward petroleum hydrocarbons than individual strains. Both Rhodococcus species were recovered successfully in cryogel granules using 16S rDNA-targeted PCR, even though the granules were previously stained with INT and extracted with ethanol. The method developed can be used for rapid detection and monitoring of gel-immobilized bacterial inocula in bioreactors or contaminated soil systems. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Simultaneous determination of sugars and picrosides in Picrorhiza species using ultrasonic extraction and high-performance liquid chromatography with evaporative light scattering detection.

    Science.gov (United States)

    Bhandari, Pamita; Kumar, Neeraj; Singh, Bikram; Kaul, Vijay K

    2008-06-20

    Sugars play a critical role in regulating overall cellular metabolism in high altitude growing plants. These plants are shown to have high levels of sugars to enhance their tolerance to abiotic stresses such as drought and freezing temperature. In the present study, a simple, sensitive, selective and reliable HPLC method based on ultrasonic extraction and evaporative light scattering detection (ELSD) has been developed and validated for the simultaneous determination of important sugars (xylose, xylitol, mannitol, glucose and sucrose) and picrosides (picroside-I and picroside-II) in two species Picrorhiza kurroa and P. scrophulariiflora. The analysis was carried out on a Zorbax amino column (250 mm x 4.6 mm i.d., 5 microm) with isocratic elution of acetonitrile:water (78:22, v/v). The method was validated for accuracy, precision, limit of detection and quantification according to International Conference on Harmonization (ICH) guidelines. The drift tube temperature of the ELSD system was set to 81 degrees C and nitrogen flow rate was 2.0 standard liter per minute (SLM). The regression equation revealed a good linear relationship (r(2)=0.9997+/-0.0012) within test ranges. The limit of detection and quantification for seven analytes in ELSD were less than 0.98 and 2.95 microg, respectively. The method showed good reproducibility for the quantification of seven analytes in Picrorhiza species with intra- and inter-day variation of less than 2.0%.

  19. Development and validation of a duplex real-time PCR assay for the simultaneous detection of three mustard species (Sinapis alba, Brassica nigra and Brassica juncea) in food.

    Science.gov (United States)

    Palle-Reisch, Monika; Cichna-Markl, Margit; Hochegger, Rupert

    2014-06-15

    The paper presents a duplex real-time PCR assay for the simultaneous detection of three potentially allergenic mustard species commonly used in food: white mustard (Sinapis alba), black mustard (Brassica nigra) and brown mustard (Brassica juncea). White mustard is detected in the "green" and black/brown mustard in the "yellow" channel. The duplex real-time PCR assay does not show cross-reactivity with other Brassicaceae species including broccoli, cauliflower, radish and rapeseed. Low cross-reactivities (difference in the Ct value ⩾ 11.91 compared with the positive control) were obtained with cumin, fenugreek, ginger, rye and turmeric. When applying 500 ng DNA per PCR tube, the duplex real-time PCR assay allowed the detection of white, black and brown mustard in brewed model sausages down to a concentration of 5mg/kg in 10 out of 10 replicates. The duplex real-time PCR assay was applied to verify correct labelling of commercial foodstuffs. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Higher-efficiency photoelectrochemical electrodes of titanium dioxide-based nanoarrays sensitized simultaneously with plasmonic silver nanoparticles and multiple metal sulfides photosensitizers

    Science.gov (United States)

    Guo, Keying; Liu, Zhifeng; Han, Jianhua; Zhang, Xueqi; Li, Yajun; Hong, Tiantian; Zhou, Cailou

    2015-07-01

    This paper describes a novel design of high-efficiency photoelectrochemical water splitting electrode, i.e., ordered TiO2 nanorod arrays (NRs) sensitized simultaneously with noble metal (Ag), binary metal sulfides (Ag2S) and ternary metal sulfides (Ag3CuS2) multiple photosensitizers for the first time. The TiO2/Ag/Ag2S/Ag3CuS2 NRs heterostructure is successfully synthesized through successive ion layer adsorption and reaction (SILAR) and a simple ion-exchange process based on ionic reaction mechanism. On the basis of an optimal quantity of Ag, Ag2S and Ag3CuS2 nanoparticles, such TiO2/Ag/Ag2S/Ag3CuS2 NRs exhibit a higher photoelectrochemical activity ever reported for TiO2-based nanoarrays in PEC water splitting, the photocurrent density is up to 9.82 mA cm-2 at 0.47 V versus Ag/AgCl, respectively. This novel architecture is able to increase electron collection efficiency and suppress carrier recombination via (i) a higher efficiency of light-harvesting through these multiple photosensitizers (Ag, Ag2S and Ag3CuS2); (ii) the efficient separation of photo-induced electrons and holes due to the direct electrical pathways; (iii) the surface plasmon resonance (SPR) effect of Ag nanoparticles, which enhances the efficient charge separation and high carrier mobility. This work is useful to explore feasible routes to further enhance the performance of oxide semiconductors for PEC water splitting to produce clean H2 energy.

  1. SU-E-T-52: A New Device for Quality Assurance of a Single Isocenter Technique for the Simultaneous Treatment of Multiple Brain Metastases

    Energy Technology Data Exchange (ETDEWEB)

    Maurer, J [Cone Health Cancer Center, Greensboro, NC (United States); Sintay, B [Cone Health, Greensboro, NC (United States); Varchena, V [Cirs, Inc., Norfolk, VA (United States)

    2015-06-15

    Purpose: Comprehensive quality assurance (QA) of a single isocenter technique for the simultaneous treatment of multiple brain metastases is presently impractical due to the time consuming nature of measuring each lesion’s dose on film or with a micro-chamber. Three dimensional diode array and full field film measurements are sometimes used to evaluate these plans, but gamma analysis may not reveal local errors that have significant effects on one or a few of several targets. This work aimed to design, build and test a phantom to simplify comprehensive measurement and evaluation. Methods: A phantom was designed with 28 stackable slabs. The top and bottom slabs are 1.5 centimeters (cm) in thickness, and central 26 slabs are 0.5 cm thick. When assembled with radiochromic film in all 27 gaps, the phantom measures 16.5 x 15 x 19 cm. Etchings were designed to aide in identification of specific film planes on computed tomography (CT) images and correlation of individual PTVs with closest bisecting planes. Patient verification plans with a total of 16 PTVs were calculated on the phantom CT, and test deliveries both with and without couch kicks were performed to test the ability to identify correct film placements and subsequent PTV specific dose distributions on the films. Results: Bisecting planes corresponding to PTV locations were easily identified, and PTV specific dose distributions were clear for all 16 targets. For deliveries with couch kicks, the phantom PTV dose distributions closely approximated those calculated on the patient’s CT. For deliveries without couch kicks, PTV specific dosimetry was also possible, although the distributions had ‘ghosts’ equaling the number of couch kicks, with distance between ghosts increasing with distance from the isocenter. Conclusion: A new phantom facilitates fast comprehensive commissioning validation and PTV specific dosimetry for a single isocenter technique for treating multiple brain metastases. This work was

  2. SU-E-T-799: Verification of a Simultaneous Treatment of Multiple Brain Metastases Using VMAT Technique by a Composite Alanine-Gel Dosimeter Phantom

    Energy Technology Data Exchange (ETDEWEB)

    Pavoni, J; Silveira, M; Filho, O Baffa [University of Sao Paulo, Ribeirao Preto, Sao Paulo (Brazil); Neves, W; Ramos, P; Haddad, C [Sirio Libanes Hospital, Sao Paulo, Sao Paulo (Brazil)

    2015-06-15

    Purpose: This work presents an end-to-end test using a Gel-Alanine phantom to validate the three-dimensional (3D) dose distribution (DD) delivered by a single isocenter VMAT technique on the simultaneous treatment of multiple brain metastases. Methods: Three cylindrical phantons containing MAGIC-f gel dosimeter were used to measure the 3D DD of a VMAT treatment, the first two were filled with the gel dosimeter (Gel 1 and 2) and the third one was filled with gel and 12 alanine dosimeters distributed along it (Gel 3). Gels 1 and 3 were irradiated and gel 2 was used to map the magnetic resonance image (MRI) scanner field inomogeneities. A CT scan of gel 3 was used for the VMAT treatment planning and 5 alanine pellets were chosen as lesions, around them a PTV was grown and different dose prescriptions were assigned for each one, varying from 5 to 9Gy. Before treatment, the plan was approved in a QA based on an ionization chamber absolute dose measurement, a radiochromic film planar dose measurement and a portal dosimetry per field verification; and also the phantons positioning were verified by ExacTrac 6D correction and OBI kV Cone Beam CT. The gels were irradiated, the MRIs were acquired 24 hours after irradiation and finally, the alanine dosimeters were analysed in a X-band Electron Spin Resonance spectrometer. Results: The association of the two detectors enabled the 3D dose evaluation by gel and punctually inside target volumes by alanine. In the gamma analyses (3%/3mm) comparing the 5 PTVs’ central images DD with TPS expected DD more than 95% of the points were approved. The alanine absolute dose measurements were in agreement with TPS by less than 5%. Conclusion: The gel-alanine phantom enabled the dosimetric validation of multiple brain metastases treatment using VMAT, being an almost ideal tool for this application. This work is partially supported by FAPESP.

  3. Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal.

    Science.gov (United States)

    Jung, Thomas; Jung, Marília Horta; Cacciola, Santa Olga; Cech, Thomas; Bakonyi, József; Seress, Diána; Mosca, Saveria; Schena, Leonardo; Seddaiu, Salvatore; Pane, Antonella; di San Lio, Gaetano Magnano; Maia, Cristiana; Cravador, Alfredo; Franceschini, Antonio; Scanu, Bruno

    2017-12-01

    During surveys of Phytophthora diversity in natural and semi-natural Fagaceae forests in Austria, Italy and Portugal, four new cryptic species were isolated from rhizosphere soil samples. Multigene phylogeny based on nuclear ITS, ß-tubulin and HSP90 and mitochondrial cox1 and NADH1 gene sequences demonstrated that two species, P. tyrrhenica and P. vulcanica spp. nov., belong to phylogenetic Clade 7a, while the other two species, P. castanetorum and P. tubulina spp. nov., clustered together with P. quercina forming a new clade, named here as Clade 12. All four new species are homothallic and have low optimum and maximum temperatures for growth and very slow growth rates at their respective optimum temperature. They differed from each other and from related species by a unique combination of morphological characters, cardinal temperatures, and growth rates. Pathogenicity of all Phytophthora species to the root system of their respective host species was demonstrated in soil infestation trials.

  4. Studies on fission with ALADIN. Precise and simultaneous measurement of fission yields, total kinetic energy and total prompt neutron multiplicity at GSI

    Science.gov (United States)

    Martin, Julie-Fiona; Taieb, Julien; Chatillon, Audrey; Bélier, Gilbert; Boutoux, Guillaume; Ebran, Adeline; Gorbinet, Thomas; Grente, Lucie; Laurent, Benoit; Pellereau, Eric; Alvarez-Pol, Héctor; Audouin, Laurent; Aumann, Thomas; Ayyad, Yassid; Benlliure, Jose; Casarejos, Enrique; Cortina Gil, Dolores; Caamaño, Manuel; Farget, Fanny; Fernández Domínguez, Beatriz; Heinz, Andreas; Jurado, Beatriz; Kelić-Heil, Aleksandra; Kurz, Nikolaus; Nociforo, Chiara; Paradela, Carlos; Pietri, Stéphane; Ramos, Diego; Rodríguez-Sànchez, Jose-Luis; Rodríguez-Tajes, Carme; Rossi, Dominic; Schmidt, Karl-Heinz; Simon, Haik; Tassan-Got, Laurent; Vargas, Jossitt; Voss, Bernd; Weick, Helmut

    2015-12-01

    A novel technique for fission studies, based on the inverse kinematics approach, is presented. Following pioneering work in the nineties, the SOFIA Collaboration has designed and built an experimental set-up dedicated to the simultaneous measurement of isotopic yields, total kinetic energies and total prompt neutron multiplicities, by fully identifying both fission fragments in coincidence, for the very first time. This experiment, performed at GSI, permits to study the fission of a wide variety of fissioning systems, ranging from mercury to neptunium, possibly far from the valley of stability. A first experiment, performed in 2012, has provided a large array of unprecedented data regarding the nuclear fission process. An excerpt of the results is presented. With this solid starter, further improvements of the experimental set-up are considered, which are consistent with the expected developments at the GSI facility, in order to measure more fission observables in coincidence. The completeness reached in the SOFIA data, permits to scrutinize the correlations between the interesting features of fission, offering a very detailed insight in this still unraveled mechanism.

  5. Non-invasive screening method for simultaneous evaluation of in vivo growth factor release profiles from multiple ectopic bone tissue engineering implants

    Science.gov (United States)

    Kempen, Diederik H.R.; Lu, Lichun; Classic, Kelly L.; Hefferan, Theresa E.; Creemers, Laura B.; Maran, Avudaiappan; Dhert, Wouter J.A.; Yaszemski, Michael J.

    2008-01-01

    The purpose of this study was to develop and validate a screening method based on scintillation probes for the simultaneous evaluation of in vivo growth factor release profiles of multiple implants in the same animal. First, we characterized the scintillation probes in a series of in vitro experiments to optimize the accuracy of the measurement setup. The scintillation probes were found to have a strong geometric dependence and experience saturation effects at high activities. In vitro simulation of 4 subcutaneous limb implants in a rat showed minimal interference of surrounding implants on local measurements at close to parallel positioning of the probes. These characteristics were taken into consideration for the design of the probe setup and in vivo experiment. The measurement setup was then validated in a rat subcutaneous implantation model using 4 different sustained release carriers loaded with 125I-BMP-2 per animal. The implants were removed after 42 or 84 days of implantation, for comparison of the non-invasive method to ex-vivo radioisotope counting. The non-invasive method demonstrated a good correlation with the ex-vivo counting method at both time-points of all 4 carriers. Overall, this study showed that scintillation probes could be successfully used for paired measurement of 4 release profiles with minimal interference of the surrounding implants, and may find use as non-invasive screening tools for various drug delivery applications. PMID:18554743

  6. Studies on fission with ALADIN. Precise and simultaneous measurement of fission yields, total kinetic energy and total prompt neutron multiplicity at GSI

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Julie-Fiona; Taieb, Julien; Chatillon, Audrey; Belier, Gilbert; Boutoux, Guillaume; Ebran, Adeline; Gorbinet, Thomas; Grente, Lucie; Laurent, Benoit; Pellereau, Eric [CEA DAM Bruyeres-le-Chatel, Arpajon (France); Alvarez-Pol, Hector; Ayyad, Yassid; Benlliure, Jose; Cortina Gil, Dolores; Caamano, Manuel; Fernandez Dominguez, Beatriz; Paradela, Carlos; Ramos, Diego; Rodriguez-Sanchez, Jose-Luis; Vargas, Jossitt [Universidad de Santiago de Compostela, Santiago de Compostela (Spain); Audouin, Laurent; Tassan-Got, Laurent [CNRS/IN2P3, IPNO, Orsay (France); Aumann, Thomas [Technische Universitaet Darmstadt, Darmstadt (Germany); Casarejos, Enrique [Universidad de Vigo, Vigo (Spain); Farget, Fanny; Rodriguez-Tajes, Carme [CNRS/IN2P3, GANIL, Caen (France); Heinz, Andreas [Chalmers University of Technology, Gothenburg (Sweden); Jurado, Beatriz [CNRS/IN2P3, CENBG, Gradignan (France); Kelic-Heil, Aleksandra; Kurz, Nikolaus; Nociforo, Chiara; Pietri, Stephane; Rossi, Dominic; Schmidt, Karl-Heinz; Simon, Haik; Voss, Bernd; Weick, Helmut [GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany)

    2015-12-15

    A novel technique for fission studies, based on the inverse kinematics approach, is presented. Following pioneering work in the nineties, the SOFIA Collaboration has designed and built an experimental set-up dedicated to the simultaneous measurement of isotopic yields, total kinetic energies and total prompt neutron multiplicities, by fully identifying both fission fragments in coincidence, for the very first time. This experiment, performed at GSI, permits to study the fission of a wide variety of fissioning systems, ranging from mercury to neptunium, possibly far from the valley of stability. A first experiment, performed in 2012, has provided a large array of unprecedented data regarding the nuclear fission process. An excerpt of the results is presented. With this solid starter, further improvements of the experimental set-up are considered, which are consistent with the expected developments at the GSI facility, in order to measure more fission observables in coincidence. The completeness reached in the SOFIA data, permits to scrutinize the correlations between the interesting features of fission, offering a very detailed insight in this still unraveled mechanism. (orig.)

  7. Implementation of the basic hazard index screening for health risks associated with simultaneous exposure to multiple chemicals using a standardized target organ and systems framework.

    Science.gov (United States)

    Adams, Valerie H; McAtee, Matthew J; Johnson, Mark S

    2017-09-01

    Environmental health risk assessments often involve assessing the potential health effects of exposure to multiple chemicals at once (i.e., complex mixtures). Because the possible number of chemical combinations is very large, few controlled in vivo toxicological studies with chemical mixtures are relevant or practical. In lieu of specific mixture toxicity data, the segregated hazard index (HI) approach has been used to determine whether simultaneous exposures may warrant further investigation due to their combined adverse effects. Each chemical is assigned to one or more target organs based on critical effects; HIs for each target organ are generated by summing the individual hazard quotients for each of the chemicals assigned to that organ or organ system. To conduct this phased risk assessment approach in a consistent manner, a comprehensive, systematized list of toxicity targets for implementing this approach is needed. We present a comprehensive and standardized list of toxicity target organs and systems (TTOS), with example data sets, for consistent implementation of the segregated HI method. This method is designed to facilitate the standardization of the widespread use of the basic segregated HI approach. The basic hazard index mixtures screening (BHIMS) tool allows for rapid identification of exposure concerns that may warrant further and more sophisticated assessment. Integr Environ Assess Manag 2017;13:852-860. Published 2017. This article is a US Government work and is in the public domain in the USA. Published 2017. This article is a US Government work and is in the public domain in the USA.

  8. No Inbreeding depression for low temperature developmental acclimation across multiple drosophila species

    DEFF Research Database (Denmark)

    Kristensen, Torsten Nygård; Loeschcke, Volker; Bilde, Trine

    2011-01-01

    is highly species specific, and differs among ecotypes (e.g., tropical and widespread species). Apart from being exposed to thermal stress many small and fragmented populations face genetic challenges due to, for example, inbreeding. Inbreeding has been shown to reduce inherent resistance levels toward...... stressful temperatures, but whether adaptation to thermal stress through plastic responses also is affected by inbreeding is so far not clear. In this study, we test inherent cold resistance and the ability to respond plastically to temperature changes through developmental cold acclimation in inbred...... and outbred lines of five tropical and five widespread Drosophila species. Our results confirm that tropical species have lower cold resistance compared to widespread species, and show that (1) inbreeding reduces inherent cold resistance in both tropical and widespread species, (2) inbreeding does not affect...

  9. Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis.

    Directory of Open Access Journals (Sweden)

    Erin L Gross

    Full Text Available Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This

  10. Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis

    Science.gov (United States)

    Gross, Erin L.; Beall, Clifford J.; Kutsch, Stacey R.; Firestone, Noah D.; Leys, Eugene J.; Griffen, Ann L.

    2012-01-01

    Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have

  11. Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis.

    Science.gov (United States)

    Gross, Erin L; Beall, Clifford J; Kutsch, Stacey R; Firestone, Noah D; Leys, Eugene J; Griffen, Ann L

    2012-01-01

    Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have

  12. Characterization of a polymerase chain reaction-based approach for the simultaneous detection of multiple animal-derived materials in animal feed.

    Science.gov (United States)

    Myers, Michael J; Yancy, Haile F; Farrell, Dorothy E

    2003-06-01

    In this study, a polymerase chain reaction (PCR) primer set capable of amplifying a mitochondrial DNA segment of multiple species (cattle, sheep, goats, deer, and elk) whose rendered remains are prohibited from being fed to ruminants was characterized. However, the primer set also amplifies DNA derived from the rendered remains of pigs and horses, which are exempt from the feed ban. PCR amplicons derived from pig DNA have a restriction endonuclease site recognized by Hinf1, while the horse DNA-derived amplicon has a unique restriction endonuclease site recognized by HypCH4III. This "universal" PCR primer produced an amplicon with DNA extracted from dairy feed containing either bovine meat and bone meal or pig blood meal. Enzymatic digestion of the PCR amplicons from these feed samples with Hinf1 resulted in cleavage products only from samples containing pig blood meal. However, Hinf1 digestion of these amplicons was not complete. Further analysis of the pig blood meal with primers specific for bovine or porcine DNA demonstrated the presence of both bovine- and porcine-derived DNA. Enzymatic digestion confirmed these findings. Additional testing was conducted with dry dog food samples labeled as containing either lamb, chicken, turkey, or chicken and fish. The universal PCR primer produced an amplicon only for the dog food containing lamb meal. This paper is the first to describe a simplified approach for the detection of the prohibited species of concern in the feed ban.

  13. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species.

    Science.gov (United States)

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, William K; Prinzing, Andreas; Dong, Ming; Cornelissen, Johannes H C

    2015-08-18

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such contribution varies among plant species at given irradiance regime, (2) whether interspecific variation in such contribution correlates with interspecific variation in the decomposition rate under shade; and (3) whether this correlation can be explained by leaf traits. We conducted a factorial experiment to determine the effects of solar radiation and environmental moisture for the mass loss and the decomposition constant k-values of 13 species litters collected in Northern China. The contribution of solar radiation to leaf litter decomposition varied significantly among species. Solar radiation accelerated decomposition in particular in the species that already decompose quickly under shade. Functional traits, notably specific leaf area, might predict the interspecific variation in that contribution. Our results provide the first empirical evidence for how the effect of solar radiation on decomposition varies among multiple species. Thus, the effect of solar radiation on the carbon flux between biosphere and atmosphere may depend on the species composition of the vegetation.

  14. Characterization of Blue Mold Penicillium Species Isolated from Stored Fruits Using Multiple Highly Conserved Loci

    Directory of Open Access Journals (Sweden)

    Guohua Yin

    2017-03-01

    Full Text Available Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locations, and years. Based on morphological and cultural characteristics and partial amplification of the β-tubulin locus, the isolates were provisionally identified as several different species of Penicillium. These isolates were investigated further using a suite of molecular DNA markers and compared to sequences of the ex-type for cognate species in GenBank, and were identified as P. expansum (3 isolates, P. solitum (3 isolates, P. carneum (1 isolate, and P. paneum (1 isolate. Three of the markers we used (ITS, internal transcribed spacer rDNA sequence; benA, β-tubulin; CaM, calmodulin were suitable for distinguishing most of our isolates from one another at the species level. In contrast, we were unable to amplify RPB2 sequences from four of the isolates. Comparison of our sequences with cognate sequences in GenBank from isolates with the same species names did not always give coherent data, reinforcing earlier studies that have shown large intraspecific variability in many Penicillium species, as well as possible errors in some sequence data deposited in GenBank.

  15. The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles.

    Science.gov (United States)

    Huang, Jen-Pan; Knowles, L Lacey

    2016-07-01

    With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status. © The Author(s) 2015

  16. Multiple origins of BBCC allopolyploid species in the rice genus (Oryza).

    Science.gov (United States)

    Zou, Xin-Hui; Du, Yu-Su; Tang, Liang; Xu, Xin-Wei; Doyle, Jeff J; Sang, Tao; Ge, Song

    2015-10-13

    In the rice genus (Oryza), about one half of the species are allopolyploids. These species are not only important resources for rice breeding but also provide a unique opportunity for studying evolution of polyploid species. In the present study, we sequenced four biparentally inherited nuclear loci and three maternally inherited chloroplast fragments from all diploid and tetraploid species with the B- and C-genome types in this genus. We detected at least three independent origins of three BC-genome tetraploid species. Specifically, the diploid O. punctata (B-genome) and O. officinalis (C-genome) were the parental progenitors of O. minuta and O. malampuzhaensis with O. punctata being the maternal donors, whereas the diploid O. punctata and O. eichingeri (C-genome) were the progenitors of tetraploid O. punctata with O. punctata being the paternal donor. Our relaxed clock analyses suggest that all the BBCC species originated within the last one million years, which is coincident with the severe climate oscillations occurred during the last ice age, implying the potential impact of climate change on their formations and dispersals. In addition, our results support previous taxonomic arguments that the tetraploid O. punctata might be better treated as a separate species (O. schweinfurthiana).

  17. Improving discrimination of savanna tree species through a multiple endmember spectral-angle-mapper (SAM) approach: canopy level analysis

    CSIR Research Space (South Africa)

    Cho, Moses A

    2010-11-01

    Full Text Available that the lowest performance for discriminating rainforest species compared to linear discriminant analysis and maximum likelihood classifiers [10]. Our research hypothesis therefore centres on the fact that a multiple-endmember approach, involving many..., "Mapping forest alliances and associations using fuzzy systems and nearest neighbor classifiers," Remote Sensing of Environment, vol. 112, pp. 1037-1050, 2008. [16] M. Analoui and M. F. Amiri, "Feature reduction of nearest neighbor classifiers using...

  18. Multiple stirred-flow chamber assembly for simultaneous automatic fractionation of trace elements in fly ash samples using a multisyringe-based flow system.

    Science.gov (United States)

    Boonjob, Warunya; Miró, Manuel; Cerdà, Víctor

    2008-10-01

    There is a current trend in automation of leaching tests for trace elements in solid matrixes by use of flow injection based column approaches. However, as a result of the downscaled dimensions of the analytical manifold and execution of a single extraction at a time, miniaturized flow-through column approaches have merely found applications for periodic investigations of trace element mobility in highly homogeneous environmental solids. A novel flow-based configuration capitalized on stirred-flow cell extraction is proposed in this work for simultaneous fractionation of trace elements in three solid wastes with no limitation of sample amount up to 1.0 g. A two-step sequential extraction scheme involving water and acetic acid (or acetic acid/acetate buffer) is utilized for accurate assessment of readily mobilizable fractions of trace elements in fly ash samples. The fully automated extraction system features high tolerance to flow rates (elements provided that exhaustive extraction is ensured. Analytical performance of the dynamic extractor is evaluated for fractionation analysis of a real coal fly ash and BCR-176R fly ash certified reference material. No significant differences were found at the 0.05 significance level between summation of leached concentrations in each fraction plus residue and concentration values of BCR-176R, thus revealing the accuracy of the automated method. Overall extractable pools of trace metals in three samples are separated in less than 115 min, even for highly contaminated ashes, versus 18-24 h per fraction in equilibrium leaching tests. The multiple stirred-flow cell assembly is thus suitable for routine risk assessment studies of industrial solid byproduct.

  19. Specific IgE Antibodies in Young Children with Atopic Dermatitis--Correlation of Multiple Allergen Simultaneous Immunoblot Test and ImmunoCap System.

    Science.gov (United States)

    Konopka, Ewa; Ceregra, Aldona; Maciorkowska, Elzbieta; Surowska, Barbara; Trojanowska, Ilona; Roszko-Kirpsza, Izabela; Cukrowska, Bozena

    2016-01-01

    Sensitization to food allergens is a common condition in pediatric atopic dermatitis (AD). Recently, the multiple allergen simultaneous test (MAST) allowing for a comprehensive assessment of atopy has been developed, but the usefulness in young AD children is not known. The aim of this study was to determine IgE specificity in AD children using MAST and to compare the results for selected food allergens with the reference ImmunoCap system. The study enrolled 50 children up to 2 years old with a diagnosis of AD. IgE antibodies were measured with the MAST-immunoblots. Children with specific IgE levels ≥ 0.35 kU/L were identified as sensitized to allergens. Most often children were sensitized to food allergens (egg white and yolk, hazelnuts, potato, cow's milk proteins, wheat flour, codfish, and soybean), but a high percentage of them also had IgE antibodies against house dust mites (12%), grass (10%), and birch (10%). Eight percent of children were sensitized to domestic animals (cats and dogs). Almost perfect (kappa index 0.8 - 1.0) and substantial (kappa index 0.6 - 0.8) agreement between MAST and ImmunoCap was found for food allergens except codfish. Pearson's analysis of antibody classes showed a very strong correlation between two methods (r = 0.8 - 1.0) for egg white, hazelnuts, potato, cow's milk proteins, wheat flour, and soybean, and a strong correlation (r = 0.6 - 0.79) was observed for peanut, egg yolk, and codfish. The study showed the frequent occurrence of IgE antibodies against food and airborne and animal allergens in young AD children and confirmed the usefulness of MAST-immunoblots for screening of sensitization in pediatric patients.

  20. Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study.

    Science.gov (United States)

    Schneeberger, Pierre H H; Becker, Sören L; Pothier, Joël F; Duffy, Brion; N'Goran, Eliézer K; Beuret, Christian; Frey, Jürg E; Utzinger, Jürg

    2016-06-01

    The intestinal microbiome is a complex community and its role in influencing human health is poorly understood. While conventional microbiology commonly attributes digestive disorders to a single microorganism, a metagenomic approach can detect multiple pathogens simultaneously and might elucidate the role of microbial communities in the pathogenesis of intestinal diseases. We present a proof-of-concept that a shotgun metagenomic approach provides useful information on the diverse composition of intestinal pathogens and antimicrobial resistance profiles in human stool samples. In October 2012, we obtained stool specimens from patients with persistent diarrhea in south Côte d'Ivoire. Four stool samples were purposefully selected and subjected to microscopy, multiplex polymerase chain reaction (PCR), and a metagenomic approach. For the latter, we employed the National Center for Biotechnology Information nucleotide database and screened for 36 pathogenic organisms (bacteria, helminths, intestinal protozoa, and viruses) that may cause digestive disorders. We further characterized the bacterial population and the prevailing resistance patterns by comparing our metagenomic datasets with a genome-specific marker database and with a comprehensive antibiotic resistance database. In the four patients, the metagenomic approach identified between eight and 11 pathogen classes that potentially cause digestive disorders. For bacterial pathogens, the diagnostic agreement between multiplex PCR and metagenomics was high; yet, metagenomics diagnosed several bacteria not detected by multiplex PCR. In contrast, some of the helminth and intestinal protozoa infections detected by microscopy were missed by metagenomics. The antimicrobial resistance analysis revealed the presence of genes conferring resistance to several commonly used antibiotics. A metagenomic approach provides detailed information on the presence and diversity of pathogenic organisms in human stool samples

  1. Statistical design-principal component analysis optimization of a multiple response procedure using cloud point extraction and simultaneous determination of metals by ICP OES.

    Science.gov (United States)

    Bezerra, Marcos A; Bruns, Roy E; Ferreira, Sergio L C

    2006-11-24

    A procedure has been developed for the simultaneous determination of traces amounts of Cd, Cr, Cu, Mn, Ni and Pb from saline oil-refinery effluents and digested vegetable samples using inductively coupled plasma optical emission spectrometry (ICP OES). The procedure is based on cloud point extraction (CPE) of these metals as 2-(bromo-2-pyridylazo)-5-diethyl-amino-phenol (Br-PADAP) complexes into a micellar phase of octylphenoxypolyethoxyethanol (Triton X-114). Optimization of the procedure was performed by response surface methodology (RSM) using a Doehlert design. Principal components (PC) were used to simplify the multiple response analysis. A response surface for the first PC score is useful in determining the optimum conditions for the Cd, Cr, Cu, Mn and Pb determinations whereas the second PC is highly correlated with the Ni response. Improvement factors of 22, 36, 46, 25, 65 and 39, along with limits of detection (3sigma(B)) of 0.081, 0.79, 0.38, 0.83, 0.28 and 0.69 microg L(-1), and precision expressed as relative standard deviation (%R.S.D., n=8, 20.0 microg L(-1)) of 1.5, 2.2, 3.5, 2.6, 2.5 and 2.5 were achieved for Cd, Cr, Cu, Mn, Ni and Pb, respectively. The accuracy was evaluated by spike tests in oil-refinery effluent samples and analysis of a vegetable certified reference material (NIST 1571, orchard leaves). Results found were in agreement with certified values.

  2. Hippocampus-Sparing Whole-Brain Radiotherapy and Simultaneous Integrated Boost for Multiple Brain Metastases From Lung Adenocarcinoma: Early Response and Dosimetric Evaluation.

    Science.gov (United States)

    Kim, Kyung Hwan; Cho, Byoung Chul; Lee, Chang Geol; Kim, Hye Ryun; Suh, Yang Gun; Kim, Jun Won; Choi, Chihwan; Baek, Jong Geal; Cho, Jaeho

    2016-02-01

    In this study, the volume response and treatment outcome after hippocampus-sparing whole-brain radiotherapy (HS-WBRT) with simultaneous integrated boost (SIB) using tomotherapy were evaluated. Patients with primary lung adenocarcinoma and multiple brain metastases who had a Karnofsky performance status ≥ 70 and exhibited well-controlled extracranial disease were treated. The prescribed dose was administered in 10 to 14 fractions as 25 to 28 Gy to whole-brain parenchyma, as 40 to 48 Gy to the gross metastatic lesion, and as 30 to 42 Gy to a 5-mm margin to the metastatic lesion. Double-dose gadolinium contrast-enhanced magnetic resonance imaging at 1-mm slice thickness was performed before treatment and at 1, 4, and 7 months post-treatment. The tumor volume reduction ratio was calculated for each follow-up. Between July 2011 and September 2012, 11 patients with 70 lesions were included in this analysis. The median number of lesions per patient was 4 (range, 2-15). The median initial tumor volume was 0.235 cm(3) (range, 0.020-10.140 cm(3)). The treatment plans were evaluated regarding conformation number (CN), target coverage (TC), and homogeneity index (HI). The median follow-up duration was 14 months (range, 3-25 months) and the 1-year intracranial control rate was 67%. The tumor volume reduction was most prominent during the first month with a median reduction rate of 0.717 (range, -0.190 to 1.000). Complete remission was seen in 22 (33%) lesions, and 45 (64%) lesions showed more than 65% reduction in tumor volume. The CN, TC, and HI values were comparable to that of previous studies, and the mean hippocampal dose was 13.65 Gy. No treatment breaks or ≥ G3 acute toxicities were observed during or after treatment. The HS-WBRT with SIB in patients with multiple brain metastases was effective and feasible for volume reduction and showed excellent intracranial control. © The Author(s) 2015.

  3. DUSTMS-D: DISPOSAL UNIT SOURCE TERM - MULTIPLE SPECIES - DISTRIBUTED FAILURE DATA INPUT GUIDE.

    Energy Technology Data Exchange (ETDEWEB)

    SULLIVAN, T.M.

    2006-01-01

    Performance assessment of a low-level waste (LLW) disposal facility begins with an estimation of the rate at which radionuclides migrate out of the facility (i.e., the source term). The focus of this work is to develop a methodology for calculating the source term. In general, the source term is influenced by the radionuclide inventory, the wasteforms and containers used to dispose of the inventory, and the physical processes that lead to release from the facility (fluid flow, container degradation, wasteform leaching, and radionuclide transport). Many of these physical processes are influenced by the design of the disposal facility (e.g., how the engineered barriers control infiltration of water). The complexity of the problem and the absence of appropriate data prevent development of an entirely mechanistic representation of radionuclide release from a disposal facility. Typically, a number of assumptions, based on knowledge of the disposal system, are used to simplify the problem. This has been done and the resulting models have been incorporated into the computer code DUST-MS (Disposal Unit Source Term-Multiple Species). The DUST-MS computer code is designed to model water flow, container degradation, release of contaminants from the wasteform to the contacting solution and transport through the subsurface media. Water flow through the facility over time is modeled using tabular input. Container degradation models include three types of failure rates: (a) instantaneous (all containers in a control volume fail at once), (b) uniformly distributed failures (containers fail at a linear rate between a specified starting and ending time), and (c) gaussian failure rates (containers fail at a rate determined by a mean failure time, standard deviation and gaussian distribution). Wasteform release models include four release mechanisms: (a) rinse with partitioning (inventory is released instantly upon container failure subject to equilibrium partitioning (sorption) with

  4. Development and validation of a triplex real-time PCR assay for the simultaneous detection of three mustard species and three celery varieties in food.

    Science.gov (United States)

    Palle-Reisch, Monika; Hochegger, Rupert; Cichna-Markl, Margit

    2015-10-01

    The paper presents a triplex real-time PCR assay allowing the simultaneous detection of three mustard species (white, black and brown mustard) and three celery varieties (celery roots, celery stalks and leaf celery) in foodstuffs. The triplex assay does not show cross-reactivity with other Brassicaceae. Low cross-reactivities were observed with fenugreek, cumin, ginger, caraway, turmeric, lovage and rye, the ΔCt values were, however, ⩾ 12 compared to positive controls. The triplex assay allows the detection of traces of DNA of the allergenic components in spite of an excess of the other DNA templates. Analysis of extracts from model sausages containing defined concentrations of mustard and celery showed that the triplex assay is applicable to both raw and processed foods. It was found to allow the detection of 1 ppm black/brown mustard and 50 ppm white mustard and celery in raw and brewed sausages with a probability ⩾ 95%. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Multiple pro-apoptotic targets of abietane diterpenoids from Salvia species.

    Science.gov (United States)

    Akaberi, M; Mehri, S; Iranshahi, M

    2015-01-01

    The genus Salvia contains a large number of biologically active diterpenoids with various skeletons including abietanes, labdanes, clerodanes, pimaranes and icetexanes. Diterpenes of Salvia species showed various biological activities, particularly cytotoxic and anti-proliferative properties. In recent years many studies have been focused on the molecular mechanisms of these diterpenes in cancer cells. It should be noted, however, that anticancer studies on diterpenoids from Salvia species were dominated by tanshinones (a class of abietanes) over the past decades. A large number of targets of diterpenes have been identified in cancer cells including NF-κB, STAT3, Bcl-xL, β-catenin, cytochrome C and caspases. These studies give us deeper insights into the mechanisms of actions and cell signaling pathways of anticancer diterpenoids from Salvia species. This paper reviews protein targets of diterpenoids from Salvia species and highlights the gaps in our knowledge deserving future research. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Multiple Plantago species (Plantaginaceae) modify floral reflectance and color in response to thermal change.

    Science.gov (United States)

    Anderson, Erin R; Lovin, Mary E; Richter, Scott J; Lacey, Elizabeth P

    2013-12-01

    Understanding how plant reproduction responds to temperature has become increasingly important because of global climate change. Temperature-sensitive plasticity in floral reflectance is likely involved in some of these responses. Such plasticity, which underlies thermoregulatory ability, affects reproductive success in Plantago lanceolata. To see whether other Plantago species also show thermal plasticity in reflectance, we measured plasticity in P. lagopus, P. coronopus, P. major, P. subulata, P. albicans, P. tomentosa, P. maritima, and P. weldenii. We induced plants to flower at two temperatures in growth chambers and recorded floral reflectance (362-800 nm). All species were thermally plastic in visible and near-IR regions. Species and populations differed in response. Some showed greater variation in reflectance at warm temperature, while the reverse was true for others. Plasticity was greatest in the P. lanceolata clade. Cosmopolitan species were not more plastic than were geographically restricted species. The data suggest that (1) thermal plasticity is an ancestral trait for Plantago, (2) plasticities in visible and near-IR regions have evolved along different pathways within the genus, and (3) phylogenetic history partially explains this evolutionary divergence. Our data combined with those of previous studies suggest that global climate change will modify floral reflectance and color in many plant species. These modifications are likely to affect plant reproductive success.

  7. Multiple phenological responses to climate change among 42 plant species in Xi'an, China

    Science.gov (United States)

    Dai, Junhu; Wang, Huanjiong; Ge, Quansheng

    2013-09-01

    Phenological data of 42 woody plants in a temperate deciduous forest from the Chinese Phenological Observation Network (CPON) and the corresponding meteorological data from 1963 to 2011 in Xi'an, Shaanxi Province, China were collected and analyzed. The first leaf date (FLD), leaf coloring date (LCD) and first flower date (FFD) are revealed as strong biological signals of climatic change. The FLD, LCD and FFD of most species are sensitive to average temperature during a certain period before phenophase onset. Regional precipitation also has a significant impact on phenophases of about half of the species investigated. Affected by climate change, the FLD and FFD of these species have advanced by 5.54 days and 10.20 days on average during 2003-2011 compared with the period 1963-1996, respectively. Meanwhile, the LCD has delayed by 10.59 days, and growing season length has extended 16.13 days. Diverse responses of phenology commonly exist among different species and functional groups during the study period. Especially for FFD, the deviations between the above two periods ranged from -20.68 to -2.79 days; biotic pollination species showed a significantly greater advance than abiotic pollination species. These results were conducive to the understanding of possible changes in both the structure of plant communities and interspecific relationships in the context of climate change.

  8. Multiple ant species tending lac insect Kerria yunnanensis (Hemiptera: Kerriidae) provide asymmetric protection against parasitoids.

    Science.gov (United States)

    Chen, Youqing; Lu, Zhixing; Li, Qiao; Hoffmann, Benjamin D; Zhang, Wei

    2014-01-01

    This study investigated the effects of ant attendance on the parasitoid community and parasitism of lac insect Kerria yunnanensis aggregations in Yunnan province, China. We manipulated ant attendance to establish three treatments: (1) ant exclusion; (2) low ant attendance by several ant species; and (3) high ant attendance by Crematogaster macaoensis. Five parasitoid species were collected, with two species contributing 82.7 and 13.2% of total abundance respectively. Total parasitoid abundance was lowest in the February sample when K. yunnanensis was in its younger life stage, being significantly lower in the ant exclusion treatment. In April, all three treatments had significantly different parasitoid abundances, being highest in the ant exclusion treatment and the lowest in the high ant attendance treatment. When ants were present, there were strong negative relationships between total parasitoid abundance and ant abundance, with the relationships being dependent upon the ant species composition and abundance. The patterns of total parasitoid abundance were driven by the two most abundant parasitoid species. Parasitoid species richness did not differ among treatments or between sample times, however, multivariate analysis confirmed that overall parasitoid community structure differed significantly among treatments and between sample times, with the high ant attendance treatment differing most from the other two treatments. Interestingly the absence of ants did not result in increased parasitism from four of the five parasitoids. Ants in lac insect farming systems have a clear role for agricultural pest management. A full understanding of the asymmetric abilities of ants to influence parasitoid communities, and affect parasitism of hosts will require further experimental manipulation to assess the relative roles of 1) the abundance of each individual ant species on parasitoid access to hosts, 2) competition among parasitoids, and 3) the interaction between the

  9. Multiple strong postmating and intrinsic postzygotic reproductive barriers isolate florally diverse species of Jaltomata (Solanaceae).

    Science.gov (United States)

    Kostyun, Jamie L; Moyle, Leonie C

    2017-06-01

    Divergence in phenotypic traits often contributes to premating isolation between lineages, but could also promote isolation at postmating stages. Phenotypic differences could directly result in mechanical isolation or hybrids with maladapted traits; alternatively, when alleles controlling these trait differences pleiotropically affect other components of development, differentiation could indirectly produce genetic incompatibilities in hybrids. Here, we determined the strength of nine postmating and intrinsic postzygotic reproductive barriers among 10 species of Jaltomata (Solanaceae), including species with highly divergent floral traits. To evaluate the relative importance of floral trait diversification for the strength of these postmating barriers, we assessed their relationship to floral divergence, genetic distance, geographical context, and ecological differences, using conventional tests and a new linear-mixed modeling approach. Despite close evolutionary relationships, all species pairs showed moderate to strong isolation. Nonetheless, floral trait divergence was not a consistent predictor of the strength of isolation; instead this was best explained by genetic distance, although we found evidence for mechanical isolation in one species, and a positive relationship between floral trait divergence and fruit set isolation across species pairs. Overall, our data indicate that intrinsic postzygotic isolation is more strongly associated with genome-wide genetic differentiation, rather than floral divergence. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  10. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  11. Bovine digital dermatitis: Possible pathogenic consortium consisting of Dichelobacter nodosus and multiple Treponema species

    DEFF Research Database (Denmark)

    Rasmussen, Marianne; Capion, Nynne; Schou, Kirstine Klitgaard

    2012-01-01

    and distribution of seventeen phylotypes of Treponema in DD lesions by fluorescent in situ hybridization (FISH) applying species/phylotype-specific oligonucleotide probes. In situ hybridization for Dichelobacter nodosus, the cause of ovine footrot, was additionally performed. We sampled 90 biopsies of DD lesions......Bovine digital dermatitis (DD) is a multifactorial disease involving at least one or more treponemal species. Virulent phylotypes of Treponema and other infectious agents contributing to disease etiology still remain to be identified. This study addressed these questions by analyzing the prevalence...... not colonized by bacteria while only four samples were found normal. We hypothesise that external noxious stimuli allow D. nodosus to break down the epidermal barrier creating a suitable environment for the secondary invaders, Treponema species, which gradually take over the infection site. The variety...

  12. Multiple endmember spectral-angle-mapper (SAM) analysis improves discrimination of Savanna tree species

    CSIR Research Space (South Africa)

    Cho, Moses A

    2009-08-01

    Full Text Available ). The measurements were made on sunlit leaves. 2.2. Data analysis First, the spectral data for each species were randomly split into the training (1/3) and test (2/3) data. A resampling procedure was adopted in the splitting the data. Ten replicates were...). The overall, users and producers classification accuracies were determined as the mean values for the ten replicates from the confusion matrices between the observed and predicted data. The effect of within species spectral similarity or dissimilarity...

  13. Multiple interkingdom horizontal gene transfers in Pyrenophora and closely related species and their contributions to phytopathogenic lifestyles.

    Directory of Open Access Journals (Sweden)

    Bao-Fa Sun

    Full Text Available Many studies have reported horizontal gene transfer (HGT events from eukaryotes, especially fungi. However, only a few investigations summarized multiple interkingdom HGTs involving important phytopathogenic species of Pyrenophora and few have investigated the genetic contributions of HGTs to fungi. We investigated HGT events in P. teres and P. tritici-repentis and discovered that both species harbored 14 HGT genes derived from bacteria and plants, including 12 HGT genes that occurred in both species. One gene coding a leucine-rich repeat protein was present in both species of Pyrenophora and it may have been transferred from a host plant. The transfer of genes from a host plant to pathogenic fungi has been reported rarely and we discovered the first evidence for this transfer in phytopathogenic Pyrenophora. Two HGTs in Pyrenophora underwent subsequent duplications. Some HGT genes had homologs in a few other fungi, indicating relatively ancient transfer events. Functional analyses indicated that half of the HGT genes encoded extracellular proteins and these may have facilitated the infection of plants by Pyrenophora via interference with plant defense-response and the degradation of plant cell walls. Some other HGT genes appeared to participate in carbohydrate metabolism. Together, these functions implied that HGTs may have led to highly efficient mechanisms of infection as well as the utilization of host carbohydrates. Evolutionary analyses indicated that HGT genes experienced amelioration, purifying selection, and accelerated evolution. These appeared to constitute adaptations to the background genome of the recipient. The discovery of multiple interkingdom HGTs in Pyrenophora, their significance to infection, and their adaptive evolution, provided valuable insights into the evolutionary significance of interkingdom HGTs from multiple donors.

  14. Multiple interkingdom horizontal gene transfers in Pyrenophora and closely related species and their contributions to phytopathogenic lifestyles.

    Science.gov (United States)

    Sun, Bao-Fa; Xiao, Jin-Hua; He, Shunmin; Liu, Li; Murphy, Robert W; Huang, Da-Wei

    2013-01-01

    Many studies have reported horizontal gene transfer (HGT) events from eukaryotes, especially fungi. However, only a few investigations summarized multiple interkingdom HGTs involving important phytopathogenic species of Pyrenophora and few have investigated the genetic contributions of HGTs to fungi. We investigated HGT events in P. teres and P. tritici-repentis and discovered that both species harbored 14 HGT genes derived from bacteria and plants, including 12 HGT genes that occurred in both species. One gene coding a leucine-rich repeat protein was present in both species of Pyrenophora and it may have been transferred from a host plant. The transfer of genes from a host plant to pathogenic fungi has been reported rarely and we discovered the first evidence for this transfer in phytopathogenic Pyrenophora. Two HGTs in Pyrenophora underwent subsequent duplications. Some HGT genes had homologs in a few other fungi, indicating relatively ancient transfer events. Functional analyses indicated that half of the HGT genes encoded extracellular proteins and these may have facilitated the infection of plants by Pyrenophora via interference with plant defense-response and the degradation of plant cell walls. Some other HGT genes appeared to participate in carbohydrate metabolism. Together, these functions implied that HGTs may have led to highly efficient mechanisms of infection as well as the utilization of host carbohydrates. Evolutionary analyses indicated that HGT genes experienced amelioration, purifying selection, and accelerated evolution. These appeared to constitute adaptations to the background genome of the recipient. The discovery of multiple interkingdom HGTs in Pyrenophora, their significance to infection, and their adaptive evolution, provided valuable insights into the evolutionary significance of interkingdom HGTs from multiple donors.

  15. Forward selection for multiple resistance across the non-selective glyphosate, glufosinate and oxyfluorfen herbicides in Lolium weed species.

    Science.gov (United States)

    Fernández, Pablo; Alcántara, Ricardo; Osuna, María D; Vila-Aiub, Martin M; Prado, Rafael De

    2017-05-01

    In the Mediterranean area, Lolium species have evolved resistance to glyphosate after decades of continual use without other alternative chemicals in perennial crops (olive, citrus and vineyards). In recent years, oxyfluorfen alone or mixed with glyphosate and glufosinate has been introduced as a chemical option to control dicot and grass weeds. Dose-response studies confirmed that three glyphosate-resistant Lolium weed species (L. rigidum, L. perenne, L. multiflorum) collected from perennial crops in the Iberian Peninsula have also evolved resistance to glufosinate and oxyfluorfen herbicides, despite their recent introduction. Based on the LD50 resistance parameter, the resistance factor was similar among Lolium species and ranged from 14- to 21-fold and from ten- to 12-fold for oxyfluorfen and glufosinate respectively. Similarly, about 14-fold resistance to both oxyfluorfen and glufosinate was estimated on average for the three Lolium species when growth reduction (GR50 ) was assessed. This study identified oxyfluorfen resistance in a grass species for the first time. A major threat to sustainability of perennial crops in the Iberian Peninsula is evident, as multiple resistance to non-selective glyphosate, glufosinate and oxyfluorfen herbicides has evolved in L. rigidum, L. perenne and L. multiflorum weeds. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  16. Above- and below-ground effects of plant diversity depend on species origin: an experimental test with multiple invaders.

    Science.gov (United States)

    Kuebbing, Sara E; Classen, Aimée T; Sanders, Nathan J; Simberloff, Daniel

    2015-11-01

    Although many plant communities are invaded by multiple nonnative species, we have limited information on how a species' origin affects ecosystem function. We tested how differences in species richness and origin affect productivity and seedling establishment. We created phylogenetically paired native and nonnative plant communities in a glasshouse experiment to test diversity-productivity relationships and responsible mechanisms (i.e. selection or complementarity effects). Additionally, we tested how productivity and associated mechanisms influenced seedling establishment. We used diversity-interaction models to describe how species' interactions influenced diversity-productivity relationships. Communities with more species had higher total biomass than did monoculture communities, but native and nonnative communities diverged in root : shoot ratios and the mechanism responsible for increased productivity: positive selection effect in nonnative communities and positive complementarity effect in native communities. Seedling establishment was 46% lower in nonnative than in native communities and was correlated with the average selection effect. Interspecific interactions contributed to productivity patterns, but the specific types of interactions differed between native and nonnative communities. These results reinforce findings that the diversity-productivity mechanisms in native and nonnative communities differ and are the first to show that these mechanisms can influence seedling establishment and that different types of interactions influence diversity-productivity relationships. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  17. Apical dominance and apical control in multiple flushing of temperate woody species.

    Science.gov (United States)

    M. Cline; C. Harrington

    2007-01-01

    In young plants of many woody species, the first flush of growth in the spring may be followed by one or more flushes of the terminal shoot if growing conditions are favorable. The occurrence of these additional flushes may significantly affect crown form and structure. Apical dominance (AD) and apical control (AC) are thought to be important control mechanisms in this...

  18. Multiple antioxidant proteins protect Chlorobaculum tepidum against oxygen and reactive oxygen species

    DEFF Research Database (Denmark)

    Li, Hui; Jubelirer, Sara; Garcia Costas, Amaya M

    2009-01-01

    The genome of the green sulfur bacterium Chlorobaculum (Cba.) tepidum, a strictly anaerobic photolithoautotroph, is predicted to encode more than ten genes whose products are potentially involved in protection from reactive oxygen species and an oxidative stress response. The encoded proteins inc...

  19. Shifted excitation Raman difference spectroscopy at multiple wavelengths for in-situ meat species differentiation

    Science.gov (United States)

    Sowoidnich, Kay; Kronfeldt, Heinz-Detlef

    2012-09-01

    Two miniaturized Raman measurement heads containing microsystem diode lasers emitting at 783 and 671 nm suitable for shifted excitation Raman difference spectroscopy (SERDS) were applied for the non-invasive in situ differentiation of selected meat species. This allows using the fingerprint characteristics of Raman spectra without a disturbing fluorescence background. At 783 nm, two emission lines with a spectral shift of 0.5 nm (7 cm-1) and optical powers of up to 110 mW were realized. For 671 nm excitation, the spectral shift amounts to 0.6 nm (12 cm-1) and optical powers of up to 40 mW were obtained. In both cases, meat Raman spectra could be recorded with integration times of 10 s. The investigations were carried out using selected cuts from the most commonly consumed meat species in the US and Europe, i.e. beef, pork, chicken, and turkey. A principal components analysis of the SERDS spectra revealed a clear separation of the meat species into four distinct groups for both excitation wavelengths. This classification is based on the myoglobin content and gradual differences of protein Raman band intensities and positions. The results demonstrate the potential of SERDS as rapid and non-destructive screening method for the discrimination of selected meat species.

  20. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    Science.gov (United States)

    Sarmentine, 1-(1-pyrrolidinyl)-(2E,4E)-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in ...

  1. Multiple start codons and phosphorylation result in discrete Rad52 protein species

    DEFF Research Database (Denmark)

    de Mayolo, A.A.; Lisby, M.; Erdeniz, N.

    2006-01-01

    protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus...

  2. Termites amplify effects of wood traits on decomposition rates among multiple bamboo and dicot woody species

    NARCIS (Netherlands)

    Liu, Guofang; Cornwell, W.K.; Cao, Kunfang; Hu, Yukun; van Logtestijn, R.S.P; Yang, Shijian; Xie, Xiufang; Zhang, Yalin; Ye, Duo; Pan, Xu; Ye, Xuehua; Huang, Zhenying; Dong, Ming; Cornelissen, J.H.C.

    2015-01-01

    Wood decomposition is a key process in the terrestrial carbon cycle, controlling carbon storage with feedback to climate. In (sub) tropical forest, termites are major players in wood decomposition, but their role relative to that of microbial decomposers and wood traits of different tree species is

  3. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

    Science.gov (United States)

    2012-01-01

    Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic) and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia) from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH). In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’), resulting in the discovery of a radiation of (at least) 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically cryptic diversity among

  4. Separation of quercetin, sexangularetin, kaempferol and isorhamnetin for simultaneous HPLC determination of flavonoid aglycones in inflorescences, leaves and fruits of three Sorbus species.

    Science.gov (United States)

    Olszewska, Monika

    2008-11-04

    A reversed-phase high-performance liquid chromatographic (RP-HPLC) method was developed and validated for the simultaneous determination of four flavonol aglycones (quercetin, QU; sexangularetin, SX; kaempferol, KA; isorhamnetin, IS) in hydrolyzed extracts from different plant parts of Sorbus aucuparia L., Sorbus aria (L.) Crantz. and Sorbus intermedia (Ehrh.) Pers. Separation of the four compounds was accomplished on a C18 Lichrosphere 100 column (5 microm, 250 mm x 4.6mm, i.d.) with a methanol gradient elution and recorded at 370 nm. The high resolution of critical bands - SX, KA and IS - was achieved with retention of the last peak (IS) in 19.5 min. The equilibration of the standard mixture by addition of HCl to an acid concentration equal that of hydrolyzed extracts injected was found to be necessary when minimizing calibration error. The correlation coefficients of all the calibration curves showed good linearity (r>0.9991) over the test range. The relative standard deviation of the method was less than 2.8% for intra- and inter-day assays, and the average recoveries were between 95.5 and 102.5%. High sensitivity was demonstrated with detection limits between 0.050 and 0.085 microg/ml. The level of total aglycones was found to be in the range of 687-1,515 mg/100g of dry weight in the inflorescences, 424-1,078 mg/100g in the leaves and 20-60 mg/100g in the fruits depending on the Sorbus species.

  5. One single standard substance for the simultaneous determination of 17 triterpenes in Ganoderma lingzhi and its related species using high-performance liquid chromatography.

    Science.gov (United States)

    Liu, Wei; Zhang, Jingsong; Han, Wei; Liu, Yanfang; Feng, Jie; Tang, Chuanhong; Feng, Na; Tang, Qingjiu

    2017-11-15

    Due to the difficulty and high cost for the preparation of triterpenes, one single standard for the simultaneous determination of multi-components (SSDMC) with high performance liquid chromatography (HPLC) is an advanced solution for multi-component analysis. Experiments were carried out to investigate the feasibility of SSDMC for the analysis of Ganoderma triterpenes, with external standard method (ESM) compared, and the samples of Ganoderma were classified by the content of Ganoderma triterpenes. The analysis was performed by using a Fortis Speed Core-C18 column (150mm×4.6mm I.D., 2.6μm) at gradient elution of 0.01% glacial acetic acid-water (V/V) and acetonitrile with diode array detection (252nm), at a flow rate of 1mL/min. The results showed that all calibration curves had good linearity (r 2 >0.9999) within test ranges. The LOD and LOQ were lower than 2.52ng and 6.43ng, respectively. The RSD for intra-day and inter-day of the seventeen analytes were less than 3.12% at three levels, and the recoveries were 91.4-103.0%. The contents of other 16 triterpenes were determined with ganoderic acid A by SSDMC, which showed that there were few differences compared with the results obtained by ESM. Moreover, the classification of 25 different species and strains of Ganoderma by using the content of triterpenes intuitively reflected the distinction among Ganoderma. In summary, the developed method could be readily utilized as a method of quality evaluation for Ganoderma triterpenes. Copyright © 2017. Published by Elsevier B.V.

  6. The simultaneous detection of mitochondrial DNA damage from sun-exposed skin of three whale species and its association with UV-induced microscopic lesions and apoptosis.

    Science.gov (United States)

    Bowman, Amy; Martinez-Levasseur, Laura M; Acevedo-Whitehouse, Karina; Gendron, Diane; Birch-Machin, Mark A

    2013-07-01

    Due to life history and physiological constraints, cetaceans (whales) are unable to avoid prolonged exposure to external environmental insults, such as solar ultraviolet radiation (UV). The majority of studies on the effects of UV on skin are restricted to humans and laboratory animals, but it is important to develop tools to understand the effects of UV damage on large mammals such as whales, as these animals are long-lived and widely distributed, and can reflect the effects of UV across a large geographical range. We and others have used mitochondrial DNA (mtDNA) as a reliable marker of UV-induced damage particularly in human skin. UV-induced mtDNA strand breaks or lesions accumulate throughout the lifespan of an individual, thus constituting an excellent biomarker for cumulative exposure. Based on our previous studies in human skin, we have developed for the first time in the literature a quantitative real-time PCR methodology to detect and quantify mtDNA lesions in skin from sun-blistered whales. Furthermore the methodology allows for simultaneous detection of mtDNA damage in different species. Therefore using 44 epidermal mtDNA samples collected from 15 blue whales, 10 fin whales, and 19 sperm whales from the Gulf of California, Mexico, we quantified damage across 4.3 kilobases, a large region of the ~16,400 base pair whale mitochondrial genome. The results show a range of mtDNA damage in the skin of the three different whale species. This previously unreported observation was correlated with apoptotic damage and microscopic lesions, both of which are markers of UV-induced damage. As is the case in human studies, this suggests the potential use of mtDNA as a biomarker for measuring the effect of cumulative UV exposure in whales and may provide a platform to help understand the effects of changing global environmental conditions. Copyright © 2013 Elsevier B.V. and Mitochondria Research Society. All rights reserved. All rights reserved.

  7. Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

    Science.gov (United States)

    Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

    2017-09-01

    The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

  8. Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

    Science.gov (United States)

    Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

    2018-02-01

    The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

  9. A Comparison of Multiple Esterases as Biomarkers of Organophosphate Exposure and Effect in Two Earthworm Species

    Science.gov (United States)

    Schneider, Ashley; Stoskopf, Michael K.

    2011-01-01

    Two different earthworm species, Eisenia fetida and Lumbricus terrestris, were exposed to 5 μg/cm2 of malathion to evaluate their usefulness as sentinels of organophosphate exposure and to assess three different esterases, as biomarkers of malathion exposure and effect. Tissue xenobiotic burdens and esterase activity were determined for each species and each esterase in order to assess variability. E. fetida exhibited 4-fold less variability in tissue burdens than did L. terrestris and had less variable basal esterase activities. An attempt was made to correlate malathion and malaoxon tissue burdens with esterase activity post-exposure. There was no malaoxon present in the earthworm tissues. No significant correlations were determined by comparing acetylcholinesterase, butyrylcholinesterase, nor carboxylesterase activities with malathion burdens. PMID:21404045

  10. Three in One--Multiple Faunal Elements within an Endangered European Butterfly Species.

    Science.gov (United States)

    Junker, Marius; Zimmermann, Marie; Ramos, Ana A; Gros, Patrick; Konvička, Martin; Nève, Gabriel; Rákosy, László; Tammaru, Toomas; Castilho, Rita; Schmitt, Thomas

    2015-01-01

    Ice ages within Europe forced many species to retreat to refugia, of which three major biogeographic basic types can be distinguished: "Mediterranean", "Continental" and "Alpine / Arctic" species. However, this classification often fails to explain the complex phylogeography of European species with a wide range of latitudinal and altitudinal distribution. Hence, we tested for the possibility that all three mentioned faunal elements are represented within one species. Our data was obtained by scoring 1,307 Euphydryas aurinia individuals (46 European locations) for 17 allozyme loci, and sequencing a subset of 492 individuals (21 sites) for a 626 base pairs COI fragment. Genetic diversity indices, F statistics, hierarchical analyses of molecular variance, individual-based clustering, and networks were used to explore the phylogeographic patterns. The COI fragment represented 18 haplotypes showing a strong geographic structure. All but one allozyme loci analysed were polymorphic with a mean FST of 0.20, supporting a pronounced among population structure. Interpretation of both genetic marker systems, using several analytical tools, calls for the recognition of twelve genetic groups. These analyses consistently distinguished different groups in Iberia (2), Italy, Provence, Alps (3), Slovenia, Carpathian Basin, the lowlands of West and Central Europe as well as Estonia, often with considerable additional substructures. The genetic data strongly support the hypothesis that E. aurinia survived the last glaciation in Mediterranean, extra-Mediterranean and perialpine refugia. It is thus a rare example of a model organism that combines attributes of faunal elements from all three of these sources. The observed differences between allozymes and mtDNA most likely result from recent introgression of mtDNA into nuclear allozyme groups. Our results indicate discrepancies with the morphologically-based subspecies models, underlining the need to revise the current taxonomy.

  11. Three in One--Multiple Faunal Elements within an Endangered European Butterfly Species.

    Directory of Open Access Journals (Sweden)

    Marius Junker

    Full Text Available Ice ages within Europe forced many species to retreat to refugia, of which three major biogeographic basic types can be distinguished: "Mediterranean", "Continental" and "Alpine / Arctic" species. However, this classification often fails to explain the complex phylogeography of European species with a wide range of latitudinal and altitudinal distribution. Hence, we tested for the possibility that all three mentioned faunal elements are represented within one species. Our data was obtained by scoring 1,307 Euphydryas aurinia individuals (46 European locations for 17 allozyme loci, and sequencing a subset of 492 individuals (21 sites for a 626 base pairs COI fragment. Genetic diversity indices, F statistics, hierarchical analyses of molecular variance, individual-based clustering, and networks were used to explore the phylogeographic patterns. The COI fragment represented 18 haplotypes showing a strong geographic structure. All but one allozyme loci analysed were polymorphic with a mean FST of 0.20, supporting a pronounced among population structure. Interpretation of both genetic marker systems, using several analytical tools, calls for the recognition of twelve genetic groups. These analyses consistently distinguished different groups in Iberia (2, Italy, Provence, Alps (3, Slovenia, Carpathian Basin, the lowlands of West and Central Europe as well as Estonia, often with considerable additional substructures. The genetic data strongly support the hypothesis that E. aurinia survived the last glaciation in Mediterranean, extra-Mediterranean and perialpine refugia. It is thus a rare example of a model organism that combines attributes of faunal elements from all three of these sources. The observed differences between allozymes and mtDNA most likely result from recent introgression of mtDNA into nuclear allozyme groups. Our results indicate discrepancies with the morphologically-based subspecies models, underlining the need to revise the current

  12. Multiple mechanism confers natural tolerance of three lilyturf species to glyphosate.

    Science.gov (United States)

    Mao, Chanjuan; Xie, Hongjie; Chen, Shiguo; Valverde, Bernal E; Qiang, Sheng

    2016-02-01

    A combination of unique EPSPS structure and increased gene copy number and expression contribute to natural glyphosate tolerance in three lilyturf species. A few plants are naturally tolerant to glyphosate, the most widely used non-selective herbicide worldwide. Here, the basis for natural tolerance to glyphosate in three lilyturf species, Ophiopogon japonicus (OJ), Liriope spicata (LS), and Liriope platyphylla (LP), is characterized. These species tolerate glyphosate at about five times the commercially recommended field dose. They share three unique amino acids in their 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) that affect glyphosate binding. These correspond to Asp71Met, Ala112Ile, and Val201Met amino acid variations compared to 231 other published plant EPSPS amino acid sequences. There was also a common deletion at 91 of a highly conserved glutamic acid. Glyphosate-treated lilyturf plants accumulated little shikimic acid but had significantly higher levels of EPSPS mRNA than initially expressed in the control. The IC50 of LsEPSPS was 14.0 µM compared to the 5.1 µM of Arabidopsis thaliana. The higher K m and K i values of LsEPSPS kinetics showed that LsEPSPS had lower substrate binding affinity to glyphosate. Overexpression of LsEPSPS in the recombinant E. coli BL21 (DE3) strain enhanced its tolerance to glyphosate. Both OJ and LS had two copies of the EPSPS gene, while LP had three copies. Therefore, a combination of unique EPSPS structure and increased gene copy number and expression contribute to natural glyphosate tolerance in the three lilyturf species.

  13. Cryptosporidium rubeyi n. sp. (Apicomplexa: Cryptosporidiidae in multiple Spermophilus ground squirrel species

    Directory of Open Access Journals (Sweden)

    Xunde Li

    2015-12-01

    Full Text Available Previously we reported the unique Cryptosporidium sp. “c” genotype (e.g., Sbey03c, Sbey05c, Sbld05c, Sltl05c from three species of Spermophilus ground squirrel (Spermophilus beecheyi, Spermophilus beldingi, Spermophilus lateralis located throughout California, USA. This follow-up work characterizes the morphology and animal infectivity of this novel genotype as the final step in proposing it as a new species of Cryptosporidium. Analysis of sequences of 18S rRNA, actin, and HSP70 genes of additional Cryptosporidium isolates from recently sampled California ground squirrels (S. beecheyi confirms the presence of the unique Sbey-c genotype in S. beecheyi. Phylogenetic and BLAST analysis indicates that the c-genotype in Spermophilus ground squirrels is distinct from Cryptosporidium species/genotypes from other host species currently available in GenBank. We propose to name this c-genotype found in Spermophilus ground squirrels as Cryptosporidium rubeyi n. sp. The mean size of C. rubeyi n. sp. oocysts is 4.67 (4.4–5.0 μm × 4.34 (4.0–5.0 μm, with a length/width index of 1.08 (n = 220. Oocysts of C. rubeyi n. sp. are not infectious to neonatal BALB/c mice and Holstein calves. GenBank accession numbers for C. rubeyi n. sp. are DQ295012, AY462233, and KM010224 for the 18S rRNA gene, KM010227 for the actin gene, and KM010229 for the HSP70 gene.

  14. Three in One—Multiple Faunal Elements within an Endangered European Butterfly Species

    Science.gov (United States)

    Junker, Marius; Zimmermann, Marie; Ramos, Ana A.; Gros, Patrick; Konvička, Martin; Nève, Gabriel; Rákosy, László; Tammaru, Toomas

    2015-01-01

    Ice ages within Europe forced many species to retreat to refugia, of which three major biogeographic basic types can be distinguished: "Mediterranean", "Continental" and "Alpine / Arctic" species. However, this classification often fails to explain the complex phylogeography of European species with a wide range of latitudinal and altitudinal distribution. Hence, we tested for the possibility that all three mentioned faunal elements are represented within one species. Our data was obtained by scoring 1,307 Euphydryas aurinia individuals (46 European locations) for 17 allozyme loci, and sequencing a subset of 492 individuals (21 sites) for a 626 base pairs COI fragment. Genetic diversity indices, F statistics, hierarchical analyses of molecular variance, individual-based clustering, and networks were used to explore the phylogeographic patterns. The COI fragment represented 18 haplotypes showing a strong geographic structure. All but one allozyme loci analysed were polymorphic with a mean FST of 0.20, supporting a pronounced among population structure. Interpretation of both genetic marker systems, using several analytical tools, calls for the recognition of twelve genetic groups. These analyses consistently distinguished different groups in Iberia (2), Italy, Provence, Alps (3), Slovenia, Carpathian Basin, the lowlands of West and Central Europe as well as Estonia, often with considerable additional substructures. The genetic data strongly support the hypothesis that E. aurinia survived the last glaciation in Mediterranean, extra-Mediterranean and perialpine refugia. It is thus a rare example of a model organism that combines attributes of faunal elements from all three of these sources. The observed differences between allozymes and mtDNA most likely result from recent introgression of mtDNA into nuclear allozyme groups. Our results indicate discrepancies with the morphologically-based subspecies models, underlining the need to revise the current taxonomy. PMID

  15. The origin of multiple clones in the parthenogenetic lizard species Darevskia rostombekowi.

    Science.gov (United States)

    Ryskov, Alexey P; Osipov, Fedor A; Omelchenko, Andrey V; Semyenova, Seraphima K; Girnyk, Anastasiya E; Korchagin, Vitaly I; Vergun, Andrey A; Murphy, Robert W

    2017-01-01

    The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species. All individuals are heterozygous at the loci. The major clone occurs in 24 individuals and involves three populations. Four rare clones involve one or several individuals from one or two populations. Most variation owes to parent-specific single nucleotide polymorphisms, which occur as heterozygotes. This result fails to reject the hypothesis of a single hybridization founder event that resulted in the initial formation of one major clone. The other clones appear to have originated via post-formation microsatellite mutations of the major clone.

  16. The origin of multiple clones in the parthenogenetic lizard species Darevskia rostombekowi.

    Directory of Open Access Journals (Sweden)

    Alexey P Ryskov

    Full Text Available The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species. All individuals are heterozygous at the loci. The major clone occurs in 24 individuals and involves three populations. Four rare clones involve one or several individuals from one or two populations. Most variation owes to parent-specific single nucleotide polymorphisms, which occur as heterozygotes. This result fails to reject the hypothesis of a single hybridization founder event that resulted in the initial formation of one major clone. The other clones appear to have originated via post-formation microsatellite mutations of the major clone.

  17. Mating rate influences female reproductive investment in a simultaneous hermaphrodite, Lymnaea stagnalis.

    NARCIS (Netherlands)

    Hoffer, J.N.A.; Schwegler, D.; Ellers, J.; Koene, J.M.

    2012-01-01

    Multiple mating often imposes direct fitness costs on females but can provide indirect benefits such as enhanced genetic diversity and offspring quality. The costs and benefits of multiple mating have been investigated extensively in separate-sex species but less so in simultaneous hermaphrodites,

  18. Multiple-technique identification of sibling species of the Anopheles quadrimaculatus complex.

    Science.gov (United States)

    Narang, S K; Seawright, J A; Mitchell, S E; Kaiser, P E; Carlson, D A

    1993-12-01

    In the past, most researchers used a single technique for identification of cryptic taxa, population structures, biosystematics, and phylogenetic studies. Our experience with the Anopheles quadrimaculatus complex shows the importance of using several methods on individual mosquitoes. This approach consists of analysis of the polytene chromosomes in ovarian nurse cells, gas chromatographic profiles of cuticular hydrocarbons, isozyme electrophoresis, and restriction site analysis of mitochondrial or genomic DNA. We recommend use of this multiple-technique approach when analyzing feral populations for the first time, or for correlating information obtained by investigators using different techniques.

  19. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A; Lane, Charles R; Thon, Michael R; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  20. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

  1. Cross-species chromosome painting tracks the independent origin of multiple sex chromosomes in two cofamiliar Erythrinidae fishes

    Directory of Open Access Journals (Sweden)

    Trifonov Vladimir

    2011-06-01

    Full Text Available Abstract Background The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X1X2Y sex systems in Hoplias malabaricus and Erythrinus erythrinus. At first, the occurrence of a same sex chromosome system within a family suggests that the sex chromosomes are correlated and originated from ancestral XY chromosomes that were either homomorphic or at an early stage of differentiation. To identify the origin and evolution of these X1X2Y sex chromosomes, we performed reciprocal cross-species FISH experiments with two sex-chromosome-specific probes designed from microdissected X1 and Y chromosomes of H. malabaricus and E. erythrinus, respectively. Results Our results yield valuable information regarding the origin and evolution of these sex chromosome systems. Our data indicate that these sex chromosomes evolved independently in these two closed related Erythrinidae species. Different autosomes were first converted into a poorly differentiated XY sex pair in each species, and additional chromosomal rearrangements produced both X1X2Y sex systems that are currently present. Conclusions Our data provide new insights into the origin and evolution of sex chromosomes, which increases our knowledge about fish sex chromosome evolution.

  2. Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

    Science.gov (United States)

    Beauparlant, Marc A; Drouin, Guy

    2014-02-01

    Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

  3. Multiple Species of Trichosporon Produce Biofilms Highly Resistant to Triazoles and Amphotericin B

    Science.gov (United States)

    Iturrieta-González, Isabel Antonieta; Padovan, Ana Carolina Barbosa; Bizerra, Fernando César; Hahn, Rosane Christine; Colombo, Arnaldo Lopes

    2014-01-01

    Invasive infections caused by Trichosporon spp. have increased considerably in recent years, especially in neutropenic and critically ill patients using catheters and antibiotics. The genus presents limited sensitivity to different antifungal agents, but triazoles are the first choice for treatment. Here, we investigated the biofilm production and antifungal susceptibility to triazoles and amphotericin B of 54 Trichosporon spp. isolates obtained from blood samples (19), urine (20) and superficial mycosis (15). All isolates and 7 reference strains were identified by sequence analysis and phylogenetic inferences of the IGS1 region of the rDNA. Biofilms were grown on 96-well plates and quantitation was performed using crystal violet staining, complemented with Scanning Electron Microscopy (SEM). Susceptibility tests for fluconazole, itraconazole, voriconazole and amphotericin B were processed using the microdilution broth method (CLSI) for planktonic cells and XTT reduction assay for biofilm-forming cells. Our results showed that T. asahii was the most frequent species identified (66.7%), followed by T. faecale (11.1%), T. asteroides (9.3%), T. inkin (7.4%), T. dermatis (3.7%) and one T. coremiiforme (1.8%). We identified 4 genotypes within T. asahii isolates (G1, G3, G4 and G5) and 2 genotypes within T. faecale (G1 and G3). All species exhibited high adhesion and biofilm formation capabilities, mainly T. inkin, T. asteroides and T. faecale. Microscopy images of high biofilm-producing isolates showed that T. asahii presented mainly hyphae and arthroconidia, whereas T. asteroides exhibited mainly short arthroconidia and few filaments. Voriconazole exhibited the best in vitro activity against all species tested. Biofilm-forming cells of isolates and reference strains were highly resistant to all antifungals tested. We concluded that levels of biofilm formation by Trichosporon spp. were similar or even greater than those described for the Candida genus. Biofilm

  4. Multiple species of Trichosporon produce biofilms highly resistant to triazoles and amphotericin B.

    Science.gov (United States)

    Iturrieta-González, Isabel Antonieta; Padovan, Ana Carolina Barbosa; Bizerra, Fernando César; Hahn, Rosane Christine; Colombo, Arnaldo Lopes

    2014-01-01

    Invasive infections caused by Trichosporon spp. have increased considerably in recent years, especially in neutropenic and critically ill patients using catheters and antibiotics. The genus presents limited sensitivity to different antifungal agents, but triazoles are the first choice for treatment. Here, we investigated the biofilm production and antifungal susceptibility to triazoles and amphotericin B of 54 Trichosporon spp. isolates obtained from blood samples (19), urine (20) and superficial mycosis (15). All isolates and 7 reference strains were identified by sequence analysis and phylogenetic inferences of the IGS1 region of the rDNA. Biofilms were grown on 96-well plates and quantitation was performed using crystal violet staining, complemented with Scanning Electron Microscopy (SEM). Susceptibility tests for fluconazole, itraconazole, voriconazole and amphotericin B were processed using the microdilution broth method (CLSI) for planktonic cells and XTT reduction assay for biofilm-forming cells. Our results showed that T. asahii was the most frequent species identified (66.7%), followed by T. faecale (11.1%), T. asteroides (9.3%), T. inkin (7.4%), T. dermatis (3.7%) and one T. coremiiforme (1.8%). We identified 4 genotypes within T. asahii isolates (G1, G3, G4 and G5) and 2 genotypes within T. faecale (G1 and G3). All species exhibited high adhesion and biofilm formation capabilities, mainly T. inkin, T. asteroides and T. faecale. Microscopy images of high biofilm-producing isolates showed that T. asahii presented mainly hyphae and arthroconidia, whereas T. asteroides exhibited mainly short arthroconidia and few filaments. Voriconazole exhibited the best in vitro activity against all species tested. Biofilm-forming cells of isolates and reference strains were highly resistant to all antifungals tested. We concluded that levels of biofilm formation by Trichosporon spp. were similar or even greater than those described for the Candida genus. Biofilm

  5. Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

    Directory of Open Access Journals (Sweden)

    Deng Minghua

    2008-12-01

    Full Text Available Abstract Background Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs. Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts. Results We constructed a hierarchical stochastic language (HSL model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or OsALYL1, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes. Conclusion Our findings indicate that 1 the HSL model can be used to accurately predict core TRRs of transcripts across species and 2 identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.

  6. Extension of Bacillus endospore gas dynamic heating studies to multiple species and test conditions.

    Science.gov (United States)

    Gates, S D; McCartt, A D; Jeffries, J B; Hanson, R K; Hokama, L A; Mortelmans, K E

    2011-10-01

    Shock wave-induced damage to a variety of Bacillus endospore species is studied for a wide range of postshock temperatures and test times in oxidative and non-oxidative gas environments. Bacillus atrophaeus and Bacillus subtilis endospores are nebulized into an aqueous aerosol, loaded into the Stanford aerosol shock tube (SAST) and subjected to shock waves of controlled strength. Endospores experience uniform test temperatures between 500 and 1000 K and pressures ranging from 2 to 7 atm, for either a short test time (∼2·5 ms) or a relatively long test time (∼45 ms). During this process, the bioaerosol is observed using in situ laser absorption and scattering diagnostics. Additionally, shock-treated samples are extracted for ex situ analysis including viability plating and flow cytometry. For short test times, results are consistent with previous studies; all endospore species begin to lose the ability to form colonies when shock-heated to temperatures above 500 K, while significant breakdown in morphology is observed for postshock temperatures above 700 K. Oxidative bath gases did not affect viability losses or morphological breakdown rates. Experiments with extended postshock test time showed increased viability loss with minimal morphological damage for shocks between 600 and 700 K. Genetic differences between B. subtilis and B. atrophaeus endospores do not confer noticeable gains in resistance to shock heating. Oxidative environments do not exacerbate shock-induced damage to endospores. Extended test time experiments reinforce our hypothesis that a temperature/time-dependent inactivation mechanism that does not involve morphological breakdown exists at low-to-moderate postshock temperatures. The methodology and experiments described in this paper extend the study of the interactions of endospores with shock/blast waves to new species and environmental conditions. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied

  7. Influence of coupling on thermal forces and dynamic friction in plasmas with multiple ion species

    CERN Document Server

    Kagan, Grigory; Daligault, Jerome

    2016-01-01

    The recently proposed effective potential theory [Phys. Rev. Lett. 110, 235001 (2013)] is used to investigate the influence of coupling on inter-ion-species diffusion and momentum exchange in multi-component plasmas. Thermo-diffusion and the thermal force are found to diminish rapidly as strong coupling onsets. For the same coupling parameters, the dynamic friction coefficient is found to tend to unity. These results provide an impetus for addressing the role of coupling on diffusive processes in inertial confinement fusion experiments.

  8. Influence of coupling on thermal forces and dynamic friction in plasmas with multiple ion species

    Science.gov (United States)

    Kagan, Grigory; Baalrud, Scott D.; Daligault, Jérôme

    2017-07-01

    The recently proposed effective potential theory [Phys. Rev. Lett. 110, 235001 (2013)] is used to investigate the influence of coupling on inter-ion-species diffusion and momentum exchange in multi-component plasmas. Thermo-diffusion and the thermal force are found to diminish rapidly as strong coupling onsets. For the same coupling parameters, the dynamic friction coefficient is found to tend to unity. These results provide an impetus for addressing the role of coupling on diffusive processes in inertial confinement fusion experiments.

  9. Mitochondrial genome analyses suggest multiple Trichuris species in humans, baboons, and pigs from different geographical regions

    DEFF Research Database (Denmark)

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.

    2015-01-01

    in primates. METHODS AND FINDINGS: We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes......) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from...

  10. A noninvasive, direct real-time PCR method for sex determination in multiple avian species

    Science.gov (United States)

    Brubaker, Jessica L.; Karouna-Renier, Natalie K.; Chen, Yu; Jenko, Kathryn; Sprague, Daniel T.; Henry, Paula F.P.

    2011-01-01

    Polymerase chain reaction (PCR)-based methods to determine the sex of birds are well established and have seen few modifications since they were first introduced in the 1990s. Although these methods allowed for sex determination in species that were previously difficult to analyse, they were not conducive to high-throughput analysis because of the laboriousness of DNA extraction and gel electrophoresis. We developed a high-throughput real-time PCR-based method for analysis of sex in birds, which uses noninvasive sample collection and avoids DNA extraction and gel electrophoresis.

  11. Evidence for retrovirus and paramyxovirus infection of multiple bat species in china.

    Science.gov (United States)

    Yuan, Lihong; Li, Min; Li, Linmiao; Monagin, Corina; Chmura, Aleksei A; Schneider, Bradley S; Epstein, Jonathan H; Mei, Xiaolin; Shi, Zhengli; Daszak, Peter; Chen, Jinping

    2014-05-16

    Bats are recognized reservoirs for many emerging zoonotic viruses of public health importance. Identifying and cataloguing the viruses of bats is a logical approach to evaluate the range of potential zoonoses of bat origin. We characterized the fecal pathogen microbiome of both insectivorous and frugivorous bats, incorporating 281 individual bats comprising 20 common species, which were sampled in three locations of Yunnan province, by combining reverse transcription polymerase chain reaction (RT-PCR) assays and next-generation sequencing. Seven individual bats were paramyxovirus-positive by RT-PCR using degenerate primers, and these paramyxoviruses were mainly classified into three genera (Rubulavirus, Henipavirus and Jeilongvirus). Various additional novel pathogens were detected in the paramyxovirus-positive bats using Illumina sequencing. A total of 7066 assembled contigs (≥200 bp) were constructed, and 105 contigs matched eukaryotic viruses (of them 103 belong to 2 vertebrate virus families, 1 insect virus, and 1 mycovirus), 17 were parasites, and 4913 were homologous to prokaryotic microorganisms. Among the 103 vertebrate viral contigs, 79 displayed low identity (retroviruses. The present study expands our understanding of the bat virome in species commonly found in Yunnan, China, and provides insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into humans.

  12. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species.

    Science.gov (United States)

    Morin, Phillip A; Archer, Frederick I; Foote, Andrew D; Vilstrup, Julia; Allen, Eric E; Wade, Paul; Durban, John; Parsons, Kim; Pitman, Robert; Li, Lewyn; Bouffard, Pascal; Abel Nielsen, Sandra C; Rasmussen, Morten; Willerslev, Eske; Gilbert, M Thomas P; Harkins, Timothy

    2010-07-01

    Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric "ecotypes" with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales but for many marine taxa. We used high-throughput sequencing to survey whole mitochondrial genome variation of 139 samples from the North Pacific, North Atlantic, and southern oceans. Phylogenetic analysis indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from approximately 150,000 to 700,000 yr ago. We recommend that three named ecotypes be elevated to full species, and that the remaining types be recognized as subspecies pending additional data. Establishing appropriate taxonomic designations will greatly aid in understanding the ecological impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times.

  13. Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms.

    Science.gov (United States)

    Nathan, Lucas M; Simmons, Megan; Wegleitner, Benjamin J; Jerde, Christopher L; Mahon, Andrew R

    2014-11-04

    The use of molecular surveillance techniques has become popular among aquatic researchers and managers due to the improved sensitivity and efficiency compared to traditional sampling methods. Rapid expansion in the use of environmental DNA (eDNA), paired with the advancement of molecular technologies, has resulted in new detection platforms and techniques. In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR) in which water samples were collected over a 24 h time period from mesocosm experiments containing a population gradient of invasive species densities. All platforms reliably detected the presence of DNA, even at low target organism densities within the first hour. The two quantitative platforms (qPCR and ddPCR) produced similar estimates of DNA concentrations. The analyses completed with ddPCR was faster from sample collection through analyses and cost approximately half the expenditure of qPCR. Although a new platform for eDNA surveillance of aquatic species, ddPCR was consistent with more commonly used qPCR and a cost-effective means of estimating DNA concentrations. Use of ddPCR by researchers and managers should be considered in future eDNA surveillance applications.

  14. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    Science.gov (United States)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  15. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    Spill, Fabian

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  16. Integrating multiple data sources in species distribution modeling: A framework for data fusion

    Science.gov (United States)

    Pacifici, Krishna; Reich, Brian J.; Miller, David A.W.; Gardner, Beth; Stauffer, Glenn E.; Singh, Susheela; McKerrow, Alexa; Collazo, Jaime A.

    2017-01-01

    The last decade has seen a dramatic increase in the use of species distribution models (SDMs) to characterize patterns of species’ occurrence and abundance. Efforts to parameterize SDMs often create a tension between the quality and quantity of data available to fit models. Estimation methods that integrate both standardized and non-standardized data types offer a potential solution to the tradeoff between data quality and quantity. Recently several authors have developed approaches for jointly modeling two sources of data (one of high quality and one of lesser quality). We extend their work by allowing for explicit spatial autocorrelation in occurrence and detection error using a Multivariate Conditional Autoregressive (MVCAR) model and develop three models that share information in a less direct manner resulting in more robust performance when the auxiliary data is of lesser quality. We describe these three new approaches (“Shared,” “Correlation,” “Covariates”) for combining data sources and show their use in a case study of the Brown-headed Nuthatch in the Southeastern U.S. and through simulations. All three of the approaches which used the second data source improved out-of-sample predictions relative to a single data source (“Single”). When information in the second data source is of high quality, the Shared model performs the best, but the Correlation and Covariates model also perform well. When the information quality in the second data source is of lesser quality, the Correlation and Covariates model performed better suggesting they are robust alternatives when little is known about auxiliary data collected opportunistically or through citizen scientists. Methods that allow for both data types to be used will maximize the useful information available for estimating species distributions.

  17. Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

    Science.gov (United States)

    Ytow, Nozomi

    2016-01-01

    The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

  18. Multiple stress effects of Vision herbicide, pH, and food on zooplankton and larval amphibian species from forest wetlands.

    Science.gov (United States)

    Chen, Celia Y; Hathaway, Kevin M; Folt, Carol L

    2004-04-01

    As part of a multiple-tier research program, interactions of the herbicide Vision (glyphosate) with two stressors, pH and food level, were examined. Effects of the formulated product Vision were tested at two test concentrations (0.75 and 1.50 mg acid equivalent/L), two pH levels (pH 5.5 and 7.5), and under high and low food concentrations. Effects of each stressor alone and in combination were examined using two common wetland taxa: Zooplankton, Simocephalus vetulus, and tadpoles (Gosner stage 25) of Rana pipiens. For S. vetulus, survival, reproduction, and development time were measured; survival was measured for R. pipiens. For both species, significant effects of the herbicide were measured at concentrations lower than the calculated worst-case value for the expected environmental concentration ([EEC], 1.40 mg acid equivalent/L). Moreover, high pH (7.5) increased the toxic effects of the herbicide on all response variables for both species even though it improved reproductive rate of S. vetulus over pH 5.5 in the absence of herbicide. Stress due to low food alone also interacted with pH 5.5 to diminish S. vetulus survival. These results support the general postulate that multiple stress interactions may exacerbate chemical effects on aquatic biota in natural systems.

  19. Virulence variation among strains of the emerging infectious fungus Batrachochytrium dendrobatidis (Bd) in multiple amphibian host species.

    Science.gov (United States)

    Dang, Trang D; Searle, Catherine L; Blaustein, Andrew R

    2017-05-11

    Emerging infectious diseases have been documented in numerous plant and animal populations. The infectious disease amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is associated with global amphibian population declines. While much Bd-amphibian research has centered on response variation in hosts, a paucity of information exists on how variation in the pathogen, such as strain differences, affects infection dynamics. To examine how different Bd strains may differentially impact multiple hosts, we conducted laboratory experiments to measure 2 infection outcomes, viz. host survival and pathogen load, in 3 amphibian host species (Pacific treefrog, western toad, and Cascades frog) after exposure to 3 different Bd strains (an additional fourth Bd strain was tested in toads only). Our results confirm that the infection response differs among host species. Western toads experienced significant mortality, but Pacific treefrogs and Cascades frogs did not. Interestingly, our experiment also captured strain-dependent virulence variation but only in 1 host species, the western toad. Increased mortality was observed in 2 of the 4 Bd strains tested in this host species. Toads were also the only host species found to have variable pathogen load dependent on strain type; individuals exposed to the Panama strain harbored significantly higher loads compared to all other strains. These findings underscore the dynamic nature of Bd infection, showing that virulence can vary contingent on host and strain type. We highlight the importance of both host- and pathogen-dependent factors in determining overall infection virulence and show the need for in vivo testing to fully assess pathogenicity.

  20. Multiple Reaction Monitoring Mode Based Liquid Chromatography-Mass Spectrometry Method for Simultaneous Quantification of Brassinolide and Other Plant Hormones Involved in Abiotic Stresses

    Directory of Open Access Journals (Sweden)

    Deepak M. Kasote

    2016-01-01

    Full Text Available Plant hormones are the key regulators of adaptive stress response. Abiotic stresses such as drought and salt are known to affect the growth and productivity of plants. It is well known that the levels of plant hormones such as zeatin (ZA, abscisic acid (ABA, salicylic acid (SA, jasmonic acid (JA, and brassinolide (BR fluctuate upon abiotic stress exposure. At present, there is not any single suitable liquid chromatography-mass spectrometry (LC-MS method for simultaneous analysis of BR and other plant hormones involved in abiotic stresses. In the present study, we developed a simple, sensitive, and rapid method for simultaneous analysis of five major plant hormones, ZA, ABA, JA, SA, and BR, which are directly or indirectly involved in drought and salt stresses. The optimized extraction procedure was simple and easy to use for simultaneous measurement of these plant hormones in Arabidopsis thaliana. The developed method is highly reproducible and can be adapted for simultaneous measurement of changes in plant hormones (ZA, ABA, JA, SA, and BR in response to abiotic stresses in plants like A. thaliana and tomato.

  1. Multiple Reaction Monitoring Mode Based Liquid Chromatography-Mass Spectrometry Method for Simultaneous Quantification of Brassinolide and Other Plant Hormones Involved in Abiotic Stresses.

    Science.gov (United States)

    Kasote, Deepak M; Ghosh, Ritesh; Chung, Jun Young; Kim, Jonggeun; Bae, Inhwan; Bae, Hanhong

    2016-01-01

    Plant hormones are the key regulators of adaptive stress response. Abiotic stresses such as drought and salt are known to affect the growth and productivity of plants. It is well known that the levels of plant hormones such as zeatin (ZA), abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), and brassinolide (BR) fluctuate upon abiotic stress exposure. At present, there is not any single suitable liquid chromatography-mass spectrometry (LC-MS) method for simultaneous analysis of BR and other plant hormones involved in abiotic stresses. In the present study, we developed a simple, sensitive, and rapid method for simultaneous analysis of five major plant hormones, ZA, ABA, JA, SA, and BR, which are directly or indirectly involved in drought and salt stresses. The optimized extraction procedure was simple and easy to use for simultaneous measurement of these plant hormones in Arabidopsis thaliana. The developed method is highly reproducible and can be adapted for simultaneous measurement of changes in plant hormones (ZA, ABA, JA, SA, and BR) in response to abiotic stresses in plants like A. thaliana and tomato.

  2. Simultaneous preconcentration of vanadium(V/IV) species with palmitoyl quinolin-8-ol bonded to amberlite XAD 2 and their separate spectrophotometric determination with 4-(2-pyridylazo)-resorcinol using CDTA as masking agent

    Energy Technology Data Exchange (ETDEWEB)

    Filik, Hayati; Berker, Kadriye Isil; Balkis, Nuray; Apak, Resat

    2004-08-02

    This paper reports the simultaneous preconcentration and separation of trace amounts of V species in synthetic solutions and seawater with palmitoyl quinolin-8-ol bonded amberlite XAD 2 copolymer resin column prior to simultaneous speciation analysis. Both V(IV) and V(V) species could be sorbed and preconcentrated by the resin. Both vanadium species were quantitatively eluted together from the resin column using HCl as stripping agent and used for speciation studies. For the speciation analysis of eluted V species, the selected route involved spectrophotometric determination of total vanadium with 4-(2-pyridylazo)-resorcinol (PAR) and vanadate estimation by masking vanadyl with 1,2 cyclohexanediaminetetraacetic acid (CDTA). The preconcentrated V species were assayed spectrophotometrically with PAR at 542 nm, and the results were compared with those of FAAS. The detection limits of V(V) with spectrophotometry and FAAS were 1.6 and 0.9 {mu}g l{sup -1}, respectively. The optimal experimental parameters such as pH, sample flow rate, desorption flow rate, redox behaviour of V(IV) and V(V) in resin and volume of eluent and sample were investigated. The values obtained for the preconcentration factor by the two methods were nearly consistent, and were in the range 150-fold. Analysis of certified reference material (IAEA-405) by the proposed method showed good agreement with the certified value. The established procedure was employed for preconcentrating the vanadium species from artificial and real seawater.

  3. Structural libraries of protein models for multiple species to understand evolution of the renin-angiotensin system.

    Science.gov (United States)

    Prokop, Jeremy W; Petri, Victoria; Shimoyama, Mary E; Watanabe, Ingrid K M; Casarini, Dulce E; Leeper, Thomas C; Bilinovich, Stephanie M; Jacob, Howard J; Santos, Robson A S; Martins, Almir S; Araujo, Fabiano C; Reis, Fernando M; Milsted, Amy

    2015-05-01

    The details of protein pathways at a structural level provides a bridge between genetics/molecular biology and physiology. The renin-angiotensin system is involved in many physiological pathways with informative structural details in multiple components. Few studies have been performed assessing structural knowledge across the system. This assessment allows use of bioinformatics tools to fill in missing structural voids. In this paper we detail known structures of the renin-angiotensin system and use computational approaches to estimate and model components that do not have their protein structures defined. With the subsequent large library of protein structures, we then created a species specific protein library for human, mouse, rat, bovine, zebrafish, and chicken for the system. The rat structural system allowed for rapid screening of genetic variants from 51 commonly used rat strains, identifying amino acid variants in angiotensinogen, ACE2, and AT1b that are in contact positions with other macromolecules. We believe the structural map will be of value for other researchers to understand their experimental data in the context of an environment for multiple proteins, providing pdb files of proteins for the renin-angiotensin system in six species. With detailed structural descriptions of each protein, it is easier to assess a species for use in translating human diseases with animal models. Additionally, as whole genome sequencing continues to decrease in cost, tools such as molecular modeling will gain use as an initial step in designing efficient hypothesis driven research, addressing potential functional outcomes of genetic variants with precompiled protein libraries aiding in rapid characterizations. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Assessment of Serum Nitrogen Species and Inflammatory Parameters in Relapsing-Remitting Multiple Sclerosis Patients Treated with Different Therapeutic Approaches

    Directory of Open Access Journals (Sweden)

    Natalia Niedziela

    2016-01-01

    Full Text Available The role of nitric oxide and its reactive derivatives (NOx is well known in the pathogenesis of multiple sclerosis, which is an inflammatory disease while NOx seems to be important in coordinating inflammatory response. The purpose of the present study was to assess serum NOx as one of the nitrogen species and inflammatory parameters in relapsing-remitting multiple sclerosis patients and to compare the effectiveness of various types of disease-modifying therapies that reduce nitric oxide and inflammatory biomarkers. Elevated NOx level was observed in patients who received the first-line disease-modifying therapy (interferons beta-1a and beta-1b in comparison with the subjects treated with the second-line disease-modifying therapy (natalizumab; fingolimod and healthy controls without significant differences in C-reactive protein and interleukin-1 beta. A negative correlation was observed between serum NOx level and the duration of multiple sclerosis confirmed in the whole study population and in subjects treated with the first-line agents. Only serum NOx, concentration could reveal a potential efficacy of disease-modifying therapy with a better reduction in NOx level due to the second-line agents of disease-modifying therapy.

  5. Development and optimization of cocktail-ELISA for a unified surveillance of zoonotic schistosomiasis in multiple host species.

    Science.gov (United States)

    Moendeg, Kharleezelle J; Angeles, Jose Ma M; Goto, Yasuyuki; Leonardo, Lydia R; Kirinoki, Masashi; Villacorte, Elena A; Rivera, Pilarita T; Inoue, Noboru; Chigusa, Yuichi; Kawazu, Shin-ichiro

    2015-03-01

    The zoonotic characteristic of the human parasite Schistosoma japonicum infecting a significant number of wild and domestic animals highlights the need to develop a unified surveillance in multiple host species for a strengthened schistosomiasis control. It has been shown in several studies that water buffaloes and dogs are considered important reservoirs in the transmission of the schistosome parasite to humans. Recombinant antigens like thioredoxin peroxidase-1 (SjTPx-1) and tandem repeat proteins (Sj1TR, Sj7TR) have been shown to be good diagnostic antigens individually in humans, water buffaloes, and dogs in previous studies. Mixing these antigens together in a cocktail-ELISA might not only improve their diagnostic potentials but rather produce a multi-host species detection means for zoonotic schistosomiasis. In this study, we aimed to develop and optimize cocktail-ELISA by testing different combinations of these recombinant antigens in humans, water buffaloes, and dogs. As compared with the diagnostic potential calculated for each of the three recombinant antigens used, their combination has presented improved specificities, positive predictive values, and kappa values. Using samples collected from various endemic areas in the Philippines, results showed that the combination of SjTPx-1/Sj7TR/Sj1TR has the highest sensitivity in humans (84.1 %), water buffaloes, and dogs (80 %) and specificity (100 %) in all host species. This study therefore suggests the use of cocktail-ELISA in improving the zoonotic surveillance in schistosomiasis endemic areas.

  6. Monitoring multiple species: Estimating state variables and exploring the efficacy of a monitoring program

    Science.gov (United States)

    Mattfeldt, S.D.; Bailey, L.L.; Grant, E.H.C.

    2009-01-01

    Monitoring programs have the potential to identify population declines and differentiate among the possible cause(s) of these declines. Recent criticisms regarding the design of monitoring programs have highlighted a failure to clearly state objectives and to address detectability and spatial sampling issues. Here, we incorporate these criticisms to design an efficient monitoring program whose goals are to determine environmental factors which influence the current distribution and measure change in distributions over time for a suite of amphibians. In designing the study we (1) specified a priori factors that may relate to occupancy, extinction, and colonization probabilities and (2) used the data collected (incorporating detectability) to address our scientific questions and adjust our sampling protocols. Our results highlight the role of wetland hydroperiod and other local covariates in the probability of amphibian occupancy. There was a change in overall occupancy probabilities for most species over the first three years of monitoring. Most colonization and extinction estimates were constant over time (years) and space (among wetlands), with one notable exception: local extinction probabilities for Rana clamitans were lower for wetlands with longer hydroperiods. We used information from the target system to generate scenarios of population change and gauge the ability of the current sampling to meet monitoring goals. Our results highlight the limitations of the current sampling design, emphasizing the need for long-term efforts, with periodic re-evaluation of the program in a framework that can inform management decisions.

  7. Role of Multiple Hosts in the Cross-Species Transmission and Emergence of a Pandemic Parvovirus

    Science.gov (United States)

    Allison, Andrew B.; Harbison, Carole E.; Pagan, Israel; Stucker, Karla M.; Kaelber, Jason T.; Brown, Justin D.; Ruder, Mark G.; Keel, M. Kevin; Dubovi, Edward J.; Holmes, Edward C.

    2012-01-01

    Understanding the mechanisms of cross-species virus transmission is critical to anticipating emerging infectious diseases. Canine parvovirus type 2 (CPV-2) emerged as a variant of a feline parvovirus when it acquired mutations that allowed binding to the canine transferrin receptor type 1 (TfR). However, CPV-2 was soon replaced by a variant virus (CPV-2a) that differed in antigenicity and receptor binding. Here we show that the emergence of CPV involved an additional host range variant virus that has circulated undetected in raccoons for at least 24 years, with transfers to and from dogs. Raccoon virus capsids showed little binding to the canine TfR, showed little infection of canine cells, and had altered antigenic structures. Remarkably, in capsid protein (VP2) phylogenies, most raccoon viruses fell as evolutionary intermediates between the CPV-2 and CPV-2a strains, suggesting that passage through raccoons assisted in the evolution of CPV-2a. This highlights the potential role of alternative hosts in viral emergence. PMID:22072763

  8. Recent trends in CE of inorganic ions: from individual to multiple elemental species analysis.

    Science.gov (United States)

    Timerbaev, Andrei R

    2007-10-01

    The major methodological developments in CE related to inorganic analysis are overviewed. This is an update to a previous review article by the author (Timerbaev, A. R., Electrophoresis 2004, 25, 4008-4031) and it covers the review work and innovative research papers published between January 2004 and the first part of 2006. As was underlined in that review, a growing interest of analytical community in providing elemental speciation information found a sound response of the CE method developers. Presently, almost every second research paper in the field of interest deals with element species analysis, the use of inductively coupled plasma MS detection and biochemical applications being the topics of utmost research efforts. On the other hand, advances in general methodology traditionally centered on a CE system modernization for improvements in sensitivity and separation selectivity have attracted less attention over the review period. While there is no indication that inorganic ion applications would surpass by the developmental rate the more matured analysis of organic analytes, CE can now be seen as an analytical technique to be before long customary in a number of inorganic analysis arenas.

  9. Quantitative profiling of PE, MMPE, DMPE, and PC lipid species by multiple precursor ion scanning: A tool for monitoring PE metabolism

    DEFF Research Database (Denmark)

    Bilgin, Mesut; Markgraf, Daniel F; Duchoslav, Eva

    2011-01-01

    We report a method for the simultaneous identification and quantification of phosphatidylethanolamine (PE), monomethyl-phosphatidylethanolamine (MMPE), dimethyl-phosphatidylethanolamine (DMPE), and phosphatidylcholine (PC) species in lipid extracts. The method employs a specific "mass-tag" strate...... metabolism in Saccharomyces cerevisiae. Finally, we benchmarked the mass-tag strategy by specific and sensitive profiling of intermediate MMPE and DMPE species in liver....... where DMPE, MMPE, and PE species are chemically methylated with deuterated methyliodide (CD(3)I) to produce PC molecules having class-specific mass offsets of 3, 6 and 9Da, respectively. The derivatized aminoglycerophospholipids release characteristic phosphorylcholine-like fragment ions having specific...

  10. Comparisons of single versus multiple bacterial species on biological control of anthurium blight.

    Science.gov (United States)

    Fukui, R; Fukui, H; Alvarez, A M

    1999-05-01

    ABSTRACT Effects of single versus multiple biological control agents (BCAs) on suppression of bacterial blight of anthurium were studied using a bioluminescent strain (V108LRUH1) of Xanthomonas campestris pv. dieffenbachiae. When five BCAs (GUT3, GUT4, GUT5, GUT6, and GUT9) were coinoculated in various combinations with V108LRUH1 into filter-sterilized guttation fluids of anthurium plants, a mixture of all five strains or four strains without GUT9 was most inhibitory to V108LRUH1. None of the individual BCAs inhibited V108LRUH1 in the guttation fluid. When BCAs were sprayed at congruent with10(8) CFU/ml on the foliage of a susceptible cultivar 1 day prior to inoculation with V108LRUH1, GUT6 alone and any mixtures containing GUT6 were highly effective in suppressing wound invasion and subsequent leaf infection by V108LRUH1. When tested on several cultivars that differed in susceptibility to the disease, the mixture of five strains or four strains without GUT9 consistently suppressed leaf infection regardless of the cultivars. In some cultivars, BCAs completely suppressed both wound and hydathode invasion by V108LRUH1, resulting in no infection in many leaves. These results indicate that application of bacterial mixtures provides anthurium cultivars with bacterial communities suppressive to X. campestris pv. dieffenbachiae. The results also suggest that selecting an effective mixture of BCAs first and then removing ineffective strains may be a better general approach to finding the most effective BCAs than finding individual strains and combining them.

  11. Is braiding an endangered river species? Converging morphological trajectories from multiple geographic contexts.

    Science.gov (United States)

    Stecca, Guglielmo; Zolezzi, Guido; Surian, Nicola; Hicks, Murray

    2017-04-01

    Observations of morphological change in braided rivers, comprising narrowing of the total and active braidplain, degradation (at least in some reaches), increase in vegetation cover, and reduction of braiding complexity towards a transitional style, have been increasingly reported worldwide in the last decades. Most of the available literature concerns rivers in Europe, with particular reference to the Alpine and pre-Alpine region (e.g., Italy, France, Austria, Switzerland). This abundance reflects the magnitude of changes in Europe, where most of braided reaches have been heavily impacted. However, contributions from other regions of Europe (e.g., the Polish Carpathians, Spain, Scotland, Corsica) and of the Earth (e.g., the South Island of New Zealand) document similar stories. These morphodynamic changes have been related to the alteration of the fundamental physical processes in braided rivers driven by the flow and sediment supply regimes, due to anthropogenic changes in constraints and controls. Multiple and context-specific sources of impact on these controls have been identified, including damming, landuse change, gravel mining, torrent control works, channelisation, introduction of alien vegetation. Here, we focus on a comparative analysis of the relatively recent (multi-decadal) evolution of braided rivers located in different geographic regions on the Earth, with particular reference to the Waitaki (New Zealand), Piave (Italy) and Dunajec (Poland) rivers. These rivers display similar morphological trajectories, which nonetheless result from very different paths of causation, i.e., from different management causes and different alteration of physical processes. We focus on the role of different physical and human geographic contexts as drivers of the river evolution, highlighting the relations between the observed trajectories and the local conditions and characteristics. We discuss the relative role of dam construction and operation in contributing to the

  12. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    Directory of Open Access Journals (Sweden)

    Franck Emmanuel Dayan

    2015-04-01

    Full Text Available Sarmentine, 1-(1-pyrrolidinyl-(2E,4E-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in response between plants treated with sarmentine and herbicidal soaps such as pelargonic acid (nonanoic acid. However, little was known about the mechanism of action leading to the rapid desiccation of foliage treated by sarmentine. In cucumber cotyledon disc-assays, sarmentine induced rapid light-independent loss of membrane integrity at 100 µM or higher concentration, whereas 3 mM pelargonic acid was required for a similar effect. Sarmentine was between 10 and 30 times more active than pelargonic acid on wild mustard, velvetleaf, redroot pigweed and crabgrass. Additionally, the potency of 30 µM sarmentine was greatly stimulated by light, suggesting that this natural product may also interfere with photosynthetic processes. This was confirmed by observing a complete inhibition of photosynthetic electron transport at that concentration. Sarmentine also acted as an inhibitor of photosystem II on isolated thylakoid membranes by competing for the binding site of plastoquinone. This can be attributed in part to structural similarities between herbicides like sarmentine and diuron. While this mechanism of action accounts for the light stimulation of the activity of sarmentine, it does not account for its ability to destabilize membranes in darkness. In this respect, sarmentine has some structural similarity to crotonoyl-CoA, the substrate of enoyl-ACP reductase, a key enzyme in the early steps of fatty acid synthesis. Inhibitors of this enzyme, such as triclosan, cause rapid loss of membrane integrity in the dark. Sarmentine inhibited the activity of enoyl-ACP reductase, with an I50app of 18.3 µM. Therefore, the herbicidal activity of sarmentine appears to

  13. High genetic diversities between isolates of the fish parasite Cryptocaryon irritans (Ciliophora) suggest multiple cryptic species.

    Science.gov (United States)

    Chi, Hongshu; Taik, Patricia; Foley, Emily J; Racicot, Alycia C; Gray, Hilary M; Guzzetta, Katherine E; Lin, Hsin-Yun; Song, Yen-Ling; Tung, Che-Huang; Zenke, Kosuke; Yoshinaga, Tomoyoshi; Cheng, Chao-Yin; Chang, Wei-Jen; Gong, Hui

    2017-07-01

    The ciliate protozoan Cryptocaryon irritans parasitizes marine fish and causes lethal white spot disease. Sporadic infections as well as large-scale outbreaks have been reported globally and the parasite's broad host range poses particular threat to the aquaculture and ornamental fish markets. In order to better understand C. irritans' population structure, we sequenced and compared mitochondrial cox-1, SSU rRNA, and ITS-1 sequences from 8 new isolates of C. irritans collected in China, Japan, and Taiwan. We detected two SSU rRNA haplotypes, which differ at three positions, separating the isolates into two main groups (I and II). Cox-1 sequences also support the division into two groups, and the cox-1 divergence between these two groups is unexpectedly high (9.28% for 1582 nucleotide positions). The divergence is much greater than that detected in Ichthyophthirius multifiliis, the ciliate protozoan causing freshwater white spot disease in fish, where intraspecies divergence on cox-1 sequence is only 1.95%. ITS-1 sequences derived from these eight isolates and from all other C. irritans isolates (deposited in the GenBank) not only support the two groups, but further suggest the presence of a third group with even greater sequence divergence. Finally, a small Ka/Ks ratio estimated from cox-1 sequences suggests that this gene in C. irritans remains under strong purifying selection. Taken together, the C. irritans species may consists of many subspecies and/or syngens. Further work is needed to determine if there is reproductive isolation between the groups we have defined. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Analysis of simultaneous space-time clusters of Campylobacter spp. in humans and in broiler flocks using a multiple dataset approach

    Science.gov (United States)

    2010-01-01

    Background Campylobacteriosis is the most frequently reported zoonosis in the EU and the epidemiology of sporadic campylobacteriosis, especially the routes of transmission, is to a great extent unclear. Poultry easily become colonised with Campylobacter spp., being symptom-less intestinal carriers. Earlier it was estimated that internationally between 50% and 80% of the cases could be attributed to chicken as a reservoir. In a Norwegian surveillance programme all broiler flocks under 50 days of age were tested for Campylobacter spp. The aim of the current study was to identify simultaneous local space-time clusters each year from 2002 to 2007 for human cases of campylobacteriosis and for broiler flocks testing positive for Campylobacter spp. using a multivariate spatial scan statistic method. A cluster occurring simultaneously in humans and broilers could indicate the presence of common factors associated with the dissemination of Campylobacter spp. for both humans and broilers. Results Local space-time clusters of humans and broilers positive for Campylobacter spp. occurring simultaneously were identified in all investigated years. All clusters but one were identified from May to August. Some municipalities were included in clusters all years. Conclusions The simultaneous occurrence of clusters of humans and broilers positive for Campylobacter spp. combined with the knowledge that poultry meat has a nation-wide distribution indicates that campylobacteriosis cases might also be caused by other risk factors than consumption and handling of poultry meat. Broiler farms that are positive could contaminate the environment with further spread to new broiler farms or to humans living in the area and local environmental factors, such as climate, might influence the spread of Campylobacter spp. in an area. Further studies to clarify the role of such factors are needed. PMID:20860801

  15. Analysis of simultaneous space-time clusters of Campylobacter spp. in humans and in broiler flocks using a multiple dataset approach

    Directory of Open Access Journals (Sweden)

    Norström Madelaine

    2010-09-01

    Full Text Available Abstract Background Campylobacteriosis is the most frequently reported zoonosis in the EU and the epidemiology of sporadic campylobacteriosis, especially the routes of transmission, is to a great extent unclear. Poultry easily become colonised with Campylobacter spp., being symptom-less intestinal carriers. Earlier it was estimated that internationally between 50% and 80% of the cases could be attributed to chicken as a reservoir. In a Norwegian surveillance programme all broiler flocks under 50 days of age were tested for Campylobacter spp. The aim of the current study was to identify simultaneous local space-time clusters each year from 2002 to 2007 for human cases of campylobacteriosis and for broiler flocks testing positive for Campylobacter spp. using a multivariate spatial scan statistic method. A cluster occurring simultaneously in humans and broilers could indicate the presence of common factors associated with the dissemination of Campylobacter spp. for both humans and broilers. Results Local space-time clusters of humans and broilers positive for Campylobacter spp. occurring simultaneously were identified in all investigated years. All clusters but one were identified from May to August. Some municipalities were included in clusters all years. Conclusions The simultaneous occurrence of clusters of humans and broilers positive for Campylobacter spp. combined with the knowledge that poultry meat has a nation-wide distribution indicates that campylobacteriosis cases might also be caused by other risk factors than consumption and handling of poultry meat. Broiler farms that are positive could contaminate the environment with further spread to new broiler farms or to humans living in the area and local environmental factors, such as climate, might influence the spread of Campylobacter spp. in an area. Further studies to clarify the role of such factors are needed.

  16. Multiple Reaction Monitoring Mode Based Liquid Chromatography-Mass Spectrometry Method for Simultaneous Quantification of Brassinolide and Other Plant Hormones Involved in Abiotic Stresses

    OpenAIRE

    Kasote, Deepak M.; Ghosh, Ritesh; Chung, Jun Young; Kim, Jonggeun; Bae, Inhwan; Bae, Hanhong

    2016-01-01

    Plant hormones are the key regulators of adaptive stress response. Abiotic stresses such as drought and salt are known to affect the growth and productivity of plants. It is well known that the levels of plant hormones such as zeatin (ZA), abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), and brassinolide (BR) fluctuate upon abiotic stress exposure. At present, there is not any single suitable liquid chromatography-mass spectrometry (LC-MS) method for simultaneous analysis of BR a...

  17. Statistical design-principal component analysis optimization of a multiple response procedure using cloud point extraction and simultaneous determination of metals by ICP OES

    OpenAIRE

    Bezerra, Marcos de Almeida; Bruns, Roy Edward; Ferreira, Sergio Luis Costa

    2006-01-01

    RESTRITO A procedure has been developed for the simultaneous determination of traces amounts of Cd, Cr, Cu, Mn, Ni and Pb from saline oil-refinery effluents and digested vegetable samples using inductively coupled plasma optical emission spectrometry (ICP OES). The procedure is based on cloud point extraction (CPE) of these metals as 2-(bromo-2-pyridylazo)-5-diethyl-amino-phenol (Br-PADAP) complexes into a micellar phase of octylphenoxypolyethoxyethanol (Triton X-114). Optimization of the ...

  18. Multiple species of ectomycorrhizal fungi are frequently detected on individual oak root tips in a tropical cloud forest.

    Science.gov (United States)

    Morris, Melissa H; Pérez-Pérez, Miguel A; Smith, Matthew E; Bledsoe, Caroline S

    2008-10-01

    The ecological importance of ectomycorrhizal (EM) fungi in tropical ecosystems is increasingly recognized, but few studies have used molecular methods to examine EM fungal communities in tropical forests. The diversity and composition of the EM community on Quercus crassifolia in a tropical montane cloud forest in southern Mexico were characterized using DNA sequencing of single root tips. Individual root tips commonly harbored multiple fungal species that resulted in mixed polymerase chain reaction (PCR) products. By cloning and performing gel extractions on mixed PCR samples, we identified two or more EM fungi on 26% of the root tips. When non-EM fungi were considered, this figure increased to 31% of root tips. A total of 44 EM taxa and nine non-EM taxa were detected on roots from 21 soil cores (104 root tips). Taxa in the families Russulaceae, Cortinariaceae, Inocybaceae, and Thelephoraceae were frequent. This is the first study to characterize the belowground EM community in a tropical montane cloud forest.

  19. A novel rapid DNA microarray assay enables identification of 37 Mycoplasma species and highlights multiple Mycoplasma infections.

    Directory of Open Access Journals (Sweden)

    Christiane Schnee

    Full Text Available Mycoplasmas comprise a conglomerate of pathogens and commensals occurring in humans and animals. The genus Mycoplasma alone contains more than 120 species at present, and new members are continuously being discovered. Therefore, it seems promising to use a single highly parallel detection assay rather than develop separate tests for each individual species. In this study, we have designed a DNA microarray carrying 70 oligonucleotide probes derived from the 23S rRNA gene and 86 probes from the tuf gene target regions. Following a PCR amplification and biotinylation step, hybridization on the array was shown to specifically identify 31 Mycoplasma spp., as well as 3 Acholeplasma spp. and 3 Ureaplasma spp. Members of the Mycoplasma mycoides cluster can be recognized at subgroup level. This procedure enables parallel detection of Mollicutes spp. occurring in humans, animals or cell culture, from mono- and multiple infections, in a single run. The main advantages of the microarray assay include ease of operation, rapidity, high information content, and affordability. The new test's analytical sensitivity is equivalent to that of real-time PCR and allows examination of field samples without the need for culture. When 60 field samples from ruminants and birds previously analyzed by denaturing-gradient gel electrophoresis (DGGE were tested by the microarray assay both tests identified the same agent in 98.3% of the cases. Notably, microarray testing revealed an unexpectedly high proportion (35% of multiple mycoplasma infections, i.e., substantially more than DGGE (15%. Two of the samples were found to contain four different Mycoplasma spp. This phenomenon deserves more attention, particularly its implications for epidemiology and treatment.

  20. Peptide-Recombinant VP6 Protein Based Enzyme Immunoassay for the Detection of Group A Rotaviruses in Multiple Host Species.

    Directory of Open Access Journals (Sweden)

    Naveen Kumar

    Full Text Available We developed a novel enzyme immunoassay for the detection of group A rotavirus (RVA antigen in fecal samples of multiple host species. The assay is based on the detection of conserved VP6 protein using anti-recombinant VP6 antibodies as capture antibodies and anti-multiple antigenic peptide (identified and constructed from highly immunodominant epitopes within VP6 protein antibodies as detector antibodies. The clinical utility of the assay was evaluated using a panel of 914 diarrhoeic fecal samples from four different host species (bovine, porcine, poultry and human collected from diverse geographical locations in India. Using VP6- based reverse transcription-polymerase chain reaction (RT-PCR as the gold standard, we found that the diagnostic sensitivity (DSn and specificity (DSp of the new assay was high [bovine (DSn = 94.2% & DSp = 100%; porcine (DSn = 94.6% & DSp = 93.3%; poultry (DSn = 74.2% & DSp = 97.7% and human (DSn = 82.1% & DSp = 98.7%]. The concordance with RT-PCR was also high [weighted kappa (k = 0.831-0.956 at 95% CI = 0.711-1.0] as compared to RNA-polyacrylamide gel electrophoresis (RNA-PAGE. The performance characteristics of the new immunoassay were comparable to those of the two commercially available ELISA kits. Our results suggest that this peptide-recombinant protein based assay may serve as a preliminary assay for epidemiological surveillance of RVA antigen and for evaluation of vaccine effectiveness especially in low and middle income settings.

  1. Drug design targeting protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning: discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 interface.

    Science.gov (United States)

    Li, Huameng; Xiao, Hui; Lin, Li; Jou, David; Kumari, Vandana; Lin, Jiayuh; Li, Chenglong

    2014-02-13

    The IL-6/GP130/STAT3 pathway is critical for the progression of multiple types of cancers. We report here the discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning approaches. Multiple drug scaffolds were simultaneously docked into hot spots of GP130 D1 domain by MLSD to compete with the key interacting residues of IL-6, followed by tethering to generate virtual hit compounds. Similarity searches of virtual hits on drug databases identified raloxifene and bazedoxifene as potential inhibitors of IL-6/GP130 interaction. In cancer cell assays both compounds bind to GP130 and demonstrated selective inhibition of IL-6 induced STAT3 phosphorylation and were significantly more potent than the previously reported natural product inhibitor MDL-A. The identified drugs represent a new class of lead compounds with piperidine, benzothiophene, and indole scaffolds to inhibit IL-6 induced homodimerization of GP130. Besides potential direct usage for clinic trials, the two compounds can also serve as lead compounds for optimization to speed the development of drugs selectively targeting the IL-6/GP130/STAT3 cancer signaling pathway.

  2. Differential recognition of the multiple banded antigen isoforms across Ureaplasma parvum and Ureaplasma urealyticum species by monoclonal antibodies.

    Science.gov (United States)

    Aboklaish, Ali F; Ahmed, Shatha; McAllister, Douglas; Cassell, Gail; Zheng, Xiaotian T; Spiller, Owen B

    2016-08-01

    Two separate species of Ureaplasma have been identified that infect humans: Ureaplasma parvum and Ureaplasma urealyticum. Most notably, these bacteria lack a cell wall and are the leading infectious organism associated with infection-related induction of preterm birth. Fourteen separate representative prototype bacterial strains, called serovars, are largely differentiated by the sequence of repeating units in the C-terminus of the major surface protein: multiple-banded antigen (MBA). Monoclonal antibodies that recognise single or small groups of serovars have been previously reported, but these reagents remain sequestered in individual research laboratories. Here we characterise a panel of commercially available monoclonal antibodies raised against the MBA and describe the first monoclonal antibody that cross-reacts by immunoblot with all serovars of U. parvum and U. urealyticum species. We also describe a recombinant MBA expressed by Escherichia coli which facilitated further characterisation by immunoblot and demonstrate immunohistochemistry of paraffin-embedded antigens. Immunoblot reactivity was validated against well characterised previously published monoclonal antibodies and individual commercial antibodies were found to recognise all U. parvum strains, only serovars 3 and 14 or only serovars 1 and 6, or all strains belonging to U. parvum and U. urealyticum. MBA mass was highly variable between strains, consistent with variation in the number of C-terminal repeats between strains. Antibody characterisation will enable future investigations to correlate severity of pathogenicity to MBA isoform number or mass, in addition to development of antibody-based diagnostics that will detect infection by all Ureaplasma species or alternately be able to differentiate between U. parvum, U. urealyticum or mixed infections. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Algivore or phototroph? Plakobranchus ocellatus (Gastropoda) continuously acquires kleptoplasts and nutrition from multiple algal species in nature.

    Science.gov (United States)

    Maeda, Taro; Hirose, Euichi; Chikaraishi, Yoshito; Kawato, Masaru; Takishita, Kiyotaka; Yoshida, Takao; Verbruggen, Heroen; Tanaka, Jiro; Shimamura, Shigeru; Takaki, Yoshihiro; Tsuchiya, Masashi; Iwai, Kenji; Maruyama, Tadashi

    2012-01-01

    The sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) retains photosynthetically active chloroplasts from ingested algae (functional kleptoplasts) in the epithelial cells of its digestive gland for up to 10 months. While its feeding behavior has not been observed in natural habitats, two hypotheses have been proposed: 1) adult P. ocellatus uses kleptoplasts to obtain photosynthates and nutritionally behaves as a photoautotroph without replenishing the kleptoplasts; or 2) it behaves as a mixotroph (photoautotroph and herbivorous consumer) and replenishes kleptoplasts continually or periodically. To address the question of which hypothesis is more likely, we examined the source algae for kleptoplasts and temporal changes in kleptoplast composition and nutritional contribution. By characterizing the temporal diversity of P. ocellatus kleptoplasts using rbcL sequences, we found that P. ocellatus harvests kleptoplasts from at least 8 different siphonous green algal species, that kleptoplasts from more than one species are present in each individual sea slug, and that the kleptoplast composition differs temporally. These results suggest that wild P. ocellatus often feed on multiple species of siphonous algae from which they continually obtain fresh chloroplasts. By estimating the trophic position of wild and starved P. ocellatus using the stable nitrogen isotopic composition of amino acids, we showed that despite the abundance of kleptoplasts, their photosynthates do not contribute greatly to the nutrition of wild P. ocellatus, but that kleptoplast photosynthates form a significant source of nutrition for starved sea slugs. The herbivorous nature of wild P. ocellatus is consistent with insights from molecular analyses indicating that kleptoplasts are frequently replenished from ingested algae, leading to the conclusion that natural populations of P. ocellatus do not rely on photosynthesis but mainly on the digestion of ingested algae.

  4. Algivore or phototroph? Plakobranchus ocellatus (Gastropoda continuously acquires kleptoplasts and nutrition from multiple algal species in nature.

    Directory of Open Access Journals (Sweden)

    Taro Maeda

    Full Text Available The sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda retains photosynthetically active chloroplasts from ingested algae (functional kleptoplasts in the epithelial cells of its digestive gland for up to 10 months. While its feeding behavior has not been observed in natural habitats, two hypotheses have been proposed: 1 adult P. ocellatus uses kleptoplasts to obtain photosynthates and nutritionally behaves as a photoautotroph without replenishing the kleptoplasts; or 2 it behaves as a mixotroph (photoautotroph and herbivorous consumer and replenishes kleptoplasts continually or periodically. To address the question of which hypothesis is more likely, we examined the source algae for kleptoplasts and temporal changes in kleptoplast composition and nutritional contribution. By characterizing the temporal diversity of P. ocellatus kleptoplasts using rbcL sequences, we found that P. ocellatus harvests kleptoplasts from at least 8 different siphonous green algal species, that kleptoplasts from more than one species are present in each individual sea slug, and that the kleptoplast composition differs temporally. These results suggest that wild P. ocellatus often feed on multiple species of siphonous algae from which they continually obtain fresh chloroplasts. By estimating the trophic position of wild and starved P. ocellatus using the stable nitrogen isotopic composition of amino acids, we showed that despite the abundance of kleptoplasts, their photosynthates do not contribute greatly to the nutrition of wild P. ocellatus, but that kleptoplast photosynthates form a significant source of nutrition for starved sea slugs. The herbivorous nature of wild P. ocellatus is consistent with insights from molecular analyses indicating that kleptoplasts are frequently replenished from ingested algae, leading to the conclusion that natural populations of P. ocellatus do not rely on photosynthesis but mainly on the digestion of ingested algae.

  5. Synthesis of Ag-ZnO with multiple rods (multipods) morphology and its application in the simultaneous photo-catalytic degradation of methyl orange and methylene blue.

    Science.gov (United States)

    Arab Chamjangali, M; Bagherian, G; Javid, A; Boroumand, S; Farzaneh, N

    2015-11-05

    In this study, the photo-decolorization of a mixture of methylene blue (MB) and methyl orange (MO) was investigated using Ag-ZnO multipods. The photo-catalyst used, ZnO multipods, was successfully synthesized. The surface of ZnO microstructure was modified by deposition of different amounts of Ag nanoparticles (Ag NPs) using the photo-reduction method. The as-prepared samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), UV-Vis and atomic absorption spectroscopy. The photo-catalytic efficiency of Ag-ZnO is mainly controlled by the amount of Ag NPs deposited on the ZnO surface. The results obtained suggest that Ag-ZnO containing 6.5% Ag NPs, has the highest photo-catalytic performance in the simultaneous photo-degradation of dyes at a shorter time. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Library design using BCUT chemistry-space descriptors and multiple four-point pharmacophore fingerprints: simultaneous optimization and structure-based diversity.

    Science.gov (United States)

    Mason, J S; Beno, B R

    2000-01-01

    New applications of fingerprints of multiple potential 4-point three-dimensional (3D) pharmacophores in combinatorial library design and virtual screening are presented. Preliminary results demonstrating the feasibility of a simulated annealing process for combinatorial reagent selection that concurrently optimizes product diversity in BCUT chemistry space and in terms of unique 4-point pharmacophores are discussed, and the advantage of using a customized chemistry-space derived for the library design is demonstrated. In addition, an extension to the multiple pharmacophore method for structure-based design that uses the shape of the target site as an additional constraint is presented. This development enables the docking process to be quantified in terms of the number and identities of the pharmacophoric hypotheses that can be matched by a compound or a library of compounds. The design of an example combinatorial library based on the Ugi condensation reaction and a serine protease active site is described.

  7. Multiple risk expert systems interventions: impact of simultaneous stage-matched expert system interventions for smoking, high-fat diet, and sun exposure in a population of parents.

    Science.gov (United States)

    Prochaska, James O; Velicer, Wayne F; Rossi, Joseph S; Redding, Colleen A; Greene, Geoffrey W; Rossi, Susan R; Sun, Xiaowu; Fava, Joseph L; Laforge, Robert; Plummer, Brett A

    2004-09-01

    Three stage-based expert system interventions for smoking, high-fat diet, and unsafe sun exposure were evaluated in a sample of 2,460 parents of teenagers. Eighty-four percent of the eligible parents were enrolled in a 2-arm randomized control trial, with the treatment group receiving individualized feedback reports for each of their relevant behaviors at 0, 6, and 12 months as well as a multiple behavior manual. At 24 months, the expert system outperformed the comparison condition across all 3 risk behaviors, resulting in 22% of the participants in action or maintenance for smoking (vs. 16% for the comparison condition), 34% for diet (vs. 26%), and 30% for sun exposure (vs. 22%). Proactive, home-based, and stage-matched expert systems can produce significant multiple behavior changes in at-risk populations where the majority of participants are not prepared to change. ((c) 2004 APA, all rights reserved)

  8. Examining the Link between Biofilm Formation and the Ability of Pathogenic Salmonella Strains to Colonize Multiple Host Species

    Science.gov (United States)

    MacKenzie, Keith D.; Palmer, Melissa B.; Köster, Wolfgang L.; White, Aaron P.

    2017-01-01

    Salmonella are important pathogens worldwide and a predominant number of human infections are zoonotic in nature. The ability of strains to form biofilms, which is a multicellular behavior characterized by the aggregation of cells, is predicted to be a conserved strategy for increased persistence and survival. It may also contribute to the increasing number of infections caused by ingestion of contaminated fruits and vegetables. There is a correlation between biofilm formation and the ability of strains to colonize and replicate within the intestines of multiple host species. These strains predominantly cause localized gastroenteritis infections in humans. In contrast, there are salmonellae that cause systemic, disseminated infections in a select few host species; these “invasive” strains have a narrowed host range, and most are unable to form biofilms. This includes host-restricted Salmonella serovar Typhi, which are only able to infect humans, and atypical gastroenteritis strains associated with the opportunistic infection of immunocompromised patients. From the perspective of transmission, biofilm formation is advantageous for ensuring pathogen survival in the environment. However, from an infection point of view, biofilm formation may be an anti-virulence trait. We do not know if the capacity to form biofilms prevents a strain from accessing the systemic compartments within the host or if loss of the biofilm phenotype reflects a change in a strain’s interaction with the host. In this review, we examine the connections between biofilm formation, Salmonella disease states, degrees of host adaptation, and how this might relate to different transmission patterns. A better understanding of the dynamic lifecycle of Salmonella will allow us to reduce the burden of livestock and human infections caused by these important pathogens. PMID:29159172

  9. Simultaneous removal of multiple pesticides from water: effect of organically modified clays as coagulant aid and adsorbent in coagulation-flocculation process.

    Science.gov (United States)

    Shabeer, T P Ahammed; Saha, Ajoy; Gajbhiye, V T; Gupta, Suman; Manjaiah, K M; Varghese, Eldho

    2014-01-01

    Contamination of drinking water sources with agrochemical residues became a major concern in the twenty-first century. Coagulation-flocculation is the most widely used water-treatment process, but the efficiency to remove pesticides and other organic pollutants are limited compared to adsorption process. Thus, simultaneous action of adsorption on normal bentonite or organo-modified montmorillonite clays [modified with octadecylamine (ODA-M) and octadecylamine + amino-propyltriethoxysilane (ODAAPS-M)] followed by coagulation-flocculation by alum and poly aluminium chloride has been evaluated for removal of 10 different pesticides, namely atrazine, lindane, metribuzin, aldrin, chlorpyriphos, pendimethalin, alpha-endosulphan, beta-endosulphan, p,p'-DDT, cypermethrin and two of its metabolites, endosulphan sulphate and p,p'-DDE, from water. The coagulation without integration of adsorption was less effective (removal % varies from 12 to 49) than the adsorption-coagulation integrated system (removal % varies from 71 to 100). Further, coagulation integrated with adsorption was more effective when organically modified montmorillonite was used as adsorbent compared to normal bentonite. The removal efficiency of organic clay depends upon the concentration of pesticides, doses of clay minerals, and efficiency was more for ODAAPS-M as compared to ODA-M. The combination of ODAAPS-M-clay with coagulants was also used efficiently for the removal of pesticides from natural and fortified natural water collected and the results exhibit the usefulness of this remediation technique for application in water decontamination and in treatment of industrial and agricultural waste waters.

  10. Design and daytime performance of laser-induced fluorescence spectrum lidar for simultaneous detection of multiple components, dissolved organic matter, phycocyanin, and chlorophyll in river water.

    Science.gov (United States)

    Saito, Yasunori; Kakuda, Kei; Yokoyama, Mizuho; Kubota, Tomoki; Tomida, Takayuki; Park, Ho-Dong

    2016-08-20

    In this work, we developed mobile laser-induced fluorescence spectrum (LIFS) lidar based on preliminary experiments on the excitation emission matrix of a water sample and a method for reducing solar background light using the synchronous detection technique. The combination of a UV short-pulse laser (355 nm, 6 ns) for fluorescence excitation with a 10-100 ns short-time synchronous detection using a gated image-intensified multi-channel CCD of the fluorescence made the LIFS lidar operation possible even in daytime. The LIFS lidar with this construction demonstrated the potential of natural river/lake water quality monitoring at the Tenryu River/Lake Suwa. Three main components in the fluorescence data of the water, dissolved organic matter, phycocyanin, and chlorophyll, were extracted by spectral analysis using the standard spectral functions of these components. Their concentrations were estimated by adapting experimentally calibrated data. Results of long-term field observations using our LIFS lidar from 2010 to 2012 show the necessity of simultaneous multi-component detection to understand the natural water environment.

  11. The potential multiple mechanisms and microbial communities in simultaneous nitrification and denitrification process treating high carbon and nitrogen concentration saline wastewater.

    Science.gov (United States)

    Wang, Jiale; Gong, Benzhou; Wang, Yingmu; Wen, Yuhui; Zhou, Jian; He, Qiang

    2017-11-01

    A simultaneous nitrification and denitrification (SND) process in sequencing batch biofilm reactor (SBBR) was established to treat high carbon and nitrogen saline wastewater in this study. Acetate, glucose and an organic mixture were applied as organic sources in three SBBRs, achieving average total nitrogen removal efficiency of 97.15%, 63.94% and 94.99% during 120days' operation, respectively. The underlying nitrogen removal mechanisms were investigated by 16S rRNA sequencing and batch tests. Results showed different carbon sources had great impact on microbial communities, and led to different nitrogen removal mechanism. Autotrophic and heterotrophic nitrification together contributed to the well performance of nitrification process. And denitrification was carried out by a combined anoxic and aerobic denitrificans. Furthermore, the SND process was mainly via nitrite not nitrate. Compared with ammonia-oxidizing bacteria, ammonia-oxidizing archaea with a much higher abundance contributed more to autotrophic nitrification. Pseudomonas_stutzeri and Bacillus_cereus were the predominant detected heterotrophic nitrification-aerobic denitrification bacterium. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Targeted analysis of ganglioside and sulfatide molecular species by LC/ESI-MS/MS with theoretically expanded multiple reaction monitoring.

    Science.gov (United States)

    Ikeda, Kazutaka; Shimizu, Takao; Taguchi, Ryo

    2008-12-01

    Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) has been applied primarily to the analysis of glycosphingolipids separated from other complex mixtures by TLC, but it is difficult to obtain quantitative profiling of each glycosphingolipid among the different spots on TLC by MALDI-MS. Thus, the development of a convenient approach that utilizes liquid chromatography/electrospray ionization (LC/ESI)-MS has received interest. However, previously reported methods have been insufficient to separate and distinguish each ganglioside class. Here we report an effective method for the targeted analysis of theoretically expected ganglioside molecular species by LC/ESI tandem mass spectrometry (LC/ESI-MS/MS) in combination with multiple reaction monitoring (MRM). MRM detection specific for sialic acid enabled us to analyze ganglioside standards such as GM1, GM2, GM3, GD1, and GT1 at picomolar to femtomolar levels. Furthermore, other gangliosides, such as GD2, GD3, GT2, GT3, and GQ1, were also detected in glycosphingolipid standard mixtures from porcine brain and acidic glycolipid extract from mouse brain by theoretically expanded MRM. We found that this approach was also applicable to sulfatides contained in the glycosphingolipid mixtures. In addition, we established a method to separate and distinguish regioisomeric gangliosides, such as GM1a and -1b, GD1a, -1b, and -1c, and GT1a, -1b, and -1c with diagnostic sugar chains in the MRM.

  13. Investigating single and multiple species fisheries management: stock status evaluation of hammerhead (Sphyrna spp.) sharks in the western North Atlantic Ocean and Gulf of Mexico.

    OpenAIRE

    Hayes, Christopher Glenn

    2007-01-01

    Three hammerhead sharks (Sphyrna spp.) are currently managed as part of the large coastal shark complex in the United States. Including multiple species in an assessment ignores the different stock dynamics of each individual species within the complex due to different life histories. This study completed individual assessments of scalloped (S. lewini), great (S. mokarran), and smooth (S. zygaena) hammerhead sharks in the U.S. Atlantic Ocean and Gulf of Mexico. Combined data for all three ...

  14. SU-F-T-510: Single Isocenter Radiosurgery for the Simultaneous Treatment of Multiple Brain Metastases: Volumetric Modulated Arc Therapy Or Dynamic Conformal Arc?

    Energy Technology Data Exchange (ETDEWEB)

    Maurer, J; Sintay, B; Manning, M; Wiant, D; Liu, H [Cone Health Cancer Center, Greensboro, NC (United States)

    2016-06-15

    Purpose: This study evaluates a novel algorithm that can be used with any treatment planning system for simple and rapid generation of stereotactic radiosurgery (SRS) plans for treating multiple brain metastases using a single isocenter dynamic conformal arc (DCA) approach. This technique is compared with a single isocenter volumetric modulated arc therapy (VMAT) technique in terms of delivery time, conformity, low dose spread and delivery accuracy. Methods: Five patients, with a total of 37 (5 – 11) targets were planned using a previously published method for generating optimal VMAT plans and using the proposed DCA algorithm. All planning target volumes (PTVs) were planned to 20 Gy, meeting a minimum 99% coverage and maximum 135 % hot spot for both techniques. Quality assurance was performed using radiochromic film, with films placed in the high dose regions of each PTV. Normal tissue volumes receiving 12 Gy and 6 Gy (V12 and V6) were computed for each plan. Conformity index (CI) and gamma evaluations (95% of points passing 4%/0.5mm) were computed for each PTV. Results: Delivery times, including beam on and table rotation times, were comparable: 17 – 22 minutes for all deliveries. V12s for DCA plans were (18.5±15.2 cc) vs. VMAT (19.7±14.4 cc). V6s were significantly lower for DCA (69.0±52.0 cc) compared with VMAT (154.0±91.0 cc) (p <<0.05). CIs for VMAT targets were (1.38±0.50) vs. DCA (1.61±0.41). 36 of 37 DCA planned targets passed gamma tests, while 29 of 37 VMAT planned targets passed. Conclusion: Single isocenter DCA plans were easily achieved. The evaluation suggests that DCA may represent a favorable technique compared with VMAT for multiple target SRS by reducing dose to normal tissue and more accurately depicting deliverable dose.

  15. Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia.

    Science.gov (United States)

    Esselstyn, Jacob A; Maharadatunkamsi; Achmadi, Anang S; Siler, Cameron D; Evans, Ben J

    2013-10-01

    In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence. © 2013 John Wiley & Sons Ltd.

  16. Simultaneous determination of heat stable peptides for eight animal and plant species in meat products using UPLC-MS/MS method.

    Science.gov (United States)

    Li, Yingying; Zhang, Yingying; Li, Huichen; Zhao, Wentao; Guo, Wenping; Wang, Shouwei

    2018-04-15

    Food adulteration and fraud is driven by economic interests; it is thus necessary to establish a high-through method that allows quantitative identification of familiar animal and plant proteins for global use. In this study, a sensitive mass spectrometric approach for the detection of eight species, including pork, beef, lamb, chicken, duck, soy, peanut, and pea, is presented and the heat stability and specificity of screened peptides are verified. To improve screening efficiency of specific peptides, several key data searching parameters, including peptides, sequence lengths, sequence coverage, and unique peptides, are investigated. Using this approach, it is possible to detect a 0.5% contamination of any of the eight species. The method is proven to have high sensitivity, specificity, repeatability, and a low quantitative detection limit with respect to adulteration of diverse types of meat products. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

    DEFF Research Database (Denmark)

    André, C.; Larsson, L. C.; Laikre, L.

    2010-01-01

    In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers...... presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species....... DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003...

  18. Developing above-ground woody biomass equations for open-grown, multiple-stemmed tree species: shelterbelt-grown Russian-olive

    Science.gov (United States)

    Xinhau Zhour; James R. Brandle; Michele M. Schoeneberger; Tala Awada

    2007-01-01

    Multiple-stemmed tree species are often used in agricultural settings, playing a significant role in natural resource conservation and carbon sequestration. Biomass estimation, whether for modeling growth under different climate scenarios, accounting for carbon sequestered, or inclusion in natural resource inventories, requires equations that can accurately describe...

  19. Simultaneous measurement of endogenous steroid hormones and their metabolites with LC-MS/MS in faeces of a New World primate species, Cebus capucinus.

    Science.gov (United States)

    Weltring, Anja; Schaebs, Franka S; Perry, Susan E; Deschner, Tobias

    2012-01-18

    We developed and validated a method to measure steroid hormones with liquid chromatography-tandem mass spectrometry (LC-MS/MS) in faecal samples of white-faced capuchins. The method includes the measurement of adrenal and gonadal hormones such as cortisol, testosterone, estrone, progesterone and a number of their faecal metabolites. This method can be used for simultaneous routine measurements of steroids in faecal samples and provides a reference method for the validation of new immunoassays in this matrix. The optimised method consists of an extraction of the dried faecal samples with 80% methanol followed by purification of the extracts by solid phase extraction, solvolytic cleavage of conjugates and liquid-liquid extraction. Extracts were measured by LC-MS/MS with an electrospray interface in positive ionisation mode. Out of 19 steroids spiked into methanol extracts, 14 showed a recovery of 79.8-118.5% with an intra-day precision of 2.5-13.0% and an inter-day precision of 7.2-15.1%. Detection limits for these steroids ranged from 0.3 to 27.0 ng/mL of extract. Five steroids did not fulfil our requirements concerning precision and accuracy and we therefore considered these to not be reliably measurable with this method. While there was no indication of considerable amounts of conjugated forms for most metabolites, 87% of the testosterone was found in the solvolysis fraction, which indicates that the majority of testosterone was conjugated. Therefore, solvolysis turned out to be crucial, especially for the quantification of the total amount of testosterone. The physiological validation of this LC-MS/MS method confirmed known physiologically caused differences in faecal steroid concentrations. This indicates the usefulness of the method in investigating variation in the levels of major steroid hormones in faeces of white-faced capuchins. The possibility to simultaneously measure hormones of the hypothalamic-pituitary-adrenal (HPA) axis and the hypothalamic

  20. Simultaneous determination of components released from dental composite resins in human saliva by liquid chromatography/multiple-stage ion trap mass spectrometry.

    Science.gov (United States)

    Hsu, Wei-Yi; Wang, Ven-Shing; Lai, Chien-Chen; Tsai, Fuu-Jen

    2012-02-01

    Dental composite resins are widely used for fixing teeth; however, the monomers used in dental composite resins have been found to be cytotoxic and genotoxic, namely triethylene glycol dimethacrylate (TEGDMA), urethane dimethacrylate (UDMA), and bisphenol A glycol dimethacrylate (Bis-GMA). In this study, we incubated dental composite resins with human saliva for demonstrating the released monomers and biodegradation products. A simple saliva sample dilution method without purification or derivatization was used for quantification. We found that liquid chromatography coupled with multiple-stage ion trap mass spectrometry (LC-MS(n) ) operated in selected reaction monitoring (SRM) mode was able to separate the three monomers within 10 min. The calibration curves were linear (R² >0.996) over a wide range for each monomer in saliva: TEGDMA, 5-500 ppb; UDMA, 5-100 ppb, and Bis-GMA, 5-700 ppb. Furthermore, several biodegradation products were discovered with data-dependent MS/MS scan techniques. Although TEGMA degradation products have previously been reported, we identified two previously unknown UDMA degradation products. The LC-MS/MS method developed in this study was able to successfully quantify monomers and their principal biodegradation products from dental composite resins in human saliva. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Processes at multiple scales affect richness and similarity of non-native plant species in mountains around the world

    Science.gov (United States)

    Tim Seipel; Christoph Kueffer; Lisa J. Rew; Curtis C. Daehler; Aníbal Pauchard; Bridgett J. Naylor; Jake M. Alexander; Peter J. Edwards; Catherine G. Parks; Jose Ramon Arevalo; Lohengrin A. Cavieres; Hansjorg Dietz; Gabi Jakobs; Keith McDougall; Rudiger Otto; Neville. Walsh

    2012-01-01

    We compared the distribution of non-native plant species along roads in eight mountainous regions. Within each region, abundance of plant species was recorded at 41-84 sites along elevational gradients using 100-m2 plots located 0, 25 and 75 m from roadsides. We used mixed-effects models to examine how local variation in species richness and...

  2. Development, validation and application of a GC-MS method for the simultaneous detection and quantification of neutral lipid species in Trypanosoma cruzi.

    Science.gov (United States)

    Santivañez-Veliz, Mery; Moreno-Viguri, Elsa; Pérez-Silanes, Silvia; Varela, Javier; Cerecetto, Hugo; González, Mercedes; Lizarraga, Elena

    2017-09-01

    The development and validation of an analytical method for the simultaneous analysis of five neutral lipids in Trypanosoma cruzi epimastigotes by GC-MS is presented in this study. The validated method meets all validation parameters for all components and the chromatographic conditions have been optimized during its development. This analytical method has demonstrated good selectivity, accuracy, within-day precision, recovery and linearity in each of the established ranges. In addition, detection and quantification limits for squalene, cholesterol, ergosterol and lanosterol have been improved and it is worth highlighting the fact that this is the first time that squalene-2,3-epoxide validation data have been reported. The new validated method has been applied to epimastigotes treated with compounds with in vitro anti-T.cruzi activity. This new methodology is straightforward and constitutes a tool for screening possible sterol biosynthesis pathway inhibitors in Trypanosoma cruzi, one of the most studied targets in Chagas disease treatment. Therefore, it is an interesting and useful contribution to medicinal chemistry research. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Simultaneous removal of multiple odorants from source water suffering from septic and musty odors: Verification in a full-scale water treatment plant with ozonation.

    Science.gov (United States)

    Guo, Qingyuan; Yang, Kai; Yu, Jianwei; Wang, Chunmiao; Wen, Xiaodong; Zhang, Liping; Yang, Min; Xia, Ping; Zhang, Dong

    2016-09-01

    Ozonation is known to be very effective in the removal of odorants from source water. However, it is not known if ozonation is effective in the removal of multiple odorants causing different types of odors. In this study, the removal performance for odors and odorants were evaluated in a Water Treatment Plant (WTP), which was equipped with coagulation, sedimentation, ozonation, biological activated carbon (BAC) filtration, sand filtration, and chlorination in succession and located in the downstream of the Huangpu (HP) River, over the period from April, 2014 to April, 2015. Flavor profile analysis (FPA) results showed that the source water was constantly associated with septic and musty odors. Geosmin and 2-MIB, with an average OAV of 4.54 and 1.38, respectively, were the major odorants for musty odor, while bis(2-chloroisopropyl) ether, DEDS and DMDS with an average OAV of 2.35, 1.65 and 0.78, respectively, might be responsible for the septic odor. While the musty odor could be removed effectively through the combination of ozonation and BAC, the septic odor and associated odorants required further treatment with sand filtration and chlorination for complete removal. It is clear that the advanced treatment process was effective for the treatment of source water containing complicated odorants. It should be noted that the sedimentation process needs careful management because release of odorants may occur during the treatment. The result of this study will be helpful for the mitigation of odors in WTP using source waters suffering from complicated odor problems. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Effects of Environment and Space on Species Turnover of Woody Plants across Multiple Forest Dynamic Plots in East Asia.

    Science.gov (United States)

    Chen, Yun; Yuan, Zhiliang; Li, Peikun; Cao, Ruofan; Jia, Hongru; Ye, Yongzhong

    2016-01-01

    Species turnover is fundamental for understanding the mechanisms that influence large-scale species richness patterns. However, few studies have described and interpreted large-scale spatial variation in plant species turnover, and the causes of this variation remain elusive. In addition, the determinants of species turnover depend on the dispersal ability of growth forms. In this study, we explored the large-scale patterns of woody species turnover across the latitude gradient based on eight large stem-mapping plots (covering 184 ha forest) in East Asia. The patterns of woody species turnover increased significantly with increasing latitude differences in East Asia. For overall woody species, environment explained 36.30, 37.20, and 48.48% of the total variance in Jaccard's (β j ), Sorenson's, (β s ), and Simpson's dissimilarity (β sim ). Spatial factors explained 47.92, 48.39, and 41.38% of the total variance in β j , β s , and β sim , respectively. The effects of pure spatial and spatially structured environments were stronger than pure environmental effects for overall woody species. Our results support the hypothesis that the effect of neutral processes on woody species turnover is more important than the effect of the environment. Neutral processes explained more variation for turnover of tree species, and environmental factors explained more variation for the turnover of shrub species on a large scale. Therefore, trees and shrubs should be subjected to different protection strategies in future biodiversity conservation efforts.

  5. Simultaneous detection of multiple mRNA markers CK19, CEA, c-Met, Her2/neu and hMAM with membrane array, an innovative technique with a great potential for breast cancer diagnosis.

    Science.gov (United States)

    Chen, Chung-Chi; Hou, Ming-Feng; Wang, Jaw-Yuan; Chang, Tsai-Wang; Lai, Dan-Yu; Chen, Yi-Fang; Hung, Sung-Yu; Lin, Shiu-Ru

    2006-08-28

    The objective of this study was mainly to develop and evaluate a membrane array-based method simultaneously detecting the expression levels of a multiple mRNA marker panel in the peripheral blood for used in complementary breast cancer diagnosis. The mRNA markers employed included cytokeratin 19 (CK-19), carcinoembryonic antigen (CEA), c-Met, Her2/neu, and mammaglobin (hMAM). The specimens of peripheral blood were collected from 80 healthy women and 102 female patients with breast cancer. The expression levels of molecular markers were evaluated by real-time Q-PCR and membrane array. Data obtained from real-time Q-PCR and membrane array were subjected to linear regression analysis, revealing that there was a high degree of correlation between the results of these two methods (r=0.979, Pmembrane array assay with a combined panel of five mRNA markers was demonstrated to achieve sensitivity of 80.6%, and specificity of 83.8% for breast cancer detection, much higher than those of analysis of single marker. In addition, we demonstrated that the membrane array method could detect circulating cancer cells at a density as low as five cancer cells per 1 ml of blood. The analysis of correlation between the outcome of membrane array and clinicopathological characteristics indicated that overexpression of the multiple marker panel was significantly correlated with tumor size (P=0.030) and TNM stage (0.009). In conclusion, the detection of circulating cancer cells by means of membrane array simultaneously monitoring five mRNA markers could significantly enhance the sensitivity and specificity for cancer cell detection.

  6. Comparative Analysis of DNA Barcoding and HPLC Fingerprint to Trace Species of Phellodendri Cortex, an Important Traditional Chinese Medicine from Multiple Sources.

    Science.gov (United States)

    Zhang, Zhipeng; Zhang, Yang; Zhang, Zhao; Yao, Hui; Liu, Haitao; Zhang, Ben'gang; Liao, Yonghong

    2016-08-01

    Phellodendri Cortex is derived from the dried barks of Phellodendron genus species, has been extensively used in traditional Chinese medicine. The cortex is divided into two odorless crude drugs Guanhuangbo and Huangbo. Historically, it has been difficult to distinguish their identities due to a lack of identification methods. This study was executed to confirm the identity and to ensure the species traceability of Phellodendri Cortex. In the current study, analysis is based on the internal transcribed spacer (ITS) and psbA-trnH intergenic spacer (psbA-trnH) barcodes and HPLC fingerprint was carried out to guarantee the species traceability of Guanhuangbo and Huangbo. DNA barcoding data successfully identified the three plants of the Phellodendron genus species by ITS+psbA-trnH, with the ability to distinguish the species origin of Huangbo. Moreover, the psbA-trnH data distinguished Guanhuangbo and Huangbo except to trace species. The HPLC fingerprint data showed that Guanhuangbo was clearly different from Huangbo, but there was no difference between the two origins of Huangbo. Additionally, the result of hierarchical clustering analysis, based on chlorogenic acid, phellodendrine, magnoflorine, jatrorrhizine, palmatine and berberine, was consistent with the HPLC fingerprint analysis. These results show that DNA barcoding and HPLC fingerprint can discriminate Guanhuangbo and Huangbo. However, DNA barcoding is more powerful than HPLC fingerprint for species traceability in the identification of related species that are genetically similar. DNA barcoding is a useful scientific tool to accurately confirm the identities of medicinal materials from multiple sources.

  7. Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand.

    Science.gov (United States)

    Laopichienpong, Nararat; Muangmai, Narongrit; Supikamolseni, Arrjaree; Twilprawat, Panupon; Chanhome, Lawan; Suntrarachun, Sunutcha; Peyachoknagul, Surin; Srikulnath, Kornsorn

    2016-12-15

    DNA barcodes of mitochondrial cytochrome c oxidase I (COI), cytochrome b (Cytb) genes, and their combined data sets were constructed from 35 snake species in Thailand. No barcoding gap was detected in either of the two genes from the observed intra- and interspecific sequence divergences. Intra- and interspecific sequence divergences of the COI gene differed 14 times, with barcode cut-off scores ranging over 2%-4% for threshold values differentiated among most of the different species; the Cytb gene differed 6 times with cut-off scores ranging over 2%-6%. Thirty-five specific nucleotide mutations were also found at interspecific level in the COI gene, identifying 18 snake species, but no specific nucleotide mutation was observed for Cytb in any single species. This suggests that COI barcoding was a better marker than Cytb. Phylogenetic clustering analysis indicated that most species were represented by monophyletic clusters, suggesting that these snake species could be clearly differentiated using COI barcodes. However, the two-marker combination of both COI and Cytb was more effective, differentiating snake species by over 2%-4%, and reducing species numbers in the overlap value between intra- and interspecific divergences. Three species delimitation algorithms (general mixed Yule-coalescent, automatic barcoding gap detection, and statistical parsimony network analysis) were extensively applied to a wide range of snakes based on both barcodes. This revealed cryptic diversity for eleven snake species in Thailand. In addition, eleven accessions from the database previously grouped under the same species were represented at different species level, suggesting either high genetic diversity, or the misidentification of these sequences in the database as a consequence of cryptic species. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. High-performance liquid chromatography-tandem mass spectrometry method for simultaneous detection of ochratoxin A and relative metabolites in Aspergillus species and dried vine fruits.

    Science.gov (United States)

    Zhang, Xiaoxu; Li, Jingming; Cheng, Zhan; Zhou, Ziying; Ma, Liyan

    2016-08-01

    A simple, sensitive and reliable quantification and identification method was developed for simultaneous analysis of ochratoxin A (OTA) and its related metabolites ochratoxin alpha (OTα), ochratoxin B (OTB) and mellein. The method was assessed by spiking analytes into blank culture media and dried vine fruits. Performance was tested in terms of accuracy, selectivity and repeatability. The method involves an ultrasonic extraction step for culture samples using methanol aqueous solution (7:3, v/v); the mycotoxin is quantified by high-performance liquid chromatography coupled with electrospray ionisation and triple quadrupole mass spectrometry (LC-ESI-MS/MS). The recoveries were 74.5-108.8%, with relative standard deviations (RSDs) of 0.4-8.4% for fungal culture. The limits of detection (LODs) were in the range of 0.03-0.87 μg l(-)(1), and the limits of quantification (LOQs) ranged from 0.07 to 2.90 μg l(-)(1). In addition, the extraction solutions and clean-up columns were optimised specifically for dried vine fruit samples to improve the performance of the method. Methanol-1% sodium bicarbonate extraction solution (6:4, v/v) was determined to be the most efficient. Solid-phase extraction (SPE) was performed as a clean-up step prior to HPLC-MS/MS analysis to reduce matrix effects. Recoveries ranged from 80.1% to 110.8%. RSDs ranged from 0.1% to 3.6%. LODs and LOQs ranged from 0.06 to 0.40 μg kg(-)(1) and from 0.19 to 1.20 μg kg(-)(1), respectively. The analytical method was established and used to identify and quantify OTA and related compounds from Aspergillus carbonarius and Aspergillus ochraceus in cultures and dried vine fruits. The results showed that A. carbonarius produced OTα, OTB and OTA, whereas A. ochraceus produced OTB, OTA and mellein after 7 days of cultivation. Of 30 commercial samples analysed, 10 were contaminated with ochratoxins; OTB, OTα and mellein were also detected in different samples.

  9. Factores de riesgo asociados a candidemias causadas por múltiples especies Risk factors associated with multiple-species candidemia

    Directory of Open Access Journals (Sweden)

    A. Benetucci

    2008-03-01

    Full Text Available Los episodios de candidemia han aumentado en la última década. Sin embargo, la publicación de casos de candidemias causadas por múltiples especies (CME es infrecuente. De un total de 155 candidemias diagnosticadas entre 1998 y 2004 en el Hospital de Clínicas de la Universidad de Buenos Aires, se identificaron 7 casos de CME (6 adultos y 1 neonato, cuyos datos clínicos y evolutivos se compararon con 21 casos de candidemias producidas por una única especie de Candida (CUE en pacientes de similar edad e igual sexo. No se hallaron mayores diferencias clínicas o evolutivas entre los pacientes con CME y CUE; sin embargo, la mediana del tiempo de internación y del tiempo promedio de permanencia de los catéteres venosos centrales con anterioridad a la candidemia (39 y 32 días para los pacientes con CME vs. 18 y 12 días para aquellos con CUE, respectivamente resultaron ser factores predisponentes relevantes. La duración de la candidemia fue más prolongada en los pacientes con CME que en los afectados por CUE (5 días vs. 1 día. En conclusión, aunque los episodios de CME son menos frecuentes que los causados por una única especie de Candida, factores de riesgo potencialmente controlables como el tiempo de internación y el tiempo de utilización de catéteres venosos centrales tienen mayor importancia en el desarrollo de CME.The incidence of fungemia has increased over the past decade. Multiple-species candidemia (MSC has been infrequently reported. From 1998 to 2004, of 155 patients with diagnosis of candidemia at the Hospital de Clínicas (University of Buenos Aires, seven cases of MSC were identified (6 adults and 1 newborn and compared with 21 cases of similar age and sex with monomicrobial candidemia. There were no differences in clinical data and outcome, except for the mediana duration of hospital stay (39 days for patients with MSC vs. 18 days for patients with monomicrobial candidemia, the mean time of central venous catheter

  10. Ion-exclusion/cation-exchange chromatography with dual detection of the conductivity and spectrophotometry for the simultaneous determination of common inorganic anionic species and cations in river and wastewater.

    Science.gov (United States)

    Nakatani, Nobutake; Kozaki, Daisuke; Mori, Masanobu; Hasebe, Kiyoshi; Nakagoshi, Nobukazu; Tanaka, Kazuhiko

    2011-01-01

    Simultaneous determinations of common inorganic anionic species (SO(4)(2-), Cl(-), NO(3)(-), phosphate and silicate) and cations (Na(+), NH(4)(+), K(+), Mg(2+) and Ca(2+)) were conducted using an ion-chromatography system with dual detection of conductivity and spectrophotometry in tandem. The separation of ionic species on a weakly acidic cation-exchange resin was accomplished using a mixture of 100 mM ascorbic acid and 4 mM 18-crown-6 as an acidic eluent (pH 2.6), after which the ions were detected using a conductivity detector. Subsequently, phosphate and silicate were analyzed based on derivatization with molybdate and spectrophotometry at 700 nm. The detection limits at S/N = 3 ranged from 0.11 to 2.9 µM for analyte ionic species. This method was applied to practical river water and wastewater with acceptable criteria for the anion-cation balance and comparisons of the measured and calculated electrical conductivity, demonstrating the usefulness of the present method for water quality monitoring.

  11. Tree demography suggests multiple directions and drivers for species range shifts in mountains of Northeastern United States.

    Science.gov (United States)

    Wason, Jay W; Dovciak, Martin

    2017-08-01

    Climate change is expected to lead to upslope shifts in tree species distributions, but the evidence is mixed partly due to land-use effects and individualistic species responses to climate. We examined how individual tree species demography varies along elevational climatic gradients across four states in the northeastern United States to determine whether species elevational distributions and their potential upslope (or downslope) shifts were controlled by climate, land-use legacies (past logging), or soils. We characterized tree demography, microclimate, land-use legacies, and soils at 83 sites stratified by elevation (~500 to ~1200 m above sea level) across 12 mountains containing the transition from northern hardwood to spruce-fir forests. We modeled elevational distributions of tree species saplings and adults using logistic regression to test whether sapling distributions suggest ongoing species range expansion upslope (or contraction downslope) relative to adults, and we used linear mixed models to determine the extent to which climate, land use, and soil variables explain these distributions. Tree demography varied with elevation by species, suggesting a potential upslope shift only for American beech, downslope shifts for red spruce (more so in cool regions) and sugar maple, and no change with elevation for balsam fir. While soils had relatively minor effects, climate was the dominant predictor for most species and more so for saplings than adults of red spruce, sugar maple, yellow birch, cordate birch, and striped maple. On the other hand, logging legacies were positively associated with American beech, sugar maple, and yellow birch, and negatively with red spruce and balsam fir - generally more so for adults than saplings. All species exhibited individualistic rather than synchronous demographic responses to climate and land use, and the return of red spruce to lower elevations where past logging originally benefited northern hardwood species indicates

  12. Effects of environment and space on species turnover of woody plants across multiple forest dynamic plots in East Asia

    Directory of Open Access Journals (Sweden)

    Yun Chen

    2016-10-01

    Full Text Available Species turnover is fundamental for understanding the mechanisms that influence large-scale species richness patterns. However, few studies have described and interpreted large-scale spatial variation in plant species turnover, and the causes of this variation remain elusive. In addition, the determinants of species turnover depend on the dispersal ability of growth forms. In this study, we explored the large-scale patterns of woody species turnover across the latitude gradient based on eight large stem-mapping plots (covering 184 ha forest in East Asia. The patterns of woody species turnover increased significantly with increasing latitude differences in East Asia. For overall woody species, environment explained 36.30%, 37.20%, and 48.48% of the total variance in Jaccard’s (βj, Sorenson’s, (βs, and Simpson’s dissimilarity (βsim. Spatial factors explained 47.92%, 48.39%, and 41.38% of the total variance in βj, βs, and βsim, respectively. The effects of pure spatial and spatially structured environments were stronger than pure environmental effects for overall woody species. Our results support the hypothesis that the effect of neutral processes on woody species turnover is more important than the effect of the environment. Neutral processes explained more variation for turnover of tree species, and environmental factors explained more variation for the turnover of shrub species on a large scale. Therefore, trees and shrubs should be subjected to different protection strategies in future biodiversity conservation efforts.

  13. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones

    Directory of Open Access Journals (Sweden)

    Zheng Tong

    2017-05-01

    Full Text Available Rubber elongation factor (REF and small rubber particle protein (SRPP are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE, each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  14. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones.

    Science.gov (United States)

    Tong, Zheng; Wang, Dan; Sun, Yong; Yang, Qian; Meng, Xueru; Wang, Limin; Feng, Weiqiang; Li, Ling; Wurtele, Eve Syrkin; Wang, Xuchu

    2017-05-02

    Rubber elongation factor (REF) and small rubber particle protein (SRPP) are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF 138,175,258 and SRPP 117,204,243 , were characterized from Hevea brasiliensis Reyan (RY) 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF 258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE), each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF 175 or REF 258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  15. Improving Discrimination of Savanna Tree Species Through a Multiple-Endmember Spectral Angle Mapper Approach: Canopy-Level Analysis

    NARCIS (Netherlands)

    Cho, M.A.; Debba, P.; Mathieu, R.; Naidoo, L.; Aardt, van J.; Asner, G.P.

    2010-01-01

    Differences in within-species phenology and structure are controlled by genetic variation, as well as topography, edaphic properties, and climatic variables across the landscape, and present important challenges to species differentiation with remote sensing. The objectives of this paper are as

  16. Concordance of seven gene genealogies compared to phenotypic data reveals multiple cryptic species in Australian dermocyboid Cortinarius (Agaricales).

    Science.gov (United States)

    Stefani, Franck O P; Jones, Rodney H; May, Tom W

    2014-02-01

    This study aims to delimit species of Australian dermocyboid fungi (Cortinarius, Agaricales) using genealogical concordance on well-characterised phenotypic species and to assess the utility of seven loci for DNA barcoding Australian Cortinarius taxa. Eighty-six collections of dermocyboid Cortinarius were sampled from across southern Australia. Phenotypic species were first recognised by performing clustering analyses on a comprehensive phenotypic dataset including morphological, colour and pigment data. Then phylogenetic species were delimited from the concordance of seven locus genealogies (ITS, nLSU, gpd, mcm7, rpb1, rpb2 and tef1). Seventeen phenotypic species were recognised while the concordance of gene genealogies recovered 35 phylogenetic species. All loci except for LSU recovered most phylogenetic species, although only rpb1 correctly identified all phylogenetic species. The ITS region is confirmed as an effective barcode for Cortinarius and a standard pairwise distance threshold of 2.0% is proposed to DNA barcode Australian Cortinarius taxa. Australian dermocyboid fungi belong in separate clades to the boreal clade Dermocybe, mostly in the clade Splendidi. This study provides a solid foundation for future ecological, taxonomic and systematic research on one of the most diverse genera of mushrooms worldwide. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Genomic characterisation of Arachis porphyrocalyx (Valls & C.E. Simpson, 2005 (Leguminosae: multiple origin of Arachis species with x = 9

    Directory of Open Access Journals (Sweden)

    Silvestri María Celeste

    2017-01-01

    Full Text Available The genus Arachis Linnaeus, 1753 comprises four species with x = 9, three belong to the section Arachis: Arachis praecox (Krapov. W.C. Greg. & Valls, 1994, Arachis palustris (Krapov. W.C. Greg. & Valls, 1994 and Arachis decora (Krapov. W.C. Greg. & Valls, 1994 and only one belongs to the section Erectoides: Arachis porphyrocalyx (Valls & C.E. Simpson, 2005. Recently, the x = 9 species of section Arachis have been assigned to G genome, the latest described so far. The genomic relationship of A. porphyrocalyx with these species is controversial. In the present work, we carried out a karyotypic characterisation of A. porphyrocalyx to evaluate its genomic structure and analyse the origin of all x = 9 Arachis species. Arachis porphyrocalyx showed a karyotype formula of 14m+4st, one pair of A chromosomes, satellited chromosomes type 8, one pair of 45S rDNA sites in the SAT chromosomes, one pair of 5S rDNA sites and pericentromeric C-DAPI+ bands in all chromosomes. Karyotype structure indicates that A. porphyrocalyx does not share the same genome type with the other three x = 9 species and neither with the remaining Erectoides species. Taking into account the geographic distribution, morphological and cytogenetic features, the origin of species with x = 9 of the genus Arachis cannot be unique; instead, they originated at least twice in the evolutionary history of the genus.

  18. Genomic characterisation of Arachis porphyrocalyx (Valls & C.E. Simpson, 2005) (Leguminosae): multiple origin of Arachis species with x = 9.

    Science.gov (United States)

    Celeste, Silvestri María; Ortiz, Alejandra Marcela; Robledo, Germán Ariel; Valls, José Francisco Montenegro; Lavia, Graciela Inés

    2017-01-01

    The genus Arachis Linnaeus, 1753 comprises four species with x = 9, three belong to the section Arachis: Arachis praecox (Krapov. W.C. Greg. & Valls, 1994), Arachis palustris (Krapov. W.C. Greg. & Valls, 1994) and Arachis decora (Krapov. W.C. Greg. & Valls, 1994) and only one belongs to the section Erectoides: Arachis porphyrocalyx (Valls & C.E. Simpson, 2005). Recently, the x = 9 species of section Arachis have been assigned to G genome, the latest described so far. The genomic relationship of Arachis porphyrocalyx with these species is controversial. In the present work, we carried out a karyotypic characterisation of Arachis porphyrocalyx to evaluate its genomic structure and analyse the origin of all x = 9 Arachis species. Arachis porphyrocalyx showed a karyotype formula of 14m+4st, one pair of A chromosomes, satellited chromosomes type 8, one pair of 45S rDNA sites in the SAT chromosomes, one pair of 5S rDNA sites and pericentromeric C-DAPI+ bands in all chromosomes. Karyotype structure indicates that Arachis porphyrocalyx does not share the same genome type with the other three x = 9 species and neither with the remaining Erectoides species. Taking into account the geographic distribution, morphological and cytogenetic features, the origin of species with x = 9 of the genus Arachis cannot be unique; instead, they originated at least twice in the evolutionary history of the genus.

  19. Oviposition behavior of the biological control agent Aphidoletes aphidimyza (Diptera: Cecidomyiidae) in environments with multiple pest aphid species (Hemiptera: Aphididae)

    Science.gov (United States)

    Natural enemies are constantly faced with oviposition decisions that have potential fitness consequences. We investigated the oviposition behavior of the aphidophagous midge Aphidoletes aphidimyza (Diptera: Cecidomyiidae) when faced with multiple prey choices, i.e. plants infested with Myzus persic...

  20. BIOTIC AND ABIOTIC FACTORS INFLUENCE DURING THE IN VITRO MULTIPLICATION PHASE OF SOME SPECIES AND VARIETIES OF THE ACER GENUS

    Directory of Open Access Journals (Sweden)

    Manuela Elena Concioiu

    2012-04-01

    Full Text Available The purpose of the research was to study the behavior of several Acer varieties: Acer palmatum 'Dissectum Atropurpureum' and Acer platanoides 'Crimson King', 'Drummondii' and 'Globosum', during the first subculture of the in vitro multiplication phase. There were used explants from the initiation phase and passed on the multiplication nutrient media. The nutrient media tested were MS, DKW and WPM and each had a different content of growth hormones. In order to determine the multiplication rate, was tested the influence of zeatin and thidiazuron, in concentration of 1.5 mg/l, on a constant level of indole-butyric acid (0.5 mg/l. In the growing chamber were a constant temperature and a photoperiod of 14 hours light/24 hours, at a luminosity of 2500 lux. From the observations and registered data was determined the multiplication rate (microshoots/explant for the four genotypes.

  1. Simultaneous determination of N(1)-methylnicotinamide, L-carnitine, and creatinine in human plasma and urine by liquid chromatography with mass spectrometry for assessing the activities of multiple renal cationic transporters.

    Science.gov (United States)

    Nobuoka, Yuji; Ogawa, Ryuichi; Echizen, Hirotoshi

    2014-09-15

    Organic cation transporters are responsible for the disposition of various endogenous and therapeutic agents in humans; thus, there is a great need for the development of a simple assay for simultaneous assessment of the activities of multiple transporters. Using liquid chromatography-mass spectrometry (LC/MS), we developed an assay that allows for simultaneous quantitation of plasma and urinary levels of N(1)-methylnicotinamide (a substrate of hOCT2/hMATEs), L-carnitine (a substrate of hOCTN2), and creatinine (an indicator of glomerular filtration). Samples were diluted with ultrapure water, deproteinized with trichloroacetic acid, filtered, and then injected on a cation exchange column. The analytes were separated with a gradient LC technique and detected by MS. The total assay time was less than 8 min. The lower detection limits for N(1)-methylnicotinamide, L-carnitine, and creatinine were 2, 10, and 24 ng/mL, respectively. Recovery of the analytes was almost complete. A preliminary clinical study conducted in 25 healthy subjects revealed that the mean±SD for the renal clearance (CLR) of N(1)-methylnicotinamide (272.7±81.0 mL/min) far exceeded the glomerular filtration rate (116.3±19.6 mL/min), indicating the involvement of active tubular secretion, while the mean CLR of clearance of L-carnitine was close to nil (1.5±1.4 mL/min), indicating almost complete tubular reabsorption. The present method is potentially useful for clinical studies on the genetic control of cationic transporter activities and the transporter-mediated drug interactions. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. The simultaneous isolation of multiple high and low frequent T-cell populations from donor peripheral blood mononuclear cells using the major histocompatibility complex I-Streptamer isolation technology.

    Science.gov (United States)

    Roex, Marthe C J; Hageman, Lois; Heemskerk, Matthias T; Veld, Sabrina A J; van Liempt, Ellis; Kester, Michel G D; Germeroth, Lothar; Stemberger, Christian; Falkenburg, J H Frederik; Jedema, Inge

    2018-02-12

    Adoptive transfer of donor-derived T cells can be applied to improve immune reconstitution in immune-compromised patients after allogeneic stem cell transplantation. The separation of beneficial T cells from potentially harmful T cells can be achieved by using the major histocompatibility complex (MHC) I-Streptamer isolation technology, which has proven its feasibility for the fast and pure isolation of T-cell populations with a single specificity. We have analyzed the feasibility of the simultaneous isolation of multiple antigen-specific T-cell populations in one procedure by combining different MHC I-Streptamers. First, the effect of combining different amounts of MHC I-Streptamers used in the isolation procedure on the isolation efficacy of target antigen-specific T cells and on the number of off-target co-isolated contaminating cells was assessed. The feasibility of this approach was demonstrated in large-scale validation procedures targeting both high and low frequent T-cell populations using the Good Manufacturing Practice (GMP)-compliant CliniMACS Plus device. T-cell products targeting up to 24 different T-cell populations could be isolated in one, simultaneous MHC I-Streptamer procedure, by adjusting the amount of MHC I- Streptamers per target antigen-specific T-cell population. Concurrently, the co-isolation of potentially harmful contaminating T cells remained below our safety limit. This technology allows the reproducible isolation of high and low frequent T-cell populations. However, the expected therapeutic relevance of direct clinical application without in vitro expansion of these low frequent T-cell populations is questionable. This study provides a feasible, fast and safe method for the generation of highly personalized MHC I-Streptamer isolated T-cell products for adoptive immunotherapy. Copyright © 2018 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

  3. A New Synthetic Allotetraploid (A1A1G2G2) between Gossypium herbaceum and G. australe: Bridging for Simultaneously Transferring Favorable Genes from These Two Diploid Species into Upland Cotton

    Science.gov (United States)

    Chen, Yu; Wang, Yingying; Chen, Jinjin; Zhang, Tianzhen; Zhou, Baoliang

    2015-01-01

    Gossypium herbaceum, a cultivated diploid cotton species (2n = 2x = 26, A1A1), has favorable traits such as excellent drought tolerance and resistance to sucking insects and leaf curl virus. G. australe, a wild diploid cotton species (2n = 2x = 26, G2G2), possesses numerous economically valuable characteristics such as delayed pigment gland morphogenesis (which is conducive to the production of seeds with very low levels of gossypol as a potential food source for humans and animals) and resistance to insects, wilt diseases and abiotic stress. Creating synthetic allotetraploid cotton from these two species would lay the foundation for simultaneously transferring favorable genes into cultivated tetraploid cotton. Here, we crossed G. herbaceum (as the maternal parent) with G. australe to produce an F1 interspecific hybrid and doubled its chromosome complement with colchicine, successfully generating a synthetic tetraploid. The obtained tetraploid was confirmed by morphology, cytology and molecular markers and then self-pollinated. The S1 seedlings derived from this tetraploid gradually became flavescent after emergence of the fifth true leaf, but they were rescued by grafting and produced S2 seeds. The rescued S1 plants were partially fertile due to the existence of univalents at Metaphase I of meiosis, leading to the formation of unbalanced, nonviable gametes lacking complete sets of chromosomes. The S2 plants grew well and no flavescence was observed, implying that interspecific incompatibility, to some extent, had been alleviated in the S2 generation. The synthetic allotetraploid will be quite useful for polyploidy evolutionary studies and as a bridge for transferring favorable genes from these two diploid species into Upland cotton through hybridization. PMID:25879660

  4. Close association between paralogous multiple isomiRs and paralogous/orthologues miRNA sequences implicates dominant sequence selection across various animal species.

    Science.gov (United States)

    Guo, Li; Zhao, Yang; Zhang, Hui; Yang, Sheng; Chen, Feng

    2013-09-25

    MicroRNAs (miRNAs) are crucial negative regulators of gene expression at the post-transcriptional level. Next-generation sequencing technologies have identified a series of miRNA variants (named isomiRs). In this study, paralogous isomiR assemblies (from the miRNA locus) were systematically analyzed based on data acquired from deep sequencing data sets. Evolutionary analysis of paralogous (members in miRNA gene family in a specific species) and orthologues (across different animal species) miRNAs was also performed. The sequence diversity of paralogous isomiRs was found to be similar to the diversity of paralogous and orthologues miRNAs. Additionally, both isomiRs and paralogous/orthologues miRNAs were implicated in 5' and 3' ends (especially 3' ends), nucleotide substitutions, and insertions and deletions. Generally, multiple isomiRs can be produced from a single miRNA locus, but most of them had lower enrichment levels, and only several dominant isomiR sequences were detected. These dominant isomiR groups were always stable, and one of them would be selected as the most abundant miRNA sequence in specific animal species. Some isomiRs might be consistent to miRNA sequences in some species but not the other. Homologous miRNAs were often detected in similar isomiR repertoires, and showed similar expression patterns, while dominant isomiRs showed complex evolutionary patterns from miRNA sequences across the animal kingdom. These results indicate that the phenomenon of multiple isomiRs is not a random event, but rather the result of evolutionary pressures. The existence of multiple isomiRs enables different species to express advantageous sequences in different environments. Thus, dominant sequences emerge in response to functional and evolutionary pressures, allowing an organism to adapt to complex intra- and extra-cellular events. © 2013.

  5. Hollow Internodes Permit a Neotropical Understory Plant to Shelter Multiple Mutualistic Ant Species, Obtaining Protection and Nutrient Provisioning (Myrmecotrophy).

    Science.gov (United States)

    Dejean, Alain; Petitclerc, Frédéric; Compin, Arthur; Azémar, Frédéric; Corbara, Bruno; Delabie, Jacques H C; Leroy, Céline

    2017-11-01

    The Neotropical understory plant Tachia guianensis (Gentianaceae)-known to shelter the colonies of several ant species in its hollow trunks and branches-does not provide them with food rewards (e.g., extrafloral nectar). We tested whether these ants are opportunistic nesters or whether mutualistic relationships exist as for myrmecophytes or plants sheltering ant colonies in specialized hollow structures in exchange for protection from enemies and/or nutrient provisioning (myrmecotrophy). We noted 37 ant species sheltering inside T. guianensis internodes, three of them accounting for 43.5% of the cases. They protect their host plants from leaf-cutting ant defoliation and termite damage because individuals devoid of associated ants suffered significantly more attacks. Using the stable isotope 15N, we experimentally showed that the tested ant species furnish their host plants with nutrients. Therefore, a mutualism exists. However, because it is associated with numerous ant species, T. guianensis can be considered a nonspecialized myrmecophyte.

  6. The Impacts of Multiple Simultaneous Climate Variations

    Science.gov (United States)

    2016-12-01

    Julian Oscillation, operational climate support 15. NUMBER OF PAGES 195 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT Unclassified 18...Interpolation HWC Hadley-Walker Circulation IL lcelandic Low IOD Indian Ocean Dipole ITCZ Intertropical Convergence Zone JAS July, August, September...latitude range where insufficient satellite data was available for our analyses—for example, in central Asia north of Afghanistan and Pakistan . We

  7. Multiple primary cancers: Simultaneously occurring prostate cancer ...

    African Journals Online (AJOL)

    , and it is becoming an increasing public health burden in sub-Saharan Africa. In our practice, we identified that prostate cancer co-existed with other primary cancers even in noncontiguous regions of the body and this co-existence impacted ...

  8. Multiple Primary Cancers: Simultaneously Occurring Prostate ...

    African Journals Online (AJOL)

    2016-05-20

    May 20, 2016 ... occurring prostate cancer and other primary tumors-our experience and ... tweak, and build upon the work non-commercially, as long as the author is credited ..... Seretis C, Seretis F, Liakos N. Multidisciplinary approach to.

  9. Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca.

    Science.gov (United States)

    Weston, Donald P; Poynton, Helen C; Wellborn, Gary A; Lydy, Michael J; Blalock, Bonnie J; Sepulveda, Maria S; Colbourne, John K

    2013-10-08

    Use of pesticides can have substantial nonlethal impacts on nontarget species, including driving evolutionary change, often with unknown consequences for species, ecosystems, and society. Hyalella azteca, a species complex of North American freshwater amphipods, is widely used for toxicity testing of water and sediment and has frequently shown toxicity due to pyrethroid pesticides. We demonstrate that 10 populations, 3 from laboratory cultures and 7 from California water bodies, differed by at least 550-fold in sensitivity to pyrethroids. The populations sorted into four phylogenetic groups consistent with species-level divergence. By sequencing the primary pyrethroid target site, the voltage-gated sodium channel, we show that point mutations and their spread in natural populations were responsible for differences in pyrethroid sensitivity. At least one population had both mutant and WT alleles, suggesting ongoing evolution of resistance. Although nonresistant H. azteca were susceptible to the typical neurotoxic effects of pyrethroids, gene expression analysis suggests the mode of action in resistant H. azteca was not neurotoxicity but was oxidative stress sustained only at considerably higher pyrethroid concentrations. The finding that a nontarget aquatic species has acquired resistance to pesticides used only on terrestrial pests is troubling evidence of the impact of chronic pesticide transport from land-based applications into aquatic systems. Our findings have far-reaching implications for continued uncritical use of H. azteca as a principal species for monitoring and environmental policy decisions.

  10. Breast-feeding multiples.

    Science.gov (United States)

    Flidel-Rimon, O; Shinwell, E S

    2002-06-01

    Human breast milk is the best nutrition for human infants. Its advantages over the milk of other species, such as cows, include both a reduced risk for infections, allergies and chronic diseases, together with the full nutritional requirements for growth and development. Breast-feeding is as important for multiples as for singletons. Despite the advantages, multiples receive less breast-feeding than singletons. Common reasons for not breast-feeding multiples include the fear of not fulfilling the infants' needs and the difficulty of coping with the demands on the mother's time. In addition, many multiples are delivered prematurely and by Caesarean section. Maternal pain and discomfort together with anxiety over the infants' condition are not conducive to successful breast-feeding. During lactation, the mother needs to add calories to her daily diet. It has been recommended to add approximately 500-600 kcal/day for each infant. Thus, between eating, nursing and sleeping, life is very busy for the mother of multiples. However, there is evidence that, with appropriate nutrition, one mother can nourish more than one infant. Also, simultaneous breast-feeding can save much time. Combined efforts of parents, close family, friends and the medical team can help to make either full or partial breast-feeding of multiples possible. However, when breast-feeding is not possible, health care workers need to carefully avoid judgmental approaches that may induce feelings of guilt.

  11. Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Marcia L Hart

    Full Text Available The gastrointestinal tract contains a vast community of microbes that to this day remain largely unculturable, making studies in this area challenging. With the newly affordable advanced sequencing technology, important breakthroughs in this exciting field are now possible. However, standardized methods of sample collection, handling, and DNA extraction have yet to be determined. To help address this, we investigated the use of 5 common DNA extraction methods on fecal samples from 5 different species. Our data show that the method of DNA extraction impacts DNA concentration and purity, successful NGS amplification, and influences microbial communities seen in NGS output dependent on the species of fecal sample and the DNA extraction method used. These data highlight the importance of careful consideration of DNA extraction method used when designing and interpreting data from cross species studies.

  12. Assessing future suitability of tree species under climate change by multiple methods: a case study in southern Germany

    Directory of Open Access Journals (Sweden)

    Helge Walentowski

    2017-07-01

    Full Text Available We compared results derived using three different approaches to assess the suitability of common tree species on the Franconian Plateau in southern Germany under projected warmer and drier climate conditions in the period 2061-2080. The study area is currently a relatively warm and dry region of Germany. We calculated species distribution models (SDMs using information on species’ climate envelopes to predict regional species spectra under 63 different climate change scenarios. We complemented this with fine-scale ecological niche analysis using data from 51 vegetation surveys in seven forest reserves in the study area, and tree-ring analysis (TRA from local populations of five tree species to quantify their sensitivity to climatic extreme years. The SDMs showed that predicted future climate change in the region remains within the climate envelope of certain species (e.g. Quercus petraea, whilst for e.g. Fagus sylvatica, future climate conditions in one third of the scenarios are too warm and dry. This was confirmed by the TRA: sensitivity to drought periods is lower for Q. petraea than for F. sylvatica. The niche analysis shows that the local ecological niches of Quercus robur and Fraxinus excelsior are mainly characterized by soils providing favorable water supply than by climate, and Pinus sylvestris (planted is strongly influenced by light availability. The best adapted species for a warmer and potentially drier climate in the study region are Acer campestre, Sorbus torminalis, S. aria, Ulmus minor, and Tilia platyphyllos, which should therefore play a more prominent role in future climate-resilient mixed forest ecosystems.

  13. Integrating fine-scale soil data into species distribution models: preparing Soil Survey Geographic (SSURGO) data from multiple counties

    Science.gov (United States)

    Matthew P. Peters; Louis R. Iverson; Anantha M. Prasad; Steve N. Matthews

    2013-01-01

    Fine-scale soil (SSURGO) data were processed at the county level for 37 states within the eastern United States, initially for use as predictor variables in a species distribution model called DISTRIB II. Values from county polygon files converted into a continuous 30-m raster grid were aggregated to 4-km cells and integrated with other environmental and site condition...

  14. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species

    NARCIS (Netherlands)

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, W.K.; Prinzing, A.; Dong, Ming; Cornelissen, J.H.C.

    2015-01-01

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such

  15. Response of Selected Woody Species to Inoculation with Phytophthora citricola and P. cactorum from European Beech Using Multiple Inoculation Methods

    Science.gov (United States)

    Phytophthora citricola and P. cactorum are important cosmopolitan plant pathogens with wide host ranges. Both species have recently been identified as the cause of bleeding canker of European beech (Fagus sylvatica) in the northeastern United States, but whether isolates from European beech had the...

  16. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization.

    Science.gov (United States)

    Gcebe, Nomakorinte; Rutten, Victor; Pittius, Nicolaas Gey van; Naicker, Brendon; Michel, Anita

    2017-04-01

    Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment, and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness, which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples. These isolates were previously identified during an NTM survey and were all found, using 16S rRNA gene sequence analysis to be closely related to Mycobacterium moriokaense. A polyphasic approach that included phenotypic characterization, antibiotic susceptibility profiling, mycolic acid profiling and phylogenetic analysis of four gene loci, 16S rRNA, hsp65, sodA and rpoB, was employed to characterize these isolates. Sequence data analysis of the four gene loci revealed that these isolates belong to a unique species of the genus Mycobacterium. This evidence was further supported by several differences in phenotypic characteristics between the isolates and the closely related species. We propose the name Mycobacterium malmesburyense sp. nov. for this novel species. The type strain is WCM 7299T (=ATCC BAA-2759T=CIP 110822T).

  17. The effect of social connections on the discovery of multiple hidden food patches in a bird species

    NARCIS (Netherlands)

    Tóth, Zoltán; Tuliozi, Beniamino; Baldan, Davide; Hoi, Herbert; Griggio, Matteo

    Social foraging is thought to provide the possibility of information transmission between individuals, but this advantage has been proved only in a handful of species and contexts. We investigated how social connections in captive flocks of house sparrows (Passer domesticus) affected the discovery

  18. [Multiple forms of NAD-dependent malate dehydrogenase in 3 species of trematodes of the genus Notocotylus (Trematoda: Notocotylidae)].

    Science.gov (United States)

    Paulauskas, A P

    1990-01-01

    NAD dependent malate dehydrogenases of three trematode species, Notocotylus attenuatus, N. ephemera and N. imbricatus, have been investigated by electrophoresis. Seven different zones with 15 isoenzymes in N. attenuatus, 16 isoenzymes in N. ephemera and 11 isoenzymes in N. imbricatus have been found in MDH spectra. Isoenzymes of MDH are controlled by seven polymorphic loci. The activity of isoenzymes of three slowly migrating zones is 10 and more times higher than that of fast zones (4-7). The genotypes of adults in one strain are genetically identical, independent ot the development in different definitive hosts. The spectra of MDH of the investigated Notocotylus species are different in slowly migrating isoenzymes (1-3 zones).

  19. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species