WorldWideScience

Sample records for biological species identification

  1. Printed Identification Key or Web-Based Identification Guide: An Effective Tool for Species Identification?

    Directory of Open Access Journals (Sweden)

    Thomas Edison E. dela Cruz

    2012-09-01

    Full Text Available Species identification is often done with the aid of traditional dichotomous keys. This printed material is based on one’s decision between two alternatives, which is followed by another pair of alternatives until the final species name is reached. With the advent of internet technology, the use of an online database offers an updatable and accumulative approach to species identification. It can also be accessed anytime, and this is very useful for fast-changing groups of organisms. In this paper, we report the preference of sophomore Bachelor of Science (B.Sc. in Microbiology students to two identification guides as a tool in taxonomy. We wish to test our hypothesis that today’s students will prefer to use web-based ID guides over printed dichotomous keys. We also describe how these printed dichotomous key and web-based ID guides were used by the students as one of their laboratory activities in the course Biology of Algae and Fungi.  

  2. Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS

    Directory of Open Access Journals (Sweden)

    Lista Florigio

    2011-12-01

    Full Text Available Abstract Background The genus Brucella contains highly infectious species that are classified as biological threat agents. The timely detection and identification of the microorganism involved is essential for an effective response not only to biological warfare attacks but also to natural outbreaks. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS is a rapid method for the analysis of biological samples. The advantages of this method, compared to conventional techniques, are rapidity, cost-effectiveness, accuracy and suitability for the high-throughput identification of bacteria. Discrepancies between taxonomy and genetic relatedness on the species and biovar level complicate the development of detection and identification assays. Results In this study, the accurate identification of Brucella species using MALDI-TOF-MS was achieved by constructing a Brucella reference library based on multilocus variable-number tandem repeat analysis (MLVA data. By comparing MS-spectra from Brucella species against a custom-made MALDI-TOF-MS reference library, MALDI-TOF-MS could be used as a rapid identification method for Brucella species. In this way, 99.3% of the 152 isolates tested were identified at the species level, and B. suis biovar 1 and 2 were identified at the level of their biovar. This result demonstrates that for Brucella, even minimal genomic differences between these serovars translate to specific proteomic differences. Conclusions MALDI-TOF-MS can be developed into a fast and reliable identification method for genetically highly related species when potential taxonomic and genetic inconsistencies are taken into consideration during the generation of the reference library.

  3. Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS

    NARCIS (Netherlands)

    Lista, F.; Reubsaet, F.A.G.; Santis, R. de; Parchen, R.R.; Jong, A.L. de; Kieboom, J.; Laaken, A.L. van der; Voskamp-Visser, I.A.I.; Fillo, S.; Jansen, H.J. de; Plas, J. van der; Paauw, A.

    2011-01-01

    Background: The genus Brucella contains highly infectious species that are classified as biological threat agents. The timely detection and identification of the microorganism involved is essential for an effective response not only to biological warfare attacks but also to natural outbreaks.

  4. Current practices in the identification of critical habitat for threatened species.

    Science.gov (United States)

    Camaclang, Abbey E; Maron, Martine; Martin, Tara G; Possingham, Hugh P

    2015-04-01

    The term critical habitat is used to describe the subset of habitat that is essential to the survival and recovery of species. Some countries legally require that critical habitat of listed threatened and endangered species be identified and protected. However, there is little evidence to suggest that the identification of critical habitat has had much impact on species recovery. We hypothesized that this may be due at least partly to a mismatch between the intent of critical habitat identification, which is to protect sufficient habitat for species persistence and recovery, and its practice. We used content analysis to systematically review critical habitat documents from the United States, Canada, and Australia. In particular, we identified the major trends in type of information used to identify critical habitat and in occupancy of habitat identified as critical. Information about population viability was used to identify critical habitat for only 1% of the species reviewed, and for most species, designated critical habitat did not include unoccupied habitat. Without reference to population viability, it is difficult to determine how much of a species' occupied and unoccupied habitat will be required for persistence. We therefore conclude that the identification of critical habitat remains inconsistent with the goal of protecting sufficient habitat to support persistence and recovery of the species. Ensuring that critical habitat identification aligns more closely with its intent will improve the accuracy of the designations and may therefore help improve the benefits to species recovery when combined with adequate implementation and enforcement of legal protections. © 2014 Society for Conservation Biology.

  5. Developing a taxonomic identification system of Phytophthora species based on microsatellites.

    Science.gov (United States)

    del Castillo-Múnera, Johanna; Cárdenas, Martha; Pinzón, Andrés; Castañeda, Adriana; Bernal, Adriana J; Restrepo, Silvia

    2013-01-01

    Phytophthora is the most important genus of the Oomycete plant pathogens. Nowadays, there are 117 described species in this genus, most of them being primary invaders of plant tissues. The different species are causal agents of diseases in a wide range of crops and plants in natural environments. In order to develop control strategies against Phytophthoraspecies, it is important to know the biology, ecology and evolutionary processes of these important pathogens. The aim of this study was to propose and validate a low cost identification system for Phytophthora species based on a set of polymorphic microsatellite (SSRs) markers. Thirty-three isolates representing Phytophthora infestans, Phytophthora andina, Phytophthora sojae, Phytophthora cryptogea, Phytophthora nicotianae, Phytophthora capsici and Phytophthora cinnamomi species were obtained, and 13 SSRs were selected as potentially transferable markers between these species. Amplification conditions, including annealing temperatures, were standardized for several markers. A subset of these markers amplified in all species, showing species-specific alleles. The adaptability and impact of the identification system in Colombia, an Andean agricultural country where different Phytophthora species co-exist in the same or in several hosts grown together, are discussed. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  6. DNA Barcoding for Species Identification of Insect Skins: A Test on Chironomidae (Diptera) Pupal Exuviae

    Science.gov (United States)

    Ekrem, Torbjørn; Stur, Elisabeth

    2017-01-01

    Abstract Chironomidae (Diptera) pupal exuviae samples are commonly used for biological monitoring of aquatic habitats. DNA barcoding has proved useful for species identification of chironomid life stages containing cellular tissue, but the barcoding success of chironomid pupal exuviae is unknown. We assessed whether standard DNA barcoding could be efficiently used for species identification of chironomid pupal exuviae when compared with morphological techniques and if there were differences in performance between temperate and tropical ecosystems, subfamilies, and tribes. PCR, sequence, and identification success differed significantly between geographic regions and taxonomic groups. For Norway, 27 out of 190 (14.2%) of pupal exuviae resulted in high-quality chironomid sequences that match species. For Costa Rica, 69 out of 190 (36.3%) Costa Rican pupal exuviae resulted in high-quality sequences, but none matched known species. Standard DNA barcoding of chironomid pupal exuviae had limited success in species identification of unknown specimens due to contaminations and lack of matching references in available barcode libraries, especially from Costa Rica. Therefore, we recommend future biodiversity studies that focus their efforts on understudied regions, to simultaneously use morphological and molecular identification techniques to identify all life stages of chironomids and populate the barcode reference library with identified sequences.

  7. Effectiveness of Reptile Species Identification--A Comparison of a Dichotomous Key with an Identification Book

    Science.gov (United States)

    Randler, Christoph; Zehender, Irene

    2006-01-01

    Species identification tasks are a prerequisite for an understanding of biodiversity. Here, we focused on different educational materials to foster the identification of six European reptile species. Our educational training unit was based on natural plastic models of six species and pupils either used an illustrated identification book or a…

  8. Biological species in the viral world.

    Science.gov (United States)

    Bobay, Louis-Marie; Ochman, Howard

    2018-06-05

    Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

  9. Genetic species identification in weatherfish and first molecular confirmation of Oriental Weatherfish Misgurnus anguillicaudatus (Cantor, 1842 in Central Europe

    Directory of Open Access Journals (Sweden)

    Belle Christina C.

    2017-01-01

    Full Text Available The Oriental Weatherfish is considered a globally invasive fish species. In Europe, several reported feral populations of Oriental Weatherfish display an overlapping distribution range with native weatherfish Misgurnus fossilis, a declining species of international conservation and aquatic management concern. Morphologically distinguishing the different weatherfish species can be difficult, as their coloration is highly variable, many species reveal high phenotypic plasticity, and morphological traits like coloration might be not obvious or might be degraded during field sampling and after preservation. Herein, we analysed suspicious weatherfish specimens from southern Germany, demonstrating the usefulness of molecular genetic species identifications in this genus. We present the first molecular genetic species record of Misgurnus anguillicaudatus in Central Europe, and confirm the range expansion of Oriental Weatherfish into the river Inn catchment in southern Germany. As accurate species identification is crucial both in the context of monitoring and conserving native endangered species, and in early detection and prevention of biological invasion, we suggest the standard use of genetic species identification if morphological traits are not obvious.

  10. Teaching Bird Identification & Vocabulary with Twitter

    Science.gov (United States)

    Hallman, Tyler A.; Robinson, W. Douglas

    2015-01-01

    Species identification is essential to biology, conservation, and management. The ability to focus on specific diagnostic characteristics of a species helps improve the speed and accuracy of identification. Birds are excellent subjects for teaching species identification because, in combination with their different shapes and sizes, their plumages…

  11. Detection and Characterization of Reactive Oxygen and Nitrogen Species in Biological Systems by Monitoring Species-Specific Products.

    Science.gov (United States)

    Hardy, Micael; Zielonka, Jacek; Karoui, Hakim; Sikora, Adam; Michalski, Radosław; Podsiadły, Radosław; Lopez, Marcos; Vasquez-Vivar, Jeannette; Kalyanaraman, Balaraman; Ouari, Olivier

    2018-05-20

    Since the discovery of the superoxide dismutase enzyme, the generation and fate of short-lived oxidizing, nitrosating, nitrating, and halogenating species in biological systems has been of great interest. Despite the significance of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in numerous diseases and intracellular signaling, the rigorous detection of ROS and RNS has remained a challenge. Recent Advances: Chemical characterization of the reactions of selected ROS and RNS with electron paramagnetic resonance (EPR) spin traps and fluorescent probes led to the establishment of species-specific products, which can be used for specific detection of several forms of ROS and RNS in cell-free systems and in cultured cells in vitro and in animals in vivo. Profiling oxidation products from the ROS and RNS probes provides a rigorous method for detection of those species in biological systems. Formation and detection of species-specific products from the probes enables accurate characterization of the oxidative environment in cells. Measurement of the total signal (fluorescence, chemiluminescence, etc.) intensity does not allow for identification of the ROS/RNS formed. It is critical to identify the products formed by using chromatographic or other rigorous techniques. Product analyses should be accompanied by monitoring of the intracellular probe level, another factor controlling the yield of the product(s) formed. More work is required to characterize the chemical reactivity of the ROS/RNS probes, and to develop new probes/detection approaches enabling real-time, selective monitoring of the specific products formed from the probes. Antioxid. Redox Signal. 28, 1416-1432.

  12. DNA barcode-based molecular identification system for fish species.

    Science.gov (United States)

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

  13. Identification of Meconopsis species by a DNA barcode sequence ...

    African Journals Online (AJOL)

    Deoxyribonucleic acid (DNA) barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Species identification is necessary for the authentication of traditional plant based medicines. Although a consensus has not been agreed regarding which DNA sequences can be used as ...

  14. Identification and Classification of Earthworm Species in Guyana

    OpenAIRE

    Preeta Saywack; Abdullah Adil Ansari

    2011-01-01

    Earthworms are very important organisms, they are both environmentally and economically beneficial and hence their correct identification and classification is very vital. Taxonomy aims to classify organisms based on their similarities and differences. The present study was carried out during the year 2006-2007 at University of Guyana, Georgetown focusing on identification and classification of local earthworm species of Guyana and comparison with a known non-native species (California red). ...

  15. Molecular identification of livestock breeds: a tool for modern conservation biology.

    Science.gov (United States)

    Yaro, Mohammed; Munyard, Kylie A; Stear, Michael J; Groth, David M

    2017-05-01

    Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been addressed. In spite of their importance, there is a growing number of reports on the alarming erosion of domestic animal genetic resources. This erosion of is happening in spite of several global conservation initiatives designed to mitigate it. Herein we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members to a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed-specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems. © 2016 Cambridge Philosophical Society.

  16. Identification of Pseudallescheria and Scedosporium Species by Three Molecular Methods▿

    Science.gov (United States)

    Lu, Qiaoyun; Gerrits van den Ende, A. H. G.; Bakkers, J. M. J. E.; Sun, Jiufeng; Lackner, M.; Najafzadeh, M. J.; Melchers, W. J. G.; Li, Ruoyu; de Hoog, G. S.

    2011-01-01

    The major clinically relevant species in Scedosporium (teleomorph Pseudallescheria) are Pseudallescheria boydii, Scedosporium aurantiacum, Scedosporium apiospermum, and Scedosporium prolificans, while Pseudallescheria minutispora, Petriellopsis desertorum, and Scedosporium dehoogii are exceptional agents of disease. Three molecular methods targeting the partial β-tubulin gene were developed and evaluated to identify six closely related species of the S. apiospermum complex using quantitative real-time PCR (qPCR), PCR-based reverse line blot (PCR-RLB), and loop-mediated isothermal amplification (LAMP). qPCR was not specific enough for the identification of all species but had the highest sensitivity. The PCR-RLB assay was efficient for the identification of five species. LAMP distinguished all six species unambiguously. The analytical sensitivities of qPCR, PCR-RLB, and LAMP combined with MagNAPure, CTAB (cetyltrimethylammonium bromide), and FTA filter (Whatman) extraction were 50, 5 × 103, and 5 × 102 cells/μl, respectively. When LAMP was combined with a simplified DNA extraction method using an FTA filter, identification to the species level was achieved within 2 h, including DNA extraction. The FTA-LAMP assay is therefore recommended as a cost-effective, simple, and rapid method for the identification of Scedosporium species. PMID:21177887

  17. Preliminary study and Identification of insects' species of forensic ...

    African Journals Online (AJOL)

    The proper identification of the insect and arthropod species of forensic importance is the most crucial element in the field of forensic entomology. The main objective in this study was the identification of insects' species of forensic importance in Urmia (37°, 33 N. and 45°, 4, 45 E.) and establishment of a preliminary ...

  18. Barcode of life: Advancing species identification and discovery

    Digital Repository Service at National Institute of Oceanography (India)

    Chandramohan, D.

    -based identification systems and the dwindling pool of taxonomists highlight the need for alternate methods for species identification which should be quick, cost effective and efficient. DNA barcoding emerges as a most favoured alternate method by the researchers..., electronics and computer science. The mission of the CBOL is to develop DNA barcoding as a global standard in taxonomy, rapidly accelerate compiling of DNA barcodes of known and newly discovered plant and animal species, establish a public library...

  19. Towards large-scale FAME-based bacterial species identification using machine learning techniques.

    Science.gov (United States)

    Slabbinck, Bram; De Baets, Bernard; Dawyndt, Peter; De Vos, Paul

    2009-05-01

    In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species

  20. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Pletscher-Frankild, Sune; Fanini, Lucia

    2013-01-01

    The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary......-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus...

  1. How automated image analysis techniques help scientists in species identification and classification?

    Science.gov (United States)

    Yousef Kalafi, Elham; Town, Christopher; Kaur Dhillon, Sarinder

    2017-09-04

    Identification of taxonomy at a specific level is time consuming and reliant upon expert ecologists. Hence the demand for automated species identification increased over the last two decades. Automation of data classification is primarily focussed on images, incorporating and analysing image data has recently become easier due to developments in computational technology. Research efforts in identification of species include specimens' image processing, extraction of identical features, followed by classifying them into correct categories. In this paper, we discuss recent automated species identification systems, categorizing and evaluating their methods. We reviewed and compared different methods in step by step scheme of automated identification and classification systems of species images. The selection of methods is influenced by many variables such as level of classification, number of training data and complexity of images. The aim of writing this paper is to provide researchers and scientists an extensive background study on work related to automated species identification, focusing on pattern recognition techniques in building such systems for biodiversity studies.

  2. Computational botany methods for automated species identification

    CERN Document Server

    Remagnino, Paolo; Wilkin, Paul; Cope, James; Kirkup, Don

    2017-01-01

    This book discusses innovative methods for mining information from images of plants, especially leaves, and highlights the diagnostic features that can be implemented in fully automatic systems for identifying plant species. Adopting a multidisciplinary approach, it explores the problem of plant species identification, covering both the concepts of taxonomy and morphology. It then provides an overview of morphometrics, including the historical background and the main steps in the morphometric analysis of leaves together with a number of applications. The core of the book focuses on novel diagnostic methods for plant species identification developed from a computer scientist’s perspective. It then concludes with a chapter on the characterization of botanists' visions, which highlights important cognitive aspects that can be implemented in a computer system to more accurately replicate the human expert’s fixation process. The book not only represents an authoritative guide to advanced computational tools fo...

  3. Learning about Bird Species on the Primary Level

    Science.gov (United States)

    Randler, Christoph

    2009-01-01

    Animal species identification is often emphasized as a basic prerequisite for an understanding of ecology because ecological interactions are based on interactions between species at least as it is taught on the school level. Therefore, training identification skills or using identification books seems a worthwhile task in biology education, and…

  4. Real-time bioacoustics monitoring and automated species identification

    Directory of Open Access Journals (Sweden)

    T. Mitchell Aide

    2013-07-01

    Full Text Available Traditionally, animal species diversity and abundance is assessed using a variety of methods that are generally costly, limited in space and time, and most importantly, they rarely include a permanent record. Given the urgency of climate change and the loss of habitat, it is vital that we use new technologies to improve and expand global biodiversity monitoring to thousands of sites around the world. In this article, we describe the acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON, a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings. The major components of the cyberinfrastructure include: a solar powered remote monitoring station that sends 1-min recordings every 10 min to a base station, which relays the recordings in real-time to the project server, where the recordings are processed and uploaded to the project website (arbimon.net. Along with a module for viewing, listening, and annotating recordings, the website includes a species identification interface to help users create machine learning algorithms to automate species identification. To demonstrate the system we present data on the vocal activity patterns of birds, frogs, insects, and mammals from Puerto Rico and Costa Rica.

  5. Mitochondrial DNA in wildlife forensic science: Species identification of tissues

    Science.gov (United States)

    Cronin, Matthew A.; Palmisciano, Daniel A.; Vyse, Ernest R.; Cameron, David G.

    1991-01-01

    A common problem in wildlife law enforcement is identifying the species of origin of carcasses, meat, or blood when morphological characters such as hair or bones are not available. Immunological and protein electrophoretic (allozyme or general protein) procedures have been used in species identification with considerable success (Bunch et al. 1976, McClymont et al. 1982, Wolfe 1983, Mardini 1984, Pex and Wolfe 1985, Dratch 1986), However, immunological tests often are not sensitive enough to distinguish closely related species. Furthermore, electrophoretically detectable protein polymorphisms may be lacking in certain populations or species and may not be species-specific.Analysis of DNA in human and wildlife forensics has been shown to be a potentially powerful tool for identification of individuals (Jeffreys et al. 1985, Vassartet al. 1987, Thommasen et al. 1989). Differences in copy number and nucleotide sequence of repetitive sequences in the nuclear (chromosomal) DNA result in hypervariability and individual-specific patterns which have been termed DNA "fingerprints." However, these patterns may be too variable for species identification necessitating analyses of more conservative parts of the genome.Mitochondrial DNA (mtDNA) is haploid, maternally inherited, similar in nucleotide sequence among conspecifics from the same geographic region, and more suitable for species identification, in contrast to hypervariable DNA fingerprints. MtDNA has several characteristics which make it useful as a species-specific marker. In mammals, individuals have a single mtDNA genotype shared by all tissues. Because mtDNA is haploid and reflects only maternal ancestry, the mtDNA gene number in a population is 4 times less than the nuclear gene number (Birky et al. 1983). This can result in relatively rapid loss or fixation of mtDNA genotypes so that all individuals in a population may be descended from a single ancestral female in as few as 4N (N = population size) generations

  6. AFSC/ABL: Juvenile rockfish DNA species identification

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Many pelagic juvenile rockfish (Sebastes) were collected in juvenile salmonid surveys in the Gulf of Alaska (GOA) from 1998 to 2002. Often species identification of...

  7. Hichrom candida agar for identification of Candida species.

    Science.gov (United States)

    Baradkar, V P; Mathur, M; Kumar, S

    2010-01-01

    Chromogenic media are frequently used in direct and rapid identification of yeasts because different Candida species produce unique colors on these media. We used 60 isolates of Candida species including 30 C. albicans, 10 C. parapsilosis, 11 C. glabrata, five C. tropicalis, and four C. dubliniensis, isolated from various clinical specimens, to evaluate the performance of HiChrome Candida agar. These strains had been identified by germ tube test, morphology on cornmeal agar, chlamydospore formation on tobacco agar and sugar assimilation tests. The sensitivity and specificity results were: C. albicans (96.55 and 96.42%); C. parapsilosis (80 and 98.03%), C. glabrata (90.90 and 88.23%), C. tropicalis (100 and 100%) and C. dubliniensis (60 and 96.55%) respectively. HiChrom Candida agaris medium has been useful and capable of presumptive, rapid identification of Candida species within 48 hours.

  8. Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species.

    Science.gov (United States)

    Naga Jogayya, K; Meganathan, P R; Dubey, Bhawna; Haque, I

    2013-05-01

    All crocodilians are under various threats due to over exploitation and these species have been listed in Appendix I or II of CITES. Lack of molecular techniques for the forensic identification of confiscated samples makes it difficult to enforce the law. Therefore, we herein present a molecular method developed on the basis on 16S rRNA gene of mitochondrial DNA for identification of crocodile species. We have developed a set of 16S rRNA primers for PCR based identification of crocodilian species. These novel primers amplify partial 16S rRNA sequences of six crocodile species which can be later combined to obtain a larger region (1290 bp) of 16S rRNA gene. This 16S rRNA gene could be used as an effective tool for forensic authentication of crocodiles. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these species. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  9. Nordic-Baltic Student Teachers' Identification of and Interest in Plant and Animal Species: The Importance of Species Identification and Biodiversity for Sustainable Development

    Science.gov (United States)

    Palmberg, Irmeli; Berg, Ida; Jeronen, Eila; Kärkkäinen, Sirpa; Norrgård-Sillanpää, Pia; Persson, Christel; Vilkonis, Rytis; Yli-Panula, Eija

    2015-01-01

    Knowledge of species, interest in nature, and nature experiences are the factors that best promote interest in and understanding of environmental issues, biodiversity and sustainable life. The aim of this study is to investigate how well student teachers identify common local species, their interest in and ideas about species identification, and…

  10. Rapid identification of the Asian gypsy moth and its related species based on mitochondrial DNA.

    Science.gov (United States)

    Wu, Ying; Du, Qiuyang; Qin, Haiwen; Shi, Juan; Wu, Zhiyi; Shao, Weidong

    2018-02-01

    The gypsy moth- Lymantria dispar (Linnaeus)-is a worldwide forest defoliator and is of two types: the European gypsy moth and the Asian gypsy moth. Because of multiple invasions of the Asian gypsy moth, the North American Plant Protection Organization officially approved Regional Standards for Phytosanitary Measures No. 33. Accordingly, special quarantine measures have been implemented for 30 special focused ports in the epidemic areas of the Asian gypsy moth, including China, which has imposed great inconvenience on export trade. The Asian gypsy moth and its related species (i.e., Lymantria monocha and Lymantria xylina ) intercepted at ports are usually at different life stages, making their identification difficult. Furthermore, Port quarantine requires speedy clearance. As such, it is difficult to identify the Asian gypsy moth and its related species only by their morphological characteristics in a speedy measure. Therefore, this study aimed to use molecular biology technology to rapidly identify the Asian gypsy moth and its related species based on the consistency of mitochondrial DNA in different life stages. We designed 10 pairs of specific primers from different fragments of the Asian gypsy moth and its related species, and their detection sensitivity met the need for rapid identification. In addition, we determined the optimal polymerase chain reaction amplification temperature of the 10 pairs of specific primers, including three pairs of specific primers for the Asian gypsy moth ( L. dispar asiatic ), four pairs of specific primers for the nun moth ( L. monocha ), and three pairs of specific primers for the casuarina moth ( L. xylina ). In conclusion, using our designed primers, direct rapid identification of the Asian gypsy moth and its related species is possible, and this advancement can help improve export trade in China.

  11. [Molecular techniques applied in species identification of Toxocara].

    Science.gov (United States)

    Fogt, Renata

    2006-01-01

    Toxocarosis is still an important and actual problem in human medicine. It can manifest as visceral (VLM), ocular (OLM) or covert (CT) larva migrans syndroms. Complicated life cycle of Toxocara, lack of easy and practical methods of species differentiation of the adult nematode and embarrassing in recognition of the infection in definitive hosts create difficulties in fighting with the infection. Although studies on human toxocarosis have been continued for over 50 years there is no conclusive answer, which of species--T. canis or T. cati constitutes a greater risk of transmission of the nematode to man. Neither blood serological examinations nor microscopic observations of the morphological features of the nematode give the satisfied answer on the question. Since the 90-ths molecular methods were developed for species identification and became useful tools being widely applied in parasitological diagnosis. This paper cover the survey of methods of DNA analyses used for identification of Toxocara species. The review may be helpful for researchers focused on Toxocara and toxocarosis as well as on detection of new species. The following techniques are described: PCR (Polymerase Chain Reaction), RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA) and SSCP (Single Strand Conformation Polymorphism).

  12. Hichrom candida agar for identification of candida species

    Directory of Open Access Journals (Sweden)

    Baradkar V

    2010-01-01

    Full Text Available Chromogenic media are frequently used in direct and rapid identification of yeasts because different Candida species produce unique colors on these media. We used 60 isolates of Candida species including 30 C. albicans, 10 C. parapsilosis, 11 C. glabrata, five C. tropicalis, and four C. dubliniensis, isolated from various clinical specimens, to evaluate the performance of HiChrome Candida agar. These strains had been identified by germ tube test, morphology on cornmeal agar, chlamydospore formation on tobacco agar and sugar assimilation tests. The sensitivity and specificity results were: C. albicans (96.55 and 96.42%; C. parapsilosis (80 and 98.03%, C. glabrata (90.90 and 88.23%, C. tropicalis (100 and 100% and C. dubliniensis (60 and 96.55% respectively. HiChrom Candida agaris medium has been useful and capable of presumptive, rapid identification of Candida species within 48 hours.

  13. Assessing biological invasions in European Seas: Biological traits of the most widespread non-indigenous species

    Science.gov (United States)

    Cardeccia, Alice; Marchini, Agnese; Occhipinti-Ambrogi, Anna; Galil, Bella; Gollasch, Stephan; Minchin, Dan; Narščius, Aleksas; Olenin, Sergej; Ojaveer, Henn

    2018-02-01

    The biological traits of the sixty-eight most widespread multicellular non-indigenous species (MWNIS) in European Seas: Baltic Sea, Western European Margin of the Atlantic Ocean and the Mediterranean Sea were examined. Data for nine biological traits was analyzed, and a total of 41 separate categories were used to describe the biological and ecological functions of these NIS. Our findings show that high dispersal ability, high reproductive rate and ecological generalization are the biological traits commonly associated with MWNIS. The functional groups that describe most of the 68 MWNIS are: photoautotrophic, zoobenthic (both sessile and motile) and nektonic predatory species. However, these 'most widespread' species comprise a wide range of taxa and biological trait profiles; thereby a clear "identikit of a perfect invader" for marine and brackish environments is difficult to define. Some traits, for example: "life form", "feeding method" and "mobility", feature multiple behaviours and strategies. Even species introduced by a single pathway, e.g. vessels, feature diverse biological trait profiles. MWNIS likely to impact community organization, structure and diversity are often associated with brackish environments. For many traits ("life form", "sociability", "reproductive type", "reproductive frequency", "haploid and diploid dispersal" and "mobility"), the categories mostly expressed by the impact-causing MWNIS do not differ substantially from the whole set of MWNIS.

  14. Identification of five sea cucumber species through PCR-RFLP analysis

    Science.gov (United States)

    Lv, Yingchun; Zheng, Rong; Zuo, Tao; Wang, Yuming; Li, Zhaojie; Xue, Yong; Xue, Changhu; Tang, Qingjuan

    2014-10-01

    Sea cucumbers are traditional marine food and Chinese medicine in Asia. The rapid expansion of sea cucumber market has resulted in various problems, such as commercial fraud and mislabeling. Conventionally, sea cucumber species could be distinguished by their morphological and anatomical characteristics; however, their identification becomes difficult when they are processed. The aim of this study was to develop a new convenient method of identifying and distinguishing sea cucumber species. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial cytochrome oxidase I gene ( COI) was used to identifing five sea cucumber species ( Apostichopus japonicus, Cucumaria frondosa, Thelenota ananas, Parastichopus californicus and Actinopyga lecanora). A 692 bp fragment of COI was searched for BamHI, KpnI, PstI, XbaI and Eco31I restriction sites with DNAMAN 6.0, which were then used to PCR-RFLP analysis. These five sea cucumber species can be discriminated from mixed sea cucumbers. The developed PCR-RFLP assay will facilitate the identification of sea cucumbers, making their source tracing and quality controlling feasible.

  15. The isolated Leptospira Spp. Identification by molecular biological techniques

    Directory of Open Access Journals (Sweden)

    Duangjai Suwancharoen

    2017-01-01

    Full Text Available Leptospirosis is a zoonotic disease caused by the bacteria of Leptospira spp. Identification of this bacterium relies on serotyping and genotyping. Data base for animal causative serovars in Thailand is limited. As the unknown serovars are found in the laboratory, they need to be sent overseas for referent identification. To reduce the cost, this research intended to develop a leptospiral identification method which is user–friendly and able to classify efficiently. Ten Leptospira isolations were cultured from urine samples. They were identified by three molecular biological techniques, including Pulsed-Field Gel Electrophoresis (PFGE, Variable Number Tandem Repeat (VNTR and Multilocus Sequence Typing (MLST. These methods were developed and compared to find the most suitable one for leptospiral identification. VNTR was found to be inappropriate since it could not identify the agents and it did not show the PCR product. PFGE and MLST gave the same results of the unknown 1 and 2 which were L.weilii sv Samin st Samin. Unknown 4 showed different results by each technique. Unknown 5 to 10 were likely to be L.meyeri sv Ranarum st ICF and Leptonema illini sv Illini st 3055 by PFGE but MLST could not identify the serovar. However, molecular biological technique for Leptospira identification should be done by several methods in order to confirm the result of each other.

  16. Sequence-based genotyping clarifies conflicting historical morphometric and biological data for 5 Eimeria species infecting turkeys.

    Science.gov (United States)

    El-Sherry, S; Ogedengbe, M E; Hafeez, M A; Sayf-Al-Din, M; Gad, N; Barta, J R

    2015-02-01

    Unlike with Eimeria species infecting chickens, specific identification and nomenclature of Eimeria species infecting turkeys is complicated, and in the absence of molecular data, imprecise. In an attempt to reconcile contradictory data reported on oocyst morphometrics and biological descriptions of various Eimeria species infecting turkey, we established single oocyst derived lines of 5 important Eimeria species infecting turkeys, Eimeria meleagrimitis (USMN08-01 strain), Eimeria adenoeides (Guelph strain), Eimeria gallopavonis (Weybridge strain), Eimeria meleagridis (USAR97-01 strain), and Eimeria dispersa (Briston strain). Short portions (514 bp) of mitochondrial cytochrome c oxidase subunit I gene (mt COI) from each were amplified and sequenced. Comparison of these sequences showed sufficient species-specific sequence variation to recommend these short mt COI sequences as species-specific markers. Uniformity of oocyst features (dimensions and oocyst structure) of each pure line was observed. Additional morphological features of the oocysts of these species are described as useful for the microscopic differentiation of these Eimeria species. Combined molecular and morphometric data on these single species lines compared with the original species descriptions and more recent data have helped to clarify some confusing, and sometimes conflicting, features associated with these Eimeria spp. For example, these new data suggest that the KCH and KR strains of E. adenoeides reported previously represent 2 distinct species, E. adenoeides and E. meleagridis, respectively. Likewise, analysis of the Weybridge strain of E. adenoeides, which has long been used as a reference strain in various studies conducted on the pathogenicity of E. adenoeides, indicates that this coccidium is actually a strain of E. gallopavonis. We highly recommend mt COI sequence-based genotyping be incorporated into all studies using Eimeria spp. of turkeys to confirm species identifications and so

  17. Identification of medically relevant Nocardia species with an abbreviated battery of tests.

    Science.gov (United States)

    Kiska, Deanna L; Hicks, Karen; Pettit, David J

    2002-04-01

    Identification of Nocardia to the species level is useful for predicting antimicrobial susceptibility patterns and defining the pathogenicity and geographic distribution of these organisms. We sought to develop an identification method which was accurate, timely, and employed tests which would be readily available in most clinical laboratories. We evaluated the API 20C AUX yeast identification system as well as several biochemical tests and Kirby-Bauer susceptibility patterns for the identification of 75 isolates encompassing the 8 medically relevant Nocardia species. There were few biochemical reactions that were sufficiently unique for species identification; of note, N. nova were positive for arylsulfatase, N. farcinica were positive for opacification of Middlebrook 7H11 agar, and N. brasiliensis and N. pseudobrasiliensis were the only species capable of liquefying gelatin. API 20C sugar assimilation patterns were unique for N. transvalensis, N. asteroides IV, and N. brevicatena. There was overlap among the assimilation patterns for the other species. Species-specific patterns of susceptibility to gentamicin, tobramycin, amikacin, and erythromycin were obtained for N. nova, N. farcinica, and N. brevicatena, while there was overlap among the susceptibility patterns for the other isolates. No single method could identify all Nocardia isolates to the species level; therefore, a combination of methods was necessary. An algorithm utilizing antibiotic susceptibility patterns, citrate utilization, acetamide utilization, and assimilation of inositol and adonitol accurately identified all isolates. The algorithm was expanded to include infrequent drug susceptibility patterns which have been reported in the literature but which were not seen in this study.

  18. Plant Species Identification by Bi-channel Deep Convolutional Networks

    Science.gov (United States)

    He, Guiqing; Xia, Zhaoqiang; Zhang, Qiqi; Zhang, Haixi; Fan, Jianping

    2018-04-01

    Plant species identification achieves much attention recently as it has potential application in the environmental protection and human life. Although deep learning techniques can be directly applied for plant species identification, it still needs to be designed for this specific task to obtain the state-of-art performance. In this paper, a bi-channel deep learning framework is developed for identifying plant species. In the framework, two different sub-networks are fine-tuned over their pretrained models respectively. And then a stacking layer is used to fuse the output of two different sub-networks. We construct a plant dataset of Orchidaceae family for algorithm evaluation. Our experimental results have demonstrated that our bi-channel deep network can achieve very competitive performance on accuracy rates compared to the existing deep learning algorithm.

  19. Species Identification, Strain Differentiation, and Antifungal Susceptibility of Dermatophyte Species Isolated From Clinically Infected Arabian Horses

    DEFF Research Database (Denmark)

    El Damaty, Hend M; Tartor, Yasmine H; Mahmmod, Yasser Saadeldien Ibrahim

    2017-01-01

    Arabian horses, the eldest equine breeds, have great economic and social significance for its long, unique, and storied history. Molecular characterization of dermatophyte species affecting Arabian horses is a crucial necessity for epidemiologic and therapeutic purposes. The objective of this study...... are more effective against T. mentagrophytes and T. verrucosum. In conclusion, PCR-RFLP technique is a reliable tool for the identification of dermatophyte species from Arabian horses. Internal transcribed spacer sequencing provides a precise and useful technique for the identification and differentiation...

  20. MASS SPECTROMETRIC ANALYSIS FOR THE IDENTIFICATION OF THUNNUS GENUS FOUR SPECIES

    Directory of Open Access Journals (Sweden)

    T. Pepe

    2011-01-01

    Full Text Available An accurate identification of similar fish species is necessary to prevent illegal substitution and is imposed by labeling regulations in UE countries (1. The genus Thunnus comprises many species of different quality and commercial value. The increasing trade of fish preparations of the species included in this genus and the consequent loss of the external anatomical and morphological features enables fraudulent substitutions. This study reports data relating to the proteomic analysis of four tuna species (T. thynnus, T. alalunga, T. albacares, T. obesus. Sarcoplasmic proteins were studied by mono and two dimensional electrophoresis. The most significant proteins for the characterization of the species were analyzed by mass spectrometric techniques. As reported in a previous study (2, an accurate identification of the species seems possible, owing to the polymorphism displayed by the species of the Thunnus genus.

  1. Diagnostic value of nested-PCR for identification of Malassezia species in dandruff

    Science.gov (United States)

    Jusuf, N. K.; Nasution, T. A.; Ullyana, S.

    2018-03-01

    Dandruff or pityriasis simplex is a condition of abnormal occurrence of formation of yellowish white scales from the scalp. Many factors play a role in the pathogenesis of dandruff, i.e.colonization of Malassezia species. Examination of Malassezia species previously done by culture as the gold standard. However, there are various difficulties in doing the culture. Identification method with anested-polymerase chain reaction (nested-PCR) is expected to provide quickly and easily detected. This study aimedto determine the diagnostic value of nested-PCR in the identification of Malassezia species in dandruff. From 21 subjects, scales from the scalp were taken and sent to the laboratory for nested-PCR identification. Statistical analysis of diagnostic test carried out to determine sensitivity, specificity, positive predictive value, and negative predictive value. The results showed nested-PCR detected 10 sample (47.6%) positive for Malassezia species consist of M. sympodialis (23.8%); M. slooffiae (9.5%); M. furfur (4.8%); M. globosa and M. furfur (4.8%); and M. restricta and M. sympodialis (4.8%). Detection of Malassezia species by nested-PCR has 100% in sensitivity whereas the specificity was 55%. Nested-PCR test has high sensitivity. Therefore nested-PCR may be considered for a faster and simpler alternative examination in identification for Malassezia species in dandruff.

  2. Mycobacterial Species Identification and Public Health Implications ...

    African Journals Online (AJOL)

    Mycobacterial Species Identification and Public Health Implications of Tuberculosis Among Nomadic Pastoralists in Three Local Governments of Plateau State, North ... Bovine and human tuberculosis is endemic in Nigeria, and apart from meat inspection at the abattoir, which is not very effective, no control measures are ...

  3. A Review on Phytoconstituents and Biological activities of Cuscuta species.

    Science.gov (United States)

    Ahmad, Ateeque; Tandon, Sudeep; Xuan, Tran Dang; Nooreen, Zulfa

    2017-08-01

    The genus Cuscuta belonging to the Cuscutaceae family comprises of about 100-170 species spread around the world. Although several species have been studied for their phytochemical characterization and biological activities but still many species are yet unexplored till date. Cuscuta are parasitic plants generally of yellow, orange, red or rarely green color. The Cuscuta species were reported rich in flavonoid and glycosidic constituents along with alkaloids, fatty acids, fixed oil, minerals, essential oil and others phytomolecules also etc. Flavonoids and other molecules of Cuscuta species were reported for different types of biological activities such as antiproliferative activity, antioxidant activity, anti-inflammatory, hepatoprotective, antimicrobial and anxiolytic activity, while some other flavonoids have exhibited potential antiviral and anticancer especially in ovarian and breast cancer activities. This review is an attempt to compile all the available data for the 24 different of Cuscuta species on the basis of different types of phytochemical constituents and biological studies as above. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  4. Species identification by conservation practitioners using online images: accuracy and agreement between experts

    Directory of Open Access Journals (Sweden)

    Gail E. Austen

    2018-01-01

    Full Text Available Emerging technologies have led to an increase in species observations being recorded via digital images. Such visual records are easily shared, and are often uploaded to online communities when help is required to identify or validate species. Although this is common practice, little is known about the accuracy of species identification from such images. Using online images of newts that are native and non-native to the UK, this study asked holders of great crested newt (Triturus cristatus licences (issued by UK authorities to permit surveying for this species to sort these images into groups, and to assign species names to those groups. All of these experts identified the native species, but agreement among these participants was low, with some being cautious in committing to definitive identifications. Individuals’ accuracy was also independent of both their experience and self-assessed ability. Furthermore, mean accuracy was not uniform across species (69–96%. These findings demonstrate the difficulty of accurate identification of newts from a single image, and that expert judgements are variable, even within the same knowledgeable community. We suggest that identification decisions should be made on multiple images and verified by more than one expert, which could improve the reliability of species data.

  5. Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil

    Directory of Open Access Journals (Sweden)

    Karine Pinto e Vairo

    2011-09-01

    Full Text Available Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.

  6. The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia.

    Science.gov (United States)

    Muangkram, Yuttamol; Wajjwalku, Worawidh; Amano, Akira; Sukmak, Manakorn

    2018-01-01

    We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.

  7. Sex identification of four penguin species using locus-specific PCR.

    Science.gov (United States)

    Zhang, Peijun; Han, Jiabo; Liu, Quansheng; Zhang, Junxin; Zhang, Xianfeng

    2013-01-01

    Traditional methods for sex identification are not applicable to sexually monomorphic species, leading to difficulties in the management of their breeding programs. To identify sex in sexually monomorphic birds, molecular methods have been established. Two established primer pairs (2550F/2718R and p8/p2) amplify the CHD1 gene region from both the Z and W chromosomes. Here, we evaluated the use of these primers for sex identification in four sexually monomorphic penguin species: king penguins (Aptenodytes patagonicus), rockhopper penguins (Eudyptes chrysocome), gentoo penguins (Pygoscelis papua), and Magellanic penguins (Spheniscus magellanicus). For all species except rockhopper penguins, primer pair 2550F/2718R resulted in two distinct CHD1Z and CHD1W PCR bands, allowing for sex identification. For rockhopper penguins, only primer pair p8/p2 yielded different CHD1Z and CHD1W bands, which were faint and similar in size making them difficult to distinguish. As a result, we designed a new primer pair (PL/PR) that efficiently determined the gender of individuals from all four penguin species. Sequencing of the PCR products confirmed that they were from the CHD1 gene region. Primer pair PL/PR can be evaluated for use in sexing other penguin species, which will be crucial for the management of new penguin breeding programs. © 2012 Wiley Periodicals, Inc.

  8. Molecular identification of Indian crocodile species: PCR-RFLP method for forensic authentication*.

    Science.gov (United States)

    Meganathan, P R; Dubey, Bhawna; Haque, Ikramul

    2009-09-01

    South East Asian countries are known for illegal poaching and trade of crocodiles clandestinely, to be used in skin, medicinal, and cosmetic industries. Besides crocodiles being listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora, India has its Wildlife Protection Act, 1972 for conservation of crocodile species. Hitherto, lack of any rapid and reliable technique for examinations of crocodile-based crime exhibits such as skin, bones, etc. has been a major problem for an effective promulgation of law on illegal trade. DNA-based identification of species using PCR-RFLP technique for an apt identification of all the three Indian crocodile species namely, Crocodylus porosus, Crocodylus palustris and Gavialis gangeticus is presented here. A 628 bp segment of cytochrome b gene was amplified using novel primers followed by restriction digestion with three enzymes i.e., HaeIII, MboI, and MwoI, separately and in combination. The technique has produced a species-specific pattern for identifying the three crocodile species individually, which fulfills the requirement for its forensic application. It is expected that the technique will prove handy in identification of all the three Indian crocodile species and strengthen conservation efforts.

  9. Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

    Science.gov (United States)

    Wang, Wen J; He, Hong S; Thompson, Frank R; Spetich, Martin A; Fraser, Jacob S

    2018-09-01

    Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are not well represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts. We investigate how species biological traits and environmental heterogeneity affect species distribution shifts. We used a species-specific, spatially explicit forest dynamic model LANDIS PRO, which incorporates site-scale tree species demography and competition, landscape-scale dispersal and disturbances, and regional-scale abiotic controls, to simulate the distribution shifts of four representative tree species with distinct biological traits in the central hardwood forest region of United States. Our results suggested that biological traits (e.g., dispersal capacity, maturation age) were important for determining tree species distribution shifts. Environmental heterogeneity, on average, reduced shift rates by 8% compared to perfect environmental conditions. The average distribution shift rates ranged from 24 to 200myear -1 under climate change scenarios, implying that many tree species may not able to keep up with climate change because of limited dispersal capacity, long generation time, and environmental heterogeneity. We suggest that climate-distribution models should include species demographic processes (e.g., fecundity, dispersal, colonization), biological traits (e.g., dispersal capacity, maturation age), and environmental heterogeneity (e.g., habitat fragmentation) to improve future predictions of species distribution shifts in response to changing climates. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Evaluation of chromogenic media and seminested PCR in the identification of Candida species

    Science.gov (United States)

    Daef, Enas; Moharram, Ahmed; Eldin, Salwa Seif; Elsherbiny, Nahla; Mohammed, Mona

    2014-01-01

    Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. seminested polymerase chain reaction (sn PCR) for identification of Candida species. One hundred and twenty seven Candida strains isolated from various clinical specimens were identified by conventional methods, four different chromogenic media and sn PCR. HiCrome Candida Differential and CHROMagar Candida media showed comparably high sensitivities and specificities in the identification of C. albicans, C. tropicalis, C. glabrata and C. krusei. CHROMagar Candida had an extra advantage of identifying all C. parapsilosis isolates. CHROMagar-Pal’s medium identified C. albicans, C. tropicalis and C. krusei with high sensitivities and specificities, but couldn’t identify C. glabrata or C. parapsilosis. It was the only medium that identified C. dubliniensis with a sensitivity and specificity of 100%. Biggy agar showed the least sensitivities and specificities. The overall concordance of the snPCR compared to the conventional tests including CHROMAgar Candida in the identification of Candida species was 97.5%. The use of CHROMAgar Candida medium is an easy and accurate method for presumptive identification of the most commonly encountered Candida spp. PMID:24948942

  11. Investigation of biological condition of fish species in lower Ogun ...

    African Journals Online (AJOL)

    The study was carried out to investigate the biological condition of fish species in lower Ogun River wetlands. A total of 175 individual fish belonging to 10 species were collected from artisanal fishermen using different types of fishing gears. Two biological indices; condition factor “K” and growth exponent “b” obtained from ...

  12. Hichrom candida agar for identification of candida species

    OpenAIRE

    Baradkar V; Mathur M; Kumar S

    2010-01-01

    Chromogenic media are frequently used in direct and rapid identification of yeasts because different Candida species produce unique colors on these media. We used 60 isolates of Candida species including 30 C. albicans, 10 C. parapsilosis, 11 C. glabrata, five C. tropicalis, and four C. dubliniensis, isolated from various clinical specimens, to evaluate the performance of HiChrome Candida agar. These strains had been identified by germ tube test, morphology on cornmeal agar, chlamydospore for...

  13. Identification of Species in Tripterygium (Celastraceae) Based on DNA Barcoding.

    Science.gov (United States)

    Zhang, Xiaomei; Li, Na; Yao, Yuanyuan; Liang, Xuming; Qu, Xianyou; Liu, Xiang; Zhu, Yingjie; Yang, Dajian; Sun, Wei

    2016-11-01

    Species of genus Tripterygium (Celastraceae) have attracted much attention owing to their excellent effect on treating autoimmune and inflammatory diseases. However, due to high market demand causing overexploitation, natural populations of genus Tripterygium have rapidly declined. Tripterygium medicinal materials are mainly collected from the wild, making the quality of medicinal materials unstable. Additionally, identification of herbal materials from Tripterygium species and their adulterants is difficult based on morphological characters. Therefore, an accurate, convenient, and stability method is urgently needed. In this wok, we developed a DNA barcoding technique to distinguish T. wilfordii HOOK. f., T. hypoglaucum (LÉVL.) HUTCH, and T. regelii SPRAGUE et TAKEDA and their adulterants based on four uniform and standard DNA regions (internal transcribed spacer 2 (ITS2), matK, rbcL, and psbA-trnH). DNA was extracted from 26 locations of fresh leaves. Phylogenetic tree was constructed with Neighbor-Joining (NJ) method, while barcoding gap was analyzed to assess identification efficiency. Compared with the other DNA barcodes applied individually or in combination, ITS2+psbA-trnH was demonstrated as the optimal barcode. T. hypoglaucum and T. wilfordii can be considered as conspecific, while T. regelii was recognized as a separate species. Furthermore, identification of commercial Tripterygium samples was conducted using BLAST against GenBank and Species Identification System for Traditional Chinese Medicine. Our results indicated that DNA barcoding is a convenient, effective, and stability method to identify and distinguish Tripterygium and its adulterants, and could be applied as the quality control for Tripterygium medicinal preparations and monitoring of the medicinal herb trade in markets.

  14. [Research on identification of species of fruit trees by spectral analysis].

    Science.gov (United States)

    Xing, Dong-Xing; Chang, Qing-Rui

    2009-07-01

    Using the spectral reflectance data (R2) of canopies, the present paper identifies seven species of fruit trees bearing fruit in the fruit mature period. Firstly, it compares the fruit tree species identification capability of six kinds of satellite sensors and four kinds of vegetation index through re-sampling the spectral data with six kinds of pre-defined filter function and the related data processing of calculating vegetation indexes. Then, it structures a BP neural network model for identifying seven species of fruit trees on the basis of choosing the best transformation of R(lambda) and optimizing the model parameters. The main conclusions are: (1) the order of the identification capability of the six kinds of satellite sensors from strong to weak is: MODIS, ASTER, ETM+, HRG, QUICKBIRD and IKONOS; (2) among the four kinds of vegetation indexes, the identification capability of RVI is the most powerful, the next is NDVI, while the identification capability of SAVI or DVI is relatively weak; (3) The identification capability of RVI and NDVI calculated with the reflectance of near-infrared and red channels of ETM+ or MODIS sensor is relatively powerful; (4) Among R(lambda) and its 22 kinds of transformation data, d1 [log(1/R(lambda))](derivative gap is set 9 nm) is the best transformation for structuring BP neural network model; (5) The paper structures a 3-layer BP neural network model for identifying seven species of fruit trees using the best transformation of R(lambda) which is d1 [log(1/R(lambda))](derivative gap is set 9 nm).

  15. Thinking beyond the Common Candida Species: Need for Species-Level Identification of Candida Due to the Emergence of Multidrug-Resistant Candida auris.

    Science.gov (United States)

    Lockhart, Shawn R; Jackson, Brendan R; Vallabhaneni, Snigdha; Ostrosky-Zeichner, Luis; Pappas, Peter G; Chiller, Tom

    2017-12-01

    Candida species are one of the leading causes of nosocomial infections. Because much of the treatment for Candida infections is empirical, some institutions do not identify Candida to species level. With the worldwide emergence of the multidrug-resistant species Candida auris , identification of Candida to species level has new clinical relevance. Species should be identified for invasive candidiasis isolates, and species-level identification can be considered for selected noninvasive isolates to improve detection of C. auris . Copyright © 2017 American Society for Microbiology.

  16. Molecular identification of Nocardia species using the sodA gene

    Directory of Open Access Journals (Sweden)

    K. Sánchez-Herrera

    2017-09-01

    Full Text Available Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sodA gene (encoding the enzyme superoxide dismutase has had good results in identifying species of other Actinomycetes. In this study the sodA gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sodA gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp, hsp65 (401 bp, secA1 (494 bp, gyrB (1195 bp and rpoB (401 bp. The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sodA genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sodA gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.

  17. Functional biology of sympatric krill species

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

    2016-01-01

    Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm....... For T. inermis, only prey size spectrum on plankton ,400 mm were investigated. The prey size ranges of both species include organisms ,400 mm, and they consequently graze on several trophic levels. However, T. inermis feed on cells ,10 mm equivalent spherical diameter (ESD), whereas M. norvegica only...

  18. Species identification of archaeological skin objects from Danish bogs

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted; Schmidt, Anne Lisbeth; Mannering, Ulla

    2014-01-01

    environment of peat bogs leading to morphological and molecular degradation within the samples. We compared species assignment results of twelve archaeological skin samples from Danish bogs using Mass Spectrometry (MS)-based peptide sequencing, against results obtained using light and scanning electron...... microscopy. While it was difficult to obtain reliable results using microscopy, MS enabled the identification of several species-diagnostic peptides, mostly from collagen and keratins, allowing confident species discrimination even among taxonomically close organisms, such as sheep and goat. Unlike previous...

  19. Statistical analysis of texture in trunk images for biometric identification of tree species.

    Science.gov (United States)

    Bressane, Adriano; Roveda, José A F; Martins, Antônio C G

    2015-04-01

    The identification of tree species is a key step for sustainable management plans of forest resources, as well as for several other applications that are based on such surveys. However, the present available techniques are dependent on the presence of tree structures, such as flowers, fruits, and leaves, limiting the identification process to certain periods of the year. Therefore, this article introduces a study on the application of statistical parameters for texture classification of tree trunk images. For that, 540 samples from five Brazilian native deciduous species were acquired and measures of entropy, uniformity, smoothness, asymmetry (third moment), mean, and standard deviation were obtained from the presented textures. Using a decision tree, a biometric species identification system was constructed and resulted to a 0.84 average precision rate for species classification with 0.83accuracy and 0.79 agreement. Thus, it can be considered that the use of texture presented in trunk images can represent an important advance in tree identification, since the limitations of the current techniques can be overcome.

  20. Source Identification of Human Biological Materials and Its Prospect in Forensic Science.

    Science.gov (United States)

    Zou, K N; Gui, C; Gao, Y; Yang, F; Zhou, H G

    2016-06-01

    Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction. Copyright© by the Editorial Department of Journal of Forensic Medicine.

  1. DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

    Science.gov (United States)

    Hassold, Sonja; Lowry, Porter P; Bauert, Martin R; Razafintsalama, Annick; Ramamonjisoa, Lolona; Widmer, Alex

    2016-01-01

    Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world's most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.

  2. ITS-2 sequences-based identification of Trichogramma species in South America

    Directory of Open Access Journals (Sweden)

    R. P. Almeida

    Full Text Available Abstract ITS2 (Internal transcribed spacer 2 sequences have been used in systematic studies and proved to be useful in providing a reliable identification of Trichogramma species. DNAr sequences ranged in size from 379 to 632 bp. In eleven T. pretiosum lines Wolbachia-induced parthenogenesis was found for the first time. These thelytokous lines were collected in Peru (9, Colombia (1 and USA (1. A dichotomous key for species identification was built based on the size of the ITS2 PCR product and restriction analysis using three endonucleases (EcoRI, MseI and MaeI. This molecular technique was successfully used to distinguish among seventeen native/introduced Trichogramma species collected in South America.

  3. DNA-based identification and phylogeny of North American Armillaria species

    Science.gov (United States)

    Amy L. Ross-Davis; John W. Hanna; Ned B. Klopfenstein

    2011-01-01

    Because Armillaria species display different ecological behaviors across diverse forest ecosystems, it is critical to identify Armillaria species accurately for any assessment of forest health. To further develop DNA-based identification methods, partial sequences of the translation elongation factor-1 alpha (EF-1α) gene were used to examine the phylogenetic...

  4. Identification and characterization of pathogenic Pestalotiopsis species to pecan tree in Brazil

    Directory of Open Access Journals (Sweden)

    Marília Lazarotto

    2014-06-01

    Full Text Available The objective of this work was to characterize and cluster isolates of Pestalotiopsis species and to identify those that are pathogenic to pecan, based on morphological and molecular characters. Pestalotiopsis spp. isolates were identified by sequencing the internal transcribed spacer (ITS and β?tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as -tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as Pestalotiopsis clavispora and three as P. cocculi. The other isolates remained as an undefined species. The morphological characters were efficient for an initial separation of the isolates, which were grouped according to differences at species level, mainly colony diameter, which was identified as an important morphological describer. Beta-tubulin gene sequencing was less informative than the ITS region sequencing for species identification.

  5. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae species reveals highly inaccurate external morphology-based species identification

    Directory of Open Access Journals (Sweden)

    Jure Jugovic

    2014-06-01

    Full Text Available Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775, M. aurelia (Nickerl, 1850 and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is also compared with the results of the other two approaches. The main conclusions are as follows: (1 small albeit significant differences in wing morphology exist among the three species and (2 while the structure of male genitalia and phylogenetic position of the three species are concordant, they are (3 in discordance with the wing morphology. The present study represents another example where identification based on external morphology would lead to highly unreliable determinations, hence identification based on phylogenetic studies and/or genitalia is strongly recommended not only for the three studied species but also more broadly within the genus. Furthermore, we show that some of the characters generally used in the identification of these three Melitaea species should be avoided in future.

  6. Construction of analytically solvable models for interacting species. [biological species competition

    Science.gov (United States)

    Rosen, G.

    1976-01-01

    The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.

  7. Detection and Identification of Arcobacter species in Poultry in Assiut Governorate, Upper Egypt

    Directory of Open Access Journals (Sweden)

    Ahmed K. Hassan

    2017-04-01

    Full Text Available This work aimed to detect, identify and study the epidemiology of Arcobacter species in avian species in Upper Egypt. A total 600 samples, including cloacal swabs and intestinal samples were collected from chickens, turkeys and ducks in Assiut Governorate in Upper Egypt. Using conventional phenotypic methods for isolation and identification, Arcobacter species could be isolated and identified with percentage 25.5% in chickens, 9.5% in turkeys and 14% in ducks. Sixteen randomly selected phenotypically identified Arcobacter species isolates were confirmed using one step multiplex PCR assay. In conclusion, Arcobacter species could be detected and identified from various avian species with variable incidence. Conventional phenotypic methods for detection and differentiation of Arcobacter species are often hampered by many limitations, while molecular methods, and PCR, in particular can provide a sensitive and rapid alternative method for detection and identification of Arcobacter species in different domestic poultry species.

  8. Identification and diversity of Fusarium species isolated from tomato fruits

    Directory of Open Access Journals (Sweden)

    Murad Nur Baiti Abd

    2016-07-01

    Full Text Available Fruit rot of tomato is a serious disease caused by Fusarium species. Sampling was conducted throughout Selangor, Malaysia and fungal species identification was conducted based on morphological and gene encoding translation elongation factor 1-α (tef1-α sequence analysis. Five species of Fusarium were discovered namely F. oxysporum (including F. oxysporum f. sp. lycopersici, F. solani, F. equiseti, F. proliferatum and F. verticillioides. Our results provide additional information regarding the diversity of Fusarium species associated with fruit rot disease of tomato.

  9. Molecular identification of tsetse fly ( Diptera: Glossinidae ) species ...

    African Journals Online (AJOL)

    Inspite of the few mixed clusters, the pattern produced in the phylogenetic trees can provide a good guide to support any other method of Glossina identification. It was recommended that evaluations be made to validate other genetic markers that can produce better resolutions to identify tsetse fly species using phylogenetic ...

  10. SSR markers: a tool for species identification in Psidium (Myrtaceae).

    Science.gov (United States)

    Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

    2015-11-01

    Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies.

  11. Ecophysiological evaluation of tree species for biomonitoring of air quality and identification of air pollution-tolerant species.

    Science.gov (United States)

    Sen, Abhishek; Khan, Indrani; Kundu, Debajyoti; Das, Kousik; Datta, Jayanta Kumar

    2017-06-01

    Identification of tree species that can biologically monitor air pollution and can endure air pollution is very much important for a sustainable green belt development around any polluted place. To ascertain the species, ten tree species were selected on the basis of some previous study from the campus of the University of Burdwan and were studied in the pre-monsoon and post-monsoon seasons. The study has been designed to investigate biochemical and physiological activities of selected tree species as the campus is presently exposed to primary air pollutants and their impacts on plant community were observed through the changes in several physical and biochemical constituents of plant leaves. As the plant species continuously exchange different gaseous pollutants in and out of the foliar system and are very sensitive to gaseous pollutants, they serve as bioindicators. Due to air pollution, foliar surface undergoes different structural and functional changes. In the selected plant species, it was observed that the concentration of primary air pollutants, proline content, pH, relative water holding capacity, photosynthetic rate, and respiration rate were higher in the pre-monsoon than the post-monsoon season, whereas the total chlorophyll, ascorbic acid, sugar, and conductivity were higher in the post-monsoon season. From the entire study, it was observed that the concentration of sulfur oxide (SO x ), nitrogen oxide (NO x ), and suspended particulate matter (SPM) all are reduced in the post-monsoon season than the pre-monsoon season. In the pre-monsoon season, SO x , NO x , and SPM do not have any significant correlation with biochemical as well as physiological parameters. SPM shows a negative relationship with chlorophyll 'a' (r = -0.288), chlorophyll 'b' (r = -0.267), and total chlorophyll (r = -0.238). Similarly, chlorophyll a, chlorophyll b, and the total chlorophyll show negative relations with SO x and NO x (p tree species according to their air

  12. Near Infrared Spectroscopy Facilitates Rapid Identification of Both Young and Mature Amazonian Tree Species.

    Science.gov (United States)

    Lang, Carla; Costa, Flávia Regina Capellotto; Camargo, José Luís Campana; Durgante, Flávia Machado; Vicentini, Alberto

    2015-01-01

    Precise identification of plant species requires a high level of knowledge by taxonomists and presence of reproductive material. This represents a major limitation for those working with seedlings and juveniles, which differ morphologically from adults and do not bear reproductive structures. Near-infrared spectroscopy (FT-NIR) has previously been shown to be effective in species discrimination of adult plants, so if young and adults have a similar spectral signature, discriminant functions based on FT-NIR spectra of adults can be used to identify leaves from young plants. We tested this with a sample of 419 plants in 13 Amazonian species from the genera Protium and Crepidospermum (Burseraceae). We obtained 12 spectral readings per plant, from adaxial and abaxial surfaces of dried leaves, and compared the rate of correct predictions of species with discriminant functions for different combinations of readings. We showed that the best models for predicting species in early developmental stages are those containing spectral data from both young and adult plants (98% correct predictions of external samples), but even using only adult spectra it is still possible to attain good levels of identification of young. We obtained an average of 75% correct identifications of young plants by discriminant equations based only on adults, when the most informative wavelengths were selected. Most species were accurately predicted (75-100% correct identifications), and only three had poor predictions (27-60%). These results were obtained despite the fact that spectra of young individuals were distinct from those of adults when species were analyzed individually. We concluded that FT-NIR has a high potential in the identification of species even at different ontogenetic stages, and that young plants can be identified based on spectra of adults with reasonable confidence.

  13. Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier.

    Science.gov (United States)

    Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Rao, A R

    2016-11-05

    DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Parasites as biological tags for stock identification of blackspot seabream, Pagellus bogaraveo, in Portuguese northeast Atlantic waters

    Directory of Open Access Journals (Sweden)

    Margarida Hermida

    2013-10-01

    Full Text Available In this study the following parasites were selected as biological tags for the identification of blackspot seabream (Pagellus bogaraveo stocks in the northeast Atlantic: Diphterostomum vividum (Digenea: Zoogonidae, Anisakis simplex s.l., A. physeteris, Anisakis sp. PB-2010 (Nematoda: Anisakidae, and Bolbosoma sp. (Acanthocephala: Polymorphidae. These parasite species point to the existence of three blackspot seabream stocks in the northeast Atlantic: one in the Azores region (ICES Area X, one in continental Portuguese shelf/slope waters (ICES Area IXa, and one in the waters around Madeira (sub-area 1.2 of FAO 34, central-eastern Atlantic.

  15. Previously unknown species of Aspergillus.

    Science.gov (United States)

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

  16. Sample Preparation and Identification of Biological, Chemical and Mid-Spectrum Agents

    National Research Council Canada - National Science Library

    Hancock, J. R; Dragon, D. C

    2005-01-01

    A general survey of sample preparation and identification techniques for biological, chemical and mid-spectrum agents was conducted as part of Canada's contribution to a joint NATO Allied Engineering Publication (AEP) handbook...

  17. New Method for Simultaneous Species-Specific Identification of Equine Strongyles (Nematoda, Strongylida) by Reverse Line Blot Hybridization▿

    Science.gov (United States)

    Traversa, Donato; Iorio, Raffaella; Klei, Thomas R.; Kharchenko, Vitaliy A.; Gawor, Jakub; Otranto, Domenico; Sparagano, Olivier A. E.

    2007-01-01

    The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species. PMID:17626168

  18. Synthetical Analysis for Morphology, biological Species, and stable Isotopes (SAMSI) of single-cell planktonic foraminifer

    Science.gov (United States)

    Ujiie, Y.; Kimoto, K.; Ishimura, T.

    2017-12-01

    Planktonic foraminifers are widely used in the studies of paleontology and paleoceanography, because the morphology of their calcareous shells is enough highly variable to identify the morphospecies and the chemical composition of the shells reflect ambient seawater condition. Although the morphospecies were believed to represent environments associating with latitudinal temperature range of the world ocean, molecular phylogeographic studies have unveiled the presence of multiple biological species in a single morphospecies and their species-specific distributions. This implicates the actual complexity of planktonic foraminiferal ecology. Conversely, these biological species have a high potential for providing novel ecological and environmental information to us. In order to reassess the morphological and geochemical characters of biological species, the DNA extraction method with the guanidium isothiocyanate buffer was developed to preserve the calcareous shells. The present study carefully tested the physical and chemical damages of the DNA extraction process to the shells, by our novel approaches with geochemical analysis of the shells after non-destructive analysis for morphometrics on a same specimen. First, we checked the changes of the shell densities between pre- and post-DNA extraction by using the micro-focus X-ray CT (MXCT) scanning. Based on the simultaneous measurement of a sample and the standard material, we confirmed no significant changes to the shell densities through the DNA extraction process. As a next step, we compared stable oxygen and carbon isotopes among individuals of three sample sets: (1) no chemical and incubation as control, (2) incubation in the DNA extraction buffer at 65-70°C for 40 minutes as standard way, and (3) incubation in the DNA extraction buffer at 65-70°C for 120 minutes, by using the microscale isotopic analytical system (MICAL3c). Consequently, there were no significant differences among the three sample sets. These

  19. MALDI-TOF MS Profiling-Advances in Species Identification of Pests, Parasites, and Vectors

    Directory of Open Access Journals (Sweden)

    Jayaseelan Murugaiyan

    2017-05-01

    Full Text Available Invertebrate pests and parasites of humans, animals, and plants continue to cause serious diseases and remain as a high treat to agricultural productivity and storage. The rapid and accurate species identification of the pests and parasites are needed for understanding epidemiology, monitoring outbreaks, and designing control measures. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS profiling has emerged as a rapid, cost effective, and high throughput technique of microbial species identification in modern diagnostic laboratories. The development of soft ionization techniques and the release of commercial pattern matching software platforms has resulted in the exponential growth of applications in higher organisms including parasitology. The present review discusses the proof-of-principle experiments and various methods of MALDI MS profiling in rapid species identification of both laboratory and field isolates of pests, parasites and vectors.

  20. MALDI-TOF MS Profiling-Advances in Species Identification of Pests, Parasites, and Vectors.

    Science.gov (United States)

    Murugaiyan, Jayaseelan; Roesler, Uwe

    2017-01-01

    Invertebrate pests and parasites of humans, animals, and plants continue to cause serious diseases and remain as a high treat to agricultural productivity and storage. The rapid and accurate species identification of the pests and parasites are needed for understanding epidemiology, monitoring outbreaks, and designing control measures. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as a rapid, cost effective, and high throughput technique of microbial species identification in modern diagnostic laboratories. The development of soft ionization techniques and the release of commercial pattern matching software platforms has resulted in the exponential growth of applications in higher organisms including parasitology. The present review discusses the proof-of-principle experiments and various methods of MALDI MS profiling in rapid species identification of both laboratory and field isolates of pests, parasites and vectors.

  1. Biological interactions and cooperative management of multiple species.

    Science.gov (United States)

    Jiang, Jinwei; Min, Yong; Chang, Jie; Ge, Ying

    2017-01-01

    Coordinated decision making and actions have become the primary solution for the overexploitation of interacting resources within ecosystems. However, the success of coordinated management is highly sensitive to biological, economic, and social conditions. Here, using a game theoretic framework and a 2-species model that considers various biological relationships (competition, predation, and mutualism), we compute cooperative (or joint) and non-cooperative (or separate) management equilibrium outcomes of the model and investigate the effects of the type and strength of the relationships. We find that cooperation does not always show superiority to non-cooperation in all biological interactions: (1) if and only if resources are involved in high-intensity predation relationships, cooperation can achieve a win-win scenario for ecosystem services and resource diversity; (2) for competitive resources, cooperation realizes higher ecosystem services by sacrificing resource diversity; and (3) for mutual resources, cooperation has no obvious advantage for either ecosystem services or resource evenness but can slightly improve resource abundance. Furthermore, by using a fishery model of the North California Current Marine Ecosystem with 63 species and seven fleets, we demonstrate that the theoretical results can be reproduced in real ecosystems. Therefore, effective ecosystem management should consider the interconnection between stakeholders' social relationship and resources' biological relationships.

  2. 75 FR 29991 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2010-05-28

    ... Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and Identification... (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., August, and September of 2010. Certain fishermen and shark dealers are required to attend a workshop to...

  3. Molecular and Morphological Identification of Mealybug Species (Hemiptera: Pseudococcidae) in Brazilian Vineyards

    Science.gov (United States)

    Pacheco da Silva, Vitor C.; Bertin, Aline; Blin, Aurélie; Germain, Jean-François; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos; Malausa, Thibaut

    2014-01-01

    Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell), Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley), Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso), Pseudococcus viburni (Signoret), Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn) and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret). Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species. PMID:25062012

  4. Improving Remote Species Identification through Efficient Training Data Collection

    Directory of Open Access Journals (Sweden)

    Claire A. Baldeck

    2014-03-01

    Full Text Available Plant species identification and mapping based on remotely-sensed spectral signatures is a challenging task with the potential to contribute enormously to ecological studies. Success in this task rests upon the appropriate collection and use of costly field-based training data, and researchers are in need of ways to improve collection efficiency based on quantitative evidence. Using imaging spectrometer data collected by the Carnegie Airborne Observatory for hundreds of field-identified tree crowns in Kruger National Park, South Africa, we developed woody plant species classification models and evaluated how classification accuracy increases with increasing numbers of training crowns. First, we show that classification accuracy must be estimated while respecting the crown as the basic unit of data; otherwise, accuracy will be overestimated and the amount of training data needed to perform successful classification will be underestimated. We found that classification accuracy and the number of training crowns needed to perform successful classification varied depending on the number and spectral separability of species in the model. We also used a modified Michaelis-Menten function to describe the empirical relationship between training crowns and model accuracy, and show how this function may be useful for predicting accuracy. This framework can assist researchers in designing field campaigns to maximize the efficiency of field data collection, and thus the amount of biodiversity information gained from remote species identification models.

  5. 75 FR 8304 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2010-02-24

    ... Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and Identification... gear, and have also been issued shark or swordfish limited access permits. Additional free workshops... Coastal Highway, Ocean City, MD 21842. Atlantic Shark Identification Workshop Since January 1, 2007, shark...

  6. STBase: one million species trees for comparative biology.

    Science.gov (United States)

    McMahon, Michelle M; Deepak, Akshay; Fernández-Baca, David; Boss, Darren; Sanderson, Michael J

    2015-01-01

    Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed

  7. STBase: one million species trees for comparative biology.

    Directory of Open Access Journals (Sweden)

    Michelle M McMahon

    Full Text Available Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies

  8. Direct identification of pure penicillium species using image analysis

    DEFF Research Database (Denmark)

    Dørge, Thorsten Carlheim; Carstensen, Jens Michael; Frisvad, Jens Christian

    2000-01-01

    This paper presents a method for direct identification of fungal species solely by means of digital image analysis of colonies as seen after growth on a standard medium. The method described is completely automated and hence objective once digital images of the reference fungi have been establish...

  9. Hierarchical Learning of Tree Classifiers for Large-Scale Plant Species Identification.

    Science.gov (United States)

    Fan, Jianping; Zhou, Ning; Peng, Jinye; Gao, Ling

    2015-11-01

    In this paper, a hierarchical multi-task structural learning algorithm is developed to support large-scale plant species identification, where a visual tree is constructed for organizing large numbers of plant species in a coarse-to-fine fashion and determining the inter-related learning tasks automatically. For a given parent node on the visual tree, it contains a set of sibling coarse-grained categories of plant species or sibling fine-grained plant species, and a multi-task structural learning algorithm is developed to train their inter-related classifiers jointly for enhancing their discrimination power. The inter-level relationship constraint, e.g., a plant image must first be assigned to a parent node (high-level non-leaf node) correctly if it can further be assigned to the most relevant child node (low-level non-leaf node or leaf node) on the visual tree, is formally defined and leveraged to learn more discriminative tree classifiers over the visual tree. Our experimental results have demonstrated the effectiveness of our hierarchical multi-task structural learning algorithm on training more discriminative tree classifiers for large-scale plant species identification.

  10. Comparing SVM and ANN based Machine Learning Methods for Species Identification of Food Contaminating Beetles.

    Science.gov (United States)

    Bisgin, Halil; Bera, Tanmay; Ding, Hongjian; Semey, Howard G; Wu, Leihong; Liu, Zhichao; Barnes, Amy E; Langley, Darryl A; Pava-Ripoll, Monica; Vyas, Himansu J; Tong, Weida; Xu, Joshua

    2018-04-25

    Insect pests, such as pantry beetles, are often associated with food contaminations and public health risks. Machine learning has the potential to provide a more accurate and efficient solution in detecting their presence in food products, which is currently done manually. In our previous research, we demonstrated such feasibility where Artificial Neural Network (ANN) based pattern recognition techniques could be implemented for species identification in the context of food safety. In this study, we present a Support Vector Machine (SVM) model which improved the average accuracy up to 85%. Contrary to this, the ANN method yielded ~80% accuracy after extensive parameter optimization. Both methods showed excellent genus level identification, but SVM showed slightly better accuracy  for most species. Highly accurate species level identification remains a challenge, especially in distinguishing between species from the same genus which may require improvements in both imaging and machine learning techniques. In summary, our work does illustrate a new SVM based technique and provides a good comparison with the ANN model in our context. We believe such insights will pave better way forward for the application of machine learning towards species identification and food safety.

  11. Identification of trace levels of selenomethionine and related organic selenium species in high-ionic-strength waters.

    Science.gov (United States)

    LeBlanc, Kelly L; Ruzicka, Josef; Wallschläger, Dirk

    2016-02-01

    A new anion-exchange chromatographic separation method was used for the simultaneous speciation analysis of selenoamino acids and the more ubiquitous inorganic selenium oxyanions, selenite and selenate. For quantification, this separation was coupled to inductively coupled plasma-mass spectrometry to achieve an instrumental detection limit of 5 ng Se L(-1) for all species. This chromatographic method was also coupled to electrospray tandem mass spectrometry to observe the negative ion mode fragmentation of selenomethionine and one of its oxidation products. Low detection limits were achieved, which were similar to those obtained using inductively coupled plasma-mass spectrometry. An extensive preconcentration and cleanup procedure using cation-exchange solid-phase extraction was developed for the identification and quantification of trace levels of selenomethionine in environmental samples. Preconcentration factors of up to five were observed for selenomethionine, which in addition to the removal of high concentrations of sulphate and chloride from industrial process waters, allowed for an unambiguous analysis that would have been impossible otherwise. Following these methods, selenomethionine was identified at an original concentration of 3.2 ng Se L(-1) in samples of effluent collected at a coal-fired power plant's biological remediation site. It is the first time that this species has been identified in the environment, outside of a biological entity. Additionally, oxidation products of selenomethionine were identified in river water and laboratory algal culture samples. High-resolution mass spectrometry was employed to postulate the chemical structures of these species.

  12. Section-Based Tree Species Identification Using Airborne LIDAR Point Cloud

    Science.gov (United States)

    Yao, C.; Zhang, X.; Liu, H.

    2017-09-01

    The application of LiDAR data in forestry initially focused on mapping forest community, particularly and primarily intended for largescale forest management and planning. Then with the smaller footprint and higher sampling density LiDAR data available, detecting individual tree overstory, estimating crowns parameters and identifying tree species are demonstrated practicable. This paper proposes a section-based protocol of tree species identification taking palm tree as an example. Section-based method is to detect objects through certain profile among different direction, basically along X-axis or Y-axis. And this method improve the utilization of spatial information to generate accurate results. Firstly, separate the tree points from manmade-object points by decision-tree-based rules, and create Crown Height Mode (CHM) by subtracting the Digital Terrain Model (DTM) from the digital surface model (DSM). Then calculate and extract key points to locate individual trees, thus estimate specific tree parameters related to species information, such as crown height, crown radius, and cross point etc. Finally, with parameters we are able to identify certain tree species. Comparing to species information measured on ground, the portion correctly identified trees on all plots could reach up to 90.65 %. The identification result in this research demonstrate the ability to distinguish palm tree using LiDAR point cloud. Furthermore, with more prior knowledge, section-based method enable the process to classify trees into different classes.

  13. Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach.

    Science.gov (United States)

    Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Beduschi, Giovanni

    2009-09-01

    Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.

  14. Differences in a ribosomal DNA sequence of Strongylus species allows identification of single eggs.

    Science.gov (United States)

    Campbell, A J; Gasser, R B; Chilton, N B

    1995-03-01

    In the current study, molecular techniques were evaluated for the species identification of individual strongyle eggs. Adult worms of Strongylus edentatus, S. equinus and S. vulgaris were collected at necropsy from horses from Australia and the U.S.A. Genomic DNA was isolated and a ribosomal transcribed spacer (ITS-2) amplified and sequenced using polymerase chain reaction (PCR) techniques. The length of the ITS-2 sequence of S. edentatus, S. equinus and S. vulgaris ranged between 217 and 235 nucleotides. Extensive sequence analysis demonstrated a low degree (0-0.9%) of intraspecific variation in the ITS-2 for the Strongylus species examined, whereas the levels of interspecific differences (13-29%) were significantly greater. Interspecific differences in the ITS-2 sequences allowed unequivocal species identification of single worms and eggs using PCR-linked restriction fragment length polymorphism. These results demonstrate the potential of the ribosomal spacers as genetic markers for species identification of single strongyle eggs from horse faeces.

  15. Molecular and morphological identification of mealybug species (Hemiptera: Pseudococcidae in Brazilian vineyards.

    Directory of Open Access Journals (Sweden)

    Vitor C Pacheco da Silva

    Full Text Available Mealybugs (Hemiptera: Pseudococcidae are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell, Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley, Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso, Pseudococcus viburni (Signoret, Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret. Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species.

  16. Estimation of Species Identification Error: Implications for Raptor Migration Counts and Trend Estimation

    Science.gov (United States)

    J.M. Hull; A.M. Fish; J.J. Keane; S.R. Mori; B.J Sacks; A.C. Hull

    2010-01-01

    One of the primary assumptions associated with many wildlife and population trend studies is that target species are correctly identified. This assumption may not always be valid, particularly for species similar in appearance to co-occurring species. We examined size overlap and identification error rates among Cooper's (Accipiter cooperii...

  17. Species identification of skins and development of sheep wool

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted

    at death for one of the animal skin samples - information not obtainable by DNA and with crucial implications for the interpretations of preferences of skins and animal husbandry. Online available protein databases used for comparison are still not complete. While the most common domesticated species...... are well described, the databases did not provide enough resolution of seals and birds to presently justify the species identification by PMF of ancient Greenlandic skin samples dating to the Saqqaq culture. Overall, the success of the analysis of ancient biomolecules is closely connected to the nature...

  18. Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

    Science.gov (United States)

    Ishitani, Y.

    2017-12-01

    Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

  19. Professional Competence of Student Teachers to Implement Species Identification in Schools – A Case Study from Germany

    Directory of Open Access Journals (Sweden)

    Petra Lindemann-Matthies

    2017-03-01

    Full Text Available This study investigates how well prepared student teachers are to implement species identification in school. Data were collected with the help of a questionnaire and a PowerPoint presentation in which local plant and animal species were presented. Participants (n = 357 correctly identified, on average, 23% of the plants and 44% of the animals. They identified plants mainly by flower characteristics and leaves, and animals mainly by shape and colour. Family and school were key sources of participants’ knowledge of species. The self-estimated competence of participants to identify species was positively correlated with their taxonomic knowledge and the amount of time they had spent on species identification during their own schooldays. The number of correctly identified plant and animal species increased with interest in identifying species and participation in species identification courses. Participants considered learner-centred education and experience-based learning, and the use of living organisms to be most important when identifying species in school.

  20. Identification of hare meat by a species-specific marker of mitochondrial origin.

    Science.gov (United States)

    Santos, Cristina G; Melo, Vitor S; Amaral, Joana S; Estevinho, Letícia; Oliveira, M Beatriz P P; Mafra, Isabel

    2012-03-01

    Meat species identification in food has gained increasing interest in recent years due to public health, economic and legal concerns. Following the consumer trend towards high quality products, game meat has earned much attention. The aim of the present work was to develop a DNA-based technique able to identify hare meat. Mitochondrial cytochrome b gene was used to design species-specific primers for hare detection. The new primers proved to be highly specific to Lepus species, allowing the detection of 0.01% of hare meat in pork meat by polymerase chain reaction (PCR). A real-time PCR assay with the new intercalating EvaGreen dye was further proposed as a specific and fast tool for hare identification with increased sensitivity (1pg) compared to end-point PCR (10pg). It can be concluded that the proposed new primers can be used by both species-specific end-point PCR or real-time PCR to accurately authenticate hare meat. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Evaluation of the Biotyper MALDI-TOF MS system for identification of Staphylococcus species.

    Science.gov (United States)

    Zhu, Wenming; Sieradzki, Krzysztof; Albrecht, Valerie; McAllister, Sigrid; Lin, Wen; Stuchlik, Olga; Limbago, Brandi; Pohl, Jan; Kamile Rasheed, J

    2015-10-01

    The Bruker Biotyper MALDI-TOF MS (Biotyper) system, with a modified 30 minute formic acid extraction method, was evaluated by its ability to identify 216 clinical Staphylococcus isolates from the CDC reference collection comprising 23 species previously identified by conventional biochemical tests. 16S rDNA sequence analysis was used to resolve discrepancies. Of these, 209 (96.8%) isolates were correctly identified: 177 (84.7%) isolates had scores ≥2.0, while 32 (15.3%) had scores between 1.70 and 1.99. The Biotyper identification was inconsistent with the biochemical identification for seven (3.2%) isolates, but the Biotyper identifications were confirmed by 16S rDNA analysis. The distribution of low scores was strongly species-dependent, e.g. only 5% of Staphylococcus epidermidis and 4.8% of Staphylococcus aureus isolates scored below 2.0, while 100% of Staphylococcus cohnii, 75% of Staphylococcus sciuri, and 60% of Staphylococcus caprae produced low but accurate Biotyper scores. Our results demonstrate that the Biotyper can reliably identify Staphylococcus species with greater accuracy than conventional biochemicals. Broadening of the reference database by inclusion of additional examples of under-represented species could further optimize Biotyper results. Published by Elsevier B.V.

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

    Science.gov (United States)

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

    2015-06-01

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

  3. Identification of endangered or threatened Costa Rican tree species by wood anatomy and fluorescence activity.

    Science.gov (United States)

    Moya, Róger; Wiemann, Michael C; Olivares, Carlos

    2013-09-01

    A total of 45 native Costa Rican tree species are threatened or in danger of extinction, but the Convention on International Trade Endangered Species (CITES) includes only eight of these in its Appendices. However, the identification of other species based on their wood anatomy is limited. The present study objective was to describe and to compare wood anatomy and fluorescence activity in some endangered or threatened species of Costa Rica. A total of 45 (22 endangered and 23 threatened with extinction) wood samples of these species, from the xylaria of the Instituto Tecnológico de Costa Rica and the Forest Products Laboratory in Madison, Wisconsin, were examined. Surface fluorescence was positive in eight species, water extract fluorescence was positive in six species and ethanol extract fluorescence was positive in 24 species. Almost all species were diffuse porous except for occasional (Cedrela odorata, C. fissilis, Cordia gerascanthus) or regular (C. salvadorensis and C. tonduzii) semi-ring porosity. A dendritic vessel arrangement was found in Sideroxylon capari, and pores were solitary in Guaiacum sanctum and Vantanea barbourii. Vessel element length was shortest in Guaiacum sanctum and longest in Humiriastrum guianensis, Minquartia guianensis and Vantanea barbourii. Finally, anatomical information and fluorescence activity were utilized to construct an identification key of species, in which fluorescence is a feature used in identification.

  4. Identification of endangered or threatened Costa Rican tree species by wood anatomy and fluorescence activity

    Directory of Open Access Journals (Sweden)

    Róger Moya

    2013-09-01

    Full Text Available A total of 45 native Costa Rican tree species are threatened or in danger of extinction, but the Convention on International Trade Endangered Species (CITES includes only eight of these in its Appendices. However, the identification of other species based on their wood anatomy is limited. The present study objective was to describe and to compare wood anatomy and fluorescence activity in some endangered or threatened species of Costa Rica. A total of 45 (22 endangered and 23 threatened with extinction wood samples of these species, from the xylaria of the Instituto Tecnológico de Costa Rica and the Forest Products Laboratory in Madison, Wisconsin, were examined. Surface fluorescence was positive in eight species, water extract fluorescence was positive in six species and ethanol extract fluorescence was positive in 24 species. Almost all species were diffuse porous except for occasional (Cedrela odorata, C. fissilis, Cordia gerascanthus or regular (C. salvadorensis and C. tonduzii semi-ring porosity. A dendritic vessel arrangement was found in Sideroxylon capari, and pores were solitary in Guaiacum sanctum and Vantanea barbourii. Vessel element length was shortest in Guaiacum sanctum and longest in Humiriastrum guianensis, Minquartia guianensis and Vantanea barbourii. Finally, anatomical information and fluorescence activity were utilized to construct an identification key of species, in which fluorescence is a feature used in identification.

  5. Rapid identification of emerging human-pathogenic Sporothrix species with rolling circle amplification

    Directory of Open Access Journals (Sweden)

    Anderson Messias Rodrigues

    2015-12-01

    Full Text Available Sporothrix infections are emerging as an important human and animal threat among otherwise healthy patients, especially in Brazil and China. Correct identification of sporotrichosis agents is beneficial for epidemiological surveillance, enabling implementation of adequate public-health policies and guiding antifungal therapy. In areas of limited resources where sporotrichosis is endemic, high-throughput detection methods that are specific and sensitive are preferred over phenotypic methods that usually result in misidentification of closely related Sporothrix species. We sought to establish rolling circle amplification (RCA as a low-cost screening tool for species-specific identification of human-pathogenic Sporothrix. We developed six species-specific padlock probes targeting polymorphisms in the gene encoding calmodulin. BLAST-searches revealed candidate probes that were conserved intraspecifically; no significant homology with sequences from humans, mice, plants or microorganisms outside members of Sporothrix were found. The accuracy of our RCA-based assay was demonstrated through the specificity of probe-template binding to 25 S. brasiliensis, 58 S. schenckii, 5 S. globosa, 1 S. luriei, 4 S. mexicana, and 3 S. pallida samples. No cross reactivity between closely related species was evident in vitro, and padlock probes yielded 100% specificity and sensitivity down to 3 x 10 6 copies of the target sequence. RCA-based speciation matched identifications via phylogenetic analysis of the gene encoding calmodulin and the rDNA operon (kappa 1.0; 95% confidence interval 1.0-1.0, supporting its use as a reliable alternative to DNA sequencing. This method is a powerful tool for rapid identification and specific detection of medically relevant Sporothrix, and due to its robustness has potential for ecological studies.

  6. Molecular identification of python species: development and validation of a novel assay for forensic investigations.

    Science.gov (United States)

    Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

    2015-05-01

    Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Biological activities of species in the genus Tulbaghia : A review ...

    African Journals Online (AJOL)

    Species of the genus Tulbaghia has been widely used in traditional medicine to treat various ailments such rheumatism, fits, fever, earache, tuberculosis etc. It is believed that the species possess several therapeutic properties. This paper evaluates some of the biological activities of the genus Tulbaghia. It is evident from ...

  8. Quantifying errors and omissions in alien species lists: The introduction status of Melaleuca species in South Africa as a case study

    Directory of Open Access Journals (Sweden)

    Llewellyn Jacobs

    2017-01-01

    Full Text Available Introduced species lists provide essential background information for biological invasions research and management. The compilation of these lists is, however, prone to a variety of errors. We highlight the frequency and consequences of such errors using introduced Melaleuca (sensu lato, including Callistemon species in South Africa as a case study. We examined 111 herbarium specimens from South Africa and noted the categories and sub-categories of errors that occurred in identification. We also used information from herbarium specimens and distribution data collected in the field to determine whether a species was introduced, naturalized and invasive. We found that 72% of the specimens were not named correctly. These were due to human error (70% (misidentification, and improved identifications and species identification problems (30% (synonyms arising from inclusion of Callistemon, and unresolved taxonomy. At least 36 Melaleuca species have been introduced to South Africa, and field observations indicate that ten of these have naturalized, including five that are invasive. While most of the errors likely have negligible impact on management, we highlight one case where incorrect identification lead to an inappropriate management approach and some instances of errors in published lists. Invasive species lists need to be carefully reviewed to minimise errors, and herbarium specimens supported by DNA identification are required where identification using morphological features is particularly challenging.

  9. A validated methodology for genetic identification of tuna species (genus Thunnus.

    Directory of Open Access Journals (Sweden)

    Jordi Viñas

    2009-10-01

    Full Text Available Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue.After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR, followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1. This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples.Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned.

  10. Sensors and actuators inherent in biological species

    Science.gov (United States)

    Taya, Minoru; Stahlberg, Rainer; Li, Fanghong; Zhao, Ying Joyce

    2007-04-01

    This paper addresses examples of sensing and active mechanisms inherent in some biological species where both plants and animals cases are discussed: mechanosensors and actuators in Venus Fly Trap and cucumber tendrils, chemosensors in insects, two cases of interactions between different kingdoms, (i) cotton plant smart defense system and (ii) bird-of-paradise flower and hamming bird interaction. All these cases lead us to recognize how energy-efficient and flexible the biological sensors and actuators are. This review reveals the importance of integration of sensing and actuation functions into an autonomous system if we make biomimetic design of a set of new autonomous systems which can sense and actuate under a number of different stimuli and threats.

  11. Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae).

    Science.gov (United States)

    Failla, A J; Vasquez, A A; Hudson, P; Fujimoto, M; Ram, J L

    2016-02-01

    Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor

  12. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China.

    Science.gov (United States)

    Laguardia, Alice; Wang, Jun; Shi, Fang-Lei; Shi, Kun; Riordan, Philip

    2015-03-18

    Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species' scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.

  13. DNA-based identification reveals illegal trade of threatened shark species in a global elasmobranch conservation hotspot.

    Science.gov (United States)

    Feitosa, Leonardo Manir; Martins, Ana Paula Barbosa; Giarrizzo, Tommaso; Macedo, Wagner; Monteiro, Iann Leonardo; Gemaque, Romário; Nunes, Jorge Luiz Silva; Gomes, Fernanda; Schneider, Horácio; Sampaio, Iracilda; Souza, Rosália; Sales, João Bráullio; Rodrigues-Filho, Luís Fernando; Tchaicka, Lígia; Carvalho-Costa, Luís Fernando

    2018-02-20

    Here, we report trading of endangered shark species in a world hotspot for elasmobranch conservation in Brazil. Data on shark fisheries are scarce in Brazil, although the northern and northeastern regions have the highest indices of shark bycatch. Harvest is made primarily with processed carcasses lacking head and fins, which hampers reliable species identification and law enforcement on illegal catches. We used partial sequences of two mitochondrial genes (COI and/or NADH2) to identify 17 shark species from 427 samples being harvested and marketed on the northern coast of Brazil. Nine species (53%) are listed under some extinction threat category according to Brazilian law and international authorities (IUCN - International Union for Conservation of Nature; CITES - Convention on International Trade of Endangered Species of Wild Fauna and Flora). The number increases to 13 (76%) if we also consider the Near Threatened category. Hammerhead sharks are under threat worldwide, and composed 18.7% of samples, with Sphyrna mokarran being the fourth most common species among samples. As illegal trade of threatened shark species is a worldwide conservation problem, molecular identification of processed meat or specimens lacking diagnostic body parts is a highly effective tool for species identification and law enforcement.

  14. Noncontact blood species identification method based on spatially resolved near-infrared transmission spectroscopy

    Science.gov (United States)

    Zhang, Linna; Sun, Meixiu; Wang, Zhennan; Li, Hongxiao; Li, Yingxin; Li, Gang; Lin, Ling

    2017-09-01

    The inspection and identification of whole blood are crucially significant for import-export ports and inspection and quarantine departments. In our previous research, we proved Near-Infrared diffuse transmitted spectroscopy method was potential for noninvasively identifying three blood species, including macaque, human and mouse, with samples measured in the cuvettes. However, in open sampling cases, inspectors may be endangered by virulence factors in blood samples. In this paper, we explored the noncontact measurement for classification, with blood samples measured in the vacuum blood vessels. Spatially resolved near-infrared spectroscopy was used to improve the prediction accuracy. Results showed that the prediction accuracy of the model built with nine detection points was more than 90% in identification between all five species, including chicken, goat, macaque, pig and rat, far better than the performance of the model built with single-point spectra. The results fully supported the idea that spatially resolved near-infrared spectroscopy method can improve the prediction ability, and demonstrated the feasibility of this method for noncontact blood species identification in practical applications.

  15. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia.

    Directory of Open Access Journals (Sweden)

    Jennifer L Ginther

    Full Text Available Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area.

  16. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia

    Science.gov (United States)

    Ginther, Jennifer L.; Mayo, Mark; Warrington, Stephanie D.; Kaestli, Mirjam; Mullins, Travis; Wagner, David M.; Currie, Bart J.; Tuanyok, Apichai; Keim, Paul

    2015-01-01

    Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area. PMID:26121041

  17. Identification of Staphylococcus species with the API STAPH-IDENT system.

    Science.gov (United States)

    Kloos, W E; Wolfshohl, J F

    1982-01-01

    The API STAPH-IDENT system was compared with conventional methods for the identification of 14 Staphylococcus species. Conventional methods included the Kloos and Schleifer simplified scheme and DNA-DNA hybridization. The API STAPH-IDENT strip utilizes a battery of 10 miniaturized biochemical tests, including alkaline phosphatase, urease, beta-glucosidase, beta-glucuronidase, and beta-galactosidase activity, aerobic acid formation from D-(+)-mannose, D-mannitol, D-(+)-trehalose, and salicin, and utilization of arginine. Reactions of cultures were determined after 5 h of incubation at 35 degrees C. Results indicated a high degree of congruence (greater than 90%) between the expedient API system and conventional methods for most species. The addition of a test for novobiocin susceptibility to the API system increased the accuracy of identification of S. saprophyticus, S. cohnii, and S. hominis, significantly. Several strains of S. hominis, S. haemolyticus, and S. warneri which were difficult to separate with the Kloos and Schleifer simplified scheme were accurately resolved by the API system. PMID:6752190

  18. Computational identification of strain-, species- and genus-specific proteins

    Directory of Open Access Journals (Sweden)

    Thiagarajan Rathi

    2005-11-01

    Full Text Available Abstract Background The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets. Description A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Proteins encoded by a given strain are preliminarily considered to be unique if BLAST, using a comprehensive protein database, fails to retrieve (with an e-value better than 0.001 any protein not encoded by the query strain, species or genus (for strain-, species- and genus-specific proteins respectively, or if BLAST, using the best hit as the query (reverse BLAST, does not retrieve the initial query protein. Results are manually inspected for homology if the initial query is retrieved in the reverse BLAST but is not the best hit. Sequences unlikely to retrieve homologs using the default BLOSUM62 matrix (usually short sequences are re-tested using the PAM30 matrix, thereby increasing the number of retrieved homologs and increasing the stringency of the search for unique proteins. The above protocol was used to examine several food- and water-borne pathogens. We find that the reverse BLAST step filters out about 22% of proteins with homologs that would otherwise be considered unique at the genus and species levels. Analysis of the annotations of unique proteins reveals that many are remnants of prophage proteins, or may be involved in virulence. The data generated from this study can be accessed and further evaluated from the CUPID (Core and Unique Protein Identification system web site (updated semi-annually at http://pir.georgetown.edu/cupid. Conclusion CUPID

  19. Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change

    Science.gov (United States)

    Wen J. Wang; Hong S. He; Frank R. Thompson; Martin A. Spetich; Jacob S. Fraser

    2018-01-01

    Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are notwell represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts.We investigate how species biological...

  20. 78 FR 73500 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2013-12-06

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., February, and March of 2014. Certain fishermen and shark dealers are required to attend a workshop to meet...

  1. 78 FR 54456 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2013-09-04

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., November, and December of 2013. Certain fishermen and shark dealers are required to attend a workshop to...

  2. 77 FR 32950 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2012-06-04

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., August, and September of 2012. Certain fishermen and shark dealers are required to attend a workshop to...

  3. 75 FR 10217 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2010-03-05

    ... Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and Identification... (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: NMFS announces free Atlantic Shark... April, May, and June of 2010. Certain fishermen and shark dealers are required to attend a workshop to...

  4. 77 FR 12574 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2012-03-01

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., May, and June of 2012. Certain fishermen and shark dealers are required to attend a workshop to meet...

  5. 77 FR 55464 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2012-09-10

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., November, and December of 2012. Certain fishermen and shark dealers are required to attend a workshop to...

  6. 77 FR 73451 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2012-12-10

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., February, and March of 2013. Certain fishermen and shark dealers are required to attend a workshop to meet...

  7. 78 FR 15709 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2013-03-12

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., May, and June of 2013. Certain fishermen and shark dealers are required to attend a workshop to meet...

  8. 75 FR 74693 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2010-12-01

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., February, and March of 2011. Certain fishermen and shark dealers are required to attend a workshop to meet...

  9. 76 FR 34209 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2011-06-13

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., August, and September of 2011. Certain fishermen and shark dealers are required to attend a workshop to...

  10. 76 FR 77214 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2011-12-12

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., February, and March of 2012. Certain fishermen and shark dealers are required to attend a workshop to meet...

  11. 76 FR 11762 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2011-03-03

    ... for Atlantic Shark Identification Workshops and Protected Species Safe Handling, Release, and... Administration (NOAA), Commerce. ACTION: Notice of public workshops. SUMMARY: Free Atlantic Shark Identification..., May, and June of 2011. Certain fishermen and shark dealers are required to attend a workshop to meet...

  12. Comparison phenotypic and genotypic identification of Staphylococcus species isolated from bovine mastitis

    Directory of Open Access Journals (Sweden)

    Felipe Freitas Guimarães

    Full Text Available ABSTRACT: In addition to Staphylococcus aureus nowadays other coagulase-positive staphylococci (CoPS and coagulase-negative staphylococci (CoNS, earlier considered of minor importance, are now accepted as relevant pathogens for humans and animals. The involvement of these microorganisms in bovine mastitis etiology and the possibility their transmission through milk to humans justify the requirement of developing reliable methods for identification of the most frequent species among them. The purpose of this study was to compare the phenotypic techniques with the genotypic method carried out by sequencing of the rpoB gene in identification of several species of the genus Staphylococcus isolated from bovine mastitis. A total of 300 staphylococci isolates of bovine mastitis cases from several Brazilian dairy herds were studied by phenotypic and genotypic techniques, respectively: 150 CoPS and 150 CoNS strains. A total of 18 CoNS different species and 4 CoPS species were identified. Among the CoNS the following species were recognized: 48 (32% Staphylococcus warneri, 22(15% S. epidermidis, 20(13% S. hyicus, 10(7% S. xylosus, 7(5% S. haemolyticus, 6(4% S. simulans, 6(4% S. schleiferi subsp schleiferi, 6(4% S. hominis, 5(3% S. pasteuri, 4(2.7% S. cohnii, 3(2% S. saprophyticus subsp. saprophyticus 3(2% S. chromogenes 3(2% S. sciuri, 2(1% S. saccharolyticus, 2(1% S. lugdunensi, 1(0,7% S. auricularis, 1(70% S. saprophyticus subsp. bovis, 1(0.7% S. capitis. And among the 150 CoPS were identified respectively: 105 (70% S. aureus, 21(14%, S. hyicus, 19(13% S. intermedius e 5(3% S. schleiferi subsp coagulans. Considering the 150 CoNS isolates, the identifications performed by phenotypic and genotypic tests presented 96.7% of concordance, kappa coefficient of agreement = 0.933, SE (standard error of kappa=0.021 (95% confidence interval: 0.893 to 0.974, Pearson’s correlation coefficient (r = 0.9977, (confidence interval 95%: 0.9938 a 0.9992 and in relation

  13. Secondary metabolites and biological activity of Pentas species: A minireview

    Directory of Open Access Journals (Sweden)

    Heba-tollah M. Sweelam

    2018-03-01

    Full Text Available The genus Pentas belongs to the Rubiaceae family, which contains approximately 40 species. Several Pentas species were reported to be used as a folk treatment by African indigenous people in treating some diseases such as malaria, tapeworms, dysentery, gonorrhea, syphilis and snake poisoning. This article covers the period from 1962 to 2017 and presents an overview of the biological activity of different Pentas species and describes their phytochemical traits. As a conclusion, the main secondary metabolites from Pentas species are quinones, highly oxygenated chromene-based structures, and iridoids. Pentas species are widely used in folk medicine but they have to be more investigated for their medicinal properties.

  14. Identification of Bottlenecks in the Plant Life Cycle for Sustainable Conservation of Rare and Endangered Species

    Directory of Open Access Journals (Sweden)

    Giovanna Aronne

    2017-07-01

    Full Text Available Long term survival of a species relies on maintenance of genetic variability and natural selection by means of successful reproduction and generation turnover. Although, basic to monitor the conservation status of a plant species, life history data are rarely available even for threatened species due to the gap between the large amount of information required and the limits in terms of time and available economic resources to gather these data. Here, the focus on bottlenecks in life-cycle of rare endangered plant species is proposed as a resolving approach to address the challenges of feasible conservation actions. Basic considerations for this approach are: (a all biological and ecological studies on plant species can be scientifically important, but not all of them are equally relevant to conservation planning and management requirements; (b under a changing environment, long term survival of a species relies on generation turnover; (c for conservation purposes, priority should be given to studies aimed to focus on bottlenecks in the succession of generations because they prevent, or slow down natural selection processes. The proposed procedure, named Systematic Hazard Analysis of Rare-endangered Plants (SHARP, consists of a preliminary survey of the already available information on the species and two main components. The first component is the identification of the bottlenecks in the life cycle by means of field surveys. The second is the diagnosis of the causes of the bottleneck by appropriate experimental methods. The target is to provide researchers, managers and practitioners with substantiated indications for sustainable conservation measures.

  15. Character’s Selection of Leaf Morphology in Some Families (Tree Habit In Sumatra Region for Species Identification

    Directory of Open Access Journals (Sweden)

    Saida Rasnovi

    2014-04-01

    Full Text Available Identification is a basic activity and one of primary objective on systematic. For plant biodiversity studies, it was the first steps that researcher performed before studying any topics in the research area. Unfortunately, species identification is usually a time consuming activity. One of the main objectives of this study was to obtain a set of leaf morphology characters that were useful and efficient enough for species identification, especially on the tree habits group in order to reduce time consuming for the identification species.  All of the leaf morphology characters were selected by correlation coefficient and separation coefficient values. Besides of that, the stability, simplicity and validity of the characters were also part of concern. The characters that had high value of separation coefficient and low value of correlation coefficient would be added one by one as in their rank, until the value of the combination separation coefficient was equal to 1 (100%. The result of this study suggested that 30 from 92 characters of leaf morphology were recommended as a set of characters that useful and efficient enough for species identification.

  16. Identification of different bacterial species in biofilms using confocal Raman microscopy

    Science.gov (United States)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2010-11-01

    Confocal Raman microspectroscopy is used to discriminate between different species of bacteria grown in biofilms. Tests are performed using two bacterial species, Streptococcus sanguinis and Streptococcus mutans, which are major components of oral plaque and of particular interest due to their association with healthy and cariogenic plaque, respectively. Dehydrated biofilms of these species are studied as a simplified model of dental plaque. A prediction model based on principal component analysis and logistic regression is calibrated using pure biofilms of each species and validated on pure biofilms grown months later, achieving 96% accuracy in prospective classification. When biofilms of the two species are partially mixed together, Raman-based identifications are achieved within ~2 μm of the boundaries between species with 97% accuracy. This combination of spatial resolution and predication accuracy should be suitable for forming images of species distributions within intact two-species biofilms.

  17. Rapid species specific identification and subtyping of Yersinia enterocolitica by MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Stephan, Roger; Cernela, Nicole; Ziegler, Dominik; Pflüger, Valentin; Tonolla, Mauro; Ravasi, Damiana; Fredriksson-Ahomaa, Maria; Hächler, Herbert

    2011-11-01

    Yersinia enterocolitica are Gram-negative pathogens and known as important causes of foodborne infections. Rapid and reliable identification of strains of the species Y. enterocolitica within the genus Yersinia and the differentiation of the pathogenic from the non-pathogenic biotypes has become increasingly important. We evaluated here the application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid species identification and subtyping of Y. enterocolitica. To this end, we developed a reference MS database library including 19 Y. enterocolitica (non-pathogenic biotype 1A and pathogenic biotypes 2 and 4) as well as 24 non-Y. enterocolitica strains, belonging to eleven different other Yersinia spp. The strains provided reproducible and unique mass spectra profiles covering a wide molecular mass range (2000 to 30,000 Da). Species-specific and biotype-specific biomarker protein mass patterns were determined for Y. enterocolitica. The defined biomarker mass patterns (SARAMIS SuperSpectrum™) were validated using 117 strains from various Y. enterocolitica bioserotypes in a blind-test. All strains were correctly identified and for all strains the mass spectrometry-based identification scheme yielded identical results compared to a characterization by a combination of biotyping and serotyping. Our study demonstrates that MALDI-TOF-MS is a reliable and powerful tool for the rapid identification of Y. enterocolitica strains to the species level and allows subtyping of strains to the biotype level. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Identification of Meloidogyne species associated with uptall ornamentals plants in Costa Rica

    International Nuclear Information System (INIS)

    Solano-Gonzalez, Stefany; Esquivel-Hernandez, Alejandro; Molina-Bravo, Ramon; Morera-Brenes, Bernal

    2015-01-01

    Nematodes species of the genus Meloidogyne associated with upland ornamental plants were identified. Ten ornamental species in a commercial nursery were sampled in San Isidro, Heredia, Costa Rica between 2011-2012. Morphometric measurements of the stylet length, the trail length, and the hyaline region of J_2s as well as perineal patterns of egg-carrying females were used for identification, Genomic DNA was extracted from single J_2s and molecular analyses were performed by amplifying the intergenic region between cytochrome oxidase subunit II of the COII and the long subunit of the ARN ribosomal genes by PCR-RFLP. Combining these methods allowed identification of five species of nematodes of the genus Meloidogyne (M. arenaria, M. hapla, M. hispanica, M. incognita and M. javanica), and new restriction enzyme patterns were reported for M. hapla and M. javanica using AluI. Additionally a preliminary report of M. hispanica was described by sequencing the 28S and 18S regions. (author) [es

  19. VEGETATIVE MORPHOLOGY FOR SPECIES IDENTIFICATION OF TROPICAL TREES: FAMILY DISTRIBUTION

    Directory of Open Access Journals (Sweden)

    Peter Hargreaves

    2006-03-01

    Full Text Available Tree specimens from the ESAL herbarium of the Universidade Federal de Lavras, Minas Gerais, Brazil, were describedby vegetative characteristics using CARipé, a Microsoft Access database application specially developed for this study. Only onespecimen per species was usually described. Thus, 2 observers described 567 herbarium species as a base to test methods ofidentification as part of a larger study. The present work formed part of that study and provides information on the distribution of22 vegetative characters among 16 families having 10 or more species described. The characters are discussed. The study foundmarked differences, even discontinuities, of distributions of characters between those families. Therefore it should be possible toincorporate phylogenetic relationships into the identification process.

  20. Meat species identification and Halal authentication analysis using mitochondrial DNA.

    Science.gov (United States)

    Murugaiah, Chandrika; Noor, Zainon Mohd; Mastakim, Maimunah; Bilung, Lesley Maurice; Selamat, Jinap; Radu, Son

    2009-09-01

    A method utilizing PCR-restriction fragment length polymorphism (RFLP) in the mitochondrial genes was developed for beef (Bos taurus), pork (Sus scrofa), buffalo (Bubalus bubali), quail (Coturnix coturnix), chicken (Gallus gallus), goat (Capra hircus), rabbit (Oryctolagus cuniculus) species identification and Halal authentication. PCR products of 359-bp were successfully obtained from the cyt b gene of these six meats. AluI, BsaJI, RsaI, MseI, and BstUI enzymes were identified as potential restriction endonucleases to differentiate the meats. The genetic differences within the cyt b gene among the meat were successfully confirmed by PCR-RFLP. A reliable typing scheme of species which revealed the genetic differences among the species was developed.

  1. Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences.

    Science.gov (United States)

    Chattaway, Marie A; Schaefer, Ulf; Tewolde, Rediat; Dallman, Timothy J; Jenkins, Claire

    2017-02-01

    Escherichia coli and Shigella species are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species of Shigella are therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982 Escherichia coli and Shigella sp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasive E. coli isolates that were misidentified as Shigella flexneri or S. boydii by the kmer ID, and 8 were S. flexneri isolates misidentified by TB&S as S. boydii due to nonfunctional S. flexneri O antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising both S. boydii and S. dysenteriae strains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data. Shigella can be differentiated from E. coli and accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species of Shigella, and identified emerging pathoadapted lineages. © Crown copyright 2017.

  2. A Review of the Composition of the Essential Oils and Biological Activities of Angelica Species

    Directory of Open Access Journals (Sweden)

    Kandasamy Sowndhararajan

    2017-09-01

    Full Text Available A number of Angelica species have been used in traditional systems of medicine to treat many ailments. Especially, essential oils (EOs from the Angelica species have been used for the treatment of various health problems, including malaria, gynecological diseases, fever, anemia, and arthritis. EOs are complex mixtures of low molecular weight compounds, especially terpenoids and their oxygenated compounds. These components deliver specific fragrance and biological properties to essential oils. In this review, we summarized the chemical composition and biological activities of EOs from different species of Angelica. For this purpose, a literature search was carried out to obtain information about the EOs of Angelica species and their bioactivities from electronic databases such as PubMed, Science Direct, Wiley, Springer, ACS, Google, and other journal publications. There has been a lot of variation in the EO composition among different Angelica species. EOs from Angelica species were reported for different kinds of biological activities, such as antioxidant, anti-inflammatory, antimicrobial, immunotoxic, and insecticidal activities. The present review is an attempt to consolidate the available data for different Angelica species on the basis of major constituents in the EOs and their biological activities.

  3. Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil

    Directory of Open Access Journals (Sweden)

    Karine Pinto e Vairo

    2011-09-01

    Full Text Available Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.Chave pictórica para a identificação das espécies de Sarcophagidae (Diptera de potencial importância forense do sul do Brasil. Espécies da subfamília Sarcophaginae são importantes para a entomologia forense devido ao seu hábito necrófago. Este trabalho apresenta uma chave pictórica para a identificação de 22 espécies de Sarcophaginae de 10 gêneros encontradas na região sul do Brasil. São fornecidas fotografias dos principais estruturas das espécies, principalmente da terminália masculina.

  4. Biological review of 82 species of coral petitioned to be included in the Endangered Species Act

    Science.gov (United States)

    Brainard, Russell E.; Birkeland, Charles; Eakin, C. Mark; McElhany, Paul; Miller, Margaret W.; Patterson, Matt; Piniak, G.A.

    2011-01-01

    list 83 coral species as threatened or endangered under the U.S. Endangered Species Act. The petition was based on a predicted decline in available habitat for the species, citing anthropogenic climate change and ocean acidification as the lead factors among the various stressors responsible for the potential decline. The NMFS identified 82 of the corals as candidate species, finding that the petition provided substantive information for a potential listing of these species. The NMFS established a Biological Review Team (BRT) to prepare this Status Review Report that examines the status of these 82 candidate coral species and evaluates extinction risk for each of them. This document makes no recommendations for listing, as that is a separate evaluation to be conducted by the NMFS.

  5. Focus stacking technique in identification of forensically important Chrysomya species (Diptera: Calliphoridae

    Directory of Open Access Journals (Sweden)

    Noha A. Elleboudy

    2016-09-01

    Recommendations: Further studies on the blowfly species that occur in Egypt and documentation of their key for identification are recommended to facilitate the diverse applications of these important insects in forensic investigations.

  6. Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species

    OpenAIRE

    Marol Serhat; Yücesoy Mine

    2003-01-01

    Abstract Background The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. Methods A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 ...

  7. CpDNA-based species identification and phylogeography: application to African tropical tree species.

    Science.gov (United States)

    Duminil, J; Heuertz, M; Doucet, J-L; Bourland, N; Cruaud, C; Gavory, F; Doumenge, C; Navascués, M; Hardy, O J

    2010-12-01

    Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations. © 2010 Blackwell Publishing Ltd.

  8. Dendritic cells and skin sensitization: Biological roles and uses in hazard identification

    International Nuclear Information System (INIS)

    Ryan, Cindy A.; Kimber, Ian; Basketter, David A.; Pallardy, Marc; Gildea, Lucy A.; Gerberick, G. Frank

    2007-01-01

    Recent advances have been made in our understanding of the roles played by cutaneous dendritic cells (DCs) in the induction of contact allergy. A number of associated changes in epidermal Langerhans cell phenotype and function required for effective skin sensitization are providing the foundations for the development of cellular assays (using DC and DC-like cells) for skin sensitization hazard identification. These alternative approaches to the identification and characterization of skin sensitizing chemicals were the focus of a Workshop entitled 'Dendritic Cells and Skin Sensitization: Biological Roles and Uses in Hazard Identification' that was given at the annual Society of Toxicology meeting held March 6-9, 2006 in San Diego, California. This paper reports information that was presented during the Workshop

  9. Genus- and species-level identification of dermatophyte fungi by surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Witkowska, Evelin; Jagielski, Tomasz; Kamińska, Agnieszka

    2018-03-01

    This paper demonstrates that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) can serve as a fast and reliable technique for detection and identification of dermatophyte fungi at both genus and species level. Dermatophyte infections are the most common mycotic diseases worldwide, affecting a quarter of the human population. Currently, there is no optimal method for detection and identification of fungal diseases, as each has certain limitations. Here, for the first time, we have achieved with a high accuracy, differentiation of dermatophytes representing three major genera, i.e. Trichophyton, Microsporum, and Epidermophyton. Two first principal components (PC), namely PC-1 and PC-2, gave together 97% of total variance. Additionally, species-level identification within the Trichophyton genus has been performed. PC-1 and PC-2, which are the most diagnostically significant, explain 98% of the variance in the data obtained from spectra of: Trichophyton rubrum, Trichophyton menatgrophytes, Trichophyton interdigitale and Trichophyton tonsurans. This study offers a new diagnostic approach for the identification of dermatophytes. Being fast, reliable and cost-effective, it has the potential to be incorporated in the clinical practice to improve diagnostics of medically important fungi.

  10. Learning About Bird Species on the Primary Level

    Science.gov (United States)

    Randler, Christoph

    2009-04-01

    Animal species identification is often emphasized as a basic prerequisite for an understanding of ecology because ecological interactions are based on interactions between species at least as it is taught on the school level. Therefore, training identification skills or using identification books seems a worthwhile task in biology education, and should already start on the primary level. On the primary level, however, complex interactions could not be taught but pupils are often interested in basic knowledge about species. We developed a hands-on, group-based and self-determined learning phase organized in workstations. About 138 pupils (2nd-4th graders) participated in this study. The two groups received an identification treatment with six different bird species. These were presented either as soft toys or as taxidermy specimen. Both groups scored similar prior and after the treatment (posttest 1) and with a delay of 6-8 weeks (posttest 2). More complex general linear modeling revealed a significant influence of prior knowledge, treatment and of grade (2nd, 3rd or 4th grade) on the first posttest while in the retention test gender differences emerged. We suggest that soft toys may be of equal value for teaching species identification on the primary level compared to natural taxidermic specimen, especially when considering pricing, insensitivity to handling, and contamination with agents used for preservation.

  11. A comparison of the application of a biological and phenetic species concept in the Hebeloma crustuliniforme complex within a phylogenetic framework

    DEFF Research Database (Denmark)

    Aanen, Duur Kornelis; Kuyper, T.W.

    2004-01-01

    a major factor. Intercompatibility tests and DNA based phylogenies indicate that most biological species are very closely related and hence provide support for the claim that correspondence between a biological species concept and a phenetic species concept in the H. crustuliniforme complex is not likely...... biological species in that complex. Based on two nuclear sequences, we present a best estimate of the phylogeny of biological species within the complex. Using this phylogeny, on the basis of strict monophyly only two species can be morphologically recognised among 22 biological species. Relaxing......A method is presented to derive an operational phenetic species concept for the Hebeloma crustuliniforme complex in northwestern Europe. The complex was found to consist of at least 22 biological species (intercompatibility groups; ICGs). Almost none of these biological species could be recognised...

  12. Morphological and biological features of seedlings of some Trifolium species

    Directory of Open Access Journals (Sweden)

    Valentina A. Kalinkina

    2013-04-01

    Full Text Available The author conducted morphological and biological characteristics of seedlings of six species belonging to three sections: Lupinaster(T. lupinasterL, T. pacificumBobr, T. eximium Steph. Ex. DC., Chronosemium(T. campestre Schreb. and Trifolium (T. arvenseL., T. pratense L. of the genus Trifolium. Dimensional and qualitative morphological characteristics of the main structural elements of the seedlings of these species are represented in the article.

  13. Identification of morphological and molecular Aspergillus species isolated from patients based on beta-tubulin gene sequencing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kheirkhah

    2017-06-01

    Full Text Available Background: Aspergillus species are opportunistic pathogens among immunocompromised patients. In terms of pathogenesis and mycotoxin production, they are in great value. The aim of the this study was to evaluate of beta-tubulin gene for identification of clinical Aspergillus species by PCR-sequencing method compared to morphological features of clinical isolates (such as conidial shape in direct microscopic examination, colony shape in culture, and physiological tests. Materials and Methods: In this study, 465 patients referred to the Shefa laboratory of Isfahan were evaluated. Morphological and molecular identification of clinical samples were performed using culture on sabouraud agar, malt extract agar, czapekdox agar, direct microscopy, and PCR-sequencing of beta tubulin gene, respectively. Sequences were analyzed in comparison with gene bank data. Results: Thirty nine out of 465 suspected cases (8.4% had aspergillosis. The most prevalent species were Aspergillus flavus (56.4%, A. oryzae (20.5%, and A. fumigatus (10.2%, respectively. Fifty nine percent of patients were females and 49% were males. Conclusion: In comparison with phenotypic tests, sequencing of beta-tubulin gene for identification of Aspergillus species is at great value. Replacement of molecular techniques with conventional tests is recommended for precise identification of microorganism for better management of infection.

  14. Identification of Meloidogyne species associated with upland ornamentals plants in Costa Rica.

    Directory of Open Access Journals (Sweden)

    Stefany Solano-González

    2015-06-01

    Full Text Available The objective of this study was to identify nematodes species of the genus Meloidogyne associated with upland ornamental plants. We sampled ten ornamental species in a commercial nursery in San Isidro, Heredia, Costa Rica between 2011-2012. Morphometric measurements of the stylet length, the tail length, and the hyaline region of J2s, as well as perineal patterns of egg-carrying females were used for identification, Genomic DNA was extracted from single J2s and molecular analyses were performed by amplifying the intergenic region between cytochrome oxidase subunit II of the COII and the long subunit of the ARN ribosomal genes by PCR-RFLP. Combining these methods allowed identification of five species of nematodes of the genus Meloidogyne (M. arenaria, M. hapla, M. hispanica, M. incognita and M. javanica, and new restriction enzyme patterns were reported for M. hapla and M. javanica using AluI. Additionally, a preliminary report of M. hispanica was described by sequencing the 28S and 18S regions.

  15. Examining the effectiveness of discriminant function analysis and cluster analysis in species identification of male field crickets based on their calling songs.

    Directory of Open Access Journals (Sweden)

    Ranjana Jaiswara

    Full Text Available Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species

  16. Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

    DEFF Research Database (Denmark)

    Smolina, I.; Kollias, S.; Poortvliet, M.

    2014-01-01

    Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers t...

  17. BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

    Directory of Open Access Journals (Sweden)

    Abi S.A. Marques

    2008-01-01

    Full Text Available The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662 and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.

  18. Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

    Science.gov (United States)

    Feng, Shang-Guo; Lu, Jiang-Jie; Gao, Ling; Liu, Jun-Jun; Wang, Hui-Zhong

    2014-04-01

    Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

  19. Description and identification of four species of plant parasitic nematodes associated with grassland, fruit trees and maize in Romania.

    Science.gov (United States)

    Badi, M; Geraert, E

    2002-01-01

    Three species of plant parasitic nematodes present in two romanian soil samples were described and identified in the present study. The species belong to order tylenchida and to taxonomical families Tylenchidae (Basiria aberrans) and Belonolaimidae (Tylenchorhynchus georgiensis and Merlinius brevidens). The identification of the present specimens was based on the classical taxonomy, following morphological and morphometrical characters in the species specific identification keys.

  20. Evaluation of matrix-assisted laser desorption/ionization time-of-fight mass spectrometry for identification of 345 clinical isolates of Aspergillus species from 11 Korean hospitals: comparison with molecular identification.

    Science.gov (United States)

    Park, Ju Heon; Shin, Jong Hee; Choi, Min Ji; Choi, Jin Un; Park, Yeon-Joon; Jang, Sook Jin; Won, Eun Jeong; Kim, Soo Hyun; Kee, Seung Jung; Shin, Myung Geun; Suh, Soon Pal

    2017-01-01

    We evaluated the ability of the Filamentous Fungi Library 1.0 of the MALDI-TOF MS Biotyper system to identify 345 clinical Aspergillus isolates from 11 Korean hospitals. Compared with results of the internal transcribed spacer region sequencing, the frequencies of correct identification at the species-complex level were 94.5% and 98.8% with cutoff values of 2.0 and 1.7, respectively. Compared with results of β-tubulin gene sequencing, the frequencies of correct identification at the species level were 96.0% (cutoff 2.0) and 100% (cutoff 1.7) for 303 Aspergillus isolates of five common, non-cryptic species, but only 4.8% (cutoff 1.7) and 0% (cutoff 2.0) for 42 Aspergillus isolates of six cryptic species (identifiable by β-tubulin or calmodulin sequencing). These results show that the MALDI Biotyper using the Filamentous Fungi Library version 1.0 enables reliable identification of the majority of common clinical Aspergillus isolates, although the database should be expanded to facilitate identification of cryptic species. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Identification of four squid species by quantitative real-time polymerase chain reaction.

    Science.gov (United States)

    Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

    2016-02-01

    Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

    DEFF Research Database (Denmark)

    Hwang, Kyu-Sang; Kim, Hyun Uk; Charusanti, Pep

    2014-01-01

    Streptomyces species continue to attract attention as a source of novel medicinal compounds. Despite a long history of studies on these microorganisms, they still have many biochemical mysteries to be elucidated. Investigations of novel secondary metabolites and their biosynthetic gene clusters...... collected in the form of databases and knowledgebases, providing predictive information and enabling one to explore experimentally unrecognized biological spaces of secondary metabolism. Herein, we review recent trends in the systems biology and biotechnology of Streptomyces species....

  3. Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology.

    Science.gov (United States)

    Margaritelis, Nikos V; Cobley, James N; Paschalis, Vassilis; Veskoukis, Aristidis S; Theodorou, Anastasios A; Kyparos, Antonios; Nikolaidis, Michalis G

    2016-04-01

    The equivocal role of reactive species and redox signaling in exercise responses and adaptations is an example clearly showing the inadequacy of current redox biology research to shed light on fundamental biological processes in vivo. Part of the answer probably relies on the extreme complexity of the in vivo redox biology and the limitations of the currently applied methodological and experimental tools. We propose six fundamental principles that should be considered in future studies to mechanistically link reactive species production to exercise responses or adaptations: 1) identify and quantify the reactive species, 2) determine the potential signaling properties of the reactive species, 3) detect the sources of reactive species, 4) locate the domain modified and verify the (ir)reversibility of post-translational modifications, 5) establish causality between redox and physiological measurements, 6) use selective and targeted antioxidants. Fulfilling these principles requires an idealized human experimental setting, which is certainly a utopia. Thus, researchers should choose to satisfy those principles, which, based on scientific evidence, are most critical for their specific research question. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Broad spectrum microarray for fingerprint-based bacterial species identification

    Directory of Open Access Journals (Sweden)

    Frey Jürg E

    2010-02-01

    Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

  5. Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

    Science.gov (United States)

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

    2017-10-17

    Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.

  6. Comparison of traditional phenotypic identification methods with partial 5' 16S rRNA gene sequencing for species-level identification of nonfermenting Gram-negative bacilli.

    Science.gov (United States)

    Cloud, Joann L; Harmsen, Dag; Iwen, Peter C; Dunn, James J; Hall, Gerri; Lasala, Paul Rocco; Hoggan, Karen; Wilson, Deborah; Woods, Gail L; Mellmann, Alexander

    2010-04-01

    Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5' 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify NFB.

  7. Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations.

    Science.gov (United States)

    Speller, Camilla F; Nicholas, George P; Yang, Dongya Y

    2011-07-28

    The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis. By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardea herodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique. By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.

  8. South African Helichrysum species: a review of the traditional uses, biological activity and phytochemistry.

    Science.gov (United States)

    Lourens, A C U; Viljoen, A M; van Heerden, F R

    2008-10-28

    In South Africa, the genus Helichrysum is widely used in traditional medicine. The uses are well documented although renaming of species and the resulting confusing taxonomic nomenclature may cause uncertainty as to which specific species was referred to in some reports. The aim of this paper is to present a collated and coherent overview of the documented traditional uses of Helichrysum species and to update the botanical identity of previously studied species. Databases (Scifinder, ISI Web of Knowledge) and several books were used to collect in information on South African Helichrysum species. The traditional uses, chemistry and biological activity of Helichrysum species have been summarized. It was attempted to give clarity as to exactly which species is refer to in the ethnobotanical literature. Although a large number of ethnopharmacological uses have been documented and the chemistry of the genus has been studied extensively, only a few South African species have been investigated for their biological activity.

  9. Molecular identification and genotyping of Microsporidia in selected hosts

    Czech Academy of Sciences Publication Activity Database

    Valenčáková, A.; Balent, P.; Ravaszová, P.; Horák, Aleš; Oborník, Miroslav; Halanová, M.; Malčeková, B.; Novotný, F.; Goldová, M.

    2012-01-01

    Roč. 110, č. 2 (2012), s. 689-693 ISSN 0932-0113 Institutional research plan: CEZ:AV0Z60220518 Keywords : ENCEPHALITOZOON-CUNICULI * RIBOSOMAL-RNA * SPECIES IDENTIFICATION * AIDS PATIENTS * PET RABBITS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.852, year: 2012

  10. Molecular detection and species-specific identification of medically important Aspergillus species by real-time PCR in experimental invasive pulmonary aspergillosis.

    Science.gov (United States)

    Walsh, Thomas J; Wissel, Mark C; Grantham, Kevin J; Petraitiene, Ruta; Petraitis, Vidmantas; Kasai, Miki; Francesconi, Andrea; Cotton, Margaret P; Hughes, Johanna E; Greene, Lora; Bacher, John D; Manna, Pradip; Salomoni, Martin; Kleiboeker, Steven B; Reddy, Sushruth K

    2011-12-01

    Diagnosis of invasive pulmonary aspergillosis (IPA) remains a major challenge to clinical microbiology laboratories. We developed rapid and sensitive quantitative PCR (qPCR) assays for genus- and species-specific identification of Aspergillus infections by use of TaqMan technology. In order to validate these assays and understand their potential diagnostic utility, we then performed a blinded study of bronchoalveolar lavage (BAL) fluid specimens from well-characterized models of IPA with the four medically important species. A set of real-time qPCR primers and probes was developed by utilizing unique ITS1 regions for genus- and species-specific detection of the four most common medically important Aspergillus species (Aspergillus fumigatus, A. flavus, A. niger, and A. terreus). Pan-Aspergillus and species-specific qPCRs with BAL fluid were more sensitive than culture for detection of IPA caused by A. fumigatus in untreated (P < 0.0007) and treated (P ≤ 0.008) animals, respectively. For infections caused by A. terreus and A. niger, culture and PCR amplification from BAL fluid yielded similar sensitivities for untreated and treated animals. Pan-Aspergillus PCR was more sensitive than culture for detection of A. flavus in treated animals (P = 0.002). BAL fluid pan-Aspergillus and species-specific PCRs were comparable in sensitivity to BAL fluid galactomannan (GM) assay. The copy numbers from the qPCR assays correlated with quantitative cultures to determine the pulmonary residual fungal burdens in lung tissue. Pan-Aspergillus and species-specific qPCR assays may improve the rapid and accurate identification of IPA in immunocompromised patients.

  11. [Identification of mycobacteria to the species level by molecular methods in the Public Health Laboratory of Bogotá, Colombia].

    Science.gov (United States)

    Hernández-Toloza, Johana Esther; Rincón-Serrano, María de Pilar; Celis-Bustos, Yamile Adriana; Aguillón, Claudia Inés

    2016-01-01

    Global epidemiology of non-tuberculous mycobacteria (NTM) is unknown due to the fact that notification is not required in many countries, however the number of infection reports and outbreaks caused by NTM suggest a significant increase in the last years. Traditionally, mycobacteria identification is made through biochemical profiles which allow to differentiate M. tuberculosis from NTM, and in some cases the mycobacteria species. Nevertheless, these methods are technically cumbersome and time consuming. On the other hand, the introduction of methods based on molecular biology has improved the laboratory diagnosis of NTM. To establish the NTM frequency in positive cultures for acid-fast bacilli (AAFB) which were sent to Laboratorio de Salud Pública de Bogotá over a 12 month period. A total of 100 positive cultures for acid-fast bacilli from public and private hospitals from Bogotá were identified by both biochemical methods and the molecular methods PRA (PCR-restriction enzyme analysis) and multiplex-PCR. Furthermore, low prevalence mycobacteria species and non-interpretable results were confirmed by 16SrDNA sequentiation analysis. Identification using the PRA method showed NMT occurrence in 11% of cultures. In addition, this molecular methodology allowed to detect the occurrence of more than one mycobacteria in 4% of the cultures. Interestingly, a new M. kubicae pattern of PCR-restriction analysis is reported in our study. Using a mycobacteria identification algorithm, which includes the molecular method PRA, improves the diagnostic power of conventional methods and could help to advance both NTM epidemiology knowledge and mycobacteriosis control. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  12. DNA Barcoding: Amplification and sequence analysis of rbcl and matK genome regions in three divergent plant species

    Directory of Open Access Journals (Sweden)

    Javed Iqbal Wattoo

    2016-11-01

    Full Text Available Background: DNA barcoding is a novel method of species identification based on nucleotide diversity of conserved sequences. The establishment and refining of plant DNA barcoding systems is more challenging due to high genetic diversity among different species. Therefore, targeting the conserved nuclear transcribed regions would be more reliable for plant scientists to reveal genetic diversity, species discrimination and phylogeny. Methods: In this study, we amplified and sequenced the chloroplast DNA regions (matk+rbcl of Solanum nigrum, Euphorbia helioscopia and Dalbergia sissoo to study the functional annotation, homology modeling and sequence analysis to allow a more efficient utilization of these sequences among different plant species. These three species represent three families; Solanaceae, Euphorbiaceae and Fabaceae respectively. Biological sequence homology and divergence of amplified sequences was studied using Basic Local Alignment Tool (BLAST. Results: Both primers (matk+rbcl showed good amplification in three species. The sequenced regions reveled conserved genome information for future identification of different medicinal plants belonging to these species. The amplified conserved barcodes revealed different levels of biological homology after sequence analysis. The results clearly showed that the use of these conserved DNA sequences as barcode primers would be an accurate way for species identification and discrimination. Conclusion: The amplification and sequencing of conserved genome regions identified a novel sequence of matK in native species of Solanum nigrum. The findings of the study would be applicable in medicinal industry to establish DNA based identification of different medicinal plant species to monitor adulteration.

  13. Hazard identification and risk assessment for biologics targeting the immune system.

    Science.gov (United States)

    Weir, Andrea B

    2008-01-01

    Biologic pharmaceuticals include a variety of products, such as monoclonal antibodies, fusion proteins and cytokines. Products in those classes include immunomodulatory biologics, which are intended to enhance or diminish the activity of the immune system. Immunomodulatory biologics have been approved by the U.S. FDA for a variety of indications, including cancer and inflammatory conditions. Prior to gaining approval for marketing, sponsoring companies for all types of products must demonstrate a product's safety in toxicology studies conducted in animals and show safety and efficacy in clinical trials conducted in patients. The overall goal of toxicology studies, which applies to immunomodulatory and other product types, is to identify the hazards that products pose to humans. Because biologics are generally highly selective for specific targets (receptors/epitopes), conducting toxicology studies in animal models with the target is essential. Such animals are referred to as pharmacologically relevant. Endpoints routinely included in toxicology studies, such as hematology, organ weight and histopathology, can be used to assess the effect of a product on the structure of the immune system. Additionally, specialized endpoints, such as immunophenotyping and immune function tests, can be used to define effects of immunomodulatory products on the immune system. Following hazard identification, risks posed to patients are assessed and managed. Risks can be managed through clinical trial design and risk communication, a practice that applies to immunomodulatory and other product types. Examples of risk management in clinical trial design include establishing a safe starting dose, defining the appropriate patient population and establishing appropriate patient monitoring. Risk communication starts during clinical trials and continues after product approval. A combination of hazard identification, risk assessment and risk management allows for drug development to proceed

  14. Cross-species genome-wide identification of evolutionary conserved microproteins

    DEFF Research Database (Denmark)

    Straub, Daniel; Wenkel, Stephan

    2017-01-01

    Protein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known micro...... act in plant transcriptional regulation, signal transduction and anatomical structure development. MiPFinder is freely available to find microProteins in any genome and will aid in the identification of novel microProteins in plants and animals....

  15. Molecular identification of broomrape species from a single seed by High Resolution Melting analysis

    Directory of Open Access Journals (Sweden)

    Mathieu Rolland

    2016-12-01

    Full Text Available Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (P. aegyptiaca, O. cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90 %. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples. The described assay fulfils its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.

  16. Toxocariasis in Carnivora from Argentinean Patagonia: Species molecular identification, hosts, and geographical distribution

    Directory of Open Access Journals (Sweden)

    R.M. Vega

    2018-04-01

    Full Text Available Twenty four specimens of seven species belonging to the families Felidae, Mustelidae, and Canidae were obtained in Lanín and Nahuel Huapi National Parks from March 1996 to April 2016. Specimens were processed by necropsy in order to contribute to the knowledge of toxocariasis in wild carnivores of Argentinean Patagonia. The only Puma concolor and the seven Leopardus geoffroyi were positive for Toxocara cati. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP of the ITS-1 region from larval and adult DNA was carried out to confirm parasite species identification. This is the first molecular determination of T. cati from wild felids in Argentina and the study also fill gaps about the spatial distribution and hosts for Toxocara cati. Keywords: Toxocara cati, Puma concolor, Leopardus geoffroyi, Molecular identification, Argentina

  17. Forensic timber identification: a case study of a CITES listed species, Gonystylus bancanus (Thymelaeaceae).

    Science.gov (United States)

    Ng, Kevin Kit Siong; Lee, Soon Leong; Tnah, Lee Hong; Nurul-Farhanah, Zakaria; Ng, Chin Hong; Lee, Chai Ting; Tani, Naoki; Diway, Bibian; Lai, Pei Sing; Khoo, Eyen

    2016-07-01

    Illegal logging and smuggling of Gonystylus bancanus (Thymelaeaceae) poses a serious threat to this fragile valuable peat swamp timber species. Using G. bancanus as a case study, DNA markers were used to develop identification databases at the species, population and individual level. The species level database for Gonystylus comprised of an rDNA (ITS2) and two cpDNA (trnH-psbA and trnL) markers based on a 20 Gonystylus species database. When concatenated, taxonomic species recognition was achieved with a resolution of 90% (18 out of the 20 species). In addition, based on 17 natural populations of G. bancanus throughout West (Peninsular Malaysia) and East (Sabah and Sarawak) Malaysia, population and individual identification databases were developed using cpDNA and STR markers respectively. A haplotype distribution map for Malaysia was generated using six cpDNA markers, resulting in 12 unique multilocus haplotypes, from 24 informative intraspecific variable sites. These unique haplotypes suggest a clear genetic structuring of West and East regions. A simulation procedure based on the composition of the samples was used to test whether a suspected sample conformed to a given regional origin. Overall, the observed type I and II errors of the databases showed good concordance with the predicted 5% threshold which indicates that the databases were useful in revealing provenance and establishing conformity of samples from West and East Malaysia. Sixteen STRs were used to develop the DNA profiling databases for individual identification. Bayesian clustering analyses divided the 17 populations into two main genetic clusters, corresponding to the regions of West and East Malaysia. Population substructuring (K=2) was observed within each region. After removal of bias resulting from sampling effects and population subdivision, conservativeness tests showed that the West and East Malaysia databases were conservative. This suggests that both databases can be used independently

  18. MORPHOLOGICAL AND MOLECULAR IDENTIFICATION OF Fusarium SPECIES AND THEIR PATHOGENICITY FOR WHEAT

    Directory of Open Access Journals (Sweden)

    Jelena Poštić

    2012-12-01

    Full Text Available From the root and lower stem parts of weeds and plant debris of maize, wheat, oat and sunflower we isolated 300 isolates of Fusarium spp. and performed morphological and molecular identification. With molecular identification using AFLP method we determined 14 Fusarium species: F. acuminatum, F. avenaceum, F. concolor, F. crookwellense, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. semitectum, F. solani, F. sporotrichioides, F. subglutinans, F. venenatum and F. verticillioides.By comparing results of morphological and molecular identification we found out that determination of 16,7% isolates was incorrect. Out of 300 isolates identified with molecular methods, 50 did not belong to the species determined with morphological determination.With pathogenicity tests of 30 chosen Fusarium isolates we determined that many of them were pathogenic to wheat and maize seedlings and to wheat heads. The most pathogenic were isolates of F. graminearum from A. retroflexus, A. theophrasti and C. album, F. venenatum from maize debris and and A. theophrasti, F. crookwellense from A. lappa. Antifungal influence of 11 essential oils on mycelia growth and sporulation of chosen Fusarium isolates determined that essential oils of T. vulgaris, P. anisum and E. caryophyllus had the strongest effect on mycelial growth. Influence of essential oils on sporulation was not statistically significant.

  19. Brine shrimp bioassay: importance of correct taxonomic identification of Artemia (Anostraca) species.

    Science.gov (United States)

    Ruebhart, David R; Cock, Ian E; Shaw, Glen R

    2008-08-01

    Despite the common use of the brine shrimp bioassay in toxicology, there is confusion in the literature regarding citation of the correct taxonomic identity of the Artemia species used. The genus Artemia, once thought to be represented by a single species Artemia salina, is now known to be composed of several bisexual species as well as parthenogenetic populations. Artemia franciscana is the best studied of the Artemia species and is considered to represent the vast majority of studies in which Artemia is used as an experimental test organism. We found that in studies referring to the use of A. salina, the zoogeography of the cyst harvest site indicated that the species used was actually A. franciscana. Those performing bioassays with Artemia need to exercise diligence in assigning correct species identification, as the identity of the test organism is an important parameter in assuring the validity of the results of the assay.

  20. PCR-based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa

    Science.gov (United States)

    Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainabl...

  1. Identification of important nodes in directed biological networks: a network motif approach.

    Directory of Open Access Journals (Sweden)

    Pei Wang

    Full Text Available Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA, this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine.

  2. Identification / characterisation and authentication of microbial strains by MALDI-TOF ICMS

    OpenAIRE

    Santos, C.; Lima, Nelson

    2011-01-01

    The identification of species is an important goal in microbial taxonomy. Information about each microorganism (e.g. morphological description, physiological and biochemical properties, molecular biology sequencings, ecological roles, and societal risks or benefits) is key element in this process. Identifications can been a long and seemingly never-ended process with frequent revisions of the taxonomic schemes. The application of sound tolls to smooth the progress of identifica...

  3. Stochastic dynamics for two biological species and ecological niches

    Science.gov (United States)

    Ruziska, Flávia M.; Arashiro, Everaldo; Tomé, Tânia

    2018-01-01

    We consider an ecological system in which two species interact with two niches. To this end we introduce a stochastic model with four states. Our analysis is founded in three approaches: Monte Carlo simulations of the model on a square lattice, mean-field approximation, and birth and death master equation. From this last approach we obtain a description in terms of Langevin equations which show in an explicit way the role of noise in population biology. We focus mainly on the description of time oscillations of the species population and the alternating dominance between them. The model treated here may provide insights on these properties.

  4. Potentials of single-cell biology in identification and validation of disease biomarkers.

    Science.gov (United States)

    Niu, Furong; Wang, Diane C; Lu, Jiapei; Wu, Wei; Wang, Xiangdong

    2016-09-01

    Single-cell biology is considered a new approach to identify and validate disease-specific biomarkers. However, the concern raised by clinicians is how to apply single-cell measurements for clinical practice, translate the message of single-cell systems biology into clinical phenotype or explain alterations of single-cell gene sequencing and function in patient response to therapies. This study is to address the importance and necessity of single-cell gene sequencing in the identification and development of disease-specific biomarkers, the definition and significance of single-cell biology and single-cell systems biology in the understanding of single-cell full picture, the development and establishment of whole-cell models in the validation of targeted biological function and the figure and meaning of single-molecule imaging in single cell to trace intra-single-cell molecule expression, signal, interaction and location. We headline the important role of single-cell biology in the discovery and development of disease-specific biomarkers with a special emphasis on understanding single-cell biological functions, e.g. mechanical phenotypes, single-cell biology, heterogeneity and organization of genome function. We have reason to believe that such multi-dimensional, multi-layer, multi-crossing and stereoscopic single-cell biology definitely benefits the discovery and development of disease-specific biomarkers. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  5. Identification of fine-leaved species of genus Festuca by molecular methods

    International Nuclear Information System (INIS)

    Stukonis, V.; Armoniene, R.; Kemesyte, V.

    2015-01-01

    Festuca (L.) is a taxonomically complex genus of family Poaceae. The fine-leaved species of fescue are well adapted to grow in sandy and dry habitats, therefore, they can be used for establishment of lawns of minimal maintenance as well as recultivations of damaged soils. Breeding for the new varieties to meet these purposes requires reliable methods for identification of the species. The discrimination of fine-leaved fescue species based on morphological features is rather difficult, therefore reliable molecular marker would greatly facilitate it and eliminate the need to wait till floral organs are fully formed. Seven fine-leaved species of genus Festuca collected in Lithuania, namely, F. ovina, F. trachyphylla, F. polesica, F. psammophila, F. sabulosa, F. pseudovina and F. wolgensis were investigated at the Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry. The ISSR markers, seed storage proteins and isozymes were tested for their ability to distinguish between the fine-leaved species of the genus Festuca. Seed storage protein and ISSR fingerprint profiles could be used to distinguish between fine-leaved species of Festuca, except for closely related F. sabulosa and F. polesica species. Isozyme fingerprints did not contain sufficient number of species specific bands and were not feasible to discriminate between species. (author)

  6. The influence of culture conditions on the identification of Mycobacterium species by MALDI-TOF MS profiling.

    Science.gov (United States)

    Balážová, Tereza; Makovcová, Jitka; Šedo, Ondrej; Slaný, Michal; Faldyna, Martin; Zdráhal, Zbyněk

    2014-04-01

    Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) represents a simple reliable approach for rapid bacterial identification based on specific peptide/protein fingerprints. However, cell-wall characteristics of mycobacterial species, and their well known stability, complicate MALDI-TOF MS profiling analysis. In this study, we tested two recently published protocols for inactivation and disruption of mycobacteria, and we also examined the influence of different culture conditions (four culture media and five cultivation times) on mass spectral quality and the discriminatory power of the method. We found a significant influence of sample pretreatment method and culture medium on species identification and differentiation for a total of 10 strains belonging to Mycobacterium phlei and Mycobacterium smegmatis. Optimum culture conditions yielding the highest identification success rate against the BioTyper database (Bruker Daltonics) and permitting the possibility of automatic acquisition of mass spectra were found to be distinct for the two mycobacterial species examined. Similarly, individual changes in growth conditions had diverse effects on the two species. For these reasons, thorough control over cultivation conditions should always be employed to maximize the performance and discriminatory power of MALDI-TOF MS profiling, and cultivation conditions must be optimized separately for individual groups of mycobacterial species/strains. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  7. A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification.

    Science.gov (United States)

    Szemiako, Kasjan; Śledzińska, Anna; Krawczyk, Beata

    2017-08-01

    Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.

  8. Identification of most tolerant lichen species to vehicular traffic's pollutants at Batu Pahat area

    Science.gov (United States)

    Khairuddin, Nur Ain; Muhammad, Norhayati; Hashim, Nor Haslina; Yusof, Hasliza; Jusoh, Samsiah; Abas, Azlan; Talip, Balkis A.; Abdullah, Norazlin; Din, Laily B.

    2017-10-01

    Bio-indicators are organisms that can be used for the identification and qualitative determination of human generated environmental factors. The decreasing population of sensitive lichens in specific regions around the world due to low air quality level has make lichens as a bio-indicator for air pollution. Lichen is a result of symbiotic association of fungus and alga and well known for having wide variety of sensitivity towards environmental stressors such as air quality and climate change. The aim of this study is to identify the most tolerant lichen species to vehicular traffic's pollutant at Batu Pahat urban and suburban areas. This study was conducted by using Index of Atmospheric Purity (IAP) method and followed by morphological and chemicals testing for species identification. Dirinaria picta has been identified as the most tolerant lichen species against pollutants from vehicle traffic. The results also indicated that the air quality of Batu Pahat town/urban area could be considered as moderately clean.

  9. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures.

    Directory of Open Access Journals (Sweden)

    Francesca Bertolini

    Full Text Available The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43% in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97 and lower for avian species (0.70. PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.

  10. 76 FR 59661 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2011-09-27

    ...; Charleston, SC; and Madeira Beach, FL. The Protected Species Safe Handling, Release, and Identification....-4 p.m., Madeira Beach City Hall, 300 Municipal Drive, Madeira Beach, FL 33708. Registration To...

  11. Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.

    Directory of Open Access Journals (Sweden)

    Atsushi Ebihara

    Full Text Available BACKGROUND: DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking. METHODOLOGY/PRINCIPAL FINDINGS: The Japanese pteridophyte flora (733 taxa including subspecies and varieties was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0% taxa for rbcL and 617 (84.2% taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52% was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only. CONCLUSIONS/SIGNIFICANCE: This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially

  12. Detection and Identification of Bursaphelenchus Species with DNA Fingerprinting and Polymerase Chain Reaction

    OpenAIRE

    Harmey, Judith H.; Harmey, Matthew A.

    1993-01-01

    We have evaluated the potential of DNA-based methods to identify and differentiate Bursaphelenchus spp. and isolates. The isolation of a DNA probe, designated X14, and development of a DNA fingerprinting method for the identification and differentiation of Bursaphelenchus species and strains is described. Polymerase chain reaction (PCR) amplification of DNA isolated from Bursaphelenchus species using two primers derived from the sequence of the cloned repetitive DNA fragment X14 resulted in m...

  13. An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

    Science.gov (United States)

    Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

    2006-10-01

    Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

  14. Identification of Yeast Species In the Oral Cavity of Iranian Soldiers By Disk Diffusion Method

    Directory of Open Access Journals (Sweden)

    M. Imami

    2008-02-01

    Full Text Available Background:The disk diffusion method for identification of yeasts species was performed based on different but distinct susceptibilities of yeasts spp.to chemicals:janus green, ethidium bromide,2,3,5-triphenyltetrazolium chloride, brilliant green, cycloheximide and rhodamine 6G. Methods: Atotal of 568 Iranian soldiers went under study for isolation and identification of Yeast species from their oral cavity. Asterile swab was used for each individual and specimens were collected from the nasopharynx region, then inoculated to petri dishes containing Sabouraud Dextrose Agar and incubated for 48 hrs at 37 °C. All colonies were counted and stocked in distilled water and stored in a refrigerator for further analysis. The yeasts were identified by the “disk diffusion test” [6,8]. This is a simple, rapid, accurate, and inexpensive technique presented by Sobczak [8]. By this method we identified yeast species within 24-48 hrs. Results: 51.4% of petri dishes were positive for yeast species and 318 strains were identified. Candida albicans, Candida kefyr, Candida tropicalis and Candida guilliermondii were the most common yeast species isolated from the oral cavity of soldiers. Conclusion: We used this method because of its simplicity and other beneficial characteristics for rapid identification of large and numerous isolates and the results were compared with other morphological characters such as chlamydospore and germ tube production. In addition,we used some type strains (Candida parapsilosis: PTCC 5089,Candida tropicalis: PTCC 5028,Saccharomyces cerevisiae:PTCC 5052,Candida lipolytica: PTCC 5063,Candida lipolytica:PTCC 5064,and the results were acceptable.

  15. The Influence of the Academic Conservation Biology Literature on Endangered Species Recovery Planning

    Directory of Open Access Journals (Sweden)

    John Stinchcombe

    2002-12-01

    Full Text Available Despite the volume of the academic conservation biology literature, there is little evidence as to what effect this work is having on endangered species recovery efforts. Using data collected from a national review of 136 endangered and threatened species recovery plans, we evaluated whether recovery plans were changing in response to publication trends in four areas of the academic conservation biology literature: metapopulation dynamics, population viability analysis, conservation corridors, and conservation genetics. We detected several changes in recovery plans in apparent response to publication trends in these areas (e.g., the number of tasks designed to promote the recovery of an endangered species shifted, although these tasks were rarely assigned a high priority. Our results indicate that, although the content of endangered species recovery plans changes in response to the literature, results are not uniform across all topics. We suggest that academic conservation biologists need to address the relative importance of each topic for conservation practice in different settings. [See Erratum

  16. Species identification and molecular typing of human Brucella isolates from Kuwait.

    Science.gov (United States)

    Mustafa, Abu S; Habibi, Nazima; Osman, Amr; Shaheed, Faraz; Khan, Mohd W

    2017-01-01

    Brucellosis is a zoonotic disease of major concern in Kuwait and the Middle East. Human brucellosis can be caused by several Brucella species with varying degree of pathogenesis, and relapses are common after apparently successful therapy. The classical biochemical methods for identification of Brucella are time-consuming, cumbersome, and provide information limited to the species level only. In contrast, molecular methods are rapid and provide differentiation at intra-species level. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-8, MLVA-11 and MLVA-16 were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. 16S rRNA gene sequencing of all isolates showed 90-99% sequence identity with B. melitensis and real-time PCR with genus- and species- specific primers identified all isolates as B. melitensis. The results of ERIC-PCR suggested the existence of 75 ERIC genotypes of B. melitensis with a discriminatory index of 0.997. Cluster classification of these genotypes divided them into two clusters, A and B, diverging at ~25%. The maximum number of genotypes (n = 51) were found in cluster B5. MLVA-8 analysis identified all isolates as B. melitensis, and MLVA-8, MLVA-11 and MLVA-16 typing divided the isolates into 10, 32 and 71 MLVA types, respectively. Furthermore, the combined minimum spanning tree analysis demonstrated that, compared to MLVA types discovered all over the world, the Kuwaiti isolates were a distinct group of MLVA-11 and MLVA-16 types in the East Mediterranean Region.

  17. Morphology of caterpillars and pupae of European Maculinea species (Lepidoptera: Lycaenidae) with an identification table

    DEFF Research Database (Denmark)

    Sliwinska, Ewa B.; Nowicki, Piotr; Nash, David Richard

    2006-01-01

    the caterpillars of these species for effective conservation. We present the morphology of the larvae and pupae of these three species, and a simple key to their identification. Inter-specific differences among larvae and pupae, and within-species differences among larval instars, are underlined in order to enable...

  18. Comparison of three methods for identification of pathogenic Neisseria species

    Energy Technology Data Exchange (ETDEWEB)

    Appelbaum, P.C.; Lawrence, R.B.

    1979-05-01

    A radiometric procedure was compared with the Minitek and Cystine Trypticase Agar sugar degradation methods for identification of 113 Neisseria species (58 Neisseria meningitidis, 51 Neisseria gonorrhoeae, 2 Neisseria lactamica, 2 Neisseria sicca). Identification of meningococci and gonoccoi was confirmed by agglutination and fluorescent antibody techniques, respectively. The Minitek method identified 97% of meningococci, 92% of gonococci, and 100% of other Neisseria after 4 h of incubation. The radiometric (Bactec) procedure identified 100% of gonococci and 100% of miscellaneous Neisseria after 3 h, but problems were encountered with meningococci: 45% of the later strains yielded index values for fructose between 20 and 28 (recommended negative cut-off point, less than 20), with strongly positive (greater than 100) glucose and maltose and negative o-nitrophenyl-beta-0-galactopyranoside reactions in all 58 strains. The Cystine Trypticase Agar method identified 91% of meningococci, ases.

  19. Identification of listeria species isolated in Tunisia by Microarray based assay : results of a preliminary study

    International Nuclear Information System (INIS)

    Hmaied, Fatma; Helel, Salma; Barkallah, Insaf; Leberre, V.; Francois, J.M.; Kechrid, A.

    2008-01-01

    Microarray-based assay is a new molecular approach for genetic screening and identification of microorganisms. We have developed a rapid microarray-based assay for the reliable detection and discrimination of Listeria spp. in food and clinical isolates from Tunisia. The method used in the present study is based on the PCR amplification of a virulence factor gene (iap gene). the PCR mixture contained cyanine Cy5labeled dCTP. Therefore, The PCR products were fluorescently labeled. The presence of multiple species-specific sequences within the iap gene enabled us to design different oligoprobes per species. The species-specific sequences of the iap gene used in this study were obtained from genBank and then aligned for phylogenetic analysis in order to identify and retrieve the sequences of homologues of the amplified iap gene analysed. 20 probes were used for detection and identification of 22 food isolates and clinical isolates of Listeria spp (L. monocytogenes, L. ivanovi), L. welshimeri, L. seeligeri, and L. grayi). Each bacterial gene was identified by hybridization to oligoprobes specific for each Listeria species and immobilized on a glass surface. The microarray analysis showed that 5 clinical isolates and 2 food isolates were identified listeria monocytogenes. Concerning the remaining 15 food isolates; 13 were identified listeria innocua and 2 isolates could not be identified by microarray based assay. Further phylogenetic and molecular analysis are required to design more species-specific probes for the identification of Listeria spp. Microarray-based assay is a simple and rapid method used for Listeria species discrimination

  20. Identification of Candida species isolated from vulvovaginitis in Mashhad, Iran by Use of MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Majid Alizadeh

    2017-12-01

     Of the 65 isolates analyzed, 61 (93.8% were recognised by MALDI-TOF mass spectrometry and for four isolates (6.1% only not relabile identifications were achieved. In this study, the most frequently isolated species were Candida albicans (58.5%, followed by Candida tropicalis (16.9%, Candida glabrata (7.7%, Candida parapsilosis (7.7% and Candida guillermondii (3.1%.  Conclusion presented results demonstrate that the MALDI TOF mass spectrometry is a fast and reliable technique, and has the potential to replace conventional phenotypic identification of Candida species and other yeast strains routinely isolated in clinical microbiology laboratories.

  1. Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry.

    Science.gov (United States)

    Alizadeh, Majid; Kolecka, Anna; Boekhout, Teun; Zarrinfar, Hossein; Ghanbari Nahzag, Mohamad A; Badiee, Parisa; Rezaei-Matehkolaei, Ali; Fata, Abdolmajid; Dolatabadi, Somayeh; Najafzadeh, Mohammad J

    2017-12-01

    Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran. This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification. Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%). As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non- albicans Candida species.

  2. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fast and accurate identification of clinically relevant Aspergillus species.

    Science.gov (United States)

    Alanio, A; Beretti, J-L; Dauphin, B; Mellado, E; Quesne, G; Lacroix, C; Amara, A; Berche, P; Nassif, X; Bougnoux, M-E

    2011-05-01

    New Aspergillus species have recently been described with the use of multilocus sequencing in refractory cases of invasive aspergillosis. The classical phenotypic identification methods routinely used in clinical laboratories failed to identify them adequately. Some of these Aspergillus species have specific patterns of susceptibility to antifungal agents, and misidentification may lead to inappropriate therapy. We developed a matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)-based strategy to adequately identify Aspergillus species to the species level. A database including the reference spectra of 28 clinically relevant species from seven Aspergillus sections (five common and 23 unusual species) was engineered. The profiles of young and mature colonies were analysed for each reference strain, and species-specific spectral fingerprints were identified. The performance of the database was then tested on 124 clinical and 16 environmental isolates previously characterized by partial sequencing of the β-tubulin and calmodulin genes. One hundred and thirty-eight isolates of 140 (98.6%) were correctly identified. Two atypical isolates could not be identified, but no isolate was misidentified (specificity: 100%). The database, including species-specific spectral fingerprints of young and mature colonies of the reference strains, allowed identification regardless of the maturity of the clinical isolate. These results indicate that MALDI-TOF MS is a powerful tool for rapid and accurate identification of both common and unusual species of Aspergillus. It can give better results than morphological identification in clinical laboratories. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

  3. Optimizations for the EcoPod field identification tool

    Directory of Open Access Journals (Sweden)

    Yu YuanYuan

    2008-03-01

    Full Text Available Abstract Background We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questions that guide the operator towards identification. Historic observation data from the census geographic area helps minimize question volume. We explore how much historic data is required to boost performance, and whether the use of history negatively impacts identification of rare species. We also explore how characteristics of the matrix interact with the algorithm, and how best to predict the probability of observing a previously unseen species. Results Point counts of birds taken at Stanford University's Jasper Ridge Biological Preserve between 2000 and 2005 were used to examine the algorithm. A computer identified species by correctly answering, and counting the algorithm's questions. We also explored how the character density of the key matrix and the theoretical minimum number of questions for each bird in the matrix influenced the algorithm. Our investigation of the required probability smoothing determined whether Laplace smoothing of observation probabilities was sufficient, or whether the more complex Good-Turing technique is required. Conclusion Historic data improved identification speed, but only impacted the top 25% most frequently observed birds. For rare birds the history based algorithms did not impose a noticeable penalty in the number of questions required for identification. For our dataset neither age of the historic data, nor the number of observation years impacted the algorithm. Density of characters for different taxa in the identification matrix did not impact the algorithms. Intrinsic differences in identifying different birds did affect the algorithm, but the differences affected the baseline method of not using historic data to exactly the same degree. We found that Laplace smoothing

  4. A multiplex PCR method for the identification of commercially important salmon and trout species (Oncorhynchus and Salmo) in North America.

    Science.gov (United States)

    Rasmussen Hellberg, Rosalee S; Morrissey, Michael T; Hanner, Robert H

    2010-09-01

    The purpose of this study was to develop a species-specific multiplex polymerase chain reaction (PCR) method that allows for the detection of salmon species substitution on the commercial market. Species-specific primers and TaqMan® probes were developed based on a comprehensive collection of mitochondrial 5' cytochrome c oxidase subunit I (COI) deoxyribonucleic acid (DNA) "barcode" sequences. Primers and probes were combined into multiplex assays and tested for specificity against 112 reference samples representing 25 species. Sensitivity and linearity tests were conducted using 10-fold serial dilutions of target DNA (single-species samples) and DNA admixtures containing the target species at levels of 10%, 1.0%, and 0.1% mixed with a secondary species. The specificity tests showed positive signals for the target DNA in both real-time and conventional PCR systems. Nonspecific amplification in both systems was minimal; however, false positives were detected at low levels (1.2% to 8.3%) in conventional PCR. Detection levels were similar for admixtures and single-species samples based on a 30 PCR cycle cut-off, with limits of 0.25 to 2.5 ng (1% to 10%) in conventional PCR and 0.05 to 5.0 ng (0.1% to 10%) in real-time PCR. A small-scale test with food samples showed promising results, with species identification possible even in heavily processed food items. Overall, this study presents a rapid, specific, and sensitive method for salmon species identification that can be applied to mixed-species and heavily processed samples in either conventional or real-time PCR formats. This study provides a newly developed method for salmon and trout species identification that will assist both industry and regulatory agencies in the detection and prevention of species substitution. This multiplex PCR method allows for rapid, high-throughput species identification even in heavily processed and mixed-species samples. An inter-laboratory study is currently being carried out to

  5. Morphological identification of Candida species on glucose agar, rice extract agar and corn meal agar with and without Tween-80.

    Science.gov (United States)

    Joshi, K R; Solanki, A; Prakash, P

    1993-01-01

    A comparative study for the identification of 32 known strains of Candida species on the basis of morphology on glucose agar, rice extract agar and corn meal agar with and without Tween 80 revealed that when Tween 80 is incorporated in the media identification is possible for 96.8% of the species within 48 hours on rice extract agar and for 96.8% of the species within 48 hours on rice extract agar and for 90.6% of the species on glucose agar. The germ tubes and chlamydospores were also produced more on rice extract agar than on 0.1% glucose agar. Rice extract agar with Tween 80 can be used as single medium for morphologic identification of Candida species. The inoculated medium is first incubated at 37 degrees C for 3 hours and examined for germ tube formation and then incubated at 25 degrees C for 24 to 72 hours and examined for appearance of chlamydospores and mycelial morphology.

  6. Computational identification of 18 micrornas and their targets in three species of rose

    International Nuclear Information System (INIS)

    Baloch, I.A.; Barozai, M.Y.K.; Achakzai, A.K.K.

    2015-01-01

    MicroRNAs (miRNAs) are non-protein coding, small endogenous RNAs. Their length ranges from 18-26 nucleotides (nt). The miRNAs convergence property becomes a rational approach for the hunt of novel miRNAs in other organisms by homology search. As presently very little miRNAs are reported for rose species, so this study deals with the identification of miRNAs in different species of rose. Consequently 18 miRNA belonging to 17 miRNA families were identified in 3 species of rose (Rosa hybrid, Rosa chinensis and Rosa virginiana). All of the identified miRNA families (miR156, 160, 164, 166, 398, 482, 831, 837, 838, 841, 847, 3436, 3627, 6135, 6285, 6287 and 6288) are being reported for the first time in rose. Precursors of the identified miRNAs form stable minimum free energy (MFE) stem-loop structures and the mature miRNAs are found in the stem portions of their corresponding precursors. 11 putative targets of the miRNAs have also been identified. The identified targets are various proteins including transcription factors. Identification of 18 miRNAs will be supportive to explore the gene regulation phenomenon in various species of roses and it will be a good contribution for understanding the post transcriptional gene regulation in various stages of the life cycles of roses. (author)

  7. Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species

    Directory of Open Access Journals (Sweden)

    Marol Serhat

    2003-10-01

    Full Text Available Abstract Background The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. Methods A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 Trichosporon spp., 4 C. kefyr, 2 C. lusitaniae, 1 Saccharomyces cerevisiae and 1 Geotrichum candidum were included. The strains were first identified by germ tube test, morphological characteristics on cornmeal tween 80 agar and Vitek 32 and API 20 C AUX systems. In parallel, they were also streaked onto CHROMagar Candida and bismuth sulphite glucose glycine yeast agar plates. The results were read according to the color, morphology of the colonies and the existance of halo around them after 48 hours of incubation at 37°C. Results The sensitivity and specificity values for C. albicans strains were found to be 99.4, 100% for CHROMagar Candida and 87.0, 75.2% for BiGGY agar, respectively. The sensitivity of CHROMagar Candida to identify C. tropicalis, C. glabrata and C. krusei ranged between 90.9 and 100% while the specificity was 100%. The sensitivity rates for BiGGY agar were 66.6 and 100% while the specificity values were found to be 95.4 and 100% for C. tropicalis and C. krusei, respectively. Conclusions It can be concluded that the use of CHROMagar Candida is an easy and reliable method for the presumptive identification of most commonly isolated Candida species especially C. albicans, C. tropicalis and C. krusei. The lower sensitivity and specificity of BiGGY agar to identify commonly isolated Candida species potentially limits the clinical usefulness of this agar.

  8. Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species.

    Science.gov (United States)

    Yücesoy, Mine; Marol, Serhat

    2003-10-29

    The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 Trichosporon spp., 4 C. kefyr, 2 C. lusitaniae, 1 Saccharomyces cerevisiae and 1 Geotrichum candidum were included. The strains were first identified by germ tube test, morphological characteristics on cornmeal tween 80 agar and Vitek 32 and API 20 C AUX systems. In parallel, they were also streaked onto CHROMagar Candida and bismuth sulphite glucose glycine yeast agar plates. The results were read according to the color, morphology of the colonies and the existance of halo around them after 48 hours of incubation at 37 degrees C. The sensitivity and specificity values for C. albicans strains were found to be 99.4, 100% for CHROMagar Candida and 87.0, 75.2% for BiGGY agar, respectively. The sensitivity of CHROMagar Candida to identify C. tropicalis, C. glabrata and C. krusei ranged between 90.9 and 100% while the specificity was 100%. The sensitivity rates for BiGGY agar were 66.6 and 100% while the specificity values were found to be 95.4 and 100% for C. tropicalis and C. krusei, respectively. It can be concluded that the use of CHROMagar Candida is an easy and reliable method for the presumptive identification of most commonly isolated Candida species especially C. albicans, C. tropicalis and C. krusei. The lower sensitivity and specificity of BiGGY agar to identify commonly isolated Candida species potentially limits the clinical usefulness of this agar.

  9. Identification of Cronobacter species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with an optimized analysis method.

    Science.gov (United States)

    Wang, Qi; Zhao, Xiao-Juan; Wang, Zi-Wei; Liu, Li; Wei, Yong-Xin; Han, Xiao; Zeng, Jing; Liao, Wan-Jin

    2017-08-01

    Rapid and precise identification of Cronobacter species is important for foodborne pathogen detection, however, commercial biochemical methods can only identify Cronobacter strains to genus level in most cases. To evaluate the power of mass spectrometry based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS) for Cronobacter species identification, 51 Cronobacter strains (eight reference and 43 wild strains) were identified by both MALDI-TOF MS and 16S rRNA gene sequencing. Biotyper RTC provided by Bruker identified all eight reference and 43 wild strains as Cronobacter species, which demonstrated the power of MALDI-TOF MS to identify Cronobacter strains to genus level. However, using the Bruker's database (6903 main spectra products) and Biotyper software, the MALDI-TOF MS analysis could not identify the investigated strains to species level. When MALDI-TOF MS analysis was performed using the combined in-house Cronobacter database and Bruker's database, bin setting, and unweighted pair group method with arithmetic mean (UPGMA) clustering, all the 51 strains were clearly identified into six Cronobacter species and the identification accuracy increased from 60% to 100%. We demonstrated that MALDI-TOF MS was reliable and easy-to-use for Cronobacter species identification and highlighted the importance of establishing a reliable database and improving the current data analysis methods by integrating the bin setting and UPGMA clustering. Copyright © 2017. Published by Elsevier B.V.

  10. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Directory of Open Access Journals (Sweden)

    Tilton Susan C

    2012-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single

  11. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Science.gov (United States)

    2012-01-01

    Background MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP) miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM) v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf) results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis

  12. Identification of herbarium whole-leaf samples of Epilobium species by ATR-IR spectroscopy.

    Science.gov (United States)

    Strgulc Krajsek, Simona; Buh, Primoz; Zega, Anamarija; Kreft, Samo

    2008-02-01

    A simple, high-accuracy FT-IR method based on attenuated total reflection (ATR) was developed for the rapid determination of leaf samples of Epilobium species. The method is superior to other analytical techniques, since there is no need of laborious sample preparation such as grinding or extraction and solvent removal. A total of 70 herbarium specimens, belonging to all 13 Epilobium and to 2 Chamerion species growing in Slovenia, were analyzed. With the 100 most-informative wavenumbers in the range 700-1800 cm(-1), we obtained over 90% accuracy of species identification, with discriminant multivariate statistical analysis on the measurements made on whole dried leaves.

  13. Enhancing the effectiveness of biological control programs of invasive species through a more comprehensive pest management approach.

    Science.gov (United States)

    DiTomaso, Joseph M; Van Steenwyk, Robert A; Nowierski, Robert M; Vollmer, Jennifer L; Lane, Eric; Chilton, Earl; Burch, Patrick L; Cowan, Phil E; Zimmerman, Kenneth; Dionigi, Christopher P

    2017-01-01

    Invasive species are one of the greatest economic and ecological threats to agriculture and natural areas in the US and the world. Among the available management tools, biological control provides one of the most economical and long-term effective strategies for managing widespread and damaging invasive species populations of nearly all taxa. However, integrating biological control programs in a more complete integrated pest management approach that utilizes increased information and communication, post-release monitoring, adaptive management practices, long-term stewardship strategies, and new and innovative ecological and genetic technologies can greatly improve the effectiveness of biological control. In addition, expanding partnerships among relevant national, regional, and local agencies, as well as academic scientists and land managers, offers far greater opportunities for long-term success in the suppression of established invasive species. In this paper we direct our recommendations to federal agencies that oversee, fund, conduct research, and develop classical biological control programs for invasive species. By incorporating these recommendations into adaptive management strategies, private and public land managers will have far greater opportunities for long-term success in suppression of established invasive species. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  14. Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA).

    Science.gov (United States)

    Salimi, Nima; Loh, Kar Hoe; Kaur Dhillon, Sarinder; Chong, Ving Ching

    2016-01-01

    Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies.

  15. Morphological and molecular identification of phytophthora species from maple trees in Serbia

    Directory of Open Access Journals (Sweden)

    Milenković Ivan

    2014-01-01

    Full Text Available The paper presents the results of the study performed with aims to determine the presence and diversity of Phytophthora species on maple trees in Serbia. Due to high aggressiveness and their multicyclic nature, presence of these pathogens is posing significant threat to forestry and biodiversity. In total, 29 samples of water, soil and tissues were taken from 10 different localities, and six different maple hosts were tested. After the isolation tests, 17 samples from five different maple hosts were positive for the presence of Phytophthora spp., and 31 isolates were obtained. After the detailed morphological and physiological classification, four distinct groups of isolates were separated. DNA was extracted from selected representative isolates and molecular identification with sequencing of ITS region was performed. Used ITS4 and ITS6 primers successfully amplified the genomic DNA of chosen isolates and morphological identification of obtained isolates was confirmed after the sequencing. Four different Phytophthora species were detected, including P. cactorum, P. gonapodyides, P. plurivora and P. lacustris. The most common isolated species was homothallic, and with very variable and semipapillate sporangia, P. plurivora with 22 obtained isolates. This is the first report of P. plurivora and P. gonapodyides on A. campestre, P. plurivora and P. lacustris on Acer heldreichii and first report of P. lacustris on A. pseudoplatanus and A. tataricum in Serbia. [Projekat Ministarstva nauke Republike Srbije, br. TR 37008

  16. Identification of novel sRNAs in mycobacterial species.

    Directory of Open Access Journals (Sweden)

    Chen-Hsun Tsai

    Full Text Available Bacterial small RNAs (sRNAs are short transcripts that typically do not encode proteins and often act as regulators of gene expression through a variety of mechanisms. Regulatory sRNAs have been identified in many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Here, we use a computational algorithm to predict sRNA candidates in the mycobacterial species M. smegmatis and M. bovis BCG and confirmed the expression of many sRNAs using Northern blotting. Thus, we have identified 17 and 23 novel sRNAs in M. smegmatis and M. bovis BCG, respectively. We have also applied a high-throughput technique (Deep-RACE to map the 5' and 3' ends of many of these sRNAs and identified potential regulators of sRNAs by analysis of existing ChIP-seq datasets. The sRNAs identified in this work likely contribute to the unique biology of mycobacteria.

  17. Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics.

    Science.gov (United States)

    Vitecek, Simon; Kučinić, Mladen; Previšić, Ana; Živić, Ivana; Stojanović, Katarina; Keresztes, Lujza; Bálint, Miklós; Hoppeler, Felicitas; Waringer, Johann; Graf, Wolfram; Pauls, Steffen U

    2017-06-06

    Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.

  18. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

    Directory of Open Access Journals (Sweden)

    Natasha R Serrao

    Full Text Available Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway

  19. Identification of bester hybrid and its parental species (♀ Huso huso Linnaeus, 1758 and ♂ Acipenser ruthenus Linnaeus, 1758 by nuclear markers

    Directory of Open Access Journals (Sweden)

    Andreea Dudu

    2015-05-01

    Full Text Available In Romania, sturgeon farming is gaining advance, different species being raised for commercial purposes and for restocking activities. A correct identification of individuals is imposed since severe ecological damages might occur if non-native species or hybrids are used for restocking. Such identification is required also for commercial reasons, the meat and caviar from different species having different prices. The aim of our study was to analyze two sturgeon species, Huso huso and Acipenser ruthenus and their interspecific hybrid - bester, using nuclear markers, in order to set up a molecular method for their accurate identification. The genetic pattern of the species was inferred from the analysis of nine microsatellite loci (LS19, LS34, LS39, LS54, AoxD234, AnacC11, LS68, Aox45 and Aox27 amplified by multiplex PCR reactions. The genotype data were analyzed with GENETIX v4.05 and STRUCTURE. The FCA analysis grouped the individuals in three distinct clusters corresponding to each of the pure species and to the interspecific hybrids. The admixture analysis performed in STRUCTURE also assigned three groups, confirming the results highlighted by FCA. We can conclude that the selected microsatellite markers allow the unambiguously identification of the bester hybrid and its genitor species from Romanian farms.

  20. Reliable and reproducible method for rapid identification of Nocardia species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Toyokawa, Masahiro; Kimura, Keigo; Nishi, Isao; Sunada, Atsuko; Ueda, Akiko; Sakata, Tomomi; Asari, Seishi

    2013-01-01

    Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenged for the identification of Nocardia species. However, the standard ethanol-formic acid extraction alone is insufficient in allowing the membrane proteins of Nocardia species to be ionized by the matrix. We therefore aimed to establish our new extraction method for the MALDI-TOF MS-based identification of Nocardia species isolates. Our modified extraction procedure is through dissociation in 0.5% Tween-20 followed by bacterial heat-inactivation, mechanical breaking of the cell wall by acid-washed glass beads and protein extraction with formic acid and acetonitrile. As reference methods for species identification, full-length 16S rRNA gene sequencing and some phenotypical tests were used. In a first step, we made our own Nocardia database by analyzing 13 strains (13 different species including N. elegans, N. otitidiscaviarum, N. asiatica, N. abscessus, N. brasiliensis, N. thailandica, N. farcinica, N. nova, N. mikamii, N. cyriacigeorgica, N. asteroids, Nocardiopsis alba, and Micromonospora sp.) and registered to the MALDI BioTyper database. Then we established our database. The analysis of 12 challenge strains using the our database gave a 100% correct identification, including 8 strains identified to the species level and 4 strains to the genus level (N. elegans, N. nova, N. farcinica, Micromonospora sp.) according to the manufacture's log score specifications. In the estimation of reproducibility of our method intended for 4 strains, both within-run and between-run reproducibility were excellent. These data indicates that our method for rapid identification of Nocardia species is with reliability, reproducibility and cost effective.

  1. Remote Sensing Dynamic Monitoring of Biological Invasive Species Based on Adaptive PCNN and Improved C-V Model

    Directory of Open Access Journals (Sweden)

    PENG Gang

    2014-12-01

    Full Text Available Biological species invasion problem bring serious damage to the ecosystem, and have become one of the six major enviromental problems that affect the future economic development, also have become one of the hot topic in domestic and foreign scholars. Remote sensing technology has been successfully used in the investigation of coastal zone resources, dynamic monitoring of the resources and environment, and other fields. It will cite a new remote sensing image change detection algorithm based on adaptive pulse coupled neural network (PCNN and improved C-V model, for remote sensing dynamic monitoring of biological species invasion. The experimental results show that the algorithm is effective in the test results of biological species invasions.

  2. Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation.

    Science.gov (United States)

    Trtkova, Jitka; Pavlicek, Petr; Ruskova, Lenka; Hamal, Petr; Koukalova, Dagmar; Raclavsky, Vladislav

    2009-11-10

    Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD). Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification. A simple fully automated algorithm based on normalized melting data identified 80% of the isolates correctly. When this algorithm was supplemented by semi-automated matching of decisive peaks in first derivative plots, 87% of the isolates were identified correctly. However, a computer-aided visual matching of derivative plots showed the best performance with average 98.3% of the accurately identified isolates, almost matching the 99.4% performance of traditional RAPD fingerprinting. Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance.

  3. Differential identification of Candida species and other yeasts by analysis of [35S]methionine-labeled polypeptide profiles

    International Nuclear Information System (INIS)

    Shen, H.D.; Choo, K.B.; Tsai, W.C.; Jen, T.M.; Yeh, J.Y.; Han, S.H.

    1988-01-01

    This paper describes a scheme for differential identification of Candida species and other yeasts based on autoradiographic analysis of protein profiles of [ 35 S]methionine-labeled cellular proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using ATCC strains as references, protein profile analysis showed that different Candida and other yeast species produced distinctively different patterns. Good agreement in results obtained with this approach and with other conventional systems was observed. Being accurate and reproducible, this approach provides a basis for the development of an alternative method for the identification of yeasts isolated from clinical specimens

  4. Identification and Differentiation of Monilinia Species Causing Brown Rot of Pome and Stone Fruit using High-Resolution Melting (HRM) Analysis.

    Science.gov (United States)

    Papavasileiou, Antonios; Madesis, Panagiotis B; Karaoglanidis, George S

    2016-09-01

    Brown rot is a devastating disease of stone fruit caused by Monilinia spp. Among these species, Monilinia fructicola is a quarantine pathogen in Europe but has recently been detected in several European countries. Identification of brown rot agents relies on morphological differences or use of molecular methods requiring fungal isolation. The current study was initiated to develop and validate a high-resolution melting (HRM) method for the identification of the Monilinia spp. and for the detection of M. fructicola among other brown rot pathogens. Based on the sequence of the cytb intron from M. laxa, M. fructicola, M. fructigena, M. mumecola, M. linhartiana, and M. yunnanensis isolates originating from several countries, a pair of universal primers for species identification and a pair of primers specific to M. fructicola were designed. The specificity of the primers was verified to ensure against cross-reaction with other fungal species. The melting curve analysis using the universal primers generated six different HRM curve profiles, each one specific for each species. Τhe HRM analysis primers specific to M. fructicola amplified a 120-bp region with a distinct melt profile corresponding to the presence of M. fructicola, regardless of the presence of other species. HRM analysis can be a useful tool for rapid identification and differentiation of the six Monilinia spp. using a single primer pair. This novel assay has the potential for simultaneous identification and differentiation of the closely related Monilinia spp. as well as for the differentiation of M. fructicola from other common pathogens or saprophytes that may occur on the diseased fruit.

  5. Comparison of CHROMagar, polymerase chain reaction-restriction fragment length polymorphism, and polymerase chain reaction-fragment size for the identification of Candida species.

    Science.gov (United States)

    Jafari, Zahra; Motamedi, Marjan; Jalalizand, Nilufar; Shokoohi, Gholam R; Charsizadeh, Arezu; Mirhendi, Hossein

    2017-09-01

    The epidemiological alteration in the distribution of Candida species, as well as the significantly increasing trend of either intrinsic or acquired resistance of some of these fungi highlights the need for a reliable method for the identification of the species. Polymerase chain reaction (PCR) is one of the methods facilitating the quick and precise identification of Candida species. The aim of this study was to compare the efficiency of CHROMagar, PCR-restriction fragment length polymorphism (PCR-RFLP), and PCR-fragment size polymorphism (PCR-FSP) assays in the identification of Candida species to determine the benefits and limitations of these methods. This study was conducted on 107 Candida strains, including 20 standard strains and 87 clinical isolates. The identification of the isolates was accomplished by using CHROMagar as a conventional method. The PCR-RFLP assay was performed on the entire internal transcribed spacer (ITS) region of ribosomal DNA (rDNA), and the consequent enzymatic digestion was compared with PCR-FSP results in which ITS1 and ITS2 regions were separately PCR amplified. In both molecular assays, yeast identification was carried out through the specific electrophoretic profiles of the PCR products. According to the results, the utilization of CHROMagar resulted in the identification of 29 (33.3%) Candida isolates, while the PCR-RFLP and PCR-FSP facilitated the identification of 83 (95.4%) and 80 (91.9%) clinical isolates, respectively. The obtained concordances between CHROMagar and PCR-RFLP, between CHROMagar and PCR-FSP, as well as between PCR-RFLP and PCR-FSP were 0.23, 0.20, and 0.77, respectively. The recognition of the benefits and limitations of PCR methods allows for the selection of the most efficient technique for a fast and correct differentiation. The PCR-RFLP and PCR-FSP assays had satisfactory concordance. The PCR-FSP provides a rapid, technically simple, and cost-effective method for the identification of Candida species

  6. DNA barcodes and molecular diagnostics to distinguish an introduced and native Laricobius (Coleoptera: Derodontidae) species in eastern North America

    Science.gov (United States)

    G.A. Davis; N.P. Havill; Z.N. Adelman; A. Caccone; L.T. Kok; S.M. Salom

    2011-01-01

    Molecular diagnostics based on DNA barcodes can be powerful identification tools in the absence of distinctive morphological characters for distinguishing between closely related species. A specific example is distinguishing the endemic species Laricobius rubidus from Laricobius nigrinus, a biological control agent of hemlock...

  7. Specific primer design of mitochondrial 12S rRNA for species identification in raw meats

    Science.gov (United States)

    Cahyadi, M.; Puruhita; Barido, F. H.; Hertanto, B. S.

    2018-01-01

    Polymerase chain reaction (PCR) is a molecular technique that widely used in agriculture area including species identification in animal-based products for halalness and food safety reasons. Amplification of DNA using PCR needs a primer pair (forward and reverse primers) to isolate specific DNA fragment in the genome. This objective of this study was to design specific primer from mitochondrial 12S rRNA region for species identification in raw beef, pork and chicken meat. Three published sequences, HQ184045, JN601075, and KT626857, were downloaded from National Center for Biotechnology Information (NCBI) website. Furthermore, those reference sequences were used to design specific primer for bovine, pig, and chicken species using primer3 v.0.4.0. A total of 15 primer pairs were picked up from primer3 software. Of these, an universal forward primer and three reverse primers which are specific for bovine, pig, and chicken species were selected to be optimized using multiplex-PCR technique. The selected primers were namely UNIF (5’-ACC GCG GTC ATA CGA TTA AC-3’), SPR (5’-AGT GCG TCG GCT ATT GTA GG-3’), BBR (5’-GAA TTG GCA AGG GTT GGT AA-3’), and AR (5’-CGG TAT GTA CGT GCC TCA GA-3’). In addition, the PCR products were visualized using 2% agarose gels under the UV light and sequenced to be aligned with reference sequences using Clustal Omega. The result showed that those primers were specifically amplified mitochondrial 12S rRNA regions from bovine, pig, and chicken using PCR. It was indicated by the existence of 155, 357, and 611 bp of DNA bands for bovine, pig, and chicken species, respectively. Moreover, sequence analysis revealed that our sequences were identically similar with reference sequences. It can be concluded that mitochondrial 12S rRNA may be used as a genetic marker for species identification in meat products.

  8. Multiplex-PCR As a Rapid and Sensitive Method for Identification of Meat Species in Halal-Meat Products.

    Science.gov (United States)

    Alikord, Mahsa; Keramat, Javad; Kadivar, Mahdi; Momtaz, Hassan; Eshtiaghi, Mohammad N; Homayouni-Rad, Aziz

    2017-01-01

    Species identification and authentication in meat products are important subjects for ensuring the health of consumers. The multiplex-PCR amplification and species- specific primer set were used for the identification of horse, donkey, pig and other ruminants in raw and processed meat products. Oligonucleotid primers were designed and patented for amplification of species-specific mitochondrial DNA sequences of each species and samples were prepared from binary meat mixtures. The results showed that meat species were accurately determined in all combinations by multiplex-PCR, and the sensitivity of this method was 0.001 ng, rendering this technique open to and suitable for use in industrial meat products. It is concluded that more fraud is seen in lower percentage industrial meat products than in higher percentage ones. There was also more fraud found in processed products than in raw ones. This rapid and useful test is recommended for quality control firms for applying more rigorous controls over industrial meat products, for the benefit of target consumers. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  9. Molecular Identification of Eimeria Species in Broiler Chickens in Trinidad, West Indies

    Directory of Open Access Journals (Sweden)

    Arianne Brown Jordan

    2018-01-01

    Full Text Available Coccidiosis is an intestinal disease of chickens of major economic importance to broiler industries worldwide. Species of coccidia found in chickens include Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox, and Eimeria tenella. In recent years, polymerase chain reaction (PCR has been developed to provide accurate and rapid identification of the seven known Eimeria species of chickens. The aim of this study was to use species-specific real-time PCR (qPCR to identify which of the seven Eimeria species are present in Trinidad poultry. Seventeen pooled fecal samples were collected from 6 broiler farms (2–5 pens per farm across Trinidad. Feces were also collected from birds showing clinical signs of coccidiosis in two live bird markets (pluck shops. qPCR revealed the presence of five species of Eimeria (E. acervulina, E. maxima, E. mitis, E. necatrix, and E. tenella, but not E. brunetti or E. praecox. Mixed infections were detected on all broiler farms, and DNA of two highly pathogenic Eimeria species (E. tenella and E. necatrix was detected in feces taken from clinically sick birds sampled from the two pluck shops.

  10. Identification of surface species by vibrational normal mode analysis. A DFT study

    Science.gov (United States)

    Zhao, Zhi-Jian; Genest, Alexander; Rösch, Notker

    2017-10-01

    Infrared spectroscopy is an important experimental tool for identifying molecular species adsorbed on a metal surface that can be used in situ. Often vibrational modes in such IR spectra of surface species are assigned and identified by comparison with vibrational spectra of related (molecular) compounds of known structure, e. g., an organometallic cluster analogue. To check the validity of this strategy, we carried out a computational study where we compared the normal modes of three C2Hx species (x = 3, 4) in two types of systems, as adsorbates on the Pt(111) surface and as ligands in an organometallic cluster compound. The results of our DFT calculations reproduce the experimental observed frequencies with deviations of at most 50 cm-1. However, the frequencies of the C2Hx species in both types of systems have to be interpreted with due caution if the coordination mode is unknown. The comparative identification strategy works satisfactorily when the coordination mode of the molecular species (ethylidyne) is similar on the surface and in the metal cluster. However, large shifts are encountered when the molecular species (vinyl) exhibits different coordination modes on both types of substrates.

  11. Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to noninvasive sampling.

    Science.gov (United States)

    Barbosa, S; Pauperio, J; Searle, J B; Alves, P C

    2013-01-01

    Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt-b)] and one nuclear gene [interphotoreceptor retinoid-binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation. © 2012 Blackwell Publishing Ltd.

  12. Chemical constituents and biological activities of species of Justicia: a review

    Directory of Open Access Journals (Sweden)

    Geone M. Corrêa

    2012-02-01

    Full Text Available The Acanthaceae family is an important source of therapeutic drugs, and the ethnopharmacological knowledge of this family requires urgent documentation as several of its species are near extinction. Justicia is the largest genus of Acanthaceae, with approximately 600 species. The present work provides a review addressing the chemistry and pharmacology of the genus Justicia. In addition, the biological activities of compounds isolated from the genus are also covered. The chemical and pharmacological information in the present work may inspire new biomedical applications for the species of Justicia, considering atom economy, the synthesis of environmentally benign products without producing toxic by-products, the use of renewable sources of raw materials, and the search for processes with maximal efficiency of energy.

  13. DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

    Science.gov (United States)

    Bucklin, Ann; Hopcroft, Russell R.; Kosobokova, Ksenia N.; Nigro, Lisa M.; Ortman, Brian D.; Jennings, Robert M.; Sweetman, Christopher J.

    2010-01-01

    Zooplankton species diversity and distribution are important measures of environmental change in the Arctic Ocean, and may serve as 'rapid-responders' of climate-induced changes in this fragile ecosystem. The scarcity of taxonomists hampers detailed and up-to-date monitoring of these patterns for the rarer and more problematic species. DNA barcodes (short DNA sequences for species recognition and discovery) provide an alternative approach to accurate identification of known species, and can speed routine analysis of zooplankton samples. During 2004-2008, zooplankton samples were collected during cruises to the central Arctic Ocean and Chukchi Sea. A ˜700 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was amplified and sequenced for 82 identified specimens of 41 species, including cnidarians (six hydrozoans, one scyphozoan), arthropod crustaceans (five amphipods, 24 copepods, one decapod, and one euphausiid); two chaetognaths; and one nemertean. Phylogenetic analysis used the Neighbor-Joining algorithm with Kimura-2-Parameter (K-2-P) distances, with 1000-fold bootstrapping. K-2-P genetic distances between individuals of the same species ranged from 0.0 to 0.2; genetic distances between species ranged widely from 0.1 to 0.7. The mtCOI gene tree showed monophyly (at 100% bootstrap value) for each of the 26 species for which more than one individual was analyzed. Of seven genera for which more than one species was analyzed, four were shown to be monophyletic; three genera were not resolved. At higher taxonomic levels, only the crustacean order Copepoda was resolved, with bootstrap value of 83%. The mtCOI barcodes accurately discriminated and identified known species of 10 taxonomic groups of Arctic Ocean holozooplankton. A comprehensive DNA barcode database for the estimated 300 described species of Arctic holozooplankton will allow rapid assessment of species diversity and distribution in this climate-vulnerable ocean ecosystem.

  14. High-throughput gender identification of penguin species using melting curve analysis.

    Science.gov (United States)

    Tseng, Chao-Neng; Chang, Yung-Ting; Chiu, Hui-Tzu; Chou, Yii-Cheng; Huang, Hurng-Wern; Cheng, Chien-Chung; Liao, Ming-Hui; Chang, Hsueh-Wei

    2014-04-03

    Most species of penguins are sexual monomorphic and therefore it is difficult to visually identify their genders for monitoring population stability in terms of sex ratio analysis. In this study, we evaluated the suitability using melting curve analysis (MCA) for high-throughput gender identification of penguins. Preliminary test indicated that the Griffiths's P2/P8 primers were not suitable for MCA analysis. Based on sequence alignment of Chromo-Helicase-DNA binding protein (CHD)-W and CHD-Z genes from four species of penguins (Pygoscelis papua, Aptenodytes patagonicus, Spheniscus magellanicus, and Eudyptes chrysocome), we redesigned forward primers for the CHD-W/CHD-Z-common region (PGU-ZW2) and the CHD-W-specific region (PGU-W2) to be used in combination with the reverse Griffiths's P2 primer. When tested with P. papua samples, PCR using P2/PGU-ZW2 and P2/PGU-W2 primer sets generated two amplicons of 148- and 356-bp, respectively, which were easily resolved in 1.5% agarose gels. MCA analysis indicated the melting temperature (Tm) values for P2/PGU-ZW2 and P2/PGU-W2 amplicons of P. papua samples were 79.75°C-80.5°C and 81.0°C-81.5°C, respectively. Females displayed both ZW-common and W-specific Tm peaks, whereas male was positive only for ZW-common peak. Taken together, our redesigned primers coupled with MCA analysis allows precise high throughput gender identification for P. papua, and potentially for other penguin species such as A. patagonicus, S. magellanicus, and E. chrysocome as well.

  15. The emerging role of reactive oxygen and nitrogen species in redox biology and some implications for plasma applications to medicine and biology

    Science.gov (United States)

    Graves, David B.

    2012-07-01

    Reactive oxygen species (ROS) and the closely related reactive nitrogen species (RNS) are often generated in applications of atmospheric pressure plasmas intended for biomedical purposes. These species are also central players in what is sometimes referred to as ‘redox’ or oxidation-reduction biology. Oxidation-reduction biochemistry is fundamental to all of aerobic biology. ROS and RNS are perhaps best known as disease-associated agents, implicated in diabetes, cancer, heart and lung disease, autoimmune disease and a host of other maladies including ageing and various infectious diseases. These species are also known to play active roles in the immune systems of both animals and plants and are key signalling molecules, among many other important roles. Indeed, the latest research has shown that ROS/RNS play a much more complex and nuanced role in health and ageing than previously thought. Some of the most potentially profound therapeutic roles played by ROS and RNS in various medical interventions have emerged only in the last several years. Recent research suggests that ROS/RNS are significant and perhaps even central actors in the actions of antimicrobial and anti-parasite drugs, cancer therapies, wound healing therapies and therapies involving the cardiovascular system. Understanding the ways ROS/RNS act in established therapies may help guide future efforts in exploiting novel plasma medical therapies. The importance of ROS and RNS to plant biology has been relatively little appreciated in the plasma biomedicine community, but these species are just as important in plants. It appears that there are opportunities for useful applications of plasmas in this area as well.

  16. The emerging role of reactive oxygen and nitrogen species in redox biology and some implications for plasma applications to medicine and biology

    International Nuclear Information System (INIS)

    Graves, David B

    2012-01-01

    Reactive oxygen species (ROS) and the closely related reactive nitrogen species (RNS) are often generated in applications of atmospheric pressure plasmas intended for biomedical purposes. These species are also central players in what is sometimes referred to as ‘redox’ or oxidation-reduction biology. Oxidation-reduction biochemistry is fundamental to all of aerobic biology. ROS and RNS are perhaps best known as disease-associated agents, implicated in diabetes, cancer, heart and lung disease, autoimmune disease and a host of other maladies including ageing and various infectious diseases. These species are also known to play active roles in the immune systems of both animals and plants and are key signalling molecules, among many other important roles. Indeed, the latest research has shown that ROS/RNS play a much more complex and nuanced role in health and ageing than previously thought. Some of the most potentially profound therapeutic roles played by ROS and RNS in various medical interventions have emerged only in the last several years. Recent research suggests that ROS/RNS are significant and perhaps even central actors in the actions of antimicrobial and anti-parasite drugs, cancer therapies, wound healing therapies and therapies involving the cardiovascular system. Understanding the ways ROS/RNS act in established therapies may help guide future efforts in exploiting novel plasma medical therapies. The importance of ROS and RNS to plant biology has been relatively little appreciated in the plasma biomedicine community, but these species are just as important in plants. It appears that there are opportunities for useful applications of plasmas in this area as well. (topical review)

  17. Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory

    Science.gov (United States)

    Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

    2018-04-01

    Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2 = 41.336, P clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. [Figure not available: see fulltext.

  18. Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.

    Science.gov (United States)

    Poovitha, Sundar; Stalin, Nithaniyal; Balaji, Raju; Parani, Madasamy

    2016-12-01

    The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%-9.6% with individual markers, which increased to 0%-12.5% and 0.8%-20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.

  19. Recognition and identification of bumblebee species in the Bombus lucorum-complex (Hymenoptera, Apidae – A review and outlook

    Directory of Open Access Journals (Sweden)

    Silas Bossert

    2015-02-01

    Full Text Available The recognition of cryptic species represents one of the major challenges in current taxonomy and affects our understanding of global diversity. In practice, the process from discovery to acceptance in the scientific community can take an extensive length of time. A prime example is the traditionally difficult taxonomy of the cryptic bumblebee species belonging to the Bombus lucorum-complex. The status of the three European species in the group – Bombus lucorum and the closely related Bombus cryptarum and Bombus magnus – has recently become widely accepted, primarily due to investigations of nucleotide sequences and marking pheromones. In contrast, doubts prevail concerning the validity of species identification based on morphology. As a consequence, our knowledge of the species is muddled in a mire of unreliable and confusing literature data from a large number of authors over the centuries. To clarify this issue, this paper provides a recapitulation of the historical literature and highlights the milestones in the process of species recognition. Further, the possibility of a morphologically based species identification is discussed in the context of new molecular data. Finally, this review outlines the current challenges and provides directions for future issues.

  20. Aspergillus fumigatus and Related Species

    Science.gov (United States)

    Sugui, Janyce A.; Kwon-Chung, Kyung J.; Juvvadi, Praveen R.; Latgé, Jean-Paul; Steinbach, William J.

    2015-01-01

    The genus Aspergillus contains etiologic agents of aspergillosis. The clinical manifestations of the disease range from allergic reaction to invasive pulmonary infection. Among the pathogenic aspergilli, Aspergillus fumigatus is most ubiquitous in the environment and is the major cause of the disease, followed by Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus nidulans, and several species in the section Fumigati that morphologically resemble A. fumigatus. Patients that are at risk for acquiring aspergillosis are those with an altered immune system. Early diagnosis, species identification, and adequate antifungal therapy are key elements for treatment of the disease, especially in cases of pulmonary invasive aspergillosis that often advance very rapidly. Incorporating knowledge of the basic biology of Aspergillus species to that of the diseases that they cause is fundamental for further progress in the field. PMID:25377144

  1. Candida colonization and species identification by two methods in NICU newborn

    Directory of Open Access Journals (Sweden)

    Narges Sadat Taherzadeh

    2016-02-01

    Full Text Available Background: Over the last two decades invasive candidiasis has become an increasing problem in neonatal intensive care units (NICUs. Colonization of skin and mucous membranes with Candida spp. is important factor in the pathogenesis of neonatal infection and several colonized sites are major risk factors evoking higher frequencies of progression to invasive candidiasis. The aim of this study was to detect Candida colonization in NICU patients. Methods: This cross-sectional study was conducted on 93 neonates in NICUs at Imam Khomeini and Children Medical Center Hospitals in Tehran. Cutaneous and mucous membrane samples obtained at first, third, and seventh days of patients’ stay in NICUs during nine months from August 2013 to May 2014. The samples were primarily cultured on CHROMagar Candida medium. The cultured media were incubated at 35°C for 48h and evaluated based on colony color produced on CHROMagar Candida. In addition, isolated colonies were cultured on Corn Meal Agar medium supplemented with tween 80 for identification of Candida spp. based on their morphology. Finally, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method was performed for definite identification of isolated species. Results: Colonization by Candida spp. was occurred in 20.43% of neonates. Fifteen and four patients colonized with one and two different Candida spp., respectively. Isolated Candida spp. identified as; C. parapsilosis (n: 10, C. albicans (n: 7, C. tropicalis (n: 3, C. guilliermondii (n: 2, and C. krusei (n: 1. In present study non-albicans Candia species were dominant (69.56% and C. parapsilosis was the most frequent isolate (43.47%. Using Fisher's exact test, the correlation between fungal colonization with low birth weight, low gestational age, and duration of hospital stay was found to be statistically significant (P=0.003. Conclusion: The results of this study imply to the candida species colonization of neonates

  2. New occurrences and biological aspects to four species of rodents (Mammalia: Cricetidae from Brazil

    Directory of Open Access Journals (Sweden)

    Felipe Santana Machado

    2015-07-01

    Full Text Available The most representative group among mammals are rodents for presenting high ratio to the total of species. However, rodents are considered a "taxonomic chaos" and some species such as Blarinomys breviceps, Bibimys labiosus, Akodon lindberghi and Pseudoryzomys simplex are little known. That can be explained because of low occurrence of small terrestrial mammals in wildlife inventories and/or reduced abundance. The objective is to describe the occurrence of these species and analyze these locations presenting descriptive comments about their biological aspects. Therefore, in addition to specimens collected in the field, some scientific collections were visited and reviews in relevant literature were conducted in order to obtain information about the locations and biological aspects. Akodon lindberghi was found in five sites, Bibimys labiosus was found in 15, Blarinomys breviceps in 39 and Pseudoryzomys simplex  in 13. Each species has specific information and they are included in two threatened areas, Atlantic Forest and Cerrado. The occurrences are disconnected and related to taxonomic and methodological problems. Keywords: New records. Rodentia. Sigmodontinae. Occurence area.

  3. A High Throughput Ambient Mass Spectrometric Approach to Species Identification and Classification from Chemical Fingerprint Signatures

    Science.gov (United States)

    Musah, Rabi A.; Espinoza, Edgard O.; Cody, Robert B.; Lesiak, Ashton D.; Christensen, Earl D.; Moore, Hannah E.; Maleknia, Simin; Drijfhout, Falko P.

    2015-01-01

    A high throughput method for species identification and classification through chemometric processing of direct analysis in real time (DART) mass spectrometry-derived fingerprint signatures has been developed. The method entails introduction of samples to the open air space between the DART ion source and the mass spectrometer inlet, with the entire observed mass spectral fingerprint subjected to unsupervised hierarchical clustering processing. A range of both polar and non-polar chemotypes are instantaneously detected. The result is identification and species level classification based on the entire DART-MS spectrum. Here, we illustrate how the method can be used to: (1) distinguish between endangered woods regulated by the Convention for the International Trade of Endangered Flora and Fauna (CITES) treaty; (2) assess the origin and by extension the properties of biodiesel feedstocks; (3) determine insect species from analysis of puparial casings; (4) distinguish between psychoactive plants products; and (5) differentiate between Eucalyptus species. An advantage of the hierarchical clustering approach to processing of the DART-MS derived fingerprint is that it shows both similarities and differences between species based on their chemotypes. Furthermore, full knowledge of the identities of the constituents contained within the small molecule profile of analyzed samples is not required. PMID:26156000

  4. Rapid identification of probiotic Lactobacillus species by multiplex PCR using species-specific primers based on the region extending from 16S rRNA through 23S rRNA.

    Science.gov (United States)

    Kwon, Hyuk-Sang; Yang, Eun-Hee; Yeon, Seung-Woo; Kang, Byoung-Hwa; Kim, Tae-Yong

    2004-10-15

    This study aimed to develop a novel multiplex polymerase chain reaction (PCR) primer set for the identification of seven probiotic Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus delbrueckii, Lactobacillus casei, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus reuteri and Lactobacillus rhamnosus. The primer set, comprising of seven specific and two conserved primers, was derived from the integrated sequences of 16S and 23S rRNA genes and their rRNA intergenic spacer region of each species. It was able to identify the seven target species with 93.6% accuracy, which exceeds that of the general biochemical methods. The phylogenetic analyses, using 16S rDNA sequences of the probiotic isolates, also provided further support that the results from the multiplex PCR assay were trustworthy. Taken together, we suggest that the multiplex primer set is an efficient tool for simple, rapid and reliable identification of seven Lactobacillus species.

  5. Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India

    Science.gov (United States)

    Peddayelachagiri, Bhavani V.; Paul, Soumya; Nagaraj, Sowmya; Gogoi, Madhurjya; Sripathy, Murali H.; Batra, Harsh V.

    2016-01-01

    Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha

  6. Species identification of tephritids across a broad taxonomic range using ribosomal D

    International Nuclear Information System (INIS)

    Armstrong, Karen F; Cameron, Charlotte M.

    2000-01-01

    International trade and passenger travel are significant factors in the spread of economically important fruit fly species. The risk of accidental introduction via infested fruit is high, and in New Zealand the recent Medfly incursion in Auckland demonstrated the reality of this threat (Frampton, 2000). There are no economically important species of fruit fly established in New Zealand at present, but 31 are considered high risk in terms of their potential colonisation (refer to the Biosecurity (Notifiable Organisms) Amendment Order 1997). These are amongst a background of non-pest and low risk pest species that may also arrive in fruit from neighbouring countries or trading partners. Quarantine officials closely monitor fruit fly host material at the New Zealand borders (Frampton, 2000). In terms of the action to be taken should an infestation be discovered, there is significant benefit from being able to accurately identify species from the immature life stages, or at least to distinguish the high and low risk groups (Armstrong et al. 1997a). The need for this quarantine application was also highlighted by White (1996) at the previous fruit fly symposium in Sand Keys, Florida, where he summarised the advances made in larval taxonomy over the last decade. Despite this, morphological keys such as those of Steck et al. (1990) and White and Elson Harris (1992), are still only available for about a third of ca. 250 pest species. For those species, even so, identification is not easy and only possible for good quality late instar larvae; there are no morphological characters for early instars or eggs. Until recently in New Zealand, the identification of immature life stages depended entirely on rearing through to adults. This was time consuming and often unsuccessful (Armstrong et al. 1997b). A rapid molecular technique has since been described as a feasible alternative or supplementary quarantine tool (Armstrong et al. 1997a). The method is based on the polymerase

  7. MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex.

    Directory of Open Access Journals (Sweden)

    Carolina Firacative

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

  8. Identification of Eastern United States Reticulitermes Termite Species via PCR-RFLP, Assessed Using Training and Test Data

    Directory of Open Access Journals (Sweden)

    Ryan C. Garrick

    2015-06-01

    Full Text Available Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP assay, with banding patterns resolved via agarose gel electrophoresis. The assay was designed using a large set of training data obtained from a public DNA sequence database, then evaluated using an independent test panel of Reticulitermes from the Southern Appalachian Mountains, for which species assignments were determined via phylogenetic comparison to reference sequences. After refining the interpretive framework, the PCR-RFLP assay was shown to provide accurate identification of four co-occurring species (the fifth species, R. hageni, was absent from the test panel, so accuracy cannot yet be extended to training data. The assay is cost- and time-efficient, and will help improve knowledge of Reticulitermes species distributions.

  9. Rapid Identification of Seven Waterborne Exophiala Species by RCA DNA Padlock Probes.

    Science.gov (United States)

    Najafzadeh, M J; Vicente, V A; Feng, Peiying; Naseri, A; Sun, Jiufeng; Rezaei-Matehkolaei, A; de Hoog, G S

    2018-03-05

    The black yeast genus Exophiala includes numerous potential opportunistic species that potentially cause systematic and disseminated infections in immunocompetent individuals. Species causing systemic disease have ability to grow at 37-40 °C, while others consistently lack thermotolerance and are involved in diseases of cold-blooded, waterborne vertebrates and occasionally invertebrates. We explain a fast and sensitive assay for recognition and identification of waterborne Exophiala species without sequencing. The ITS rDNA region of seven Exophiala species (E. equina, E. salmonis, E. opportunistica, E. pisciphila, E. aquamarina, E. angulospora and E. castellanii) along with the close relative Veronaea botryosa was sequenced and aligned for the design of specific padlock probes for the detection of characteristic single-nucleotide polymorphisms. The assay demonstrated to successfully amplify DNA of target fungi, allowing detection at the species level. Amplification products were visualized on 1% agarose gels to confirm specificity of probe-template binding. Amounts of reagents were reduced to prevent the generation of false positive results. The simplicity, tenderness, robustness and low expenses provide padlock probe assay (RCA) a definite place as a very practical method among isothermal approaches for DNA diagnostics.

  10. Molecular species identification of Central European ground beetles (Coleoptera: Carabidae using nuclear rDNA expansion segments and DNA barcodes

    Directory of Open Access Journals (Sweden)

    Raupach Michael J

    2010-09-01

    Full Text Available Abstract Background The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous. Results We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97% of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95% of the studied Carabidae. Conclusion Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.

  11. Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes.

    Science.gov (United States)

    Raupach, Michael J; Astrin, Jonas J; Hannig, Karsten; Peters, Marcell K; Stoeckle, Mark Y; Wägele, Johann-Wolfgang

    2010-09-13

    The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI) gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous. We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97%) of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95%) of the studied Carabidae. Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.

  12. Detection and identification of Rickettsia species in Ixodes tick populations from Estonia.

    Science.gov (United States)

    Katargina, Olga; Geller, Julia; Ivanova, Anna; Värv, Kairi; Tefanova, Valentina; Vene, Sirkka; Lundkvist, Åke; Golovljova, Irina

    2015-09-01

    A total of 1640 ticks collected in different geographical parts of Estonia were screened for the presence of Rickettsia species DNA by real-time PCR. DNA of Rickettsia was detected in 83 out of 1640 questing ticks with an overall prevalence of 5.1%. The majority of the ticks infected by rickettsiae were Ixodes ricinus (74 of 83), while 9 of the 83 positive ticks were Ixodes persulcatus. For rickettsial species identification, a part of the citrate synthase gltA gene was sequenced. The majority of the positive samples were identified as Rickettsia helvetica (81 out of 83) and two of the samples were identified as Rickettsia monacensis and Candidatus R. tarasevichiae, respectively. Genetic characterization based on the partial gltA gene showed that the Estonian sequences within the R. helvetica, R. monacensis and Candidatus R. tarasevichiae species demonstrated 100% similarity with sequences deposited in GenBank, originating from Rickettsia species distributed over large territories from Europe to Asia. Copyright © 2015 Elsevier GmbH. All rights reserved.

  13. Species identification in meat products: A new screening method based on high resolution melting analysis of cyt b gene.

    Science.gov (United States)

    Lopez-Oceja, A; Nuñez, C; Baeta, M; Gamarra, D; de Pancorbo, M M

    2017-12-15

    Meat adulteration by substitution with lower value products and/or mislabeling involves economic, health, quality and socio-religious issues. Therefore, identification and traceability of meat species has become an important subject to detect possible fraudulent practices. In the present study the development of a high resolution melt (HRM) screening method for the identification of eight common meat species is reported. Samples from Bos taurus, Ovis aries, Sus scrofa domestica, Equus caballus, Oryctolagus cuniculus, Gallus gallus domesticus, Meleagris gallopavo and Coturnix coturnix were analyzed through the amplification of a 148 bp fragment from the cyt b gene with a universal primer pair in HRM analyses. Melting profiles from each species, as well as from several DNA mixtures of these species and blind samples, allowed a successful species differentiation. The results demonstrated that the HRM method here proposed is a fast, reliable, and low-cost screening technique. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus

    Science.gov (United States)

    2011-01-01

    Background Streptococcus is an economically important genus as a number of species belonging to this genus are human and animal pathogens. The genus has been divided into different groups based on 16S rRNA gene sequence similarity. The variability observed among the members of these groups is low and it is difficult to distinguish them. The present study was taken up to explore 16S rRNA gene sequence to develop methods that can be used for preliminary identification and can supplement the existing methods for identification of clinically-relevant isolates of the genus Streptococcus. Methods 16S rRNA gene sequences belonging to the isolates of S. dysgalactiae, S. equi, S. pyogenes, S. agalactiae, S. bovis, S. gallolyticus, S. mutans, S. sobrinus, S. mitis, S. pneumoniae, S. thermophilus and S. anginosus were analyzed with the purpose to define genetic variability within each species to generate a phylogenetic framework, to identify species-specific signatures and in-silico restriction enzyme analysis. Results The framework based analysis was used to segregate Streptococcus spp. previously identified upto genus level. This segregation was validated using species-specific signatures and in-silico restriction enzyme analysis. 43 uncharacterized Streptococcus spp. could be identified using this approach. Conclusions The markers generated exploring 16S rRNA gene sequences provided useful tool that can be further used for identification of different species of the genus Streptococcus. PMID:21702978

  15. Detection of cryptic species

    International Nuclear Information System (INIS)

    Cockburn, A.F.; Jensen, T.; Seawright, J.A.

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author)

  16. Assessment of compatibility among Armillaria cepistipes, A. sinapina, and North American biological species X and XI, using culture morphology and molecular biology

    Science.gov (United States)

    Mark T. Banik; Harold H. Burdsall

    1998-01-01

    Ten single-spore isolates each of Armillaria sinapina, A. cepistipes, and North American biological species (NABS)X and XI were paired in all combinations. A second set of ten single-spore isolates of each species was likewise paired. Each pairing was duplicated for a total of 3280 pairs. Using the standard morphological criteria (e.g., fluffy, crustose) to assess the...

  17. Osmiine bees of the genus Haetosmia (Megachilidae, Osmiini): biology, taxonomy and key to species.

    Science.gov (United States)

    Müller, Andreas; Griswold, Terry

    2017-11-29

    Haetosmia is a species-poor genus of osmiine bees (Megachilidae) containing six species, which inhabit deserts and semideserts from the Canary Islands to Central Asia. Formerly considered to be restricted to the southern Palaearctic region, the genus is shown here to occur also in the northern Afrotropical region. The females of all six Haetosmia species collect pollen from the narrow-tubed flowers of Heliotropium (Boraginaceae) with the aid of specialized pollen-harvesting bristles on the proboscis. Current knowledge suggests that Haetosmia species are restricted to sandy habitats, excavate their nests in the ground and use chewed leaves to construct their urn-shaped brood cells, which are placed side by side in an enlarged chamber at the end of the nesting burrow. The taxonomic revision of Haetosmia revealed the existence of two undescribed species, H. ethiopiensis spec. nov. from eastern Africa and H. pakistaniensis spec. nov. from Pakistan. Due to clear morphological gaps and overlapping distribution area with the nominotypical subspecies, H. brachyura altera (Peters 1974) is elevated to species rank. Keys for the identification of the six Haetosmia species are provided.

  18. Species identification of smoked and gravad fish products by sodium dodecylsulphate polyacrylamide gel electrophoresis, urea isoelectric focusing and native isoelectric focusing : a collaborative study

    DEFF Research Database (Denmark)

    Mackie, I.; Craig, A.; Etienne, M.

    2000-01-01

    A collaborative study on the use of sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE), urea-isoelectric focusing (urea-IEF) and native isoelectric focusing for the identification of species of smoked salmonids, gravad salmonids and smoked eels was carried out by eight laborator......A collaborative study on the use of sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE), urea-isoelectric focusing (urea-IEF) and native isoelectric focusing for the identification of species of smoked salmonids, gravad salmonids and smoked eels was carried out by eight...... laboratories. With SDS-PAGE, minor changes took place in the profiles of the processed salmonid species making it impossible or Very difficult to identify closely related species. With urea-IEF, there were fewer changes in the profiles due to processing and the system generally had greater species......-discriminating power for the processed salmonids than SDS-PAGE. The profiles of the eel species as obtained on SDS-PAGE or urea-IEF were not affected by smoking. Urea-IEF had greater species- discriminating power than SDS-PAGE for the eel species. Native IEF was useful in providing supplementary identification...

  19. [Comparison between conventional methods, ChromAgar Candida® and PCR method for the identification of Candida species in clinical isolates].

    Science.gov (United States)

    Estrada-Barraza, Deyanira; Dávalos Martínez, Arturo; Flores-Padilla, Luis; Mendoza-De Elias, Roberto; Sánchez-Vargas, Luis Octavio

    2011-01-01

    The increase in the incidence of yeast species causing fungemia in susceptible immunocompromised patients in the last two decades and the low sensitivity of conventional blood culture has led to the need to develop alternative approaches for the early detection and identification of causative species. The aim of this study was to compare the usefulness of molecular testing by the polymerase chain reaction (PCR) and conventional methods to identify clinical isolates of different species, using the ID32C ATB system (bioMérieux, France), chromogenic culture Chromagar Candida® (CHROMagar, France) and morphogenesis in corn meal agar. We studied 79 isolates, in which the most prevalent species using the system ID32C and PCR was C. albicans, followed by C. tropicalis, C. glabrata and C .krusei. PCR patterns obtained for the identification of clinical isolates were stable and consistent in the various independent studies and showed good reproducibility, concluding that PCR with species-specific primers that amplify genes ITS1 and ITS2 for rRNA or topoisomerase II primers is a very specific and sensitive method for the identification of C. glabrata, C. krusei, C. albicans, and with less specificity for C. tropicalis. Copyright © 2010 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  20. The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

    Science.gov (United States)

    Poussin, Carine; Mathis, Carole; Alexopoulos, Leonidas G; Messinis, Dimitris E; Dulize, Rémi H J; Belcastro, Vincenzo; Melas, Ioannis N; Sakellaropoulos, Theodore; Rhrissorrakrai, Kahn; Bilal, Erhan; Meyer, Pablo; Talikka, Marja; Boué, Stéphanie; Norel, Raquel; Rice, John J; Stolovitzky, Gustavo; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

    2014-01-01

    The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to 'translate' the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies.

  1. The species translation challenge—A systems biology perspective on human and rat bronchial epithelial cells

    Science.gov (United States)

    Poussin, Carine; Mathis, Carole; Alexopoulos, Leonidas G; Messinis, Dimitris E; Dulize, Rémi H J; Belcastro, Vincenzo; Melas, Ioannis N; Sakellaropoulos, Theodore; Rhrissorrakrai, Kahn; Bilal, Erhan; Meyer, Pablo; Talikka, Marja; Boué, Stéphanie; Norel, Raquel; Rice, John J; Stolovitzky, Gustavo; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

    2014-01-01

    The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to ‘translate’ the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies. PMID:25977767

  2. Automated species-level identification and segmentation of planktonic foraminifera using convolutional neural networks

    Science.gov (United States)

    Marchitto, T. M., Jr.; Mitra, R.; Zhong, B.; Ge, Q.; Kanakiya, B.; Lobaton, E.

    2017-12-01

    Identification and picking of foraminifera from sediment samples is often a laborious and repetitive task. Previous attempts to automate this process have met with limited success, but we show that recent advances in machine learning can be brought to bear on the problem. As a `proof of concept' we have developed a system that is capable of recognizing six species of extant planktonic foraminifera that are commonly used in paleoceanographic studies. Our pipeline begins with digital photographs taken under 16 different illuminations using an LED ring, which are then fused into a single 3D image. Labeled image sets were used to train various types of image classification algorithms, and performance on unlabeled image sets was measured in terms of precision (whether IDs are correct) and recall (what fraction of the target species are found). We find that Convolutional Neural Network (CNN) approaches achieve precision and recall values between 80 and 90%, which is similar precision and better recall than human expert performance using the same type of photographs. We have also trained a CNN to segment the 3D images into individual chambers and apertures, which can not only improve identification performance but also automate the measurement of foraminifera for morphometric studies. Given that there are only 35 species of extant planktonic foraminifera larger than 150 μm, we suggest that a fully automated characterization of this assemblage is attainable. This is the first step toward the realization of a foram picking robot.

  3. Integrating biological and social values when prioritizing places for biodiversity conservation.

    Science.gov (United States)

    Whitehead, Amy L; Kujala, Heini; Ives, Christopher D; Gordon, Ascelin; Lentini, Pia E; Wintle, Brendan A; Nicholson, Emily; Raymond, Christopher M

    2014-08-01

    The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes. © 2014 Society for Conservation Biology.

  4. Diversity of Secondary Metabolites from Marine Bacillus Species: Chemistry and Biological Activity

    Science.gov (United States)

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Islam, Mohammad Tofazzal

    2013-01-01

    Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed. PMID:23941823

  5. Systematics and biology of Cotesia typhae sp. n. (Hymenoptera, Braconidae, Microgastrinae, a potential biological control agent against the noctuid Mediterranean corn borer, Sesamia nonagrioides

    Directory of Open Access Journals (Sweden)

    Laure Kaiser

    2017-07-01

    Full Text Available Many parasitoid species are subjected to strong selective pressures from their host, and their adaptive response may result in the formation of genetically differentiated populations, called host races. When environmental factors and reproduction traits prevent gene flow, host races become distinct species. Such a process has recently been documented within the Cotesia flavipes species complex, all of which are larval parasitoids of moth species whose larvae are stem borers of Poales. A previous study on the African species C. sesamiae, incorporating molecular, ecological and biological data on various samples, showed that a particular population could be considered as a distinct species, because it was specialized at both host (Sesamia nonagrioides and plant (Typha domingensis levels, and reproductively isolated from other C. sesamiae. Due to its potential for the biological control of S. nonagrioides, a serious corn pest in Mediterranean countries and even in Iran, we describe here Cotesia typhae Fernandez-Triana sp. n. The new species is characterized on the basis of morphological, molecular, ecological and geographical data, which proved to be useful for future collection and rapid identification of the species within the species complex. Fecundity traits and parasitism success on African and European S. nonagrioides populations, estimated by laboratory studies, are also included.

  6. Identification of clinical isolates of Aspergillus, including cryptic species, by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Vidal-Acuña, M Reyes; Ruiz-Pérez de Pipaón, Maite; Torres-Sánchez, María José; Aznar, Javier

    2017-12-08

    An expanded library of matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been constructed using the spectra generated from 42 clinical isolates and 11 reference strains, including 23 different species from 8 sections (16 cryptic plus 7 noncryptic species). Out of a total of 379 strains of Aspergillus isolated from clinical samples, 179 strains were selected to be identified by sequencing of beta-tubulin or calmodulin genes. Protein spectra of 53 strains, cultured in liquid medium, were used to construct an in-house reference database in the MALDI-TOF MS. One hundred ninety strains (179 clinical isolates previously identified by sequencing and the 11 reference strains), cultured on solid medium, were blindy analyzed by the MALDI-TOF MS technology to validate the generated in-house reference database. A 100% correlation was obtained with both identification methods, gene sequencing and MALDI-TOF MS, and no discordant identification was obtained. The HUVR database provided species level (score of ≥2.0) identification in 165 isolates (86.84%) and for the remaining 25 (13.16%) a genus level identification (score between 1.7 and 2.0) was obtained. The routine MALDI-TOF MS analysis with the new database, was then challenged with 200 Aspergillus clinical isolates grown on solid medium in a prospective evaluation. A species identification was obtained in 191 strains (95.5%), and only nine strains (4.5%) could not be identified at the species level. Among the 200 strains, A. tubingensis was the only cryptic species identified. We demonstrated the feasibility and usefulness of the new HUVR database in MALDI-TOF MS by the use of a standardized procedure for the identification of Aspergillus clinical isolates, including cryptic species, grown either on solid or liquid media. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For

  7. Final Report NESPMAN: improving the knowledge of the biology and the fisheries of the new species for management

    NARCIS (Netherlands)

    Heessen, H.J.L.

    2010-01-01

    The NESPMAN (New Species for Management) project is meant to improve the knowledge of the biology and the fisheries of the new species for management. Apart from highly priced turbot, brill, striped red mullet and sea bass, these 12 species comprise also 3 gurnard species and 4 flatfishes. This

  8. Simple Identification of Human Taenia Species by Multiplex Loop-Mediated Isothermal Amplification in Combination with Dot Enzyme-Linked Immunosorbent Assay

    Science.gov (United States)

    Nkouawa, Agathe; Sako, Yasuhito; Okamoto, Munehiro; Ito, Akira

    2016-01-01

    For differential detection of Taenia solium, Taenia saginata, and Taenia asiatica, loop-mediated isothermal amplification (LAMP) assay targeting the cytochrome c oxidase subunit 1 gene has been recently developed and shown to be sensitive, specific, and effective. However, to achieve differential identification, one specimen requires three reaction mixtures containing a primer set of each Taenia species separately, which is complex and time consuming and increases the risk of cross-contamination. In this study, we developed a simple differential identification of human Taenia species using multiplex LAMP (mLAMP) in combination with dot enzyme-linked immunosorbent assay (dot-ELISA). Forward inner primers of T. solium, T. saginata, and T. asiatica labeled with fluorescein isothiocyanate (FITC), digoxigenin (DIG), and tetramethylrhodamine (TAMRA), respectively, and biotin-labeled backward inner primers were used in mLAMP. The mLAMP assay succeeded in specific amplification of each respective target gene in a single tube. Furthermore, the mLAMP product from each species was easily distinguished by dot-ELISA with an antibody specific for FITC, DIG, or TAMRA. The mLAMP assay in combination with dot-ELISA will make identification of human Taenia species simpler, easier, and more practical. PMID:27044566

  9. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

    Directory of Open Access Journals (Sweden)

    Fan Yang

    2018-01-01

    Full Text Available Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

  10. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine.

    Science.gov (United States)

    Yang, Fan; Ding, Fei; Chen, Hong; He, Mingqi; Zhu, Shixin; Ma, Xin; Jiang, Li; Li, Haifeng

    2018-01-01

    Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

  11. In vitro biological test of resistance to oxidation: application to identification of irradiated food

    International Nuclear Information System (INIS)

    Blache, D.; Prost, M.; Raffi, J.

    1991-01-01

    The test presented here for the identification of ionized food is a direct application of a biological test of resistance to oxidation, put on for an evaluation of antioxidant properties of pharmaceutic molecules and for the study of free radicals in biology. Consequently, the main part of this datum is relative to this biological test. We only point out, when necessary, how we plan to use it for food items. Our aim in this paper is to present a simple biological test (SPIRAL Patent Pending) to measure the total anti oxidative defence status of individuals utilizing some easy to handle cells: circulating cells. In this presentation, we only limited to red blood cells, but any cell could be used after suitable adaptation of the procedure. The first experiments carried out on irradiated foods are promising, even for foodstuffs in liquid state, but we have surely to do a lot of new ones in order to improve the specificity of this test with regard to irradiation and to define with which food it can be used. (9 refs; 15 figs)

  12. Palaearctic Hoplitis bees of the subgenus Platosmia (Megachilidae, Osmiini): biology, taxonomy and key to species.

    Science.gov (United States)

    Müller, Andreas

    2015-03-18

    Platosmia, a subgenus of the osmiine bee genus Hoplitis (Megachilidae), contains ten species, which are confined to desertic and semidesertic areas of the Palaearctic region. Analysis of female pollen loads and field observations indicate that several H. (Platosmia) species are strictly oligolectic on Reseda (Resedaceae) and possibly Hedysareae (Fabaceae), while others are mesolectic on both Reseda and Fabaceae. The few data available so far suggest that preexisting cavities in stones and rocks serve as nesting sites of H. (Platosmia). The taxonomic revision of H. (Platosmia) revealed the existence of an undescribed species from the Arabian peninsula, H. arabiae spec. nov.. Hoplitis incognita Zanden, 1996 and H. quarzazati (Zanden, 1998) are newly synonymized with H. maghrebensis (Zanden, 1992) and H. platalea (Warncke, 1990), respectively. Identification keys for all H. (Platosmia) species are given including the hitherto unknown male or female sex of three species.

  13. A nuclear DNA-based species determination and DNA quantification assay for common poultry species.

    Science.gov (United States)

    Ng, J; Satkoski, J; Premasuthan, A; Kanthaswamy, S

    2014-12-01

    DNA testing for food authentication and quality control requires sensitive species-specific quantification of nuclear DNA from complex and unknown biological sources. We have developed a multiplex assay based on TaqMan® real-time quantitative PCR (qPCR) for species-specific detection and quantification of chicken (Gallus gallus), duck (Anas platyrhynchos), and turkey (Meleagris gallopavo) nuclear DNA. The multiplex assay is able to accurately detect very low quantities of species-specific DNA from single or multispecies sample mixtures; its minimum effective quantification range is 5 to 50 pg of starting DNA material. In addition to its use in food fraudulence cases, we have validated the assay using simulated forensic sample conditions to demonstrate its utility in forensic investigations. Despite treatment with potent inhibitors such as hematin and humic acid, and degradation of template DNA by DNase, the assay was still able to robustly detect and quantify DNA from each of the three poultry species in mixed samples. The efficient species determination and accurate DNA quantification will help reduce fraudulent food labeling and facilitate downstream DNA analysis for genetic identification and traceability.

  14. Biological activities of undescribed North American lichen species.

    Science.gov (United States)

    Yeash, Erik A; Letwin, Lyndon; Malek, Lada; Suntres, Zacharias; Knudsen, Kerry; Christopher, Lew P

    2017-11-01

    Lichens provide a large array of compounds with the potential for pharmaceutical development. In the present study, extracts from three previously undescribed North American lichen species were examined for antioxidant, antibacterial and anticancer activities. The results from this study demonstrated the following: (i) Acarospora socialis ethanol extract exhibited significant DPPH antioxidant scavenging activities, which were concentration dependent; (ii) acetone and ethyl acetate extracts of Xanthoparmelia mexicana inhibited Gram-positive bacteria but had no effect on Gram-negative bacteria; X. mexicana acetone extract yielded a minimum inhibitory concentration (MIC) of 20.9 µg mL -1 against Staphylococcus aureus, and 41.9 µg mL -1 against Enterococcus faecalis; (iii) acetone extract of Lobothallia alphoplaca inhibited growth of cultured breast cancer MCF-7 cells with an effective concentration (EC 50 ) of 87 µg mL -1 ; the MCF-7 cell cycle appears arrested in the G2 phase, whereas the DNA synthesis cell cycle (S) may be inhibited. New lichen species that possess strong biological activities have been identified. These lichens comprise secondary metabolites that possess antioxidant, antibacterial and anticancer properties. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  15. Direct maldi-tof mass spectrometry assay of blood culture broths for rapid identification of Candida species causing bloodstream infections: an observational study in two large microbiology laboratories.

    Science.gov (United States)

    Spanu, Teresa; Posteraro, Brunella; Fiori, Barbara; D'Inzeo, Tiziana; Campoli, Serena; Ruggeri, Alberto; Tumbarello, Mario; Canu, Giulia; Trecarichi, Enrico Maria; Parisi, Gabriella; Tronci, Mirella; Sanguinetti, Maurizio; Fadda, Giovanni

    2012-01-01

    We evaluated the reliability of the Bruker Daltonik's MALDI Biotyper system in species-level identification of yeasts directly from blood culture bottles. Identification results were concordant with those of the conventional culture-based method for 95.9% of Candida albicans (187/195) and 86.5% of non-albicans Candida species (128/148). Results were available in 30 min (median), suggesting that this approach is a reliable, time-saving tool for routine identification of Candida species causing bloodstream infection.

  16. Characterization of Aspergillus species on Brazil nut from the Brazilian Amazonian region and development of a PCR assay for identification at the genus level

    Science.gov (United States)

    2014-01-01

    Background Brazil nut is a protein-rich extractivist tree crop in the Amazon region. Fungal contamination of shells and kernel material frequently includes the presence of aflatoxigenic Aspergillus species from the section Flavi. Aflatoxins are polyketide secondary metabolites, which are hepatotoxic carcinogens in mammals. The objectives of this study were to identify Aspergillus species occurring on Brazil nut grown in different states in the Brazilian Amazon region and develop a specific PCR method for collective identification of member species of the genus Aspergillus. Results Polyphasic identification of 137 Aspergillus strains isolated from Brazil nut shell material from cooperatives across the Brazilian Amazon states of Acre, Amapá and Amazonas revealed five species, with Aspergillus section Flavi species A. nomius and A. flavus the most abundant. PCR primers ASP_GEN_MTSSU_F1 and ASP_GEN_MTSSU_R1 were designed for the genus Aspergillus, targeting a portion of the mitochondrial small subunit ribosomal RNA gene. Primer specificity was validated through both electronic PCR against target gene sequences at Genbank and in PCR reactions against DNA from Aspergillus species and other fungal genera common on Brazil nut. Collective differentiation of the observed section Flavi species A. flavus, A. nomius and A. tamarii from other Aspergillus species was possible on the basis of RFLP polymorphism. Conclusions Given the abundance of Aspergillus section Flavi species A. nomius and A. flavus observed on Brazil nut, and associated risk of mycotoxin accumulation, simple identification methods for such mycotoxigenic species are of importance for Hazard Analysis Critical Control Point system implementation. The assay for the genus Aspergillus represents progress towards specific PCR identification and detection of mycotoxigenic species. PMID:24885088

  17. Invasive Species Guidebook for Department of Defense Installations in the Chesapeake Bay Watershed: Identification, Control, and Restoration

    Science.gov (United States)

    2007-11-01

    Crown vetch Coronilla varia MD, VA 14 Leafy spurge Euphorbia esula VA 15 Ground ivy Glechoma hederacea DC, MD, PA, VA, WV 17 Cogongrass Imperata ...INSTALLATIONS IN THE CHESAPEAKE BAY WATERSHED IDENTIFICATION AND CONTROL METHODS Cogongrass ( Imperata cylindrica) Description & Biology – A large

  18. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

    Science.gov (United States)

    Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

    2016-01-19

    Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Identification of salivary Lactobacillus rhamnosus species by DNA profiling and a specific probe.

    Science.gov (United States)

    Richard, B; Groisillier, A; Badet, C; Dorignac, G; Lonvaud-Funel, A

    2001-03-01

    The Lactobacillus genus has been shown to be associated with the dental carious process, but little is known about the species related to the decay, although Lactobacillus rhamnosus is suspected to be the most implicated species. Conventional identification methods based on biochemical criteria lead to ambiguous results, since the Lactobacillus species found in saliva are phenotypically close. To clarify the role of this genus in the evolution of carious disease, this work aimed to find a rapid and reliable method for identifying the L. rhamnosus species. Methods based on hybridization with DNA probes and DNA amplification by PCR were used. The dominant salivary Lactobacillus species (reference strains from the ATCC) were selected for this purpose as well as some wild strains isolated from children's saliva. DNA profiling using semirandom polymorphic DNA amplification (semi-RAPD) generated specific patterns for L. rhamnosus ATCC 7469. The profiles of all L. rhamnosus strains tested were similar and could be grouped; these strains shared four common fragments. Wild strains first identified with classic methods shared common patterns with the L. rhamnosus species and could be reclassified. One fragment of the profile was purified, cloned, used as a probe and found to be specific to the L. rhamnosus species. These results may help to localize this species within its ecological niche and to elucidate the progression of the carious process.

  20. PCR Amplification of Ribosomal DNA for Species Identification in the Plant Pathogen Genus Phytophthora

    Science.gov (United States)

    Ristaino, Jean B.; Madritch, Michael; Trout, Carol L.; Parra, Gregory

    1998-01-01

    We have developed a PCR procedure to amplify DNA for quick identification of the economically important species from each of the six taxonomic groups in the plant pathogen genus Phytophthora. This procedure involves amplification of the 5.8S ribosomal DNA gene and internal transcribed spacers (ITS) with the ITS primers ITS 5 and ITS 4. Restriction digests of the amplified DNA products were conducted with the restriction enzymes RsaI, MspI, and HaeIII. Restriction fragment patterns were similar after digestions with RsaI for the following species: P. capsici and P. citricola; P. infestans, P. cactorum, and P. mirabilis; P. fragariae, P. cinnamomi, and P. megasperma from peach; P. palmivora, P. citrophthora, P. erythroseptica, and P. cryptogea; and P. megasperma from raspberry and P. sojae. Restriction digests with MspI separated P. capsici from P. citricola and separated P. cactorum from P. infestans and P. mirabilis. Restriction digests with HaeIII separated P. citrophthora from P. cryptogea, P. cinnamomi from P. fragariae and P. megasperma on peach, P. palmivora from P. citrophthora, and P. megasperma on raspberry from P. sojae. P. infestans and P. mirabilis digests were identical and P. cryptogea and P. erythroseptica digests were identical with all restriction enzymes tested. A unique DNA sequence from the ITS region I in P. capsici was used to develop a primer called PCAP. The PCAP primer was used in PCRs with ITS 1 and amplified only isolates of P. capsici, P. citricola, and P. citrophthora and not 13 other species in the genus. Restriction digests with MspI separated P. capsici from the other two species. PCR was superior to traditional isolation methods for detection of P. capsici in infected bell pepper tissue in field samples. The techniques described will provide a powerful tool for identification of the major species in the genus Phytophthora. PMID:9501434

  1. 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 fragment...... 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....

  2. Evaluation of the MIT RMID 1000 system for the identification of Listeria species.

    Science.gov (United States)

    Ricardi, John; Haavig, David; Cruz, Lasaunta; Paoli, George; Gehring, Andrew

    2010-01-01

    The Micro Imaging Technology (MIT) 1000 Rapid Microbial Identification (RMID) System is a device that uses the principles of light scattering coupled with proprietary algorithms to identify bacteria after being cultured and placed in a vial of filtered water. This specific method is for pure culture identification of Listeria spp. A total of 81 microorganisms (55 isolates) were tested by the MIT 1000 System, of which 25 were Listeria spp. and 30 a variety of other bacterial species. In addition, a total of 406 tests over seven different ruggedness parameters were tested by the MIT 1000 System to determine its flexibility to the specifications stated in the MIT 1000 System User Guide in areas where they might be deviated by a user to shorten the test cycle. Overall, MIT concluded that the MIT 1000 System had an accuracy performance that should certify this Performance Test Method for the identification of Listeria spp. This report discusses the tests performed, results achieved, and conclusions, along with several reference documents to enable a higher understanding of the technology used by the MIT 1000 System.

  3. A 1.5 hour procedure for identification of Enterococcus Species directly from blood cultures.

    Science.gov (United States)

    Morgan, Margie A; Marlowe, Elizabeth; Novak-Weekly, Susan; Miller, J M; Painter, T M; Salimnia, Hossein; Crystal, Benjamin

    2011-02-10

    Enterococci are a common cause of bacteremia with E. faecalis being the predominant species followed by E. faecium. Because resistance to ampicillin and vancomycin in E. faecalis is still uncommon compared to resistance in E. faecium, the development of rapid tests allowing differentiation between enterococcal species is important for appropriate therapy and resistance surveillance. The E. faecalis OE PNA FISH assay (AdvanDx, Woburn, MA) uses species-specific peptide nucleic acid (PNA) probes in a fluorescence in situ hybridization format and offers a time to results of 1.5 hours and the potential of providing important information for species-specific treatment. Multicenter studies were performed to assess the performance of the 1.5 hour E. faecalis/OE PNA FISH procedure compared to the original 2.5 hour assay procedure and to standard bacteriology methods for the identification of enterococci directly from a positive blood culture bottle.

  4. Exploration and classification of chromatographic fingerprints as additional tool for identification and quality control of several Artemisia species.

    Science.gov (United States)

    Alaerts, Goedele; Pieters, Sigrid; Logie, Hans; Van Erps, Jürgen; Merino-Arévalo, Maria; Dejaegher, Bieke; Smeyers-Verbeke, Johanna; Vander Heyden, Yvan

    2014-07-01

    The World Health Organization accepts chromatographic fingerprints as a tool for identification and quality control of herbal medicines. This is the first study in which the distinction, identification and quality control of four different Artemisia species, i.e. Artemisia vulgaris, A. absinthium, A. annua and A. capillaris samples, is performed based on the evaluation of entire chromatographic fingerprint profiles developed with identical experimental conditions. High-Performance Liquid Chromatography (HPLC) with Diode Array Detection (DAD) was used to develop the fingerprints. Application of factorial designs leads to methanol/water (80:20 (v/v)) as the best extraction solvent for the pulverised plant material and to a shaking bath for 30 min as extraction method. Further, so-called screening, optimisation and fine-tuning phases were performed during fingerprint development. Most information about the different Artemisia species, i.e. the highest number of separated peaks in the fingerprint, was acquired on four coupled Chromolith columns (100 mm × 4.6 mm I.D.). Trifluoroacetic acid 0.05% (v/v) was used as mobile-phase additive in a stepwise linear methanol/water gradient, i.e. 5, 34, 41, 72 and 95% (v/v) methanol at 0, 9, 30, 44 and 51 min, where the last mobile phase composition was kept isocratic till 60 min. One detection wavelength was selected to perform data analysis. The lowest similarity between the fingerprints of the four species was present at 214 nm. The HPLC/DAD method was applied on 199 herbal samples of the four Artemisia species, resulting in 357 fingerprints. The within- and between-day variation of the entire method, as well as the quality control fingerprints obtained during routine analysis, were found acceptable. The distinction of these Artemisia species was evaluated based on the entire chromatographic profiles, developed by a shared method, and visualised in score plots by means of the Principal Component Analysis (PCA) exploratory data

  5. Morphological, molecular and biological evidence reveal two cryptic species in Mecinus janthinus Germar (Coleoptera, Curculionidae), a successful biological control agent of Dalmatian toadflax, Linaria dalmatica (Lamiales, Plantaginaceae)

    Science.gov (United States)

    Ivo Tosevski; Roberto Caldara; Jelena Jovic; Gerardo Hernandez-Vera; Cosimo Baviera; Andre Gassmann; Brent C. Emerson

    2011-01-01

    A combined morphological, molecular and biological study shows that the weevil species presently named Mecinus janthinus is actually composed of two different cryptic species: M. janthinus Germar, 1821 and M. janthiniformis Tosevski & Caldara sp.n. These species are morphologically distinguishable from each other by a few very subtle morphological characters. On...

  6. The biological activities and chemical composition of Pereskia species (Cactaceae)--a review.

    Science.gov (United States)

    Pinto, Nícolas de Castro Campos; Scio, Elita

    2014-09-01

    The exploration of nature as a source of sustainable, novel bioactive substances continues to grow as natural products play a significant role in the search for new therapeutic and agricultural agents. In this context, plants of the genus Pereskia (Cactaceae) have been studied for their biological activities, and are evolving as an interesting subject in the search for new, bioactive compounds. These species are commonly used as human foodstuffs and in traditional medicine to treat a variety of diseases. This review focuses on the bioactivity and chemical composition of the genus Pereskia, and aims to stimulate further studies on the chemistry and biological potential of the genus.

  7. Identification of Colletotrichum species causing anthracnose on Tahiti lime, tree tomato and mango

    Directory of Open Access Journals (Sweden)

    Martínez Erika P.

    2009-08-01

    Full Text Available

    In Colombia, citrus, tree tomato and mango crops are likely to suffer considerable losses from anthracnose caused by several Colletotrichum species, which were identified by the present study on infected organs of the three fruit crops, sampled in different regions of the country. Identification was based on their morphological and molecular characteristics, as well as on fungicide (benomyl and copper hydroxide sensitivity and pathogenicity tests. The latter assessed infectivity on both the original hosting crop and the other two crops (crossed infection, by putting the fungi in contact with organs taken from the three fruit crops. Molecular identification of the Colletotrichum species was carried out through amplification of rDNA ITS regions by means of C. gloeosporioides (CgInt and C. acutatum (CaInt2 specific primer PCR combining the use of ITS4 universal primer. The results indicate that C. acutatum is the infectious agent in Tahiti lime and tree tomato, and so is C. gloeosporioides in mango. Although C. acutatum is the infectious agent in two diferent fruit species, the strains proved to be specific of their original hosts.

  8. Cimicifuga species identification by high performance liquid chromatography-photodiode array/mass spectrometric/evaporative light scattering detection for quality control of black cohosh products

    Science.gov (United States)

    He, Kan; Pauli, Guido F.; Zheng, Bolin; Wang, Huikang; Bai, Naisheng; Peng, Tangsheng; Roller, Marc; Zheng, Qunyi

    2006-01-01

    Black cohosh has become one of the most important herbal products in the U.S. dietary supplements market. It is manufactured from roots and rhizomes of Cimicifuga racemosa (Ranunculaceae). Botanical identification of the raw starting material is a key step in the quality control of black cohosh preparations. The present report summarizes a fingerprinting approach based on HPLC-PDA/MS/ELSD that has been developed and validated using a total of ten Cimicifuga species. These include three North American species, C. racemosa, C. americana, C. rubifolia, and seven Asian species, C. acerina, C. biternat, C. dahurica, C. heracleifolia, C. japonica, C. foetida, and C. simplex. The chemotaxonomic distinctiveness of the HPLC fingerprints allows identification of all ten Cimicifuga species. The triterpene glycosides cimigenol-3-O-arabinoside (3), cimifugin (12), and cimifugin-3-O-glucoside (18) were determined to be suitable species-specific markers for the distinction of C. racemosa from the other Cimicifuga species. In addition to identification, the fingerprint method provided insight into chemical interconversion processes occurring between the diverse triterpene glycosides contained in black cohosh. The reported method has proven its usefulness in the botanical standardization and quality control of black cohosh products. PMID:16515793

  9. Comparison of the identification results of Candida species obtained by BD Phoenix™ and Maldi-TOF (Bruker Microflex LT Biotyper 3.1).

    Science.gov (United States)

    Marucco, Andrea P; Minervini, Patricia; Snitman, Gabriela V; Sorge, Adriana; Guelfand, Liliana I; Moral, Laura López

    2018-02-05

    In patients with invasive fungal infections, the accurate and rapid identification of the genus Candida is of utmost importance since antimycotic sensitivity is closely related to the species. The aim of the present study was to compare the identification results of species of the genus Candida obtained by BD Phoenix™ (Becton Dickinson [BD]) and Maldi-TOF MS (Bruker Microflex LT Biotyper 3.1). A total of 192 isolates from the strain collection belonging to the Mycology Network of the Autonomous City of Buenos Aires, Argentina, were analyzed. The observed concordance was 95%. Only 10 strains (5%) were not correctly identified by the BD Phoenix™ system. The average identification time with the Yeast ID panels was 8h 22min. The BD Phoenix™ system proved to be a simple, reliable and effective method for identifying the main species of the genus Candida. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  10. Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings

    Science.gov (United States)

    Nadeem, Sayyada Ghufrana; Hakim, Shazia Tabassum; Kazmi, Shahana Urooj

    2010-01-01

    Introduction Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. Material and methods A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal–tween 80 agar and biochemical methods by using API 20 C AUX. Results The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. Conclusion The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients. PMID:21483597

  11. Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings

    Directory of Open Access Journals (Sweden)

    Sayyada Ghufrana Nadeem

    2010-02-01

    Full Text Available Introduction: Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. Material and methods: A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal–tween 80 agar and biochemical methods by using API 20 C AUX. Results: The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. Conclusion: The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients.

  12. Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings.

    Science.gov (United States)

    Nadeem, Sayyada Ghufrana; Hakim, Shazia Tabassum; Kazmi, Shahana Urooj

    2010-02-09

    Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal-tween 80 agar and biochemical methods by using API 20 C AUX. The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients.

  13. The species of the genus Diamesa (Diptera, Chironomidae) known to occur in Italian Alps and Apennines.

    Science.gov (United States)

    Montagna, Matteo; Urbanelli, Sandra; Rossaro, Bruno

    2016-11-15

    Some rare species from Italian Alps, belonging to the genus Diamesa Meigen, 1835 (Diptera, Chironomidae) are here redescribed as adult males, because only old, incomplete descriptions are available for these taxa. Terminology of male genitalia is reviewed, diagnostic features are illustrated in detail, and notes on biology and geographical distribution of the examined species are provided. An identification key to the known adult males is presented.

  14. Detection of cryptic species

    Energy Technology Data Exchange (ETDEWEB)

    Cockburn, A F; Jensen, T; Seawright, J A [United States Dept. of Agriculture, Agricultural Research Service, Medical and Veterinary Entomology Research Lab., Gainesville, FL (United States)

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author). 11 refs, 2 figs, 2 tabs.

  15. Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

    Science.gov (United States)

    Ayyadurai, Saravanan; Flaudrops, Christophe; Raoult, Didier; Drancourt, Michel

    2010-11-12

    Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species. When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes. These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates.

  16. Plant Identification Based on Leaf Midrib Cross-Section Images Using Fractal Descriptors.

    Directory of Open Access Journals (Sweden)

    Núbia Rosa da Silva

    Full Text Available The correct identification of plants is a common necessity not only to researchers but also to the lay public. Recently, computational methods have been employed to facilitate this task, however, there are few studies front of the wide diversity of plants occurring in the world. This study proposes to analyse images obtained from cross-sections of leaf midrib using fractal descriptors. These descriptors are obtained from the fractal dimension of the object computed at a range of scales. In this way, they provide rich information regarding the spatial distribution of the analysed structure and, as a consequence, they measure the multiscale morphology of the object of interest. In Biology, such morphology is of great importance because it is related to evolutionary aspects and is successfully employed to characterize and discriminate among different biological structures. Here, the fractal descriptors are used to identify the species of plants based on the image of their leaves. A large number of samples are examined, being 606 leaf samples of 50 species from Brazilian flora. The results are compared to other imaging methods in the literature and demonstrate that fractal descriptors are precise and reliable in the taxonomic process of plant species identification.

  17. Zymography Methods to Simultaneously Analyze Superoxide Dismutase and Catalase Activities: Novel Application for Yeast Species Identification.

    Science.gov (United States)

    Gamero-Sandemetrio, Esther; Gómez-Pastor, Rocío; Matallana, Emilia

    2017-01-01

    We provide an optimized protocol for a double staining technique to analyze superoxide dismutase enzymatic isoforms Cu-Zn SOD (Sod1) and Mn-SOD (Sod2) and catalase in the same polyacrylamide gel. The use of NaCN, which specifically inhibits yeast Sod1 isoform, allows the analysis of Sod2 isoform while the use of H 2 O 2 allows the analysis of catalase. The identification of a different zymography profiling of SOD and catalase isoforms in different yeast species allowed us to propose this technique as a novel yeast identification and classification strategy.

  18. Validity of photo-identification technique to analyze natural markings in Melanophryniscus montevidensis (Anura: Bufonidae

    Directory of Open Access Journals (Sweden)

    Ernesto Elgue

    2014-08-01

    Full Text Available Individual identification is useful for answering a variety of biological questions about animal life histories. Most of the techniques used to mark amphibians are invasive and can cause negative effects, compromising individual survivorship and biasing studies. Photo-identification consists in the identification of specimens based on photographic records of unique color-design patterns. This technique has been used with success in several amphibian species. Melanophryniscus montevidensis is an endangered anuran species inhabiting the Uruguayan Atlantic coast. The general pattern of coloration is black with red and yellow blotches on the belly. In this study, we validated the technique of photo-identification assisted by software for individual recognition in M. montevidensis using natural markings. Field trips were performed over 16 months during which, the ventral color pattern of specimens was photographed. The photos were edited and analyzed with the Wild-ID 1.0 software for photographic reconnaissance. An efficiency of 100% was obtained in the visual recognition and 90% in the detection of recaptures using the software. The use of photo-identification using natural marks is an effective technique in this species, because the color pattern of the belly was highly variable among individuals and remained unchanged in individuals over the 16 month period. In this evaluation the use of software for photo-identification was necessary for the treatment of large databases.

  19. Simple Identification of Human Taenia Species by Multiplex Loop-Mediated Isothermal Amplification in Combination with Dot Enzyme-Linked Immunosorbent Assay.

    Science.gov (United States)

    Nkouawa, Agathe; Sako, Yasuhito; Okamoto, Munehiro; Ito, Akira

    2016-06-01

    For differential detection of Taenia solium, Taenia saginata, and Taenia asiatica, loop-mediated isothermal amplification (LAMP) assay targeting the cytochrome c oxidase subunit 1 gene has been recently developed and shown to be sensitive, specific, and effective. However, to achieve differential identification, one specimen requires three reaction mixtures containing a primer set of each Taenia species separately, which is complex and time consuming and increases the risk of cross-contamination. In this study, we developed a simple differential identification of human Taenia species using multiplex LAMP (mLAMP) in combination with dot enzyme-linked immunosorbent assay (dot-ELISA). Forward inner primers of T. solium, T. saginata, and T. asiatica labeled with fluorescein isothiocyanate (FITC), digoxigenin (DIG), and tetramethylrhodamine (TAMRA), respectively, and biotin-labeled backward inner primers were used in mLAMP. The mLAMP assay succeeded in specific amplification of each respective target gene in a single tube. Furthermore, the mLAMP product from each species was easily distinguished by dot-ELISA with an antibody specific for FITC, DIG, or TAMRA. The mLAMP assay in combination with dot-ELISA will make identification of human Taenia species simpler, easier, and more practical. © The American Society of Tropical Medicine and Hygiene.

  20. Species identification of Candida isolated from clinical specimens in a tertiary care hospital

    Directory of Open Access Journals (Sweden)

    lsmet Nigar

    2016-07-01

    Full Text Available Background: Candida species are responsible for various clinical manifestations from mucocutaneous overgrowth to blood stream infections especially in immunocompromized situations. Although C. albicans is the most prevalent species, high incidence of non-albicans Candida species with antifungal resistance are emerging which is posing a serious threat to the patients care.Objective: This study aimed to isolate and identify different species of Candida from different clinical specimens. Methods: A total of 100 different clinical specimens were studied of which 35 were oral swab, 28 were high vaginal swab, 15 were urine, 14 were nail, 04 were bronchoalveolar lavage and peritoneal fluid were 04. Among 100 clinical specimens, Candida isolates were identified in 64 specimens. Isolation of Candida species was done by primary culture in SDA. Subsequent identification of species were performed by germ tube test, subculture in chromo­genic agar medium and carbohydrate assimilation test with commonly used twelve sugars.Results: Out of 64 isolated Candida species, Candida albicans were 51.56% and the non-albicans Candida species were 48.44%. The most prevalent Candida species was C. albicans 33 (51.53% followed by C. tropicalis 17 (26.56%. C. glabrata 4 (6.25%, C. parapsilo­sis 4 (6.25%, C. krusei 3 (4.68% and C. guilliermondii 2 (3.2%. One of the isolated Candida species was unidentified.Conclusion: Though Candida albicans was found as the most common species, but non-albicans Candida species are appearing as emerging pathogens as well. Exposure to chemotherapy appeared to be the commonest predisposing factor for Candida infection followed by indwelling urinary catheter in situ for prolong period.

  1. Mayfly and fish species identification and sex determination in bleak (Alburnus alburnus) by MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Maasz, G; Takács, P; Boda, P; Varbiro, G; Pirger, Z

    2017-12-01

    Besides food quality control of fish or cephalopods, the novel mass spectrometry (MS) approaches could be effective and beneficial methods for the investigation of biodiversity in ecological research. Our aims were to verify the applicability of MALDI-TOF MS in the rapid identification of closely related species, and to further develop it for sex determination in phenotypically similar fish focusing on the low mass range. For MALDI-TOF MS spectra analysis, ClinProTools software was applied, but our observed classification was also confirmed by Self Organizing Map. For verifying the wide applicability of the method, brains from invertebrate and vertebrate species were used in order to detect the species related markers from two mayflies and eight fish as well as sex-related markers within bleak. Seven Ephemera larvae and sixty-one fish species related markers were observed and nineteen sex-related markers were identified in bleak. Similar patterns were observed between the individuals within one species. In contrast, there were markedly diverse patterns between the different species and sexes visualized by SOMs. Two different Ephemera species and male or female fish were identified with 100% accuracy. The various fish species were classified into 8 species with a high level of accuracy (96.2%). Based on MS data, dendrogram was generated from different fish species by using ClinProTools software. This MS-based dendrogram shows relatively high correspondence with the phylogenetic relationships of both the studied species and orders. In summary, MALDI-TOF MS provides a cheap, reliable, sensitive and fast identification tool for researchers in the case of closely related species using mass spectra acquired in a low mass range to define specific molecular profiles. Moreover, we presented evidence for the first time for determination of sex within one fish species by using this method. We conclude that it is a powerful tool that can revolutionize ecological and

  2. A comparison of PCR-based markers for the molecular identification of Sphagnum species of the section Acutifolia

    Directory of Open Access Journals (Sweden)

    Jakub Sawicki

    2011-07-01

    Full Text Available RAPDs, ISJs, ISSRs, ITS and katGs were applied to determine genetic relationships between common Sphagnum species of the section Acutifolia. Twenty populations were genotyped using ten ISJ primers, 12 pairs of katG primers, 10 ISSR and 10 RAPD primers, and a restriction analysis of ITS1 and ITS2. ISSR and katG markers revealed the greatest number of species-specific bands. An analysis of ITS1 and ITS2 regions with restriction enzymes also proved to be a highly effective tool for species identification.

  3. Comparative biology of decellularized lung matrix: Implications of species mismatch in regenerative medicine.

    Science.gov (United States)

    Balestrini, Jenna L; Gard, Ashley L; Gerhold, Kristin A; Wilcox, Elise C; Liu, Angela; Schwan, Jonas; Le, Andrew V; Baevova, Pavlina; Dimitrievska, Sashka; Zhao, Liping; Sundaram, Sumati; Sun, Huanxing; Rittié, Laure; Dyal, Rachel; Broekelmann, Tom J; Mecham, Robert P; Schwartz, Martin A; Niklason, Laura E; White, Eric S

    2016-09-01

    Lung engineering is a promising technology, relying on re-seeding of either human or xenographic decellularized matrices with patient-derived pulmonary cells. Little is known about the species-specificity of decellularization in various models of lung regeneration, or if species dependent cell-matrix interactions exist within these systems. Therefore decellularized scaffolds were produced from rat, pig, primate and human lungs, and assessed by measuring residual DNA, mechanical properties, and key matrix proteins (collagen, elastin, glycosaminoglycans). To study intrinsic matrix biologic cues, human endothelial cells were seeded onto acellular slices and analyzed for markers of cell health and inflammation. Despite similar levels of collagen after decellularization, human and primate lungs were stiffer, contained more elastin, and retained fewer glycosaminoglycans than pig or rat lung scaffolds. Human endothelial cells seeded onto human and primate lung tissue demonstrated less expression of vascular cell adhesion molecule and activation of nuclear factor-κB compared to those seeded onto rodent or porcine tissue. Adhesion of endothelial cells was markedly enhanced on human and primate tissues. Our work suggests that species-dependent biologic cues intrinsic to lung extracellular matrix could have profound effects on attempts at lung regeneration. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

    DEFF Research Database (Denmark)

    Welker, F.

    2018-01-01

    Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identificati......Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein...... not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against......), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations...

  5. Simultaneous multi-species determination of trimethyllead, monomethylmercury and three butyltin compounds by species-specific isotope dilution GC-ICP-MS in biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Poperechna, Nataliya; Heumann, Klaus G. [Johannes Gutenberg-University Mainz (Germany). Institute of Inorganic Chemistry and Analytical Chemistry

    2005-09-01

    An accurate and sensitive multi-species species-specific isotope dilution GC-ICP-MS method was developed for the simultaneous determination of trimethyllead (Me{sub 3}Pb{sup +}), monomethylmercury (MeHg{sup +}) and the three butyltin species Bu{sub 3}Sn{sup +}, Bu{sub 2}Sn{sup 2+}, and BuSn{sup 3+} in biological samples. The method was validated by three biological reference materials (CRM 477, mussel tissue certified for butyltins; CRM 463, tuna fish certified for MeHg{sup +}; DORM 2, dogfish muscle certified for MeHg{sup +}). Under certain conditions, and with minor modifications of the sample pretreatment procedure, this method could also be transferred to environmental samples such as sediments, as demonstrated by analyzing sediment reference material BCR 646 (freshwater sediment, certified for butyltins). The detection limits of the multi-species GC-ICP-IDMS method for biological samples were 1.4 ng g{sup -1} for MeHg{sup +}, 0.06 ng g{sup -1} for Me{sub 3}Pb{sup +}, 0.3 ng g{sup -1} for BuSn{sup 3+} and Bu{sub 3}Sn{sup +}, and 1.2 ng g{sup -1} for Bu{sub 2}Sn{sup 2+}. Because of the high relevance of these heavy metal alkyl species to the quality assurance of seafood, the method was also applied to corresponding samples purchased from a supermarket. The methylated lead fraction in these samples, correlated to total lead, varied over a broad range (from 0.01% to 7.6%). On the other hand, the MeHg{sup +} fraction was much higher, normally in the range of 80-100%. Considering that we may expect tighter legislative limitations on MeHg{sup +} levels in seafood in the future, we found the highest methylmercury contents (up to 10.6 {mu}g g{sup -1}) in two shark samples, an animal which is at the end of the marine food chain, whereas MeHg{sup +} contents of less than 0.2 {mu}g g{sup -1} were found in most other seafood samples; these results correlate with the idea that MeHg{sup +} is usually of biological origin in the marine environment. The concentration of

  6. Identification of colletotrichum species causing anthracnose on tahiti lime, tree tomato and mango

    OpenAIRE

    Martínez, Erika P.; Hío, Juan C.; Osorio1, Jairo A.; Torres, María F.

    2009-01-01

    In Colombia, citrus, tree tomato and mango crops are likely to suffer considerable losses from anthracnose caused by several Colletotrichum species, which were identified by the present study on infected organs of the three fruit crops, sampled in different regions of the country. Identification was based on their morphological and molecular characteristics, as well as on fungicide (benomyl and copper hydroxide) sensitivity and pathogenicity tests. The latter assessed infectivity on both the ...

  7. On-site identification of meat species in processed foods by a rapid real-time polymerase chain reaction system.

    Science.gov (United States)

    Furutani, Shunsuke; Hagihara, Yoshihisa; Nagai, Hidenori

    2017-09-01

    Correct labeling of foods is critical for consumers who wish to avoid a specific meat species for religious or cultural reasons. Therefore, gene-based point-of-care food analysis by real-time Polymerase Chain Reaction (PCR) is expected to contribute to the quality control in the food industry. In this study, we perform rapid identification of meat species by our portable rapid real-time PCR system, following a very simple DNA extraction method. Applying these techniques, we correctly identified beef, pork, chicken, rabbit, horse, and mutton in processed foods in 20min. Our system was sensitive enough to detect the interfusion of about 0.1% chicken egg-derived DNA in a processed food sample. Our rapid real-time PCR system is expected to contribute to the quality control in food industries because it can be applied for the identification of meat species, and future applications can expand its functionality to the detection of genetically modified organisms or mutations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Measuring management success for protected species: Looking beyond biological outcomes

    Directory of Open Access Journals (Sweden)

    Kathryn D Bisack

    2016-05-01

    Full Text Available The complexity of the ocean ecosystem, including the human component, is such that a single fishery may require multiple policy instruments to support recovery and conservation of protected species, in addition to those for fisheries management. As regulations multiply, the need for retrospective analysis and evaluation grows in order to inform future policy. To accurately evaluate policy instruments, clear objectives and their link to outcomes are necessary, as well as identifying criteria to evaluate outcomes. The Northeast United States sink gillnet groundfish fishery provides a case study of the complexity of regulations and policy instruments implemented under the Marine Mammal Protection Act and the Endangered Species Act to address bycatch of marine mammals. The case study illustrates a range of possible objectives for the policy instruments including biological, economic, social-normative and longevity factors. We highlight links between possible objectives, outcomes and criteria for the four factors, as well as areas for consideration when undertaking ex-post analyses. To support learning from past actions, we call for a coordinated effort involving multiple disciplines and jurisdictions to undertake retrospective analyses and evaluations of key groups of policy instruments used for protected species.

  9. Essential Oils from Neotropical Piper Species and Their Biological Activities

    Science.gov (United States)

    da Trindade, Rafaela; Alves, Nayara Sabrina; Figueiredo, Pablo Luís; Maia, José Guilherme S.; Setzer, William N.

    2017-01-01

    The Piper genus is the most representative of the Piperaceae reaching around 2000 species distributed in the pantropical region. In the Neotropics, its species are represented by herbs, shrubs, and lianas, which are used in traditional medicine to prepare teas and infusions. Its essential oils (EOs) present high yield and are chemically constituted by complex mixtures or the predominance of main volatile constituents. The chemical composition of Piper EOs displays interspecific or intraspecific variations, according to the site of collection or seasonality. The main volatile compounds identified in Piper EOs are monoterpenes hydrocarbons, oxygenated monoterpenoids, sesquiterpene hydrocarbons, oxygenated sesquiterpenoids and large amounts of phenylpropanoids. In this review, we are reporting the biological potential of Piper EOs from the Neotropical region. There are many reports of Piper EOs as antimicrobial agents (fungi and bacteria), antiprotozoal (Leishmania spp., Plasmodium spp., and Trypanosoma spp.), acetylcholinesterase inhibitor, antinociceptive, anti-inflammatory and cytotoxic activity against different tumor cells lines (breast, leukemia, melanoma, gastric, among others). These studies can contribute to the rational and economic exploration of Piper species, once they have been identified as potent natural and alternative sources to treat human diseases. PMID:29240662

  10. Identification and Differentiation of Verticillium Species and V. longisporum Lineages by Simplex and Multiplex PCR Assays

    Science.gov (United States)

    Inderbitzin, Patrik; Davis, R. Michael; Bostock, Richard M.; Subbarao, Krishna V.

    2013-01-01

    Accurate species identification is essential for effective plant disease management, but is challenging in fungi including Verticillium sensu stricto (Ascomycota, Sordariomycetes, Plectosphaerellaceae), a small genus of ten species that includes important plant pathogens. Here we present fifteen PCR assays for the identification of all recognized Verticillium species and the three lineages of the diploid hybrid V. longisporum. The assays were based on DNA sequence data from the ribosomal internal transcribed spacer region, and coding and non-coding regions of actin, elongation factor 1-alpha, glyceraldehyde-3-phosphate dehydrogenase and tryptophan synthase genes. The eleven single target (simplex) PCR assays resulted in amplicons of diagnostic size for V. alfalfae, V. albo-atrum, V. dahliae including V. longisporum lineage A1/D3, V. isaacii, V. klebahnii, V. nonalfalfae, V. nubilum, V. tricorpus, V. zaregamsianum, and Species A1 and Species D1, the two undescribed ancestors of V. longisporum. The four multiple target (multiplex) PCR assays simultaneously differentiated the species or lineages within the following four groups: Verticillium albo-atrum, V. alfalfae and V. nonalfalfae; Verticillium dahliae and V. longisporum lineages A1/D1, A1/D2 and A1/D3; Verticillium dahliae including V. longisporum lineage A1/D3, V. isaacii, V. klebahnii and V. tricorpus; Verticillium isaacii, V. klebahnii and V. tricorpus. Since V. dahliae is a parent of two of the three lineages of the diploid hybrid V. longisporum, no simplex PCR assay is able to differentiate V. dahliae from all V. longisporum lineages. PCR assays were tested with fungal DNA extracts from pure cultures, and were not evaluated for detection and quantification of Verticillium species from plant or soil samples. The DNA sequence alignments are provided and can be used for the design of additional primers. PMID:23823707

  11. Improved identification of primary biological aerosol particles using single-particle mass spectrometry

    Directory of Open Access Journals (Sweden)

    M. A. Zawadowicz

    2017-06-01

    Full Text Available Measurements of primary biological aerosol particles (PBAP, especially at altitudes relevant to cloud formation, are scarce. Single-particle mass spectrometry (SPMS has been used to probe aerosol chemical composition from ground and aircraft for over 20 years. Here we develop a method for identifying bioaerosols (PBAP and particles containing fragments of PBAP as part of an internal mixture using SPMS. We show that identification of bioaerosol using SPMS is complicated because phosphorus-bearing mineral dust and phosphorus-rich combustion by-products such as fly ash produce mass spectra with peaks similar to those typically used as markers for bioaerosol. We have developed a methodology to differentiate and identify bioaerosol using machine learning statistical techniques applied to mass spectra of known particle types. This improved method provides far fewer false positives compared to approaches reported in the literature. The new method was then applied to two sets of ambient data collected at Storm Peak Laboratory and a forested site in Central Valley, California to show that 0.04–2 % of particles in the 200–3000 nm aerodynamic diameter range were identified as bioaerosol. In addition, 36–56 % of particles identified as biological also contained spectral features consistent with mineral dust, suggesting internal dust–biological mixtures.

  12. Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples.

    Directory of Open Access Journals (Sweden)

    Faith M Walker

    Full Text Available Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces based on a segment of the mitochondrial gene cytochrome c oxidase I (COI. The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species, and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets and community (using combined pellets collected from across long-term roost sites analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/ that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and

  13. The large carpenter bees of central Saudi Arabia, with notes on the biology of Xylocopa sulcatipes Maa (Hymenoptera, Apidae, Xylocopinae

    Directory of Open Access Journals (Sweden)

    Mohammed Hannan

    2012-06-01

    Full Text Available The large carpenter bees (Xylocopinae, Xylocopa Latreille occurring in central Saudi Arabia are reviewed. Two species are recognized in the fauna, Xylocopa (Koptortosoma aestuans (Linnaeus and X. (Ctenoxylocopa sulcatipes Maa. Diagnoses for and keys to the species of these prominent components of the central Saudi Arabian bee fauna are provided to aid their identification by pollination researchers active in the region. Females and males of both species are figured and biological notes provided for X. sulcatipes. Notes on the nesting biology and ecology of X. sulcatipes are appended. As in studies for this species from elsewhere, nests were found in dried stems of Calotropis procera (Aiton (Asclepiadaceae and Phoenix dactylifera L. (Arecaceae.

  14. Identification of microorganisms involved in nitrogen removal from wastewater treatment systems by means of molecular biology techniques

    International Nuclear Information System (INIS)

    Figueroa, M.; Alonso-Gutierrez, J.; Campos, J. L.; Mendez, R.; Mosquera-Corral, A.

    2010-01-01

    The identification of the main bacteria populations present in the granular biomass from a biological reactor treating wastewater has been performed by applying two different molecular biology techniques. By means of the DGGE technique five different genera of heterotrophic bacteria (Thiothrix, Thauera, Cloroflexi, Comamonas y Zoogloea) and one of ammonia oxidizing bacteria (Nitrosomanas) were identified. The FISH technique, based on microscopy, allowed the in situ visualization and quantification of those microorganisms. Special attention was paid to filamentous bacteria distribution (Thiothrix and Cloroflexi) which could exert a structural function in aerobic granular sludge. (Author) 26 refs.

  15. The combined rapid detection and species-level identification of yeasts in simulated blood culture using a colorimetric sensor array.

    Science.gov (United States)

    Shrestha, Nabin K; Lim, Sung H; Wilson, Deborah A; SalasVargas, Ana Victoria; Churi, Yair S; Rhodes, Paul A; Mazzone, Peter J; Procop, Gary W

    2017-01-01

    A colorimetric sensor array (CSA) has been demonstrated to rapidly detect and identify bacteria growing in blood cultures by obtaining a species-specific "fingerprint" of the volatile organic compounds (VOCs) produced during growth. This capability has been demonstrated in prokaryotes, but has not been reported for eukaryotic cells growing in culture. The purpose of this study was to explore if a disposable CSA could differentially identify 7 species of pathogenic yeasts growing in blood culture. Culture trials of whole blood inoculated with a panel of clinically important pathogenic yeasts at four different microorganism loads were performed. Cultures were done in both standard BacT/Alert and CSA-embedded bottles, after adding 10 mL of spiked blood to each bottle. Color changes in the CSA were captured as images by an optical scanner at defined time intervals. The captured images were analyzed to identify the yeast species. Time to detection by the CSA was compared to that in the BacT/Alert system. One hundred sixty-two yeast culture trials were performed, including strains of several species of Candida (Ca. albicans, Ca. glabrata, Ca. parapsilosis, and Ca. tropicalis), Clavispora (synonym Candida) lusitaniae, Pichia kudriavzevii (synonym Candida krusei) and Cryptococcus neoformans, at loads of 8.2 × 105, 8.3 × 103, 8.5 × 101, and 1.7 CFU/mL. In addition, 8 negative trials (no yeast) were conducted. All negative trials were correctly identified as negative, and all positive trials were detected. Colorimetric responses were species-specific and did not vary by inoculum load over the 500000-fold range of loads tested, allowing for accurate species-level identification. The mean sensitivity for species-level identification by CSA was 74% at detection, and increased with time, reaching almost 95% at 4 hours after detection. At an inoculum load of 1.7 CFU/mL, mean time to detection with the CSA was 6.8 hours (17%) less than with the BacT/Alert platform. The CSA

  16. Identification of the facultative heterochromatic X chromosome in females of 25 rodent species.

    Science.gov (United States)

    Kanda, N; Yosida, T H

    1979-01-01

    Treatment of the chromosomes of 25 rodent species with a 50 degrees C hypotonic solution and Giemsa staining permitted identification of the heterochromatic X chromosome in 24 species. With this technique, the facultative of the heterochromatic X chromosome or the facultative portion of large, composite-type X chromosoms is stained darker than the other chromosomes, allowing it to be distinguished from the homologous euchromatic X chromosome in female metaphase cells. Intense staining of the single X chromosome was not observed in male metaphase cells. It is suggested that this differential staining of one of the two X chromosomes might be due to qualitative differences in chromosomal proteins rather than to differences in the degree of chromosomal condensation or in DNA base sequence.

  17. Detection of biosurfactants in Bacillus species: genes and products identification.

    Science.gov (United States)

    Płaza, G; Chojniak, J; Rudnicka, K; Paraszkiewicz, K; Bernat, P

    2015-10-01

    To screen environmental Bacillus strains for detection of genes encoding the enzymes involved in biosurfactant synthesis and to evaluate their products e.g. surfactin, iturin and fengycin. The taxonomic identification of isolated from the environment Bacillus strains was performed by Microgene ID Bacillus panel and GEN III Biolog system. The polymerase chain reaction (PCR) strategy for screening of genes in Bacillus strains was set up. Liquid chromatography-mass spectrometry (LC-MS/MS) method was used for the identification of lipopeptides (LPs). All studied strains exhibited the presence of srfAA gene and produced surfactin mostly as four homologues (C13 to C16). Moreover, in 2 strains (KP7, T'-1) simultaneous co-production of 3 biosurfactants: surfactin, iturin and fengycin was observed. Additionally, it was found out that isolate identified as Bacillus subtilis ssp. subtilis (KP7), beside LPs co-production, synthesizes surfactin with the efficiency much higher than other studied strains (40·2 mg l(-1) ) and with the yield ranging from 0·8 to 8·3 mg l(-1) . We showed that the combined methodology based on PCR and LC-MS/MS technique is an optimal tool for the detection of genes encoding enzymes involved in biosurfactant synthesis as well as their products, e.g. surfactin, iturin and fengycin. This approach improves the screening and the identification of environmental Bacillus co-producing biosurfactants-stimulating and facilitating the development of this area of science. The findings of this work will help to improve screening of biosurfactant producers. Discovery of novel biosurfactants and biosurfactants co-production ability has shed light on their new application fields and for the understanding of their interactions and properties. © 2015 The Society for Applied Microbiology.

  18. Identification of a biomarker for propetamphos and development of a biological monitoring assay.

    Science.gov (United States)

    K Jones G Wang S J Garfitt J Cocker

    1999-01-01

    This paper describes the identification of a human metabolite of propetamphos ((E-O-2-isopropylcarbonyl-1-methylvinyl-O-methylethylphosphoramidothioate), formed by the hydrolytic cleavage of the enol-vinyl-phosphate bond, and the development of an analytical method suitable for biological monitoring of propetamphos exposure. The metabolite has been detected in the urine of exposed workers but not in that of control subjects. The analytical method involves azeotropic distillation of the urine with acetonitrile, followed by derivatization with pentafluorobenzyl bromide and analysis using gas chromatography with flame photometric detection.

  19. Molecular Identification of Necrophagous Muscidae and Sarcophagidae Fly Species Collected in Korea by Mitochondrial Cytochrome c Oxidase Subunit I Nucleotide Sequences

    Directory of Open Access Journals (Sweden)

    Yu-Hoon Kim

    2014-01-01

    Full Text Available Identification of insect species is an important task in forensic entomology. For more convenient species identification, the nucleotide sequences of cytochrome c oxidase subunit I (COI gene have been widely utilized. We analyzed full-length COI nucleotide sequences of 10 Muscidae and 6 Sarcophagidae fly species collected in Korea. After DNA extraction from collected flies, PCR amplification and automatic sequencing of the whole COI sequence were performed. Obtained sequences were analyzed for a phylogenetic tree and a distance matrix. Our data showed very low intraspecific sequence distances and species-level monophylies. However, sequence comparison with previously reported sequences revealed a few inconsistencies or paraphylies requiring further investigation. To the best of our knowledge, this study is the first report of COI nucleotide sequences from Hydrotaea occulta, Muscina angustifrons, Muscina pascuorum, Ophyra leucostoma, Sarcophaga haemorrhoidalis, Sarcophaga harpax, and Phaonia aureola.

  20. Direct identification and recognition of yeast species from clinical material by using albicans ID and CHROMagar Candida plates.

    OpenAIRE

    Baumgartner, C; Freydiere, A M; Gille, Y

    1996-01-01

    Two chromogenic media, Albicans ID and CHROMagar Candida agar plates, were compared with a reference medium, Sabouraud-chloramphenicol agar, and standard methods for the identification of yeast species. This study involved 951 clinical specimens. The detection rates for the two chromogenic media for polymicrobial specimens were 20% higher than that for the Sabouraud-chloramphenicol agar plates. The rates of identification of Candida albicans for Albicans ID and CHROMagar Candida agar plates w...

  1. Identification of the same polyomavirus species in different African horseshoe bat species is indicative of short-range host-switching events.

    Science.gov (United States)

    Carr, Michael; Gonzalez, Gabriel; Sasaki, Michihito; Dool, Serena E; Ito, Kimihito; Ishii, Akihiro; Hang'ombe, Bernard M; Mweene, Aaron S; Teeling, Emma C; Hall, William W; Orba, Yasuko; Sawa, Hirofumi

    2017-10-06

    Polyomaviruses (PyVs) are considered to be highly host-specific in different mammalian species, with no well-supported evidence for host-switching events. We examined the species diversity and host specificity of PyVs in horseshoe bats (Rhinolophus spp.), a broadly distributed and highly speciose mammalian genus. We annotated six PyV genomes, comprising four new PyV species, based on pairwise identity within the large T antigen (LTAg) coding region. Phylogenetic comparisons revealed two instances of highly related PyV species, one in each of the Alphapolyomavirus and Betapolyomavirus genera, present in different horseshoe bat host species (Rhinolophus blasii and R. simulator), suggestive of short-range host-switching events. The two pairs of Rhinolophus PyVs in different horseshoe bat host species were 99.9 and 88.8 % identical with each other over their respective LTAg coding sequences and thus constitute the same virus species. To corroborate the species identification of the bat hosts, we analysed mitochondrial cytb and a large nuclear intron dataset derived from six independent and neutrally evolving loci for bat taxa of interest. Bayesian estimates of the ages of the most recent common ancestors suggested that the near-identical and more distantly related PyV species diverged approximately 9.1E4 (5E3-2.8E5) and 9.9E6 (4E6-18E6) years before the present, respectively, in contrast to the divergence times of the bat host species: 12.4E6 (10.4E6-15.4E6). Our findings provide evidence that short-range host-switching of PyVs is possible in horseshoe bats, suggesting that PyV transmission between closely related mammalian species can occur.

  2. Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi.

    Science.gov (United States)

    Normand, Anne-Cécile; Cassagne, Carole; Ranque, Stéphane; L'ollivier, Coralie; Fourquet, Patrick; Roesems, Sam; Hendrickx, Marijke; Piarroux, Renaud

    2013-04-08

    The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera.Identification effectiveness was improved by increasing the number of both RMS per strain (plibrary markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi.

  3. Shortcomings of the Commercial MALDI-TOF MS Database and Use of MLSA as an Arbiter in the Identification of Nocardia Species

    Science.gov (United States)

    Carrasco, Gema; de Dios Caballero, Juan; Garrido, Noelia; Valdezate, Sylvia; Cantón, Rafael; Sáez-Nieto, Juan A.

    2016-01-01

    Nocardia species are difficult to identify, a consequence of the ever increasing number of species known and their homogeneous genetic characteristics. 16S rRNA analysis has been the gold standard for identifying these organisms, but proteomic techniques such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF MS) and housekeeping gene analysis, have also been explored. One hundred high (n = 25), intermediate (n = 20), and low (n = 55) prevalence (for Spain) Nocardia strains belonging to 30 species were identified via 16S rRNA and MALDI-TOF MS analysis. The manufacturer-provided database MALDI Biotyper library v4.0 (5.627 entries, Bruker Daltonik) was employed. In the high prevalence group (Nocardia farcinica, N. abscessus, N. cyriacigeorgica and N. nova), the 16S rRNA and MALDI-TOF MS methods provided the same identification for 76% of the strains examined. For the intermediate prevalence group (N. brasiliensis, N. carnea, N. otitidiscaviarum and N. transvalensis complex), this figure fell to 45%. In the low-prevalence group (22 species), these two methods were concordant only in six strains at the species level. Tetra-gene multi-locus sequencing analysis (MLSA) involving the concatemer gyrB-16S rRNA-hsp65-secA1 was used to arbitrate between discrepant identifications (n = 67). Overall, the MLSA confirmed the results provided at species level by 16S rRNA analysis in 34.3% of discrepancies, and those provided by MALDI-TOF MS in 13.4%. MALDI-TOF MS could be a strong candidate for the identification of Nocardia species, but only if its reference spectrum database improves, especially with respect to unusual, recently described species and species included in the described Nocardia complexes. PMID:27148228

  4. Portuguese Thymbra and Thymus species volatiles: chemical composition and biological activities.

    Science.gov (United States)

    Figueiredo, A C; Barroso, J G; Pedro, L G; Salgueiro, L; Miguel, M G; Faleiro, M L

    2008-01-01

    Thymbra capitata and Thymus species are commonly known in Portugal as thyme and they are currently used as culinary herbs, as well as for ornamental, aromatizing and traditional medicinal purposes. The present work reports on the state of the art on the information available on the taxonomy, ethnobotany, cell and molecular biology of the Portuguese representatives of these genera and on the chemotaxonomy and antibacterial, antifungal and antioxidant activities of their essential oils and other volatile-containing extracts.

  5. Identification of Chlamydiae and Mycoplasma species in ruminants with ocular infections.

    Science.gov (United States)

    Gupta, S; Chahota, R; Bhardwaj, B; Malik, P; Verma, S; Sharma, M

    2015-02-01

    Infectious keratoconjunctivitis (IKC) is a highly contagious ocular inflammatory condition, which is often reported in domestic small and large ruminants. Multiple infectious aetiologies are reported to be involved, but information about the role of certain fastidious bacterial pathogens such as chlamydiae and mycoplasmas is limited in India. Hence, this study was performed to determine the role of these pathogens and their identification by molecular approach. A total of 53 samples from 31 ovine, 14 caprine and eight bovine having clinical symptoms were collected and tested using species-specific PCR tests for chlamydiae and mycoplasmas followed by nucleotide sequence analysis. The results showed 77.41, 14.29 and 25% samples were chlamydiae positive in ovine, caprine and bovine, respectively, whereas 41.93, 14.29 and 37.5% prevalence of mycoplasma infection was detected in ovine, caprine and bovines, respectively. Chlamydophila abortus, Chlamydophila psittaci, Mycoplasma arginini and Mycoplasma hyorhinis were detected from tested samples. To the best of our knowledge, this is the first time these species are identified in IKC cases from India. Coinfection of both chlamydial and mycoplasmal species was detected in eight IKC cases of ovine which suggest synergistic roles played by both chlamydiae and mycoplasma in IKC samples. © 2014 The Society for Applied Microbiology.

  6. Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes.

    Science.gov (United States)

    Yuan, Qing-Jun; Zhang, Bin; Jiang, Dan; Zhang, Wen-Jing; Lin, Tsai-Yun; Wang, Nian-He; Chiou, Shu-Jiau; Huang, Lu-Qi

    2015-03-01

    DNA barcodes have been increasingly used in authentication of medicinal plants, while their wide application in materia medica is limited in their accuracy due to incomplete sampling of species and absence of identification for materia medica. In this study, 95 leaf accessions of 23 species (including one variety) and materia medica of three Pharmacopoeia-recorded species of Angelica in China were collected to evaluate the effectiveness of four DNA barcodes (rbcL, matK, trnH-psbA and ITS). Our results showed that ITS provided the best discriminatory power by resolving 17 species as monophyletic lineages without shared alleles and exhibited the largest barcoding gap among the four single barcodes. The phylogenetic analysis of ITS showed that Levisticum officinale and Angelica sinensis were sister taxa, which indicates that L. officinale should be considered as a species of Angelica. The combination of ITS + rbcL + matK + trnH-psbA performed slight better discriminatory power than ITS, recovering 23 species without shared alleles and 19 species as monophyletic clades in ML tree. Authentication of materia medica using ITS revealed that the decoction pieces of A. sinensis and A. biserrata were partially adulterated with those of L. officinale, and the temperature around 80 °C processing A. dahurica decoction pieces obviously reduced the efficiency of PCR and sequencing. The examination of two cultivated varieties of A. dahurica from different localities indicated that the four DNA barcodes are inefficient for discriminating geographical authenticity of conspecific materia medica. This study provides an empirical paradigm in identification of medicinal plants and their materia medica using DNA barcodes. © 2014 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  7. Species identification of Aspergillus, Fusarium and Mucorales with direct surface analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    De Carolis, E; Posteraro, B; Lass-Flörl, C; Vella, A; Florio, A R; Torelli, R; Girmenia, C; Colozza, C; Tortorano, A M; Sanguinetti, M; Fadda, G

    2012-05-01

    Accurate species discrimination of filamentous fungi is essential, because some species have specific antifungal susceptibility patterns, and misidentification may result in inappropriate therapy. We evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for species identification through direct surface analysis of the fungal culture. By use of culture collection strains representing 55 species of Aspergillus, Fusarium and Mucorales, a reference database was established for MALDI-TOF MS-based species identification according to the manufacturer's recommendations for microflex measurements and MALDI BioTyper 2.0 software. The profiles of young and mature colonies were analysed for each of the reference strains, and species-specific spectral fingerprints were obtained. To evaluate the database, 103 blind-coded fungal isolates collected in the routine clinical microbiology laboratory were tested. As a reference method for species designation, multilocus sequencing was used. Eighty-five isolates were unequivocally identified to the species level (≥99% sequence similarity); 18 isolates producing ambiguous results at this threshold were initially rated as identified to the genus level only. Further molecular analysis definitively assigned these isolates to the species Aspergillus oryzae (17 isolates) and Aspergillus flavus (one isolate), concordant with the MALDI-TOF MS results. Excluding nine isolates that belong to the fungal species not included in our reference database, 91 (96.8%) of 94 isolates were identified by MALDI-TOF MS to the species level, in agreement with the results of the reference method; three isolates were identified to the genus level. In conclusion, MALDI-TOF MS is suitable for the routine identification of filamentous fungi in a medical microbiology laboratory. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

  8. Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding.

    Science.gov (United States)

    Nithaniyal, Stalin; Vassou, Sophie Lorraine; Poovitha, Sundar; Raju, Balaji; Parani, Madasamy

    2017-02-01

    Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.

  9. Does scale matter? A systematic review of incorporating biological realism when predicting changes in species distributions.

    Science.gov (United States)

    Record, Sydne; Strecker, Angela; Tuanmu, Mao-Ning; Beaudrot, Lydia; Zarnetske, Phoebe; Belmaker, Jonathan; Gerstner, Beth

    2018-01-01

    There is ample evidence that biotic factors, such as biotic interactions and dispersal capacity, can affect species distributions and influence species' responses to climate change. However, little is known about how these factors affect predictions from species distribution models (SDMs) with respect to spatial grain and extent of the models. Understanding how spatial scale influences the effects of biological processes in SDMs is important because SDMs are one of the primary tools used by conservation biologists to assess biodiversity impacts of climate change. We systematically reviewed SDM studies published from 2003-2015 using ISI Web of Science searches to: (1) determine the current state and key knowledge gaps of SDMs that incorporate biotic interactions and dispersal; and (2) understand how choice of spatial scale may alter the influence of biological processes on SDM predictions. We used linear mixed effects models to examine how predictions from SDMs changed in response to the effects of spatial scale, dispersal, and biotic interactions. There were important biases in studies including an emphasis on terrestrial ecosystems in northern latitudes and little representation of aquatic ecosystems. Our results suggest that neither spatial extent nor grain influence projected climate-induced changes in species ranges when SDMs include dispersal or biotic interactions. We identified several knowledge gaps and suggest that SDM studies forecasting the effects of climate change should: 1) address broader ranges of taxa and locations; and 1) report the grain size, extent, and results with and without biological complexity. The spatial scale of analysis in SDMs did not affect estimates of projected range shifts with dispersal and biotic interactions. However, the lack of reporting on results with and without biological complexity precluded many studies from our analysis.

  10. Reactive species in non-equilibrium atmospheric-pressure plasmas: Generation, transport, and biological effects

    Energy Technology Data Exchange (ETDEWEB)

    Lu, X., E-mail: luxinpei@hotmail.com [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240 (China); Naidis, G.V. [Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412 (Russian Federation); Laroussi, M. [Plasma Engineering & Medicine Institute, Old Dominion University, Norfolk, VA 23529 (United States); Reuter, S. [Leibniz Institute for Plasma Science and Technology, Felix-Hausdorff-Strasse 2, 17489 Greifswald (Germany); Graves, D.B. [Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720 (United States); Ostrikov, K. [Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000 (Australia); School of Physics, Chemistry, and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD 4000 (Australia); Commonwealth Scientific and Industrial Research Organization, P.O.Box 218, Lindfield, NSW 2070 (Australia); School of Physics, The University of Sydney, Sydney, NSW 2006 (Australia)

    2016-05-04

    Non-equilibrium atmospheric-pressure plasmas have recently become a topical area of research owing to their diverse applications in health care and medicine, environmental remediation and pollution control, materials processing, electrochemistry, nanotechnology and other fields. This review focuses on the reactive electrons and ionic, atomic, molecular, and radical species that are produced in these plasmas and then transported from the point of generation to the point of interaction with the material, medium, living cells or tissues being processed. The most important mechanisms of generation and transport of the key species in the plasmas of atmospheric-pressure plasma jets and other non-equilibrium atmospheric-pressure plasmas are introduced and examined from the viewpoint of their applications in plasma hygiene and medicine and other relevant fields. Sophisticated high-precision, time-resolved plasma diagnostics approaches and techniques are presented and their applications to monitor the reactive species and plasma dynamics in the plasma jets and other discharges, both in the gas phase and during the plasma interaction with liquid media, are critically reviewed. The large amount of experimental data is supported by the theoretical models of reactive species generation and transport in the plasmas, surrounding gaseous environments, and plasma interaction with liquid media. These models are presented and their limitations are discussed. Special attention is paid to biological effects of the plasma-generated reactive oxygen and nitrogen (and some other) species in basic biological processes such as cell metabolism, proliferation, survival, etc. as well as plasma applications in bacterial inactivation, wound healing, cancer treatment and some others. Challenges and opportunities for theoretical and experimental research are discussed and the authors’ vision for the emerging convergence trends across several disciplines and application domains is presented to

  11. Infinite graphs in systematic biology, with an application to the species problem.

    Science.gov (United States)

    Alexander, Samuel A

    2013-06-01

    We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T. A. Knight and C. Darwin, and sketch a decomposition result involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels' question, "Can biology lead to new theorems?"

  12. Identifications of Captive and Wild Tilapia Species Existing in Hawaii by Mitochondrial DNA Control Region Sequence

    Science.gov (United States)

    Wu, Liang; Yang, Jinzeng

    2012-01-01

    Background The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis. Methodology/Principal Findings In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization. Conclusions/Significance This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species

  13. A systematic identification of species-specific protein succinylation sites using joint element features information

    Directory of Open Access Journals (Sweden)

    Hasan MM

    2017-08-01

    Full Text Available Md Mehedi Hasan,1 Mst Shamima Khatun,2 Md Nurul Haque Mollah,2 Cao Yong,3 Dianjing Guo1 1School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, People’s Republic of China; 2Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh; 3Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen, People’s Republic of China Abstract: Lysine succinylation, an important type of protein posttranslational modification, plays significant roles in many cellular processes. Accurate identification of succinylation sites can facilitate our understanding about the molecular mechanism and potential roles of lysine succinylation. However, even in well-studied systems, a majority of the succinylation sites remain undetected because the traditional experimental approaches to succinylation site identification are often costly, time-consuming, and laborious. In silico approach, on the other hand, is potentially an alternative strategy to predict succinylation substrates. In this paper, a novel computational predictor SuccinSite2.0 was developed for predicting generic and species-specific protein succinylation sites. This predictor takes the composition of profile-based amino acid and orthogonal binary features, which were used to train a random forest classifier. We demonstrated that the proposed SuccinSite2.0 predictor outperformed other currently existing implementations on a complementarily independent dataset. Furthermore, the important features that make visible contributions to species-specific and cross-species-specific prediction of protein succinylation site were analyzed. The proposed predictor is anticipated to be a useful computational resource for lysine succinylation site prediction. The integrated species-specific online tool of SuccinSite2.0 is publicly

  14. A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models

    Science.gov (United States)

    Holsman, Kirstin K.; Ianelli, James; Aydin, Kerim; Punt, André E.; Moffitt, Elizabeth A.

    2016-12-01

    Multi-species statistical catch at age models (MSCAA) can quantify interacting effects of climate and fisheries harvest on species populations, and evaluate management trade-offs for fisheries that target several species in a food web. We modified an existing MSCAA model to include temperature-specific growth and predation rates and applied the modified model to three fish species, walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus) and arrowtooth flounder (Atheresthes stomias), from the eastern Bering Sea (USA). We fit the model to data from 1979 through 2012, with and without trophic interactions and temperature effects, and use projections to derive single- and multi-species biological reference points (BRP and MBRP, respectively) for fisheries management. The multi-species model achieved a higher over-all goodness of fit to the data (i.e. lower negative log-likelihood) for pollock and Pacific cod. Variability from water temperature typically resulted in 5-15% changes in spawning, survey, and total biomasses, but did not strongly impact recruitment estimates or mortality. Despite this, inclusion of temperature in projections did have a strong effect on BRPs, including recommended yield, which were higher in single-species models for Pacific cod and arrowtooth flounder that included temperature compared to the same models without temperature effects. While the temperature-driven multi-species model resulted in higher yield MBPRs for arrowtooth flounder than the same model without temperature, we did not observe the same patterns in multi-species models for pollock and Pacific cod, where variability between harvest scenarios and predation greatly exceeded temperature-driven variability in yield MBRPs. Annual predation on juvenile pollock (primarily cannibalism) in the multi-species model was 2-5 times the annual harvest of adult fish in the system, thus predation represents a strong control on population dynamics that exceeds temperature

  15. [Comparison of Phoenix™ Yeast ID Panel and API® ID 32C commercial systems for the identification of Candida species isolated from clinical samples].

    Science.gov (United States)

    Gayibova, Ülkü; Dalyan Cılo, Burcu; Ağca, Harun; Ener, Beyza

    2014-07-01

    Opportunistic fungal pathogens are one of the important causes of nosocomial infections, and several different types of yeasts, especially Candida species are increasingly recovered from immunocompromised patients. Since many of the yeasts are resistant to the commonly used antifungal agents, the introduction of appropriate therapy depends on rapid and accurate identification. The aims of this study were to compare the commercial identification systems namely API® ID 32C (bioMerieux, France) and Phoenix™ Yeast ID Panel (Becton Dickinson Diagnostics, USA) for the identification of Candida species and to evaluate the effect of morphological findings in the identification process. A total of 211 yeast strains isolated from different clinical samples (111 urine, 34 blood/vascular catheter, 27 upper/lower respiratory tract, 16 abscess/pus, 13 throat/vagina swabs and 10 sterile body fluids) of 137 patients hospitalized in Uludag University Health and Research Center between October 2013 to January 2014, were included in the study. Samples were cultured on blood agar, chromogenic agar (CHROMagar Candida, BD, USA) and Saboraud's dextrose agar (SDA), and isolated yeast colonies were evaluated with germ tube test and morphological examination by microscopy on cornmeal/Tween-80 agar. The isolates were identified as well by two commercial systems according to the manufacturers' recommendations. Discrepant results between the systems were tried to be resolved by using morphological characteristics of the yeasts. Of the isolates 159 were identified identical by both of the systems, and the concordance between those systems were estimated as 75.4%. According to the concordant identification, the most frequently isolated species was C.albicans (44.1%) followed by C.tropicalis (9.9%), C.glabrata (9.5%), C.parapsilosis (8.5%) and C.kefyr (8.1%). The concordance rate was 81.7% in identification of frequently isolated species (C.albicans, C.tropicalis, C.parapsilosis, C.glabrata, C

  16. Identification of liquid-phase decomposition species and reactions for guanidinium azotetrazolate

    International Nuclear Information System (INIS)

    Kumbhakarna, Neeraj R.; Shah, Kaushal J.; Chowdhury, Arindrajit; Thynell, Stefan T.

    2014-01-01

    Highlights: • Guanidinium azotetrazolate (GzT) is a high-nitrogen energetic material. • FTIR spectroscopy and ToFMS spectrometry were used for species identification. • Quantum mechanics was used to identify transition states and decomposition pathways. • Important reactions in the GzT liquid-phase decomposition process were identified. • Initiation of decomposition occurs via ring opening, releasing N 2 . - Abstract: The objective of this work is to analyze the decomposition of guanidinium azotetrazolate (GzT) in the liquid phase by using a combined experimental and computational approach. The experimental part involves the use of Fourier transform infrared (FTIR) spectroscopy to acquire the spectral transmittance of the evolved gas-phase species from rapid thermolysis, as well as to acquire spectral transmittance of the condensate and residue formed from the decomposition. Time-of-flight mass spectrometry (ToFMS) is also used to acquire mass spectra of the evolved gas-phase species. Sub-milligram samples of GzT were heated at rates of about 2000 K/s to a set temperature (553–573 K) where decomposition occurred under isothermal conditions. N 2 , NH 3 , HCN, guanidine and melamine were identified as products of decomposition. The computational approach is based on using quantum mechanics for confirming the identity of the species observed in experiments and for identifying elementary chemical reactions that formed these species. In these ab initio techniques, various levels of theory and basis sets were used. Based on the calculated enthalpy and free energy values of various molecular structures, important reaction pathways were identified. Initiation of decomposition of GzT occurs via ring opening to release N 2

  17. [Evaluation of PNA-FISH method for direct identification of Candida species in blood culture samples and its potential impact on guidance of antifungal therapy].

    Science.gov (United States)

    Doğan, Özlem; İnkaya, Ahmet Çağkan; Gülmez, Dolunay; Uzun, Ömrüm; Akova, Murat; Arıkan Akdağlı, Sevtap

    2016-10-01

    Early antifungal therapy has a major influence on survival in candidemia. Rapid identification of the species has importance for the treatment, prediction of the species-specific primary resistance and variable antifungal susceptibility. Recently, molecular-based methods attempt to reduce the time between the positive signal of a blood culture and identification of the fungus. PNA-FISH (Peptide nucleic acid fluorescence in situ hybridization) assay distinguishes a number of frequently isolated Candida species in groups following the growth in blood culture. The aim of this study was to investigate the correlation of the species identified by PNA-FISH with conventional identification methods in yeast positive blood cultures and its influence on the selection of antifungal therapy. Specimens of adult patients diagnosed as yeast with Gram stain in signal-positive blood cultures between August to December 2013, were included in the study. The strains were concomitantly cultivated by subculturing from the blood culture bottles onto solid media and identified by conventional methods (germ tube test, ID32C and morphology on cornmeal Tween 80 agar). Rapid species identification was performed by Yeast Traffic Light PNA-FISH, which generates green flourescence for Candida albicans and Candida parapsilosis, yellow for Candida tropicalis, and red for Candida krusei and Candida glabrata. C.tropicalis was identified as a single species whereas the others were identified in pairs. The time points when the yeast positive blood culture bottle was received by the mycology laboratory and reporting of the species identification results by PNA-FISH and the conventional methods were recorded. Seven C.albicans, six C.glabrata, three C.parapsilosis, one C.tropicalis, one C.krusei, one Cryptococcus neoformans, one Saprochaete capitata (Blastoschizomyces capitatus), one C.albicans and Candida dubliniensis, one C.krusei and C.dubliniensis, and one C.glabrata and C.parapsilosis were

  18. Ribosomal subunit protein typing using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification and discrimination of Aspergillus species.

    Science.gov (United States)

    Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Kusuya, Yoko; Takahashi, Hiroki; Yaguchi, Takashi

    2017-04-26

    Accurate identification of Aspergillus species is a very important subject. Mass spectral fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is generally employed for the rapid identification of fungal isolates. However, the results are based on simple mass spectral pattern-matching, with no peak assignment and no taxonomic input. We propose here a ribosomal subunit protein (RSP) typing technique using MALDI-TOF MS for the identification and discrimination of Aspergillus species. The results are concluded to be phylogenetic in that they reflect the molecular evolution of housekeeping RSPs. The amino acid sequences of RSPs of genome-sequenced strains of Aspergillus species were first verified and compared to compile a reliable biomarker list for the identification of Aspergillus species. In this process, we revealed that many amino acid sequences of RSPs (about 10-60%, depending on strain) registered in the public protein databases needed to be corrected or newly added. The verified RSPs were allocated to RSP types based on their mass. Peak assignments of RSPs of each sample strain as observed by MALDI-TOF MS were then performed to set RSP type profiles, which were then further processed by means of cluster analysis. The resulting dendrogram based on RSP types showed a relatively good concordance with the tree based on β-tubulin gene sequences. RSP typing was able to further discriminate the strains belonging to Aspergillus section Fumigati. The RSP typing method could be applied to identify Aspergillus species, even for species within section Fumigati. The discrimination power of RSP typing appears to be comparable to conventional β-tubulin gene analysis. This method would therefore be suitable for species identification and discrimination at the strain to species level. Because RSP typing can characterize the strains within section Fumigati, this method has potential as a powerful and reliable tool in

  19. An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2002-03-01

    Full Text Available Abstract Background The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However, it shows also great promise for other small organisms that are taxonomically difficult to tract. Results We have devised here an algorithm that aims to find the optimal probes for any given set of sequences. The program requires only a crude alignment of these sequences as input and is optimized for performance to deal also with very large datasets. The algorithm is designed such that the position of mismatches in the probes influences the selection and makes provision of single nucleotide outloops. Program implementations are available for Linux and Windows.

  20. The utricular otoliths, lapilli, of teleosts: their morphology and relevance for species identification and systematics studies

    Directory of Open Access Journals (Sweden)

    Carlos A. Assis

    2005-06-01

    Full Text Available The present study describes the general morphology of the utricular otoliths, lapilli, of teleost fishes, proposes a terminology for their parts, identifies their two major morphological types, provides some examples of their use in species identification, and discusses their usefulness in studies of fish phylogeny and systematics.

  1. Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants.

    Science.gov (United States)

    Zhang, Wei; Fan, Xiaohong; Zhu, Shuifang; Zhao, Hong; Fu, Lianzhong

    2013-01-01

    Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling-through this, DNA barcoding will greatly benefit the current fields of its application.

  2. Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Bernard La Scola

    Full Text Available BACKGROUND: With long delays observed between sampling and availability of results, the usefulness of blood cultures in the context of emergency infectious diseases has recently been questioned. Among methods that allow quicker bacterial identification from growing colonies, matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF mass spectrometry was demonstrated to accurately identify bacteria routinely isolated in a clinical biology laboratory. In order to speed up the identification process, in the present work we attempted bacterial identification directly from blood culture bottles detected positive by the automate. METHODOLOGY/PRINCIPAL FINDINGS: We prospectively analysed routine MALDI-TOF identification of bacteria detected in blood culture by two different protocols involving successive centrifugations and then lysis by trifluoroacetic acid or formic acid. Of the 562 blood culture broths detected as positive by the automate and containing one bacterial species, 370 (66% were correctly identified. Changing the protocol from trifluoroacetic acid to formic acid improved identification of Staphylococci, and overall correct identification increased from 59% to 76%. Lack of identification was observed mostly with viridans streptococci, and only one false positive was observed. In the 22 positive blood culture broths that contained two or more different species, only one of the species was identified in 18 samples, no species were identified in two samples and false species identifications were obtained in two cases. The positive predictive value of bacterial identification using this procedure was 99.2%. CONCLUSIONS/SIGNIFICANCE: MALDI-TOF MS is an efficient method for direct routine identification of bacterial isolates in blood culture, with the exception of polymicrobial samples and viridans streptococci. It may replace routine identification performed on colonies, provided improvement for the specificity of blood culture

  3. Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry.

    Science.gov (United States)

    La Scola, Bernard; Raoult, Didier

    2009-11-25

    With long delays observed between sampling and availability of results, the usefulness of blood cultures in the context of emergency infectious diseases has recently been questioned. Among methods that allow quicker bacterial identification from growing colonies, matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF) mass spectrometry was demonstrated to accurately identify bacteria routinely isolated in a clinical biology laboratory. In order to speed up the identification process, in the present work we attempted bacterial identification directly from blood culture bottles detected positive by the automate. We prospectively analysed routine MALDI-TOF identification of bacteria detected in blood culture by two different protocols involving successive centrifugations and then lysis by trifluoroacetic acid or formic acid. Of the 562 blood culture broths detected as positive by the automate and containing one bacterial species, 370 (66%) were correctly identified. Changing the protocol from trifluoroacetic acid to formic acid improved identification of Staphylococci, and overall correct identification increased from 59% to 76%. Lack of identification was observed mostly with viridans streptococci, and only one false positive was observed. In the 22 positive blood culture broths that contained two or more different species, only one of the species was identified in 18 samples, no species were identified in two samples and false species identifications were obtained in two cases. The positive predictive value of bacterial identification using this procedure was 99.2%. MALDI-TOF MS is an efficient method for direct routine identification of bacterial isolates in blood culture, with the exception of polymicrobial samples and viridans streptococci. It may replace routine identification performed on colonies, provided improvement for the specificity of blood culture broths growing viridans streptococci is obtained in the near future.

  4. Rapid detection and identification of Stachybotrys and Chaetomium species using tissue PCR analysis

    DEFF Research Database (Denmark)

    Lewinska, Anna Malgorzata; Peuhkuri, Ruut Hannele; Rode, Carsten

    2016-01-01

    level is essential for health risk assessment and building remediation. This study focuses on molecular identification of two common indoor fungal genera: Stachybotrys and Chaetomium. This study proposes two new DNA barcode candidates for Stachybotrys and Chaetomium: the gene encoding mitogen activated...... protein kinase (hogA) and the intergenic region between histone 3 and histone 4 (h3-h4) as well as it introduces a rapid - 3.5 h - protocol for direct Stachybotrys and Chaetomium species identification, which bypasses culture cultivation, DNA extraction and DNA sequencing....

  5. The genus Scrophularia: a source of iridoids and terpenoids with a diverse biological activity.

    Science.gov (United States)

    Pasdaran, Ardalan; Hamedi, Azadeh

    2017-12-01

    Scrophularia genus (Scrophulariaceae) includes about 350 species commonly known as figwort. Many species of this genus grow wild in nature and have not been cultivated yet. However, some species are in danger of extinction. This paper reviews the chemical compounds, biological activities and the ethnopharmacology of some Scrophularia species. All information was obtained through reported data on bibliographic database such as Scopus, United States National Agricultural Library, Biological Abstracts, EMBASE, PubMed, MedlinePlus, PubChem and Springer Link (1934-2017). The information in different Pharmacopoeias on this genus was also gathered from 1957 to 2007. The structures of 204 compounds and their biological activity were presented in the manuscript: glycoside esters, iridoid glycosides and triterpenoids are the most common compounds in this genus. Among them, scropolioside like iridoids have shown potential for anti-inflammatory, hepatoprotective and wound healing activity. Among the less frequently isolated compounds, resin glycosides such as crypthophilic acids have shown potent antiprotozoal and antimicrobial activities. The Scrophularia genus seems to be a rich source of iridoids and terpenoids, but isolation and identification of its alkaloids have been a neglected area of scientific study. The diverse chemical compounds and biological activities of this genus will motivate further investigation on Scrophularia genus as a source of new therapeutic medications.

  6. Molecular identification and antifungal susceptibility profile of Candida species isolated from patients with vulvovaginitis in Tehran, Iran.

    Science.gov (United States)

    Sharifynia, Somayeh; Falahati, Mehraban; Akhlaghi, Lame; Foroumadi, Alireza; Fateh, Roohollah

    2017-01-01

    Rapid and accurate identification and evaluation of antifungal susceptibility pattern of Candida isolates are crucial to determine suitable antifungal drugs for the treatment of patients with vulvovaginitis candidiasis. Vaginal samples were collected from 150 women with suspicious vaginal candidiasis, and then cultured on Sabouraoud's Dextrose Agar with chloramphenicol to isolate Candida species. After identification of Candida isolates using polymerase chain reaction-restriction fragment length polymorphism technique, antifungal susceptibility testing of four azolic antifungal drugs was carried out using broth microdilution method according to the CLSI M27-A3. Candida species were isolated from eighty suspected patients (61.79%). The most common pathogen was Candida albicans (63.75%). Resistance to fluconazole and ketoconazole was observed in 27.5% and 23.75% of Candida isolates, respectively, and only 2% of Candida isolates were resistant to miconazole. Interestingly, resistance to fluconazole in C. albicans was more than other Candida species. The results indicated that therapy should be selected according to the antifungal susceptibility tests for the prevention of treatment failure and miconazole therapy can be considered as the best therapeutic choice in the management of vulvovaginitis.

  7. Molecular identification and antifungal susceptibility profile of Candida species isolated from patients with vulvovaginitis in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    Somayeh Sharifynia

    2017-01-01

    Full Text Available Background: Rapid and accurate identification and evaluation of antifungal susceptibility pattern of Candida isolates are crucial to determine suitable antifungal drugs for the treatment of patients with vulvovaginitis candidiasis. Materials and Methods: Vaginal samples were collected from 150 women with suspicious vaginal candidiasis, and then cultured on Sabouraoud's Dextrose Agar with chloramphenicol to isolate Candida species. After identification of Candida isolates using polymerase chain reaction-restriction fragment length polymorphism technique, antifungal susceptibility testing of four azolic antifungal drugs was carried out using broth microdilution method according to the CLSI M27-A3. Results: Candida species were isolated from eighty suspected patients (61.79%. The most common pathogen was Candida albicans (63.75%. Resistance to fluconazole and ketoconazole was observed in 27.5% and 23.75% of Candida isolates, respectively, and only 2% of Candida isolates were resistant to miconazole. Interestingly, resistance to fluconazole in C. albicans was more than other Candida species. Conclusion: The results indicated that therapy should be selected according to the antifungal susceptibility tests for the prevention of treatment failure and miconazole therapy can be considered as the best therapeutic choice in the management of vulvovaginitis.

  8. Drivers of extinction risk in African mammals: the interplay of distribution state, human pressure, conservation response and species biology.

    Science.gov (United States)

    Di Marco, Moreno; Buchanan, Graeme M; Szantoi, Zoltan; Holmgren, Milena; Grottolo Marasini, Gabriele; Gross, Dorit; Tranquilli, Sandra; Boitani, Luigi; Rondinini, Carlo

    2014-01-01

    Although conservation intervention has reversed the decline of some species, our success is outweighed by a much larger number of species moving towards extinction. Extinction risk modelling can identify correlates of risk and species not yet recognized to be threatened. Here, we use machine learning models to identify correlates of extinction risk in African terrestrial mammals using a set of variables belonging to four classes: species distribution state, human pressures, conservation response and species biology. We derived information on distribution state and human pressure from satellite-borne imagery. Variables in all four classes were identified as important predictors of extinction risk, and interactions were observed among variables in different classes (e.g. level of protection, human threats, species distribution ranges). Species biology had a key role in mediating the effect of external variables. The model was 90% accurate in classifying extinction risk status of species, but in a few cases the observed and modelled extinction risk mismatched. Species in this condition might suffer from an incorrect classification of extinction risk (hence require reassessment). An increased availability of satellite imagery combined with improved resolution and classification accuracy of the resulting maps will play a progressively greater role in conservation monitoring.

  9. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

    Science.gov (United States)

    Welker, F

    2018-02-20

    The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized

  10. Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice.

    Science.gov (United States)

    Li, Jingjian; Xiong, Chao; He, Xia; Lu, Zhaocen; Zhang, Xin; Chen, Xiaoyang; Sun, Wei

    2018-01-01

    Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided.

  11. Recent Advances in Target Characterization and Identification by Photoaffinity Probes

    Directory of Open Access Journals (Sweden)

    Sang J. Chung

    2013-08-01

    Full Text Available Target identification of biologically active molecules such as natural products, synthetic small molecules, peptides, and oligonucleotides mainly relies on affinity chromatography, activity-based probes, or photoaffinity labeling (PAL. Amongst them, activity-based probes and PAL have offered great advantages in target identification technology due to their ability to form covalent bonds with the corresponding targets. Activity-based probe technology mainly relies on the chemical reactivity of the target proteins, thereby limiting the majority of the biological targets to enzymes or proteins which display reactive residues at the probe-binding site. In general, the probes should bear a reactive moiety such as an epoxide, a Michael acceptor, or a reactive alkyl halide in their structures. On the other hand, photoaffinity probes (PAPs are composed of a target-specific ligand and a photoactivatable functional group. When bound to the corresponding target proteins and activated with wavelength-specific light, PAPs generate highly reactive chemical species that covalently cross-link proximal amino acid residues. This process is better known as PAL and is widely employed to identify cellular targets of biologically active molecules. This review highlights recent advances in target identification by PAL, with a focus on the structure and chemistry of the photoaffinity probes developed in the recent decade, coupled to the target proteins identified using these probes.

  12. Systematics and biology of Xylocopa subgenus Schonnherria (Hymenoptera, Apidae) in Argentina.

    Science.gov (United States)

    Lucia, Mariano; Gonzalez, Victor H; Abrahamovich, Alberto H

    2015-01-01

    Biological information on the species of the large carpenter bee Xylocopa subgenus Schonnherria occurring in Argentina is revised. Based on the appraisal of museum specimens, the study of type material, and field surveys conducted across 15 provinces between 2007 and 2011, the following seven species are recognized for the country: Xylocopa bambusae Schrottky, Xylocopa chrysopoda Schrottky, Xylocopa macrops Lepeletier de Saint Fargeau, Xylocopa simillima Smith Xylocopa splendidula Lepeletier de Saint Fargeau, Xylocopa pulchra Smith, and Xylocopa viridis Smith. Previous literature records of Xylocopa dimidiata Latreille, Xylocopa subcyanea Pérez, and Xylocopa varians Smith for the province of Misiones appear to have been misidentified specimens, although the presence of these species in Argentina cannot be entirely ruled out given the proximity of this province to Brazil and Paraguay where they occur; Xylocopa boops Maidl was described from a male specimen with unusually enlarged eyes and is newly synonymized under Xylocopa macrops. Males and females of all species are diagnosed, described, and figured, including details of the male genitalia. Taxonomic comments, data on the geographical distribution and nesting substrates, and identification keys to all Argentinean species of Schonnherria are provided. The nesting biologies of Xylocopa splendidula and Xylocopa viridis are documented.

  13. Reproductive biology and natural hybridization between two endemic species of Pitcairnia (Bromeliaceae).

    Science.gov (United States)

    Wendt, T; Canela, M B; Gelli de Faria, A P; Rios, R I

    2001-10-01

    We investigated pollination biology and breeding systems in hybridizing populations of Pitcairnia albiflos and P. staminea; both species are endemic to rocky outcrops at Rio de Janeiro, Brazil. These species are morphologically distinct and easily recognized by floral color: white in P. albiflos and red in P. staminea. Putative hybrids show a large range of intermediate pink floral colors. The showy hermaphroditic flowers offer pollen and nectar that attract many visitors including bees, butterflies, hawk moths, and bats. Although the flowers of both parental species and hybrids open at night, only P. albiflos had other adaptations for nocturnal pollination. Flowering times overlapped during three consecutive years of observation. Bees visited both species and putative hybrids. Cross-pollinations were performed within and among parental species and hybrids in a greenhouse using plants transplanted from the field. Pitcairnia staminea and hybrids are self-compatible and could be spontaneously self-pollinated, whereas P. albiflos, though self-compatible, needs pollinators' services for self-pollination. Facultative agamospermy was found in the parental species. Prezygotic and postzygotic reproductive barriers between these taxa were weak. Reciprocal hand-pollinations between parental species and with hybrids yielded high fruit sets with viable seeds. Evaluations of fruit set, seed set, seed germination, and pollen viability were undertaken to compare the fitness of the hybrids relative to their parents. The hybrids showed equivalent fitness, except for lower pollen viability. Some conservation implications are noted.

  14. High-resolution melting of 12S rRNA and cytochrome b DNA sequences for discrimination of species within distinct European animal families.

    Directory of Open Access Journals (Sweden)

    Jana Naue

    Full Text Available The cheap and easy identification of species is necessary within multiple fields of molecular biology. The use of high-resolution melting (HRM of DNA provides a fast closed-tube method for analysis of the sequence composition of the mitochondrial genes 12S rRNA and cytochrome b. We investigated the potential use of HRM for species identification within eleven different animal groups commonly found in Europe by animal-group-specific DNA amplification followed by DNA melting. Influence factors as DNA amount, additional single base alterations, and the existence of mixed samples were taken into consideration. Visual inspection combined with mathematical evaluation of the curve shapes did resolve nearly all species within an animal group. The assay can therefore not only be used for identification of animal groups and mixture analysis but also for species identification within the respective groups. The use of a universal 12S rRNA system additionally revealed a possible approach for species discrimination, mostly by exclusion. The use of the HRM assay showed to be a reliable, fast, and cheap method for species discrimination within a broad range of different animal species and can be used in a flexible "modular" manner depending on the question to be solved.

  15. Biological Macro and Micro Systems Co-existing in the “Fountain of the Two Dragons”, Palermo

    Directory of Open Access Journals (Sweden)

    Enza Di Carlo

    2017-06-01

    Full Text Available Stone works of art located outdoors are exposed to natural deterioration, due to several physical, chemical and biological factors. Biological macro- and micro-systems (e.g. weeds, insects, algae, mosses, fungi and bacteria may induce the biodeterioration of stone materials. In February 2014, the state of conservation of the Fountain of the two Dragons in Palermo was examined, during which time biological colonization in some areas of the fountain and statues, was also detected. The monument represents an excellent substrate for the development and growth of microrganisms and organisms that need a continuous supply of water. Direct solar irradiance promotes the development of photoautotrophic organisms, bryophyte flora, in addition to several microbial genera, responsible for pigmentation, discoloring, efflorescence. After autotrophic colonization, some organisms find an ideal habitat also during wintertime, including two species of gastropods and two species of Hemiptera, omnivorous, a species of Collembola, mostly fungivorous. This interdisciplinary study has enabled the detection and identification of different biological communities, providing information for a subsequent project of preventive conservation of the fountain and its surroundings.

  16. Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media

    Directory of Open Access Journals (Sweden)

    Ying Li

    2017-06-01

    Full Text Available We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381 of the isolates to the species level (score values of ≥2.000 and 49.3% to the genus level (score values of 1.700–1.999. When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates.

  17. Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media.

    Science.gov (United States)

    Li, Ying; Wang, He; Zhao, Yu-Pei; Xu, Ying-Chun; Hsueh, Po-Ren

    2017-01-01

    We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700-1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates.

  18. Species Identification and Virulence Attributes of Saccharomyces boulardii (nom. inval.)

    Science.gov (United States)

    McCullough, Michael J.; Clemons, Karl V.; McCusker, John H.; Stevens, David A.

    1998-01-01

    Saccharomyces boulardii (nom. inval.) has been used for the treatment of several types of diarrhea. Recent studies have confirmed that S. boulardii is effective in the treatment of diarrhea, in particular chronic or recurrent diarrhea, and furthermore that it is a safe and well-tolerated treatment. The aim of the present study was to identify strains of S. boulardii to the species level and assess their virulence in established murine models. Three strains of S. boulardii were obtained from commercially available products in France and Italy. The three S. boulardii strains did not form spores upon repeated testing. Therefore, classical methods used for the identification of Saccharomyces spp. could not be undertaken. Typing by using the restriction fragment length polymorphisms (RFLPs) of the PCR-amplified intergenic transcribed spacer regions (including the 5.8S ribosomal DNA) showed that the three isolates of S. boulardii were not separable from authentic isolates of Saccharomyces cerevisiae with any of the 10 restriction endonucleases assessed, whereas 9 of the 10 recognized species of Saccharomyces could be differentiated. RFLP analysis of cellular DNA with EcoRI showed that all three strains of S. boulardii had identical patterns and were similar to other authentic S. cerevisiae isolates tested. Therefore, the commercial strains of S. boulardii available to us cannot be genotypically distinguished from S. cerevisiae. Two S. boulardii strains were tested in CD-1 and DBA/2N mouse models of systemic disease and showed intermediate virulence compared with virulent and avirulent strains of S. cerevisiae. The results of the present study show that these S. boulardii strains are asporogenous strains of the species S. cerevisiae, not representatives of a distinct and separate species, and possess moderate virulence in murine models of systemic infection. Therefore, caution should be advised in the clinical use of these strains in immunocompromised patients until

  19. The status of Botryosphaeriaceae species infecting grapevines

    Directory of Open Access Journals (Sweden)

    Jose Ramón URBEZ-TORRES

    2011-12-01

    Full Text Available Normal 0 MicrosoftInternetExplorer4 Normal 0 MicrosoftInternetExplorer4 Species in the Botryosphaeriaceae have a cosmopolitan distribution, and occur on a wide range of annual and perennial hosts including grapevines. To date, morphological and taxonomic studies, as well as analyses of nucleotide sequences of multiple genes, have allowed the identification of at least 21 different species in the Botryosphaeriaceae occurring in grapevines worldwide. Grapevine disease symptoms caused by members of this family include leaf spots, fruit rots, shoot dieback, bud necrosis, vascular discoloration of the wood, and perennial cankers, and their current status as pathogens is reviewed. Additionally, the disease name Botryosphaeria dieback is proposed here to describe the different grapevine trunk disease symptoms caused by species of Botryosphaeriaceae. Much has been written during the last decade about the association between species in the Botryosphaeriaceae and grapevine trunk diseases, which has contributed to a better understanding of the role that these fungal taxa play in grapevine diseases. Although virulence has been shown to vary between species and isolates of the same species in different countries, these fungi have become well-recognized as important grapevine pathogens worldwide. Latest and novel findings from studies conducted in different countries, on disease etiology and species distribution, epidemiology and biology are discussed. Much progress has been achieved in the development and implementation of novel diagnostic and detection techniques.Vineyard sanitation techniques, as well as chemical, biological, and cultural control strategies available at the present time to reduce the infection caused by botryosphaeriaceous fungi, are presented in this review. 

  20. Variability in secondary structure of 18S ribosomal RNA as topological marker for identification of Paramecium species.

    Science.gov (United States)

    Shakoori, Farah R; Tasneem, Fareeda; Al-Ghanim, K; Mahboob, S; Al-Misned, F; Jahan, Nusrat; Shakoori, Abdul Rauf

    2014-12-01

    Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continuous mutational bias towards G.C base pairing in H. sapiens. © 2014 Wiley Periodicals, Inc.

  1. Shortcomings of of the commercial MALDI-TOF MS database and use of MLSA as an arbiter in the identification of Nocardia species

    Directory of Open Access Journals (Sweden)

    Gema eCarrasco

    2016-04-01

    Full Text Available Nocardia species are difficult to identify, a consequence of the ever increasing number of species known and their homogeneous genetic characteristics. 16S rRNA analysis has been the gold standard for identifying these organisms, but proteomic techniques such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF MS and housekeeping gene analysis, have also been explored. One hundred high (n=25, intermediate (n=20 and low (n=55 prevalence (for Spain Nocardia strains belonging to 30 species were identified via 16S rRNA and MALDI-TOF MS analysis. The manufacturer-provided database MALDI Biotyper library v4.0 (5.627 entries, Bruker Daltonik was employed. In the high prevalence group (N. farcinica, N. abscessus, N. cyriacigeorgica and N. nova, the 16S rRNA and MALDI-TOF MS methods provided the same identification for 76% of the strains examined. For the intermediate prevalence group (N. brasiliensis, N. carnea, N. otitidiscaviarum and N. transvalensis complex, this figure fell to 45%. In the low-prevalence group (22 species, these two methods were concordant only in six strains at the species level. Tetra-gene multi-locus sequencing analysis (MLSA involving the concatemer gyrB-16S rRNA-hsp65-secA1 was used to arbitrate between discrepant identifications (n=67. Overall, the MLSA confirmed the results provided at species level by 16S rRNA analysis in 34.3% of discrepancies, and those provided by MALDI-TOF MS in 13.4%. MALDI-TOF MS could be a strong candidate for the identification of Nocardia species, but only if its reference spectrum database improves, especially with respect to unusual, recently described species and species included in the described Nocardia complexes.

  2. The combined rapid detection and species-level identification of yeasts in simulated blood culture using a colorimetric sensor array.

    Directory of Open Access Journals (Sweden)

    Nabin K Shrestha

    Full Text Available A colorimetric sensor array (CSA has been demonstrated to rapidly detect and identify bacteria growing in blood cultures by obtaining a species-specific "fingerprint" of the volatile organic compounds (VOCs produced during growth. This capability has been demonstrated in prokaryotes, but has not been reported for eukaryotic cells growing in culture. The purpose of this study was to explore if a disposable CSA could differentially identify 7 species of pathogenic yeasts growing in blood culture.Culture trials of whole blood inoculated with a panel of clinically important pathogenic yeasts at four different microorganism loads were performed. Cultures were done in both standard BacT/Alert and CSA-embedded bottles, after adding 10 mL of spiked blood to each bottle. Color changes in the CSA were captured as images by an optical scanner at defined time intervals. The captured images were analyzed to identify the yeast species. Time to detection by the CSA was compared to that in the BacT/Alert system.One hundred sixty-two yeast culture trials were performed, including strains of several species of Candida (Ca. albicans, Ca. glabrata, Ca. parapsilosis, and Ca. tropicalis, Clavispora (synonym Candida lusitaniae, Pichia kudriavzevii (synonym Candida krusei and Cryptococcus neoformans, at loads of 8.2 × 105, 8.3 × 103, 8.5 × 101, and 1.7 CFU/mL. In addition, 8 negative trials (no yeast were conducted. All negative trials were correctly identified as negative, and all positive trials were detected. Colorimetric responses were species-specific and did not vary by inoculum load over the 500000-fold range of loads tested, allowing for accurate species-level identification. The mean sensitivity for species-level identification by CSA was 74% at detection, and increased with time, reaching almost 95% at 4 hours after detection. At an inoculum load of 1.7 CFU/mL, mean time to detection with the CSA was 6.8 hours (17% less than with the BacT/Alert platform

  3. Molecular and morphological identification of fungal species isolated from bealmijang meju.

    Science.gov (United States)

    Kim, Ji Yeun; Yeo, Soo-Hwan; Baek, Sung Yeol; Choi, Hye Sun

    2011-12-01

    Bealmijang is a short-term aged paste made from meju, which is a brick of fermented soybeans and other ingredients. Different types of bealmijang are available depending on the geographic region or ingredients used. However, no study has clarified the microbial diversity of these types. We identified 17 and 14 fungal species from black soybean meju (BSM) and buckwheat meju (BWM), respectively, on the basis of morphology, culture characteristics, and internal transcribed spacer and beta-tubulin gene sequencing. In both meju, Aspergillus oryzae, Rhizopus oryzae, Penicillium polonicum, P. steckii, Cladosporium tenuissimum, C. cladosporioides, C. uredinicola, and yeast species Pichia burtonii were commonly found. Moreover, A. flavus, A. niger, P. crustosum, P. citrinum, Eurotium niveoglaucum, Absidia corymbifera, Setomelanomma holmii, Cladosporium spp. and unclassified species were identified from BSM. A. clavatus, Mucor circinelloides, M. racemosus, P. brevicompactum, Davidiella tassiana, and Cladosporium spp. were isolated from BWM. Fast growing Zygomycetous fungi is considered important for the early stage of meju fermentation, and A. oryae and A. niger might play a pivotal role in meju fermentation owing to their excellent enzyme productive activities. It is supposed that Penicillium sp. and Pichia burtonii could contribute to the flavor of the final food products. Identification of this fungal diversity will be useful for understanding the microbiota that participate in meju fermentation, and these fungal isolates can be utilized in the fermented foods and biotechnology industries.

  4. The Role of Reactive Oxygen Species (ROS in the Biological Activities of Metallic Nanoparticles

    Directory of Open Access Journals (Sweden)

    Ahmed Abdal Dayem

    2017-01-01

    Full Text Available Nanoparticles (NPs possess unique physical and chemical properties that make them appropriate for various applications. The structural alteration of metallic NPs leads to different biological functions, specifically resulting in different potentials for the generation of reactive oxygen species (ROS. The amount of ROS produced by metallic NPs correlates with particle size, shape, surface area, and chemistry. ROS possess multiple functions in cellular biology, with ROS generation a key factor in metallic NP-induced toxicity, as well as modulation of cellular signaling involved in cell death, proliferation, and differentiation. In this review, we briefly explained NP classes and their biomedical applications and describe the sources and roles of ROS in NP-related biological functions in vitro and in vivo. Furthermore, we also described the roles of metal NP-induced ROS generation in stem cell biology. Although the roles of ROS in metallic NP-related biological functions requires further investigation, modulation and characterization of metallic NP-induced ROS production are promising in the application of metallic NPs in the areas of regenerative medicine and medical devices.

  5. Direct analysis and identification of pathogenic Lichtheimia species by matrix-assisted laser desorption ionization-time of flight analyzer-mediated mass spectrometry.

    Science.gov (United States)

    Schrödl, Wieland; Heydel, Tilo; Schwartze, Volker U; Hoffmann, Kerstin; Grosse-Herrenthey, Anke; Walther, Grit; Alastruey-Izquierdo, Ana; Rodriguez-Tudela, Juan Luis; Olias, Philipp; Jacobsen, Ilse D; de Hoog, G Sybren; Voigt, Kerstin

    2012-02-01

    Zygomycetes of the order Mucorales can cause life-threatening infections in humans. These mucormycoses are emerging and associated with a rapid tissue destruction and high mortality. The resistance of Mucorales to antimycotic substances varies between and within clinically important genera such as Mucor, Rhizopus, and Lichtheimia. Thus, an accurate diagnosis before onset of antimycotic therapy is recommended. Matrix-assisted laser desorption ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) is a potentially powerful tool to rapidly identify infectious agents on the species level. We investigated the potential of MALDI-TOF MS to differentiate Lichtheimia species, one of the most important agents of mucormycoses. Using the Bruker Daltonics FlexAnalysis (version 3.0) software package, a spectral database library with m/z ratios of 2,000 to 20,000 Da was created for 19 type and reference strains of clinically relevant Zygomycetes of the order Mucorales (12 species in 7 genera). The database was tested for accuracy by use of 34 clinical and environmental isolates of Lichtheimia comprising a total of five species. Our data demonstrate that MALDI-TOF MS can be used to clearly discriminate Lichtheimia species from other pathogenic species of the Mucorales. Furthermore, the method is suitable to discriminate species within the genus. The reliability and robustness of the MALDI-TOF-based identification are evidenced by high score values (above 2.3) for the designation to a certain species and by moderate score values (below 2.0) for the discrimination between clinically relevant (Lichtheimia corymbifera, L. ramosa, and L. ornata) and irrelevant (L. hyalospora and L. sphaerocystis) species. In total, all 34 strains were unequivocally identified by MALDI-TOF MS with score values of >1.8 down to the generic level, 32 out of 34 of the Lichtheimia isolates (except CNM-CM 5399 and FSU 10566) were identified accurately with score values of >2 (probable species

  6. Direct Analysis and Identification of Pathogenic Lichtheimia Species by Matrix-Assisted Laser Desorption Ionization–Time of Flight Analyzer-Mediated Mass Spectrometry

    Science.gov (United States)

    Schrödl, Wieland; Heydel, Tilo; Schwartze, Volker U.; Hoffmann, Kerstin; Große-Herrenthey, Anke; Walther, Grit; Alastruey-Izquierdo, Ana; Rodriguez-Tudela, Juan Luis; Olias, Philipp; Jacobsen, Ilse D.; de Hoog, G. Sybren

    2012-01-01

    Zygomycetes of the order Mucorales can cause life-threatening infections in humans. These mucormycoses are emerging and associated with a rapid tissue destruction and high mortality. The resistance of Mucorales to antimycotic substances varies between and within clinically important genera such as Mucor, Rhizopus, and Lichtheimia. Thus, an accurate diagnosis before onset of antimycotic therapy is recommended. Matrix-assisted laser desorption ionization (MALDI)–time of flight (TOF) mass spectrometry (MS) is a potentially powerful tool to rapidly identify infectious agents on the species level. We investigated the potential of MALDI-TOF MS to differentiate Lichtheimia species, one of the most important agents of mucormycoses. Using the Bruker Daltonics FlexAnalysis (version 3.0) software package, a spectral database library with m/z ratios of 2,000 to 20,000 Da was created for 19 type and reference strains of clinically relevant Zygomycetes of the order Mucorales (12 species in 7 genera). The database was tested for accuracy by use of 34 clinical and environmental isolates of Lichtheimia comprising a total of five species. Our data demonstrate that MALDI-TOF MS can be used to clearly discriminate Lichtheimia species from other pathogenic species of the Mucorales. Furthermore, the method is suitable to discriminate species within the genus. The reliability and robustness of the MALDI-TOF-based identification are evidenced by high score values (above 2.3) for the designation to a certain species and by moderate score values (below 2.0) for the discrimination between clinically relevant (Lichtheimia corymbifera, L. ramosa, and L. ornata) and irrelevant (L. hyalospora and L. sphaerocystis) species. In total, all 34 strains were unequivocally identified by MALDI-TOF MS with score values of >1.8 down to the generic level, 32 out of 34 of the Lichtheimia isolates (except CNM-CM 5399 and FSU 10566) were identified accurately with score values of >2 (probable species

  7. Gastric fluid versus amniotic fluid analysis for the identification of intra-amniotic infection due to Ureaplasma species.

    Science.gov (United States)

    Kim, Sun Min; Romero, Roberto; Lee, JoonHo; Chaemsaithong, Piya; Docheva, Nikolina; Yoon, Bo Hyun

    2016-01-01

    % specificity in the identification of intra-amniotic infection with Ureaplasma species. However, the detection of Ureaplasma species by culture or PCR in the gastric fluid of neonates at birth did not identify these microorganisms in two-thirds of cases with microbial invasion of the amniotic cavity. Thus, amniotic fluid analysis is superior to that of gastric fluid in the identification of intra-amniotic infection.

  8. Molecular DNA Analysis in Forensic Identification.

    Science.gov (United States)

    Dumache, Raluca; Ciocan, Veronica; Muresan, Camelia; Enache, Alexandra

    2016-01-01

    Serological and biochemical identification methods used in forensics have several major disadvantages, such as: long time in processing biological sample and lack of sensitivity and specificity. In the last 30 years, DNA molecular analysis has become an important tool in forensic investigations. DNA profiling is based on the short tandem repeats (STR) and aids in human identification from biological samples. Forensic genetics, can provide information on the events which occurred at the crime scene or to supplement other methods of forensic identification. Currently, the methods used in identification are based on polymerase chain reaction (PCR) analyses. This method analyses the autosomal STRs, the Y-chromosome, and the mitochondrial DNA. Correlation of biological samples present at the crime scene with identification, selection, and the probative value factor is therefore the first aspect to be taken into consideration in the forensic genetic analysis. In the last decade, because of the advances in the field of molecular biology, new biomarkers such as: microRNAs (miR), messenger RNA (mRNA), and DNA methylation have been studied and proposed to be used in the forensic identifications of body fluids.

  9. A comparison of Api 20A vs MALDI-TOF MS for routine identification of clinically significant anaerobic bacterial strains to the species level.

    Science.gov (United States)

    Kierzkowska, Marta; Majewska, Anna; Kuthan, Robert T; Sawicka-Grzelak, Anna; Młynarczyk, Grażyna

    2013-02-15

    Adequate identification of anaerobic bacteria still presents a challenge for laboratories conducting microbiological diagnostics. The aim of this study was to compare the use of Api 20A and MALDI-TOF MS techniques for identification of obligate anaerobes. The results indicate that MALDI-TOF MS ensures a rapid and accurate identification of the species isolated from patients. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

    Science.gov (United States)

    Shao, Jin; Wan, Zhe; Li, Ruoyu; Yu, Jin

    2018-04-01

    This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis , Mucor hiemalis , Mucor racemosus , Cunninghamella bertholletiae , Cunninghamella phaeospora , and Cunninghamella echinulata All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales. Copyright © 2018 American Society for Microbiology.

  11. A PCR-based method for identification of bifidobacteria from the human alimentary tract at the species level

    NARCIS (Netherlands)

    Venema, K.; Maathuis, A.J.H.

    2003-01-01

    A polymerase chain reaction (PCR)-based method was developed for the identification of isolates of Bifidobacterium at the species level. Using two Bifidobacterium-specific primers directed against the 16S ribosomal gene (Bif164 and Bif662), a PCR product was obtained from the type strains of 12

  12. A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus).

    Science.gov (United States)

    Toli, E-A; Calboli, F C F; Shikano, T; Merilä, J

    2016-11-01

    In heterogametic species, biological differences between the two sexes are ubiquitous, and hence, errors in sex identification can be a significant source of noise and bias in studies where sex-related sources of variation are of interest or need to be controlled for. We developed and validated a universal multimarker assay for reliable sex identification of three-spined sticklebacks (Gasterosteus aculeatus). The assay makes use of genotype scores from three sex-linked loci and utilizes Bayesian probabilistic inference to identify sex of the genotyped individuals. The results, validated with 286 phenotypically sexed individuals from six populations of sticklebacks representing all major genetic lineages (cf. Pacific, Atlantic and Japan Sea), indicate that in contrast to commonly used single-marker-based sex identification assays, the developed multimarker assay should be 100% accurate. As the markers in the assay can be scored from agarose gels, it provides a quick and cost-efficient tool for universal sex identification of three-spined sticklebacks. The general principle of combining information from multiple markers to improve the reliability of sex identification is transferable and can be utilized to develop and validate similar assays for other species. © 2016 John Wiley & Sons Ltd.

  13. Morphology, Diet Composition, Distribution and Nesting Biology of Four Lark Species in Mongolia

    Directory of Open Access Journals (Sweden)

    Galbadrakh Mainjargal

    2013-12-01

    Full Text Available We aimed to enhance existing knowledge of four lark species (Mongolian lark , Horned lark, Eurasian skylark, and Lesser short-toed lark, with respect to nesting biology, distribution, and diet, using long-term dataset collected during 2000–2012. Nest and egg measurements substantially varied among species. For pooled data across species, the clutch size averaged 3.72 ± 1.13 eggs and did not differ among larks. Body mass of nestlings increased signi fi cantly with age at weighing. Daily increase in body mass of lark nestlings ranged between 3.09 and 3.89 gram per day. Unsurprisingly, the majority of lark locations occurred in steppe ecosystems, followed by human created systems; whereas only 1.8% of the pooled locations across species were observed in forest ecosystem. Diet composition did not vary among species in the proportions of major food categories consumed. The most commonly occurring food items were invertebrates and frequently consumed were being beetles (e.g. Coleoptera: Carabidae, Scarabaeidae, and Curculionidae and grasshoppers (e.g. Orthoptera: Acrididae, and their occurrences accounted for 63.7% of insect related food items. Among the fi ve morphological traits we measured, there were signi fi cant differences in wing span, body mass, bill, and tarsus; however tail lengths did not differ across four species.

  14. Identification of biological corridors in highly fragmented landscapes through GIS tools Case study Microcuenca La Bolsa, Marinilla Town

    International Nuclear Information System (INIS)

    Ruiz Osorio, Catalina; Cardona Hernandez, Dorotea; Duque J, Jose Luis

    2012-01-01

    The study object is to identify biological corridors as recovery time strategy in highly fragmented landscapes through tools of Geographic Information Systems, taking as a case study of microcuenca La Balsa, Marinilla Town. GIS tools such as V- Late, allowed assessing landscape structure through statistical analysis of forest fragments of local biodiversity importance, that from a cost raster that allowed the tracing of the biological corridor using Cost weight, shortest path and a buffer width of 100 meters as optimal for the use of certain animal species such as small and medium-sized mammals and birds. This allowed us to propose the biological corridor that will allow functional linkage of strategic ecosystems of the watershed and the recovery time, preservation and protection of biodiversity in the areas. Importantly, the use of birds as indicators of biodiversity and ecosystem disruption with which you intend to measure susceptibility to fragmentation, risk status due to loss of habitat and migratory frugivorous species which are sensitive to these changes and allow monitoring by evaluating the success of the biological corridor, because although the present study took a hypothetical data, the use of these indicators are intended to establish the need to identify key species of flora and fauna that allow for monitoring and verifying the success or otherwise of posed recovery strategy.

  15. Identification of invasive and expansive plant species based on airborne hyperspectral and ALS data

    Science.gov (United States)

    Szporak-Wasilewska, Sylwia; Kuc, Gabriela; Jóźwiak, Jacek; Demarchi, Luca; Chormański, Jarosław; Marcinkowska-Ochtyra, Adriana; Ochtyra, Adrian; Jarocińska, Anna; Sabat, Anita; Zagajewski, Bogdan; Tokarska-Guzik, Barbara; Bzdęga, Katarzyna; Pasierbiński, Andrzej; Fojcik, Barbara; Jędrzejczyk-Korycińska, Monika; Kopeć, Dominik; Wylazłowska, Justyna; Woziwoda, Beata; Michalska-Hejduk, Dorota; Halladin-Dąbrowska, Anna

    2017-04-01

    The aim of Natura 2000 network is to ensure the long term survival of most valuable and threatened species and habitats in Europe. The encroachment of invasive alien and expansive native plant species is among the most essential threat that can cause significant damage to protected habitats and their biodiversity. The phenomenon requires comprehensive and efficient repeatable solutions that can be applied to various areas in order to assess the impact on habitats. The aim of this study is to investigate of the issue of invasive and expansive plant species as they affect protected areas at a larger scale of Natura 2000 network in Poland. In order to determine the scale of the problem we have been developing methods of identification of invasive and expansive species and then detecting their occurrence and mapping their distribution in selected protected areas within Natura 2000 network using airborne hyperspectral and airborne laser scanning data. The aerial platform used consists of hyperspectral HySpex scanner (451 bands in VNIR and SWIR), Airborne Laser Scanner (FWF) Riegl Lite Mapper and RGB camera. It allowed to obtain simultaneous 1 meter resolution hyperspectral image, 0.1 m resolution orthophotomaps and point cloud data acquired with 7 points/m2. Airborne images were acquired three times per year during growing season to account for plant seasonal change (in May/June, July/August and September/October 2016). The hyperspectral images were radiometrically, geometrically and atmospherically corrected. Atmospheric correction was performed and validated using ASD FieldSpec 4 measurements. ALS point cloud data were used to generate several different topographic, vegetation and intensity products with 1 m spatial resolution. Acquired data (both hyperspectral and ALS) were used to test different classification methods including Mixture Tuned Matched Filtering (MTMF), Spectral Angle Mapper (SAM), Random Forest (RF), Support Vector Machines (SVM), among others

  16. The development and validation of a single SNaPshot multiplex for tiger species and subspecies identification--implications for forensic purposes.

    Science.gov (United States)

    Kitpipit, Thitika; Tobe, Shanan S; Kitchener, Andrew C; Gill, Peter; Linacre, Adrian

    2012-03-01

    The tiger (Panthera tigris) is currently listed on Appendix I of the Convention on the International Trade in Endangered Species of Wild Fauna and Flora; this affords it the highest level of international protection. To aid in the investigation of alleged illegal trade in tiger body parts and derivatives, molecular approaches have been developed to identify biological material as being of tiger in origin. Some countries also require knowledge of the exact tiger subspecies present in order to prosecute anyone alleged to be trading in tiger products. In this study we aimed to develop and validate a reliable single assay to identify tiger species and subspecies simultaneously; this test is based on identification of single nucleotide polymorphisms (SNPs) within the tiger mitochondrial genome. The mitochondrial DNA sequence from four of the five extant putative tiger subspecies that currently exist in the wild were obtained and combined with DNA sequence data from 492 tiger and 349 other mammalian species available on GenBank. From the sequence data a total of 11 SNP loci were identified as suitable for further analyses. Five SNPs were species-specific for tiger and six amplify one of the tiger subspecies-specific SNPs, three of which were specific to P. t. sumatrae and the other three were specific to P. t. tigris. The multiplex assay was able to reliably identify 15 voucher tiger samples. The sensitivity of the test was 15,000 mitochondrial DNA copies (approximately 0.26 pg), indicating that it will work on trace amounts of tissue, bone or hair samples. This simple test will add to the DNA-based methods currently being used to identify the presence of tiger within mixed samples. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  17. Development of standardized methodology for identifying toxins in clinical samples and fish species associated with tetrodotoxin-borne poisoning incidents

    Directory of Open Access Journals (Sweden)

    Tai-Yuan Chen

    2016-01-01

    Full Text Available Tetrodotoxin (TTX is a naturally occurring toxin in food, especially in puffer fish. TTX poisoning is observed frequently in South East Asian regions. In TTX-derived food poisoning outbreaks, the amount of TTX recovered from suspicious fish samples or leftovers, and residual levels from biological fluids of victims are typically trace. However, liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry methods have been demonstrated to qualitatively and quantitatively determine TTX in clinical samples from victims. Identification and validation of the TTX-originating seafood species responsible for a food poisoning incident is needed. A polymerase chain reaction-based method on mitochondrial DNA analysis is useful for identification of fish species. This review aims to collect pertinent information available on TTX-borne food poisoning incidents with a special emphasis on the analytical methods employed for TTX detection in clinical laboratories as well as for the identification of TTX-bearing species.

  18. Identification and strain differentiation of 'Bacteroides fragilis group' species and Prevotella bivia by PCR fingerprinting.

    Science.gov (United States)

    Claros, M; Schönian, G; Gräser, Y; Montag, T; Rodloff, A C; Citron, D M; Goldstein, E J

    1995-08-01

    Using single consensus primers of genomic nucleotide sequences, PCR-generated fingerprints were used for identification and differentiation of the Bacteroides fragilis group (B. fragilis, B. thetaiotaomicron, B. ovatus, B. distasonis, B. vulgatus) and Prevotella bivia (B. bivius) by comparing the DNA profiles with those of reference strains from the American Type Culture Collection and German Culture Collection. When primed by a single primer phage M13 core sequence, intra-species specific differences and species-specific bands were detected. Using primers derived from the evolutionarily conserved tRNA gene sequence, species-specific patterns were produced. A computer program, GelManager, was used to analyze the profiles and generate dendrograms. The correlation coefficients determined from the DNA fingerprint profiles of the clinical isolates (using the M13 core primer) fell within a narrow range, reflecting a high level of homology within the species. Based on the dendrograms, strains of one species were clearly differentiated from strains of other species. For comparison, SDS-PAGE analysis of whole cell extracts was also performed to obtain protein band patterns of various strains. Because of the simplicity of the PCR fingerprinting method and the ease of performance of computerized evaluation of data, this technique is a useful method for both species and strain differentiation, as well as for characterization of Bacteroides species and Prevotella bivia.

  19. DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes.

    Science.gov (United States)

    Vanhaecke, Delphine; Garcia de Leaniz, Carlos; Gajardo, Gonzalo; Young, Kyle; Sanzana, Jose; Orellana, Gabriel; Fowler, Daniel; Howes, Paul; Monzon-Arguello, Catalina; Consuegra, Sofia

    2012-01-01

    The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.

  20. Genetic variability and identification of the intermediate snail hosts of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Teofânia HDA Vidigal

    1998-01-01

    Full Text Available Studies based on shell or reproductive organ morphology and genetic considerations suggest extensive intraspecific variation in Biomphalaria snails. The high variability at the morphological and genetic levels, as well as the small size of some specimens and similarities between species complicate the correct identification of these snails. Here we review our work using methods based on polymerase chain reaction (PCR amplification for analysis of genetic variation and identification of Biomphalaria snails from Brazil, Argentina, Uruguay and Paraguay. Arbitrarily primed-PCR revealed that the genome of B. glabrata exihibits a remarkable degree of intraespecific polymorphism. Low stringency-PCR using primers for 18S rRNA permited the identification of B. glabrata, B. tenagophila and B. occidentalis. The study of individuals obtained from geographically distinct populations exhibits significant intraspecific DNA polymorphism, however specimens from the same species, exhibit some species specific LSPs. We also showed that PCR-restriction fragment of length polymorphism of the internal transcribed spacer region of Biomphalaria rDNA, using DdeI permits the differentiation of the three intermediate hosts of Schistosoma mansoni. The molecular biological techniques used in our studies are very useful for the generation of new knowledge concerning the systematics and population genetics of Biomphalaria snails.

  1. Identification of forensically important Chrysomya (Diptera: Calliphoridae) species using the second ribosomal internal transcribed spacer (ITS2).

    Science.gov (United States)

    Nelson, Leigh A; Wallman, James F; Dowton, Mark

    2008-05-20

    The identification of forensically important blowflies of the genus Chrysomya (Diptera: Calliphoridae) may be hampered by their close morphological similarities, especially as immatures. In contrast to most previous studies, the utility of a nuclear rather than mitochondrial genetic marker was investigated to solve this problem. The second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) was amplified and sequenced from all nine Chrysomya species known from Australia. Difficulties encountered with direct sequencing of ITS2 for Chrysomya flavifrons necessitated cloning prior to sequencing for this species, which revealed a low level (0-0.23%) of intraindividual variation. Five restriction enzymes (DraI, BsaXI, BciVI, AseI and HinfI) were identified that were able to differentiate most members of the genus by polymerase chain reaction (PCR) restriction fragment length polymorphism (PCR-RFLP). The PCR-RFLP analysis revealed characteristic restriction profiles for all species except the closely related species pairs Chrysomya latifrons+Chrysomya semimetallica and Chrysomya incisuralis+Chrysomya rufifacies. Ch. incisuralis and Ch. rufifacies were able to be separated using the size differences resulting from amplification of the entire ITS region. The lack of intraspecific ITS2 sequence variation among eight Ch. incisuralis specimens was verified by the identical restriction profiles generated from these specimens. A DNA-based approach, such as PCR-RFLP, has the capacity to be useful for the identification of forensic entomological evidence in cases where morphological characters are unreliable.

  2. Biology of primate relaxin: A paracrine signal in early pregnancy?

    Directory of Open Access Journals (Sweden)

    Hayes Eric S

    2004-06-01

    Full Text Available Abstract Relaxin is a peptide hormone that exerts numerous effects in a variety of tissues across a broad range of species. Although first identified more than 75 years ago interest in relaxin biology has waxed and waned over the years consistent with peaks and troughs of new experimental data on its wide-ranging biological effects and advances in relaxin enabling technologies. Recent insights into species-dependent differences in relaxin biology during pregnancy have once again stimulated a relative surge of interest in the study of relaxin's reproductive biology. Identification and pharmacological characterization of orphaned relaxin receptors and exploration of its paracrine effects on pregnancy using genomic and proteomic technologies have succeeded in fueling current interest in relaxin research. Primates and non-primate vertebrates exhibit very disparate profiles of relaxin genomics, proteomics and functional biology. Non-human primates appear to exhibit a very close similarity to humans with respect to relaxin reproductive biology but the similarities and subtle differences are only just beginning to be understood. We, and others, have shown that relaxin produces significant changes to the non-human primate endometrium during the peri-implantation period that are consistent with relaxin's long perceived role as a paracrine modulator of pregnancy. The purpose of this review is to summarize the reproductive biology of relaxin in non-human primates with a specific emphasis on the paracrine role of ovarian and endometrial relaxin during embryo implantation and early pregnancy.

  3. Floral and reproductive biology of Alcantarea nahoumii (Bromeliaceae, a vulnerable endemic species of the Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Maria Josirene Souza Moreira Bastos

    Full Text Available ABSTRACT Alcantarea nahoumii occurs exclusively in the state of Bahia, Brazil, and is classified as vulnerable due to deforestation and frequent fires in the region. Knowledge of floral and reproductive biology is fundamental to understanding ecological interactions, as well as the reproductive success of plant species. The objective of this study was to evaluate the floral and reproductive biology of A. nahoumii in an Atlantic Forest fragment with regard to phenology, pollen viability, stigma receptivity, pollination ecology and reproductive systems, all of which are important parameters for of the development of conservation strategies for the species. Anthesis is diurnal and heterogeneous, starting at 6:30 a.m. and lasting until 8:00 a.m. Highest germination percentages and greatest pollen tube lengths were obtained in BK culture medium. Histochemical tests revealed high pollen viability (89.71 %. Stigma receptivity occurred during anthesis and lasted for up to 24 hours after floral opening. Alcantarea nahoumii exhibited preferential allogamy and self-compatibility, and required a pollinator to production of viable seeds. Sixteen species of pollinators were observed visiting A. nahoumii, among which were five hummingbird species. Even though its reproductive system is efficient, this bromeliad remains threatened mainly due to habitat fragmentation caused by deforestation, burning and predatory extractivism.

  4. Cloth-based hybridization array system for expanded identification of the animal species origin of derived materials in feeds.

    Science.gov (United States)

    Murphy, Johanna; Armour, Jennifer; Blais, Burton W

    2007-12-01

    A cloth-based hybridization array system (CHAS) previously developed for the detection of animal species for which prohibited materials have been specified (cattle, sheep, goat, elk, and deer) has been expanded to include the detection of animal species for which there are no prohibitions (pig and horse) in Canadian and American animal feeds. Animal species were identified by amplification of mitochondrial DNA sequences by PCR and subsequent hybridization of the amplicons with an array of species-specific oligonucleotide capture probes immobilized on a polyester cloth support, followed by an immunoenzymatic assay of the bound PCR products. The CHAS permitted sensitive and specific detection of meat meals from different animal species blended in a grain-based feed and should provide a useful adjunct to microscopic examination for the identification of prohibited materials in animal feeds.

  5. Identification of some Fusarium species from selected crop seeds using traditional method and BIO-PCR

    Directory of Open Access Journals (Sweden)

    Tomasz Kulik

    2012-12-01

    Full Text Available We identified a species level of the fungal cultures isolated from selected crop seeds using traditional method and BIO-PCR. The use of BIO-PCR did not correspond completely to the morphological analyses. Both methods showed increased infection with F. poae in winter wheat seed sample originated from north Poland. Fungal culture No 40 (isolated from faba bean and identified with traditional method as mixed culture with F. culmorum and F. graminearum did not produce expected product after PCR reaction with species specific primers OPT18F470, OPT18R470. However, the use of additional primers Fc01F, Fc01R allowed for reliable identification of F. culmorum in the culture.

  6. The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.

    Science.gov (United States)

    Cortese-Krott, Miriam M; Koning, Anne; Kuhnle, Gunter G C; Nagy, Peter; Bianco, Christopher L; Pasch, Andreas; Wink, David A; Fukuto, Jon M; Jackson, Alan A; van Goor, Harry; Olson, Kenneth R; Feelisch, Martin

    2017-10-01

    Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.

  7. New applications in EPA’s ECOTOX Knowledge System: Assimilating relative potencies of metals across chemical and biological species from literature-based toxicity effects data.

    Science.gov (United States)

    Toxicity of metals in field settings can vary widely among ionic chemical species and across biological receptors. Thus, a challenge often found in developing TRVs for the risk assessment of metals is identifying the most appropriate metal and biological species combinations for...

  8. Entedoninae wasps (Hymenoptera, Chalcidoidea, Eulophidae) associated with ants (Hymenoptera, Formicidae) in tropical America, with new species and notes on their biology

    Science.gov (United States)

    Hansson, Christer; Lachaud, Jean-Paul; Pérez-Lachaud, Gabriela

    2011-01-01

    Abstract Three new species of Eulophidae associated, or presumed to be associated with ants are described: two species of Horismenus Walker and one species of Microdonophagus Schauff. Information on the biology is also included. The two Horismenus species are from Chiapas, Mexico. Horismenus myrmecophagus sp. n. is known only from females and is a gregarious endoparasitoid in larvae of the weaver ant Camponotus sp. ca. textor. The parasitoids pupate inside the host larva, and an average of 6.7 individuals develops per host. This is the second time a species of genus Horismenus is found parasitizing the brood of a formicine ant of genus Camponotus. Horismenus microdonophagus sp. n. is described from both males and females, and is a gregarious endoparasitoid attacking the larvae of Microdon sp. (Diptera: Syrphidae), a predator on ant brood found in nests of Camponotus sp. ca. textor. The new species of Microdonophagus, Microdonophagus tertius, is from Costa Rica, and known only from the female. Nothing is known about its biology but since another species in same genus, Microdonophagus woodleyi Schauff, is associated with ants through its host, Microdon larva (with same biology as Horismenus microdonophagus), it is possible that also Microdonophagus tertius has this association. A new distributional record for Microdonophagus woodleyi is also reported, extending its distribution from Panama and Colombia to Brazil. PMID:22140342

  9. The biology and preimaginal morphology of Italian endemic species Isturgia sparsaria (Hübner, 1809 (Lepidoptera, Geometridae

    Directory of Open Access Journals (Sweden)

    Hossein Rajaei

    2017-02-01

    Full Text Available The geometrid species Isturgia sparsaria (Hübner, 1809 is restricted to Italy and its biology is unknown. Recently, several individuals of this species have been successfully reared in captivity. Experiments with various potential host plants are reported. The larva was reared successfully on Genista tinctoria L. and Ulex europaeus L. (both from family Fabaceae. Adult insects, as well as ovum, larva, and pupa are illustrated and/or briefly described.

  10. Allergens/Antigens, toxins and polyketides of important Aspergillus species.

    Science.gov (United States)

    Bhetariya, Preetida J; Madan, Taruna; Basir, Seemi Farhat; Varma, Anupam; Usha, Sarma P

    2011-04-01

    The medical, agricultural and biotechnological importance of the primitive eukaryotic microorganisms, the Fungi was recognized way back in 1920. Among various groups of fungi, the Aspergillus species are studied in great detail using advances in genomics and proteomics to unravel biological and molecular mechanisms in these fungi. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Aspergillus nidulans and Aspergillus terreus are some of the important species relevant to human, agricultural and biotechnological applications. The potential of Aspergillus species to produce highly diversified complex biomolecules such as multifunctional proteins (allergens, antigens, enzymes) and polyketides is fascinating and demands greater insight into the understanding of these fungal species for application to human health. Recently a regulator gene for secondary metabolites, LaeA has been identified. Gene mining based on LaeA has facilitated new metabolites with antimicrobial activity such as emericellamides and antitumor activity such as terrequinone A from A. nidulans. Immunoproteomic approach was reported for identification of few novel allergens for A. fumigatus. In this context, the review is focused on recent developments in allergens, antigens, structural and functional diversity of the polyketide synthases that produce polyketides of pharmaceutical and biological importance. Possible antifungal drug targets for development of effective antifungal drugs and new strategies for development of molecular diagnostics are considered.

  11. Protists as bioindicators in activated sludge: Identification, ecology and future needs.

    Science.gov (United States)

    Foissner, Wilhelm

    2016-08-01

    When the activated sludge process was developed, operators and scientists soon recognized protists as valuable indicators. However, only when Curds et al. (1968) showed with a few photographs the need of ciliates for a clear plant effluent, sewage protistology began to bloom but was limited by the need of species identification. Still, this is a major problem although several good guides are available. Thus, molecular kits should be developed for identification. Protists are indicators in two stages of wastewater treatment, viz., in the activated sludge and in the environmental water receiving the plant effluent. Continuous control of the protist and bacterial communities can prevent biological sludge foaming and bulking and may greatly save money for sludge oxygenation because several protist species are excellent indicators for the amount of oxygen present. The investigation of the effluent-receiving rivers gives a solid indication about the long term function of sewage works. The literature on protist bioindication in activated sludge is widely distributed. Thus, I compiled the data in a simple Table, showing which communities and species indicate good, mediocre, or poor plant performance. Further, many details on indication are provided, such as sludge loading and nitrifying conditions. Such specific features should be improved by appropriate statistics and more reliable identification of species. Then, protistologists have a fair chance to become important in wastewater works. Activated sludge is a unique habitat for particular species, often poorly or even undescribed. As an example, I present two new species. The first is a minute (∼30μm) Metacystis that makes an up to 300μm-sized mucous envelope mimicking a sludge floc. The second is a Phialina that is unique in having the contractile vacuole slightly posterior to mid-body. Finally, I provide a list of species which have the type locality in sewage plants. Copyright © 2016 Elsevier GmbH. All rights

  12. Biology and Epidemiology of Venturia Species Affecting Fruit Crops: A Review

    Directory of Open Access Journals (Sweden)

    Elisa González-Domínguez

    2017-09-01

    Full Text Available The fungal genus Venturia Sacc. (anamorph Fusicladium Bonord. includes plant pathogens that cause substantial economic damage to fruit crops worldwide. Although Venturia inaequalis is considered a model species in plant pathology, other Venturia spp. also cause scab on other fruit trees. Relative to the substantial research that has been conducted on V. inaequalis and apple scab, little research has been conducted on Venturia spp. affecting other fruit trees. In this review, the main characteristics of plant-pathogenic species of Venturia are discussed with special attention to V. inaequalis affecting apple, V. pyrina affecting European pear, V. nashicola affecting Asian pear, V. carpophila affecting peach and almond, Fusicladium oleagineum affecting olive, F. effusum affecting pecan, and F. eriobotryae affecting loquat. This review has two main objectives: (i to identify the main gaps in our knowledge regarding the biology and epidemiology of Venturia spp. affecting fruit trees; and (ii to identify similarities and differences among these Venturia spp. in order to improve disease management. A thorough review has been conducted of studies regarding the phylogenetic relationships, host ranges, biologies, and epidemiologies of Venturia spp. A multiple correspondence analysis (CA has also been performed on the main epidemiological components of these Venturia spp. CA separated the Venturia spp. into two main groups, according to their epidemiological behavior: the first group included V. inaequalis, V. pyrina, V. nashicola, and V. carpophila, the second F. oleagineum and F. eriobotryae, with F. effusum having an intermediate position. This review shows that Venturia spp. affecting fruit trees are highly host-specific, and that important gaps in understanding the life cycle exist for some species, including V. pyrina; gaps include pseudothecia formation, ascospore and conidia germination, and mycelial growth. Considering the epidemiological

  13. Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae determined by a polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta Lima

    1998-01-01

    Full Text Available The freshwater snails Biomphalaria straminea, B. intermedia, B. kuhniana and B. peregrina, are morphologically similar; based on this similarity the first three species were therefore grouped in the complex B. straminea. The morphological identification of these species is based on characters such as vaginal wrinkling, relation between prepuce: penial sheath:deferens vas and number of muscle layers in the penis wall. In this study the polymerase chain reaction restriction fragment length polymorphism technique was used for molecular identification of these molluscs. This technique is based on the amplification of the internal transcribed spacer regions ITS1 e ITS2 of the ribosomal RNA gene and subsequent digestion of these fragments by restriction enzymes. Six enzymes were tested: Dde I, Mnl I, Hae III, Rsa I, Hpa II e Alu I. The restriction patterns obtained with DdeI presented the best profile for separation of the four species of Biomphalaria. The profiles obtained with all the enzymes were used to estimate the genetic distances among the species through analysis of common banding patterns.

  14. Advances toward DNA-based identification and phylogeny of North American Armillaria species using elongation factor-1 alpha gene

    Science.gov (United States)

    Amy L. Ross-Davis; John W. Hanna; Mee-Sook Kim; Ned B. Klopfenstein

    2012-01-01

    The translation elongation factor-1 alpha gene was used to examine the phylogenetic relationships among 30 previously characterized isolates representing ten North American Armillaria species: A. solidipes (=A. ostoyae), A. gemina, A. calvescens, A. sinapina, A. mellea, A. gallica, A. nabsnona, North American biological species X, A. cepistipes, and A. tabescens. The...

  15. Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems

    DEFF Research Database (Denmark)

    Justesen, Ulrik Stenz; Holm, Anette; Knudsen, Elisa

    2011-01-01

    We compared two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Shimadzu/SARAMIS and Bruker) on a collection of consecutive clinically important anaerobic bacteria (n = 290). The Bruker system had more correct identifications to the species level...... (67.2% versus 49.0%), but also more incorrect identifications (7.9% versus 1.4%). The system databases need to be optimized to increase identification levels. However, MALDI-TOF MS in its present version seems to be a fast and inexpensive method for identification of most clinically important...

  16. Biology, ecology and control of the Penthaleus species complex (Acari: Penthaleidae).

    Science.gov (United States)

    Umina, Paul A; Hoffmann, Ary A; Weeks, Andrew R

    2004-01-01

    Blue oat mites, Penthaleus spp. (Acari: Penthaleidae), are major agricultural pests in southern Australia and other parts of the world, attacking various pasture, vegetable and crop plants. Management of these mites has been complicated by the recent discovery of three cryptic pest species of Penthaleus, whereas prior research had assumed a single species. The taxonomy, population genetics, ecology, biology and control of the Penthaleus spp. complex are reviewed. Adult Penthaleus have a dark blue-black body approximately 1 mm in length, and eight red-orange legs. Within Australia, they are winter pests completing two or three generations a season, depending on conditions. The summer is passed as diapausing eggs, when long-distance dispersal is thought to occur. The Penthaleus spp. reproduce by thelytokous parthenogenesis, with populations comprising clones that differ ecologically. The three pest Penthaleus spp. differ markedly in their distributions, plant hosts, timing of diapause egg production and response to pesticides, highlighting the need to develop control strategies that consider each species separately. Chemicals are the main weapons used in current control programs, however research continues into alternative more sustainable management options. Host plant resistance, crop rotations, conservation of natural enemies, and improved timing of pesticide application would improve the management of these pests. The most cost-effective and environmentally acceptable means of control will result from the integration of these practices combined with the development of a simple field-based kit to distinguish the different mite species.

  17. Short communication: Identification of coagulase-negative staphylococcus species from goat milk with the API Staph identification test and with transfer RNA-intergenic spacer PCR combined with capillary electrophoresis.

    Science.gov (United States)

    Koop, G; De Visscher, A; Collar, C A; Bacon, D A C; Maga, E A; Murray, J D; Supré, K; De Vliegher, S; Haesebrouck, F; Rowe, J D; Nielen, M; van Werven, T

    2012-12-01

    Coagulase-negative staphylococci (CNS) are the most commonly isolated bacteria from goat milk, but they have often been identified with phenotypic methods, which may have resulted in misclassification. The aims of this paper were to assess the amount of misclassification of a phenotypic test for identifying CNS species from goat milk compared with transfer RNA intergenic spacer PCR (tDNA-PCR) followed by capillary electrophoresis, and to apply the tDNA-PCR technique on different capillary electrophoresis equipment. Milk samples were collected from 416 does in 5 Californian dairy goat herds on 3 occasions during lactation. In total, 219 CNS isolates were identified at the species level with tDNA-PCR and subjected to the API 20 Staph identification test kit (API Staph; bioMérieux, Durham, NC). If the same species was isolated multiple times from the same udder gland, only the first isolate was used for further analyses, resulting in 115 unique CNS isolates. According to the tDNA-PCR test, the most prevalent CNS species were Staphylococcus epidermidis, Staphylococcus caprae, and Staphylococcus simulans. Typeability with API staph was low (72%). Although the API Staph test was capable of identifying the majority of Staph. epidermidis and Staph. caprae isolates, sensitivity for identification of Staph. simulans was low. The true positive fraction was high for the 3 most prevalent species. It was concluded that the overall performance of API Staph in differentiating CNS species from goat milk was moderate to low, mainly because of the low typeability, and that genotypic methods such as tDNA-PCR are preferred. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  18. Parasites as biological tags in marine fisheries research: European Atlantic waters.

    Science.gov (United States)

    Mackenzie, K; Hemmingsen, W

    2015-01-01

    Studies of the use of parasites as biological tags for stock identification and to follow migrations of marine fish, mammals and invertebrates in European Atlantic waters are critically reviewed and evaluated. The region covered includes the North, Baltic, Barents and White Seas plus Icelandic waters, but excludes the Mediterranean and Black Seas. Each fish species or ecological group of species is treated separately. More parasite tag studies have been carried out on Atlantic herring Clupea harengus than on any other species, while cod Gadus morhua have also been the subject of many studies. Other species that have been the subjects of more than one study are: blue whiting Micromesistius poutassou, whiting Merlangius merlangus, haddock Melanogrammus aeglefinus, Norway pout Trisopterus esmarkii, horse mackerel Trachurus trachurus and mackerel Scomber scombrus. Other species are dealt with under the general headings redfishes, flatfish, tunas, anadromous fish, elasmobranchs, marine mammals and invertebrates. A final section highlights how parasites can be, and have been, misused as biological tags, and how this can be avoided. It also reviews recent developments in methodology and parasite genetics, considers the potential effects of climate change on the distributions of both hosts and parasites, and suggests host-parasite systems that should reward further research.

  19. Differential effects of plant species on a mite pest (Tetranychus utricae) and its predator (Phytoseiulus persimilis): implications for biological control.

    Science.gov (United States)

    Skirvin, D J; de Courcy Williams, M

    1999-06-01

    The influence of plant species on the population dynamics of the spider mite pest, Tetranychus urticae, and its predator, Phytoseiulus persimilis, was examined as a prerequisite to effective biological control on ornamental nursery stock. Experiments have been done to investigate how the development, fecundity and movement of T. urticae, and the movement of P. persimilis were affected by plant species. A novel experimental method, which incorporates plant structure, was used to investigate the functional response of P. persimilis. Development times for T. urticae were consistent with published data and did not differ with plant species in a biologically meaningful way. Plant species was shown to have a major influence on fecundity (P < 0.001) and movement of the pest mite (P < 0.01), but no influence on the movement of the predator. The movement of both pest and predator was shown to be related to the density of the adult pest mites on the plant (P < 0.001). Plant structure affected the functional response, particularly in relation to the ability of the predator to locate prey at low densities. The impact of these findings on the effective use of biological control on ornamental nursery stock is discussed.

  20. BP Neural Network Could Help Improve Pre-miRNA Identification in Various Species

    Directory of Open Access Journals (Sweden)

    Limin Jiang

    2016-01-01

    Full Text Available MicroRNAs (miRNAs are a set of short (21–24 nt noncoding RNAs that play significant regulatory roles in cells. In the past few years, research on miRNA-related problems has become a hot field of bioinformatics because of miRNAs’ essential biological function. miRNA-related bioinformatics analysis is beneficial in several aspects, including the functions of miRNAs and other genes, the regulatory network between miRNAs and their target mRNAs, and even biological evolution. Distinguishing miRNA precursors from other hairpin-like sequences is important and is an essential procedure in detecting novel microRNAs. In this study, we employed backpropagation (BP neural network together with 98-dimensional novel features for microRNA precursor identification. Results show that the precision and recall of our method are 95.53% and 96.67%, respectively. Results further demonstrate that the total prediction accuracy of our method is nearly 13.17% greater than the state-of-the-art microRNA precursor prediction software tools.

  1. A new species of Cacatuocotyle (Monogenea, Dactylogyridae) parasitizing Astyanax spp. (Characiformes, Characidae) from Brazil, including molecular data and a key to species identification.

    Science.gov (United States)

    Zago, Aline Cristina; Franceschini, Lidiane; Müller, Maria Isabel; Silva, Reinaldo José da

    2018-06-26

    The present study describes Cacatuocotyle papilionis n. sp. (Monogenea, Dactylogyridae) from the skin of the characid fishes Astyanax lacustris (Lütken, 1875) (=Astyanax altiparanae Garutti & Britski, 2000) and Astyanax fasciatus (Cuvier, 1819) (Characiformes, Characidae) from the Southeast of Brazil, supported by morphological and molecular data. The new species differs from all congeners, mainly due to the morphology of the ventral bar (resembling a butterfly), accessory piece, and the number of rings of the male copulatory organ (MCO), comprising a coiled tube with 4.5-5.5 counterclockwise rings. The first molecular data for this monogenean genus is provided in this study, using the partial sequences of the ribosomal gene (28S), as well as providing an identification key to the species.

  2. Identification of Thrips Species on Garlic Fields in Hamedan Province and Determination of Dominant Species

    Directory of Open Access Journals (Sweden)

    Majid Mirab-balou

    2016-09-01

    consisted of about 6000 species placed in two suborders and nine families. A large number of thrips species are considered pests, because they feed on economical crops. In this study, a total of eight species in seven genera and three families were collected and identified, including Aeolothrips intermedius Bagnall and Rhipidothrips gratiosus Uzel from family Aeolothripidae, Aptinothrips rufus (Haliday, Frankliniella intonsa (Trybom, Scolothrips longicornis Priesner, Thrips alliorum (Priesner and Thrips tabaci Lindeman from family Thripidae, and Haplothrips reuteri (Karny from family Phlaeothripidae. All of the species existed in two years in both two regions. Thrips tabaci was the dominant species (64.89% in garlic fields. Among the predatory thrips, Aeolothrips intermedius and Scolothrips longicornis were present in greater numbers. However, their number was not enough to reduce the number of phytophagous thrips. The predatory species feeds mainly on the larvae and imagoes of onion thrips but they feed on mites as well. An identification key for thrips species associated with garlic is also given. Conclusion: In this study, eight species of thrips were collected on garlic fields of Hamedan province which Thrips tabaci was dominant species (64.89%; and three of which were identified as predatory species. Up to the present, several thrips were collected and recorded from Hamedan province by the author, but there is no study on thrips associated to garlic; therefore, this study was firstly carried out in Hamedan province. There are several insect pests on garlic, and T. tabaci was also reported as important pest on garlic fileds in this province. Onion thrips, T. tabaci is one of the important pests in the world, and it has more than 300 host plants. At present, it is widely distributed in Iran and is a key insect pest in most onion and cotton cultivation areas as well as ornamental plants. In addition, thrips species in the genera Thrips and Frankliniella spread plant

  3. First Identification of Palytoxin-Like Molecules in the Atlantic Coral Species Palythoa canariensis.

    Science.gov (United States)

    Fraga, María; Vilariño, Natalia; Louzao, M Carmen; Molina, Lucía; López, Yanira; Poli, Mark; Botana, Luis M

    2017-07-18

    Palytoxin (PLTX) is a complex marine toxin produced by Zoanthids (Palyhtoa), dinoflagellates (Ostreopsis), and cyanobacteria (Trichodesmium). Contact with PLTX-like compounds present in aerosols or marine organisms has been associated with adverse effects on humans. The worldwide distribution of producer species and seafood contaminated with PLTX-like molecules illustrates the global threat to human health. The identification of species capable of palytoxin production is critical for human safety. We studied the presence of PLTX analogues in Palythoa canariensis, a coral species collected in the Atlantic Ocean never described as a PLTX-producer before. Two methodologies were used for the detection of these toxins: a microsphere-based immunoassay that offered an estimation of the content of PLTX-like molecules in a Palythoa canariensis extract and an ultrahigh-pressure liquid chromatography coupled to an ion trap with a time-of-flight mass spectrometer (UPLC-IT-TOF-MS) that allowed the characterization of the toxin profile. The results demonstrated the presence of PLTX, hydroxy-PLTX and, at least, two additional compounds with PLTX-like profile in the Palythoa canariensis sample. The PLTX content was estimated in 0.27 mg/g of lyophilized coral using UPLC-IT-TOF-MS. Therefore, this work demonstrates that Palythoa canariensis produces a mixture of PLTX-like molecules. This is of special relevance to safeguard human health considering Palythoa species are commonly used for decoration by aquarium hobbyists.

  4. Gamma-irradiated onions as a biological indicator of radiation dose

    International Nuclear Information System (INIS)

    Vaijapurkar, S.G.; Agarwal, Deepshikha; Chaudhuri, S.K.; Ram Senwar, Kana; Bhatnagar, P.K.

    2001-01-01

    Post-irradiation identification and dose estimation are required to assess the radiation-induced effects on living things in any nuclear emergency. In this study, radiation-induced morphological/cytological changes i.e., number of root formation and its length, shooting length, reduction in mitotic index, micronuclei formation and chromosomal aberrations in the root tip cells of gamma-irradiated onions at lower doses (50-2000 cGy) are reported. The capabilities of this biological species to store the radiation-induced information are also studied

  5. Identification of squid species by melting temperature shifts on fluorescence melting curve analysis (FMCA) using single dual-labeled probe

    Science.gov (United States)

    Koh, Eunjung; Song, Ha Jeong; Kwon, Na Young; Kim, Gi Won; Lee, Kwang Ho; Jo, Soyeon; Park, Sujin; Park, Jihyun; Park, Eun Kyeong; Hwang, Seung Yong

    2017-06-01

    Real time PCR is a standard method for identification of species. One of limitations of the qPCR is that there would be false-positive result due to mismatched hybridization between target sequence and probe depending on the annealing temperature in the PCR condition. As an alternative, fluorescence melting curve analysis (FMCA) could be applied for species identification. FMCA is based on a dual-labeled probe. Even with subtle difference of target sequence, there are visible melting temperature (Tm) shift. One of FMCA applications is distinguishing organisms distributed and consumed globally as popular food ingredients. Their prices are set by species or country of origin. However, counterfeiting or distributing them without any verification procedure are becoming social problems and threatening food safety. Besides distinguishing them in naked eye is very difficult and almost impossible in any processed form. Therefore, it is necessary to identify species in molecular level. In this research three species of squids which have 1-2 base pair differences each are selected as samples since they have the same issue. We designed a probe which perfectly matches with one species and the others mismatches 2 and 1 base pair respectively and labeled with fluorophore and quencher. In an experiment with a single probe, we successfully distinguished them by Tm shift depending on the difference of base pair. By combining FMCA and qPCR chip, smaller-scale assay with higher sensitivity and resolution could be possible, andc furthermore, enabling results analysis with smart phone would realize point-of-care testing (POCT).

  6. Molecular identification of Nocardia species using the sodA gene: Identificación molecular de especies de Nocardia utilizando el gen sodA.

    Science.gov (United States)

    Sánchez-Herrera, K; Sandoval, H; Mouniee, D; Ramírez-Durán, N; Bergeron, E; Boiron, P; Sánchez-Saucedo, N; Rodríguez-Nava, V

    2017-09-01

    Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sod A gene (encoding the enzyme superoxide dismutase) has had good results in identifying species of other Actinomycetes. In this study the sod A gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sod A gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp), hsp 65 (401 bp), sec A1 (494 bp), gyr B (1195 bp) and rpo B (401 bp). The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sod A genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sod A gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.

  7. Identification And Study Of Fish Species In Karkheh River (Iran

    Directory of Open Access Journals (Sweden)

    Khoshnood Zahra

    2014-10-01

    Full Text Available For the investigation of fish from Karkheh River, sampling was performed in a six month period from August 2014 to January 2015. All sampled fish were measured for biometrical values (length and weight. General results of the sampling and identification of the fish showed the presence of 14 species from four fish families of Cyprinidae, Mugilidae, Siluridae and Macrostomidae, out of which the Cyprinidae family were the most frequent of the sampled fish. The most significant abundance belongs to Cyprinus carpio. The fish sampled in the present study were: Liza abu, Ctenopharyngodon idella, Barbel sp., Cyprinion macrostomum, Barbus sharpeyi, Hypophthalmichthys molitrix, Barbus esocinus, Barbus barbulus, Barbus luteus, Barbus grypus, Cyprinus carpio, Silurus triostegus, Mastacembelus circumcinctus and Capoeta trutta. Shannon Index results showed that the fish biodiversity in the studyed area followed a uniform path and additionally that the considered area at the studied period has good fish biodiversity.

  8. Molecular identification and distribution profile of Candida species isolated from Iranian patients.

    Science.gov (United States)

    Mohammadi, Rasoul; Mirhendi, Hossein; Rezaei-Matehkolaei, Ali; Ghahri, Mohammad; Shidfar, Mohammad Reza; Jalalizand, Nilufar; Makimura, Koichi

    2013-08-01

    A total of 855 yeast strains isolated from different clinical specimens, mainly nail (42%) and vulva-vagina (25%) were identified by a set of polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Genomic DNA was extracted from fresh colonies using Whatman FTA Card technology. PCR assays were performed on the complete ribosomal DNA internal transcribed spacer (rDNA-ITS) region for all isolates and species identification was carried out through their specific electrophoretic profiles after digestion with the enzyme MspI. Those isolates suspected as Candida parapsilosis group were then subjected to amplification of the secondary alcohol dehydrogenase (SADH) gene and restriction digestion with NlaIII enzyme. In total, 71.1% of the strains were obtained from females and 28.9% from males. The age group of 31-40 years consisted of the highest frequency of patients with candidiasis. Candida albicans was the predominant species (58.6%) followed by C. parapsilosis (11.0%), C. glabrata (8.3%), C. tropicalis (7.0%), C. kefyr (5.8%), C. krusei (4.4%), C. orthopsilosis (2.1%), and C. guilliermondii (0.6%). A few strains of C. lusitaniae, C. rugosa, C. intermedia, C. inconspicua, C. neoformans and S. cerevisiae were isolated. We could not identify 8 (0.9%) isolates. Candida albicans remains the most frequently species isolated from Iranian patients; however, the number of non-C. albicans Candida species looks to be increasing. The simple and reliable PCR-RFLP system used in the study has the potential to identify most clinically isolated yeasts.

  9. A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients.

    Science.gov (United States)

    Taira, Cleison Ledesma; Okay, Thelma Suely; Delgado, Artur Figueiredo; Ceccon, Maria Esther Jurfest Rivero; de Almeida, Margarete Teresa Gottardo; Del Negro, Gilda Maria Barbaro

    2014-07-21

    Nosocomial candidaemia is associated with high mortality rates in critically ill paediatric patients; thus, the early detection and identification of the infectious agent is crucial for successful medical intervention. The PCR-based techniques have significantly increased the detection of Candida species in bloodstream infections. In this study, a multiplex nested PCR approach was developed for candidaemia detection in neonatal and paediatric intensive care patients. DNA samples from the blood of 54 neonates and children hospitalised in intensive care units with suspected candidaemia were evaluated by multiplex nested PCR with specific primers designed to identify seven Candida species, and the results were compared with those obtained from blood cultures. The multiplex nested PCR had a detection limit of four Candida genomes/mL of blood for all Candida species. Blood cultures were positive in 14.8% of patients, whereas the multiplex nested PCR was positive in 24.0% of patients, including all culture-positive patients. The results obtained with the molecular technique were available within 24 hours, and the assay was able to identify Candida species with 100% of concordance with blood cultures. Additionally, the multiplex nested PCR detected dual candidaemia in three patients. Our proposed PCR method may represent an effective tool for the detection and identification of Candida species in the context of candidaemia diagnosis in children, showing highly sensitive detection and the ability to identify the major species involved in this infection.

  10. [Applylication of new type combined fragments: nrDNA ITS+ nad 1-intron 2 for identification of Dendrobium species of Fengdous].

    Science.gov (United States)

    Geng, Li-xia; Zheng, Rui; Ren, Jie; Niu, Zhi-tao; Sun, Yu-long; Xue, Qing-yun; Liu, Wei; Ding, Xiao-yu

    2015-08-01

    In this study, 17 kinds of Dendrobium species of Fengdous including 39 individuals were collected from 4 provinces. Mitochondrial gene sequences co I, nad 5, nad 1-intron 2 and chloroplast gene sequences rbcL, matK amd psbA-trnH were amplified from these materials, as well as nrDNA ITS. Furthermore, suitable sequences for identification of Dendrobium species of Fengdous were screened by K-2-P and P-distance. The results showed that during the mentioned 7 sequences, nrDNA ITS, nad 1-intron 2 and psbA-trnH which had a high degree of variability could be used to identify Dendrobium species of Fengdous. However, single fragment could not be used to distinguish D. moniliforme and D. huoshanense. Moreover, compared to other combined fragments, new type combined fragments nrDNA ITS+nad 1-intron 2 was more effective in identifying the original plants of Dendrobium species and could be used to identify D. huoshanense and D. moniliforme. Besides, according to the UPGMA tree constructed with nrDNA ITS+nad 1-intron 2, 3 inspected Dendrobium plants were identified as D. huoshanense, D. moniliforme and D. officinale, respectively. This study identified Dendrobium species of Fengdous by combined fragments nrDNA ITS+nad 1-intron 2 for the first time, which provided a more effective basis for identification of Dendrobium species. And this study will be helpful for regulating the market of Fengdous.

  11. Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur.

    Science.gov (United States)

    Naseeb, Samina; James, Stephen A; Alsammar, Haya; Michaels, Christopher J; Gini, Beatrice; Nueno-Palop, Carmen; Bond, Christopher J; McGhie, Henry; Roberts, Ian N; Delneri, Daniela

    2017-06-01

    Two strains, D5088T and D5095, representing a novel yeast species belonging to the genus Saccharomyces were isolated from oak tree bark and surrounding soil located at an altitude of 1000 m above sea level in Saint Auban, France. Sequence analyses of the internal transcribed spacer (ITS) region and 26S rRNA D1/D2 domains indicated that the two strains were most closely related to Saccharomyces mikatae and Saccharomyces paradoxus. Genetic hybridization analyses showed that both strains are reproductively isolated from all other Saccharomyces species and, therefore, represent a distinct biological species. The species name Saccharomyces jurei sp. nov. is proposed to accommodate these two strains, with D5088T (=CBS 14759T=NCYC 3947T) designated as the type strain.

  12. Enzymatic fingerprints of polysaccharides of Dendrobium officinale and their application in identification of Dendrobium species.

    Science.gov (United States)

    Zha, Xue-Qiang; Pan, Li-Hua; Luo, Jian-Ping; Wang, Jun-Hui; Wei, Peng; Bansal, Vibha

    2012-07-01

    Enzymatic fingerprinting of polysaccharides from Dendrobium officinale was studied and applied to authenticate Dendrobium species. Results showed that Dendrobium officinale species from Anhui province, Fujian province, Yunnan province, Guangdong province and Guangxi province of China, could be identified by polysaccharide analysis using carbohydrate gel electrophoresis (PACE). However, the fingerprints of Dendrobium officinale from Jiangxi province, Hu'nan province and Wenzhou, Yandangshan and Fuyang in Zhejiang province were very similar. As far as the fingerprints of different Dendrobium species were concerned, the differences between Dendrobium officinale, Dendrobium huoshanense, Dendrobium moniliforme, Dendrobium devonianum, Dendrobium aphyllum, Dendrobium wilsonii and Dendrobium crystallinum were obvious. Moreover, the genetic relationships between different samples were analyzed by using principal component analysis and unweighted pair group method with arithmetic mean cluster analysis. Results suggested that polysaccharide fingerprint analysis by PACE has the potential to become a valuable new method for the identification and control of quality of herbal medicines in future.

  13. Conservation Genetics of Threatened Dalbergia Timber Species in Indochina

    DEFF Research Database (Denmark)

    Hartvig, Ida

    Tropical forests all over the world are disappearing at high rates primarily due to anthropogenic ecosystem changes. A high number of tropical tree species is threatened with extinction due to deforestation and unsustainable levels of logging, and the implementation of effective conservation plans...... is often hindered by the lack of basic knowledge of their biology. This study represents the first region-wide analysis of population genetic diversity for tree species in Indochina and provides valuable knowledge on how threatened tree species are affected by landscape features, ancient or recent habitat...... as several separate species and accurately identified the CITES-listed D. cochinchinensis. The results can be used to update threat assessments with correct taxonomic information and the method can be implemented as an identification tool in field studies as well as in enforcement of CITES regulations...

  14. Identification of Staphylococcus species and subspecies with the MicroScan Pos ID and Rapid Pos ID panel systems.

    Science.gov (United States)

    Kloos, W E; George, C G

    1991-01-01

    The accuracies of the MicroScan Pos ID and Rapid Pos ID panel systems (Baxter Diagnostic Inc., MicroScan Division, West Sacramento, Calif.) were compared with each other and with the accuracies of conventional methods for the identification of 25 Staphylococcus species and 4 subspecies. Conventional methods included those used in the original descriptions of species and subspecies and DNA-DNA hybridization. The Pos ID panel uses a battery of 18 tests, and the Rapid Pos ID panel uses a battery of 42 tests for the identification of Staphylococcus species. The Pos ID panel has modified conventional and chromogenic tests that can be read after 15 to 48 h of incubation; the Rapid Pos ID panel has tests that use fluorogenic substrates or fluorometric indicators, and test results can be read after 2 h of incubation in the autoSCAN-W/A. Results indicated that both MicroScan systems had a high degree of congruence (greater than or equal to 90%) with conventional methods for the species S. capitis, S. aureus, S. auricularis, S. saprophyticus, S. cohnii, S. arlettae, S. carnosus, S. lentus, and S. sciuri and, in particular, the subspecies S. capitis subsp. capitis and S. cohnii subsp. cohnii. The Rapid Pos ID panel system also had greater than or equal to 90% congruence with conventional methods for S. epidermidis, S. caprae, S. warneri subsp. 2, S. xylosus, S. kloosii, and S. caseolyticus. For both MicroScan systems, congruence with conventional methods was 80 to 90% for S. haemolyticus subsp. 1, S. equorum, S. intermedius, and S. hyicus; and in addition, with the Rapid Pos ID panel system congruence was 80 to 89% for S. capitis subsp. ureolyticus, S. warneri subsp. 1, S. hominis, S. cohnii subsp. urealyticum, and S. simulans. The MicroScan systems identified a lower percentage (50 to 75%) of strains of S. lugdunensis, S. gallinarum, S. schleiferi, and S. chromogenes, although the addition of specific tests to the systems might increase the accuracy of identification

  15. Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists.

    Science.gov (United States)

    Zhao, Yan; Yi, Zhenzhen; Gentekaki, Eleni; Zhan, Aibin; Al-Farraj, Saleh A; Song, Weibo

    2016-01-01

    Ciliates comprise a highly diverse protozoan lineage inhabiting all biotopes and playing crucial roles in regulating microbial food webs. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. Here, we use the species-rich taxon Frontonia and employ both nuclear and mitochondrial loci. We attempt to assess the level of genetic diversity and evaluate the potential of each marker in delineating species of Frontonia. Morphological features and ecological characteristics are also integrated into genetic results, in an attempt to resolve conflicts of species identification based on morphological and molecular methods. Our studies reveal: (1) the mitochondrial cox1 gene, nuclear ITS1 and ITS2 as well as the hypervariable D2 region of LSU rDNA are promising candidates for species delineation; (2) the cox1 gene provides the best resolution for analyses below the species level; (3) the V2 and V4 hypervariable regions of SSU rDNA, and D1 of LSU rDNA as well as the 5.8S rDNA gene do not show distinct barcoding gap due to overlap between intra- and inter-specific genetic divergences; (4) morphological character-based analysis shows promise for delimitation of Frontonia species; and (5) all gene markers and character-based analyses demonstrate that the genus Frontonia consists of three groups and monophyly of the genus Frontonia is questionable. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. High-resolution melt analysis for species identification of coagulase-negative staphylococci derived from bovine milk.

    Science.gov (United States)

    Ajitkumar, Praseeda; Barkema, Herman W; Zadoks, Ruth N; Morck, Douglas W; van der Meer, Frank J U M; De Buck, Jeroen

    2013-03-01

    Coagulase-negative staphylococci (CNS) are the most frequently isolated pathogens isolated from bovine milk. In this study, we report a rapid assay for species identification of CNS using high-resolution melt analysis (HRMA) of 16S rDNA sequences. Real-time polymerase chain reaction amplification of 16S rRNA gene fragment, spanning the variable region V1 and V2, was performed with a resulting amplicon of 215 bp. A library of distinct melt curves of reference strains of 13 common CNS species was created using HRMA. Sequencing of 16S rRNA and rpoB genes, and, when needed, tuf gene, of 100 CNS isolates obtained from Canadian Bovine Mastitis Research Network was done to determine their species identity, allowing for subsequent evaluation of the performance of HRMA for field isolates of bovine CNS. A combination of HRMA and sequencing revealed that Staphylococcus chromogenes, S. xylosus, S. simulans, and S. sciuri had multiple genotypes, complicating their resolution by HRMA. As the 3 genotypes of S. chromogenes had distinct melt curves, the 3 distinct genotypes were employed as reference strains in a blinded trial of 156 CNS isolates to identify S. chromogenes. HRMA correctly identified all S. chromogenes isolates which were later confirmed by sequencing. Staphylococcus chromogenes (68%) was most frequently found among the CNS isolates, followed by S. haemolyticus (10%) and S. xylosus (6%). The present study revealed that HRMA of 16S rRNA gene (V1-V2) could be used as a rapid, efficient, low-cost, and minimally cumbersome technique for S. chromogenes identification, the most common CNS derived from bovine milk. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Comparison of VITEK 2 YST Card and API 20C AUX system in identification of non- albicans Candida species

    Directory of Open Access Journals (Sweden)

    Süleyman Durmaz

    2012-03-01

    Full Text Available Objectives: In the present study, it was aimed to compare results obtained by using VITEK 2 YST Card (bioMérieux, France with those obtained by using API 20C AUX (bioMérieux, France for identification of non- albicans Candida species, which was isolated from various clinical samples, at level of species.Materials and methods: Forty-one non-albicans Candida isolates, which were isolated from 28 urine, 10 blood and 3 vaginal swab specimens, and found to be negative by germ tube test, were identified by using VITEK 2 YST Card (bioMérieux, France. In addition, microscopic morphology was assessed in corn-meal Tween 80 agar, while carbohydrate assimilation was assessed by using commercially available API 20C AUX kit (bioMérieux, France.Results: Thirty-four isolates (82.9% were identified as identical species by these 2 systems, while different results were obtained in 7 isolates (17.1%. 5 isolates, identified as Candida glabrata by API 20C AUX system, were identified as Candida tropicalis (n=2, Candida krusei, Candida lipolitica and Candida kefyr by VITEK 2 YST Card. One other isolate, identified as C.tropicalis, was identified as Candida parapsilosis; and additional one isolate, identified as C.parapsilosis, was identified as C.tropicalis.Conclusion: It was concluded that one should be cautious in the identification of C.glabrata, in particular, C.tropicalis and C.parapsilosis, although between VITEK 2 YST Card and API 20C AUX system results was found largely similarity in identification of non-albicans Candida spp.

  18. Redescription of Liza bandialensis (Teleostei: Mugilidae) with an identification key to mullet species of Eastern Central Atlantic.

    Science.gov (United States)

    Trape, Sébastien; Harrison, Ian J; Diouf, Papa Samba; Durand, Jean-Dominique

    2012-02-01

    Liza bandialensis Diouf 1991 is redescribed because previous descriptions have not been in well-distributed publications and have lacked sufficient detail or reference to voucher specimens. The description provided here is based on specimens from the Sine Saloum estuary, Senegal (West Africa), from where the species was originally described. The distinctness of the species is confirmed both by meristic and molecular criteria. L. bandialensis presents a unique combination of characters with a low number of scales in the longitudinal series (32-33), 10.5-12 transverse scale rows, and distinctly yellowish dorsal, anal, and caudal fins. The currently known distribution of L. bandialensis includes coastal waters of Senegal, Gambia and Guinea Bissau. Finally, we provide a morphological identification key for the sixteen species of Mugilidae species occurring along the eastern central Atlantic coast of Africa. Copyright © 2011 Académie des sciences. All rights reserved.

  19. [Patient identification errors and biological samples in the analytical process: Is it possible to improve patient safety?].

    Science.gov (United States)

    Cuadrado-Cenzual, M A; García Briñón, M; de Gracia Hills, Y; González Estecha, M; Collado Yurrita, L; de Pedro Moro, J A; Fernández Pérez, C; Arroyo Fernández, M

    2015-01-01

    Patient identification errors and biological samples are one of the problems with the highest risk factor in causing an adverse event in the patient. To detect and analyse the causes of patient identification errors in analytical requests (PIEAR) from emergency departments, and to develop improvement strategies. A process and protocol was designed, to be followed by all professionals involved in the requesting and performing of laboratory tests. Evaluation and monitoring indicators of PIEAR were determined, before and after the implementation of these improvement measures (years 2010-2014). A total of 316 PIEAR were detected in a total of 483,254 emergency service requests during the study period, representing a mean of 6.80/10,000 requests. Patient identification failure was the most frequent in all the 6-monthly periods assessed, with a significant difference (Perrors. However, we must continue working with this strategy, promoting a culture of safety for all the professionals involved, and trying to achieve the goal that 100% of the analytical and samples are properly identified. Copyright © 2015 SECA. Published by Elsevier Espana. All rights reserved.

  20. PCR-RFLP on β-tubulin gene for rapid identification of the most clinically important species of Aspergillus.

    Science.gov (United States)

    Nasri, Tuba; Hedayati, Mohammad Taghi; Abastabar, Mahdi; Pasqualotto, Alessandro C; Armaki, Mojtaba Taghizadeh; Hoseinnejad, Akbar; Nabili, Mojtaba

    2015-10-01

    Aspergillus species are important agents of life-threatening infections in immunosuppressed patients. Proper speciation in the Aspergilli has been justified based on varied fungal virulence, clinical presentations, and antifungal resistance. Accurate identification of Aspergillus species usually relies on fungal DNA sequencing but this requires expensive equipment that is not available in most clinical laboratories. We developed and validated a discriminative low-cost PCR-based test to discriminate Aspergillus isolates at the species level. The Beta tubulin gene of various reference strains of Aspergillus species was amplified using the universal fungal primers Bt2a and Bt2b. The PCR products were subjected to digestion with a single restriction enzyme AlwI. All Aspergillus isolates were subjected to DNA sequencing for final species characterization. The PCR-RFLP test generated unique patterns for six clinically important Aspergillus species, including Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus terreus, Aspergillus clavatus and Aspergillus nidulans. The one-enzyme PCR-RFLP on Beta tubulin gene designed in this study is a low-cost tool for the reliable and rapid differentiation of the clinically important Aspergillus species. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Predicting how altering propagule pressure changes establishment rates of biological invaders across species pools.

    Science.gov (United States)

    Brockerhoff, Eckehard G; Kimberley, Mark; Liebhold, Andrew M; Haack, Robert A; Cavey, Joseph F

    2014-03-01

    Biological invasions resulting from international trade can cause major environmental and economic impacts. Propagule pressure is perhaps the most important factor influencing establishment, although actual arrival rates of species are rarely recorded. Furthermore, the pool of potential invaders includes many species that vary in their arrival rate and establishment potential. Therefore, we stress that it is essential to consider the size and composition of species pools arriving from source regions when estimating probabilities of establishment and effects of pathway infestation rates. To address this, we developed a novel framework and modeling approach to enable prediction of future establishments in relation to changes in arrival rate across entire species pools. We utilized 13 828 border interception records from the United States and New Zealand for 444 true bark beetle (Scolytinae) and longhorned beetle (Cerambycidae) species detected between 1949 and 2008 as proxies for arrival rates to model the relationship between arrival and establishment rates. Nonlinearity in this relationship implies that measures intended to reduce the unintended transport of potential invaders (such as phytosanitary treatments) must be highly effective in order to substantially reduce the rate of future invasions, particularly if trade volumes continue to increase.

  2. ConSpeciFix: Classifying prokaryotic species based on gene flow.

    Science.gov (United States)

    Bobay, Louis-Marie; Ellis, Brian Shin-Hua; Ochman, Howard

    2018-05-16

    Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML. ljbobay@uncg.edu.

  3. Species Identification of Fox-, Mink-, Dog-, and Rabbit-Derived Ingredients by Multiplex PCR and Real-Time PCR Assay.

    Science.gov (United States)

    Wu, Qingqing; Xiang, Shengnan; Wang, Wenjun; Zhao, Jinyan; Xia, Jinhua; Zhen, Yueran; Liu, Bang

    2018-05-01

    Various detection methods have been developed to date for identification of animal species. New techniques based on PCR approach have raised the hope of developing better identification methods, which can overcome the limitations of the existing methods. PCR-based methods used the mitochondrial DNA (mtDNA) as well as nuclear DNA sequences. In this study, by targeting nuclear DNA, multiplex PCR and real-time PCR methods were developed to assist with qualitative and quantitative analysis. The multiplex PCR was found to simultaneously and effectively distinguish four species (fox, dog, mink, and rabbit) ingredients by the different sizes of electrophoretic bands: 480, 317, 220, and 209 bp. Real-time fluorescent PCR's amplification profiles and standard curves showed good quantitative measurement responses and linearity, as indicated by good repeatability and coefficient of determination R 2  > 0.99. The quantitative results of quaternary DNA mixtures including mink, fox, dog, and rabbit DNA are in line with our expectations: R.D. (relative deviation) varied between 1.98 and 12.23% and R.S.D. (relative standard deviation) varied between 3.06 and 11.51%, both of which are well within the acceptance criterion of ≤ 25%. Combining the two methods is suitable for the rapid identification and accurate quantification of fox-, dog-, mink-, and rabbit-derived ingredients in the animal products.

  4. Sensitive identification of mycobacterial species using PCR-RFLP on bronchial washings.

    Science.gov (United States)

    Hidaka, E; Honda, T; Ueno, I; Yamasaki, Y; Kubo, K; Katsuyama, T

    2000-03-01

    In 98 patients (24 with active pulmonary tuberculosis [TB] lesions, 28 with cured TB lesions, and 46 with nontuberculous opacities [control group] in chest CT scans), we examined whether washing the bronchus after brushing the lesion, then applying polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to the bronchial washings might be useful for diagnosing TB and nontuberculous mycobacteriosis (NTMosis). After biopsy and brushing with a bronchoscope, the bronchus connecting to the lesion was washed with 20 ml saline. The saline used for washing the brushes (5 ml; brushing sample), and 3 to 10 ml saline aspirated through the forceps channel (washing sample) were examined by PCR-RFLP, which proved able to identify Mycobacterium tuberculosis and seven species of nontuberculous mycobacteria (NTM). The values obtained for the sensitivity of the PCR-RFLP with respect to the brushing sample, the washing sample, and both samples mixed together were 70, 76, and 91%, respectively, when only patients who were culture-positive or radiologically improved after antituberculous therapy were considered as showing true infection. A mixture of brushing and washing samples provides useful material for PCR and culture, and the PCR-RFLP used here is a good method for the simultaneous identification of several species of mycobacterium (including M. tuberculosis).

  5. A High Throughput Ambient Mass Spectrometric Approach to Species Identification and Classification from Chemical Fingerprint Signatures

    OpenAIRE

    Musah, Rabi A.; Espinoza, Edgard O.; Cody, Robert B.; Lesiak, Ashton D.; Christensen, Earl D.; Moore, Hannah E.; Maleknia, Simin; Drijfhout, Falko P.

    2015-01-01

    A high throughput method for species identification and classification through chemometric processing of direct analysis in real time (DART) mass spectrometry-derived fingerprint signatures has been developed. The method entails introduction of samples to the open air space between the DART ion source and the mass spectrometer inlet, with the entire observed mass spectral fingerprint subjected to unsupervised hierarchical clustering processing. A range of both polar and non-polar chemotypes a...

  6. Performance of chromogenic media for Candida in rapid presumptive identification of Candida species from clinical materials

    OpenAIRE

    Pravin Charles, M. V.; Kali, Arunava; Joseph, Noyal Mariya

    2015-01-01

    Background: In perspective of the worldwide increase in a number of immunocompromised patients, the need for identification of Candida species has become a major concern. The development of chromogenic differential media, introduced recently, facilitate rapid speciation. However, it can be employed for routine mycology workup only after an exhaustive evaluation of its benefit and cost effectiveness. This study was undertaken to evaluate the benefit and cost effectiveness of chromogenic media ...

  7. The tiger beetles (Coleoptera, Cicindelidae) of the southern Levant and adjacent territories: from cybertaxonomy to conservation biology.

    Science.gov (United States)

    Assmann, Thorsten; Boutaud, Estève; Buse, Jörn; Gebert, Jörg; Drees, Claudia; Friedman, Ariel-Leib-Leonid; Khoury, Fares; Marcus, Tamar; Orbach, Eylon; Ittai Renan; Schmidt, Constantin; Zumstein, Pascale

    2018-01-01

    The tiger beetles of the southern Levant (Egypt: Sinai, Israel, Jordan) and adjacent regions of the neighboring countries Lebanon, Syria, Iraq, Saudi Arabia and Egypt are reviewed in terms of species taxonomy, ecological and distributional traits and conservation biology. An illustrated dichotomous identification key from the species of this region is provided. Based on the classical identification key, we developed a digital identification application for smartphones and tablets. The species status of Calomera aulicoides (J.R. Sahlberg, 1913) is (re-) established (stat. rest.) as this taxon can be found sympatrically and parapatrically together with Calomera littoralis winkleri (Mandl, 1934). Morphological character states are discussed to identify Cicindela javetii Chaudoir, 1861 and C. herbacea Klug, 1832. Calomera aphrodisia (Baudi di Selve, 1864) is recorded for the first time from Israel. The presence of Calomera aulica (Dejean, 1831) and Grammognatha euphratica (Dejean, 1822) is confirmed by new records. At least five taxa are threatened or extinct in Israel. For one of these species, Israel has a national responsibility for the conservation as the main part of the distribution range is within this country. The application TIGER BEETLE ID for Android devices can be freely downloaded at https://doi.org/10.3897/zookeys.734.21989.suppl1. See also disclaimer of warranties.

  8. Identification of Forensically Important Calliphoridae and Sarcophagidae Species Collected in Korea Using SNaPshot Multiplex System Targeting the Cytochrome c Oxidase Subunit I Gene

    Directory of Open Access Journals (Sweden)

    Ji Hye Park

    2018-01-01

    Full Text Available Estimation of postmortem interval (PMI is paramount in modern forensic investigation. After the disappearance of the early postmortem phenomena conventionally used to estimate PMI, entomologic evidence provides important indicators for PMI estimation. The age of the oldest fly larvae or pupae can be estimated to pinpoint the time of oviposition, which is considered the minimum PMI (PMImin. The development rate of insects is usually temperature dependent and species specific. Therefore, species identification is mandatory for PMImin estimation using entomological evidence. The classical morphological identification method cannot be applied when specimens are damaged or have not yet matured. To overcome this limitation, some investigators employ molecular identification using mitochondrial cytochrome c oxidase subunit I (COI nucleotide sequences. The molecular identification method commonly uses Sanger’s nucleotide sequencing and molecular phylogeny, which are complex and time consuming and constitute another obstacle for forensic investigators. In this study, instead of using conventional Sanger’s nucleotide sequencing, single-nucleotide polymorphisms (SNPs in the COI gene region, which are unique between fly species, were selected and targeted for single-base extension (SBE technology. These SNPs were genotyped using a SNaPshot® kit. Eleven Calliphoridae and seven Sarcophagidae species were covered. To validate this genotyping, fly DNA samples (103 adults, 84 larvae, and 4 pupae previously confirmed by DNA barcoding were used. This method worked quickly with minimal DNA, providing a potential alternative to conventional DNA barcoding. Consisting of only a few simple electropherogram peaks, the results were more straightforward compared with those of the conventional DNA barcoding produced by Sanger’s nucleotide sequencing.

  9. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  10. Molecular identification of two Culex (Culex species of the neotropical region (Diptera: Culicidae.

    Directory of Open Access Journals (Sweden)

    Magdalena Laurito

    Full Text Available Culex bidens and C. interfor, implicated in arbovirus transmission in Argentina, are sister species, only distinguishable by feature of the male genitalia; however, intermediate specimens of the species in sympatry have been found. Fourth-instar larvae and females of both species share apomorphic features, and this lack of clear distinction creates problems for specific identification. Geometric morphometric traits of these life stages also do not distinguish the species. The aim of the present study was to assess the taxonomic status of C. bidens and C. interfor using two mitochondrial genes and to determine the degree of their reproductive isolation using microsatellite loci. Sequences of the ND4 and COI genes were concatenated in a matrix of 993 nucleotides and used for phylogenetic and distance analyses. Bayesian and maximum parsimony inferences showed a well resolved and supported topology, enclosing sequences of individuals of C. bidens (0.83 BPP, 73 BSV and C. interfor (0.98 BPP, 97 BSV in a strong sister relationship. The mean K2P distance within C. bidens and C. interfor was 0.3% and 0.2%, respectively, and the interspecific variation was 2.3%. Bayesian clustering also showed two distinct mitochondrial lineages. All sequenced mosquitoes were successfully identified in accordance with the best close match algorithm. The low genetic distance values obtained indicate that the species diverged quite recently. Most morphologically intermediate specimens of C. bidens from Córdoba were heterozygous for the microsatellite locus GT51; the significant heterozygote excess observed suggests incomplete reproductive isolation. However, C. bidens and C. interfor should be considered good species: the ventral arm of the phallosome of the male genitalia and the ND4 and COI sequences are diagnostic characters.

  11. Indoors forensic entomology: colonization of human remains in closed environments by specific species of sarcosaprophagous flies.

    Science.gov (United States)

    Pohjoismäki, Jaakko L O; Karhunen, Pekka J; Goebeler, Sirkka; Saukko, Pekka; Sääksjärvi, Ilari E

    2010-06-15

    Fly species that are commonly recovered on human corpses concealed in houses or other dwellings are often dependent on human created environments and might have special features in their biology that allow them to colonize indoor cadavers. In this study we describe nine typical cases involving forensically relevant flies on human remains found indoors in southern Finland. Eggs, larvae and puparia were reared to adult stage and determined to species. Of the five species found the most common were Lucilia sericata Meigen, Calliphora vicina Robineau-Desvoidy and Protophormia terraenovae Robineau-Desvoidy. The flesh fly Sarcophaga caerulescens Zetterstedt is reported for the first time to colonize human cadavers inside houses and a COI gene sequence based DNA barcode is provided for it to help facilitate identification in the future. Fly biology, colonization speed and the significance of indoors forensic entomological evidence are discussed. (c) 2010 Elsevier Ireland Ltd. All rights reserved.

  12. Comparison of identification methods for oral asaccharolytic Eubacterium species.

    Science.gov (United States)

    Wade, W G; Slayne, M A; Aldred, M J

    1990-12-01

    Thirty one strains of oral, asaccharolytic Eubacterium spp. and the type strains of E. brachy, E. nodatum and E. timidum were subjected to three identification techniques--protein-profile analysis, determination of metabolic end-products, and the API ATB32A identification kit. Five clusters were obtained from numerical analysis of protein profiles and excellent correlations were seen with the other two methods. Protein profiles alone allowed unequivocal identification.

  13. Molecular identification of birds: performance of distance-based DNA barcoding in three genes to delimit parapatric species.

    Directory of Open Access Journals (Sweden)

    Mansour Aliabadian

    Full Text Available DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (cox1 or COI has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species.In this study we extend the sample size of prior studies in birds for cox1 (2776 sequences, 756 species and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species, we include also DNA sequences of two other mitochondrial genes: cytochrome b (cob (4614 sequences, 2087 species and 16S (708 sequences, 498 species. Our results confirm the existence of a wide gap between intra- and interspecies divergences for both cox1 and cob, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both cox1 and cob.DNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.

  14. Simultaneous detection and identification of Aspergillus and mucorales species in tissues collected from patients with fungal rhinosinusitis.

    Science.gov (United States)

    Zhao, Zuotao; Li, Lili; Wan, Zhe; Chen, Wei; Liu, Honggang; Li, Ruoyu

    2011-04-01

    Rapid detection and differentiation of Aspergillus and Mucorales species in fungal rhinosinusitis diagnosis are desirable, since the clinical management and prognosis associated with the two taxa are fundamentally different. We describe an assay based on a combination of broad-range PCR amplification and reverse line blot hybridization (PCR/RLB) to detect and differentiate the pathogens causing fungal rhinosinusitis, which include five Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. nidulans) and seven Mucorales species (Mucor heimalis, Mucor racemosus, Mucor cercinelloidea, Rhizopus arrhizus, Rhizopus microsporus, Rhizomucor pusillus, and Absidia corymbifera). The assay was validated with 98 well-characterized clinical isolates and 41 clinical tissue specimens. PCR/RLB showed high sensitivity and specificity, with 100% correct identifications of 98 clinical isolates and no cross-hybridization between the species-specific probes. Results for five control isolates, Candida albicans, Fusarium solani, Scedosporium apiospermum, Penicillium marneffei, and Exophiala verrucosa, were negative as judged by PCR/RLB. The analytical sensitivity of PCR/RLB was found to be 1.8 × 10(-3) ng/μl by 10-fold serial dilution of Aspergillus genomic DNA. The assay identified 35 of 41 (85.4%) clinical specimens, exhibiting a higher sensitivity than fungal culture (22 of 41; 53.7%) and direct sequencing (18 of 41; 43.9%). PCR/RLB similarly showed high specificity, with correct identification 16 of 18 specimens detected by internal transcribed spacer (ITS) sequencing and 16 of 22 detected by fungal culture, but it also has the additional advantage of being able to detect mixed infection in a single clinical specimen. The PCR/RLB assay thus provides a rapid and reliable option for laboratory diagnosis of fungal rhinosinusitis.

  15. Simultaneous Detection and Identification of Aspergillus and Mucorales Species in Tissues Collected from Patients with Fungal Rhinosinusitis▿

    Science.gov (United States)

    Zhao, Zuotao; Li, Lili; Wan, Zhe; Chen, Wei; Liu, Honggang; Li, Ruoyu

    2011-01-01

    Rapid detection and differentiation of Aspergillus and Mucorales species in fungal rhinosinusitis diagnosis are desirable, since the clinical management and prognosis associated with the two taxa are fundamentally different. We describe an assay based on a combination of broad-range PCR amplification and reverse line blot hybridization (PCR/RLB) to detect and differentiate the pathogens causing fungal rhinosinusitis, which include five Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. nidulans) and seven Mucorales species (Mucor heimalis, Mucor racemosus, Mucor cercinelloidea, Rhizopus arrhizus, Rhizopus microsporus, Rhizomucor pusillus, and Absidia corymbifera). The assay was validated with 98 well-characterized clinical isolates and 41 clinical tissue specimens. PCR/RLB showed high sensitivity and specificity, with 100% correct identifications of 98 clinical isolates and no cross-hybridization between the species-specific probes. Results for five control isolates, Candida albicans, Fusarium solani, Scedosporium apiospermum, Penicillium marneffei, and Exophiala verrucosa, were negative as judged by PCR/RLB. The analytical sensitivity of PCR/RLB was found to be 1.8 × 10−3 ng/μl by 10-fold serial dilution of Aspergillus genomic DNA. The assay identified 35 of 41 (85.4%) clinical specimens, exhibiting a higher sensitivity than fungal culture (22 of 41; 53.7%) and direct sequencing (18 of 41; 43.9%). PCR/RLB similarly showed high specificity, with correct identification 16 of 18 specimens detected by internal transcribed spacer (ITS) sequencing and 16 of 22 detected by fungal culture, but it also has the additional advantage of being able to detect mixed infection in a single clinical specimen. The PCR/RLB assay thus provides a rapid and reliable option for laboratory diagnosis of fungal rhinosinusitis. PMID:21325541

  16. Sea Cucumber (Holothuroidea Species of Turkey

    Directory of Open Access Journals (Sweden)

    Mehmet AYDIN

    2016-11-01

    Full Text Available There are nearly 1200 sea cucumber species in the world oceans, while only 37 species from Holothuroidea class lives in the Mediterranean Sea. This preliminary study aims identification sea cucumbers species of the Turkish waters. The sea cucumber samples used in this study were obtained from a series of different studies between the years of 2008 and 2014. Identification of the species are mainly based on the morphometric characteristics while some of species are determined from their calcareous spicules. Eight sea species were identified in this research which are; Holothuria tubulosa, Holothuria polii, Holothuria mammata, Holothuria (Platyperona sanctori, Holothuria forskali, Stichopus regalis, Synaptula reciprocans and Stereoderma kirschbergi. There are limited number of studies in the literature focusing on the identification of the sea cucumber species spread in our seas. Therefore, this study is believed to play an important role in guiding future researches.

  17. Identification and characterization of phenolics and terpenoids from ethanolic extracts of Phyllanthus species by HPLC-ESI-QTOF-MS/MS

    Institute of Scientific and Technical Information of China (English)

    Sunil Kumar; Awantika Singh; Brijesh Kumar

    2017-01-01

    Phyllanthus species plants are a rich source of phenolics and widely used due to their medicinal properties. A liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was developed using high-pressure liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (HPLC-ESI-QTOF-MS/MS) for the identification and characterization of quercetin, kaempferol, ellagic acid and their derivatives in ethanolic extracts of Phyllanthus species. The chromatographic separation was carried out on Thermo Betasil C8 column (250 mm×4.5 mm, 5 μm) using 0.1% formic acid in water and 0.1% formic acid in methanol as the mobile phase. The identification of diagnostic fragment ions and optimization of collision energies were carried out using 21 reference standards. Totally 51 compounds were identified which include 21 compounds identified and characterized unambiguously by comparison with their authentic standards and the remaining 30 were tentatively identified and characterized in ethanolic extracts of P. emblica, P. fraternus, P. amarus and P. niruri.

  18. Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains

    Science.gov (United States)

    Jaklitsch, Walter; Gazis, Romina; Degenkolb, Thomas; Samuels, Gary J.

    2016-01-01

    Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture ‘T. harzianum T22’ was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex. PMID:25661720

  19. Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains.

    Science.gov (United States)

    Chaverri, Priscila; Branco-Rocha, Fabiano; Jaklitsch, Walter; Gazis, Romina; Degenkolb, Thomas; Samuels, Gary J

    2015-01-01

    Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture 'T. harzianum T22' was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex. © 2015 by The Mycological Society of America.

  20. Identification of receptors of main sex-pheromone components of three Lepidopteran species.

    Science.gov (United States)

    Mitsuno, Hidefumi; Sakurai, Takeshi; Murai, Masatoshi; Yasuda, Tetsuya; Kugimiya, Soichi; Ozawa, Rika; Toyohara, Haruhiko; Takabayashi, Junji; Miyoshi, Hideto; Nishioka, Takaaki

    2008-09-01

    Male moths discriminate conspecific female-emitted sex pheromones. Although the chemical components of sex pheromones have been identified in more than 500 moth species, only three components in Bombyx mori and Heliothis virescens have had their receptors identified. Here we report the identification of receptors for the main sex-pheromone components in three moth species, Plutella xylostella, Mythimna separata and Diaphania indica. We cloned putative sex-pheromone receptor genes PxOR1, MsOR1 and DiOR1 from P. xylostella, M. separata and D. indica, respectively. Each of the three genes was exclusively expressed with an Or83b orthologous gene in male olfactory receptor neurons (ORNs) that are surrounded by supporting cells expressing pheromone-binding-protein (PBP) genes. By two-electrode voltage-clamp recording, we tested the ligand specificity of Xenopus oocytes co-expressing PxOR1, MsOR1 or DiOR1 with an OR83b family protein. Among the seven sex-pheromone components of the three moth species, the oocytes dose-dependently responded only to the main sex-pheromone component of the corresponding moth species. In our study, PBPs were not essential for ligand specificity of the receptors. On the phylogenetic tree of insect olfactory receptors, the six sex-pheromone receptors identified in the present and previous studies are grouped in the same subfamily but have no relation with the taxonomy of moths. It is most likely that sex-pheromone receptors have randomly evolved from ancestral sex-pheromone receptors before the speciation of moths and that their ligand specificity was modified by mutations of local amino acid sequences after speciation.

  1. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.

    Science.gov (United States)

    Suwannasai, Nuttika; Martín, María P; Phosri, Cherdchai; Sihanonth, Prakitsin; Whalley, Anthony J S; Spouge, John L

    2013-01-01

    Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and

  2. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.

    Directory of Open Access Journals (Sweden)

    Nuttika Suwannasai

    Full Text Available Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI, we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1 Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2 Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3 Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in

  3. Genetic identification of eggs from four species of Ophichthidae and Congridae (Anguilliformes) in the northern East China Sea

    Science.gov (United States)

    Choi, Hae-young; Oh, Jina

    2018-01-01

    We report the first genetic identification of eggs of four species of Anguilliformes caught in the northern East China Sea during August 2016, where leptocephali and adults have been collected. The species were Ophisurus macrorhynchos and Echelus uropterus belonging to the Ophichthidae, and Ariosoma majus and Gnathophis heterognathos belonging to the Congridae. The eggs were identified using three molecular genetic markers (mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit 1), sequences obtained from local adult specimens, and geographical distribution data. All eggs were in the early or middle developmental stages. For all species except A. majus, the eggs were found near the range of small leptocephali in the East China Sea and the southern Korean Peninsula, which indicates these species had spawned along the continental near these areas during the summer. PMID:29621326

  4. Technical Note: "Mitochondrial and nuclear DNA approaches for reliable identification of Lucilia (Diptera, Calliphoridae) species of forensic interest from Southern Europe".

    Science.gov (United States)

    GilArriortua, Maite; Saloña-Bordas, Marta I; Cainé, Laura M; Pinheiro, Fátima; M de Pancorbo, Marian

    2015-12-01

    In forensic entomology, rapid and unambiguous identification of blowfly species is a critical prerequisite for accurately estimating the post-mortem interval (PMI). The conventional diagnosis of cadaveric entomofauna based on external characters is hampered by the morphological similarities between species, especially in immature stages. Genetic analysis has been shown to allow precise and reliable diagnosis and delimitation of insect species. Nevertheless, the taxonomy of some species remains unresolved. This study was focused on improving the effectiveness and accuracy of analysis based on the widely used cytochrome c oxidase subunit I barcode region (COI barcode, 658 bp), complemented by other mitochondrial and nuclear regions, such as cytochrome b (Cyt-b, 307 bp) and the second internal transcribed spacer (ITS2, 310-331 bp), for the identification of Southern European blowflies. We analyzed a total of 209 specimens, collected from 38 human corpses, belonging to three Calliphoridae genera and seven species: Chrysomya (Ch. albiceps), Calliphora (C. vicina and C. vomitoria), and Lucilia (L. sericata, L. ampullacea, L. caesar and L. illustris). These species are the most common PMI indicators in Portugal. The results revealed that unambiguous separation of species of the Lucilia genus requires different loci from the barcode region. Furthermore, we conclude that the ITS2 (310-331 bp) molecular marker is a promising diagnostic tool because its inter-specific discriminatory power enables unequivocal and consistent distinctions to be made, even between closely related species (L. caesar-L. illustris). This work also contributes new genetic data that may be of interest in performing species diagnosis for Southern European blowflies. Notably, to the best of our knowledge, we provide the first records of the Cyt-b (307 bp) locus for L. illustris and the ITS2 (310-331 bp) region for Iberian Peninsula Lucilia species. Copyright © 2015 Elsevier Ireland Ltd. All rights

  5. LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species.

    Science.gov (United States)

    Moolhuijzen, P; Cakir, M; Hunter, A; Schibeci, D; Macgregor, A; Smith, C; Francki, M; Jones, M G K; Appels, R; Bellgard, M

    2006-06-01

    The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume

  6. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to rpoB gene sequencing for species identification of bloodstream infection staphylococcal isolates.

    Science.gov (United States)

    Spanu, T; De Carolis, E; Fiori, B; Sanguinetti, M; D'Inzeo, T; Fadda, G; Posteraro, B

    2011-01-01

    As a result of variable expression of biochemical characters, misidentification by conventional phenotypic means often occurs with clinical isolates belonging to Staphylococcus species. Therefore, we evaluated the use of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of 450 blood isolates of the most relevant staphylococcal species, using sequence analysis of the rpoB gene as the reference method. A correct species identification by MALDI-TOF was obtained in 99.3% (447/450), with only three isolates being misidentified. In addition, MALDI-TOF correctly identified all the staphylococcal subspecies studied, including Staphylococcus capitis subsp. capitis and subsp. urealyticus, Staphylococcus cohnii subsp. urealyticus, Staphylococcus hominis subsp. novobiosepticus and subsp. hominis, Staphylococcus saprophyticus subsp. saprophyticus, Staphylococcus schleiferi subsp. schleiferi and Staphylococcus sciuri subsp. sciuri. Thus, MALDI-TOF MS-based species identification of staphylococci can be routinely achieved without any substantial costs for consumables or the time needed for labour-intensive DNA sequence analysis. © 2010 The Authors. Journal Compilation © 2010 European Society of Clinical Microbiology and Infectious Diseases.

  7. A Universal Method for Species Identification of Mammals Utilizing Next Generation Sequencing for the Analysis of DNA Mixtures

    Science.gov (United States)

    Tillmar, Andreas O.; Dell'Amico, Barbara; Welander, Jenny; Holmlund, Gunilla

    2013-01-01

    Species identification can be interesting in a wide range of areas, for example, in forensic applications, food monitoring and in archeology. The vast majority of existing DNA typing methods developed for species determination, mainly focuses on a single species source. There are, however, many instances where all species from mixed sources need to be determined, even when the species in minority constitutes less than 1 % of the sample. The introduction of next generation sequencing opens new possibilities for such challenging samples. In this study we present a universal deep sequencing method using 454 GS Junior sequencing of a target on the mitochondrial gene 16S rRNA. The method was designed through phylogenetic analyses of DNA reference sequences from more than 300 mammal species. Experiments were performed on artificial species-species mixture samples in order to verify the method’s robustness and its ability to detect all species within a mixture. The method was also tested on samples from authentic forensic casework. The results showed to be promising, discriminating over 99.9 % of mammal species and the ability to detect multiple donors within a mixture and also to detect minor components as low as 1 % of a mixed sample. PMID:24358309

  8. Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh,

    Directory of Open Access Journals (Sweden)

    Suaad S. AlWakeel

    2017-09-01

    Full Text Available This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis, alpha-hemolytic streptococci, Staphylococcus hominis, coagulase-negative staphylococci, Leuconostoc mesenteroides, Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (<60% sensitivity to the antibiotics ampicillin, erythromycin, clarithromycin and norfloxacin were observed. Ninety-seven percent similarity to the microbial bank species was noted when the isolates were compared to it. Most hematological indices recorded were within the normal range. In conclusion, exposure to toxic fumes and compounds within fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

  9. A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys.

    Science.gov (United States)

    Watanabe, Shun; Minegishi, Yuki; Yoshinaga, Tatsuki; Aoyama, Jun; Tsukamoto, Katsumi

    2004-01-01

    To compensate for the limited number of morphological characteristics of fish eggs and larvae, we established a convenient and robust method of species identification for eggs of the Japanese eel (Anguilla japonica) using a real-time polymerase chain reaction (PCR) that can be performed onboard research ships at sea. A total of about 1.2 kbp of the mitochondrial 16S ribosomal RNA gene sequences from all species of Anguilla and 3 other anguilliform species were compared to design specific primer pairs and a probe for A. japonica. This real-time PCR amplification was conducted for a total of 44 specimens including A. japonica, A. marmorata, A. bicolor pacifica, and 6 other anguilliform species. Immediate PCR amplification was only observed in A. japonica. We then tested this method under onboard conditions and obtained the same result as had been produced in the laboratory. These results suggest that real-time PCR can be a powerful tool for detecting Japanese eel eggs and newly hatched larvae immediately after onboard sampling during research cruises and will allow targeted sampling efforts to occur rapidly in response to any positive onboard identification of the eggs and larvae of this species.

  10. Genetic identification of the main opportunistic Mucorales by PCR-restriction fragment length polymorphism.

    Science.gov (United States)

    Machouart, M; Larché, J; Burton, K; Collomb, J; Maurer, P; Cintrat, A; Biava, M F; Greciano, S; Kuijpers, A F A; Contet-Audonneau, N; de Hoog, G S; Gérard, A; Fortier, B

    2006-03-01

    Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera Absidia, Mucor, Rhizopus, and Rhizomucor, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis.

  11. Identification of Nematode Fauna in Vineyards of South of Western Azerbaijan and Determination of the Dominant Parasitic Species

    Directory of Open Access Journals (Sweden)

    E. Mohajeri

    2017-12-01

    Full Text Available Introduction: Grapevine belongs to the Vitaceae family that consists of 14 genera and about 700 species. Only in the genus Vitis fruits are edible. Italy is the largest producer of grapes and Iran has the seventh position in the world from this point of view. Western Azarbaijan province comprises a high diversity of crops including wild grapes. Although, some nematodes are free living and antagonists of another soil microfauna, the other are plant parasitic agents. Most of which live in the agricultural soils where they are widely dispersed. Effectiveness of the disease management strategies are affected by the accurate identification of the plant disease causal agents and the nematodal diseases are not the exception from this rule. Therefore, for control of the diseases caused by the nematodes, it is necessary to separate the parasitic nematodes from the suspected contaminated soils and identify them. Although separation and identification of the nematodes are partly time-consuming, it is not very complicated. Some nematodes likeXiphinema, Longidorus and Ditylenchus are cosmopolitan and catastrophic nematodes in vineyards worldwide. So far no study has been performed regarding the plant parasitic nematode in vineyards of the south of Western Azerbaijan. Therefore, in this study as an introduction to the management ofthe vineyard parasitic nematodes, the dominant nematodes of the plant were identified. In the next step, investigation of nematodes bioecology, the interaction of nematodes with the other plant pathogens, their host range and their damages to the host plants would be studied. Materials and Methods: In order to identify the fauna of plant parasitic nematodes in vineyards of the south of Western Azarbaijan, during 2013-2014, 50 soil samples were collected from the rhizosphere of grapevine. The sampling was carried out from the vineyards of five grapevine growing cities including Mahabad, Bookan, Sardasht, Piranshahr and Miyandoab. The

  12. Identification of Trichoderma Species Using Partial Sequencing of nrRNA and tef1α Genes with Report of Trichoderma capillare in Iran Mycoflore

    Directory of Open Access Journals (Sweden)

    mehdi Mehrabi-Koushki

    2018-01-01

    Full Text Available Introduction: Trichoderma is monophyletic (16, with teleomorphs in the genus Hypocrea. Some cryptic Trichoderma species are hidden within morphological species complexes and can only be elucidated by in-depth molecular studies. The genealogical concordance phylogenetic species recognition (GCPSR using several non-linked genes are needed to give accurate identification of Trichoderma spp. (6. Although the ITS region has been successfully used for species delimitation of Trichoderma and Hypocrea (5, but, it is not sufficient for accurate identification of some species. Translation elongation factor 1α gene (tef1α is a reliable barcode for Fusarium (9, Trichoderma and Hypocrea (5. Here, ITS and tef1α genes were selected as candidate DNA barcodes to identify Trichoderma isolates. Material and methods: 40 Trichoderma isolates used in this study were from a fungal collection archived in the plant pathology laboratory in the Department of Plant Protection at the Shahid Chamran University of Ahvaz. Spore suspension (105/ml prepared from single spore cultures of each Trichoderma isolates was added into flasks containing PDB medium. The flasks were shaken at 180 rpm for 10-15 days at 28ºC and the biomass was harvested by passing through sterilized filter papers. The mycelia were freeze-dried (Freeze-Dryer, Alpha 1-2LD Plus, Christ and powdered in the mortar containing liquid nitrogen by pestle. The genomic DNA was isolated according to modified method established by Raeder and Broda (21. The universal primers (ITS1–F; 5'-TCCGTAGGTGAACCTGCGG-3' and ITS4-R; 5'-TCCTCCGCTTATTGATATGC-3' were employed for amplifying around 700bp from 18s, ITS1, 5.8s, ITS2 and 28s rDNA regions (27. The specific primers (tef1α71-f; 5'-CAAAATGGGTAAGGAGGASAAGAC-3' and tef1997-R; 5'-CAGTACCGGCRGCRATRATSAG-3' were employed for amplifying around 950bp from tef1α gene (24. PCR products were purified through ethanol-precipitation method and then sequenced using forward and

  13. Identification of potential essential fish habitats for skates based on fishers' knowledge.

    Science.gov (United States)

    Serra-Pereira, Bárbara; Erzini, Karim; Maia, Catarina; Figueiredo, Ivone

    2014-05-01

    Understanding of spatio-temporal patterns of sensitive fish species such as skates (Rajidae) is essential for implementation of conservation measures. With insufficient survey data available for these species in Portuguese Continental waters, this study shows that fishery-dependent data associated with fishers' knowledge can be used to identify potential Essential Fish Habitats (EFH) for seven skate species. Sites with similar geomorphology were associated with the occurrence of juveniles and/or adults of the same group of species. For example, sites deeper than 100 m with soft sediment include predominantly adults of Raja clavata, and are the habitat for egg deposition of this species. Raja undulata and R. microocellata are the more coastal species, preferring sand or gravel habitats, while coastal areas with rocks and sand seabed are potential nursery areas for R. brachyura, R. montagui and R. clavata. The main output of this study is the identification of preferential fishing sites enclosing potential EFH for some species, associated with egg-laying and nursery grounds. The location of these areas will be considered for future seasonal closures, and studies will be conducted to evaluate the biological and socio-economic impacts of such measures. As in the past, fishermen will collaborate in the process of evaluating those impacts, since they have practical and applied knowledge that is extremely valuable for evaluating the advantages and disadvantages of such closures. In conclusion, this study is a first contribution to the understanding and identification of EFH for skate species, associated with nursery and egg deposition sites, with direct application to management.

  14. Identification of Potential Essential Fish Habitats for Skates Based on Fishers' Knowledge

    Science.gov (United States)

    Serra-Pereira, Bárbara; Erzini, Karim; Maia, Catarina; Figueiredo, Ivone

    2014-05-01

    Understanding of spatio-temporal patterns of sensitive fish species such as skates (Rajidae) is essential for implementation of conservation measures. With insufficient survey data available for these species in Portuguese Continental waters, this study shows that fishery-dependent data associated with fishers' knowledge can be used to identify potential Essential Fish Habitats (EFH) for seven skate species. Sites with similar geomorphology were associated with the occurrence of juveniles and/or adults of the same group of species. For example, sites deeper than 100 m with soft sediment include predominantly adults of Raja clavata, and are the habitat for egg deposition of this species. Raja undulata and R. microocellata are the more coastal species, preferring sand or gravel habitats, while coastal areas with rocks and sand seabed are potential nursery areas for R. brachyura, R. montagui and R. clavata. The main output of this study is the identification of preferential fishing sites enclosing potential EFH for some species, associated with egg-laying and nursery grounds. The location of these areas will be considered for future seasonal closures, and studies will be conducted to evaluate the biological and socio-economic impacts of such measures. As in the past, fishermen will collaborate in the process of evaluating those impacts, since they have practical and applied knowledge that is extremely valuable for evaluating the advantages and disadvantages of such closures. In conclusion, this study is a first contribution to the understanding and identification of EFH for skate species, associated with nursery and egg deposition sites, with direct application to management.

  15. Limitations of the Current Microbial Identification System for Identification of Clinical Yeast Isolates

    Science.gov (United States)

    Kellogg, James A.; Bankert, David A.; Chaturvedi, Vishnu

    1998-01-01

    The ability of the rapid, computerized Microbial Identification System (MIS; Microbial ID, Inc.) to identify a variety of clinical isolates of yeast species was compared to the abilities of a combination of tests including the Yeast Biochemical Card (bioMerieux Vitek), determination of microscopic morphology on cornmeal agar with Tween 80, and when necessary, conventional biochemical tests and/or the API 20C Aux system (bioMerieux Vitek) to identify the same yeast isolates. The MIS chromatographically analyzes cellular fatty acids and compares the results with the fatty acid profiles in its database. Yeast isolates were subcultured onto Sabouraud dextrose agar and were incubated at 28°C for 24 h. The resulting colonies were saponified, methylated, extracted, and chromatographically analyzed (by version 3.8 of the MIS YSTCLN database) according to the manufacturer’s instructions. Of 477 isolates of 23 species tested, 448 (94%) were given species names by the MIS and 29 (6%) were unidentified (specified as “no match” by the MIS). Of the 448 isolates given names by the MIS, only 335 (75%) of the identifications were correct to the species level. While the MIS correctly identified only 102 (82%) of 124 isolates of Candida glabrata, the predictive value of an MIS identification of unknown isolates as C. glabrata was 100% (102 of 102) because no isolates of other species were misidentified as C. glabrata. In contrast, while the MIS correctly identified 100% (15 of 15) of the isolates of Saccharomyces cerevisiae, the predictive value of an MIS identification of unknown isolates as S. cerevisiae was only 47% (15 of 32), because 17 isolates of C. glabrata were misidentified as S. cerevisiae. The low predictive values for accuracy associated with MIS identifications for most of the remaining yeast species indicate that the procedure and/or database for the system need to be improved. PMID:9574676

  16. Contribution to biology and distribution studies on some ground beetles species (Coleoptera, Carabidae registered in the Red Data Book of Krasnodarsky Krai

    Directory of Open Access Journals (Sweden)

    Alexander S. Bondarenko

    2017-05-01

    Full Text Available Some biological features and distributional data on seven species of the ground beetles, registered in the Red Data Book of Krasnodarsky Krai, are presented, namely Carabus obtusus, Carabus kaljuzhnyji, Carabus miroshnikovi, Carabus caucasicus, Leistus spinibarbis, Poecilus lyroderus, and Harpalus petri. The results of the field researches, carried out by the authors in 2010–2015, expanded considerably the knowledge of their biological features and regional distribution areas; furthermore, life cycles were reconstructed for four of the above listed species.

  17. Real-time PCR for Leishmania species identification: Evaluation and comparison with classical techniques.

    Science.gov (United States)

    de Morais, Rayana Carla Silva; da Costa Oliveira, Cintia Nascimento; de Albuquerque, Suênia da Cunha Gonçalves; Mendonça Trajano Silva, Lays Adrianne; Pessoa-E-Silva, Rômulo; Alves da Cruz, Heidi Lacerda; de Brito, Maria Edileuza Felinto; de Paiva Cavalcanti, Milena

    2016-06-01

    Cutaneous leishmaniasis (CL) is a parasitic disease caused by various Leishmania species. Several studies have shown that real time quantitative PCR (qPCR) can be used for Leishmania spp. identification by analyzing the melting temperature (Tm). Thus, the aim of this study was to evaluate the viability of qPCR for differentiating eight closely related Leishmania species that cause the same clinical form of the disease and to compare the results with classical techniques. qPCR assays for standardizing the Tm using reference strains were performed. After the CL diagnosis on blood samples of domestic animals, positive samples were analyzed by their Tm and qPCR products were purified and sequenced. Ten human samples previously characterized by Multilocus Enzyme Electrophoresis (MLEE) were also analyzed by Tm. A Restriction Fragment Length Polymorphism (RFLP) assay, a reference test, was also standardized, by using the reference strains. Through standardization of Tm for Leishmania spp., two Tm ranges were created for analysis: 1 (Tm = 78-79.99 °C) included Leishmania (V.) braziliensis, Leishmania (V.) panamensis, Leishmania (V.) lainsoni, Leishmania (V.) guyanensis and Leishmania (V.) shawi; and 2 (Tm = 80-82.2 °C) included Leishmania (V.) naiffi, Leishmania (L.) amazonensis and Leishmania (L.) mexicana. A total of 223 positive blood samples were analyzed, with 58 included in range 1 and 165 in range 2. L. (V.) braziliensis, L. (V.) panamensis and L. (V.) guyanensis were identified by sequencing, while L. (V.) braziliensis, L. (L.) mexicana and L. (V.) panamensis were identified by RFLP analysis. Ten human samples previously characterized by Multilocus Enzyme Electrophoresis (MLEE) were also analyzed by qPCR Tm analysis; five were classified in range 1 and five in range 2. A concordance of 80% was calculated between qPCR and the gold-standard (MLEE) with no significant difference between the methods (p = 0.6499); a similar result was observed for sequencing

  18. Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region.

    Science.gov (United States)

    Yao, Hui; Song, Jing-Yuan; Ma, Xin-Ye; Liu, Chang; Li, Ying; Xu, Hong-Xi; Han, Jian-Ping; Duan, Li-Sheng; Chen, Shi-Lin

    2009-05-01

    DNA barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Although a consensus has not been reached regarding which DNA sequences can be used as the best plant barcodes, the psbA-trnH spacer region has been tested extensively in recent years. In this study, we hypothesize that the psbA-trnH spacer regions are also effective barcodes for Dendrobium species. We have sequenced the chloroplast psbA-trnH intergenic spacers of 17 Dendrobium species to test this hypothesis. The sequences were found to be significantly different from those of other species, with percentages of variation ranging from 0.3 % to 2.3 % and an average of 1.2 %. In contrast, the intraspecific variation among the Dendrobium species studied ranged from 0 % to 0.1 %. The sequence difference between the psbA-trnH sequences of 17 Dendrobium species and one Bulbophyllum odoratissimum ranged from 2.0 % to 3.1 %, with an average of 2.5 %. Our results support the notion that the psbA-trnH intergenic spacer region could be used as a barcode to distinguish various Dendrobium species and to differentiate Dendrobium species from other adulterating species. Copyright Georg Thieme Verlag KG Stuttgart. New York.

  19. Identification of cultured isolates of clinically important yeast species using fluorescent fragment length analysis of the amplified internally transcribed rRNA spacer 2 region

    Directory of Open Access Journals (Sweden)

    Muylaert An

    2002-07-01

    Full Text Available Abstract Background The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2, followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts. Results A rapid DNA-extraction method, based on simple boiling-freezing was introduced. Of the 26 species tested, 22 could be identified unambiguously by scoring the length of the ITS2-region. No distinction could be made between the species Trichosporon asteroides and T. inkin or between T. mucoides and T. ovoides. The two varieties of Cryptococcus neoformans (var. neoformans and var. gattii could be differentiated from each other due to a one bp length difference of the ITS2 fragment. The three Cryptococcus laurentii isolates were split into two groups according to their ITS2-fragment lengths, in correspondence with the phylogenetic groups described previously. Since the obtained fragment lengths compare well to those described previously and could be exchanged between two laboratories, an internationally usable library of ITS2 fragment lengths can be constructed. Conclusions The existing ITS2 size based library enables identification of most of the clinically important yeast species within 6 hours starting from a single colony and can be easily updated when new species are described. Data can be exchanged between laboratories.

  20. Genotypic versus phenotypic identification of staphylococcal species of canine origin with special reference to Staphylococcus schleiferi subsp. coagulans.

    Science.gov (United States)

    Jousson, Olivier; Di Bello, Domenica; Vanni, Michele; Cardini, Giovanni; Soldani, Giulio; Pretti, Carlo; Intorre, Luigi

    2007-07-20

    A comparative study was performed to examine the respective accuracy of 16S rDNA sequencing and of the commercial biochemical assay ID32 STAPH (bioMérieux, Marcy l'Etoile, France) in the identification of 232 staphylococcal samples representing 20 species and subspecies isolated from 367 dogs. Notable differences in species distribution were observed by comparing genotypic and phenotypic data. Partial sequencing of 16S rDNA resulted in an unambiguous identification of 226 (97.4%) of the isolates, whereas the phenotypic approach resulted in a correct diagnosis of 162 (69.8%) of the isolates. Statistical agreement between genotypic and phenotypic identification of staphylococci was substantial (Kappa coefficient of 0.6-0.8) for Staphylococcus aureus, S. hominis, S. warneri, S. cohnii subsp. urealyticus, and S. simulans, and "almost perfect" (Kappa coefficient of 0.8-1) for S. intermedius, S. epidermidis, S. equorum, S. haemolyticus, S. sciuri, and S. kloosi. No agreement above that expected by chance (Kappa coefficient=0) was observed for S. schleiferi subsp. coagulans, which was either confounded with S. intermedius and S. capitis, or categorized as unacceptable by the biochemical assay. Given the growing importance of this pathogen in veterinary medicine and its frequent misidentification with related staphylococci, a PCR-RFLP approach producing a S. schleiferi-specific restriction profile was developed. This fast and reliable assay represents a valuable tool in assisting in the monitoring of this pathogen.

  1. Environmental DNA (eDNA From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification

    Directory of Open Access Journals (Sweden)

    C. Scott Baker

    2018-04-01

    Full Text Available Genetic sampling for identification of species, subspecies or stock of whales, dolphins and porpoises at sea remains challenging. Most samples have been collected with some form of a biopsy dart requiring a close approach of a vessel while the individual is at the surface. Here we have adopted droplet digital (ddPCR technology for detection and species identification of cetaceans using environmental (eDNA collected from seawater. We conducted a series of eDNA sampling experiments during 25 encounters with killer whales, Orcinus orca, in Puget Sound (the Salish Sea. The regular habits of killer whales in these inshore waters allowed us to locate pods and collect seawater, at an initial distance of 200 m and at 15-min intervals, for up to 2 h after the passage of the whales. To optimize detection, we designed a set of oligonucleotide primers and probes to target short fragments of the mitochondrial (mtDNA control region, with a focus on identification of known killer whale ecotypes. We confirmed the potential to detect eDNA in the wake of the whales for up to 2 h, despite movement of the water mass by several kilometers due to tidal currents. Re-amplification and sequencing of the eDNA barcode confirmed that the ddPCR detection included the “southern resident community” of killer whales, consistent with the calls from hydrophone recordings and visual observations.

  2. Identification of species and geographical strains of Sitophilus oryzae and Sitophilus zeamais using the visible/near-infrared hyperspectral imaging technique.

    Science.gov (United States)

    Cao, Yang; Zhang, Chaojie; Chen, Quansheng; Li, Yanyu; Qi, Shuai; Tian, Lin; Ren, YongLin

    2015-08-01

    Identifying stored-product insects is essential for granary management. Automated, computer-based classification methods are rapidly developing in many areas. A hyperspectral imaging technique could potentially be developed to identify stored-product insect species and geographical strains. This study tested and adapted the technique using four geographical strains of each of two insect species, the rice weevil and maize weevil, to collect and analyse the resultant hyperspectral data. Three characteristic images that corresponded to the dominant wavelengths, 505, 659 and 955 nm, were selected by multivariate image analysis. Each image was processed, and 22 morphological and textural features from regions of interest were extracted as the inputs for an identification model. We found the backpropagation neural network model to be the superior method for distinguishing between the insect species and geographical strains. The overall recognition rates of the classification model for insect species were 100 and 98.13% for the calibration and prediction sets respectively, while the rates of the model for geographical strains were 94.17 and 86.88% respectively. This study has demonstrated that hyperspectral imaging, together with the appropriate recognition method, could provide a potential instrument for identifying insects and could become a useful tool for identification of Sitophilus oryzae and Sitophilus zeamais to aid in the management of stored-product insects. © 2014 Society of Chemical Industry.

  3. A real-time polymerase chain reaction method for the identification of four commercially important salmon and trout species.

    Science.gov (United States)

    Feng, Junli; Wu, Zhigang; Xie, Xiao; Dai, Zhiyuan; Liu, Shasha

    2017-01-01

    A duplex quantitative real-time PCR (qPCR) assay was developed for rapid and accurate identification of four commercially important salmon and trout species (Oncorhynchus keta, Oncorhynchus nerka, Oncorhynchus mykiss, and Salmo salar) commonly used for production process of fish in China. The assays targeting the mitochondrial control region (CR) and 16S rRNA gene were able to simultaneously discriminate four target species and the family Salmonidae from processed as well as fresh fish. The qPCR efficiency of each reaction was calculated according to the standard curve, and the method was validated by amplification DNA extracted from single or artificial mixtures prepared with the reference salmon and trout species. Testing of 11 commercial salmon and trout products by the established qPCR assay demonstrated that it was really a useful and academic technique to identify four commercially important salmon and trout species.

  4. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species.

    Science.gov (United States)

    Stevenson, Lindsay G; Drake, Steven K; Shea, Yvonne R; Zelazny, Adrian M; Murray, Patrick R

    2010-10-01

    We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid identification of yeast species. Using Bruker Daltonics MALDI BioTyper software, we created a spectral database library with m/z ratios of 2,000 to 20,000 Da for 109 type and reference strains of yeast (44 species in 8 genera). The database was tested for accuracy by use of 194 clinical isolates (23 species in 6 genera). A total of 192 (99.0%) of the clinical isolates were identified accurately by MALDI-TOF MS. The MALDI-TOF MS-based method was found to be reproducible and accurate, with low consumable costs and minimal preparation time.

  5. Molecular approaches for blood meal analysis and species identification of mosquitoes (Insecta: Diptera: Culicidae) in rural locations in southern England, United Kingdom.

    Science.gov (United States)

    Hernández-Triana, Luis Miguel; Brugman, Victor Albert; Prosser, Sean Williams John; Weland, Chris; Nikolova, Nadya; Thorne, Leigh; Marco, Mar Fernández DE; Fooks, Anthony Richard; Johnson, Nicholas

    2017-04-03

    Thirty-four species of Culicidae are present in the UK, of which 15 have been implicated as potential vectors of arthropod-borne viruses such as West Nile virus. Identification of mosquito feeding preferences is paramount to the understanding of vector-host-pathogen interactions which, in turn, would assist in the control of disease outbreaks. Results are presented on the application of DNA barcoding for vertebrate species identification in blood-fed female mosquitoes in rural locations. Blood-fed females (n = 134) were collected in southern England from rural sites and identified based on morphological criteria. Blood meals from 59 specimens (44%) were identified as feeding on eight hosts: European rabbit, cow, human, barn swallow, dog, great tit, magpie and blackbird. Analysis of the cytochrome c oxidase subunit I mtDNA barcoding region and the internal transcribed spacer 2 rDNA region of the specimens morphologically identified as Anopheles maculipennis s.l. revealed the presence of An. atroparvus and An. messeae. A similar analysis of specimens morphologically identified as Culex pipiens/Cx. torrentium showed all specimens to be Cx. pipiens (typical form). This study demonstrates the importance of using molecular techniques to support species-level identification in blood-fed mosquitoes to maximize the information obtained in studies investigating host feeding patterns.

  6. DNA-based identification of invasive alien species in relation to Canadian federal policy and law, and the basis of rapid-response management.

    Science.gov (United States)

    Thomas, Vernon G; Hanner, Robert H; Borisenko, Alex V

    2016-11-01

    Managing invasive alien species in Canada requires reliable taxonomic identification as the basis of rapid-response management. This can be challenging, especially when organisms are small and lack morphological diagnostic features. DNA-based techniques, such as DNA barcoding, offer a reliable, rapid, and inexpensive toolkit for taxonomic identification of individual or bulk samples, forensic remains, and even environmental DNA. Well suited for this requirement, they could be more broadly deployed and incorporated into the operating policy and practices of Canadian federal departments and should be authorized under these agencies' articles of law. These include Fisheries and Oceans Canada, Canadian Food Inspection Agency, Transport Canada, Environment Canada, Parks Canada, and Health Canada. These efforts should be harmonized with the appropriate provisions of provincial jurisdictions, for example, the Ontario Invasive Species Act. This approach necessitates that a network of accredited, certified laboratories exists, and that updated DNA reference libraries are readily accessible. Harmonizing this approach is vital among Canadian federal agencies, and between the federal and provincial levels of government. Canadian policy and law must also be harmonized with that of the USA when detecting, and responding to, invasive species in contiguous lands and waters. Creating capacity in legislation for use of DNA-based identifications brings the authority to fund, train, deploy, and certify staff, and to refine further developments in this molecular technology.

  7. Environmental isolation, biochemical identification, and antifungal drug susceptibility of Cryptococcus species

    Directory of Open Access Journals (Sweden)

    Valter Luis Iost Teodoro

    2013-12-01

    Full Text Available Introduction The incidence of opportunistic fungal infections has increased in recent years and is considered an important public health problem. Among systemic and opportunistic mycoses, cryptococcosis is distinguished by its clinical importance due to the increased risk of infection in individuals infected by human immunodeficiency virus. Methods To determine the occurrence of pathogenic Cryptococcus in pigeon excrement in the City of Araraquara, samples were collected from nine environments, including state and municipal schools, abandoned buildings, parks, and a hospital. The isolates were identified using classical tests, and susceptibility testing for the antifungal drugs (fluconazole, itraconazole, voriconazole, and amphotericin B independently was also performed. After collection, the excrement samples were plated on Niger agar and incubated at room temperature. Results A total of 87 bird dropping samples were collected, and 66.6% were positive for the genus Cryptococcus. The following species were identified: Cryptococcus neoformans (17.2%, Cryptococcus gattii (5.2%, Cryptococcus ater (3.5%, Cryptococcus laurentti (1.7%, and Cryptococcus luteolus (1.7%. A total of 70.7% of the isolates were not identified to the species level and are referred to as Cryptococcus spp. throughout the manuscript. Conclusions Although none of the isolates demonstrated resistance to antifungal drugs, the identification of infested areas, the proper control of birds, and the disinfection of these environments are essential for the epidemiological control of cryptococcosis.

  8. Rapid identification of drug resistant Candida species causing recurrent vulvovaginal candidiasis.

    Science.gov (United States)

    Diba, Kambiz; Namaki, Atefeh; Ayatolahi, Haleh; Hanifian, Haleh

    2012-01-01

    Some yeast agents including Candida albicans, Candida tropicalis and Candida glabrata have a role in recurrent vulvovaginal candidiasis. We studied the frequency of both common and recurrent vulvovaginal candidiasis in symptomatic cases which were referred to Urmia Medical Sciences University related gynecology clinics using morphologic and molecular methods. The aim of this study was the identification of Candida species isolated from recurrent vulvovaginal candidiasis cases using a rapid and reliable molecular method. Vaginal swabs obtained from each case, were cultured on differential media including cornmeal agar and CHROM agar Candida. After 48 hours at 37℃, the cultures were studied for growth characteristics and color production respectively. All isolates were identified using the molecular method of PCR - restriction fragment length polymorphism. Among all clinical specimens, we detected 19 ( 16 % ) non fungal agents, 87 ( 82.1 % ) yeasts and 2 ( 1.9 % ) multiple infections. The yeast isolates identified morphologically included Candida albicans ( n = 62 ), Candida glabrata ( n = 9 ), Candida tropicalis ( n = 8 ), Candida parapsilosis ( n = 8 ) and Candida guilliermondii and Candida krusei ( n = 1 each ). We also obtained very similar results for Candida albicans, Candida glabrata and Candida tropicalis as the most common clinical isolates, by using PCR - Restriction Fragment Length Polymorphism. Use of two differential methods, morphologic and molecular, enabled us to identify most medically important Candida species which particularly cause recurrent vulvovaginal candidiasis.

  9. Molecular characterization of Fasciola species isolated from imported sheep in Taif region (Saudi Arabia).

    Science.gov (United States)

    Shalaby, I; Gherbawy, Y; Banaja, A

    2013-03-01

    Accurate identification of Fasciola species, followed by biological and ecological characterization, is important with concern to the planning for field control. Because there are many variations in morphological characteristics, exact distinguishing of Fasciola species is usually difficult by simple traditional microscopic measurements and, therefore, the morphometric characterization may be insufficient for the species identification. Hence, the present work was proposed to collect 100 liver samples from 100 imported sheep from Sudan from slaughterhouses in Taif region. The samples were firstly examined macroscopically and microscopically to ensure the presence or absence of infection. The collected worms were subjected for RAPD-PCR analysis using different primers and ITS1 sequences for accurate identification. Using RAPD-PCR analysis, two primers were selected to amplify the DNA of each Fasciola. The results show that the amplification fragments were between 500 and 1500 bp and, the use of random genetic markers allowed to discriminate among the different collected species. Using Internal transcribed spacer region (ITS) sequencing, the imported sheep in Taif region consisted of 630 bps including complete ITS1, partial 18S and 5.8S and had 5 variable nucleotide positions. This is the first demonstration of the existence of both F. hepatica, F. gigantica and hybrid and/or introgressed populations of liver flukes bearing genetic material from both F. hepatica and F. gigantica in the imported sheep in Saudi Arabia by a genetic approach.

  10. Characterization and identification of newly isolated Acinetobacter baumannii strain serdang 1 for phenol removal

    Science.gov (United States)

    Yadzir, Z. H. M.; Shukor, M. Y.; Nazir, M. S.; Abdullah, M. A.

    2012-09-01

    A new indigenous bacterial strain from Malaysian soil contaminated with petroleum waste had been successfully isolated, characterized and identified for phenol removal. The gram negative bacteria showed 98% identity with Acinetobacter baumannii based on Biolog{trade mark, serif} Identification System and the determination of a partial 16S ribosomal RNA (rRNA) sequence. The isolate clustered with species belonging to Acinetobacter clade in a 16S rDNA-based neighbour-joining phylogenetic tree.

  11. Population genetics and cryptic species

    International Nuclear Information System (INIS)

    McPheron, Bruce A.

    2000-01-01

    Does the definition of a species matter for pest management purposes? Taxonomists provide us with tools - usually morphological characters - to identify a group of organisms that we call a species. The implication of this identification is that all of the individuals that fit the provided description are members of the species in question. The taxonomists have considered the range of variation among individuals in defining the species, but this variation is often forgotten when we take the concept of species to the level of management. Just as there is morphological variation among individuals, there is also variation in practically any character we might imagine, which has implications for the short and long term success of our management tactics. The rich literature on insecticide resistance should be a constant reminder of the fact that the pressure on pest survival and reproduction applied by our management approaches frequently leads to evolutionary changes within the pest species. The degree of variation within a particular species is a defining characteristic of that species. This level of variability may have very important implications for successful management, so it is very important to measure variation and, whenever possible, the genetic basis of that variation, in a target species. Population genetic approaches can provide evidence of genetic structure (or lack thereof) among populations of a species. These types of data can be used to discuss the movement of pest populations on a local or global scale. In other cases, we may have a complex of species that share some, but not all, characteristics. Species complexes that share morphological characters (i.e., cannot be easily distinguished) but not biological characters are referred to as sibling or cryptic species

  12. Comparative analysis of storage conditions and homogenization methods for tick and flea species for identification by MALDI-TOF MS.

    Science.gov (United States)

    Nebbak, A; El Hamzaoui, B; Berenger, J-M; Bitam, I; Raoult, D; Almeras, L; Parola, P

    2017-12-01

    Ticks and fleas are vectors for numerous human and animal pathogens. Controlling them, which is important in combating such diseases, requires accurate identification, to distinguish between vector and non-vector species. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was applied to the rapid identification of arthropods. The growth of this promising tool, however, requires guidelines to be established. To this end, standardization protocols were applied to species of Rhipicephalus sanguineus (Ixodida: Ixodidae) Latreille and Ctenocephalides felis felis (Siphonaptera: Pulicidae) Bouché, including the automation of sample homogenization using two homogenizer devices, and varied sample preservation modes for a period of 1-6 months. The MS spectra were then compared with those obtained from manual pestle grinding, the standard homogenization method. Both automated methods generated intense, reproducible MS spectra from fresh specimens. Frozen storage methods appeared to represent the best preservation mode, for up to 6 months, while storage in ethanol is also possible, with some caveats for tick specimens. Carnoy's buffer, however, was shown to be less compatible with MS analysis for the purpose of identifying ticks or fleas. These standard protocols for MALDI-TOF MS arthropod identification should be complemented by additional MS spectrum quality controls, to generalize their use in monitoring arthropods of medical interest. © 2017 The Royal Entomological Society.

  13. Application of otolith shape analysis for stock discrimination and species identification of five goby species (Perciformes: Gobiidae) in the northern Chinese coastal waters

    Science.gov (United States)

    Yu, Xin; Cao, Liang; Liu, Jinhu; Zhao, Bo; Shan, Xiujuan; Dou, Shuozeng

    2014-09-01

    We tested the use of otolith shape analysis to discriminate between species and stocks of five goby species ( Ctenotrypauchen chinensis, Odontamblyopus lacepedii, Amblychaeturichthys hexanema, Chaeturichthys stigmatias, and Acanthogobius hasta) found in northern Chinese coastal waters. The five species were well differentiated with high overall classification success using shape indices (83.7%), elliptic Fourier coefficients (98.6%), or the combination of both methods (94.9%). However, shape analysis alone was only moderately successful at discriminating among the four stocks (Liaodong Bay, LD; Bohai Bay, BH; Huanghe (Yellow) River estuary HRE, and Jiaozhou Bay, JZ stocks) of A. hasta (50%-54%) and C. stigmatias (65.7%-75.8%). For these two species, shape analysis was moderately successful at discriminating the HRE or JZ stocks from other stocks, but failed to effectively identify the LD and BH stocks. A large number of otoliths were misclassified between the HRE and JZ stocks, which are geographically well separated. The classification success for stock discrimination was higher using elliptic Fourier coefficients alone (70.2%) or in combination with shape indices (75.8%) than using only shape indices (65.7%) in C. stigmatias whereas there was little difference among the three methods for A. hasta. Our results supported the common belief that otolith shape analysis is generally more effective for interspecific identification than intraspecific discrimination. Moreover, compared with shape indices analysis, Fourier analysis improves classification success during inter- and intra-species discrimination by otolith shape analysis, although this did not necessarily always occur in all fish species.

  14. The genus Alterosa Blahnik, 2005 (Trichoptera, Philopotamidae, Philopotaminae) in northeastern Brazil, including the description of three new species and an identification key for the genus

    Science.gov (United States)

    Dumas, Leandro Lourenço; Calor, Adolfo Ricardo; Nessimian, Jorge Luiz

    2013-01-01

    Abstract Alterosa Blahnik, 2005 contains 35 described species distributed in southern and southeastern Brazil. Three new species of Alterosa from northeastern Brazil are described and illustrated, Alterosa amadoi sp. n., Alterosa castroalvesi sp. n. and Alterosa caymmii sp. n., the first records of the genus from northeastern Brazil. An identification key for all known species of the genus is also presented. PMID:23950667

  15. Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA)

    NARCIS (Netherlands)

    Decat, E.; van Mechelen, E.; Saerens, B.; Vermeulen, S.J.T.; Boekhout, T.; de Blaiser, S.; Vaneechoutte, M.; Deschaght, P.

    2013-01-01

    Rapid identification of clinically important yeasts can facilitate the initiation of anti-fungal therapy, since susceptibility is largely species-dependent. We evaluated melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA) as an identification

  16. Diagnostic Cytochrome b gene profiles for the identification of paca (Cuniculus paca bushmeat: implications for the monitoring of illegal hunting and wildlife trade

    Directory of Open Access Journals (Sweden)

    A. A. Silva-Neto

    Full Text Available Abstract Paca (Cuniculus paca Linnaeus, 1766 is the second largest rodent found in Brazil. The quality of the meat and a long tradition of hunting have contributed to the decline of the natural populations of this species. Hunting of paca is strictly prohibited in Brazil, but in spite of this restriction, no forensic tools are available for the identification of the meat. We describe an efficient method, based on single nucleotide polymorphisms of the cytochrome b gene, that can be used to differentiate biological material derived from paca from those of domestic species commonly used as sources of meat. The identification of the presence of C. paca in the samples was 100% reliable.

  17. Diagnostic Cytochrome b gene profiles for the identification of paca (Cuniculus paca) bushmeat: implications for the monitoring of illegal hunting and wildlife trade.

    Science.gov (United States)

    Silva-Neto, A A; Ferreira, P B; Torres, R A; Texeira, R H F; Duarte, J M B; Barbosa, A C; Vargas, R C; Garcia, J E

    2016-02-01

    Paca (Cuniculus paca Linnaeus, 1766) is the second largest rodent found in Brazil. The quality of the meat and a long tradition of hunting have contributed to the decline of the natural populations of this species. Hunting of paca is strictly prohibited in Brazil, but in spite of this restriction, no forensic tools are available for the identification of the meat. We describe an efficient method, based on single nucleotide polymorphisms of the cytochrome b gene, that can be used to differentiate biological material derived from paca from those of domestic species commonly used as sources of meat. The identification of the presence of C. paca in the samples was 100% reliable.

  18. Evaluation of a simple protein extraction method for species identification of clinically relevant staphylococci by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    Science.gov (United States)

    Matsuda, Naoto; Matsuda, Mari; Notake, Shigeyuki; Yokokawa, Hirohide; Kawamura, Yoshiaki; Hiramatsu, Keiichi; Kikuchi, Ken

    2012-12-01

    In clinical microbiology, bacterial identification is labor-intensive and time-consuming. A solution for this problem is the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this study, we evaluated a modified protein extraction method of identification performed on target plates (on-plate extraction method) with MALDI-TOF (Bruker Microflex LT with Biotyper version 3.0) and compared it to 2 previously described methods: the direct colony method and a standard protein extraction method (standard extraction method). We evaluated the species of 273 clinical strains and 14 reference strains of staphylococci. All isolates were characterized using the superoxide dismutase A sequence as a reference. For the species identification, the on-plate, standard extraction, and direct colony methods identified 257 isolates (89.5%), 232 isolates (80.8%), and 173 isolates (60.2%), respectively, with statistically significant differences among the three methods (P extraction method is at least as good as standard extraction in identification rate and has the advantage of a shorter processing time.

  19. Biological species is the only possible form of existence for higher organisms: the evolutionary meaning of sexual reproduction

    Directory of Open Access Journals (Sweden)

    Shcherbakov Victor P

    2010-03-01

    Full Text Available Abstract Consistent holistic view of sexual species as the highest form of biological existence is presented. The Weismann's idea that sex and recombination provide the variation for the natural selection to act upon is dominated in most discussions of the biological meaning of the sexual reproduction. Here, the idea is substantiated that the main advantage of sex is the opposite: the ability to counteract not only extinction but further evolution as well. Living systems live long owing to their ability to reproduce themselves with a high fidelity. Simple organisms (like bacteria reach the continued existence due to the high fidelity of individual genome replication. In organisms with a large genome and complex development, the achievable fidelity of DNA replication is not enough for the precise reproduction of the genome. Such species must be capable of surviving and must remain unchanged in spite of the continuous changes of their genes. This problem has no solution in the frame of asexual ("homeogenomic" lineages. They would rapidly degrade and become extinct or blurred out in the course of the reckless evolution. The core outcome of the transition to sexual reproduction was the creation of multiorganismic entity - biological species. Individual organisms forfeited their ability to reproduce autonomously. It implies that individual organisms forfeited their ability to substantive evolution. They evolve as a part of the biological species. In case of obligatory sexuality, there is no such a thing as synchronic multi-level selection. Natural selection cannot select anything that is not a unit of reproduction. Hierarchy in biology implies the functional predestination of the parts for the sake of the whole. A crucial feature of the sexual reproduction is the formation of genomes of individual organisms by random picking them over from the continuously shuffled gene pool instead of the direct replication of the ancestor's genome. A clear anti

  20. A new species of jumping spider Neonella Gertsch, with notes on the genus and male identification key (Araneae, Salticidae)

    Science.gov (United States)

    Rubio, Gonzalo D.; Argañaraz, Carina I.; Gleiser, Raquel M.

    2015-01-01

    Abstract The American genus Neonella Gertsch, 1936 consists of very small jumping spiders whose biology is not well known. The genus currently includes eleven valid species, of which eight are known from both sexes and two are only known from one sex. This paper describes and illustrates a new species Neonella acostae sp. n., demonstrates male palpal variation in Neonella montana Galiano, 1988, and provides some information on the ecology of three sympatric species. New records of Neonella montana and Neonella minuta Galiano, 1965 are reported. Because the previously described species of Neonella were well illustrated and diagnosed, a dichotomous key to males is given along with genital illustrations of both sexes for all known species. PMID:26692804

  1. Towards the identification of flower-specific genes in Citrus spp

    Directory of Open Access Journals (Sweden)

    Marcelo Carnier Dornelas

    2007-01-01

    Full Text Available Citrus sinensis is a perennial woody species, for which genetic approaches to the study of reproductive development are not readily amenable. Here, the usefulness of the CitEST Expressed Sequence Tag (EST database is demonstrated as a reliable new resource for identifying novel genes exclusively related to Citrus reproductive biology. We performed the analysis of an EST dataset of the CitEST Project containing 4,330 flower-derived cDNA sequences. Relying on bioinformatics tools, sequences exclusively present in this flower-derived sequence collection were selected and used for the identification of Citrus putative flower-specific genes. Our analysis revealed several Citrus sequences showing significant similarity to conserved genes known to have flower-specific expression and possessing functions related to flower metabolism and/or reproductive development in diverse plant species. Comparison of the Citrus flower-specific sequences with all available plant peptide sequences unraveled 247 unique transcripts not identified elsewhere within the plant kingdom. Additionally, 49 transcripts, for which no biological function could be attributed by means of sequence comparisons, were found to be conserved among plant species. These results allow further gene expression analysis and possibly novel approaches to the understanding of reproductive development in Citrus.

  2. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections.

    Science.gov (United States)

    Chambers, E Anne; Hebert, Paul D N

    2016-01-01

    High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.

  3. Identification and characterization of bacterial symbionts in three species of filth fly parasitoids.

    Science.gov (United States)

    Betelman, Kfir; Caspi-Fluger, Ayelet; Shamir, Maayan; Chiel, Elad

    2017-09-01

    Facultative bacterial symbionts are widespread among insects and have diverse effects on their biology. Here, we focused on bacterial symbionts of three ecologically and economically important filth flies parasitoid species-Spalangia cameroni, Spalangia endius and Muscidifurax raptor. Both Spalangia species harbored a Sodalis bacterium that is closely related to Spalangia praecaptivus (a free-living bacterium) and to Sodalis symbionts of weevils. This is the only case of Sodalis infection in the important order Hymenoptera. We also found, for the first time in this parasitoid guild, a Rickettsia infecting the two Spalangia spp., albeit in much higher prevalence in S. cameroni. Molecular and phylogenetic analyses revealed that it is closely related to Rickettsia felis and other Rickettsia species from the 'transitional' group. All three parasitoid species harbored Wolbachia. Using multi-locus sequence typing, we found that M. raptor harbors a single Wolbachia strain whereas the Spalangia spp. have multiple strains. By controlled crossings, we found that Wolbachia infection in S. endius causes incomplete cytoplasmic incompatibility and increased longevity, thereby promoting Wolbachia's spread. In contrast, no effects of Wolbachia on the reproduction and longevity of M. raptor were found. This study underscores the diversity and nature of symbiotic interactions between microbes and insects. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Using aquatic macroinvertebrate species traits to build test batteries for sediment toxicity assessment: accounting for the diversity of potential biological responses to toxicants.

    Science.gov (United States)

    Ducrot, Virginie; Usseglio-Polatera, Philippe; Péry, T Alexandre R R; Mouthon, Jacques; Lafont, Michel; Roger, Marie-Claude; Garric, Jeanne; Férard, Jean-François

    2005-09-01

    An original species-selection method for the building of test batteries is presented. This method is based on the statistical analysis of the biological and ecological trait patterns of species. It has been applied to build a macroinvertebrate test battery for the assessment of sediment toxicity, which efficiently describes the diversity of benthic macroinvertebrate biological responses to toxicants in a large European lowland river. First, 109 potential representatives of benthic communities of European lowland rivers were selected from a list of 479 taxa, considering 11 biological traits accounting for the main routes of exposure to a sediment-bound toxicant and eight ecological traits providing an adequate description of habitat characteristics used by the taxa. Second, their biological and ecological trait patterns were compared using coinertia analysis. This comparison allowed the clustering of taxa into groups of organisms that exhibited similar life-history characteristics, physiological and behavioral features, and similar habitat use. Groups exhibited various sizes (7-35 taxa), taxonomic compositions, and biological and ecological features. Main differences among group characteristics concerned morphology, substrate preferendum and habitat utilization, nutritional features, maximal size, and life-history strategy. Third, the best representatives of the mean biological and ecological characteristics of each group were included in the test battery. The final selection was composed of Chironomus riparius (Insecta: Diptera), Branchiura sowerbyi (Oligochaeta: Tubificidae), Lumbriculus variegatus (Oligochaeta: Lumbriculidae), Valvata piscinalis (Gastropoda: Valvatidae), and Sericostoma personatum (Trichoptera: Sericostomatidae). This approach permitted the biological and ecological variety of the battery to be maximized. Because biological and ecological traits of taxa determine species sensitivity, such maximization should permit the battery to better account

  5. Detection and identification of six Cryptospordium species in livestock in Slovakia by amplification of SSU and GP60 genes with the use of PCR analysis

    Directory of Open Access Journals (Sweden)

    Oľga Danišová

    2016-06-01

    The findings suggest that livestock can be an important source of zoonotic species or genotypes of Cryptosporidium , which may adversely affect the public health of human populations. This is the first time in our country that the Cryptosporidium species has been identified in livestock in Slovakia. The identification and genotyping of this pathogen in Slovakia, completes the epidemiological situation in Europe for Cryptosporidum species.

  6. Use of species-specific PCR for the identification of 10 sea cucumber species

    Science.gov (United States)

    Wen, Jing; Zeng, Ling

    2014-11-01

    We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

  7. Molecular biological identification of Babesia, Theileria, and Anaplasma species in cattle in Egypt using PCR assays, gene sequence analysis and a novel DNA microarray.

    Science.gov (United States)

    El-Ashker, Maged; Hotzel, Helmut; Gwida, Mayada; El-Beskawy, Mohamed; Silaghi, Cornelia; Tomaso, Herbert

    2015-01-30

    In this preliminary study, a novel DNA microarray system was tested for the diagnosis of bovine piroplasmosis and anaplasmosis in comparison with microscopy and PCR assay results. In the Dakahlia Governorate, Egypt, 164 cattle were investigated for the presence of piroplasms and Anaplasma species. All investigated cattle were clinically examined. Blood samples were screened for the presence of blood parasites using microscopy and PCR assays. Seventy-one animals were acutely ill, whereas 93 were apparently healthy. In acutely ill cattle, Babesia/Theileria species (n=11) and Anaplasma marginale (n=10) were detected. Mixed infections with Babesia/Theileria spp. and A. marginale were present in two further cases. A. marginale infections were also detected in apparently healthy subjects (n=23). The results of PCR assays were confirmed by DNA sequencing. All samples that were positive by PCR for Babesia/Theileria spp. gave also positive results in the microarray analysis. The microarray chips identified Babesia bovis (n=12) and Babesia bigemina (n=2). Cattle with babesiosis were likely to have hemoglobinuria and nervous signs when compared to those with anaplasmosis that frequently had bloody feces. We conclude that clinical examination in combination with microscopy are still very useful in diagnosing acute cases of babesiosis and anaplasmosis, but a combination of molecular biological diagnostic assays will detect even asymptomatic carriers. In perspective, parallel detection of Babesia/Theileria spp. and A. marginale infections using a single microarray system will be a valuable improvement. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  8. Molecular identification of Aspergillus and Eurotium species isolated from rice and their toxin-producing ability.

    Science.gov (United States)

    Yazdani, D; Zainal Abidin, M A; Tan, Y H; Kamaruzaman, S

    2011-01-01

    Thirty milled rice samples were collected from retailers in 4 provinces of Malaysia. These samples were evaluated for Aspergillus spp. infection by direct plating on malt extract salt agar (MESA). All Aspergillus holomorphs were isolated and identified using nucleotide sequences of ITS 1 and ITS 2 of rDNA. Five anamorphs (Aspergillus flavus, A. oryzae, A. tamarii, A. fumigatus and A. niger) and 5 teleomorphs (Eurotium rubrum, E. amstelodami, E. chevalieri, E. cristatum and E. tonophilum) were identified. The PCR-sequencing based technique for sequences of ITS 1 and ITS 2 is a fast technique for identification of Aspergillus and Eurotium species, although it doesn't work flawlessly for differentiation of Eurotium species. All Aspergillus and Eurotium isolates were screened for their ability to produce aflatoxin and ochratoxin A (OTA) by HPLC and TLC techniques. Only A. flavus isolate UPM 89 was able to produce aflatoxins B1 and B2.

  9. DNA barcoding for species identification from dried and powdered plant parts: a case study with authentication of the raw drug market samples of Sida cordifolia.

    Science.gov (United States)

    Vassou, Sophie Lorraine; Kusuma, G; Parani, Madasamy

    2015-03-15

    The majority of the plant materials used in herbal medicine is procured from the markets in the form of dried or powdered plant parts. It is essential to use authentic plant materials to derive the benefits of herbal medicine. However, establishing the identity of these plant materials by conventional taxonomy is extremely difficult. Here we report a case study in which the species identification of the market samples of Sida cordifolia was done by DNA barcoding. As a prelude to species identification by DNA barcoding, 13 species of Sida were collected, and a reference DNA barcode library was developed using rbcL, matK, psbA-trnH and ITS2 markers. Based on the intra-species and inter-species divergence observed, psbA-trnH and ITS2 were found to be the best two-marker combination for species identification of the market samples. The study showed that none of the market samples belonged to the authentic species, S. cordifolia. Seventy-six per cent of the market samples belonged to other species of Sida. The predominant one was Sida acuta (36%) followed by S. spinosa (20%), S. alnifolia (12%), S. scabrida (4%) and S. ravii (4%). Such substitutions may not only fail to give the expected therapeutic effect, but may also give undesirable effects as in case of S. acuta which contains a 6-fold higher amount of ephedrine compared to the roots of S. cordifolia. The remaining 24% of the samples were from other genera such as Abutilon sp. (8%), Ixonanthes sp., Terminalia sp., Fagonia sp., and Tephrosia sp. (4% each). This observation is in contrast to the belief that medicinal plants are generally substituted or adulterated with closely related species. The current study strongly suggests that the raw drug market samples of herbal medicines need to be properly authenticated before use, and DNA barcoding has been found to be suitable for this purpose. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.

    Science.gov (United States)

    Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

    2013-10-29

    Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

  11. Screening and identification of antioxidants in biological samples using high-performance liquid chromatography-mass spectrometry and its application on Salacca edulis Reinw.

    Science.gov (United States)

    Shui, Guanghou; Leong, Lai Peng

    2005-02-23

    In this study, a new approach was developed for screening and identifying antioxidants in biological samples. The approach was based on significant decreases of the intensities of ion peaks obtained from high-performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) upon reaction with 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radicals. HPLC-MS/MS was further applied to elucidate structures of antioxidant peaks characterized in a spiking test. The new approach could also be used to monitor the reactivity of antioxidants in biological sample with free radicals. The approach was successfully applied to the identification of antioxidants in salak (Salacca edulis Reinw), a tropical fruit that is reported to be a very good source of natural antioxidants, but it was still not clear which compounds were responsible for its antioxidant property. The antioxidants in salak were identified to be chlorogenic acid, (-)-epicatechin, and singly linked proanthocyanidins that mainly existed as dimers through hexamers of catechin or epicatechin. In salak, chlorogenic acid was identified to be an antioxidant of the slow reaction type as it reacted with free radicals much more slowly than either (-)-epicatechin or proanthocyanidins. The new approach was proved to be useful for the characterization and identification of antioxidants in biological samples as a mass detector combined with an HPLC separation system not only serves as an ideal tool to monitor free radical active components but also provides their possible chemical structures in a biological sample.

  12. Ants of the Monomorium monomorium species-group (Hymenoptera: Formicidae in the Arabian Peninsula with description of a new species from southwestern Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Mostafa Sharaf

    2018-02-01

    Full Text Available We revise the taxonomy of the myrmicine ants of the Monomorium monomorium species-group for the Arabian Peninsula. Six species are recognized: Monomorium aeyade Collingwood & Agosti, 1996, M. clavicorne André, 1881, M. exiguum Forel, 1894, M. holothir Bolton, 1987, M. mohammedi sp. n., and M. sarawatense Sharaf & Aldawood, 2013. On the basis of the worker caste, we describe Monomorium mohammedi sp. n. from the southwestern region of the Kingdom of Saudi Arabia (KSA. We designate a neotype for Monomorium aeyade Collingwood & Agosti and redescribe and illustrate the worker caste. Furthermore, we provide a worker-based species identification key, distribution maps for the treated species, and ecological and biological notes, if available. Monomorium holothir is recorded for the first time from the KSA. Also, we propose M. clavicorne var. punica Santschi, 1915a as a junior synonym of M. clavicorne, as well as M. dryhimi Aldawood & Sharaf, 2011 and M. montanum Collingwood & Agosti, 1996 to be treated as junior synonyms of Monomorium exiguum.

  13. Comparison of Vitek Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Versus Conventional Methods in Candida Identification.

    Science.gov (United States)

    Keçeli, Sema Aşkın; Dündar, Devrim; Tamer, Gülden Sönmez

    2016-02-01

    Candida species are generally identified by conventional methods such as germ tube or morphological appearance on corn meal agar, biochemical methods using API kits and molecular biological methods. Alternative to these methods, rapid and accurate identification methods of microorganisms called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDİ-TOF MS) has recently been described. In this study, Candida identification results by API Candida kit, API 20C AUX kit and identifications on corn meal agar (CMA) are compared with the results obtained on Vitek-MS. All results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Totally, 97 Candida strains were identified by germ tube test, CMA, API and Vitek-MS. Vitek-MS results were compatible with 74.2 % of API 20C AUX and 81.4 % of CMA results. The difference between the results of API Candida and API 20C AUX was detected. The ratio of discrepancy between Vitek-MS and API 20C AUX was 25.8 %. Candida species mostly identified as C. famata or C. tropicalis by and not compatible with API kits were identified as C. albicans by Vitek-MS. Sixteen Candida species having discrepant results with Vitek-MS, API or CMA were randomly chosen, and ITS sequence analysis was performed. The results of sequencing were compatible 56.2 % with API 20C AUX, 50 % with CMA and 93.7 % with Vitek-MS. When compared with conventional identification methods, MS results are more reliable and rapid for Candida identification. MS system may be used as routine identification method in clinical microbiology laboratories.

  14. Phenotypic polymorphism of Chrysomya albiceps (Wiedemann) (Diptera: Calliphoridae) may lead to species misidentification.

    Science.gov (United States)

    Grella, Maicon D; Savino, André G; Paulo, Daniel F; Mendes, Felipe M; Azeredo-Espin, Ana M L; Queiroz, Margareth M C; Thyssen, Patricia J; Linhares, Arício X

    2015-01-01

    Species identification is an essential step in the progress and completion of work in several areas of biological knowledge, but it is not a simple process. Due to the close phylogenetic relationship of certain species, morphological characters are not always sufficiently distinguishable. As a result, it is necessary to combine several methods of analysis that contribute to a distinct categorization of taxa. This study aimed to raise diagnostic characters, both morphological and molecular, for the correct identification of species of the genus Chrysomya (Diptera: Calliphoridae) recorded in the New World, which has continuously generated discussion about its taxonomic position over the last century. A clear example of this situation was the first record of Chrysomya rufifacies in Brazilian territory in 2012. However, the morphological polymorphism and genetic variability of Chrysomya albiceps studied here show that both species (C. rufifacies and C. albiceps) share very similar character states, leading to misidentification and subsequent registration error of species present in our territory. This conclusion is demonstrated by the authors, based on a review of the material deposited in major scientific collections in Brazil and subsequent molecular and phylogenetic analysis of these samples. Additionally, we have proposed a new taxonomic key to separate the species of Chrysomya found on the American continent, taking into account a larger number of characters beyond those available in current literature. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. DNA species surveillance: Monitoring bushmeat poaching and ...

    African Journals Online (AJOL)

    DNA species identification has applications in such areas as forensic science, systematics, conservation genetics and agriculture. One key anthropogenic activity threatening large wildlife fauna is illegal exploitation. In Kenya, species identification of raw and processed meat products remains a constraint to effective ...

  16. Molecular identification of species of Taenia causing bovine cysticercosis in Ethiopia.

    Science.gov (United States)

    Hailemariam, Z; Nakao, M; Menkir, S; Lavikainen, A; Iwaki, T; Yanagida, T; Okamoto, M; Ito, A

    2014-09-01

    Bovine cysticercosis causing damage to the beef industry is closely linked to human taeniasis due to Taenia saginata. In African countries, Taenia spp. from wildlife are also involved as possible sources of infections in livestock. To identify the aetiological agents of bovine cysticercosis in Ethiopia, cysticerci were collected from 41 cattle slaughtered in the eastern and central areas during 2010-2012. A single cysticercus per animal was subjected to the polymerase chain reaction (PCR)-based DNA sequencing of mitochondrial cytochrome c oxidase subunit 1 gene, and the resultant sequence was compared with those of members of the genus Taenia. Although 38 out of 41 cysticerci (92.7%) were identified as T. saginata, three samples (7.3%) showed the hitherto unknown sequences of Taenia sp., which is distantly related to Taenia solium, Taenia arctos and Taenia ovis. Old literatures suggest it to be Taenia hyaenae, but morphological identification of species could not be completed by observing only the larval samples.

  17. Review-An overview of Pistacia integerrima a medicinal plant species: Ethnobotany, biological activities and phytochemistry.

    Science.gov (United States)

    Bibi, Yamin; Zia, Muhammad; Qayyum, Abdul

    2015-05-01

    Pistacia integerrima with a common name crab's claw is an ethnobotanically important tree native to Asia. Traditionally plant parts particularly its galls have been utilized for treatment of cough, asthma, dysentery, liver disorders and for snake bite. Plant mainly contains alkaloids, flavonoids, tannins, saponins and sterols in different parts including leaf, stem, bark, galls and fruit. A number of terpenoids, sterols and phenolic compounds have been isolated from Pistacia integerrima extracts. Plant has many biological activities including anti-microbial, antioxidant, analgesic, cytotoxicity and phytotoxicity due to its chemical constituents. This review covers its traditional ethnomedicinal uses along with progresses in biological and phytochemical evaluation of this medicinally important plant species and aims to serve as foundation for further exploration and utilization.

  18. Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh, Saudi Arabia.

    Science.gov (United States)

    AlWakeel, Suaad S

    2017-09-01

    This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis , alpha-hemolytic streptococci, Staphylococcus hominis , coagulase-negative staphylococci, Leuconostoc mesenteroides , Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

  19. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus).

    Science.gov (United States)

    Moody, Michael L; Rieseberg, Loren H

    2012-07-01

    The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

  20. Direct identification and recognition of yeast species from clinical material by using albicans ID and CHROMagar Candida plates.

    Science.gov (United States)

    Baumgartner, C; Freydiere, A M; Gille, Y

    1996-02-01

    Two chromogenic media, Albicans ID and CHROMagar Candida agar plates, were compared with a reference medium, Sabouraud-chloramphenicol agar, and standard methods for the identification of yeast species. This study involved 951 clinical specimens. The detection rates for the two chromogenic media for polymicrobial specimens were 20% higher than that for the Sabouraud-chloramphenicol agar plates. The rates of identification of Candida albicans for Albicans ID and CHROMagar Candida agar plates were, respectively, 37.0 and 6.0% after 24 h of incubation and 93.6 and 92.2% after 72 h of incubation, with specificities of 99.8 and 100%. Furthermore, CHROMagar Candida plates identified 13 of 14 Candida tropicalis and 9 of 12 Candida krusei strains after 48 h of incubation.