1. bookVolume 56 (2017): Issue 3 (January 2017)
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Journal
eISSN
2545-3149
First Published
01 Mar 1961
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4 times per year
Languages
English, Polish
access type Open Access

Genetic differentiation methods of microorganisms in the soil – plant system

Published Online: 22 May 2019
Volume & Issue: Volume 56 (2017) - Issue 3 (January 2017)
Page range: 341 - 352
Received: 01 Dec 2016
Accepted: 01 Mar 2017
Journal Details
License
Format
Journal
eISSN
2545-3149
First Published
01 Mar 1961
Publication timeframe
4 times per year
Languages
English, Polish
Abstract

Biodiversity is a key concept in finding important features of new microorganisms. Microorganisms play an important role in the soil ecosystem and participate, among others, in such processes as the maintenance of soil structure, humification, release of organic compounds, disposal of pollutants and transformation of organic matter. The maintenance of competent state of soil microbial communities, i.e. the appropriate microorganism count, activity and diversity, is a necessary condition for the functioning of a highly complex system such as the soil. Phyllosphere bacteria have the potential to influence plant biogeography and ecosystem function through their influence on plant performance under different environmental conditions, but the drivers of variation in leaf-associated bacterial biodiversity among host plants are not well understood. Hence, undoubtedly, an important research aspect is the selection and development of indicators to evaluate microbial biodiversity of the soil and plant phyllosphere. In this publication, selected molecular methods used for the diversity assessment of microorganisms have been presented.

1. Introduction. 2. Denaturing Gradient Gel Electrophoresis DGGE, Temperature Gradient Gel Electrophoresis TGGE, 3. SSCP – single strand conformation polymorphism. 4. Real-Time Quantitative PCR. 5. Summary

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Adhitya A., Thomas F.I.M., Ward B.B.: Diversity of assimilatory nitrate reductase genes from plankton and epiphytes associated with a seagrass bed. Microbial Ecol. 54, 587–597 (2007).10.1007/s00248-006-9175-0Search in Google Scholar

Andreote F.D., Azevedo J.L., Araújo W.A.: Assessing the diversity of bacterial communities associated with plants. Braz. J. Microbiol. 40, 417–432 (2009)Search in Google Scholar

Brons J.K., van Elsas J.D.: Analysis of Bacterial Communities in Soil by Use of Denaturing Gradient Gel Electrophoresis and Clone Libraries, as Influenced by Different Reverse Primers. Appl. Environ. Microbiol.74, 2717–2727 (2008)10.1128/AEM.02195-07Search in Google Scholar

Bustin S.A.: Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25, 169–193 (2000)Search in Google Scholar

Cetecioglu Z., Ince O., Ince B.: Gel Electrophoresis Based Genetic Fingerprinting Techniques on Environmental Ecology (w) Gel electrophoresis – advanced techniques, red. S. Magdeldin, Rijeka, Croatia, 2012, s. 51–6610.5772/37063Search in Google Scholar

Cleary T.J., Roudel G., Casillas O., Miller N.: Rapid and specific detection of Mycobacterium tuberculosis by using the Smart Cycler instrument and a specific fluorogenic probe. J. Clin. Microbiol. 41, 4783–4786 (2003)Search in Google Scholar

Da Silva K.R.A., Salles J.F., Seldin L., van Elsas J.D.: Application of a novel Paenibacillus-specific PCR-DGGE method and sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere. J. Microbiol. Meth. 54, 213–231 (2003)Search in Google Scholar

Dorigo U., Volatier L., Humbert J.F.: Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Res. 39, 2207–2218 (2005)10.1016/j.watres.2005.04.007Search in Google Scholar

Duelli P., Obrist M.K.: Biodiversity indicators: the choice of values and measures. Agriculture, Ecosystems& Environment. 98, 87–98 (2003)10.1016/S0167-8809(03)00072-0Search in Google Scholar

Fakruddin M., Mannan K.S.B.: Methods for Analyzing Diversity of Microbial Communities in Natural Environments. Ceylon J. Sci. (Biol. Sci.) 42, 19–33 (2013)Search in Google Scholar

Fischer S.G., Lerman L.S.: DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. USA, 80, 1579–1583 (1983)10.1073/pnas.80.6.1579Search in Google Scholar

Fischer S.G., Lerman L.S.: Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell, 16, 191–200 (1979)10.1016/0092-8674(79)90200-9Search in Google Scholar

Fjellbirkeland A., Torsvik V., Ovreas L.: Methanotrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences. Anton. Leeuw. Int. J.G.79, 209–217 (2001)10.1023/A:1010221409815Search in Google Scholar

Gałązka A., Gałązka R.: Phytoremediation of polycyclic aromatic hydrocarbons in soils artificially polluted using plant-associated-endophytic bacteria and Dactylis glomerata as the bioremediation plant. Pol. J. Microbiol.64, 239–250 (2015)10.5604/01.3001.0009.2119Search in Google Scholar

Gałązka A., Król M., Perzyński A.: The Efficiency of Rhizosphere Bioremediation with Azospirillum sp. and Pseudomonas stutzeri in Soils Freshly Contaminated with PAHs and Diesel Fuel. Pol. J. Environ. Stud.21, 345–353 (2012)Search in Google Scholar

Garbeva P., van Veen J.A.; van Elsa, J.D.: Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes. FEMS Microbiol. Ecol. 47, 51–64 (2004)Search in Google Scholar

Gasser I., Muller H., Berg G.: Ecology and characterization of polyhydroxyalkanoate-producing microorganisms on and in plant. FEMS Microbiol. Ecol. 70, 142–150 (2009)Search in Google Scholar

Głowaciński Z. Różnorodność gatunkowa – jej interpretacja i obliczanie. W: Różnorodność biologiczna: pojęcia, oceny, zagadnienia ochrony i kształtowania, Zeszyty Naukowe Komitetu "Człowiek i Środowisko”, 15, 57–70 (1996)Search in Google Scholar

Gomes N. C. M., Heuer H., Schönfeld J., Costa R., Mendonça-Hagler L., Smalla K.: Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil.232, 167–180 (2001)10.1007/978-94-010-0566-1_17Search in Google Scholar

Harper J.L., Hawksworth D.L.: Biodiversity: measurement and estimation. Phil. Trans. R. Soc. Lond. B. 345, 5–12 (1994)Search in Google Scholar

Heid C.A., Stevens J., Livak K.J., Williams P.M.: Real time quantitative PCR. Genome Res.6, 986–994 (1996)10.1101/gr.6.10.986Search in Google Scholar

Henckel T., Friedrich M., Conrad R.: Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. App. Environ. Microbiol.65, 1980–1990 (1999)10.1128/AEM.65.5.1980-1990.1999Search in Google Scholar

Heuer H., Krsek M., Baker P., Smalla K., Wellington E.M.H.: Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63, 3233–3241 (1997)Search in Google Scholar

Heuer H., Smalla K.: Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities (w) Modern Soil Microbiology, red. J.D. van Elsas, J.T. Trevors, E.M.H. Wellington, Marcel Dekker, New York. 1997, s. 353–373Search in Google Scholar

Heuer H., Krsek M., Baker P., Smalla K., Wellington E.M.H.: Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63, 3233–3241 (1997)Search in Google Scholar

Higuchi R., Fockler C., Dollinger G., Watson R.: Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology, 11, 1026–1030 (1993)Search in Google Scholar

Huang J., Kang Z.: Detection of Thielaviopsis basicola in soil with real-time quantitative PCR assays. Microbiol. Res.165, 411–417 (2010)10.1016/j.micres.2009.09.001Search in Google Scholar

Ji S.C., Kim D., Yoon J.H., Lee C.H.: Metagenomic Analysis of BTEX-Contaminated Forest Soil Microcosm. J. Microbiol. Biotechn.17, 668–672 (2007)Search in Google Scholar

Kembel S.W., O’Connor T.K., Arnold H.K., Hubbell S.P., Wright S.J., Green J.L.: Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. PANS, 111, 13715–13720 (2014)10.1073/pnas.1216057111Search in Google Scholar

Kirk J.L., Beaudette L.A., Hart M., Moutoglis P., Klironomos J.N., Lee H., Trevors J.T.: Methods of studying soil microbial diversity. J. Microbiol. Meth. 58, 169–188 (2004)Search in Google Scholar

Kokoskova B., Pankova I., Krejzar V.: Characteristics of polyclonal antisera for detection and determination of Clavibacter michiganensis subsp. insidiosus. Plant Protect. Sci. 36, 46–52 (2000)Search in Google Scholar

Krajowa strategia ochrony i zrównoważonego użytkowania różnorodności biologicznej wraz z Programem działań na lata 2007–2013. Załącznik do uchwały nr 270/2007 Rady Ministrów z dnia 26.10.2007Search in Google Scholar

Krawczyk B.: Diagnostyka molekularna w zakażeniach szpitalnych. Postęp. Mikrobiol. 46, 367–378 (2007)Search in Google Scholar

Kucharska K., Wachowska U.: Mikrobiom roślin uprawnych. Post. Mikrobiol. 53, 4: 352–359 (2014)Search in Google Scholar

Kumar R., Joshi S.R.: Microbial Ecology of Soil: Studying the diversity of microorgansims in the most complex of the environments – A review. Adv. Appl. Microbiol.19, 267–279 (2015)Search in Google Scholar

Lee D.H., Zo Y.G., Kim S.J.: Nonradioactive method to study genetic profiles of natural bacterial communities by PCR single strand conformation polymorphism. Appl. Environ. Microbiol.62, 3112–3120 (1996)10.1128/aem.62.9.3112-3120.1996Search in Google Scholar

Leys N.M.E., Ryngaert A., Bastiaens L., Verstraete W., Top E.M., Springael D.: Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. App. Environ. Microbiol. 70, 1944–1955 (2004)Search in Google Scholar

Libczańska A., Woźniak A., Wawrocka A., Krawczyński M.R.: Techniki wykorzystywane w diagnostyce molekularnej chorób jednogenowych. Nowiny Lekarskie, 75, 486–490 (2006)Search in Google Scholar

Łyszcz M., Gałązka A.: Metody oparte o amplifikację DNA techniką PCR wykorzystywane w ocenie bioróżnorodnościci mikroorganizmów glebowych. Kosmos, Varia; no 2, 2017 (w druku)Search in Google Scholar

Łyszcz M., Gałązka A.: Wybrane metody molekularne wykorzystywane w ocenie bioróżnorodności mikroorganizmów glebowych. Post. Mikrobiol. 55, 309–319 (2016)Search in Google Scholar

Maarit-Niemi R., Heiskanen I., Wallenius K., Lindstrom K.: Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J. Microbiol. Meth.45, 155–165 (2001)10.1016/S0167-7012(01)00253-6Search in Google Scholar

Maarit-Niemi R., Heiskanen I., Wallenius K., Lindstrom K.: Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J. Microbiol. Meth.45, 155–165 (2001)10.1016/S0167-7012(01)00253-6Search in Google Scholar

Mackay I.M., Arden K.E., Nitsche A.: Real-time PCR in virology. Nucleic Acids Res. 15, 1292–1305 (2002)10.1093/nar/30.6.129210134311884626Search in Google Scholar

MacNaughton S.J., Stephen J.R., Venosa A.D., Davis G.A., Chang Y.J., White D.C.: Microbial population changes during bioremediation of an experimental oil spill. App. Environ. Microbiol.65, 3566–3574 (1999)10.1128/AEM.65.8.3566-3574.19999153510427050Search in Google Scholar

Malik S., Beer M., Megharaj M., Naidu R.: The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ. Int.34, 265–276 (2008)10.1016/j.envint.2007.09.00118083233Search in Google Scholar

Marefat A., Ophel-Keller K., McKay A.: A real-time PCR assay for detection of Clavibacter michiganensis subsp. insidiosus in Lucerne. Australas. Plant. Path. 36, 262–269 (2007)Search in Google Scholar

Miller K.M., Ming T.J., Schulze A.D., Withler R.E.: Denaturing Gradient Gel Electrophoresis (DGGE): a rapid and sensitive technique to screen nucleotide sequence variation in populations. BioTechniques, 27, 1016–1030 (1999)10.2144/99275rr02Search in Google Scholar

Milling A., Smalla K., Maidl F.X., Schloter M., Munch J.C.: Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi. Plant Soil,266, 23–39 (2004)10.1007/s11104-005-4906-4Search in Google Scholar

Morrison T.B., Weis J.J., Wittwer C.T.: Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification, Biotechniques, 24, 954–958 (1998)Search in Google Scholar

Mühling M., Woolven-Allen J., Murrell J.C., Joint I.: Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J. 2, 379–392 (2008)10.1038/ismej.2007.97Search in Google Scholar

Mullis K.B., Faloona F.A.: Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods. Enzymol. 155, 335–350 (1987)10.1016/0076-6879(87)55023-6Search in Google Scholar

Mullis K.B.: The unusual origin of the polymerase chain reaction. Sci Am. 262, 56–61, (199010.1038/scientificamerican0490-56Search in Google Scholar

Muyzer G., Brinkhoff T., Nubel U., Santegoeds C., Schafer H., Wawer C.: Denaturing gradient gel electrophoresis (DGGE) in microbial ecology (w) Molecular Microbial Ecology Manual, red. A. Kowalchuk, F.J de Bruijn., A.D.L Akkermans, J.D van Elsas. Kluwer Academic Publishers Dordrecht, 2004, s. 743–769Search in Google Scholar

Muyzer G., Smalla K.: Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Anton. Leeuw. 73, 127–141 (1998)10.1023/A:1000669317571Search in Google Scholar

Muyzer G., Waal E.C.D., Uitterlinden A.G.: Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 5, 695–700 (1993)10.1128/aem.59.3.695-700.1993Search in Google Scholar

Muyzer, G.: DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2, 317–322 (1999)Search in Google Scholar

Nakatsu C.H.: Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis. Soil Sci. Soc. Am. 71, 562–571 (2007)Search in Google Scholar

Orita M., Suzuki Y., Sekiya T., Hayashi K.: A rapid and sensitive detection of point mutations and genetic polymorphisms using polymerase chain reaction. Genomics.5, 874–879 (1989)10.1016/0888-7543(89)90129-8Search in Google Scholar

Peixoto R.S., Coutinho H.L.D., Rumjanek N.G., Macrae A., Rosado A.S.: Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGE. Lett. Appl. Microbiol. 35, 316–320 (2002)Search in Google Scholar

Pereira T.P., Do Amaral F.P., Dall’Asta P., Brod F.C.A., Aris A.C.M.: Real-time PCR quantification of the plant growth promoting bacteria Herbaspirillum seropedicae strain SmR1 in maize roots. Mol. Biotechnol.56, 660–670 (2014)10.1007/s12033-014-9742-424563376Search in Google Scholar

Rao X., Lai D., Huang X.: A New Method for Quantitative Real-Time Polymerase Chain Reaction Data Analysis. J. Comput. Biol. 20, 703–711 (2013)Search in Google Scholar

Rastogi G., Sani R.K.: Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment (w) Microbes and Microbial Technology Agricultural and Environmental Applications, red. I. Ahmad, F. Ahmad, J. Pichtel, Springer Science+Business, New York Dordrechet Heidelberg London. 2011, s. 29–5710.1007/978-1-4419-7931-5_2Search in Google Scholar

Rincon-Florez V.A., Carvalhais L.C., Schenk P.M.: Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology. Diversity, 5, 581–612 (2013)10.3390/d5030581Search in Google Scholar

Rosado A.S., Duarte G.F., Seldin L., Van Elsa J.D.: Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. Appl. Environ. Microbiol.64, 2770–2779 (1998)10.1128/AEM.64.8.2770-2779.1998Search in Google Scholar

Rosenbaum V., Riesner D.: Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys. Chemist. 26, 235–246 (1987)Search in Google Scholar

Salles J.F., De Souza F.A., van Elsas J.D.: Molecular method to assess the diversity of Burkholderia species in environmental samples. Appl. Environ. Microbiol. 68, 1595–1603 (2002)Search in Google Scholar

Saragih S.A., Takemoto S., Hisamoto Y., Fujii M., Sato H., Kamata N.: Quantitative real-time PCR (qPCR) – Based tool for detection and quantification of Cordyceps militaris in soil. J. Invertebr. Pathol. 124, 70–72 (2015)Search in Google Scholar

Sluijter J.P.G., Pasterkamp G., de Kleijn D.P.V.: Quantitative Real-Time PCR (w) Cardiovascular Research New Technologies, Methods, and Applications, red. G. Pasterkamp, D. de Kleijn, Springer, New York, 2005, 75–8310.1007/0-387-23329-6_4Search in Google Scholar

Smalla K., Oros-Sichler M., Milling A., Heuer H., Baumgarte S., Becker R., Neuber G., Kropf S., Ulrich A., Tebbe C.C.: Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results. J. Microbiol. Methods. 69, 470–479 (2007).Search in Google Scholar

Studzińska A., Tyburski J., Daca P., Tretyn A.: PCR w czasie rzeczywistym. Istota metody i strategie monitorowania przebiegu reakcji. Biotechnologia.1, 71–85 (2008)Search in Google Scholar

Sugden D., de Winter P.: Quantification of mRNA Using Real Time RT-PCR (w) Molecular Biomethods Handbook, red. J.M. Walker, R. Rapley, Humana Press, Totowa, NJ, 2008, s. 149–16810.1007/978-1-60327-375-6_11Search in Google Scholar

Sugden D.: Quantitative PCR (w) Medical BioMethods Handbook, red. J.M. Walker, R. Ralph, Humana Press, New York, 2005, s. 327–34510.1385/1-59259-870-6:327Search in Google Scholar

Theron J., Cloete T.E.: Molecular techniques for determining microbial diversity and community structure in natural environments. Crc. Cr. Rev. Microbiol. 26, 37–57, (2000)10.1080/10408410091154174Search in Google Scholar

Tichopad A., Didier A., Pfaffl M.W.: Inhibition of real-time RT-PCR quantification due to tissue-specific contaminants. Mol. Cell. Probes. 18, 45–50 (2004)Search in Google Scholar

Tichopad A., Dilger M., Schwarz G., Pfaffl M.W.: Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res. 3, 1–6 (2003)10.1093/nar/gng122Search in Google Scholar

Tiedje J.M., Asuming-Brempong S., Nusslein K., Marsh T.L., Flynn S.J.: Opening the black box of soil microbial diversity. Appl. Soil. Ecol.13, 109–122 (1999)10.1016/S0929-1393(99)00026-8Search in Google Scholar

Tyburski J., Studzińska A., Daca P., Tretyn A.: PCR w czasie rzeczywistym. Metody analizy danych. Biotechnologia, 1, 86–96 (2008)Search in Google Scholar

Valasek M.A., Repa J.R.: The power of real-time PCR. Adv. Physiol. Educ.29, 151–159 (2005)10.1152/advan.00019.200516109794Search in Google Scholar

Valášková V., Baldrian P.: Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities. Plant. Soil. Environ. 55, 10, 413–423 (2009)Search in Google Scholar

Vallaeys T., Topp E., Muyzer G., Macheret V., Laguerre G., Soulas G.: Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24, 279–285 (1997)Search in Google Scholar

VanGuilder H.D., Vrana K.E., Freeman W.M.: Twenty-five years of quantitative PCR for gene expression analysis. BioTechniques.44, 619–626 (2008)10.2144/00011277618474036Search in Google Scholar

Vendan R.T., Lee S.H., Yu Y.J., Rhee Y.H.: Analysis of Bacterial Community in the Ginseng Soil Using Denaturing Gradient Gel Electrophoresis (DGGE). Indian J. Microbiol. 52, 286–288 (2012)Search in Google Scholar

Widmer F., Seidler R.J. Gillevet P.M. Watrud L.S. Di Giovanni G.D.: A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl. Environ. Microbiol. 64, 2545–255 (1998)Search in Google Scholar

Wilhelm J., Pingoud A.: Real-time polymerase chain reaction. Chem. Biochem. 4, 1120–1128 (2003)Search in Google Scholar

Wong M.L., Medrano J.F.: Real-time PCR for mRNA quantitation. BioTechniques.39, 75–85 (2005)10.2144/05391RV0116060372Search in Google Scholar

Yang C.H., Crowley D.E., Borneman J., Kee N.T.: Microbial phyllosphere populations are more complex than previously realized. P. Natl. Acad. Sci. USA, 98, 3889–3894 (2001)10.1073/pnas.0516338983114811274410Search in Google Scholar

Ziembińska-Buczyńska A., Cema G., Kalbarczyk M., Żabczyński S.: Wykorzystanie metody PCR-DGGE do badania zmien- ności genotypowej bakterii zasiedlających złoże tarczowe oczyszczające modelowe ścieki koksownicze. Ochr. Śr. 36, 3–8 (2014)Search in Google Scholar

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