ORIGINAL_ARTICLE
Detection of Polymorphism in Ancient Tempranillo Clones (Vitis vinifera L.) Using Microsatellite and Retrotransposon Markers
Tempranillo is one of the most widely cultivated grapevine varieties in Spain. After several years of clone selection, some highly recommended old clones have been identified in terms of both their qualitative and production characteristics. This study was designed to discriminate among 28 ancient clones of the cultivar Tempranillo (Vitis vinifera). DNA samples from clones were analysed using two different molecular markers; microsatellites or simple sequence repeats (SSR) and retrotransposons. The results of this study indicate that one variant genotype was expressed as three alleles. Further analysis revealed the presence of a chimera, in which the third allele was present in the leaf but not root or wood tissue, indicating a functionally double-layered apical meristem. The present research also showed that one of the retrotranposon marker was able to discriminate one grapevine clone (VP1) from the remaining clones.
https://www.ijbiotech.com/article_7121_b76bd22f268803ea298c7058d25eab22.pdf
2010-01-01
1
6
Vitis vinifera L
Intravarietal variability
microsatellites
retrotransposon
Claudia
Carcamo
1
INIA-CBGP, Dpto. Biotecnología, Campus Montegancedo (Autovia M40-Km38), Pozuelo de Alarcón, 28223 Madrid, Spain
AUTHOR
Ignacio
Provedo
2
Viveros Provedo, Logroño, Spain
AUTHOR
Rosa
Arroyo-García
rarroyo@inia.es
3
INIA-CBGP, Dpto. Biotecnología, Campus Montegancedo (Autovia M40-Km38), Pozuelo de Alarcón, 28223 Madrid, Spain
LEAD_AUTHOR
Bowers Je, Dangl GS, Meredith CP (1999). Development and characterization of additional microsatellite DNA markers for grape. Am J Enol Vitic. 50: 243-24.
1
Benjak A, Forneck A, Casacubierta JM (2008). Genome-wide analysis of the “Cut-and-Paste” transposon of grapevine. PLos One. 3: e3107.
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Bertsch C, Kieffer F, Maillot P, Farine S, Butterlin G, Merdinuglu D, Walker B (2005). Genetic chimerism of Vitis vinifera cv Chardonnay 96 is maintained through organogenesis but not somatic embryogenesis. BMC Plant Biology. 5:20.
3
Branco CJS, Vieira EA, Malone G, Cop MM, Bernardes A, Mistura C, Carvalho F, Oliveira CA (2007). IRAP and REMAP assessment of genetic similarity in rice. J Appl Genet. 7: 107-113.
4
Crespan M (2003). Evidence on the evolution of polymorphisms of microsatellite markers in varieties of Vitis vinifera L. Theor Appl Genet. 108: 231-237.
5
Crespan M, Milani N (2001). The Muscats: molecular analysis of synonyms, homonyms and genetic relationships within a large family of grapevine cultivars. Vitis 38: 87-92.
6
Dangl GS, Mendum ml, Prins BH, Walker MA, Meredith CP, Simon CJ (2001). Simple sequence repeat analysis of a clonally propagated species: a tool for managing a grape germplasm collection. Genome 44: 432-438.
7
Franks T, Botta R, Thomas MR (2002). Chimerism in grapevines: implications for cultivars identification, ancestry and genetic improvement. Theor Appl Genet. 104: 192-199.
8
González-Techera A, Jubany S, Ponce de Leon I, Boido E, Dellacasa E, Carrau FM. (2004) Molecular diversity within clones of cv. Tannat (Vitis vinifera L.). Vitis 43: 179-185.
9
Hartmann HT, Kester DE, Davis FT, Genev RL (1997). Plant Propagation: Principal and Practices. Prentice Hall, New Yersey.
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11
Ibañez J, De Andres MT, Molino A, Borrego J (2003). Genetic study of key Spanish grapevine varieties using microsatellite analysis. Am J Enol Vitic. 54: 22-30.
12
Imazio S, Labra M, Grassi F, Winfield M, Bardini M, Scienza A (2002). Molecular tools for clone identification: the case of the grapevine cultivar “Traminer”. Plant Breed. 121: 531-535.
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16
Merdinoglu F, ButterlinG, Bevilacqua I, Chiquet V, Adam-Blondom AF, Decroq S (2005). Development and characterization of a large set of microsatellites markers in grapevine. Mol Breed. 15: 349-366.
17
Pelsy F. (2007) Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis. Theor Appl Genet. 116: 15-27.
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Pereira HS, Barao A, Delgado M, Morais-Cecilio L, Viegas W (2005). Genomic analysis of Grapevine Retrotransposon 1 (Gret1) in Vitis vinifera. Theor Appl Genet. 111: 871-878.
19
Regner F, Wiedeck E, Stadlbauer A (2000). Differentiation and identification of White Riesling clones by genetic markers. Vitis 39: 103-107.
20
Riaz S, Garrison KE, Dangl GS, Boursiquot JM, Meredith CP (2002). Genetic diversity and chimerism within ancient asexually propagated winegrape cultivars. J Am Soc Hortic Sci. 127: 508-514.
21
Schellenbaum P, Mohler V, Wenzel G, Walker B (2008). Variation in DNA methylation of grapevine somaclones (Vitis vinifera L). BMC Plant Biology. 8: 78-98.
22
Sefc KM, Regner F, Turetshek G, Glosel J, Steinkeller H (1999). Identification of microsatellites sequences in Vitis riparia and their applicability for genotyping of different Vitis specires. Genome 42: 367-373.
23
Thompson NM, Olmo HP (1963). Cytohistological studies of cytochimeric and tetraploid grapes. Amer J Bot. 50: 901-906.
24
Wegscheider E, Benjak A, Forneck A (2009). Clonal Variation in Pinot noir revealed by S-SAP involving universal retrotransposon-based sequences. Am J Enol Vitic. 60: 1.
25
ORIGINAL_ARTICLE
The Phylogeny of Calligonum and Pteropyrum (Polygonaceae) Based on Nuclear Ribosomal DNA ITS and Chloroplast trnL-F Sequences
This study represents phylogenetic analyses of two woody polygonaceous genera Calligonum and Pteropyrum using both chloroplast fragment (trnL-F) and the nuclear ribosomal internal transcribed spacer (nrDNA ITS) sequence data. All inferred phylogenies using parsimony and Bayesian methods showed that Calligonum and Pteropyrum are both monophyletic and closely related taxa. They have no affinity with Atraphaxis, instead allied with a clade in which the genus is nested. Infrageneric relationships in Calligonum, due to the paucity of informative nucleotide sites in both DNA regions are not resolved.
https://www.ijbiotech.com/article_7122_8bd56f575495dae5615f19f45213c9de.pdf
2010-01-01
7
15
Calligonum
cpDNA trnL-F
Molecular phylogeny
nrDNA ITS
Pteropyrum
Polygonaceae
Solmaz
Tavakkoli
1
Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175,Tehran, Iran
AUTHOR
Shahrokh
Kazempour Osaloo
skosaloo@modares.ac.ir and skosaloo@yahoo.com
2
Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175,Tehran, Iran
LEAD_AUTHOR
Ali Asghar
Maassoumi
maassoumi@yahoo.com
3
Department of Botany, Research Institute of Forests and Rangelands, P.O. Box 13185-116, Tehran, Iran
AUTHOR
Akhani H (2004). A new spiny, cushion-like Euphorbia (Euphorbiaceae) from south-west Iran with special reference to the phytogeographic importance of local endemic species. Bot J Linn Soc. 146: 107-121.
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Al-Khayat AH (1990). Pteropyrum naufelum (Polygonaceae), a new species from Iraq. Nord J Bot. 13: 33-35.
2
Aparicio A (1989). Números cromosomáticos de plantas occidentals. Anales del Jardín Botánico de Madrid. 45: 483-494.
3
Bao B, Grabovskaya AE (2003). Calligonum, In: Flora of China. Vol. 5, ZY Wu, PH Raven and DY Hong, (eds). Science Press, Beijing, and Missouri Botanical Garden Press, St. Louis. PP. 324-328.
4
Brandbyge J (1993). Polygonaceae. In: K. Kubitzki, J.C. Rohwer, and V. Bittrich, eds The families and genera of vascular plants, Springer-Verlag, Berlin. 2: 531-544.
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Kim MH, Won H, Park C (2005). Molecular phylogeny of Polygonaceae based on chloroplast matK sequences.XVII international Botanical Congress, Vienna, Austria. Abstract 1487.
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Lamb Frye AS, Kron KA (2003). rbcL Phylogeny and character evolution in Polygonaceae. Syst Bot. 28: 326-332.
16
Li A, Grabovskaya-Borodina AE (2003). Pteroxygonum (Polygonaceae). In: Flora of China. Vol. 5, ZY Wu, PH Raven and DY Hong, (eds). Science Press, Beijing, and Missouri Botanical Garden Press, St. Louis. PP. 323.
17
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Mao Z, Yang G, Wang C (1983). Studies on chromosome numbers and anatomy of young branches of Calligonum of Xingang in relation to the evolution of some species. Acta Phytotax Sinica. 21: 44-49.
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Navajes-P΄eres R, Herran Rdl, Gonalez GL, Jamilerna M, Lozano R, Rejon CR, Rejon MR (2005). The evolution of reproductive systems and sex-determination mechanisms within Rumex (Polygovaeae) inferred from nuclear and chloroplastidial sequences data. Mol Biol Evol. 22: 1929-1939.
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26
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28
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29
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33
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35
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36
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37
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38
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39
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40
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41
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42
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43
ORIGINAL_ARTICLE
Genetic Similarities Among Iranian Populations of Festuca, Lolium, Bromus and Agropyron Using Amplified Fragments Length Polymorphism (AFLP) Markers
The study of genetic variation and phylogenetic relationships is essential for the efficient selection of superior plant material and conducting introgression breeding programs. In Iran, despite the wide geographical distribution of grasses no report is available on the genetic diversity and relationships of cool season grass populations. In this study amplified fragment length polymorphism (AFLP) was used to study 42 populations from eight species of Festuca arundinacea Schereb., Festuca. pratensis Huds., Festuca. rubra L., Festuca. ovina L., Lolium perenne L., L. rigidum Gaud., Bromus tomentellus Boiss. and Agropyron cristatum (L) Gaertn. The number of amplified products ranged from 11 to 78 per primer combination and a total of 497 markers were scored. Jaccard’s genetic similarity coefficients among populations ranged from 0.15 to 0.88 showing high levels of inter and intra-specific genetic diversity. The cluster analysis and principle coordinate analysis (PCOA) reflected the phylogenetic relationships among species and clearly demonstrated differences in the degree of similarity among accessions. Results indicated that AFLP is a useful technique to reveal genetic diversity at different taxonomic levels of grasses and might facilitate the selective introgression of useful genes in plant breeding programs.
https://www.ijbiotech.com/article_7123_742c30a85e28e6b6a75c78b635047cb9.pdf
2010-01-01
16
23
Genetic similarity
Grasses
AFLP marker
Mohammad Mahdi
Majidi
majidi@cc.iut.ac.ir
1
Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, P.O. Box 84156-8311, I.R. Iran
LEAD_AUTHOR
Aghafakhr
Mirlohi
2
Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, P.O. Box 84156-8311, I.R. Iran
AUTHOR
Darbyshire SJ, Warwick SI (1992). Phylogeny of North American Festuca and related genera using chloroplast DNA restriction site variation. Can J Bot. 70: 2415-2429.
1
Dellaporta SL, Wood J, Hicks JB (1983). A plant minipreparation. Plant Mol Biol Rep. 4: 19-21.
2
Dewey DR (1984). The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. In: Gustafson J.P. (ed.), Gene Manipulation in Plant Improvement. Plenum Press, New York. PP. 209-279.
3
Fjellheim S, Rognli OA (2005). Genetic Diversity within and among Nordic Meadow Fescue (Festuca pratensis Huds.) Cultivars Determined on the Basis of AFLP Markers. Crop Sci. 45: 2081-2086.
4
Guthridge KM, Dupal MP, Jones ES, Kolliker R, Smith KF, Forster JW (2001). AFLP analysis of genetic diversity within and between populations of perennial ryegrass (Lolium perenne L.). In: Plant and Animal Genome. The 9th Inter. Conf. on the Status of Plant and Animal Genome Research, San Diego. Scherago Int., New York. PP. 141-152.
5
Krauss S, Peakall R (1998). An evaluation of the AFLP fingerprinting technique for the analysis of paternity in natural population of Persoonia mollis (Proteaceae). Aust J Bot. 46: 533-546.
6
Love A (1984). Conspectus of the Triticeae. Feddes Repertorium. 95: 425-521.
7
Mian AR, Hopkins AA, Zwonitzer JC (2002). Determination of genetic diversity in tall fescue with AFLP markers. Crop Sci. 42:944-950.
8
Mirlohi A, Sabzalian MR, Sharifnabi B, Khayyam-Nekoui M (2006). Widespread occurrence of Neotyphodium like endophyte in populations of Bromus tomentellus Boiss. In Iran. FEMS Microbiol Lett. 256: 126-131.
9
Pillay M and Myers GO (1999). Genetic diversity in cotton assessed by variation in ribosomal RNA genes and AFLP markers. Crop Sci. 39: 1881-1886.
10
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13
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14
Saha MC, Mian R, Zwonitzer JC, Chekhovskiy K, Hopkins AA (2005). An SSR and AFLP based genetic linkage map of tall fescue (Festuca arundinacea Schreb.). Theor Appl Genet. 110: 323-336.
15
Seal AG (1983). DNA variation in Festuca. Heredity 50: 225-236.
16
Sleper DA (1985). Breeding tall fescue. Plant Breed Rev. 3: 313-342.
17
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Turgen AJ (1985). Turf Grass Managements. Reston publishing company. Reston Virginia. PP. 416.
20
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21
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22
Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Frijters A, Pot J, Pleman J, Kuiper M, Zabeau M (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acid Res. 23: 4407-4414.
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24
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25
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26
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27
ORIGINAL_ARTICLE
Simple Sequence Repeats Amplification: a Tool to Survey the Genetic Background of Olive Oils
A reliable DNA extraction method for use on extra virgin olive oil based on a commercial kit was defined, and the possibility of using this DNA for fingerprinting the original cultivar was demonstrated. The genetic traceability of single-cultivar virgin olive oil from two cultivars (Carolea and Frantoio) was achieved by identifying the varieties from which they were produced. This involved the analysis of DNA sequences using a panel of seven simple sequence repeats (SSRs) to provide genotype-specific allelic profiles. The amplified SSR fragments and the DNA profiles from the monovarietal oil corresponded to the profiles from the leaves of the same cultivar. The most reliable SSR in providing correct allele sizing in distinguishing either single-cultivar olive oil samples or the different ratios of their blends are DCA3, DCA4, DCA16, DCA17, and GAPU101, while DCA9, GAPU59 produced less concordance against data obtained by the genetic analysis of leaf samples. To have reproducible results, PCR product purification and selection of a set of markers with a highly robust amplification pattern is suggested.
https://www.ijbiotech.com/article_7124_3cc51ad7d3a51f476eae119d708dac54.pdf
2010-01-01
24
31
DNA fingerprinting
Genetic traceability
Olive oil
Simple Sequence Repeats (SSRs)
Zohreh
Rabiei
rabiei@nigeb.ac.ir
1
Department of Biotechnology, Faculty of New Technologies and Energy Engineering, Shahid Beheshti University, G.C. Tehran, I.R. Iran
LEAD_AUTHOR
Sattar
Tahmasebi Enferadi
tahmasebi@nigeb.ac.ir
2
Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology, P.O. BOX 14965/161, Tehran, I.R. Iran
AUTHOR
Abbas
Saidi
3
Department of Biotechnology, Faculty of New Technologies and Energy Engineering, Shahid Beheshti University, G.C. Tehran, I.R. Iran
AUTHOR
Sonia
Patui
4
Università degli Studi di Udine, Dipartimento di Biologia e Protezione delle Piante, via delle Scienze 91-33100 Udine, Italy
AUTHOR
Gian
Paolo Vannozzi
5
Università degli Studi di Udine, Dipartimento di Scienze Agrarie e Ambientali, via delle Scienze 208-33100 Udine, Italy
AUTHOR
Alba V, Sabetta W, Blanco A, Pasqualone A, Montemurro C (2009). Microsatellite markers to identify specific alleles in DNA extracted from monovarietal virgin olive oils, Eur Food Res Techno DOI 10.1007/s00217-009-1062-8.
1
Angiolillo A, Mencuccini M, Baldoni L (1999). Olive genetic diversity assessed using amplified fragment length polymorphisms. Theor Appl Genet. 98: 411-421.
2
Baldoni, L, Angiolillo A, Pellegrini M, Mencuccini M (1999). A linkage genome map for olive as an important tool for marker-assisted selection, Metzidakis and Voyiatzis ed., Proc 3rd Int ISHS Symp on Olive Growing, Acta Hort., Volume: 474. PP. 111-115.
3
Bandelj D, Jakše J, Javornik B (2002). DNA Fingerprinting of olive varieties by microsatellite markers. Food Technol Biotechnol. 40: 185-190.
4
Bautista R, Cánovas FM, Claros MG (2003). Genomic evidence for a repetitive nature of the RAPD polymorphisms in Olea europaea (olive-tree). Euphytica 130: 185-190.
5
Belaj A, Cipriani G, Testolin R (2004). Characterization and identification of the main Spanish and Italian olive cultivar by simple-sequence-repeat markers. HortScience 39: 1557-1561.
6
Besnard G, Berville´ A (2000). Multiple origins for Mediterranean olive (Olea europaea L. subsp. europaea) based upon mitochondrial DNA polymorphisms. C R Acad Sci III. 323: 173-181.
7
Bianchi G, Giansante L, Shaw A, Kell DB (2001). Chemometric criteria for the characterisation of Italian protected denomination of origin (DOP) olive oils from their metabolic profiles. Eur J Lipid Sci Technol. 103: 141-150.
8
Breton C, Claux D, Metton I, Skorski G, Bervillè A (2004). Comparative Study of Methods for DNA Preparation from Olive Oil Samples to Identify Cultivar SSR Alleles in Commercial Oil Samples: Possible Forensic Applications. J Agric Food Chem. 52: 531-537.
9
Busconi M, Foroni C, Corradi M, Bongiorni C, Cattapan F, Fogher C (2003). DNA extraction from olive oil and its use in the identification of the production cultivar. Food Chem. 83: 127-134.
10
Caponio F, Gomes T, Pasqualone A (2001). Phenolic compounds in virgin olive oils: influence of the degree of olive ripeness on organoleptic characteristics and shelf-life. Eur Food Res Technol. 212: 329-333.
11
Carriero F, Fontanazza G, Cellini F, Giorio G (2002). Identification of simple sequence repeats (SSRs) in olive (Olea europea L.). Theor Appl Genet. 104: 301-307.
12
Cipriani G, Marrazzo MT, Marconi R, Cimato A, Testolin R (2002). Microsatellite markers isolated in olive (Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars. Theor Appl Genet. 104: 223-228.
13
Claros MG, Crespillo R, Aguilar ML, Cánovas FM (2000). DNA fingerprinting and classification of geographically related genotypes of olive-tree (Olea europaea L.). Euphytica 116: 131-142.
14
Cresti M, Linskens HF, Mulcahy DL, Bush S, di Stilio V, Xu MY, Vigani R, Cimato A (1997). Comunicación preliminar sobre la identificación del DNA de las hojas y el aceite de oliva de Olea europaea. Olivae 69: 36-37.
15
De La Rosa R, James CM, Tobutt KR (2002). Isolation and characterization of polymorphic microsatellites in olive (Olea europaea L.) and their transferability to other genera in the Oleaceae. Mol Ecol Notes. 2: 265-267.
16
De la Torre F, Bautista R, Cánovas FM, Claros G (2004). Isolation of DNA from olive oil and oil sediments: application in oil fingerprinting. Food Agric Envir. 2: 84-9.
17
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19
Doveri S, Lee D (2007). Development of Sensitive Crop-Specific Polymerase Chain Reaction Assays Using 5S DNA: Applications in Food Traceability. J Agric Food Chem. 55: 4640-4644.
20
Ettayebi k, Errachidi F, Jamai L, Tahri-Jouti MA, Sendide K, Ettayebi M (2003). Biodegradation of polyphenols with immobilized Candida tropicalis under metabolic induction. FEMS Microbiol Letters. 23: 215-219.
21
Fabbri A, Hormaza JI, Polito VS (1995). Random Amplified Polymorphic DNA analysis of olive (Olea europeae) cultivars. J Amer Soc Hort Sci. 120: 538-542.
22
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23
Hannachi H, Sommerlatte H, Breton C, Msallem M, El Gazzah M, El Hadj SB, Berville´ A (2009). Oleaster (var. sylvestris) and subsp. cuspidata are suitable genetic resources for improvement of the olive (Olea europaea subsp. europaea var. europaea). Genet Resour Crop Evol. 56: 393-403.
24
Hannachi H, , Breton C, Msallem M, El Hadj SB, El Gazzah M, Berville´ A (2008). Differences between native and introduced olive cultivars as revealed by morphology of drupes, oil composition and SSR polymorphisms: A case study in Tunisia Scientia. Horticulturae 116: 280-290.
25
Hernández P, de la Rosa R, Rallo L, Martin A, Dorado G (2001). First evidence of a retrotransposon-like element in olive (Olea europaea): Implications in plant variety identification by SCAR marker development. Theor Appl Genet. 102: 1082-1087.
26
Jakupciak JP, Wang W, Markowitz ME, Ally D, Coble M, Srivastava S, Maitra A, Barker PE, Sidransky D, O’Connell CD (2005). Mitochondrial DNA as a Cancer Biomarker. J Mol Diagn.7: 258-267.
27
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30
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31
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34
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35
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36
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37
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38
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39
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40
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42
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43
ORIGINAL_ARTICLE
Inhibitory Effects of Lactobacillus salivarius and Lactobacillus crispatus Isolated from Chicken Gastrointestinal Tract on Salmonella enteritidis and Escherichia coli Growth
Probiotics are live cultures of microbes; often lactic acid bacteria, but also some other species, which when fed to animals, improve their health and growth through altering the intestinal microbial balance. In the present research, healthy chickens’ gastrointestinal (GI) tracts were screened for the presence of lactic acid bacteria with probiotic properties. The probiotic properties of the isolates taken from different parts of the GI tract were evaluated. They were examined for resistance to 2% (w/v) bile salts and acidic pH, capability to adhere to the intestinal epithelium and inhibitory effects on the growth of Salmonella enteritidis and Escherichia coli. Fermentation profile analyses and sequencing data of the conserved 16S rRNA genes showed that from a total of five selected clones, four clones isolated from the duodenum and caeca were Lactobacillus salivarius and the fifth clone, isolated from the duodenum, was Lactobacillus crispatus. All the selected clones were able to adhere to the chicken’s epithelial cells. The lactobacilli isolated from different parts of the GI tract had probiotic properties suitable for use in animal feed. Due to the inhibitory effects of the isolated lactic acid bacteria on the growth of pathogenic microbiota, it can be concluded that these bacteria are good candidates for treatment of chicken GI infectious diseases.
https://www.ijbiotech.com/article_7125_453c4f5516993105f951d30f8cafe1f5.pdf
2010-01-01
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37
Chicken
Lactic acid bacteria
Probiotic
E. coli
Salmonella enteritidis
Mehrnaz
Nouri
1
Department of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. Iran
AUTHOR
Fatemeh
Rahbarizadeh
rahbarif@modares.ac.ir
2
Department of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. Iran
LEAD_AUTHOR
Davoud
Ahmadvand
3
Department of Clinical Biochemistry, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. Iran
AUTHOR
Farhad
Moosakhani
4
Department of Veterinary Medicine, Azad University, Karaj, I.R. Iran 4Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
AUTHOR
Elham
Sadeqzadeh
5
Department of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. Iran
AUTHOR
Shahram
Lavasani
6
Department of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. Iran
AUTHOR
Vahid
Khoddami Vishteh
7
Department of Medical Biotechnology, School of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-333, Tehran, I.R. Iran
AUTHOR
Abee T, Klaenhammer TR, Letellier L (1994). Kinetic studies of the action of lactacin F, a bacteriocin produced by Lactobacillus johnsonii that forms poration complexes in the cytoplasmic membrane. Appl Environ Microbiol. 60: 1006-1013.
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2
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3
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4
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5
Collado MC, Jalonen L, Meriluoto J, Salminen S (2006). Protection mechanism of probiotic combination against human pathogens: in vitro adhesion to human intestinal mucus. Asia Pac J Clin Nutr. 15: 570-575.
6
de Vos WM, Kleerebezem M, Kuipers OP (2005). Lactic acid bacteria - genetics, metabolism and application. FEMS Microbiol Rev. 29: 391.
7
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8
Fuller R, Gibson GR (1997). Modification of the intestinal microbiota using probiotics and prebiotics. Scand J Gastroentero Suppl. 222: 28-31.
9
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10
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11
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12
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13
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14
Jacobsen CN, Rosenfeldt-Nielsen V, Hayford AE, Møller PL, Michaelsen KF, Paerregaard A, Sandström B, Tvede M, Jakobsen M (1999). Screening of probiotic activities of forty-seven strains of Lactobacillus spp by in vitro techniques and evaluation of the colonization ability of five selected strains in humans. Appl Environ Microbiol. 65: 4949-4956.
15
Madsen K, Cornish A, Soper P, McKaigney C, Jijon H, Yachimec C, Doyle J, Jewell L, De Simone C (2001). Probiotic bacteria enhance murine and human intestinal epithelial barrier function. Gastroenterology 121: 580-591.
16
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17
Mead GC (1989). Microbes of the avian caeca: types present and substrates utilized. J Exp Zool Suppl. 3: 48-54.
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Metchnikoff E (1908). The Nature of Man In: Studies in Optimistic Philosophy, William Heinemann, London.
19
Mishu B, Griffin PM, Tauxe RV, Cameron DN, Hutcheson RH, Schaffner W (1991). Salmonella enteritidis gastroenteritis transmitted by intact chicken eggs. Ann Intern Med. 115: 190-194.
20
Netherwood T, Gilbert HJ, Parker DS, O’Donnell AG (1999). Probiotics shown to change bacterial community structure in the avian gastrointestinal tract. Appl Environ Microb. 65: 5134-8.
21
Nurmi E, Rantala M (1973). New aspects of Salmonella infection in broiler production. Nature 241: 210-211.
22
Olivares M, Díaz-Ropero MP, Martín R, Rodríguez JM, Xaus J (2006). Antimicrobial potential of four Lactobacillus strains isolated from breast milk. J Appl Microbiol. 101: 72-79.
23
Patterson JA, Burkholder KM (2003). Application of prebiotics and probiotics in poultry production. Poultry Sci. 82: 627-631.
24
Rehman H, Böhm J, Zentek J (2008). Effects of differentially fermentable carbohydrates on the microbial fermentation profile of the gastrointestinal tract of broilers. J Anim Physiol Anim Nutr (Berl). 92: 471-480.
25
Saelinger CA, Lewbart GA, Christian LS, Lemons CL (2006). Prevalence of Salmonella spp in cloacal, faecal, and gastrointestinal mucosal samples from wild North American turtles. J Am Vet Med Assoc. 229: 266-268.
26
Salminen S, Bouley C, Boutron-Ruault MC, Cummings JH, Franck A, Gibson GR, Isolauri E, Moreau MC, Roberfroid M, Rowland I (1998). Functional food science and gastrointestinal physiology and function. Brit J Nutr. 80: S147-S171.
27
Sambrook J, Russell DW (2001). Molecular Cloning: a Laboratory Manual, 3rd ed, Cold Spring Harbor Laboratory Press, Cold Spring Harbor: NY.
28
Servin AL (2004). Antagonistic activities of lactobacilli and ifidobacteria against microbial pathogens. FEMS Microbiol Rev. 28: 405-440.
29
Shin MS, Han SK, Ji AR, Kim KS, Lee WK (2008). Isolation and characterization of bacteriocin-producing bacteria from the gastrointestinal tract of broiler chickens for probiotic use. J Appl Microbiol. 105: 2203-2212.
30
Tannock GW (2003). Probiotics: time for a dose of realism. Curr Issues Intest Microbiol. 4: 33-42.
31
Tierney J, Gowing H, Van Sinderen D, Flynn S, Stanley L, McHardy N, Hallahan S, Mulcahy G (2004). In vitro inhibition of Eimeria tenella invasion by indigenous chicken Lactobacillus species. Vet Parasitol. 122: 171-182.
32
Vicente JL, Torres-Rodriguez A, Higgins SE, Pixley C, Tellez G, Donoghue AM, Hargis BM (2008). Effect of a selected Lactobacillus spp-based probiotic on Salmonella entericaserovar enteritidis-infected broiler chicks. Avian Dis. 52: 143-146.
33
Waldenstedt L, Lundén A, Elwinger K, Thebo P, Uggla A (1999). Comparison between a live, attenuated anticoccidial vaccine and an anticoccidial ionophore, on performance of broilers raised with or without a growth promoter,in an initially Eimeria-free environment. ACTA Vet Scand. 40: 11-21.
34
Walter J (2008). Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol. 74: 4985-96.
35
Woo PC, Fung AM, Lau SK, Yuen KY (2002). Identification by 16S rRNA gene sequencing of Lactobacillus salivarius bacteremic cholecystitis. J Clin Microbiol. 40: 265-267.
36
ORIGINAL_ARTICLE
Effect of Whey Permeate and Yeast Extract on Metabolic Activity of Bifidobacterium Animalis Subsp. Lactis Bb 12
In fermented products containing Bifidobacteria, factors such as organic acid concentration and b-galactosidase activity are important in the development of flavor and texture of final products. Both the process conditions and medium components have significant effects on fluctuation of such factors. The effects of whey permeate powder and yeast extract concentrations, as nitrogen sources was investigated, on metabolic activity of Bifidobacterium animalis subsp. lactis Bb 12 in skim milk based media. Development of organic acids, growth rate and b-galactosidase activity under uncontrolled pH conditions was also monitored. Media with high concentrations of nitrogen sources showed maximum viable counts of B. animalis. The activity of b-galactosidase increased during the logarithmic phase and the initial stage of the stationary phase of growth and then decreased thereafter. Increasing the yeast extract concentration resulted in an increase in the specific sugar consumption rate with concomitant reduction in formation of acetic acid and formic acid. Consequently, the molar ratio of acetic acid to lactic acid was decreased. Using limited amounts of nitrogen sources resulted in more organic acid production in the tested microorganism. During the early hours of fermentation in which the amounts of nitrogen levels were limited, the specific rate of b-glactosidase activity was very high. Therefore, by evaluating the activity of this enzyme we can estimate the amount nutrient components in the medium.The production of succinic acid was observed during logarithmic and stationary phase in all fermentation media. Citric acid that naturally exists in whey and skim milk powder was consumed during the stationary phase of growth by B. animalis and its consumption correlated significantly with the production of succinic acid at this stage.
https://www.ijbiotech.com/article_7126_e9a89f520366ccd6b4aad0387fe6fbea.pdf
2010-01-01
38
45
Bifidobacterium
Nitrogen source
Metabolic activity
Hasan
Jalili
1
Departmant of Food Science, Technology and Engineering, Faculty of Agricultural Engineering and Technology, Agricultural Campus, University of Tehran, P.O. Box 4111, Karaj, I.R. Iran
AUTHOR
Hadi
Razavi
srazavi@ut.ac.ir
2
Departmant of Food Science, Technology and Engineering, Faculty of Agricultural Engineering and Technology, Agricultural Campus, University of Tehran, P.O. Box 4111, Karaj, I.R. Iran
LEAD_AUTHOR
Mohammad
Safari
3
Departmant of Food Science, Technology and Engineering, Faculty of Agricultural Engineering and Technology, Agricultural Campus, University of Tehran, P.O. Box 4111, Karaj, I.R. Iran
AUTHOR
ABU-Tarboush, AL-Dagal MM, AL-Royli MA (1998). Growth, viability, and proteolytic activity of Bifidobacteria in whole camel milk. J Dairy Sci. 81: 354-361.
1
Amrane A, Prigent Y (1998a). Influence of yeast extract concentration on batch cultures of Lactobacillus helveticus: growth and production coupling. World J Microbiol Biotechnol. 14: 529-534.
2
Amrane A, Prigent Y (1998b). Lactic acid production rates during the different growth phases of Lactobacillus helveticus cultivated on whey supplemented with yeast extract. Biotechnol letter 20: 379-383.
3
Astapovich NI, Ryabaya DNE (2006). Patterns of growth and b-galactosidase production by Bifidobacteria. Microbiology 75: 274-278.
4
Beal C, Corrieu G (1995). On-line indirect measurements of biological variables and their kinetics during pH controlled batch cultures of thermophilic lactic acid bacteria. J Food eng. 26: 511-525.
5
Buck LM, Gilliland SE (1994). Comparisons of freshly isolated strains of Lactobacillus acidophilus, of human intestinal origin for ability to assimilate, cholesterol during growth. J Dairy Sci. 77: 2925-292.
6
Dave RI, Shah NP (1998). Ingredient supplementation effects on viability of probiotic bacteria in yogurt. J Dairy Sci. 81: 2804-2816.
7
Desjardins ML, Roy D, Toupin C, Goulet J (1990). Uncoupling of growth and acids production in Bifidobacterium ssp. J Dairy Sci. 73: 1478-1484.
8
Doleyres Y, Fliss I, Lacroix C (2004). Increased stress tolerance of Bifidobacterium longum and Lactococcus lactis produced during continuous mixed-strain immobilized-cell fermentation. J Appl Microbiol. 97: 527-539.
9
Dudley EG, Steele JL (2005). Succinate production and citrate catabolism by Cheddar cheese nonstarter lactobacilli. J Appl Microbiol. 98: 14-23.
10
Dunne C, Shanahan F (2002). Role of probiotics in the treatment of intestinal infections and inflammation. Curr Opin Gastroenterol. 18: 40-45.
11
Gomes AMP, Malcata FX (1999). Bifidobacterium spp. and Lactobacillus acidophilus: biological, biochemical, technological and therapeutical properties relevant for use as probiotics. Trend Food Sci Technol. 10: 139-157.
12
Hsu CA, Yu RC, Chou CC (2005). Production of b-galactosidase by Bifidobacteria as influenced by various culture conditions. Int J Food Microbiol. 104: 197-206.
13
Ibrahim SA, Bezkorovainty A (1994). Growth-promoting factors for Bifidobacterium longum. J Food Sci. 59: 189-191.
14
Janer C, Arigoni F, Lee BH, Pelaez C, Requena T (2005). Enzymatic ability of Bifidobacterium animalis subsp. lactis to hydrolyze milk proteins: identification and characterization of endopeptidase O. Appl Env Microbiol. 71: 8460-8465.
15
Macfarlane GT, Macfarlane S (1997). Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria. Scan J Gastroenterol. 32: 3-9.
16
Madiedo PR, Hernandez-Barranco A, Margolles A, Reyes-Gavilan CGDL (2005). A bile salt-resistant derivative of Bifidobacterium animalis has an altered fermentation pattern when grown on glucose and maltose. Appl Env Microbiol. 71: 6564-6570.
17
Marisa SG, Aguirre L, Savoy Gdg (2006). Biological activity of Bifidobacterium longum in response to environmental pH. Appl Microbiol Biotechnol. 70: 612-617.
18
Meulen, RVD, Makras L, Verbrugghe K, Adriany T, Vuyst LD (2006). In vitro kinetic analysis of oligofructose consumption by Bacteroides and Bifidobacterium spp. Indicates different degradation mechanisms. Appl Env Microbiol. 72: 1006-1012.
19
Mlobeli NT, Gutierreza NA, Maddox S (1998). Physiology and kinetics of Bifidobacterium bifidum during growth on different sugars. Appl Microbiol Biotechnol. 50: 125-128.
20
Neves A , Pool AW, Kok J, Kuipers OP, Santos H (2005). Overview on sugar metabolism and its control in Lactococcus lactis-The input from in vivo NMR. FEMS Microbiol Reviews. 29: 531-554.
21
Østile MH, Treimo j, Narvhus JA (2005). Effect of temperature on growth and metabolism of probiotic bacteria in milk. Int Dairy J. 15: 989-997.
22
Schmidt G, Zink R (2000). Basic features of the stress response in three species of bifidobacteria: B. longum, B. adolescentis, and B. breve. Int J Food Microbiol. 55: 41-45.
23
Hekmat S, Macmahon DJ (1992). Survival of lactobacillus acidophilus and bifidobacterium bifidum in ice cream for use as a probiotic food. J Dairy Sci. 75: 1415-1422.
24
Taniguchi M, KO N, Kobayashi T (1987). High concentration cultivation of Bifidobacterium longum in fermenter with cross-flow filtration. Appl Microbiol Biotechnol. 25: 438-444.
25
Tormo M, Izco JM (2004). Alternative reversed-phase high-performance liquid chromatography method to analyses organic acids in dairy products. J Chromatography A. 1033: 305-310.
26
Vasiljevic T, Jelen P (2002). Drying and storage of crude b-galactosidase extracts from Lactobacillus delbrueckii ssp. bulgaricus 11842. Inno Food Sci Emerg Technol. 3: 175-184.
27
Wang-june K, Seong-kwan C (1995). Culture conditions and growth characteristics of Bifidobacterium longum. J Microbiol Biotechnol. 5: 351-357.
28
Wolin M, Zhang YC, Bank S, Yerry S, Miller TL (1998). NMR detection of 3CH313COOH from 3- 13C-glucose: a signature for Bifidobacterium fermentation in the intestinal tract. J Nutr. 128: 91-96.
29
ORIGINAL_ARTICLE
Molecular Detection of Lipase A gene in Putative Bacillus subtilis Strains Isolated from Soil
The present study was undertaken to screen the soil samples collected in Iran for the presence of the Bacillus subtilis lipase A gene. The bacterial colonies obtained from the collected soil samples were examined by physical appearance, biochemical tests and the polymerase chain reaction (PCR). Only four colonies were identified as putative B. subtilis strains and all contained the lipase A gene. However, the intensities of the DNA bands were different and correlated with the differences obtained from the biochemical tests. Polymorphism of the lipase gene was also determined in samples using SSCP assay. In conclusion, this study demonstrates an easy and reliable method for detection of the lipase gene in B. subtilis strains. Further screening of the soil by this method will enable the detection and identification of industrially more favorable lipases.
https://www.ijbiotech.com/article_7095_8b3deb50385951db5f5b4d31665798ce.pdf
2010-01-01
46
49
Lipase A gene
PCR
Bacillus subtilis
Soil
Detection
Hamid
Mir Mohammad Sadeghi
h_sadeghi@pharm.mui.ac.ir
1
Department of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
and
Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
LEAD_AUTHOR
Mohammad
Rabbani
2
Department of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
AUTHOR
Fatemeh
Moazen
3
Department of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
AUTHOR
Sareh
Homami
4
Department of Biotechnology and Isfahan Pharmaceutical Research Center, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
AUTHOR
Acharya P, Rajakumar AE, Sankaranarayanan R, RaomNM (2004). Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. J Mol Biol. 341: 1271-1281.
1
Brockerhoff H and Jensen RG (1974). Lipolytic Enzymes. Academic Press, New York.
2
Dorge MJ, Ruggeberg CJ, Van der Sloot AM, Schimmel J, Dijkstra DS, Verhaert RM, Reetz MT, Quax WJ (2003). Binding of phage displayed Bacillus subtilis lipase A to a phosphonate suicide inhibitor, J Biotechnol. 101: 19-28.
3
Gupta R, Gupta N, Rathi P (2004). Bacterial lipases: an overview of production, purification and biochemical properties. Appl Microbiol Biotechnol. 64: 763-781.
4
Jaeger KE, Dijkstra BW, Reetz MT (1999). Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu Rev Microbiol. 53: 315-351.
5
Mc Fadden JF (2000). Biochemical tests for identification of medical bacteria. 3rd ed. Philadelphia: Lippincott, Williams, and Wilkins ed. PP. 45-53.
6
Masayama A, Kuwana R, Takamatsu H, Hemmi H, Yoshimura T, Watabe K, Moriyama R (2007). A novel lipolytic enzyme, YcsK (lipC), located in the spore coat of Bacillus subtilis, is involved in spore germination. J Bacteriol. 189: 2369-2375.
7
Mir Mohammad Sadeghi H, Jahanian NA, Abedi D, Jafarian DA (2008). Identification of an isolate of Pseudomonas aeroginosa deposited in PTCC as a PHA producer strain: Comparison of three different bacterial genomic DNA extraction methods. J Biol Sci. 8: 826-830.
8
Pinchuk IV, Bressolier P, Sorokulova IB, Verneuil B, Urdaci MC (2002). Amicoumacin antibiotic production and genetic diversity of Bacillus subtilis strains isolated from different habitats. Res Microbil. 153: 269-276.
9
Reetz MT, Carballeira JD (2007). Iterative saturation mutagenesis (ISM) for rapid directed evolution of enzymes. Nat protoc. 2: 891-903.
10
Ruiz C, Pastor FI, Diaz P (2005). Isolation of lipid- and polysaccharide-degrading micro-organisms from subtropical forest soil, and analysis of lipolytic strain Bacillus sp. CR-179. Lett Appl Microbiol, February 2005, vol. 40, no. 3, p.218-227 351.
11
Sambrook J, Russell DV (2001). Molecular cloning, a laboratory manual. 3rd ed. Cold Spring Harbor Laboratory Press. PP. A9.6- A9.7.
12
ORIGINAL_ARTICLE
Comparison of Four Different Purification Methods for Isolation of Anti Echis carinatus Antivenom Antibodies from Immunized Chicken Egg Yolk
Egg-laying hens were immunized with the Echis carinatus venom and the resulting antibodies were extracted from egg yolk by four different purification methods. The chicken egg yolk antibodies were purified by the water dilution method, polyethylene glycol (PEG) and ammonium sulphate precipitation method, chloroform extraction and the Lithium sulphate precipitation method. These methods were compared in terms of total protein content, immunospecific anti E. carinatus immunoglobulin Y (IgY) activity and in vitro and in vivo neutralizing capacity of IgY against the E. carinatus venom. Total IgY concentrations varied from 1.6 to 7.0 mg per ml of egg yolk. In neutralization studies, IgY purified by PEG and ammonium sulphate precipitation (PEG-AS) showed better results when compared to other purification methods. Approximately 1.25 mg of IgY (PEG-AS) was able to neutralize 2Lethal Dose50 of the E. carinatus venom. Purification of IgY by PEG and ammonium sulphate yielded very pure IgY at high quantities (93% ± 5% of total egg yolk protein), which was also capable of neutralizing toxic and lethal components of the E. carinatus venom.
https://www.ijbiotech.com/article_7102_05037eab02bdb81853d24dba459f3a52.pdf
2010-01-01
50
55
Venom
IgY
Lethality
Haemorrhagic
PLA2
Subramani
Meenatchisundaram
drmscbe@gmail.com
1
Department of Microbiology, Nehru Arts and Science College, Coimbatore, India
LEAD_AUTHOR
Antonysamy
Michael
2
Department of Microbiology, PSG College of Arts and Science, Coimbatore, India
AUTHOR
Akita EM, Nakai S (1992). Immunoglobulins from egg yolk: Isolation and Purification. J Food Sci. 57: 629-634.
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ORIGINAL_ARTICLE
Investigation of Culture Conditions for Biosynthesis of Silver Nanoparticles Using Aspergillus fumigatus
In this study, silver nanoparticles were synthesized using the fungus, Aspergillus fumigatus. The effects of three independent variables including glucose content of culture media, initial pH and initial spore concentration on biosynthesis of silver nanoparticles were investigated. These variables affect cell morphology, cell mass, size and morphology of silver nanoparticles and degree of silver ion reduction. The formation of silver nanoparticles was confirmed spectrophotomterically. Size and morphology of silver nanoparticles were investigated using transmission electron microscopy (TEM). The effects of culture conditions on cell mass concentration as well as the amount and size of synthesized silver nanoparticles were studied. As a result, the optimum culture condition for biosynthesis of silver nanoparticles consisted of a glucose concentration of 16 g/l, pH of 4.5 and spore concentration of 1.5×107 spore/l. TEM micrographs showed that the size of nanoparticles in the sample synthesized under optimized condition was in the range of 7-19 nm.
https://www.ijbiotech.com/article_7105_c3fbcec8c7fea14e26734b0255cb32c9.pdf
2010-01-01
56
61
Silver nanoparticles
Biosynthesis
Aspergillus fumigatus
Culture conditions
Zahra
Ranjbar Navazi
1
Environmental Group, Department of Energy, Materials and Energy Research Center, Karaj, I.R. Iran
AUTHOR
Mohammad
Pazouki
mpazouki@merc.ac.ir, mpaz6@yahoo.com
2
Environmental Group, Department of Energy, Materials and Energy Research Center, Karaj, I.R. Iran
LEAD_AUTHOR
Farah Sadat
Halek
3
Environmental Group, Department of Energy, Materials and Energy Research Center, Karaj, I.R. Iran
AUTHOR
Ahmad A, Senapati S, Khan MI, Kumar R, Sastry M (2003). Extracellular biosynthesis of monodispersed gold nanoparticles by a novel extermophillic actinomycete, Thermonospora sp. Langmuir 19: 3550-3553.
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