Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 Isolation of Lactobacillus acidophilus from Sharbabk city yoghurt and its molecular characterization Isolation of Lactobacillus acidophilus from Sharbabk city yoghurt and its molecular characterization 1 12 366 10.22103/jab.2012.366 FA Moeen Izadi Mohammad Hassan Fooladi GHolamreza SHarifi Sirchi Javid Amini Journal Article 2012 11 12 Lactobacillus acidophilus bacterium is one of the most useful specieses of lactobacillus genus, which can be seen as a probiotic microorganism in dairy products like yoghourt, milk and some portions of mammal digestive systems like human intestine. The bacterium is positive gram and negative catalaze, and has the best growth in 37 °C during 72 hours in microaerophil condition. In this research, local strains of Lactobacillus acidophilus are dissected from 20 yoghourt samples of Shahr babak city of kerman. In order to identify this bacterium from non-molecular methods including growth study in different degrees, studying of sensitivity or resistance to antibiotic disks and surveying growth behavior regarding to carbohydrate fermentation, As well as molecular methods partial 16S rRNA gene sequencing were used. Using these examinations, 12 isolates of Lactobacillus acidophilus were extracted, where coincidanced with the positive samples noted in the bergey´s manual of systematic bacteriology. This is the first state report for isolation of Lactobacillus acidophilus isolates for local yoghourt of Shahr babak city of kerman. Lactobacillus acidophilus bacterium is one of the most useful specieses of lactobacillus genus, which can be seen as a probiotic microorganism in dairy products like yoghourt, milk and some portions of mammal digestive systems like human intestine. The bacterium is positive gram and negative catalaze, and has the best growth in 37 °C during 72 hours in microaerophil condition. In this research, local strains of Lactobacillus acidophilus are dissected from 20 yoghourt samples of Shahr babak city of kerman. In order to identify this bacterium from non-molecular methods including growth study in different degrees, studying of sensitivity or resistance to antibiotic disks and surveying growth behavior regarding to carbohydrate fermentation, As well as molecular methods partial 16S rRNA gene sequencing were used. Using these examinations, 12 isolates of Lactobacillus acidophilus were extracted, where coincidanced with the positive samples noted in the bergey´s manual of systematic bacteriology. This is the first state report for isolation of Lactobacillus acidophilus isolates for local yoghourt of Shahr babak city of kerman.

https://jab.uk.ac.ir/article_366_e8250e482fad322c5dbbc0d0ba45ec8a.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 Phytases: enzymology, molecular and biochemical characteristic and applications Phytases: enzymology, molecular and biochemical characteristic and applications 13 40 367 10.22103/jab.2012.367 FA Mohammadreza Sarikhani Mohammad Ali Malboobi Journal Article 2012 02 08 Phytases are a special class of phosphatses that catalyze the step-wise release of phosphate from phytate, the principle storage form of phosphate in plant seeds. These enzymes have a wide distribution in plants, microorganisms and in some animal tissues; however, microbial sources are more promising for the production. They are added to animal feedstuff to reduce phosphate pollution in the environment, since monogastric animals such as pigs, poultry and fish are unable to metabolize phytate. The first commercial phytase product became available on the market around 20 years ago. Based on biochemical properties and amino acid sequence alignment, phytases can be categorized into four major classes, histidine acid phosphatase, b-propller phytase, cystein phosphatase and purpule acid phosphatase. In general, phytases behave like a monomeric enzyme with molecular masses between 40 and 100 kDa. Up to now two main types of phytases have been identified based on optimal pH for activity; acid phytases with a pH optimum around 5 and alkaline phytases with a pH optimum around 8. Most of identified phytases depending upon the source of origin they have generally pH and temperature optima around 4.5-6 and 45-60 °C .Some of phytases show broad substrate specificity and hydrolyzes metal-free phytate, in contrast some of them exhibit strict substrate specificity for the calcium-phytate. Phytases are different according to the number of released phosphate groups from phytate and in general they have capability to release 3 to 5 phosphate groups. This article reviews enzymology, application and biochemical and catalytic characteristic of microbial phytases. Phytases are a special class of phosphatses that catalyze the step-wise release of phosphate from phytate, the principle storage form of phosphate in plant seeds. These enzymes have a wide distribution in plants, microorganisms and in some animal tissues; however, microbial sources are more promising for the production. They are added to animal feedstuff to reduce phosphate pollution in the environment, since monogastric animals such as pigs, poultry and fish are unable to metabolize phytate. The first commercial phytase product became available on the market around 20 years ago. Based on biochemical properties and amino acid sequence alignment, phytases can be categorized into four major classes, histidine acid phosphatase, b-propller phytase, cystein phosphatase and purpule acid phosphatase. In general, phytases behave like a monomeric enzyme with molecular masses between 40 and 100 kDa. Up to now two main types of phytases have been identified based on optimal pH for activity; acid phytases with a pH optimum around 5 and alkaline phytases with a pH optimum around 8. Most of identified phytases depending upon the source of origin they have generally pH and temperature optima around 4.5-6 and 45-60 °C .Some of phytases show broad substrate specificity and hydrolyzes metal-free phytate, in contrast some of them exhibit strict substrate specificity for the calcium-phytate. Phytases are different according to the number of released phosphate groups from phytate and in general they have capability to release 3 to 5 phosphate groups. This article reviews enzymology, application and biochemical and catalytic characteristic of microbial phytases.

https://jab.uk.ac.ir/article_367_bd7d68fd0a7491f96e9f1f55784f7fb6.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 DNA polymorphism among mycelial compatibility groups of Sclerotinia sclerotiorum using ISSR marker DNA polymorphism among mycelial compatibility groups of Sclerotinia sclerotiorum using ISSR marker 41 55 368 10.22103/jab.2012.368 FA Elham Karimi Nasser Safaie Masoud Shamsbakhsh Journal Article 2010 05 02 To assess the genetic structure of 38 Sclerotinia sclerotiorum isolates, representing 38 MCGs (Mycelial Comatibility Groups), collected from canola fields in Golestan, Mazandaran and Western Azarbaijan provinces, ISSR marker were used. Six out of 19 ISSR primers were reproducible and could amplify 2124 bands ranging in size from approximately 120 bp to 3800 bp. ISSR09, ISSr10 and P1 primers had discriminatory power and marker index more than the others, indicating the efficiency of these three primers in discriminating of isolates. ISSR markers could differentiate 38 isolates into 36 genotypes, suggesting in S. sclerotiorum populations each MCG is genetically different from others. To assess the genetic structure of 38 Sclerotinia sclerotiorum isolates, representing 38 MCGs (Mycelial Comatibility Groups), collected from canola fields in Golestan, Mazandaran and Western Azarbaijan provinces, ISSR marker were used. Six out of 19 ISSR primers were reproducible and could amplify 2124 bands ranging in size from approximately 120 bp to 3800 bp. ISSR09, ISSr10 and P1 primers had discriminatory power and marker index more than the others, indicating the efficiency of these three primers in discriminating of isolates. ISSR markers could differentiate 38 isolates into 36 genotypes, suggesting in S. sclerotiorum populations each MCG is genetically different from others.

https://jab.uk.ac.ir/article_368_9c84f7b7af4301bbe006a9e128ffbcbc.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 Whole-genome scan of population differentiation in Zel and Lori-Bakhtiari sheep breeds Whole-genome scan of population differentiation in Zel and Lori-Bakhtiari sheep breeds 57 70 369 10.22103/jab.2012.369 FA Mohammad Hossein Moradi Ardeshir Nejati Mohammad Moradi Shahrbabak professor of Animal Science, Tehran University, Tehran, Iran 0000-0002-5255-609X Ken Dodds Senior scientists, Centre for Reproduction and Genomics, AgResearch, Invermay, New Zealand John McEwan Senior scientists, Centre for Reproduction and Genomics, AgResearch, Invermay, New Zealand. Journal Article 2011 11 26 Selection for increasing of frequency in new mutations that are advantageous only in a subset of populations leaves some signatures in the genome. Detecting these genomic regions is one of the most important areas of research in animal genetics since locations of selection signatures are often correlated with QTLs affecting economically important traits. In this paper, a whole genome scan using ~54000 SNP markers was performed in two main Iranian sheep breeds, namely Zel and Lori-Baktiari, with the aim of identifying divergently selected regions of the genome. Study of population differentiation across the genome using Weir and Cockerham’s FST test revealed some regions showing evidence of selection. In this paper, five regions which were in the 99.99 percentile of the genome distribution of FST scores were selected for further analysis. These regions were located in chromosomes 2, 5, 7 (two areas) and X. To evaluate the selection sweep, due to linkage disequilibrium, associated with these signatures we employed the Extended Haplotype Homozygosity (EHH) test. The results of this test as well as a study of haplotype bifurcation diagrams in these breeds also confirmed large allele differentiation in these regions. Finally, study of reported QTL regions in the orthologous areas of the cattle genome showed that they overlapped with the reported cattle QTLs, representing economically important traits such as carcass yield and reproductive traits. In conclusion, the results from this study provide one of the first attempts to develop a genome-wide map of selection footprints in the sheep genome and may facilitate the identification of genes affecting traits which are divergent in these two Iranian sheep breeds Selection for increasing of frequency in new mutations that are advantageous only in a subset of populations leaves some signatures in the genome. Detecting these genomic regions is one of the most important areas of research in animal genetics since locations of selection signatures are often correlated with QTLs affecting economically important traits. In this paper, a whole genome scan using ~54000 SNP markers was performed in two main Iranian sheep breeds, namely Zel and Lori-Baktiari, with the aim of identifying divergently selected regions of the genome. Study of population differentiation across the genome using Weir and Cockerham’s FST test revealed some regions showing evidence of selection. In this paper, five regions which were in the 99.99 percentile of the genome distribution of FST scores were selected for further analysis. These regions were located in chromosomes 2, 5, 7 (two areas) and X. To evaluate the selection sweep, due to linkage disequilibrium, associated with these signatures we employed the Extended Haplotype Homozygosity (EHH) test. The results of this test as well as a study of haplotype bifurcation diagrams in these breeds also confirmed large allele differentiation in these regions. Finally, study of reported QTL regions in the orthologous areas of the cattle genome showed that they overlapped with the reported cattle QTLs, representing economically important traits such as carcass yield and reproductive traits. In conclusion, the results from this study provide one of the first attempts to develop a genome-wide map of selection footprints in the sheep genome and may facilitate the identification of genes affecting traits which are divergent in these two Iranian sheep breeds

https://jab.uk.ac.ir/article_369_b309f0a5ffe84f6eb569553584ee7690.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 Analysis of ovine transferrin polymorphisms and their relationship with blood metabolite variation in Makoei sheep breed Analysis of ovine transferrin polymorphisms and their relationship with blood metabolite variation in Makoei sheep breed 71 82 370 10.22103/jab.2012.370 FA Hossein Moradi Amir Hossein KHellatabadi Farahani Mohammad Moradi Shahrbabak Hossein Mohammadi Journal Article 2011 04 09 In order to determine polymorphism of ovine transferrin and its association with blood metabolite in Makoei sheep, blood samples were collected from 576 male and female lambs using two types of Venoject (with or without EDTA). Plasma and serum were then separated and kept in -20₀C. Transferrin polymorphisms were determined by vertical electrophoresis of polyacrylamid gels. Results indicated a total of 24 genotypes involving the 10 alleles C, B, D, A, E, G, L, K, M and O, ordered on the basis of their frequencies. Among these the C allele was the most frequent (0.29) and the M allele was the rarest (0.004). Association of the transferrin polymorphisms with triglyceride and total protein blood was very significant (P<0.01). So that the AA genotype the most amount cholesterol and total protein blood and AQ genotype has the lowest amount cholesterol and total protein blood. But, there was no significant association between genotypes of various transferrin proteins with cholesterol and glucose blood. Further investigation should be on the molecular level of transferrin gene, using treatment samples. In order to determine polymorphism of ovine transferrin and its association with blood metabolite in Makoei sheep, blood samples were collected from 576 male and female lambs using two types of Venoject (with or without EDTA). Plasma and serum were then separated and kept in -20₀C. Transferrin polymorphisms were determined by vertical electrophoresis of polyacrylamid gels. Results indicated a total of 24 genotypes involving the 10 alleles C, B, D, A, E, G, L, K, M and O, ordered on the basis of their frequencies. Among these the C allele was the most frequent (0.29) and the M allele was the rarest (0.004). Association of the transferrin polymorphisms with triglyceride and total protein blood was very significant (P<0.01). So that the AA genotype the most amount cholesterol and total protein blood and AQ genotype has the lowest amount cholesterol and total protein blood. But, there was no significant association between genotypes of various transferrin proteins with cholesterol and glucose blood. Further investigation should be on the molecular level of transferrin gene, using treatment samples.

https://jab.uk.ac.ir/article_370_90688768d29137b7f6c11e32c183e680.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 Comparison of polymorphism of STAT5A gene in Simmental and Holstein cows Comparison of polymorphism of STAT5A gene in Simmental and Holstein cows 83 96 378 10.22103/jab.2012.378 FA Mojtaba Najafi GHodratallah Rahimi Masoud Babaee Zarbakht Ansari Journal Article 2011 01 10 Signal transducer and activator of transcription 5A(STAT5A) is a crucial signaling protein mediating the biological effects of prolactin hormone which in turn activates the transcription of milk proteins genes. In order to study the polymorphisms of STAT5A gene total blood samples were collected randomly from one hundred of Holstein and Simmental cattle. DNA was extracted using modified salting out method and polymerase chain reactions (PCR) were carried out using a specific primer pairs for amplification a fragment of 281 bp from part of exon 15 and intron 16 of STAT5A gene. All of individuals were genotyped by single stranded conformation polymorphism (SSCP) analyses using silver staining. Two SSCP patterns of A and B were identified with the frequency of 0.91 and 0.09 and 0.88 and 0.12 in Holstein and Simmental cattle, respectively. Two genotypes of AA (0.82) and AB (0.18) were found in Holstein and AA (0.76) and AB (0.24) in Simmental individuals. The results revealed that the marker site of STAT5A gene is polymorph in studied Holstein and Simmental cattle and the SSCP technique has a great potential for detection of such polymorphism. Furthermore, a comparison of gene and genotype frequencies showed no any statistical differences (P>0.05) between Holstein and Simmental cattle breed that have genotyped in the present study. Signal transducer and activator of transcription 5A(STAT5A) is a crucial signaling protein mediating the biological effects of prolactin hormone which in turn activates the transcription of milk proteins genes. In order to study the polymorphisms of STAT5A gene total blood samples were collected randomly from one hundred of Holstein and Simmental cattle. DNA was extracted using modified salting out method and polymerase chain reactions (PCR) were carried out using a specific primer pairs for amplification a fragment of 281 bp from part of exon 15 and intron 16 of STAT5A gene. All of individuals were genotyped by single stranded conformation polymorphism (SSCP) analyses using silver staining. Two SSCP patterns of A and B were identified with the frequency of 0.91 and 0.09 and 0.88 and 0.12 in Holstein and Simmental cattle, respectively. Two genotypes of AA (0.82) and AB (0.18) were found in Holstein and AA (0.76) and AB (0.24) in Simmental individuals. The results revealed that the marker site of STAT5A gene is polymorph in studied Holstein and Simmental cattle and the SSCP technique has a great potential for detection of such polymorphism. Furthermore, a comparison of gene and genotype frequencies showed no any statistical differences (P>0.05) between Holstein and Simmental cattle breed that have genotyped in the present study.

https://jab.uk.ac.ir/article_378_c5b6aeb943ec813bdd415401d0e2abfc.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 2 2 2010 11 22 The generating methods of transgenic chickens and its potential application in biotechnology The generating methods of transgenic chickens and its potential application in biotechnology 97 124 379 10.22103/jab.2012.379 FA Mohamadreza Nassiri Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, P. O. Box: 91775-1163, Iran Shahrokh Ghovvati Animal Science Department, Faculty of Agriculture, University of Guilan, Rasht, Iran Mohammadreza Mohammadabadi Department of Animal Science, Faculty of Agriculture, College of Agriculture, Shahid Bahonar University of Kerman Hamid Ariannezhad Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, P. O. Box: 91775-1163, Iran Ali Doosti Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, P. O. Box: 91775-1163, Iran Journal Article 2010 03 04 During the last decades, potential of genetic modifications at the molecular level has created great revolution in biology. Transgenic technology has provided the possibility of connection between different techniques in field of embryology, cellular biology and molecular genetics. Nowadays, transgenic chicken are used as efficient research tools in many institutions. So, many researchers believe that before any research in the field of genetic manipulation, these methods should be optimized. Regarding to the remarkable progress of biotechnology, direct manipulation of chicken embryo by DNA or viral vectors is possible but generally, using this methods can not create a specific site and target genes for genetic manipulation. To fix this problem, recently, many scientists have proposed and improved different methods to generate transgenic chickens based on Blastodermal cells (BDCs), Embryonic stem cells (ESCs), Primordial germ cells (PGCs) and Spermatogonial stem cells (SSCs). By the way, recently the complicated system for the isolation, expansion, transfection, selection and re-expansion embryonic stem cell cultures and the subsequent production of high-grade somatic chimeras was improved and their results were published in scientific papers. In recent years, the results of several studies have shown testicular culture method from spermatogonial somatic cells (SSCs) is the newest, easiest and most efficient method of transgenic chicken generation. This method has been used biological process of sperm production and SSCs as inducer in transgenic chicken. Although, use of the viral systems can be lead to gene transfer with high efficiency, but the safety issues limited its practical applications. Nowadays, the methods of chimeras germ cells production and pluripotent stem cells manipulation are combined and used to generate transgenic birds. This review has attempted to describe the most important methods of generating transgenic chickens, the methods of gene transfer and also the application of transgenic chickens as bioreactor in biology. During the last decades, potential of genetic modifications at the molecular level has created great revolution in biology. Transgenic technology has provided the possibility of connection between different techniques in field of embryology, cellular biology and molecular genetics. Nowadays, transgenic chicken are used as efficient research tools in many institutions. So, many researchers believe that before any research in the field of genetic manipulation, these methods should be optimized. Regarding to the remarkable progress of biotechnology, direct manipulation of chicken embryo by DNA or viral vectors is possible but generally, using this methods can not create a specific site and target genes for genetic manipulation. To fix this problem, recently, many scientists have proposed and improved different methods to generate transgenic chickens based on Blastodermal cells (BDCs), Embryonic stem cells (ESCs), Primordial germ cells (PGCs) and Spermatogonial stem cells (SSCs). By the way, recently the complicated system for the isolation, expansion, transfection, selection and re-expansion embryonic stem cell cultures and the subsequent production of high-grade somatic chimeras was improved and their results were published in scientific papers. In recent years, the results of several studies have shown testicular culture method from spermatogonial somatic cells (SSCs) is the newest, easiest and most efficient method of transgenic chicken generation. This method has been used biological process of sperm production and SSCs as inducer in transgenic chicken. Although, use of the viral systems can be lead to gene transfer with high efficiency, but the safety issues limited its practical applications. Nowadays, the methods of chimeras germ cells production and pluripotent stem cells manipulation are combined and used to generate transgenic birds. This review has attempted to describe the most important methods of generating transgenic chickens, the methods of gene transfer and also the application of transgenic chickens as bioreactor in biology.

https://jab.uk.ac.ir/article_379_c98192903815e3b1184df5ff6668c859.pdf