Growth hormone affects a lot of physiological processes and traits, such as metabolism, milk and meat production. Polymorphism at DNA level might affect gene function and consequently the trait. The aim of this study was to identify the variation in the growth hormone gene between and within species (cattle, sheep and goat). The results showed that all variations between species located at intronic region, whereas exon 3 didn’t have any species-specific genetic variations. There is no SNPs identified between the breeds of cattle, whereas the variation within breeds of sheep and goat located at an intronic and exonic region.
{"title":"INTER AND INTRASPECIFIC COMPARATIVE ANALYSIS OF GROWTH HORMONE GENE FOR SOME FARM RUMINANT SPECIES","authors":"M. Rashed, A. Kadry, D. Aboul-Seoud, F. Sharara","doi":"10.21608/EJGC.2016.9584","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9584","url":null,"abstract":"Growth hormone affects a lot of physiological processes and traits, such as metabolism, milk and meat production. Polymorphism at DNA level might affect gene function and consequently the trait. The aim of this study was to identify the variation in the growth hormone gene between and within species (cattle, sheep and goat). The results showed that all variations between species located at intronic region, whereas exon 3 didn’t have any species-specific genetic variations. There is no SNPs identified between the breeds of cattle, whereas the variation within breeds of sheep and goat located at an intronic and exonic region.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"27 1","pages":"323-331"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Heba Abdel-Azyem, Amal M. Abdel-Aziz, R. Elbaz, A. Eldesoky, Wael S. Abdel-Mageed
Polymorphisms in cytokine genes responsible for inflammatory and immune responses are associated with risk of hepatocellular carcinoma (HCC) in Egyptian population. HCC study had conducted on 75 HCC patients and 75 matched control subjects of Egyptian population. Genetic variants in the IL-101082, TNF-α308 and IL-1β511 genes were analyzed by SNP. The logistic regression method was used to analyze the data, relative to the putative high-activity genotypes; individual low-activity genotypes were associated with statistically non-significant increases in HCC risk. The genotypic frequencies in the cases were not similar to that of the controls, TNF-α308 differences being statistically significant (P = 0.001). Using the GG genotype as the reference genotype, AA was significantly associated with increased risk of HCC (adjusted OR = 7.034, 95% CI, 2 = 54.399). Furthermore, we found A allele was significantly associated with increased risk of HCC, compared with G allele (2 = 53.034, OR-95% CI = 0.134 - 7.469). No such significant difference was found for cytokines (IL-1β and IL-10). Conclusion: Our study showed that TNF-α−308 G > A polymorphism was associated with increased HCC risk in Egypt population
{"title":"SINGLE NUCLEOTIDE POLYMORPHISM IN CYTOKINES AND RISK OF HEPATOCELLULAR CARCINOMA IN EGYPTIAN PATIENTS","authors":"Heba Abdel-Azyem, Amal M. Abdel-Aziz, R. Elbaz, A. Eldesoky, Wael S. Abdel-Mageed","doi":"10.21608/EJGC.2016.9579","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9579","url":null,"abstract":"Polymorphisms in cytokine genes responsible for inflammatory and immune responses are associated with risk of hepatocellular carcinoma (HCC) in Egyptian population. HCC study had conducted on 75 HCC patients and 75 matched control subjects of Egyptian population. Genetic variants in the IL-101082, TNF-α308 and IL-1β511 genes were analyzed by SNP. The logistic regression method was used to analyze the data, relative to the putative high-activity genotypes; individual low-activity genotypes were associated with statistically non-significant increases in HCC risk. The genotypic frequencies in the cases were not similar to that of the controls, TNF-α308 differences being statistically significant (P = 0.001). Using the GG genotype as the reference genotype, AA was significantly associated with increased risk of HCC (adjusted OR = 7.034, 95% CI, 2 = 54.399). Furthermore, we found A allele was significantly associated with increased risk of HCC, compared with G allele (2 = 53.034, OR-95% CI = 0.134 - 7.469). No such significant difference was found for cytokines (IL-1β and IL-10). Conclusion: Our study showed that TNF-α−308 G > A polymorphism was associated with increased HCC risk in Egypt population","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"245-259"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samah M. M. Eldemery, K. Abdellatif, E. A. El-Absawy, H. Emara, W. E. Rodeny, A. M. Zakaria
Twenty five faba bean (Vicia faba L.) genotypes were evaluated under broomrape (Orobanche crenata L.) natural infestation conditions for their growth and yield characteristics as well as the gene expression of some tolerance genes. Analysis of variance of the morphological traits revealed highly significant differences among the genotypes for all the morphological traits. The results of some yield related traits such as number of pods/plant, number of seeds/pod and number of seeds/plant were significantly increased in the Egyptian broomrape-tolerant genotypes “Giza843”, “Misr1” and “Misr3” and in the foreign genotype “FAB476”. On the other hand, “Nubaria1” genotype was worst genotype to defeat broomrape growth in which the highest number of O. crenata spikes/row and O. crenata spikes/plant was obtained (broomrape-susceptible genotypes). Cluster analysis of yield related traits distingweshed between broomrape tolerant and susceptible genotypes as well as between Egyptian and foreigner genotypes. Gene expression was assessed using Reverse Transcriptase PCR (RT-PCR) to study genes transcript accumulation during early (35 days) and late stages (50 days) of infestation. RT-PCR results revealed a kind of coexpression in common defense genes such as (HMG gene) and broomrape specific defense genes such as (C4H gene) in the most tolerant genotype “Misr1”. It is possible to conclude that yield related traits and the molecular results revealed that faba bean cultivar “Misr1” was the most broomrape tolerant cultivar and “Nubaria1” was the broomrape susceptible cultivar.
{"title":"GENE EXPRESSION INDUCED IN FABA BEAN (Vicia faba L.) BY Orobanche crenata AND ITS IMPACT ON THE FIELD LEVEL","authors":"Samah M. M. Eldemery, K. Abdellatif, E. A. El-Absawy, H. Emara, W. E. Rodeny, A. M. Zakaria","doi":"10.21608/EJGC.2016.9581","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9581","url":null,"abstract":"Twenty five faba bean (Vicia faba L.) genotypes were evaluated under broomrape (Orobanche crenata L.) natural infestation conditions for their growth and yield characteristics as well as the gene expression of some tolerance genes. Analysis of variance of the morphological traits revealed highly significant differences among the genotypes for all the morphological traits. The results of some yield related traits such as number of pods/plant, number of seeds/pod and number of seeds/plant were significantly increased in the Egyptian broomrape-tolerant genotypes “Giza843”, “Misr1” and “Misr3” and in the foreign genotype “FAB476”. On the other hand, “Nubaria1” genotype was worst genotype to defeat broomrape growth in which the highest number of O. crenata spikes/row and O. crenata spikes/plant was obtained (broomrape-susceptible genotypes). Cluster analysis of yield related traits distingweshed between broomrape tolerant and susceptible genotypes as well as between Egyptian and foreigner genotypes. Gene expression was assessed using Reverse Transcriptase PCR (RT-PCR) to study genes transcript accumulation during early (35 days) and late stages (50 days) of infestation. RT-PCR results revealed a kind of coexpression in common defense genes such as (HMG gene) and broomrape specific defense genes such as (C4H gene) in the most tolerant genotype “Misr1”. It is possible to conclude that yield related traits and the molecular results revealed that faba bean cultivar “Misr1” was the most broomrape tolerant cultivar and “Nubaria1” was the broomrape susceptible cultivar.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"279-295"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The NADPH-Thioredoxin System (NTS) and NADPH Glutathione System (NGS) are the two major thiol reduction systems that play a key role in the maintenance of cellular redox homeostasis and several plant developmental processes. Crosstalk between these two thiol reduction systems has been studied by associating TRX reductase (ntra ntrb) and glutathione biosynthesis (cad2) mutations. Triple ntra ntrb cad2 mutant revealed a new phenotype related to flower meristem development. Unfortunately, this mutant is unfertile and therefore it cannot be maintained at a homozygous stage. In this study, we used the RNAi technique to obtain close similar phenotype to this mutant, but that are fertile. RNAi strategy is performed by down-regulating the expression of both NTR genes by introducing RNAi construct harbouring two head-to-tail copies of the NTRA gene in the genetic background of the cad2 mutant. The transformed plants obtained exhibit attenuated phenotypes compared to the ntra ntrb cad2 mutant. Remarkably, no plants exhibit the characteristic pin-like phenotype of the ntra ntrb cad2 mutant was obtained. However, some plants looks fertile but show a decrease of the apical dominance. Others are more affected and show unfertile flowers. Our data show that the RNAi strategy is an efficient strategy to generate fertile plants with down-regulated NTS and NGS reduction systems and to investigate the crosstalk between these two thiol systems.
{"title":"DOWN-REGULATION OF NTR GENES BY RNAi IN THE cad2 MU-TANT IMPAIRS PLANT DEVELOPMENT OF Arabidopsis thaliana","authors":"T. Bashandy, J. Reichheld","doi":"10.21608/EJGC.2016.9578","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9578","url":null,"abstract":"The NADPH-Thioredoxin System (NTS) and NADPH Glutathione System (NGS) are the two major thiol reduction systems that play a key role in the maintenance of cellular redox homeostasis and several plant developmental processes. Crosstalk between these two thiol reduction systems has been studied by associating TRX reductase (ntra ntrb) and glutathione biosynthesis (cad2) mutations. Triple ntra ntrb cad2 mutant revealed a new phenotype related to flower meristem development. Unfortunately, this mutant is unfertile and therefore it cannot be maintained at a homozygous stage. In this study, we used the RNAi technique to obtain close similar phenotype to this mutant, but that are fertile. RNAi strategy is performed by down-regulating the expression of both NTR genes by introducing RNAi construct harbouring two head-to-tail copies of the NTRA gene in the genetic background of the cad2 mutant. The transformed plants obtained exhibit attenuated phenotypes compared to the ntra ntrb cad2 mutant. Remarkably, no plants exhibit the characteristic pin-like phenotype of the ntra ntrb cad2 mutant was obtained. However, some plants looks fertile but show a decrease of the apical dominance. Others are more affected and show unfertile flowers. Our data show that the RNAi strategy is an efficient strategy to generate fertile plants with down-regulated NTS and NGS reduction systems and to investigate the crosstalk between these two thiol systems.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"235-244"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Rashed, M. Swelim, S. H. Abdel-Aziz, I. M. Elkalamawy
This study presented important data about the gap between serology screening (surface antigen) and nucleic acid testing (NAT) testing of blood donors. Effectiveness of NAT for blood donors screening is a debating area in blood transfusion. This study highlight on the riskiness of transfuse blood contain integrated HBV DNA owing to the carcinogenic effect of integrated HBV in human liver. Wide-national study is required to ensure blood transfusion safety and effectiveness by using traditional (surface antigen, core antigen as a serological test) confirmed by NAT testing to screen blood donors and introduce new techniques for the detection of viral integrated with the human genome.
{"title":"PREVALENCE OF INTEGRATED HBV DNA AMONG BLOOD DONORS IN EGYPT","authors":"M. Rashed, M. Swelim, S. H. Abdel-Aziz, I. M. Elkalamawy","doi":"10.21608/EJGC.2016.9576","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9576","url":null,"abstract":"This study presented important data about the gap between serology screening (surface antigen) and nucleic acid testing (NAT) testing of blood donors. Effectiveness of NAT for blood donors screening is a debating area in blood transfusion. This study highlight on the riskiness of transfuse blood contain integrated HBV DNA owing to the carcinogenic effect of integrated HBV in human liver. Wide-national study is required to ensure blood transfusion safety and effectiveness by using traditional (surface antigen, core antigen as a serological test) confirmed by NAT testing to screen blood donors and introduce new techniques for the detection of viral integrated with the human genome.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"205-213"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ability to improve productivity and agronomic traits of sweetpotato through breeding programs depends on assessing the genetic variation of their germplasm and genetic relationship to other genotypes. In addition, studying genetic diversity supports the conservation of genetic resources. In this study, three different DNA-based markers, random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and selective amplification of microsatellite polymorphic loci (SAMPL) were used for fingerprinting and detecting genetic variation for ten germplasm of sweetpotato. Results indicated that RAPD assays using 18 primers produced 213 bands, 145 of which were polymorphic with a percentage of 68.1%. AFLP using five primers yielded 344 amplified products with a percentage of 71.8% polymorphism. SAMPL using two primers combinations amplified 132 bands in which 85 being polymorphic representing 64.4%. Genetic relationship was estimated using Dice’s coefficient values between different accessions, ranging from 0.655 to 0.939 in RAPD, 0.749 to 0.936 in AFLP, and 0.742 to 0.928 for SAMPL. The UPGMA algorithm was used for grouping all germplasm based on their genetic distances. In total, the three molecular marker systems were compared on the basis of multiplex ratio, marker index and average heterozygosity and revealed that AFLP was the bestsuited molecular assay for fingerprinting and assessing genetic relationships. All analysis confirmed the relatively high genetic diversity present in sweetpotato germplasm used. Also, distinct DNA fingerprinting profile could be obtained with all the three molecular marker systems. These results clearly indicate the usefulness of DNA fingerprinting for the identification of sweetpotato germplasm, and their potentiality to eliminate accessions duplicates from gene banks around the world.
{"title":"FINGERPRINTING OF SWEETPOTATO GERMPLASM USING AFLP, RAPD, AND SAMPL ANALYSIS","authors":"Amina A. Mohamed, Mervat M. M. El Far, M. Saad","doi":"10.21608/EJGC.2016.9591","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9591","url":null,"abstract":"The ability to improve productivity and agronomic traits of sweetpotato through breeding programs depends on assessing the genetic variation of their germplasm and genetic relationship to other genotypes. In addition, studying genetic diversity supports the conservation of genetic resources. In this study, three different DNA-based markers, random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and selective amplification of microsatellite polymorphic loci (SAMPL) were used for fingerprinting and detecting genetic variation for ten germplasm of sweetpotato. Results indicated that RAPD assays using 18 primers produced 213 bands, 145 of which were polymorphic with a percentage of 68.1%. AFLP using five primers yielded 344 amplified products with a percentage of 71.8% polymorphism. SAMPL using two primers combinations amplified 132 bands in which 85 being polymorphic representing 64.4%. Genetic relationship was estimated using Dice’s coefficient values between different accessions, ranging from 0.655 to 0.939 in RAPD, 0.749 to 0.936 in AFLP, and 0.742 to 0.928 for SAMPL. The UPGMA algorithm was used for grouping all germplasm based on their genetic distances. In total, the three molecular marker systems were compared on the basis of multiplex ratio, marker index and average heterozygosity and revealed that AFLP was the bestsuited molecular assay for fingerprinting and assessing genetic relationships. All analysis confirmed the relatively high genetic diversity present in sweetpotato germplasm used. Also, distinct DNA fingerprinting profile could be obtained with all the three molecular marker systems. These results clearly indicate the usefulness of DNA fingerprinting for the identification of sweetpotato germplasm, and their potentiality to eliminate accessions duplicates from gene banks around the world.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"383-401"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68481042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Screening experiment was performed on twelve genotypes of bread wheat (Ttriticum aestivum L.) to select the most stem rust resistant genotype (Misr1) and the most stem rust susceptible genotypes (Line 37 and Line 92) according to stem rust reaction. Crosses were carried out between the resistant parent (Misr1) with each of the susceptible parents as well as between the two susceptible parents (Line 37 and Line 92) to obtain the F1 kernels. Some of the F1 kernels were sown in the field and selfed to obtain the F2 kernels for each cross. These three selected parents, their F1 and the most resistant and susceptible F2 plant groups for the three crosses were evaluated for their response to stem rust resistance by recording some stem rust–related traits. However, infected condition caused a reduction in the values of all traits except spike length and number of spikelets per spike traits. The three parents, their F1 plants and some individual plants of the two contrasting F2 plant groups (the most resistant and the most susceptible F2 groups) for the three crosses were used to develop some molecular genetic markers associated with stem rust resistance using SSR and STS markers. The results indicated the presence of two positive markers out of the three SSR and three STS primers which used in this study. Sr2 (SSR) and Sr25 (STS) primers gave positive markers at fragment sizes of 120 and 130 bp, respectively, for stem rust resistance that could be considered as reliable markers for stem rust resistance in bread wheat (Ttriticum aestivum L.).
{"title":"DEVELOPMENT OF SSR STS MOLECULAR MARKERS ASSO-CIATED WITH STEM RUST RESISTANCE IN BREAD WHEAT (Triticum aestivum L.)","authors":"M. Rashed, A. Atta, T. S. El-din, A. Mostafa","doi":"10.21608/EJGC.2016.9580","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9580","url":null,"abstract":"Screening experiment was performed on twelve genotypes of bread wheat (Ttriticum aestivum L.) to select the most stem rust resistant genotype (Misr1) and the most stem rust susceptible genotypes (Line 37 and Line 92) according to stem rust reaction. Crosses were carried out between the resistant parent (Misr1) with each of the susceptible parents as well as between the two susceptible parents (Line 37 and Line 92) to obtain the F1 kernels. Some of the F1 kernels were sown in the field and selfed to obtain the F2 kernels for each cross. These three selected parents, their F1 and the most resistant and susceptible F2 plant groups for the three crosses were evaluated for their response to stem rust resistance by recording some stem rust–related traits. However, infected condition caused a reduction in the values of all traits except spike length and number of spikelets per spike traits. The three parents, their F1 plants and some individual plants of the two contrasting F2 plant groups (the most resistant and the most susceptible F2 groups) for the three crosses were used to develop some molecular genetic markers associated with stem rust resistance using SSR and STS markers. The results indicated the presence of two positive markers out of the three SSR and three STS primers which used in this study. Sr2 (SSR) and Sr25 (STS) primers gave positive markers at fragment sizes of 120 and 130 bp, respectively, for stem rust resistance that could be considered as reliable markers for stem rust resistance in bread wheat (Ttriticum aestivum L.).","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"261-278"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The diversity of Oreochromis niloticus gut microbiome domains, eukaryotes, bacteria and archaea, was studied to understand the contribution of microbiota to the health of the fish. Fishes were collected from four different Khors, Kalabsha, Wadi Abyad, Tushka and Korosko, of Lake Nasser, Egypt. The approach of this study depends on culture-independent PCR/DGGE and sequence of small subunit of rRNA genes, 18S rRNA gene and 16S rRNA gene. The DGGE patterns displayed 5, 12 and 5 band groups, phylotypes, for eukaryotic 18S rRNA gene, bacterial and archaeal 16S rRNA genes, respectively, in gut contents from the studied khors. DGGE showed bands, which were common and specific for each site and could be used as a bar code to certify the origin of the fish. Statistical analyses, using binary matrix, showed numbers of DGGE bands, 1, 2 and 2, for eukaryotes, bacteria and archaea, respectively, were commonly occurred in all studied khors. The DGGE phylotype, 3.Euk.Kr characterized eukaryotes in Khor Korosko. Phylogenetic analyses showed that two of eukaryotic phylotypes, 1.Euk.Kl.Kr and 2.Euk.Common, were belonged to crustacean Ostracoda. Bacterial phylotypes in all studied khors were located in the branch of cyanobacteria, alpha proteobacteria, but most of them constituted unique phylogenetic lineages within the branch of uncultured environmental bacteria. All archaeal phylotypes were located in the branch of methanogenic uncultured euryarchaeota. Some helminthes, of the genera Neoechinorhynchus and Catenula, -like rRNA gene phylotypes were recorded in guts from Kalabsha, Tushka and Korosko, suggesting common gut parasitic worms. The DGGE patterns and sequence analyses showed high similarities of eukaryote, bacteria and archaea rRNA gene phylotype compositions in fish guts from distant khors, implicating core gut microbiome. This is the first survey of all microbiome domains in tilapia guts at Lake Nasser based on molecular approaches.
{"title":"BIODIVERSITY OF GUT MICROFLORA OF Oreochromis niloticus BASED ON CULTURE-INDEPENDENT rRNA GENE ANALYSES AT LAKE NASSER, EGYPT","authors":"Mai A. Wassel, H. Elsaied, M. Rashed","doi":"10.21608/EJGC.2016.9577","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9577","url":null,"abstract":"The diversity of Oreochromis niloticus gut microbiome domains, eukaryotes, bacteria and archaea, was studied to understand the contribution of microbiota to the health of the fish. Fishes were collected from four different Khors, Kalabsha, Wadi Abyad, Tushka and Korosko, of Lake Nasser, Egypt. The approach of this study depends on culture-independent PCR/DGGE and sequence of small subunit of rRNA genes, 18S rRNA gene and 16S rRNA gene. The DGGE patterns displayed 5, 12 and 5 band groups, phylotypes, for eukaryotic 18S rRNA gene, bacterial and archaeal 16S rRNA genes, respectively, in gut contents from the studied khors. DGGE showed bands, which were common and specific for each site and could be used as a bar code to certify the origin of the fish. Statistical analyses, using binary matrix, showed numbers of DGGE bands, 1, 2 and 2, for eukaryotes, bacteria and archaea, respectively, were commonly occurred in all studied khors. The DGGE phylotype, 3.Euk.Kr characterized eukaryotes in Khor Korosko. Phylogenetic analyses showed that two of eukaryotic phylotypes, 1.Euk.Kl.Kr and 2.Euk.Common, were belonged to crustacean Ostracoda. Bacterial phylotypes in all studied khors were located in the branch of cyanobacteria, alpha proteobacteria, but most of them constituted unique phylogenetic lineages within the branch of uncultured environmental bacteria. All archaeal phylotypes were located in the branch of methanogenic uncultured euryarchaeota. Some helminthes, of the genera Neoechinorhynchus and Catenula, -like rRNA gene phylotypes were recorded in guts from Kalabsha, Tushka and Korosko, suggesting common gut parasitic worms. The DGGE patterns and sequence analyses showed high similarities of eukaryote, bacteria and archaea rRNA gene phylotype compositions in fish guts from distant khors, implicating core gut microbiome. This is the first survey of all microbiome domains in tilapia guts at Lake Nasser based on molecular approaches.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"215-233"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Assement of genotoxins-induced DNA damage at molecular level is important in eco-genotoxicology. In this research, ISSR and SRAP were used to detect DNA damage in barley (Hordeum vulgare L.) seeding exposed to toxic ascending Pb at concentration of 50,100, and 150 mg/l for 15 days. Substantial inhibition of root growth was observed with an increase in the Pb concentration, whereas shoot growth was non significantly inhibited compared to the unexposed plantlets. The alternations in the SDS-PAGE of seed proteins are indicative of the ability of lead (Pb) to alter the gene expression in exposed plant. For the ISSR analyses, 9 ISSR primers were found to produce a total of 53 amplification products (loci) from the nine primers were identified in the control seedlings ranging from 410-1927 bp in molecular size (primer ISSR-9 and primer ISSR-8 respectively). The detected % of polymorphisms was 32.08%, 33.96% and 71.70% for 50, 100 and 150 mg/l lead treatment, respectively. While for the SRAP analyses, three ISSR primers were found to produce a total of 17 amplification products (loci) from the three combinations primers were identified in the control seedlings ranging from 127-1883 bp in molecular size. Different polymorphic bands were detected at each concentration of lead for different primers. The detected % of polymorphisms 52.94%, 58.82% and 70.59% for 50, 100 and 150 mg/l lead treatment, respectively. The number of disappearing SRAP bands was the highest (7) in Pb treated seedlings 150 mg/l. Moreover, the number of appearing SRAP bands was the highest (4) in Pb treated seedlings 100 and 50 mg/l. Results produced from SDS-PAGE, ISSR and SRAP analysis indicated that the evident changes of exposed barley seedlings included gain or loss of bands compared with the control seedlings. The polymorphisms detected by both of SDS-PAGE, ISSR and SRAP profiles can be applied as a tool in risk assessment of Pb stress on plants. The results suggested that genomic template stability (GTS) reflecting changes in SDS-PAGE, ISSR and SRAP profiles was the most sensitive endpoint compared with the traditional indices such as root and shoot growth.
{"title":"ASSESSMENT OF LEAD STRESS USING GENOME TEMPLATE STABILITY IN Hordeum vulgare","authors":"H. Mahfouz, Walaa A. Rayan","doi":"10.21608/EJGC.2016.9583","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9583","url":null,"abstract":"Assement of genotoxins-induced DNA damage at molecular level is important in eco-genotoxicology. In this research, ISSR and SRAP were used to detect DNA damage in barley (Hordeum vulgare L.) seeding exposed to toxic ascending Pb at concentration of 50,100, and 150 mg/l for 15 days. Substantial inhibition of root growth was observed with an increase in the Pb concentration, whereas shoot growth was non significantly inhibited compared to the unexposed plantlets. The alternations in the SDS-PAGE of seed proteins are indicative of the ability of lead (Pb) to alter the gene expression in exposed plant. For the ISSR analyses, 9 ISSR primers were found to produce a total of 53 amplification products (loci) from the nine primers were identified in the control seedlings ranging from 410-1927 bp in molecular size (primer ISSR-9 and primer ISSR-8 respectively). The detected % of polymorphisms was 32.08%, 33.96% and 71.70% for 50, 100 and 150 mg/l lead treatment, respectively. While for the SRAP analyses, three ISSR primers were found to produce a total of 17 amplification products (loci) from the three combinations primers were identified in the control seedlings ranging from 127-1883 bp in molecular size. Different polymorphic bands were detected at each concentration of lead for different primers. The detected % of polymorphisms 52.94%, 58.82% and 70.59% for 50, 100 and 150 mg/l lead treatment, respectively. The number of disappearing SRAP bands was the highest (7) in Pb treated seedlings 150 mg/l. Moreover, the number of appearing SRAP bands was the highest (4) in Pb treated seedlings 100 and 50 mg/l. Results produced from SDS-PAGE, ISSR and SRAP analysis indicated that the evident changes of exposed barley seedlings included gain or loss of bands compared with the control seedlings. The polymorphisms detected by both of SDS-PAGE, ISSR and SRAP profiles can be applied as a tool in risk assessment of Pb stress on plants. The results suggested that genomic template stability (GTS) reflecting changes in SDS-PAGE, ISSR and SRAP profiles was the most sensitive endpoint compared with the traditional indices such as root and shoot growth.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"297-321"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68480949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hydrolytic enzymes producing Trichoderma species have long been recognized as an agent for controlling plant diseases caused by various phytopathogenic fungi. This study aims to isolate and characterize of new bio fungicides from Egyptian soils and assess of their antagonistic activity against some pathogenic fungi (Fusarium semitectum and Alternaria alternata). Four isolates of the Trichoderma asperellum were isolated from rhizosphere soil of different host plants collected from Fayoum governorate, Egypt. The isolates were characterized according to morphological characterization, microscopic observations and confirmed by sequencing of the ITS region of 18S rRNA. Trichoderma asperellum isolates were evaluated for their potential to antagonize the plant pathogenic fungi (F. semitectum and A. alternata) in vitro using the dual culture technique. Four out of twenty Trichoderma isolates (20%) were identified as T. asperellum based on morphological characteristics and confirmed by sequencing of ITS region of 18SrRNA. The four selected T. asperellum isolates (Tas1, Tas2, Tas3 and Tas4) were screened for their ability to produce chitinase on solid agar medium using bromocresol purple for developing the clear zone around colonies, and characterized due to its antagonistic effect against mycelial growth of pathogenic fungi. These results indicate that molecular systematic studies based on the sequence of ITS region are important for confirmation of phenotypic characterization of Trichoderma isolates. To the best of our knowledge, there is no information on the occurrence of T. asperellum in Egypt and this is the first report of the occurrence and isolation of T. asperellum from Egyptian soils.
{"title":"In vitro ASSESSMENT OF Trichoderma asperellum ISOLATED FROM PLANT RHIZOSPHERE AND EVALUATION OF THEIR POTEN-TIAL ACTIVITY AGAINST SOME PATHOGENIC FUNGI","authors":"G. Hassan, Nada F Hemeda","doi":"10.21608/EJGC.2016.9701","DOIUrl":"https://doi.org/10.21608/EJGC.2016.9701","url":null,"abstract":"Hydrolytic enzymes producing Trichoderma species have long been recognized as an agent for controlling plant diseases caused by various phytopathogenic fungi. This study aims to isolate and characterize of new bio fungicides from Egyptian soils and assess of their antagonistic activity against some pathogenic fungi (Fusarium semitectum and Alternaria alternata). Four isolates of the Trichoderma asperellum were isolated from rhizosphere soil of different host plants collected from Fayoum governorate, Egypt. The isolates were characterized according to morphological characterization, microscopic observations and confirmed by sequencing of the ITS region of 18S rRNA. Trichoderma asperellum isolates were evaluated for their potential to antagonize the plant pathogenic fungi (F. semitectum and A. alternata) in vitro using the dual culture technique. Four out of twenty Trichoderma isolates (20%) were identified as T. asperellum based on morphological characteristics and confirmed by sequencing of ITS region of 18SrRNA. The four selected T. asperellum isolates (Tas1, Tas2, Tas3 and Tas4) were screened for their ability to produce chitinase on solid agar medium using bromocresol purple for developing the clear zone around colonies, and characterized due to its antagonistic effect against mycelial growth of pathogenic fungi. These results indicate that molecular systematic studies based on the sequence of ITS region are important for confirmation of phenotypic characterization of Trichoderma isolates. To the best of our knowledge, there is no information on the occurrence of T. asperellum in Egypt and this is the first report of the occurrence and isolation of T. asperellum from Egyptian soils.","PeriodicalId":31811,"journal":{"name":"Egyptian Journal of Genetics and Cytology","volume":"45 1","pages":"113-128"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68481744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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