Human intestinal tract contained a diverse number of microbial communities which performed a significant role in human health. The presence of gut microbiota was affected mainly by diet. Camel milk is the source of nutrition and provides all the essential nutrients for growth. It has great significance in the treatment of liver, spleen, and anemic infections. Camel urine has also many medical advantages. In this study we examined the effect of camel milk and urine and a mixture of both (milk + urine) on the growth of Gut microbiota using an in vivo animal model. Fresh fecal samples were collected before and after administration of the tested materials. After that, the microbial analysis was conducted via culturing, denaturing gradient gel electrophoresis and metabolic analysis via high-performance liquid chromatography (HPLC). The result indicated that the numbers of bacterial groups were increased after the first dose. Coliform group have significant increase when given a mix of milk and urine compared to control group with P < 0.05. Bifidobacterium group have significant increase in their number in the Milk and Mix groups compared to control group with P < 0.05. The concentration of Short-chain fatty acids in fecal samples was increased in Milk and Mix groups compared to control group. In conclusion, drinking camal milk, urine or a mix of both increased the growth of Gut microbiota.
{"title":"Effects of Oral Administration of Camel Milk and Urine on Gut Microbiota: Biochemical and Microbiological Profiling in Rats","authors":"S. Noor, Manal S. Alenini","doi":"10.4236/AJMB.2018.81001","DOIUrl":"https://doi.org/10.4236/AJMB.2018.81001","url":null,"abstract":"Human intestinal tract contained a diverse number of microbial communities which performed a significant role in human health. The presence of gut microbiota was affected mainly by diet. Camel milk is the source of nutrition and provides all the essential nutrients for growth. It has great significance in the treatment of liver, spleen, and anemic infections. Camel urine has also many medical advantages. In this study we examined the effect of camel milk and urine and a mixture of both (milk + urine) on the growth of Gut microbiota using an in vivo animal model. Fresh fecal samples were collected before and after administration of the tested materials. After that, the microbial analysis was conducted via culturing, denaturing gradient gel electrophoresis and metabolic analysis via high-performance liquid chromatography (HPLC). The result indicated that the numbers of bacterial groups were increased after the first dose. Coliform group have significant increase when given a mix of milk and urine compared to control group with P < 0.05. Bifidobacterium group have significant increase in their number in the Milk and Mix groups compared to control group with P < 0.05. The concentration of Short-chain fatty acids in fecal samples was increased in Milk and Mix groups compared to control group. In conclusion, drinking camal milk, urine or a mix of both increased the growth of Gut microbiota.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"08 1","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70513193","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 present work presents an iin silicoi analysis of Upstream Regulatory Modules (URMs) of genes expressed in tapetum specific manner in dicotyledon and monocotyledon plants. In the current analysis, we identified several motifs conserved in these URMs of which ten were observed to be part of known icisi-elements using tools and databases like MEME, PLACE, MAST and TFSEARCH. We also identified that binding sites for two transcription factors, DOF and WRKY71 were found to be present in majority of the URMs.
{"title":"An in silico Analysis of Upstream Regulatory Modules (URMs) of Tapetum Specific Genes to Identify Regulatory cis -Elements and Transcription Factors","authors":"P. Sharma, P. Burma","doi":"10.4236/AJMB.2018.81002","DOIUrl":"https://doi.org/10.4236/AJMB.2018.81002","url":null,"abstract":"The present work presents an iin silicoi analysis of Upstream Regulatory Modules (URMs) of genes expressed in tapetum specific manner in dicotyledon and monocotyledon plants. In the current analysis, we identified several motifs conserved in these URMs of which ten were observed to be part of known icisi-elements using tools and databases like MEME, PLACE, MAST and TFSEARCH. We also identified that binding sites for two transcription factors, DOF and WRKY71 were found to be present in majority of the URMs.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"08 1","pages":"13-25"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70513202","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}
F. Lobato, C. Damasceno, Daniela Soares Leite, Â. Ribeiro-dos-Santos, Sylvain Darnet, C. L. Francês, N. Vijaykumar, Á. Santana
New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process; 2) adaptation and development of new protocols for sample preparation; 3) the assignment of a degree of confidence to the data generated; and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.
{"title":"Data Analysis of Multiplex Sequencing at SOLiD Platform: A Probabilistic Approach to Characterization and Reliability Increase","authors":"F. Lobato, C. Damasceno, Daniela Soares Leite, Â. Ribeiro-dos-Santos, Sylvain Darnet, C. L. Francês, N. Vijaykumar, Á. Santana","doi":"10.4236/AJMB.2018.81003","DOIUrl":"https://doi.org/10.4236/AJMB.2018.81003","url":null,"abstract":"New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process; 2) adaptation and development of new protocols for sample preparation; 3) the assignment of a degree of confidence to the data generated; and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"08 1","pages":"26-38"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70513239","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}
E. Ekerette, E. Ikpeme, O. Udensi, M. Ozoje, O. Etukudo, A. Umoyen, So Durosaro, M. Wheto
Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p < 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.
{"title":"Phylogenetics and Molecular Divergence of Tilapia Fish (Oreochromis Species) Using Mitochondrial D-Loop and Cytochrome b Regions","authors":"E. Ekerette, E. Ikpeme, O. Udensi, M. Ozoje, O. Etukudo, A. Umoyen, So Durosaro, M. Wheto","doi":"10.4236/AJMB.2018.81004","DOIUrl":"https://doi.org/10.4236/AJMB.2018.81004","url":null,"abstract":"Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p < 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"1 1","pages":"39-57"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70513255","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}
D. Nascimento, O. Dellagostin, D. S. Matos, D. McIntosh, R. Hirata, G. M. Pereira, A. Mattos-Guaraldi, G. R. Armôa
Diphtheria is a fulminant bacterial disease caused by toxigenic strains of Corynebacterium diphtheriae whose local and systemic manifestations are due to the action of the diphtheria toxin (DT). The vaccine which is used to prevent diphtheria worldwide is a toxoid obtained by detoxifying DT. Although associated with high efficacy in the prevention of disease, the current anti-diphtheria vaccine, one of the components of DTP (diphtheria, tetanus and pertussis triple vaccine), may present post vaccination effects such as toxicity and reactogenicity resulting from the presence of contaminants in the vaccine that originated during the process of production and/or detoxification. Therefore, strategies to develop a less toxic and at the same time economically viable vaccine alternatives are needed to improve existing vaccines in use worldwide. In this study, the Moreau substrain of BCG which is used in Brazil as a live vaccine against human tuberculosis was genetically modified to carry and express the gene encoding for the diphtheria toxin fragment B (DTB). As such, the DNA sequence encoding the dtb gene was cloned into the pUS977 shuttle vector for cytoplasmic expression and successfully introduced into BCG cells by electroporation. Mice immunized with recombinant BCG expressing DTB showed seroconversion with the detection of specific antibodies against DTB. Also, rBCGs stably expressing DTB persisted up to 60 days in the absence of selective pressure in mice and cell viability did not change significantly during the period tested. Finally, immune sera from BALB/c mice vaccinated with rBCGpUS977dtbPW8 were preliminarily tested for their capacity of neutralizing the diphtheria toxin in the Vero Cells assay.
{"title":"Mycobacterium bovis BCG as a Delivery System for the dtb Gene Antigen from Diphtheria Toxin","authors":"D. Nascimento, O. Dellagostin, D. S. Matos, D. McIntosh, R. Hirata, G. M. Pereira, A. Mattos-Guaraldi, G. R. Armôa","doi":"10.4236/AJMB.2017.74014","DOIUrl":"https://doi.org/10.4236/AJMB.2017.74014","url":null,"abstract":"Diphtheria is a fulminant bacterial disease caused by toxigenic strains of Corynebacterium diphtheriae whose local and systemic manifestations are due to the action of the diphtheria toxin (DT). The vaccine which is used to prevent diphtheria worldwide is a toxoid obtained by detoxifying DT. Although associated with high efficacy in the prevention of disease, the current anti-diphtheria vaccine, one of the components of DTP (diphtheria, tetanus and pertussis triple vaccine), may present post vaccination effects such as toxicity and reactogenicity resulting from the presence of contaminants in the vaccine that originated during the process of production and/or detoxification. Therefore, strategies to develop a less toxic and at the same time economically viable vaccine alternatives are needed to improve existing vaccines in use worldwide. In this study, the Moreau substrain of BCG which is used in Brazil as a live vaccine against human tuberculosis was genetically modified to carry and express the gene encoding for the diphtheria toxin fragment B (DTB). As such, the DNA sequence encoding the dtb gene was cloned into the pUS977 shuttle vector for cytoplasmic expression and successfully introduced into BCG cells by electroporation. Mice immunized with recombinant BCG expressing DTB showed seroconversion with the detection of specific antibodies against DTB. Also, rBCGs stably expressing DTB persisted up to 60 days in the absence of selective pressure in mice and cell viability did not change significantly during the period tested. Finally, immune sera from BALB/c mice vaccinated with rBCGpUS977dtbPW8 were preliminarily tested for their capacity of neutralizing the diphtheria toxin in the Vero Cells assay.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"07 1","pages":"176-189"},"PeriodicalIF":0.0,"publicationDate":"2017-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43115268","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}
A. Hirao, Yoshihiko Onda, Rie Shimizu‐Inatsugi, J. Sese, K. Shimizu, T. Kenta
Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations; however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.
{"title":"Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq","authors":"A. Hirao, Yoshihiko Onda, Rie Shimizu‐Inatsugi, J. Sese, K. Shimizu, T. Kenta","doi":"10.4236/AJMB.2017.74012","DOIUrl":"https://doi.org/10.4236/AJMB.2017.74012","url":null,"abstract":"Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations; however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"07 1","pages":"1031-1046"},"PeriodicalIF":0.0,"publicationDate":"2017-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45399217","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}
Takanari Wakayama, K. Ohashi, Y. Fujimoto, M. Maeda
The P19CL6 mouse embryonic carcinoma cells efficiently differentiate into cardiac muscle cells in the presence of DMSO. A reporter plasmid for cardiac muscle differentiation was constructed by connecting the CMV enhancer and a 250 bp MLC-2v promoter in front of the GFP gene to further evaluate the role of the CMV enhancer. This plasmid (pCBVenh/MLC-2vpro/EGFP) was stably introduced into P19CL6 cells, and the transfectant differentiated into cardiomyocytes with DMSO. Upon DMSO addition, GFP was immediately transcribed (within 2 days) and the amount of the transcript increased with cultivation. Concomitantly, GFP fluorescence was detected in the cells under a microscope. However, native MLC-2v was transcribed later on day 4. This expression time course is different from that of GFP. Clearly the CMV enhancer responded immediately to DMSO. Since GATA DNA-binding proteins play crucial roles in the initiation of cardiomyocyte differentiation, such a response could be ascribed to the presence of multiple GATA motifs in the enhancer sequence but not in the native MLC-2v promoter. Thus the CMV enhancer may be not only useful for gene therapy and monitoring cell differentiation but also the study of the role of GATA transcription factors expressed in P19CL6 cells.
{"title":"The Cytomegalovirus Enhancer Induces an Immediate Response to the Myosin Light Chain 2v Promoter during P19CL6 Cell Differentiation","authors":"Takanari Wakayama, K. Ohashi, Y. Fujimoto, M. Maeda","doi":"10.4236/AJMB.2017.74015","DOIUrl":"https://doi.org/10.4236/AJMB.2017.74015","url":null,"abstract":"The P19CL6 mouse embryonic carcinoma cells efficiently differentiate into cardiac muscle cells in the presence of DMSO. A reporter plasmid for cardiac muscle differentiation was constructed by connecting the CMV enhancer and a 250 bp MLC-2v promoter in front of the GFP gene to further evaluate the role of the CMV enhancer. This plasmid (pCBVenh/MLC-2vpro/EGFP) was stably introduced into P19CL6 cells, and the transfectant differentiated into cardiomyocytes with DMSO. Upon DMSO addition, GFP was immediately transcribed (within 2 days) and the amount of the transcript increased with cultivation. Concomitantly, GFP fluorescence was detected in the cells under a microscope. However, native MLC-2v was transcribed later on day 4. This expression time course is different from that of GFP. Clearly the CMV enhancer responded immediately to DMSO. Since GATA DNA-binding proteins play crucial roles in the initiation of cardiomyocyte differentiation, such a response could be ascribed to the presence of multiple GATA motifs in the enhancer sequence but not in the native MLC-2v promoter. Thus the CMV enhancer may be not only useful for gene therapy and monitoring cell differentiation but also the study of the role of GATA transcription factors expressed in P19CL6 cells.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"07 1","pages":"190-203"},"PeriodicalIF":0.0,"publicationDate":"2017-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43625867","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}
Angelina Mandadzhieva, Daniela Avdzhieva-Tzavella, T. Todorov, S. Tincheva, V. Sinigerska, M. Ivanova, A. Savov, V. Mitev, A. Todorova
Wolman disease is a rare autosomal recessive disorder caused by mutations in the LIPA gene (10q23.31). The LIPA gene encodes lysosomal acid lipase (LAL), which plays a key role in hydrolysis of the cholesteryl esters and triglycerides. Two unrelated families from Bulgaria were referred for genetic testing with clinical diagnosis Wolman disease. Sanger sequencing of all coding exons and exon-intron boundaries of the LIPA gene was performed. The index patients were found to be homozygous for two different mutations in the LIPA gene: a missense mutation, c.260G > T, p.Gly87Val, which affects the enzyme active site and a splice-site change, c.822+1G > A, which most probably destroys the enzyme polypeptide chain. These two completely different types of mutations along the LIPA gene resulted in a very similar phenotype involving liver, kidney, gastrointestinal, muscle and blood disturbances. As consanguinity is not typical for the Bulgarian population, a possible explanation of the homozygosity could be presence of endemic regions for given mutations. To check this hypothesis, selective screening for these mutations was performed in two presumable endemic regions in Bulgaria. Altogether, 100 newborns were screened for p.Gly87Val mutation and the detected carrier frequency was about 1% (1/100), while in the group of 100 newborns screened for the c.822 + 1G > A mutation the detected carrier frequency was 2% (2/100). The results indicate a high recurrence risk of Wolman disease in these particular Bulgarian regions of about 1:10000. These findings are from crucial importance for the inhabitants of the corresponding parts of Bulgaria. They may benefit from early genetic testing and adequate genetic counselling during family planning.
{"title":"Wolman Disease in Bulgarian Patients: Selective Genetic Screening in Two Presumable Endemic Regions","authors":"Angelina Mandadzhieva, Daniela Avdzhieva-Tzavella, T. Todorov, S. Tincheva, V. Sinigerska, M. Ivanova, A. Savov, V. Mitev, A. Todorova","doi":"10.4236/AJMB.2017.74013","DOIUrl":"https://doi.org/10.4236/AJMB.2017.74013","url":null,"abstract":"Wolman disease is a rare autosomal recessive disorder caused by mutations in the LIPA gene (10q23.31). The LIPA gene encodes lysosomal acid lipase (LAL), which plays a key role in hydrolysis of the cholesteryl esters and triglycerides. Two unrelated families from Bulgaria were referred for genetic testing with clinical diagnosis Wolman disease. Sanger sequencing of all coding exons and exon-intron boundaries of the LIPA gene was performed. The index patients were found to be homozygous for two different mutations in the LIPA gene: a missense mutation, c.260G > T, p.Gly87Val, which affects the enzyme active site and a splice-site change, c.822+1G > A, which most probably destroys the enzyme polypeptide chain. These two completely different types of mutations along the LIPA gene resulted in a very similar phenotype involving liver, kidney, gastrointestinal, muscle and blood disturbances. As consanguinity is not typical for the Bulgarian population, a possible explanation of the homozygosity could be presence of endemic regions for given mutations. To check this hypothesis, selective screening for these mutations was performed in two presumable endemic regions in Bulgaria. Altogether, 100 newborns were screened for p.Gly87Val mutation and the detected carrier frequency was about 1% (1/100), while in the group of 100 newborns screened for the c.822 + 1G > A mutation the detected carrier frequency was 2% (2/100). The results indicate a high recurrence risk of Wolman disease in these particular Bulgarian regions of about 1:10000. These findings are from crucial importance for the inhabitants of the corresponding parts of Bulgaria. They may benefit from early genetic testing and adequate genetic counselling during family planning.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"07 1","pages":"169-175"},"PeriodicalIF":0.0,"publicationDate":"2017-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45630712","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}
Reverse transcriptase (rt) fragments from LINE retrotransposons in the mulberry genome were analyzed in terms of heterogeneity, phylogeny, and chromosomal distribution. We amplified and characterized conserved domains of the rt using degenerate primer pairs. Sequence analyses indicated that the rt fragments were highly heterogeneous and rich in A/T bases. The sequence identity ranged from 31.8% to 99.4%. Based on sequence similarities, the rt fragments were categorized into eight groups. Furthermore, similar stop codon distribution patterns among a series of clones in the same group indicated that they underwent a similar evolutionary process. Interestingly, phylogenetic analyses of the rt fragments isolated from mulberry and 13 other plant species revealed that two distantly related taxa (mulberry and Paeonia suffruticosa) grouped together. It does not appear that this phenomenon resulted from horizontal transposable element transfer. Fluorescence in situ hybridization analysis revealed that most of the rt fragments were concentrated in the subtelomeric and pericentromeric regions of the mulberry chromosomes, but that these elements were not abundant in the mulberry genome. Future studies will focus on the potential roles of these elements in the subtelomeric and pericentromeric regions of the mulberry genome.
{"title":"Identification and Characterization of Reverse Transcriptase Fragments of Long Interspersed Nuclear Elements (LINEs) in the Morus notabilis Genome","authors":"Bi Ma, Youchao Xin, L. Kuang, Fei Hou, Ningjia He","doi":"10.4236/AJMB.2017.73011","DOIUrl":"https://doi.org/10.4236/AJMB.2017.73011","url":null,"abstract":"Reverse transcriptase (rt) fragments from LINE retrotransposons in the mulberry genome were analyzed in terms of heterogeneity, phylogeny, and chromosomal distribution. We amplified and characterized conserved domains of the rt using degenerate primer pairs. Sequence analyses indicated that the rt fragments were highly heterogeneous and rich in A/T bases. The sequence identity ranged from 31.8% to 99.4%. Based on sequence similarities, the rt fragments were categorized into eight groups. Furthermore, similar stop codon distribution patterns among a series of clones in the same group indicated that they underwent a similar evolutionary process. Interestingly, phylogenetic analyses of the rt fragments isolated from mulberry and 13 other plant species revealed that two distantly related taxa (mulberry and Paeonia suffruticosa) grouped together. It does not appear that this phenomenon resulted from horizontal transposable element transfer. Fluorescence in situ hybridization analysis revealed that most of the rt fragments were concentrated in the subtelomeric and pericentromeric regions of the mulberry chromosomes, but that these elements were not abundant in the mulberry genome. Future studies will focus on the potential roles of these elements in the subtelomeric and pericentromeric regions of the mulberry genome.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"07 1","pages":"138-152"},"PeriodicalIF":0.0,"publicationDate":"2017-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47019399","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}
Ten Egyptian barley genotypes (2 commercial varieties and 8 breeding lines) were cultivated under normal condition at the Experimental Farm of Sakha Agricultural Research station and exposed to salinity stress condition at the Experimental Farm of El-hosainia plain Agricultural Research station, Elsharkia Governorate, Egypt, in an attempt to identify the relative salinity tolerant genotypes. A susceptibility index (SI) was used to estimate the relative stress loss because it accounted for variation in yield potential and stress intensity. Giza 123, Line-1, Line-5, Line-6 and Line-8 genotypes were considered as saline tolerant genotypes on the basis of their highly tolerance indices values. Barley genotypes were characterized by seven SSR markers and three SCoT primers in different combinations to discern the extent of genetic variation and develop a fingerprinting key. Normal SCoT reactions amplify single segments of DNA which are 15- to 19-mer long. A new strategy was used to increase SCoT potential in genetic diversity studies by using two and three different primer combinations per reaction. Amplification products scored a polymorphism percentage of 94.44% for Triple-SCoT and 90.91% for SSR, while the average no. of polymorphic fragments/primer was 17 and 7.14 in the two marker systems, respectively. On the other side, Triple-SCoT exhibited the highest average number of positive and negative genotype-specific markers. The cluster analysis of the studied genotypes using these different marker systems revealed four dendrograms varied in their topology. The dendrogram based on Triple-SCoT data exhibited the closest relationships to those illustrated by SSR dendrogram.
{"title":"Efficiency of Triple-SCoT Primer in Characterization of Genetic Diversity and Genotype-Specific Markers against SSR Fingerprint in Some Egyptian Barley Genotypes","authors":"A. A. Aboulila, M. Mansour","doi":"10.4236/AJMB.2017.73010","DOIUrl":"https://doi.org/10.4236/AJMB.2017.73010","url":null,"abstract":"Ten Egyptian barley genotypes (2 commercial varieties and 8 breeding lines) were cultivated under normal condition at the Experimental Farm of Sakha Agricultural Research station and exposed to salinity stress condition at the Experimental Farm of El-hosainia plain Agricultural Research station, Elsharkia Governorate, Egypt, in an attempt to identify the relative salinity tolerant genotypes. A susceptibility index (SI) was used to estimate the relative stress loss because it accounted for variation in yield potential and stress intensity. Giza 123, Line-1, Line-5, Line-6 and Line-8 genotypes were considered as saline tolerant genotypes on the basis of their highly tolerance indices values. Barley genotypes were characterized by seven SSR markers and three SCoT primers in different combinations to discern the extent of genetic variation and develop a fingerprinting key. Normal SCoT reactions amplify single segments of DNA which are 15- to 19-mer long. A new strategy was used to increase SCoT potential in genetic diversity studies by using two and three different primer combinations per reaction. Amplification products scored a polymorphism percentage of 94.44% for Triple-SCoT and 90.91% for SSR, while the average no. of polymorphic fragments/primer was 17 and 7.14 in the two marker systems, respectively. On the other side, Triple-SCoT exhibited the highest average number of positive and negative genotype-specific markers. The cluster analysis of the studied genotypes using these different marker systems revealed four dendrograms varied in their topology. The dendrogram based on Triple-SCoT data exhibited the closest relationships to those illustrated by SSR dendrogram.","PeriodicalId":65391,"journal":{"name":"美国分子生物学期刊(英文)","volume":"07 1","pages":"123-137"},"PeriodicalIF":0.0,"publicationDate":"2017-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41483418","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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