ABSTRACT
During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protege as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.
Subject(s)
Biology , Dataset , Gene Ontology , Genome , Genome, Microbial , Geographic Information Systems , Rumen , SemanticsABSTRACT
Background and Aim: The Y-chromosome azoospermic factor [AZF] regions consist of genes whose specific roles and functions in spermatogenesis and fertility have not been completely clarified. Hence, recognition of the association between AZF microdeletions and male infertility has suggestions for the diagnosis, treatment, and genetic counseling. The main objective of the present study was investigation of Y chromosome microdeletions in the non-obstructive azoospermic and oligospermic patients in Mashhad and identification of appropriate STS markers associated with azoospermia and oligospermia
Materials and Methods: This descriptive-analytical study was performed on 45 infertile men with azoospermia and oligospermia with normal karyotypes referred to infertility center of Montaseriyeh hospital in Mashhad. Molecular screening technique was performed by using Multiplex PCR and sequence-tagged sites [STS] primers according to the EAA/EMQN guideline for detection of microdeletions in Y-chromosomal AZF regions and the Y specific sequences
Results: Three out of 45 infertile men had deletions in the AZFc and AZFa regions. Among every 3 infertile men, two patients [7.7%] and one patient [5%] had microdeletion in the AZFc region and in the AZFa, respectively. The results indicated that AZF microdeletions had a significant effect on azoospermia and oligospermia in infertile men
Conclusion: Y-chromosome microdeletion analysis can be recommended as an important molecular test for infertile males to obtain reliable genetic information before the administration of assisted-reproductive techniques. It will help to decrease the cost and technical difficulty of the procedure
ABSTRACT
The aim of present study was cloning and expression of phiC31 integrase cDNA in a bacterial expression vector. Thus, an intra molecular assay vector was applied to show in vitro activity of recombinant protein. In this experimental study, phiC31 cDNA was subcloned into a prokaryotic expression vector and transformed into E.coli Bl21 [DE3]. Recombinant phiC31 integrase was purified form the bacterial cell lysates and its activity was verified by an in vitro functional assessment. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis [SDS-PAGE] of the purified phiC31 integrase confirmed the size of protein [70 kDa]. Finally, the functionality of purified phiC31 integrase was verified. The results of this study indicated that the purified integrase has a great potential application for in vitro site-specific integration