ABSTRACT
Resumen Los biobancos son infraestructuras multidisciplinares y esta investigación integradora pretende exponer su concepto a las diferentes ciencias que lo construyen e interpretan, para entender sus elementos esenciales de forma holística. La revisión integradora se realizó siguiendo la guía PRISMA y la evaluación de la calidad según CASPe dando como resultado un total de 30 trabajos. El análisis de los datos se realizó a través de las categorías aristotélicas y los resultados se interpretaron según el paradigma de la complejidad de Edgar Morin. El concepto de Biobanco fue aclarado al considerarlo como la representación de un fenómeno bio-socio-cultural en el que los campos científicos desarrollan relaciones de tipo: complementarias, antagónicas y ambiguas de conocimientos y prácticas. Esta red de significación, desde la filosofía, impacta en la construcción de la subjetividad y en las formas de socialización.
Abstract Biobanks are multidisciplinary infrastructures and, accordingly, this integrative research seeks to bring out the concept of biobank in the various sciences that construct and interpret it, so as to arrive at a holistic understanding of its essential components. This integrative review - guided by PRISMA and with quality assessment following CASPe - resulted in a selection of 30 articles. Data were analysed by Aristotelian categories and the results were interpreted on the complexity paradigm of Edgar Morin. The biobank concept was clarified by considering it to be the representation of a biological, social and cultural phenomenon in which knowledge and practices from diverse scientific fields enter into complementary, antagonistic and ambiguous types of relationship. This network of signification, analysed here using categories from Aristotelian philosophy, has impacts on the construction of subjectivity and forms of socialisation.
Subject(s)
Humans , Philosophy , Biological Specimen BanksABSTRACT
This study aimed to isolate and identify a novel bacterial isolate potential resistant to Mn2+ as well as to investigate the biosorption isotherms of Mn2+ removal from aqueous solutions by the freeze-dried biomass of this bacterium. Sixty three manganese resistant bacterial isolates were recovered from 20 industrial wastewater samples. Interestingly, among them, the isolate number 2120 was able to resist up to 140 ppm of Mn2+ and was selected for the further processes. This isolate was phenotypically characterized and identified by 16S rRNA gene sequencing as Proteus penneri and assigned accession number KY712431 in the GenBank database. The effects of pH and contact time on the biosorption process were studied and optimum pH for biosorption equilibrium was 6 while the optimum contact time was 30 min at room temperature. The maximum adsorption capacity (qmax) of Mn2+ removal from aqueous solutions by the freeze-dried biomass of Proteus penneri 2120 was 175.4 mg/g. According to Freundlich and Langmuir models, the correlation coefficients (R2) were 0.9977 and 0.5525, respectively. Therefore the studied biosorption isotherms are fit well with Freundlich model rather than the Langmuir model. Our findings suggest that the dried biomass of the isolate Proteus penneri 2120 is potentially applicable for manganese metal ion removal from the industrial waste water.
ABSTRACT
Objective: To establish a polymerase chain reaction (PCR) technique based on cytochrome b (cytb) gene of mitochondria DNA (mtDNA) for blood meal identification. Methods: The PCR technique was established based on published information and validated using blood sample of laboratory animals of which their whole gene sequences are available in GenBank. PCR was next performed to compile gene sequences of different species of wild rodents. The primers used were complementary to the conserved region of the cytb gene of vertebrate’s mtDNA. A total of 100 blood samples, both from laboratory animals and wild rodents were collected and analyzed. The obtained unknown sequences were compared with those in the GenBank database using BLAST program to identify the vertebrate animal species. Results: Gene sequences of 11 species of wild animals caught in 9 localities of Peninsular Malaysia were compiled using the established PCR. The animals involved were Rattus (rattus) tanezumi, Rattus tiomanicus, Leopoldamys sabanus,Tupaia glis, Tupaia minor, Niviventor cremoriventor, Rhinosciurus laticaudatus, Callosciurus caniseps, Sundamys muelleri, Rattus rajah and Maxomys whiteheadi. The BLAST results confirmed the host with exact or nearly exact matches (>89% identity). Ten new gene sequences have been deposited in GenBank database since September 2010. Conclusions: This study indicates that the PCR direct sequencing system using universal primer sets for vertebrate cytb gene is a promising technique for blood meal identification.
ABSTRACT
Although abundant biology data have been accumulated in public biology databases, such as GenBank and PIR, few easy-interface services are provided for users to access or update them. We have developed a system, named BioStore, that is composed of several programs to aid users to not only access public data but also share their own data easily. The service can be used for maintaining a local database as a repository of raw data files of several public databases and distributing the data files to other users. Currently, BioStore manipulates major bio-databases and will expand to include more databases and more useful interfaces.
Subject(s)
Biology , Databases, Nucleic Acid , Formycins , Ribonucleotides , Information Storage and RetrievalABSTRACT
We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.
Subject(s)
Abstracting and Indexing , Databases, Nucleic Acid , Databases, ProteinABSTRACT
Many bioinformatics sites have managed local bio-databases, including major databases such as GenBank and PIR with update load. We have developed several programs to monitor the update status of these databases and to FTP them automatically. These programs can be used for maintaining local bio-databases as recent versions and providing up-to-date databases through FTP sites. Currently, the program serves major bio-databases and will extend to accommodate many more bio-databases.