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Lopes Pinto, Fernando
Publications (4 of 4) Show all publications
Drabek, J., Smolikova, M., Kalendar, R., Lopes Pinto, F. A., Pavlousek, P., KleparnIk, K. & Frebort, I. (2016). Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars. Electrophoresis, 37(23-24), 3059-3067
Open this publication in new window or tab >>Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars
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2016 (English)In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 37, no 23-24, p. 3059-3067Article in journal (Refereed) Published
Abstract [en]

Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.

Keywords
Grapevine DNA analysis, Multiplex PCR, STRs, Vitis vinifera L
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-316142 (URN)10.1002/elps.201600068 (DOI)000392421400003 ()27696463 (PubMedID)
Available from: 2017-03-03 Created: 2017-03-03 Last updated: 2017-11-29Bibliographically approved
Lopes Pinto, F. (2009). Development of Molecular Biology and Bioinformatics Tools: From Hydrogen Evolution to Cell Division in Cyanobacteria. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Development of Molecular Biology and Bioinformatics Tools: From Hydrogen Evolution to Cell Division in Cyanobacteria
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The use of fossil fuels presents a particularly interesting challenge - our society strongly depends on coal and oil, but we are aware that their use is damaging the environment. Currently, this awareness is gaining momentum, and pressure to evolve towards an energetically cleaner planet is very strong. Molecular hydrogen (H2) is an environmentally suitable energy carrier that could initially supplement or even substitute fossil fuels.

Ideally, the primary energy source to produce hydrogen gas should be renewable, and the process of conversion back to energy without polluting emissions, making this cycle environmentally clean. Photoconversion of water to hydrogen can be achieved using the following strategies: 1) the use of photochemical fuel cells, 2) by applying photovoltaics, or 3) by promoting production of hydrogen by photosynthetic microorganisms, either phototrophic anoxygenic bacteria and cyanobacteria or eukaryotic green algae. For photobiological H2 production cyanobacteria are among the ideal candidates since they: a) are capable of H2 evolution, and b) have simple nutritional requirements - they can grow in air (N2 and CO2), water and mineral salts, with light as the only energy source.

As this project started, a vision and a set of overall goals were established. These postulated that improved H2 production over a long period demanded: 1) selection of strains taking in consideration their specific hydrogen metabolism, 2) genetic modification in order to improve the H2 evolution, and 3) cultivation conditions in bioreactors should be exmined and improved. Within these goals, three main research objectives were set: 1) update and document the use of cyanobacteria for hydrogen production, 2) create tools to improve molecular biology work at the transcription analysis level, and 3) study cell division in cyanobacteria.

This work resulted in: 1) the publication of a review on hydrogen evolution by cyanobacteria, 2) the development of tools to assist understanding of transcription, and 3) the start of a new fundamental research approach to ultimately improve the yield of H2 evolution by cyanobacteria.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. p. 66
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 697
Keywords
Cyanobacteria, hydrogen, RNA, bioinformatics, RT-PCR, RACE, transcription
National Category
Biochemistry and Molecular Biology Bioinformatics and Systems Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:uu:diva-110842 (URN)978-91-554-7678-6 (ISBN)
Public defence
2010-01-20, Häggsalen, Ångströmlaboratoriet, Lägerhyddsv. 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2009-12-21 Created: 2009-11-26 Last updated: 2010-12-22Bibliographically approved
Lopes Pinto, F., Svensson, H. & Lindblad, P. (2007). Webtag: A new web tool providing tags/anchors for RT-PCR experiments with prokaryotes. BMC Biotechnology, 7, 73
Open this publication in new window or tab >>Webtag: A new web tool providing tags/anchors for RT-PCR experiments with prokaryotes
2007 (English)In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 7, p. 73-Article in journal (Refereed) Published
Abstract [en]

Background: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome. These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination. Results: The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures. Conclusion: This new web tool allows scientists to easily and rapidly obtain suitable tags for RTPCR experiments, and is available at http://www.egs.uu.se/software/webtag/.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-13840 (URN)10.1186/1472-6750-7-73 (DOI)000251903100001 ()17961214 (PubMedID)
Available from: 2008-01-28 Created: 2008-01-28 Last updated: 2017-12-11Bibliographically approved
Lopes Pinto, F., Svensson, H. & Lindblad, P. (2006). Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR. BMC Biotechnology, 6, 31
Open this publication in new window or tab >>Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR
2006 (English)In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 6, p. 31-Article in journal (Refereed) Published
Abstract [en]

Background

In order to overcome genomic DNA contamination in transcriptional studies, reverse template-specific polymerase chain reaction, a modification of reverse transcriptase polymerase chain reaction, is used. The possibility of using tags whose sequences are not found in the genome further improves reverse specific polymerase chain reaction experiments. Given the absence of software available to produce genome suitable tags, a simple tool to fulfill such need was developed.

Results

The program was developed in Perl, with separate use of the basic local alignment search tool, making the tool platform independent (known to run on Windows XP and Linux). In order to test the performance of the generated tags, several molecular experiments were performed. The results show that Tagenerator is capable of generating tags with good priming properties, which will deliberately not result in PCR amplification of genomic DNA.

Conclusion

The program Tagenerator is capable of generating tag sequences that combine genome absence with good priming properties for RT-PCR based experiments, circumventing the effects of genomic DNA contamination in an RNA sample.

Keywords
Tagenerator, RT-PCR
National Category
Biochemistry and Molecular Biology Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:uu:diva-81352 (URN)10.1186/1472-6750-6-31 (DOI)16820068 (PubMedID)
Available from: 2006-08-18 Created: 2006-08-18 Last updated: 2017-12-14Bibliographically approved
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