Publications by authors named "Roberta Fogliatto Mariot"

9 Publications

  • Page 1 of 1

The development of miniSTRs as a method for high-speed direct PCR.

Electrophoresis 2021 Apr 3. Epub 2021 Apr 3.

Department of Chemistry, Florida International University (FIU), Miami, Florida, USA.

There are situations in which it would be very valuable to have a DNA profile within a short time; for example, in mass disasters or airport security. In previous work, we have promoted reduced size STR amplicons for the analysis of degraded DNA. We also noticed that shorter amplicons are more robust during amplification, making them inhibition resistant, and potentially applicable to high-speed direct PCR. Here, we describe a set of miniSTRs capable of rapid direct PCR amplification. The selected markers are a subset of the Combined DNA Index System (CODIS) loci modified to permit high-speed amplification. Using the proposed protocol, the amplification of eight loci plus amelogenin directly from a saliva sample can be completed in 7 min and 38 s using a two-step PCR with 30 cycles of 98°C for 2 s and 62°C for 7 s on a Streck Philisa thermocycler. Selection of DNA polymerase, optimization of the two-step PCR cycling conditions, the primer concentrations, and the dilution of saliva is described. This method shows great potential as a quick screening method to obtain a presumptive DNA profile when time is limited, particularly when combined with high-speed separation and detection methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/elps.202100066DOI Listing
April 2021

Geographic origin determination of Brazilian Cannabis sativa L. (Marihuana) by multi-element concentration.

Forensic Sci Int 2020 Oct 11;315:110459. Epub 2020 Aug 11.

Soil Science Department, Agronomy Faculty, Federal University of Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 7712, CEP 91540-000 Porto Alegre, Rio Grande do Sul, Brazil; National Institute of Forensic Science and Technology (INCT Forense), Brazil.

The Marihuana Polygon production of Cannabis sativa L. supplies the northeastern region of Brazil and represents 30% of the nation's market. The international trend of indoor cultivation is also occurring in Brazil, and the Brazilian Federal Police (BFP) has been increasing its apprehension of cannabis seeds sent by mail. The present work aims to assess the utility of the multi-element composition of different cannabis plant parts and soil samples where the plants were cultivated to determine their geographic origin. Statistical tools were applied to classification of marijuana samples from distinct geographic regions within northeastern Brazil, including indoor cultivated samples. The multi-element quantification was determined using inductively-coupled plasma - optical emission spectrometry (ICP-OES), and the data were compared by the Kruskal-Wallis H test, and subsequently, multiple discriminant analysis (MDA). The results of the multi-element concentration of cannabis plant samples were also subjected to a principal component analysis (PCA) and an orthogonal partial least squares discriminant analysis (OPLS-DA). The cannabis plant samples from the Marihuana Polygon could be clearly separated from those cultivated indoors, and the distance between them was detectable. The MDA revealed that phosphorus, calcium, magnesium, selenium, and arsenic concentrations were used as variables for this separation. Our results demonstrate that multi-element composition analysis can be used to indicate the origin or cultivation location of cannabis plants. Routine laboratory analyses consisting of multi-element composition combined with statistical analyses provide a reliable tool by which C. sativa movement, cultivation, and interdiction efforts in Brazil may be assessed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.forsciint.2020.110459DOI Listing
October 2020

Evaluation of two 13-loci STR multiplex system regarding identification and origin discrimination of Brazilian Cannabis sativa samples.

Int J Legal Med 2020 Sep 25;134(5):1603-1612. Epub 2020 Jun 25.

Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.

According to the Brazilian Federal Police (BFP), the Brazilian Cannabis sativa illicit market is mainly supplied by drugs originated from Paraguay and Northeastern Brazil (Marijuana Polygon region). These two known routes, the increasing indoor cultivations (supported by online market), and drugs from Uruguay are also in BFP's sight. Forensic tools to aid police intelligence were published in the past years. In genetics, microsatellites have gained attention due to their individualization capability. This study aims to evaluate the effectiveness and efficiency of two STR multiplex systems previously proposed in 94 Cannabis sativa samples seized in Brazil. Principal coordinate analyses (PCoA), forensic parameters, and genetic structure analysis were executed. Both panels were effective in individualizing and origin discriminating all samples, and the system proposed in 2015 demonstrated better results. For this marker set, the probability of identity for a random individual is approximately one in 65 billion; also, the PCoA shows a clear genetic distinction among samples according to its origin. Bayesian inference populational structure analysis indicated a significant genetic diversity among seizure groups, matching with its origin. Overall, the STR multiplex systems were able to achieve its purpose in individualizing and differentiating, according to geographic region, Brazilian Cannabis sp. samples.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00414-020-02338-5DOI Listing
September 2020

Forensic DNA Analysis.

Anal Chem 2019 01 20;91(1):673-688. Epub 2018 Dec 20.

Department of Chemistry , Florida International University , Miami , Florida 33199 , United States.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.8b05318DOI Listing
January 2019

13-loci STR multiplex system for Brazilian seized samples of marijuana: individualization and origin differentiation.

Int J Legal Med 2019 Mar 15;133(2):373-384. Epub 2018 Oct 15.

Soil Science Department, Agronomy Faculty, Federal University of Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 7712, Porto Alegre, Rio Grande do Sul, CEP 91540-000, Brazil.

It is known that Cannabis in Brazil could either originate from Paraguay or be cultivated in Brazil. While consumer markets in the North and Northeast regions are maintained by national production, the rest of the country is supplied with Cannabis from Paraguay. However, the Brazilian Federal Police (BFP) has exponentially increased the seizure number of Cannabis seeds sent by mail. For this reason, the aim of the study was to assess the 13-loci short tandem repeat (STR) multiplex system proposed by Houston et al. (2015) to evaluate the power of such markers in individualization and origin differentiation of Cannabis sativa samples seized in Brazil by the BFP. To do so, 72 Cannabis samples seized in Brazil by BFP were analyzed. The principal coordinate analysis (PCoA) and probability identity (PI) analysis were computed. Additionally, the Cannabis samples' genotypes were subjected to comparison by Kruskal-Wallis H, followed by a multiple discriminant analysis (MDA). All samples analyzed revealed a distinct genetic profile. PCoA clearly discriminated the seizure sets based on their geographic origin. A combination of seven loci was enough to differentiate samples' genotypes, and the PI for a random sample is approximately one in 50 billion. The Cannabis samples were 100% correct as classified by Kruskal-Wallis H, followed by an MDA. The results of this study demonstrate that the 13-loci STR multiplex system successfully achieved the aim of sample individualization and origin differentiation and suggest that it could be a useful tool to help BFP intelligence in tracing back-trade routes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00414-018-1940-3DOI Listing
March 2019

Complete Genome Sequence of Enterococcus faecalis Strain P8-1 Isolated from Wild Magellanic Penguin (Spheniscus magellanicus) Feces on the South Coast of Brazil.

Genome Announc 2016 Jan 14;4(1). Epub 2016 Jan 14.

Basic Health Sciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.

Enterococcus faecalis strains have a ubiquitous nature that allows them to survive in different niches. Studies involving enterococci isolated from marine animals are scarce. Therefore, in this study, we report the complete genome sequence of E. faecalis strain P8-1 isolated from feces of a Magellanic penguin on the south coast of Brazil.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.01531-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714110PMC
January 2016

Characterization and Transcriptional Profile of Genes Involved in Glycoalkaloid Biosynthesis in New Varieties of Solanum tuberosum L.

J Agric Food Chem 2016 Feb 25;64(4):988-96. Epub 2016 Jan 25.

RIKILT Food Safety Institute, Wageningen University , 6708 PB Wageningen, The Netherlands.

Before commercial release, new potato (Solanum tuberosum) varieties must be evaluated for content of toxic compounds such as glycoalkaloids (GAs), which are potent poisons. GA biosynthesis proceeds via the cholesterol pathway to α-chaconine and α-solanine. The goal of this study was to evaluate the relationship between total glycoalkaloid (TGA) content and the expression of GAME, SGT1, and SGT3 genes in potato tubers. TGA content was measured by HPLC-MS, and reverse transcription quantitative polymerase chain reactions were performed to determine the relative expression of GAME, SGT1, and SGT3 genes. We searched for cis-elements of the transcription start site using the PlantPAN database. There was a relationship between TGA content and the relative expression of GAME, SGT1, and SGT3 genes in potato tubers. Putative promoter regions showed the presence of several cis-elements related to biotic and abiotic stresses and light. These findings provide an important step toward understanding TGA regulation and variation in potato tubers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jafc.5b05519DOI Listing
February 2016

Complete Genome Sequences of Two Listeria monocytogenes Serovars, 1/2a and 4b, Isolated from Dairy Products in Brazil.

Genome Announc 2015 Dec 17;3(6). Epub 2015 Dec 17.

Food Science Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil

Listeria monocytogenes is the foodborne pathogen responsible for a bacterial infection called listeriosis. Here, we present the whole-genome sequences of two L. monocytogenes serovars, 1/2a and 4b, which are considered the most prevalent in food processing plants and listeriosis outbreaks, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.01494-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683241PMC
December 2015

Selection of reference genes for transcriptional analysis of edible tubers of potato (Solanum tuberosum L.).

PLoS One 2015 1;10(4):e0120854. Epub 2015 Apr 1.

Food Science Department, Food Science and Technology Institute, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.

Potato (Solanum tuberosum) yield has increased dramatically over the last 50 years and this has been achieved by a combination of improved agronomy and biotechnology efforts. Gene studies are taking place to improve new qualities and develop new cultivars. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a bench-marking analytical tool for gene expression analysis, but its accuracy is highly dependent on a reliable normalization strategy of an invariant reference genes. For this reason, the goal of this work was to select and validate reference genes for transcriptional analysis of edible tubers of potato. To do so, RT-qPCR primers were designed for ten genes with relatively stable expression in potato tubers as observed in RNA-Seq experiments. Primers were designed across exon boundaries to avoid genomic DNA contamination. Differences were observed in the ranking of candidate genes identified by geNorm, NormFinder and BestKeeper algorithms. The ranks determined by geNorm and NormFinder were very similar and for all samples the most stable candidates were C2, exocyst complex component sec3 (SEC3) and ATCUL3/ATCUL3A/CUL3/CUL3A (CUL3A). According to BestKeeper, the importin alpha and ubiquitin-associated/ts-n genes were the most stable. Three genes were selected as reference genes for potato edible tubers in RT-qPCR studies. The first one, called C2, was selected in common by NormFinder and geNorm, the second one is SEC3, selected by NormFinder, and the third one is CUL3A, selected by geNorm. Appropriate reference genes identified in this work will help to improve the accuracy of gene expression quantification analyses by taking into account differences that may be observed in RNA quality or reverse transcription efficiency across the samples.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120854PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382326PMC
December 2015