Publications by authors named "Cíntia Alves"

58 Publications

Species assignment in forensics and the challenge of hybrids.

Forensic Sci Int Genet 2020 09 17;48:102333. Epub 2020 Jun 17.

Forensic Science Unit, Forensic Genetics Laboratory, Basque Country Police-Ertzaintza Larrauri Mendotxe 18, 48950 Erandio Bizkaia, Spain.

Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.
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http://dx.doi.org/10.1016/j.fsigen.2020.102333DOI Listing
September 2020

Low-level laser therapy attenuates lung inflammation and airway remodeling in a murine model of idiopathic pulmonary fibrosis: Relevance to cytokines secretion from lung structural cells.

J Photochem Photobiol B 2020 Jan 4;203:111731. Epub 2019 Dec 4.

Post Graduate Program in Biphotonic Applied to Health Sciences, Nove de Julho University (UNINOVE), São Paulo, SP, Brazil.

Idiopathic pulmonary fibrosis (IPF) is a progressive and chronic inflammatory disease with a poor prognosis and very few available treatment options. Low-level laser therapy (LLLT) has been gaining prominence as a new and effective anti-inflammatory and immunomodulatory agent. Can lung inflammation and the airway remodeling be regulated by LLLT in an experimental model of IPF in C57Bl/6 mice? The present study investigated if laser attenuates cellular migration to the lungs, the airway remodeling as well as pro-fibrotic cytokines secretion from type II pneumocytes and fibroblasts. Mice were irradiated (780 nm and 30 mW) and then euthanized fifteen days after bleomycin-induced lung fibrosis. Lung inflammation and airway remodeling were evaluated through leukocyte counting in bronchoalveolar lavage fluid (BALF) and analysis of collagen in lung, respectively. Inflammatory cells in blood were also measured. For in vitro assays, bleomycin-activated fibroblasts and type II pneumocytes were irradiated with laser. The pro- and anti-inflammatory cytokines level in BALF as well as cells supernatant were measured by ELISA, and the TGFβ in lung was evaluated by flow cytometry. Lung histology was used to analyze collagen fibers around the airways. LLLT reduced both migration of inflammatory cells and deposition of collagen fibers in the lungs. In addition, LLLT downregulated pro-inflammatory cytokines and upregulated the IL-10 secretion from fibroblasts and pneumocytes. Laser therapy greatly reduced total lung TGFβ. Systemically, LLLT also reduced the inflammatory cells counted in blood. There is no statistical difference in inflammatory parameters studied between mice of the basal group and the laser-treated mice. Data obtained indicate that laser effectively attenuates the lung inflammation, and the airway remodeling in experimental pulmonary fibrosis is driven to restore the balance between the pro- and anti-inflammatory cytokines in lung and inhibit the pro-fibrotic cytokines secretion from fibroblasts.
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http://dx.doi.org/10.1016/j.jphotobiol.2019.111731DOI Listing
January 2020

Effect of Low-Level Laser Therapy (LLLT) in Pulmonary Inflammation in Asthma Induced by House Dust Mite (HDM): Dosimetry Study.

Int J Inflam 2019 21;2019:3945496. Epub 2019 Mar 21.

Post-Graduate Program in Biophotonics Applied to Health Sciences, University Nove de Julho (UNINOVE), Sao Paulo, Brazil.

Asthma is characterized by chronic inflammation in the airways. Several models have been proposed for the discovery of new therapies. Low-Level Laser Therapy (LLLT) is relatively new and effective, very low cost, with no side effects. However, there is still no consensus on the optimal dose to be used. In this sense, the objective of the present study was to evaluate the best dose in an experimental model of asthma induced by House Dust Mite (HDM). Balb/c mice received administration of 100 ug/animal HDM and LLLT applications (diode laser: 660 nm, 100 mW and four different energies 1J, 3J, 5J, and 7.5J) for 16 days. After 24 hours, we studied inflammatory, functional, and structural parameters. The results showed that LBI was able to modulate the pulmonary inflammation observed by reducing the number of cells in Bronchoalveolar Lavage Fluid (BALF) as well as reducing the percentage of neutrophils, eosinophils and T lymphocytes. On the other hand, LLLT increased the level of IL-10 and reduced levels of IL-4, IL-5 and IL-13 in BALF. LLLT was able to reduce the production of mucus, peribronchial eosinophils, collagen deposition, bronchoconstriction index, and bronchial and muscular thickening in the airways. We concluded that the use of LLLT in the treatment of chronic inflammation of the airways attenuated the inflammatory process and functional and structural parameters. We emphasize, in general, that the 1J and 3J laser presented better results. Thus, photobiomodulation may be considered a promising tool for the treatment of chronic pulmonary allergic inflammation observed in asthma.
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http://dx.doi.org/10.1155/2019/3945496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448342PMC
March 2019

Low-Level Laser Therapy Reduces Lung Inflammation in an Experimental Model of Chronic Obstructive Pulmonary Disease Involving P2X7 Receptor.

Oxid Med Cell Longev 2018 4;2018:6798238. Epub 2018 Mar 4.

Post Graduate Program in Biophotonics Applied to Health Sciences, University Nove de Julho (UNINOVE), Sao Paulo, SP, Brazil.

Chronic obstructive pulmonary disease (COPD) is a progressive disease characterized by irreversible airflow limitation, airway inflammation and remodeling, and enlargement of alveolar spaces. COPD is in the top five leading causes of deaths worldwide and presents a high economic cost. However, there are some preventive measures to lower the risk of developing COPD. Low-level laser therapy (LLLT) is a new effective therapy, with very low cost and no side effects. So, our objective was to investigate if LLLT reduces pulmonary alterations in an experimental model of COPD. C57BL/6 mice were submitted to cigarette smoke for 75 days (2x/day). After 60 days to smoke exposure, the treated group was submitted to LLLT (diode laser, 660 nm, 30 mW, and 3 J/cm) for 15 days and euthanized for morphologic and functional analysis of the lungs. Our results showed that LLLT significantly reduced the number of inflammatory cells and the proinflammatory cytokine secretion such as IL-1, IL-6, and TNF- in bronchoalveolar lavage fluid (BALF). We also observed that LLLT decreased collagen deposition as well as the expression of purinergic P2X7 receptor. On the other hand, LLLT increased the IL-10 release. Thus, LLLT can be pointed as a promising therapeutic approach for lung inflammatory diseases as COPD.
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http://dx.doi.org/10.1155/2018/6798238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5857317PMC
September 2018

Genuine sildenafil tablets sold in Brazil disguised as MDMA.

Forensic Sci Int 2018 Feb 20;283:e8-e12. Epub 2017 Dec 20.

Seção Técnica de Física e Química Legal - Divisão de Laboratório, Instituto de Criminalística da Polícia Civil de Minas Gerais, Rua Juiz de Fora, 400, CEP 30180-060, Belo Horizonte, MG, Brazil; Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, CEP 31270-901, Belo Horizonte, MG, Brazil.

MDMA and sildenafil are two examples among many substances consumed in "raves", as well as in other types of "recreative" social events nowadays. During the first six months of 2017, five cases of supposedly MDMA tablets seized by local law enforcement forces in the state of Minas Gerais, Brazil, and brought to our forensic laboratory for examination, attracted our attention among dozens of others, as the tablets apprehended in these cases were, in fact, colorfully painted versions of genuine, pentagon-shaped, sildenafil tablets, freely available for sale in local pharmacies and drugstores. Physical profiling, together with ATR-FTIR spectral matching, multi-component/deconvolution analysis and correlation were employed to prove that these tablets were genuine sildenafil tablets from a specific manufacturer, painted in a colorful way so that they could be marketed as MDMA tablets to unsuspecting buyers.
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http://dx.doi.org/10.1016/j.forsciint.2017.12.006DOI Listing
February 2018

Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise.

Forensic Sci Int Genet 2017 05 7;28:219-224. Epub 2017 Mar 7.

Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal. Electronic address:

DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis. The exercise was organized during 2014 by a Working Commission of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG), created in 2013. The 24 participating laboratories from 10 countries were asked to identify the species in 11 DNA samples from previous GHEP-ISFG proficiency tests using a SPInDel primer mix and control samples of the 10 target species. A computer software was also provided to the participants to assist the analyses of the results. All samples were correctly identified by 22 of the 24 laboratories, including samples with low amounts of DNA (hair shafts) and mixtures of saliva and blood. Correct species identifications were obtained in 238 of the 241 (98.8%) reported SPInDel profiles. Two laboratories were responsible for the three cases of misclassifications. The SPInDel was efficient in the identification of species in mixtures considering that only a single laboratory failed to detect a mixture in one sample. This result suggests that SPInDel is a valid method for mixture analyses without the need for DNA sequencing, with the advantage of identifying more than one species in a single reaction. The low frequency of wrong (5.0%) and missing (2.1%) alleles did not interfere with the correct species identification, which demonstrated the advantage of using a method based on the analysis of multiple loci. Overall, the SPInDel method was easily implemented by laboratories using different genotyping platforms, the interpretation of results was straightforward and the SPInDel software was used without any problems. The results of this collaborative exercise indicate that the SPInDel method can be applied successfully in forensic casework investigations.
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http://dx.doi.org/10.1016/j.fsigen.2017.03.003DOI Listing
May 2017

Expiratory Reserve Volume During Slow Expiration With Glottis Opened in Infralateral Decubitus Position (ELTGOL) in Chronic Pulmonary Disease: Technique Description and Reproducibility.

Respir Care 2015 Mar 9;60(3):406-11. Epub 2014 Dec 9.

Postgraduate Program in Rehabilitation Sciences, Universidade Nove de Julho (UNINOVE), São Paulo, Brazil.

Background: There has not been a detailed description of expiratory reserve volume (ERV) during slow expiration with glottis open in infralateral decubitus position (ELTGOL, for Expiration Lente Totale Glotte Ouverte en infraLatéral) and its reproducibility. The aim of this study was to determine ERV during ELTGOL and to evaluate ERV intra-observer and inter-observer reliability.

Methods: In this prospective study, subjects were 30-70 y of age with chronic lung disease. ELTGOL (an active-passive or active physiotherapy technique) was applied in random order by 3 observers: 2 trained physiotherapists (PT 1 and PT 2) and the subject him/herself. Two ELTGOL compressions (A and B) were applied by PT 1, PT 2, and the subject.

Results: Thirty-two subjects were evaluated with moderate lung obstruction, FEV1: 47.7 ± 15.4, and ERV: 61.7 ± 29.4. The mean value of ERV for PT 1 was 51.4 ± 24.8%; for PT 2, it was 54.3 ± 31.8%; and for the subject, it was 53.5 ± 26.2% (P = .49). Considering the mean value of ERV, the ELTGOL mobilized more than 80% of ERV. There was good reliability intra-PT: PT 1, intraclass correlation coefficient (ICC) 0.85 (0.70-0.93), P < .0001; PT 2, ICC 0.90 (0.80-0.95), P < .0001, and inter-PT (ICC 0.86 [95% CI 0.71-0.93], P < .001). The Bland-Altman plot with mean bias and limits of agreement for ERV of PT 1 and PT 2 was -3.3 (-42.7 to 35.9).

Conclusions: ELTGOL mobilized more than 80% of ERV in subjects with moderate airway obstruction; there is no difference in ERV exhaled during the technique applied by a physiotherapist or by the subject. ELTGOL is a reproducible technique, determined by inter- and intra-observer testing.
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http://dx.doi.org/10.4187/respcare.03384DOI Listing
March 2015

Portuguese mitochondrial DNA genetic diversity-An update and a phylogenetic revision.

Forensic Sci Int Genet 2015 Mar 14;15:27-32. Epub 2014 Oct 14.

Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.

In recent years a large amount of mitochondrial population data for forensic purposes has been produced. Current efforts are focused at increasing the number of studied populations while generating updated genetic information of forensic quality. However, complete mitochondrial control region sequences are still scarce for most populations and even more so for complete mitochondrial genomes. In the case of Portugal, previous population genetics studies have already revealed the general portrait of HVS-I and HVS-II mitochondrial diversity, becoming now important to update and expand the mitochondrial region analysed. Accordingly, a total of 292 complete control region sequences from continental Portugal were obtained, under a stringent experimental design to ensure the quality of data through double sequencing of each target region. Furthermore, H-specific coding region SNPs were examined to detail haplogroup classification and complete mitogenomes were obtained for all sequences belonging to haplogroups U4 and U5. In general, a typical Western European haplogroup composition was found in mainland Portugal, associated to high level of mitochondrial genetic diversity. Within the country, no signs of substructure were detected. The typing of extra coding region SNPs has provided the refinement or confirmation of the previous classification obtained with EMMA tool in 96% of the cases. Finally, it was also possible to enlarge haplogroup U phylogeny with 28 new U4 and U5 mitogenomes.
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http://dx.doi.org/10.1016/j.fsigen.2014.10.004DOI Listing
March 2015

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Authors:
Josephine Purps Sabine Siegert Sascha Willuweit Marion Nagy Cíntia Alves Renato Salazar Sheila M T Angustia Lorna H Santos Katja Anslinger Birgit Bayer Qasim Ayub Wei Wei Yali Xue Chris Tyler-Smith Miriam Baeta Bafalluy Begoña Martínez-Jarreta Balazs Egyed Beate Balitzki Sibylle Tschumi David Ballard Denise Syndercombe Court Xinia Barrantes Gerhard Bäßler Tina Wiest Burkhard Berger Harald Niederstätter Walther Parson Carey Davis Bruce Budowle Helen Burri Urs Borer Christoph Koller Elizeu F Carvalho Patricia M Domingues Wafaa Takash Chamoun Michael D Coble Carolyn R Hill Daniel Corach Mariela Caputo Maria E D'Amato Sean Davison Ronny Decorte Maarten H D Larmuseau Claudio Ottoni Olga Rickards Di Lu Chengtao Jiang Tadeusz Dobosz Anna Jonkisz William E Frank Ivana Furac Christian Gehrig Vincent Castella Branka Grskovic Cordula Haas Jana Wobst Gavrilo Hadzic Katja Drobnic Katsuya Honda Yiping Hou Di Zhou Yan Li Shengping Hu Shenglan Chen Uta-Dorothee Immel Rüdiger Lessig Zlatko Jakovski Tanja Ilievska Anja E Klann Cristina Cano García Peter de Knijff Thirsa Kraaijenbrink Aikaterini Kondili Penelope Miniati Maria Vouropoulou Lejla Kovacevic Damir Marjanovic Iris Lindner Issam Mansour Mouayyad Al-Azem Ansar El Andari Miguel Marino Sandra Furfuro Laura Locarno Pablo Martín Gracia M Luque Antonio Alonso Luís Souto Miranda Helena Moreira Natsuko Mizuno Yasuki Iwashima Rodrigo S Moura Neto Tatiana L S Nogueira Rosane Silva Marina Nastainczyk-Wulf Jeanett Edelmann Michael Kohl Shengjie Nie Xianping Wang Baowen Cheng Carolina Núñez Marian Martínez de Pancorbo Jill K Olofsson Niels Morling Valerio Onofri Adriano Tagliabracci Horolma Pamjav Antonia Volgyi Gusztav Barany Ryszard Pawlowski Agnieszka Maciejewska Susi Pelotti Witold Pepinski Monica Abreu-Glowacka Christopher Phillips Jorge Cárdenas Danel Rey-Gonzalez Antonio Salas Francesca Brisighelli Cristian Capelli Ulises Toscanini Andrea Piccinini Marilidia Piglionica Stefania L Baldassarra Rafal Ploski Magdalena Konarzewska Emila Jastrzebska Carlo Robino Antti Sajantila Jukka U Palo Evelyn Guevara Jazelyn Salvador Maria Corazon De Ungria Jae Joseph Russell Rodriguez Ulrike Schmidt Nicola Schlauderer Pekka Saukko Peter M Schneider Miriam Sirker Kyoung-Jin Shin Yu Na Oh Iulia Skitsa Alexandra Ampati Tobi-Gail Smith Lina Solis de Calvit Vlastimil Stenzl Thomas Capal Andreas Tillmar Helena Nilsson Stefania Turrina Domenico De Leo Andrea Verzeletti Venusia Cortellini Jon H Wetton Gareth M Gwynne Mark A Jobling Martin R Whittle Denilce R Sumita Paulina Wolańska-Nowak Rita Y Y Yong Michael Krawczak Michael Nothnagel Lutz Roewer

Forensic Sci Int Genet 2014 Sep 28;12:12-23. Epub 2014 Apr 28.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. Electronic address:

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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http://dx.doi.org/10.1016/j.fsigen.2014.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127773PMC
September 2014

Comparative performance between "next generation" multiplex systems and the new European Standard Set of STR markers in the Portuguese Population.

Forensic Sci Int Genet 2014 Jan 8;8(1):137-42. Epub 2013 Sep 8.

Department of Biology, Faculty of Sciences, University of Porto, Portugal; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal.

Various multiplex STR systems have been developed by the major commercial companies in the forensic genetics field to comply with the recent establishment of the global European Standard Set (ESS) of markers. Of the various alternatives available, our laboratory decided to test the recent ESSplex Plus system (Qiagen) and the NGM kit (Life Technologies), which share the same 15 STR loci and comprise the most recently established ESS markers (D1S1656, D2S441, D10S1248, D12S391 and D22S1045). Apart from evaluating the kits' technical performances, a population and segregation study was carried out on a Portuguese sample, with the aim of introducing the ESS markers in routine forensic casework. A total of 370 individuals were sampled for this purpose, comprising 120 true trios (125 fathers, 125 mothers and 120 sons/daughters). No deviations from Hardy-Weinberg equilibrium were detected for the five new loci in the Portuguese population and no genotyping inconsistencies were observed between kits. Parameters of forensic interest revealed that, of the five ESS markers, D1S1656 was the most informative in our sample. Comparison of performances between all autosomal multiplex systems available in our laboratory (ESSplex Plus, NGM, Identifiler Plus and Powerplex 16 HS), revealed that the multiplex kits with the ESS markers generally showed better performances and, among these, the ESSplex Plus kit showed slightly higher sensitivity and a better detection of degraded DNA information.
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http://dx.doi.org/10.1016/j.fsigen.2013.08.015DOI Listing
January 2014

American tegumentary leishmaniasis: effectiveness of an immunohistochemical protocol for the detection of Leishmania in skin.

PLoS One 2013 21;8(5):e63343. Epub 2013 May 21.

Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil.

Background: American tegumentary leishmaniasis (ATL) is endemic in Latin America, where Brazil has over 27 thousand cases per year. The aim of the present study was to develop an immunohistochemical method (IHC) for ATL diagnosis. For this purpose, we used serum from a dog naturally infected with Leishmania (L) infantum (canine hyperimmune serum) as the primary antibody, followed by a detection system with a secondary biotinylated antibody.

Methodology: Skin samples were obtained from 73 patients in an endemic area of Caratinga, Minas Gerais (MG) State, Brazil all testing positive for ATL with the Montenegro skin test, microscopy, and PCR. Canine hyperimmune serum of a dog naturally infected with Leishmania (L.) infantum was employed as a primary antibody in an immunohistochemical diagnostic method using streptavidin-biotin peroxidase. To assess the specificity of this reaction, IHC assays employing two monoclonal antibodies were carried out. As the polymer-based technology is less time-consuming and labor intensive than the IHC labeled streptavidin-biotin peroxidase method, we compared the two methods for all samples.

Results: The IHC method detected ATL in 67 of the 73 cases (91.8%). Immunolabeled parasites were primarily detected inside macrophages either in the superficial or the deep dermis. Detection was facilitated by the high contrast staining of amastigotes (dark brown) against the light blue background. A lower detection rate (71.2%) was observed with the both of the monoclonal Leishmania antibodies compared to the canine hyperimmune serum. This may have been due to a non-specific background staining observed in all histological samples rendering positive detection more difficult. The higher efficacy of the canine hyperimmune serum in the IHC method was confirmed by the method using streptavidin-biotin peroxidase as well as that with the polymer-based technology (biotin-avidin-free system).

Conclusions: The data are encouraging with regard to validating IHC as a standard alternative method for ATL diagnosis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063343PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660443PMC
December 2013

Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs.

Int J Legal Med 2012 Nov 1;126(6):917-21. Epub 2012 Sep 1.

Institute of Molecular Pathology and Immunology, University of Porto, 4200-465, Porto, Portugal.

Kinship investigations such as paternity are currently solved using sets of (commercially available) highly polymorphic autosomal short tandem repeats (STRs), which lead to powerful likelihood ratios (LR). Still, some difficult cases arise whenever the kinship is much more remote or if the alternative hypotheses are not correctly formulated due to the lack of information (for e.g. there is an unknown relationship between the alleged and the true fathers). In these situations, beyond the routinely used marker set, laboratories usually enlarge the number and/or the type of markers analysed. Among these, autosomal indels and X-chromosome STRs have gained popularity. The aim of this study was to compare the results obtained after complementing an initial set of autosomal STRs with indels or with X-chromosome-specific STRs in simulated paternity cases where the alleged father is a close relative of the real one. Results show that in paternity cases where a low number of incompatibilities are observed, the best strategy is to increase the number of autosomal STRs under analysis. Nevertheless, if these are not available, our study globally shows that in father-daughter duos, a set of 12 X-STRs is more advantageous than 38 highly diverse autosomal biallelic markers. Additionally, the usefulness of X-STRs was also evaluated in cases where only a close relative of the alleged parent (father or mother) is available for testing. For those situations where these markers have the power to exclude, strong LR values are obtained. In the remaining cases, LRs are usually weak and sometimes the results are more likely under the wrong kinship hypothesis.
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http://dx.doi.org/10.1007/s00414-012-0768-5DOI Listing
November 2012

Assessing paternities with inconclusive STR results: The suitability of bi-allelic markers.

Forensic Sci Int Genet 2013 Jan 1;7(1):16-21. Epub 2012 Jun 1.

IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal.

In paternity testing the genetic profiles of the individuals are used to compare the relative likelihoods of the alleged father and the child being related as father/offspring against, usually, being unrelated. In the great majority of the cases, analyses with the widely used sets of short tandem repeat markers (STRs) provide powerful statistical evidence favouring one of the alternative hypotheses. Nevertheless, there are situations where the final statistical result is ambiguous, mostly because the alleged father shows incompatible genotypes at a few loci along with a very high paternity index in the remaining systems. In these cases, the possibility that the alleged father is actually a close relative of the real one (son, father or brother) can reasonably be raised. In such cases, when the statistical evidence obtained is considered as insufficient, the common practice is to extend the set of analysed markers. In this context, many authors have suggested that bi-allelic markers, such as single nucleotide (SNP) or insertion/deletion (Indel) polymorphisms, are markers of choice, as they are incomparably less prone to mutation than STRs. In this work we address the soundness of this claim and the consequences of this strategy, analyzing the a priori odds both for (a) expected number of Mendelian incompatibilities, and (b) expected values for the final likelihood ratios. Moreover, one hundred real pairs of second degree relatives, typed for two sets of markers: 15 STRs plus 38 Indels, were used to simulate paternity testing. Our data show that, for the number of markers commonly considered, the results from an extended battery of SNPs or Indels should be interpreted with caution when relatives are possibly involved.
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http://dx.doi.org/10.1016/j.fsigen.2012.05.002DOI Listing
January 2013

Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome.

Forensic Sci Int Genet 2012 Dec 27;6(6):778-84. Epub 2012 Mar 27.

Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität Kiel, Brunswiker Straße 10, 24105 Kiel, Germany.

A large number of short tandem repeat (STR) markers spanning the entire human X chromosome have been described and established for use in forensic genetic testing. Due to their particular mode of inheritance, X-STRs often allow easy and informative haplotyping in kinship analyses. Moreover, some X-STRs are known to be tightly linked so that, in combination, they constitute even more complex genetic markers than each STR taken individually. As a consequence, X-STRs have proven particularly powerful in solving complex cases of disputed blood relatedness. However, valid quantification of the evidence provided by X-STR genotypes in the form of likelihood ratios requires that the recombination rates between markers are exactly known. In a collaborative family study, we used X-STR genotype data from 401 two- and three-generation families to derive valid estimates of the recombination rates between 12 forensic markers widely used in forensic testing, namely DXS10148, DXS10135, DXS8378 (together constituting linkage group I), DXS7132, DXS10079, DXS10074 (linkage group II), DXS10103, HPRTB, DXS10101 (linkage group III), DXS10146, DXS10134 and DXS7423 (linkage group IV). Our study is the first to simultaneously allow for mutation and recombination in the underlying likelihood calculations, thereby obviating the bias-prone practice of excluding ambiguous transmission events from further consideration. The statistical analysis confirms that linkage groups I and II are transmitted independently from one another whereas linkage groups II, III and IV are characterised by inter-group recombination fractions that are notably smaller than 50%. Evidence was also found for recombination within all four linkage groups, with recombination fraction estimates ranging as high as 2% in the case of DXS10146 and DXS10134.
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http://dx.doi.org/10.1016/j.fsigen.2012.02.015DOI Listing
December 2012

Capillary electrophoresis of an X-chromosome STR decaplex for kinship deficiency cases.

Methods Mol Biol 2012 ;830:57-71

IPATIMUP-Institute of Pathology and Molecular Immunology of the University of Porto, Porto, Portugal.

During the two last decades, STR markers located on the autosomes have been gaining relevance and have nearly replaced the use of other type of markers in most cases of genetic identification, paternity testing, as well as in other situations of kinship analysis. Nevertheless, in some complex cases, independently of the number of polymorphisms being typed, autosomal markers convey very little information. Depending on the parentage constellation available for analysis, as well as the gender of the subjects, this problem can sometimes be solved by using markers that have different modes of transmission. Therefore, most forensic laboratories are nowadays prepared to analyse lineage markers (Y chromosome and mtDNA) and many have recently set up methods for the analysis of X-STRs. In the present chapter, a method is described for the typing of ten X chromosome-specific markers in a single PCR amplification reaction, followed by capillary electrophoresis separation and fluorescent detection in an ABI Genetic Analyser apparatus. This typing strategy was developed and optimized for the simultaneous amplification of ten X-linked specific STRs well distributed along the chromosome: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 and DXS7423.
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http://dx.doi.org/10.1007/978-1-61779-461-2_5DOI Listing
March 2012

Allele frequencies for 15 autosomal STR markers in the Libyan population.

Ann Hum Biol 2012 Jan 1;39(1):80-3. Epub 2011 Nov 1.

Laboratory of Molecular Genetics, Immunology and Human Pathologies, Faculty of Sciences, University of Tunis El Manar, Tunis, Tunisia.

Background: Until recently Libya remained the only state of the Maghreb without genetic evolution investigations of the genetic landscape of its population. Apart from some studies of Libyan Jews and Libyan Tuareg, only two recent investigations, based on autosomal ancestry informative SNP and mitochondrial DNA markers, have concerned the general Libyan population.

Aim: The present work is the first to describe STR markers polymorphism in the general Libyan population in order to contribute to the analysis of its genetic diversity for forensic purposes.

Subjects And Methods: Allele frequencies for 15 STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, D19S433) included in the AmpFlSTR Identifiler kit were determined in a sample of 99 unrelated individuals originating from the general Libyan population.

Results: No deviations from Hardy-Weinberg equilibrium were observed, with the exception of CSF1PO. Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999. Comparisons with data from other North African populations showed significant differences between Libyans and Tunisians, Moroccans and Egyptians.

Conclusions: The high informativity observed for these 15 STRs in a Libyan population demonstrates their usefulness for forensic and parental purposes.
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http://dx.doi.org/10.3109/03014460.2011.630678DOI Listing
January 2012

Reconstructing the Indian origin and dispersal of the European Roma: a maternal genetic perspective.

PLoS One 2011 Jan 10;6(1):e15988. Epub 2011 Jan 10.

Institute of Evolutionary Biology (CSIC-UPF), CEXS-UPF-PRBB, Barcelona, Spain.

Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015988PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018485PMC
January 2011

Nilotes from Karamoja, Uganda: haplotype data defined by 17 Y-chromosome STRs.

Forensic Sci Int Genet 2010 Jul 3;4(4):e83-6. Epub 2009 Aug 3.

Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal.

In this work 118 Nilote male samples were genotyped from Karamoja region, in Northeast Uganda, through 17 Y-chromosomal short tandem repeats (STRs)-DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. A total of 94 different haplotypes were found, where 19 were shared by at least two individuals, and haplotype diversity amounted to 0.9958+/-0.0017. When considering only the nine Y-STRs included in the minimal haplotype (YHRD) the haplotype diversity decreased to 0.9807+/-0.0048, a similar value to those found in other African populations such as Mozambique, Angola and Guinea-Bissau. Population comparisons were performed between our sample and nine other African populations. Significant R(st) genetic distances were obtained between the Nilote population from Karamoja and all African populations used for comparison, except Xhosa sample from South Africa. In the multidimensional scaling (MDS) plot, the Karamoja sample is well separated from all other populations, standing between the Ethiopia and the Bantu samples, although closer to this last group.
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http://dx.doi.org/10.1016/j.fsigen.2009.07.001DOI Listing
July 2010

Genetic profiles and sex identification of found-dead wolves determined by the use of an 11-loci PCR multiplex.

Forensic Sci Int Genet 2010 Feb 23;4(2):68-72. Epub 2009 Jun 23.

Instituto de Patologia e Imunologia da Universidade do Porto, Porto, Portugal.

A previously described canine-specific 9-STR multiplex, now including two markers for sex determination, was tested for the genotyping of 23 wolves from Northern and Central Portugal. The samples were collected at necropsies and presented varying states of preservation. Complete profiles were obtained in 74% of the samples, partial profiles in 22% and one completely null profile. This survey revealed 15 alleles not previously described in dogs, distributed among 6 STR loci. It is shown that this genotyping system, previously tested in domestic dogs, can be reliably used for obtaining complete genetic profiles in wolves with a matching probability of 2.45 x 10(-9) and compatible sex identification, even in sub-optimal samples. Moreover, a population structure analysis using the observed genotypes revealed that this multiplexed 11-loci panel may potentially be used for discriminating between wolves and dogs.
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http://dx.doi.org/10.1016/j.fsigen.2009.05.003DOI Listing
February 2010

A framework for the development of STR genotyping in domestic animal species: characterization and population study of 12 canine X-chromosome loci.

Electrophoresis 2010 Jan;31(2):303-8

Instituto de Patologia e Imunologia da Universidade do Porto, Porto, Portugal.

This study reports the methodology used to search, select and characterize STR loci on the canine X chromosome using publicly available genome resources and following the current guidelines for human and non-human forensic testing. After several rounds of selection, 12 X-STR markers were optimized for simultaneous co-amplification in a single PCR, and genetic profiles were determined in a sample of 103 unrelated dogs. Mendelian inheritance was verified and mutation rates were assessed using family groups. Alleles that varied in size were sequenced to create a standardized nomenclature proposal based on the number of repeats. All loci conformed to Hardy-Weinberg expectations. The resulting panel showed high forensic efficiency, presenting high values of power of discrimination (in males and females) and mean exclusion chance, both in trios involving female offspring and in duos composed of dam and male offspring. Its use may complement the information obtained by autosomal STR analysis and contribute to the resolution of complex cases of kinship in dogs. The presented methodology for the de novo construction of an STR multiplex may also provide a helpful framework for analogous work in other animal species. As an increasing number of reference genomes become available, convenient tools for individual identification and parentage testing based on STR loci selected from autosomes or sex chromosomes' sequences may be created following this strategy.
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http://dx.doi.org/10.1002/elps.200900389DOI Listing
January 2010

Forensic analysis of dog (Canis lupus familiaris) mitochondrial DNA sequences: an inter-laboratory study of the GEP-ISFG working group.

Forensic Sci Int Genet 2009 Dec 20;4(1):49-54. Epub 2009 May 20.

Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.

A voluntary collaborative exercise aiming at the mitochondrial analysis of canine biological samples was carried out in 2006-2008 by the Non-Human Forensic Genetics Commission of the Spanish and Portuguese Working Group (GEP) of the International Society for Forensic Genetics (ISFG). The participating laboratories were asked to sequence two dog samples (one bloodstain and one hair sample) for the mitochondrial D-loop region comprised between positions 15,372 and 16,083 using suggested primers and PCR conditions, and to compare their results against a reference sequence. Twenty-one participating laboratories reported a total of 67.5% concordant results, 15% non-concordant results, and 17.5% no results. The hair sample analysis presented more difficulty to the participants than the bloodstain analysis, with a high percentage (29%) failing to obtain a result. The high level of participation showed the interest of the community in the analysis of dog forensic samples but the results reveal that crucial methodological issues need to be addressed and further training is required in order to respond proficiently to the demands of forensic casework.
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http://dx.doi.org/10.1016/j.fsigen.2009.04.008DOI Listing
December 2009

A genetic historical sketch of European Gypsies: The perspective from autosomal markers.

Am J Phys Anthropol 2010 Apr;141(4):507-14

IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto 4200-465, Portugal.

In this study, 123 unrelated Portuguese Gypsies were analyzed for 15 highly polymorphic autosomal short tandem repeats (STRs). Average gene diversity across the 15 markers was 76.7%, which is lower than that observed in the non-Gypsy Portuguese population. Subsets of STRs were used to perform comparisons with other Gypsy and corresponding host populations. Interestingly, diversity reduction in Gypsy groups compared to their non-Gypsy surrounding populations apparently varied according to an East-West gradient, which parallels their dispersion in Europe as well as a decrease in complexity of their internal structure. Analysis of genetic distances revealed that the average level of genetic differentiation between Gypsy groups was much larger than that observed between the corresponding non-Gypsy populations. The high rate of heterogeneity among Gypsies can be explained by strong genetic drift and limited intergroup gene flow. However, when genetic relationships were addressed through principal component analysis, all Gypsy populations clustered together and was clearly distinguished from other populations, a pattern that suggests their common origin. Concerning the putative ancestral genetic component, admixture analysis did not reveal strong Indian ancestry in the current Gypsy gene pools, in contrast to the high admixture estimates for either Europeans or Western Asians.
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http://dx.doi.org/10.1002/ajpa.21166DOI Listing
April 2010

A new multiplex for human identification using insertion/deletion polymorphisms.

Electrophoresis 2009 Nov;30(21):3682-90

Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.

Human identification is usually based on the study of STRs or SNPs depending on the particular characteristics of the investigation. However, other types of genetic variation such as insertion/deletion polymorphisms (indels) have considerable potential in the field of identification, since they can combine the desirable characteristics of both STRs and SNPs. In this study, a set of 38 non-coding bi-allelic autosomal indels reported to be polymorphic in African, European, and Asian populations were selected. We developed a sensitive genotyping assay, which is able to characterize all 38 bi-allelic markers using a single multiplex PCR and detected with standard CE analyzers. Amplicon length was designed to be shorter than 160 bp. Complete profiles were obtained using 0.3 ng of DNA, and full genotyping of degraded samples was possible in cases where standard STR typing had partially failed. A total of 306 individuals from Angola, Mozambique, Portugal, Macau, and Taiwan were studied and population data are presented. All indels were polymorphic in the three population groups studied and the random match probabilities of the set ranged in orders of magnitude from 10(-14) to 10(-15). Therefore, the indel-plex represents a valuable approach in human identification studies, especially in challenging DNA cases, as a more straightforward and efficient alternative to SNP typing.
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http://dx.doi.org/10.1002/elps.200900274DOI Listing
November 2009

Hepatic extracellular matrix alterations in dogs naturally infected with Leishmania (Leishmania) chagasi.

Int J Exp Pathol 2009 Oct;90(5):538-48

Depto. de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.

Summary The aim of this work was to study alterations in the extracellular matrix of liver in dogs naturally infected with Leishmania (Leishmania) chagasi that are correlated with clinical aspects and with histological, parasitological and immunological findings. The study was carried out on 30 dogs, 10 uninfected (control group) and 20 infected. The infected animals were further divided into two groups: an asymptomatic group of 10 dogs without clinical signs of the disease; and a symptomatic group of 10 dogs with classical clinical signs. All thirty animals were mongrel dogs of undefined age, obtained from the municipality of Belo Horizonte, MG, metropolitan area. During necropsy, liver fragments were collected and fixed in 10% buffered formaldehyde for histological examination. Paraffined sections of the tissues were stained with haematoxylin-eosin, Gomori's ammoniacal silver stain for reticular fibres and strepto-avidin peroxidase for immunohistochemical detection of Leishmania amastigotes. Frozen tissue sections were stained by immunofluorescence for fibronectin (FN) and laminin (LN). Liver collagen deposition was significantly greater in the infected than the control animals and differed significantly between the symptomatic and asymptomatic dogs. There was a positive correlation between the parasite load and liver collagen deposition. The increased collagen deposition in infected animal livers may be associated with the parasite burden. Adhesive FN and LN fibres were significantly more highly expressed in the livers of symptomatic than of asymptomatic dogs. Our results demonstrate that canine visceral leishmaniasis causes fibrogenesis in liver, associated with the parasite load and degenerative processes.
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http://dx.doi.org/10.1111/j.1365-2613.2009.00681.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768152PMC
October 2009

Substructure of a Tunisian Berber population as inferred from 15 autosomal short tandem repeat loci.

Hum Biol 2008 Aug;80(4):435-48

Laboratory of Molecular Genetics, Immunology and Human Pathology, Faculty of Sciences, University of Tunis El Manar, Tunis, Tunisia.

Currently, language and cultural practices are the only criteria to distinguish between Berber autochthonous Tunisian populations. To evaluate these populations' possible genetic structure and differentiation, we have analyzed 15 autosomal short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, and D19S433) in three southern Tunisian Berber groups: Sened, Matmata, and Chenini-Douiret. The exact test of population differentiation based on allele frequencies at the 15 loci shows significant P values at 7 loci between Chenini-Douiret and both Sened and Matmata, whereas just 5 loci show significant P values between Sened and Matmata. Comparative analyses between the three Berber groups based on genetic distances show that P values for F(ST) distances are significant between the three Berber groups. Population analysis performed using Structure shows a clear differentiation between these Berber groups, with strong genetic isolation of Chenini-Douiret. These results confirm at the autosomal level the high degree of heterogeneity of Tunisian Berber populations that had been previously reported for uniparental markers.
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http://dx.doi.org/10.3378/1534-6617-80.4.435DOI Listing
August 2008

Population data defined by 15 autosomal STR loci in Karamoja population (Uganda) using AmpF/STR Identifiler kit.

Forensic Sci Int Genet 2009 Mar 25;3(2):e55-8. Epub 2008 Jul 25.

Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal.

Karamoja is a region located in the northeast edge of Uganda where it borders Kenya and Sudan. The majority of inhabitants of this region belong to Karimojong ethnic groups. In this work, we present allele frequencies for 15 STRs included in the AmpF/STR Identifiler kit (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) in 218 unrelated individuals from Karamoja region. Observed genotype distributions for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. When comparing allele frequencies, for each locus, with other five African samples (Equatorial Guinea, Mozambique, Cabinda (Angola), Rwanda and Tanzania) the only population that did not show significant differences with Karamoja (Uganda) was Rwanda.
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http://dx.doi.org/10.1016/j.fsigen.2008.06.005DOI Listing
March 2009

A new autosomal STR nineplex for canine identification and parentage testing.

Electrophoresis 2009 Jan;30(2):417-23

IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.

A single multiplex PCR assay capable of simultaneously amplifying nine canine-specific autosomal STR markers (FH3210, FH3241, FH2004, FH2658, FH4012, REN214L11, FH2010, FH2361 and the newly described C38) was developed for individual identification and parentage testing in domestic dogs. In order to increase genotyping efficiency, amplicon sizes were optimized for a 90-350 bp range, with fluorescently labelled primers for use in Applied Biosystems, Inc., platforms. The performance of this new multiplex system was tested in 113 individuals from a case-study population and 12 random dogs from mixed-breed origin. Co-dominant inheritance of STR alleles was investigated in 101 father, mother and son trios. Expected heterozygosity values vary between 0.5648 for REN214L11 and 0.9050 for C38. The high level of genetic diversity observed for most markers provides this multiplex with a very high discriminating power (matching probability=1.63/10(10) and matching probability among siblings=4.9/10(3)). Allele sequences and a proposal for standardized nomenclature are also herein presented, aiming at implementing the use of this system in forensic DNA typing and population genetic studies. This approach resulted in an optimized and well-characterized canine DNA genotyping system that is highly performing and straightforward to integrate and employ routinely. Although this STR multiplex was developed for use and tested in a case-study population, the Portuguese breed Cão de Gado Transmontano, it proved to be useful for general identification purposes or parentage testing.
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http://dx.doi.org/10.1002/elps.200800307DOI Listing
January 2009

Expression of IFN-gamma, TNF-alpha, IL-10 and TGF-beta in lymph nodes associates with parasite load and clinical form of disease in dogs naturally infected with Leishmania (Leishmania) chagasi.

Vet Immunol Immunopathol 2009 Apr 17;128(4):349-58. Epub 2008 Nov 17.

Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil.

American visceral leishmaniasis is a zoonosis of the New World. Dogs are the main reservoir of the disease and there is much interest in the understanding of mechanisms implicated in protection against canine infection. Nevertheless, most studies in dogs have not been carried out in organs that are targets of infection. This work is first to report the profile of cytokines and parasite burdens, as determined by real-time PCR, in the lymph nodes of dogs naturally infected with Leishmania chagasi. With this purpose, 18 mongrel dogs were divided in three groups: control non-infected dogs (n=6) and naturally infected animals with L. chagasi, asymptomatic (n=6) and symptomatic (n=6). Parasite burden in lymph nodes was 73-fold greater in symptomatic than asymptomatic animals. Prescapular lymph nodes of asymptomatic dogs had the highest expression of IFN-gamma and TNF-alpha and low parasite burden, indicating that these cytokines play a role in protection against infection. Highest expression of IL-10 and TGF-beta and high parasite burden were observed in symptomatic dogs, suggesting a role for these cytokines in the progression of disease. Hence, the balance of expression of IFN-gamma and TNF-alpha (protective) and IL-10 and TGF-beta (disease progression) in lymph nodes determine parasite burden and clinical expression in naturally infected dogs.
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http://dx.doi.org/10.1016/j.vetimm.2008.11.020DOI Listing
April 2009

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations.

Int J Legal Med 2009 May 12;123(3):227-34. Epub 2008 Dec 12.

IPATIMUP Institute of Pathology and Molecular Immunology, University of Porto, Porto, Portugal.

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (> or =1 in 5 x 10(5)) and females (> or =1 in 3 x 10(9)), as well as high mean exclusion chance in father/daughter duos (> or =99.953%) and in father/mother/daughter trios (> or =99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.
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http://dx.doi.org/10.1007/s00414-008-0309-4DOI Listing
May 2009

Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study.

Int J Legal Med 2008 Nov 24;122(6):529-33. Epub 2008 Jul 24.

University of Santiago de Compostela, C/San Francisco, A Coruña, Spain.

A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25 x 10(-4) (95% CI 0.05 x 10(-3)-1.53 x 10(-3)) at DYS438 and 6.36 x 10(-3) (95% CI 2.75 x 10(-3)-12.49 x 10(-3)) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice.
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http://dx.doi.org/10.1007/s00414-008-0265-zDOI Listing
November 2008