59 results on '"Amato ME"'
Search Results
2. Towards complete male individualization with rapidly mutating Y-chromosomal STRs
- Author
-
Ballantyne, KN, Ralf, A, Aboukhalid, R, Achakzai, NM, Anjos, MJ, Ayub, Q, Balažic, J, Ballantyne, J, Ballard, DJ, Berger, B, Bobillo, C, Bouabdellah, M, Burri, H, Butler, J, Capal, T, Caratti, S, Carracedo, A, Cartault, F, Carvalho, EF, Cheng, B, Coble, MD, Comas, D, Corach, D, D'Amato, ME, Davison, S, de Carvalho, EF, de Knijff, Peter, de Ungria, M, Decorte, Ronny, Dobosz, T, Dupuy, BM, Elmrghni, S, Gliwinski, M, Gomes, SC, Grol, L, Haas, C, Hanson, E, Henke, J, Hill, CR, Holmlund, G, Honda, K, Immel, U, Inoue, S, Jobling, MA, Kaddura, M, Kim, JS, Kim, SH, Kim, W, King, TE, Klausriegler, E, Kling, D, Kovacevic, LL, Kovatsi, L, Krajewski, P, Kravchenko, S, Larmuseau, Maarten, Lee, EY, Lee, SH, Lessig, R, Livshits, LA, Marjanovic, D, Minarik, M, Mizuno, N, Moreira, H, Morling, N, Mukherjee, M, Nagaraju, J, Neuhuber, F, Nie, S, Nilasitsataporn, P, Nishi, T, Oh, HH, Olofsson, J, Onofri, V, Palo, JU, Pamjav, H, Parson, W, Payet, C, Petlach, M, Phillips, C, Ploski, R, Prasad, SPR, Primorac, D, Purnnomo, GA, Purps, J, Rangel, H, Rebala, K, Rerkamnuaychoke, B, Rey, D, Robino, C, Rodríguez, F, Roewer, L, Rosa, A, Sajantila, A, Sala, A, Salvador, J, Sanz, P, Schmitt, C, Sharma, AK, Silva, DA, Shin, KJ, Sijen, T, Sirker, M, Siváková, D, Skaro, V, Solano-Matamoros, C, Souto, L, Stenzl, V, Sudoyo, H, Syndercombe-Court, D, Tagliabracci, A, Taylor, D, Tillmar, A, Tsybovsky, IS, Tyler-Smith, C, van der Gaag, K, Vanek, D, Völgyi, A, Ward, D, Willemse, P, Winkler, C, Yap, EPH, Yong, RYY, Zupanic Pajnic, I, and Kayser, M
- Subjects
haplotypes ,paternal lineage ,RM YSTRs ,Y-STRs ,forensic ,Y-chromosome - Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database. ispartof: Human Mutation vol:35 issue:8 pages:1021-1032 status: published
- Published
- 2014
3. Static and Moving Frontiers: The Genetic Landscape of Southern African Bantu-Speaking Populations
- Author
-
Marks, Sj, Montinaro, F, Levy, H, Brisighelli, F, Ferri, G, Bertoncini, S, Batini, C, Busby, Gbj, Arthur, C, Mitchell, P, Stewart, Ba, Oosthuizen, O, Oosthuizen, E, D'Amato, Me, Davison, S, Pascali, V, Capelli, C, Brisighelli, F (ORCID:0000-0001-5469-4413), Pascali, V (ORCID:0000-0001-6520-5224), Marks, Sj, Montinaro, F, Levy, H, Brisighelli, F, Ferri, G, Bertoncini, S, Batini, C, Busby, Gbj, Arthur, C, Mitchell, P, Stewart, Ba, Oosthuizen, O, Oosthuizen, E, D'Amato, Me, Davison, S, Pascali, V, Capelli, C, Brisighelli, F (ORCID:0000-0001-5469-4413), and Pascali, V (ORCID:0000-0001-6520-5224)
- Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still amatter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by amoving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.
- Published
- 2015
4. Static and Moving Frontiers: The Genetic Landscape of Southern African Bantu-Speaking Populations
- Author
-
Marks, Sj, Montinaro, F, Levy, H, Brisighelli, Francesca, Ferri, G, Bertoncini, S, Batini, C, Busby, Gbj, Arthur, C, Mitchell, P, Stewart, Ba, Oosthuizen, O, Oosthuizen, E, D'Amato, Me, Davison, S, Pascali, V, Capelli, C., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Marks, Sj, Montinaro, F, Levy, H, Brisighelli, Francesca, Ferri, G, Bertoncini, S, Batini, C, Busby, Gbj, Arthur, C, Mitchell, P, Stewart, Ba, Oosthuizen, O, Oosthuizen, E, D'Amato, Me, Davison, S, Pascali, V, Capelli, C., and Brisighelli, Francesca (ORCID:0000-0001-5469-4413)
- Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.
- Published
- 2014
5. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci
- Author
-
Purps, J, Siegert, S, Willuweit, S, Nagy, M, Alves, C, Salazar, R, Angustia, Sm, Santos, Lh, Anslinger, K, Bayer, B, Ayub, Q, Wei, W, Xue, Y, Tyler Smith, C, Bafalluy, Mb, Martínez Jarreta, B, Balitzki, B, Tschumi, S, Ballard, D, Court, D, Barrantes, X, Bäßler, G, Wiest, T, Berger, B, Niederstätter, H, Parson, W, Davis, C, Budowle, B, Burri, H, Borer, U, Koller, C, Carvalho, Ef, Domingues, Pm, Chamoun, Wt, Coble, Md, Hill, Cr, Corach, D, Caputo, M, D'Amato, Me, Davison, S, Decorte, R, Larmuseau, Mh, Ottoni, C, Rickards, O, Jonkisz, A, Frank, We, Furac, I, Gehrig, C, Castella, V, Grskovic, B, Haas, C, Wobst, J, Hadzic, G, Drobnic, K, Immel, Ud, Lessig, R, Jakovski, Z, Ilievska, T, Klann, Ae, García, Cc, De Knijff, P, Kondili, A, Miniati, P, Vouropoulou, M, Kovacevic, L, Marjanovic, D, Lindner, I, Mansour, I, Al Azem, M, Andari, Ae, Marino, M, Furfuro, S, Locarno, L, Martín, P, Luque, Gm, Alonso, A, Miranda, L, Moreira, H, Neto, R, Nogueira, Tl, Morling, N, Onofri, V, Tagliabracci, A, Pamjav, H, Pelotti, S, Abreu Glowacka, M, Cárdenas, J, Rey Gonzalez, D, Salas, A, Brisighelli, Francesca, Capelli, C. Et Al, Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Purps, J, Siegert, S, Willuweit, S, Nagy, M, Alves, C, Salazar, R, Angustia, Sm, Santos, Lh, Anslinger, K, Bayer, B, Ayub, Q, Wei, W, Xue, Y, Tyler Smith, C, Bafalluy, Mb, Martínez Jarreta, B, Balitzki, B, Tschumi, S, Ballard, D, Court, D, Barrantes, X, Bäßler, G, Wiest, T, Berger, B, Niederstätter, H, Parson, W, Davis, C, Budowle, B, Burri, H, Borer, U, Koller, C, Carvalho, Ef, Domingues, Pm, Chamoun, Wt, Coble, Md, Hill, Cr, Corach, D, Caputo, M, D'Amato, Me, Davison, S, Decorte, R, Larmuseau, Mh, Ottoni, C, Rickards, O, Jonkisz, A, Frank, We, Furac, I, Gehrig, C, Castella, V, Grskovic, B, Haas, C, Wobst, J, Hadzic, G, Drobnic, K, Immel, Ud, Lessig, R, Jakovski, Z, Ilievska, T, Klann, Ae, García, Cc, De Knijff, P, Kondili, A, Miniati, P, Vouropoulou, M, Kovacevic, L, Marjanovic, D, Lindner, I, Mansour, I, Al Azem, M, Andari, Ae, Marino, M, Furfuro, S, Locarno, L, Martín, P, Luque, Gm, Alonso, A, Miranda, L, Moreira, H, Neto, R, Nogueira, Tl, Morling, N, Onofri, V, Tagliabracci, A, Pamjav, H, Pelotti, S, Abreu Glowacka, M, Cárdenas, J, Rey Gonzalez, D, Salas, A, Brisighelli, Francesca, Capelli, C. Et Al, and Brisighelli, Francesca (ORCID:0000-0001-5469-4413)
- Abstract
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.
- Published
- 2014
6. Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages
- Author
-
Batini, C, Ferri, G, Destro Bisol, G, Brisighelli, Francesca, Luiselli, D, Sanchez Diz, P, Rocha, J, Simonson, T, Brehm, A, Montano, V, Elwali, Ne, Spedini, G, D'Amato, Me, Myres, N, Ebbesen, P, Comas, D, Capelli, C., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Batini, C, Ferri, G, Destro Bisol, G, Brisighelli, Francesca, Luiselli, D, Sanchez Diz, P, Rocha, J, Simonson, T, Brehm, A, Montano, V, Elwali, Ne, Spedini, G, D'Amato, Me, Myres, N, Ebbesen, P, Comas, D, Capelli, C., and Brisighelli, Francesca (ORCID:0000-0001-5469-4413)
- Abstract
The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture, and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad data set of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high-resolution single nucleotide polymorphism analysis with short tandem repeats variation of their subclades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional preagricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.
- Published
- 2011
7. X-RAY STRUCTURE DETERMINATION OF CYCLOBUTANE PHOTODIMERS FROM (Z)-ALPHA, BETA-DIARYLACRYLONITRILES
- Author
-
Amato, Me, Musumarra, Giuseppe, Scarlata, G, Lamba, D, and Spagna, R.
- Published
- 1989
8. X-ray, NMR and theoretical studies of the structure and conformation of the nootropic agent tenilsetam
- Author
-
Amato, ME, Bandoli, G, Grassi, A, Marletta, A, and Perly, B
- Published
- 1991
- Full Text
- View/download PDF
9. Improving paediatric movement disorders care: Insights on rating scales utilization and clinical practice.
- Author
-
Amato ME, Darling A, Stovickova L, Attard S, Eggink H, Engelen M, Freilinger M, Grosso S, Hadzsiev K, Moroni I, Nardocci N, Neubauer D, Nicita F, Pagliano E, Siegert S, Soler D, van de Pol LA, Vasco G, Vidailhet M, Willemsen MA, Zibordi F, Zorzi G, Zumrova A, Reinhard C, Sevin C, Wolf N, Rodriguez-Blazquez C, Sival DA, and Ortigoza-Escobar JD
- Subjects
- Humans, Child, Europe, Transition to Adult Care standards, Pediatrics standards, Pediatrics methods, Severity of Illness Index, Adolescent, Movement Disorders therapy, Movement Disorders diagnosis
- Abstract
Aim: This exploratory study evaluates rating scale usage by experts from the European Reference Network for Rare Neurological Diseases (ERN-RND) for paediatric MD, considering factors like diagnosis, intellectual disability, age, and transition to adult care. The aim is to propose a preliminary framework for consistent application., Methods: A multicentre survey among 25 ERN-RND experts from 10 European countries examined rating scale usage in paediatric MD, categorizing MD into acute, non-progressive, and neurodegenerative types. Factors influencing scale choice and the transition to adult care practices were analysed. A comprehensive literature search was conducted to identify the earliest age of application of these scales in paediatric patients., Results: The study identifies various rating scales and establishes their usage frequencies for different MDs. Experts highlighted the need for standardized scales and proposed preliminary evaluation strategies based on clinical contexts. Challenges in applying scales to young, non-cooperative patients were acknowledged., Interpretation: The study recommends developing standardized rating scales for paediatric MDs to improve evaluations and data collection. It suggests potential scales for specific clinical scenarios to better evaluate disease progression. Comprehensive, patient-centred care remains crucial during the transition to adult care, despite the identified challenges. This exploratory approach aims to enhance patient outcomes and care., Competing Interests: Declaration of competing interest We hereby affirm that all authors involved in the preparation of this manuscript declare no conflicts of interest. This includes financial, personal, or professional relationships that could potentially influence the interpretation of the work presented herein., (Copyright © 2024 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
10. Ethical considerations for Forensic Genetic Frequency databases: First Report conception and development.
- Author
-
D'Amato ME, Joly Y, Lynch V, Machado H, Scudder N, and Zieger M
- Subjects
- Humans, Gene Frequency, Databases, Genetic, Databases, Nucleic Acid ethics, DNA Fingerprinting ethics, Forensic Genetics ethics
- Abstract
The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received., Competing Interests: Declaration of Competing Interest The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
11. On the ethics of informed consent in genetic data collected before 1997.
- Author
-
Zieger M, Joly Y, and D'Amato ME
- Subjects
- Humans, Datasets as Topic ethics, Datasets as Topic history, History, 20th Century, Human Genetics ethics, Human Genetics history, Informed Consent ethics, Informed Consent history, Data Collection ethics, Data Collection history
- Published
- 2024
- Full Text
- View/download PDF
12. Novel buffer for long-term preservation of DNA in biological material at room temperature.
- Author
-
Kasu M, Ristow PG, Burrows AM, Kuplik Z, Gibbons MJ, and D'Amato ME
- Subjects
- Animals, Humans, Buffers, Preservation, Biological methods, Scyphozoa genetics, Time Factors, DNA analysis, DNA isolation & purification, DNA genetics, DNA chemistry, Temperature, Saliva chemistry, Specimen Handling methods
- Abstract
The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish Pelagia noctiluca comb jelly Beroe sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.
- Published
- 2024
- Full Text
- View/download PDF
13. Genetic heritage of the Baphuthi highlights an over-ethnicized notion of "Bushman" in the Maloti-Drakensberg, southern Africa.
- Author
-
Daniels RJ, D'Amato ME, Lesaoana M, Kasu M, Ehlers K, Chauke PA, Lecheko P, Challis S, Rockett K, Montinaro F, González-Santos M, and Capelli C
- Subjects
- Humans, Africa, Southern, Black People genetics, Ethnicity genetics, Genetic Variation, Genetics, Population
- Abstract
Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear, as ethnicity labels have been changed through time and most communities were decimated if not extirpated. The eastern KhoeSan may have had genetic distinctions from neighboring communities who speak Bantu languages and KhoeSan further away; alternatively, the identity may not have been tied to any notion of biology, instead denoting communities with a nomadic "lifeway" distinct from African agro-pastoralism. The Baphuthi of the 1800s in the Maloti-Drakensberg, southern Africa had a substantial KhoeSan constituency and a lifeway of nomadism, cattle raiding, and horticulture. Baphuthi heritage could provide insights into the history of the eastern KhoeSan. We examine genetic affinities of 23 Baphuthi to discern whether the narrative of KhoeSan descent reflects distinct genetic ancestry. Genome-wide SNP data (Illumina GSA) were merged with 52 global populations, for 160,000 SNPs. Genetic analyses show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu speakers. The Baphuthi have strong affinities with early-arriving southern Bantu-speaking (Nguni) communities, as the later-arriving non-Nguni show strong evidence of recent African admixture possibly related to late-Iron Age migrations. The references to communities as "San" and "Bushman" in historic literature has often been misconstrued as notions of ethnic/biological distinctions. The terms may have reflected ambiguous references to non-sedentary polities instead, as seems to be the case for the eastern "Bushman" heritage of the Baphuthi., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
14. Coexistence of junctional epidermolysis bullosa, autosomal recessive deafness type 57, and Angelman syndrome: A case report.
- Author
-
Amato ME, Ricart S, Vicente MA, Martorell L, Armstrong J, Fernández Isern G, Mascaro JM, Balsells S, Alonso I, Serrano M, and Ortigoza-Escobar JD
- Abstract
Key Clinical Message: The presence of more than one genetic/genomic disorder is not uncommon. It is therefore essential to continuously consider new signs and symptoms over time. Administration of gene therapy could be extremely difficult in particular situations., Abstract: A 9-month-old boy presented to our department for evaluation of developmental delay. We found that he was affected by intermediate junctional epidermolysis bullosa (COL17A1, c.3766 + 1G > A, homozygous), Angelman syndrome (5,5 Mb deletion of 15q11.2-q13.1), and autosomal recessive deafness type 57 (PDZD7, c.883C > T, homozygous)., Competing Interests: The authors have no conflict of interest to declare., (© 2023 The Authors. Clinical Case Reports published by John Wiley & Sons Ltd.)
- Published
- 2023
- Full Text
- View/download PDF
15. The genetic landscape of South African males: A Y-STR perspective.
- Author
-
Kasu M, Cloete KW, Pitere R, Tsiana KJ, and D'Amato ME
- Subjects
- Black People genetics, Genetic Variation, Haplotypes, Humans, Male, Microsatellite Repeats, South Africa, Chromosomes, Human, Y, Genetics, Population
- Abstract
The profiles of 2188 SA males obtained with 10 Y-STR highly informative markers were analyzed for their information content for forensic and population studies. The samples comprised a total of 16 populations, represented by Bantu-speaking groups, KhoeSan descendants, out-of-Africa descendants and admixed groups. The country hosts approximately 58 million inhabitants, 80% native and the remaining with ancestry external to Africa and admixed. The forensic parameters indicated high levels of diversity in all populations and lower in the Nguni, who showed elevated number of repeated haplotypes, thus displaying the lowest DC values. Population comparative analysis with MDS showed concordant results with the historical record. Non-hierarchical and hierarchical AMOVA over ethnolinguistic groups and administrative divisions showed significant variation in all cases, with higher differences due to ethnicity than to geopolitical subdivision. The haplotypes were further analyzed by hierarchical kmeans clustering. The identified clusters differed in their relative contribution to the gene pool of the 16 analyzed populations. Geostatistical analysis of the clusters evidenced areas of higher density for some clusters in correspondence with language, while other clusters were more homogeneously distributed. In addition, a few rare microvariants were identified with very restricted geographic occurrence. The results emphasize the forensic value of a highly informative set of markers in a country with high genetic diversity and complex population history., (Copyright © 2022 Elsevier B.V. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
16. DNA commission of the International Society of Forensic Genetics (ISFG): Recommendations on the interpretation of Y-STR results in forensic analysis.
- Author
-
Roewer L, Andersen MM, Ballantyne J, Butler JM, Caliebe A, Corach D, D'Amato ME, Gusmão L, Hou Y, de Knijff P, Parson W, Prinz M, Schneider PM, Taylor D, Vennemann M, and Willuweit S
- Subjects
- Alleles, Databases, Genetic standards, Genetics, Population, Haplotypes, Humans, Models, Statistical, Chromosomes, Human, Y, DNA Fingerprinting standards, Forensic Genetics standards, Microsatellite Repeats
- Abstract
Forensic genetic laboratories perform a large amount of STR analyses of the Y chromosome, in particular to analyze the male part of complex DNA mixtures. However, the statistical interpretation of evidence retrieved from Y-STR haplotypes is challenging. Due to the uni-parental inheritance mode, Y-STR loci are connected to each other and thus haplotypes show patterns of relationship on the familial and population level. This precludes the treatment of Y-STR loci as independently inherited variables and the application of the product rule. Instead, the dependency structure of Y-STRs needs to be included in the haplotype frequency estimation process affecting also the current paradigm of a random match probability that is in the autosomal case approximated by the population frequency assuming unrelatedness of sampled individuals. Information on the degree of paternal relatedness in the suspect population as well as on the familial network is however needed to interpret Y-chromosomal results in the best possible way. The previous recommendations of the DNA commission of the ISFG on the use of Y-STRs in forensic analysis published more than a decade ago [1] cover the interpretation issue only marginally. The current recommendations address a number of topics (frequency estimators, databases, metapopulations, LR formulation, triage, rapidly mutating Y-STRs) with relevance for the Y-STR statistics and recommend a decision-based procedure, which takes into account legal requirements as well as availability of population data and statistical methods., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
17. Ethical publication of research on genetics and genomics of biological material: guidelines and recommendations.
- Author
-
D'Amato ME, Bodner M, Butler JM, Gusmão L, Linacre A, Parson W, Schneider PM, Vallone P, and Carracedo A
- Subjects
- Animal Experimentation ethics, Animal Experimentation legislation & jurisprudence, Animals, Biological Specimen Banks ethics, Biological Specimen Banks legislation & jurisprudence, DNA, Environmental, Humans, Ethics, Research, Genetics, Guidelines as Topic, Periodicals as Topic, Publishing ethics
- Abstract
Forensic Science International: Genetics and Forensic Science International: Reports communicate research on a variety of biological materials using genetics and genomic methods. Numerous guidelines have been produced to secure standardization and quality of results of scientific investigations. Yet, no specific guidelines have been produced for the ethical acquisition of such data. These guidelines summarize universally adopted principles for conducting ethical research on biological materials, and provide details of the general procedures for conducting ethical research on materials of human, animal, plant and environmental origin. Finally, the minimal ethics requirements for submission of research material are presented., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
18. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters.
- Author
-
Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, and Balaresque P
- Subjects
- DNA Fingerprinting, Humans, Male, Multiplex Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Forensic Genetics methods, Haplotypes, Machine Learning, Microsatellite Repeats, Mutation Rate
- Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
19. Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449.
- Author
-
Kasu M, Fredericks J, Fraser M, Labuschagne C, Lesaoana M, and D'Amato ME
- Subjects
- 5' Flanking Region, Alleles, DNA Fingerprinting, Genetic Markers, Humans, Male, Polymerase Chain Reaction, Chromosomes, Human, Y, Genetic Variation, Microsatellite Repeats, Sequence Analysis, DNA
- Abstract
In forensic casework, Y-chromosome short tandem repeats (Y-STRs) are essential for differentiating between unrelated males and resolving the male component of admixed biological evidence. While the majority of Y-STRs are adequate for discriminating between different paternal lineages, rapidly mutating Y-STRs are necessary for improving discrimination between males within populations of low Y-chromosome diversity and between paternal relatives. Alternatively, sequencing of Y-STRs may also improve the discrimination between isometric Y-STR alleles by identifying variation in the repeat unit pattern arrangements and by identifying SNPs in the flanking region or within the STR repeat unit itself. In this report, a total of 153 DNA sequences are presented across the Y-STR loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. A total of 94 Y-STR sequences provided herein are reported for the first time, of which 37 sequences represent alleles showing size homoplasy, 34 sequences of known alleles for which sequence data has been unavailable and a total of 23 novel allele sequences across loci DYS644, DS447, DYS710 and DYS504. This study further encountered a rare sequence variant in the 5' flanking region of DYS385 and a total of two SNPs in the repeat structure at DYS481 and DYS449.
- Published
- 2019
- Full Text
- View/download PDF
20. A nano-junction of self-assembled mixed-metal-centre molecular wires on transparent conductive oxides.
- Author
-
Vitale S, Laramée-Milette B, Amato ME, Hanan GS, Tuccitto N, and Licciardello A
- Abstract
The fabrication of stable, highly conductive molecular nano-junctions is one of the main research goals in the field of molecular electronics. In this paper we report on the self-assembly and functional characterisation of highly conductive molecular wires, based on mixed-metal polynuclear complexes, at the surface of a transparent conductive oxide. The adopted synthetic approach involves metal-coordination reactions on oxide surfaces, pre-functionalised with a monolayer of terpyridine moieties that are used as anchoring sites for the integration of ditopic, redox-active ruthenium-bisterpyridine molecules through iron(ii) centres. By the stepwise iteration of the iron-coordination reaction, molecular wires of the desired length can be prepared, which alternate iron and ruthenium centres in the wire backbone. The stepwise assembly of the wires at the transparent conductive oxide surface was characterised by means of UV-Vis spectroscopy and, at the nanoscale, by means of ToF-SIMS measurements. The electrical characteristics of the wires were obtained by the liquid-metal eutectic-gain nano-junction technique, with results that show good electron transport capabilities along the wires. The demonstrated feasibility of the integration of these metal-polypyridinic, redox-active, conductive wires at the surface of a transparent and conductive oxide, and the evidence for good electrical conduction indicates prospective applications in the field of nanoscale molecular optoelectronics.
- Published
- 2019
- Full Text
- View/download PDF
21. Characterization of a null TPOX allele for AmpFℓSTR ® Identifiler ® Plus kit.
- Author
-
Ristow PG and D'Amato ME
- Subjects
- Genetic Linkage, Genotype, High-Throughput Nucleotide Sequencing, Humans, Mutation, Sequence Analysis, DNA, Alleles, Genetic Loci, Microsatellite Repeats, Polymerase Chain Reaction instrumentation
- Published
- 2018
- Full Text
- View/download PDF
22. A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations.
- Author
-
Pereira R, Alves C, Aler M, Amorim A, Arévalo C, Betancor E, Braganholi D, Bravo ML, Brito P, Builes JJ, Burgos G, Carvalho EF, Castillo A, Catanesi CI, Cicarelli RMB, Coufalova P, Dario P, D'Amato ME, Davison S, Ferragut J, Fondevila M, Furfuro S, García O, Gaviria A, Gomes I, González E, Gonzalez-Liñan A, Gross TE, Hernández A, Huang Q, Jiménez S, Jobim LF, López-Parra AM, Marino M, Marques S, Martínez-Cortés G, Masciovecchio V, Parra D, Penacino G, Pinheiro MF, Porto MJ, Posada Y, Restrepo C, Ribeiro T, Rubio L, Sala A, Santurtún A, Solís LS, Souto L, Streitemberger E, Torres A, Vilela-Lamego C, Yunis JJ, Yurrebaso I, and Gusmão L
- Subjects
- DNA Fingerprinting, Databases, Nucleic Acid, Ethnicity genetics, Gene Frequency, Genotype, Humans, Laboratories statistics & numerical data, Microsatellite Repeats, Genetics, Population, INDEL Mutation, Polymorphism, Single Nucleotide, Racial Groups genetics
- Abstract
A collaborative effort was carried out by the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) to promote knowledge exchange between associate laboratories interested in the implementation of indel-based methodologies and build allele frequency databases of 38 indels for forensic applications. These databases include populations from different countries that are relevant for identification and kinship investigations undertaken by the participating laboratories. Before compiling population data, participants were asked to type the 38 indels in blind samples from annual GHEP-ISFG proficiency tests, using an amplification protocol previously described. Only laboratories that reported correct results contributed with population data to this study. A total of 5839 samples were genotyped from 45 different populations from Africa, America, East Asia, Europe and Middle East. Population differentiation analysis showed significant differences between most populations studied from Africa and America, as well as between two Asian populations from China and East Timor. Low F
ST values were detected among most European populations. Overall diversities and parameters of forensic efficiency were high in populations from all continents., (Copyright © 2017 Elsevier B.V. All rights reserved.)- Published
- 2018
- Full Text
- View/download PDF
23. Evaluation of the InnoTyper ® 21 genotyping kit in multi-ethnic populations.
- Author
-
Ristow PG, Barnes N, Murphy GP, Brown H, Cloete KW, and D'Amato ME
- Subjects
- Alleles, Amelogenin genetics, Discriminant Analysis, Humans, Microsatellite Repeats, Sex Determination Analysis, DNA Fingerprinting instrumentation, Ethnicity genetics, Genetics, Population, Genotype
- Abstract
We report the findings of the evaluation of the InnoTyper
® 21 genotyping kit for the use of human identification (HID) and paternity testing in South Africa. This novel forensic kit evaluates 20 retrotransposable elements (AC4027, MLS26, ALU79712, NBC216, NBC106, RG148, NBC13, AC2265, MLS09, AC1141, TARBP, AC2305, HS4.69, NBC51, ACA1766, NBC120, NBC10, NBC102, SB19.12 and NBC148) and the Amelogenin locus for sex determination. The evaluation of the genotyping performance showed no significant spectral pull-up for peak heights between 100 and 30,000 RFUs. All loci presented biallelic patterns except the triallelic RG148 locus resulting from a variant insertion allele, named RG148I-1, observed exclusively in the Bantu. The InnoTyper® 21 kit was found to be highly discriminatory between the 507 unrelated individuals of the Afrikaaner, Asian Indian, Coloured, amaXhosa and amaZulu groups. The HID parameters: the CPD ranged between 0.99999987 and 0.9999999845, and the CMP between 1.0335×10-7 and 1.5506×10-8 . The paternity parameters: the CPI ranged between 0.0202 and 0.3177, and the CPE between 0.9161 and 0.9749. There were no significant signs of deviations from HWE or linkage disequilibrium (LD) after applying a Bonferroni correction. This kit also showed minor levels of population structure which could differentiate between the African and non-African population groups. Finally, in challenging casework with severely degraded biological material, the InnoTyper® 21 genotyping kit was compatible with GlobalFiler® and Investigator DIPplex® to increase the HID parameters., (Copyright © 2017 Elsevier B.V. All rights reserved.)- Published
- 2017
- Full Text
- View/download PDF
24. Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci.
- Author
-
Tau T, Wally A, Fanie TP, Ngono GL, Mpoloka SW, Davison S, and D'Amato ME
- Subjects
- Alleles, Botswana, Geography, Humans, Likelihood Functions, Genetic Loci, Genetic Variation, Genetics, Population, Microsatellite Repeats genetics
- Abstract
Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10
-19 . CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0.9999582029 and 0.9999922652 respectively. CMP ranged from 6.28 × 10-19 (Khoisan Tuu) to 1,02 × 10-18 (Northwest district). Using pairwise genetic distances (FST ), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and TESS, ethno-linguistics were found to have a greater influence on population structure than geography. FCA showed clustering between Bantu and Khoisan, and within the Bantu. This Bantu sub-structuring was not seen with STRUCTURE and TESS, which detected clustering only between Bantu and Khoisan. The patterns of population structure revealed highlight the need for regional reference databases that include ethno-linguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications.- Published
- 2017
- Full Text
- View/download PDF
25. Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis.
- Author
-
Cloete KW, Ristow PG, Kasu M, and D'Amato ME
- Subjects
- Automation, Laboratory methods, Electrophoresis, Capillary methods, Fluorescent Dyes chemistry, Genotyping Techniques methods, Research Design, Automation, Laboratory standards, Electrophoresis, Capillary standards, Fluorescent Dyes analysis, Fluorescent Dyes standards, Genotyping Techniques standards
- Abstract
CE equipment detects and deconvolutes mixtures containing up to six fluorescently labeled DNA fragments. This deconvolution is done by the collection software that requires a spectral calibration file. The calibration file is used to adjust for the overlap that occurs between the emission spectra of fluorescence dyes. All commercial genotyping and sequencing kits require the installation of a corresponding matrix standard to generate a calibration file. Due to the differences in emission spectrum overlap between fluorescent dyes, the application of existing commercial matrix standards to the electrophoretic separation of DNA labeled with other fluorescent dyes can yield undesirable results. Currently, the number of fluorescent dyes available for oligonucleotide labeling surpasses the availability of commercial matrix standards. Therefore, in this study we developed and evaluated a customized matrix standard using ATTO 633, ATTO 565, ATTO 550, ATTO Rho6G, and 6-FAM dyes for which no commercial matrix standard is available. We highlighted the potential genotyping errors of using an incorrect matrix standard by evaluating the relative performance of our custom dye set using six matrix standards. The specific performance of two genotyping kits (UniQTyper™ Y-10 version 1.0 and PowerPlex® Y23 System) was also evaluated using their specific matrix standards. The procedure we followed for the construction of our custom dye matrix standard can be extended to other fluorescent dyes., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2017
- Full Text
- View/download PDF
26. GlobalFiler(®) Express DNA amplification kit in South Africa: Extracting the past from the present.
- Author
-
Ristow PG, Cloete KW, and D'Amato ME
- Subjects
- Ethnicity genetics, Genetic Variation, Humans, Likelihood Functions, South Africa, DNA Fingerprinting, Genetics, Population, Microsatellite Repeats, Polymerase Chain Reaction instrumentation
- Abstract
In this study, the GlobalFiler(®) Express amplification kit was evaluated for forensic use in 541 South African individuals belonging to the Afrikaaner, amaXhosa,(1) amaZulu,(1) Asian Indian and Coloured population groups. Allelic frequencies, genetic diversity parameters and forensic informative metrics were calculated for each population. A total of 301 alleles were observed ranging between 5 and 44.2 repeat units, 43 were rarely observed partial repeats and seven were novel. The combined match probability (CMP) ranged from 2.21×10(-26) (Coloured) to 5.21×10(-25) (AmaZulu), and the combined power of exclusion (CPE) 0.9999999978 (Afrikaaner) to 0.99999999979 (AmaZulu) respectively. No significant departures from Hardy-Weinberg equilibrium (HWE) were observed after Bonferroni correction. Strong evidence of genetic structure was detected using the coancestry coefficient θ, Analysis of Molecular Variance (AMOVA) and an unsupervised Bayesian clustering method (STRUCTURE). The efficiency of assignment of individuals to population groups was evaluated by applying likelihood ratios with WHICHRUN, and the individual ancestral membership probabilities inferred by STRUCTURE. Likelihood ratios performed the best in the assignment of individuals to population groups. Signs of positive selection were detected for TH01 and D13S317 and purifying/balancing selection for locus SE33. These three loci also displayed the largest informativeness for assignment (In) values. The results of this study supports the use of the GlobalFiler(®) STR profiling kit for forensic applications in South Africa with the additional capability to predict ethnicity or continental origin of a random sample., (Copyright © 2016. Published by Elsevier Ireland Ltd.)
- Published
- 2016
- Full Text
- View/download PDF
27. Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa.
- Author
-
Hefke G, Davison S, and D'Amato ME
- Subjects
- Asian People genetics, Humans, South Africa, Black People genetics, Forensic Sciences methods, Genetics, Population methods, Genotyping Techniques methods, INDEL Mutation genetics
- Abstract
The utilization of binary markers in human individual identification is gaining ground in forensic genetics. We analyzed the polymorphisms from the first commercial indel kit Investigator DIPplex (Qiagen) in 512 individuals from Afrikaner, Indian, admixed Cape Colored, and the native Bantu Xhosa and Zulu origin in South Africa and evaluated forensic and population genetics parameters for their forensic application in South Africa. The levels of genetic diversity in population and forensic parameters in South Africa are similar to other published data, with lower diversity values for the native Bantu. Departures from Hardy-Weinberg expectations were observed in HLD97 in Indians, Admixed and Bantus, along with 6.83% null homozygotes in the Bantu populations. Sequencing of the flanking regions showed a previously reported transition G>A in rs17245568. Strong population structure was detected with Fst, AMOVA, and the Bayesian unsupervised clustering method in STRUCTURE. Therefore we evaluated the efficiency of individual assignments to population groups using the ancestral membership proportions from STRUCTURE and the Bayesian classification algorithm in Snipper App Suite. Both methods showed low cross-assignment error (0-4%) between Bantus and either Afrikaners or Indians. The differentiation between populations seems to be driven by four loci under positive selection pressure. Based on these results, we draw recommendations for the application of this kit in SA., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2015
- Full Text
- View/download PDF
28. Polymorphisms at 17 Y-STR loci in Botswana populations.
- Author
-
Tau T, Davison S, and D'Amato ME
- Subjects
- Africa South of the Sahara, Botswana, Databases, Genetic, Ethnicity genetics, Genetics, Population methods, Haplotypes, Humans, Male, Polymorphism, Genetic, Chromosomes, Human, Y, Microsatellite Repeats
- Abstract
Seventeen Y-chromosomal short tandem repeats (YSTRs)-DYS19, DYS389I, DYS389II, DYS385a/b, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4-were analyzed in 252 unrelated male individuals from Botswana. A total of 238 unique haplotypes were identified. The discrimination capacity (DC) was 0.9444 whereas the haplotype diversity (HD) was 0.9990. A database search of the 238 unique haplotypes in the Y chromosome haplogroup database (YHRD) yielded three African American, six Sub-Saharan African, and two admixed South American matches. Five additional African-American matches were detected in the Applied Biosystems Y-STR database. RST, multi-dimensional scaling (MDS) and AMOVA were used to investigate population differentiation in Sub-Saharan Africa and in Botswana. The populations in Sub-Saharan Africa were found to be heterogeneous, with Botswana showing significant differences from its neighbors. No geographic regional or ethnic differentiation was observed within Botswana. Regional and ethnic variation can be useful in forensic working hypotheses., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
29. NMDA blockade inhibits experience-dependent modification of anterior thalamic head direction cells.
- Author
-
Berkowitz LE, Ybarra I, Jones JA, Amato ME, Rodriguez AM, and Calton JL
- Subjects
- Animals, Anterior Thalamic Nuclei drug effects, Female, Motor Activity, Neurons drug effects, Orientation drug effects, Rats, Rats, Long-Evans, Spatial Behavior drug effects, Anterior Thalamic Nuclei physiology, Excitatory Amino Acid Antagonists pharmacology, Neuronal Plasticity drug effects, Neurons physiology, Orientation physiology, Spatial Behavior physiology
- Abstract
Head Direction (HD) cells of the rodent Papez circuit are thought to reflect the spatial orientation of the animal. Because NMDA transmission is important for spatial behavior, we sought to determine the effects of NMDA blockade on the basic directional signal carried by HD cells and on experience-dependent modification of this system. In Experiment 1, HD cells were recorded from the anterior dorsal thalamus in female Long-Evans rats while they foraged in a familiar enclosure following administration of the NMDA antagonist CPP or saline. While the drug produced a significant decrease in peak firing rates, it failed to affect the overall directional specificity and landmark control of HD cells. Experiment 2 took place over 2 days and assessed whether the NMDA antagonist would interfere with the stabilization of the HD network in a novel environment. On Day 1 the animal was administered CPP or saline and placed in a novel enclosure to allow the stabilization of the HD signal relative to the new environmental landmarks. On Day 2 the animal was returned to the formerly novel enclosure to determine if the enclosure specific direction-dependent activity established on Day 1 was maintained. In contrast to HD cells from control animals, cells from animals receiving CPP during the initial exposure to the novel enclosure did not maintain the same direction-dependent activity relative to the enclosure in the subsequent drug-free exposure. These findings demonstrate that plasticity in the HD system is dependent on NMDA transmission similar to many other forms of spatial learning., ((PsycINFO Database Record (c) 2015 APA, all rights reserved).)
- Published
- 2015
- Full Text
- View/download PDF
30. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations.
- Author
-
Marks SJ, Montinaro F, Levy H, Brisighelli F, Ferri G, Bertoncini S, Batini C, Busby GB, Arthur C, Mitchell P, Stewart BA, Oosthuizen O, Oosthuizen E, D'Amato ME, Davison S, Pascali V, and Capelli C
- Subjects
- Africa, Southern ethnology, Emigration and Immigration, Female, Genetic Variation, Genetics, Population, Humans, Male, Principal Component Analysis, Regression Analysis, Black People ethnology, Black People genetics, Chromosomes, Human, Y genetics, DNA, Mitochondrial genetics
- Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2015
- Full Text
- View/download PDF
31. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
- Author
-
Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MH, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RS, Nogueira TL, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MM, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MC, Rodriguez JJ, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LS, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RY, Krawczak M, Nothnagel M, and Roewer L
- Subjects
- Alleles, Forensic Genetics, Humans, Chromosomes, Human, Y, Haplotypes, Microsatellite Repeats
- Abstract
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., (Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
32. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.
- Author
-
Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, De Ungria MC, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MH, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SP, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Skaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EP, Yong RY, Pajnič IZ, and Kayser M
- Subjects
- Africa, Alleles, Americas, Asia, DNA Fingerprinting statistics & numerical data, Europe, Gene Frequency, Genetic Variation, Humans, Male, Paternity, Pedigree, Rural Population, Urban Population, Chromosomes, Human, Y chemistry, DNA Fingerprinting methods, Genetics, Population, Haplotypes, Microsatellite Repeats
- Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database., (© 2014 The Authors. **Human Mutation published by Wiley Periodicals, Inc.)
- Published
- 2014
- Full Text
- View/download PDF
33. Doppler echocardiographic evidence of pulmonary hypertension in dogs: a retrospective clinical investigation.
- Author
-
Paradies P, Spagnolo PP, Amato ME, Pulpito D, and Sasanelli M
- Subjects
- Animals, Dog Diseases physiopathology, Dogs, Female, Hypertension, Pulmonary diagnostic imaging, Hypertension, Pulmonary physiopathology, Linear Models, Male, Retrospective Studies, Dog Diseases diagnostic imaging, Echocardiography, Doppler veterinary, Hypertension, Pulmonary veterinary
- Abstract
Pulmonary hypertension (PH) decreases resistance to fatigue and life expectancy. The aim of this study was to correlate some indirect Doppler indices of PH with tricuspid and pulmonary regurgitation criteria and to relate PH on different indices with the severity of clinical signs. Furthermore the pathogenetic mechanisms associated to PH development were discussed. Dogs with Doppler echocardiographic evidence of PH diagnosed by assessment of pulmonary and tricuspid regurgitant jet velocity were selected, their clinical records were reviewed and a clinical score was computed. Seventeen cases of PH were identified. The degree of PH was assessed based on systolic or diastolic pulmonary pressure and the indirect Doppler indices (AT/ET and Tei Index) were calculated; data were statistically evaluated. Indirect Doppler indices were calculated also in a control group of seven healthy dogs. The most common clinical signs were coughing, dyspnea and syncope; the most common condition associated to PH development was the left-sided valvular heart disease. A significant positive correlation was found between Tei Index and both the systolic pressure and the severity of PH while no correlations were found between PH on different indices and clinical score and/or severity of clinical signs. Results of this study suggest that Tei-index could be an useful support not only to reveal PH but also to give information on the severity of PH. The clinical picture in dogs with PH is apparently unpredictable and not strictly correlated with the severity of PH.
- Published
- 2014
- Full Text
- View/download PDF
34. Selective oxidation reactions of natural compounds with hydrogen peroxide mediated by methyltrioxorhenium.
- Author
-
Amato ME, Ballistreri FP, Pappalardo A, Tomaselli GA, Toscano RM, and Sfrazzetto GT
- Subjects
- Molecular Structure, Oxidation-Reduction, Hydrogen Peroxide chemistry, Organometallic Compounds chemistry
- Abstract
We have investigated the oxidative behaviour of natural compounds such as methyl abietate (1), farnesyl acetate (2), α-ionone (3), β-ionone (4), methyl linolelaidate (5), methyl linolenate (6) and bergamottin (7) with the oxidant system methyltrioxo-rhenium/ H2O2/pyridine. The reactions, performed in CH2Cl2/H2O at 25 °C, have shown good regio- and stereoselectivity. The oxidation products were isolated by HPLC or silica gel chromatography and characterized by MS(EI), 1H-, 13C-NMR, APT, gCOSY, HSQC, TOCSY and NOESY measurements. The selectivity seems to be controlled by the nucleophilicity of double bonds and by stereoelectronic and steric effects.
- Published
- 2013
- Full Text
- View/download PDF
35. A ratiometric naphthalimide sensor for live cell imaging of copper(I).
- Author
-
Satriano C, Sfrazzetto GT, Amato ME, Ballistreri FP, Copani A, Giuffrida ML, Grasso G, Pappalardo A, Rizzarelli E, Tomaselli GA, and Toscano RM
- Subjects
- Cell Line, Tumor, Humans, Microscopy, Confocal, Molecular Structure, Naphthalimides chemical synthesis, Neurons pathology, Copper analysis, Naphthalimides chemistry, Neurons chemistry
- Abstract
A new naphthalimide derivative bearing a tetrathia-azacrown for high affinity and selective binding to Cu(+) was synthesised. Copper recognition properties in solution were evaluated using (1)H NMR and fluorescence spectroscopy. Live cell imaging by confocal microscopy highlighted the capabilities of the new sensor for the two-wavelength detection of intracellular monovalent copper in neuronal cells.
- Published
- 2013
- Full Text
- View/download PDF
36. Where is the game? Wild meat products authentication in South Africa: a case study.
- Author
-
D'Amato ME, Alechine E, Cloete KW, Davison S, and Corach D
- Abstract
Background: Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species., Results: The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species., Conclusions: The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
- Published
- 2013
- Full Text
- View/download PDF
37. Monitoring the reverse to normal of clinico-pathological findings and the disease free interval time using four different treatment protocols for canine leishmaniosis in an endemic area.
- Author
-
Paradies P, Sasanelli M, Amato ME, Greco B, De Palo P, and Lubas G
- Subjects
- Allopurinol administration & dosage, Animals, Antiprotozoal Agents administration & dosage, Dog Diseases parasitology, Dogs, Drug Therapy, Combination, Female, Leishmaniasis drug therapy, Leishmaniasis pathology, Male, Meglumine administration & dosage, Meglumine Antimoniate, Organometallic Compounds administration & dosage, Time Factors, Allopurinol therapeutic use, Antiprotozoal Agents therapeutic use, Dog Diseases drug therapy, Endemic Diseases veterinary, Leishmaniasis veterinary, Meglumine therapeutic use, Organometallic Compounds therapeutic use
- Abstract
Twenty-four dogs naturally infected by Leishmania spp. were treated with four different protocols using meglumine antimoniate (aNm) and allopurinol in combination or in monotherapy. Aiming to compare the efficacy of the different treatments the reverse to normal of clinico-pathological findings and the disease free interval time (DFIT) were evaluated. Treated dogs were monitored for 1 year and, in absence of relapses, the DFIT was postponed to the last available follow-up. Seven dogs treated with aNm alone showed relapses during the year of observation. In the group of dogs treated with the combination of aNm (50 mg/kg/SC 12 hourly up to clinico-pathological recovery) and allopurinol (15 mg/kg/PO 12 hourly administered for 6months) no relapses were registered in the year of monitoring and the DFIT reached up to 65 months. Our results showed that this combination represents the best choice to treat canine leishmaniosis compared to other protocols., (Copyright © 2012 Elsevier Ltd. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
38. Pair of diastereomeric uranyl salen cavitands displaying opposite enantiodiscrimination of α-amino acid ammonium salts.
- Author
-
Pappalardo A, Amato ME, Ballistreri FP, Tomaselli GA, Toscano RM, and Trusso Sfrazzetto G
- Subjects
- Molecular Conformation, Stereoisomerism, Amino Acids chemistry, Ethers, Cyclic chemistry, Ethylenediamines chemistry, Organometallic Compounds chemistry, Quaternary Ammonium Compounds chemistry, Resorcinols chemistry, Uranium chemistry
- Abstract
A pair of diastereomeric salen cavitands and their uranyl complexes combine a chiral (R,R) salen bridge and an inherent chiral tris-bridged quinoxaline cup within the same molecule. Whereas the free ligands show a preference for the same enantiomer of an α-amino acid pair, the corresponding UO(2) complexes display opposite enantiodiscrimination and exceptionally high enantioselectivities (K(D)/K(L) = 26.4).
- Published
- 2012
- Full Text
- View/download PDF
39. Novel inhibitors of nitric oxide synthase with antioxidant properties.
- Author
-
Salerno L, Modica MN, Romeo G, Pittalà V, Siracusa MA, Amato ME, Acquaviva R, Di Giacomo C, and Sorrenti V
- Subjects
- Animals, Humans, Imidazoles chemistry, Imidazoles pharmacology, Lipid Peroxidation drug effects, Nitric Oxide Synthase Type I metabolism, Nitric Oxide Synthase Type III metabolism, Rats, Antioxidants chemistry, Antioxidants pharmacology, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, Nitric Oxide Synthase Type I antagonists & inhibitors, Nitric Oxide Synthase Type III antagonists & inhibitors
- Abstract
We previously described a series of imidazole-based inhibitors substituted at N-1 with an arylethanone chain as interesting inhibitors of neuronal nitric oxide synthase (nNOS), endowed with good selectivity vs endothelial nitric oxide synthase (eNOS). As a follow up of these studies, several analogs characterized by the presence of substituted imidazoles or other mono or bicyclic nitrogen-containing heterocycles instead of simple imidazole were synthesized, and their biological evaluation as in vitro inhibitors of both nNOS and eNOS is described herein. Most of these compounds showed improved nNOS and eNOS inhibitory activity with respect to reference inhibitors. Selected compounds were also tested to analyze their antioxidant properties. Some of them displayed good capacity to scavenge free radicals and ability to reduce lipid peroxidation., (Copyright © 2012 Elsevier Masson SAS. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
40. Signatures of the preagricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages.
- Author
-
Batini C, Ferri G, Destro-Bisol G, Brisighelli F, Luiselli D, Sánchez-Diz P, Rocha J, Simonson T, Brehm A, Montano V, Elwali NE, Spedini G, D'Amato ME, Myres N, Ebbesen P, Comas D, and Capelli C
- Subjects
- Africa South of the Sahara, Black People, DNA, Mitochondrial genetics, Emigration and Immigration, Humans, Microsatellite Repeats genetics, Chromosomes, Human, Y genetics, Demography, Genetics, Population, Haplotypes genetics, Phylogeography
- Abstract
The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture, and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad data set of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high-resolution single nucleotide polymorphism analysis with short tandem repeats variation of their subclades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional preagricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.
- Published
- 2011
- Full Text
- View/download PDF
41. Allele frequencies of six non-CODIS miniSTR loci (D1S1627, D3S4529, D5S2500, D6S1017, D8S1115 and D9S2157) in three South African populations.
- Author
-
Abrahams Z, D'Amato ME, Davison S, and Benjeddou M
- Subjects
- DNA Fingerprinting, Humans, Male, Polymerase Chain Reaction, South Africa, Ethnicity genetics, Gene Frequency, Genetics, Population, Microsatellite Repeats
- Published
- 2011
- Full Text
- View/download PDF
42. Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system.
- Author
-
D'Amato ME, Bajic VB, and Davison S
- Subjects
- DNA Primers, Genetic Markers, Humans, Male, Polymerase Chain Reaction, Racial Groups genetics, South Africa, Chromosomes, Human, Y, DNA Fingerprinting methods, Tandem Repeat Sequences
- Abstract
The Y-chromosome STRs (short tandem repeat) markers are routinely utilized in the resolution of forensic casework related to sexual assault. For this, the forensic community has adopted a set of eleven (core) Y-STR that is incorporated in all commercial diagnostic systems. Our previous studies of Y-STR polymorphisms in the South African population identified low levels of diversity and discrimination capacity for many commercial marker sets, determining a limited applicability of these systems to the local population groups. To overcome this shortcoming, we designed a Y-STR 10-plex system that shows higher discriminatory capacity (DC) than available commercial systems. The markers were selected from a population group of 283 individuals with African, European and Asian ancestry genotyped at 45 Y-STRs, applying an optimization based selection procedure to achieve the highest possible DC with the minimal number of markers. The 10-plex was satisfactorily subjected to developmental validation tests following the SWGDAM guidelines and shows potential for its application to genealogical and evolutionary studies., (Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
43. Quality traits of conventional and transgenic lettuce (Lactuca sativa L.) at harvesting by NMR metabolic profiling.
- Author
-
Sobolev AP, Testone G, Santoro F, Nicolodi C, Iannelli MA, Amato ME, Ianniello A, Brosio E, Giannino D, and Mannina L
- Subjects
- Amino Acids analysis, Amino Acids metabolism, Gene Expression Regulation, Plant, Lactuca genetics, Lactuca growth & development, Magnetic Resonance Spectroscopy, Plant Leaves chemistry, Plant Leaves genetics, Plant Leaves growth & development, Plant Leaves metabolism, Plant Proteins analysis, Plant Proteins metabolism, Plants, Genetically Modified genetics, Plants, Genetically Modified growth & development, Lactuca chemistry, Lactuca metabolism, Metabolome, Plants, Genetically Modified chemistry, Plants, Genetically Modified metabolism
- Abstract
Metabolism of genetically modified (GM) lettuce (Lactuca sativa L.) leaves was investigated by comparing NMR metabolic profiles of three lines (T(3)B12, T(7)B7, and T(7)B14) overexpressing the E. coli asparagine synthetase A gene with those of the wild type (WT) at 24, 56, and 64 days after sowing (DAS). Statistical analyses based on hydro-soluble compound profiles significantly and maximally discriminated the WT from GM-lines at optimal harvest time (56 DAS). The T(7)B14 metabolic variations were opposite to those of both T(3)B12/T(7)B7 lines, suggesting that unexpected effects of transgenesis had occurred. Compared to controls, the T(3)B12/T(7)B7 plants shared the leaf mass increase, higher amino acid (asparagine, glutamine, valine, and isoleucine) and protein levels, and lower nitrate contents, accompanied by a modest sink of organic acids (alpha-chetoglutarate, succinate, fumarate, and malate), sucrose, fructose, and inulins. Incongruously, the T(7)B14 butter heads were less leafy than the controls and showed lowered amino acid/protein contents and overstored inulin. To further investigate the metabolic discrepancies among the GM-lines, a set of key nitrogen and inulin genes was monitored. The T(3)B12/T(7)B7 lines shared comparable gene expression changes, including the induction of the endogenous asparagine synthetase1 and nitrate reductase1 that supported the targeted enhancement of nitrogen status. Transgene product malfunctioning and T-DNA rearrangements throughout generations were proposed to explain the decreased asparagine content and the complex expression pattern of N genes in T(7)B14 leaves. In the latter, the inulin accumulation was associated with the upregulation of fructan biosynthesis genes and the intense repression of fructan hydrolases.
- Published
- 2010
- Full Text
- View/download PDF
44. Synthesis and conformational study of a novel macrocyclic chiral(salen) ligand and its uranyl and Mn complexes.
- Author
-
Amato ME, Ballistreri FP, Pappalardo A, Tomaselli GA, and Toscano RM
- Subjects
- Ligands, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Conformation, Stereoisomerism, Macrocyclic Compounds chemistry, Manganese chemistry, Uranium chemistry
- Abstract
A novel chiral macrocyclic ligand incorporating a chiral salen moiety into a framework containing two biphenyl units was synthesized. Structural properties and conformational aspects of the free ligand and an UO2 complex were studied by using NMR spectroscopy in solution and MM calculations. The Mn(III) complex was tested as catalyst in enantioselective oxidation of prochiral unfunctionalized olefins to the corresponding optically active epoxides under very mild conditions.
- Published
- 2010
- Full Text
- View/download PDF
45. Recognition of achiral and chiral ammonium salts by neutral ditopic receptors based on chiral salen-UO2 macrocycles.
- Author
-
Amato ME, Ballistreri FP, Gentile S, Pappalardo A, Tomaselli GA, and Toscano RM
- Subjects
- Aldehydes chemistry, Bridged-Ring Compounds chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, Solutions, Macrocyclic Compounds chemistry, Quaternary Ammonium Compounds chemistry, Uranium chemistry
- Abstract
A mononuclear (M20) and a dinuclear (M40) uranyl chiral macrocyclic complex, incorporating both a salen unit containing two phenyl rings linked to a chiral diimine bridge and the (R)-BINOL unit, behaves as an efficient ditopic receptor for achiral and chiral quaternary ammonium salts. Binding affinities in chloroform solution have been measured for 1:1 complexes of many quaternary salts encompassing tetramethylammonium (TMA), tetraethylammonium (TEA), tetrabutylammonium (TBA), and acetylcholine (ACh), as well as trimethylanilinium (TriMAn), benzyltrimethylammonium (BnTriMA), (alpha-methylbenzyl)trimethylammonium and pyrrolidinium cations. The anion of the salt is bound by the hard Lewis acidic uranyl site, with an increasing binding efficiency on increasing the anion hardness (I(-) < Br(-) < Cl(-)), whereas CH-pi or pi-pi attractions by binapthyl moiety, or the salicylaldehyde unit, or the phenyl rings of diimine bridge ensure the recognition of the cation partner. Optimized structures of receptor-anion-cation ternary complexes obtained by MM calculations are supported by 2D-ROESY NMR measurements.
- Published
- 2010
- Full Text
- View/download PDF
46. Simulation of Y-chromosomal haplotype data.
- Author
-
Koen C and D'Amato ME
- Subjects
- Algorithms, Evolution, Molecular, Gene Frequency genetics, Genetics, Population methods, Humans, Male, Microsatellite Repeats genetics, Statistics, Nonparametric, Sweden, Chromosomes, Human, Y genetics, Computer Simulation, Haplotypes genetics, Models, Genetic
- Abstract
The non-recombining nature of the Y-chromosome determines the non-independence of alleles between loci. The evolution of short tandem repeat (STR) loci in the Y-chromosome is the result of different factors such as differential mutation rates, mutation modes, gene conversion, selection and demographic processes. The degree of correlation between loci is dependent on the magnitude of these processes. The simulation of data is a routine tool used for testing hypotheses in population and evolutionary studies. The most basic parameters hitherto used in lineage haplotype simulations are the allele frequency distributions and mutation rates, assuming either full independence or linkage between loci. In this study we introduce use of the Spearman correlation coefficient to estimate the degree of dependence between non-recombining loci. Then, both the interdependence between loci and the allele frequency distributions at multi-allelic loci are incorporated in an algorithm for simulating haplotypes. We illustrate the method using published and unpublished Y-chromosome STR data.
- Published
- 2010
- Full Text
- View/download PDF
47. Threading the calix[5]arene annulus.
- Author
-
Gattuso G, Notti A, Parisi MF, Pisagatti I, Amato ME, Pappalardo A, and Pappalardo S
- Published
- 2010
- Full Text
- View/download PDF
48. Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710.
- Author
-
D'Amato ME, Ehrenreich L, Cloete K, Benjeddou M, and Davison S
- Subjects
- Base Sequence, Black People genetics, Chromosome Mapping, Chromosomes, Human, Y chemistry, DNA genetics, DNA isolation & purification, DNA Primers, Evolution, Molecular, Genealogy and Heraldry, Genetic Variation, Genotype, Humans, India ethnology, Male, Polymerase Chain Reaction, South Africa, White People genetics, Chromosomes, Human, Y genetics, Microsatellite Repeats genetics
- Abstract
During the study of genetic diversity at non-core Y-STRs in South African population groups, we identified loci with high discrimination capacity. In this study we present a detailed account of the allele diversity, allele sequence data, gene diversity, allele frequency spectrum and informativeness for assignment in the European English, Asian Indian and Xhosa population groups at loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710. The suitability of these loci for forensic, genealogical and evolutionary studies is discussed, and nomenclature for loci DYS518, DYS612, DYS626 and DYS644 is suggested.
- Published
- 2010
- Full Text
- View/download PDF
49. Analysis of seventeen Y-chromosome STR loci in the Cape Muslim population of South Africa.
- Author
-
Cloete K, Ehrenreich L, D'Amato ME, Leat N, Davison S, and Benjeddou M
- Subjects
- Alleles, Genetic Loci, Haplotypes, Humans, Male, Mouth Mucosa diagnostic imaging, Ultrasonography, Chromosomes, Human, Y, DNA analysis, Forensic Genetics methods, Tandem Repeat Sequences
- Abstract
Two Y-STR genotyping systems were evaluated for usefulness in forensic casework in the Cape Muslim population of South Africa. Samples were collected from 105 males, and genotyped for 17 loci amplified in two multiplexes. Allele and haplotype frequencies were determined for nine Y-STR loci used to define the minimal haplotype (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, and the duplicated locus DYS385) amplified in one multiplex, as well as for eight widely used loci amplified in a second multiplex and consisting of DYS449, DYS481, DYS518, DYS557, DYS570, DYS607, DYS612 and DYS614. When analysing the samples for all the loci, 104 unique haplotypes were obtained, and the discrimination capacity was 0.990. When considering only the nine Y-STRs included in the minimal haplotype, 91 unique haplotypes were obtained, and the discrimination capacity was 0.866. In the case of the remaining eight Y-STR loci, values of 97 and 0.924 were obtained, respectively.
- Published
- 2010
- Full Text
- View/download PDF
50. Synthesis of new arylpiperazinylalkylthiobenzimidazole, benzothiazole, or benzoxazole derivatives as potent and selective 5-HT1A serotonin receptor ligands.
- Author
-
Siracusa MA, Salerno L, Modica MN, Pittalà V, Romeo G, Amato ME, Nowak M, Bojarski AJ, Mereghetti I, Cagnotto A, and Mennini T
- Subjects
- Alkylation, Benzothiazoles chemistry, Ligands, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Structure, Piperazine, Protein Binding, Receptor, Serotonin, 5-HT1A metabolism, Structure-Activity Relationship, Benzothiazoles chemical synthesis, Benzothiazoles pharmacology, Piperazines chemistry, Serotonin 5-HT1 Receptor Antagonists
- Abstract
A series of new compounds containing a benzimidazole, benzothiazole, or benzoxazole nucleus linked to an arylpiperazine by different thioalkyl chains was prepared. They were tested in radioligand binding experiments to evaluate their affinity for 5-HT 1A and 5-HT 2A serotonergic, alpha 1 adrenergic, D1, and D2 dopaminergic receptors. Many of tested compounds showed an interesting binding profile; in particular, 36 displayed very high 5-HT 1A receptor affinity and selectivity over all the other investigated receptors. Selected compounds, evaluated in functional assays, showed antagonistic or partial agonistic activity at 5-HT 1A receptor. An extensive conformational research using both NMR and modeling techniques indicated that extended conformations predominated in vacuum, in solution and during interactions with 5-HT 1A receptor. Finally, the elaborated binding mode of selected compounds at 5-HT 1A receptor was used to explain the influence of spacer length on ligands affinity.
- Published
- 2008
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.