Ethical considerations for Forensic Genetic Frequency databases: First Report conception and development.

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.

The genetic landscape of South African males: A Y-STR perspective.

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.

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations.

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 FST values were detected among most European populations. Overall diversities and parameters of forensic efficiency were high in populations from all continents.

Doppler echocardiographic evidence of pulmonary hypertension in dogs: a retrospective clinical investigation.

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.

Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system.

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.

Simulation of Y-chromosomal haplotype data.

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.

Structural studies of wheat flour glutenin polymers by CD spectroscopy.

A dissolution procedure of unreduced glutenin polymers of three wheat flour varieties (WRU 6981, Alisei 1, and Alisei 2) by sonication in the presence of SDS (sodium dodecyl sulphate), after the elimination of albumins, globulins, and gliadins, was achieved, and the molecular weight distribution of glutenin polymers obtained by this method was measured by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. A structural study by CD spectroscopy at different temperatures of WRU 6981 glutenin polymer and of 1Ax1 high-M(r) (relative molecular mass) glutenin subunit, which is the only high-M(r) subunit contained in WRU 6981 flour, was undertaken to understand if the information obtained from the single subunit were applicable to the total polymer. CD spectroscopy also has been employed to study the glutenin polymers obtained by Alisei 1 and Alisei 2 wheat flours; Alisei 1 biotype contained 1Bx7 and 1Dx2+1Dy12 high-M(r) subunits, whereas the Alisei 2 biotype contained only 1Bx7 and 1Dy12 subunits. A conformational study was undertaken by CD spectroscopy at different temperatures and in the presence of some chemical denaturant agents, such as urea and sodium dodecyl sulphate, in order to obtain information about their intrinsic stability and to verify if the 1Dx2 subunit presence determined a different structural behavior between Alisei 1 and Alisei 2 polymers. MALDI-TOF mass spectrometric experiments showed that the glutenin polymers molecular weights were in the mass range of 500000-5000000. CD spectra indicated that a single conformational state did not predominate in the temperature range studied but equilibrium between two distinct conformational states existed; moreover, all the changes induced by urea and by SDS followed a multistep transition process.

Conformational studies of wheat flour high relative molecular mass glutenin subunits by circular dichroism spectroscopy.

Conformational studies of 1Dx2, 1Bx7, and 1Dy12 high relative molecular mass glutenin subunits, extracted from Alisei 1 flour, are reported. Circular dichroism (CD) spectroscopy is employed to study their conformational polymorphism induced by urea and by urea in the presence of 1% sodium dodecyl sulfate (SDS). The CD spectra indicate that SDS promotes ordered structures. The addition of urea to the SDS-acetate solution of 1Dx2, 1Bx7, and 1Dy12 subunits eliminates the effect of SDS. Its addition to the acetate solution of proteins induces conformational transitions to form a poly-L-proline II-like structure. All the changes induced by urea follow a multistep transition process that is typical of proteins consisting of different domains.

Structural features and molecular assembly of amorphous phosphazenic materials in the bulk--combined theoretical and experimental techniques: Tris-(2,2'-dioxy-1,1'-binaphthyl)cyclotriphosphazen.

The structure and the assembly of tris-(2,2'-dioxy-binaphthyl)cyclotriphosphazene [(+)-[NP3(O2C20H12)3], DBNP, in the solid amorphous state was studied using molecular dynamics (MD) including ad hoc quantum mechanically derived force field (FF) parameters, in combination with the energy dispersive X-ray diffraction (EDXD) technique. The atom-atom radial distribution function (RDF) curve obtained through the EDXD experiment revealed low intensity peaks not attributable to the intramolecular distances of the single molecule, but clearly featuring a low energy state of long-distance three-dimensional assembly. The radial distribution functions (RDF) were calculated for various models of DBNP submitted to theoretical MD simulations. Based on the comparison of theoretically calculated RDFs and those obtained from the EDXD experiment, the predominant structural motif of the material in the bulk was found to have DBNP molecules laid one upon the other to form tubular nanostructures. These contain eight DBNP units each (length ca. 46 A) with two and three of these units aligned in parallel and held together. The material can be represented as a bulk of tubular snake-like chains undergoing distortions with a step of eight DBNP units. The bending angles, that vary randomly, attain limited values sufficient to induce disorder and thus nonperiodic structure. The present application of MD simulations combined with EDXD data appear to be a general approach to solve for the first time otherwise intractable issues concerning structural features and assembly of molecular materials in the bulk.

Repetitive DNA sequences as an insight into Aeglidae (Crustacea, Anomura) evolution.

The evolutionary relationships of five Atlantic Aeglidae species (Aegla neuquensis affinis, A. humahuaca, A. jujuyana, A. platensis, and A. uruguayana) were studied by (i) satellite DNA analysis using a restriction enzyme digestion and hybridization pattern approach and (ii) genome screening by using randomly amplified polymorphic DNA (RAPD) typing. The identical restriction patterns and intense interspecific hybridization patterns obtained in this study strongly suggest a recent cladogenetic event for the Aeglidae. The species-specific amplification products which were detected using RAPD markers allowed species characterization. A total of 49 amplification products were used to construct trees by cluster analysis. The new scheme agrees in part with previous proposals based on biogeography and morphology. We considered that the subdivision northwestern-platensis species was probably due to the rising of the Andes, which started in the Middle Miocene. Divergence due to altitude is suggested by the different altitudinal distribution of three northwestern species along the same river. The possible role of selection by ecological factor/s was observed at the population level in A. jujuyana, which has a wider altitudinal range distribution. RAPD markers revealed a high level of intraspecific diversity and important genetic flow among populations. However, a few markers showed significant differences in frequency or H between the lowermost population and the other populations, located in a different biogeographical region. The differences were not in relation to geographical distance, and we interpreted them as being due to selection. Repetitive sequences constitute an important reservoir of genetic variation, and these results show their usefulness in testing and proposing evolutionary hypothesis in crabs. These sequences seem to have played an important role in aeglid evolution. Ecological factors related to altitude have probably influenced macro- and microevolutionary processes, at least in northwestern species.

Molecular modeling of beta-cyclodextrin complexes with nootropic drugs.

The geometry and structural features of the inclusion complexes of beta-cyclodextrin (beta-CD) with the chiral antiamnesic drugs (+/-)-1-benzyl-4-hydroxymethylpyrrolidin-2-one (WEB-1868). (+/-)-1-benzenesulfonyl-5-ethoxypyrrolidin-2-one (RU-35929), and (+/-)-1-(3-pyridinlysulfonyl)-5-ethoxypyrrolidin-2-one (RU-47010) were studied by the molecular modeling method (MacroModel interactive computer program). Docking procedures yielded the most stable complexes, which showed the aromatic ring of the guests inside the cavity and the pyrrolidinone ring out from the side of the beta-CD secondary hydroxyl groups. The binding energies were essentially due to hydrogen-bonded structures involving the C=O group of the guests. Selective interactions allowed chiral discrimination, and accordingly, separate beta-CD complexes of the R and S enantiomers of each guest compound were studied. The almost round beta-CD structure, in all the cases, assumed an elliptic shape on passing from the isolated molecule to the docked complex. The optimized structures and conformations of beta-CD and its inclusion compounds showed acceptable general agreement with information from proton nuclear magnetic resonance studies.