Search Results (43)

Genetic similarity determines the extent to which two genotypes share common genetic material. It can be measured in various ways, such as by comparing DNA sequences, proteins, or other genetic markers. The significance of genetic similarity is multifaceted and encompasses various fields, including evolutionary biology, medicine, forensic science, animal and plant breeding, and anthropology. Genetic similarity is an important concept with wide application across different scientific disciplines. The research material included 21 rapeseed genotypes (ten interspecific Brassicaceae hybrids of F₂ generation and 11 of their parental forms) and 146 alleles obtained using 21 ISSR molecular markers. In the presented study, six measures for calculating genetic similarity were compared: Euclidean, Jaccard, Kulczyński, Sokal and Michener, Nei, and Rogers. Genetic similarity values were estimated between all pairs of examined genotypes using the six measures proposed above. For each genetic similarity measure, the average, minimum, maximum values, and coefficient of variation were calculated. Correlation coefficients between the genetic similarity values obtained from each measure were determined. The obtained genetic similarity coefficients were used for the hierarchical clustering of objects using the unweighted pair group method with an arithmetic mean. A multiple regression model was written for each method, where the independent variables were the remaining methods. For each model, the coefficient of multiple determination was calculated. Genetic similarity values ranged from 0.486 to 0.993 (for the Euclidean method), from 0.157 to 0.986 (for the Jaccard method), from 0.275 to 0.993 (for the Kulczyński method), from 0.272 to 0.993 (for the Nei method), from 0.801 to 1.000 (for the Rogers method) and from 0.486 to 0.993 (for the Sokal and Michener method). The results indicate that the research material was divided into two identical groups using any of the proposed methods despite differences in the values of genetic similarity coefficients. Two of the presented measures of genetic similarity (the Sokal and Michener method and the Euclidean method) were the same. Full article

Throughout history, it has been observed that human populations have buried the deceased members of their communities following different patterns. During the Copper Age and the Bronze Age—periods on which this study focuses—in the northern sub-plateau of the Iberian Peninsula, we identified different patterns of multiple or collective burial. This work analyzes a total of 58 individuals buried in different multiple or collective graves, to investigate whether the practice of these burials implies a family or biological link between individuals buried together. With this aim, STR markers of nuclear DNA were analyzed, as well as the hypervariable regions I and II of mitochondrial DNA, establishing both close kinship relationships and relationships through maternal lineage. We observed different burial patterns, detecting certain maternal lines preserved in some common burials maintained over time. Close family relationships were observed to a lesser extent, with some occasional exceptions. The results of the analysis formed the basis for a discussion on the concepts of family and community. Full article

Acanthocephalans are dioecious parasites that gain sexual maturity in the alimentary canal of their definitive hosts (gnathostome vertebrates). This initial survey by light and transmission electron microscopy was conducted on the functional organization of the ovarian balls and uterine bell in mature females and on Saefftigen’s pouch and the copulatory bursa in males. We studied these structures via the example of Centrorhynchus globocaudatus (Palaeacanthocephala) in Falco tinnunculus and Buteo buteo, from the Province of Ferrara (Northern Italy). Our study confirms that the ovarian balls have surface microvilli and consist of a multinucleate supporting syncytium and a cellular region with oogonial syncytium, single germ cells, zygotes, and shelled eggs. Germ cells are embedded in the supporting syncytium. The ultrastructural features of these components and data on fertilization, shell formation, and release from the ovarian ball, alongside insights into the likely egg sorting function of the uterine bell, are provided. We also present light and electron microscopy observations of Saefftigen’s pouch and a suggestion regarding its hydrostatic functioning in the eversion of the copulatory bursa. Full article

Mitochondrial (mt) DNA plays an important role in the fields of forensic and clinical genetics, molecular anthropology, and population genetics, with mixture interpretation being of particular interest in medical and forensic genetics. The high copy number, haploid state (only a single haplotype contributed per individual), high mutation rate, and well-known phylogeny of mtDNA, makes it an attractive marker for mixture deconvolution in damaged and low quantity samples of all types. Given the desire to deconvolute mtDNA mixtures, the goals of this study were to (1) create a new software, MixtureAceMT™, to deconvolute mtDNA mixtures by assessing and combining two existing software tools, MixtureAce™ and Mixemt, (2) create a dataset of in-silico MPS mixtures from whole mitogenome haplotypes representing a diverse set of population groups, and consisting of two and three contributors at different dilution ratios, and (3) since amplicon targeted sequencing is desirable, and is a commonly used approach in forensic laboratories, create biological mixture data associated with two amplification kits: PowerSeq™ Whole Genome Mito (Promega™, Madison, WI, USA) and Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific by AB™, Waltham, MA, USA) to further validate the software for use in forensic laboratories. MixtureAceMT™ provides a user-friendly interface while reducing confounding features such as NUMTs and noise, reducing traditionally prohibitive processing times. The new software was able to detect the correct contributing haplogroups and closely estimate contributor proportions in sequencing data generated from small amplicons for mixtures with minor contributions of ≥5%. A challenge of mixture deconvolution using small amplicon sequencing is the potential generation of spurious haplogroups resulting from private mutations that differ from Phylotree. MixtureAceMT™ was able to resolve these additional haplogroups by including known haplotype/s in the evaluation. In addition, for some samples, the inclusion of known haplotypes was also able to resolve trace contributors (minor contribution 1–2%), which remain challenging to resolve even with deep sequencing. Full article

Endemic to the Indian subcontinent, the sloth bear (Melursus ursinus) is a threatened species, present in fragmented habitats across India. Field techniques such as direct observation and camera trapping alone are not sufficient and may not be explicit enough to understand a monomorphic species like the sloth bear at larger spatial scales. In this study, we looked into the genetic structure, variability and population demographics amongst the extant sloth bear populations in the highly fragmented Vidarbha landscape, using a panel of 13 microsatellite markers with a cumulative PID value of 1.48 × 10⁻⁵ PID_sibs. Our results revealed genetic clustering (K = 5) and moderate structuring amongst the study populations. Despite being geographically distant and placed in two different genetic clusters, sloth bears from the Melghat Tiger Reserve and Sahyadri Tiger Reserve shared genetic signatures, indicating connectivity, while migration was detected amongst other study areas as well. The findings from this study can serve as baseline assessment for future genetic monitoring of the species in the human-dominated landscape and assist in managerial decisions to step up protection of fragmented forest patches and reduce human–bear conflicts without compromising on the genetic connectivity. Full article

The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics. Full article

The chronological period from the beginning of the Chalcolithic Age to the end of the Bronze Age on the Iberian northern sub-plateau of the Iberic Peninsula involves interesting social and cultural phenomena, such as the appearance of the Bell Beaker and, later, the Cogotas I cultures. This work constructs a genetic characterisation of the maternal lineages of the human population that lived on the northern sub-plateau between 5000 and 3000 years ago through an analysis of mitochondrial DNA (mtDNA), a kind of genetic marker that is inherited through maternal lineages, unaltered from generation to generation. Population and cultural questions are investigated through mtDNA analyses. This study intends to shed light on the following questions. Were individuals who were buried together in multiple or collective burials biologically related through their maternal lineages? Were there distinct maternal human lineages in the same or different geographical areas if different material cultures (Bell Beaker and Cogotas I) were associated with the arrival of new human populations who established close biological relationships with the endogenous populations? Or could this be the result of the transmission of knowledge without human populations mixing? Another important question is whether the material cultures were related to the female populations. We analysed 91 individuals from 28 different archaeological sites of the Iberian northern sub-plateau from four different chrono-cultural periods (Pre-Bell Beaker, Bell Beaker, Proto-Cogotas I, and Cogotas I), from the end of the Chalcolithic Age up to the Bronze Age. There were two historical moments of new populations arriving: the first during the Pre-Bell Beaker period, associated with the K mtDNA haplogroup, and the second during the Proto-Cogotas I culture, with new lineages of the H, HVO, and T haplogroups. Neither of these new population flows were directly associated with the maximum development of the two main material cultures Bell Beaker and Cogotas I, so they must have occurred immediately beforehand, during the Pre-Bell Beaker and Proto-Cogotas I periods, respectively. However, we cannot discard an association between the populations and material cultures. Curiously, it has also been observed that there was also a tendency towards multiple burials, in which the individuals who were buried together belonged to the same maternal lineage, during these two periods of population change. This study has shed some light on the populational changes that occurred through these different periods in this specific geographical area of the northern sub-plateau of the Iberian Peninsula. Full article

Seafood constitutes the primary source of exposure to the organic form of mercury in the general population, and the Trieste Gulf is considered a hotspot of mercury contamination. We used a newly developed quantitative food frequency questionnaire to obtain an estimation of the intake of mercury through seafood consumption in a sample of 32 individuals from Trieste. Then, we validated the results obtained from the questionnaire against those of the analysis of total mercury measured in the hair of the same individuals through Spearman rank correlation coefficients, Cohen’s weighted Kappa statistic, and a Bland–Altman plot. The Spearman rank correlation coefficient and Cohen’s weighted Kappa statistic were 0.76 and 0.69, respectively. In the Bland–Altman plot, 93.75% of the data points lay within the acceptability range. The plot revealed an ever-increasing overestimation of mercury intake by the questionnaires as the hair mercury increased. By applying a standardized filtering procedure to the results of the questionnaires, we obtained a Spearman rank correlation coefficient and Cohen’s weighted Kappa statistic of 0.69 and 0.57, respectively. In this Bland–Altman plot, 93.75% of the data points lay within the acceptability range. In this latter plot, the proportionality between the mean difference and the magnitude of the measurement was more subtle compared to that observed in the plot built upon the non-filtered questionnaires. This preliminary study shows the high accuracy of the reported questionnaire in the estimation of habitual mercury intake, similar to the one measured through the analysis of hair. Full article

A large body of evidence indicates that environmental agents can induce alterations in DNA methylation (DNAm) profiles. Radiofrequency electromagnetic fields (RF-EMFs) are radiations emitted by everyday devices, which have been classified as “possibly carcinogenic”; however, their biological effects are unclear. As aberrant DNAm of genomic repetitive elements (REs) may promote genomic instability, here, we sought to determine whether exposure to RF-EMFs could affect DNAm of different classes of REs, such as long interspersed nuclear elements-1 (LINE-1), Alu short interspersed nuclear elements and ribosomal repeats. To this purpose, we analysed DNAm profiles of cervical cancer and neuroblastoma cell lines (HeLa, BE(2)C and SH-SY5Y) exposed to 900 MHz GSM-modulated RF-EMF through an Illumina-based targeted deep bisulfite sequencing approach. Our findings showed that radiofrequency exposure did not affect the DNAm of Alu elements in any of the cell lines analysed. Conversely, it influenced DNAm of LINE-1 and ribosomal repeats in terms of both average profiles and organisation of methylated and unmethylated CpG sites, in different ways in each of the three cell lines studied. Full article

Older adults with dementia present an increased risk of mortality due to seasonal influenza. Despite concerning evidence, the influenza vaccination program has been unsuccessful, with low rates of uptake in Italian people ≥65 years. In addition, being vaccinated does not eliminate the risk of contracting a virus, especially by coming into close contact with other possibly unvaccinated people, such as family caregivers in the home environment. Therefore, the refusal of family caregivers to get vaccinated for seasonal influenza could have dire consequences for their relatives with dementia. The aims of this study were to investigate the predictive role of the Theory of Planned Behavior model (TPB) and past vaccination behavior on the intention to receive a seasonal influenza vaccine among family caregivers of people with dementia. Data were collected from seventy-one respondents during July–September 2021 using a cross-sectional web-based survey design. Results of hierarchical binary logistic regression showed that TPB (i.e., attitudes towards vaccination, subjective norms, and perceived behavioral control) explained 51.6% of the variance in intention to receive a seasonal influenza vaccine; past vaccination behavior increased this to 58.8%. In conclusion, past vaccination behavior and the theory of planned behavior variables effectively predict influenza vaccine willingness of family caregivers of people with dementia and should be targeted in vaccination campaigns. Full article

Human APOE is a 299-amino acid long protein expressed and secreted in several tissues and body districts, where it exerts different functions mainly related to lipid metabolism, with specific activities around cholesterol transport and absorption/elimination. It has three main isoforms, determined by the pair of mutations rs7412-C/T and rs429358-C/T, which gives rise to the functionally different APOE variants ε2, ε3, and ε4. These have a distinct impact on lipid metabolism and are differentially implicated in Alzheimer’s disease and neurodegeneration, cardiovascular disease, and dyslipidemia. A plethora of other single nucleotide variants along the sequence of the APOE gene have been studied in cohorts of affected individuals, where they also modulate the influence of the three main isoforms to determine the risk of developing the disease. However, no contextual analysis of gene-long haplotypes has been carried out so far, and never extensively in cohorts of healthy individuals from different worldwide populations. Leveraging a rich population genomics dataset, this study elucidates the distribution of APOE variants and haplotypes that are shared across populations and to specific macroareas, revealing a variety of risk-allele associations that distinguish specific ancestral backgrounds and can be leveraged for specific ancestry-informed screenings in medicine and public health. Full article

The skeletal sex and ancestry of unidentified human crania can be inferred both from physical and from molecular features. This paper depicts and discusses the experiences of physical and molecular anthropologists on a set of commingled crania from the largest Mediterranean shipwreck disaster on 18 April 2015, in order to facilitate identification of human crania. Twenty-one disarticulated crania that were recovered from the above-mentioned shipwreck were analyzed to estimate skeletal sex and ancestry, following a physical and a molecular pipeline. The physical analyses applied morphological and metric methods that provided posterior probabilities for the crania to be classified into a sex or ancestral group. The molecular analyses were performed on petrous bones via a shotgun sequencing approach that allowed us to determine the sex of each individual and to retrieve the complete mitochondrial genome, Y chromosome single nucleotide polymorphisms, up to 597573 SNPs across the human genome from each individual. The morphometric sex analyses showed that most crania belonged to male individuals, although some estimations remained uncertain or undetermined. Inconsistent results were obtained for ancestry estimation as well, since morphological methods classified the crania mostly as European/White, in contrast to the most numerous African forms determined by craniometric analyses. This quite agreed with molecular analyses that identified only African males. Overall, undetermined and contrasting results were obtained between disciplines, preventing the creation of reliable and sound biological profiles that could provide guidance on the sex and ancestral group of the victims. Therefore, the times may not be mature for a merger of physical and molecular anthropology. However, future investigations of this research avenue would pave the way to the possible development of novel tools, methods, and wider reference databases that could address the limitations of both disciplines. Full article

In our experience, university students enrolling in health science and forensic science degrees show difficulty in retaining and integrating basic scientific knowledge learned in their first academic year. Furthermore, in the forensic sciences case, many students have oversimplified and unrealistic expectations as a result of the exposure to crime TV shows, internet blogs, and other social media platforms. Our pedagogical proposal is focused on second-year university students, aiming at promoting effective learning and the integration of scientific knowledge from previous courses, in this particular example, molecular and cell biology and biochemistry, with more advanced forensic courses, such as forensic anthropology and odontology. Teams composed of students and tutors from the teaching staff, with the help of dichotomous keys, are challenged to analyze a crime scene and choose the relevant evidence to further investigate, determine the scientific approach, execute the experimental work, interpret the results and, finally, resolve the case. To assess the pedagogical advantages and the receptivity of this project, a survey is to be carried out among students, and respective statistical analysis is also proposed. Finally, we hope this project outline may be adapted to other subjects, and, therefore, be used to address different pedagogical questions in forensic studies. Full article

Alzheimer’s disease (AD) represents the most prevalent type of dementia in elderly people, primarily characterized by brain accumulation of beta-amyloid (Aβ) peptides, derived from Amyloid Precursor Protein (APP), in the extracellular space (amyloid plaques) and intracellular deposits of the hyperphosphorylated form of the protein tau (p-tau; tangles or neurofibrillary aggregates). The Nerve growth factor receptor (NGFR/p75^NTR) represents a low-affinity receptor for all known mammalians neurotrophins (i.e., proNGF, NGF, BDNF, NT-3 e NT-4/5) and it is involved in pathways that determine both survival and death of neurons. Interestingly, also Aβ peptides can blind to NGFR/p75^NTR making it the “ideal” candidate in mediating Aβ-induced neuropathology. In addition to pathogenesis and neuropathology, several data indicated that NGFR/p75^NTR could play a key role in AD also from a genetic perspective. Other studies suggested that NGFR/p75^NTR could represent a good diagnostic tool, as well as a promising therapeutic target for AD. Here, we comprehensively summarize and review the current experimental evidence on this topic. Full article

Epigenetic clocks were initially developed to track chronological age, but accumulating evidence indicates that they can also predict biological age. They are usually based on the analysis of DNA methylation by genome-wide methods, but targeted approaches, based on the assessment of a small number of CpG sites, are advisable in several settings. In this study, we developed a targeted epigenetic clock purposely optimized for the measurement of biological age. The clock includes six genomic regions mapping in ELOVL2, NHLRC1, AIM2, EDARADD, SIRT7 and TFAP2E genes, selected from a re-analysis of existing microarray data, whose DNA methylation is measured by EpiTYPER assay. In healthy subjects (n = 278), epigenetic age calculated using the targeted clock was highly correlated with chronological age (Spearman correlation = 0.89). Most importantly, and in agreement with previous results from genome-wide clocks, epigenetic age was significantly higher and lower than expected in models of increased (persons with Down syndrome, n = 62) and decreased (centenarians, n = 106; centenarians’ offspring, n = 143; nutritional intervention in elderly, n = 233) biological age, respectively. These results support the potential of our targeted epigenetic clock as a new marker of biological age and open its evaluation in large cohorts to further promote the assessment of biological age in healthcare practice. Full article