Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.- Background - Results -- Authentication of a preserved oral biofilm in calculus samples -- Dental calculus and plaque biofilm communities are distinct -- Health-associated communities of dental plaque and calculus are distinct -- Signatures of health and of disease are shared in modern and historic calculus samples -- Microbial community differences between health and disease in calculus are poorly resolved -- Absence of caries-specific microbial profiles in dental calculus -- Microbial co-exclusion patterns in plaque and calculus reflect biofilm maturity -- Microbial complexes in plaque and calculus -- Functional prediction in calculus is poorly predictive of health status -- Proteomic profiles of historic healthy site calculus -- Correlations between taxonomic, proteomic, and metabolomic profiles - Discussion - Conclusions - Materials and methods --Historic and modern calculus sample collection DNA extraction -- DNA library construction and high-throughput sequencing -- DNA sequence processing -- Genetic assessment of historic calculus sample preservation -- Genetic microbial taxonomic profiling -- Principal component analysis -- Assessment of differentially abundant taxa -- Sparse partial least squares-discriminant analysis -- Assessment of microbial co-exclusion patterns -- Gene functional categorization with SEED -- Proteomics -- Metabolomics -- Regularized canonical correlation analysi

The emergence of the brain non-CpG methylation system in vertebrates

Mammalian brains feature exceptionally high levels of non-CpG DNA methylation alongside the canonical form of CpG methylation. Non-CpG methylation plays a critical regulatory role in cognitive function, which is mediated by the binding of MeCP2, the transcriptional regulator that when mutated causes Rett Syndrome. However, it is unclear if the non-CpG neural methylation system is restricted to mammalian species with complex cognitive abilities or has deeper evolutionary origins. To test this, we investigated brain DNA methylation across 12 distant animal lineages, revealing that non-CpG methylation is restricted to vertebrates. We discovered that in vertebrates, non-CpG methylation is enriched within a highly conserved set of developmental genes transcriptionally repressed in adult brains, indicating that it demarcates a deeply conserved regulatory program. Concomitantly, we found that the writer of non-CpG methylation, DNMT3A, and the reader, MeCP2, originated at the onset of vertebrates as a result of the ancestral vertebrate whole genome duplication. Together, we demonstrate how this novel layer of epigenetic information assembled at the root of vertebrates and gained new regulatory roles independent of the ancestral form of the canonical CpG methylation. This suggests the emergence of non-CpG methylation may have fostered the evolution of sophisticated cognitive abilities found in the vertebrate lineage

Dental metric standards for sex estimation in archaeological populations from Iran

Sex estimation of skeletal remains is one of the major components of forensic identification of unknown individuals. Teeth are a potential source of information on sex and are often recovered in archaeological or forensic contexts due to their post-mortem longevity. Currently there is limited data on dental sexual dimorphism of archaeological populations from Iran. This dissertation represents the first study to provide a dental sex estimation method for Iron Age populations. The current study was conducted on the skeletal remains of 143 adults from two Iron Age populations in close temporal and geographic proximity in the Solduz Valley (West Azerbaijan Province of Iran). 2D and 3D cervical mesiodistal and buccolingual and root volume measurements of maxillary and mandibular teeth were used to investigate the degree of sexual dimorphism in permanent dentition and to assess their applicability in sex estimation. In total 1327, 457, and 480 anterior and posterior teeth were used to collect 2D cervical, 3D cervical, and root volume measurements respectively. 2D cervical measurements were taken using Hillson-Fitzgerald dental calliper and 3D measurements were collected using CT images provided by Open Research Scan Archive (ORSA) - Penn Museum. 3D models of the teeth were created using manual segmentation in the Amira 6.01 software package. Since tooth density largely differs from crown to apex, root segmentation required two threshold levels: the segmentation of the root from the jaw and the segmentation of the crown from the root. Thresholds used for root segmentation were calculated using the half maximum height protocol of Spoor et al. (1993) for each skull, and thresholds used for crown segmentation were set visually for each tooth separately. Data was analysed using discriminant function analysis and posterior probabilities were calculated for all produced formulae where sex was previously assessed from morphological features of pelvis and skull. Bootstrapping was used to account for small sample sizes in the analysis. Statistical analysis was carried out using SPSS 23. The percentage of sexual dimorphism was also used to quantify the amount of sexual dimorphism in the sample. The results showed that incisors and canines were the most sexually dimorphic teeth, providing percentages of correct sex classification between 80% and 100% depending on the measurement used. Root volume measurement was shown to be the most sexually dimorphic variable providing an accuracy of over 90% in all functions. The present study provided the first dental metric standards for sex estimation using odontometric data in Iranian archaeological populations. Dental measurements, particularly root volume measurements, were found to be of value for sex assessment and the method presented here could be a useful tool for establishing accurate demographic data from skeletal remains of the Iron Age from Iran

A comparison of three established age estimation methods on an adult Spanish sample.

Most current methods for adult skeletal age-at-death estimation are based on American samples comprising individuals of European and African ancestry. Our limited understanding of population variability hampers our efforts to apply these techniques to various skeletal populations around the world, especially in global forensic contexts. Further, documented skeletal samples are rare, limiting our ability to test our techniques. The objective of this paper is to test three pelvic macroscopic methods (1-Suchey-Brooks; 2- Lovejoy; 3- Buckberry and Chamberlain) on a documented modern Spanish sample. These methods were selected because they are popular among Spanish anthropologists and because they never have been tested in a Spanish sample. The study sample consists of 80 individuals (55 ♂ and 25 ♀) of known sex and age from the Valladolid collection. Results indicate that in all three methods, levels of bias and inaccuracy increase with age. The Lovejoy method performs poorly (27%) compared with Suchey-Brooks (71%) and Buckberry and Chamberlain (86%). However, the levels of correlation between phases and chronological ages are low and comparable in the three methods (< 0.395). The apparent accuracy of the Suchey-Brooks and Buckberry and Chamberlain methods is largely based on the broad width of the methods" estimated intervals. This study suggests that before systematic application of these three methodologies in Spanish populations, further statistical modeling and research into the co-variance of chronological age with morphological change is necessary. Future methods should be developed specific to various world populations, and should allow for both precision and flexibility in age estimation

Degenerative changes of the sacroiliac auricular joint surface?validation of influential factors

The purpose of this study was to clarify the relevance of degenerative changes in the sacroiliac joint (SIJ) and the joints in the lower limb and lumbar spine using age estimation methods. We also examined the shape of the auricular surface to determine the effect of degenerative changes on each joint. A total of 200 iliac auricular surfaces from 100 Japanese male skeletons were examined macroscopically in accordance with conventional methods of age estimation. From the obtained estimated age, we calculated the deflection values, which represented the degree of degenerative changes of the joints. For comparison, we used osteophyte score data of the hip, knee, and zygapophyseal joints in lumbar spines from previous studies which had used the same bone specimens. As a quantitative indicator of auricular surface morphology, we defined the constriction ratio (CR) of the auricular surface and compared the CR values obtained with various measured values. Degenerative changes in the SIJ were positively correlated with those in both the hip joint and zygapophyseal joint, but a correlation with knee joints was found only on the left side. In skeletons from individuals aged ?60 years as time of death, the CR was significantly different between the group with high scores and those with low scores in both the hip and sacroiliac joints. It has been suggested that degenerative changes in SIJs interact with those in the hip joint and zygapophyseal joint. In addition, the shape of the auricular surface may also be a relevant factor for degenerative changes in these joints

Anglo-Saxon concepts of dis/ability: Placing disease at Great Chesterford in its wider context

Within Anglo-Saxon society, individuals obtained their status on the basis of their ability to undertake required and prescribed social roles. People experiencing impairment, be that as a result of disease or some other process including trauma or pregnancy, might thus have reduced ability to undertake socially required activities. These people would have been highly visible within contemporary society by their very inability to undertake all required roles. These ideas are explored using a cluster of inhumations from the early Anglo-Saxon cemetery at Great Chesterford. Cemetery topography, visibility of difference, liminality, and etiology are explored in order to suggest the importance of the development of a sample-based approach to osteobiography. These might then be used to establish local understandings of disability,whereby individuals are viewed as people with focus placed on ability

The iliac crest in forensic age estimation: evaluation of three methods in pelvis X-rays

Age assessment in children and young adults is a relevant forensic issue. It is requested not only in evaluating criminal responsibility in youths without proper identification documents, often in relation to age thresholds, but also for release of a residency permit, and asylum seekers of minors. The analysis of the Risser sign and the iliac crest ossification process has been proposed as a useful tool for forensic age estimation. We evaluated the applicability of three different age estimation methods on a sample of 497 pelvic radiographs of Italian individuals between 10 and 25 years of age. Each method showed high reliability for both reproducibility and repeatability. The staging technique inspired by Kreitner and Kellinghaus methods (KK-MS) is easier than the Risser method in applicability, as it is not affected by the variations of ossification. We observed that all subjects who attained stage 3c of KK-MS and 5 of Risser Fr were >14 years, suggesting the benefits of these methods for that age threshold. The applicability of the area measurement method, inspired by Cameriere’s approach, ranged between 12 and 20 years, but the statistical analysis showed only a moderate correlation with age. In order to evaluate the possible use of this approach it is therefore necessary to clarify and exclude external factors influencing the parameter. In conclusion, the iliac crest ossification is of interest in age estimation for forensic purposes. The evaluation of the pelvis X-ray, in addition to the other common dental and skeletal methods, could become a useful supplementary tool in age estimation for the 14 year threshold in order to fulfill forensic-level requirements