The effects of graded levels of calorie restriction : I. impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse

We acknowledge the BSU staff for their invaluable help with caring for the animals and anonymous referees for their inputs. The work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) of the UK (Standard grant BB/G009953/1 and China partnering award BB/JO20028/1). The authors declare no competing interests.Peer reviewedPublisher PD

Primate Skeletal Epigenetics: Evolutionary Implications of DNA Methylation Patterns in the Skeletal Tissues of Human and Nonhuman Primates

abstract: Within the primate lineage, skeletal traits that contribute to inter-specific anatomical variation and enable varied niche occupations and forms of locomotion are often described as the result of environmental adaptations. However, skeletal phenotypes are more accurately defined as complex traits, and environmental, genetic, and epigenetic mechanisms, such as DNA methylation which regulates gene expression, all contribute to these phenotypes. Nevertheless, skeletal complexity in relation to epigenetic variation has not been assessed across the primate order. In order to gain a complete understanding of the evolution of skeletal phenotypes across primates, it is necessary to study skeletal epigenetics in primates. This study attempts to fill this gap by identifying intra- and inter-specific variation in primate skeletal tissue methylation in order to test whether specific features of skeletal form are related to specific variations in methylation. Specifically, methylation arrays and gene-specific methylation sequencing are used to identify DNA methylation patterns in femoral trabecular bone and cartilage of several nonhuman primate species. Samples include baboons (Papio spp.), macaques (Macaca mulatta), vervets (Chlorocebus aethiops), chimpanzees (Pan troglodytes), and marmosets (Callithrix jacchus), and the efficiencies of these methods are validated in each taxon. Within one nonhuman primate species (baboons), intra-specific variations in methylation patterns are identified across a range of comparative levels, including skeletal tissue differences (bone vs. cartilage), age cohort differences (adults vs. juveniles), and skeletal disease state differences (osteoarthritic vs. healthy), and some of the identified patterns are evolutionarily conserved with those known in humans. Additionally, in all nonhuman primate species, intra-specific methylation variation in association with nonpathological femur morphologies is assessed. Lastly, inter-specific changes in methylation are evaluated among all nonhuman primate taxa and used to provide a phylogenetic framework for methylation changes previously identified in the hominin lineage. Overall, findings from this work reveal how skeletal DNA methylation patterns vary within and among primate species and relate to skeletal phenotypes, and together they inform our understanding of epigenetic regulation and complex skeletal trait evolution in primates.Dissertation/ThesisDoctoral Dissertation Anthropology 201

Mobility and economic transition in the 5th to the 2nd millennium B.C. in the population of the Central Iranian Plateau, Tepe Hissar

Iranian archaeology has had a keen interest in exploring unexplained events occurring during the 5th to the 2nd millennium B.C. on the Central Iranian Plateau. This is represented by transformations in material culture, a differentiation in mortuary practices, and site abandonment and reoccupation, and has traditionally been explained by the influx of new populations into Central Plateau sites. The site of Tepe Hissar, the subject of this research, located in the north-east region of the Central Plateau and appears to have undergone these changes during its existence (late 5th to the early 2nd millennium B.C.). This research uses a bioarchaeological approach to tests the hypotheses that the socio-cultural-economic changes that occurred at Tepe Hissar over time, accompanied by influxes of new people into the site, particularly in Hissar periods II and III; ultimately impacted on subsistence economy, diet, and general health, and also resulted in a rise in tension and interpersonal violence. The biological affinity data suggest that the changes at Tepe Hissar were not accompanied by large scale population replacement/immigration/or invasion. Rather, there was more small scale population replacement over time, although these changes were accompanied by interpersonal violence. These changes did not greatly impact on the general health of people over time, although people in each period experienced different frequencies of stress and disease, and periods of malnutrition; both females and males were affected equally in each period. The dental disease data showed that changes during Hissar II and III had a significant impact on the oral-health of people, and Hissar I experienced better oral-health compared to later periods; this may be due to changes in subsistence economy and diet, food preparation techniques, and how the teeth were used as tools. The data indicate that males possibly suffered poorer dental health compared to females at this site; they may have had a different diet, or possibly used their teeth as a third hand more than females. The isotopic data (C/N) showed that the inhabitants had access to similar food resources across all periods; individuals from each period, both sexes from different age-categories, had a similar diet based on C3 plants and animal protein, as well as a small contribution from fresh water resources. Overall, this research suggests that the society who lived at Tepe Hissar overall may have had an appropriate social structure and adequate food resources to withstand socio-cultural-economic changes, enabling the community to be more centralised socially, economically, and politically such that the changes and events they experienced did not markedly affect their health or nutritional status

A zinc oxide-modified hydroxyapatite-based cement facilitated new crystalline-stoichiometric and amorphous apatite precipitation on dentine.

Aim: To evaluate the remineralization ability of two dentin canal sealer cements. Methodology: Dentin surfaces were subjected to: i) 37% phosphoric acid (PA) or ii) 0.5 M ethylenediaminetetraacetic acid (EDTA) conditioning prior to the application of two experimental hydroxyapatite-based cements, containing sodium hydroxide (calcypatite) or zinc oxide (oxipatite), respectively. Samples were stored in simulated body fluid during 24 h or 21 d. Remineralization of the dentin surfaces were studied by Raman spectroscopy, mapping with K-means cluster and hierarchical cluster analysis were done. Nano-roughness and collagen fibrils width measurements were performed by means of an atomic force microscopy. Results: PA+oxipatite promoted both the highest dentin mineralization and crystallographic maturity at the dentin surface. Non-crystalline amorphous-like apatites were also formed. Dentin treated with PA+calcypatite attained the roughest surface with minimal fibril width. Crosslinking of collagen only raised in the group PA+oxipatite, after 21 d. The maximum relative mineral concentration and structure of collagen referred to amide I and ratio amide III/AGEs was achieved after using PA+calcypatite at 21 d time point. EDTA produced a lower stoichiometric hydroxyapatite with decreased maturity, at the expense of the carbonate band widening, though it favored the nucleation of carbonated calcium phosphate. Conclusions: Surfaces treated with PA+oxipatite attained the highest dentin remineralization with both crystalline-stoichiometric and amorphous apatites, at long term. EDTA conditioning facilitated amorphous-bulk mineral precipitation. This amorphization, more intense after using oxipatite, provided an ion-rich environment favoring in situ dentin remineralization.This work was supported by the Ministry of Economy and Competitiveness (MINECO) [Project MAT2014-52036-P] and European Regional Development Fund (FEDER)

Recent Advances in Forensic Anthropological Methods and Research

Forensic anthropology, while still relatively in its infancy compared to other forensic science disciplines, adopts a wide array of methods from many disciplines for human skeletal identification in medico-legal and humanitarian contexts. The human skeleton is a dynamic tissue that can withstand the ravages of time given the right environment and may be the only remaining evidence left in a forensic case whether a week or decades old. Improved understanding of the intrinsic and extrinsic factors that modulate skeletal tissues allows researchers and practitioners to improve the accuracy and precision of identification methods ranging from establishing a biological profile such as estimating age-at-death, and population affinity, estimating time-since-death, using isotopes for geolocation of unidentified decedents, radiology for personal identification, histology to assess a live birth, to assessing traumatic injuries and so much more

Harnessing label-free Raman spectroscopy for metastatic cancer diagnosis and biologic development

Optical spectroscopy is unique amongst experimental techniques in that it can be performed in near-physiological conditions, achieve high molecular specificity, and explore dynamics on timescales ranging from nanoseconds to days. In particular, Raman spectroscopy has emerged in the last two decades as a uniquely versatile method to investigate the structures and properties of molecules in diverse environments through interpreting vibrational transitions. In this thesis, we present four interconnected biomedical and biopharmaceutical applications of Raman spectroscopy that exploit its exquisite molecular specificity, non-perturbative nature, and near real-time measurement capability. In the first presented study, we harness spontaneous Raman spectroscopy in conjunction with multivariate analysis to rapidly and quantitatively determine antibody-drug conjugate aggregation with the goal of eventual application as an in-line tool for monitoring protein particle formation. By exploring subtle, but consistent, differences in spectral vibrational modes of various monoclonal antibodies (mAb) aggregations, a support vector machine-based regression model is developed which is able to accurately predict a wide range of protein aggregation. In addition, the investigation of these spectral vibrational modes also offers new insights into mAb product-specific aggregation mechanisms. Second, leveraging surface-enhanced Raman scattering (SERS) and localized surface plasmon resonance (LSPR), we present a design of plasmonic nanostructures based on rationally structured metal-dielectric combinations, which we call composite scattering probes (CSP). Specifically, we design CSP configurations that have several prominent resonance peaks enabling higher tunability and sensitivity for self-referenced multiplexed analyte sensing. The CSP prototypes were used to demonstrate differentiation of subtle changes in refractive index (as low as 0.001) as well as acquire complementary untargeted plasmon-enhanced Raman measurements from the biospecimen’s compositional contributors. In the third study, we demonstrate that Raman spectroscopy offers vital biomolecular information for early diagnosis and precise localization of breast cancer-colonized bone alterations. We show that as early as two weeks after intracardiac injections of breast cancer cells in mouse models, Raman measurements in femur and spine uncover consistent changes in both bone matrix and mineral composition. This research effort opens the door for improved understanding of breast metastatic tumor-related bone remodeling and establishing a non-invasive tool for detection of early metastasis and prediction of fracture risk. In parallel with this effort, we also seek to identify the differences between organ-specific isogenic metastatic breast cancer cells. By interpreting the informative spectral bands, we are able to unambiguously identify these isogenic cell lines as unique biological entities. Our spectroscopic study and corresponding metabolic research indicate that tissue-specific adaptations generate biomolecular alterations on cancer cells