Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The effect of eraser sampling for proteomic analysis on Palaeolithic bone surface microtopography.

ABSTRACT: Bone surface modifications are crucial for understanding human subsistence and dietary behaviour, and can inform about the techniques employed in the production and use of bone tools. Permission to destructively sample such unique artefacts is not always granted. The recent development of non-destructive proteomic extraction techniques has provided some alternatives for the analysis of rare and culturally significant artefacts, including bone tools and personal ornaments. The Eraser Extraction Method (EEM), first developed for ZooMS analysis of parchment, has recently been applied to bone and ivory specimens. To test the potential impact of the EEM on ancient bone surfaces, we analyse six anthropogenically modified Palaeolithic bone specimens from Bacho Kiro Cave (Bulgaria) through a controlled sampling experiment using qualitative and 3D quantitative microscopy. Although the overall bone topography is generally preserved, our findings demonstrate a slight flattening of the microtopography alongside the formation of micro-striations associated with the use of the eraser for all bone specimens. Such modifications are similar to ancient use-wear traces. We therefore consider the EEM a destructive sampling approach for Palaeolithic bone surfaces. Together with low ZooMS success rates in some of the reported studies, the EEM might not be a suitable approach to taxonomically identify Pleistocene bone specimens.

SUBMITTER: Sinet-Mathiot V

PROVIDER: S-EPMC8655045 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Surface microtopography modulates sealing zone development in osteoclasts cultured on bone.

Project description:Bone homeostasis is continuously regulated by the coordinated action of bone-resorbing osteoclasts and bone-forming osteoblasts. Imbalance between these two cell populations leads to pathological bone diseases such as osteoporosis and osteopetrosis. Osteoclast functionality relies on the formation of sealing zone (SZ) rings that define the resorption lacuna. It is commonly assumed that the structure and dynamic properties of the SZ depend on the physical and chemical properties of the substrate. Considering the unique complex structure of native bone, elucidation of the relevant parameters affecting SZ formation and stability is challenging. In this study, we examined in detail the dynamic response of the SZ to the microtopography of devitalized bone surfaces, taken from the same area in cattle femur. We show that there is a significant enrichment in large and stable SZs (diameter larger than 14 µm; lifespan of hours) in cells cultured on rough bone surfaces, compared with small and fast turning over SZ rings (diameter below 7 µm; lifespan approx. 7 min) formed on smooth bone surfaces. Based on these results, we propose that the surface roughness of the physiologically relevant substrate of osteoclasts, namely bone, affects primarily the local stability of growing SZs.

| S-EPMC5332580 | biostudies-literature

RGB-D microtopography: A comprehensive dataset for surface analysis and characterization techniques.

Project description:The dataset presented contains microtopographies of various materials and processing methods. These microtopographies were measured using a Confocal Laser Scanning Microscope, which provides RGB-D data. This means the dataset comprises accurate height maps for each measurement and microscopic RGB images. The height maps can be used to quantify and characterize small-scale surface features such as pits and grooves, surface roughness, texture direction, and surface anisotropy. These features can significantly impact a material's properties and behavior, making them essential in many fields, such as biomaterials and tribology. Additionally, the dataset contains metadata about the specimens and the measurement conditions, such as material, surface processing method, roughness, and optical magnification. Therefore, this dataset provides an opportunity to develop and test surface classification and characterization algorithms.

| S-EPMC10114499 | biostudies-literature

Proteomic analysis of bone proteins adsorbed onto the surface of titanium dioxide.

Project description:Osseointegration is the structural and functional connection between bone tissues and implants such as titanium dioxide (TiO2). The bone-TiO2 interface is thought to contain proteoglycans. However, exhaustive analysis of the proteins in this layer has not been performed. In this study, we evaluated the bone protein adhered on the surface of TiO2 comprehensively. Pig bone protein was extracted by sequential elutions with guanidine, 0.1 M EDTA, and again with guanidine. The proteins obtained from these extractions were allowed to adhere to an HPLC column packed with TiO2 and were eluted with 0.2 M NaOH. The eluted proteins were identified by LC/MS/MS and included not only proteoglycans but also other proteins such as extracellular matrix proteins, enzymes, and growth factors. Calcium depositions were observed on TiO2 particles incubated with bone proteins, guanidine-extracted proteins adhered to TiO2 displayed significantly high amounts of calcium depositions.

| S-EPMC5613647 | biostudies-literature

The Effect of Exogenous Zinc Concentration on the Responsiveness of MC3T3-E1 Pre-Osteoblasts to Surface Microtopography: Part I (Migration).

Project description:Initial cell-surface interactions are guided by the material properties of substrate topography. To examine if these interactions are also modulated by the presence of zinc, we seeded murine pre-osteoblasts (MC3T3-E1, subclone 4) on micropatterned polydimethylsiloxane (PDMS) containing wide (20 µm width, 30 µm pitch, 2 µm height) or narrow (2 µm width, 10 µm pitch, 2 µm height) ridges, with flat PDMS and tissue culture polystyrene (TC) as controls. Zinc concentration was adjusted to mimic deficient (0.23 µM), serum-level (3.6 µM), and zinc-rich (50 µM) conditions. Significant differences were observed in regard to cell morphology, motility, and contact guidance. We found that cells exhibited distinct anisotropic migration on the wide PDMS patterns under either zinc-deprived (0.23 µM) or serum-level zinc conditions (3.6 µM). However, this effect was absent in a zinc-rich environment (50 µM). These results suggest that the contact guidance of pre-osteoblasts may be partly influenced by trace metals in the microenvironment of the extracellular matrix.

| S-EPMC5452741 | biostudies-literature

Silicone implant surface microtopography modulates inflammation and tissue repair in capsular fibrosis.

Project description:Excessive fibrous capsule formation around silicone mammary implants (SMI) involves immune reactions to silicone. Capsular fibrosis, a common SMI complication linked to host responses, worsens with specific implant topographies. Our study with 10 patients investigated intra- and inter-individually, reduced surface roughness effects on disease progression, wound responses, chronic inflammation, and capsular composition. The results illuminate the significant impact of surface roughness on acute inflammatory responses, fibrinogen accumulation, and the subsequent fibrotic cascade. The reduction of surface roughness to an average roughness of 4 μm emerges as a promising approach for mitigating detrimental immune reactions, promoting healthy wound healing, and curbing excessive fibrosis. The identified proteins adhering to rougher surfaces shed light on potential mediators of pro-inflammatory and pro-fibrotic processes, further emphasizing the need for meticulous consideration of surface design. The composition of the implant capsule and the discovery of intracapsular HSP60 expression highlight the intricate web of stress responses and immune activation that can impact long-term tissue outcomes.

| S-EPMC10985323 | biostudies-literature

An Upper Palaeolithic engraved human bone associated with ritualistic cannibalism.

Project description:Cut-marked and broken human bones are a recurrent feature of Magdalenian (~17-12,000 years BP, uncalibrated dates) European sites. Human remains at Gough's Cave (UK) have been modified as part of a Magdalenian mortuary ritual that combined the intensive processing of entire corpses to extract edible tissues and the modification of skulls to produce skull-cups. A human radius from Gough's Cave shows evidence of cut marks, percussion damage and human tooth marks, indicative of cannibalism, as well as a set of unusual zig-zagging incisions on the lateral side of the diaphysis. These latter incisions cannot be unambiguously associated with filleting of muscles. We compared the macro- and micro-morphological characteristics of these marks to over 300 filleting marks on human and non-human remains and to approximately 120 engraved incisions observed on two artefacts from Gough's Cave. The new macro- and micro-morphometric analyses of the marks, as well as further comparisons with French Middle Magdalenian engraved artefacts, suggest that these modifications are the result of intentional engraving. The engraved motif comfortably fits within a Magdalenian pattern of design; what is exceptional in this case, however, is the choice of raw material (human bone) and the cannibalistic context in which it was produced. The sequence of the manipulations suggests that the engraving was a purposeful component of the cannibalistic practice, implying a complex ritualistic funerary behaviour that has never before been recognized for the Palaeolithic period.

| S-EPMC5549908 | biostudies-literature

Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue.

Project description:Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m2. Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm2 as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm2 to 1 mm2 were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm2 area to 2400 in the 1 mm2 area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.

| S-EPMC8502231 | biostudies-literature

Precision Surface Microtopography Regulates Cell Fate via Changes to Actomyosin Contractility and Nuclear Architecture.

Project description:Cells are able to perceive complex mechanical cues from their microenvironment, which in turn influences their development. Although the understanding of these intricate mechanotransductive signals is evolving, the precise roles of substrate microtopography in directing cell fate is still poorly understood. Here, UV nanoimprint lithography is used to generate micropillar arrays ranging from 1 to 10 µm in height, width, and spacing to investigate the impact of microtopography on mechanotransduction. Using mesenchymal stem cells (MSCs) as a model, stark pattern-specific changes in nuclear architecture, lamin A/C accumulation, chromatin positioning, and DNA methyltransferase expression, are demonstrated. MSC osteogenesis is also enhanced specifically on micropillars with 5 µm width/spacing and 5 µm height. Intriguingly, the highest degree of osteogenesis correlates with patterns that stimulated maximal nuclear deformation which is shown to be dependent on myosin-II-generated tension. The outcomes determine new insights into nuclear mechanotransduction by demonstrating that force transmission across the nuclear envelope can be modulated by substrate topography, and that this can alter chromatin organisation and impact upon cell fate. These findings have potential to inform the development of microstructured cell culture substrates that can direct cell mechanotransduction and fate for therapeutic applications in both research and clinical sectors.

| S-EPMC7967085 | biostudies-literature

The Effect of Exogenous Zinc Concentration on the Responsiveness of MC3T3-E1 Pre-Osteoblasts to Surface Microtopography: Part II (Differentiation).

Project description:Osseointegration of bone implants is a vital part of the recovery process. Numerous studies have shown that micropatterned geometries can promote cell-substrate associations and strengthen the bond between tissue and the implanted material. As demonstrated previously, exogenous zinc levels can influence the responsiveness of pre-osteoblasts to micropatterns and modify their migratory behavior. In this study, we sought to determine the effect of exogenous zinc on differentiation of osteoblasts cultured on micropatterned vs. planar substrates. Levels of activated metalloproteinase-2 (MMP-2) and transforming growth factor-beta 1 (TGF-β1), as well as early stage differentiation marker alkaline phosphatase, were altered with the addition of zinc. These results suggest that exogenous zinc concentration and micropatterning may interdependently modulate osteoblast differentiation.

| S-EPMC5453094 | biostudies-other

Proteomic analysis of gingival tissue and alveolar bone during alveolar bone healing.

Project description:Bone tissue regeneration is orchestrated by the surrounding supporting tissues and involves the build-up of osteogenic cells, which orchestrate remodeling/healing through the expression of numerous mediators and signaling molecules. Periodontal regeneration models have proven useful for studying the interaction and communication between alveolar bone and supporting soft tissue. We applied a quantitative proteomic approach to analyze and compare proteins with altered expression in gingival soft tissue and alveolar bone following tooth extraction. For target identification and validation, hard and soft tissue were extracted from mini-pigs at the indicated times after tooth extraction. From triplicate experiments, 56 proteins in soft tissue and 27 proteins in alveolar bone were found to be differentially expressed before and after tooth extraction. The expression of 21 of those proteins was altered in both soft tissue and bone. Comparison of the activated networks in soft tissue and alveolar bone highlighted their distinct responsibilities in bone and tissue healing. Moreover, we found that there is crosstalk between identified proteins in soft tissue and alveolar bone with respect to cellular assembly, organization, and communication. Among these proteins, we examined in detail the expression patterns and associated networks of ATP5B and fibronectin 1. ATP5B is involved in nucleic acid metabolism, small molecule biochemistry, and neurological disease, and fibronectin 1 is involved in cellular assembly, organization, and maintenance. Collectively, our findings indicate that bone regeneration is accompanied by a profound interaction among networks regulating cellular resources, and they provide novel insight into the molecular mechanisms involved in the healing of periodontal tissue after tooth extraction.

| S-EPMC3790282 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data