Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

Bioarchitectural Design of Bioactive Biopolymers: Structure-Function Paradigm for Diabetic Wound Healing

Chronic wounds such as diabetic ulcers are a major complication in diabetes caused by hyperglycemia, prolonged inflammation, high oxidative stress, and bacterial bioburden. Bioactive biopolymers have been found to have a biological response in wound tissue microenvironments and are used for developing advanced tissue engineering strategies to enhance wound healing. These biopolymers possess innate bioactivity and are biodegradable, with favourable mechanical properties. However, their bioactivity is highly dependent on their structural properties, which need to be carefully considered while developing wound healing strategies. Biopolymers such as alginate, chitosan, hyaluronic acid, and collagen have previously been used in wound healing solutions but the modulation of structural/physico-chemical properties for differential bioactivity have not been the prime focus. Factors such as molecular weight, degree of polymerization, amino acid sequences, and hierarchical structures can have a spectrum of immunomodulatory, anti-bacterial, and anti-oxidant properties that could determine the fate of the wound. The current narrative review addresses the structure-function relationship in bioactive biopolymers for promoting healing in chronic wounds with emphasis on diabetic ulcers. This review highlights the need for characterization of the biopolymers under research while designing biomaterials to maximize the inherent bioactive potency for better tissue regeneration outcomes, especially in the context of diabetic ulcers.

A physicochemical evaluation of ossein-hydroxyapatite within the bovine bone matrix revealed demineralization and making type I collagen available as a result of processing and solubilization by acids

Bovine bone is an animal-origin matrix rich in type I collagen (COL I) and it necessitates prior demineralization and makes COL I available. This study investigated the ossein-hydroxyapatite physicochemical properties evaluation as a result of processing and solubilization by acids and revealed the bone matrix demineralization and making COL I available. The tibia residue from bovine sources was processed, ground, and transformed into bone matrix powder. The bone matrix was solubilized in acetic acid followed by lactic acid. The bone matrix was evaluated as a result of processing and solubilization by acids: ossein and hydroxyapatite percentages by nitrogen and ash content, mineral content, particle size distribution, Fourier-transformation infrared spectroscopy, x-ray diffraction, and scanning electron microscope. For the obtained residual extracts, pH and mineral content were evaluated. The solubilization by acids affected the ossein-hydroxyapatite physicochemical properties, and the bone matrix solubilized by acetic and lactic acid showed the preservation of the ossein alongside the loss of hydroxyapatite. The processing and the solubilization by acids were revealed to be a  alternative to bone matrix demineralization and enabling the accessibility of bone COL I. PRACTICAL APPLICATION: Bovine bone is an abundant type I collagen source, but processing maneuvers and demineralization effect present limitations due to the rigidity of the structural components. Exploring methodologies to process and demineralize will allow type I collagen to be obtained from the bone source, and direct and amplify the potentialities in the chemical and food industries. The research focused on bone sources and collagen availability holds paramount significance, and promotes repurposing agribusiness residues and development of protein-base products.

Proteomic Analysis of Collagen: a Mass Spectrometry Approach to Material Identification of Shadow Puppet Cultural Relics

Shadow puppets are a popular art form in various regions, including China, Indonesia, and Turkey, and are rich in cultural significance. However, there is a considerable lack of research on the materials, diseases and conservation techniques related to shadow puppet relics. Material identification is the basis for understanding the production process of ancient shadow puppet relics and evaluating their deterioration degree. The microscopic morphology and infrared spectroscopy results in our experiments showed that the traditional methods of ancient skin identification were not effective in the shadow puppet samples. In order to achieve accurate identification, we used biological mass-spectrometry in proteomics to examine two puppet relics and commercially available modern shadow puppets. The results showed that the above samples could be detected by mass spectrometry with abundant peptides, including peptides specific for bovine skin. These peptides cannot be found in other commonly used materials for making shadow puppets, including the skins of pig, sheep, deer and horse. It is worth mentioning that we have found the peptides specific to yellow cowhide in two ancient shadow puppet relics samples. Therefore, the proteomic evidence shows that the raw materials of the two shadow puppet relics samples are yellow cowhide. Four modern samples also confirmed the reliability of material identification using proteomics. The proteomic evidence shows that the biological mass spectrometry will contribute to the scientific research of shadow puppet relics and other skin and leather cultural relics.

Cheminformatics-Based Design and Synthesis of Hydroxyapatite/Collagen Nanocomposites for Biomedical Applications

This paper presents a novel cheminformatics approach for the design and synthesis of hydroxyapatite/collagen nanocomposites, which have potential biomedical applications in tissue engineering, drug delivery, and orthopedic and dental implants. The nanocomposites are synthesized by the co-precipitation method with different ratios of hydroxyapatite and collagen. Their mechanical, biological, and degradation properties are analyzed using various experimental and computational techniques. Attenuated total reflection-Fourier-transform infrared spectroscopy, thermogravimetric analysis, and X-ray diffraction unveil the low crystallinity and nanoscale particle size of hydroxyapatite (22.62 nm) and hydroxyapatite/collagen composites (14.81 nm). These findings are substantiated by scanning electron microscopy with energy-dispersive X-ray spectroscopy, confirming the Ca/P ratio between 1.65 and 1.53 and attesting to the formation of non-stoichiometric apatites in all samples, further validated by molecular simulation. The antimicrobial activity of the nanocomposites is evaluated in vitro against several bacterial and fungal strains, demonstrating their medical potential. Additionally, in silico analyses are performed to predict the absorption, distribution, metabolism, and excretion properties and the bioavailability of the collagen samples. This study paves the way for the development of novel biomaterials using chemoinformatics tools and methods, facilitating the optimization of design and synthesis parameters, as well as the prediction of biological outcomes. Future research directions should encompass the investigation of in vivo biocompatibility and bioactivity of the nanocomposites, while exploring further applications and functionalities of these innovative materials.

The Efficient Extraction Method of Collagen from Deteriorated Leather Artifacts

Collagen is the most crucial component of leather artifacts and analyzing collagen can provide vital information for studying and conserving such artifacts. However, collagen in leather artifacts often faces challenges such as degradation, denaturation, and contamination, which make it difficult to achieve an ideal protein extract using traditional extraction methods. This study aimed to find an efficient collagen extraction strategy for aging leather by comparing and improving commonly used methods. The results of comparing different extraction methods indicated that a NaOH solution was highly effective in extracting collagen from aged leather. To determine the optimal conditions for collagen extraction from the NaOH solution, we conducted orthogonal experiments. The results revealed that a NaOH concentration of 0.05 mol/L, a dissolution temperature of 80 °C, and a dissolution time of 12 h were the most favorable conditions. To validate the effectiveness of this method, we performed SDS-PAGE and biological mass spectrometry tests on collagen extracts from leather samples with varying degrees of aging. All collagen extracts exhibited distinct bands in the gel, and the molecular weight of collagen in each sample exceeded 20 kDa. Furthermore, even with a reduced sample mass of 1 mg (micro-destructive sampling), biological mass spectrometry identified 124 peptides in the protein extract. Notably, four of these peptides were unique to cattle hide collagen and were not present in the collagen of pig, sheep, horse, deer, or human skins. These experimental findings confirm the efficacy of the NaOH solution for extracting collagen from aging leather, suggesting that it can serve as a significant method for collagen identification and analysis in leather artifacts.

Secondary ion mass spectrometry, a powerful tool for revealing ink formulations and animal skins in medieval manuscripts

Book production by medieval scriptoria have gained growing interest in recent studies. In this context, identifying ink compositions and parchment animal species from illuminated manuscripts is of great importance. Here, we introduce time-of-flight secondary ion mass spectrometry (ToF-SIMS) as a non-invasive tool to identify both inks and animal skins in manuscripts, at the same time. For this purpose, both positive and negative ion spectra in inked and non-inked areas were recorded. Chemical compositions of pigments (decoration) or black inks (text) were determined by searching for characteristic ion mass peaks. Animal skins were identified by data processing of raw ToF-SIMS spectra using principal component analysis (PCA). In illuminated manuscripts from the fifteenth to sixteenth century, malachite (green), azurite (blue), cinnabar (red) inorganic pigments, as well as iron-gall black ink, were identified. Carbon black and indigo (blue) organic pigments were also identified. Animal skins were identified in modern parchments of known animal species by a two-step PCA procedure. We believe the proposed method will find extensive application in material studies of medieval manuscripts, as it is non-invasive, highly sensitive and able to identify both inks and animal skins at the same time, even from traces of pigments and tiny scanned areas.

Duplex droplet digital PCR (ddPCR) for simultaneous quantification of bovine and porcine gelatin in capsules

Detection of bovine and porcine in gelatin-based products is important as species fraud and product mislabeling may have a detrimental impact on customers who have health, ethical, and religious concerns about animal products. The duplex droplet digital PCR (ddPCR) assay using double-quenched probes has been developed for quantification and detection of porcine and bovine DNA in gelatin capsules. A DNA mixture derived from gelatin was found to have a limit of detection as low as 0.001 ng/µl for porcine samples and 0.01 ng/µl for bovine samples. DNA from 12 other distinct species was tested with the bovine and porcine probes, showing high specificity for this method. The test was validated using fifty-five commercial supplement and pharmaceutical capsules, of which 17 were positive for bovine and/or porcine DNA. This study shows that the duplex ddPCR is reliable for routine analysis in the identification of bovine and porcine origins for gelatin capsules.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01204-x.

Introduction to new guidelines for validation of methods to examine visually recognisable substances

Visual examination of visually recognisable substances, including microscopy, focus on targets or contaminants such as particles of animal origin, plant seeds, spore bodies of moulds, sclerotia, packaging material, microplastic and 'Besatz' (everything that differs from the norm). The two principal results are counts (numbers) and weights for macroscopic methods, or presence/absence for microscopic methods. The level of detection equals at least the size of one unit, usually with a weight exceeding 1 mg, which is in the range of parts per million (ppm). These parameters do not follow a normal distribution but Poisson (counts), lognormal (weights) or binomial (Booleans) distributions, with effect on the interpretation of validation parameters. As for other domains, examination methods for visual monitoring need to be properly validated and quality control during actual application is needed. In most cases procedures for validation of visual methods are based on principles adopted from other domains, such as chemical analysis. A series of examples from publications show inconsistent or not correct implementations of these validation procedures, which stress the need for dedicated validation procedures. Identification of legal ingredients and composition analysis in the domain of visual examination relies on the expertise of the laboratory staff, therefore validation of a method usually includes the validation of the expert. In the view of these specific circumstances, a Guidance for quality assurance and control of visual methods has been developed, which are being presented and discussed in this paper. The general framework of the Guidance is adopted from ISO standards (17023, 17043, 13528). Part 1 of the Guidance includes the general background, theory and principles. Part 2 presents the actual validation procedures with experimental designs and equations for calculating the relevant parameters, and can be used as blueprint for a SOP in a quality management system. An EURL and NRL network for physical hazards is strongly recommended.

Identification and quantification of fox meat in meat products by liquid chromatography-tandem mass spectrometry

Over the years, food adulteration has become an important global problem, threatening public health safety and the healthy development of food industry. This study established a liquid chromatography-tandem mass (LC-MS/MS) method for accurate identification and quantitative analysis of fox meat products. High-resolution mass was used for data collection, and Proteome Discoverer was used for data analysis to screen fox-specific peptides. Multivariate statistical analysis was conducted using the data obtained from the label-free analysis of different contents of simulated samples. Samples with different contents were distinguished without interfering with each other, suggesting the feasibility of quantitative analysis of fox meat content. The linear correlation coefficient and recovery rate were calculated to determine the fox peptides that can be used for accurate quantification. The established LC-MS/MS method can be used for the accurate identification and quantification of actual samples. In addition, this method can provide technical support for law enforcement departments.

Neanderthals on the Lower Danube: Middle Palaeolithic evidence in the Danube Gorges of the Balkans

The article presents evidence about the Middle Palaeolithic and Middle to Upper Palaeolithic transition interval in the karst area of the Danube Gorges in the Lower Danube Basin. We review the extant data and present new evidence from two recently investigated sites found on the Serbian side of the Danube River - Tabula Traiana and Dubočka-Kozja caves. The two sites have yielded layers dating to both the Middle and Upper Palaeolithic and have been investigated by the application of modern standards of excavation and recovery along with a suite of state-of-the-art analytical procedures. The presentation focuses on micromorphological analyses of the caves' sediments, characterisation of cryptotephra, a suite of new radiometric dates (accelerator mass spectrometry and optically stimulated luminescence) as well as proteomics (zooarchaeology by mass spectrometry) and stable isotope data in discerning patterns of human occupation of these locales over the long term.

Effect of enzymatic hydrolyzed protein from pig bones on some biological and functional properties

Pig bone residue is considered a potential source of hydrolysates from its protein with added value uses in the food industry. This work deals with the enzyme hydrolysis of pig bone protein. The conditions for extracting the protein hydrolysate were optimized and the equation obtained allowed samples with different degrees of hydrolysis (DH) to be extracted to study how the biological properties of in-vitro hydrolized protein affected digestibility, determination of the inhibitory activity of the angiotensin-converting enzyme and the antioxidant activity and its functional properties. It was found that the emulsifying capacity and emulsion stability increased at intermediate DH values, after which these properties decreased with the increase in DH. The in-vitro digestibility and angiotensin-converting enzyme (ACE) of the hydrolysates are also clearly affected by the DH. The amino acid composition of the hydrolized protein is also determined.

Authentication of three main commercial Pheretima based on amino acids analysis

Pheretima has been used as an animal-derived traditional Chinese medicine for thousands of years in Asian countries due to its multi-activities. However, more than half of the commercial Pheretima are adulterants according to the previous research. Besides, the standards of Pheretima are still inadequate in the identification of Pheretima species. In this study, an amino acids (AAs) analytical method established based on the ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS) in multiple reaction monitoring (MRM) mode through derivatization with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) was used for qualitative and quantitative analysis of the total AAs of three main commercial Pheretima (two major Pheretima species, Amynthas aspergillum, Metaphire vulgaris, and one main counterfeit, M. magna). As a result, 16 AAs were detected and quantitated in their hydrolyzed samples. Then, multivariate statistical analysis was applied to distinguish the three commercial Pheretima based on their AAs level. Finally, four AAs (Thr, Glu, Asp, and Arg) were screened as species-differential AAs, which may be used as chemical markers to distinguish the three commercial Pheretima. This study deeply described the outline of AAs in Pheretima and offered a good reference for its species authentication.

Changes in the Molecular Characteristics of Bovine and Marine Collagen in the Presence of Proteolytic Enzymes as a Stage Used in Scaffold Formation

Biopolymers, in particular collagen and fibrinogen, are the leading materials for use in tissue engineering. When developing technology for scaffold formation, it is important to understand the properties of the source materials as well as the mechanisms that determine the formation of the scaffold structures. Both factors influence the properties of scaffolds to a great extent. Our present work aimed to identify the features of the molecular characteristics of collagens of different species origin and the changes they undergo during the enzymatic hydrolysis used for the process of scaffold formation. For this study, we used the methods of gel-penetrating chromatography, dynamic light scattering, reading IR spectra, and scanning electron microscopy. It was found that cod collagen (CC) and bovine collagen (BC) have different initial molecular weight parameters, and that, during hydrolysis, the majority of either type of protein is hydrolyzed by the proteolytic enzymes within the first minute. The differently sourced collagen samples were also hydrolyzed with the formation of two low molecular fractions: Mw ~ 10 kDa and ~20 kDa. In the case of CC, the microstructure of the final scaffolds contained denser, closely spaced fibrillar areas, while the BC-sourced scaffolds had narrow, short fibrils composed of unbound fibers of hydrolyzed collagen in their structure.

Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250-283 Ma and ∼120-133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.

A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry

Proteogenomics is an increasingly common method for species identification as it allows for rapid and inexpensive interrogation of an unknown organism’s proteome—even when the proteome is partially degraded. The proteomic method typically uses tandem mass spectrometry to survey all peptides detectable in a sample that frequently contains hundreds or thousands of proteins. Species identification is based on detection of a small numbers of species-specific peptides. Genetic analysis of proteins by mass spectrometry, however, is a developing field, and the bone proteome, typically consisting of only two proteins, pushes the limits of this technology. Nearly 20% of highly confident spectra from modern human bone samples identify non-human species when searched against a vertebrate database—as would be necessary with a fragment of unknown bone. These non-human peptides are often the result of current limitations in mass spectrometry or algorithm interpretation errors. Consequently, it is difficult to know if a “species-specific” peptide used to identify a sample is actually present in that sample. Here we evaluate the causes of peptide sequence errors and propose an unbiased, probabilistic approach to determine the likelihood that a species is correctly identified from bone without relying on species-specific peptides.

Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California Channel Islands

An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interdisciplinary hypothesis-testing toolkit, limiting their scope and application. Here we illustrate the use of such an integrative approach and report the occurrence of North America's largest terrestrial mammalian carnivore, the short-faced bear, Arctodus simus, from Daisy Cave (CA-SMI-261), an important early human occupation site on the California Channel Islands. We identified the specimen by corroborating morphological, protein, and mitogenomic lines of evidence, and evaluated the potential natural and anthropogenic mechanisms of its transport and deposition. While representing just a single specimen, our combination of techniques opened a window into the behavior of an enigmatic species, suggesting that A. simus was a wide-ranging scavenger utilizing terrestrial and marine carcasses. This discovery highlights the utility of bridging archaeological and paleontological datasets to disentangle complex biogeographic scenarios and reveal unexpected biodiversity for island systems worldwide.

A Dermonutrient Containing Special Collagen Peptides Improves Skin Structure and Function: A Randomized, Placebo-Controlled, Triple-Blind Trial Using Confocal Laser Scanning Microscopy on the Cosmetic Effects and Tolerance of a Drinkable Collagen Supplement

The purpose of this randomized, placebo-controlled, triple-blind trial on 60 healthy female volunteers was to assess the cosmetic effects on skin quality of a food supplement containing special collagen peptides together with acerola extract, vitamin C, vitamin E, biotin, and zinc after an intake of 12 weeks (Elasten^®, QUIRIS Healthcare, Germany). To reduce assessment bias maximally and increase the accuracy and objectivity of the outcomes, the trial design was triple blinded in a manner that neither the subjects nor the person administering the products nor the person who assessed the primary outcomes knew which subjects had received the test product and which had received the placebo. The expert grader assessing the confocal laser scanning microscopy images was additionally blinded regarding the time when the image was taken (on days 1 or 85). The objective, blinded, and validated image analyses using confocal laser scanning microscopy showed a significant improvement of the collagen structure of facial skin (primary endpoint) after intake of the test product, while no improvements were found after intake of the placebo. The proven positive nutritional effect on the collagen structure was fully consistent with positive subjective evaluations of relevant skin parameters such as elasticity, crinkliness/wrinkliness, and evenness in different body areas such as face, hands, décolleté, neck, backside, legs, and belly, all serving as secondary endpoints. The test product was found to be safe and very well tolerated. A cosmetically relevant improvement of the facial skin was demonstrated after administration of the collagen supplement.

Hydroxyproline determination for initial detection of halal-critical food ingredients (gelatin and collagen)

Gelatin and collagen are considered halal-critical ingredients as they are typically derived from either bovine or porcine animals. Current analytical methods for determining the sources of gelatin and collagen suffer from limitations in terms of robustness and false positives in peptide matching. Thus, the aim of this study was to investigate the utility of monitoring hydroxyproline, a signature amino acid for gelatin and collagen, for identifying potentially haram foodstuffs. To determine the hydroxyproline profiles among animal- and plant-based samples, one-way univariate analysis of variance followed by pair-wise comparison was used to establish statistical significance. Multivariate chemometric analysis through principal component analysis revealed a discrete distribution pattern among 59 samples due to hydroxyproline variability. Finally, inter- and intra-laboratory comparisons demonstrated the validity and robustness of hydroxyproline determination according to ISO 17025. Thus, this preliminary identification technique will aid the identification of potentially haram foodstuffs.

Structural feature and self-assembly properties of type II collagens from the cartilages of skate and sturgeon

Acid-soluble collagen (ASC) and pepsin-soluble collagen (PSC) were extracted and purified from the cartilages of skate and sturgeon. Their typical structure and physicochemical properties were evaluated by circular dichroism (CD), X-ray diffraction (XRD), and so on. Results showed that the extracted collagen was likely identified as collagen-II composed of three α-chains (135 kDa), with the typical peptide sequence of Gly-X-Y. It showed the collagen retained the native and intact triple helical structure, and its intensity ratio of the positive and negative absorption peaks (Rpn) was 0.19-0.25. In addition, the extracted collagen exhibited obvious self-assembly behavior with the concentration above 0.3 mg/mL, the adjustment of pH 7.4-7.6 and the NaCl concentration of 120 mmol/L. The critical aggregate mass concentrations of pepsin-soluble collagens from skate and sturgeon were 0.93 and 0.86 g/L, respectively. Therefore, collagens from skate and sturgeon cartilages have potential commercial application.

How to get your goat: automated identification of species from MALDI-ToF spectra

Motivation

Classification of archaeological animal samples is commonly achieved via manual examination of matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-ToF sample, provided the collagen sequences for each candidate species are available. The approach derives a set of peptide masses from the sequence data for comparison with the sample data, which is carried out by cross-correlation. A novel way of combining evidence from multiple marker peptides is used to interpret the raw alignments and arrive at a classification with an associated confidence measure.

Results

To illustrate the efficacy of the approach, we tested the new method with a previously published classification of parchment folia from a copy of the Gospel of Luke, produced around 1120 C.E. by scribes at St Augustine’s Abbey in Canterbury, UK. In total, 80 of the 81 samples were given identical classifications by both methods. In addition, the new method gives a quantifiable level of confidence in each classification.

Availability and implementation

The software can be found at https://github.com/bioarch-sjh/bacollite, and can be installed in R using devtools.

Supplementary information

Supplementary data are available at Bioinformatics online.

A Collagen Supplement Improves Skin Hydration, Elasticity, Roughness, and Density: Results of a Randomized, Placebo-Controlled, Blind Study

The purpose of this randomized, placebo-controlled, blind study was to investigate the effects of the drinkable nutraceutical ELASTEN^® (QUIRIS Healthcare, Gütersloh, Germany) on skin aging and skin health. Drinking ampoules provides a blend of 2.5 g of collagen peptides, acerola fruit extract, vitamin C, zinc, biotin, and a native vitamin E complex. This controlled interventional trial was performed on 72 healthy women aged 35 years or older. They received either the food supplement (n = 36) or a placebo (n = 36) for twelve weeks. A skin assessment was carried out and based on objective validated methods, including corneometry (skin hydration), cutometry (elasticity), the use of silicon skin replicas with optical 3D phase-shift rapid in-vivo measurements (PRIMOS) (roughness), and skin sonography (density). The verum group was followed for an additional four weeks (without intake of the test product) to evaluate the sustainability of the changes induced by the intake of the test product. The test product significantly improved skin hydration, elasticity, roughness, and density. The differences between the verum group and the placebo group were statistically significant for all test parameters. These positive effects were substantially retained during the follow-up. The measured effects were fully consistent with the subjective assessments of the study participants. The nutraceutical was well tolerated.

Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites

Advancements in molecular science are continually improving our knowledge of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here, we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to approximately 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley (Lepidochelys kempii) and olive ridley (L. olivacea) turtles, which can be separated to genus level, having diverged from one another only approximately 5 Ma. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples, Chelonia spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle (Chelonia spp.; 63%), with hawksbill (Eretmochelys imbricata; 17%) and ridley turtles (Lepidochelys spp.; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle (Caretta caretta) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor.

Characterization of proteins in cultural heritage using MALDI–TOF and LC–MS/MS mass spectrometric techniques

Identification of proteinaceous materials in artworks is of high interest to restorers-conservators, art historians and archaeologists, because it helps to shed light on the used painting techniques, to attribute unknown artworks, to make conclusions on prehistoric diets, etc. The chapter is devoted to the mass spectrometry instrumentation, evaluation of obtained data and it is showing several examples of the application of matrix-assisted laser desorption/ionization–time-of-flight and liquid chromatography–electrospray ionization–quadrupole–time-of-flight mass spectrometers on cultural heritage samples.

Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand

Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.

Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan

The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan’s high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies.

Association between protein profile and postmortem interval in human bone remains

Proteomic techniques in bones forensic samples are increasingly, being applied. The main aim of forensic sciences is the estimation of postmortem interval. Most current techniques are useful for the first post-mortem stages. However, in the case of osseous remains, these techniques may be difficult to use due to the high level of decomposition of the sample. Our objective was to attempt to know whether there is a protein profile in human bone remains that would enable a late postmortem. interval ranging from 5 to 20 years postmortem to be estimated. A total of 40 femur bones from 40 different cadavers (data range 5-20 years) were use. Of the 275 total proteins, we excluded the circulating ones (n = 227), leaving a total of 48 proteins (29 structural and 19 functional) were found. A multiple correspondence analysis was applied on the 48 proteins. Finally selecting 32 proteins that allowed us to discriminate between the. two groups of postmortem interval. Analysis of the protein profile present in bone permits an approximation of the date of death within the studied interval, and could be used to complement other tests for estimating the postmortem interval.

Lymphatic cannulation models in sheep: Recent advances for immunological and biomedical research

Lymphatic cannulation models are useful tools for studying the immunobiology of the lymphatic system and the immunopathology of specific tissues in diseases. Sheep cannulations have been used extensively, as models for human physiology, fetal and neonatal development, human diseases, and for studies of ruminant pathobiology. The development of new and improved cannulation techniques in recent years has meant that difficult to access sites, such as mucosal associated tissues, are now more readily available to researchers. This review highlights the new approaches to cannulation and how these, in combination with advanced omics technologies, will direct future research using the sheep model.

Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones

Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Here, we evaluated the proteomes obtained from five distinct subsamples of different skeletal elements from buried pig carcasses to ascertain the extent of variation within and between individuals. We found that reproducibility of data depends on the skeletal element used for sampling and that intrabone differences exceed those observed between the same skeletal element sampled from different individuals. Interestingly, the abundance of several serum proteins appeared to correlate with biological age with relative concentrations of alpha-1 antitrypsin and chromogranin-A increasing and those of fetuin-A decreasing. We also observed a surprising level of divergence in data from different LC-MS/MS runs on aliquots of similar samples analyzed months apart, adding constraints to the comparison of results of such methods across different studies.

Collagen: a network for regenerative medicine

The basic building block of the extra-cellular matrix in native tissue is collagen. As a structural protein, collagen has an inherent biocompatibility making it an ideal material for regenerative medicine. Cellular response, mediated by integrins, is dictated by the structure and chemistry of the collagen fibers. Fiber formation, via fibrillogenesis, can be controlled in vitro by several factors: pH, ionic strength, and collagen structure. After formation, fibers are stabilized via cross-linking. The final bioactivity of collagen scaffolds is a result of both processes. By considering each step of fabrication, scaffolds can be tailored for the specific needs of each tissue, improving their therapeutic potential.