Biology subjects

Collins, M. J.

Publications and source records attributed to Collins, M. J..

14 recordsLinked to original sources

bioRxiv2025

An unclean slate, discrepancies between food input and recovered protein signal from experimental foodcrusts

Organic residues are a rich source of biomolecular information on ancient diets. In particular, foodcrusts, charred residues on ceramics, are commonly analysed for their lipid content and to a lesser extent protein in order to identify foods, culinary practices and material culture use in past populations. However, the composition of foodcrusts and the factors behind their formation are not well understood. Here we analyse proteomic data (available via ProteomeXchange with identifier PXD059930) from foodcrusts made using a series of mixtures of protein- (salmon flesh), lipid- (beef fat) and carbohydrate-rich (beetroot) foods to investigate the relationship between the biomolecular composition of the input and the recovered signal using conventional methods applied to archaeological material. Additionally, using 3D modelling we quantify the volume of foodcrust generated by different ingredient combinations The results highlight biases in the data obtained in the analyses of organic residues both in terms of identified resources reflecting the cooked foodstuffs, e.g. an overrepresentation of fish proteins, as well as with regards to the abundance of foodcrust, for example mixtures of only salmon and beef fat resulted in relatively small amounts of foodcrust, and suggest caution in interpreting the composition of residues formed from complex mixtures of foodstuffs.

biochemistry↗

bioRxiv2024

Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics

While metaproteomics provides invaluable insight into microbial communities and functions, significant bioinformatics challenges persist due to data complexity and the limitations of database searching. We introduce Orthrus, a hybrid approach combining transformer-based de novo sequencing (Casanovo) and database searching with rescoring (Sage+Mokapot). Benchmarking against PEAKS(R)11, MaxQuant, and MetaNovo, Orthrus demonstrates high peptide outputs, taxonomic diversity, and proteome coverage. Orthrus is Python-based and accessible to all via Google Colaboratory.

bioinformatics↗

bioRxiv2024

Anubis: a multi-level authentication scale for ancient proteins using random forest classification

Deamidation is a time-dependent, post-translational modification with wide applications in clinical proteomics and palaeoproteomics as ageing indicators and authentication markers. Despite its significance, the use of deamidation for authenticating ancient proteins remains controversial, primarily due to variability in deamidation kinetics and context-specific protein preservation. We propose Anubis, an open-source, Python-based pipeline to evaluate relative deamidation patterns and authenticate ancient proteins. Anubis leverages random forest classification based on a range of tandem mass spectrometry-based features and physico-chemical characteristics. We use a combination of ancient and experimentally degraded beta-lactoglobulin to demonstrate that Anubis can authenticate a putative ancient dairy protein using position-specific deamidation patterns, relative deamidation (asparagine vs. glutamine), and overall modification patterns using trypsin processed in the same batch as a baseline. This multi-level approach addresses the complexities of ancient protein deamidation and paves the way for automated, reliable authentication across different archaeological substrates.

bioinformatics↗

bioRxiv2024

The Survival of β-lactoglobulin Peptides in the Archaeological Record: Vulnerability vs. Sequence Variation

It is a strange observation, given the cultural co-evolution of dairying, that milk proteins are more commonly reported than any other food proteins in the archaeological record. The whey protein {beta}-lactoglobulin and in particular its eleven amino acid long peptide T125PEVDXEALEK135 seems to be preferentially preserved in both ceramic vessels and teeth (dental calculus). An amino acid substitution in the middle of the chain is valuable to track livestock management because it permits differentiation between key animal species used in dairying. The persistence of this peptide is, however, unusual as its acidic nature makes it more vulnerable to hydrolysis. Moreover, selection for the ability to digest raw milk - more specifically, the continued production of the milk sugar enzyme lactase beyond the age of normal weaning - did not begin until the early Bronze Age. It is therefore unclear why it is a milk peptide, in particular a peptide associated with the lactose-rich whey fraction, that is one of the most commonly recovered dietary peptides. The unexpected preservation of T125PEVDXEALEK135 thus presents a good case study to uncover patterns of protein survival in the archaeological record. We have previously explored the dynamics of the bovine variation of the peptide (X=Asp130) and its likelihood to undergo hydrolysis in solution. In this study, we turn our attention to the ovine (X=Asn130) and the caprine (X=Lys130) variations of the {beta}-lactoglobulin peptide to determine how the mutation in the amino acid in position 6 affects peptide conformations and vulnerability in bulk water. To do this, we use Molecular Dynamics as implemented in GROMACS 2020, with the Amber14SB forcefield and the SPC/E water model. We first perform extensive conformational analysis of both peptides in solution to determine stable structures. Then, using analogous methodology to that developed in our earlier study of the bovine peptide, we identify geometric arrangements between water and peptide that may be more prone to hydrolysis.

biophysics↗

bioRxiv2024

The impact of cooking and burial on proteins: a characterisation of experimental foodcrusts and ceramics

Foodcrusts have received relatively little attention in the burgeoning field of proteomic analysis of ancient cuisine. We remain ignorant of how cooking and burial impacts protein survival, and crucially, the extent to which the extractome reflects the composition of input ingredients. Therefore, through experimental analogues we explore the extent of protein survival in unburied and buried foodcrusts and ceramics using typical Mesolithic ingredients (red deer, Atlantic salmon and sweet chestnut). We then explore a number of physiochemical properties theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, input ingredient strongly influences protein preservation, and that degradation is not universal nor linear between proteins, indicating that multiple protein physiochemical properties are at play. While certain properties such as hydrophobicity apparently aid protein preservation, none single-handedly explain why particular proteins/peptides survive in buried foodcrusts: this complex interplay requires further investigation. The findings demonstrate that proteins indicative of the input ingredient can be identifiable in foodcrust, but that the full proteome is unlikely to preserve. While this shows promise for the survival of proteins in archaeological foodcrust, further research is needed to accurately interpret foodcrust extractomes.

biochemistry↗

bioRxiv2023

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of good practice to interrogate our data. However, there is a lack of a systematic exploration of how these affect the identification of peptides, post-translational modifications (PTMs), proteins and their significance (through the False Discovery Rate) and correctness. We systematically investigated the performance of a wide range of sequencing tools and search engines in a controlled system: the experimental degradation of the single purified bovine {beta}-lactoglobulin (BLG), heated at 95 {degrees}C and pH 7 for 0, 4 and 128 days. We target BLG since it is one of the most robust and ubiquitous proteins in the archaeological record. We tested different reference database choices, a targeted dairy protein one, and the whole bovine proteome and the three digestion options (tryptic-, semi-tryptic- and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. We also explored alternative strategies, including open search that allows for the global identification of PTMs based upon wide precursor mass tolerance and de novo sequencing to boost sequence coverage. We analysed the samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe and DeNovoGUI (pepNovo+, DirecTag, Novor), benchmarked these tools and discuss the optimal strategy for the characterisation of ancient proteins. We also studied physicochemical properties of the BLG that correlate with bias in the identification coverage.

bioinformatics↗

bioRxiv2022

Survival of mineral-bound peptides into the Miocene

The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in extant species and consistent with the Liushu Struthio sp. ootaxon. These findings push the preservation of ancient proteins back to the Miocene and highlight their potential for paleontology, paleoecology and evolutionary biology.

paleontology↗

bioRxiv2022

RNase E biomolecular condensates stimulate PNPase activity

Bacterial Ribonucleoprotein bodies (BR-bodies) play an essential role in organizing RNA degradation via liquid-liquid phase separation in the cytoplasm of bacteria. BR-bodies mediate multi-step mRNA decay through the concerted activity of the endoribonuclease RNase E coupled with the 3-5 exonuclease Polynucleotide Phosphorylase (PNPase). Our past in vivo studies indicated that the loss of PNPase recruitment into BR-bodies led to a significant build-up of RNA decay intermediates in Caulobacter crescentus. We reconstituted RNase Es C-terminal domain together with PNPase to understand how RNase E biomolecular condensates can tailor the functions of PNPase. We found that PNPase catalytic activity is accelerated when colocalized with the RNase E biomolecular condensates. In contrast, disruption of the RNase E-PNPase protein-protein interaction led to a loss of PNPase recruitment into the BR-bodies and a loss of ribonuclease rate enhancement. We also found that BR-bodies could enhance the decay of select RNA substrates, as we observed a 3.4-fold enhancement of polyadenylic acid (poly(A)) degradation and no impact upon poly(U) degradation. Our investigation into the origins of the 3.4-fold rate enhancement for poly(A) decay indicates a combination of scaffolding and mass action effects impact due to the concentrated biomolecular condensate environment accelerating RNA decay. Consistent with our past in vivo work, these studies suggest BR-bodies are sites of accelerated RNA decay that can shape the available transcriptome.

biochemistry↗

bioRxiv2022

Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)2. During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this study, we propose a simple three-step workflow, developed as an R package called MALDIpqi(), to estimate deamidation in parchment derived collagen using low-resolution MALDI-TOF spectra. After pre-processing raw spectra, we used weighted least-squares linear regression to estimate Q deamidation levels from the convoluted isotopic envelope for seven collagen-peptide markers. Finally, we employed a linear mixed effect model to predict the overall deamidation level of a parchment sample termed Parchment Glutamine Index (PQI). To test the robustness of the workflow, we applied MALDIpqi() to previously published ZooMS data generated from almost an entire library of the Cistercian monastery at Orval Abbey, Belgium. In addition to reliably predicting PQI, we observed interesting patterns pertaining to parchment production. MALDIpqi() holds excellent potential for biocodicological and other archaeological studies involving collagen, such as bone, but we also foresee its application in the food and biomedical industry.

bioinformatics↗

bioRxiv2020

Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis

In this paper we describe a dry non-invasive extraction method to detect palaeoproteomic evidence from stained manuscripts. The manuscript analysed in this study is a medieval parchment birth girdle (Wellcome Collection Western MS. 632) made in England and thought to be used by pregnant women while giving birth. Using a dry non-invasive sampling method we were able to extract both human and non-human peptides from the stains, including evidence for the use of honey, cereals, ovicaprine milk and legumes. In addition, a large number of human peptides were detected on the birth roll, many of which are found in cervico-vaginal fluid. This suggests that the birth roll was actively used during childbirth. This study is the first to extract and analyse non-collagenous peptides from a parchment document using a dry non-invasive sampling method and demonstrates the potential of this type of analysis for stained manuscripts, providing direct biomolecular evidence for active use.

molecular biology↗

bioRxiv2020

NON-AVIAN DINOSAUR EGGSHELL CALCITE CONTAINS ANCIENT, ENDOGENOUS AMINO ACIDS

Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, thermally matured, sub-fossil, and ~3.8 Ma avian eggshell, as well as ~30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, along with similar concentrations of free versus total hydrolysable amino acids, likely suggests complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, suggestive of kerogen formation deriving from eggshell lipids. Raman spectroscopy yields bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation even if such reactions might be slowed in exceptional circumstances. The evidence for complete hydrolysis and degradation of most amino acids in the eggshell raises concern about the validity of reported polypeptide sequences from open-system non-avian dinosaur bone and other Mesozoic fossils.

paleontology↗

bioRxiv2020

Survival of environmental DNA in natural environments: Surface charge and topography of minerals as driver for DNA storage

Extraction of environmental DNA (eDNA) from sediments are providing ground-breaking views of the past ecosystems and biodiversity. Despite this rich source of information, it is still unclear which sediments favour preservation and why. Here we used atomic force microscopy and molecular dynamics simulations to explore the DNA-mineral interaction to assess how mineralogy and interfacial geochemistry play a role in the preservation of environmental DNA on mineral substrates. We demonstrate that mineral composition, surface topography and surface charge influence DNA adsorption behavior as well as preservation. Modeling and experimental data show that DNA damage can be induced by mineral binding if there is a strong driving force for adsorption. The study shows that knowledge of the mineralogical composition of a sediment and the environmental conditions can be useful for assessing if a deposit is capable of storing extracellular DNA and to what extent the DNA would be preserved. Our data adds to the understanding of eDNA taphonomy and highlights that, for some mineral systems, fragmented DNA may not represent old DNA.

biochemistry↗

bioRxiv2018

Stone Age \"chewing gum\" yields 5,700 year-old human genome and oral microbiome

We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous \"chewing gum\" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,8585,661 cal. BP (GrM13305;5,007{+/-}11). We sequenced the genome to an average depth-of coverage of 2.3x and find that the individual who chewed the resin was female and genetically more closely related to western hunter gatherers from mainland Europe, than hunter gatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

genomics↗

bioRxiv2017

The York Gospels: a one thousand year biological palimpsest

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA we report a cost effective and simple-to-use biomolecular sampling technique. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1,000 year lifespan of this cherished object that remains an active participant in the life of York Minster. This biological data provides insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.

genomics↗