Hydrolysis of proteins

Dairy and plant based protein beverages: In vitro digestion behaviour and effect on intestinal barrier biomarkers

The consumer demand for protein-enriched food products continues to grow, in parallel with consumers' interest in plant based alternatives. The replacement of milk protein by plant protein is likely to be occur predominantly in prepared consumer foods such as nutritional beverages. This study aimed to compare and contrast powder beverages formulated with commercially available dairy versus plant ingredients in terms of protein digestion and gut barrier health. After simulated static in vitro gastrointestinal digestion, the release of free amino acids increased for all model beverages. In addition, the majority of peptides present in digested beverages were < 0.8 kDa in size. Gastrointestinal digestion did not increase the degree of protein hydrolysis in beverages formulated with prehydrolysed milk protein, whey or pea ingredients. A 2 h permeability assessment of digested beverages across the intestinal barrier, using Caco-2/HT-29/MTX co-cultures, revealed reduced transcription of tight junction protein 1, claudin-1 and mucus protein 2 albeit gut barrier impedance was unchanged. IL-8 mRNA levels in cell monolayers was significantly increased with digested fluids treatment but even more so with digesta from hydrolysed milk protein beverage. Overall, the response observed on intestinal biomarkers with digested plant beverages was similar to dairy based beverages supporting the replacement of dairy with plant proteins in powder beverage formulations.

Under Conditions of Amyloid Formation Bovine Carbonic Anhydrase B Undergoes Fragmentation by Acid Hydrolysis

The development of many severe human diseases is associated with the formation of amyloid fibrils. Most of the available information on the process of amyloid formation has been obtained from studies of small proteins and peptides, wherein the features of complex proteins’ aggregation remain insufficiently investigated. Our work aimed to research the amyloid aggregation of a large model protein, bovine carbonic anhydrase B (BCAB). It has previously been demonstrated that, when exposed to an acidic pH and elevated temperature, this protein forms amyloid fibrils. Here, we show that, under these conditions and before amyloid formation, BCAB undergoes fragmentation by acid hydrolysis to give free individual peptides and associated peptides. Fragments in associates contain a pronounced secondary structure and act as the main precursor of amyloid fibrils, wherein free peptides adopt mostly unstructured conformation and form predominantly irregular globular aggregates. Reduced acidity decreases the extent of acid hydrolysis, causing BCAB to form amorphous aggregates lacking the thioflavin T binding β-structure. The presented results provide new information on BCAB amyloid formation and show the importance of protein integrity control when working even in mildly acidic conditions.

The degradation of intracrystalline mollusc shell proteins: A proteomics study of Spondylus gaederopus

Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a "molecular clock" for geochronological applications. But despite seventy years of ancient protein research, the fundamental aspects of diagenesis-induced changes to protein structures and sequences remain elusive. In this study we investigate the degradation of intracrystalline proteins by performing artificial degradation experiments on the shell of the thorny oyster, Spondylus gaederopus, which is particularly important for archaeological research. We used immunochemistry and tandem mass tag (TMT) quantitative proteomics to simultaneously track patterns of structural loss and of peptide bond hydrolysis. Powdered and bleached shell samples were heated in water at four different temperatures (80, 95, 110, 140 °C) for different time durations. The structural loss of carbohydrate and protein groups was investigated by immunochemical techniques (ELLA and ELISA) and peptide bond hydrolysis was studied by tracking the changes in protein/peptide relative abundances over time using TMT quantitative proteomics. We find that heating does not induce instant organic matrix decay, but first facilitates the uncoiling of cross-linked structures, thus improving matrix detection. We calculated apparent activation energies of structural loss: E_a (carbohydrate groups) = 104.7 kJ/mol, E_a (protein epitopes) = 104.4 kJ/mol, which suggests that secondary matrix structure degradation may proceed simultaneously with protein hydrolysis. While prolonged heating at 110 °C (10 days) results in complete loss of the structural signal, surviving peptide sequences were still observed. Eight hydrolysis-prone peptide bonds were identified in the top scoring shell sequence, the uncharacterised protein LOC117318053 from Pecten maximus. Interestingly, these were not the expected "weak" bonds based on published theoretical stabilities calculated for peptides in solution. This further confirms that intracrystalline protein degradation patterns are complex and that the overall microchemical environment plays an active role in protein stability. Our TMT approach represents a major stepping stone towards developing a model for studying protein diagenesis in biomineralised systems.

Functional and Bioactive Properties of Protein Extracts Generated from Spirulina platensis and Isochrysis galbana T-Iso

There is growing consumer demand for food products derived from microalgae, driven largely by the perceived health benefits associated with them. The functional and bioactive potential of proteins isolated from two microalgae—Spirulina sp. and Isochrysis galbana T-Iso—were determined. The results obtained show the potential of microalgal protein extracts for use in the beverage industry, based on solubility values and other functional characteristics, including water and oil holding capacities, foaming, emulsifying activities and stabilities, water activities, solubility and pH. The solubility of algal proteins was pH-dependent, and they were largely insoluble at pH values between 2 and 11. However, the proteins were increasingly soluble at a pH of 12, and they have potential use in formulating foods with higher viscosities or gels, where they could act as fillers to strengthen networks. Compared with whey and flaxseed proteins, the Spirulina sp. protein extract had a superior oil-holding capacity (OHC). The OHC is important in developing texture in food products such as meats. Overall, better foam stability was observed for both Spirulina sp. and Isochrysis sp. soluble protein extracts, compared with flaxseed protein at pH values from 2 to 10 over a period of 120 min. The foam capacity and stability increase the physical properties of foods. However, the emulsion activity and stability values for soluble algal protein extracts were less than the values observed for flaxseed and whey proteins. Algal proteins would not be suitable for use in creaming and food processing involving flocculation. In addition, algal protein extracts inhibited Angiotensin-converting enzyme-I (ACE-I) and renin, and they have potential for use in functional food ingredient applications to maintain heart health and also to act as meat substitutes.

Engineering of sustainable biomaterial composites from cellulose and silk fibroin: Fundamentals and applications

This review addresses composites prepared from cellulose (Cel) and silk fibroin (SF) to generate multifunctional, biocompatible, biodegradable materials such as fibers, films and scaffolds for tissue engineering. First, we discuss briefly the molecular structures of Cel and SF. Their structural features explain why certain solvents, e.g., ionic liquids, inorganic electrolyte solutions dissolve both biopolymers. We discuss the mechanisms of Cel dissolution because in many cases they also apply to (much less studied) SF dissolution. Subsequently, we discuss the fabrication and characterization of Cel/SF composite biomaterials. We show how the composition of these materials beneficially affects their mechanical properties, compared to those of the precursor biopolymers. We also show that Cel/SF materials are excellent and versatile candidates for biomedical applications because of the inherent biocompatibility of their components.

Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing

Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. SIGNIFICANCE: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.

Extraction of Protein from Four Different Seaweeds Using Three Different Physical Pre-Treatment Strategies

Seaweeds are a rich source of protein and can contain up to 47% on the dry weight basis. It is challenging to extract proteins from the raw biomass of seaweed due to resilient cell-wall complexes. Four species of macroalgae were used in this study-two brown, Fucus vesiculosus and Alaria esculenta, and two red, Palmaria palmata and Chondrus crispus. Three treatments were applied individually to the macroalgal species: (I) high-pressure processing (HPP); (II) laboratory autoclave processing and (III) a classical sonication and salting out method. The protein, ash and lipid contents of the resulting extracts were estimated. Yields of protein recovered ranged from 3.2% for Fucus vesiculosus pre-treated with high pressure processing to 28.9% protein recovered for Chondrus crispus treated with the classical method. The yields of protein recovered using the classical, HPP and autoclave pre-treatments applied to Fucus vesiculosus were 35.1, 23.7% and 24.3%, respectively; yields from Alaria esculenta were 18.2%, 15.0% and 17.1% respectively; yields from Palmaria palmata were 12.5%, 14.9% and 21.5% respectively, and finally, yields from Chondrus crispus were 35.2%, 16.1% and 21.9%, respectively. These results demonstrate that while macroalgal proteins may be extracted using either physical or enzymatic methods, the specific extraction procedure should be tailored to individual species.

Biopolymeric photonic structures: design, fabrication, and emerging applications

Biological photonic structures can precisely control light propagation, scattering, and emission via hierarchical structures and diverse chemistry, enabling biophotonic applications for transparency, camouflaging, protection, mimicking and signaling. Corresponding natural polymers are promising building blocks for constructing synthetic multifunctional photonic structures owing to their renewability, biocompatibility, mechanical robustness, ambient processing conditions, and diverse surface chemistry. In this review, we provide a summary of the light phenomena in biophotonic structures found in nature, the selection of corresponding biopolymers for synthetic photonic structures, the fabrication strategies for flexible photonics, and corresponding emerging photonic-related applications. We introduce various photonic structures, including multi-layered, opal, and chiral structures, as well as photonic networks in contrast to traditionally considered light absorption and structural photonics. Next, we summarize the bottom-up and top-down fabrication approaches and physical properties of organized biopolymers and highlight the advantages of biopolymers as building blocks for realizing unique bioenabled photonic structures. Furthermore, we consider the integration of synthetic optically active nanocomponents into organized hierarchical biopolymer frameworks for added optical functionalities, such as enhanced iridescence and chiral photoluminescence. Finally, we present an outlook on current trends in biophotonic materials design and fabrication, including current issues, critical needs, as well as promising emerging photonic applications.

Ancient amino acids from fossil feathers in amber

Ancient protein analysis is a rapidly developing field of research. Proteins ranging in age from the Quaternary to Jurassic are being used to answer questions about phylogeny, evolution, and extinction. However, these analyses are sometimes contentious, and focus primarily on large vertebrates in sedimentary fossilisation environments; there are few studies of protein preservation in fossils in amber. Here we show exceptionally slow racemisation rates during thermal degradation experiments of resin enclosed feathers, relative to previous thermal degradation experiments of ostrich eggshell, coral skeleton, and limpet shell. We also recover amino acids from two specimens of fossil feathers in amber. The amino acid compositions are broadly similar to those of degraded feathers, but concentrations are very low, suggesting that much of the original protein has been degraded and lost. High levels of racemisation in more apolar, slowly racemising amino acids suggest that some of the amino acids were ancient and therefore original. Our findings indicate that the unique fossilisation environment inside amber shows potential for the recovery of ancient amino acids and proteins.

A method for analyzing the composition of viral nucleoprotein complexes, produced by heterologous expression in bacteria

Viral genomes are protected and organized by virally encoded packaging proteins. Heterologous production of these proteins often results in formation of particles resembling the authentic viral capsid or nucleocapsid, with cellular nucleic acids packaged in place of the viral genome. Quantifying the total protein and nucleic acid content of particle preparations is a recurrent biochemical problem. We describe a method for resolving this problem, developed when characterizing particles resembling the Menangle Virus nucleocapsid. The protein content was quantified using the biuret assay, which is largely independent of amino acid composition. Bound nucleic acids were quantified by determining the phosphorus content, using inductively coupled plasma mass spectrometry. Estimates for the amount of RNA packaged within the particles were consistent with the structurally-characterized packaging mechanism. For a bacterially-produced nucleoprotein complex, phosphorus usually provides a unique elemental marker of bound nucleic acids, hence this method of analysis should be routinely applicable.

Utilization of Slaughterhouse Waste in Value-Added Applications: Recent Advances in the Development of Wood Adhesives

Globally, slaughterhouses generate large volumes of animal byproducts. While these byproducts are an important resource of industrial protein that could potentially be utilized in various value-added applications, they are currently either underutilized in high-value applications or being used for production of relatively low-value products such as animal feed and pet food. Furthermore, some of the byproducts of animal slaughtering cannot enter food and feed chains and thus their disposal possesses a serious environmental concern. An innovative utilization of the proteinaceous waste generated by slaughterhouses comprises of waste processing to extract proteins, which are then incorporated into industrial processes to produce value-added bio-based products. In this report, we review the current processes for extraction of protein from proteinaceous waste of slaughterhouses, and utilization of the recovered protein in the development of protein-based wood adhesives.

Atlantic salmon (Salmo salar) co-product-derived protein hydrolysates: A source of antidiabetic peptides

Large quantities of low-value protein rich co-products, such as salmon skin and trimmings, are generated annually. These co-products can be upgraded to high-value functional ingredients. The aim of this study was to assess the antidiabetic potential of salmon skin gelatin and trimmings-derived protein hydrolysates in vitro. The gelatin hydrolysate generated with Alcalase 2.4L and Flavourzyme 500L exhibited significantly higher (p < 0.001) insulin and GLP-1 secretory activity from pancreatic BRIN-BD11 and enteroendocrine GLUTag cells, respectively, when tested at 2.5 mg/mL compared to hydrolysates generated with Alcalase 2.4L or Promod 144MG. The gelatin hydrolysate generated with Alcalase 2.4L and Flavourzyme 500L showed significantly more potent (p < 0.01) DPP-IV inhibitory activity than those generated with Alcalase 2.4L or Promod 144MG. No significant difference was observed in the insulinotropic activity mediated by any of the trimmings-derived hydrolysates when tested at 2.5 mg/mL. However, the trimmings hydrolysate generated with Alcalase 2.4L and Flavourzyme 500L exhibited significantly higher DPP-IV inhibitory (p < 0.05:Alcalase 2.4L and p < 0.01:Promod 144MG) and GLP-1 (p < 0.001, 2.5 mg/mL) secretory activity than those generated with Alcalase 2.4L or Promod 144MG. The salmon trimmings hydrolysate generated with Alcalase 2.4L and Flavourzyme 500L when subjected to simulated gastrointestinal digestion (SGID) was shown to retain its GLP-1 secretory and DPP-IV inhibitory activities, in addition to improving its insulin secretory activity. However, the gelatin hydrolysate generated with Alcalase 2.4L and Flavourzyme 500L was shown to lose GLP-1 secretory activity following SGID. A significant increase in membrane potential (p < 0.001) and intracellular calcium (p < 0.001) by both co-product hydrolysates generated with Alcalase 2.4L and Flavourzyme 500L suggest that both hydrolysates mediate their insulinotropic activity through the K_ATP channel-dependent pathway. Additionally, by stimulating a significant increase in intracellular cAMP release (p < 0.05) it is likely that the trimmings-derived hydrolysate may also mediate insulin secretion through the protein kinase A pathway. The results presented herein demonstrate that salmon co-product hydrolysates exhibit promising in vitro antidiabetic activity.

Assessment of the functional properties of protein extracted from the brown seaweed Himanthalia elongata (Linnaeus) S. F. Gray

A protein extract from the brown seaweed Himanthalia elongata (Linnaeus) S. F. Gray was prepared and its functional properties, colour and amino acid composition were assessed for its potential future use by the food industry. The total content of amino acids was determined as 54.02±0.46gaminoacids/kg dry weight, with high levels of the essential amino acids lysine and methionine. SDS-PAGE showed 5 protein bands with molecular weights of 71.6, 53.7, 43.3, 36.4 and 27.1kDa. The water holding capacity and oil holding capacity were determined as 10.27±0.09gH2O/g and 8.1±0.07goil/g respectively. Foaming activity and stability were higher at alkaline pH values. The emulsifying capacity and stability of the extract varied depending on the pH and oil used. These results demonstrate the potential use of Himanthalia elongata protein extract in the food industry.

Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution

The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.

Dietary modulation of cortical excitation and inhibition

The balance of excitatory and inhibitory neurotransmitters in the brain affects both neural responses and behaviour in humans and animals. Here we investigated whether dietary intervention aimed at increasing levels of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) can influence neural responses to basic sensory stimuli. Using a steady-state electroencephalography (EEG) paradigm, we found that the neural response to visual patterns was reduced in individuals who consumed a yeast extract product rich in substances associated with the production of GABA (glutamate and B vitamins), but not in a control group who consumed a placebo substance ( n = 14 per group). This demonstrates that the balance of excitation and inhibition in the brain can be influenced by dietary interventions, suggesting possible clinical benefits in conditions (e.g. epilepsy) where inhibition is abnormal.

Identification of the earliest collagen- and plant-based coatings from Neolithic artefacts (Nahal Hemar cave, Israel)

Mortuary practices in human evolution record cognitive, social changes and technological innovations. The Neolithic Revolution in the Levant was a watershed in this domain that has long fascinated the archaeological community. Plaster modelled skulls are well known at Jericho and several other Neolithic sites, and in Nahal Hemar cave (Israel, ca. 8200 -7300 cal. BC) excavations yielded six unique human skulls covered with a black organic coating applied in a net pattern evoking a headdress. This small cave was used as storage for paraphernalia in the semi-arid area of the Judean desert and the dry conditions preserved other artefacts such as baskets coated with a similar dark substance. While previous analysis had revealed the presence of amino acids consistent with a collagen signature, in the present report, specific biomarkers were characterised using combined proteomic and lipid approaches. Basket samples yielded collagen and blood proteins of bovine origin (Bos genus) and a large sequence coverage of a plant protein charybdin (Charybdis genus). The skull residue samples were dominated by benzoate and cinnamate derivatives and triterpenes consistent with a styrax-type resin (Styrax officinalis), thus providing the earliest known evidence of an odoriferous plant resin used in combination with an animal product.

Use of the 2-chlorotrityl chloride resin for microwave-assisted solid phase peptide synthesis

A fast and efficient microwave (MW)-assisted solid-phase peptide synthesis protocol using the 2-chlorotrityl chloride resin and the Fmoc/tBu methodology, has been developed. The established protocol combines the advantages of MW irradiation and the acid labile 2-chlorotrityl chloride resin. The effect of temperature during the MW irradiation, the degree of resin substitution during the coupling of the first amino acids and the rate of racemization for each amino acid were evaluated. The suggested solid phase methodology is applicable for orthogonal peptide synthesis and for the synthesis of cyclic peptides.

Biomineralisation by earthworms - an investigation into the stability and distribution of amorphous calcium carbonate

BACKGROUND

Many biominerals form from amorphous calcium carbonate (ACC), but this phase is highly unstable when synthesised in its pure form inorganically. Several species of earthworm secrete calcium carbonate granules which contain highly stable ACC. We analysed the milky fluid from which granules form and solid granules for amino acid (by liquid chromatography) and functional group (by Fourier transform infrared (FTIR) spectroscopy) compositions. Granule elemental composition was determined using inductively coupled plasma-optical emission spectroscopy (ICP-OES) and electron microprobe analysis (EMPA). Mass of ACC present in solid granules was quantified using FTIR and compared to granule elemental and amino acid compositions. Bulk analysis of granules was of powdered bulk material. Spatially resolved analysis was of thin sections of granules using synchrotron-based μ-FTIR and EMPA electron microprobe analysis.

RESULTS

The milky fluid from which granules form is amino acid-rich (≤ 136 ± 3 nmol mg^-1 (n = 3; ± std dev) per individual amino acid); the CaCO₃ phase present is ACC. Even four years after production, granules contain ACC. No correlation exists between mass of ACC present and granule elemental composition. Granule amino acid concentrations correlate well with ACC content (r ≥ 0.7, p ≤ 0.05) consistent with a role for amino acids (or the proteins they make up) in ACC stabilisation. Intra-granule variation in ACC (RSD = 16%) and amino acid concentration (RSD = 22-35%) was high for granules produced by the same earthworm. Maps of ACC distribution produced using synchrotron-based μ-FTIR mapping of granule thin sections and the relative intensity of the ν₂: ν₄ peak ratio, cluster analysis and component regression using ACC and calcite standards showed similar spatial distributions of likely ACC-rich and calcite-rich areas. We could not identify organic peaks in the μ-FTIR spectra and thus could not determine whether ACC-rich domains also had relatively high amino acid concentrations. No correlation exists between ACC distribution and elemental concentrations determined by EMPA.

CONCLUSIONS

ACC present in earthworm CaCO₃ granules is highly stable. Our results suggest a role for amino acids (or proteins) in this stability. We see no evidence for stabilisation of ACC by incorporation of inorganic components. Graphical abstractSynchrotron-based μ-FTIR mapping was used to determine the spatial distribution of amorphous calcium carbonate in earthworm-produced CaCO₃ granules.

Wet degradation of keratin proteins: linking amino acid, elemental and isotopic composition

RATIONALE

Archaeological keratin samples are increasingly the subject of palaeodietary, provenancing and dating studies. Keratin samples from wet archaeological contexts are microbiologically and chemically degraded, causing differential diagenesis of protein structures in hair fibres. The effects of these processes on the analytical parameters of interest are currently unknown.

METHODS

This study examined the impact of degradation of wool fibres on isotopic (δ(13)C, δ(15)N, un-exchangeable δ(2)H and δ(18)O values) composition. It compared two models of archaeological protein degradation in wet burial environments: (1) short term (up to 8 years) experimental burial in three contrasting soil environments; and (2) laboratory wet conditions, in which elevated temperature (80 °C, 110 °C, and 140 °C) and pressure simulated longer exposure. Elemental and amino acid (AA) composition were also measured.

RESULTS

In experimentally soil-buried samples, AA, elemental and isotopic composition changes were small, despite extensive macroscopic alteration. Isothermally heated samples showed preferential loss of hydrophilic AAs (Asx, Glx, Ser, Gly) from wool residues, with depletion in (2)H and (18)O at higher temperatures (up to -73‰ change in δ(2)H and -2.6‰ in δ(18)O values). The δ(13)C and δ(15)N values showed little change except in densely pigmented samples at low temperatures only. Samples dyed with madder/alum were better preserved than undyed samples.

CONCLUSIONS

Diagenesis in experimentally soil-buried wool textiles was consistent with microbiological, non-protein-selective activity, in contrast to highly AA-selective hydrolytic behaviour under laboratory wet conditions. Changes in δ(2)H and δ(18)O values were correlated with degree of AA change, but the δ(13)C and δ(15)N values were not. The results contribute to a baseline for interpreting analytical data from archaeological hair samples preserved by burial in wet environments.

A Levallois Knapping Site at West Thurrock, Lower Thames, UK: its Quaternary Context, Environment and Age

Levallois knapping debris is present beneath the sides of a disused tramway cutting connected to Lion Pit, West Thurrock, Essex. This occurrence, first recorded during the early 20th century, is in the basal gravel of the Taplow/Mucking Formation, which dates from the end of Marine Oxygen Isotope Stage (MIS) 8. The relatively undisturbed nature of this knapping debris is confirmed by the incidence of refitting material, although finer debitage is absent, presumably winnowed out. The Levallois character of the assemblage is demonstrated by the occurrence of characteristic ‘tortoise’ cores and flakes with faceted striking platforms. The artefact-bearing gravel is overlain by >10 m of predominantly fine-grained sediments, including fossiliferous sands and massive clayey silt, as well as laminated silts, clays, and sands of possible estuarine origin. These are attributed to deposition under temperate conditions during MIS 7. To the south, a younger fluvial gravel, attributed to MIS 6, has been incised into the interglacial sequence. The top of the estuarine sequence has been affected by pedogenesis, both before and after its burial by an unbedded solifluction gravel.

Excavations at the Lower Palaeolithic site at Elveden, Suffolk, UK

The Lower Palaeolithic site at Elveden, Suffolk, was the subject of new excavations from 1995–1999. Excavations around the edge and in the centre of the former clay-pit revealed sediments infilling a lake basin that had formed in Lowestoft till, overlying Chalk, the till being attributed to the Anglian glaciation (MIS 12). The lake sediments contain pollen that can be assigned to pollen zones HoI and HoIIa of the early Hoxnian (MIS 11). Overlying grey clays contain ostracods, molluscs, vertebrates, and carbonate concretions. Together they are indicative of a fluvial environment in a temperate climate. AAR ratios (amino acid racemisation) on the molluscs also suggest correlation with MIS 11. Further indications of a fluvial context are indicated by thin spreads of lag gravel along opposite sides of the clay-pit, marking the edges of a channel. The gravel forms the raw material for the human industries which consist of handaxes, flake tools, flakes, and cores. Further artefacts are found in the overlying black clay, which is interpreted as a palaeosol that formed with the silting-up of the channel. The basin was further infilled with colluvial ‘brickearths’, which also contain artefacts that are probably derived from the underlying gravel. Further evidence of soil formation was identified in the ‘brickearth’. Coversands with periglacial involutions overlie the ‘brickearth’ at the top of the sequence. These probably formed in the last cold stage, the Devensian (MIS 5d-2).

New experimental evidence for in-chain amino acid racemization of serine in a model peptide

The facile racemization of protein-bound amino acids plays an important role in the aging and pathologies of living tissues, and it can be exploited for protein geochronological studies in subfossil biominerals. However, the in-chain degradation pathways of amino acids are complex and difficult to elucidate. Serine has proven to be particularly elusive, and its ability to racemize as a peptide-bound residue (like asparagine and aspartic acid) has not been demonstrated. This study investigates the patterns of degradation of a model peptide (WNSVWAW) at elevated temperatures, quantifying the extent of racemization and peptide bond hydrolysis using reverse-phase high-performance liquid chromatography (RP-HPLC) and tracking the presence of degradation products by MALDI-MS. We provide direct evidence that, under these experimental conditions, both serine and asparagine are able to undergo racemization as internally bound residues, which shows their potential for initiating protein breakdown and provides an explanation for the presence of d-enantiomers in living mammalian tissues.

Intra-crystalline protein diagenesis (IcPD) in Patella vulgata. Part II: Breakdown and temperature sensitivity

Artificial diagenesis of the intra-crystalline proteins isolated from Patella vulgata was induced by isothermal heating at 140 °C, 110 °C and 80 °C. Protein breakdown was quantified for multiple amino acids, measuring the extent of peptide bond hydrolysis, amino acid racemisation and decomposition. The patterns of diagenesis are complex; therefore the kinetic parameters of the main reactions were estimated by two different methods: 1) a well-established approach based on fitting mathematical expressions to the experimental data, e.g. first-order rate equations for hydrolysis and power-transformed first-order rate equations for racemisation; and 2) an alternative model-free approach, which was developed by estimating a "scaling" factor for the independent variable (time) which produces the best alignment of the experimental data. This method allows the calculation of the relative reaction rates for the different temperatures of isothermal heating. High-temperature data were compared with the extent of degradation detected in sub-fossil Patella specimens of known age, and we evaluated the ability of kinetic experiments to mimic diagenesis at burial temperature. The results highlighted a difference between patterns of degradation at low and high temperature and therefore we recommend caution for the extrapolation of protein breakdown rates to low burial temperatures for geochronological purposes when relying solely on kinetic data.

Assessing amino acid racemization variability in coral intra-crystalline protein for geochronological applications

Over 500 Free Amino Acid (FAA) and corresponding Total Hydrolysed Amino Acid (THAA) analyses were completed from eight independently-dated, multi-century coral cores of massive Porites sp. colonies. This dataset allows us to re-evaluate the application of amino acid racemization (AAR) for dating late Holocene coral material, 20 years after Goodfriend et al. (GCA56 (1992), 3847) first showed AAR had promise for developing chronologies in coral cores. This re-assessment incorporates recent method improvements, including measurement by RP-HPLC, new quality control approaches (e.g. sampling and sub-sampling protocols, statistically-based data screening criteria), and cleaning steps to isolate the intra-crystalline skeletal protein. We show that the removal of the extra-crystalline contaminants and matrix protein is the most critical step for reproducible results and recommend a protocol of bleaching samples in NaOCl for 48 h to maximise removal of open system proteins while minimising the induced racemization. We demonstrate that AAR follows closed system behaviour in the intra-crystalline fraction of the coral skeletal proteins. Our study is the first to assess the natural variability in intra-crystalline AAR between colonies, and we use coral cores taken from the Great Barrier Reef, Australia, and Jarvis Island in the equatorial Pacific to explore variability associated with different environmental conditions and thermal histories. Chronologies were developed from THAA Asx D/L, Ala D/L, Glx D/L and FAA Asx D/L for each core and least squares Monte Carlo modelling applied in order to quantify uncertainty of AAR age determinations and assess the level of dating resolution possible over the last 5 centuries. AAR within colonies follow consistent stratigraphic aging. However, there are systematic differences in rates between the colonies, which would preclude direct comparison from one colony to another for accurate age estimation. When AAR age models are developed from a combined dataset to include this natural inter-colony variability THAA Asx D/L, Glx D/L and Ala D/L give a 2σ age uncertainty of ±19, ±38 and ±29 year, for the 20th C respectively; in comparison 2σ age uncertainties from a single colony are ±12, ±12 and ±14 year. This is the first demonstration of FAA D/L for dating coral and following strict protocols 2σ precisions of ±24 years can be achieved across different colonies in samples from the last 150 years, and can be ±10 years within a core from a single colony. Despite these relatively large error estimates, AAR would be a valuable tool in situations where a large number of samples need to be screened rapidly and cheaply (e.g. identifying material from mixed populations in beach or uplift deposits), prior to and complementing the more time-consuming geochronological tools of U/Th or seasonal isotopic timeseries.

Protein and mineral characterisation of rendered meat and bone meal

We report the characterisation of meat and bone meal (MBM) standards (Set B-EFPRA) derived from cattle, sheep, pig and chicken, each rendered at four different temperatures (133, 137, 141 and 145 °C). The standards, prepared for an EU programme STRATFEED (to develop new methodologies for the detection and quantification of illegal addition of mammalian tissues in feeding stuffs), have been widely circulated and used to assess a range of methods for identification of the species composition of MBM. The overall state of mineral alteration and protein preservation as a function of temperature was monitored using small angle X-ray diffraction (SAXS), amino acid composition and racemization analyses. Progressive increases in protein damage and mineral alteration in chicken and cattle standards was observed. In the case of sheep and pig, there was greater damage to the proteins and alteration of the minerals at the lowest treatment temperature (133 °C), suggesting that the thermal treatments must have been compromised in some way. This problem has probably impacted upon the numerous studies which tested methods against these heat treatments. We use protein mass spectrometric methods to explore if thermostable proteins could be used to identify rendered MBM. In more thermally altered samples, so-called 'thermostable' proteins such as osteocalcin which has been proposed as a ideal target to speciate MBM were no longer detectable, but the structural protein type I collagen could be used to differentiate all four species, even in the most thermally altered samples.

Amino acid geochronology of the type Cromerian of West Runton, Norfolk, UK

Aminostratigraphic studies of continental deposits in the UK have hitherto relied almost exclusively on data from the aragonitic shells of non-marine molluscs for dating Pleistocene sequences. This is usually based on the d/l value of a single amino acid, d-alloisoleucine/l-isoleucine (A/I), in the total shell proteins. Two genera of freshwater gastropods (Valvata and Bithynia) are used to explore the value of using multiple amino acids from the intra-crystalline fraction, which should be more protected from the effects of diagenesis than the inter-crystalline component. Results are compared from both the aragonitic shells and opercula composed of calcite, a more stable form of calcium carbonate. In order to put the amino acid data from the West Runton Freshwater Bed into perspective, statistical analyses are used to compare them with results from the Hoxnian (MIS 11) site at Clacton-on-Sea, Essex. Twelve protein decomposition indicators revealed that the results from the shells were not as clear-cut as those from the opercula. Five indicators from the Valvata shell suggest that West Runton is older than Clacton (at a 95% significance level), but two actually suggested a younger age. Seven indicators show that the Bithynia shells from West Runton are older than congeneric shells from Clacton. In marked contrast, all 12 indicators isolated from the opercula demonstrate that West Runton is significantly older than Clacton. The data are also compared with results from Waverley Wood, an important archaeological site in the English Midlands falling within the 'Cromerian Complex'. Contrary to earlier interpretations, the new amino acid data from Bithynia opercula indicate that West Runton is older than Waverley Wood, a relationship now consistent with the available biostratigraphy.

Racemization of Amino Acids in Dipeptides Shows COOH > NH2 for Non-Sterically Hindered Residues

The relative rates of racemization for amino acid residues at the NH(2) and COOH ends of 37 different dipeptides were determined. In nine dipeptides containing alanine, leucine, phenylalanine, aspartic acid, and methionine, the amino acid residue racemized faster at the COOH-terminal position than at the NH(2)-terminal position (COOH > NH(2)). The sterically hindered amino acids isoleucine and valine showed NH(2) > COOH. Six proline dipeptides showed NH(2) > COOH. Intramolecular effects have been invoked to explain these surprising results.

Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells

When mollusc shells are analysed conventionally for amino acid geochronology, the entire population of amino acids is included, both inter- and intra-crystalline. This study investigates the utility of removing the amino acids that are most susceptible to environmental effects by isolating the fraction of amino acids encapsulated within mineral crystals of mollusc shells (intra-crystalline fraction). Bleaching, heating and leaching (diffusive loss) experiments were undertaken on modern and fossil Corbicula fluminalis, Margaritifera falcata, Bithynia tentaculata and Valvata piscinalis shells. Exposure of powdered mollusc shells to concentrated NaOCl for 48 h effectively reduced the amino acid content of the four taxa to a residual level, assumed to represent the intra-crystalline fraction. When heated in water at 140 degrees C for 24 h, only 1% of amino acids were leached from the intra-crystalline fraction of modern shells compared with 40% from whole shell. Free amino acids were more effectively retained in the intra-crystalline fraction, comprising 55% (compared with 18%) of the whole shell after 24 h at 140 degrees C. For fossil gastropods, the inter-shell variability in D/L values for the intra-crystalline fraction of a single-age population was reduced by 50% compared with conventionally analysed shells. In contrast, analysis of the intra-crystalline fraction of C. fluminalis does not appear to improve the results for this taxon, possibly due to variability in shell ultrastructure. Nonetheless, the intra-crystalline fraction in gastropods approximates a closed system of amino acids and appears to provide a superior subset of amino acids for geochronological applications.

Testing the aminostratigraphy of fluvial archives: the evidence from intra-crystalline proteins within freshwater shells

Until recently few studies of amino acid racemization of fossil bivalves and gastropods collected from river terrace deposits in Europe were based on the analysis of the intra-crystalline fraction. Instead they were based on the epimerization (racemization) of a single amino acid, isoleucine, and its inter-conversion to alloisoleucine. This paper presents data from the analysis of the intra-crystalline fraction of the shells, using a preparation technique of sample bleaching to remove the leachable matrix, thus leaving a component that exhibits closed-system behaviour. Reverse-phase HPLC separation with fluorescence detection allows the interpretation of four amino acids in detail: aspartic acid, glutamic acid, alanine and valine. The intra-crystalline fraction offers greater potential for improved resolution, especially when combined with the analysis of multiple amino acid d/l values, which racemize at different rates. This is explored using three species of freshwater gastropods (Bithynia tentaculata and troschelii, Valvata piscinalis) and the bivalve Corbicula. Sites of different ages within the Lower Thames river terrace sequence are used as a stratigraphical framework, with samples from other southern UK sites providing supplementary evidence. The results indicate better resolution using the intra-crystalline fraction over that obtained using unbleached shells, with differentiation possible at sites of up to MIS 7 age. However, for older sites, although values are always higher, the separation is less successful. A species effect has been identified between the gastropod shells. Despite the analysis of intra-crystalline protein, amino acid data from Corbicula remain problematical. Preliminary data on the opercula from Bithynia indicate that better resolution is possible, particularly at older sites.

The application of amino acid racemization in the acid soluble fraction of enamel to the estimation of the age of human teeth

Estimation of age-at-death for skeletonised forensic remains is one of the most significant problems in forensic anthropology. The majority of existing morphological and histological techniques are highly inaccurate, and show a bias towards underestimating the age of older individuals. One technique which has been successful in forensic age estimation is amino acid racemization in dentine. However, this method cannot be used on remains where the post-mortem interval is greater than 20 years. An alternative approach is to measure amino acid racemization in dental enamel, which is believed to be more resistant to change post-mortem. The extent of amino acid racemization in the acid soluble fraction of the enamel proteins was determined for modern known age teeth. A strong correlation was observed between the age of the tooth and the extent of racemization. No systematic bias in the direction of age estimation errors was detected. For the majority of teeth analyzed, the presence of dental caries did not affect the results obtained. In a minority of cases, carious teeth showed a higher level of racemization than would be expected given the age of the individual. These results indicate that amino acid racemization in enamel has the potential to be used in age estimation of skeletal remains.

Characterisation of proteinaceous binders in artistic paintings by chromatographic techniques

This review discusses the application of chromatographic techniques (GC, HPLC and Py-GC) for the characterisation of proteinaceous materials in artistic paintings. The focus is on the various analytical steps that are needed to determine these natural materials in paint samples, from sampling and sample pre-treatment, including various methods of hydrolysis and derivatisation for GC and HPLC, to approaches for data evaluation.

Increased albumin and fibrinogen synthesis rate in patients with chronic renal failure

BACKGROUND

Hypoalbuminemia and hyperfibrinogenemia are frequently observed in patients with chronic renal failure (CRF) and are both associated with cardiovascular diseases. The mechanisms responsible for hypoalbuminemia and hyperfibrinogenemia in CRF are unknown.

METHODS

In the present study, both albumin and fibrinogen kinetics were measured in vivo in predialysis patients (N = 6), patients on peritoneal dialysis (N = 7) and control subjects (N = 8) using l-[1-13C]-valine.

RESULTS

Plasma albumin concentration was significantly lower in patients on peritoneal dialysis compared to control subjects (P < 0.05). Plasma fibrinogen was significantly increased in both predialysis patients (P < 0.01) as well as patients on peritoneal dialysis (P < 0.001) in comparison to control subjects. In contrast to albumin, fibrinogen is only lost in peritoneal dialysate and not in urine. The absolute synthesis rates (ASR) of albumin and fibrinogen were increased in patients on peritoneal dialysis (ASR albumin, 125 +/- 9 mg/kg/day versus 93 +/- 9 mg/kg/day, P < 0.05; ASR fibrinogen, 45 +/- 4 mg/kg/day versus 29 +/- 3 mg/kg/day, P < 0.01) compared to control subjects. Albumin synthesis is strongly correlated with fibrinogen synthesis (r2 = 0.665, P < 0.0001, N = 21). In this study, the observed hypoalbuminemia in patients on peritoneal dialysis is likely not explained by malnutrition, inadequate dialysis, inflammation, metabolic acidosis, or insulin resistance. We speculate that peritoneal albumin loss is of relevance.

CONCLUSION

Synthesis rate of albumin and fibrinogen are coordinately up-regulated. Both albumin and fibrinogen are lost in peritoneal dialysis fluid. To compensate protein loss, albumin synthesis is up-regulated, but the response, in contrast to predialysis patients, does not fully correct plasma albumin concentrations in peritoneal dialysis patients. The increase in fibrinogen synthesis introduces an independent risk factor for atherosclerosis, since plasma fibrinogen pool is enlarged.

Transferrin synthesis is increased in nephrotic patients insufficiently to replace urinary losses

The urinary loss of transferrin is sufficient to reduce plasma transferrin concentrations in the nephrotic syndrome. Hypotransferrinemia may lead to iron loss and microcytic anemia. The mechanism responsible for the hypotransferrinemia in the nephrotic syndrome is, however, unknown. In the present study, synthesis rate of transferrin was measured in vivo in nephrotic patients (n = 7) compared with control subjects (n = 6) using L-[1-(13)C]-valine. Plasma transferrin and iron concentration in the patients were significantly lower than in control subjects (transferrin, 1.39 +/- 0.08 versus 2.57 +/- 0.11 g/L, P < 0.0001; iron, 10.2 +/- 0.8 versus 21.1 +/- 4.5 micromol/L, P = 0.02). Furthermore, albuminuria correlated with transferrinuria (r(2) = 0.901, P = 0.001). The absolute synthesis rate of transferrin was increased in the patients (10.0 +/- 1.1 versus 7.4 +/- 0.7 mg/kg per d, P = 0.07), although this value failed to achieve significance. C-reactive protein, plasma iron, and proteinuria did not correlate with transferrin synthesis. In contrast, transferrin synthesis correlated with albumin synthesis (r(2) = 0.648, P = 0.03; n = 7). The present study indicates that increased transferrin synthesis occurs in nephrotic patients but is insufficient to compensate for urinary losses. Because, overall, no significant relationship was found between transferrin synthesis and either C-reactive protein or iron, it is unlikely that inflammation suppresses or that iron deficiency stimulates increased transferrin synthesis in these patients. The correlation between transferrin synthesis and albumin synthesis suggests that transferrin synthesis is a component of a general response in hepatic protein synthesis in the nephrotic syndrome. This suggests that a therapeutic approach to maximize plasma transferrin concentrations in nephrotic patients should be aimed primarily at reducing urinary protein excretion.

Positive and negative aspects of the human immunodeficiency virus protease: development of inhibitors versus its role in AIDS pathogenesis

In this review we summarize multiple aspects of the human immunodeficiency virus (HIV) protease from both structural and functional viewpoints. After an introductory overview, we provide an up-to-date status report on protease inhibitors (PI). This proceeds from a discussion of PI structural design, to how PI are optimally utilized in highly active antiretroviral triple therapy (one PI along with two reverse transcriptase inhibitors), the emergence of PI resistance, and the natural role of secretory leukocyte PI. Then we switch to another focus: the interaction of HIV protease with other genes in acute and persistent infection, which in turn may have an effect on AIDS pathogenesis. We conclude with a discussion on future directions in HIV treatment, involving multiple-target anti-HIV therapy, vaccine development, and novel reactivation-inhibitory reagents.

Glycine insertion in the hinge region of lactose repressor protein alters DNA binding

Amino acid alterations were designed at the C terminus of the hinge segment (amino acids approximately 51-59) that links two functional domains within lactose repressor protein (LacI). Gly was introduced between Gly(58) and Lys(59) to generate Gly(58+1); Gln(60) was changed to Gly or Pro, and up to three additional glycines were inserted following Gln(60) --> Gly. All mutant proteins exhibited purification behavior, CD spectra, assembly state, and inducer binding properties similar to wild-type LacI and only small differences in trypsin proteolysis patterns. In contrast, significant differences were observed in DNA binding properties. Gly(58+1) exhibited a decrease of approximately 100-fold in affinity for O(1) operator, and sequential Gly insertion C-terminal to Gln(60) --> Gly resulted in progressively decreased affinity for O(1) operator, approaching nonspecific levels for insertion of >/=2 glycines. Where sufficient affinity for O(1) operator existed, decreased binding to O(1) in the presence of inducer indicated no disruption in the allosteric response for these proteins. Collectively, these results indicate that flexibility and/or spacing between the core and N-terminal domains did not significantly affect folding or assembly, but these alterations in the hinge domain profoundly altered affinity of the lactose repressor protein for its wild-type target sequence.

Renal clearance of branched-chain L-amino and 2-oxo acids in maple syrup urine disease

In maple syrup urine disease (MSUD), branched-chain L-amino (BCAA) and 2-oxo acids (BCOA) accumulate in body fluids owing to an inherited deficiency of branched-chain 2-oxo acid dehydrogenase complex activity. In MSUD, little information is available on the significance of urinary disposal of branched-chain compounds. We examined the renal clearance of leucine, valine, isoleucine and alloisoleucine, and their corresponding 2-oxo acids 4-methyl-2-oxopentanoate (KIC), 3-methyl-2-oxobutanoate (KIV), (S)-(S-KMV), and (R)-3-methyl-2-oxopentanoate (R-KMV), using pairs of plasma and urine samples (n = 63) from 10 patients with classical MSUD. The fractional renal excretion of free BCAA was in the normal range (< 0.5%) and independent of the plasma concentrations. The excretion of bound (N-acylated) BCAA was normal and not significantly dependent on the BCAA plasma concentrations. The fractional renal excretion of BCOA was in the order KIC << KIV < R-KMV < or = S-KMV (range (%): KIC 0.1-25; KIV 0.14-21.3; S-KMV 0.26-24.6; R-KMV 0.1-35.9), significantly correlated with the KIC plasma concentrations, and generally higher than that of the related BCAA. The results show that the renal excretion of free BCAA as well as of the acylated derivatives is negligible. The renal excretion of BCOA, however, to some extent counteracts increases in BCAA concentrations and thus contributes to the lowering of total BCAA pools in MSUD.