Bayesian hierarchical reconstruction of protein profiles including a digestion model

Introduction : Mass spectrometry approaches are very attractive to detect protein panels in a sensitive and high speed way. MS can be coupled to many proteomic separation techniques. However, controlling technological variability on these analytical chains is a critical point. Adequate information processing is mandatory for data analysis to take into account the complexity of the analysed mixture, to improve the measurement reliability and to make the technology user friendly. Therefore we develop a hierarchical parametric probabilistic model of the LC-MS analytical chain including the technological variability. We introduce a Bayesian reconstruction methodology to recover the protein biomarkers content in a robust way. We will focus on the digestion step since it brings a major contribution to technological variability. Method : In this communication, we introduce a hierarchical model of the LC-MS analytical chain. Such a chain is a cascade of molecular events depicted by a graph structure, each node being associated to a molecular state such as protein, peptide and ion and each branch to a molecular processing such as digestion, ionisation and LC-MS separation. This molecular graph defines a hierarchical mixture model. We extend the Bayesian statistical framework we have introduced previously [1] to this hierarchical description. As an example, we will consider the digestion step. We describe the digestion process on a pair of peptides within the targeted protein as a Bernoulli random process associated with a cleavage probability controlled by the digestion kinetic law.Comment: pr\'esentation orale; 59th American Society for Mass Spectrometry Conference, Dallas : France (2011

Anaerobic digestion - it’s a gas

The article in the Soil Association's Organic Farming magazine introduces the subject of anaerobic digestion, exploring some of the benefits and of installing this technology on farms and some of the difficulties encountered. Potential sources of funding and further information (eg: relevant ebsites) are also listed

A comparison of the Si/Al and Si/time wet-alkaline digestion methods for measurement of biogenic silica in lake sediments

Existing techniques for measuring sediment Biogenic Silica (BSi) concentrations rely largely on conventional (Si-only) wet-alkaline digestion methods. Although results have provided detailed palaeoenvironmental information, potential errors can arise in accounting for sources of non-BSi. Here, I compare a conventional Si-only method to a Si/Al wet-alkaline digestion method, which in theory provides a more robust correction for concentrations of non-BSi. Late glacial/Holocene-aged sediment from Lake Baikal, Russia was used for the comparison. Results showed no significant difference between the two techniques, indicating that existing Si-only BSi methods are suitable for reconstructing environmental changes when levels of digested non-BSi are low to moderate

Behaviour of milk protein ingredients and emulsions stabilised by milk protein ingredients in the simulated gastrointestinal tract : a thesis presented in partial fulfilment of the requirements for the degree of Master of Food Technology, Massey University, Manawatu, New Zealand

Milk clotting behaviours in the stomach impact the digestion rates of protein and fat. A variety of milk protein products are applied as functional ingredients in many foods. This research was conducted to investigate the digestion behaviours of various commercial dairy ingredients and lipids in emulsions stabilised by these ingredients using a dynamic in vitro digestion model, i.e., a human gastric simulator (HGS), with a focus on the effect of different structures of clots formed in dairy ingredients during gastric digestion on hydrolysis of proteins and/or lipids. Skim milk powder (SMP), milk protein concentrate (MPC) 4851, MPC 4861, sodium caseinate, whey protein isolate (WPI) and heated (90°C, 20 min) WPI were used in the present study. Results showed that SMP and MPC 4851, which contained casein micelles, formed ball-like clots with a relatively dense network after 10 min of gastric digestion. These clots did not disintegrate after 220 min of digestion. MPC 4861 and sodium caseinate generated clots at around 40 min, and a loose, fragmented structure was observed at the end of the gastric digestion due to a lacking micellar structure of caseins. No clot was observed in WPI or heated WPI after 220 min gastric digestion, although aggregation occurred at around 40 min in heated WPI. These differences in coagulation behaviours apparently affected the rate of gastric emptying and protein hydrolysis by pepsin in the gastric system. In SMP and MPC 4851, the gastric emptying and hydrolysis of caseins was much slower than that observed in MPC 4861 and sodium caseinate. The most rapid gastric emptying of proteins was observed in the WPI samples both with and without heating. This is attributed to the formation of varied structured clots at different times under the gastric conditions. The effect of protein concentration on the gastric behaviour of these dairy ingredients in solution was then examined, with a particular emphasis on the structure of clots. SMP and MPC 4851 have been selected as model protein ingredients. Their gastric behaviours were investigated over a protein concentration range of 0.5-5.0% (w/w). The results showed that the digestion behaviour of SMP and MPC 4851 followed a similar pattern. The rate of pH changes in the emptied digesta during digestion was protein concentration dependent. With an increase in protein concentration, the decrease in pH slowed. The protein concentration had no apparent impact on the casein clotting time. Clots were formed in the first 10 min of digestion in all samples. However, in both SMP and MPC 4851, when protein concentration was lower than 2.0% (w/w) the clots consisted of small protein pieces with a loose, porous and open structure after a 220 min digestion. Whereas a cheese ball-like clot with a denser network was observed at the end of gastric digestion when the protein concentration varied from 2.0% to 5.0% (w/w). Such a difference in the structure apparently affected the rate of protein hydrolysis. A more rapid hydrolysis (P < 0.05) of the clotted protein was observed when protein concentration was lower than 2.0% (w/w) compared to the samples containing a higher proportion of protein (2.0%-5.0%, w/w). To study the effect of different coagulation behaviours on the digestion of oil droplets in oil-in-water emulsions, these dairy ingredients (with the exception of SMP) were used to prepare an oil-in-water emulsion (20.0% soy oil and 4.0% protein, w/w). They were digested under the dynamic gastric conditions using the HGS. The gastric digesta was emptied at 20 min intervals. Then all digesta were mixed to investigate the lipid digestion under the small intestinal conditions. Changes in physicochemical properties of emulsions, involving the particle size, the microstructure, the oil content of the emptied gastric digesta and the amount of free fatty acids (FFAs) released during the small intestine stage, were determined using an in vitro small intestinal digestion model. Aggregation of MPC 4851-stabilised emulsion took place after 5 min of digestion in the HGS with the largest size. The aggregates remained in the stomach and did not disappear during the whole gastric digestion. The hydrolysis of the aggregated network by pepsin was largely slowed by the reduced ability of the simulated gastric fluid (SGF, containing pepsin) to diffuse into the larger sized aggregates. MPC 4851-stabilised emulsion thus resulted in the slowest release of oil droplets into the small intestine. In comparison, MPC 4861 and sodium caseinate-stabilised emulsions aggregated in the stomach at approximately 40 min, forming smaller sized aggregates. These aggregates disintegrated at the mid and late-stages of digestion in these two emulsions. Therefore, MPC 4861 and sodium caseinate-stabilised emulsions had a more rapid delivery of oil droplets into the small intestine. In relation to the WPI-stabilised emulsions both with and without heating, the aggregations formed at a similar time to that which was observed in MPC 4861 and sodium caseinate-stabilised-emulsions; i.e., at approximately 40 min. However, they had the smallest sized aggregates amongst all samples and they disintegrated quickly with further digestion. WPI-stabilised emulsions both with and without heating had the fastest gastric emptying and hydrolysis by pepsin in the early and mid-stages of the gastric digestion process. Thus, the highest level of oil content contained in the emptied gastric digesta was produced from both WPI-stabilised emulsions. In the mixed gastric digesta, which were subjected to the small intestinal digestion, the oil contents contained in the different emulsion samples varied. This difference impacted the extent of lipid digestion by pancreatic lipase. The sample with a higher oil content released a greater amount of FFAs compared to the sample with a lower oil content. The extent of lipid digestion of different emulsion samples adhered to the following pattern: MPC 4851-stabilised emulsion < MPC 4861-stabilised emulsion < sodium caseinate-stabilised emulsion, WPI-stabilised emulsions both with and without heating. Overall, the gastric behaviours of dairy ingredients either in solutions or emulsions were affected by the formation of structured clots/aggregates. The differences in clotting/aggregation times and their structures were greatly dependent on the component and structure of protein, the processing prior to digestion and the susceptibility to proteases. These differences in protein coagulation/aggregation behaviour impacted the rates of protein hydrolysis and gastric emptying. The oil content and protein composition of the gastric digesta transferred into small intestine and the extent of lipid digestion in small intestine were also affected. These results are important in an application perspective. They provide useful information for the design and development of healthier food products by allowing greater control over the manipulation of protein bioavailability, which subsequently provides greater control over lipid metabolism

Characterisation of food fibres and their effect on starch digestion in an in-vitro system at physiological shear rates : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Anatomy and Physiology at Massey University, New Zealand

Material removed from thesis for copyright reasons: Appendix 5 - Hardacre, A.K., Yap, S-Y., Lentle, R.G., Janssen, P.W.M., & Monro, J.A. (2014). The partitioning of water in aggregates of undigested and digested dietary particles, Food Chemistry, 142, 446-454. https://doi.org/10.1016/j.foodchem.2013.07.063 Appendix 6 - Hardacre, A.K., Yap, S-Y., Lentle, R.G., & Monro, J.A. (2015). The effect of fibre and gelatinised starch type on amylolysis and apparent viscosity during in vitro digestion at a physiological shear rate, Carbohydrate Polymers, 123, 80-88. https://doi.org/10.1016/j.carbpol.2015.01.013 Appendix 7 - Hardacre, A.K., Lentle, R.G., Yap, S-Y., & Monro, J.A. (2016). Does viscosity or structure govern the rate at which starch granules are digested? Carbohydrate Polymers, 136, 667-675. https://doi.org/10.1016/j.carbpol.2015.08.060The fast pace of life promotes the excessive consumption of processed starchy food containing high levels of sugar, salt and oil; which can increase the prevalence of type II diabetes, colon and cardiovascular diseases. The addition of dietary fibres in the diet increases the viscosity of digesta, delays mixing in the gut, and promotes laxation. However, few studies attempt to quantify the possible physical and chemical effects of either soluble (food gums) and insoluble (largely cellulose) fibre in the diet. These effects may encompass the retention of water inside the fibre particles, between particles in the fibre mass and direct effects of the chemical nature of the fibre on the digestion process. In this study, the fractions of water held in the various partitions of insoluble particulate dietary fibres are quantified. The relationship between the volume fraction of soluble and insoluble dietary fibres in simulated digesta at physiological concentrations and the rheological properties of the suspension at physiological shear rates is determined. Furthermore, the impact of fibre and shear rates on the digestion of starch in-vitro at physiological shear rates was measured. This work provides the first quantitative assessment of the effects of the physical attributes of dietary fibre on the digestion of starch in-vitro, at physiological shear rates. In this work, four insoluble fibre types were used to construct aqueous suspensions containing solid volume fractions similar to those of pig digesta from the small intestine; these suspensions also were shown to have similar rheological properties to those of pig digesta at physiological shear rates. In addition, a soluble fibre (Guar gum) was used to construct solutions with viscosities comparable to those of the particulate suspensions. Gelatinised and partially gelatinised starch was added to these suspensions and its rate of digestion at 37°C under simulated small intestinal conditions was measured at shear rates covering the reported physiological range. Important results from this work include: - The proportion of water retained by a given volume of hydrated mass of large fibre particles (AllBran®) was double that of smaller particles (wheat fibre). For all of the solid particles used, the proportion of water sequestered by the intra-particulate voids was less than 4% of the volume of the particles, similar proportions were determined for indigestible particles recovered from the colon of pigs and from human faeces. - Food fibre systems containing less than 20% by volume (solid volume fraction, φ = 0.20) of insoluble dietary fibres showed Newtonian rheological properties and the viscosity of these suspensions could be predicted from φ by the Maron-Pierce model. Starch/fibre suspensions prepared with φ below 20% (φ = 0.68-0.98) had a similar viscosity to that of starch/guar suspension comprising 10% (w/v) starch and 0.4% (w/v) guar. During in-vitro digestion, the viscosity of the starch/fibre suspensions decreased logarithmically over the first 20 minutes during which about 30% of the starch was hydrolysed, this was followed by a prolonged period of slow digestion as the slowly digested starch (SDS) and resistant starch (RS) were hydrolysed. The rate of starch digestion was independent of the type of insoluble fibre and was not affected by suspension viscosities used providing shear rates could be maintained within physiological levels. For guar, rates of digestion were slowed probably due to non-competitive inhibition of the amylase by the guar. - When shear rates were below the physiological range (0.1 s-1) or gelatinisation was incomplete, the rate of digestion became linear over the first 20 minutes of digestion suggesting that the rate of digestion was limited by transport processes at low shear in viscous suspensions. - This study provides useful information regarding the limiting concentration of particles and hence viscosity of digesta in the gut if rates of digestion are to be maximised. Additionally, it is suggested that guar, even at low concentration may reduce glycemia by reducing rates of amylolysis

Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity

The process of anaerobic digestion in which waste biomass is transformed to methane by complex microbial communities has been modeled for more than 16 years by parametric gray box approaches that simplify process biology and do not resolve intracellular microbial activity. Information on such activity, however, has become available in unprecedented detail by recent experimental advances in metatranscriptomics and metaproteomics. The inclusion of such data could lead to more powerful process models of anaerobic digestion that more faithfully represent the activity of microbial communities. We augmented the Anaerobic Digestion Model No. 1 (ADM1) as the standard kinetic model of anaerobic digestion by coupling it to Flux-Balance-Analysis (FBA) models of methanogenic species. Steady-state results of coupled models are comparable to standard ADM1 simulations if the energy demand for non-growth associated maintenance (NGAM) is chosen adequately. When changing a constant feed of maize silage from continuous to pulsed feeding, the final average methane production remains very similar for both standard and coupled models, while both the initial response of the methanogenic population at the onset of pulsed feeding as well as its dynamics between pulses deviates considerably. In contrast to ADM1, the coupled models deliver predictions of up to 1,000s of intracellular metabolic fluxes per species, describing intracellular metabolic pathway activity in much higher detail. Furthermore, yield coefficients which need to be specified in ADM1 are no longer required as they are implicitly encoded in the topology of the species’ metabolic network. We show the feasibility of augmenting ADM1, an ordinary differential equation-based model for simulating biogas production, by FBA models implementing individual steps of anaerobic digestion. While cellular maintenance is introduced as a new parameter, the total number of parameters is reduced as yield coefficients no longer need to be specified. The coupled models provide detailed predictions on intracellular activity of microbial species which are compatible with experimental data on enzyme synthesis activity or abundance as obtained by metatranscriptomics or metaproteomics. By providing predictions of intracellular fluxes of individual community members, the presented approach advances the simulation of microbial community driven processes and provides a direct link to validation by state-of-the-art experimental techniques

Decoding Information from noisy, redundant, and intentionally-distorted sources

Advances in information technology reduce barriers to information propagation, but at the same time they also induce the information overload problem. For the making of various decisions, mere digestion of the relevant information has become a daunting task due to the massive amount of information available. This information, such as that generated by evaluation systems developed by various web sites, is in general useful but may be noisy and may also contain biased entries. In this study, we establish a framework to systematically tackle the challenging problem of information decoding in the presence of massive and redundant data. When applied to a voting system, our method simultaneously ranks the raters and the ratees using only the evaluation data, consisting of an array of scores each of which represents the rating of a ratee by a rater. Not only is our appraoch effective in decoding information, it is also shown to be robust against various hypothetical types of noise as well as intentional abuses.Comment: 19 pages, 5 figures, accepted for publication in Physica

Small-scale anaerobic digestion : case studies in Western Europe

This brochure is intended to meet farmers’ demand for more information concerning the current market situation of the small-scale anaerobic digestion technology. The authors aim to quickly guide those who are interested in the technology so that they can adopt a targeted approach in their search for information. This brochure elaborates on how the implementation of small-scale anaerobic digestion can take place at the company level, based on five practical examples. A broad market study in a second part of this brochure shows that there are already many European providers that focus on small-scale digestion. Some are still in a pilot phase, while others have already realized full-scale operational installations

Inoculum selection influences the biochemical methane potential of agro-industrial substrates

Obtaining a reliable estimation of the methane potential of organic waste streams in anaerobic digestion, for which a biochemical methane potential (BMP) test is often used, is of high importance. Standardization of this BMP test is required to ensure inter-laboratory repeatability and accuracy of the BMP results. Therefore, guidelines were set out; yet, these do not provide sufficient information concerning origin of and the microbial community in the test inoculum. Here, the specific contribution of the methanogenic community on the BMP test results was evaluated. The biomethane potential of four different substrates (molasses, bio-refinery waste, liquid manure and high-rate activated sludge) was determined by means of four different inocula from full-scale anaerobic digestion plants. A significant effect of the selected inoculum on the BMP result was observed for two out of four substrates. This inoculum effect could be attributed to the abundance of methanogens and a potential inhibiting effect in the inoculum itself, demonstrating the importance of inoculum selection for BMP testing. We recommend the application of granular sludge as an inoculum, because of its higher methanogenic abundance and activity, and protection from bulk solutions, compared with other inocula