Towards Reliable Automatic Protein Structure Alignment

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based on local structure similarity. In this work, we propose a method to incorporate global information in obtaining optimal alignments and superpositions. Our method, when applied to optimizing the TM-score and the GDT score, produces significantly better results than current state-of-the-art protein structure alignment tools. Specifically, if the highest TM-score found by TMalign is lower than (0.6) and the highest TM-score found by one of the tested methods is higher than (0.5), there is a probability of (42%) that TMalign failed to find TM-scores higher than (0.5), while the same probability is reduced to (2%) if our method is used. This could significantly improve the accuracy of fold detection if the cutoff TM-score of (0.5) is used. In addition, existing structure alignment algorithms focus on structure similarity alone and simply ignore other important similarities, such as sequence similarity. Our approach has the capacity to incorporate multiple similarities into the scoring function. Results show that sequence similarity aids in finding high quality protein structure alignments that are more consistent with eye-examined alignments in HOMSTRAD. Even when structure similarity itself fails to find alignments with any consistency with eye-examined alignments, our method remains capable of finding alignments highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Gaia Early Data Release 3: The celestial reference frame (Gaia-CRF3)

Context. Gaia-CRF3 is the celestial reference frame for positions and proper motions in the third release of data from the Gaia mission, Gaia DR3 (and for the early third release, Gaia EDR3, which contains identical astrometric results). The reference frame is defined by the positions and proper motions at epoch 2016.0 for a specific set of extragalactic sources in the (E)DR3 catalogue. Aims. We describe the construction of Gaia-CRF3 and its properties in terms of the distributions in magnitude, colour, and astrometric quality. Methods. Compact extragalactic sources in Gaia DR3 were identified by positional cross-matching with 17 external catalogues of quasi-stellar objects (QSO) and active galactic nuclei (AGN), followed by astrometric filtering designed to remove stellar contaminants. Selecting a clean sample was favoured over including a higher number of extragalactic sources. For the final sample, the random and systematic errors in the proper motions are analysed, as well as the radio-optical offsets in position for sources in the third realisation of the International Celestial Reference Frame (ICRF3). Results. Gaia-CRF3 comprises about 1.6 million QSO-like sources, of which 1.2 million have five-parameter astrometric solutions in Gaia DR3 and 0.4 million have six-parameter solutions. The sources span the magnitude range G = 13-21 with a peak density at 20.6 mag, at which the typical positional uncertainty is about 1 mas. The proper motions show systematic errors on the level of 12 μas yr-1 on angular scales greater than 15 deg. For the 3142 optical counterparts of ICRF3 sources in the S/X frequency bands, the median offset from the radio positions is about 0.5 mas, but it exceeds 4 mas in either coordinate for 127 sources. We outline the future of Gaia-CRF in the next Gaia data releases. Appendices give further details on the external catalogues used, how to extract information about the Gaia-CRF3 sources, potential (Galactic) confusion sources, and the estimation of the spin and orientation of an astrometric solution

Modelling of the effect of HRT on anaerobic CSTR performance based on a specific characterisation of wastes from agro-industry

International audienceThe aim of this article is to investigate the effect of the Hydraulic Retention Time (HRT) on the anaerobic CSTR digester performance in term of methane production using modelling combined with a specific characterization of wastes. Hence, a recently developed methodology (“anaerobic respirometry”) has been applied to define input state variable set for the “Anaerobic Digestion Model n°1” (ADM1) adapted to each substrate including also hydrolysis rates. Then, ADM1 was used to simulate CSTRs with different HRT for each substrate. The results obtained for 12 common organic wastes from agro-industries (slaughterhouses and meat industry) are significantly different in function of the considered substrates. As an example, an HRT of 7 days is sufficient to reach 80% of the maximal methane production for bovine blood whereas HRT values of 32 and 78 days are required for waste activated sludge and rumen content, respectively, to reach the same yield. These results highlight the interest in the adaptation of the reactor design according to the composition of the reactor feed

Modelling of the effect of HRT on anaerobic CSTR performance based on a specific characterisation of wastes from agro-industry

International audienceThe aim of this article is to investigate the effect of the Hydraulic Retention Time (HRT) on the anaerobic CSTR digester performance in term of methane production using modelling combined with a specific characterization of wastes. Hence, a recently developed methodology (“anaerobic respirometry”) has been applied to define input state variable set for the “Anaerobic Digestion Model n°1” (ADM1) adapted to each substrate including also hydrolysis rates. Then, ADM1 was used to simulate CSTRs with different HRT for each substrate. The results obtained for 12 common organic wastes from agro-industries (slaughterhouses and meat industry) are significantly different in function of the considered substrates. As an example, an HRT of 7 days is sufficient to reach 80% of the maximal methane production for bovine blood whereas HRT values of 32 and 78 days are required for waste activated sludge and rumen content, respectively, to reach the same yield. These results highlight the interest in the adaptation of the reactor design according to the composition of the reactor feed

La "respirométrie anaérobie", un outil pour la caractérisation des substrats dans un objectif de modélisation de la digestion anaérobie des effluents d'élevage

International audienceModelling of anaerobic digestion is more and more used as a tool for process optimization or interpreting observed phenomena within research projects. The most used model is the Anaerobic Digestion Model n°1 (ADM1) but some other models are also available (either simpler or more complex). Whatever the model, one of the major key issue is the fractionation and characterisation of the influent. For substrates like activated sludge from wastewater treatment plants, detailed influent characterisation models have been developed. But, the other substrates more complex as slurries or those from co-digestion systems require a more detailed input characterisation. Chemical analysis can be used to give the basic splits required into proteins, fats, and carbohydrates. However, this does not provide biodegradability. Moreover, this required a conversion of analysis results into COD fractions often used as unit in models which lead to difficulty in term of mass balance. The aim of this approach is to develop a method for the characterisation of the influent of anaerobic digestion models. Named anaerobic respirometry, this method is based on the interpretation of the results (in term of methane production kinetics) of batch experiment performed at low substrate to biomass ratio. Already used specifically for the characterisation of sludges from wastewater treatment plants (Yasui et al., 2008), here this method was applied on more complex substrates (livestock effluents and common co-substrates). In this work, eight similar mesophilic batch reactors (1L of working volume) on which biogas and methane production rates are continuously measured were developed to perform anaerobic respirometry for substrate characterisation. After a study concerning the optimal conditions in term of substrate to biomass ratio and influence of the origin of biomass, substrates commonly used for anaerobic co-digestion were characterized including piggery slurry, wastes from slaughterhouse (fat, blood, sludges,), green waste, Three origin of sludge have been tested. The results show a low influence of the choice of the sludge it is not too much specialized for a specific substrate. Four substrate/biomass ratios have been evaluated between 0.05 and 0.35 gCODbiodegradable/gVSS with an optimum at 0.14 gCODbiodegradable/gVSS. From these results, substrates were characterized as presented on figure 1 allowing to determine a kinetic fractionation. On most of substrates a readily and a slowly biodegradable fraction of COD could be identified with the help of a simplified version of ADM1. These results could be useful for the modelling and optimization of anaerobic digestion processes

Anaerobic co-digestion of waste activated sludge and greasy sludge from flotation process: Batch versus CSTR experiments to investigate optimal design

In this study, the maximum ratio of greasy sluvdge to incorporate with waste activated sludge was investigated in batch and CSTR experiments. In batch experiments, inhibition occurred with a greasy sludge ratio of more than 20-30% of the feed COD. In CSTR experiments, the optimal greasy sludge ratio was 60% of the feed COD and inhibition occurred above a ratio of 80%. Hence, batch experiments can predict the CSTR yield when the degradation phenomenon are additive but cannot be used to determine the maximum ratio to be used in a CSTR configuration. Additionally, when the ratio of greasy sludge increased from 0% to 60% of the feed COD, CSTR methane production increased by more than 60%. When the greasy sludge ratio increased from 60% to 90% of the feed COD, the reactor yield decreased by 75%

A waste characterisation procedure for ADM1 implementation based on degradation kinetics

International audienceIn this study, a procedure accounting for degradation kinetics was developed to split the total COD of a substrate into each input state variable required for Anaerobic Digestion Model n(degrees)1. The procedure is based on the combination of batch experimental degradation tests ("anaerobic respirometry") and numerical interpretation of the results obtained (optimisation of the ADM1 input state variable set). The effects of the main operating parameters, such as the substrate to inoculum ratio in batch experiments and the origin of the inoculum, were investigated. Combined with biochemical fractionation of the total COD of substrates, this method enabled determination of an ADM1-consistent input state variable set for each substrate with affordable identifiability. The substrate to inoculum ratio in the batch experiments and the origin of the inoculum influenced input state variables. However, based on results modelled for a CSTR fed with the substrate concerned, these effects were not significant. Indeed, if the optimal ranges of these operational parameters are respected, uncertainty in COD fractionation is mainly limited to temporal variability of the properties of the substrates. As the method is based on kinetics and is easy to implement for a wide range of substrates, it is a very promising way to numerically predict the effect of design parameters on the efficiency of an anaerobic CSTR. This method thus promotes the use of modelling for the design and optimisation of anaerobic processes

Réduction de la production des boues à l'aide d'ultrasons

The study presented here has taken place in the light of a LIFE Environment project directed by the Water and Waste Water Service of Angers Loire Metropole. The treatment of a part stream of recycled sludge (Waste water treatment plants of 6300 population equivalents) has reduced sludge production by about 26 %. The treatment by ultrasounds seems to have no impact on the water treatment performance, on the quality of thickened sludge, neither on the direct emission of greenhouse gases. The only exception is a decrease of the treatment performance of phosphorus. The treatment is not valuable from an economical point for this small waste water treatment plant with low sludge handling costs (10 /ton). Extrapolation of the results show that after some modifications, the process could be economically feasible for waste water treatment plants with a sizee 100 000 population equivalent and with final sludge eliminution costs > 11 /ton (DM 20%). If a digestor is present, it is preferable to apply ultrasounds to the sludge file in order to increase biogas production. This final application has proved itself all over the world (Hein, 2008; Nickel, 2008)