Amino acid sequence conservation and taxonomic distribution

Funding Information: FMS is recipient of fellowship by Fundação para a Ciência e a Tecnologia ( PD/BD/128213/2016 , within the scope of the PhD program Molecular Biosciences PD/00133/2012 ). The work was funded by Fundação para a Ciência e a Tecnologia ( PTDC/BIA-BQM/2599/2021 ). The project was supported by UIDB/04046/2020 and UIDP/04046/2020 Centre grants from FCT , Portugal (to BioISI), by LISBOA-01-0145-FEDER-007660 co-funded by FEDER through COMPETE2020-POCI. Publisher Copyright: © 2023 The Author(s)Pyruvate:quinone oxidoreductases (PQOs) catalyse the oxidative decarboxylation of pyruvate to acetate and concomitant reduction of quinone to quinol with the release of CO2. They are thiamine pyrophosphate (TPP) and flavin-adenine dinucleotide (FAD) containing enzymes, which interact with the membrane in a monotopic way. PQOs are considered as part of alternatives to most recognized pyruvate catabolizing pathways, and little is known about their taxonomic distribution and structural/functional relationship. In this bioinformatics work we tackled these gaps in PQO knowledge. We used the KEGG database to identify PQO coding genes, performed a multiple sequence analysis which allowed us to study the amino acid conservation on these enzymes, and looked at their possible cellular function. We observed that PQOS are enzymes exclusively present in prokaryotes with most of the sequences identified in bacteria. Regarding the amino acid sequence conservation, we found that 75 amino acid residues (out of 570, on average) have a conservation over 90 %, and that the most conserved regions in the protein are observed around the TPP and FAD binding sites. We systematized the presence of conserved features involved in Mg2+, TPP and FAD binding, as well as residues directly linked to the catalytic mechanism. We also established the presence of a new motif named “HEH lock”, possibly involved in the dimerization process. The results here obtained for the PQO protein family contribute to a better understanding of the biochemistry of these respiratory enzymes.publishersversionpublishe

The alternative complex III of Rhodothermus marinus and its structural and functional association with caa3 oxygen reductase

AbstractAn alternative complex III (ACIII) is a respiratory complex with quinol:electron acceptor oxidoreductase activity. It is the only example of an enzyme performing complex III function that does not belong to bc1 complex family. ACIII from Rhodothermus (R.) marinus was the first enzyme of this type to be isolated and characterized, and in this work we deepen its characterization. We addressed its interaction with quinol substrate and with the caa3 oxygen reductase, whose coding gene cluster follows that of the ACIII. There is at least, one quinone binding site present in R. marinus ACIII as observed by fluorescence quenching titration of HQNO, a quinone analogue inhibitor. Furthermore, electrophoretic and spectroscopic evidences, taken together with mass spectrometry revealed a structural association between ACIII and caa3 oxygen reductase. The association was also shown to be functional, since quinol:oxygen oxidoreductase activity was observed when the two isolated complexes were put together. This work is thus a step forward in the recognition of the structural and functional diversities of prokaryotic respiratory chains

Recovery of valuable aromas from sardine cooking wastewaters by pervaporation with fractionated condensation: matrix effect and model validation

Due to the lack of studies addressing the influence of real food matrices on integrated organophilic pervaporation/fractionated condensation processes, the present work analyses the impact of the real matrix of sardine cooking wastewaters on the fractionation of aromas. In a previous study, a thermodynamic/material balance model was developed to describe the integrated pervaporation—a fractionated condensation process of aroma recovery from model solutions that emulate seafood industry aqueous effluents, aiming to define the best conditions for off-flavour removal. This work assesses whether the previously developed mathematical model, validated only with model solutions, is also applicable in predicting the fractionation of aromas of different chemical families from real effluents (sardine cooking wastewaters), aiming for off-flavour removals. It was found that the food matrix does not influence substantial detrimental consequences on the model simulations, which validates and extends the applicability of the model.info:eu-repo/semantics/publishedVersio

Quality Evaluation of Machine Learning-based Point Cloud Coding Solutions

In this paper, a quality evaluation of three point cloud coding solutions based on machine learning technology is presented, notably, ADLPCC, PCC_GEO_CNN, and PCGC, as well as LUT_SR, which uses multi-resolution Look-Up Tables. Moreover, the MPEG G-PCC was used as an anchor. A set of six point clouds, representing both landscapes and objects were coded using the five encoders at different bit rates, and a subjective test, where the distorted and reference point clouds were rotated in a video sequence side by side, is carried out to assess their performance. Furthermore, the performance of point cloud objective quality metrics that usually provide a good representation of the coded content is analyzed against the subjective evaluation results. The obtained results suggest that some of these metrics fail to provide a good representation of the perceived quality, and thus are not suitable to evaluate some distortions created by machine learning-based solutions. A comparison between the analyzed metrics and the type of represented scene or codec is also presented.This research was funded by the Portuguese FCT-Fundação para a Ciência e Tecnologia under the project UIDB/50008/2020, PLive X-0017-LX-20, and by operation Centro-01-0145-FEDER-000019 - C4 - Centro de Competencias em Cloud Computing.info:eu-repo/semantics/acceptedVersio

On the stability of point cloud machine learning based coding

This paper analyses the performance of two of the most well known deep learning-based point cloud coding solutions, considering the training conditions. Several works have recently been published on point cloud machine learning-based coding, following the recent tendency on image coding. These codecs are typically seen as a set of predefined trained machines. However, the performance of such models is usually very dependent of their training, and little work has been considered on the stability of the codecs’ performance, as well as the possible influence of the loss function parameters, and the increasing number of training epochs. The evaluation experiments are supported in a generic test set with point clouds representing objects and also more complex scenes, using the point to point metric (PSNR D1), as several studies revealed the good quality representation of this geometry-only point cloud metric.Research funded by the Portuguese FCT-Fundação para a Ciência e Tecnologia under the project UIDB/50008/2020, PLive X-0017-LX-20, and by operation Centro-01-0145-FEDER-000019 - C4 - Centro de Competencias em Cloud Computing.info:eu-repo/semantics/acceptedVersio

Fish and cephalopods associated with the squid Loligo vulgaris Lamarck, 1798 in Portuguese waters

Fish and cephalopod taxa occurring in association with Loligo vulgaris, in Portuguese waters between Lisbon and Vila Real de Santo António, were investigated by sampling with bottom trawling equipment between 1990-1991 and 1993-1995. The family Triglidae, the genera Pagellus and Trachurus and the four species Alloteuthis subulata, Boops boops, Callionymus lyra, and Merluccius merluccius were found, on average, in at least 75% of the trawls with L. vulgaris. Conversely, that cephalopod was found in at least 75% of the trawls with the family Trachinidae, the genera Dentex, Diplodus, Liza and Torpedo and the six species, Hyperoplus lanceolatus, Pagrus pagrus, Pomatoschistus m. minutus, Psetta m. maxima, Scophthalmus rhombus and Spicara flexuosa. An index of "affinity" (ranging from -∞ to 1) between L. vulgaris and the other taxa was used in order to highlight co-occurrences of an unlikely coincidental nature. Lists of taxa with high affinity index scores (0.5 to 1) are given for 5 different situations: all samples together; samples grouped by bottom depth; samples grouped by research cruise; research cruises grouped by season and by year. Pair wise comparisons between all taxa lists for each of the 5 situations were made, indicating a greater influence of depth than any other factor in the composition of the lists. The significance of the degree of similarity between lists of taxa, "preferred" under different circumstances and the reasons for those "preferences" are discussed

Subjective Quality Evaluation of Point Clouds Using a Head Mounted Display

This paper reports on a subjective quality evaluation of static point clouds encoded with the MPEG codecs V-PCC and G-PCC, the deep learning-based codec RS-DLPCC, and the popular Draco codec. 18 subjects visualized 3D representations of distorted point clouds using a Head Mounted Display, which allowed for a direct comparison with their reference. The Mean Opinion Scores (MOS) obtained in this subjective evaluation were compared with the MOS from two previous studies, where the same content was visualized either on a 2D display or a 3D stereoscopic display, through the Pearson Correlation, Spearman Rank Order Correlation, Root Mean Square Error, and the Outlier Ratio. The results indicate that the three studies are highly correlated with one another. Moreover, a statistical analysis between all evaluations showed no significant differences between them

Motion estimation with chessboard pattern prediction strategy

Due to high correlations among the adjacent blocks, several algorithms utilize movement information of spatially and temporally correlated neighboring blocks to adapt their search patterns to that information. In this paper, this information is used to define a dynamic search pattern. Each frame is divided into two sets, black and white blocks, like a chessboard pattern and a different search pattern, is defined for each set. The advantage of this definition is that the number of spatially neighboring blocks is increased for each current block and it leads to a better prediction for each block. Simulation results show that the proposed algorithm is closer to the Full-Search algorithm in terms of quality metrics such as PSNR than the other state-of-the-art algorithms while at the same time the average number of search points is less.info:eu-repo/semantics/publishedVersio

Stress response of European seabass (Dicentrarchus labrax) fed plant-based diets supplemented with swine blood hydrolysates

To improve fish welfare, it is essential that aquafeeds are designed to help fish cope with the stressful conditions of fish farms. One effective strategy to achieve this goal is to supplement the diet with bioactive hydrolysates. Here, diet supplementation to modulate oxidative stress after air exposure was investigated in European seabass, using swine blood hydrolysates (BH), obtained either by autohydrolysis (AH) or enzymatically. The enzymatically produced BH were further submitted to a micro- (RMF) and nanofiltration (RNF). Four isolipidic, isoproteic and isoenergetic diets were developed: a plant-based diet with low (12.5%) fishmeal levels (control, CTRL) and three diets where 3% of each BH (RMF, RNF and AH) was added to the CTRL. Diets were assigned to triplicate groups of 71 European seabass juveniles (initial weight 12.3 ± 1.4 g). After 12 weeks, 9 fish per treatment were either immediately sampled or air-exposed for 1 min and let to recover in a new system for 6 h prior to sampling. Stress response increased cortisol levels, followed by an increment in plasma lactate. The challenge increased liver lipid peroxidation (LPO) due to reactive oxygen species (ROS) accumulation. Carbonyls decreased post-stress, maybe due to a possible interaction with the LPO radicals, reducing protein oxidation. None of the BH improved plasma stress response. By reducing catalase levels without increasing LPO, the RNF treatment appears to adjust European seabass' antioxidant defences, indicating its potential to supply exogenous antioxidants to combat oxidative stress induced by ROS. However, this impact was not sufficient to lower LPO levels compared to a control plant-based diet. The tested diets seemed to affect the fish oxidative stress response in the liver, possibly due to the presence of bioactive peptides, which aided in the non-enzymatic modulation of stress response, as observed by the total antioxidant capacity values in the liver.info:eu-repo/semantics/publishedVersio