RLPredictiOme,a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins,Reveals Novel Classes of Transmembrane Receptors

Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes.     

Circulating Extracellular Vesicles: The Missing Link between Physical Exercise and Depression Management?

Depression is associated with an increased risk of aging-related diseases. It is also seemingly a common psychological reaction to pandemic outbreaks with forced quarantines and lockdowns. Thus, depression represents, now more than ever, a major global health burden with therapeutic management challenges. Clinical data highlights that physical exercise is gaining momentum as a non-pharmacological intervention in depressive disorders. Although it may contribute to the reduction of systemic inflammation associated with depression, the mechanisms underlying the beneficial physical exercise effects in emotional behavior remain to be elucidated. Current investigations indicate that a rapid release of extracellular vesicles into the circulation might be the signaling mediators of systemic adaptations to physical exercise. These biological entities are now well-established intercellular communicators, playing a major role in relevant physiological and pathophysiological functions, including brain cell–cell communication. We also reviewed emerging evidence correlating depression with modified circulating extracellular vesicle surfaces and cargo signatures (e.g., microRNAs and proteins), envisioned as potential biomarkers for diagnosis, efficient disease stratification and appropriate therapeutic management. Accordingly, the clinical data summarized in the present review prompted us to hypothesize that physical exercise-related circulating extracellular vesicles contribute to its antidepressant effects, particularly through the modulation of inflammation. This review sheds light on the triad “physical exercise–extracellular vesicles–depression” and suggests new avenues in this novel emerging field.     

Fast prototyping of network protocols through ns-3 simulation model reuse

In the networking research and development field, one recurring problem faced is the duplication of effort to write first simulation and then implementation code. We posit an alternative development process that takes advantage of the built in network emulation features of Network Simulator 3 (ns-3) and allows developers to share most code between simulation and implementation of a protocol. Tests show that ns-3 can handle a data plane processing large packets, but has difficulties with small packets. When using ns-3 for implementing the control plane of a protocol, we found that ns-3 can even outperform a dedicated implementation.     

Consumers’ quality perception of national branded, national store branded, and imported store branded beef

This study investigated the differences in the consumers’ quality perception of national branded, national store branded, and imported store branded beef. Partial Least Squares analysis is used for modelling the quality perception process. Results show that consumers perceived national branded Carnalentejana beef, as better on all quality cues and quality aspects than the other two store branded beefs. Preference for Carnalentejana beef stayed highly consistent even after the blind test, where consumers differentiated this beef from the other two beef brands on all sensory dimensions: taste, tenderness, and juiciness, and chose it as the preferred one. Consumers utilized more perceived intrinsic cues to infer expected eating quality of store branded beefs.     

Effect of cooking methods on fatty acids,conjugated isomers of linoleic acid and nutritional quality of beef intramuscular fat

The effect of boiling, microwaving and grilling on the composition and nutritional quality of beef intramuscular fat from cattle fed with two diets was investigated. Longissimus lumborum muscle from 15 Alentejano young bulls fed on concentrate or pasture was analyzed. Cooking losses and, consequently, total lipids, increased directly with the cooking time and internal temperature reached by meat (microwaving > boiling > grilling). The major changes in fatty acid composition, which implicated 16 out of 34 fatty acids, resulted in higher percentages in cooked beef of SFA and MUFA and lower proportions of PUFA, relative to raw meat, while conjugated linoleic acid (CLA) isomers revealed a great stability to thermal processes. Heating decreased the PUFA/SFA ratio of meat but did not change its n−6/n−3 index. Thermal procedures induced only slight oxidative changes in meat immediately after treatment but hardly affected the true retention values of its individual fatty acids (72–168%), including CLA isomers (81–128%).     

Irradiation effect on fatty acid composition and conjugated linoleic acid isomers in frozen lamb meat

The effect of gamma radiation processing on the lipid content, fatty acid composition and conjugated linoleic acid (CLA) profile in frozen lamb meat was investigated. Samples of longissimus thoracis muscle from lambs fed lucerne basal diets either unsupplemented or supplemented with polyunsaturated vegetable oils were irradiated (7 kGy) and analysed. CLA contents in lamb meat did not affect (P > 0.05) the levels of lipid oxidation induced by the irradiation. No significant differences (P > 0.05) were observed for fatty acid composition, related nutritional indexes (n − 6/n − 3 and PUFA/SFA), as well as for total lipid and CLA contents, between non-irradiated (control) and irradiated meat samples. In contrast, meat irradiation affected the relative proportions of total trans, trans and cis/trans CLA isomers (P < 0.001), in addition to the percentage of some minor individual CLA isomers (t11, t13 and t9, t11, with P < 0.05 and P < 0.001, respectively). The percentage of total cis/trans CLA isomers slightly decreased in irradiated samples, while the relative proportion of total trans, trans isomers slightly increased. This observation may be explained by the higher susceptibility to autoxidation of the cis double bond relative to the trans configuration.     

Challenges and alternatives for unmanned underwater vehicular research in the Amazon basin: Towards a more sustainable management of water resources and the environment

The Amazon basin is one of the largest hydrographic systems in the world, possessing a great diversity of natural resources in need of more sustainable water and environmental management. However, as much of what lies beneath the surface of Amazonian waters is still unexplored, underwater exploration technologies are seen as a means of research and monitoring. The present work therefore aims to answer two research questions: What are the current technologies that could be implemented for unmanned underwater research in the Amazon waters? What are the main limitations and existing alternatives for using unmanned underwater vehicles in the rivers of this region to provide more sustainable water and environment management? Our results demonstrate that remotely operated vehicles (ROVs) and autonomous underwater vehicles (AUVs) are possible options in the short and long terms, respectively. The main challenges in implementing these technologies are related to the variations in hydraulic geometry, current velocities and turbidity of the rivers, as well as the preservation of the region's biodiversity. This research can be taken as a starting point for planners and decision makers seeking more sustainable underwater and environmental exploration of the Amazon river system.     

In Pursuit of Zero 2.0: Recent Developments in Nonfouling Polymer Brushes for Immunoassays

“Nonfouling” polymer brush surfaces can greatly improve the performance of in vitro diagnostic (IVD) assays due to the reduction of nonspecific protein adsorption and consequent improvement of signal-to-noise ratios. The development of synthetic polymer brush architectures that suppress adventitious protein adsorption is reviewed, and their integration into surface plasmon resonance and fluorescent sandwich immunoassay formats is discussed. Also, highlighted is a novel, self-contained immunoassay platform (the D4 assay) that transforms time-consuming laboratory-based assays into a user-friendly and point-of-care format with a sensitivity and specificity comparable or better than standard enzyme-linked immunosorbent assay (ELISA) directly from unprocessed samples. These advancements clearly demonstrate the utility of nonfouling polymer brushes as a substrate for ultrasensitive and robust diagnostic assays that may be suitable for clinical testing, in field and laboratory settings.