SUMMARY
Soybean (Glycine max L. Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the ...past 5 years generated an enormous amount of RNA‐seq data, encompassing various tissues, developmental conditions and genotypes. In this study, we have collected data from 1298 publicly available soybean transcriptome samples, processed the raw sequencing reads and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground and seed/seed‐related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1349 genes showed heavily biased expression patterns towards particular tissues. A transcript‐level analysis revealed that 95% (70 963 of 74 490) of the assembled transcripts have intron chains exactly matching those from known transcripts, whereas 3256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user‐friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.
Significance Statement
Here we report an integrative and systematic analysis of 1298 RNA‐Seq samples to build a soybean gene expression atlas. This resource is accessible via a user‐friendly web interface as well as available for download.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Ethanol is the main biofuel produced by fermentation route and the search for new feedstocks to produce fuel ethanol is still a great challenge. This work aims to compare the ethanol production from ...a new irrigated rice cultivar BRS AG to the conventional cultivar BRS PAMPA applied in Brazil. Six different commercial strains of Saccharomyces cerevisiae (BG-1, CAT-1, FT-858, JP-1, PE-2, and SA-1) were applied in fermentation reactions. Fermentations performed with BRS PAMPA rice revealed that the highest yields were achieved with strain SA-1, corresponding to 93.0% of the theoretical maximum and final ethanol concentration of 58.92 g L
, and with CAT-1, a yield of 92.7% and final ethanol concentration of 58.93 g L
. For the fermentations with BRS AG rice, the highest yields were obtained with strain FT-858, exhibiting a 89.6% yield and final ethanol concentration of 62.45 g L
, and with CAT-1, 87.9% yield and final ethanol concentration of 61.25 g L
were achieved. The most appropriate microorganism for ethanol production using BRS PAMPA rice and BRS AG rice was CAT-1. Comparatively, the ethanol yield and productivity using BRS AG were higher than those observed for BRS PAMPA for all strains, except for PE-2 and SA-1 that led to very similar results. The experimental results showed that the giant rice BRS AG is an excellent feedstock for fuel ethanol production in lowland fields.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Main conclusion
We report a soybean gene co-expression network built with data from 1284 RNA-Seq experiments, which was used to identify important regulators, modules and to elucidate the fates of ...gene duplicates.
Soybean (
Glycine max
(L.) Merr.) is one of the most important crops worldwide, constituting a major source of protein and edible oil. Gene co-expression networks (GCN) have been extensively used to study transcriptional regulation and evolution of genes and genomes. Here, we report a soybean GCN using 1284 publicly available RNA-Seq samples from 15 distinct tissues. We found modules that are differentially regulated in specific tissues, comprising processes such as photosynthesis, gluconeogenesis, lignin metabolism, and response to biotic stress. We identified transcription factors among intramodular hubs, which probably integrate different pathways and shape the transcriptional landscape in different conditions. The top hubs for each module tend to encode proteins with critical roles, such as succinate dehydrogenase and RNA polymerase subunits. Importantly, gene essentiality was strongly correlated with degree centrality and essential hubs were enriched in genes involved in nucleic acids metabolism and regulation of cell replication. Using a guilt-by-association approach, we predicted functions for 93 of 106 hubs without functional description in soybean. Most of the duplicated genes had different transcriptional profiles, supporting their functional divergence, although paralogs originating from whole-genome duplications (WGD) are more often preserved in the same module than those from other mechanisms. Together, our results highlight the importance of GCN analysis in unraveling key functional aspects of the soybean genome, in particular those associated with hub genes and WGD events.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
In the last decade, the automotive industry has undergone a paradigm shift towards electrification. Electric vehicles have become increasingly popular, but so far, they have almost solely utilized ...single-ratio gearboxes. The use of multiple gear ratios has several potential benefits, including enabling the electric traction machine and inverter to operate in a more efficient region, increasing vehicle acceleration, gradeability, and top speed, and reducing overall traction system mass and volume. Performance vehicles, light to heavy-duty trucks, and buses may especially benefit from multi-speed gearboxes due to their high torque and power requirements. This paper covers the fundamentals of applying multi-speed gearboxes to EVs, the latest designs, and future trends. The efforts of both academia and industry in this field are covered. A range of topics are discussed, including gearbox topologies, gear ratio selection, gearbox losses, noise vibration and harshness, gearbox control, shift scheduling, and regenerative braking. Prior studies are presented showing that depending on the drive cycle, vehicle type, and gearbox configuration, drivetrain energy consumption may be reduced slightly or increased anywhere from a few percent to thirty percent when utilizing a multi-speed configuration. While multi-speed EV traction systems do show considerable promise, more investigation is needed to conclusively determine in what cases they can outperform highly optimized single-speed systems.
The present work addresses the modeling and simulation of the addition of copolymerizations of styrene and methyl methacrylate in batch mode, and the formation of tailored vinyl acetate/acrylic acid ...copolymers is evaluated through stochastic optimization procedures based on the Monte Carlo method. A kinetic model of the free-radical reaction was proposed in order to predict the behavior of the reaction system taking into consideration the presence of the penultimate unit effect. The profiles of conversion and copolymer composition were also evaluated considering the effect of the medium viscosity (kinetic phenomena related to gel and glass effects) on the reaction performance. It was shown that the proposed model for chain-growth copolymerization is able to describe strong nonlinear behaviors such as autoacceleration of the polymerization and drift of copolymer composition. It was also shown that copolymers with homogeneous composition can be successfully synthesized through manipulation of the monomer feed flow rate based on a stochastic optimization procedure.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Much evidence suggests that Amazonia and the Atlantic Forest were connected through at least three dispersion routes in the past: the Eastern route, the central route, and the Western route. However, ...few studies have assessed the use of these routes based on multiple species. Here we present a compilation of mammal species that potentially have dispersed between the two forest regions and which may serve to investigate these connections. We evaluate the present-day geographic distributions of mammals occurring in both Amazonia and the Atlantic Forest and the likely connective routes between these forests. We classified the species per habitat occupancy (strict forest specialists, species that prefer forest habitat, or generalists) and compiled the genetic data available for each species. We found 127 mammalian species presently occurring in both Amazonia and the Atlantic Forest for which, substantial genetic data was available. Hence, highlighting their potential for phylogeographic studies investigating the past connections between the two forests. Differently from what was previously proposed, the present-day geographic distribution of mammal species found in both Amazonia and the Atlantic Forest points to more species in the eastern portion of the dry diagonal (and adjoining forested habitats). The Central route was associated with the second most species. Although it remains to be seen how this present-day geography reflects the paleo dispersal routes, our results show the potential of using mammal species to investigate and bring new insights about the past connections between Amazonia and the Atlantic Forest.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Medical devices are important diagnosis and therapy tools for several diseases which include a wide range of products. Technological advances in this area have been proposed to reduce adverse ...complication incidences. New technologies and manufacturing processes, as well as the development of new materials or medical devices with modified surface and the use of biodegradable polymeric devices such as a substrate for cell culture in the field of tissue engineering, have attracted considerable attention in recent years by the scientific community intended to produce medical devices with superior properties and morphology. This review article focused on implantable devices, addresses the major advances in the biomedical field related to the devices manufacture processes such as 3D printing and hot melting extrusion, and the use of polymer matrices composed of copolymers, blends, nanocomposites or grafted with antiproliferative drugs for manufacturing and/or coating the devices surface.
The increase in pollution and carbon dioxide in the transportation sector motivates many countries to establish rules to reduce the emission and carbon footprint. The partial or total electrification ...of the automotive propulsion system is mandatory to minimize the impact of transportation on the environment. There are multiple possible architectures to electrify the vehicle propulsion system, with different degrees of electrification, and each of the architectures can provide a different balance between energy efficiency, vehicle performance, comfort, drivability, and safety. This article aims to present the definition of the automotive propulsion system electrification, the various degrees of electrification and operation modes, and the possible configurations of an electrified propulsion system by the electric machine position. This article also introduces the definition of the subsystems of the propulsion systems and their components, with an explanation of the subsystem and each of their parts. Based on the state-of-the-art technology development, it intends to present the industry's common sense and knowledge on automotive propulsion system electrification and proposes a process to follow in the electrified propulsion system architecture selection.
Abstract Despite the disjunct distribution of the Amazonian and the Atlantic forests, three historical connections between those biomes have been hypothesized: through Northeast Brazil, the Brazilian ...Cerrado, and the Southeast–Northwest. Temporal variation has been suggested to occur in these connections, with recent connections for the Northeast and older connections for the Southeast–Northwest. We tested for the hypothesis of temporal variation in these connections using Neotropical mammals as a study group. Phylogenetic and spatial data of sister groups from each forest were combined to access the spatiotemporal patterns of these connections. The relationship between distance route and divergence times was tested using linear regression. The results revealed that the previously suggested spatiotemporal pattern was corroborated only for Rodentia but not for Didelphimorphia and Chiroptera, showing both old and recent connections for all routes. In addition, each family revealed specific connections at different times. We refute the previously proposed absence of old connections through the Northeast route. Rather, temporal variation in the Northeast differs among the mammalian groups according to their evolutionary histories. Owing to the biogeographical history of each group, different connections were found at different times. Therefore, connections between these forests cannot be explained by a single spatiotemporal pattern.
The Oseberg Viking ship burial is one of the most extensive collections of Viking wooden artefacts ever excavated in Norway. In the early twentieth century, many of these artefacts were treated with ...alum in order to preserve them, inadvertently leading to their current degraded state. It is therefore crucial to develop new bioinspired polymers which could be used to conserve these artefacts and prevent further disintegration. Two hydroxylated polymers were synthesised (TPA6 and TPA7), using α-pinene- and oleic acid-derived monomers functionalised with an acrylate moiety. Characterisation using biomolecular hydrodynamics (analytical ultracentrifugation and high precision viscometry) has shown that these polymers have properties which would potentially make them good wood consolidants. Conformation analyses with the viscosity increment (ν) universal hydrodynamic parameter and ELLIPS1 software showed that both polymers had extended conformations, facilitating in situ networking when applied to wood. SEDFIT-MSTAR analyses of sedimentation equilibrium data indicates a weight average molar mass M
of (3.9 ± 0.8) kDa and (4.2 ± 0.2) kDa for TPA6 and TPA7 respectively. Analyses with SEDFIT (sedimentation velocity) and MultiSig however revealed that TPA7 had a much greater homogeneity and a lower proportion of aggregation. These studies suggest that both these polymers-particularly TPA7-have characteristics suitable for wood consolidation, such as an optimal molar mass, conformation and a hydroxylated nature, making them interesting leads for further research.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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