Brazilian Center for Research in Energy and Materials

BACKGROUND: System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. RESULTS: Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. CONCLUSIONS: Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

New remote sensing data on vegetation cover and restoration opportunities bring hope to the Brazilian Atlantic Forest, one of the hottest of the 36 global biodiversity hotspots. Available estimates of remaining vegetation cover in the biome currently range from 11% to 16%. However, our new land-cover map, prepared at the highest resolution ever (5 m), reveals a current vegetation cover of 28%, or 32 million hectares (Mha) of native vegetation. Simultaneously, we found 7.2 Mha of degraded riparian areas, of which 5.2 Mha at least must be restored before 2038 by landowners for legislation compliance. Restoring the existing legal debt could increase native vegetation cover in the Atlantic Forest up to 35%. Such effort, if well planned and implemented, could reduce extinction processes by increasing connectivity of vegetation remnants and rising total native cover to above the critical biodiversity threshold established for different taxonomic groups. If undertaken, this process can be adaptive to climate change and boost sustainable development in this most populous biome in Brazil, turning it into a hopespot.

Abstract Recent advances in experimental and computational methods are increasing the quantity and complexity of generated data. This massive amount of raw data needs to be stored and interpreted in order to advance the materials science field. Identifying correlations and patterns from large amounts of complex data is being performed by machine learning algorithms for decades. Recently, the materials science community started to invest in these methodologies to extract knowledge and insights from the accumulated data. This review follows a logical sequence starting from density functional theory as the representative instance of electronic structure methods, to the subsequent high-throughput approach, used to generate large amounts of data. Ultimately, data-driven strategies which include data mining, screening, and machine learning techniques, employ the data generated. We show how these approaches to modern computational materials science are being used to uncover complexities and design novel materials with enhanced properties. Finally, we point to the present research problems, challenges, and potential future perspectives of this new exciting field.

BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

There is growing interest in biodegradable polymers (BP), in particular poly(butylene adipate‐ co ‐terephthalate) (PBAT), due to environmental problems associated with the disposal of non‐biodegradable polymers into the environment. However, high production cost and low thermo‐mechanical properties restrict the use of this sustainable material, making its biodegradability advantageous only when it is decisively required. The addition of different compositions of monomers and selective addition of natural fillers have been reported as alternatives to develop more accessible PBAT‐based bioplastics with performance that could match or even exceed that of the most widely used commodity plastics. This review explores the recent progress of the applications and biodegradation of PBAT. The addition of natural fillers and its effect on the final performance of the PBAT‐based composites is also reported with respect to improving the properties of composites. The advance of polymerization reaction engineering combined with sustainable trend offers great opportunities for innovative green chemical manufacturing. POLYM. ENG. SCI., 59:E7–E15, 2019. © 2017 Society of Plastics Engineers

All living organisms rely on nutrients to sustain cell metabolism and energy production, which in turn need to be adjusted based on available resources. The evolutionarily conserved target of rapamycin (TOR) protein kinase is a central regulatory hub that connects environmental information about the quantity and quality of nutrients to developmental and metabolic processes in order to maintain cellular homeostasis. TOR is activated by both nitrogen and carbon metabolites and promotes energy-consuming processes such as cell division, mRNA translation, and anabolism in times of abundance while repressing nutrient remobilization through autophagy. In animals and yeasts, TOR acts antagonistically to the starvation-induced AMP-activated kinase (AMPK)/sucrose nonfermenting 1 (Snf1) kinase, called Snf1-related kinase 1 (SnRK1) in plants. This review summarizes the immense knowledge on the relationship between TOR signaling and nutrients in nonphotosynthetic organisms and presents recent findings in plants that illuminate the crucial role of this pathway in conveying nutrient-derived signals and regulating many aspects of metabolism and growth.

In this paper we describe a new Benders decomposition approach to solve power transmission network expansion planning problems. This new approach is characterized by using a linear (0-1) disjuntictive model that ensures the optimality of the solution found and by using additional constraints, iteratively evaluated, besides the traditional Benders cuts. The results obtained, considering a real world power transmission network expansion planning study with the southeastem Brazilian system, show the efficiency of this approach.

This paper presents a model for active distribution systems expansion planning based on genetic algorithms, where distributed generation (DG) integration is considered together with conventional alternatives for expansion, such as rewiring, network reconfiguration, installation of new protection devices, etc. The novel approach of planning DG integration together with network expansion is a requirement for the modern active distribution network. However, the uncertainties related to DG power generation and load response growth must be taken into account in order to plan a safe system at a minimum cost. Thus, two different methodologies for uncertainties incorporation through the use of multiple scenarios analysis are proposed and compared. The multiple objectives optimization algorithm applied in the model takes into account the costs of reliability, losses, power imported from transmission, and network investments.

Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.

We compared the amount of lignin as determined by the three most traditional methods for lignin measurement in three tissues (sugarcane bagasse, soybean roots and soybean seed coat) contrasting for lignin amount and composition. Although all methods presented high reproducibility, major inconsistencies among them were found. The amount of lignin determined by thioglycolic acid method was severely lower than that provided by the other methods (up to 95%) in all tissues analyzed. Klason method was quite similar to acetyl bromide in tissues containing higher amounts of lignin, but presented lower recovery of lignin in the less lignified tissue. To investigate the causes of the inconsistencies observed, we determined the monomer composition of all plant materials, but found no correlation. We found that the low recovery of lignin presented by the thioglycolic acid method were due losses of lignin in the residues disposed throughout the procedures. The production of furfurals by acetyl bromide method does not explain the differences observed. The acetyl bromide method is the simplest and fastest among the methods evaluated presenting similar or best recovery of lignin in all the tissues assessed.

Silver nanoparticles are one of the most important materials in the nanotechnology industry. Additionally, the protein corona is emerging as a key entity at the nanobiointerface; thus, a comprehensive understanding of the interactions between proteins and silver nanoparticles is imperative. Therefore, literature reporting studies involving both single molecule protein coronas (i.e., bovine and human serum albumin, tubulin, ubiquitin and hyaluronic-binding protein) and complex protein coronas (i.e., fetal bovine serum and yeast extract proteins) were selected to demonstrate the effects of protein coronas on silver nanoparticle cytotoxicity and antimicrobial activity. There is evidence that distinct and differential protein components may yield a "protein corona signature" that is related to the size and/or surface curvature of the silver nanoparticles. Therefore, the formation of silver nanoparticle protein coronas together with the biological response to these coronas (i.e., oxidative stress, inflammation and cytotoxicity) as well as other cellular biophysicochemical mechanisms (i.e., endocytosis, biotransformation and biodistribution) will be important for nanomedicine and nanotoxicology. Researchers may benefit from the information contained herein to improve biotechnological applications of silver nanoparticles and to address related safety concerns. In summary, the main aim of this mini-review is to highlight the relationship between the formation of silver nanoparticle protein coronas and toxicity.

The structural complexity of composite biomaterials and biomineralized particles arises from the hierarchical ordering of inorganic building blocks over multiple scales. Although empirical observations of complex nanoassemblies are abundant, the physicochemical mechanisms leading to their geometrical complexity are still puzzling, especially for nonuniformly sized components. We report the self-assembly of hierarchically organized particles (HOPs) from polydisperse gold thiolate nanoplatelets with cysteine surface ligands. Graph theory methods indicate that these HOPs, which feature twisted spikes and other morphologies, display higher complexity than their biological counterparts. Their intricate organization emerges from competing chirality-dependent assembly restrictions that render assembly pathways primarily dependent on nanoparticle symmetry rather than size. These findings and HOP phase diagrams open a pathway to a large family of colloids with complex architectures and unusual chiroptical and chemical properties.

Glutamine is an essential nutrient for cancer cell proliferation, especially in the context of citric acid cycle anaplerosis. In this manuscript we present results that collectively demonstrate that, of the three major mammalian glutaminases identified to date, the lesser studied splice variant of the gene gls, known as Glutaminase C (GAC), is important for tumor metabolism. We show that, although levels of both the kidney-type isoforms are elevated in tumor vs. normal tissues, GAC is distinctly mitochondrial. GAC is also most responsive to the activator inorganic phosphate, the content of which is supposedly higher in mitochondria subject to hypoxia. Analysis of X-ray crystal structures of GAC in different bound states suggests a mechanism that introduces the tetramerization-induced lifting of a "gating loop" as essential for the phosphate-dependent activation process. Surprisingly, phosphate binds inside the catalytic pocket rather than at the oligomerization interface. Phosphate also mediates substrate entry by competing with glutamate. A greater tendency to oligomerize differentiates GAC from its alternatively spliced isoform and the cycling of phosphate in and out of the active site distinguishes it from the liver-type isozyme, which is known to be less dependent on this ion.

Abstract Sugarcane is currently the main renewable energy source in Brazil. Due to the importance of the cane industry and its contribution to a wide range of biobased energy and other products, LCA studies regarding cane‐derived products are needed to assess their environmental benefits. The main objective of this work was the assessment of life cycle energy use and greenhouse gas (GHG) emissions related to cane sugar and ethanol, considering bagasse and electricity surpluses as coproducts. We performed an overall balance for the Brazilian Center‐South Region, adopting different methods to evaluate sugar and ethanol production separately. The GREET 1.8c.0 model was used for the ‘well‐to‐wheels’ calculations but adapted to the comprehensive set of Brazilian parameters that best represent the Center‐South Region. For the reference case, fossil energy use and GHG emissions related to sugar production were evaluated as 721 kJ/kg and 234 g CO 2 eq/kg, respectively. For the ethanol life cycle, these values were 80 kJ/MJ and 21.3 g CO 2 eq/MJ. Special attention was paid to the variation of some parameters among producing units based on data collected by industry. The consequent uncertainties in ethanol life cycle emissions were assessed through a Monte Carlo analysis based on assigned distribution of probability curves for eleven selected parameters and informed by partial statistical data available from industry for distribution generation. Projections were also made for 2020 scenario parameters based on the best in current class technologies and technological improvements deemed commercially possible today. Published in 2011 by John Wiley & Sons, Ltd

Abstract Large‐scale bioenergy demand has triggered new approaches to straw management in Brazilian sugarcane fields. With the progressive shift from a burned to a nonburned harvest system, most of the straw presently retained on the soil surface has become economically viable feedstock for bioenergy production. The trade‐offs between the need to preserve soil quality and produce more bioenergy have been the subject of intense discussion. This study presents a synthesis of available information on the magnitude of the main impacts of straw removal from sugarcane fields for bioenergy production and therefore represents an easily available resource to guide management decisions on the recommended amount of straw to be maintained on the field to take advantage of the agronomic, environmental, and industrial benefits. Crop residues remaining on sugarcane fields provide numerous ecosystem services including nutrient recycling, soil biodiversity, water storage, carbon accumulation, control of soil erosion, and weed infestation. Furthermore, several studies reported higher sugarcane production under straw retention on the field, while few suggest that straw may jeopardize biomass production in cold regions and under some specific soil conditions. Pest control is among the parameters favored by straw removal, while N 2 O emissions are increased only if straw is associated with the application of N fertilizer and vinasse. An appropriate recommendation, which is clearly site specific, should be based on a minimum mass of straw on the field to provide those benefits. Overall, this review indicates that most of the agronomic and environmental benefits are achieved when at least 7 Mg ha −1 of dry straw is maintained on the soil surface. However, modeling efforts are of paramount importance to assess the magnitude and rates of straw removal considering the several indicators involved in this complex equation, so that an accurate straw recovery rate could be provided to producers and industry toward greater sustainability.

mutants display enhanced resistance against different classes of pathogens, such as bacteria, oomycete, and fungi. Notably, disease resistance correlates with increased salicylic acid (SA) levels and transcriptional activation of immune responses. Furthermore, we demonstrate that SlDMR6-1 and SlDMR6-2 display SA-5 hydroxylase activity, thus contributing to the elucidation of the enzymatic function of DMR6. We then propose that SlDMR6 duplication in tomato resulted in subsequent subfunctionalization, in which SlDMR6-2 specialized in balancing SA levels in flowers/fruits, while SlDMR6-1 conserved the ability to fine-tune SA levels during pathogen infection of the plant vegetative tissues. Overall, this work not only corroborates a mechanism underlying SA homeostasis in plants, but also presents a promising strategy for engineering broad-spectrum and durable disease resistance in crops.

The target of rapamycin (TOR) pathway is a major regulator of growth in all eukaryotes, integrating energy, nutrient and stress signals into molecular decisions. By using large-scale MS-based metabolite profiling of primary, secondary and lipid compounds in combination with array-based transcript profiling, we show that the TOR protein not only regulates growth but also influences nutrient partitioning and central energy metabolism. The study was performed on plants exhibiting conditional down-regulation of AtTOR expression, revealing strong regulation of genes involved in pathways such as the cell cycle, cell-wall modifications and senescence, together with major changes in transcripts and metabolites of the primary and secondary metabolism. In agreement with these results, our morphological and metabolic analyses disclosed major metabolic changes leading to massive accumulations of storage lipids and starch. The implications of these data in the context of the general role of TOR in eukaryotic systems are discussed in parallel with the plant-specific aspects of TOR function. Finally, we propose a role for harnessing the plant TOR pathway by utilizing it as a potent metabolic switch, offering a possible route for biotechnological optimization of plant energy content and carbon partitioning for the production of bioenergy.

This review discusses recent advances in the synthesis, characterization and toxicity of metal oxide nanoparticles obtained mainly through biogenic (green) processes. The in vitro and in vivo toxicities of these oxides are discussed including a consideration of the factors important for safe use of these nanomaterials. The toxicities of different metal oxide nanoparticles are compared. The importance of biogenic synthesized metal oxide nanoparticles has been increasing in recent years; however, more studies aimed at better characterizing the potent toxicity of these nanoparticles are still necessary for nanosafely considerations and environmental perspectives. In this context, this review aims to inspire new research in the design of green approaches to obtain metal oxide nanoparticles for biomedical and technological applications and to highlight the critical need to fully investigate the nanotoxicity of these particles.

Cell wall storage polysaccharides (CWSPs) are found as the principal storage compounds in seeds of many taxonomically important groups of plants. These groups developed extremely efficient biochemical mechanisms to disassemble cell walls and use the products of hydrolysis for growth. To accumulate these storage polymers, developing seeds also contain relatively high activities of noncellulosic polysaccharide synthases and thus are interesting models to seek the discovery of genes and enzymes related to polysaccharide biosynthesis. CWSP systems offer opportunities to understand phenomena ranging from polysaccharide deposition during seed maturation to the control of source-sink relationship in developing seedlings. By studying polysaccharide biosynthesis and degradation and the consequences for cell and physiological behavior, we can use these models to develop future biotechnological applications.

A sustainable nanomaterial, cellulose nanofibril (CNF) was used to prepare aerogel sorbents to remove various contaminants in wastewater. A mussel-inspired coating strategy was used to introduce polydopamine onto the surface of CNFs, which were cross-linked with polyethylenimine (PEI) to form the aerogels. The synthetic procedure was optimized to achieve a minimal consumption of raw materials to produce a robust porous structure. The aerogels possessed a low density (25.0 mg/cm3), high porosity (98.5%) and shape recovery in air and water. Adsorption studies were conducted on two representative contaminants, Cu (II) and methyl orange (MO). The kinetic data obeyed the pseudo 2nd order kinetic model and the mechanism of adsorption could be described by the intra-particle diffusion model. The Langmuir model fitting yielded a maximum adsorption capacity of 103.5 mg/g and 265.9 mg/g for Cu (II) and MO, respectively. The effects of pH on the adsorption performance were evaluated, confirming that the aerogels can maintain a high adsorption capacity over a wide pH range.