Showing papers by "Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto published in 2018"

Metagenomic Approaches for Understanding New Concepts in Microbial Science.

Abstract: Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of “hidden” genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.

Field methods for sampling tree height for tropical forest biomass estimation

Abstract: Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally-derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally-derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with estimates using measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even remarkably limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.

On the relationship between fire regime and vegetation structure in the tropics

Abstract: We assessed data from 11 experiments examining the effects of the timing and/or frequency of fire on tropical forest and/or savanna vegetation structure over one decade or more. The initial 'control treatment' in many such cases consisted of previously cleared land. This is as opposed to natural vegetation subject to some sort of endogenous fire regime before the imposition of fire treatments. Effects of fire on fractional foliar cover are up to 10-fold greater when clearing pre-treatments are imposed. Moreover, because many of the 'classic' fire trials were initialised with applied management questions in mind, most have also used burning regimes much more frequent and/or severe than those occurring in the absence of human activity. Once these factors are taken into account, our modelling analysis shows that nonanthropogenic fire regimes serve to reduce canopy vegetative cover to a much lower extent than has previously been argued to be the case. These results call into question the notion that fire effects on tropical vegetation can be of a sufficient magnitude to maintain open-type savanna ecosystems under climatic/soil regimes otherwise sufficient to give rise to a more luxurious forest-type vegetation cover.

Chemical composition and antibacterial activity of essential oils from Citrus aurantifolia leaves and fruit peel against oral pathogenic bacteria.

Abstract: Tooth decay is a major public health problem which affects a large number of people in several countries. Even though more than 700 bacterial species have been detected in the oral cavity, Streptococcus and Lactobacillus stand out as the genera that cause tooth decay and other periodontal diseases. In this study, essential oils from Citrus aurantifolia leaves (CL-EO) and fruit peel (CP-EO) were obtained by hydrodistillation by a Clevenger-type apparatus whereas their chemical composition was analyzed by gas chromatography-flame ionization detector (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Limonene (77.5 %), linalool (20.1 %), citronellal (14.5 %) and citronellol (14.2 %) were the main constituents found in the essential oils from C. aurantifolia leaves and fruit peel. Antibacterial activity of essential oils was evaluated in terms of its minimum inhibitory concentration (MIC) values by the broth microdilution method in 96-well microplates. Both CL-EO and CP-EO displayed some activity against all oral pathogens under investigation; MIC values ranged from 20 to 200 µg/mL. CL-EO and CP-EO not only had promising activity against Streptococcus mutans (MIC = 20 µg/mL) and Lactobacillus casei (31.25 µg/mL), but also displayed antibacterial activity against all studied cariogenic bacteria. Efficacy of essential oils against S. mutans and L. casei is noteworthy and should be further investigated.

N-Ethyl Pentylone (Ephylone) Intoxications: Quantitative Confirmation and Metabolite Identification in Authentic Human Biological Specimens.

Abstract: N-ethyl pentylone (ephylone) has been identified as the most recent novel stimulant to emerge into the arena of evolving novel psychoactive substances (NPS). Due to its novelty, information regarding case reports with associated quantitative confirmations, biotransformation pathways, and identified unique metabolites will assist the scientific community in understanding the implications of the emergence and risks associated with N-ethyl pentylone use. Authentic blood specimens (n = 26) submitted as part of toxicological death investigations or drugged driving casework tested positive for N-ethyl pentylone, and were quantitatively analyzed by liquid chromatography tandem mass spectrometry (LC-MS-MS). N-ethyl pentylone concentrations ranged from 12 to 1,200 ng/mL, with mean (±standard deviation) and median concentrations of 313 (±366) and 125 ng/mL, respectively, excluding one case measured at 50,000 ng/mL. N-ethyl pentylone was often found in combination with other drugs of abuse and NPS, include a variety of novel opioids including fentanyl analogs. Oral fluid specimens (n = 5), collected from recreational drug users at a dance music festival, were quantitatively analyzed using LC-MS-MS. Concentrations ranged from 12.6 to 1,377 ng/mL. Additional analysis was performed to characterize the metabolic profile of N-ethyl pentylone using human liver microsomes (HLM), followed by confirmation of the presence of the proposed metabolites in a subset of the blood specimens and oral fluid specimens. Metabolomic analysis was performed using a liquid chromatograph quadrupole time-of-flight mass spectrometer (LC-QTOF), followed by data processing using MetabolitePilot™ software. In vivo verification of in vitro HLM-generated metabolites resulted in the confirmation of four metabolites. Reduction of the beta-ketone to an alcohol resulted in the most prominent metabolite found in the authentic specimens, and its uniqueness to N-ethyl pentylone leads to this metabolite being an appropriate biomarker to determine N-ethyl pentylone ingestion. This is the first study to report N-ethyl pentylone concentrations and to characterize the metabolic profile of N-ethyl pentylone.

Pyrazines from bacteria and ants: convergent chemistry within an ecological niche

Abstract: Ants use pheromones to coordinate their communal activity. Volatile pyrazines, for instance, mediate food resource gathering and alarm behaviors in different ant species. Here we report that leaf-cutter ant-associated bacteria produce a family of pyrazines that includes members previously identified as ant trail and alarm pheromones. We found that L-threonine induces the bacterial production of the trail pheromone pyrazines, which are common for the host leaf-cutter ants. Isotope feeding experiments revealed that L-threonine along with sodium acetate were the biosynthetic precursors of these natural products and a biosynthetic pathway was proposed.

Why Could the Nature of Surface Facets Lead to Differences in the Activity and Stability of Cu2O-Based Electrocatalytic Sensors?

Abstract: By a combination of theoretical and experimental design, we unraveled the effect of {111} and {100} surface facets on the electrocatalytic sensing activities and stabilities of metal oxides by employing Cu2O crystals as a model substrate and glucose as the analyte. We started by theoretically investigating the potential energy curves for the glucose interaction with the Cu2O {111} and {100} surface facets. We found that the glucose interaction energy was significantly higher for the {100} facets than for the {111} facets. Then, we experimentally observed that their electrocatalytic sensing performance displayed shape-dependent behavior. While the catalytic activities followed the order cubes > cuboctahedrons > octahedrons, their stabilities showed the opposite trend. The higher catalytic activity enabled by the {100} facets is explained by their stronger interaction with glucose. On the other hand, the higher stability allowed by the {111} facets is justified by their lower concentration of oxygen vacanci...

The impact of early Quaternary climate change on the diversification and population dynamics of a South American cactus species

Abstract: AIM: Climatic oscillations have been suggested to promote speciation and changes in species distributions, mostly in connection with the Last Glacial Maximum (LGM). However, the LGM is just the most recent of the 20+ glacial‐interglacial periods that characterise the Quaternary. Here, we investigate the role of climatic changes and geomorphological features in shaping the evolution, distribution and population dynamics of the South American cactus Cereus hildmannianus. LOCATION: South‐eastern South America. METHODS: We built a large fossil‐calibrated phylogeny for cacti (family Cactaceae), comprising 128 species distributed in all subfamilies, using a Bayesian relaxed clock. We used the results to derive a secondary calibration for a population‐level phylogeny in C. hildmannianus. We amplified two plastid (trnQ‐5′rps16 and psbJ‐petA) and one nuclear marker (PhyC) for 24 populations. We estimated population dynamics, ancestral areas, and species distribution models to infer the clade's evolutionary history in time and space. RESULTS: Our results show a major population divergence of C. hildmannianus at c. 2.60 Ma, which is strikingly coincident with the transition of the Pliocene–Pleistocene and onset of Quaternary glaciations. This was followed by a complex phylogeographic scenario involving population expansions across ecologically diverse regions. MAIN CONCLUSIONS: Contrary to the dominant research focus on the LGM, our study indicates a major impact of the first Quaternary glaciation on the distribution and population divergence of a South American plant species. Further intraspecific events seem related to successive climatic changes and geomorphology, including the development of the coastal plain and its peculiar diversity. We propose that the first Quaternary glaciation acted as a major evolutionary bottleneck, whereby many warm‐adapted lineages succumbed, while those that survived could diversify and better cope with subsequent climatic oscillations.

Human mitochondrial pyruvate carrier 2 as an autonomous membrane transporter

Abstract: The active transport of glycolytic pyruvate across the inner mitochondrial membrane is thought to involve two mitochondrial pyruvate carrier subunits, MPC1 and MPC2, assembled as a 150 kDa heterotypic oligomer. Here, the recombinant production of human MPC through a co-expression strategy is first described; however, substantial complex formation was not observed, and predominantly individual subunits were purified. In contrast to MPC1, which co-purifies with a host chaperone, we demonstrated that MPC2 homo-oligomers promote efficient pyruvate transport into proteoliposomes. The derived functional requirements and kinetic features of MPC2 resemble those previously demonstrated for MPC in the literature. Distinctly, chemical inhibition of transport is observed only for a thiazolidinedione derivative. The autonomous transport role for MPC2 is validated in cells when the ectopic expression of human MPC2 in yeast lacking endogenous MPC stimulated growth and increased oxygen consumption. Multiple oligomeric species of MPC2 across mitochondrial isolates, purified protein and artificial lipid bilayers suggest functional high-order complexes. Significant changes in the secondary structure content of MPC2, as probed by synchrotron radiation circular dichroism, further supports the interaction between the protein and ligands. Our results provide the initial framework for the independent role of MPC2 in homeostasis and diseases related to dysregulated pyruvate metabolism.

Functional characterization of a lytic polysaccharide monooxygenase from the thermophilic fungus Myceliophthora thermophila

Abstract: Thermophilic fungi are a promising source of thermostable enzymes able to hydrolytically or oxidatively degrade plant cell wall components. Among these enzymes are lytic polysaccharide monooxygenases (LPMOs), enzymes capable of enhancing biomass hydrolysis through an oxidative mechanism. Myceliophthora thermophila (synonym Sporotrichum thermophile), an Ascomycete fungus, expresses and secretes over a dozen different LPMOs. In this study, we report the overexpression and biochemical study of a previously uncharacterized LPMO (MtLPMO9J) from M. thermophila M77 in Aspergillus nidulans. MtLPMO9J is a single-domain LPMO and has 63% sequence similarity with the catalytic domain of NcLPMO9C from Neurospora crassa. Biochemical characterization of MtLPMO9J revealed that it performs C4-oxidation and is active against cellulose, soluble cello-oligosaccharides and xyloglucan. Moreover, biophysical studies showed that MtLPMO9J is structurally stable at pH above 5 and at temperatures up to 50°C. Importantly, LC-MS analysis of the peptides after tryptic digestion of the recombinantly produced protein revealed not only the correct processing of the signal peptide and methylation of the N-terminal histidine, but also partial autoxidation of the catalytic center. This shows that redox conditions need to be controlled, not only during LPMO reactions but also during protein production, to protect LPMOs from oxidative damage.

Factors influencing ocelot occupancy in Brazilian Atlantic Forest reserves

Abstract: Over 80% of Atlantic Forest remnants are <50 ha and protected areas are embedded in a matrix dominated by human activities, undermining the long-term persistence of carnivores. The ocelot (Leopardus pardalis) is an opportunistic species, but little is known about its tolerance to habitat alterations and the influence of other species on its occupancy in Atlantic Forest remnants. We used camera traps to assess ocelot occupancy in protected areas of Atlantic Forest in southeastern Brazil. We found a positive correlation between the occupancy of ocelots and top predators (jaguars, Panthera onca, and pumas, Puma concolor), and a weaker negative effect between the number of domestic dogs (Canis familiaris) detected and ocelot occupancy. Ocelot detection was higher at sites with more eucalyptus, suggesting that ocelots frequently use these areas. Better-protected areas surrounded by permeable matrices may be critical to the persistence of ocelots in the fragmented Atlantic Forest.

Mechanistic Insights and Controlled Synthesis of Radioluminescent ZnSe Quantum Dots Using a Microfluidic Reactor

Abstract: We describe the controlled colloidal synthesis and characterization of ZnSe quantum dots using a continuous-flow microfluidic reactor. A systematic investigation of the synthetic route reveals a po...

Brazil's government attacks biodiversity.

Abstract: To address the rapid and massive loss of biodiversity worldwide, scientific research must inform agile decision-making. The political leaders of Brazil, the country with the planet's greatest biological wealth ([ 1 ][1]), continue to undermine this goal. In 2001, citing the laudable objective of

Essential oils from Piper aduncum inflorescences and leaves: chemical composition and antifungal activity against Sclerotinia sclerotiorum

Abstract: Even though essential oils from Piper aduncum (Piperaceae) have different biological activities, little is known about their application to agricultural areas. White mold is a plant disease caused by the phytopathogen Sclerotinia sclerotiorum, which needs to be controlled by alternative measures. This study aimed at evaluating the effect of essential oils from P. aduncum leaves (PL-EO) and inflorescences (PI-EO) on the mycelial growth of S. sclerotiorum. Essential oils from P. aduncum were obtained by hydrodistillation by a Clevenger-type apparatus while their chemical composition was analyzed by GC-MS and GC-FID. Piperitone (23.4 %), myristicin (12.4 %), terpinen-4-ol (12.3 %), β-caryophyllene (7.2 %), α-humulene (6.9 %), germacrene-D (6.9 %) and dillapiol (6.3 %) were the main constituents found in oils from P. aduncum. The in vitro antifungal activity showed that PI-EO dose above 30 µL inhibited mycelial growth in 100 %, whereas PL-EO at 50 µL inhibited it in 98.74 %. This is the first report of the chemical composition of PI-EO and results suggest that the essential oils under evaluation have high potential to control the phytopathogenic fungus S. sclerotiorum.

Protein Engineering Strategies to Expand CRISPR-Cas9 Applications

Abstract: The development of precise and modulated methods for customized manipulation of DNA is an important objective for the study and engineering of biological processes and is essential for the optimization of gene therapy, metabolic flux, and synthetic gene networks. The clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 is an RNA-guided site-specific DNA-binding complex that can be reprogrammed to specifically interact with a desired DNA sequence target. CRISPR-Cas9 has been used in a wide variety of applications ranging from basic science to the clinic, such as gene therapy, gene regulation, modifying epigenomes, and imaging chromosomes. Although Cas9 has been successfully used as a precise tool in all these applications, some limitations have also been reported, for instance (i) a strict dependence on a protospacer-adjacent motif (PAM) sequence, (ii) aberrant off-target activity, (iii) the large size of Cas9 is problematic for CRISPR delivery, and (iv) lack of modulation of protein binding and endonuclease activity, which is crucial for precise spatiotemporal control of gene expression or genome editing. These obstacles hinder the use of CRISPR for disease treatment and in wider biotechnological applications. Protein-engineering approaches offer solutions to overcome the limitations of Cas9 and generate robust and efficient tools for customized DNA manipulation. Here, recent protein-engineering approaches for expanding the versatility of the Streptococcus pyogenes Cas9 (SpCas9) is reviewed, with an emphasis on studies that improve or develop novel protein functions through domain fusion or splitting, rational design, and directed evolution.

The Baurusuchidae vs Theropoda record in the Bauru Group (Upper Cretaceous, Brazil): a taphonomic perspective

Abstract: The Bauru Group is worldwide known due to its high diversity of archosaurs, especially that of Crocodyliformes. Recently, it has been suggested that the Crocodyliformes, especially the Baurusuchidae, were the top predators of the Bauru Group, based on their anatomical convergence with theropods and the dearth of those last ones in the fossil record of this geological group. Here, we erect the hypothesis that assumption is taphonomically biased. For this purpose, we made a literature survey on all the published specimens of Theropoda, Baurusuchidae and Titanosauria from all geological units from the Bauru Group. Also, we gathered data from the available literature, and we classified each fossil find under a taphonomic class proposed on this work. We show that those groups have different degrees of bone representativeness and different qualities of preservation pattern. Also, we suggest that baurusuchids lived close to or in the abundant flood plains, which explains the good preservation of their remains. Theropods and titanosaurs did not live in association with such environments and the quality of their preservation has thus been negatively affected. We support the idea that the Baurusuchidae played an important role in the food chain of the ecological niches of the Late Cretaceous Bauru Group, but the possible biases in their fossil record relative to Theropoda do not support the conclusion that baurusuchids outcompeted theropods. Rather, this taphonomic bias must be tackled first, which previous studies have not regarded.

Chemical composition and evaluation of antileishmanial and cytotoxic activities of the essential oil from leaves of Cryptocarya aschersoniana Mez. (Lauraceae Juss.)

Abstract: Leishmaniasis is an endemic disease caused by protozoa of the genus Leishmania, which affects around two million people worldwide. One major drawback in the treatment of leishmaniasis is the emergence of resistance to current chemotherapeutics. Medicinal and aromatic plants constitute a major source of natural organic compounds. In this study, the leaf essential oil of Cryptocarya aschersoniana was obtained by hydrodistillation in a Clevenger-type apparatus, and the chemical composition was analyzed by GC-MS and GC-FID. The essential oil of these species was predominantly constituted by monoterpene hydrocarbons (48.8%). Limonene (42.3%), linalool (9.7%) and nerolidol (8.6%) were the main constituents in the oil of C. aschersoniana. The in vitro activity of the oil was evaluated against the promastigote forms of Leishmania amazonensis, the causative agent of cutaneous leishmaniasis in humans. The essential oil of C. aschersoniana showed high activity against L. amazonensis promastigote forms (IC50 = 4.46 µg/mL), however, it also demonstrated a relatively high cytotoxicity on mouse peritoneal macrophages (CC50 = 7.71 µg/mL). This is the first report of the chemical composition and the leishmanicidal and cytotoxic activities of the leaf essential oil of C. aschersoniana.