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Exponential model for population growth (exponential model) is a foundation to evaluate population dynamics in Population Ecology field. Here, we used a didactic experiment to teach exponential model for an undergraduate course of Population Ecology. We built nine populations of weevils with three different initial population sizes: eight, 16, and 32 individuals with three replicates each. We provided equal food resource availability, and counted their population sizes weekly for 12 weeks. We estimated the intrinsic growth rate (i.e., r parameter), by trials and errors with an exponential model build in an Excel spreadsheet. The population growth rate (i.e., dN/dt parameter) was estimated using r values. Replicates with eight and 16 individuals reached the highest values of r and dN/dt, while replicates with 32 individuals reached the lowest values. Beyond of exponential model, two density dependency issues acting in populations were observed. First, in the lowest initial population sizes we observed the effect of demographic stochasticity acting in both r and dN/dt in one of the three populations. Second, we observed the intraspecific competition reducing r values in largest initial populations. Therefore, we highlight the importance of didactic experiment into learning exponential model in Population Ecology course, both for teaching and learning practices.

Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.

Oysters are sessile, filter-feeding bivalve molluscs widely distributed in estuarine and coastal habitats worldwide. They constitute a valuable resource for fisheries and extensive aquaculture and provide essential ecological services. Yet, their genetic diversity and distribution remain understudied. The variability in shell morphology complicates species classification, which is influenced by environmental and genetic factors. Although molecular phylogenetics research has refined oyster taxonomy and identified approximately 100 extant species, numerous taxonomic uncertainties persist. In the present study, we aimed to document the occurrence of small flat oysters of the genus Ostrea along the Mediterranean coastal areas of Liguria and Sardinia (Italy). Specifically, 16S rRNA sequence data were used to identify Ostrea species. Our findings offer novel insights into the O. stentina species complex and O. neostentina, a new species in the Mediterranean coastal areas of Italy. The study data further our understanding of Ostrea species diversity, distribution, and evolutionary patterns.

Abstract Background Melanoma is one of the deadliest tumors in the world. Early detection is critical for first-line therapy in this tumor pathology and it remains challenging due to the need for histological analysis to ensure correctness in diagnosis. Therefore, multiple computer-aided diagnosis (CAD) systems working on melanoma images were proposed to mitigate the need of a biopsy. However, although the high global accuracy is declared in literature results, the CAD systems for the health fields must focus on the lowest false negative rate (FNR) possible to qualify as a diagnosis support system. The final goal must be to avoid classification type 2 errors to prevent life-threatening situations. Another goal could be to create an easy-to-use system for both physicians and patients. Results To achieve the minimization of type 2 error, we performed a wide exploratory analysis of the principal convolutional neural network (CNN) architectures published for the multiple image classification problem; we adapted these networks to the melanoma clinical image binary classification problem (MCIBCP). We collected and analyzed performance data to identify the best CNN architecture, in terms of FNR, usable for solving the MCIBCP problem. Then, to provide a starting point for an easy-to-use CAD system, we used a clinical image dataset (MED-NODE) because clinical images are easier to access: they can be taken by a smartphone or other hand-size devices. Despite the lower resolution than dermoscopic images, the results in the literature would suggest that it would be possible to achieve high classification performance by using clinical images. In this work, we used MED-NODE, which consists of 170 clinical images (70 images of melanoma and 100 images of naevi). We optimized the following CNNs for the MCIBCP problem: Alexnet, DenseNet, GoogleNet Inception V3, GoogleNet, MobileNet, ShuffleNet, SqueezeNet, and VGG16. Conclusions The results suggest that a CNN built on the VGG or AlexNet structure can ensure the lowest FNR (0.07) and (0.13), respectively. In both cases, discrete global performance is ensured: 73% (accuracy), 82% (sensitivity) and 59% (specificity) for VGG; 89% (accuracy), 87% (sensitivity) and 90% (specificity) for AlexNet.

Myrmecophaga tridactyla Linnaeus, 1758, Giant Anteater, is a very sensitive species in the Quadrilátero Ferrífero, a region of the Brazilian state of Minas Gerais responsible for a large part of the country’s iron ore production. Information on the occurrence of this species in the area is limited to literature reviews, data papers, and interviews. Here, we present the first record of M. tridactyla from the Reserva Particular do Patrimônio Natural Poço Fundo (a natural heritage private reserve) and what is likely to be only the fifth record from the Quadrilátero Ferrífero region. We highlight the importance of larger, connected areas for the long-term survival of this threat-ened species.

Cognitive abilities tend to decline with aging, with variation between individuals, and many studies seek to identify genetic biomarkers that more accurately anticipate risks related to pathological aging. We investigated the influence of BDNF, NTRK2, and FNDC5 single nucleotide polymorphisms (SNPs) on the cognitive performance of young and older adults with contrasting educational backgrounds. We addressed three questions: (1) Is education associated with reduced age-related cognitive decline? (2) Does the presence of SNPs explain the variation in cognitive performance observed late in life? (3) Is education differentially associated with cognition based on the presence of BDNF, NTRK2, or FNDC5 polymorphisms? We measured the cognitive functions of young and older participants, with lower and higher education, using specific and sensitive tests of the Cambridge Automated Neuropsychological Test Assessment Battery. A three-way ANOVA revealed that SNPs were associated with differential performances in executive functions, episodic memory, sustained attention, mental and motor response speed, and visual recognition memory and that higher educational levels improved the affected cognitive functions. The results revealed that distinct SNPs affect cognition late in life differentially, suggesting their utility as potential biomarkers and emphasizing the importance of cognitive stimulation that advanced education early in life provides.

Cholecystokinin 8 (CCK8) is an entero-octapeptide that participates in crosstalk with components of intestinal immunity via the CCK receptor (CCKR), but its role in modulation of the IgA response is not fully known under physiological conditions. Male eight-week-old BALB/c mice each were intraperitoneally injected once during 7 days with CCK8, devazapide (CCKR1 antagonist), L365,260 (CCKR2 antagonist) or vehicle (sham group). In intestinal lavages, total and secretory IgA (SIgA) were determined by ELISA; in lamina propria, IgA+ B lymphocytes and IgA+ plasma cells were analyzed by flow cytometry; mRNA levels of polymeric immunoglobulin receptor (pIgR) in epithelial cells and α chain, interleukins (ILs) in lamina propria cells were assessed by qRTPCR. Regarding the sham conditions, IgA+ plasma-cell percentage and IL-2, IL-5, IL-10 and transforming growth factor-β (TGF-β) mRNA levels were either increased by CCK8 or decreased by both CCKR antagonists. For IgA/SIgA responses, IL-4/IL-6 mRNA levels were decreased by all drugs and pIgR mRNA was increased by CCK8 and reduced by L365,260. IgA+ B cell percentage and α chain mRNA levels were elicited by CCK8 and L365,260. Data suggested a presumable differential role of CCK/CCKR on the IgA-response; outcome of L365,260 on the elicitation of IgA+ B cells and α chain mRNA needs further examination.

Currently, the antioxidants (AOs) used in foods are mainly synthetic, often questioned on health grounds. So, the need for innocuous natural AOs has increased in last years. The peanut skin (PS) is an industrial by-product of low added value, but rich in bioactive phenolic compounds. In this study, the antioxidant capacity of a PS extract (PSE) was examined in a chia oil-based mayonnaise stored during six months (25 °C). The mayonnaise was made using chia oil (68% w/w) added with PSE (2 mg/g fat) and without any AO (control). For the storage test, 30 g were placed in 100 mL amber bottles and at 2, 4 and 6 months the oily phase was extracted (chloroform: methanol). Peroxide index (PI), acidity index (AI), K232, K270, p-Anisidine (pAnV) and TOTOX values were measured. Moreover, the presence of 2,4 heptadienal and 3,5-octadiene-2-one was analyzed by static headspace GC-MS. At the end of the assay, PI, AI, K232, K270, and pAnV for control and PSE mayonnaises were 74.7 and 13.4 meq O2/kg oil; 2.4 and 2.0 mg KOH/kg oil, 10 and 3.55, 1.34 and 0.64, 3.7 and 0.98, respectively. The TOTOX value of the control was approximately six times higher than PSE mayonnaise. 2,4 Heptadienal and 3,5-octadiene-2-one were not detected at initial time but in the control treatment at the end reached 3.75 and 2.15 µg/g, respectively. Differently, in PSE mayonnaise, 3,5-octadiene-2-one was undetected and 2,4 Heptadienal was 0.83 µg/g. In conclusion, PSE represents a potential natural AO to preserve the oxidative stability of chia oil-based mayonnaise.

[This corrects the article DOI: 10.1371/journal.ppat.1010631.].

Primary cilia are sensory membrane protrusions whose dysfunction causes ciliopathies. INPP5E is a ciliary phosphoinositide phosphatase mutated in ciliopathies like Joubert syndrome. INPP5E regulates numerous ciliary functions, but how it accumulates in cilia remains poorly understood. Herein, we show INPP5E ciliary targeting requires its folded catalytic domain and is controlled by four conserved ciliary localization signals (CLSs): LLxPIR motif (CLS1), W383 (CLS2), FDRxLYL motif (CLS3) and CaaX box (CLS4). We answer two long-standing questions in the field. First, partial CLS1-CLS4 redundancy explains why CLS4 is dispensable for ciliary targeting. Second, the essential need for CLS2 clarifies why CLS3-CLS4 are together insufficient for ciliary accumulation. Furthermore, we reveal that some Joubert syndrome mutations perturb INPP5E ciliary targeting, and clarify how each CLS works: (i) CLS4 recruits PDE6D, RPGR and ARL13B, (ii) CLS2-CLS3 regulate association to TULP3, ARL13B, and CEP164, and (iii) CLS1 and CLS4 cooperate in ATG16L1 binding. Altogether, we shed light on the mechanisms of INPP5E ciliary targeting, revealing a complexity without known parallels among ciliary cargoes.

Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype. As the name suggests, the Red River Hog is a wild member of the pig family living in Africa, in particular through the West and Central African rainforest. To date, very few studies have analysed the gut microbiota of Red River Hogs (RRHs) both housed under controlled conditions and in wild habitats. This study analysed the intestinal microbiota and the distribution of Bifidobacterium species in five Red River Hog (RRH) individuals (four adults and one juvenile), hosted in two different modern zoological gardens (Parco Natura Viva, Verona, and Bioparco, Rome) with the aim of disentangling the possible effects of captive different lifestyle and host genetics. Faecal samples were collected and studied both for bifidobacterial counts and isolation by means of culture-dependent method and for total microbiota analysis through the high-quality sequences of the V3–V4 region of bacterial 16S rRNA. Results showed a host-specific bifidobacterial species distribution. Indeed, B. boum and B. thermoacidophilum were found only in Verona RRHs, whereas B. porcinum species were isolated only in Rome RRHs. These bifidobacterial species are also typical of pigs. Bifidobacterial counts were about 106 CFU/g in faecal samples of all the individuals, with the only exception for the juvenile subject, showing 107 CFU/g. As in human beings, in RRHs a higher count of bifidobacteria was also found in the young subject compared with adults. Furthermore, the microbiota of RRHs showed qualitative differences. Indeed, Firmicutes was found to be the dominant phylum in Verona RRHs whereas Bacteroidetes was the most represented in Roma RRHs. At order level, Oscillospirales and Spirochaetales were the most represented in Verona RRHs compared with Rome RRHs, where Bacteroidales dominated over the other taxa. Finally, at the family level, RRHs from the two sites showed the presence of the same families, but with different levels of abundance. Our results highlight that the intestinal microbiota seems to reflect the lifestyle (i.e., the diet), whereas age and host genetics are the driving factors for the bifidobacterial population.

In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.

Habitat fragmentation has been shown to be constantly growing and increasingly affecting the conservation of species that require large areas for their populations to subsist, as is the case for most large animals. In Minas Gerais, there are 45 species threatened with extinction in the Brazilian Red List and for most mammal species there is not yet sufficient data on their populations and distributions, which makes it difficult to understand their conservation status. To understand the composition of medium and large mammals in two Private Natural Heritage Reserves (RPPNs) in the Quadrilátero Ferrífero of Minas Gerais (Cata Branca and Córrego Seco), in a transition zone between the Atlantic Forest and the Cerrado, a camera trapping survey of mastofauna was carried out between November 2019 and May 2020. The combined RPPNs have a rich diversity with 20 species of medium and large mammals and provide a fundamental service for the protection of animals threatened with extinction, in addition to harbouring important species for the maintenance of local ecosystems. However, they are areas with a strong anthropic impact and have a lower richness than some other reserves also located in the Quadrilátero Ferrífero, especially Cata Branca, which had a lower richness than Córrego Seco.

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

About twenty molecules sharing 1H-chromeno[3,2-c]pyridine as the scaffold and differing in the degree of saturation of the pyridine ring, oxidation at C10, 1-phenylethynyl at C1 and 1H-indol-3-yl fragments at C10, as well as a few small substituents at C6 and C8, were synthesized starting from 1,2,3,4-tetrahydro-2-methylchromeno[3,2-c]pyridin-10-ones (1,2,3,4-THCP-10-ones, 1) or 2,3-dihydro-2-methyl-1H-chromeno[3,2-c]pyridines (2,3-DHPCs, 2). The newly synthesized compounds were tested as inhibitors of the human isoforms of monoamine oxidase (MAO A and B) and cholinesterase (AChE and BChE), and the following main SARs were inferred: (i) The 2,3-DHCP derivatives 2 inhibit MAO A (IC50 about 1 μM) preferentially; (ii) the 1,2,3,4-THCP-10-one 3a, bearing the phenylethynyl fragment at C1, returned as a potent MAO B inhibitor (IC50 0.51 μM) and moderate inhibitor of both ChEs (IC50s 7–8 μM); (iii) the 1H-indol-3-yl fragment at C10 slightly increases the MAO B inhibition potency, with the analog 6c achieving MAO B IC50 of 3.51 μM. The MAO B inhibitor 3a deserves further pharmacological studies as a remedy in the symptomatic treatment of Parkinson’s disease and neuroprotectant for Alzheimer’s disease. Besides the established neuroprotective effects of MAO inhibitors, the role of MAOs in tumor insurgence and progression has been recently reported. Herein, antiproliferative assays with breast (MCF-7), colon (HCT116) and cisplatin-resistant ovarian (SK-OV-3) tumor cells revealed that the 10-indolyl-bearing 2,3,4,10-THCP analog 6c exerts anti-tumor activity with IC50s in the range 4.83–11.3 μM.

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer in the world. Single nucleotide variants (SNVs) in miRNA and genes encoding proteins of the miRNA synthesis complex (SC) may affect the processing of drugs used in the treatment of ALL, resulting in treatment-related toxicities (TRTs). We investigated the role of 25 SNVs in microRNA genes and genes encoding proteins of the miRNA SC, in 77 patients treated for ALL-B from the Brazilian Amazon. The 25 SNVs were investigated using the TaqMan® OpenArray™ Genotyping System. SNVs rs2292832 (MIR149), rs2043556 (MIR605), and rs10505168 (MIR2053) were associated with an increased risk of developing Neurological Toxicity, while rs2505901 (MIR938) was associated with protection from this toxicity. MIR2053 (rs10505168) and MIR323B (rs56103835) were associated with protection from gastrointestinal toxicity, while DROSHA (rs639174) increased the risk of development. The rs2043556 (MIR605) variant was related to protection from infectious toxicity. SNVs rs12904 (MIR200C), rs3746444 (MIR499A), and rs10739971 (MIRLET7A1) were associated with a lower risk for severe hematologic toxicity during ALL treatment. These findings reveal the potential for the use of these genetic variants to understand the development of toxicities related to the treatment of ALL in patients from the Brazilian Amazon region.

A soil polluted by waste motor oil (WMO) is inhibiting organic matter mineralization and caused losing its fertility. An alternative solution is to enrich soil and a plant to eliminate WMO at concentration value lower than 4400 ppm, maximum value accepted by the Mexican environmental regulation called NOM-138-SEMARNAT/SSA1-2003 (NOM-138). The objective of this research was to treat a soil polluted by 35,000 ppm of WMO with Phaseolus vulgaris inoculated with Azotobacter vinelandii and Paenibacillus polymyxa to reduce the WMO´s concentration at lower value than the maximum accepted by the NOM-138. The variable responses for recovering soil ‘fertility of this experiment was a) the initial and final concentration of WMO by Soxhlet, and b) for P. vulgaris the percentage (%) of germination, the phenology: height of plant, length of root; and biomass: aereal and radical fresh/dry weight at seedlings and reflooring stages. Experimental data were analyzed by Tukey 0.05%. Results showed that soil enriched to facilitate that P. vulgaris with A. vinelandii and P. polymyxa at e-flowering, could reducing ARA until 1152 ppm, lower concentration than the maximum allowed by NOM-138 for recovering soil´s fertility.

We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids-Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid-on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.

Phosphate fertilization is indispensable for carrot cultivation, as it contributes to plant development, formation of marketable roots and higher yields. In this context, the objective of this study was to evaluate the production and nutritional efficiency of carrot cultivars under phosphate fertilization. The experiments were carried out from July to November 2016 and from June to October 2017, at the Rafael Fernandes experimental farm, District of Alagoinha, Mossoró, RN, Brazil. The experimental design was in randomized blocks, in a 4×4 factorial scheme with 4 replicates. The treatments consisted of the combination of carrot cultivars (Brasília, Planalto, Suprema and Nativa) with phosphorus (P) doses (0, 90, 180 and 270 kg ha-1 P2O5). The characteristics analyzed were: P content in the diagnostic leaf, plant dry matter, plant height, marketable and total yields, and the classification of cultivars for efficiency and response to phosphate fertilization. The increments promoted by phosphate fertilization were 64% in plant height, 444% in dry matter and 284% in marketable yield. The maximum marketable yield was obtained with doses from 186.8 to 243.5 kg ha-1, depending on the cultivar. The Native cultivar was classified as more efficient in the use of P.

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding. Author summary In Eukaryotic cells, DNA epigenetic modifications play an important role in gene expression and regulation, and protein recognition. In this work we investigate the physical implications of cytosine 5-hydroxymethylation on DNA, its structural and flexibility differences with methylated and unmodified cytosine using molecular dynamics, biophysical experiments and NMR spectroscopy. In particular the effect of hydroxyl group on free energy of nucleosome and Methyl binding Protein (MBD) binding, comparing in silico and experimental data to shed light on the effect of the reduced flexibility and the direct protein-DNA recognition.

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

3D Representation Sharing (3dRS) is a web-based tool designed to share biomolecular structure representations, including 4D ensembles derived from Molecular Dynamics (MD) trajectories. The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers. The web tool allows an easy upload of structures and trajectories in different formats. The 3D representation, powered by NGL viewer, offers an interactive display with smooth visualization in modern web browsers. Multiple structures can be loaded and superposed in the same scene. 1D sequences from the loaded structures are presented and linked to the 3D representation. Multiple, pre-defined 3D molecular representations are available. The powerful NGL selection syntax allows the definition of molecular regions that can be then displayed using different representations. Important descriptors such as distances or interactions can be easily added into the representation. Trajectory frames can be explored using a common video player control panel. Trajectories are efficiently stored and transferred to the NGL viewer thanks to an MDsrv-based data streaming. The server design offers all functionalities in one single web page, with a curated user experience, involving a minimum learning curve. Extended documentation is available, including a gallery with a collection of scenes. The server requires no registration and is available at https://mmb.irbbarcelona.org/3dRS.

Multiple prediction models for risk of in-hospital mortality from COVID-19 have been developed, but not applied, to patient cohorts different to those from which they were derived. The MEDLINE, EMBASE, Scopus, and Web of Science (WOS) databases were searched. Risk of bias and applicability were assessed with PROBAST. Nomograms, whose variables were available in a well-defined cohort of 444 patients from our site, were externally validated. Overall, 71 studies, which derived a clinical prediction rule for mortality outcome from COVID-19, were identified. Predictive variables consisted of combinations of patients′ age, chronic conditions, dyspnea/taquipnea, radiographic chest alteration, and analytical values (LDH, CRP, lymphocytes, D-dimer); and markers of respiratory, renal, liver, and myocardial damage, which were mayor predictors in several nomograms. Twenty-five models could be externally validated. Areas under receiver operator curve (AUROC) in predicting mortality ranged from 0.71 to 1 in derivation cohorts; C-index values ranged from 0.823 to 0.970. Overall, 37/71 models provided very-good-to-outstanding test performance. Externally validated nomograms provided lower predictive performances for mortality in their respective derivation cohorts, with the AUROC being 0.654 to 0.806 (poor to acceptable performance). We can conclude that available nomograms were limited in predicting mortality when applied to different populations from which they were derived.

On 1 April 2022, the AlfaCrux CubeSat was launched by the Falcon 9 Transporter-4 mission, the fourth SpaceX dedicated smallsat rideshare program mission, from Space Launch Complex 40 at Cape Canaveral Space Force Station in Florida into a Sun-synchronous orbit at 500 km. AlfaCrux is an amateur radio and educational mission to provide learning and scientific benefits in the context of small satellite missions. It is an opportunity for theoretical and practical learning about the technical management, systems design, communication, orbital mechanics, development, integration, and operation of small satellites. The AlfaCrux payload, a software-defined radio hardware, is responsible for two main services, which are a digital packet repeater and a store-and-forward system. In the ground segment, a cloud-computing-based command and control station has been developed, together with an open access online platform to access and visualize the main information of the AlfaCrux telemetry and user data and experiments. It also becomes an in-orbit database reference to be used for different studies concerned with, for instance, radio propagation, attitude reconstruction, data-driven calibration algorithms for satellite sensors, among others. In this context, this paper describes the AlfaCrux mission, its main subsystems, and the achievements obtained in the early orbit phase. Scientific and engineering assessments conducted with the spacecraft operations to tackle unexpected behaviors in the ground station and also to better understand the space environment are also presented and discussed.

Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum.

Cyperus difformis L. is a Cyperaceae, annual, of natural occurrence in marshy environments in southern Brazil, considered a weed in irrigated rice crops. Studies on its development are scarce, especially regarding its cycle and thermal requirements. Therefore, the objective of this work was to determine the base temperature, the thermal sum and the duration of the different sub-periods of the biological cycle of the species. The experiment was carried out at the Campus of the Universidade Federal de Santa Maria – UFSM, Santa Maria, Rio Grande do Sul, in four sowing seasons. In a completely delineated design and factorial scheme involving five soil water conditions (water depth and 50% soil water retention capacity [WRC]) from the sowing, water depth and 50% WRC introduced 21 days after emergence and 100% WRC during the whole cycle, with six repetitions each. Each experimental unit consisted of a cultivated in pot plant with 11 L capacity filled with soil. The cycle of the plants was subdivided into the sowing-emergence sub-periods, emergence-emission of the floral tassel and emission of the floral-maturing physiological tassel, being estimated the thermal requirements for the species. The conditions of the soil water condition the base temperature, the sum of the degree-days and the duration of the species cycle. The base temperature varies for each treatment, the sum of degrees-day decreases with the water deficit and the plants under flood accelerate the biological cycle.

The extensive use of antibiotics has contributed to the current antibiotic resistance crisis. Livestock infections of Salmonella spp, Clostridium spp. and E. coli antimicrobial-resistant bacteria represent a public threat to human and animal health. To reduce the incidence of these zoonoses, essential oils (EOs) could be effective antibiotic alternatives. This study aims at identifying EOs safe for use, effective both in complementary therapy and in the environmental sanitization of intensive farming. Natural products were chemo-characterized by gas chromatography. Three S. Typhimurium, three C. perfringens and four E. coli strains isolated from poultry and swine farms were used to assess the antimicrobial properties of nine EOs and a modified GR-OLI (mGR-OLI). The toxicity of the most effective ones (Cinnamomum zeylanicum, Cz; Origanum vulgare, Ov) was also evaluated on porcine spermatozoa and Galleria mellonella larvae. Cz, Ov and mGR-OLI showed the strongest antimicrobial activity; their volatile components were also able to significantly inhibit the growth of tested strains. In vitro, Ov toxicity was slightly lower than Cz, while it showed no toxicity on G. mellonella larvae. In conclusion, the study confirms the importance of evaluating natural products to consolidate the idea of safe EO applications in reducing and preventing intensive livestock infections.

The essential oils (EOs) of Origanum compactum and Satureja montana chemotyped (CT) at carvacrol, two Thymus vulgaris CT at thujanol and thymol, and Hydrolates (Hys) of S. montana and Citrus aurantium var. amara were chosen for studying their bactericidal efficacy against few phytobacterial pathogens. The Minimal Inhibitory Concentration (MIC) and Bactericidal Concentration (MBC) were found by microdilution assay. The essential oils of O. compactum (MBC 0.06% v/v), T. vulgaris CT thymol (MBC 0.06% v/v), and Hy of C. aurantium (MBC 6.25% v/v) resulted in being the most effective against Erwinia amylovora; thus, they were used as starting concentrations for ex vivo assays. Despite the great in vitro effectiveness, the disease incidence and the population dynamic ex vivo assays showed no significant results. On the other hand, EO of O. compactum and Hy of C. aurantium (at 0.03% and 4.5% v/v, respectively) showed resistance induction in tomato plants against Xanthomonas vesicatoria infections; both treatments resulted in approximately 50% protection. In conclusion, EOs and Hys could be promising tools for agricultural defense, but further studies will be necessary to stabilize the EOs emulsions, while Hys application could be an effective method to prevent bacterial diseases when used as resistance inducer by pre-transplantation treatment at roots.

Summary: Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities. Remarkably, the protein is also capable of template-dependent de novo DNA synthesis, i.e., DNA-priming activity, thereby breaking the long-standing dogma that replicative DNA polymerases require a pre-existing primer for DNA synthesis. We suggest that piPolBs are involved in self-replication of pipolins and may also contribute to bacterial DNA damage tolerance. : Redrejo-Rodríguez et al. report and characterize a DNA polymerase group (piPolB) from the B family that can perform primer-independent DNA replication. PiPolBs are encoded by Pipolins, diverse self-replicating genetic elements that are widespread among bacterial phyla and in mitochondria. Keywords: DNA replication, translesion synthesis, primer-independent DNA synthesis, de novo DNA synthesis, family B DNA polymerase, self-replicating mobile element, DNA damage

Abstract Background Global literature describes differences in the incidence of gastric cancer among populations. For instance, Europeans have lower incidence rates of gastric cancer in relation to Latin and Asian populations, particularly Korean and Japanese populations. However, only a few studies have been able to verify the occurrence of gastric cancer in admixed populations with high interethnic degree mix, such as the Brazilian Amazon region. Results We observed an increase in European ancestry in the control group compared to the case group (47% vs. 41%). Using increments of 10%, compared to categorical distribution of European ancestry in the sample, we found a difference in the contribution between cases and controls (p = 0.03). Multiple logistic regression was performed to determine the influence of European ancestry in susceptibility to gastric cancer in the sample. According to the adopted model, for each 10% increase in European ancestry, there is a 20% decrease chance of developing gastric cancer (P = 0.0121; OR = 0.81; 95% CI 0.54–0.83). Conclusion Overall, the results suggest that a greater contribution of European ancestry can be a protective factor for the development of gastric cancer in the studied Amazon population. It can help to establish protocols able to predict susceptibility to gastric cancer in admixed populations.

Bacillus virus Bam35 is the model Betatectivirus and member of the family Tectiviridae, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. Interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, which are known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein–protein interactions (PPIs) network for a tectivirus–host system by studying the Bam35–Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and high-throughput sequencing (Y2H-HTS). We generated and thoroughly analyzed a genomic library of Bam35′s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait–prey couples. Initial analysis of the raw data enabled the identification of over 4000 candidate interactions, which were sequentially filtered to produce 182 high-confidence interactions that were defined as part of the core virus–host interactome. Overall, host metabolism proteins and peptidases were particularly enriched within the detected interactions, distinguishing this host–phage system from the other reported host–phage PPIs. Our approach also suggested biological roles for several Bam35 proteins of unknown function, including the membrane structural protein P25, which may be a viral hub with a role in host membrane modification during viral particle morphogenesis. This work resulted in a better understanding of the Bam35–B. thuringiensis interaction at the molecular level and holds great potential for the generalization of the Y2H-HTS approach for other virus–host models.

High-risk neuroblastoma (HR-NB) still remains the most dangerous tumor in early childhood. For this reason, the identification of new therapeutic approaches is of fundamental importance. Recently, we combined the conventional pharmacological approach to NB, represented by cisplatin, with fendiline hydrochloride, an inhibitor of several transporters involved in multidrug resistance of cancer cells, which demonstrated an enhancement of the ability of cisplatin to induce apoptosis. In this work, we co-administrated acetazolamide, a carbonic anhydrase isoform IX (CAIX) inhibitor which was reported to increase chemotherapy efficacy in various cancer types, to the cisplatin/fendiline approach in SKNBE2 xenografts in NOD-SCID mice with the aim of identifying a novel and more effective treatment. We observed that the combination of the three drugs increases more than twelvefold the differences in the cytotoxic activity of cisplatin alone, leading to a remarkable decrease of the expression of malignancy markers. Our conclusion is that this approach, based on three FDA-approved drugs, may constitute an appropriate improvement of the pharmacological approach to HR-NB.

Summary: Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines. : Working as part of the NHLBI NextGen consortium, Panopoulos and colleagues report the derivation and characterization of 222 publicly available iPSCs from ethnically diverse individuals with corresponding genomic data including SNP arrays, RNA-seq, and whole-genome sequencing. This collection provides a powerful resource to investigate the function of genetic variants. Keywords: iPSCORE, iPSC, GWAS, molecular traits, physiological traits, cardiac disease, NHLBI Next Gen, LQT2, KCNH2, iPSC-derived cardiomyocytes

El propósito de esta investigación es describir dos nuevas especies de Chersodoma de Bolivia: Chersodoma filifolia y C. tarijensis. Ambas especies presentan hábito arbustivo de porte pequeño y cespitoso; se diferencian por el número de flores por capítulo, por el indumento de la hoja y por su distribución geográfica: Chersodoma filifolia habita en el centro de Bolivia y C. tarijensis en el extremo sur de Bolivia. Adicionalmente, se provee una clave para las especies bolivianas de género, una tabla comparativa entre las dos especies nuevas y las especies más afines y un mapa con la distribución de las dos especies nuevas.

The application of plant growth regulators can promote better development of the seedlings, essential for the success of fruit growing. The current study aims to evaluate the use of plant growth regulators in fig tree seedlings ‘Roxo de Valinhos’. The experiment was carried out in a suspended nursery covered with plastic, using rooted cuttings of the cultivar Roxo de Valinhos. Four applications were made with a commercial product, known as Stimulate®, at doses of 0, 50, 100, 150, and 200 mL L-1. Using a randomized block experimental design, the study was subdivided into plots (doses X days of the last application [after 0, 7, 14 and 21]). The following traits were evaluated: stem and root length; stem diameter; root volume; leaf number; leaf area; stem, leaf and root dry mass; specific leaf area, leaf weight ratio; leaf area ratio; and chlorophyll total. Results indicated that the product promoted greater seedlings development at a dose range from 100 to 150 mL L-1. Different dose levels did not vary according to the days after product application. Furthermore, using such technique enabled seedlings of higher quality and vigour.

The application of plant growth regulators can promote better development of the seedlings, essential for the success of fruit growing. The current study aims to evaluate the use of plant growth regulators in fig tree seedlings ‘Roxo de Valinhos’. The experiment was carried out in a suspended nursery covered with plastic, using rooted cuttings of the cultivar Roxo de Valinhos. Four applications were made with a commercial product, known as Stimulate®, at doses of 0, 50, 100, 150, and 200 mL L-1. Using a randomized block experimental design, the study was subdivided into plots (doses X days of the last application [after 0, 7, 14 and 21]). The following traits were evaluated: stem and root length; stem diameter; root volume; leaf number; leaf area; stem, leaf and root dry mass; specific leaf area, leaf weight ratio; leaf area ratio; and chlorophyll total. Results indicated that the product promoted greater seedlings development at a dose range from 100 to 150 mL L-1. Different dose levels did not vary according to the days after product application. Furthermore, using such technique enabled seedlings of higher quality and vigour.

Neuroblastoma (NB) is a heterogeneous developmental tumor occurring in childhood, which arises from the embryonic sympathoadrenal cells of the neural crest. Although the recent progress that has been done on this tumor, the mechanisms involved in NB are still partially unknown. Despite some genetic aberrations having been identified, the sporadic cases represent the majority. Due to its wide heterogeneity in clinical behavior and etiology, NB represents a challenge in terms of prevention and treatment. Since a definitive therapy is lacking so far, there is an urgent necessity to unveil the molecular mechanisms behind NB onset and progression to develop new therapeutic approaches. Long non-coding RNAs (lncRNAs) are a group of RNAs longer than 200 nucleotides. Whether lncRNAs are destined to become a protein or not, they exert multiple biological functions such as regulating gene expression and functions. In recent decades, different research has highlighted the possible role of lncRNAs in the pathogenesis of many diseases, including cancer. Moreover, lncRNAs may represent potential markers or targets for diagnosis and treatment of diseases. This mini-review aimed to briefly summarize the most recent findings on the involvement of some lncRNAs in NB disease by focusing on their mechanisms of action and possible role in unveiling NB onset and progression.

Equine genital squamous cell carcinomas (egSCCs) are among the most common equine tumors after sarcoids, severely impairing animal health and welfare. Equus caballus papillomavirus type 2 (EcPV2) infection is often related to these tumors. The aim of this study was to clarify the molecular mechanisms behind egSCCs associated with EcPV2 infection, investigating receptor activator of nuclear factor-kappa B ligand (RANKL) signaling in NF-kB pathway, together with the Wnt and IL17 signaling pathways. We analyzed the innate immune response through gene expression evaluation of key cytokines and transcription factors. Moreover, Ki67 index was assessed with immunohistochemistry. EcPV2-E6 DNA was checked, and viral presence was confirmed in 21 positive out to 23 cases (91%). Oncogene expression was confirmed in 14 cases (60.8%) for E6 and in 8 (34.7%) for E2. RANKL, nuclear factor kappa-light-chain-enhancer of activated B cells (NFKB)-p50, NFKBp65, interleukin (IL)-6, IL17, IL23p19, IL8, IL12p35, IL12p40, β-catenin (BCATN1), FOS like 1 (FOSL1), and lymphoid enhancer binding factor 1 (LEF1) showed a significant upregulation in tumor samples compared to healthy tissues. Our results describe an inflammatory environment characterized by the activation of RANKL/RANK and IL17 with the relative downstream pathways, and a positive modulation of inflammatory cytokines genes such as IL6 and IL8. Moreover, the increase of BCATN1, FOSL1, and LEF1 gene expression suggests an activation of both canonical and non-canonical Wnt signaling pathway that could be critical for carcinogenesis and tumor progression.

The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.

To overcome the lack of effective pharmacological treatments for high-risk neuroblastoma (HR-NB), the development of novel in vitro and in vivo models that better recapitulate the disease is required. Here, we used an in vitro multiclonal cell model encompassing NB cell differentiation stages, to identify potential novel pharmacological targets. This model allowed us to identify, by low-density RT-PCR arrays, two gene sets, one over-expressed during NB cell differentiation, and the other up-regulated in more malignant cells. Challenging two HR-NB gene expression datasets, we found that these two gene sets are related to high and low survival, respectively. Using mouse NB cisplatin-treated xenografts, we identified two genes within the list associated to the malignant stage (MCM2 and carbonic anhydrase 9), whose expression is positively correlated with tumor growth. Thus, we tested their pharmacological targeting as potential therapeutic strategy. We measured mice survival and tumor growth rate after xenografts of human NB treated with cisplatin in the presence of MCM2/carbonic anhydrase 9 inhibitors (ciprofloxacin and acetazolamide). MCM2 or carbonic anhydrase 9 inhibition significantly increased cisplatin activity, supporting their possible testing for NB therapy.

Chronic hepatitis B virus (HBV) infection may be reactivated by immunosuppressive drugs in patients with autoimmune inflammatory rheumatic diseases. This study evaluates HBV serum markers’ prevalence in rheumatic outpatients belonging to Spondyloarthritis, Chronic Arthritis and Connective Tissue Disease diagnostic groups in Italy. The study enrolled 302 subjects, sex ratio (M/F) 0.6, mean age ± standard deviation 57 ± 15 years, 167 (55%) of whom were candidates for immunosuppressive therapy. The Spondyloarthritis group included 146 subjects, Chronic Arthritis 75 and Connective Tissue Disease 83 (two patients had two rheumatic diseases; thus, the sum is 304 instead of 302). Ten subjects (3%) reported previous anti-HBV vaccination and tested positive for anti-HBs alone with a titer still protective (>10 IU/mL). Among the remaining 292 subjects, the prevalence of positivity for HBsAg, isolated anti-HBc, anti-HBc/anti-HBs, and any HBV marker was 2%, 4%, 18%, and 24%, respectively. A total of 26/302 (9%) patients with γ-globulin levels ≤0.7 g/dL were more frequently (p = 0.03455) prescribed immunosuppressive therapy, suggesting a more severe rheumatic disease. A not negligible percentage of rheumatic patients in Italy are at potential risk of HBV reactivation related to immunosuppressive therapy. Before starting treatment, subjects should be tested for HBV markers. Those resulting positive should receive treatment or prophylaxis with Nucleos (t) ides analogue (NUCs) at high barrier of resistance, or pre-emptive therapy, according to the pattern of positive markers. HB vaccination is recommended for those who were never exposed to the virus.

Abstract This study aimed to inventory the herbivore insects associated with Enterolobium contortisiliquum (Vell.) Morong (Fabaceae) fruits and seeds and their primary and secondary parasitoids. Six samples collected between May and October 2013 yielded 210 fruits, from which 326 insects of six orders emerged: Coleoptera, Hymenoptera, Lepidoptera, Diptera, Thysanoptera and Psocoptera. Coleoptera (five families) was represented by the seed consumers Merobruchus bicoloripes Pic, Stator sp. Bridwell (Chrysomelidae, Bruchinae), two species of Silvanidae, one species of Scolytinae (Curculionidae), one species of Nitidulidae and one species of Cerambycidae. The cerambycid was also observed forming galleries on fruit mesocarp. Immature individuals of Lepidoptera were observed consuming the fruits and seeds. From the seven Hymenoptera families, only two species were associated with Coleoptera, being Horismenus Walker sp. (Eulophidae) as parasitoid of M. bicoloripes, and Neoheterospilus falcatus (Marsh) (Braconidae) as parasitoid of Scolytinae. The Lepidoptera parasitoids represented four genera: Pseudophanerotoma Zetel, Chelonus Panzer (Braconidae), Orgilus Nees (Braconidae) and Goniozus Forster (Bethylidae). The host associations for the reared parasitoids Bracon Fabricius (Braconidae), Pimplinae sp. (Ichneumonidae) and Perilampus Forster (Perilampidae) were not confirmed. We obtained a single representative of Diptera (Tachinidae) associated with Lepidoptera hosts in this food web.

In Brazil, the improvement of papaya agribusiness is correlated to the estimation of genetic parameters and evaluation of agronomic descriptors; thus enabling less favourable areas for the development and implementation of papaya crops. Therefore, the current study aimed to evaluate quantitative descriptors and to estimate genetic parameters in genotypes of papaya grown under subtropical climate in the state of São Paulo. The experimental design was randomized in block. The experimental units were grouped into seven blocks of five plants each and three treatments, which consisted of three different varieties: Sunrise Solo, Tainung nº1 and local. The psychochemical properties were analysed for plant height; intersection height of first fruits; stem diameter; male, female and hermaphroditic flower percentage; fruit number per plant; production; yield; normal fruits percentage, carpeloid and pentandric fruits; pulp matter; pulp length; pulp diameter; pulp shape; pulp cavity; pulp thickness; peel performance; pulp performance; seeds performance; seeds number; soluble solids; pH; titratable acidity; ratio; technological index; ascorbic acid and reducing sugars. Furthermore, most agronomic descriptors showed high heritability; besides that, the varieties Sunrise Solo and Tainung nº1 performed the best results in Botucatu.

In Brazil, the improvement of papaya agribusiness is correlated to the estimation of genetic parameters and evaluation of agronomic descriptors; thus enabling less favourable areas for the development and implementation of papaya crops. Therefore, the current study aimed to evaluate quantitative descriptors and to estimate genetic parameters in genotypes of papaya grown under subtropical climate in the state of São Paulo. The experimental design was randomized in block. The experimental units were grouped into seven blocks of five plants each and three treatments, which consisted of three different varieties: Sunrise Solo, Tainung nº1 and local. The psychochemical properties were analysed for plant height; intersection height of first fruits; stem diameter; male, female and hermaphroditic flower percentage; fruit number per plant; production; yield; normal fruits percentage, carpeloid and pentandric fruits; pulp matter; pulp length; pulp diameter; pulp shape; pulp cavity; pulp thickness; peel performance; pulp performance; seeds performance; seeds number; soluble solids; pH; titratable acidity; ratio; technological index; ascorbic acid and reducing sugars. Furthermore, most agronomic descriptors showed high heritability; besides that, the varieties Sunrise Solo and Tainung nº1 performed the best results in Botucatu.

This protocol analyzes the direct interaction between two DNA-binding proteins by pull-down co-immunoprecipitation. One of the proteins is overexpressed in E. coli as HA-tagged recombinant protein and cell-free extracts are immunoprecipitated in HA-affinity resin. Cell extracts are treated with nuclease to degrade DNA and RNA, which rules out nucleic acid-mediated indirect interaction. Then, a second immunoprecipitation step is performed using the purified putative partner protein. Co-immunoprecipitated proteins can be detected either by Coomassie Blue staining and/or Western blotting (WB) if a specific antibody is available. Moreover, many DNA/RNA binding proteins are highly electropositive, which can hinder WB under standard conditions, as has been shown in histones and histone-like proteins. In this case, we show that the high isoelectric point of the putative partner results in a poor transfer. Tips to troubleshot WB transfer of highly electropositive DNA-binding proteins are provided.

Mango is quite popular among tropical fruits, and has traits of a fast-expanding market. There is a huge variety of mango cultivars and their potential should be studied in order to be introduced in new producing regions with favourable edaphoclimatic characteristics for planting. The current study aimed to evaluate mango productive performance under subtropical conditions in the state of São Paulo, Brazil. The experiment was conducted with 'Espada Vermelha', 'Keitt' and 'Palmer' cultivars grafted onto rootstock 'Espada' over three crop cycles 2012-2013, 2013-2014 and 2014-2015. The experimental design was a randomized complete block, consisting of 3x3 factorial design, in which the first factor corresponds to the cultivars and the second factor to the evaluated crop cycles, with 10 replications and one plant per plot. The following variables were evaluated: number of fruits per panicle, number of fruits per plant, panicles percentage to the full aborted fruits, fruit fresh weight, production, yield, canopy volume, production efficiency and crop seasonality. Data analysis by Tukey test and Pearson´s correlation coefficients. Among the evaluated cultivars, Palmer has stood out with the best productive performance under the experiment conditions in the three evaluated crop cycles. The seasonal availability of cultivars should be explored so that there are fruit productions over a longer period of time. Correlations among productive traits varies according to the cultivar.Â

Mango is quite popular among tropical fruits, and has traits of a fast-expanding market. There is a huge variety of mango cultivars and their potential should be studied in order to be introduced in new producing regions with favourable edaphoclimatic characteristics for planting. The current study aimed to evaluate mango productive performance under subtropical conditions in the state of São Paulo, Brazil. The experiment was conducted with 'Espada Vermelha', 'Keitt' and 'Palmer' cultivars grafted onto rootstock 'Espada' over three crop cycles 2012-2013, 2013-2014 and 2014-2015. The experimental design was a randomized complete block, consisting of 3x3 factorial design, in which the first factor corresponds to the cultivars and the second factor to the evaluated crop cycles, with 10 replications and one plant per plot. The following variables were evaluated: number of fruits per panicle, number of fruits per plant, panicles percentage to the full aborted fruits, fruit fresh weight, production, yield, canopy volume, production efficiency and crop seasonality. Data analysis by Tukey test and Pearson´s correlation coefficients. Among the evaluated cultivars, Palmer has stood out with the best productive performance under the experiment conditions in the three evaluated crop cycles. The seasonal availability of cultivars should be explored so that there are fruit productions over a longer period of time. Correlations among productive traits varies according to the cultivar.Â

This survey aimed to characterize a Urochloa humidicola methanol extract regarding the presence of secondary metabolites classes and to determine its bromatological composition. U. humidicola samples were dried under shade, milled on a 2-mm sieve by a Willey mill. The solution obtained was filtered using filter paper and concentrated in a rotary evaporator under reduced pressure; the concentrated residue was then placed in an open vessel to complete solvent removal using continuous air flow dryers. Phytochemical prospection tests and bromatological composition analyses were performed on the dry methanol extract, and the results were compared to in natura U. humidicola. The methanol extract had 10.2% CP and 35% EE and in natura U. humidicola had 5.17% CP and 1.57% EE, with a difference (P < 0.05) of 5% by Fisher's test. In natura U. humidicola had 75.59% NDF, 40.77% ADF, 38.82% HEM, 29.93% CEL, and 7.19% LIG. Methanol extraction by cold maceration reduced the LIG (0.17%) and CEL (0.21%) contents as only soluble constituents were extracted. A phytochemical assay was positive for the presence of saponins, tannins, alkaloids, non-protein amino acids, carbohydrates, cardiac glycosides, steroids, tripernoids, catechins, and saccharides and was negative for the presence of flavonoids and purines. The U. humidicola methanol extract possesses traits that allow its use as a phytogenic and natural additive.

This survey aimed to characterize a Urochloa humidicola methanol extract regarding the presence of secondary metabolites classes and to determine its bromatological composition. U. humidicola samples were dried under shade, milled on a 2-mm sieve by a Willey mill. The solution obtained was filtered using filter paper and concentrated in a rotary evaporator under reduced pressure; the concentrated residue was then placed in an open vessel to complete solvent removal using continuous air flow dryers. Phytochemical prospection tests and bromatological composition analyses were performed on the dry methanol extract, and the results were compared to in natura U. humidicola. The methanol extract had 10.2% CP and 35% EE and in natura U. humidicola had 5.17% CP and 1.57% EE, with a difference (P < 0.05) of 5% by Fisher's test. In natura U. humidicola had 75.59% NDF, 40.77% ADF, 38.82% HEM, 29.93% CEL, and 7.19% LIG. Methanol extraction by cold maceration reduced the LIG (0.17%) and CEL (0.21%) contents as only soluble constituents were extracted. A phytochemical assay was positive for the presence of saponins, tannins, alkaloids, non-protein amino acids, carbohydrates, cardiac glycosides, steroids, tripernoids, catechins, and saccharides and was negative for the presence of flavonoids and purines. The U. humidicola methanol extract possesses traits that allow its use as a phytogenic and natural additive.

Many foods are susceptible to fungal contamination. Grains, such as peanuts, are commonly affected, with consequences including compromised integrity and infeasibility for human and animal consumption. Furthermore, some fungi may pose a health risk, largely due the production of mycotoxins. Among these, aflatoxins produced by Aspergillus flavus and A. parasiticus produce various carcinogenic, teratogenic, immunosuppressive, hepatotoxic and nephrotoxic effects. Molecular techniques have been used to identify and distinguish fungal species in foods. The objective of this study was molecular detection of Aspergillus species in peanut samples collected in stores in Maringá-PR, by amplification of fungal genetic material with specific primers for the intergenic spacer aflR-aflJ and later cutting with restriction enzymes. Of the 50 peanut samples analyzed, 27 were positive for the intergenic spacer aflR-aflJ, seven of which were identified as Aspergillus flavus. Our results demonstrate that peanuts sold in retail stores in this region have potential for contamination with toxigenic fungi.