Miracle-dz/UniFAR-FTUs huggingface dataset:
Estudo molecular de genótipos não usuais de rotavírus A em crianças com gastrenterite aguda da Região Metropolitana de Belém, Pará-Brasil (2008 a 2011)

The epidemiology of rotavirus A (RVA) infection is a complex phenomenon and subjected to variation due to its wide genetic diversity. Despite genotypic characteristics, the most prevalent genotypes globally are: G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] e G12P[8]. In Brazil, unusual genotypes are represented by genotypes that differ from the six most prevalent types found globally. This study aimed to conduct genetic analyses of rotavirus A unusual genotypes circulating in children with acute gastroenteritis in metropolitan area of Bélem, Pará, from 2008 to 2011. The samples were submitted to genomic amplification and nucleotide sequencing. Samples that were classified as unusual were selected for genotype constellation determination, as well as for phylogenetic and evolutionary analyses. Out 122 samples previously untyped, it was possible to obtain the genotypic combination in 106 (86.9%). It was detected usual genotypes: G1P[8] (n=18), G2P[4] (n=11), G3P[8] (n=1) and G12P[8] (n=6) and unusual genotypes: G3P[9] (n=1), G12P[6] (n=58) and G12P[9] (n=4). Infections by multiple genotypes were also detected. G3P[9] genotype showed constellation G3P[9]-I18-R3-C3-Mx-A19-N3-T3-E3-H6. Phylogentic analyses showed a closer relationship among VP7, VP1, NSP3, NSP4 and NSP5 genes with genes of animal origin, such as chiropter, alpaca, equine and simian. In addition, VP6 and NSP1 genes belong to novel genotypes I18 and A19, respectively. With respect G12P[6] strains, nucleotide sequencing of 30 samples demonstrated that 16 (53.3%), 13 (43.3%) and one sample (3.4%) displayed Wa-like (Wa-like G12), DS-1-like (DS-1-like G12) and Wa x DS-1-like (Wa x DS1-like G12) constellations, respectively. Genetic analyzes suggested that Wa-like G12P[6] and DS-1-like G12P[6] Brazilian strains are distinct evolutionarily in their VP7 and VP4 genes. Bayesian analysis of VP6 gene indicated that Wa-like G12 strains were related to G1P[8] strains, while DS-1-like G12 strains were related to G2P[4] strains. With regards to G12P[9] strains, four samples were classified into AU-1-like constellation. The genes of these samples were related to 18974/Brazil sample, being NSP1 gene related to bovine origin. The time of the most recent common ancestor for VP7 G12 dated from 1998, with estimated evolution rates of 2.5 × 10 −3 substitutions/site/year. This study confirms the importance of unusual genotypes and the role of animals in ecology and evolution of RVA, in addition to providing evolutionary data on G12 genotype. The emergence of unusual strains may eventually interfere with the efficacy of the RVA vaccine, which highlights the importance of continuous and prolonged monitoring, as well as the need for further studies to better determine the origin and evolution of this agent.
Biodiversity and medicinal uses of globe artichoke (Cynara scolymus L.) plant

Globe artichoke (Cynara scolymus L.) is a vegetable crop native of the Mediterranean basin and it is grown mainly for its immature flower buds. The edible parts of artichoke have important nutrition values to their content of inulin, fibers and minerals. Furthermore, artichoke is recognized as a medicinal plant where leaves and heads are rich source of polyphenolic compounds. It is recommended for the treatment of gallstones, liver disease or damage and poor liver function. The pharmaceutical properties of artichoke are linked to their special chemical composition, which includes high levels of polyphenols such as cynarin, along with its biosynthetic precursor chlorogenic acid. Globe artichoke is characterized by a wide range of biodiversity which represents a prerequisite for genetic improvement. However, there are many factors including biotic and abiotic stresses threatening the genetic resources of globe artichoke. Such factors could result in genetic erosion due to crop failure and loss of cultivars. Therefore, there is a great need to preserve the globe artichoke diversity for future genetic improvement. Because most cultivars are highly heterozygous, maintenance of globe artichoke germplasm in seed form is restricted. Otherwise, conservation in the field presents major drawbacks, which limit its efficacy and threaten the safety of germplasm conserved in this way. The application of biotechnology tools, i.e. plant tissue culture and molecular biology technique can provide reliable methods for supporting the exploitation and conservation of globe artichoke biodiversity. Furthermore, in vitro culture techniques could be used for the controlled production of artichoke secondary metabolites. This article discusses the biodiversity, conservation and nutritional and medicinal aspects of globe artichoke plant. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 39-54
Protein Binding to mRNA 3′ Isoforms

Here we describe CLIP‐READS, a technique that combines elements of crosslinking and immunoprecipitation (CLIP) and 3′ region extraction and deep sequencing (READS), to provide a genome‐wide map of mRNA 3′ isoform binding by a given messenger ribonucleoprotein (mRNP). In CLIP‐READS, cells are grown to logarithmic phase and are irradiated with UV light (254 nm) to form RNA–protein adducts. The protein−mRNA complexes are immunoprecipitated from cell extracts with an antibody specific to the protein of interest, after which the protein component is digested away with Pronase. Messenger RNAs are then subjected to 3′ READS. An input sample processed by 3′ READS in parallel allows for the relative quantification of isoform‐specific binding by the mRNP of interest. © 2019 by John Wiley & Sons, Inc.
The role of cell-cell interactions in population level dynamics of partial EMT states

Author(s): Paulson, Amanda Kay | Advisor(s): Gartner, Zev J | Abstract: The epithelial-mesenchymal transition (EMT) plays a key role in invasion and metastasis. Recent studies have demonstrated that many discrete states exist along the EMT spectrum, with partial or hybrid EMT phenotypes as the most metastatic. These states have variable plasticity, must compete for the proliferative niche, and also remodel each other’s microenvironment which modifies each other’s behavior. How the steady state distributions of these populations can be maintained, and how different EMT states compete and cooperate to define population-level phenotypes, has not been explored. In order to understand the contribution of this spectrum of states to the behavior of an entire heterogeneous population, we use a model transformed cell line that exhibits partial EMT cell states. In this cell line, a partial early-EMT state spontaneously gives rise to a later-EMT state with no evidence for reversion. The early-EMT cell population dominates the mixture while later-EMT cells exist in smaller fractions. We refer to this as a “top-heavy” lineage hierarchy to contrast it with healthy stem cell lineages where the populations is dominated by more differentiated progeny. A mathematical model suggests that in the top-heavy regime, differential proliferation limits the emergence of slower growing late-EMT cells or further differentiated progeny. The model also predicts perturbations that destabilize the top-heavy regime, and we validate the predictions experimentally. Intriguingly, we find that fully mesenchymal states emerge after destabilization of the top-heavy regime. These fully mesenchymal cells are more drug resistant, migratory, and grow in soft agar. Further, these cells dramatically modify their microenvironment which promotes a more mesenchymal and migratory phenotype in the more abundant partial EMT cells. These findings highlight the importance of studying the population-level dynamics that regulate cell-state proportions as well as the interactions among states that determine their collective behaviors.
The effect of chemical distances, physical distances, and the presence of sexuals on aggression in Cataglyphis desert ants

In social insects, non-nestmates interactions are typically agonistic and many factors may influence the degree of exhibited aggression. Two of these factors are the physical proximity between nests and the chemical dissimilarity between colonies’ chemical signatures. We studied a population sample of 43 colonies of Cataglyphis niger ants distributed along a transect of ∼4KM. This geographic distribution allowed us to examine correlations of aggression levels with physical and chemical distances. Ants were collected before mating season, when sexuals (unmated gynes and drones) could be found in nests. In our sample, colonies had either gynes or drones but never both. The presence of sexuals, therefore, was another factor we took into account in our behavioral analyses. Workers from nests with sexuals were more aggressive towards conspecifics than workers from nests where sexuals were absent. We also found those workers to be more vigorously active towards colonies with greater chemical distances, while workers from nests without sexuals were indifferent to chemical distances. We therefore concluded that ants are able to detect differences in chemical dissimilarity, but their aggression levels are mainly determined by other mechanisms. A possible additional mechanism is associative learning and long term memory of the chemical signatures of neighboring colonies. Such learning is supported by our finding that aggression is higher towards neighboring nests, which is in line with the previously reported ‘nasty neighbour’ effect in Cataglyphis ants. These results suggest that previous experience and learning of neural templates representing neighbors’ chemical cues is a stronger component than chemical dissimilarity in the mechanisms which determine aggression towards conspecifics in this species. We discuss possible explanations for the observed effect of the presence of sexuals on agonistic behavior and responsiveness to chemical distances.
Transcriptome analysis of Zi geese (Anser cygnoides) prehierarchical follicles and verification of related genes in arginine metabolic pathway

Arginine metabolism plays a pivotal role in the mammalian reproductive system by controlling various physiological processes of the reproductive organs including follicular development, ovulatory mechanisms and egg production. However little is known about the molecular mechanisms regulating arginine metabolism at early stages of folliculogenesis. The objective of the current study was to determine the arginine metabolic pathways in prehierarchical follicles of Zi geese through the Illumina Hiseq 2500 platform and their transcripts through the de novo assembly. In this study, five different stages of the geese prehierarchical follicles transcriptome were sequenced. A total of 31722729162 bp from 224929214 high quality clean sequences was obtained. There were 74.75% transcripts annotated pathways, and 106 unigenes were mapped in the Arginine and proline metabolism pathway. Combined with Gene Ontology (GO) functions, ArgE , NOS and ODC were selected as the candidate genes to explore the arginine metabolic pathway and determine their relative expression in the prehierarchical follicles of geese. The results showed that the three genes were expressed in all five prehierarchical stages of geese follicles, with the predominant expression in primary follicles (p ˂ 0.05), indicating promotion of follicular development. This study provides useful inclusive gene expression profiling information that would certainly provide basic theory for future research studies on follicular development in Zi geese.
Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases

Finding similar 3D structures is crucial for discovering potential structural, evolutionary, and functional relationships among proteins. As the number of known protein structures has dramatically increased, traditional methods can no longer provide the life science community the adequate informatics capability to conduct large-scale and complex analyses. A suite of highthroughput and accurate protein structure search and comparison methods is essential. To meet the needs of the community, we develop several bioinformatics methods for protein binding site comparison and global structure alignment. First, we developed an efficient protein binding site search that is based on extracting geometric features both locally and globally. Second, we developed an approach for accurate protein binding site comparison by applying a two-level heuristic process which progressively refines alignment results from coarse surface point level to accurate residue atom level. Finally, we introduced a parallel algorithm for global protein structure alignment by exploiting the parallelism of Graphics Processing Units (GPUs). Our findings can be applied in various research areas, such as prediction of protein interactions and screening in drug discoveries. The uniqueness of our methods is its ability to manipulate the big data of protein structures by integrating the featureand alignment-based search and comparison approaches together, thus enabling more efficient and accurate analysis of large-scale protein structures for the research community.
Current Advances in Red Blood Cell Generation Using Stem Cells from Diverse Sources

Blood transfusions hold an indispensable part in the modern healthcare system. Up to date, the blood supply is largely dependent on donations. Unfortunately, collecting the clinical-grade blood products has become a challenging mission due to accelerated population aging, which not only increases the need for blood transfusions but also decreases the number of healthy donors. Moreover, individuals with severe hematological abnormalities or rare blood phenotypes need alternative therapeutic approaches instead of conventional blood transfusion. In these aspects, the concept of in vitro/ex vivo production of blood cells has been emerging and many attempts have been focused on manufacturing mature erythrocytes, so-called red blood cells (RBCs), the most common and important component among the blood derivatives. In this review, we provide a general overview regarding the current strategies for generating RBCs from various stem cell sources including pluripotent stem cells (PSCs) as well as circulating blood stem cells and the remaining challenges that must be overcome prior to their practical application.
Single-cell radioluminescence microscopy with two-fold higher sensitivity using dual scintillator configuration

Radioluminescence microscopy (RLM) is an imaging technique that allows quantitative analysis of clinical radiolabeled drugs and probes in single cells. However, the modality suffers from slow data acquisition (10 – 15 minutes), thus critically affecting experiments with short-lived radioactive drugs. To overcome this issue, we suggest an approach that significantly accelerates data collection. Instead of using a single scintillator to image the decay of radioactive molecules, we sandwiched the radiolabeled cells between two scintillators. As proof of concept, we imaged cells labeled with [18F]FDG, a radioactive glucose popularly used in oncology to image tumors. Results show that the double scintillator configuration increases the microscope sensitivity by two-fold, thus reducing the image acquisition time by half to achieve the same result as the single scintillator approach. The experimental results were also compared with Geant4 Monte Carlo simulation to confirm the two-fold increase in sensitivity with only minor degradation in spatial resolution. Overall, these findings suggest that the double scintillator configuration can be used to perform time-sensitive studies such as cell pharmacokinetics or cell uptake of short-lived radiotracers.
Characterization of a Novel Thrombin-like Enzyme, Globlase from the Venom of Gloydius blomhoffii (Japanese Mamushi)

Aims: To elucidate the coagulation mechanisms of a novel clotting factor isolated from Gloydius blomhoffii venom, its hydrolytic activity on various substrates were examined. Furthermore the primary structure was determined and compared with the other snake venom components. Methodology: A thrombin-like enzyme was isolated from the crude venom of G. blomhoffii by DE52 Cellulose and CM52 Cellulose column chromatography. Enzyme activity was measured by using synthetic substrates (arginine esters, MCA-substrates and 3-(Acyloxy)-4-nitrobenzoic acid). Effect on fibrinogen was detected with bovine and human fibrinogen. Isoelectric point and molecular mass were measured by polyacrylamide gel electrophoresis and MALDI-TOF-MS. Amino acid sequence was decided with a protein sequencer by analyzing enzymatically cleaved peptides. Results: A clotting factor was found to be homologous as indicated by a single band on SDS-PAGE, and the final preparation was named as globlase. Molecular mass of this enzyme was determined to be 13,876.36 Da and the isoelectric point was 8.8. Globlase showed arginine ester hydrolytic activity, and specificity for substrates of thrombin. Proteolytic activity and phospholipase A2 (PLA2) activity were not detected. Complete amino acid sequence analysis indicated that the primary structure of globlase is similar to PLA2. However the aspartic acid which exists in the active site of PLA2 was found to be substituted by glutamine. Conclusion: It was shown in our current investigation that globlase is a novel thrombin-like enzyme isolated from G. blomhoffii venom. It was revealed that this enzyme had structure unlike the serine-protease such as the other thrombin-like enzymes.
WAVELET ANALYSIS OF SHORT GLOBULAR HOMOLOGOUS PROTEINS IN MESOPHILE AND THERMOPHILE PROKARYOTES

This study looked to identify features related to thermal stability and function in the amino acid chains of short globular proteins from mesophile and thermophile species, within the constraint that the protein fold to perform a specific function. To do so 540 homologous pairs of proteins were studied. The amino acid chains were converted to hydrophobicity signals by assigning a hydropathy score to each residue in the polypeptide. The hydrophobicity signals were passed through a wavelet packet transform and the resulting spectra analyzed. Bootstrapping was used to generate a control data set to determine if the true ordering of amino acids codes for a non-random fluctuation in hydropathy along the length of the polypeptide. A method to relate the spectral characteristics to the function of a protein making use of gene ontologies was developed as a proof of concept. As a group, mesophile and thermophile proteins have very similar total power. However, on a protein-toprotein basis the thermophile contains a greater total power in 489 of the 540 pairs (90.56%). The hydrophobicity scale used in this study is strongly correlated with Gibbs free energy. The total power of a protein is also strongly correlated to the Gibbs free energy, so that the thermophile protein contains a greater free energy than its corresponding mesophile partner. It has been noted in the experimental literature that thermophile proteins are stabilized by increasing their Gibbs free energy. The statistical measures skew and kurtosis were adapted so that a spectrum of skew and kurtosis values were generated for each protein. These values indicate that the fluctuation in hydropathy is non random and position dependent. Thermophile proteins have larger power at frequency bands 21 through 31 (average intervals of 100 to 77 amino acids), and 44 to 56 (on average 46 to 19 amino acids), which may contribute to their having greater total power in 90.56% of the pairs. Increases to the fluctuation in hydropathy within certain lengths throughout the total amino acid chain of a protein may be a means of raising the temperature at which a protein denatures.
Prolonging Rotation of Chinese Fir to over 25 Years Could Maintain a Better Soil Status in Subtropical China

Although Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important species for wood production in subtropical China, it serious declines in soil nutrients and timber productivity in plantations have been reported, probably caused by successive rotation and inappropriate cutting time. Although the significant effect of stand age on soil properties has been widely recognized, research on soil enzymes and microbial communities is relatively rare. In this study, assuming that short rotation period is one important reason for soil degradation, we measured soil physicochemical properties, microbial community composition, and enzyme activity in 3-, 15-, 25- and 45-year Chinese fir forests in Jiangxi province of China. Soil organic carbon (SOC) content decreased from 3-year to 25-year stands and then increased in 45-year stands. Despite the significant relationship between SOC and the abundance of total phospholipid fatty acids (PLFAs), no notable changes in the abundance of PLFAs were detected with increasing tree ages, except for the abundances of arbuscular mycorrhizal fungi (AMF) which were significantly higher in 25-year stands. However, the ratios of gram-positive to gram-negative bacteria (G+/G−) and fungi to bacteria (F/B) both decreased with increasing stand age. 45-year stands showed the highest activities of both phosphatase and β-glucosidase. Total potassium (TK) content and net N mineralization rate both had significant links with soil microbial community structure. Collectively, our study emphasized that stand age could significantly affect soil physicochemical properties and the microbial community. In general, 25-year stands showed poorer soil status compared to that of 45-year stands. Thus, the cutting age of Chinese fir should be increased to over 25 years to maintain a better soil status.
Culturing Simpler and Bacterial Wilt Suppressive Microbial Communities from Tomato Rhizosphere

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to Ralstonia solanacearum inoculation. The disease progress indicated that the upland MM9 1st transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 1st transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family Enterobacteriaceae of Proteobacteria was the dominant member (86.76%) of the total population of which genus Enterobacter composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.