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The amount of available data is continuously growing. This phenomenon promotes a new concept, named big data. The highlight technologies related to big data are cloud computing (infrastructure) and Not Only SQL (NoSQL; data storage). In addition, for data analysis, machine learning algorithms such as decision trees, support vector machines, artificial neural networks, and clustering techniques present promising results. In a biological context, big data has many applications due to the large number of biological databases available. Some limitations of biological big data are related to the inherent features of these data, such as high degrees of complexity and heterogeneity, since biological systems provide information from an atomic level to interactions between organisms or their environment. Such characteristics make most bioinformatic-based applications difficult to build, configure, and maintain. Although the rise of big data is relatively recent, it has contributed to a better understanding of the underlying mechanisms of life. The main goal of this article is to provide a concise and reliable survey of the application of big data-related technologies in biology. As such, some fundamental concepts of information technology, including storage resources, analysis, and data sharing, are described along with their relation to biological data.

The genomes of two Penicillium strains were sequenced and studied in this study: strain 2HH was isolated from the digestive tract of Anobium punctatum beetle larva in 1979 and the cellulase hypersecretory strain S1M29, derived from strain 2HH by a long-term mutagenesis process. With these data, the strains were reclassified and insight is obtained on molecular features related to cellulase hyperproduction and the albino phenotype of the mutant. Both strains were previously identified as Penicillium echinulatum and this investigation indicated that these should be reclassified. Phylogenetic and phenotype data showed that these strains represent a new Penicillium species in series Oxalica, for which the name Penicillium ucsense is proposed here. Six additional strains (SFC101850, SFCP10873, SFCP10886, SFCP10931, SFCP10932 and SFCP10933) collected from the marine environment in the Republic of Korea were also classified as this species, indicating a worldwide distribution of this new taxon. Compared to the closely related strain Penicillium oxalicum 114-2, the composition of cell wall-associated proteins of P. ucsense 2HH shows five fewer chitinases, considerable differences in the number of proteins related to β-D-glucan metabolism. The genomic comparison of 2HH and S1M29 highlighted single amino-acid substitutions in two major proteins (BGL2 and FlbA) that can be associated with the hyperproduction of cellulases. The study of melanin pathways shows that the S1M29 albino phenotype resulted from a single amino-acid substitution in the enzyme ALB1, a precursor of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis. Our study provides important knowledge towards understanding species distribution, molecular mechanisms, melanin production and cell wall biosynthesis of this new Penicillium species.

In the course of 40 years of research, different strains of the filamentous fungus Penicillium echinulatum were employed in biotechnological studies at University of Caxias do Sul (UCS). This systematic literature review proposes a historic analysis of research findings on this fungus. Bearing this in mind, a methodology composed of four steps was adopted, including: (i) question formulation; (ii) repository election; (iii) paper filtration; and (iv) reading, organization, analysis and result interpretation. A total of 37 scientific articles and 12 theses and dissertations were referred. Based on the encountered papers, it was evidenced that most works citing P. echinulatum were published by a single research group at UCS. These studies focus mainly on lignocellulolytic enzymes, including enhancement of biotechnological processes and selection of hyper-productive lineages. Furthermore, P. echinulatum has also appeared in a variety of distinct studies. While the strains used in investigations by UCS are all derived from the 2HH wild isolate, other research groups report isolation of the same species from several different sources, including red algae, blue grape mold, ham, soil samples, cheese, and subglacial ice. Additionally, it was evidenced that integrative approaches are essential in modern taxonomy. In conclusion, this review allowed the construction of a global picture of P. echinulatum throughout science, emphasizing the promising biotechnological application in enzyme production. Keywords: Penicillium echinulatum. Lignocellulolytic Enzymes. Biotechnology. Fungi Resumo No decorrer de 40 anos de pesquisa, diferentes linhagens do fungo filamentoso Penicillium echinulatum foram empregadas em estudos na área da biotecnologia na Universidade de Caxias do Sul (UCS). Esta revisão sistemática da literatura propõe uma análise histórica das investigações científicas com esse fungo. Desse modo, uma metodologia composta de quatro etapas foi adotada, incluindo: (i) formulação de questões; (ii) seleção de repositórios; (iii) escolha de artigos; e (iv) leitura, organização, análise e interpretação de resultados. Um total de 37 artigos científicos e 12 teses e dissertações foram encontrados. Baseado nos artigos referidos foi evidenciado que grande parte dos trabalhos citando P. echinulatum foram publicados por um único grupo de pesquisa na UCS. O grande foco desses estudos são enzimas lignocelulolíticas, incluindo o aprimoramento de processos biotecnológicos e seleção de linhagens hiperprodutoras. Além disso, a espécie P. echinulatum também foi utilizada em outros estudos. Enquanto as linhagens utilizadas na UCS foram todas derivadas do isolado selvagem 2HH, nos outros grupos de pesquisa essa foi isolada em diferentes locais, incluindo algas vermelhas, videira, presunto, amostras de solo, queijo, e gelo subglacial. Adicionalmente, é salientado que uma abordagem taxonômica integrativa é essencial para a correta identificação dos isolados. Em conclusão, esta revisão sistemática permitiu a construção de um panorama global do P. echinulatum na ciência, dando ênfase na aplicação biotecnológica promissora de produção enzimática. Palavras-chave: Penicillium echinulatum. Enzimas Lignocelulolíticas. Biotecnologia. Fungos

Introdução: O advento das tecnologias de edição gênica permitem modificar organismos de modo específico. Desta forma, pode-se selecionar um organismo com potencial biotecnológico e melhorar a produção de suas enzimas e metabólitos. Objetivo: Este trabalho tem como objetivo elencar as técnicas de edição gênica utilizadas em fungos nos últimos 5 anos (2015-2019). Metodologia: Foi empregada uma revisão sistemática da literatura. Para tal, realizou-se as seguintes etapas: Elaboração das perguntas a serem respondidas; Determinação das strings de busca e dos bancos de dados; Definição de critérios de inclusão e exclusão de artigos; Seleção, extração, análise e interpretação dos resultados. Resultados: Obteve-se 32 artigos, os quais descrevem 9 técnicas de edição gênica: Mutagênese Clássica; Nocaute gênico induzido por transposon (TAGK); Integração mediada por enzimas de restrição (REMI); Meganucleases; Recombinação homóloga; Nucleases efetoras do tipo ativadoras de transcrição (TALENs); Nucleases dedo de Zinco (ZFNs); Transformação mediada por Agrobacterium tumefaciens (ATMT); e Clustered, regularly interspaced, short palindromic repeats associado a nuclease Cas9 (CRISPR/Cas9). Sendo CRISPR/Cas9 a tecnologia predominante nos trabalhos. Conclusão: Para realização da engenharia genética em um organismo, além da técnica de edição gênica é necessário a escolha de um vetor e de uma técnica de transformação, bem como conhecimento acerca do mecanismo de reparo de DNA na espécie-alvo. Existem diferentes tecnologias, com diferentes fundamentos, a escolha de qual técnica utilizar dependerá da avaliação da equipe e do objetivo da pesquisa.

Penicillium echinulatum 2HH is an ascomycete well known for its production of cellulolytic enzymes. Understanding lignocellulolytic and sugar uptake systems is essential to obtain efficient fungi strains for the production of bioethanol. In this study we performed a genome-wide functional annotation of carbohydrate-active enzymes and sugar transporters involved in the lignocellulolytic system of P. echinulatum 2HH and S1M29 strains (wildtype and mutant, respectively) and eleven related fungi. Additionally, signal peptide and orthology prediction were carried out. We encountered a diverse assortment of cellulolytic enzymes in P. echinulatum, especially in terms of β-glucosidases and endoglucanases. Other enzymes required for the breakdown of cellulosic biomass were also found, including cellobiohydrolases, lytic cellulose monooxygenases and cellobiose dehydrogenases. The S1M29 mutant, which is known to produce an increased cellulase activity, and the 2HH wild type strain of P. echinulatum did not show significant differences between their enzymatic repertoire. Nevertheless, we unveiled an amino acid substitution for a predicted intracellular β-glucosidase of the mutant, which might contribute to hyperexpression of cellulases through a cellodextrin induction pathway. Most of the P. echinulatum enzymes presented orthologs in P. oxalicum 114-2, supporting the presence of highly similar cellulolytic mechanisms and a close phylogenetic relationship between these fungi. A phylogenetic analysis of intracellular β-glucosidases and sugar transporters allowed us to identify several proteins potentially involved in the accumulation of intracellular cellodextrins. These may prove valuable targets in the genetic engineering of P. echinulatum focused on industrial cellulases production. Our study marks an important step in characterizing and understanding the molecular mechanisms employed by P. echinulatum in the enzymatic hydrolysis of lignocellulosic biomass.

Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 are well-known cellulase fungal producers. However, few studies addressing global mechanisms for gene regulation of these two important organisms are available so far. A recent finding that the 2HH wild-type is closely related to P. oxalicum leads to a combined study of these two species. Firstly, we provide a global gene regulatory network for P. echinulatum 2HH and P. oxalicum 114-2, based on TF-TG orthology relationships, considering three related species with well-known regulatory interactions combined with TFBSs prediction. The network was then analyzed in terms of topology, identifying TFs as hubs, and modules. Based on this approach, we explore numerous identified modules, such as the expression of cellulolytic and xylanolytic systems, where XlnR plays a key role in positive regulation of the xylanolytic system. It also regulates positively the cellulolytic system by acting indirectly through the cellodextrin induction system. This remarkable finding suggests that the XlnR-dependent cellulolytic and xylanolytic regulatory systems are probably conserved in both P. echinulatum and P. oxalicum. Finally, we explore the functional congruency on the genes clustered in terms of communities, where the genes related to cellular nitrogen, compound metabolic process and macromolecule metabolic process were the most abundant. Therefore, our approach allows us to confer a degree of accuracy regarding the existence of each inferred interaction.

Em laboratórios científicos são criados dados que necessitam de gerenciamento apropriado. Nesse sentido, surgiram os sistemas de informação aplicados para esses ambientes, desde cadernos físicos de anotação até plataformas eletrônicas personalizadas. Com o passar do tempo, os instrumentos físicos de anotação passaram a não ser mais suficientes para suprir a demanda existente em ambientes dinâmicos de pesquisa. Assim, este trabalho teve como objetivo apresentar uma revisão narrativa sobre os elementos-chave para o desenvolvimento de sistemas de informação eficientes aplicados a laboratórios científicos. Ainda, salienta-se que é imprescindível a construção de sistemas personalizados que consigam atender de forma específica as necessidades dos usuários. Este trabalho também exemplifica a contribuição de sistemas de informação digitais para pesquisas científicas nas áreas das ciências da vida e saúde. Para isso, os principais conceitos e fundamentos envolvidos no desenvolvimento de sistemas de informação aplicados à pesquisa científica são descritos, podendo ser utilizados para o planejamento de novas plataformas.

Background: The production of bioethanol using lignocellulosic feedstocks has proved to be a cutting-edge technology. However, this technology faces limitations such as cost and yield of enzymatic systems, required to degrade efficiently the polysaccharides of plant cell walls. Penicillium echinulatum 2HH is a widely studied ascomycete, known by its efficient cellulolytic cocktails. One strategy to improve the saccharification yields for commercial exploitation is the design of hypersecreting strains. However, molecular knowledge about the lignocellulolytic system of this specific fungus is scarce. Understanding both lignocellulolytic and sugar uptake systems is essential to obtain industrial strains with adequate efficiency for bioethanol production. Results: We report a comprehensive in silico characterization of CAZymes and sugar transporters of P. echinulatum 2HH. The CAZyome reveals an outstanding repertoire of enzymes involved in plant biomass degradation. Among them, we highlight the cellulolytic enzyme system whose genes are predominantly orthologous to P. oxalicum 114-2, demonstrating the high similarity of these phylogenetically related enzyme producers. We also report a LPMO-type enzyme of the AA16 family described for the first time in these fungi. In addition to the well-known high activity of ß-glucosidases, we found that coding genes for the AA16, GH5-4 and GH45 families comprehend the main differences in the cellulolytic complexes of P. echinulatum 2HH and P. oxalicum 114-2, when both are compared to commercial producers. Our phylogenetic analysis of the sugar transportome suggests that P. echinulatum 2HH diversity and specificity of STs include eight major families with specificity to different groups of sugars. Finally, our phylogenetic analyses enabled the identification of several iBGLs and STs potentially involved in the accumulation of intracellular cellodextrins.Conclusions: Overall, both CAZyome and sugar transportome of P. echinulatum revealed new insights into the mechanisms underlying a flexible and highly functional metabolism to degrade plant biomass. Peculiarities found in our study help to highlight the cellulolytic complex of P. echinulatum 2HH, contributing to the commercial ascendance of Penicillium spp. as cellulolytic enzyme producers. Furthermore, the first phylogenetic classification of STs and iBGLs shed new light into the role of these genes regarding the preferred carbon source during fungal growth. Along these lines, these iBGLs and STs comprise valuable gene targets to understand the regulatory mechanisms underlying cellulolytic enzymes and to design hypersecreting strains with adequate efficiency for bioethanol production in large-scale.

Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 are well-known cellulase fungal producers. However, few studies addressing global mechanisms for gene regulation of these two important organisms are available so far. A recent finding that the 2HH wild-type is closely related to P. oxalicum leads to a combined study of these two species. Firstly, we provide a global gene regulatory network for P. echinulatum 2HH and P. oxalicum 114-2, based on TF-TG orthology relationships, considering three related species with well-known regulatory interactions combined with TFBSs prediction. The network was then analyzed in terms of topology, identifying TFs as hubs, and modules. Based on this approach, we explore numerous identified modules, such as the expression of cellulolytic and xylanolytic systems, where XlnR plays a key role in positive regulation of the xylanolytic system. It also regulates positively the cellulolytic system by acting indirectly through the cellodextrin induction system. This remarkable finding suggests that the XlnR-dependent cellulolytic and xylanolytic regulatory systems are probably conserved in both P. echinulatum and P. oxalicum. Finally, we explore the functional congruency on the genes clustered in terms of communities, where the genes related to cellular nitrogen, compound metabolic process and macromolecule metabolic process were the most abundant. Therefore, our approach allows us to confer a degree of accuracy regarding the existence of each inferred interaction.

The current paper aims to perform data mining and artificial intelligence algorithms for genealogical data related to creole horses awarded in the “Expointer” competition, in order to uncover patterns and characteristics of winning animals. The dataset was obtained on a repository from the “Associacao Brasileira de Criadores de Cavalos Crioulos”. The techniques and algorithms employed were frequency analysis, means comparison and linear regression. In total, information from 1866 animals was extracted, which were organized in two groups according to the competition events of “Morfologia” and “Freio de Ouro”. The paternal lineage with better performance out of the champions from both events was Aculeo Vastago. In comparison, the more successful maternal branches demonstrated higher variability; Nevertheless, a dominance was observed for the families Torhuela, Che Pitanga 565 and BT Fuzarca in the “Morfologia” event. The mean comparison analyses revealed a statistically signifficant difference (p