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Background Organoid cultivation in suspension culture requires agitation at low shear stress to allow for nutrient diffusion, which preserves tissue structure. Multiplex systems for organoid cultivation have been proposed, but whether they meet similar shear stress parameters as the regularly used spinner flask and its correlation with the successful generation of brain organoids has not been determined. Results Here we used computational fluid dynamics (CFD) to simulate two multiplex culture conditions: steering plates on an orbital shaker and the use of a previously described bioreactor. The bioreactor had low speed and high shear stress regions that may affect cell aggregate growth, depending on volume, whereas the computed variables of the steering plates were closer to those of the spinning flask. Conclusion Our protocol improves the initial steps of the standard brain organoid formation, and the produced organoids displayed regionalized brain structures, including retinal pigmented cells. Overall, we conclude that suspension culture on orbital steering plates is a cost-effective practical alternative to previously described platforms for the cultivation of brain organoids for research and multiplex testing. Electronic supplementary material The online version of this article (10.1186/s12861-019-0183-y) contains supplementary material, which is available to authorized users.

Two general strategies have been proposed for microbial cellulose degradation: filamentous fungi and aerobic bacteria secrete uncomplexed cellulases, while some anaerobic bacteria produce a cell-associated and large extracellular multienzymatic complex called cellulosomes. By using a combination of 1D-blue native (BN)-PAGE, 2D-BN/SDS-PAGE, zymography, and LC-MS/MS methods, we demonstrate here that Streptomyces sp. I1.2, an aerobic bacterium associated with the land snail Achatina fulica, is able to degrade both crystalline cellulose and sugarcane bagasse through the production of cellulolytic multienzymatic complexes containing different combinations of cellobiohydrolases, endo-glucanases, xylanases, lytic polysaccharide monooxygenases (LPMOs), and peptidases. The assembly and subunit composition of these complexes is specifically affected by the carbon source, while the multienzymatic complexes produced after growth in crystalline cellulose are composed mainly by one cellobiohydrolase and chitinase, in which the complexes produced in response to sugarcane bagasse are more heterogeneous and contain cellobiohydrolases, endo-glucanases, pectate lyases, one LPMO, β-1,3-glucanases, and one xylanase. Our results suggest that Streptomyces sp. I1.2 displays an alternative mechanism for deconstruction of cellulose that depends upon a noncellulosomic association of catalytic subunits into high molecular weight complexes in order to achieve higher catalytic efficiencies.

The fungus Trichoderma reesei is a major producer of plant cell wall-degrading enzymes, such as cellulases and hemicellulases. These enzymes have been used to hydrolyze agro-industrial wastes in processes of second-generation biofuel production. The disaccharide lactose, the main by-product of dairy industry, is considered the most attractive substrate for the commercial production of cellulases by T. reesei. In the present work, it was shown that T. reesei, cultivated in media supplemented with either lactose or galactose, secrete proteins which behave as multi-enzymatic complexes. Blue Native electrophoresis (BN-PAGE) displayed two major bands which were specific or present in higher amounts in each secretome sample, complex I in galactose medium and complex II in lactose medium. The protein components of complexes I and II were identified by means of LC-MS/MS. The complexes were composed of different glycosyl hydrolases and predicted proteins related to biopolymer metabolism. Zymography coupled to BN-PAGE showed that T. reesei secretome presents higher cellulolytic and xylanolytic activities in lactose than in galactose-induced medium. The results presented here corroborate the existence of hydrolysis based on multi-enzymatic complexes in T. reesei secretome, as observed previously in other fungi, such as Trichoderma harzianum and Penicillium purpurogenum.

The protein composition of animal venoms is usually determined by peptide-centric proteomics approaches (bottom-up proteomics). However, this technique cannot, in most cases, distinguish among toxin proteoforms, herein called toxiforms, because of the protein inference problem. Top-down proteomics (TDP) analyzes intact proteins without digestion and provides high quality data to identify and characterize toxiforms. Denaturing top-down proteomics is the most disseminated subarea of TDP, which performs qualitative and quantitative analyzes of proteoforms up to ~30 kDa in high-throughput and automated fashion. On the other hand, native top-down proteomics provides access to information on large proteins (> 50 kDA) and protein interactions preserving non-covalent bonds and physiological complex stoichiometry. The use of native and denaturing top-down venomics introduced novel and useful techniques to toxinology, allowing an unprecedented characterization of venom proteins and protein complexes at the toxiform level. The collected data contribute to a deep understanding of venom natural history, open new possibilities to study the toxin evolution, and help in the development of better biotherapeutics.

Chromobacterium violaceum is a free-living bacillus with several genes that enables it survival under different harsh environments such as oxidative and temperature stresses. Here we performed a label-free quantitative proteomic study to unravel the molecular mechanisms that enable C. violaceum to survive oxidative stress. To achieve this, total proteins extracted from control and C. violaceum cultures exposed during two hours with 8 mM hydrogen peroxide were analyzed using GeLC-MS proteomics. Analysis revealed that under the stress condition, the bacterium expressed proteins that protected it from the damage caused by reactive oxygen condition and decreasing the abundance of proteins responsible for bacterial growth and catabolism. GeLC-MS proteomics analysis provided an overview of the metabolic pathways involved in the response of C. violaceum to oxidative stress ultimately aggregating knowledge of the response of this organism to environmental stress. This study identified approximately 1500 proteins, generating the largest proteomic coverage of C. violaceum so far. We also detected proteins with unknown function that we hypothesize to be part of new mechanisms related to oxidative stress defense. Finally, we identified the mechanism of clustered regularly interspaced short palindromic repeats (CRISPR), which has not yet been reported for this organism.

Background Culex quinquefasciatus is a hematophagous insect from the Culicidae family that feeds on the blood of humans, dogs, birds and livestock. This species transmits a wide variety of pathogens between humans and animals. The midgut environment is the first location of pathogen-vector interactions for blood-feeding mosquitoes and the expression of specific peptidases in the early stages of feeding could influence the outcome of the infection. Trypsin-like serine peptidases belong to a multi-gene family that can be expressed in different isoforms under distinct physiological conditions. However, the confident assignment of the trypsin genes that are expressed under each condition is still a challenge due to the large number of trypsin-coding genes in the Culicidae family and most likely because they are low abundance proteins. Methods We used zymography for the biochemical characterization of the peptidase profile of the midgut from C. quinquefasciatus females fed on sugar. Protein samples were also submitted to SDS-PAGE followed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis for peptidase identification. The peptidases sequences were analyzed with bioinformatics tools to assess their distinct features. Results Zymography revealed that trypsin-like serine peptidases were responsible for the proteolytic activity in the midgut of females fed on sugar diet. After denaturation in SDS-PAGE, eight trypsin-like serine peptidases were identified by LC-MS/MS. These peptidases have structural features typical of invertebrate digestive trypsin peptidases but exhibited singularities at the protein sequence level such as: the presence of different amino acids at the autocatalytic motif and substrate binding regions as well as different number of disulfide bounds. Data mining revealed a group of trypsin-like serine peptidases that are specific to C. quinquefasciatus when compared to the culicids genomes sequenced so far. Conclusion We demonstrated that proteomics approaches combined with bioinformatics tools and zymographic analysis can lead to the functional annotation of trypsin-like serine peptidases coding genes and aid in the understanding of the complexity of peptidase expression in mosquitoes.

Background Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy generates bewildering amounts of data whose biological interpretation is a challenge. Results Here we present a new algorithm, termed GO Explorer (GOEx), that leverages the gene ontology (GO) to aid in the interpretation of proteomic data. GOEx stands out because it combines data from protein fold changes with GO over-representation statistics to help draw conclusions. Moreover, it is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. Its usefulness is demonstrated by applying it to help interpret the effects of perillyl alcohol, a natural chemotherapeutic agent, on glioblastoma multiform cell lines (A172). We used a new multi-surfactant shotgun proteomic strategy and identified more than 2600 proteins; GOEx pinpointed key sets of differentially expressed proteins related to cell cycle, alcohol catabolism, the Ras pathway, apoptosis, and stress response, to name a few. Conclusion GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at http://pcarvalho.com/patternlab.

A continuous murine cell line (GRX) was obtained from fibrotic granulomas induced in C3H/HeN mice liver by experimental infection with Schistosoma mansoni. This anchorage-dependent line produces composite connective tissue/extracellular matrix, displays morphological characteristics of myofibroblasts, and can, under appropriate conditions, accumulate fat droplets. GRX cells produce viral particles of retrovirus type. We consider GRX cell line to be representative of liver connective tissue cells, responsible for fibroplasia in liver fibrotic and granulomatous reactions.