BioPipeline Creator-a user-friendly Java-based GUI for managing and customizing biological data pipelines.

Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline. To solve this problem, we have developed the BioPipeline Creator, a user-friendly Java-based GUI that allows different software tools to be integrated into the repertoire while ensuring easy user interaction via an accessible graphical interface. Consisting of client and server software components, BioPipeline Creator provides an intuitive graphical interface that simplifies the use of various bioinformatics tools for users without advanced computer skills. It can run on less sophisticated devices or workstations, allowing users to keep their operating system without having to switch to another compatible system. The server is responsible for the processing tasks and can perform the analysis in the user's local or remote network structure. Compatible with the most important operating systems, available at https://github.com/allanverasce/bpc.git .

Red-on-Yellow Queen: Bio-Layer Interferometry Reveals Functional Diversity Within Micrurus Venoms and Toxin Resistance in Prey Species.

Snakes in the family Elapidae largely produce venoms rich in three-finger toxins (3FTx) that bind to the α 1 subunit of nicotinic acetylcholine receptors (nAChRs), impeding ion channel activity. These neurotoxins immobilize the prey by disrupting muscle contraction. Coral snakes of the genus Micrurus are specialist predators who produce many 3FTx, making them an interesting system for examining the coevolution of these toxins and their targets in prey animals. We used a bio-layer interferometry technique to measure the binding interaction between 15 Micrurus venoms and 12 taxon-specific mimotopes designed to resemble the orthosteric binding region of the muscular nAChR subunit. We found that Micrurus venoms vary greatly in their potency on this assay and that this variation follows phylogenetic patterns rather than previously reported patterns of venom composition. The long-tailed Micrurus tend to have greater binding to nAChR orthosteric sites than their short-tailed relatives and we conclude this is the likely ancestral state. The repeated loss of this activity may be due to the evolution of 3FTx that bind to other regions of the nAChR. We also observed variations in the potency of the venoms depending on the taxon of the target mimotope. Rather than a pattern of prey-specificity, we found that mimotopes modeled after snake nAChRs are less susceptible to Micrurus venoms and that this resistance is partly due to a characteristic tryptophan → serine mutation within the orthosteric site in all snake mimotopes. This resistance may be part of a Red Queen arms race between coral snakes and their prey.

Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants.

Synthetic biology has the potential to revolutionize biotechnology, public health, and agriculture. Recent studies have shown the enormous potential of plants as chassis for synthetic biology applications. However, tools to precisely manipulate metabolic pathways for bioproduction in plants are still needed. We used bacterial allosteric transcription factors (aTFs) that control gene expression in a ligand-specific manner and tested their ability to repress semi-synthetic promoters in plants. We also tested the modulation of their repression activity in response to specific plant metabolites, especially phenylpropanoid-related molecules. Using these aTFs, we also designed synthetic genetic circuits capable of computing Boolean logic operations. Three aTFs, CouR, FapR, and TtgR, achieved c. 95% repression of their respective target promoters. For TtgR, a sixfold de-repression could be triggered by inducing its ligand accumulation, showing its use as biosensor. Moreover, we designed synthetic genetic circuits that use AND, NAND, IMPLY, and NIMPLY Boolean logic operations and integrate metabolite levels as input to the circuit. We showed that biosensors can be implemented in plants to detect phenylpropanoid-related metabolites and activate a genetic circuit that follows a predefined logic, demonstrating their potential as tools for exerting control over plant metabolic pathways and facilitating the bioproduction of natural products.

Unveiling the peptidome diversity of Lachesismuta snake venom: Discovery of novel fragments of metalloproteinase, l-amino acid oxidase, and bradykinin potentiating peptides.

Snake venoms are known to be major sources of peptides with different pharmacological properties. In this study, we comprehensively explored the venom peptidomes of three specimens of Lachesismuta, the largest venomous snake in South America, using mass spectrometry techniques. The analysis revealed 19 main chromatographic peaks common to all specimens. A total of 151 peptides were identified, including 69 from a metalloproteinase, 58 from the BPP-CNP precursor, and 24 from a l-amino acid oxidase. To our knowledge, 126 of these peptides were reported for the first time in this work, including a new SVMP-derived peptide fragment, Lm-10a. Our findings highlight the dynamic nature of toxin maturation in snake venoms, driven by proteolytic processing, post-translational modifications, and cryptide formation.

Involvement of phospholipase A2 in the neuromuscular blockade caused by coralsnake (Micrurus spp.) venoms in mouse phrenic nerve-diaphragm preparations in vitro.

In this work, we examined the neuromuscular blockade caused by venoms from four South-American coralsnakes (Micrurus altirostris - MA, M. corallinus - MC, M. spixii - MS, and M. dumerilii carinicauda - MDC) and the ability of varespladib (VPL), a phospholipase A2 (PLA2) inhibitor, to attenuate this blockade. PLA2 activity was determined using a colorimetric assay and a fixed amount of venom (10 µg). Neurotoxicity was assayed using a single concentration of venom (10 µg/ml) in mouse phrenic nerve-diaphragm (PND) preparations mounted for myographic recordings and then subjected to histological analysis. All venoms showed PLA2 activity, with MS and MA venoms having the highest (15.53 ± 1.9 A425 nm/min) and lowest (0.23 ± 0.14 A425 nm/min) activities, respectively. VPL (292 and 438 µM) inhibited the PLA2 activity of all venoms, although that of MA venom was least affected. All venoms caused neuromuscular blockade, with MS and MDC venoms causing the fastest and slowest 100% blockade [in 40 ± 3 min and 120 ± 6 min (n = 4), respectively]; MA and MC produced complete blockade within 90-100 min. Preincubation of venoms with 292 µM VPL attenuated the blockade to varying degrees: the greatest inhibition was seen with MDC venom and blockade by MS venom was unaffected by this inhibitor. These results indicate that PLA2 has a variable contribution to coralsnake venom-induced neuromuscular blockade in vitro, with the insensitivity of MS venom to VPL suggesting that blockade by this venom is mediated predominantly by post-synaptically-active α-neurotoxins.

The Efficacy of Bisphosphonate in the Treatment of Giant Cell Tumour of the Bone: A Systematic Review and Meta-Analysis.

Introduction: Anti-osteoclastic mechanism of Bisphosphonate (BP) is crucial to treat Giant Cell Tumour of the Bone (GCTB), however no established guidelines of its use have been published. This systematic review and meta-analysis is the first to summarise recent clinical studies on the subject. Materials and methods: A systematic search was performed based on PRISMA guidelines for clinical trials of BP administration in GCTB. Baseline data including BP regimen, dose and timing was summarised. The primary outcomes assessed were recurrence rate, metastases, survival rate, functional outcome, clinical outcome, radiological outcome, and adverse effect. Results: We identified 8 articles from 2008-2020. Most studies administer 4mg of Zoledronic acid post-operatively, with five studies mentioning pre-operative administration and six studies describing post-operative administration. There was a total of 181 GCTB cases analysed in this study. The BP group presented lower recurrence rate than control group (three studies; Odds Ratio [OR] 0.15; 95% Confidence Interval [CI], 0.05 - 0.43; p<0.05; heterogeneity, I2=0%). As for survival rate, BP group is comparable to control group (two studies; OR 1.67; 95% CI, 0.06 - 48.46; p=0.77; heterogeneity, I2=65%). Conclusion: Bisphosphonate therapy offers satisfactory recurrence rate, functional outcome, clinical outcome, radiological outcome, survival rate and metastases rate in patients with GCTB, with minimal adverse effects. Pre- and post-operative administration of bisphosphonates in combination might be the most beneficial in minimalising the recurrence rate.

Integration of multiple stress signals in plants using synthetic Boolean logic gates.

As photosynthetic organisms, plants have a potential role in the sustainable production of high-value products such as medicines, biofuels, and chemical feedstocks. With effective engineering using synthetic biology approaches, plant-based platforms could conceivably be designed to minimize the costs and waste of production for materials that would otherwise be uneconomical. Additionally, modern agricultural crops could be engineered to be more productive, resilient, or restorative in different or rapidly changing environments and climates. Information-processing genetic devices and circuits containing multiple interacting parts that behave predictably must be developed to achieve these complex goals. A genetic Boolean AND logic gate is a device that computes the presence or absence of 2 inputs (signals and stimuli) and produces an output (response) only when both inputs are present. We optimized individual genetic components and used synthetic protein heterodimerizing domains to rationally assemble genetic AND logic gates that integrate 2 hormonal inputs in transgenic Arabidopsis thaliana plants. These AND gates produce an output only in the presence of both abscisic acid and auxin but not when either or neither hormone is present. The AND logic gate can also integrate signals resulting from 2 plant stresses, cold temperature and bacterial infection, to produce a response. The design principles used here are generalizable, and, therefore, multiple orthogonal AND gates could be assembled and rationally layered to process complex genetic information in plants. These layered logic gates may be used in genetic circuits to probe fundamental questions in plant biology, such as hormonal crosstalk, in addition to plant engineering for bioproduction.

A logical way to reprogram plants.

Living cells constantly monitor their external and internal environments for changing conditions, stresses or developmental cues. Networks of genetically encoded components sense and process these signals following pre-defined rules in such a way that specific combinations of the presence or absence of certain signals activate suitable responses. Many biological signal integration mechanisms approximate Boolean logic operations, whereby presence or absence of signals are computed as variables with values described as either true or false, respectively. Boolean logic gates are commonly used in algebra and in computer sciences, and have long been recognized as useful information processing devices in electronic circuits. In these circuits, logic gates integrate multiple input values and produce an output signal according to pre-defined Boolean logic operations. Recent implementation of these logic operations using genetic components to process information in living cells has allowed genetic circuits to enable novel traits with decision-making capabilities. Although several literature reports describe the design and use of these logic gates to introduce new functions in bacterial, yeast and mammalian cells, similar approaches in plants remain scarce, likely due to challenges posed by the complexity of plants and the lack of some technological advances, e.g., species-independent genetic transformation. In this mini review, we have surveyed recent reports describing synthetic genetic Boolean logic operators in plants and the different gate architectures used. We also briefly discuss the potential of deploying these genetic devices in plants to bring to fruition a new generation of resilient crops and improved biomanufacturing platforms.

BADASS: BActeriocin-Diversity ASsessment Software.

BACKGROUND: Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease treatment, food conservation, and probiotics. However, even with a large industrial and biotechnological application potential, these peptides are still poorly studied and explored. BADASS is software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. RESULTS: The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes of bacteriocins. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. BADASS has a complete pipeline that starts with the quality assessment of the raw data. At the end of the analysis, BADASS generates several plots of richness and abundance automatically as well as tabular files containing information about the main bacteriocins detected. The user is able to change the main parameters of the analysis in the graphical interface. To demonstrate how the software works, we used four datasets from WMS studies using default parameters. Lantibiotics were the most abundant bacteriocins in the four datasets. This class of bacteriocin is commonly produced by Streptomyces sp. CONCLUSIONS: With a user-friendly graphical interface and a complete pipeline, BADASS proved to be a powerful tool for prospecting bacteriocin sequences in Whole-Metagenome Shotgun Sequencing (WMS) data. This tool is publicly available at https://sourceforge.net/projects/badass/ .

Ejaculate characteristics over seasons in five species of lancehead pitvipers (Bothrops spp) kept in captivity.

Due to their major medical importance in Latin America, lancehead pitvipers are frequently kept and bred in captivity for venom extraction to the production of antivenom serums. Nevertheless, despite the great contribution given to captive breeding, much of the knowledge of Bothrops' reproductive biology derived from sporadic and insufficient data provided by zoological collections. Thus, we aimed to investigate seasonal changes in gonadosomatic index (GSI) and seminal parameters (e.g., volume, concentration, motility, viability, and acrosome integrity) of five species of lancehead pitvipers from different biomes and phylogenetic groups, maintained in the indoors serpentarium at Butantan Institute (Brazil). Patterns of variation in GSI and semen parameters differed from one species to another, suggesting that captive populations should perhaps be managed distinctly to maximize reproductive success. Furthermore, in none of the studied species did changes in GSI occur concomitantly with seminal variations. GSI remained unaltered year-round for Jararaca (Bothrops jararaca) and Brazilian lancehead (Bothrops moojeni), whereas it peaked in the autumn for Common lancehead (Bothrops atrox), Jararacussu (Bothrops jararacussu), and Whitetail lancehead (Bothrops leucurus). But surprisingly, the scenario was inverted when we estimated the total number of motile spermatozoa per season, as Jararaca and Brazilian lancehead displayed seasonal differences and the other species did not vary throughout the year. Potential ecological and evolutionary factors underlying these differences were also discussed in the present article. Together, these findings can help to better define breeding management strategies for each species in captivity, in addition to optimizing the future use of artificial insemination and semen cryopreservation.

Tuning the Transcriptional Activity of the CaMV 35S Promoter in Plants by Single-Nucleotide Changes in the TATA Box.

Synthetic biology uses genetically encoded devices and circuits to implement novel complex functions in living cells and organisms. A hallmark of these genetic circuits is the interaction among their individual parts, according to predefined rules, to process cellular information and produce a circuit output or response. As the number of individual components in a genetic circuit increases, so does the number of interactions needed to achieve the correct behavior, and hence, a greater need to fine-tune the levels of expression of each component. Transcriptional promoters play a key regulatory role in genetic circuits, as they influence the levels of RNA and proteins produced. In multicellular organisms, such as plants, they can also determine developmental, spatial, and tissue-specific patterns of gene expression. The 35S promoter from the Cauliflower Mosaic Virus (CaMV 35S) is widely used in plant biotechnology to direct high levels of gene expression in a variety of plant species. We produced a library of 21 variants of the CaMV 35S promoter by introducing all single nucleotide substitutions to the promoter's TATA box sequence. We then characterized the activity of all variants in homozygous transgenic plants and showed that some of these variants have lower activity than the wild type in plants. These promoter variants could be used to fine-tune the behavior of synthetic genetic circuits in plants.

Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin.

Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel ß-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.

Re-engineering Plant Phenylpropanoid Metabolism With the Aid of Synthetic Biosensors.

Phenylpropanoids comprise a large class of specialized plant metabolites with many important applications, including pharmaceuticals, food nutrients, colorants, fragrances, and biofuels. Therefore, much effort has been devoted to manipulating their biosynthesis to produce high yields in a more controlled manner in microbial and plant systems. However, current strategies are prone to significant adverse effects due to pathway complexity, metabolic burden, and metabolite bioactivity, which still hinder the development of tailor-made phenylpropanoid biofactories. This gap could be addressed by the use of biosensors, which are molecular devices capable of sensing specific metabolites and triggering a desired response, as a way to sense the pathway's metabolic status and dynamically regulate its flux based on specific signals. Here, we provide a brief overview of current research on synthetic biology and metabolic engineering approaches to control phenylpropanoid synthesis and phenylpropanoid-related biosensors, advocating for the use of biosensors and genetic circuits as a step forward in plant synthetic biology to develop autonomously-controlled phenylpropanoid-producing plant biofactories.

The effect of the volumetric flow rate and endotracheal tube diameter on the pressure distribution in human airways.

The comprehension of the fluid flow in the upper airways is of paramount importance when treating patients under clinical conditions that demand mechanical ventilation. Barotrauma and overdistension are related to undesirable pressures and might be responsible for morbidity and mortality. In the current work we use computational fluid dynamics to investigate the pressure field in the upper respiratory airways. We performed a set of simulations varying the volumetric flow rate of mechanical ventilators and we have shown that the pressure profile can be calculated by means of the volumetric flow rate in accordance with a mathematical expression given by Pav=aV˙2, where Pav is the average pressure at selected sections of the upper airways and V˙ is the volumetric flow rate. Numerical findings provide evidence that the constant a varies with the location of the plane in the upper airways. We also show that some particular diameters of endotracheal tubes (ETT) must be used with care for a given range of volumetric flow rates. Overall, we document an important relationship among pressure, volumetric flow rate and selected internal diameters from ETT.

3D micromixer for nanoliposome synthesis: a promising advance in high mass productivity.

This paper addresses an important breakthrough in the high mass production of liposomes by microfluidics technology. We investigated the synthesis of liposomes using a high flow rate microfluidic device (HFR-MD) with a 3D-twisted cross-sectional microchannel to favor chaotic advection. A simple construction scaffold technique was used to manufacture the HFR-MD. The synthesis of liposomes combined the effects of high flow and high concentration of lipids, resulting in high mass productivity (2.27 g of lipid per h) which, to our knowledge, has never been registered by only one microdevice. We assessed the effects of the flow rate ratio (FRR), total flow rate (TFR), and lipid concentration on the liposome physicochemical properties. HFR-MD liposomes were monodisperse (0.074) with a size around 100 nm under the condition of an FRR of 1 (50% v/v ethanol) and TFR of 5 ml min-1 (expandable to 10 ml min-1). We demonstrated that the mixing conditions are not the only parameter controlling liposome synthesis using experimental and computational fluid dynamics analysis. A vacuum concentrator was used for ethanol removal, and there is no further modification after processing in accordance with the structural (SAXS) and morphological (cryo-TEM) analysis. Hence, the HFR-MD can be used to prepare nanoliposomes. It emerges as an innovative tool with high mass production.

What's in a mass?

This short essay pretends to make the reader reflect on the concept of biological mass and on the added value that the determination of this molecular property of a protein brings to the interpretation of evolutionary and translational snake venomics research. Starting from the premise that the amino acid sequence is the most distinctive primary molecular characteristics of any protein, the thesis underlying the first part of this essay is that the isotopic distribution of a protein's molecular mass serves to unambiguously differentiate it from any other of an organism's proteome. In the second part of the essay, we discuss examples of collaborative projects among our laboratories, where mass profiling of snake venom PLA2 across conspecific populations played a key role revealing dispersal routes that determined the current phylogeographic pattern of the species.

The absence of thrombin-like activity in Bothrops erythromelas venom is due to the deletion of the snake venom thrombin-like enzyme gene.

Snake venom thrombin-like enzymes (SVTLEs) are serine proteinases that clot fibrinogen. SVTLEs are distributed mainly in venoms from snakes of the Viperidae family, comprising venomous pit viper snakes. Bothrops snakes are distributed throughout Central and South American and are responsible for most venomous snakebites. Most Bothrops snakes display thrombin-like activity in their venoms, but it has been shown that some species do not present it. In this work, to understand SVTLE polymorphism in Bothrops snake venoms, we studied individual samples from two species of medical importance in Brazil: Bothrops jararaca, distributed in Southeastern Brazil, which displays coagulant activity on plasma and fibrinogen, and Bothrops erythromelas, found in Northeastern Brazil, which lacks direct fibrinogen coagulant activity but shows plasma coagulant activity. We tested the coagulant activity of venoms and the presence of SVTLE genes by a PCR approach. The SVTLE gene structure in B. jararaca is similar to the Bothrops atrox snake, comprising five exons. We could not amplify SVTLE sequences from B. erythromelas DNA, except for a partial pseudogene. These genes underwent a positive selection in some sites, leading to an amino acid sequence diversification, mostly in exon 2. The phylogenetic tree constructed using SVTLE coding sequences confirms that they are related to the chymotrypsin/kallikrein family. Interestingly, we found a B. jararaca specimen whose venom lacked thrombin-like activity, and its gene sequence was a pseudogene with SVTLE structure, presenting nonsense and frameshift mutations. Our results indicate an association of the lack of thrombin-like activity in B. jararaca and B. erythromelas venoms with mutations and deletions of snake venom thrombin-like enzyme genes.

Comparative gender peptidomics of Bothrops atrox venoms: are there differences between them?

BACKGROUND: Bothrops atrox is known to be the pit viper responsible for most snakebites and human fatalities in the Amazon region. It can be found in a wide geographical area including northern South America, the east of Andes and the Amazon basin. Possibly, due to its wide distribution and generalist feeding, intraspecific venom variation was reported by previous proteomics studies. Sex-based and ontogenetic variations on venom compositions of Bothrops snakes were also subject of proteomic and peptidomic analysis. However, the venom peptidome of B. atrox remains unknown. METHODS: We conducted a mass spectrometry-based analysis of the venom peptides of individual male and female specimens combining bottom-up and top-down approaches. RESULTS: We identified in B. atrox a total of 105 native peptides in the mass range of 0.4 to 13.9 kDa. Quantitative analysis showed that phospholipase A2 and bradykinin potentiating peptides were the most abundant peptide families in both genders, whereas disintegrin levels were significantly increased in the venoms of females. Known peptides processed at non-canonical sites and new peptides as the Ba1a, which contains the SVMP BATXSVMPII1 catalytic site, were also revealed in this work. CONCLUSION: The venom peptidomes of male and female specimens of B. atrox were analyzed by mass spectrometry-based approaches in this work. The study points to differences in disintegrin levels in the venoms of females that may result in distinct pathophysiology of envenomation. Further research is required to explore the potential biological implications of this finding.

Developing a microbial consortium for removing nutrients in dishwasher wastewater: towards a biofilter for its up-cycling.

Microbial consortia are effective biofilters to treat wastewaters, allowing for resource recovery and water remediation. To reuse and save water in the domestic cycle, we assembled a suspended biofilm, a 'biofilter' to treat dishwasher wastewater. Bacterial monocultures of both photo- and heterotrophs were assembled in an increasingly complex fashion to test their nutrient stripping capacity. This 'biofilter' is the core of an integrated system (Zero Mile System) devoted to reusing and upcycling of reconditioned wastewater, partly in subsequent dishwasher cycles and partly into a vertical garden for plant food cultivation. The biofilter was assembled based on a strain of the photosynthetic, filamentous cyanobacterium Trichormus variabilis, selected to produce an oxygen evolving scaffold, and three heterotrophic aerobic bacterial isolates coming from the dishwasher wastewater itself: Acinetobacter, Exiguobacterium and Pseudomonas spp. The consortium was constructed starting with 16 isolates tested one-to-one with T. variabilis and then selecting the heterotrophic microbes up to a final one-to-three consortium, which included two dominant and a rare component of the wastewater community. This consortium thrives in the wastewater much better than T. variabilis alone, efficiently stripping N and P in short time, a pivotal step for the reuse and saving of water in household appliances.