Cytoscape.js 2023 update: a graph theory library for visualization and analysis.

SUMMARY: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Differential consumption of malic acid and fructose in apple musts by Pichia kudriavzevii strains.

AIMS: To assess the capability of Pichia kudriavzevii strains isolated from wine, cider, and natural environments in North Patagonia to produce ciders with reduced malic acid levels. METHODS AND RESULTS: Fermentation kinetics and malic acid consumption were assessed in synthetic media and in regional acidic apple musts. All P. kudriavzevii strains degraded malic acid and grew in synthetic media with malic acid as the sole carbon source. Among these strains, those isolated from cider exhibited higher fermentative capacity, mainly due to increased fructose utilization; however, a low capacity to consume sucrose present in the must was also observed for all strains. The NPCC1651 cider strain stood out for its malic acid consumption ability in high-malic acid Granny Smith apple must. Additionally, this strain produced high levels of glycerol as well as acceptable levels of acetic acid. On the other hand, Saccharomyces cerevisiae ÑIF8 reference strain isolated from Patagonian wine completely consumed reducing sugars and sucrose and showed an important capacity for malic acid consumption in apple must fermentations. CONCLUSIONS: Pichia kudriavzevii NPCC1651 strain isolated from cider evidenced interesting features for the consumption of malic acid and fructose in ciders.

Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations.

Different species can find convergent solutions to adapt their genome to the same evolutionary constraints, although functional convergence promoted by chromosomal rearrangements in different species has not previously been found. In this work, we discovered that two domesticated yeast species, Saccharomyces cerevisiae, and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentation environments. We found two new heterologous chromosomal translocations in fermentative strains of S. uvarum at the SSU1 locus, involved in sulfite resistance, an antimicrobial additive widely used in food production. These are convergent events that share similarities with other SSU1 locus chromosomal translocations previously described in domesticated S. cerevisiae strains. In S. uvarum, the newly described VIIXVI and XIXVI chromosomal translocations generate an overexpression of the SSU1 gene and confer increased sulfite resistance. This study highlights the relevance of chromosomal rearrangements to promote the adaptation of yeast to anthropic environments.

Presence of Saccharomyces eubayanus in fermentative environments reveals a new adaptive scenario in Patagonia.

Patagonia (Argentina and Chile) harbors the highest Saccharomyces eubayanus genomic diversity and its widest predominance in natural environments. In this work, S. eubayanus was isolated for the first time from a fermentative environment. This species was found dominating both a traditional apple chicha fermentation as well as feral apple trees in the Andean region of Aluminé (Argentina). S. eubayanus was the only Saccharomyces species found in the isolation substrates, although it coexisted with other non-Saccharomyces species. The absence of strong fermentative competitors of the Saccharomyces genus (like Saccharomyces uvarum or Saccharomyces cerevisiae) in the feral apples could promote the development and implantation of S. eubayanus in a spontaneous apple must fermentation. Phylogeographic analyses revealed a high intraspecific diversity in S. eubayanus, enabling the characterization of strains belonging to the genomic subpopulations PA1, PA2, and PB1 according to the sequences obtained for the intFR gene region. This result evidence that the studied sampling area represents a natural habitat for the species. Being a novel finding, studying the causes that allowed this species to prosper in a fermentative environment becomes essential. Hence, the physiological profile of the new isolates, including their ability to grow at different temperature, nitrogen, and ethanol concentrations was evaluated in comparison with a set of S. eubayanus strains previously isolated from natural environment and representing different genomic subpopulations. Greater physiological diversity was evidenced when strains isolated from both natural and fermentative environments were analyzed overall. Furthermore, no direct relationship between genomic population and physiological behavior was observed; on the opposite, strains appeared to exhibit similar behavior, primarily grouped by isolation origin.

Contaminated Perry in Patagonia Argentina: A Case Study.

Perry is a beverage obtained by fermentation of pear juice, popular in the North Hemisphere. In Argentina it is an emerging market, particularly in the Patagonian region. The aim of this work is to describe and to evaluate the spoilage yeasts associated to six perry samples showing signs of microbiological contamination from a local craft perry company in North Patagonian region. Eighteen yeasts were isolated from four of the six perry samples where Brettanomyces custersianus, Brettanomyces bruxellensis and Zygosaccharomyces parabailii were identified. The growth capacity of these isolates in the presence of antimicrobial agents (sulfite and potassium sorbate) was analyzed in solid media. Growth parameters in sterile perry must was evaluated and the production of undesirable compounds were evaluated, products were characterized in terms of their aromatic and physicochemical features. The yeasts Z. parabailii NPCC1791 was able to grow on plates containing sulfite concentrations of up to 4 mM and produced high methanol concentrations in perry. Additionally, B. bruxellensis NPPC1792 was able to produce methanol as well as high concentrations of volatile phenols including 4-ethylphenol and 4-ethylguaiacol. These results demonstrate the potential of these species as perry contaminants. Given the lack of studies describing the contaminating yeasts in perry production, this work represents the first report about perry spoilage yeasts in Argentina, with this knowledge, control strategies can be developed to prevent microbiological contamination and minimize product loss.

Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids.

The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history.

Regioselective generation and reactivity control of subnanometric platinum clusters in zeolites for high-temperature catalysis.

Subnanometric metal species (single atoms and clusters) have been demonstrated to be unique compared with their nanoparticulate counterparts. However, the poor stabilization of subnanometric metal species towards sintering at high temperature (>500 °C) under oxidative or reductive reaction conditions limits their catalytic application. Zeolites can serve as an ideal support to stabilize subnanometric metal catalysts, but it is challenging to localize subnanometric metal species on specific sites and modulate their reactivity. We have achieved a very high preference for localization of highly stable subnanometric Pt and PtSn clusters in the sinusoidal channels of purely siliceous MFI zeolite, as revealed by atomically resolved electron microscopy combining high-angle annular dark-field and integrated differential phase contrast imaging techniques. These catalysts show very high stability, selectivity and activity for the industrially important dehydrogenation of propane to form propylene. This stabilization strategy could be extended to other crystalline porous materials.

A Lamellar MWW Zeolite With Silicon and Niobium Oxide Pillars: A Catalyst for the Oxidation of Volatile Organic Compounds.

In this work, an MWW-type zeolite with pillars containing silicon and niobium oxide was synthesized to obtain a hierarchical zeolite. The effect of niobium insertion in the pillaring process was determined by combining a controllable acidity and accessibility in the final material. All pillared materials had niobium occupying framework positions in pillars and extra-framework positions. The pillared material, Pil-Nb-4.5 with 4.5 wt % niobium, did not compromise the mesoporosity formed by pillaring, while the increase of niobium in the structure gradually decreased the mesoporosity and ordering of lamellar stacking. The morphology of the pillared zeolites and the niobium content were found to directly affect the catalytic activity. Specifically, we report on the activity of the MWW-type zeolites with niobium catalyzing the gas-phase oxidation of volatile organic compounds (VOCs), which is an important reaction for clean environmental. All produced MWW-type zeolites with niobium were catalytically active, even at low temperatures and low niobium loading, and provided excellent conversion efficiencies.

MOF-Mediated Synthesis of Supported Fe-Doped Pd Nanoparticles under Mild Conditions for Magnetically Recoverable Catalysis*.

Metal-organic framework (MOF)-driven synthesis is considered as a promising alternative for the development of new catalytic materials with well-designed active sites. This synthetic approach is used here to gradually transform a new bimetallic MOF, with Pd and Fe as the metal components, by the in situ generation of aniline under mild conditions. This methodology results in a compositionally homogeneous nanocomposite formed by Fe-doped Pd nanoparticles that, in turn, are supported on iron oxide-doped carbon. The nanocomposite has been fully characterized by several techniques such as IR and Raman spectroscopy, TEM, XPS, and XAS. The performance of this nanocomposite as an heterogeneous catalyst for hydrogenation of nitroarenes and nitrobenzene coupling with benzaldehyde has been evaluated, proving it to be an efficient and reusable catalyst.

GeneMANIA update 2018.

GeneMANIA (http://genemania.org) is a flexible user-friendly web site for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA finds functionally similar genes using a wealth of genomics and proteomics data. In this mode, it weights each functional genomic dataset according to its predictive value for the query. Another use of GeneMANIA is gene function prediction. Given a single query gene, GeneMANIA finds genes likely to share function with it based on their interactions with it. Enriched Gene Ontology categories among this set can point to the function of the gene. Nine organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Escherichia coli, Homo sapiens, Mus musculus, Rattus norvegicus and Saccharomyces cerevisiae). Hundreds of data sets and hundreds of millions of interactions have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze. We have recently updated the user interface to GeneMANIA to make it more intuitive and make more efficient use of visual space. GeneMANIA can now be used effectively on a variety of devices.

Use of Alkylarsonium Directing Agents for the Synthesis and Study of Zeolites.

Expanding the previously known family of -onium (ammonium, phosphonium, and sulfonium) organic structure-directing agents (OSDAs) for the synthesis of zeolite MFI, a new member, the arsonium cation, is used for the first time. The new group of tetraalkylarsonium cations has allowed the synthesis of the zeolite ZSM-5 with several different chemical compositions, opening a route for the synthesis of zeolites with a new series of OSDA. Moreover, the use of As replacing N in the OSDA allows the introduction of probe atoms that facilitate the study of these molecules by powder X-ray diffraction (PXRD), solid-state nuclear magnetic resonance (MAS NMR), and X-ray absorption spectroscopy (XAS). Finally, the influence of trivalent elements such as B, Al, or Ga isomorphically replacing Si atoms in the framework structure and its interaction with the As species has been studied. The suitability of the tetraalkylarsonium cation for carrying out the crystallization of zeolites is demonstrated along with the benefit of the presence of As atoms in the occluded OSDA, which allows its advanced characterization as well as the study of its evolution during OSDA removal by thermal treatments.

Incorporation of Brazilian Diatomite in the Synthesis of An MFI Zeolite.

The need for greener procedures is a fact to reduce residues, to decrease industrial costs, and to accomplish the environmental agreements. In an attempt to address this question, we propose the addition of a natural resource, Brazilian diatomite, to an MFI zeolite traditional synthesis. We have characterized the resulting product with different techniques, such as X-ray diffraction, microscopy, and gas sorption, and, afterwards, we evaluate the greenness of the process by the Green Star method. The results were promising: We obtained the desired topology in the form of small crystallites aggregated and a pore diameter of 0.8 nm. In conclusion, the product has the necessary characteristics for an adsorption or catalytic future tests and escalation to industrial production.

Phylogeography of the wild Lager-brewing ancestor (Saccharomyces eubayanus) in Patagonia.

Saccharomyces eubayanus is the close relative of the Lager-brewing yeast and was firstly found in North Patagonia associated with Nothofagus trees. In recent years additional strains were found in North America, Asia and New Zealand, and genomic analyses showed the existence of two main populations of this yeast, both of them present in Patagonia. Here, we performed the most comprehensive study of S. eubayanus in Patagonia natural environments (400 samples) and confirmed that this region has the highest isolation success rate for this species described worldwide (more than 10-fold). The genetic characterization of 200 isolates (COX2, DCR1, intFR) revealed five geographically structured subpopulations. We hypothesized that marine ingressions and glaciations, which shaped the Patagonian landscape, contributed on population differentiation. The first large screening of fermentation performance of 60 wild S. eubayanus strains indicated which subpopulations would be more suitable for beer production.

Saccharomyces cerevisiae × Saccharomyces uvarum hybrids generated under different conditions share similar winemaking features.

Interspecific hybrids among species in the Saccharomyces genus are frequently detected in anthropic habitats and can also be obtained easily in the laboratory. This occurs because the most important genetic barriers among Saccharomyces species are post-zygotic. Depending on several factors, including the involved strains, the hybridization mechanism and stabilization conditions, hybrids that bear differential genomic constitutions, and hence phenotypic variability, can be obtained. In the present study, Saccharomyces cerevisiae × Saccharomyces uvarum hybrids were constructed using genetically and physiologically different S. uvarum parents at distinct temperatures (13 and 20°C). The effect of those variables on the main oenological features of the wines obtained with these hybrids was evaluated. Hybrids were successfully obtained in all cases. However, genetic stabilization based on successive fermentations in white wine at 13°C was significantly longer than that at 20°C. Our results demonstrated that, irrespective of the S. uvarum parent and temperature used for hybrid generation and stabilization, similar physicochemical and aromatic features were found in wines. The hybrids generated herein were characterized by low ethanol production, high glycerol synthesis and the capacity to grow at low temperature and to produce malic acid with particular aroma profiles. These features make these hybrids useful for the new winemaking industry within the climate change era frame. Copyright © 2017 John Wiley & Sons, Ltd.

An in situ XAS study of the activation of precursor-dependent Pd nanoparticles.

The activation of precursor-dependent Pd nanoparticles was comprehensively followed by in situ X-ray absorption spectroscopy on two inorganic supports for rationalizing the final catalytic activity. Two series of Pd-based catalysts (7 wt% Pd) were prepared by impregnation of γ-Al2O3 and activated carbon supports varying the metal precursor (Pd(NO3)2, PdCl2 and Pd(OAc)2). The most relevant physicochemical properties of the studied catalysts were determined by several techniques including ICP-OES, XRD, N2 adsorption and XAS. The results indicate that the thermal stability of the metal precursor plays an important role in the size and speciation of the formed Pd nanoparticles after the activation process. The Cl-based precursor, which presents high thermal stability, passes through a PdOxCly mixed phase when submitted to calcination on Pd/Al2O3 and leaves Cl-species after metal reduction on Pd/C (which can be detrimental to catalytic reactions). Differently, Pd(OAc)2 and Pd(NO3)2 promote the formation of larger species due to different precursor decomposition pathways. Ordered PdO is observed even before calcination when Pd(NO3)2 was used as a metallic source, which translates into large nanoparticles after reduction in H2. By using the average coordination numbers of Pd species obtained from EXAFS data of the as-reduced catalysts, a correlation was observed comparing the three precursors: PdCl2 generates smaller nanoparticles than Pd(OAc)2, which in turn generates smaller nanoparticles than Pd(NO3)2, regardless of the support used for catalyst preparation.

Confined Pt1 1+ Water Clusters in a MOF Catalyze the Low-Temperature Water-Gas Shift Reaction with both CO2 Oxygen Atoms Coming from Water.

The synthesis and reactivity of single metal atoms in a low-valence state bound to just water, rather than to organic ligands or surfaces, is a major experimental challenge. Herein, we show a gram-scale wet synthesis of Pt1 1+ stabilized in a confined space by a crystallographically well-defined first water sphere, and with a second coordination sphere linked to a metal-organic framework (MOF) through electrostatic and H-bonding interactions. The role of the water cluster is not only isolating and stabilizing the Pt atoms, but also regulating the charge of the metal and the adsorption of reactants. This is shown for the low-temperature water-gas shift reaction (WGSR: CO + H2 O → CO2 + H2 ), where both metal coordinated and H-bonded water molecules trigger a double water attack mechanism to CO and give CO2 with both oxygen atoms coming from water. The stabilized Pt1+ single sites allow performing the WGSR at temperatures as low as 50 °C.

Cytoscape.js: a graph theory library for visualisation and analysis.

UNLABELLED: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. CONTACT: gary.bader@utoronto.ca.

Saccharomyces uvarum is responsible for the traditional fermentation of apple chicha in Patagonia.

Apple chicha is a fresh low alcoholic beverage elaborated by aboriginal communities of Andean Patagonia (Argentina and Chile). In the present work, we identified the yeast microbiota associated with this fermentation, and characterized genetically those belonging to the genus Saccharomyces. Both Saccharomyces cerevisiae and S. uvarum were found in the analyzed fermentations. Phylogenetic and population structure analyses based on genes sequence analysis were carried out for both S. cerevisiae and S. uvarum strains obtained in this study and a set of additional strains from diverse origins. The results demonstrate that S. cerevisiae strains from apple chicha belong to the big group of wine/European strains of this species, while S. uvarum strains were included in the Holartic population of this species. Additionally, some S. uvarum strains from chichas evidenced as an admixture of both pure Holartic and pure South American populations. Our results suggest that Holartic strains could have been introduced in South America together with the domestication of apple trees by Mapuche communities. This Holartic population suffered admixis with the naturally present South American population of this species, originating strains bearing genetic features from the two populations, detectable in both chichas and natural habitats.

GeneMANIA prediction server 2013 update.

GeneMANIA (http://www.genemania.org) is a flexible user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. GeneMANIA can also be used in a function prediction setting: given a query gene, GeneMANIA finds a small set of genes that are most likely to share function with that gene based on their interactions with it. Enriched Gene Ontology categories among this set can sometimes point to the function of the gene. Seven organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens, Rattus norvegicus and Saccharomyces cerevisiae), and hundreds of data sets have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze.

Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia.

Mudai is a traditional fermented beverage, made from the seeds of the Araucaria araucana tree by Mapuche communities. The main goal of the present study was to identify and characterize the yeast microbiota responsible of Mudai fermentation as well as from A. araucana seeds and bark from different locations in Northern Patagonia. Only Hanseniaspora uvarum and a commercial bakery strain of Saccharomyces cerevisiae were isolated from Mudai and all Saccharomyces isolates recovered from A. araucana seed and bark samples belonged to the cryotolerant species Saccharomyces eubayanus and Saccharomyces uvarum. These two species were already reported in Nothofagus trees from Patagonia; however, this is the first time that they were isolated from A. araucana, which extends their ecological distribution. The presence of these species in A. araucana seeds and bark samples, led us to postulate a potential role for them as the original yeasts responsible for the elaboration of Mudai before the introduction of commercial S. cerevisiae cultures. The molecular and genetic characterization of the S. uvarum and S. eubayanus isolates and their comparison with European S. uvarum strains and S. eubayanus hybrids (S. bayanus and S. pastorianus), allowed their ecology and evolution us to be examined.