Biology subjects

Casadevall, A.

Publications and source records attributed to Casadevall, A..

13 recordsLinked to original sources

bioRxiv2018

The buoyant cell density of Cryptococcus neoformans is affected by capsule size

Cryptococcus neoformans is an environmental pathogenic fungus with a worldwide geographical distribution that is responsible for hundreds of thousands human cryptococcosis cases each year. During infection, the yeast undergoes a morphological transformation involving capsular enlargement that increases microbial volume. To understand the factors that play a role in environmental dispersal of C. neoformans and C. gatii we evaluated the buoyant cell density of Cryptococcus using Percoll isopycnic gradients. We found differences in the buoyant cell density of strains belonging to C. neoformans and C. gatti species complexes. The buoyant cell density of C. neoformans strains varied depending on growth medium conditions. In minimal medium, the cryptococcal capsule made a major contribution to the buoyant cell density such that cells with larger capsules had lower density than those with smaller capsules. Removing the capsule, both by chemical or mechanical methods, decreased the C. neoformans cell density. Melanization of the C. neoformans cell wall, which also contributes to virulence, produced a small but consistent increase in cell density. C. neoformans sedimented much slower in seawater as its density approached the density of water. Our results suggest a new function for the capsule whereby it can function as a flotation device to facilitate transport and dispersion in aqueous fluids.

microbiology↗

bioRxiv2018

The capsule of Cryptococcus neoformans modulates phagosomal pH through its acid-base properties

Phagosomal acidification is a critical cellular mechanism for the inhibition and killing of ingested microbes by phagocytic cells. The acidic environment activates microbicidal proteins and creates an unfavorable environment for the growth of many microbes. Consequently, numerous pathogenic microbes have developed strategies for countering phagosomal acidification through various mechanisms that include interference with phagosome maturation. The human pathogenic fungus Cryptococcus neoformans resides in acidic phagosome after macrophage ingestion that actually provides a favorable environment for replication since the fungus replicates faster at acidic pH. We hypothesized that the glucuronic acid residues in the capsular polysaccharide had the capacity to affect phagosome acidity through their acid-base properties. A ratiometric fluorescence comparison of imaged phagosomes containing C. neoformans to those containing beads showed that the latter were significantly more acidic. Similarly, phagosomes containing non-encapsulated C. neoformans cells were more acidic than those containing encapsulated cells. Acid-base titrations of isolated C. neoformans polysaccharide revealed that it behaves as a weak acid with maximal buffering capacity around pH 4-5. We interpret these results as indicating that the glucuronic acid residues in the C. neoformans capsular polysaccharide can buffer phagosomal acidification. Interference with phagosomal acidification represents a new function for the cryptococcal capsule in virulence and suggests the importance of considering the acid-base properties of microbial capsules in the host-microbe interaction for other microbes with charged residues in their capsules.\n\nImportanceCryptococcus neoformans is the causative agent of cryptococcosis, a devastating fungal disease that affects thousands of individuals worldwide. This fungus has the capacity to survive inside phagocytic cells, which contributes to persistence of infection and dissemination. One of the major mechanisms of host phagocytes is to acidify the phagosomal compartment after ingestion of microbes. This study shows that the capsule of C. neoformans can interfere with full phagosomal acidification by serving as a buffer.

microbiology↗

bioRxiv2018

Dragotcytosis: Elucidation of the Mechanism for Cryptococcus neoformans Macrophage-to-Macrophage Transfer

Cryptococcus neoformans is a pathogenic yeast capable of a unique and intriguing form of cell-to-cell transfer between macrophage cells. The mechanism for cell-to-cell transfer is not understood. Here we imaged macrophages with CellTracker Green CMFDA-labeled cytosol to ascertain whether cytosol was shared between donor and acceptor macrophages. Analysis of several transfer events detected no transfer of cytosol from donor to acceptor macrophages. However, blocking Fc and complement receptors resulted in a major diminution of cell-to-cell transfer events. The timing cell-to-cell transfer (11.17 min) closely approximated the sum of phagocytosis (4.18 min) and exocytosis (6.71 min) times. We propose that macrophage cell-to-cell transfer represents a non-lytic exocytosis event followed by phagocytosis into a macrophage that is in close proximity and name this process Dragotcytosis (Dragot is a Greek surname meaning Sentinel) as it represents sharing of a microbe between two sentinel cells of the innate immune system.

microbiology↗

bioRxiv2018

Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience

The present study analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009-2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 42 corrections, 5 retractions and 12 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, ~10% of papers with inappropriate image duplications in MCB were retracted. If this proportion is representative, then as many as 35,000 papers in the literature are candidates for retraction due to image duplication. The resolution of inappropriate image duplication concerns after publication required an average of 6 h of journal staff time per published paper. MCB instituted a pilot program to screen images of accepted papers prior to publication that identified 12 manuscripts (14.5% out of 83) with image concerns in two months. The screening and correction of papers before publication required an average of 30 min of staff time per problematic paper. Image screening can identify papers with problematic images prior to publication, reduces post-publication problems and requires significantly less staff time than the correction of problems after publication.

scientific communication and education↗

bioRxiv2018

Opsonin-free, real-time imaging of Cryptococcus neoformans capsule during budding

Cryptococcus neoformans is a unicellular fungal pathogen that causes meningoencephalitis, killing hundreds of thousands of patients each year. Its most distinctive characteristic is a polysaccharide capsule that envelops the whole cell. It is the major virulence attribute and the antigen for serologic diagnosis. We have developed a method for easy observation of the capsule and its growth dynamics using the cell-separation reagent Percoll and differential interference contrast (DIC) microscopy. Percoll suspension is far less disruptive of cell physiology than methods relying on antibody binding to the capsule, and measurements made with it are equivalent with India ink. Time-lapse microscopy observations using this method suggest that during budding, a dividing cell can regulate whether the capsule polysaccharide it produces is deposited on the capsule of the bud or on its own. This observation has important implications for our understanding of the C. neoformans capsule induction process during budding.\n\nList of abbreviations and acronyms

microbiology↗

bioRxiv2018

Serum-mediated cleavage of Bacillus anthracis Protective Antigen is a two-step process that involves a serum carboxypeptidase

Much our understanding of the activity of anthrax toxin is based on in-vitro systems, which delineate the interaction between B. anthracis toxins and the cell surface. These systems however, fail to account for the intimate association of B. anthracis with the circulatory system, including the contribution of serum proteins to the host response and processing of anthrax toxins. Using variety immunologic techniques to inhibit serum processing of B. anthracis Protective Antigen (PA) along with mass spectrometry analysis, we demonstrate that serum digests PA via 2 distinct reactions. In the first reaction, serum cleaves PA83 into 2 fragments to produce PA63 and PA20 fragments, similar to that observed following furin digestion. This is followed by carboxypeptidase-mediated removal of the carboxy-terminal arginine and lysine residues from PA20.

microbiology↗

bioRxiv2017

Disequilibrium in Gender Ratios among Authors who Contributed Equally

In recent decades, the biomedical literature has witnessed an increasing number of authors per article together with a concomitant increase of authors claiming to have contributed equally. In this study, we analyzed over 3000 publications from 1995-2017 claiming equal contributions for authors sharing the first author position for author number, gender, and gender position. The frequency of dual pairings contributing equally was male-male > mixed gender > female-female. For mixed gender pairs males were more often at the first position although the disparity has lessened in the past decade. Among author associations claiming equal contribution and containing three or more individuals, males predominated in both the first position and number of gender exclusive groupings. Our results show a disequilibrium in gender ratios among authors who contributed equally from expected ratios had the ordering been done randomly or alphabetical. Given the importance of the first author position in assigning credit for a publication, the finding of fewer than expected females in associations involving shared contributions raises concerns about women not receiving their fair share of expected credit. The results suggest a need for journals to request clarity on the method used to decide author order among individuals claiming to have made equal contributions to a scientific publication.

scientific communication and education↗

bioRxiv2017

Divalent metal cations potentiate the predatory capacity of amoeba for Cryptococcus neoformans

Among the best studied interaction between soil phagocytic predators and a human pathogenic fungus is that of Acanthamoeba castellanii and Cryptococcus neoformans. The experimental conditions used in amoeba-fungal confrontation assays can have major effects on whether the fungus or the protozoan is ascendant in the interaction. In the presence of Mg2+ and Ca2+ in PBS, C. neoformans was consistently killed when incubated with A. castellanii. A. castellanii survived better in the presence of Mg2+ and Ca2+, even when incubated with C. neoformans. In the absence of Mg2+ and Ca2+, C. neoformans survived when incubated with A. castellanii, and the percentage of dead amoeba was higher than when incubated without yeast cells. These results show that the presence of Mg2+ and Ca2+ can make a decisive contribution toward tilting the outcome of the interaction in favor of amoeba. Of the two metals Mg2+ had a stronger effect than Ca2+. Cations enhanced A. castellanii activity against C. neoformans through enhanced phagocytosis, which is the major mechanism for amoeba to kill fungal cells. We found no evidence that amoeba uses extracellular killing mechanisms in their interactions with C. neoformans. In summary, the presence of Mg2+ and Ca2+ enhanced cell adhesion on surface and motility of amoeba, thus increasing the chance for contact of C. neoformans and the frequency of phagocytosis. Our findings imply that divalent cation concentration in soils could be an important variable for whether amoeba can control C. neoformans in the environment.\n\nImportanceGrazing of soil organisms by phagocytic predators such as amoeba is thought to select for traits that allow some of them to acquire the capacity for virulence in animals. Consequently, knowledge about the interactions between amoeba and soil microbes, such as pathogenic fungi, is important for understanding how virulence can emerge. We show that the interaction between amoeba and the pathogenic fungus C. neoformans is influenced by the presence of magnesium and calcium in the assay, which potentiate amoeba. The results may also have practical applications since enriching soils with divalent cations may reduce C. neoformans numbers in contaminated soils.

microbiology↗

bioRxiv2017

Listeria monocytogenes virulence factors are secreted in biologically active Extracellular Vesicles

Outer membrane vesicles produced by Gram-negative bacteria have been studied for half a century but the possibility that Gram-positive bacteria secreted extracellular vesicles (EVs) was not pursued due to the assumption that the thick peptidoglycan cell wall would prevent their release to the environment. However, following discovery in fungi, which also have cell walls, EVs have now been described for a variety of Gram-positive bacteria. EVs purified from Gram-positive bacteriaare implicated in virulence, toxin release and transference to host cells, eliciting immune responses, and spread of antibiotic resistance. Listeria monocytogenes is a Gram-positive bacterium that is the etiological agent of listeriosis. Here we report that L. monocytogenes produces EVs with diameter ranging from 20-200 nm, containing the pore-forming toxin listeriolysin O(LLO) and phosphatidylinositol-specific phospholipase C (PI-PLC). Using simultaneous metabolite, protein, and lipid extraction (MPLEx) multi-omics we characterized protein, lipid and metabolite composition of bacterial cells and secreted EVs and found that EVs carry the majority of listerial virulence proteins. Cell-free EV preparations were toxic to the murine macrophage cell line J774.16, in a LLO-dependent manner, evidencing EV biological activity. The deletion of plcA increased EV toxicity, suggesting PI-PLC can restrain LLO activity. Using immunogold electron microscopy we detect LLO localization at several organelles within infected human epithelial cells and with high-resolution fluorescence imaging we show that dynamic lipid structures are released from L. monocytogenes that colocalize with LLO during infection. Our findings demonstrate that L. monocytogenes utilize EVs for toxin release and implicate these structures in mammalian cytotoxicity.

microbiology↗

bioRxiv2017

Integrin alpha 4/beta 1 (CD49d/CD29) is a component of the murine IgG3 receptor

Antibodies exert several of their effector functions by binding to cell surface receptors. For murine IgG3 (mIgG3) the identity of its receptors (and the very existence of a receptor) is still under debate, as not all mIgG3 functions can be explained by interaction with Fc{gamma}-receptor I (Fc{gamma}RI). This implies the existence of an alternate receptor, whose identity we sought to pinpoint. We found that blockage of the alpha4/beta1 integrin (Itga4/Itgb1) selectively hampered binding of mIgG3 to macrophages and mIgG3-mediated phagocytosis. Manganese, an integrin activator, increased mIgG3 binding to macrophages. Blockage of Fc{gamma}RI or Itgb1 inhibited binding of different mIgG3 antibodies to variable extents. Our results indicate an integrin component in the mIgG3 receptor. Given the more ancient origin of integrins in comparison with Fc{gamma}R, this observation could have far ranging implications for our understanding of the evolution of antibody-mediated immunity, as well as in immunity to microorganisms, pathogenesis of autoimmune diseases and antibody engineering.

immunology↗

bioRxiv2017

Identification of environmental and genetic factors important for Cryptococcus neoformans titan cell formation using new in vitro inducing conditions

The pathogenic fungus Cryptococcus neoformans exhibits morphological changes in cell size during lung infection, producing both typical size 5 to 7 {micro}m cells and large titan cells (> 10 {micro}m and up to 100 {micro}m). We found and optimized in vitro conditions that produce titan cells in order to identify the ancestry of titan cells, the environmental determinants, and the key gene regulators of titan cell formation. Titan cells generated in vitro harbor the main characteristics of titan cells produced in vivo including their large cell size (>10 {micro}m), polyploidy with a single nucleus, large vacuole, dense capsule, and thick cell wall. Here we show titan cells derived from the enlargement of progenitor cells in the population independent of yeast growth rate. Change in the incubation medium, hypoxia, nutrient starvation and low pH were the main factors that trigger titan cell formation, while quorum sensing factors like the initial inoculum concentration, pantothenic acid, and the quorum sensing peptide Qsp1p also impacted titan cell formation. Inhibition of ergosterol, protein and nucleic acid biosynthesis altered titan cell formation, as did serum, phospholipids and anti-capsular antibodies in our settings. We explored genetic factors important for titan cell formation using three approaches. Using H99-derivative strains with natural genetic differences, we showed that titan cell formation was dependent on LMP1 and SGF29 genes. By screening a gene deletion collection, we also confirmed that GPR4/5-RIM101, and CAC1 genes were required to generate titan cells and that the PKR1, TSP2, USV101 genes negatively regulated titan cell formation. Furthermore, analysis of spontaneous Pkr1 loss-of-function clinical isolates confirmed the important role of the Pkr1 protein as a negative regulator of titan cell formation. Through development of a standardized and robust in vitro assay, our results provide new insights into titan cell biogenesis with the identification of multiple important factors/pathways.\n\nAuthor SummaryCryptococcus neoformans is a yeast that is capable of morphological change upon interaction with the host. Particularly, in the lungs of infected mice, a subpopulation of yeast enlarges, producing cells up to 100 {micro}m in cell body diameter - referred to as titan cells. Along with their large size, the titan cells have other unique characteristics such as thickened cell wall, dense capsule, polyploidization, large vacuole with peripheral nucleus and cellular organelles. The generation of a large number of such cells outside the lungs of mice has been described but was not reproducible nor standardized. Here we report standardized, reproducible, robust conditions for generation of titan cells and explored the environmental and genetic factors underlying the genesis of these cells. We showed that titan cells were generated upon stresses such as change in the incubation medium, nutrient deprivation, hypoxia and low pH. Using collections of well characterized reference strains and clinical isolates, we validated with our model that the cAMP/PKA/Rim101 pathway is a major genetic determinant of titan cell formation. This study opens the way for a more comprehensive picture of the ontology of morphological changes in Cryptococcus neoformans and its impact on pathobiology of this deadly pathogen.

microbiology↗

bioRxiv2017

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)

Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,630,066 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8,656 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.

microbiology↗

bioRxiv2017

Why Do Scientists Fabricate And Falsify Data? A Matched-Control Analysis Of Papers Containing Problematic Image Duplications

It is commonly hypothesized that scientists are more likely to engage in data falsification and fabrication when they are subject to pressures to publish, when they are not restrained by forms of social control, when they work in countries lacking policies to tackle scientific misconduct, and when they are male. Evidence to test these hypotheses, however, is inconclusive due to the difficulties of obtaining unbiased data.\n\nHere we report a pre-registered test of these four hypotheses, conducted on papers that were identified in a previous study as containing problematic image duplications through a systematic screening of the journal PLoS ONE. Image duplications were classified into three categories based on their complexity, with category 1 being most likely to reflect unintentional error and category 3 being most likely to reflect intentional fabrication. Multiple parameters connected to the hypotheses above were tested with a matched-control paradigm, by collecting two controls for each paper containing duplications.\n\nCategory 1 duplications were mostly not associated with any of the parameters tested, in accordance with the assumption that these duplications were mostly not due to misconduct. Category 2 and 3, however, exhibited numerous statistically significant associations. Results of univariable and multivariable analyses support the hypotheses that academic culture, peer control, cash-based publication incentives and national misconduct policies might affect scientific integrity. Significant correlations between the risk of image duplication and individual publication rates or gender, however, were only observed in secondary and exploratory analyses.\n\nCountry-level parameters generally exhibited effects of larger magnitude than individual-level parameters, because a subset of countries was significantly more likely to produce problematic image duplications. Promoting good research practices in all countries should be a priority for the international research integrity agenda.

scientific communication and education↗