bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct activities of Scrib module proteins organize epithelial polarity
Authors: Khoury Mark J. , Bilder David 
Published: December 2019

ABSTRACTA polarized architecture is central to both epithelial structure and function. In many cells, polarity involves mutual antagonism between the Par complex and the Scrib module. While molecular mechanisms underlying Par-mediated apical determination are well-understood, how Scrib module proteins specify the basolateral domain remains unknown. Here, we demonstrate dependent and independent activities of Scrib, Dlg and Lgl using the Drosophila follicle epithelium. Our data support a linear hierarchy for localization, but rule out previously proposed protein-protein interactions as essential for polarization. Membrane recruitment of Scrib does not require palmitoylation or polar phospholipid binding but instead an independent cortically-stabilizing activity of Dlg. Scrib and Dlg do not directly antagonize aPKC, but may instead restrict aPKC localization by enabling the aPKC-inhibiting activity of Lgl. Importantly, while Scrib, Dlg and Lgl are each required, all three together are not sufficient to antagonize the Par complex. Our data demonstrate previously unappreciated diversity of function within the Scrib module and begin to define the elusive molecular functions of Scrib and Dlg.SIGNIFICANCE STATEMENTTo enable their physiological functions, cells must polarize their plasma membrane. In many epithelia, polarity is regulated by balanced activity of the apical Par complex and basolateral Scribble module. While the former is understood in molecular detail, little is known about how the latter works. We identify distinct functions of the three Scribble module proteins, separating independent roles in a localization hierarchy from cooperative roles in apical polarity antagonism and showing that they are not together sufficient to specify basolateral identity. This work establishes an essential basis for a mechanistic understanding of this core polarity machinery that controls processes ranging from stem cell divisions to organ morphogenesis across animal species.
An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells
Authors: Jones Ross D. , Qian Yili , Siciliano Velia , DiAndreth Breanna , Huh Jin , Weiss Ron , Vecchio Domitilla Del 
Published: December 2019

AbstractSynthetic biology has the potential to bring forth advanced genetic devices for applications in healthcare and biotechnology. However, accurately predicting the behavior of engineered genetic devices remains difficult due to lack of modularity, wherein a device’s output does not depend only on its intended inputs but also on its context. One contributor to lack of modularity is competition among genes for shared cellular resources, such as those required for transcription and translation, which can induce ‘coupling’ among otherwise independently-regulated genes. Here, we quantify the effects of resource sharing on engineered genetic systems in mammalian cells and develop an endoribonuclease-based incoherent feedforward loop (iFFL) to make gene expression levels robust to changes in resource availability. Our iFFL accurately controls gene expression levels in various cell lines and in the presence of significant resource sequestration by transcriptional activators. In addition to mitigating resource sharing, our iFFL also adapts gene expression to multiple log decades of DNA copy number variation, substantially improving upon previously-described miRNA-based iFFLs. Ultimately, our iFFL device will enable predictable, robust, and context-independent control of gene expression in mammalian cells.
Adaptation to transients disrupts spatial coherence in binocular rivalry
Authors: Naber Marnix , Stuit Sjoerd , de Kloe Yentl , Van der Stigchel Stefan , Paffen Chris L.E. 
Published: December 2019

AbstractWhen the two eyes are presented with incompatible images, the visual system fails to create a single, fused, coherent percept. Instead, it creates an ongoing alternation between each eye’s image; a phenomenon dubbed binocular rivalry (BR). Such alternations in awareness are separated by brief, intermediate states during which a spatially mixed (incoherent) pattern of both images is perceived. A recent study proposed that the precedence of mixed percepts positively correlates with the degree of adaptation to conflict between the eyes. However, it neglected the role of visual transients, which covaried with the degree of conflict in the stimulus design. We here study whether the presence of visual transients drive adaptation to interocular conflict and explain incidence rates of spatially incoherent BR. Across three experiments we created several adaptation conditions in which we systematically varied the frequency of transients and the degree of conflict between the eyes. Transients consisted of grating orientation reversals, blanks, and plaids. The results showed that the pattern of variations in the fractions mixed percepts across conditions was best explained by variations in the frequency of visual transients, rather than the degree of conflict between the eyes. We propose that the prolonged presentation of transients to both eyes evokes a chain of events consisting of (1) the exogenous allocation of attention to both images, (2) the increase in perceptual dominance of both rivalling images, (3) the speed up of adaptation of interocular suppression, and eventually (4) the facilitation of mixed perception during BR after adaptation.Author summaryWhen one eye is presented with an image that is distinct from the image presented to the other eye, the eyes start to rival and suppress each other’s image. Binocular rivalry leads to perceptual alternations between the images of each eye, during which only one of the images is perceived at a time. However, when the eyes exert weak and shallow mutual suppression, observers tend to perceive both images intermixed more often. Here we designed an experiment and a model to investigate how stereoscopic stimuli can be designed to alter the degree of interocular suppression. We find that prolonged and repeated observations of strong visual transients, such as sudden changes in contrast, can facilitate the adaptation to suppression between the eyes, resulting in that observers report more mixed percepts. This novel finding is relevant to virtual- and augmented reality for which it is crucial to design stereoscopic environments in which binocular rivalry is limited.
The evolutionary origin of the universal distribution of mutation fitness effect
Authors: Barlukova Ayuna , Rouzine Igor M. 
Published: December 2019

AbstractAn intriguing fact long defying explanation is the observation of a universal exponential distribution of beneficial mutations in fitness effect for different microorganisms. Here we use a general and straightforward analytic model to demonstrate that, regardless of the inherent distribution of mutation fitness effect across genomic sites, an observed exponential distribution of fitness effects emerges naturally in the long term, as a consequence of the evolutionary process. This result follows from the exponential statistics of the frequency of the less-fit alleles f predicted to evolve, in the long term, for both polymorphic and monomorphic sites. The exponential distribution disappears when the system arrives at the steady state, when it is replaced with the classical mutation-selection result, f = μ/s. Based on these findings, we develop a technique to measure selection coefficients for specific genomic sites from two single-time sequence sets. Our results demonstrate the striking difference between the distribution of fitness effects observed experimentally, for naturally occurring mutations, and the “inherent” distribution obtained in a directed-mutagenesis experiment, which can have any shape depending on organism. Based on these results, we develop a new method to measure fitness effects of mutations for each variable residue based on DNA sequences isolated from an adapting population at two time points. This new method is not sensitive to linkage effects and does not require one-site model assumptions.
HBV DNA is a substrate for the cGAS/STING pathway but is not sensed in infected hepatocytes
Authors: Lauterbach-Rivière Lise , Bergez Maïwenn , Mönch Saskia , Qu Bingqian , Riess Maximilian , Vondran Florian W. R. , Liese Juliane , Hornung Veit , Urban Stephan , König Renate 
Published: December 2019

AbstractHBV chronic infection is a critical risk factor for hepatocellular carcinoma. Although debated, the absence of innate immune response to HBV infection in hepatocytes is becoming the current view. However the underlying reasons are poorly understood. This study aims to define potential viral pathogen-associated molecular patterns (PAMPs) and the pattern recognition receptors (PRRs), and to elucidate whether HBV counteracts the innate pathways.The innate immune response to HBV infection was monitored by interferon-stimulated gene 54 (ISG54) mRNA, a direct downstream transcriptional target of Interferon Regulatory Factor 3 (IRF3), or IRF3 phosphorylation. The immunostimulatory potential of naked HBV DNAs or RNAs and the respective PRRs were determined upon viral nucleic acid transfection in immunocompetent cells including knockout cells lacking key molecules of innate pathways. The expression and functionality of DNA and RNA sensing pathways in primary human hepatocytes (PHH) were assessed. The inhibition of the DNA-sensing pathway by HBV was tested using IRF3 nuclear translocation assay.Our study revealed that HBV infection does not induce an innate response in infected hepatocytes, even in absence of HBV X protein. HBV relaxed-circular DNA (rcDNA) and DNA replication intermediates, but not HBV RNAs, are immunostimulatory and sensed by Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase (cGAS) and Stimulator of Interferon Genes (STING). Although PHH express DNA sensors to reduced levels compared to myeloid cells, they can respond to naked HBV rcDNA. However, we show that the absence of innate response to HBV infection in hepatocytes is not due to an active inhibition of the DNA sensing pathway by the virus.HBV passively evades the innate immune response in infected hepatocytes by (i) producing non-immunostimulatory RNAs, (ii) avoiding sensing of its DNAs by cGAS/STING without active inhibition of the pathway, possibly through shielding of the viral DNAs by the capsid.Author summaryInnate immune responses are the first line of defense against viral infections. They lead to the production of antiviral factors after recognition of specific viral features by the infected cells. Here we show that HBV, a major cause of liver cirrhosis and cancer, avoids recognition by infected hepatocytes through different means. First, HBV RNAs, contrarily to other viral RNAs, are not immunostimulatory. Second, we show that naked HBV DNAs are recognized by cGAS/STING and induce an innate immune response. Furthermore, we demonstrate that this pathway is active in hepatocytes and is not inhibited by the virus. Instead, we propose that HBV DNAs are not accessible to cGAS/STING in the context of an infection. This might be due to shielding of the viral DNA by the viral capsid.
Bacterial and plant produced lipids can exacerbate the Olive Quick Decline Syndrome caused byXylella
Authors: Scala Valeria , Pucci Nicoletta , Salustri Manuel , Modesti Vanessa , L’Aurora Alessia , Scortichini Marco , Zaccaria Marco , Momeni Babak , Reverberi Massimo , Loreti Stefania 
Published: December 2019

AbstractXylella fastidiosais an insect vector-transmitted bacterial plant pathogen associated with severe diseases in a wide range of plants. In last decades,X. fastidiosawas detected in several European countries. AmongX. fastidiosasubspecies, here we studyX. fastidiosasubsp.paucaassociated with the Olive Quick Decline Syndrome (OQDS) causing severe losses in Southern Italy. First, we collectedOlea europaeaL. (cv. Ogliarola salentina) samples in groves located in infected zones and uninfected zones. Secondly, the untargeted LC-TOF analysis of the lipid profiles of OQDS positive (+) and negative (-) plants showed a significant clustering of OQDS+ samples apart from OQDS-ones. Thirdly, using HPLC-MS/MS targeted methods and chemometric analysis, we identified a shortlist of 10 lipids significantly different in the infected versus healthy samples. Last, we observed a clear impact onX. fastidiosasubsp.paucagrowth and biofilm formationin vitroliquid cultures supplemented with these compounds.Considering that growth and biofilm formation are primary ways by whichX. fastidiosacauses disease, our results demonstrate that lipids produced as part of the plant’s immune response can exacerbate the disease. This is reminiscent of an allergic reaction in animal systems, offering the depression of plant immune response as a potential strategy for OQDS treatment.Author summaryGlobal trade and climate change are re-shaping the distribution map of pandemic pathogens. One major emerging concern isXylella fastidiosa, a tropical bacterium recently introduced into Europe from America. Its impact has been dramatic: in the last 5-years only, Olive Quick Decline Syndrome (OQDS) has caused thousands of 200 years old olive trees to be felled in the southern Italy.Xylella fastidiosathrough a tight coordination of the adherent biofilm and the planktonic states, invades the host systemically. The planktonic phase is correlated to low cell density and vessel colonization. Increase in cell density triggers a quorum sensing system based on cis 2-enoic fatty acids—diffusible signalling factors (DSF) that promote stickiness and biofilm. Xylem vessels are occluded by the combined effect of bacterial biofilm and plant defences (e.g. tyloses). This study provides novel insight on howX. fastidiosasubsp.paucabiology relates to the Olive Quick Decline Syndrome. We found that some class of lipids increase their amount in the infected olive tree. These lipid entities, provided toX. fastidiosasubsp.paucabehave as hormone-like molecules: modulating the dual phase, e.g. planktonicversusbiofilm. Probably, part of these lipids represents a reaction of the plant to the bacterial contamination.
Characterization, modelling and mitigation of gene expression burden in mammalian cells
Authors: Frei T , Cella F , Tedeschi F , Gutierrez J , Stan GB , Khammash M , Siciliano V 
Published: December 2019

AbstractDespite recent advances in genome engineering, the design of genetic circuits in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here we demonstrate that competition for limited transcriptional and translational resources dynamically couples otherwise independent co-expressed exogenous genes, leading to diminished performance and contributing to the divergence between intended and actual function. We also show that the expression of endogenous genes is likewise impacted when genetic payloads are expressed in the host cells. Guided by a resource-aware mathematical model and our experimental finding that post-transcriptional regulators have a large capacity for resource redistribution, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the novel use of endogenous miRNAs as integral components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement ofin vivosynthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.
Variation in cell surface hydrophobicity amongCryptococcus neoformansstrains influences interactions with amoeba
Authors: Vij Raghav , Crawford Conor J. , Casadevall Arturo 
Published: December 2019

ABSTRACTCryptococcus neoformansandCryptococcus gattiiare pathogenic fungi that cause significant morbidity and mortality. Cell surface hydrophobicity (CSH) is a biophysical parameter that influences the adhesion of fungal cells or spores to biotic and abiotic surfaces.C. neoformansis encased by polysaccharide capsule that is highly hydrophilic and is a critical determinant of virulence. In this study, we report large differences in the CSH of someC. neoformansandC. gattiistrains. The capsular polysaccharides ofC. neoformansstrains differ in repeating motifs, and therefore vary in the number of hydroxyl groups, which along with higher-order structure of the capsule, may contribute to the variation in hydrophobicity that we observed. ForC. neoformans, CSH correlated with phagocytosis by natural soil predatorAcanthamoeba castellani. Furthermore, capsular binding of the protective antibody (18B7), but not the non-protective (13F1) antibody altered the CSH ofC. neoformansstrains. Variability in CSH could be an important characteristic when comparing the biological properties of cryptococcal strains.IMPORTANCEThe interaction of a microbial cell with its environment is influenced by the biophysical properties of a cell. The affinity of the cell surface for water, defined by the Cell Surface Hydrophobicity (CSH), is a biophysical parameter that varied amongst different strains ofCryptococcus neoformans. The CSH influenced the phagocytosis of the yeast by its natural predator in the soil, Amoeba. Studying variation in biophysical properties like CSH gives us insight into the dynamic host-predator interaction, and host-pathogen interaction in a damage-response framework.
BAX and SMAC Regulate Bistable Properties of the Apoptotic Caspase System
Authors: McKenna Stephanie , García-Gutiérrez Lucía , Matallanas David , Fey Dirk 
Published: December 2019

AbstractThe initiation of apoptosis is a core mechanism in cellular biology by which organisms control the removal of damaged or unnecessary cells. The irreversible activation of caspases is essential for apoptosis, and mathematical models have demonstrated that the process is tightly regulated by positive feedback and a bistable switch. BAX and SMAC are often dysregulated in diseases such as cancer or neurodegeneration and are two key regulators that interact with the caspase system generating the apoptotic switch. Here we present a mathematical model of how BAX and SMAC control the apoptotic switch. Formulated as a system of ordinary differential equations, the model summarises experimental and computational evidence form the literature and incorporates the biochemical mechanisms of how BAX and SMAC interact with the components of the caspase system. Using simulations and bifurcation analysis, we find that both BAX and SMAC regulate the time-delay and activation threshold of the apoptotic switch. Interestingly, the model predicted that BAX (not SMAC) controls the amplitude of the apoptotic switch. Cell culture experiments using siRNA mediated BAX and SMAC knockdowns this model prediction. We further validated the model on data of the NCI-60 cell line panel using BAX protein expression as cell-line specific parameter and show that model simulations correlated with the cellular response to DNA damaging drugs and established a defined threshold for caspase activation that could distinguish between sensitive and resistant melanoma cells. In summary, we present an experimentally validated dynamic model that summarises our current knowledge of how BAX and SMAC regulate the bistable properties of irreversible caspase activation during apoptosis.
A genome-wide loss-of-function screen identifiesToxoplasma gondiigenes that determine fitness in interferon gamma-activated murine macrophages
Authors: Wang Yifan , Sangaré Lamba Omar , Paredes-Santos Tatiana C. , Krishnamurthy Shruthi , Hassan Musa A. , Furuta Anna M. , Markus Benedikt M. , Lourido Sebastian , Saeij Jeroen P.J. 
Published: December 2019

ABSTRACTMacrophages play an essential role in the early immune response againstToxoplasmaand are the cell type preferentially infected by the parasitein vivo. Interferon gamma (IFNγ) elicits a variety of anti-Toxoplasmaactivities in macrophages. Using a genome-wide CRISPR screen we identified ∼130Toxoplasmagenes that determine parasite fitness in naїve macrophages and ∼466 genes that determine fitness in IFNγ-stimulated murine macrophages, seven of which we investigated and confirmed. We show that one of these genes encodes dense granule protein GRA45, which contains a putative chaperone-like domain, and which we show is critical in preventing other GRA effectors from aggregating. Parasites lackingGRA45mislocalize GRA effectors upon secretion, are more susceptible to IFNγ-mediated growth inhibition, and have reduced virulence in mice. Our results provide a resource for the community to further explore the function ofToxoplasmagenes that determine fitness in IFNγ-stimulated macrophages.IMPORTANCEThe intracellular parasiteToxoplasma gondiican cause congenital infections and severe disease in immunocompromised patients. The cytokine IFNγ can block parasite replication by upregulating a variety of toxoplasmacidal mechanisms in many cells, including macrophages.Toxoplasmapreferentially infects macrophages. Therefore, the parasite has evolved mechanisms to survive in these cells in the presence of IFNγ. Here, we generated pools ofToxoplasmamutants for every gene and determined which mutants were specifically depleted in IFNγ-stimulated macrophages, thus identifying parasite genes determining fitness in these cells. We show that one of these genes encodes for a dense granule protein (GRA45) that plays an important role in preventing other GRA effectors from aggregating. Parasites without GRA45 mislocalize GRA effectors upon secretion, have enhanced susceptibility to IFNγ-mediated growth inhibition, and are avirulent in mice. Thus, our screen provides a resource to theToxoplasmacommunity to determine the function ofToxoplasmagenes that affect its fitness in IFNγ-stimulated macrophages.
Phylogeography of equine infectious anemia virus
Authors: Jara Manuel , Frias-De-Diego Alba , Machado Gustavo 
Published: December 2019

ABSTRACTEquine Infectious Anemia virus (EIAV) is the causative agent of one of the most impacting infectious diseases affecting equids. EIAV is genetically diverse with several lineages circulating globally. To elucidate EIAV global spread patterns, we studied its spatiotemporal dynamics applying Bayesian phylodynamic analyses, using a worldwide compiled dataset composed of unique sequences of the gag gene. In addition, we performed a scoping review of 1.470 publications on EIAV to characterize the spatiotemporal trends in EAIV research. Phylogeographic reconstruction suggested Hungary as the most likely country of origin for current EIAV circulation (root state posterior probability = 0.21), and one of the most important centers of diversification for the disease. Historical EIAV spread was predominantly characterized by long-distance spread across continents. As a result, we found that the American and Asian circulating EIAV (i.e., Mongolia) are more related to European lineages than to other Asian countries, being Europe the continent with the highest EIAV phylogenetic diversity. Our bibliometric analysis showed a continuous increment in the number of publications per year, where the United States and China appeared as the countries with highest EIAV-related scientific production. This study provides a historical geographic mapping of the EIAV linages’ spread patterns. In addition, we identified important asymmetry between the current research effort and the availability of genetic data which restricted our abilities to quantify for example the time frame of virus dispersal.