bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging toxin-induced neuroinflammation in mice using hyperpolarized13C magnetic resonance spectroscopy
Authors: Le Page Lydia M , Guglielmetti Caroline , Najac Chloé , Tiret Brice , Chaumeil Myriam M 
Published: April 2019

AbstractLipopolysaccharide (LPS) is a commonly used agent for induction of neuroinflammation in preclinical studies. Upon injection, LPS causes activation of microglia and astrocytes, whose metabolism alters to favor glycolysis. Assessingin vivoneuroinflammation and its modulation following therapy remains challenging, and new non-invasive methods allowing for longitudinal monitoring would be greatly valuable. Hyperpolarized (HP)13C magnetic resonance spectroscopy (MRS) is a promising technique for assessingin vivometabolism. In addition to applications in oncology, the most commonly used probe of [1-13C] pyruvate has shown potential in assessing neuroinflammation-linked metabolism in mouse models of multiple sclerosis and traumatic brain injury. Here, we wished to investigate LPS-induced neuroinflammatory changes using HP [1-13C] pyruvate and HP13C urea.2D chemical shift imaging following simultaneous intravenous injection of HP [1-13C] pyruvate and HP13C urea was performed at baseline (day 0), day 3 and day 7 post intracranial injection of LPS (n=6) or saline (n=5). Immunofluorescence (IF) analyses were performed for Iba1 (resting and activated microglia/macrophages), GFAP (resting and reactive astrocytes) and CD68 (activated microglia/macrophages).A significant increase in HP [1-13C] lactate production was observed in the injected (ipsilateral) side at 3 and 7 days of the LPS-treated mouse brain, but not in either the contralateral side or saline-injected animals. HP13C lactate/pyruvate ratio, without and with normalization to urea, was also significantly increased in the ipsilateral LPS-injected brain at 7 days compared to baseline. IF analyses showed a significant increase in CD68 and GFAP at 3 days, followed by increased numbers of Iba1 and GFAP positive cells at 7 days post-LPS injection.In conclusion, we can detect LPS-induced changes in the mouse brain using HP13C MRS, in alignment with increased numbers of microglia/macrophages and astrocytes. This study demonstrates that HP13C spectroscopy holds much potential for providing non-invasive information on neuroinflammation.
Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers
Authors: Santillan E. , Phua W. X. , Constancias F. , Wuertz S. 
Published: April 2019

AbstractSustained disturbances are relevant for environmental biotechnology as they can lead to alternative stable states in a system that may not be reversible. Here, we tested the effect of a sustained organic loading alteration (food-to-biomass ratio, F:M, and carbon-to-nitrogen ratio, C:N) on activated sludge bioreactors, focusing on the stability of nitrification and nitrifiers. Two sets of replicate 5-liter sequencing batch reactors were operated at different, low and high, F:M (0.19-0.36 mgCOD/mgTSS/d) and C:N (3.5-6.3 mgCOD/mgTKN) conditions for a period of 74 days, following 53 days of sludge acclimation. Recovery and resilience were tested during the last 14 days by operating all reactors at low F:M and C:N (henceforth termed F:M-C:N). Stable nitrite accumulation (77%) was achieved through high F:M-C:N loading with a concurrent reduction in the abundance of Nitrospira. Subsequently, only two of the three reactors experiencing a switch back from high to low F:M-C:N recovered the nitrite oxidation function, with an increase in Nitrobacter as the predominant NOB, without a recovery of Nitrospira. The AOB community was more diverse, resistant and resilient than the NOB community. We showed that functional recovery and resilience can vary across replicate reactors, and that nitrification recovery need not coincide with a return to the initial nitrifying community structure.
A fence function for adherens junctions in epithelial cell polarity
Authors: Aguilar-Aragon Mario , Tournier Alex , Thompson Barry J 
Published: April 2019

AbstractAdherens junctions are a defining feature of all epithelial cells, providing cell-cell adhesion and being essential for cell and tissue morphology. InDrosophila, adherens junctions are concentrated between the apical and basolateral plasma membrane domains, but whether they contribute to apical-basal polarisation itself has been unclear. Here we show that, in the absence of adherens junctions, apical-basal polarity determinants can still segregate into complementary domains, but control of apical versus basolateral domain size is lost. Manipulation of the level of apical or basal polarity determinants in experiments and in computer simulations suggests that junctions provide a moveable diffusion barrier, or fence, that restricts the diffusion of polarity determinants to enable precise domain size control. Movement of adherens junctions in response to mechanical forces during morphogenetic change thus enables spontaneous adjustment of apical versus basolateral domain size as an emergent property of the polarising system.
Topological analysis of the type 3 secretion system translocon pore protein IpaC following its native delivery to the plasma membrane during infection
Authors: Russo Brian C. , Duncan Jeffrey K. , Goldberg Marcia B. 
Published: April 2019

AbstractMany Gram-negative bacterial pathogens require a type 3 secretion system (T3SS) to deliver effector proteins into eukaryotic cells. Contact of the tip complex of the T3SS with a target eukaryotic cell initiates the secretion of the two bacterial proteins that assemble into the translocon pore in the plasma membrane. The translocon pore functions to regulate effector protein secretion and is the conduit for effector protein translocation across the plasma membrane. To generate insights into how the translocon pore regulates effector protein secretion, we defined the topology of theShigellatranslocon pore protein IpaC in the plasma membrane following its native delivery by the T3SS. Using single-cysteine substitution mutagenesis and site-directed labeling with a membrane-impermeant chemical probe, we mapped residues accessible from the extracellular surface of the cell. Our data support a model in which the N-terminus of IpaC is extracellular and the C-terminus of IpaC is intracellular. These findings resolve previously conflicting data on IpaC topology that were based on non-native delivery of IpaC to membranes.Salmonella entericaserovar Typhimurium also requires the T3SS for effector protein delivery into eukaryotic cells. Although the sequence of IpaC is closely related to theSalmonellatranslocon pore protein SipC, the two proteins have unique functional attributes during infection. We showed a similar overall topology for SipC and IpaC and identified subtle topological differences between their transmembrane α-helixes and C-terminal regions. Together, our data suggest that topological differences among distinct translocon pore proteins may dictate organism-specific functional differences of the T3SSs during infection.ImportanceThe type 3 secretion system (T3SS) is a nanomachine required for virulence of many bacterial pathogens that infect humans. The system delivers bacterial virulence proteins into the cytosol of human cells, where the virulence proteins promote bacterial infection. The T3SS forms a translocon pore in the membrane of target cells. This pore is the portal through which bacterial virulence proteins are delivered by the T3SS into the eukaryotic cytosol. The pore also regulates the secretion of these virulence proteins. Our work defines the topology of translocon pore proteins in their native context during infection, resolves previously conflicting reports about the topology of theShigellatranslocon pore protein IpaC, and provides new insights into how interactions of the pore with the T3SS likely produce signals that activate secretion of virulence proteins.
Loss of spatacsin impairs cholesterol trafficking and calcium homeostasis
Authors: Boutry Maxime , Pierga Alexandre , Matusiak Raphaël , Branchu Julien , Houllegatte Marc , Ibrahim Yoan , Balse Elise , El Hachimi Khalid-Hamid , Brice Alexis , Stevanin Giovanni , Darios Frédéric 
Published: April 2019

AbstractMutations in SPG11, leading to loss of spatacsin function, impair the formation of membrane tubules in lysosomes and cause the accumulation of lipids in lysosome compartment. However, the full nature of lipids accumulating in lysosomes and the physiological consequences of such accumulation are not known. Here we show that loss of spatacsin, but also downregulation of clathrin, inhibited the formation of tubules on late endosomes/lysosomes and prevented the clearance of cholesterol from this subcellular compartment. Using spatacsin-deficient cells, we evaluated the consequences of impaired cholesterol clearance from late endosomes/lysosomes. The accumulation of cholesterol in late endosomes/lysosomes led to lower cholesterol levels in the plasma membrane, enhancing the entry of extracellular calcium by store-operated calcium entry and increasing resting cytosolic calcium levels. Higher cytosolic calcium levels promoted the nuclear translocation of the master regulator of lysosomes TFEB. Downregulation of TFEB or decrease in resting calcium levels in absence of spatacsin partially corrected the formation of tubules and the accumulation of cholesterol in lysosomes, suggesting that spatacsin could be indirectly implicated in the formation of tubules. Our work reveals a homeostatic balance between cholesterol trafficking and cytosolic calcium levels and shows that loss of spatacsin impairs this homeostatic equilibrium.
Experimentally-induced and real-world acute anxiety have no effect on goal-directed behaviour
Authors: Gillan CM , Vaghi MM , Hezemans FH , van Ghesel Grothe S , Dafflon J , Brühl AB , Savulich G , Robbins TW 
Published: April 2019

AbstractCompulsivity is associated with failures in goal-directed control, an important cognitive faculty that protects against developing habits. But might this effect be explained by co-occurring anxiety? Previous studies have found goal-directed deficits in other anxiety disorders, and to some extent when healthy individuals are stressed, suggesting this is plausible. We carried out a causal test of this hypothesis in two experiments (between-subject N=88; within-subject N=50) that used the inhalation of hypercapnic gas (7.5% CO2) to induce an acute state of anxiety in healthy volunteers. In both experiments, we successfully induced anxiety, assessed physiologically and psychologically, but this did not affect goal-directed performance. In a third experiment (N=1413), we used a correlational design to test if real-life anxiety-provoking events (panic attacks, stressful events) impair goal-directed control. While small effects were observed, none survived controlling for individual differences in compulsivity. These data suggest that anxiety has no meaningful impact on goal-directed control.
Polygenic risk score based on weight gain trajectories is predictive of childhood obesity
Authors: Craig Sarah J. C. , Kenney Ana M. , Lin Junli , Paul Ian M. , Birch Leann L. , Savage Jennifer S. , Marini Michele E. , Chiaromonte Francesca , Reimherr Matthew L. , Makova Kateryna D. 
Published: April 2019

AbstractObesity is highly heritable, yet only a small fraction of its heritability has been attributed to specific genetic variants. These variants are traditionally ascertained from genome-wide association studies (GWAS), which utilize samples with tens or hundreds of thousands of individuals for whom a single summary measurement (e.g., BMI) is collected. An alternative approach is to focus on a smaller, more deeply characterized sample in conjunction with advanced statistical models that leverage detailed phenotypes. Here we use novel functional data analysis (FDA) techniques to capitalize on longitudinal growth information and construct a polygenic risk score (PRS) for obesity in children followed from birth to three years of age. This score, comprised of 24 single nucleotide polymorphisms (SNPs), is significantly higher in children with (vs. without) rapid infant weight gain—a predictor of obesity later in life. Using two independent cohorts, we show that genetic variants identified in early childhood are also informative in older children and in adults, consistent with early childhood obesity being predictive of obesity later in life. In contrast, PRSs based on SNPs identified by adult obesity GWAS are not predictive of weight gain in our cohort of children. Our research provides an example of a successful application of FDA to GWAS. We demonstrate that a deep, statistically sophisticated characterization of a longitudinal phenotype can provide increased statistical power to studies with relatively small sample sizes. This study shows how FDA approaches can be used as an alternative to the traditional GWAS.Author SummaryFinding genetic variants that confer an increased risk of developing a particular disease has long been a focus of modern genetics. Genome wide association studies (GWAS) have catalogued single nucleotide polymorphisms (SNPs) associated with a variety of complex diseases in humans, including obesity, but by and large have done so using increasingly large samples-- tens or even hundreds of thousands of individuals, whose phenotypes are thus often only superficially characterized. This, in turn, may hide the intricacies of the genetic influence on disease. GWAS findings are also usually study-population dependent. We found that genetic risk scores based on SNPs from large adult obesity studies are not predictive of the propensity to gain weight in very young children. However, using a small cohort of a few hundred children deeply characterized with growth trajectories between birth and two years, and leveraging such trajectories through novel functional data analysis (FDA) techniques, we were able to produce a strong childhood obesity genetic risk score.
Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase
Authors: Cromer Laurence , Jolivet Sylvie , Singh Dipesh Kumar , Berthier Floriane , De Winne Nancy , De Jaeger Geert , Komaki Shinichiro , Prusicki Maria Ada , Schnittger Arp , Guérois Raphael , Mercier Raphael 
Published: April 2019

AbstractChromosome distribution at anaphase of mitosis and meiosis is triggered by separase, an evolutionarily conserved protease. Separase must be tightly regulated to prevent the untimely release of chromatid cohesion and disastrous chromosome distribution defects. Securin is the key inhibitor of separase in animals and fungi, but has not been identified in other eukaryotic lineages. Here, we identified PATRONUS1 and PATRONUS2 (PANS1 and PANS2) as the Arabidopsis homologues of securin. Disruption of PANS1 is known to lead to the premature separation of chromosomes at meiosis, and the simultaneous disruption of PANS1 and PANS2 is lethal. Here, we show that PANS1 targeting by the anaphase-promoting-complex is required to trigger chromosome separation, mirroring the regulation of securin. We showed that PANS1 acts independently from Shugosins. In a genetic screen for pans1 suppressors, we identified SEPARASE mutants, showing that PANS1 and SEPARASE have antagonistic functions in vivo. Finally, we showed that the PANS1 and PANS2 proteins interact directly with SEPARASE. Altogether, our results show that PANS1 and PANS2 act as a plant securin. Remote sequence similarity was identified between the plant patronus family and animal securins, suggesting that they indeed derive from a common ancestor. Identification of patronus as the elusive plant securin illustrates the extreme sequence divergence of this central regulator of mitosis and meiosis.
The Virulence Index: A Metric for Quantitative Analysis of Phage Virulence
Authors: Storms Zachary , Teel Matthew R. , Mercurio Kevin , Sauvageau Dominic 
Published: April 2019

AbstractBackgroundOne of the main challenges in developing phage therapy and manufacturing phage products is the reliable evaluation of their efficacy, performance and quality. Since phage virulence is intrinsically difficult to fully capture, researchers have turned to rapid but partially inadequate methods for its evaluation.Materials and MethodsThe present study demonstrates a standardized, quantitative method to assess phage virulence based on three parameters: the Virulence Index (VP) – quantifying the virulence of a phage against a host, the local virulence (vi) – assessing killing potential at given MOIs, and MV50 – the MOI at which the phage achieves 50% of its maximum theoretical virulence. This was shown through comparative analysis of the virulence of phages T4, T5 and T7.ResultsUnder the conditions tested, phage T7 displayed the highest virulence, followed by phage T4 and, finally, phage T5. The impact of parameters such as temperature and medium composition on virulence was shown for each phage. The use of the method to evaluate the virulence of combinations of phages – e.g. for cocktail formulation – is also shown with phages T5 and T7.ConclusionsThe method presented provides a platform for high-throughput quantitative assessment of phage virulence and quality control of phage products. It can also be applied to phage screening, evaluation of phage strains, phage mutants, infection conditions and/or the susceptibility of host strains, and the formulation of phage cocktails.
Endothelial sphingosine 1-phosphate receptors promote vascular normalization to influence tumor growth and metastasis
Authors: Cartier Andreane , Leigh Tani , Liu Catherine H. , Hla Timothy 
Published: April 2019

AbstractSphingosine 1-phosphate receptor-1 (S1PR1) is essential for embryonic vascular development and maturation. In the adult, it is a key regulator of vascular barrier function and inflammatory processes. Its roles in tumor angiogenesis, tumor growth and metastasis are not well understood. In this report, we show that S1PR1 is expressed and active in tumor vessels. Tumor vessels that lack S1PR1 (S1pr1 ECKO) show excessive vascular sprouting and branching, decreased barrier function, and poor perfusion accompanied by loose attachment of pericytes. Compound knockout of S1pr1, 2 and 3 genes further exacerbated these phenotypes, suggesting compensatory function of endothelial S1PR2 and 3 in the absence of S1PR1. On the other hand, tumor vessels with high expression of S1PR1 (S1pr1 ECTG) show less branching, tortuosity and enhanced pericyte coverage. Larger tumors and enhanced lung metastasis were seen in S1pr1 ECKO whereas S1pr1 ECTG showed smaller tumors and reduced metastasis. Furthermore, anti-tumor activity of doxorubicin was more effective in S1pr1 ECTG than the wild-type counterparts. These data suggest that tumor endothelial S1PR1 induces vascular normalization and influences tumor growth, evolution and spread. Strategies to enhance S1PR1 signaling in tumor vessels may be an important adjunct to standard cancer therapy.SignificanceEndothelial sphingosine 1-phosphate receptors modulate tumor angiogenesis by inducing vascular normalization, which allows better blood circulation and enhanced anti-tumor therapeutic efficacy.
Reliable Phylogenetic Regressions for Multivariate Comparative Data: Illustration with the MANOVA and Application to the Effect of Diet on Mandible Morphology in Phyllostomid Bats
Authors: Clavel Julien , Morlon Hélène 
Published: April 2019

ABSTRACTUnderstanding what shapes species phenotypes over macroevolutionary time scales from comparative data requires the use of reliable phylogenetic regression techniques and associated tests (e.g. phylogenetic Generalized Least Squares, pGLS and phylogenetic analyses of variance and covariance, pANOVA, pANCOVA). While these tools are well established for univariate data, their multivariate counterparts are lagging behind. This is particularly true for high dimensional phenotypic data, such as morphometric data. Here we implement well-needed likelihood-based multivariate pGLS, pMANOVA and pMANCOVA, and use a recently-developed penalized likelihood framework to extend their application to the difficult case when the number of traitspapproaches or exceeds the number of speciesn. We then focus on the pMANOVA and use intensive simulations to assess the performance of the approach aspincreases, under various levels of phylogenetic signal and correlations between the traits, phylogenetic structure in the predictors, and under various types of phenotypic differences across species groups. We show that our approach outperforms available alternatives under all circumstances, with a greater power to detect phenotypic differences across species group when they exist, and a low risk to improperly detect inexistent differences. Finally, we provide an empirical illustration of our pMANOVA on a geometric-morphometric dataset describing mandible morphology in phyllostomid bats along with data on their diet preferences. Our approach, implemented in the R package mvMORPH, provides efficient multivariate phylogenetic regression tools for understanding what shapes phenotypic differences across species.
More than efficacy revealed by single-cell analysis of antiviral therapeutics
Authors: Liu Wu , Caglar Mehmet U. , Mao Zhangming , Woodman Andrew , Arnold Jamie J. , Wilke Claus O. , Cameron Craig E. 
Published: April 2019

SUMMARYDevelopment of antiviral therapeutics emphasizes minimization of the effective dose and maximization of the toxic dose, first in cell culture and later in animal models. Long-term success of an antiviral therapeutic is determined not only by its efficacy but also by the duration of time required for drug-resistance to evolve. We have developed a microfluidic device comprised of ~6000 wells, with each well containing a microstructure to capture single cells. We have used this device to characterize enterovirus inhibitors with distinct mechanisms of action. In contrast to population methods, single-cell analysis reveals that each class of inhibitor interferes with the viral infection cycle in a manner that can be distinguished by principal component analysis. Single-cell analysis of antiviral candidates reveals not only efficacy but also properties of the members of the viral population most sensitive to the drug, the stage of the lifecycle most affected by the drug, and perhaps even if the drug targets an interaction of the virus with its host.
Spatiotemporal organization of branched microtubule networks
Authors: Thawani Akanksha , Stone Howard A , Shaevitz Joshua W , Petry Sabine 
Published: April 2019

AbstractTo understand how chromosomes are segregated, it is necessary to explain the precise spatiotemporal organization of microtubules (MTs) in the mitotic spindle. We useXenopusegg extracts to study the nucleation and dynamics of MTs in branched networks, a process that is critical for spindle assembly. Surprisingly, new branched MTs preferentially originate near the minus-ends of pre-existing MTs. A sequential reaction model, consisting of deposition of nucleation sites on an existing MT, followed by rate-limiting nucleation of branches, reproduces the measured spatial profile of nucleation, the distribution of MT plus-ends and tubulin intensity. By regulating the availability of the branching effectors TPX2, augmin and γ-TuRC, combined with single-molecule observations, we show that first TPX2 is deposited on pre-existing MTs, followed by binding of augmin/γ-TuRC to result in the nucleation of branched MTs. In sum, regulating the localization and kinetics of nucleation effectors governs the architecture of branched MT networks.Impact StatementA sequential reaction pathway involving TPX2, augmin and γ-TuRC governs the assembly and architecture of branched microtubule networks.