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https://www.readbyqxmd.com/read/29351294/a-had-family-phosphatase-csp-6-regulates-the-circadian-output-pathway-in-neurospora-crassa
#1
Xiaoying Zhou, Bin Wang, Jillian M Emerson, Carol S Ringelberg, Scott A Gerber, Jennifer J Loros, Jay C Dunlap
Circadian clocks are ubiquitous in eukaryotic organisms where they are used to anticipate regularly occurring diurnal and seasonal environmental changes. Nevertheless, little is known regarding pathways connecting the core clock to its output pathways. Here, we report that the HAD family phosphatase CSP-6 is required for overt circadian clock output but not for the core oscillation. The loss of function Δcsp-6 deletion mutant is overtly arrhythmic on race tubes under free running conditions; however, reporter assays confirm that the FREQUENCY-WHITE COLLAR COMPLEX core circadian oscillator is functional, indicating a discrete block between oscillator and output...
January 19, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29351209/the-prognostic-significance-of-histone-demethylase-utx-in-esophageal-squamous-cell-carcinoma
#2
Shau-Hsuan Li, Hung-I Lu, Wan-Ting Huang, Wan-Yu Tien, Ya-Chun Lan, Wei-Che Lin, Hsin-Ting Tsai, Chang-Han Chen
The dysregulation of the ubiquitously transcribed TPR gene on the X chromosome (UTX) has been reported to be involved in the oncogenesis of several types of cancers. However, the expression and significance of UTX in esophageal squamous cell carcinoma (ESCC) remains largely undetermined. Immunohistochemistry was performed in 106 ESCC patients, and correlated with clinicopathological features and survival. The functional role of UTX in ESCC cells was determined by UTX-mediated siRNA. Univariate analyses showed that high UTX expression was associated with superior overall survival (OS, p = 0...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29351066/contamination-of-swimming-pools-and-hot-tubs-biofilms-with-acanthamoeba
#3
Behroz Mahdavi Poor, Abdolhossein Dalimi, Fatemeh Ghafarifar, Fariba Khoshzaban, Jalal Abdolalizadeh
The members of Acanthamoeba genus are ubiquitous amoeba which could be a pathogenic parasite. The amoeba is resistant to the common chlorine concentration that used for disinfecting the swimming pool water. Therefore, the pools can be suitable environments for the survival and multiplication of the amoeba. In this cross sectional study, 10 indoor recreational water centers from different regions of Tabriz city were selected and sampling was done from fixed and floating biofilms of the swimming pools and hot tubs...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29350420/over-expression-of-dec1-inhibits-myogenic-differentiation-by-modulating-myog-activity-in-bovine-satellite-cell
#4
Yongzhen Huang, Xinsheng Lai, Linyong Hu, Chuzhao Lei, Xianyong Lan, Chunlei Zhang, Yun Ma, Li Zheng, Yue-Yu Bai, Fengpeng Lin, Hong Chen
Differentiated embryo chondrocyte 1 (DEC1), a member of basic-helix-loop-helix transcription factor Bhlhe40, also called stimulated by retinoic acid 13, STRA13, plays an important role in the regulation of adipogenesis, tumorigenesis, peripheral circadian output, response to hypoxia and development of metabolic syndrome. Previous studies suggested that DEC1 was involved in skeletal muscle development; however, its precise role in myoblast differentiation has not been determined. In the present study, we showed that DEC1 expressed ubiquitously in different bovine tissues and was down-regulated in differentiated bovine satellite cells...
January 19, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29350268/the-epitope-mediated-mmp-activation-assay-detection-and-quantification-of-the-activation-of-mmp2-in-vivo-in-the-zebrafish-embryo
#5
Emma J Jeffrey, Bryan D Crawford
Matrix remodeling is a consequence of tightly regulated matrix metalloproteinase (MMP) activity. MMPs are synthesized as inactive precursors with auto-inhibitory N-terminal propeptides, the proteolytic removal of which exposes the catalytic zinc ion, rendering the protease active. The regulation of MMP activation has been investigated primarily in tissue culture and biochemical assays that lack important biological context. Here we present the epitope-mediated MMP activation (EMMA) assay and use it to observe the activation of Mmp2 (gelatinase A) by endogenous mechanisms in the intact zebrafish embryo...
January 19, 2018: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/29350232/impact-of-droplets-on-immiscible-liquid-films
#6
Zhizhao Che, Omar K Matar
The impact of droplets on liquid films is a ubiquitous phenomenon not only in nature but also in many industrial applications. Compared to the widely-studied impact of droplets on films of identical fluids, the impact of droplets on immiscible films has received far less attention. In the present work, we show using high-speed imaging that immiscibility has a profound effect on the impact dynamics. The impact of a water droplet on an oil film leads to the formation of a compound crown followed by a central jet, whereas that of an oil droplet on a water film results in rapid spreading on the film surface driven by a large, positive spreading factor...
January 19, 2018: Soft Matter
https://www.readbyqxmd.com/read/29350155/yersinia-pestis-survival-and-replication-in-potential-ameba-reservoir
#7
David W Markman, Michael F Antolin, Richard A Bowen, William H Wheat, Michael Woods, Mercedes Gonzalez-Juarrero, Mary Jackson
Plague ecology is characterized by sporadic epizootics, then periods of dormancy. Building evidence suggests environmentally ubiquitous amebae act as feral macrophages and hosts to many intracellular pathogens. We conducted environmental genetic surveys and laboratory co-culture infection experiments to assess whether plague bacteria were resistant to digestion by 5 environmental ameba species. First, we demonstrated that Yersinia pestis is resistant or transiently resistant to various ameba species. Second, we showed that Y...
February 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29349818/nanocrystalline-precursors-for-the-co-assembly-of-crack-free-metal-oxide-inverse-opals
#8
Katherine R Phillips, Tanya Shirman, Elijah Shirman, Anna V Shneidman, Theresa M Kay, Joanna Aizenberg
Inorganic microstructured materials are ubiquitous in nature. However, their formation in artificial self-assembly systems is challenging as it involves a complex interplay of competing forces during and after assembly. For example, colloidal assembly requires fine-tuning of factors such as the size and surface charge of the particles and electrolyte strength of the solvent to enable successful self-assembly and minimize crack formation. Co-assembly of templating colloidal particles together with a sol-gel matrix precursor material helps to release stresses that accumulate during drying and solidification, as previously shown for the formation of high-quality inverse opal (IO) films out of amorphous silica...
January 19, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29349291/spontaneous-infraslow-fluctuations-modulate-hippocampal-epsp-ps-coupling
#9
Michael B Dash, Stephen Ajayi, Lynde Folsom, Paul E Gold, Donna L Korol
Extensive trial-to-trial variability is a hallmark of most behavioral, cognitive, and physiological processes. Spontaneous brain activity (SBA), a ubiquitous phenomenon that coordinates levels and patterns of neuronal activity throughout the brain, may contribute to this variability by dynamically altering neuronal excitability. In freely-behaving male rats, we observed extensive variability of the hippocampal evoked response across 28-min recording periods despite maintaining constant stimulation parameters of the medial perforant path...
January 2018: ENeuro
https://www.readbyqxmd.com/read/29348582/nanostructured-titanium-surfaces-exhibit-recalcitrance-towards-staphylococcus-epidermidis-biofilm-formation
#10
Yunyi Cao, Bo Su, Subash Chinnaraj, Saikat Jana, Leon Bowen, Sam Charlton, Pengfei Duan, Nicholas S Jakubovics, Jinju Chen
Titanium-based implants are ubiquitous in the healthcare industries and often suffer from bacterial attachment which results in infections. An innovative method of reducing bacterial growth is to employ nanostructures on implant materials that cause contact-dependent cell death by mechanical rupture of bacterial cell membranes. To achieve this, we synthesized nanostructures with different architectures on titanium surfaces using hydrothermal treatment processes and then examined the growth of Staphylococcus epidermidis on these surfaces...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348423/a-tissue-mimetic-nano-fibrillar-hybrid-injectable-hydrogel-for-potential-soft-tissue-engineering-applications
#11
Neda Latifi, Meisam Asgari, Hojatollah Vali, Luc Mongeau
While collagen type I (Col-I) is commonly used as a structural component of biomaterials, collagen type III (Col-III), another fibril forming collagen ubiquitous in many soft tissues, has not previously been used. In the present study, the novel concept of an injectable hydrogel with semi-interpenetrating polymeric networks of heterotypic collagen fibrils, with tissue-specific Col-III to Col-I ratios, in a glycol-chitosan matrix was investigated. Col-III was introduced as a component of the novel hydrogel, inspired by its co-presence with Col-I in many soft tissues, its influence on the Col-I fibrillogenesis in terms of diameter and mechanics, and its established role in regulating scar formation...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29347928/chronic-obstructive-pulmonary-disease-guidelines-in-europe-a-look-into-the-future
#12
REVIEW
Marc Miravitlles, Nicolas Roche, João Cardoso, David Halpin, Zaurbek Aisanov, Hannu Kankaanranta, Vladimir Kobližek, Paweł Śliwiński, Leif Bjermer, Michael Tamm, Francesco Blasi, Claus F Vogelmeier
Clinical practice guidelines are ubiquitous and are developed to provide recommendations for the management of many diseases, including chronic obstructive pulmonary disease. The development of these guidelines is burdensome, demanding a significant investment of time and money. In Europe, the majority of countries develop their own national guidelines, despite the potential for overlap or duplication of effort. A concerted effort and consolidation of resources between countries may alleviate the resource-intensity of maintaining individual national guidelines...
January 18, 2018: Respiratory Research
https://www.readbyqxmd.com/read/29347918/somatic-evolutionary-timings-of-driver-mutations
#13
Karen Gomez, Sayaka Miura, Louise A Huuki, Brianna S Spell, Jeffrey P Townsend, Sudhir Kumar
BACKGROUND: A unified analysis of DNA sequences from hundreds of tumors concluded that the driver mutations primarily occur in the earliest stages of cancer formation, with relatively few driver mutation events detected in the late-arising subclones. However, emerging evidence from the sequencing of multiple tumors and tumor regions per individual suggests that late-arising subclones with additional driver mutations are underestimated in single-sample analyses. METHODS: To test whether driver mutations generally map to early tumor development, we examined multi-regional tumor sequencing data from 101 individuals reported in 11 published studies...
January 18, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29347702/orbitals-for-classical-arbitrary-anisotropic-colloidal-potentials
#14
Martin Girard, Trung Dac Nguyen, Monica Olvera de la Cruz
Coarse-grained potentials are ubiquitous in mesoscale simulations. While various methods to compute effective interactions for spherically symmetric particles exist, anisotropic interactions are seldom used, due to their complexity. Here we describe a general formulation, based on a spatial decomposition of the density fields around the particles, akin to atomic orbitals. We show that anisotropic potentials can be efficiently computed in numerical simulations using Fourier-based methods. We validate the field formulation and characterize its computational efficiency with a system of colloids that have Gaussian surface charge distributions...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347533/model-of-chromosomal-loci-dynamics-in-bacteria-as-fractional-diffusion-with-intermittent-transport
#15
Marco Gherardi, Ludovico Calabrese, Mikhail Tamm, Marco Cosentino Lagomarsino
The short-time dynamics of bacterial chromosomal loci is a mixture of subdiffusive and active motion, in the form of rapid relocations with near-ballistic dynamics. While previous work has shown that such rapid motions are ubiquitous, we still have little grasp on their physical nature, and no positive model is available that describes them. Here, we propose a minimal theoretical model for loci movements as a fractional Brownian motion subject to a constant but intermittent driving force, and compare simulations and analytical calculations to data from high-resolution dynamic tracking in E...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347218/effect-of-particle-size-dynamics-on-properties-of-dense-spongy-particle-systems-approach-towards-equilibrium
#16
Monica E A Zakhari, Patrick D Anderson, Markus Hütter
Open-porous deformable particles, often envisaged as sponges, are ubiquitous in biological and industrial systems (e.g., casein micelles in dairy products and microgels in cosmetics). The rich behavior of these suspensions is owing to the elasticity of the supporting network of the particle, and the viscosity of permeating solvent. Therefore, the rate-dependent size change of these particles depends on their structure, i.e., the permeability. This work aims at investigating the effect of the particle-size dynamics and the underlying particle structure, i...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347126/requisite-ingredients-for-thermal-rectification
#17
Emmanuel Pereira
The present work is devoted to an analytical investigation of the thermal rectification mechanism. More specifically, we attempt to find the requisite ingredients for such a phenomenon to occur. Starting from the linearization of the time evolution equations of anharmonic chains of oscillators, we propose some effective harmonic toy models with a potential that is dependent on temperature, and we investigate their steady heat currents. This unusual temperature-dependent potential is the footprint of nonlinearity in the final effective linear model...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346992/existence-and-construction-of-large-stable-food-webs
#18
Jan O Haerter, Namiko Mitarai, Kim Sneppen
Ecological diversity is ubiquitous despite the restrictions imposed by competitive exclusion and apparent competition. To explain the observed richness of species in a given habitat, food-web theory has explored nonlinear functional responses, self-interaction, or spatial structure and dispersal-model ingredients that have proven to promote stability and diversity. We return instead here to classical Lotka-Volterra equations, where species-species interaction is characterized by a simple product and spatial restrictions are ignored...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346984/mechanical-failure-in-amorphous-solids-scale-free-spinodal-criticality
#19
Itamar Procaccia, Corrado Rainone, Murari Singh
The mechanical failure of amorphous media is a ubiquitous phenomenon from material engineering to geology. It has been noticed for a long time that the phenomenon is "scale-free," indicating some type of criticality. In spite of attempts to invoke "Self-Organized Criticality," the physical origin of this criticality, and also its universal nature, being quite insensitive to the nature of microscopic interactions, remained elusive. Recently we proposed that the precise nature of this critical behavior is manifested by a spinodal point of a thermodynamic phase transition...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346886/predictability-of-escape-for-a-stochastic-saddle-node-bifurcation-when-rare-events-are-typical
#20
Corentin Herbert, Freddy Bouchet
Transitions between multiple stable states of nonlinear systems are ubiquitous in physics, chemistry, and beyond. Two types of behaviors are usually seen as mutually exclusive: unpredictable noise-induced transitions and predictable bifurcations of the underlying vector field. Here, we report a different situation, corresponding to a fluctuating system approaching a bifurcation, where both effects collaborate. We show that the problem can be reduced to a single control parameter governing the competition between deterministic and stochastic effects...
September 2017: Physical Review. E
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