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https://www.readbyqxmd.com/read/29045877/self-organization-of-ftsz-polymers-in-solution-reveals-spacer-role-of-the-disordered-c-terminal-tail
#1
Sonia Huecas, Erney Ramírez-Aportela, Albert Vergoñós, Rafael Núñez-Ramírez, Oscar Llorca, J Fernando Díaz, David Juan-Rodríguez, María A Oliva, Patricia Castellen, José M Andreu
FtsZ is a self-assembling GTPase that forms, below the inner membrane, the mid-cell Z-ring guiding bacterial division. FtsZ monomers polymerize head to tail forming tubulin-like dynamic protofilaments, whose organization in the Z-ring is an unresolved problem. Rather than forming a well-defined structure, FtsZ protofilaments laterally associate in vitro into polymorphic condensates typically imaged on surfaces. We describe here nanoscale self-organizing properties of FtsZ assemblies in solution that underlie Z-ring assembly, employing time-resolved x-ray scattering and cryo-electron microscopy...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045862/the-two-state-prehensile-tail-of-the-antibacterial-toxin-colicin-n
#2
Christopher L Johnson, Alexandra S Solovyova, Olli Hecht, Colin Macdonald, Helen Waller, J Günter Grossmann, Geoffrey R Moore, Jeremy H Lakey
Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045454/insights-into-the-inhibited-form-of-the-redox-sensitive-sufe-like-sulfur-acceptor-csde
#3
Esther Peña-Soler, Juan Aranda, Miguel López-Estepa, Sara Gómez, Fernando Garces, Miquel Coll, Francisco J Fernández, Iñaki Tuñon, M Cristina Vega
Sulfur trafficking in living organisms relies on transpersulfuration reactions consisting in the enzyme-catalyzed transfer of S atoms via activated persulfidic S across protein-protein interfaces. The recent elucidation of the mechanistic basis for transpersulfuration in the CsdA-CsdE model system has paved the way for a better understanding of its role under oxidative stress. Herein we present the crystal structure of the oxidized, inactivated CsdE dimer at 2.4 Å resolution. The structure sheds light into the activation of the Cys61 nucleophile on its way from a solvent-secluded position in free CsdE to a fully extended conformation in the persulfurated CsdA-CsdE complex...
2017: PloS One
https://www.readbyqxmd.com/read/29044377/heparosan-coated-liposomes-for-drug-delivery
#4
Rachel S Lane, F Michael Haller, Anais A E Chavaroche, Andrew Almond, Paul L DeAngelis
Liposomal encapsulation is a useful drug delivery strategy for small molecules, especially chemotherapeutic agents such as doxorubicin. Doxil® is a doxorubicin-containing liposome ("dox-liposome") that passively targets drug to tumors while reducing side effects caused by free drug permeating and poisoning healthy tissues. Polyethylene glycol (PEG) is the hydrophilic coating of Doxil® that protects the formulation from triggering the mononuclear phagocyte system (MPS). Evading the MPS prolongs dox-liposome circulation time thus increasing drug deposition at the tumor site...
November 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/29044206/emergence-of-the-stoner-wohlfarth-astroid-in-thin-films-at-dynamic-regime
#5
José Luis F Cuñado, Alberto Bollero, Tomás Pérez-Castañeda, Paolo Perna, Fernando Ajejas, Javier Pedrosa, Adrian Gudín, Ana Maldonado, Miguel Angel Niño, Rubén Guerrero, David Cabrera, Francisco J Terán, Rodolfo Miranda, Julio Camarero
The Stoner-Wohlfarth (SW) model is the simplest model that describes adequately the magnetization reversal of nanoscale systems that are small enough to contain single magnetic domains. However for larger sizes where multi-domain effects are present, e.g., in thin films, this simple macrospin approximation fails and the experimental critical curve, referred as SW astroid, is far from its predictions. Here we show that this discrepancy could vanish also in extended system. We present a detailed angular-dependent study of magnetization reversal dynamics of a thin film with well-defined uniaxial magnetic anisotropy, performed over 9 decades of applied field sweep rate (dH/dt)...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044178/use-of-pixe-pige-for-sequential-ca-and-f-measurements-in-root-carious-model
#6
K Yagi, H Yamamoto, R Uemura, Y Matsuda, K Okuyama, T Ishimoto, T Nakano, M Hayashi
The progress of caries has conventionally been evaluated by checking changes in mineral density using transverse microradiography (TMR). Recent advances have seen development of a new measurement system, using in-air micro proton induced X-ray/gamma-ray emission (PIXE/PIGE). PIXE/PIGE enables analysis of distributions and concentrations of multiple mineral elements in a carious lesion. The aim of this study was to evaluate the effectiveness of PIXE/PIGE for investigating the development of root caries. In summary, we successfully established a multi-elemental sequential measuring method using in-air micro-PIXE/PIGE to identify the dynamic distributions and concentrations of Ca and F in human root dentin...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044152/a-machine-learning-assisted-label-free-non-invasive-approach-for-somatic-reprogramming-in-induced-pluripotent-stem-cell-colony-formation-detection-and-prediction
#7
Ke Fan, Sheng Zhang, Ying Zhang, Jun Lu, Mike Holcombe, Xiao Zhang
During cellular reprogramming, the mesenchymal-to-epithelial transition is accompanied by changes in morphology, which occur prior to iPSC colony formation. The current approach for detecting morphological changes associated with reprogramming purely relies on human experiences, which involve intensive amounts of upfront training, human error with limited quality control and batch-to-batch variations. Here, we report a time-lapse-based bright-field imaging analysis system that allows us to implement a label-free, non-invasive approach to measure morphological dynamics...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044127/engineered-in-vitro-cell-line-mixtures-and-robust-evaluation-of-computational-methods-for-clonal-decomposition-and-longitudinal-dynamics-in-cancer
#8
Hossein Farahani, Camila P E de Souza, Raewyn Billings, Damian Yap, Karey Shumansky, Adrian Wan, Daniel Lai, Anne-Marie Mes-Masson, Samuel Aparicio, Sohrab P Shah
Characterization and quantification of tumour clonal populations over time via longitudinal sampling are essential components in understanding and predicting the response to therapeutic interventions. Computational methods for inferring tumour clonal composition from deep-targeted sequencing data are ubiquitous, however due to the lack of a ground truth biological data, evaluating their performance is difficult. In this work, we generate a benchmark data set that simulates tumour longitudinal growth and heterogeneity by in vitro mixing of cancer cell lines with known proportions...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044110/hyperconnected-molecular-glass-network-architectures-with-exceptional-elastic-properties
#9
Joseph A Burg, Mark S Oliver, Theo J Frot, Mark Sherwood, Victor Lee, Geraud Dubois, Reinhold H Dauskardt
Hyperconnected network architectures can endow nanomaterials with remarkable mechanical properties that are fundamentally controlled by designing connectivity into the intrinsic molecular structure. For hybrid organic-inorganic nanomaterials, here we show that by using 1,3,5 silyl benzene precursors, the connectivity of a silicon atom within the network extends beyond its chemical coordination number, resulting in a hyperconnected network with exceptional elastic stiffness, higher than that of fully dense silica...
October 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/29043776/art-advancing-science-filmmaking-leads-to-molecular-insights-at-the-nanoscale
#10
Charles Reilly, Donald E Ingber
Many have recognized the potential value of facilitating activities that span the art-science interface for the benefit of society; however, there are few examples that demonstrate how pursuit of an artistic agenda can lead to scientific insights. Here, we describe how we set out to produce an entertaining short film depicting the fertilization of the egg by sperm as a parody of a preview for another Star Wars movie to excite the public about science, but ended up developing a simulation tool for multiscale modeling...
October 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/29043773/coherence-spectroscopy-in-the-condensed-phase-insights-into-molecular-structure-environment-and-interactions
#11
Jacob C Dean, Gregory D Scholes
The role of coherences, or coherently excited superposition states, in complex condensed-phase systems has been the topic of intense interest and debate for a number of years. In many cases, coherences have been utilized as spectators of ultrafast dynamics or for identifying couplings between electronic states. In rare cases, they have been found to drive excited state dynamics directly. Interestingly though, the utilization of coherences as a tool for high-detail vibronic spectroscopy has largely been overlooked until recently, despite their encoding of key information regarding molecular structure, electronically sensitive vibrational modes, and intermolecular interactions...
October 18, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29043641/measuring-dynamic-behavior-of-trinucleotide-repeat-tracts-in-vivo-in-saccharomyces-cerevisiae
#12
Gregory M Williams, Jennifer A Surtees
Trinucleotide repeat (TNR) tracts are inherently unstable during DNA replication, leading to repeat expansions and/or contractions. Expanded tracts are the cause of over 40 neurodegenerative and neuromuscular diseases. In this chapter, we focus on the (CNG)n repeat sequences that, when expanded, lead to Huntington's disease (HD), myotonic dystrophy type 1 (DM1), and a number of other neurodegenerative diseases. We describe a series of in vivo assays, using the model system Saccharomyces cerevisiae, to determine and characterize the dynamic behavior of TNR tracts that are in the early stages of expansion, i...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043627/quantitative-bromodeoxyuridine-immunoprecipitation-analyzed-by-high-throughput-sequencing-qbrdu-seq-or-qbu
#13
Joanna E Haye-Bertolozzi, Oscar M Aparicio
Incorporation into DNA of nucleoside analogs like 5-bromo-2'-deoxyuridine (BrdU) is a powerful tool for in vivo studies of DNA synthesis during replication and repair. Immunoprecipitation of BrdU-labeled DNA analyzed by DNA sequencing (BrdU-IP-seq) allows for genome-wide, sequence-specific tracking of replication origin and replication fork dynamics under different conditions, such as DNA damage and replication stress, and in mutant strains. We have recently developed a quantitative method for BrdU-IP-seq (qBrdU-seq) involving DNA barcoding to enable quantitative analysis of multiple experimental samples subjected to BrdU-IP-seq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043353/machine-learnt-bond-order-potential-to-model-metal-organic-co-c-heterostructures
#14
Badri Narayanan, Henry Chan, Alper Kinaci, Fatih G Sen, Stephen K Gray, Maria K Y Chan, Subramanian K R S Sankaranarayanan
A fundamental understanding of the inter-relationships between structure, morphology, atomic scale dynamics, chemistry, and physical properties of mixed metallic-covalent systems is essential to design novel functional materials for applications in flexible nano-electronics, energy storage and catalysis. To achieve such knowledge, it is imperative to develop robust and computationally efficient atomistic models that describe atomic interactions accurately within a single framework. Here, we present a unified Tersoff-Brenner type bond order potential (BOP) for a Co-C system, trained against lattice parameters, cohesive energies, equation of state, and elastic constants of different crystalline phases of cobalt as well as orthorhombic Co2C derived from density functional theory (DFT) calculations...
October 18, 2017: Nanoscale
https://www.readbyqxmd.com/read/29042780/frequencies-of-circulating-b-and-t-lymphocytes-as-indicators-for-stroke-outcomes
#15
Yanling Wang, Jihong Liu, Xuemei Wang, Zongjian Liu, Fengwu Li, Fenghua Chen, Xiaokun Geng, Zhili Ji, Huishan Du, Xiaoming Hu
BACKGROUND: Stroke has high mortality and morbidity. Biomarkers are required for to predict stroke outcomes, which could help clinicians to provide rationale approaches for patient management. The dynamic changes in circulating immune cells have been reported in stroke patients and animal models of stroke. AIM: The aim of this study was to explore biomarkers to predict stroke outcomes by investigating the relationship between the frequencies of circulating immune cells and stroke outcomes...
2017: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/29042666/equation-of-state-and-self-bound-droplet-in-rabi-coupled-bose-mixtures
#16
Alberto Cappellaro, Tommaso Macrì, Giovanni F Bertacco, Luca Salasnich
Laser induced transitions between internal states of atoms have been playing a fundamental role to manipulate atomic clouds for many decades. In absence of interactions each atom behaves independently and their coherent quantum dynamics is described by the Rabi model. Since the experimental observation of Bose condensation in dilute gases, static and dynamical properties of multicomponent quantum gases have been extensively investigated. Moreover, at very low temperatures quantum fluctuations crucially affect the equation of state of many-body systems...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042538/volcanic-suppression-of-nile-summer-flooding-triggers-revolt-and-constrains-interstate-conflict-in-ancient-egypt
#17
Joseph G Manning, Francis Ludlow, Alexander R Stine, William R Boos, Michael Sigl, Jennifer R Marlon
Volcanic eruptions provide tests of human and natural system sensitivity to abrupt shocks because their repeated occurrence allows the identification of systematic relationships in the presence of random variability. Here we show a suppression of Nile summer flooding via the radiative and dynamical impacts of explosive volcanism on the African monsoon, using climate model output, ice-core-based volcanic forcing data, Nilometer measurements, and ancient Egyptian writings. We then examine the response of Ptolemaic Egypt (305-30 BCE), one of the best-documented ancient superpowers, to volcanically induced Nile suppression...
October 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29042301/towards-a-first-implementation-of-the-wlimes-approach-in-living-system-studies-advancing-the-diagnostics-and-therapy-in-personalized-medicine
#18
Plamen L Simeonov, Andrée C Ehresmann
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design...
October 14, 2017: Bio Systems
https://www.readbyqxmd.com/read/29041600/analysis-of-a-lens-array-modulated-coaxial-holographic-data-storage-system-with-considering-recording-dynamics-of-material
#19
Yeh-Wei Yu, Chi-Hsiang Yang, Tsung-Hsun Yang, Shiuan-Huei Lin, Ching-Cherng Sun
In the first time, a simulation model with considering the recording dynamics of material is built and is used to simulate evolution of the grating strength of the recorded hologram in a coaxial volume holographic memory system. In addition, phase modulation by lens array in the reference is introduced and observed to perform better diffracted signal quality and higher shifting selectivity, in both simulation and experiment. The use of lens array is found to provide multiple advantages in volume holographic memory system...
September 18, 2017: Optics Express
https://www.readbyqxmd.com/read/29040743/anger-sensitive-networks-characterising-neural-systems-recruited-during-aggressive-social-interactions-using-data-driven-analysis
#20
Frederike Beyer, Ulrike M Krämer, Christian F Beckmann
Social neuroscience uses increasingly complex paradigms to improve ecological validity, as investigating aggressive interactions with functional magnetic resonance imaging (fMRI; Krämer, Jansma, Tempelmann, & Münte, 2007). Standard analyses for fMRI data typically use general linear models (GLM), which require a priori models of task effects on neural processes. These may inadequately model non-stimulus-locked or temporally overlapping cognitive processes, as mentalizing about other agents.We used the data-driven approach of independent component analysis (ICA) to investigate neural processes involved in a competitive interaction...
October 4, 2017: Social Cognitive and Affective Neuroscience
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