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structural connectivity

Keisuke Handa, Syouta Abe, V Venkata Suresh, Yoshiyasu Fujieda, Masaki Ishikawa, Ai Orimoto, Yoko Kobayashi, Satoru Yamada, Satoko Yamaba, Shinya Murakami, Masahiro Saito
OBJECTIVE: Marfan syndrome (MFS) is a systemic connective tissue disorder caused by insufficient fibrillin-1 (FBN-1), a major component of microfibrils that controls the elasticity and integrity of connective tissues. FBN-1 insufficiency in MFS leads to structural weakness, which causes various tissue disorders, including cardiovascular and periodontal disease. However, the role of FBN-1 insufficiency in the destruction and regeneration of connective tissue has not yet been clarified...
March 6, 2018: Archives of Oral Biology
Renata Gruszka, Magdalena Zakrzewska
The fundamental function of ribonucleic acids is to transfer genetic information from DNA to protein during translation process, however, this is not the only way connecting active RNA sequences with essential biological processes. Up until now, many RNA subclasses of different size, structure, and biological function were identified. Among them, there are non-coding single-stranded microRNAs (miRNAs). This subclass comprises RNAs of 19-25 nucleotides in length that modulate the activity of well-defined coding RNAs and play a crucial role in many physiological and pathological processes...
March 16, 2018: International Journal of Molecular Sciences
Ognjen Perišić
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM...
March 16, 2018: Pharmaceuticals
Ariel Talavera, Jelle Hendrix, Wim Versées, Dukas Jurėnas, Katleen Van Nerom, Niels Vandenberk, Ranjan Kumar Singh, Albert Konijnenberg, Steven De Gieter, Daniel Castro-Roa, Anders Barth, Henri De Greve, Frank Sobott, Johan Hofkens, Nikolay Zenkin, Remy Loris, Abel Garcia-Pino
Bacterial protein synthesis is intricately connected to metabolic rate. One of the ways in which bacteria respond to environmental stress is through posttranslational modifications of translation factors. Translation elongation factor Tu (EF-Tu) is methylated and phosphorylated in response to nutrient starvation upon entering stationary phase, and its phosphorylation is a crucial step in the pathway toward sporulation. We analyze how phosphorylation leads to inactivation of Escherichia coli EF-Tu. We provide structural and biophysical evidence that phosphorylation of EF-Tu at T382 acts as an efficient switch that turns off protein synthesis by decoupling nucleotide binding from the EF-Tu conformational cycle...
March 2018: Science Advances
Anna Szewczyk, Julie Gehl, Malgorzata Daczewska, Jolanta Saczko, Stine Krog Frandsen, Julita Kulbacka
Calcium electroporation (CaEP) describes the use of electric pulses (electroporation) to transiently permeabilize cells to allow supraphysiological doses of calcium to enter the cytosol. Calcium electroporation has successfully been investigated for treatment of cutaneous metastases in a clinical study. This preclinical study explores the possible use of calcium electroporation for treatment of sarcoma. A normal murine muscle cell line (C2C12), and a human rhabdomyosarcoma cell line (RD) were used in the undifferentiated and differentiated state...
February 20, 2018: Oncotarget
Guillermo de Anda-Jáuregui, Kai Guo, Brett A McGregor, Junguk Hur
The quintessential biological response to disease is inflammation. It is a driver and an important element in a wide range of pathological states. Pharmacological management of inflammation is therefore central in the clinical setting. Anti-inflammatory drugs modulate specific molecules involved in the inflammatory response; these drugs are traditionally classified as steroidal and non-steroidal drugs. However, the effects of these drugs are rarely limited to their canonical targets, affecting other molecules and altering biological functions with system-wide effects that can lead to the emergence of secondary therapeutic applications or adverse drug reactions (ADRs)...
2018: Frontiers in Physiology
Luqing Wei, Hong Chen, Guo-Rong Wu
The neurovisceral integration model has shown a key role of the amygdala in neural circuits underlying heart rate variability (HRV) modulation, and suggested that reciprocal connections from amygdala to brain regions centered on the central autonomic network (CAN) are associated with HRV. To provide neuroanatomical evidence for these theoretical perspectives, the current study used covariance analysis of MRI-based gray matter volume (GMV) to map structural covariance network of the amygdala, and then determined whether the interregional structural correlations related to individual differences in HRV...
2018: Frontiers in Human Neuroscience
Zhenyu Zhu, Rubin Wang, Fengyun Zhu
Based on the Hodgkin-Huxley model, the present study established a fully connected structural neural network to simulate the neural activity and energy consumption of the network by neural energy coding theory. The numerical simulation result showed that the periodicity of the network energy distribution was positively correlated to the number of neurons and coupling strength, but negatively correlated to signal transmitting delay. Moreover, a relationship was established between the energy distribution feature and the synchronous oscillation of the neural network, which showed that when the proportion of negative energy in power consumption curve was high, the synchronous oscillation of the neural network was apparent...
2018: Frontiers in Neuroscience
S N Beznosov, M G Pyatibratov, O V Fedorov
At the end of 1980s, regions of the polypeptide chain of bacterial flagella subunits (flagellins) responsible for different properties of these protein polymers were identified by structural studies. It was found that the N- and C-terminal regions are responsible for the polymerization properties of subunits, and the central region is responsible for antigenic properties of the flagellum. Soon after that, it was proposed to use variability of the central flagellin domain for directed modification to impart new properties to the flagellum surface...
January 2018: Biochemistry. Biokhimii︠a︡
Luis M Sesé
The problem of the equilibrium triplet structures in fluids with quantum behavior is discussed. Theoretical questions of interest to the real space structures are addressed by studying the three types of structures that can be determined via path integrals (instantaneous, centroid, and total thermalized-continuous linear response). The cases of liquid para-H2 and liquid neon on their crystallization lines are examined with path-integral Monte Carlo simulations, the focus being on the instantaneous and the centroid triplet functions (equilateral and isosceles configurations)...
March 14, 2018: Journal of Chemical Physics
K Beltako, F Michelini, N Cavassilas, L Raymond
Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse...
March 14, 2018: Journal of Chemical Physics
F Calvo, E Yurtsever
A flexible and polarizable interatomic potential has been developed to model hydrogen clusters interacting with one hydrogen anion, (H2 )n H- , in a broad range of sizes n = 1-54 and parametrized against coupled cluster quantum chemical calculations. Using path-integral molecular dynamics simulations at 1 K initiated from the putative classical global minima, the equilibrium structures are found to generally rely on icosahedral shells with the hydrogen molecules pointing toward the anion, producing geometric magic numbers at sizes n = 12, 32, and 44 that are in agreement with recent mass spectrometry measurements...
March 14, 2018: Journal of Chemical Physics
Viktor Müller, Johanna Sänger, Ulman Lindenberger
When playing music in an ensemble, musicians need to precisely coordinate their actions with one another. As shown in our previous studies on guitar duets, interbrain synchronization plays an essential role during such interactions. In this study, we simultaneously recorded electroencephalograms from four guitarists during quartet playing, to explore the extent and the functional significance of synchronized cortical activity across four brains. We found that hyperbrain networks based on intra- and interbrain connectivity across four brains dwell on higher frequencies for intrabrain communication and on lower frequencies for interbrain connections...
March 15, 2018: Annals of the New York Academy of Sciences
Jacobus H Visser, Nigel C Bennett, Bettine Jansen van Vuuren
The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis)...
2018: PloS One
Christopher Ebsch, Robert Rosenbaum
Understanding the relationship between external stimuli and the spiking activity of cortical populations is a central problem in neuroscience. Dense recurrent connectivity in local cortical circuits can lead to counterintuitive response properties, raising the question of whether there are simple arithmetical rules for relating circuits' connectivity structure to their response properties. One such arithmetic is provided by the mean field theory of balanced networks, which is derived in a limit where excitatory and inhibitory synaptic currents precisely balance on average...
March 15, 2018: PLoS Computational Biology
Colin K Egan, Francesco Paesani
The importance of many-body effects in the hydration of the hydroxide ion (OH- is investigated through a systematic analysis of the many-body expansion of the inter- action energy carried out at the CCSD(T) level of theory, extrapolated to the complete basis set limit, for the low-lying isomers of OH- (H2 O)n clusters, with n = 1 - 5. This is ac- complished by partitioning individual fragments extracted from the whole clusters into "groups" that are classified by both the number of OH- and H2 O molecules and the hydrogen bonding connectivity within each fragment...
March 15, 2018: Journal of Chemical Theory and Computation
Qing Li, Biao Yang, Jonas Björk, Qigang Zhong, Huanxin Ju, Junjie Zhang, Nan Cao, Ziliang Shi, Haiming Zhang, Daniel Ebeling, Andre Schirmeisen, Junfa Zhu, Lifeng Chi
Hierarchical control of chemical reactions is being considered as one of the most ambitious and challenging topics in modern organic chemistry. In this study, we have realized the one-by-one scission of the X-H bonds (X=N and C) of aromatic amines in a controlled fashion on the Cu(111) surface. Each dehydrogenation reaction leads to certain metal-organic supramolecular structures, which were monitored in single-bond resolution via scanning tunneling microscopy and non-contact atomic force microscopy. Moreover, the reaction pathways were elucidated from X-ray photoelectron spectroscopy measurements and density functional theory calculations...
March 15, 2018: Journal of the American Chemical Society
Alana Grech, Emmanuel Hanert, Len McKenzie, Michael Rasheed, Christopher Thomas, Samantha Tol, Mingzhu Wang, Michelle Waycott, Jolan Wolter, Rob Coles
The rate of exchange, or connectivity, among populations effects their ability to recover after disturbance events. However, there is limited information on the extent to which populations are connected or how multiple disturbances affect connectivity, especially in coastal and marine ecosystems. We used network analysis and the outputs of a biophysical model to measure potential functional connectivity and predict the impact of multiple disturbances on seagrasses in the central Great Barrier Reef World Heritage Area (GBRWHA), Australia...
March 15, 2018: Global Change Biology
Evgeny J Chumin, Joaquín Goñi, Meredith E Halcomb, Timothy C Durazzo, Mario Džemidžić, Karmen K Yoder
BACKGROUND: Diffusion weighted imaging (DWI) has been widely used to investigate the integrity of white matter (WM; indexed by fractional anisotropy, FA) in alcohol dependence and cigarette smoking. These disorders are highly comorbid, yet cigarette use has often not been adequately controlled in neuroimaging studies of alcohol dependent populations. In addition, information on white matter deficits in currently drinking, nontreatment-seeking (NTS) individuals with alcohol dependence is limited...
March 15, 2018: Alcoholism, Clinical and Experimental Research
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