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https://www.readbyqxmd.com/read/29341613/what-gives-an-insulin-hexamer-its-unique-shape-and-stability-role-of-ten-confined-water-molecules
#1
Saumyak Mukherjee, Sayantan Mondal, Ashish Anilrao Deshmukh, Balasubramanian Gopal, Biman Bagchi
Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn2+, Ca2+ etc. in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations and X-ray analyses to discover that a team of approximately ten water molecules confined inside a barrel-shaped nano-cavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly...
January 17, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29341020/mri-in-the-study-of-animal-models-of-stroke
#2
Pedro Ramos-Cabrer, Daniel Padro
Stroke consists of the loss of cerebral functions resulting from the interruption of blood supply to a region of the brain, and represents the second cause of death and the leading cause of major disability in adults in Europe. Stroke is a very active field of research at preclinical and clinical levels, and Magnetic Resonance Imaging (MRI) is one of the most powerful tools that scientist and clinicians have for the study of the onset, evolution and consequences of this devastating disease, as well as for the monitoring of the success of available treatments, or for the development of novel therapeutic strategies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29340803/robust-exponential-memory-in-hopfield-networks
#3
Christopher J Hillar, Ngoc M Tran
The Hopfield recurrent neural network is a classical auto-associative model of memory, in which collections of symmetrically coupled McCulloch-Pitts binary neurons interact to perform emergent computation. Although previous researchers have explored the potential of this network to solve combinatorial optimization problems or store reoccurring activity patterns as attractors of its deterministic dynamics, a basic open problem is to design a family of Hopfield networks with a number of noise-tolerant memories that grows exponentially with neural population size...
January 16, 2018: Journal of Mathematical Neuroscience
https://www.readbyqxmd.com/read/29340399/landscape-of-gene-networks-for-random-parameter-perturbation
#4
Chunhe Li
Landscape approaches have been exploited to study the stochastic dynamics of gene networks. However, how to calculate the landscape with a wide range of parameter variations and how to investigate the influence of the network topology on the global properties of gene networks remain to be elucidated. Here, I developed an approach for the landscape of random parameter perturbation (LRPP) to address this issue. Based on a self-consistent approximation approach, by making perturbations to parameters in a given range, I obtained the landscape for gene network systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29340250/integrated-genomic-analyses-of-lung-squamous-cell-carcinoma-for-identification-of-a-possible-competitive-endogenous-rna-network-by-means-of-tcga-datasets
#5
Pengbo Ning, Zhongxing Wu, Aoxue Hu, Xuepeng Li, Jun He, Xiaocheng Gong, Yuqiong Xia, Yukui Shang, Huijie Bian
The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play important roles in the initiation, progression, and metastasis of human cancers. Nonetheless, a mechanistic understanding of noncoding RNA functions in lung squamous cell carcinoma (LUSC) is lacking. To fill this critical gap in knowledge, we obtained mRNA, miRNA, and lncRNA expression data on patients with LUSC from the updated Cancer Genome Atlas (TCGA) database (2016)...
2018: PeerJ
https://www.readbyqxmd.com/read/29340037/systemic-bioinformatics-analysis-of-recurrent-aphthous-stomatitis-gene-expression-profiles
#6
Jian Wu, Zheng-Ping Chen, An-Quan Shang, Wei-Wei Wang, Zong-Ning Chen, Yun-Juan Tao, Yue Zhou, Wan-Xiang Wang
Recurrent aphthous stomatitis (RAS) represents the most common chronic oral diseases with the prevalence ranges from 5% to 25% for different populations. Its pathogenesis remains poorly understood, which limits the development of effective drugs and treatment methods. In this study, we conducted systemic bioinformatics analysis of gene expression profiles from the Gene Expression Omnibus (GEO) to identify potential drug targets for RAS. We firstly downloaded the gene microarray datasets with the accession number of GSE37265 from GEO and performed robust multi-array (RMA) normalization with affy R programming package...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339553/engineering-abiotic-stress-response-in-plants-for-biomass-production
#7
Sneh Lata Singla-Pareek, Rohit Joshi, Ashwani Pareek
One of the major challenges in today's agriculture is to achieve enhanced plant growth and biomass even under adverse environmental conditions. Recent advancements in genetics and molecular biology have enabled identification of a complex signaling network contributing towards plant growth and development on the one hand and abiotic stress response on the other. As an outcome of these studies, three major approaches have been identified having a potential to improve biomass production in plants under abiotic stress conditions...
January 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29339492/cytocapsular-tubes-conduct-cell-translocation
#8
Tingfang Yi, Gerhard Wagner
Cell locomotion is essential for multicellular organism embryo development, organ homeostasis, tissue regeneration, immune responses, and tumor metastasis. Here we report that single mammalian cells can generate two extracellular membranous compartments: cytocapsulae and cytocapsular tubes. Cells migrate in cytocapsulae and engender cytocapsular tubes, which exhibit pleiotropic biological functions and provide tubular routes for directed cell transportation. Ultrastructural analysis by electron microscope revealed that nanoprotrusions surround and anchor cytocapsular tubes in place...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339075/up-regulated-lncrna-msx2p1-promotes-the-growth-of-il-22-stimulated-keratinocytes-by-inhibiting-mir-6731-5p-and-activating-s100a7
#9
Meng Qiao, Ronghua Li, Xintong Zhao, Jianjun Yan, Qing Sun
Competitive endogenous RNAs (ceRNAs) regulate RNA transcripts by competing for shared miRNAs and play critical roles in disease development. Psoriasis is a long-lasting, recurring chronic inflammatory skin disease characterized by hyperproliferation of keratinocytes. The keratinocyte response is triggered by the activation of inflammatory cytokines, like interleukin-22 (IL-22). We used lncRNA array analysis to detect differentially expressed lncRNAs in skin (HaCaT) cells treated with or without IL-22. We used hematoxylin and eosin (H&E) staining to determine the pathological changes in skin cells and immunohistochemistry to evaluate the expression of S100A7...
January 12, 2018: Experimental Cell Research
https://www.readbyqxmd.com/read/29338708/patterns-of-illness-disclosure-among-indian-slum-dwellers-a-qualitative-study
#10
Moumita Das, Federica Angeli, Anja J S M Krumeich, Onno C P van Schayck
BACKGROUND: Slum dwellers display specific traits when it comes to disclosing their illnesses to professionals. The resulting actions lead to poor health-seeking behaviour and underutilisation of existing formal health facilities. The ways that slum people use to communicate their feelings about illness, the type of confidants that they choose, and the supportive and unsupportive social and cultural interactions to which they are exposed have not yet been studied in the Indian context, which constitutes an important knowledge gap for Indian policymakers and practitioners alike...
January 16, 2018: BMC International Health and Human Rights
https://www.readbyqxmd.com/read/29338560/scientists-instruments-and-even-brains-in-transfer-german-spanish-postwar-networks-and-the-construction-of-the-neuroendocrine-system-1952-1960
#11
Raúl Velasco Morgado
This article presents the process of relocation of hegemonies and "center-periphery" dynamics in neuroanatomy after World War II through the study of the links between the Spanish anatomical school of José Escolar García and some German institutions. We have analyzed their works on the morphology of the neuroendocrine system as a case study, showing how the first contacts of the Spaniards with the United States started a material transfer process between centers on both sides of the Atlantic Ocean through the mediation-and adaptation-of the periphery...
January 1, 2018: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
https://www.readbyqxmd.com/read/29338122/no-co-and-h2-s-what-about-gasotransmitters-in-fish-and-amphibian-hearts
#12
REVIEW
Sandra Imbrogno, Mariacristina Filice, Maria Carmela Cerra, Alfonsina Gattuso
The gasotransmitters nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2 S), long considered only toxicant, are produced in vivo during the catabolism of common biological molecules, and are crucial for a large variety of physiological processes. Mounting evidence is emerging that in poikilotherm vertebrates, as in mammals, they modulate the basal performance of the heart and the response to stress challenges. In this review, we will focus on teleost fish and amphibians to highlight the evolutionary importance in vertebrates of the cardiac control elicited by NO, CO and H2 S, and the conservation of the intracellular cascades they activate...
January 16, 2018: Acta Physiologica
https://www.readbyqxmd.com/read/29337486/improving-risk-stratification-among-veterans-diagnosed-with-prostate-cancer-impact-of-the-17-gene-prostate-score-assay
#13
Julie A Lynch, Megan P Rothney, Raoul R Salup, Cesar E Ercole, Sharad C Mathur, David A Duchene, Joseph W Basler, Javier Hernandez, Michael A Liss, Michael P Porter, Jonathan L Wright, Michael C Risk, Mark Garzotto, Olga Efimova, Laurie Barrett, Brygida Berse, Michael J Kemeter, Phillip G Febbo, Atreya Dash
BACKGROUND: Active surveillance (AS) has been widely implemented within Veterans Affairs' medical centers (VAMCs) as a standard of care for low-risk prostate cancer (PCa). Patient characteristics such as age, race, and Agent Orange (AO) exposure may influence advisability of AS in veterans. The 17-gene assay may improve risk stratification and management selection. OBJECTIVES: To compare management strategies for PCa at 6 VAMCs before and after introduction of the Oncotype DX Genomic Prostate Score (GPS) assay...
January 2018: American Journal of Managed Care
https://www.readbyqxmd.com/read/29337412/metallic-nanodot-patterns-with-unique-symmetries-templated-from-abc-triblock-terpolymer-networks
#14
Karim Aissou, Muhammad Mumtaz, Alberto Alvarez-Fernandez, Jean Mercat, Ségolène Antoine, Gilles Pécastaings, Virginie Ponsinet, Cécile Dobrzynski, Guillaume Fleury, Georges Hadziioannou
Nanotemplates derived from the self-assembly of AB-type block copolymers provide an elegant route to achieve well-defined metallic dot arrays, even if the variety of pattern symmetries is restricted due to the limited number of structures offered by microphase separated diblock copolymers. A strategy that relies on the use of complex network structures accessible through the self-assembly of linear ABC-type terpolymers is presented for the formation of metallic nanodots arrays with "outside-the-box" symmetries...
January 16, 2018: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/29337288/network-based-method-for-detecting-dysregulated-pathways-in-glioblastoma-cancer
#15
Hao Wu, Jihua Dong, Jicheng Wei
The knowledge on the biological molecular mechanisms underlying cancer is important for the precise diagnosis and treatment of cancer patients. Detecting dysregulated pathways in cancer can provide insights into the mechanism of cancer and help to detect novel drug targets. Based on the wide existing mutual exclusivity among mutated genes and the interrelationship between gene mutations and expression changes, this study presents a network-based method to detect the dysregulated pathways from gene mutations and expression data of the glioblastoma cancer...
February 2018: IET Systems Biology
https://www.readbyqxmd.com/read/29337287/revealing-determinants-of-two-phase-dynamics-of-p53-network-under-gamma-irradiation-based-on-a-reduced-2d-relaxation-oscillator-model
#16
Gökhan Demirkıran, Güleser Kalaycı Demir, Cüneyt Güzeliş
This study proposes a two-dimensional (2D) oscillator model of p53 network, which is derived via reducing the multidimensional two-phase dynamics model into a model of ataxia telangiectasia mutated (ATM) and Wip1 variables, and studies the impact of p53-regulators on cell fate decision. First, the authors identify a 6D core oscillator module, then reduce this module into a 2D oscillator model while preserving the qualitative behaviours. The introduced 2D model is shown to be an excitable relaxation oscillator...
February 2018: IET Systems Biology
https://www.readbyqxmd.com/read/29337284/method-for-identification-of-sensitive-nodes-in-boolean-models-of-biological-networks
#17
Pooja A Dnyane, Shraddha S Puntambekar, Chetan J Gadgil
Biological systems are often represented as Boolean networks and analysed to identify sensitive nodes which on perturbation disproportionately change a predefined output. There exist different kinds of perturbation methods: perturbation of function, perturbation of state and perturbation in update scheme. Nodes may have defects in interpretation of the inputs from other nodes and calculation of the node output. To simulate these defects and systematically assess their effect on the system output, two new function perturbations, referred to as 'not of function' and 'function of not', are introduced...
February 2018: IET Systems Biology
https://www.readbyqxmd.com/read/29337088/cross-regulatory-network-in-pseudomonas-aeruginosa-biofilm-genes-and-tio2-anatase-induced-molecular-perturbations-in-key-proteins-unraveled-by-a-systems-biology-approach
#18
Rani Anupama, S Sajitha Lulu, Amitava Mukherjee, Subramanian Babu
A systems biology approach was used to study all the biofilm related genes of P. aeruginosa PAO1, and the interaction of titanium dioxide (TiO2) anatase with biofilm related proteins. Among the 71 genes, the interactions of all the nodal pairs were extracted by STRING 10.5 database. The inter-relationship among these genes was predicted by constructing complete PPI network and visualized in Cytoscape v 3.4.0. Total number of nodes of the network was found to be 335 and edges were 795. The network was further investigated for its clusters and the best cluster was further analyzed for the hub proteins which significantly contribute in cross-regulation of the biofilm related process...
January 11, 2018: Gene
https://www.readbyqxmd.com/read/29336875/systems-pharmacology-dissection-of-the-anti-stroke-mechanism-for-the-chinese-traditional-medicine-xing-nao-jing
#19
Yuhua Chen, Yue Sun, Wende Li, Hong Wei, Tianlin Long, Hua Li, Quanhua Xu, Wei Liu
Xing-Nao-Jing (XNJ) is a well-known injection that has been extensively applied in clinical treatment of stroke in China. However, the underlying mechanism of clinical administration of XNJ in stroke remains unclear. In this study, a systems pharmacology strategy based on pharmacokinetic and pharmacodynamics data was applied to analyze the pharmacological effect of XNJ on stroke. Sixteen active compounds were filtered from XNJ through Drug-likeness (DL) and Brain-blood-barrier (BBB) evaluations. Ninety-four potential targets of these active components were identified by SysDT and SEA...
December 20, 2017: Journal of Pharmacological Sciences
https://www.readbyqxmd.com/read/29336158/chromosome-gene-orientations-inversion-networks-goins-of-plasmodium-proteome
#20
Viviana F Quevedo-Tumailli, Bernabe Ortega-Tenezaca, Humbert Gonzalez-Diaz
The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans and many more are organised in larger clusters. This raises intriguing questions asked by different authors before. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? In this paper, we define a new kind of network coined as the Gene Orientation Inversion Network (GOIN)...
January 16, 2018: Journal of Proteome Research
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