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https://www.readbyqxmd.com/read/28545060/signet-a-signaling-network-data-simulator-to-enable-signaling-network-inference
#1
Elizabeth A Coker, Costas Mitsopoulos, Paul Workman, Bissan Al-Lazikani
Network models are widely used to describe complex signaling systems. Cellular wiring varies in different cellular contexts and numerous inference techniques have been developed to infer the structure of a network from experimental data of the network's behavior. To objectively identify which inference strategy is best suited to a specific network, a gold standard network and dataset are required. However, suitable datasets for benchmarking are difficult to find. Numerous tools exist that can simulate data for transcriptional networks, but these are of limited use for the study of signaling networks...
2017: PloS One
https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#2
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544832/percutaneous-antegrade-trans-septal-closure-of-mitral-paravalvular-leak-without-creation-of-an-arteriovenous-wire-loop-in-patients-with-coexistent-mechanical-aortic-valve
#3
Teoman Kilic, Senol Coskun, Kurtulus Karauzum, Sadan Yavuz, Tayfun Sahin
BACKGROUND: Various approaches such as antegrade trans-septal, retrograde transfemoral and transapical techniques have been used to close mitral paravalvular leak (PVL) in patients with an aortic prosthesis. During the implementation of these techniques, an arteriovenous guidewire loop is often created for device delivery. However, passing through a mechanical aortic valve may cause hemodynamic compromise and prolong the procedure. To date, no studies have evaluated antegrade mitral PVL closure without the use of an arteriovenous wire loop in patients with a mechanical aortic prosthesis...
January 2017: Journal of Heart Valve Disease
https://www.readbyqxmd.com/read/28544810/the-best-models-of-metabolism
#4
REVIEW
Eberhard O Voit
Biochemical systems are among of the oldest application areas of mathematical modeling. Spanning a time period of over one hundred years, the repertoire of options for structuring a model and for formulating reactions has been constantly growing, and yet, it is still unclear whether or to what degree some models are better than others and how the modeler is to choose among them. In fact, the variety of options has become overwhelming and difficult to maneuver for novices and experts alike. This review outlines the metabolic model design process and discusses the numerous choices for modeling frameworks and mathematical representations...
May 19, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28544801/nanotherapeutic-systems-for-local-treatment-of-brain-tumors
#5
REVIEW
Rami Walid Chakroun, Pengcheng Zhang, Ran Lin, Paula Schiapparelli, Alfredo Quinones-Hinojosa, Honggang Cui
Malignant brain tumor, including the most common type glioblastoma, are histologically heterogeneous and invasive tumors known as the most devastating neoplasms with high morbidity and mortality. Despite multimodal treatment including surgery, radiotherapy, chemotherapy, and immunotherapy, the disease inevitably recurs and is fatal. This lack of curative options has motivated researchers to explore new treatment strategies and to develop new drug delivery systems (DDSs); however, the unique anatomical, physiological, and pathological features of brain tumors greatly limit the effectiveness of conventional chemotherapy...
May 24, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28544800/reinforced-microextraction-of-polycyclic-aromatic-hydrocarbons-from-polluted-soil-samples-using-an-in-needle-coated-fiber-with-polypyrrole-graphene-oxide-nanocomposite
#6
Mina Behfar, Ali Reza Ghiasvand, Fatemeh Yazdankhah
The surface of a stainless-steel wire was platinized using electrophoretic deposition method to create a high-surface-area, porous and cohesive substrate. The platinized fiber was coated by the polypyrrole/graphene oxide nanocomposite by electropolymerization and accommodated into a stainless-steel needle to fabricate an in-needle coated fiber. The developed setup was coupled to gas chromatography with flame ionization detection and applied to extract and determine polycyclic aromatic hydrocarbons (naphthalene, fluorene, phenanthrene, fluoranthene and pyrene) in complicated solid matrices, along with reinforcement of the extraction by cooling the sorbent, using liquid carbon dioxide...
May 25, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28544658/the-evolution-of-stories-from-mimesis-to-language-from-fact-to-fiction
#7
REVIEW
Brian Boyd
Why a species as successful as Homo sapiens should spend so much time in fiction, in telling one another stories that neither side believes, at first seems an evolutionary riddle. Because of the advantages of tracking and recombining true information, capacities for event comprehension, memory, imagination, and communication evolved in a range of animal species-yet even chimpanzees cannot communicate beyond the here and now. By Homo erectus, our forebears had reached an increasing dependence on one another, not least in sharing information in mimetic, prelinguistic ways...
May 24, 2017: Wiley Interdisciplinary Reviews. Cognitive Science
https://www.readbyqxmd.com/read/28544556/electrophysiological-analysis-of-synaptic-transmission-in-drosophila
#8
REVIEW
Maria Bykhovskaia, Alexander Vasin
Synaptic transmission is dynamic, plastic, and highly regulated. Drosophila is an advantageous model system for genetic and molecular studies of presynaptic and postsynaptic mechanisms and plasticity. Electrical recordings of synaptic responses represent a wide-spread approach to study neuronal signaling and synaptic transmission. We discuss experimental techniques that allow monitoring synaptic transmission in Drosophila neuromuscular and central systems. Recordings of synaptic potentials or currents at the larval neuromuscular junction (NMJ) are most common and provide numerous technical advantages due to robustness of the preparation, large and identifiable muscles, and synaptic boutons which can be readily visualized...
May 24, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28544521/oral-nucleic-acid-therapy-using-multicompartmental-delivery-systems
#9
REVIEW
Husain Attarwala, Murui Han, Jonghan Kim, Mansoor Amiji
Nucleic acid-based therapeutics has the potential for treating numerous diseases by correcting abnormal expression of specific genes. Lack of safe and efficacious delivery strategies poses a major obstacle limiting clinical advancement of nucleic acid therapeutics. Oral route of drug administration has greater delivery challenges, because the administered genes or oligonucleotides have to bypass degrading environment of the gastrointestinal (GI) tract in addition to overcoming other cellular barriers preventing nucleic acid delivery...
May 24, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28544514/dynamic-enhancer-function-in-the-chromatin-context
#10
REVIEW
Ido Goldstein, Gordon L Hager
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding...
May 22, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28544497/cell-tracking-using-gold-nanoparticles-and-computed-tomography-imaging
#11
REVIEW
Rinat Meir, Rachela Popovtzer
Cell-based therapies utilize transplantation of living cells with therapeutic traits to alleviate numerous diseases and disorders. The use of such biological agents is an attractive alternative for diseases that existing medicine cannot effectively treat. Although very promising, translating cell therapy to the clinic has proven to be challenging, due to inconsistent results in preclinical and clinical studies. To examine the underlying cause for these inconsistencies, it is crucial to noninvasively monitor the accuracy of cell injection, and cell survival and migration patterns...
May 24, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28544390/phenotypic-plasticity-and-remodeling-in-the-stress-induced-caenorhabditis-elegans-dauer
#12
REVIEW
Rebecca J Androwski, Kristen M Flatt, Nathan E Schroeder
Organisms are often capable of modifying their development to better suit their environment. Under adverse conditions, the nematode Caenorhabditis elegans develops into a stress-resistant alternative larval stage called dauer. The dauer stage is the primary survival stage for C. elegans in nature. Large-scale tissue remodeling during dauer conveys resistance to harsh environments. The environmental and genetic regulation of the decision to enter dauer has been extensively studied. However, less is known about the mechanisms regulating tissue remodeling...
May 24, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28541362/preparation-of-graphene-by-electrical-explosion-of-graphite-sticks
#13
Xin Gao, Chunxiao Xu, Hao Yin, Xiaoguang Wang, Qiuzhi Song, Pengwan Chen
Graphene nanosheets were produced by electrical explosion of high-purity graphite sticks in distilled water at room temperature. The as-prepared samples were characterized by various techniques to find different forms of carbon phases, including graphite nanosheets, few-layer graphene, and especially, mono-layer graphene with good crystallinity. Delicate control of energy injection is critical for graphene nanosheet formation, whereas mono-layer graphene was produced under the charging voltage of 22.5-23.5 kV...
May 25, 2017: Nanoscale
https://www.readbyqxmd.com/read/28541304/digital-logic-circuits-in-yeast-with-crispr-dcas9-nor-gates
#14
Miles W Gander, Justin D Vrana, William E Voje, James M Carothers, Eric Klavins
Natural genetic circuits enable cells to make sophisticated digital decisions. Building equally complex synthetic circuits in eukaryotes remains difficult, however, because commonly used components leak transcriptionally, do not arbitrarily interconnect or do not have digital responses. Here, we designed dCas9-Mxi1-based NOR gates in Saccharomyces cerevisiae that allow arbitrary connectivity and large genetic circuits. Because we used the chromatin remodeller Mxi1, our gates showed minimal leak and digital responses...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28541035/three-dimensional-printing-of-silver-microarchitectures-using-newtonian-nanoparticle-inks
#15
Sanghyeon Lee, Jung Hyun Kim, Muhammad Wajahat, Hwakyung Jeong, Won Suk Chang, Sung Ho Cho, Ji Tae Kim, Seung Kwon Seol
Although three-dimensional (3D) printing has recently emerged as a technology to potentially bring about the next industrial revolution, the limited selection of usable materials restricts its use to simple prototyping. In particular, metallic 3D printing with submicrometer spatial resolution is essential for the realization of 3D-printed electronics. Herein, a meniscus-guided 3D printing method that exploits a low-viscosity (∼7 mPa·s) silver nanoparticle (AgNP) ink meniscus with Newtonian fluid characteristics (which is compatible with conventional inkjet printers) to fabricate 3D silver microarchitectures is reported...
May 25, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28540635/wire-bias-in-coronary-measurement-using-optical-coherence-tomography
#16
Edward James Danson, Peter Hansen, Ravinay Bhindi
OCT is widely used for accurate coronary stent sizing; however, the impact of coronary tortuosity or guide wire weight on the accuracy of OCT in assessing coronary dimensions is not known. This study sought to determine whether guide wire properties impact on coronary diameter and length estimation by optical coherence tomography (OCT) in tortuous segments of coronary artery. OCT coronary diameters were determined in selected patients with tortuous arteries before and after removal of a supportive guide wire to obtain unobscured images...
May 24, 2017: Cardiovascular Intervention and Therapeutics
https://www.readbyqxmd.com/read/28540569/altered-purinergic-signaling-in-uridine-adenosine-tetraphosphate-induced-coronary-relaxation-in-swine-with-metabolic-derangement
#17
Zhichao Zhou, Oana Sorop, Vincent J de Beer, Ilkka Heinonen, Caroline Cheng, A H Jan Danser, Dirk J Duncker, Daphne Merkus
We previously demonstrated that uridine adenosine tetraphosphate (Up4A) induces potent and partially endothelium-dependent relaxation in the healthy porcine coronary microvasculature. We subsequently showed that Up4A-induced porcine coronary relaxation was impaired via downregulation of P1 receptors after myocardial infarction. In view of the deleterious effect of metabolic derangement on vascular function, we hypothesized that the coronary vasodilator response to Up4A is impaired in metabolic derangement, and that the involvement of purinergic receptor subtypes and endothelium-derived vasoactive factors (EDVFs) is altered...
May 24, 2017: Purinergic Signalling
https://www.readbyqxmd.com/read/28539882/function-and-dysfunction-of-microglia-during-brain-development-consequences-for-synapses-and-neural-circuits
#18
REVIEW
Rosa C Paolicelli, Maria T Ferretti
Many diverse factors, ranging from stress to infections, can perturb brain homeostasis and alter the physiological activity of microglia, the immune cells of the central nervous system. Microglia play critical roles in the process of synaptic maturation and brain wiring during development. Any perturbation affecting microglial physiological function during critical developmental periods could result in defective maturation of synaptic circuits. In this review, we critically appraise the recent literature on the alterations of microglial activity induced by environmental and genetic factors occurring at pre- and early post-natal stages...
2017: Frontiers in Synaptic Neuroscience
https://www.readbyqxmd.com/read/28539397/variations-on-a-theme-species-differences-in-synaptic-connectivity-do-not-predict-central-pattern-generator-activity
#19
Charuni A Gunaratne, Akira Sakurai, Paul S Katz
A fundamental question in comparative neuroethology is the extent to which synaptic wiring determines behavior versus the extent to which it is constrained by phylogeny. We investigated this by examining the connectivity and activity of homologous neurons in different species. Melibe leonina and Dendronotus iris (Mollusca, Gastropoda, Nudibranchia) have homologous neurons and exhibit homologous swimming behaviors consisting of alternating left-right (LR) whole body flexions. Yet, a homologous interneuron (Si1) differs between the two species in its participation in the swim motor pattern (SMP) and synaptic connectivity...
May 24, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28539389/let-s-burn-whatever-you-have-mitofusin-2-metabolically-re-wires-brown-adipose-tissue
#20
Marcel Scheideler, Stephan Herzig
No abstract text is available yet for this article.
May 24, 2017: EMBO Reports
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