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Complex system in biology

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https://www.readbyqxmd.com/read/30117918/label-free-multimodal-coherent-anti-stokes-raman-scattering-analysis-of-microparticles-in-unconstrained-microfluidics
#1
K O'Dwyer, R Mouras, A A Mani, D Rice, M Gleeson, N Liu, S A M Tofail, C Silien
Fast, label-free optical identification and quantification of biomolecules and other relevant biological materials in microfluidic devices and the vascular system will play a major role in liquid biopsy and related diagnoses. An optical microscope probing simultaneously non-linear coherent anti-Stokes Raman scattering (CARS) and linear scattering (LS) was used to probe microparticles in aqueous solutions flowed unconstrained in microfluidic channels. Despite the optical complexity of these systems, where out-of-focus microparticles randomly impede CARS and LS, and where water CARS generates a substantial background, we demonstrate that in-focus microparticles can be individually and unambiguously detected when CARS and LS are co-analyzed...
August 1, 2018: Applied Optics
https://www.readbyqxmd.com/read/30116818/automated-screening-of-c-elegans-neurodegeneration-mutants-enabled-by-microfluidics-and-image-analysis-algorithms
#2
Ivan de Carlos Cáceres, Daniel A Porto, Ivan Gallotta, Pamela Santonicola, Josue Rodríguez-Cordero, Elia Di Schiavi, Hang Lu
Spinal muscular atrophy (SMA) is a degenerative disorder that selectively deteriorates motor neurons due to a deficiency of survival motor neuron protein (SMN). The illness is the leading genetic cause of death in infants and is difficult to study in complex biological systems such as humans. A simpler model system, such as the nematode C. elegans, can be used to study potential mechanisms underlying this disease; C. elegans expresses the smn-1 gene, a homologue of SMN; powerful genetic tools in C. elegans research can be used to discover novel genes whose effect on SMN remains unknown or uncharacterized...
August 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/30116749/venom-from-bothrops-lanceolatus-a-snake-species-native-to-martinique-potently-activates-the-complement-system
#3
Marie Delafontaine, Isadora Maria Villas-Boas, Giselle Pidde, Carmen W van den Berg, Laurence Mathieu, Joël Blomet, Denise V Tambourgi
Bothrops lanceolatus snake venom causes systemic thrombotic syndrome but also local inflammation involving extensive oedema, pain, and haemorrhage. Systemic thrombotic syndrome may lead to fatal pulmonary embolism and myocardial and cerebral infarction. Here, we investigated the ability of B. lanceolatus venom to activate the Complement system (C) in order to improve the understanding of venom-induced local inflammation. Data presented show that B. lanceolatus venom is able to activate all C-pathways. In human serum, the venom strongly induced the generation of anaphylatoxins, such as C5a and C4a, and the Terminal Complement complex...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/30116502/antagonistic-phenomena-in-network-dynamics
#4
Adilson E Motter, Marc Timme
Recent research on the network modeling of complex systems has led to a convenient representation of numerous natural, social, and engineered systems that are now recognized as networks of interacting parts. Such systems can exhibit a wealth of phenomena that not only cannot be anticipated from merely examining their parts, as per the textbook definition of complexity, but also challenge intuition even when considered in the context of what is now known in network science. Here we review the recent literature on two major classes of such phenomena that have far-reaching implications: (i) antagonistic responses to changes of states or parameters and (ii) coexistence of seemingly incongruous behaviors or properties-both deriving from the collective and inherently decentralized nature of the dynamics...
March 2018: Annual Review of Condensed Matter Physics
https://www.readbyqxmd.com/read/30115913/transcriptomic-signatures-of-schizophrenia-revealed-by-dopamine-perturbation-in-an-ex-vivo-model
#5
Jubao Duan, Harald H H Göring, Alan R Sanders, Winton Moy, Jessica Freda, Eugene I Drigalenko, Mark Kos, Deli He, Pablo V Gejman
The dopaminergic hypothesis of schizophrenia (SZ) postulates that dopaminergic over activity causes psychosis, a central feature of SZ, based on the observation that blocking dopamine (DA) improves psychotic symptoms. DA is known to have both receptor- and non-receptor-mediated effects, including oxidative mechanisms that lead to apoptosis. The role of DA-mediated oxidative processes in SZ has been little studied. Here, we have used a cell perturbation approach and measured transcriptomic profiles by RNAseq to study the effect of DA exposure on transcription in B-cell transformed lymphoblastoid cell lines (LCLs) from 514 SZ cases and 690 controls...
August 16, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/30115912/adiporon-an-adiponectin-receptor-agonist-acts-as-an-antidepressant-and-metabolic-regulator-in-a-mouse-model-of-depression
#6
Sarah Nicolas, Delphine Debayle, Catherine Béchade, Luc Maroteaux, Anne-Sophie Gay, Pascale Bayer, Catherine Heurteaux, Alice Guyon, Joëlle Chabry
Major depression is a psychiatric disorder with complex etiology. About 30% of depressive patients are resistant to antidepressants that are currently available, likely because they only target the monoaminergic systems. Thus, identification of novel antidepressants with a larger action spectrum is urgently required. Epidemiological data indicate high comorbidity between metabolic and psychiatric disorders, particularly obesity and depression. We used a well-characterized anxiety/depressive-like mouse model consisting of continuous input of corticosterone for seven consecutive weeks...
August 16, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/30114364/kinetic-trans-assembly-of-dna-nanostructures
#7
Jihoon Shin, Junghoon Kim, Sung Ha Park, Tai Hwan Ha
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic paradigms of DNA nanotechnology, we present a rationally designed synthetic platform which functions in an analogous manner to create complex DNA nanostructures. Starting from one type of DNA nanostructure, DNA strand displacement circuits were designed to interact and pass along the information encoded in the initial structure to mediate the self-assembly of a different type of structure, the final output structure depending on the type of circuit triggered...
August 16, 2018: ACS Nano
https://www.readbyqxmd.com/read/30113814/minimizing-context-dependency-of-gene-networks-using-artificial-cells
#8
Yunfeng Ding, Luis Eduardo Contreras-Llano, Eliza Morris, Michelle Mao, Cheemeng Tan
The functioning of synthetic gene circuits depends on their local chemical context defined by the types and concentrations of biomolecules in the surrounding milieu that influence gene transcription and translation. This chemical-context dependence of synthetic gene circuits arises from significant yet unknown crosstalk between engineered components, host cells, and environmental factors, and has been a persistent challenge for synthetic biology. Here, we show that the sensitivity of synthetic gene networks to their chemical contexts can be minimized and their designed functions rendered robust using artificial cells, which are synthetic biomolecular compartments engineered from the bottom-up using liposomes that encapsulate the gene networks...
August 16, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30113427/germline-variants-and-risk-for-pancreatic-cancer-a-systematic-review-and-emerging-concepts
#9
Wei Zhan, Celeste A Shelton, Phil J Greer, Randall E Brand, David C Whitcomb
Pancreatic cancer requires many genetic mutations. Combinations of underlying germline variants and environmental factors may increase the risk of cancer and accelerate the oncogenic process. We systematically reviewed, annotated, and classified previously reported pancreatic cancer-associated germline variants in established risk genes. Variants were scored using multiple criteria and binned by evidence for pathogenicity, then annotated with published functional studies and associated biological systems/pathways...
September 2018: Pancreas
https://www.readbyqxmd.com/read/30113078/evolving-systems-biology-approaches-to-understanding-non-coding-rnas-in-pulmonary-hypertension
#10
Lloyd D Harvey, Stephen Y Chan
Our appreciation of the roles of non-coding RNAs, in particular microRNAs, in the manifestation of pulmonary hypertension (PH) has advanced considerably over the past decade. Comprised of small nucleotide sequences, microRNAs have demonstrated critical and broad regulatory roles in the pathogenesis of PH via the direct binding to messenger RNA transcripts for degradation or inhibition of translation, thereby exerting profound influence on cellular activity. Yet, as inherently pleiotropic molecules, microRNAs have been difficult to study using traditional, reductionist approaches alone...
August 16, 2018: Journal of Physiology
https://www.readbyqxmd.com/read/30112931/the-burden-of-non-infectious-intraocular-inflammatory-eye-diseases-a-systematic-literature-review
#11
J Bradford Rice, Alan G White, Lauren M Scarpati, George J Wan, Winnie W Nelson
OBJECTIVE: Non-infectious inflammatory eye diseases (IEDs), although rare, are complex and varied and may result in detrimental effects. A systematic literature review was conducted on the clinical outcome and economic burden of IED. METHODS: The Ovid search platform (Wolters Kluwer) was used to access scientific literature databases, including MEDLINE, Embase, Cochrane libraries, Health Technology Assessment, and the NHS Economic Evaluation database. The search strategy targeted clinical and economic outcomes research in 2009-2016...
August 16, 2018: Current Medical Research and Opinion
https://www.readbyqxmd.com/read/30112764/cancer-and-dementia-two-sides-of-the-same-coin
#12
REVIEW
Kimberly D van der Willik, Sanne B Schagen, M Arfan Ikram
Non-central nervous system cancer and the brain share an interesting and complex relation, with an emerging body of evidence showing that cancer patients are at an increased risk of developing cognitive problems. In contrast, epidemiological studies consistently find an inverse link between cancer and dementia, i.e. patients with dementia having a lower risk of subsequently developing cancer, and cancer patients being less often diagnosed with dementia. Different biological processes such as inversely activated cell proliferation and survival pathways have been suggested to have an important role underlying this inverse association...
August 15, 2018: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/30112671/the-brain-adipocyte-gut-network-linking-obesity-and-depression-subtypes
#13
REVIEW
Carla M Patist, Nicolas J C Stapelberg, Eugene F Du Toit, John P Headrick
Major depressive disorder (MDD) and obesity are dominant and inter-related health burdens. Obesity is a risk factor for MDD, and there is evidence MDD increases risk of obesity. However, description of a bidirectional relationship between obesity and MDD is misleading, as closer examination reveals distinct unidirectional relationships in MDD subtypes. MDD is frequently associated with weight loss, although obesity promotes MDD. In contrast, MDD with atypical features (MDD-AF) is characterised by subsequent weight gain and obesity...
August 15, 2018: Cognitive, Affective & Behavioral Neuroscience
https://www.readbyqxmd.com/read/30112567/-progress-on-ionomics-of-complex-diseases
#14
Hui-Min Ying, Yan Zhang
Ionomics is a new multidisciplinary scientific field for investigating the composition and distribution of all chemical elements in specific biological systems as well as their variations under different physiological and pathological conditions. It combines both high-throughput techniques for element profile measurement and bioinformatic methods, which provides new ideas for obtaining a systems-level understanding of biological utilization and functions of these elements. More and more results of researches suggest that ionomics has important theoretical and practical values in etiological study, early diagnosis and screening, and therapeutic strategy selection for complex diseases...
August 25, 2018: Sheng Li Xue Bao: [Acta Physiologica Sinica]
https://www.readbyqxmd.com/read/30112081/synthesis-and-photophysical-studies-of-a-multivalent-photoreactive-ru-ii-calix-4-arene-complex-bearing-rgd-containing-cyclopentapeptides
#15
Sofia Kajouj, Lionel Marcelis, Alice Mattiuzzi, Adrien Grassin, Damien Dufour, Pierre Van Antwerpen, Didier Boturyn, Eric Defrancq, Mathieu Surin, Julien De Winter, Pascal Gerbaux, Ivan Jabin, Cécile Moucheron
Photoactive ruthenium-based complexes are actively studied for their biological applications as potential theragnostic agents against cancer. One major issue of these inorganic complexes is to penetrate inside cells in order to fulfil their function, either sensing the internal cell environment or exert a photocytotoxic activity. The use of lipophilic ligands allows the corresponding ruthenium complexes to passively diffuse inside cells but limits their structural and photophysical properties. Moreover, this strategy does not provide any cell selectivity...
2018: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/30111790/cooperative-asymmetric-reactions-combining-photocatalysis-and-enzymatic-catalysis
#16
Zachary C Litman, Yajie Wang, Huimin Zhao, John F Hartwig
Living organisms rely on simultaneous reactions catalysed by mutually compatible and selective enzymes to synthesize complex natural products and other metabolites. To combine the advantages of these biological systems with the reactivity of artificial chemical catalysts, chemists have devised sequential, concurrent, and cooperative chemoenzymatic reactions that combine enzymatic and artificial catalysts1-9 . Cooperative chemoenzymatic reactions consist of interconnected processes that generate products in yields and selectivities that cannot be obtained when the two reactions are carried out sequentially with their respective substrates2,7 ...
August 2018: Nature
https://www.readbyqxmd.com/read/30110840/structural-bifurcation-analysis-in-chemical-reaction-networks
#17
Takashi Okada, Je-Chiang Tsai, Atsushi Mochizuki
In living cells, chemical reactions form complex networks. Dynamics arising from such networks are the origins of biological functions. We propose a mathematical method to analyze bifurcation behaviors of network systems using their structures alone. Specifically, a whole network is decomposed into subnetworks, and for each of them the bifurcation condition can be studied independently. Further, parameters inducing bifurcations and chemicals exhibiting bifurcations can be determined on the network. We illustrate our theory using hypothetical and real networks...
July 2018: Physical Review. E
https://www.readbyqxmd.com/read/30110836/insights-into-noise-modulation-in-oligomerization-systems-of-increasing-complexity
#18
Fabrizio Pucci, Marianne Rooman
Understanding under which conditions the increase of systems complexity is evolutionarily advantageous, and how this trend is related to the modulation of the intrinsic noise, are fascinating issues of utmost importance for synthetic and systems biology. To get insights into these matters, we analyzed a series of chemical reaction networks with different topologies and complexity, described by mass-action kinetics. We showed, analytically and numerically, that the global level of fluctuations at the steady state, measured by the sum over all species of the Fano factors of the number of molecules, is directly related to the network's deficiency...
July 2018: Physical Review. E
https://www.readbyqxmd.com/read/30109746/extremely-stable-high-molecular-mass-soluble-multiprotein-complex-from-eggs-of-sea-urchin-strongylocentrotus-intermedius-with-phosphatase-activity
#19
Svetlana E Soboleva, Evgeniya E Burkova, Pavel S Dmitrenok, Dmitrii V Bulgakov, Natalia I Menzorova, Valentina N Buneva, Georgy A Nevinsky
It was proposed that most biological processes are performed by different protein complexes. In contrast to individual proteins and enzymes, their complexes usually have other biological functions, and their formation may be important system process for the expansion of diversity and biological functions of different molecules. Identification and characterization of embryonic components including proteins and their multiprotein complexes seem to be very important for an understanding of embryo function. We have isolated and analyzed for the first time a very stable multiprotein complex (SPC; approximately 1100 kDa) from the soluble fraction of extracts of the sea urchin embryos...
August 14, 2018: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/30109563/transcriptional-regulation-of-osmotic-stress-tolerance-in-wheat-triticum-aestivum-l
#20
REVIEW
Shabir H Wani, Prateek Tripathi, Abbu Zaid, Ghana S Challa, Anuj Kumar, Vinay Kumar, Jyoti Upadhyay, Rohit Joshi, Manoj Bhatt
The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses...
August 14, 2018: Plant Molecular Biology
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