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Complex system in biology

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https://read.qxmd.com/read/30771388/tuning-physicochemical-and-biological-properties-of-chitosan-through-complexation-with-transition-metal-ions
#1
Anamarija Rogina, Andrea Lončarević, Maja Antunović, Inga Marijanović, Marica Ivanković, Hrvoje Ivanković
The synthesis of biologically active scaffolds is focused on the design of cell-sensitive surface by applying cell-adhesive proteins or bioceramic micro (nano) particles. The emerging new strategy for manipulating the biological properties lies in the modification by trace metals found in the living organism. In this work, we have prepared biocompatible chitosan hydrogels modified by copper (II) and zinc (II) ions through complexation interactions. Due to the strong affinity of metal ions towards amino groups of chitosan, we obtained defined and ordered structures of metal ion-chitosan hydrogel without the formation of additional metal species...
February 13, 2019: International Journal of Biological Macromolecules
https://read.qxmd.com/read/30770736/parameter-estimation-in-models-of-biological-oscillators-an-automated-regularised-estimation-approach
#2
Jake Alan Pitt, Julio R Banga
BACKGROUND: Dynamic modelling is a core element in the systems biology approach to understanding complex biosystems. Here, we consider the problem of parameter estimation in models of biological oscillators described by deterministic nonlinear differential equations. These problems can be extremely challenging due to several common pitfalls: (i) a lack of prior knowledge about parameters (i.e. massive search spaces), (ii) convergence to local optima (due to multimodality of the cost function), (iii) overfitting (fitting the noise instead of the signal) and (iv) a lack of identifiability...
February 15, 2019: BMC Bioinformatics
https://read.qxmd.com/read/30770678/micron-resolution-high-fidelity-three-dimensional-vascular-optical-imaging-phantoms
#3
Callum D Little, Radhika K Poduval, Richard Caulfield, Sacha Noimark, Richard J Colchester, Chris D Loder, Manish K Tiwari, Roby D Rakhit, Ioannis Papakonstantinou, Adrien E Desjardins
Microscopic and mesoscale optical imaging techniques allow for three-dimensional (3-D) imaging of biological tissue across millimeter-scale regions, and imaging phantom models are invaluable for system characterization and clinical training. Phantom models that replicate complex 3-D geometries with both structural and molecular contrast, with resolution and lateral dimensions equivalent to those of imaging techniques (<20  μm), have proven elusive. We present a method for fabricating phantom models using a combination of two-photon polymerization (2PP) to print scaffolds, and microinjection of tailored tissue-mimicking materials to simulate healthy and diseased tissue...
February 2019: Journal of Biomedical Optics
https://read.qxmd.com/read/30769902/analysis-of-topological-parameters-of-complex-disease-genes-reveals-the-importance-of-location-in-a-biomolecular-network
#4
Xiaohui Zhao, Zhi-Ping Liu
Network biology and medicine provide unprecedented opportunities and challenges for deciphering disease mechanisms from integrative viewpoints. The disease genes and their products perform their dysfunctions via physical and biochemical interactions in the form of a molecular network. The topological parameters of these disease genes in the interactome are of prominent interest to the understanding of their functionality from a systematic perspective. In this work, we provide a systems biology analysis of the topological features of complex disease genes in an integrated biomolecular network...
February 14, 2019: Genes
https://read.qxmd.com/read/30769331/excel-combining-u-ex-u-trusion-printing-on-u-ce-u-llulose-scaffolds-with-u-l-u-amination-to-create-i-in-vitro-i-biological-models
#5
Alireza Shahin-Shamsabadi, P Ravi Selvaganapathy
Bioprinting is rapidly developing to be a powerful tool in tissue engineering for both whole tissue printing and development of in vitro models that can be used in drug discovery, toxicology and as in vitro bioreactors. Nevertheless, the ability to create complex 3D culture systems with different types of cells, extracellular matrices integrated with perfusable channels has been a challenge. Here we develop an approach that combines xurography of a scaffold material (cellulose) with extrusion printing of bioinks on it, followed by assembly in a layer by layer fashion to create complex 3D culture systems that could be used as in vitro models of biological processes...
February 15, 2019: Biofabrication
https://read.qxmd.com/read/30768256/correlation-between-drug-loading-content-and-biological-activity-the-complexity-demonstrated-in-paclitaxel-loaded-glycopolymer-micelle-system
#6
Cheng Cao, Jiacheng Zhao, Mingxia Lu, Christopher J Garvey, Martina H Stenzel
Drug delivery carriers are now widely established as they can increase the therapeutic efficiency of drugs. In general, the aim in this field is to create effective carriers that have large amounts of drugs loaded in order to minimize drug carrier material that needs to be disposed of. However, there was little attention so far in the literature on the effect of the amount of loaded drugs on the biological activity. In this paper, we are trying to answer the question how the drug loading content will affect the in vitro activity...
February 15, 2019: Biomacromolecules
https://read.qxmd.com/read/30767846/group-a-streptococcus-mediated-host-cell-signaling
#7
Vijay Pancholi
In the past decade, the field of the cellular microbiology of group A Streptococcus ( S. pyogenes ) infection has made tremendous advances and touched upon several important aspects of pathogenesis, including receptor biology, invasive and evasive phenomena, inflammasome activation, strain-specific autophagic bacterial killing, and virulence factor-mediated programmed cell death. The noteworthy aspect of S. pyogenes -mediated cell signaling is the recognition of the role of M protein in a variety of signaling events, starting with the targeting of specific receptors on the cell surface and on through the induction and evasion of NETosis, inflammasome, and autophagy/xenophagy to pyroptosis and apoptosis...
January 2019: Microbiology Spectrum
https://read.qxmd.com/read/30767754/synthesis-spectroscopic-properties-crystal-structure-and-biological-evaluation-of-new-platinum-complexes-with-5-methyl-5-2-thiomethyl-ethyl-hydantoin
#8
Adriana Georgieva Bakalova, Rossen Todorov Buyukliev, Rositsa Petrova Nikolova, Boris Lubomirov Shivachev, Rositsa Asenova Mihaylovac, Spiro Mihaylov Konstantinov
BACKGROUND: The accidental discovery of cisplatin's growth-inhibiting properties a few decades ago led to resurgence of interest in metal-based chemotherapeutics. A number of well-discussed factors such as severe systemic toxicity and unfavourable physicochemical properties further limit the clinical application of the platinating agents. Great efforts have been placed in the development of alternative platinum derivatives with an extended antitumor spectrum and amended toxicity profile as compared to the reference drug cisplatin...
February 13, 2019: Anti-cancer Agents in Medicinal Chemistry
https://read.qxmd.com/read/30767681/mucosal-rna-and-protein-expression-as-the-next-frontier-in-ibs-abnormal-function-despite-morphologically-intact-small-intestinal-mucosa
#9
Bruno Kotska Rodino-Janeiro, Cristina Pardo-Camacho, Javier Santos, Cristina Martinez
Irritable bowel syndrome is one of the commonest gastrointestinal disorders. Although long-time considered a pure functional disorder, intense research in past years has rendered a very complex and varied array of observations indicating the presence of structural and molecular abnormalities underlying characteristic motor and sensitive changes and clinical manifestations. Analysis of gene and protein expression in the intestinal mucosa has shed light on the molecular mechanisms implicated in IBS physiopathology...
February 15, 2019: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://read.qxmd.com/read/30765530/mobile-platform-for-rapid-sub-picogram-per-milliliter-multiplexed-digital-droplet-detection-of-proteins
#10
Venkata Yelleswarapu, Joshua R Buser, Margalit Haber, Jonathan Baron, Eshwar Inapuri, David Issadore
Digital droplet assays-in which biological samples are compartmentalized into millions of femtoliter-volume droplets and interrogated individually-have generated enormous enthusiasm for their ability to detect biomarkers with single-molecule sensitivity. These assays have untapped potential for point-of-care diagnostics but are currently mainly confined to laboratory settings, due to the instrumentation necessary to serially generate, control, and measure tens of millions of droplets/compartments. To address this challenge, we developed an optofluidic platform that miniaturizes digital assays into a mobile format by parallelizing their operation...
February 14, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30763455/dietary-black-raspberries-impact-the-colonic-microbiome-and-phytochemical-metabolites-in-mice
#11
Junnan Gu, Jennifer M Thomas-Ahner, Kenneth M Riedl, Michael T Bailey, Yael Vodovotz, Steven J Schwartz, Steven K Clinton
SCOPE: Black raspberries (BRB) are a rich source of bioactive phytochemicals, including anthocyanins and ellagitannins. These phytochemicals are poorly absorbed and we hypothesize that upon reaching the colon they may be transformed by gut microbiota into various metabolites that may impact the colonic mucosa or upon absorption have systemic bioactivity. The objective of this study was to define the impact of a BRB-containing diet on the colon microbiome in mice and quantify the phytochemical metabolites in the colon contents and the circulation...
February 14, 2019: Molecular Nutrition & Food Research
https://read.qxmd.com/read/30763315/iris-eda-an-integrated-rna-seq-interpretation-system-for-gene-expression-data-analysis
#12
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies...
February 14, 2019: PLoS Computational Biology
https://read.qxmd.com/read/30763096/the-diverse-nature-of-ion-speciation-at-the-nanoscale-hydrophobic-water-interface
#13
Evangelia Zdrali, Marcel D Baer, Halil I Okur, Christopher Mundy, Sylvie Roke
Many biological systems are composed of nanoscale structures having hydrophobic and hydrophilic groups adjacent to one another and in contact with aqueous electrolyte solution. The interaction of ions with such structures is of fundamental importance. Although many studies have focused on characterizing planar extended (often air/water) interfaces, little is known about ion speciation at complex nanoscale biological systems. To start understanding the complex mechanisms involved, we use a hexadecane nanodroplet system, stabilized with a dilute monolayer of positively charged (DTA+) groups in contact with an electrolyte solution (NaSCN)...
February 14, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30762928/bioinformatic-analysis-of-cacybp-associated-proteins-using-human-glioma-databases
#14
Chengmin Xuan, Yong Gao, Mingwei Jin, Shumei Xu, Lei Wang, Yuan Wang, Rui Han, Kunpeng Shi, Xincheng Chen, Qi An
The ubiquitin-proteasome system is the primary cellular pathway for protein degradation, mediating 80% of intracellular protein degradation. Because of the widespread presence of ubiquitin-modified protein substrates, ubiquitination can regulate a variety of cellular activities including cell proliferation, apoptosis, autophagy, endocytosis, DNA damage repair, and immune responses. With the continuous generation of genomics data in recent years it has become particularly important to analyze these data effectively and reasonably...
February 14, 2019: IUBMB Life
https://read.qxmd.com/read/30761299/hypoxia-modified-cancer-cell-metabolism
#15
REVIEW
Wafaa Al Tameemi, Tina P Dale, Rakad M Kh Al-Jumaily, Nicholas R Forsyth
While oxygen is critical to the continued existence of complex organisms, extreme levels of oxygen within a system, known as hypoxia (low levels of oxygen) and hyperoxia (excessive levels of oxygen), potentially promote stress within a defined biological environment. The consequences of tissue hypoxia, a result of a defective oxygen supply, vary in response to the gravity, extent and environment of the malfunction. Persistent pathological hypoxia is incompatible with normal biological functions, and as a result, multicellular organisms have been compelled to develop both organism-wide and cellular-level hypoxia solutions...
2019: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/30761179/mcimpute-matrix-completion-based-imputation-for-single-cell-rna-seq-data
#16
Aanchal Mongia, Debarka Sengupta, Angshul Majumdar
Motivation: Single-cell RNA sequencing has been proved to be revolutionary for its potential of zooming into complex biological systems. Genome-wide expression analysis at single-cell resolution provides a window into dynamics of cellular phenotypes. This facilitates the characterization of transcriptional heterogeneity in normal and diseased tissues under various conditions. It also sheds light on the development or emergence of specific cell populations and phenotypes. However, owing to the paucity of input RNA, a typical single cell RNA sequencing data features a high number of dropout events where transcripts fail to get amplified...
2019: Frontiers in Genetics
https://read.qxmd.com/read/30761041/disarming-ex-combatants-minds-toward-situated-reintegration-process-in-post-conflict-colombia
#17
Sandra Baez, Hernando Santamaría-García, Agustín Ibáñez
Collective violence in the context of armed conflict impacts the economy, health systems, and social stability of affected countries. This is considered a complex phenomenon with interwoven biological, psychological, social, cultural, and political factors. However, most of the research on this topic still lacks suitable established integrative approaches to assess multilevel perspectives. Social, cognitive and affective mental processes (SCAMP) are critical factors that should be considered in multilevel approaches...
2019: Frontiers in Psychology
https://read.qxmd.com/read/30760983/applications-of-light-sheet-microscopy-in-microdevices
#18
REVIEW
Ignacio Albert-Smet, Asier Marcos-Vidal, Juan José Vaquero, Manuel Desco, Arrate Muñoz-Barrutia, Jorge Ripoll
Light-sheet fluorescence microscopy (LSFM) has been present in cell biology laboratories for quite some time, mainly as custom-made systems, with imaging applications ranging from single cells (in the micrometer scale) to small organisms (in the millimeter scale). Such microscopes distinguish themselves for having very low phototoxicity levels and high spatial and temporal resolution, properties that make them ideal for a large range of applications. These include the study of cellular dynamics, in particular cellular motion which is essential to processes such as tumor metastasis and tissue development...
2019: Frontiers in Neuroanatomy
https://read.qxmd.com/read/30760751/the-oxytocinergic-system-mediates-synchronized-interpersonal-movement-during-dance
#19
Liad Josef, Pavel Goldstein, Naama Mayseless, Liat Ayalon, Simone G Shamay-Tsoory
Because the oxytocinergic (OT) system has previously been linked to regulation of complex social cognition and behavior, we examined whether intranasal administration of OT would modulate synchronization during a real-life dance paradigm. The current study examined pairs of friends while dancing after intranasal administration of OT or placebo. Motion tracking software and a computational model were utilized to measure synchrony between the partners as manifested in the velocity of their movements. In line with our predictions, OT increased synchrony between partners...
February 13, 2019: Scientific Reports
https://read.qxmd.com/read/30760596/atomic-level-characterization-of-protein-protein-association
#20
Albert C Pan, Daniel Jacobson, Konstantin Yatsenko, Duluxan Sritharan, Thomas M Weinreich, David E Shaw
Despite the biological importance of protein-protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein-protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)-based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events...
February 13, 2019: Proceedings of the National Academy of Sciences of the United States of America
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