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Biological reaction network

K Hu, S S Sheiko
Biological networks are capable of programming temporal evolution of their crosslinking and dissociation reactions. However, replicating this feature in synthetic self-assemblies is challenging. Herein we report the design of dynamic polymeric hydrogels that undergo delayed dissociation with an onset time precisely tuned from minutes to hours by a reaction relay.
May 23, 2018: Chemical Communications: Chem Comm
Jelili Oyelade, Itunuoluwa Isewon, Efosa Uwoghiren, Olufemi Aromolaran, Olufunke Oladipupo
Malaria is an infectious disease that affects close to half a million individuals every year and Plasmodium falciparum is a major cause of malaria. The treatment of this disease could be done effectively if the essential enzymes of this parasite are specifically targeted. Nevertheless, the development of the parasite in resisting existing drugs now makes discovering new drugs a core responsibility. In this study, a novel computational model that makes the prediction of new and validated antimalarial drug target cheaper, easier, and faster has been developed...
2018: BioMed Research International
Guido Bolognesi, Mark S Friddin, Ali Salehi-Reyhani, Nathan E Barlow, Nicholas J Brooks, Oscar Ces, Yuval Elani
Constructing higher-order vesicle assemblies has discipline-spanning potential from responsive soft-matter materials to artificial cell networks in synthetic biology. This potential is ultimately derived from the ability to compartmentalise and order chemical species in space. To unlock such applications, spatial organisation of vesicles in relation to one another must be controlled, and techniques to deliver cargo to compartments developed. Herein, we use optical tweezers to assemble, reconfigure and dismantle networks of cell-sized vesicles that, in different experimental scenarios, we engineer to exhibit several interesting properties...
May 14, 2018: Nature Communications
Chikara Furusawa, Kunihiko Kaneko
A reduction in high-dimensional phenotypic states to a few degrees of freedom is essential to understand biological systems. Here, we show evolutionary robustness causes such reduction which restricts possible phenotypic changes in response to a variety of environmental conditions. First, global protein expression changes in Escherichia coli after various environmental perturbations were shown to be proportional across components, across different types of environmental conditions. To examine if such dimension reduction is a result of evolution, we analyzed a cell model-with a huge number of components, that reproduces itself via a catalytic reaction network-and confirmed that common proportionality in the concentrations of all components is shaped through evolutionary processes...
April 2018: Physical Review. E
Pablo I Nikel, Víctor de Lorenzo
The itinerary followed by Pseudomonas putida from being a soil-dweller and plant colonizer bacterium to become a flexible and engineer-able platform for metabolic engineering stems from its natural lifestyle, which is adapted to harsh environmental conditions and all sorts of physicochemical stresses. Over the years, these properties have been capitalized biotechnologically owing to the expanding wealth of genetic tools designed for deep-editing the P. putida genome. A suite of dedicated vectors inspired in the core tenets of synthetic biology have enabled to suppress many of the naturally-occurring undesirable traits native to this species while enhancing its many appealing properties, and also to import catalytic activities and attributes from other biological systems...
May 11, 2018: Metabolic Engineering
Rong-Quan He, Li Gao, Jie Ma, Zu-Yun Li, Xiao-Hua Hu, Gang Chen
Despite the fact that previous studies have reported the aberrant expression of miR‑183‑5p in lung adenocarcinoma (LUAD), the oncogenic role of miR‑183‑5p in LUAD and its underlying mechanisms have remained elusive. Hence, we attempted to elucidate the clinicopathological significance of miR‑183‑5p expression in LUAD and identify the biological function of miR‑183‑5p in LUAD in this study. Meta‑analysis of Gene Expression Omnibus (GEO) data, data mining of The Cancer Genome Atlas (TCGA) and real‑time quantitative polymerase chain reaction (qPCR) were performed to evaluate the clinicopathological significance of miR‑183‑5p in LUAD...
May 9, 2018: Oncology Reports
Yifan Lyu, Cuichen Wu, Charles Heinke, Da Han, Ren Cai, I-Ting Teng, Yuan Liu, Hui Liu, Xiao-Bing Zhang, Qiaoling Liu, Weihong Tan
A DNA reaction network is like a biological algorithm that can respond to 'molecular input signals,' such as biological molecules, while the artificial cell is like a micron-robot whose function is powered by the encapsulated DNA reaction network. In this work, we describe the feasibility of using a DNA reaction network as the computational core of a protocell, which will perform an artificial immune response in a concise way to eliminate a mimicked pathogenic challenge. Such a DNA reaction network-powered protocell can realize the connection of logical computation and biological recognition due to the natural programmability and biological prop-erties of DNA...
May 10, 2018: Journal of the American Chemical Society
Juan Wang, Hu Yang
Dendrimers exhibit super atomistic features by virtue of their well-defined discrete quantized nanoscale structures. Here, we show that hyperbranched amine-terminated polyamidoamine (PAMAM) dendrimer G4.0 reacts with linear polyethylene glycol (PEG) diacrylate (575 g/mol) via the aza-Michael addition reaction at a subzero temperature (-20 °C), namely cryo-aza-Michael addition, to form a macroporous superelastic network, i.e., dendrimer cryogel. Dendrimer cryogels exhibit biologically relevant Young's modulus, high compression elasticity and super resilience at ambient temperature...
May 8, 2018: Scientific Reports
Frédéric Auvré, Julien Coutier, Michèle T Martin, Nicolas O Fortunel
Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized...
May 8, 2018: Methods in Molecular Biology
D Thirumalai, Changbong Hyeon
Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. Allostery describes the responses of a complex to binding of ligands at sites that are spatially well separated from the binding region. We describe the structural perturbation method, based on phonon propagation in solids, which can be used to determine the signal-transmitting allostery wiring diagram (AWD) in large but finite-sized biological complexes. Application to the bacterial chaperonin GroEL-GroES complex shows that the AWD determined from structures also drives the allosteric transitions dynamically...
June 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Humberto A Filho, Jeaneth Machicao, Odemir M Bruno
Modeling the basic structure of metabolic machinery is a challenge for modern biology. Some models based on complex networks have provided important information regarding this machinery. In this paper, we constructed metabolic networks of 17 plants covering unicellular organisms to more complex dicotyledonous plants. The metabolic networks were built based on the substrate-product model and a topological percolation was performed using the kcore decomposition. The distribution of metabolites across the percolation layers showed correlations between the metabolic integration hierarchy and the network topology...
2018: PloS One
Chelsea Yongxi Hu, Melissa K Takahashi, Yan Zhang, Julius B Lucks
RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal noise. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs...
May 7, 2018: ACS Synthetic Biology
Erik E Augspurger, Muhit Rana, Mehmet Veysel Yigit
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. DNA-based technologies' recent prominence in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions and solvent types...
May 7, 2018: ACS Sensors
Jeonghyun Lee, Hyosung Park, Jiyoung Eom, Seung Goo Kang
The germinal center reaction is a key event of humoral immunity, providing long-lived immunological memory. Follicular helper T (TFH ) cells are a specialized subset of CD4+ T cells located in the follicles, which help B cells and thus control the germinal center reaction. TFH cell development is achieved by multi-step processes of interactions with dendritic cells and B cells along with the coordination of various transcription factors. Since the T helper cell fate decision program is determined by subtle changes in regulatory molecules, fine tuning of these dynamic interactions is crucial for the generation functional TFH cells...
April 2018: Immune Network
Sergio Bordel
In order to choose optimal personalized anticancer treatments, transcriptomic data should be analyzed within the frame of biological networks. The best known human biological network (in terms of the interactions between its different components) is metabolism. Cancer cells have been known to have specific metabolic features for a long time and currently there is a growing interest in characterizing new cancer specific metabolic hallmarks. In this article it is presented a method to find personalized therapeutic windows using RNA-seq data and Genome Scale Metabolic Models...
April 13, 2018: Oncotarget
Laura Martínez-Muñoz, Ricardo Villares, José Luis Rodríguez-Fernández, José Miguel Rodríguez-Frade, Mario Mellado
The chemokines direct leukocyte recruitment in both homeostatic and inflammatory conditions, and are therefore critical for immune reactions. By binding to members of the class A G protein-coupled receptors, the chemokines play an essential role in numerous physiological and pathological processes. In the last quarter century, the field has accumulated much information regarding the implications of these molecules in different immune processes, as well as mechanistic insight into the signaling events activated through their binding to their receptors...
May 2, 2018: Journal of Leukocyte Biology
Yuki Shindo, Yohei Kondo, Yasushi Sako
Mathematical modeling and analysis of biochemical reaction networks are key routines in computational systems biology and biophysics; however, it remains difficult to choose the most valid model. Here, we propose a computational framework for data-driven and systematic inference of a nonlinear biochemical network model. The framework is based on the expectation-maximization algorithm combined with particle smoother and sparse regularization techniques. In this method, a "redundant" model consisting of an excessive number of nodes and regulatory paths is iteratively updated by eliminating unnecessary paths, resulting in an inference of the most likely model...
May 1, 2018: Scientific Reports
Lorenzo Duso, Christoph Zechner
Stochastic simulations of biochemical networks are of vital importance for understanding complex dynamics in cells and tissues. However, existing methods to perform such simulations are associated with computational difficulties and addressing those remains a daunting challenge to the present. Here we introduce the selected-node stochastic simulation algorithm (snSSA), which allows us to exclusively simulate an arbitrary, selected subset of molecular species of a possibly large and complex reaction network...
April 28, 2018: Journal of Chemical Physics
Daryl Sivakumaran, Emilia Bakaic, Scott B Campbell, Fei Xu, Eva Mueller, Todd Hoare
While various smart materials have been explored for a variety of biomedical applications (e.g., drug delivery, tissue engineering, bioimaging, etc.), their ultimate clinical use has been hampered by the lack of biologically-relevant degradation observed for most smart materials. This is particularly true for temperature-responsive hydrogels, which are almost uniformly based on polymers that are functionally non-degradable (e.g., poly(N-isopropylacrylamide) (PNIPAM) or poly(oligoethylene glycol methacrylate) (POEGMA))...
April 16, 2018: Journal of Visualized Experiments: JoVE
Zhe Wang, Panpan Xu, Biyue Chen, Zheyu Zhang, Chunhu Zhang, Qiong Zhan, Siqi Huang, Zi-An Xia, Weijun Peng
Alzheimer's disease (AD) is the most common form of dementia worldwide. Accumulating evidence indicates that non-coding RNAs are strongly implicated in AD-associated pathophysiology. However, the role of these ncRNAs remains largely unknown. In the present study, we used microarray analysis technology to characterize the expression patterns of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNAs in hippocampal tissue from Aβ1-42 -induced AD model rats, to integrate interaction data and thus provide novel insights into the mechanisms underlying AD...
April 27, 2018: Aging
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