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https://www.readbyqxmd.com/read/29792823/principles-of-systems-biology-no-29
#1
(no author information available yet)
This month: in silico labeling of microscopy images (Christiansen/Finkbeiner), single-cell lineage trees and data integration (Rajewsky, Satija), gene expression (Weinberger/Simpson, Tavazoie, Ameres/Zuber), and signalling networks (Mercer/Wollscheid, Fussenegger).
May 23, 2018: Cell Systems
https://www.readbyqxmd.com/read/29789543/rapid-pathway-prototyping-and-engineering-using-in-vitro-and-in-vivo-synthetic-genome-scramble-in-methods
#2
Wei Liu, Zhouqing Luo, Yun Wang, Nhan T Pham, Laura Tuck, Irene Pérez-Pi, Longying Liu, Yue Shen, Chris French, Manfred Auer, Jon Marles-Wright, Junbiao Dai, Yizhi Cai
Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed "SCRaMbLE-in") to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29788828/mechanistic-kinetic-modeling-generates-system-independent-p-glycoprotein-mediated-transport-elementary-rate-constants-for-inhibition-and-in-combination-with-3d-sim-microscopy-elucidates-the-importance-of-microvilli-morphology-on-p-glycoprotein-mediated-efflux
#3
Harma Ellens, Zhou Meng, Sylvain J Le Marchand, Joe Bentz
Introduction In vitro transporter kinetics are typically analyzed by steady-state Michaelis-Menten (MM) approximations. However, no clear evidence exists that these approximations, applied to multiple transporters in biological membranes, yield system-independent mechanistic parameters needed for reliable in vivo hypothesis generation and testing. Areas covered The classical mass action model has been developed for P-glycoprotein mediated transport across confluent polarized cell monolayers. Numerical integration of the mass action equations for transport using a stable global optimization program, yields fitted elementary rate constants that are system-independent...
May 23, 2018: Expert Opinion on Drug Metabolism & Toxicology
https://www.readbyqxmd.com/read/29787708/emerging-links-between-lipid-droplets-and-motor-neuron-diseases
#4
Giuseppa Pennetta, Michael A Welte
Lipid droplets (LDs) are ubiquitous fat storage organelles and play key roles in lipid metabolism and energy homeostasis; in addition, they contribute to protein storage, folding, and degradation. However, a role for LDs in the nervous system remains largely unexplored. We discuss evidence supporting an intimate functional connection between LDs and motor neuron disease (MND) pathophysiology, examining how LD functions in systemic energy homeostasis, in neuron-glia metabolic coupling, and in protein folding and clearance may affect or contribute to disease pathology...
May 21, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29787445/deployment-of-the-dosikit-system-under-operational-conditions-experience-from-a-french-defense-national-nuclear-exercise
#5
F Entine, J Bensimon Etzol, C Bettencourt, M Dondey, X Michel, G Gagna, G Gellie, Y Corre, N Ugolin, S Chevillard, J-C Amabile
Estimation of the dose received by accidentally irradiated victims is based on a tripod: clinical, biological, and physical dosimetry. The DosiKit system is an operational and mobile biodosimetry device allowing the measurement of external irradiation directly on the site of a radiological accident. This tool is based on capillary blood sample and hair follicle collection. The aim is to obtain a whole-body and local-surface dose assessment. This paper is about the technical evaluation of the DosiKit; the analytical process and scientific validation are briefly described...
July 2018: Health Physics
https://www.readbyqxmd.com/read/29785401/rheumatoid-arthritis-and-mirnas-a-critical-review-through-a-functional-view
#6
REVIEW
Maria Cristina Moran-Moguel, Stefania Petarra-Del Rio, Evangelina E Mayorquin-Galvan, Maria G Zavala-Cerna
Rheumatoid arthritis (RA) is a systemic autoimmune disease with severe joint inflammation and destruction associated with an inflammatory environment. The etiology behind RA remains to be elucidated; most updated concepts include the participation of environmental, proteomic, epigenetic, and genetic factors. Epigenetic is considered the missing link to explain genetic diversification among RA patients. Within epigenetic factors participating in RA, miRNAs are defined as small noncoding molecules with a length of approximately 22 nucleotides, capable of gene expression modulation, either negatively through inhibition of translation and degradation of the mRNA or positively through increasing the translation rate...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29785042/inducible-high-efficiency-crispr-cas9-targeted-gene-editing-and-precision-base-editing-in-african-trypanosomes
#7
Eva Rico, Laura Jeacock, Julie Kovářová, David Horn
The Cas9 endonuclease can be programmed by guide RNA to introduce sequence-specific breaks in genomic DNA. Thus, Cas9-based approaches present a range of novel options for genome manipulation and precision editing. African trypanosomes are parasites that cause lethal human and animal diseases. They also serve as models for studies on eukaryotic biology, including 'divergent' biology. Genome modification, exploiting the native homologous recombination machinery, has been important for studies on trypanosomes but often requires multiple rounds of transfection using selectable markers that integrate at low efficiency...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784963/single-entity-resolution-valving-of-nanoscopic-species-in-liquids
#8
Patric Eberle, Christian Höller, Philipp Müller, Maarit Suomalainen, Urs F Greber, Hadi Eghlidi, Dimos Poulikakos
Investigating biological and synthetic nanoscopic species in liquids, at the ultimate resolution of single entity, is important in diverse fields1-5 . Progress has been made6-10 , but significant barriers need to be overcome such as the need for intense fields, the lack of versatility in operating conditions and the limited functionality in solutions of high ionic strength for biological applications. Here, we demonstrate switchable electrokinetic nanovalving able to confine and guide single nano-objects, including macromolecules, with sizes down to around 10 nanometres, in a lab-on-chip environment...
May 21, 2018: Nature Nanotechnology
https://www.readbyqxmd.com/read/29783016/systematic-investigation-of-the-erigeron-breviscapus-mechanism-for-treating-cerebrovascular-disease
#9
Jiangmei Wang, Yangyang Chen, Baoshi Liu, Qian Wang, Lulu Zhang, Zhenzhong Wang, Jun Zhou, Wei Xiao, Chunli Zheng, Yonghua Wang
ETHNOPHARMACOLOGICAL RELEVANCE: Cerebrovascular diseases (CBVDs), characterized by striking morbidity and mortality, have become the most common life-threatening diseases. The existing drugs of CBVDs target one or a few of pathogenic factors, the efficacy of which is limited because of the complexity of CBVDs. Traditional Chinese medicine (TCM), featured by multi-component and multi-target endows the great effectiveness in CBVDs treatment. For instance, Erigeron breviscapus (vant.) Hand...
May 18, 2018: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29782973/enhanced-retinal-pigment-epithelium-rpe-regeneration-using-curcumin-alginate-hydrogels-in-vitro-evaluation
#10
Jong Ho Park, Eun Yeong Shin, Myeong Eun Shin, Min Joung Choi, Cristiano Carlomagno, Jeong Eun Song, Gilson Khang
The retinal pigment epithelium (RPE) plays a significant role in retaining structural integrity of eye. Factors such as reduction in cell regeneration due to aging and physical injury pose a major hurdle in RPE regeneration. In this study, we exploited the use of alginate (AGT) incorporated with Curcumin (CCI) forming a hydrogel based system CCI/AGT. The fabricated hydrogel could anchor RPE cell in it. In vitro cell analysis revealed that the CCI/AGT hydrogel shows good biocompatibility, enhanced cell growth ability and higher ECM formation compared to the pure AGT hydrogel...
May 18, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29782246/precision-medicine-and-radiogenomics-in-breast-cancer-new-approaches-toward-diagnosis-and-treatment
#11
Katja Pinker, Joanne Chin, Amy N Melsaether, Elizabeth A Morris, Linda Moy
Precision medicine is medicine optimized to the genotypic and phenotypic characteristics of an individual and, when present, his or her disease. It has a host of targets, including genes and their transcripts, proteins, and metabolites. Studying precision medicine involves a systems biology approach that integrates mathematical modeling and biology genomics, transcriptomics, proteomics, and metabolomics. Moreover, precision medicine must consider not only the relatively static genetic codes of individuals, but also the dynamic and heterogeneous genetic codes of cancers...
June 2018: Radiology
https://www.readbyqxmd.com/read/29782191/lipid-protein-and-microrna-composition-within-mesenchymal-stem-cell-derived-exosomes
#12
Hao Deng, Chun Sun, Yingxin Sun, Huhu Li, Lin Yang, Danbin Wu, Qing Gao, Xijuan Jiang
Mesenchymal stem cells (MSCs) were regarded as one of the most promising type of seed cells in tissue engineering due to its easy accessibility and multipotent feature of being able to differentiate into adipocyte, osteoblast, cardiomyocytes, and neurons. For years, MSCs have been applied in treating cardiovascular disease, reconstructing kidney injury, and remodeling immune system with remarkable achievements. Basic researches revealed that its clinic effects are not only due to their pluripotent ability but also through their paracrine function that they synthesize and secrete a broad spectrum of growth factors and cytokines...
May 21, 2018: Cellular Reprogramming
https://www.readbyqxmd.com/read/29781276/light-induced-hypoxia-triggered-living-nanocarriers-for-synergistic-cancer-therapy
#13
Wenliang Wang, Lin Lin, Xiaojing Ma, Bo Wang, Sanrong Liu, Xinxin Yan, Shengran Li, Huayu Tian, Xifei Yu
Living drug delivery system has been proposed as new concept materials since it is able to communicate with biological system, sense subtle changes of body microenvironment caused by disease and then make rapid response to cure in early stage of disease. Herein, taking full advantage of the tumor hypoxia physiology and successive effects of photodynamic therapy (PDT), we designed a new living delivery system via combining the PDT and hypoxia-responsive chemotherapy, abbreviated as Ce6-PEG-Azo-PCL. Then, according to the facts that oxygen can be converted into reactive oxygen species during irradiation of the photosensitizer, tumor cells could be killed after the poly(ethylene glycol) (PEG) conjugated photosensitizer chlorine e6 were irradiated at tumor site...
May 21, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29780970/three-challenges-for-future-research-on-cochlear-implants
#14
REVIEW
David B Pisoni, William G Kronenberger, Michael S Harris, Aaron C Moberly
Cochlear implants (CIs) often work very well for many children and adults with profound sensorineural (SNHL) hearing loss. Unfortunately, while many CI patients display substantial benefits in recognizing speech and understanding spoken language following cochlear implantation, a large number of patients achieve poor outcomes. Understanding and explaining the reasons for poor outcomes following implantation is a very challenging research problem that has received little attention despite the pressing clinical significance...
December 2017: World Journal of Otorhinolaryngology—Head and Neck Surgery
https://www.readbyqxmd.com/read/29776387/integrative-genomics-approaches-validate-ppyuc11-like-as-candidate-gene-for-the-stony-hard-trait-in-peach-p-persica-l-batsch
#15
Marco Cirilli, Daniela Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, Alessandro Liverani, Daniele Bassi
BACKGROUND: Texture is one of the most important fruit quality attributes. In peach, stony hard (SH) is a recessive monogenic trait (hd/hd) that confers exceptionally prolonged firm flesh to fully ripe fruit. Previous studies have shown that the SH mutation affects the fruit ability to synthesize appropriate amounts of indol-3-acetic acid (IAA), which orchestrates the ripening processes through the activation of system 2 ethylene pathway. Allelic variation in a TC microsatellite located within the first intron of PpYUC11-like (a YUCCA-like auxin-biosynthesis gene) has been recently proposed as the causal mutation of the SH phenotype...
May 18, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29776158/clusters-in-nonsmooth-oscillator-networks
#16
Rachel Nicks, Lucie Chambon, Stephen Coombes
For coupled oscillator networks with Laplacian coupling, the master stability function (MSF) has proven a particularly powerful tool for assessing the stability of the synchronous state. Using tools from group theory, this approach has recently been extended to treat more general cluster states. However, the MSF and its generalizations require the determination of a set of Floquet multipliers from variational equations obtained by linearization around a periodic orbit. Since closed form solutions for periodic orbits are invariably hard to come by, the framework is often explored using numerical techniques...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775648/towards-a-quantitative-model-to-predict-the-toxicity-pathogenicity-potential-of-mineral-fibers
#17
Alessandro F Gualtieri
A number of mineral fibers represent a health hazard because they are classified as cancer-causing chemical/physical toxicants upon (chronic) dust inhalation. Although in the last decades they have been the subject of intensive multidisciplinary investigations, the mechanisms by which mineral fibers induce toxic and pathogenic adverse effects on human health and environment are not yet fully understood. The major intricacy of the biological approach that prevents the design of a conclusive shared model of behavior of mineral fibers in a biological system stems from their very nature with intrinsic variability in chemical, molecular, structural and morphometric parameters, biodurability and surface reactivity...
May 15, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29772073/julius-sachs-1868-the-father-of-plant-physiology
#18
Ulrich Kutschera, Karl J Niklas
The year 2018 marks the 150th anniversary of the first publication of Julius von Sachs' (1832-1897) Lehrbuch der Botanik (Textbook of Botany), which provided a comprehensive summary of what was then known about the plant sciences. Three years earlier, in 1865, Sachs produced the equally impressive Handbuch der Experimental-Physiologie der Pflanzen (Handbook of Experimental Plant Physiology), which summarized the state of knowledge in all aspects of the discipline known today as plant physiology. Both of these books provided numerous insights based on Sachs' seminal experiments...
May 17, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29770938/evaluating-a-5-year-metal-contamination-remediation-and-the-biomonitoring-potential-of-a-freshwater-gastropod-along-the-xiangjiang-river-china
#19
Deliang Li, Jie Pi, Ting Zhang, Xiang Tan, Dylan J Fraser
Effective remediation of heavy metal pollution in aquatic systems is desired in many regions, but it requires integrative assessments of sediments, water, and biota that can serve as robust biomonitors. We assessed the effects of a 5-year metal contamination remediation along the Xiangjiang River, China, by comparing concentrations of trace metals in water and surface sediments between 2010-2011 and 2016. We also explored the trace metal biomonitoring potential of a freshwater gastropod (Bellamya aeruginosa)...
May 16, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29768936/nutrient-removal-and-biomass-production-advances-in-microalgal-biotechnology-for-wastewater-treatment
#20
Sudharsanam Abinandan, Suresh R Subashchandrabose, Kadiyala Venkateswarlu, Mallavarapu Megharaj
Owing to certain drawbacks, such as energy-intensive operations in conventional modes of wastewater treatment (WWT), there has been an extensive search for alternative strategies in treatment technology. Biological modes for treating wastewaters are one of the finest technologies in terms of economy and efficiency. An integrated biological approach with chemical flocculation is being conventionally practiced in several-sewage and effluent treatment plants around the world. Overwhelming responsiveness to treat wastewaters especially by using microalgae is due to their simplest photosynthetic mechanism and ease of acclimation to various habitats...
May 17, 2018: Critical Reviews in Biotechnology
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