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Niche construction

Jinah Jang, Hun-Jun Park, Seok-Won Kim, Heejin Kim, Ju Young Park, Soo Jin Na, Hyeon Ji Kim, Moon Nyeo Park, Seung Hyun Choi, Sun Hwa Park, Sung Won Kim, Sang-Mo Kwon, Pum-Joon Kim, Dong-Woo Cho
Stem cell therapy is a promising therapeutic method for the treatment of ischemic heart diseases; however, some challenges prohibit the efficacy after cell delivery due to hostile microenvironment of the injured myocardium. 3D printed pre-vascularized stem cell patch can enhance the therapeutic efficacy for cardiac repair through promotion of rapid vascularization after patch transplantation. In this study, stem cell-laden decellularized extracellular matrix bioinks are used in 3D printing of pre-vascularized and functional multi-material structures...
October 14, 2016: Biomaterials
Zhen Wang, Jun-Qiang Chen, Jin-Lu Liu, Lei Tian
Tumor microenvironment (TME) plays an integral part in the biology of cancer, participating in tumor initiation, progression, and response to therapy. Exosome is an important part of TME. Exosomes are small vesicles formed in vesicular bodies with a diameter of 30-100 nm and a classic "cup" or "dish" morphology. They can contain microRNAs, mRNAs, DNA fragments and proteins, which are shuttled from a donor cell to recipient cells. Exosomes secreted from tumor cells are called tumor-derived (TD) exosomes. There is emerging evidence that TD exosomes can construct a fertile environment to support tumor proliferation, angiogenesis, invasion and premetastatic niche preparation...
October 19, 2016: Journal of Translational Medicine
Ardeshir Kianercy, Kenneth J Pienta
Bone, which includes several cell populations and numerous cytokines and chemokines that provide cell-cell signaling, is a common destination for many cancer metastases. Bone metastasis skews this signaling to develop vicious cycles between immune, bone and cancer populations that lead to abnormal bone remodeling during cancer niche construction. Temporal models utilize positive feedback systems as an integrative tool providing insights into the rate-limiting processes that determine multiple stages of the bone metastasis...
2016: Advances in Experimental Medicine and Biology
Nanbo Liu, Sha Huang, Bin Yao, Jiangfan Xie, Xu Wu, Xiaobing Fu
3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro...
October 3, 2016: Scientific Reports
Alissa C Rothchild, James R Sissons, Shahin Shafiani, Christopher Plaisier, Deborah Min, Dat Mai, Mark Gilchrist, Jacques Peschon, Ryan P Larson, Andreas Bergthaler, Nitin S Baliga, Kevin B Urdahl, Alan Aderem
The regulation of host-pathogen interactions during Mycobacterium tuberculosis (Mtb) infection remains unresolved. MicroRNAs (miRNAs) are important regulators of the immune system, and so we used a systems biology approach to construct an miRNA regulatory network activated in macrophages during Mtb infection. Our network comprises 77 putative miRNAs that are associated with temporal gene expression signatures in macrophages early after Mtb infection. In this study, we demonstrate a dual role for one of these regulators, miR-155...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Breda M Zimkus, Lucinda P Lawson, Michael Barej, Christopher D Barratt, Alan Channing, Katrina M Dash, J Maximilian Dehling, Louis Du Preez, Philip-Sebastian Gehring, Eli Greenbaum, Václav Gvoždík, James Harvey, Jos Kielgast, Chifundera Kusamba, Zoltán T Nagy, Maciej Pabijan, Johannes Penner, Mark-Oliver Rödel, Miguel Vences, Stefan Lötters
The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals...
September 21, 2016: Molecular Phylogenetics and Evolution
Huawang Shi, Hang Yin, Lianyu Wei
The process of bid/no-bid decision-making is su bjected to uncertainty and influence of complex criteria. This paper proposed an application of the integration of rough sets (RS) and improved general regression neural network (GRNN) based on niche particle swarm optimization (NPSO) algorithm for tendering decision making. The decision table of RS and the attribution reduction was processed by MIBARK algorithm to simply the samples of GRNN. In order to improve the general regression neural network (GRNN) network performance, the niche particle swarm optimization (NPSO) was used to optimize the spread parameter σ of GRNN neural network, then a novel Bid/no-bid decision model was established based on RS and NPSO-GRNN neural network algorithm...
2016: SpringerPlus
Zhiye Li, Ruikai Ba, Zhifa Wang, Jianhua Wei, Yimin Zhao, Wei Wu
: : Craniofacial deformities caused by congenital defects or trauma remain challenges for clinicians, whereas current surgical interventions present limited therapeutic outcomes. Injection of bone marrow-derived mesenchymal stem cells (BMSCs) into the defect is highly desirable because such a procedure is microinvasive and grafts are more flexible to fill the lesions. However, preventing hypertrophic transition and morphological contraction remain significant challenges. We have developed an "all host derived" cell transplantation system composed of chondrocyte brick (CB)-enriched platelet-rich plasma (P) gel and BMSCs (B)...
September 14, 2016: Stem Cells Translational Medicine
Joel S Brown
Humans have marvelled at the fit of form and function, the way organisms' traits seem remarkably suited to their lifestyles and ecologies. While natural selection provides the scientific basis for the fit of form and function, Darwin found certain adaptations vexing or particularly intriguing: sex ratios, sexual selection and altruism. The logic behind these adaptations resides in frequency-dependent selection where the value of a given heritable phenotype (i.e. strategy) to an individual depends upon the strategies of others...
September 14, 2016: Proceedings. Biological Sciences
Yu Guo, Katherine Alexander, Andrew G Clark, Andrew Grimson, Haiyuan Yu
Analysis of transcription regulatory networks has revealed many principal features that govern gene expression regulation. MicroRNAs (miRNAs) have emerged as another major class of gene regulators that influence gene expression post-transcriptionally, but there remains a need to assess quantitatively their global roles in gene regulation. Here, we have constructed an integrated gene regulatory network comprised of transcription factors (TFs), miRNAs, and their target genes and analyzed the effect of regulation on target mRNA expression, target protein expression, protein-protein interaction, and disease association...
September 7, 2016: RNA
Svetlana Rodgers
This paper offers a concise review of technical and operational concepts underpinning commercialization of minimally processed functional foods (FFs), foods with fresh-like qualities commanding premium prices. The growing number of permitted nutritional content/health claims, many of which relate to well-being, coupled with emerging extraction and food processing technologies offers new exciting opportunities for small and medium size enterprises (SMEs) specializing in fresh produce to play an active role in the health market...
October 2016: Journal of Food Science
Yanguang Zhou, Ming Hu
Thermoelectrics offer an attractive pathway for addressing an important niche in the globally growing landscape of energy demand. Nanoengineering existing low-dimensional thermoelectric materials pertaining to realizing fundamentally low thermal conductivity has emerged as an efficient route to achieve high energy conversion performance for advanced thermoelectrics. In this paper, by performing nonequilibrium and Green-Kubo equilibrium molecular dynamics simulations we report that the thermal conductivity of Si nanowires (NWs) in polycrystalline form can reach a record low value substantially below the Casimir limit, a theory of diffusive boundary limit that regards the direction-averaged mean free path is limited by the characteristic size of the nanostructures...
October 12, 2016: Nano Letters
Pritesh Sundar Roy, Gundimeda Jwala Narasimha Rao, Sudipta Jena, Rashmita Samal, Ashok Patnaik, Sasank Sekhar Chyau Patnaik, Nitiprasad Namdeorao Jambhulkar, Srigopal Sharma, Trilochan Mohapatra
A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified...
2016: PloS One
Yee-Chin Wong, Moataz Abd El Ghany, Raeece Naeem, Kok-Wei Lee, Yung-Chie Tan, Arnab Pain, Sheila Nathan
Burkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B...
2016: Frontiers in Microbiology
Anandika Dhaliwal, Matthew Brenner, Paul Wolujewicz, Zheng Zhang, Yong Mao, Mona Batish, Joachim Kohn, Prabhas V Moghe
: A predictive framework for the evolution of stem cell biology in 3-D is currently lacking. In this study we propose deep image informatics of the nuclear biology of stem cells to elucidate how 3-D biomaterials steer stem cell lineage phenotypes. The approach is based on high content imaging informatics to capture minute variations in the 3-D spatial organization of splicing factor SC-35 in the nucleoplasm as a marker to classify emergent cell phenotypes of human mesenchymal stem cells (hMSCs)...
November 2016: Acta Biomaterialia
Colin J Carlson, Eric R Dougherty, Wayne Getz
The current outbreak of Zika virus poses a severe threat to human health. While the range of the virus has been cataloged growing slowly over the last 50 years, the recent explosive expansion in the Americas indicates that the full potential distribution of Zika remains uncertain. Moreover, many studies rely on its similarity to dengue fever, a phylogenetically closely related disease of unknown ecological comparability. Here we compile a comprehensive spatially-explicit occurrence dataset from Zika viral surveillance and serological surveys based in its native range, and construct ecological niche models to test basic hypotheses about its spread and potential establishment...
August 2016: PLoS Neglected Tropical Diseases
Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C Willison, Richard E Lenski, Orkun S Soyer, Dominique Schneider
BACKGROUND: Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli...
2016: BMC Evolutionary Biology
Jordan B Bemmels, Pascal O Title, Joaquín Ortego, L Lacey Knowles
Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species-specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade-offs in functional traits, and local-scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation...
October 2016: Molecular Ecology
Jing Hu, Peter H Seeberger, Jian Yin
Given the important roles of carbohydrates in numerous signalling pathways, cell-cell interactions and cell-matrix interactions, a variety of scaffolds based on natural polysaccharides and glycoproteins that are mostly found in the native extracellular matrix (ECM) have been established and investigated as stem cell culture systems. Stem cells have been extensively used in cell therapy and tissue engineering, and the ability to create a suitable environment to direct stem cell behavior is critical for such endeavors...
October 7, 2016: Organic & Biomolecular Chemistry
Maria Helena Hällfors, Jishan Liao, Jason Dzurisin, Ralph Grundel, Marko Hyvärinen, Kevin Towle, Grace C Wu, Jessica J Hellmann
Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account may lead to incorrect range prediction and therefore misplaced conservation efforts...
June 2016: Ecological Applications: a Publication of the Ecological Society of America
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