Specification of spatial relationships in directed graphs of cell signaling networks

Graph theory provides a useful and powerful tool for the analysis of cellular signaling networks. Intracellular components such as cytoplasmic signaling proteins, transcription factors and genes are connected by links, representing various types of chemical interactions that result in functional consequences. However, these graphs lack important information regarding the spatial distribution of cellular components. The ability of two cellular components to interact depends not only on their mutual chemical affinity but also on co-localization to the same subcellular region. Localization of components is often used as a regulatory mechanism to achieve specific effects in response to different receptor signals. Here we describe an approach for incorporating spatial distribution into graphs, and for the development of mixed graphs where links are specified by mutual chemical affinity as well as colocalization. We suggest that such mixed graphs will provide more accurate descriptions of functional cellular networks and their regulatory capabilities and aid in the development of large-scale predictive models of cellular behavior

Behavior of prostate cancer cells in a nanohydroxyapatite/collagen bone scaffold

Prostate cancer (PCa) is the second leading cause of death among men in Europe and U.S. The metastatic dissemination pattern of PCa is unique, developing bone metastasis as the only site of progression, consequently with a prognosis very poor. The cancer cells interactions within the surrounding bone environment are critical for tumor growth and progression. Secreted protein, acidic and rich in cysteine (SPARC) is described to be involved in PCa cells migration and invasion into bone. Three-dimensional (3D) in vitro systems that are able to closely resemble the in vivo microenvironment are recently taking importance in cancer research. Original nanohydroxyapatite/collagen scaffolds were designed to resemble bone microenvironment in order to be applied as substitutes in bone defects and as potential biomaterials to mimic skeletal tumors. In fact, these 3D structures were cytocompatible and able to support osteoblast (MC3T3-E1) colonization and to promote bone ingrowth. Additionally, SPARC adsorption onto the scaffolds affected PC3 and LNCaP PCa cell lines behavior. PC3 cells were found to adapt and colonize the scaffolds, differing from LNCaP where cells underwent morphogenic changes and grew as clusters. Furthermore, for the tested SPARC concentration, SPARC plays a role in retaining LNCaP cells at the latter time points while with PC3 cells no significant differences were observed. This characterization study is required to establish a bone model to provide new insights into the poorly understood PCa mechanisms of metastasis to bone and the generation of improved therapies.info:eu-repo/semantics/publishedVersio

Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism

Streptococcus pneumoniae is a strictly fermentative human pathogen that relies on carbohydrate metabolism to generate energy for growth. The nasopharynx colonised by the bacterium is poor in free sugars, but mucosa lining glycans can provide a source of sugar. In blood and inflamed tissues glucose is the prevailing sugar. As a result during progression from colonisation to disease S. pneumoniae has to cope with a pronounced shift in carbohydrate nature and availability. Thus, we set out to assess the pneumococcal response to sugars found in glycans and the influence of glucose (Glc) on this response at the transcriptional, physiological and metabolic levels. Galactose (Gal), N-acetylglucosamine (GlcNAc) and mannose (Man) affected the expression of 8 to 14% of the genes covering cellular functions including central carbon metabolism and virulence. The pattern of end-products as monitored by in vivo 13C-NMR is in good agreement with the fermentation profiles during growth, while the pools of phosphorylated metabolites are consistent with the type of fermentation observed (homolactic vs. mixed) and regulation at the metabolic level. Furthermore, the accumulation of α-Gal6P and Man6P indicate metabolic bottlenecks in the metabolism of Gal and Man, respectively. Glc added to cells actively metabolizing other sugar(s) was readily consumed and elicited a metabolic shift towards a homolactic profile. The transcriptional response to Glc was large (over 5% of the genome). In central carbon metabolism (most represented category), Glc exerted mostly negative regulation. The smallest response to Glc was observed on a sugar mix, suggesting that exposure to varied sugars improves the fitness of S. pneumoniae. The expression of virulence factors was negatively controlled by Glc in a sugar-dependent manner. Overall, our results shed new light on the link between carbohydrate metabolism, adaptation to host niches and virulence

Osteogenic induction of hBMSCs by electrospun scaffolds with dexamethasone release functionality

Electrospun structures were proposed as scaffolds owing to their morphological and structural similarities with the extracellular matrix found in many native tissues. These !brous structures were also proposed as drug release systems by exploiting the direct dependence of the release rate of a drug on the surface area. An osteogenic differentiation factor, dexamethasone (DEX), was incorporated into electrospun polycaprolactone (PCL) nano!bers at different concentrations (5, 10, 15 and 20 wt.% polymer), in a single-step process. The DEX incorporated into the polymeric carrier is in amorphous state, as determined by DSC, and does not in"uence the typical nano!bers morphology. In vitro drug release studies demonstrated that the dexamethasone release was sustained over a period of 15 days. The bioactivity of the released dexamethasone was assessed by cultivating human bone marrow mesenchymal stem cells (hBMSCs) on 15 wt.% DEX-loaded PCL NFMs, under dexamethasone-absent osteogenic differentiation medium formulation. An increased concentration of alkaline phosphatase and deposition of a mineralized matrix was observed. Phenotypic and genotypic expression of osteoblastic-speci!c markers corroborates the osteogenic activity of the loaded growth/differentiation factor. Overall data suggests that the electrospun biodegradable nano!bers can be used as carriers for the sustained release of growth/differentiation factors relevant for bone tissue engineering strategies.This work was partially supported by the European Network of Excellence EXPERTISSUES (NMP3-CT-2004-500283). The Portuguese Foundation for Science and Technology was acknowledged for the PhD grant of A. Martins (SFRH/BD/24382/2005)

Exploring the gelation mechanisms and cytocompatibility of gold (III)-mediated regenerated and thiolated silk fibroin hydrogels

Accelerating the gelation of silk fibroin (SF) solution from several days or weeks to minutes or few hours is critical for several applications (e.g., cell encapsulation, bio-ink for 3D printing, and injectable controlled release). In this study, the rapid gelation of SF induced by a gold salt (Au3+) as well as the cytocompatibility of Au3+-mediated SF hydrogels are reported. The gelation behaviors and mechanisms of regenerated SF and thiolated SF (tSF) were compared. Hydrogels can be obtained immediately after mixing or within three days depending on the types of silk proteins used and amount of Au3+. Au3+-mediated SF and tSF hydrogels showed different color appearances. The color of Au-SF hydrogels was purple-red, whereas the Au-tSF hydrogels maintained their initial solution color, indicating different gelation mechanisms. The reduction of Au3+ by amino groups and further reduction to Au by tyrosine present in SF, resulting in a dityrosine bonding and Au nanoparticles (NPs) production, are proposed as underlying mechanisms of Au-SF gel formation. Thiol groups of the tSF reduced Au3+ to Au+ and formed a disulfide bond, before a formation of Au+-S bonds. Protons generated during the reactions between Au3+ and SF or tSF led to a decrease of the local pH, which affected the chain aggregation of the SF, and induced the conformational transition of SF protein to beta sheet. The cytocompatibility of the Au-SF and tSF hydrogels was demonstrated by culturing with a L929 cell line, indicating that the developed hydrogels can be promising 3D matrices for different biomedical applications.This article has been prepared with the support of REMIX Project, funded by the European Union’s Horizon 2020 Research and Innovation programme under the Maria Sklodowska-Curie grant agreement N.778078. Chavee Laomeephol acknowledges the PhD grants supported by Chulalongkorn University for “The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship” and “The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund)”. Authors also acknowledge the financial support from FCT (Portuguese Foundation for Science and Technology) for the project PTDC/CTM-BIO/4388/2014 - SPARTAN, the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) (NORTE-01-0145-FEDER-000023 FROnTHERA) and the NORTE 2020 Structured Project, co funded by Norte2020

The influence of patterned nanofiber meshes on human mesenchymal stem cell osteogenesis

A specially designed electroconductive collector enables the electrospinning of P-NFM composed of areas of parallel/uniaxially aligned fibers and areas of random/orthogonal nanofiber distribution. The biological relevance of P-NFM is demonstrated using hBMSCs as an autologous cell source. The structures induce cell orientation along the uniaxially aligned fibers, mainly during earlier culturing periods under basal and osteogenic differentiation conditions. The microtopography of the P-NFM also controls the deposition of mineralized extracellular matrix along the pre-defined fiber direction. Genotypic characterization confirms the successful differentiation into the osteogenic lineage.European Integrated Project GENOSTEM (LSH-STREP-CT-2003-503161); European Network of Excellence EXPERTISSUES (NMP3-CT-2004-500283); Portuguese Foundation for Science and Technology for the project Naturally Nano (POCI/EME/58982/2004) and the PhD grant SFRH/BD/24382/2005

Biodegradable nanofibers-reinforced microfibrous composite scaffolds for bone tissue engineering

Native bone extracellular matrix (ECM) is a complex hierarchical fibrous composite structure, resulting from the assembling of collagen fibrils at several length scales, ranging from the macro to the nanoscale. The combination of nanofibers within microfibers after conventional reinforcement methodologies seems to be a feasible solution to the rational design of highly functional synthetic ECM substitutes. The present work aims at the development of bone ECM inspired structures, conjugating electrospun chitosan (Cht) nanofibers within biodegradable polymeric microfibers [poly(butylene succinate)—PBS and PBS/Cht], assembled in a fiber mesh structure. The nanofibers-reinforced composite fiber mesh scaffolds were seeded with human bone marrow mesenchymal stem cells (hBMSCs) and cultured under osteogenic differentiation conditions. These nanofibers-reinforced composite scaffolds sustained ECM deposition and mineralization, mainly in the PBS/Cht-based fiber meshes, as depicted by the increased amount of calcium phosphates produced by the osteogenic differentiated hBMSCs. The osteogenic genotype of the cultured hBMSCs was confirmed by the expression of osteoblastic genes, namely Alkaline Phosphatase, Osteopontin, Bone Sialoprotein and Osteocalcin, and the transcription factors Runx2 and Osterix, all involved in different stages of the osteogenesis. These data represent the first report on the biological functionality of nanofibers-reinforced composite scaffolds, envisaging the applicability of the developed structures for bone tissue engineering.This work was partially supported by the European Network of Excellence EXPERTISSUES (NMP3-CT-2004-500283). It was also acknowledged by the Portuguese Foundation for Science and Technology for the Ph.D. grant of A. Martins (SFRH/BD/24382/2005)

Compartmentalized PDE4A5 signaling impairs hippocampal synaptic plasticity and long-term memory

Alterations in cAMP signaling are thought to contribute to neurocognitive and neuropsychiatric disorders. Members of the cAMP-specific phosphodiesterase 4 (PDE4) family, which contains >25 different isoforms, play a key role in determining spatial cAMP degradation so as to orchestrate compartmentalized cAMP signaling in cells. Each isoform binds to a different set of protein complexes through its unique N-terminal domain, thereby leading to targeted degradation of cAMP in specific intracellular compartments. However, the functional role of specific compartmentalized PDE4 isoforms has not been examined in vivo. Here, we show that increasing protein levels of the PDE4A5 isoform in mouse hippocampal excitatory neurons impairs a long-lasting form of hippocampal synaptic plasticity and attenuates hippocampus-dependent long-term memories without affecting anxiety. In contrast, viral expression of a truncated version of PDE4A5, which lacks the unique N-terminal targeting domain, does not affect long-term memory. Further, overexpression of the PDE4A1 isoform, which targets a different subset of signalosomes, leaves memory undisturbed. Fluorescence resonance energy transfer sensor-based cAMP measurements reveal that the full-length PDE4A5, in contrast to the truncated form, hampers forskolin-mediated increases in neuronal cAMP levels. Our study indicates that the unique N-terminal localization domain of PDE4A5 is essential for the targeting of specific cAMP-dependent signaling underlying synaptic plasticity and memory. The development of compounds to disrupt the compartmentalization of individual PDE4 isoforms by targeting their unique N-terminal domains may provide a fruitful approach to prevent cognitive deficits in neuropsychiatric and neurocognitive disorders that are associated with alterations in cAMP signaling

Cartilage tissue engineering using electrospun PCL nanofiber meshes and MSCs

Mesenchymal stem cells (MSCs) have been recognized for their ability to differentiate into cells of different tissues such as bone, cartilage, or adipose tissue, and therefore are of great interest for potential therapeutic strategies. Adherent, colony-forming, fibroblastic cells were isolated from human bone marrow aspirates, from patients undergoing knee arthroplasties, and the MSCs phenotype characterized by flow cytometry. Afterward, cells were seeded onto electrospun polycaprolactone nanofiber meshes and cultured in a multichamber flow perfusion bioreactor to determine their ability to produce cartilagineous extracellular matrix. Results indicate that the flow perfusion bioreactor increased the chondrogenic differentiation of hBM-MSCs, as confirmed either by morphological and RT-PCR analysis. Cartilage-related genes such as aggrecan, collagen type II, and Sox9 were expressed. ECM deposition was also detected by histological procedures. Collagen type II was present in the samples, as well as collagen type I. Despite no statistically significant values being obtained for gene expression, the other results support the choice of the bioreactor for this type of culture.M. Alves da Silva would like to acknowledge the Portuguese Foundation for Science and Technology (FCT) for her grant (SFRH/BD/28708/2006). The authors would like to acknowledge the patients of Hospital de S. Marcos, Braga, Portugal, for the donation of the biological samples, as well to its medical staff. The authors would also like to thank the Institute for Health and Life Sciences (ICVS), University of Minho, Braga, Portugal, for allowing the use of their research facilities. Authors would like specially to acknowledge Luis Martins for his valuable help with the histological procedures and Goreti Pinto for the aid in the microscopy. We thank Ana M. Frias for the important help with the FACS procedure. Finally, we would like to acknowledge the European NoE EXPERTISSUES (NMP3-CT-2004-500283). This work was partially supported by the European FP7 Project Find and Bind (NMP4-SL-2009-229292)

Detecting antibody-labeled BCG MNPs using a magnetoresistive biosensor and magnetic labeling technique

Tuberculosis is still a major global health concern, causing the estimated death of 1.5 million people per year and being associated with high morbidity. The development of point-of-care diagnostic tools for tuberculosis is mandatory, especially because the fast and accurate detection of the slow-growing Mycobacterium tuberculosis by the conventional diagnostic tests is difficult. The objective of this work was to develop the first steps to achieve a portable method for the diagnosis of tuberculosis, by a sandwich-immunoassay combined with magnetoresistive biochip technology. With the purpose of conjugating 250 nm streptavidin-coated magnetic nanoparticles with anti-M. tuberculosis biotinylated antibodies, Mycobacterium bovis Bacillus Calmette-Guerin was used as a surrogate for M. tuberculosis bacteria. After magnetic capture, target bacteria were brought in contact with the surface of the magnetoresistive biochip previously functionalized with a secondary anti-M. tuberculosis antibody. Magnetically labeled cells were detected by an array of spin-valve sensors, which change their electrical resistance in the presence of the fringe field of the magnetic particles. Optimization studies on the efficiency of the magnetic capture and further recognition of the bacteria by the secondary antibody on the biochip surface were conducted. The results on the magnetoresistive biochip showed a clear difference in the signal between specific and control ( nonspecific) sensors, suggesting the usefulness of this technique as a potential biorecognition tool for the development of a point-of-care diagnostic method for tuberculosis.Acknowledgments: Teresa Barroso thanks FCT for her PhD Grant SFRH/BD/33904/2009.info:eu-repo/semantics/publishedVersio