Structural and Activity Profile Relationships Between Drug Scaffolds.
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ABSTRACT:
SUBMITTER: Hu Y
PROVIDER: S-EPMC4406972 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Positively charged oligo(poly(ethylene glycol) fumarate) (OPF+) hydrogel scaffolds, implanted into a complete transection spinal cord injury (SCI), facilitate a permissive regenerative environment and provide a platform for controlled observation of repair mechanisms. Axonal regeneration after SCI is critically dependent upon nutrients and oxygen from a newly formed blood supply. Our objective was to investigate fundamental characteristics of revascularization in association with the ingrowth of axons into hydrogel scaffolds, thereby defining spatial relationships between axons and the neovasculature. A novel combination of stereologic estimates and precision image analysis techniques quantitate neurovascular regeneration in rats. Multichannel hydrogel scaffolds containing Matrigel-only (MG), Schwann cells (SCs), or SCs with rapamycin-eluting poly(lactic co-glycolic acid) microspheres (RAPA) were implanted for 6 weeks following complete spinal cord transection. Image analysis of 72 scaffold channels identified a total of 2494 myelinated and 4173 unmyelinated axons at 10 μm circumferential intervals centered around 708 individual blood vessel profiles. Blood vessel number, density, volume, diameter, intervessel distances, total vessel surface and cross-sectional areas, and radial diffusion distances were compared. Axon number and density, blood vessel surface area, and vessel cross-sectional areas in the SC group exceeded that in the MG and RAPA groups. Individual axons were concentrated within a concentric radius of 200-250 μm from blood vessel walls, in Gaussian distributions, which identified a peak axonal number (Mean Peak Amplitude) corresponding to defined distances (Mean Peak Distance) from each vessel, the highest concentrations of axons were relatively excluded from a 25-30 μm zone immediately adjacent to the vessel, and from vessel distances >150 μm. Higher axonal densities correlated with smaller vessel cross-sectional areas. A statistical spatial algorithm was used to generate cumulative distribution F- and G-functions of axonal distribution in the reference channel space. Axons located around blood vessels were definitively organized as clusters and were not randomly distributed. A scoring system stratifies 5 direct measurements and 12 derivative parameters influencing regeneration outcomes. By providing methods to quantify the axonal-vessel relationships, these results may refine spinal cord tissue engineering strategies to optimize the regeneration of complete neurovascular bundles in their relevant spatial relationships after SCI. Impact statement Vascular disruption and impaired neovascularization contribute critically to the poor regenerative capacity of the spinal cord after injury. In this study, hydrogel scaffolds provide a detailed model system to investigate the regeneration of spinal cord axons as they directly associate with individual blood vessels, using novel methods to define their spatial relationships and the physiologic implications of that organization. These results refine future tissue engineering strategies for spinal cord repair to optimize the re-development of complete neurovascular bundles in their relevant spatial architectures.
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Project description:BackgroundDetection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represented as sequence profiles is arguably the most effective homology detection strategy. However, finding the best way to represent evolutionary information of a protein sequence family in the profile, to compare profiles and to estimate the biological significance of such comparisons, remains an active area of research.ResultsHere, we present a new homology detection method based on sequence profile-profile comparison. The method has a number of new features including position-dependent gap penalties and a global score system. Position-dependent gap penalties provide a more biologically relevant way to represent and align protein families as sequence profiles. The global score system enables an analytical solution of the statistical parameters needed to estimate the statistical significance of profile-profile similarities. The new method, together with other state-of-the-art profile-based methods (HHsearch, COMPASS and PSI-BLAST), is benchmarked in all-against-all comparison of a challenging set of SCOP domains that share at most 20% sequence identity. For benchmarking, we use a reference ("gold standard") free model-based evaluation framework. Evaluation results show that at the level of protein domains our method compares favorably to all other tested methods. We also provide examples of the new method outperforming structure-based similarity detection and alignment. The implementation of the new method both as a standalone software package and as a web server is available at http://www.ibt.lt/bioinformatics/coma.ConclusionDue to a number of developments, the new profile-profile comparison method shows an improved ability to match distantly related protein domains. Therefore, the method should be useful for annotation and homology modeling of uncharacterized proteins.
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Project description:BACKGROUND:The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. RESULTS:In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs. CONCLUSIONS:Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.
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Project description:Spontaneous neural activity fluctuations have been shown to influence trial-by-trial variation in perceptual, cognitive, and behavioral outcomes. However, the complex electrophysiological mechanisms by which these fluctuations shape stimulus-evoked neural activity remain largely to be explored. Employing a large-scale magnetoencephalographic dataset and an electroencephalographic replication dataset, we investigate the relationship between spontaneous and evoked neural activity across a range of electrophysiological variables. We observe that for high-frequency activity, high pre-stimulus amplitudes lead to greater evoked desynchronization, while for low frequencies, high pre-stimulus amplitudes induce larger degrees of event-related synchronization. We further decompose electrophysiological power into oscillatory and scale-free components, demonstrating different patterns of spontaneous-evoked correlation for each component. Finally, we find correlations between spontaneous and evoked time-domain electrophysiological signals. Overall, we demonstrate that the dynamics of multiple electrophysiological variables exhibit distinct relationships between their spontaneous and evoked activity, a result which carries implications for experimental design and analysis in non-invasive electrophysiology.
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Project description:This study investigated relationships between neuroblastomas (NBs) imaging phenotypes, tumor genomic profile and patient outcome.This IRB-approved retrospective observational study included 133 NB patients (73 M, 60 F; median age 15 months, range 0-151) treated in a single institution between 1998 and 2012. A consensus review of imaging (CT-scan, MRI) categorized tumors according to both the primarily involved compartment (i.e., neck, chest, abdomen or pelvis) and the sympathetic anatomical structure the tumors rose from (i.e., cervical, paravertebral or periarterial chains, or adrenal gland). Tumor shape, volume and image-defined surgical risk factors (IDRFs) at diagnosis were recorded. Genomic profiles were assessed using array-based comparative genomic hybridization and divided into three groups: "numerical-only chromosome alterations" (NCA), "segmental chromosome alterations" (SCA) and "MYCN amplification" (MNA). Statistical analyses included Kruskal-Wallis, Chi2 and Fisher's exact tests and the Kaplan-Meier method with log-rank tests and Cox model for univariate and multivariate survival analyses.A significant association between the sympathetic structure origin of tumors and genomic profiles was demonstrated. NBs arising from cervical sympathetic chains were all NCA. Paravertebral NBs were NCA or SCA in 75% and 25%, respectively and none were MNA. Periarterial NBs were NCA, SCA or MNA in 33%, 56% and 11%, respectively. Adrenal NBs were NCA, SCA or MNA in 16%, 36% and 48%, respectively. Among MNA NBs, 92% originated from the adrenal gland. The sympathetic anatomical classification was significantly better correlated to overall survival than the compartmental classification (P < .0003). The tumor volume of MNA NBs was significantly higher than NCA or SCA NBs (P < .0001). Patients with initial volume less than 160 mL had significantly better overall survival (P < .009). A "single mass" pattern was significantly more frequent in NCA NBs (P = .0003). The number of IDRFs was significantly higher in MNA NBs (P < .0001).Imaging phenotypes of neuroblastomas, including tumor origin along the sympathetic system, correlate with tumor genomic profile and patient outcome.
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Project description:BackgroundScaffolds are of great importance in tissue engineering applications as they provide a mechanically supportive environment for cellular activity, which is particularly necessary for hard tissues such as bone. Notably, the mechanical properties of a scaffold vary with differing design parameters such as those related to scaffold height and internal structure. Thus, the present study aimed to explore the relationship between design parameters and mechanical properties of composite polycaprolactone (PCL) and nano-hydroxyapatite (nHAp) scaffolds fabricated by three-dimensional (3D) printing.MethodsWe designed and printed scaffolds with different internal structures (lattice and staggered) and varying heights (4, 6, 8 and 10 layers), and consistent porosity (50%) for the purpose of comparison. Then, we examined the scaffold microstructure (pore size and penetration between layers) using scanning electron microscopy (SEM) and mechanical properties (elastic modulus and yield strength) using compressive testing.ResultsOur results illustrated that the microstructural parameters were related to scaffold design. At higher heights, pore size increased while penetration between layers decreased; thus, mechanical properties were affected. Results of mechanical testing demonstrated that for lattice scaffolds, elastic modulus was similar for 6 vs 4, and 8 vs 4 layers but ~33% lower for 10 layers vs 4 layers. Similarly, yield strength was comparable for 6 vs 4, and 8 vs 4 layers but ~27% lower for 10 layers vs 4 layers. With staggered scaffolds, when compared to 4-layer results, elastic modulus was similar for 6 layers but was ~43% lower for 8 layers and ~38% lower for 10 layers. Staggered scaffolds had ~38%, ~51%, and ~76% lower yield strength when the number of layers were increased from 4 to 6, 8, and 10 layers, respectively. When comparing lattice and staggered scaffolds with the same layer number, elastic modulus was similar, apart from 8-layer scaffolds where the staggered design was ~42% lower than lattice. Yield strength was similar between 4-layer staggered and lattice scaffolds, while staggered scaffolds with 6, 8, and 10 number of layers showed ~43%, ~45%, ~68% lower strength, respectively, than those found in lattice scaffolds with the same layer numbers.ConclusionsMechanical properties of 3D printed scaffolds depended on scaffold height for both lattice and staggered internal structures. Staggered scaffolds had lower mechanical properties than the lattice scaffolds with the same height and were more sensitive to the change in scaffold height. Taken together, lattice scaffolds demonstrated the advantages of more stable mechanical properties over staggered scaffolds. Also, scaffolds with lower height were more promising in terms of mechanical properties compared to scaffolds with greater height.
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