133 research outputs found
Fabrication and Mechanical Evaluation of Anatomically-Inspired Quasilaminate Hydrogel Structures with Layer-Specific Formulations
A major tissue engineering challenge is the creation
of multilaminate scaffolds with layer-specific mechanical
properties representative of native tissues, such as heart valve
leaflets, blood vessels, and cartilage. For this purpose,
poly(ethylene glycol) diacrylate (PEGDA) hydrogels are
attractive materials due to their tunable mechanical and
biological properties. This study explored the fabrication of
trilayer hydrogel quasilaminates. A novel sandwich method
was devised to create quasilaminates with layers of varying
stiffnesses. The trilayer structure was comprised of two
‘‘stiff’’ outer layers and one ‘‘soft’’ inner layer. Tensile testing
of bilayer quasilaminates demonstrated that these scaffolds
do not fail at the interface. Flexural testing showed that the
bending modulus of acellular quasilaminates fell between the
bending moduli of the ‘‘stiff’’ and ‘‘soft’’ hydrogel layers.
The bending modulus and swelling of trilayer scaffolds with
the same formulations were not significantly different than
single layer gels of the same formulation. The encapsulation
of cells and the addition of phenol red within the hydrogel
layers decreased bending modulus of the trilayer scaffolds.
The data presented demonstrates that this fabrication method
can make quasilaminates with robust interfaces, integrating
layers of different mechanical properties and biofunctionalization,
and thus forming the foundation for a multilaminate
scaffold that more accurately represents native tissue
Assembly of a Three-Dimensional Multitype Bronchiole Coculture Model Using Magnetic Levitation
A longstanding goal in biomedical research has been to create organotypic cocultures that faithfully represent
native tissue environments. There is presently great interest in representative culture models of the lung, which
is a particularly challenging tissue to recreate in vitro. This study used magnetic levitation in conjunction with
magnetic nanoparticles as a means of creating an organized three-dimensional (3D) coculture of the bronchiole
that sequentially layers cells in a manner similar to native tissue architecture. The 3D coculture model was
assembled from four human cell types in the bronchiole: endothelial cells, smooth muscle cells (SMCs), fibroblasts,
and epithelial cells (EpiCs). This study represents the first effort to combine these particular cell types into
an organized bronchiole coculture. These cell layers were first cultured in 3D by magnetic levitation, and then
manipulated into contact with a custom-made magnetic pen, and again cultured for 48 h. Hematoxylin and eosin
staining of the resulting coculture showed four distinct layers within the 3D coculture. Immunohistochemistry
confirmed the phenotype of each of the four cell types and showed organized extracellular matrix formation,
particularly, with collagen type I. Positive stains for CD31, von Willebrand factor, smooth muscle a-actin,
vimentin, and fibronectin demonstrate the maintenance of the phenotype for endothelial cells, SMCs, and
fibroblasts. Positive stains for mucin-5AC, cytokeratin, and E-cadherin after 7 days with and without 1% fetal
bovine serum showed that EpiCs maintained the phenotype and function. This study validates magnetic levitation
as a method for the rapid creation of organized 3D cocultures that maintain the phenotype and induce
extracellular matrix formation
A spheroid toxicity assay using magnetic 3D bioprinting and real-time mobile device-based imaging
An ongoing challenge in biomedical research is the search for simple, yet robust assays using 3D cell cultures for toxicity screening. This study addresses that challenge with a novel spheroid assay, wherein spheroids, formed by magnetic 3D bioprinting, contract immediately as cells rearrange and compact the spheroid in relation to viability and cytoskeletal organization. Thus, spheroid size can be used as a simple metric for toxicity. The goal of this study was to validate spheroid contraction as a cytotoxic endpoint using 3T3 fibroblasts in response to 5 toxic compounds (all-trans retinoic acid, dexamethasone, doxorubicin, 5′-fluorouracil, forskolin), sodium dodecyl sulfate (+control), and penicillin-G (−control). Real-time imaging was performed with a mobile device to increase throughput and efficiency. All compounds but penicillin-G significantly slowed contraction in a dose-dependent manner (Z’ = 0.88). Cells in 3D were more resistant to toxicity than cells in 2D, whose toxicity was measured by the MTT assay. Fluorescent staining and gene expression profiling of spheroids confirmed these findings. The results of this study validate spheroid contraction within this assay as an easy, biologically relevant endpoint for high-throughput compound screening in representative 3D environments
New resampling method for evaluating stability of clusters
<p>Abstract</p> <p>Background</p> <p>Hierarchical clustering is a widely applied tool in the analysis of microarray gene expression data. The assessment of cluster stability is a major challenge in clustering procedures. Statistical methods are required to distinguish between real and random clusters. Several methods for assessing cluster stability have been published, including resampling methods such as the bootstrap.</p> <p>We propose a new resampling method based on continuous weights to assess the stability of clusters in hierarchical clustering. While in bootstrapping approximately one third of the original items is lost, continuous weights avoid zero elements and instead allow non integer diagonal elements, which leads to retention of the full dimensionality of space, i.e. each variable of the original data set is represented in the resampling sample.</p> <p>Results</p> <p>Comparison of continuous weights and bootstrapping using real datasets and simulation studies reveals the advantage of continuous weights especially when the dataset has only few observations, few differentially expressed genes and the fold change of differentially expressed genes is low.</p> <p>Conclusion</p> <p>We recommend the use of continuous weights in small as well as in large datasets, because according to our results they produce at least the same results as conventional bootstrapping and in some cases they surpass it.</p
Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum
Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon–anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera
GraphClust: alignment-free structural clustering of local RNA secondary structures
Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs
Host factors do not influence the colonization or infection by fluconazole resistant Candida species in hospitalized patients
Nosocomial yeast infections have significantly increased during the past two decades in industrialized countries, including Taiwan. This has been associated with the emergence of resistance to fluconazole and other antifungal drugs. The medical records of 88 patients, colonized or infected with Candida species, from nine of the 22 hospitals that provided clinical isolates to the Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY) program in 1999 were reviewed. A total of 35 patients contributed fluconazole resistant strains [minimum inhibitory concentrations (MICs) ≧ 64 mg/l], while the remaining 53 patients contributed susceptible ones (MICs ≦ 8 mg/l). Fluconazole resistance was more frequent among isolates of Candida tropicalis (46.5%) than either C. albicans (36.8%) or C. glabrata (30.8%). There was no significant difference in demographic characteristics or underlying diseases among patients contributing strains different in drug susceptibility
Antireflux Transoral Incisionless Fundoplication Using EsophyX: 12-Month Results of a Prospective Multicenter Study
BACKGROUND: A novel transoral incisionless fundoplication (TIF) procedure using the EsophyX system with SerosaFuse fasteners was designed to reconstruct a full-thickness valve at the gastroesophageal junction through tailored delivery of multiple fasteners during a single-device insertion. The safety and efficacy of TIF for treating gastroesophageal reflux disease (GERD) were evaluated in a prospective multicenter trial. METHODS: Patients (n = 86) with chronic GERD treated with proton pump inhibitors (PPIs) were enrolled. Exclusion criteria included an irreducible hiatal hernia > 2 cm. RESULTS: The TIF procedure (n = 84) reduced all hiatal hernias (n = 49) and constructed valves measuring 4 cm (2-6 cm) and 230 degrees (160 degrees -300 degrees ). Serious adverse events consisted of two esophageal perforations upon device insertion and one case of postoperative intraluminal bleeding. Other adverse events were mild and transient. At 12 months, aggregate (n = 79) and stratified Hill grade I tight (n = 21) results showed 73% and 86% of patients with >or=50% improvement in GERD health-related quality of life (HRQL) scores, 85% discontinuation of daily PPI use, and 81% complete cessation of PPIs; 37% and 48% normalization of esophageal acid exposure; 60% and 89% hiatal hernia reduction; and 62% and 80% esophagitis reduction, respectively. More than 50% of patients with Hill grade I tight valves had a normalized cardia circumference. Resting pressure of the lower esophageal sphincter (LES) was improved significantly (p < 0.001), by 53%. EsophyX-TIF cured GERD in 56% of patients based on their symptom reduction and PPI discontinuation. CONCLUSION: The 12-month results showed that EsophyX-TIF was safe and effective in improving quality of life and for reducing symptoms, PPI use, hiatal hernia, and esophagitis, as well as increasing the LES resting pressure and normalizing esophageal pH and cardia circumference in chronic GERD patients.Journal ArticleMulticenter StudyResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe
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