Epitaxial growth and characterization of multi-layer site-controlled InGaAs quantum dots based on the buried stressor method

We report on the epitaxial growth, theoretical modeling, and structural as well as optical investigation of multi-layer, site-controlled quantum dots fabricated using the buried stressor method. This advanced growth technique utilizes the strain from a partially oxidized AlAs layer to induce site-selective nucleation of InGaAs quantum dots. By implementing strain-induced spectral nano-engineering, we achieve separation in emission energy by about 150 meV of positioned and non-positioned quantum dots and a local increase of the emitter density in a single layer. Furthermore, we achieve a threefold increase of the optical intensity and reduce the inhomogeneous broadening of the ensemble emission by 20% via stacking three layers of site-controlled emitters, which is particularly valuable for using the SCQDs in microlaser applications. Moreover, we obtain direct control over emission properties by adjusting the growth and fabrication parameters. Our optimization of site-controlled growth of quantum dots enables the development of photonic devices with enhanced light-matter interaction and microlasers with increased confinement factor and spontaneous emission coupling efficiency

Effects of cell seeding density on real-time monitoring of anti-proliferative effects of transient gene silencing

WOS: 000390112500001PubMed ID: 27981039Background: Real-time cellular analysis systems enable impedance-based label-free and dynamic monitoring of various cellular events such as proliferation. In this study, we describe the effects of initial cell seeding density on the anti-proliferative effects of transient gene silencing monitored via real-time cellular analysis. We monitored the realtime changes in proliferation of Huh7 hepatocellular carcinoma and A7r5 vascular smooth muscle cells with different initial seeding densities following transient receptor potential canonical 1 (TRPC1) silencing using xCELLigence system. Huh7 and A7r5 cells were seeded on E-plate 96 at 10,000, 5000, 1250 and 5000, 2500 cells well(-1), respectively, following silencing vector transfection. The inhibitory effects of transient silencing on cell proliferation monitored every 30 min for 72 h. Results: TRPC1 silencing did not inhibit the proliferation rates of Huh7 cells at 10,000 cells well(-1) seeding density. However, a significant anti-proliferative effect was observed at 1250 cells well(-1) density at each time point throughout 72 h. Furthermore, significant inhibitory effects on A7r5 proliferation were observed at both 5000 and 2500 cells well(-1) for 72 h. Conclusions: Data suggest that the effects of transient silencing on cell proliferation differ depending on the initial cell seeding density. While high seeding densities mask the significant changes in proliferation, the inhibitory effects of silencing become apparent at lower seeding densities as the entry into log phase is delayed. Using the optimal initial seeding density is crucial when studying the effects of transient gene silencing. In addition, the results suggest that TRPC1 may contribute to proliferation and phenotypic switching of vascular smooth muscle cells.Scientific and Technological Research Council of Turkey (TUBITAK Research Project)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [108S072]; Novartis (Turkey)Novartis; Research Infrastructure Project, The State Planning Organization of Turkey (DPT) [2009K120640]This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK Research Project, 108S072) and Novartis (Turkey) to MT. The xCELLigence system was purchased within the Research Infrastructure Project, The State Planning Organization of Turkey (DPT, 2009K120640)

Primary skeletal muscle myoblasts from chronic heart failure patients exhibit loss of anti-inflammatory and proliferative activity

BACKGROUND: Peripheral skeletal muscle wasting is a common finding with adverse effects in chronic heart failure (HF). Whereas its clinical relevance is beyond doubt, the underlying pathophysiological mechanisms are not yet fully elucidated. We aimed to introduce and characterize the primary culture of skeletal muscle cells from individual HF patients as a supportive model to study this muscle loss. METHODS AND RESULTS: Primary myoblast and myotubes cultures were successfully propagated from the m. vastus lateralis of 6 HF patients with reduced ejection fraction (HFrEF; LVEF <45 %) and 6 age and gender-matched healthy donors. HFrEF cultures were not different from healthy donors in terms of morphology, such as myoblast size, shape and actin microfilament. Differentiation and fusion indexes were identical between groups. Myoblast proliferation in logarithmic growth phase, however, was attenuated in the HFrEF group (p = 0.032). In addition, HFrEF myoblasts are characterized by a reduced TNFR2 expression and IL-6 secretion (p = 0.017 and p = 0.016; respectively). CONCLUSION: Biopsy derived primary skeletal muscle myoblasts of HFrEF patients produce similar morphological and myogenic differentiation responses as myoblasts of healthy donors, though demonstrate loss of anti-inflammatory and proliferative activity

A microRNA Expression Profile Consisting of 12 microRNAs Is Associated with Inflammatory Breast Cancer.

Abstract Introduction: Inflammatory breast cancer (IBC) is an aggressive form of breast cancer with a dismal clinical outcome. In the past we showed that IBC is characterized by a specific gene expression pattern. In this study, we investigate if microRNAs (miRNAs) are responsible for the specific IBC gene signature.Materials and methods: 377 miRNAs were profiled in 20 IBC tumor samples and 50 non-stage matched nIBC tumour samples using the human MicroRNA A Array Set version 2.0 (Applied Biosystems). The IBC and nIBC study populations are matched for tumor grade and ER status. All miRNAs with Ct-values less than 35 in 25% of the samples were included for analysis. Data normalization was performed relative to the median miRNA expression level per sample and expression values were log2-transformed. Principal component analysis (PCA) was performed to identify metagenes of miRNAs, associated with the IBC phenotype. Relevant metagenes were compared with prognostic/predictive gene signature-classifications (wound healing response, invasiveness gene signature, 70-gene prognostic signature, genomic grade index, recurrence score, HOXB13/IL17RB-expression ratio and the molecular breast cancer subtypes). Data were validated by analysing relevant miRNA target gene sets on an IBC/nIBC gene expression data set.Results: Using PCA, we identified a metagene associated with the IBC phenotype (Hazard Ratio: 4.500; P=0.011). This metagene was also significantly associated with the Luminal B phenotype, the IBC signature and with an elevated HOXB13/IL17RB-expresion ratio (range Rs = 0.302 – 0.366; P&amp;lt;0.05). MiRNAs significantly (FDR&amp;lt;0.1) associated with this metagene were: miR29A, miR544, miR574-3p, miR548C-3p, miR451, miR548B-5p, miR24, miR28-5p, miR137, miR302B, miR148A and miR302A (range Rs: -0.367 – 0.307). Cluster analysis using this miRNA signature identified two sample clusters, one containing 70% of the IBC samples and a second one containing 64% of the nIBC samples (Pearson X2; P=0.021). Using gene set enrichment analysis for miR24-, miR28-, miR29A-, miR137-, miR148A-, miR302A- and miR302B target gene sets, we confirmed the differential expression for the above mentioned miRNAs (P&amp;lt;0.01) except for miR28. Using Oncomine analyses we were able to associate the identified miRNAs with NFkB activation (miR29, miR148), steroid receptor signalling (miR302A, miR302B, and miR137), cell adhesion (miR29), stem cell signalling (miR137, miR28) and regulation of the extracellular matrix composition (miR29, miR148).Discussion: Through PCA we identified a miRNA signature associated with IBC. The miRNA signature was partly validated on the gene expression level. Interestingly, most identified miRNAs regulate biological processes previously associated with IBC through gene expression analysis, confirming our results also at the biological level. The association of the IBC-specific miRNA-metagene with the Luminal B phenotype and elevated HOXB13/IL17RB-expression ratios confirms our data that ER+ IBC samples, which constitute the majority of the present IBC study population, generally belong to the Luminal B subtype and are associated with resistance to endocrine therapy. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6119.</jats:p

A microRNA Expression Profile Consisting of 15 microRNAs, Including miR205, Is Associated with Poor Prognosis in Breast Cancer.

Abstract Introduction: MicroRNAs (miRNA) are a class of non-coding RNAs able to regulate gene expression at the post-transcriptional level. In breast cancer, levels of specific miRNAs differ between malignant and normal breast tissue and are able to classify tumors according to clinicopathologic variables. This highlights the potential of miRNAs as novel prognostic and/or predictive indicators. In this study we sought for miRNAs denoting poor prognosis in breast cancer.Materials and methods: 377 miRNAs were profiled in 70 breast tumor samples using the human MicroRNA A Array Set version 2.0 (Applied Biosystems). All miRNAs with Ct-values less than 35 in 25% of the samples were included for analysis. Data normalization was performed relative to the median miRNA expression level per sample and expression values were log2-transformed. Principal component analysis (PCA) was performed to identify metagenes of miRNAs associated with clinicopathological variables (TNM-status, tumor stage, histological grade, ER-, PR-, ErbB2- and P53-status) and prognostic/predictive gene signature-classifications (wound healing response, invasiveness gene signature, 70-gene prognostic signature, genomic grade index, recurrence score, HOXB13/IL17RB-expression ratio and the molecular breast cancer subtypes). Results were validated by investigating relationships between the expression of a relevant miRNA target gene signature and clinicopathological variables in 5 publicly available breast cancer gene expression data sets.Results: Using PCA-analysis we identified a metagene significantly associated with the Luminal B phenotype, an elevated genomic grade index, an elevated recurrence score, an activated wound healing response, the invasiveness gene signature and poor prognosis according to the 70-gene prognostic profile (range Rs: 0.325-0.372; P&amp;lt;0.05). Using multivariate regression analysis we demonstrated that this metagene was also associated with loss of PR expression (Hazard Ratio (HR): 9.00; P=0.0001) and the presence of metastases at time of diagnosis (HR: 18.9; P=0.0002). MiRNAs significantly (FDR&amp;lt;0.1) associated with this metagene were: miR205, miR548C-5p, miR548D-5p, miR187, miR671-3p, miR492, miR365, miR499-5p, miR548D-3p, miR615-3p, miR193A, miR589, miR660, miR219-1-3p, miR888 (range Rs: -0.415 – 0.456). At the gene expression level, a miR205 target gene signature, composed of 173 unique genes, was associated with relapse-free survival (range HR: 1.225 – 1.387; P&amp;lt;0.01) and distant metastasis-free survival (HR: 3.950; P=0.006) in respectively 3 and 1 independent breast cancer data set(s).Discussion: Through principal component analysis we identified a miRNA signature associated with poor prognosis in breast cancer. This signature was composed of 15 individual miRNAs, including miR205 which is known for its role in epithelial-to-mesenchymal transition and the induction of stem cell characteristics. The association of a miR205 target gene signature with relapse-free and distant metastases-free survival confirms our results on the gene expression level. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4062.</jats:p