Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells

The retinal vascular endothelium is essential for angiogenesis and is involved in maintaining barrier selectivity and vascular tone. The aim of this study was to identify and quantify microRNAs and other small regulatory non-coding RNAs (ncRNAs) which may regulate these crucial functions. Primary bovine retinal microvascular endothelial cells (RMECs) provide a well-characterized in vitro system for studying angiogenesis. RNA extracted from RMECs was used to prepare a small RNA library for deep sequencing (Illumina Genome Analyzer). A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). In many cases, the most frequent isomiR differed from the sequence reported in miRBase. In addition, five novel microRNAs, 13 novel bovine orthologs of known human microRNAs and multiple new members of the miR-2284/2285 family were detected. Several similar to 30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one-third of all mapped reads. Inhibition of miR-21 with an LNA inhibitor significantly reduced proliferation, migration, and tube-forming capacity of RMECs. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Knockdown of miR-21 suggests a role for this microRNA in regulation of angiogenesis in the retinal microvasculature. J. Cell. Biochem. 113: 20982111, 2012. (C) 2012 Wiley Periodicals, Inc.

Deformed wing virus and drone mating flights in the honey bee (Apis mellifera): implications for sexual transmission of a major honey bee virus

Deformed wing virus (DWV) represents an ideal model to study the interaction between mode of transmission and virulence in honey bees since it exhibits both horizontal and vertical transmissions. However, it is not yet clear if venereal-vertical transmission represents a regular mode of transmission for this virus in natural honey bee populations. Here, we provide clear evidence for the occurrence of high DWV titres in the endophallus of sexually mature drones collected from drone congregation areas (DCAs). Furthermore, the endophallus DWV titres of drones collected at their maternal hives were no different from drones collected at nearby DCAs, suggesting that high-titre DWV infection of the endophallus does not hinder the ability of drones to reach the mating area. The results are discussed within the context of the dispersal of DWV between colonies and the definition of DWV virulence with respect to the transmission route and the types of tissues infected.

Physicochemical characterization and preliminary in vivo efficacy of bioadhesive, semisolid formulations containing flurbiprofen for the treatment of gingivitis

In this study, the physicochemical properties and preliminary in vivo clinical performance of formulations containing hydroxyethylcellulose (HEC; 3, 5, 10% w/w, poly(vinylpyrrolidone) (PVP; 3, 5% w/w), polycarbophil (PC; 1, 3, 5% w/w), and flurbiprofen (5% w/w) were examined. Flurbiprofen release into PBS pH 7.4 was performed at 37 degrees C. The mechanical properties (hardness, compressibility, adhesiveness, initial stress) and syringeability of formulations were determined using a texture analyzer in texture profile analysis (TPA) and compression modes, respectively. In general, the time required for release of 10 and 30% of the original mass of flurbiprofen (t(10%), t(30%)) increased as the concentration of each polymeric component increased. However, in the presence of either 5 or 10% HEC and 5% PC, increased PVP concentration decreased both t(10%), t(30%) due to excessive swelling land disintegration) of these formulations. Increased concentrations of HEC, PVP, and PC significantly increased formulation hardness, compressibility, work of syringe expression, and initial stress due to the effects of these polymers on formulation viscoelasticity. Similarly, increased concentrations of PC (primarily), HEC, and PVP increased formulation adhesiveness-due to the known bioadhesive properties of these polymers. Clinical efficacies of formulations containing 3% HEC, 3% PVP, 3% PC, and either 0% (control) of 5% (test) flurbiprofen, selected to offer optimal drug release and mechanical properties, were evaluated and clinically compared in an experimental gingivitis model. The test (flurbiprofen-containing) formulation significantly reduced gingival inflammation, as evaluated using the gingival index, and the gingival crevicular fluid volume, whereas, these clinical parameters were generally increased in volunteers who had received the control formulation. There were no observed differences in the plaque indices of the two subject groups, confirming that the observed differences in gingival inflammation could not be accredited to differences in plaque accummulation. This study has shown both the applicability of the in vitro methods used, particularly TPA, for the rational selection of formulations for clinical evaluation and, additionally, the clinical benefits of the topical application of a bioadhesive semisolid flurbiprofen-containing formulation for the treatment of experimental gingivitis.

Texture profile analysis of bioadhesive polymeric semisolids: Mechanical characterization and investigation of interactions between formulation components

This study reports the use of texture profile analysis (TPA) to mechanically characterize polymeric, pharmaceutical semisolids containing at least one bioadhesive polymer and to determine interactions between formulation components. The hardness, adhesiveness, force per unit time required for compression (compressibility), and elasticity of polymeric, pharmaceutical semisolids containing polycarbophil (1 or 5% w/w), polyvinylpyrrolidone (3 or 5% w/w), and hydroxyethylcellulose (3, 5, or 10% w/w) in phosphate buffer (pH 6.8) were determined using a texture analyzer in the TPA mode (compression depth 15 mm, compression rate 8 mm s(-1) 15 s delay period). Increasing concentrations of polycarbophil, poly vinylpyrrolidone, and hydroxyethylcellulose significantly increased product hardness, adhesiveness, and compressibility but decreased product elasticity. Statistically, interactions between polymeric formulation components were observed within the experimental design and were probably due to relative differences in the physical states of polyvinylpyrrolidone and polycarbophil in the formulations, i.e., dispersed/dissolved and unswollen/swollen, respectively. Increased product hardness and compressibility were possibly due to the effects of hydroxyethylcellulose, polyvinylpyrrolidone, and polycarbophil on the viscosity of the formulations. Increased adhesiveness was related to the concentration and, more importantly, to the physical state of polycarbophil. Decreased product elasticity was due to the increased semisolid nature of the product. TPA is a rapid, straightforward analytical technique that may be applied to the mechanical characterization of polymeric, pharmaceutical semisolids. It provides a convenient means to rapidly identify physicochemical interactions between formulation components. (C) 1996 John Wiley & Sons, Inc.

Physicochemical characterisation of injectable polymeric gels for use in the treatment of periodontal disease

The physicochemical characteristics of the injectable polymeric gels for use in the treatment of periodontal disease were investigated. The hardness, compressibility, and mucoadhesive properties of the gel were determined using a TA-XT2 Texture analyzer. The effect of of polymer concentration on the various viscoelastic, textural, bioadhesive properties and drug release were also analyzed using multifactorial analysis of variance. It was found that increased polymer concentration significantly increased gel structure, reduced polymer chain mobility and subsequently decreased the swelling/erosion and diffusion properties of the gel networks.

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Corneal biomechanical properties in primary open angle glaucoma and normal tension glaucoma

PURPOSE: To determine and compare the corneal biomechanical properties between eyes with primary open angle glaucoma (POAG) and eyes with normal tension glaucoma (NTG). PATIENTS AND METHODS: Prospective cross-sectional study. Consecutive eligible POAG and NTG patients attending the Glaucoma Clinic had assessment of their corneal biomechanical properties-corneal hysteresis (CH) and corneal resistance factor (CRF)-using the Ocular Response Analyzer by an observer masked to the diagnosis. Exclusion criteria included previous intraocular surgery, corneal pathology, inflammatory connective tissue disease, and refraction of 5-dimensional or over. If both eyes were eligible, then the right eye was used for analysis. The main outcome measures were corneal hysteresis and CRF measurements. Data analysis was performed using the t test and general linear model. RESULTS: Eighty-one patients (80 whites) were analyzed. Forty had NTG, whereas 41 had POAG. Thirty-five were females. There was a statistically significant difference in mean CH (NTG 9.6±1.3 mm Hg; POAG 9.0±1.4 mm Hg; P=0.01), but not in mean CRF (NTG 9.9±1.4; POAG 10.8±1.7; P=0.06). The highest recorded Goldmann applanation intraocular pressure (IOP) was statistically significantly associated with lower CH (P=0.01) and higher CRF (P=0.02). CONCLUSIONS: There was a small but statistically significant difference in the mean CH between POAG and NTG (CH was higher in NTG). The highest recorded Goldmann applanation IOP was also statistically significantly correlated with lower CH and higher CRF, suggesting that alterations to the corneal biomechanical properties may occur as a result of chronic raised IOP in POAG. © 2008 by Lippincott Williams & Wilkins.

Lower corneal hysteresis in glaucoma patients with acquired pit of the optic nerve (APON)

Objective: Acquired pit-like changes of the optic nerve head (APON) are characteristic of glaucomatous damage and may be a sign of a localized susceptibility of the optic nerve. Thus, it is possible that biomechanical properties of the ocular tissues may play a pressure-independent role in the pathogenesis of glaucoma. Corneal hysteresis (CH) appears to provide information of the biomechanical properties of the ocular hull tissues. The purpose of this study was to compare CH of patients with primary open angle glaucoma (POAG) with and without APON. Methods: A prospective case control study was done. POAG patients with and without APON were measured using the Ocular Response Analyzer by masked investigators. Patients in both groups were matched for sex, age, corneal thickness, and type of glaucoma according to maximal IOP (NTG or POAG). Statistical analysis was done using ANOVA. Results: Corneal hysteresis of 16 glaucomatous eyes with APON and 32 controls (glaucoma without APON) was measured. The mean (±SD) CH in the APON group was 8.89 (±1.53) and 10.2 (±1.05) in the control group. The difference is statistically significant (p = 0.005). Conclusions: Corneal hysteresis in POAG patients with APON was significantly lower than in patients that did not have such structural changes of the optic disc. These findings may reflect pressure-independent mechanisms involved in the pathogenesis of such glaucomatous optic nerve changes. © Springer-Verlag 2007.

Systematic review of the agreement of tonometers with Goldmann applanation tonometry

OBJECTIVE: To assess the agreement of tonometers available for clinical practice with the Goldmann applanation tonometer (GAT), the most commonly accepted reference device.

DESIGN: A systematic review and meta-analysis of directly comparative studies assessing the agreement of 1 or more tonometers with the reference tonometer (GAT).

PARTICIPANTS: A total of 11 582 participants (15 525 eyes) were included.

METHODS: Summary 95% limits of agreement (LoA) were produced for each comparison.

MAIN OUTCOME MEASURES: Agreement, recordability, and reliability.

RESULTS: A total of 102 studies, including 130 paired comparisons, were included, representing 8 tonometers: dynamic contour tonometer, noncontact tonometer (NCT), ocular response analyzer, Ocuton S, handheld applanation tonometer (HAT), rebound tonometer, transpalpebral tonometer, and Tono-Pen. The agreement (95% limits) seemed to vary across tonometers: 0.2 mmHg (-3.8 to 4.3 mmHg) for the NCT to 2.7 mmHg (-4.1 to 9.6 mmHg) for the Ocuton S. The estimated proportion within 2 mmHg of the GAT ranged from 33% (Ocuton S) to 66% and 59% (NCT and HAT, respectively). Substantial inter- and intraobserver variability were observed for all tonometers.

CONCLUSIONS: The NCT and HAT seem to achieve a measurement closest to the GAT. However, there was substantial variability in measurements both within and between studies.

Detection of changes of the optic disc in glaucomatous eyes:Clinical examination and image analysis with the Topcon Imagenet system

Purpose: This study was designed to evaluate the clinical agreement in the detection of optic disc changes and the ability of computerized image analysis to detect glaucomatous deterioration of the optic disc. Methods: Pairs of stereophotographs of 35 glaucomatous optic discs taken 5 years apart and of 5 glaucomatous discs photographed twice on the same day. Two glaucoma specialists examined the pairs of stereophotographs (35 cases and 5 controls) in a masked manner and judged whether the optic disc showed changes in the optic disc compatible with progression of glaucomatous damage. The stereophotographs of the five optic discs photographed twice on the same day (which by definition did not change) and of five cases judged to have deteriorated by both glaucoma specialists were analyzed by computerized image analysis with the Topcon ImageNet system. Intra- and inter-observer agreement in the detection of optic disc changes (evaluated using kappa statistic), and changes in the rim area to disc area ratio (evaluated using descriptive statistics and paired t-test). Results: Intra-observer agreement had a kappa value of 0.75 for observer 1 and 0.60 for the observer 2. Inter-observer agreement between the glaucoma specialists had a kappa value of 0.60. The image analyzer did not discriminate between controls and cases with clinically apparent glaucomatous change of the optic disc. Conclusion: Clinical agreement in detecting changes in the optic disc was moderate to substantial. Computerized image analysis with the Topcon ImageNet system appeared not to be useful in detecting glaucomatous changes of the optic disc.

Reproducibility of optic disk topographic measurements with the Topcon ImageNet and the Heidelberg Retina Tomograph

Objective: To compare the reproducibility of optic disk measurements provided by an image analyzer and a scanning laser tomograph. Methods: Ten images of the same eye of 10 normal volunteers were taken with the Heidelberg Retina Tomograph and with the Topcon ImageNet. Intraclass correlation coefficient (ICC) and coefficient of variation (CV) were used to evaluate the reproducibility of the measurements. Results: Eleven parameters were analyzed with the Topcon ImageNet. Six parameters (55%) had ICC greater than 90%. Four parameters (36%) had CV less than 10%. Twelve parameters were evaluated with the Heidelberg Retina Tomograph. Nine parameters (75%) had ICC over 90%. Nine parameters (75%) had CV less than 10%. Conclusion: Both systems provided reproducible data. The optic disk parameters provided by the Heidelberg Retina Tomograph had a better reproducibility than those obtained from the Topcon ImageNet.

From Frank Miller to Zack Snyder, and Return: Contemporary Superhero Comics and Post-Classical Hollywood

Film adaptations of superhero comic-books offer a particularly rich case study to analyse narrative strategies of contemporary Hollywood cinema. The serial structures adopted by the comics they are based on, as well as their use of the spectacular potential of the image, provide a successful model for current audiovisual productions. Without completely abandoning classical techniques, these adaptations try to find a new balance between narrative and digital phantasmagoria. This paper discusses some significant examples of this genre, including adaptations of classical DC and Marvel franchises and more recent series, as well as other comic-book influenced films such as The Matrix and Unbreakable.

A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. I. General formalism and application to open-shell states

The solution of the time-dependent Schrodinger equation for systems of interacting electrons is generally a prohibitive task, for which approximate methods are necessary. Popular approaches, such as the time-dependent Hartree-Fock (TDHF) approximation and time-dependent density functional theory (TDDFT), are essentially single-configurational schemes. TDHF is by construction incapable of fully accounting for the excited character of the electronic states involved in many physical processes of interest; TDDFT, although exact in principle, is limited by the currently available exchange-correlation functionals. On the other hand, multiconfigurational methods, such as the multiconfigurational time-dependent Hartree-Fock (MCTDHF) approach, provide an accurate description of the excited states and can be systematically improved. However, the computational cost becomes prohibitive as the number of degrees of freedom increases, and thus, at present, the MCTDHF method is only practical for few-electron systems. In this work, we propose an alternative approach which effectively establishes a compromise between efficiency and accuracy, by retaining the smallest possible number of configurations that catches the essential features of the electronic wavefunction. Based on a time-dependent variational principle, we derive the MCTDHF working equation for a multiconfigurational expansion with fixed coefficients and specialise to the case of general open-shell states, which are relevant for many physical processes of interest. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3600397]

Analog of Rabi oscillations in resonant electron-ion systems

Quantum coherence between electron and ion dynamics, observed in organic semiconductors by means of ultrafast spectroscopy, is the object of recent theoretical and computational studies. To simulate this kind of quantum coherent dynamics, we have introduced in a previous article [L. Stella, M. Meister, A. J. Fisher, and A. P. Horsfield, J. Chem. Phys. 127, 214104 (2007)] an improved computational scheme based on Correlated Electron-Ion Dynamics (CEID). In this article, we provide a generalization of that scheme to model several ionic degrees of freedom and many-body electronic states. To illustrate the capability of this extended CEID, we study a model system which displays the electron-ion analog of the Rabi oscillations. Finally, we discuss convergence and scaling properties of the extended CEID along with its applicability to more realistic problems. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3589165]

Extremely Complex Populations of Small RNAs in the Mouse Retina and RPE/Choroid

Purpose: MicroRNAs (miRNAs) are small non-coding RNAs of ~18-22 nucleotides in length that regulate gene expression. They are widely expressed in the retina, being both required for its normal development and perturbed in disease. The aim of this study was to apply new high-throughput sequencing techniques to more fully characterise the microRNAs and other small RNAs expressed in the retina and retinal pigment epithelium (RPE)/choroid of the mouse.

Methods: Retina and RPE/choroid were dissected from eyes of 3 month-old C57BL/6J mice. Small RNA libraries were prepared and deep sequencing performed on a Genome Analyzer (Illumina). Reads were annotated by alignment to miRBase, other non-coding RNA databases and the mouse genome.

Results: Annotation of 9 million reads to 320 microRNAs in retina and 340 in RPE/choroid provides the most comprehensive profiling of microRNAs to date. Two novel microRNAs were identified in retina. Members of the sensory organ specific miR-183,-182,-96 cluster were amongst the most highly expressed, retina-enriched microRNAs. Remarkably, microRNA 'isomiRs', which vary slightly in length and are differentially detected by Taqman RT-PCR assays, existed for all the microRNAs identified in both tissues. More variation occurred at the 3' ends, including non-templated additions of T and A. Drosha-independent mirtron microRNAs and other small RNAs derived from snoRNAs were also detected.

Conclusions: Deep sequencing has revealed the complexity of small RNA expression in the mouse retina and RPE/choroid. This knowledge will improve the design and interpretation of future functional studies of the role of microRNAs and other small RNAs in retinal disease.