Automatic segmentation of choroidal thickness in optical coherence tomography

The assessment of choroidal thickness from optical coherence tomography (OCT) images of the human choroid is an important clinical and research task, since it provides valuable information regarding the eye’s normal anatomy and physiology, and changes associated with various eye diseases and the development of refractive error. Due to the time consuming and subjective nature of manual image analysis, there is a need for the development of reliable objective automated methods of image segmentation to derive choroidal thickness measures. However, the detection of the two boundaries which delineate the choroid is a complicated and challenging task, in particular the detection of the outer choroidal boundary, due to a number of issues including: (i) the vascular ocular tissue is non-uniform and rich in non-homogeneous features, and (ii) the boundary can have a low contrast. In this paper, an automatic segmentation technique based on graph-search theory is presented to segment the inner choroidal boundary (ICB) and the outer choroidal boundary (OCB) to obtain the choroid thickness profile from OCT images. Before the segmentation, the B-scan is pre-processed to enhance the two boundaries of interest and to minimize the artifacts produced by surrounding features. The algorithm to detect the ICB is based on a simple edge filter and a directional weighted map penalty, while the algorithm to detect the OCB is based on OCT image enhancement and a dual brightness probability gradient. The method was tested on a large data set of images from a pediatric (1083 B-scans) and an adult (90 B-scans) population, which were previously manually segmented by an experienced observer. The results demonstrate the proposed method provides robust detection of the boundaries of interest and is a useful tool to extract clinical data.

Development and validation of anthropometric prediction equations for estimation of lean body mass and appendicular lean soft tissue in Indian men and women

Lean body mass (LBM) and muscle mass remains difficult to quantify in large epidemiological studies due to non-availability of inexpensive methods. We therefore developed anthropometric prediction equations to estimate the LBM and appendicular lean soft tissue (ALST) using dual energy X-ray absorptiometry (DXA) as a reference method. Healthy volunteers (n= 2220; 36% females; age 18-79 y) representing a wide range of body mass index (14-44 kg/m2) participated in this study. Their LBM including ALST was assessed by DXA along with anthropometric measurements. The sample was divided into prediction (60%) and validation (40%) sets. In the prediction set, a number of prediction models were constructed using DXA measured LBM and ALST estimates as dependent variables and a combination of anthropometric indices as independent variables. These equations were cross-validated in the validation set. Simple equations using age, height and weight explained > 90% variation in the LBM and ALST in both men and women. Additional variables (hip and limb circumferences and sum of SFTs) increased the explained variation by 5-8% in the fully adjusted models predicting LBM and ALST. More complex equations using all the above anthropometric variables could predict the DXA measured LBM and ALST accurately as indicated by low standard error of the estimate (LBM: 1.47 kg and 1.63 kg for men and women, respectively) as well as good agreement by Bland Altman analyses. These equations could be a valuable tool in large epidemiological studies assessing these body compartments in Indians and other population groups with similar body composition.

Effect of text type on near work-induced contrast adaptation in myopic and emmetropic young adults

Purpose Contrast adaptation has been speculated to be an error signal for emmetropization. Myopic children exhibit higher contrast adaptation than emmetropic children. This study aimed to determine whether contrast adaptation varies with the type of text viewed by emmetropic and myopic young adults. Methods Baseline contrast sensitivity was determined in 25 emmetropic and 25 spectacle-corrected myopic young adults for 0.5, 1.2, 2.7, 4.4, and 6.2 cycles per degree (cpd) horizontal sine wave gratings. The adults spent periods looking at a 6.2 cpd high-contrast horizontal grating and reading lines of English and Chinese text (these texts comprised 1.2 cpd row and 6 cpd stroke frequencies). The effects of these near tasks on contrast sensitivity were determined, with decreases in sensitivity indicating contrast adaptation. Results Contrast adaptation was affected by the near task (F2,672 = 43.0; P < 0.001). Adaptation was greater for the grating task (0.13 ± 0.17 log unit, averaged across all frequencies) than reading tasks, but there was no significant difference between the two reading tasks (English 0.05 ± 0.13 log unit versus Chinese 0.04 ± 0.13 log unit). The myopic group showed significantly greater adaptation (by 0.04, 0.04, and 0.05 log units for English, Chinese, and grating tasks, respectively) than the emmetropic group (F1,48 = 5.0; P = 0.03). Conclusions In young adults, reading Chinese text induced similar contrast adaptation as reading English text. Myopes exhibited greater contrast adaptation than emmetropes. Contrast adaptation, independent of text type, might be associated with myopia development.

Children’s accommodation during reading of Chinese and English texts

Purpose: Inaccurate accommodation during nearwork and subsequent accommodative hysteresis may influence myopia development. Myopia is highly prevalent in Singapore; an untested theory is that Chinese children are prone to these accommodation characteristics. We measured the accuracy of accommodation responses during and nearwork-induced transient myopia (NITM) after periods spent reading Chinese and English texts. Methods: Refractions of 40 emmetropic and 43 myopic children were measured with a free-space autorefractor for four reading tasks of 10-minute durations: Chinese (SimSun, 10.5 points) and English (Times New Roman, 12 points) texts at 25 cm and 33 cm. Accuracy was obtained by subtracting accommodation response from accommodation demand. Nearwork-induced transient myopia was obtained by subtracting pretask distance refraction from posttask refraction, and regression was determined as the time for the posttask refraction to return to pretask levels. Results: There were significant, but small, effects of text type (Chinese, 0.97 ± 0.32 diopters [D] vs. English, 1.00 ± 0.37 D; F1,1230 = 7.24, p = 0.007) and reading distance (33 cm, 1.01 ± 0.30 D vs. 25 cm, 0.97 ± 0.39 D; F1,1230 = 7.74, p = 0.005) on accommodation accuracy across all participants. Accuracy was similar for emmetropic and myopic children across all reading tasks. Neither text type nor reading distance had significant effects on NITM or its regression. Myopes had greater NITM (by 0.07 D) (F1,81 = 5.05, p = 0.03) that took longer (by 50s) (F1,81 = 31.08, p < 0.01) to dissipate. Conclusions: Reading Chinese text caused smaller accommodative lags than reading English text, but the small differences were not clinically significant. Myopic children had significantly greater NITM and longer regression than emmetropic children for both texts. Whether differences in NITM are a cause or consequence of myopia cannot be answered from this study.

Identification of GABA receptors in chick retinal pigment epithelium

Purpose: The retinal pigment epithelium (RPE) is a multifunctional, monolayer of cells located between the neural retina and the choroicapillaris. γ-Aminobutyric acid (GABA) is the most important inhibitory neurotransmitter in the retina and GABA receptors are known to be present in chick retina, sclera and cornea. There is a report of genes involved in GABA receptor signaling being expressed in human RPE, however, whether GABA receptors are present in chick RPE is unknown. Methods: Real time PCR and western blot were used to determine the expression of GABA receptors (alpha1 GABAA, GABABR2, and rho1 GABAC receptors) in isolated chicken RPE. Immunofluorescence using antibodies against one of the GABA receptor sub-types was used to determine receptor localization. Results: Both real-time PCR and western blot demonstrated that alpha1 GABAA, GABABR2 and rho1 GABAC receptors were expressed in isolated chick RPE. Immunofluorescence further demonstrated that GABA receptors were localized to the cell membrane and plasma of RPE cells. Conclusions: Alpha1 GABAA, GABABR2 and rho1 GABAC receptors were expressed in chick RPE. The purpose of the GABA receptors within the RPE remains to be explored.

Time course-dependent changes in the transcriptome of human skeletal muscle during recovery from endurance exercise: From inflammation to adaptive remodeling

Re-programming of gene expression is fundamental for skeletal muscle adaptations in response to endurance exercise. This study investigated the time-course dependent changes in the muscular transcriptome following an endurance exercise trial consisting of 1 h of intense cycling immediately followed by 1 h of intense running. Skeletal muscle samples were taken at baseline, 3 h, 48 h, and 96 h post-exercise from eight healthy, endurance-trained, male individuals. RNA was extracted from muscle. Differential gene expression was evaluated using Illumina microarrays and validated with qPCR. Gene set enrichment analysis identified enriched molecular signatures chosen from the Molecular Signatures Database. Three h post-exercise, 102 gene sets were up-regulated [family wise error rate (FWER), P < 0.05]; including groups of genes related with leukocyte migration, immune and chaperone activation, and cyclic AMP responsive element binding protein (CREB) 1-signaling. Forty-eight h post-exercise, among 19 enriched gene sets (FWER, P < 0.05), two gene sets related to actin cytoskeleton remodeling were up-regulated. Ninety-six h post-exercise, 83 gene sets were enriched (FWER, P < 0.05), 80 of which were up-regulated; including gene groups related to chemokine signaling, cell stress management, and extracellular matrix remodeling. These data provide comprehensive insights into the molecular pathways involved in acute stress, recovery, and adaptive muscular responses to endurance exercise. The novel 96 h post-exercise transcriptome indicates substantial transcriptional activity, potentially associated with the prolonged presence of leukocytes in the muscles. This suggests that muscular recovery, from a transcriptional perspective, is incomplete 96 h after endurance exercise involving muscle damage.

A comparison of the histochemical and image-derived proteoglycan content of articular cartilage

There are several methods for determining the proteoglycan content of cartilage in biomechanics experiments. Many of these include assay-based methods and the histochemistry or spectrophotometry protocol where quantification is biochemically determined. More recently a method based on extracting data to quantify proteoglycan content has emerged using the image processing algorithms, e.g., in ImageJ, to process histological micrographs, with advantages including time saving and low cost. However, it is unknown whether or not this image analysis method produces results that are comparable to those obtained from the biochemical methodology. This paper compares the results of a well-established chemical method to those obtained using image analysis to determine the proteoglycan content of visually normal (n=33) and their progressively degraded counterparts with the protocols. The results reveal a strong linear relationship with a regression coefficient (R2) = 0.9928, leading to the conclusion that the image analysis methodology is a viable alternative to the spectrophotometry.

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified the Arabidopsis thaliana AGO-IP tRFs. Moreover, using three degradome deep sequencing libraries, we identified four putative tRF targets. The expression pattern of tRFs, based on deep sequencing data, was also analyzed under abiotic and biotic stresses. The results obtained here represent a useful starting point for future studies on tRFs in plants. © 2013 Loss-Morais et al.; licensee BioMed Central Ltd.

RNA silencing in plants: Yesterday, today, and tomorrow

RNA silencing has become a major focus of molecular biology and biomedical research around the world. This is highlighted by a simple PubMed search for “RNA silencing,” which retrieves almost 9,000 articles. Interest in gene silencing-related mechanisms stemmed from the early 1990s, when this phenomenon was first noted as a surprise observation by plant scientists during the course of plant transformation experiments, in which the introduction of a transgene into the genome led to the silencing of both the transgene and homologous endogenes. From these initial studies, plant biologists have continued to generate a wealth of information into not only gene silencing mechanisms but also the complexity of these biological pathways as well as revealing their multilevel interactions with one another. The plant biology community has also made significant advancements in exploiting RNA silencing as a powerful tool for gene function studies and crop improvements. In this article, we (1) review the rich history of gene silencing research and the knowledge it has generated into our understanding of this fundamental mechanism of gene regulation in plants; (2) describe examples of the current applications of RNA silencing in crop plants; and (3) discuss improvements in RNA silencing technology and its potential application in plant science.

The RNA world in plants: Post-transcriptional control III

Post-transcriptional control of gene expression has gone from a curiosity involving a few special genes to a highly diverse and widespread set of processes that is truly pervasive in plant gene expression. Thus, Plant Cell readers interested in almost any aspect of plant gene expression in response to any environmental influence, or in development, are advised to read on. In May 2001, what has become the de facto third biennial Symposium on Post-Transcriptional Control of Gene Expression in Plants was held in Ames, Iowa. The meeting was hosted by the new Plant Sciences Institute of Iowa State University with additional funding from the National Science Foundation and the United States Department of Agriculture. In 1997, the annual University of California-Riverside Plant Physiology Symposium was devoted to this topic. This provided a wake-up call to the plant world, summarized in this journal (Gallie and Bailey-Serres, 1997), that not all gene expression is controlled at the level of transcription. This was expanded upon at a European Molecular Biology Organization Workshop in Leysin, Switzerland, in 1999 (Bailey-Serres et al., 1999). The 3-day meeting in Ames brought together a strong and diverse contingent of plant biologists from four continents. The participants represented an unusually heterogeneous group of disciplines ranging from virology to stress response to computational biology. The research approaches and techniques represented were similarly diverse. Here we discuss a sample of the many fascinating aspects of post-transcriptional control that were presented at this meeting; we apologize to those whose work is not described here.

Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template-Dependent, Nonvascular, Cell-to-Cell Movement

Upward long-distance mobile silencing has been shown to be phloem mediated in several different solanaceous species. We show that the Arabidopsis (Arabidopsis thaliana) seedling grafting system and a counterpart inducible system generate upwardly spreading long-distance silencing that travels not in the phloem but by template-dependent reiterated short-distance cell-to-cell spread through the cells of the central stele. Examining the movement of the silencing front revealed a largely unrecognized zone of tissue, below the apical meristem, that is resistant to the silencing signal and that may provide a gating or protective barrier against small RNA signals. Using a range of auxin and actin transport inhibitors revealed that, in this zone, alteration of vesicular transport together with cytoskeleton dynamics prevented or retarded the spread of the silencing signal. This suggests that small RNAs are transported from cell to cell via plasmodesmata rather than diffusing from their source in the phloem.

Viruses face a double defense by plant small RNAs

Plants fight viral infections with enzymes that digest viral RNA, but viruses retaliate with proteins that suppress these enzymes. To boost their antiviral response plants deploy enzymes with redundant functions.