A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.

To fully understand animal transcription networks, it is essential to accurately measure the spatial and temporal expression patterns of transcription factors and their targets. We describe a registration technique that takes image-based data from hundreds of Drosophila blastoderm embryos, each costained for a reference gene and one of a set of genes of interest, and builds a model VirtualEmbryo. This model captures in a common framework the average expression patterns for many genes in spite of significant variation in morphology and expression between individual embryos. We establish the method's accuracy by showing that relationships between a pair of genes' expression inferred from the model are nearly identical to those measured in embryos costained for the pair. We present a VirtualEmbryo containing data for 95 genes at six time cohorts. We show that known gene-regulatory interactions can be automatically recovered from this data set and predict hundreds of new interactions.

Cytomegalovirus immunoglobulin therapy for CMV retinitis post hematopoietic stem cell transplantation.

PURPOSE: To report a case of cytomegalovirus (CMV) retinitis complicated with ganciclovir-related myelosuppression, which was successfully managed with intravenous (IV) ganciclovir and CMV immunoglobulin (CMVIG) therapy. METHODS: Observational case report. RESULTS: A 51-year-old male with follicular type non-Hodgkin lymphoma post hematopoietic stem cell transplantation (HSCT) developed vision-threatening retinitis. polymerase chain reaction (PCR) of the aqueous humour showed positive for CMV. Despite myelosuppression occurred during IV ganciclovir therapy, the retinitis resolved and intraocular CMV viral load significantly improved after CMVIG therapy. CONCLUSION: Combined IV ganciclovir treatment and CMVIG therapy can significantly improve visual outcome and reduce intraocular CMV viral load in vision-threatening CMV retinitis.

Spontaneous Closure of Cyclodialysis Cleft in a Case of Normal-Tension Glaucoma Post Ab-Interno Trabeculotomy.

A cyclodialysis cleft (CDC) is the detachment of longitudinal ciliary muscle from scleral spur, causing an unusual communication between anterior chamber and suprachoroidal space, resulting in possible hypotony. We report a case of a 63-year-old woman with normal-tension glaucoma (NTG), who developed a shallow anterior chamber with relatively low intraocular pressure (IOP, 6-8 mmHg) after combined ab-interno trabeculotomy and phacoemulsification. Her vision reached good (20/20) with the mild myopic shift. After detecting subtle signs of clinical hypotony, CDC was confirmed and monitored using anterior segment optical coherence tomography. Five months after surgery, she encountered an episode of eye pain, with transient IOP elevation and deepening of the anterior chamber. Spontaneous closure of CDC was suspected and confirmed gonioscopically. To the best of our knowledge, this is the first case to describe the clinical course of spontaneous CDC closure in a patient with NTG after ab-interno trabeculotomy. It is advisable to inform the patient about potential IOP spike after spontaneous closure once CDC is diagnosed.

BIK ubiquitination by the E3 ligase Cul5-ASB11 determines cell fate during cellular stress.

The BH3-only pro-apoptotic protein BIK is regulated by the ubiquitin-proteasome system. However, the mechanism of this regulation and its physiological functions remain elusive. Here, we identify Cul5-ASB11 as the E3 ligase targeting BIK for ubiquitination and degradation. ER stress leads to the activation of ASB11 by XBP1s during the adaptive phase of the unfolded protein response, which stimulates BIK ubiquitination, interaction with p97/VCP, and proteolysis. This mechanism of BIK degradation contributes to ER stress adaptation by promoting cell survival. Conversely, genotoxic agents down-regulate this IRE1α-XBP1s-ASB11 axis and stabilize BIK, which contributes in part to the apoptotic response to DNA damage. We show that blockade of this BIK degradation pathway by an IRE1α inhibitor can stabilize a BIK active mutant and increase its anti-tumor activity. Our study reveals that different cellular stresses regulate BIK ubiquitination by ASB11 in opposing directions, which determines whether or not cells survive, and that blocking BIK degradation has the potential to be used as an anti-cancer strategy.

Glaucomatocyclitic Crises May Occur in Patients with Narrow or Closed Angles.

PURPOSE: To report cases of glaucomatocyclitic crises and discuss the possibility of occurrence in patients with narrow or closed angles. BACKGROUND: The prevalence of angle closure is much higher among Asians than among the Western population. Currently, there is no evidence for a direct relationship between the etiology and angle structure. DESIGN: A retrospective and observational case series. METHODS: We retrospectively collected data from nine adult patients (three males and six females) who were diagnosed with a glaucomatocyclitic crisis and a shallow anterior chamber over a 21-year period, from 1995 to 2016, at the Kaohsiung Medical University Hospital. A narrow angle was defined as a grade less than the Shaffer system grade II. Ophthalmic examinations, including anterior segment biomicroscopy, direct ophthalmoscopy, intraocular pressure measurements, anterior chamber reaction, visual field tests, and the grade of the anterior chamber angle according to the Shaffer system, were reviewed. RESULTS: These patients experienced at least one typical unilateral ocular hypertensive episode that fulfilled the criteria of a glaucomatocyclitic crisis without the angle feature. All patients had gonioscopically narrow or closed angles with or without peripheral anterior synechiae. CONCLUSIONS: The coexistence of narrow or closed angles and a glaucomatocyclitic crisis is possible, especially in patients of Asian descent. In patients with shallow anterior chambers, a glaucomatocyclitic crisis may be a cause of acute glaucoma episodes.

Integrating data clustering and visualization for the analysis of 3D gene expression data.

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex data sets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss 1) the integration of data clustering and visualization into one framework, 2) the application of data clustering to 3D gene expression data, 3) the evaluation of the number of clusters k in the context of 3D gene expression clustering, and 4) the improvement of overall analysis quality via dedicated postprocessing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.

Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data.

Knowledge discovery from large and complex scientific data is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the growing number of data dimensions and data objects presents tremendous challenges for effective data analysis and data exploration methods and tools. The combination and close integration of methods from scientific visualization, information visualization, automated data analysis, and other enabling technologies -such as efficient data management- supports knowledge discovery from multi-dimensional scientific data. This paper surveys two distinct applications in developmental biology and accelerator physics, illustrating the effectiveness of the described approach.

Visual exploration of three-dimensional gene expression using physical views and linked abstract views.

During animal development, complex patterns of gene expression provide positional information within the embryo. To better understand the underlying gene regulatory networks, the Berkeley Drosophila Transcription Network Project (BDTNP) has developed methods that support quantitative computational analysis of three-dimensional (3D) gene expression in early Drosophila embryos at cellular resolution. We introduce PointCloudXplore (PCX), an interactive visualization tool that supports visual exploration of relationships between different genes' expression using a combination of established visualization techniques. Two aspects of gene expression are of particular interest: 1) gene expression patterns defined by the spatial locations of cells expressing a gene and 2) relationships between the expression levels of multiple genes. PCX provides users with two corresponding classes of data views: 1) Physical Views based on the spatial relationships of cells in the embryo and 2) Abstract Views that discard spatial information and plot expression levels of multiple genes with respect to each other. Cell Selectors highlight data associated with subsets of embryo cells within a View. Using linking, these selected cells can be viewed in multiple representations. We describe PCX as a 3D gene expression visualization tool and provide examples of how it has been used by BDTNP biologists to generate new hypotheses.