Promoter analysis reveals conserved 30-base-pair core sequences controlling the nonhair-cell preferential expression of WEREWOLF in Arabidopsis.

The root epidermis of Arabidopsis (Arabidopsis thaliana) consists of two distinct cell types: hair (H) cells and non-hair (N) cells, whose patterning is regulated by a network of genes. Among these, the WEREWOLF (WER) gene, encoding an R2R3 MYB transcription factor, acts as a master regulator by promoting the expression of key downstream genes, such as GLABRA2 and CAPRICE. However, the mechanisms controlling WER expression have remained largely unexplored.

SPIRRIG is required for BRICK1 stability and salt stress induced root hair developmental plasticity in Arabidopsis.

Developmental plasticity is critical for plants to adapt to constantly changing environments. Plant root hairs display dramatic plasticity under different environments and therefore play crucial roles in defense against environmental stressors. Here, we report the isolation of an Arabidopsis mutant, salinity over-sensitive mutant 1-1 (som1-1), also exhibiting root hair developmental defects.

Negative feedback regulation of GLABRA1 contributes to epidermal cell patterning in the Arabidopsis root.

GLABRA1 (GL1), which encodes an R2R3 MYB transcription factor, is a key regulator of trichome patterning in the aerial organs of Arabidopsis (Arabidopsis thaliana). Although it has been generally assumed that GL1 functions exclusively in shoots and is not expressed in roots, reverse transcription polymerase chain reaction (RT-PCR) analysis has revealed that GL1 is indeed expressed in roots. To investigate whether GL1 plays a role in root epidermal patterning, we analyzed the effects of gl1 mutations in sensitized genetic backgrounds.

Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm.

Objectives: To determine real-life quantitative changes in OCT biomarkers in a large set of treatment naive patients in a real-life setting undergoing anti-VEGF therapy. For this purpose, we devised a novel deep learning based semantic segmentation algorithm providing the first benchmark results for automatic segmentation of 11 OCT features including biomarkers for neovascular age-related macular degeneration (nAMD).

Methods: Training of a Deep U-net based semantic segmentation ensemble algorithm for state-of-the-art semantic segmentation performance which was used to analyze OCT features prior to, after 3 and 12 months of anti-VEGF therapy.

TRANSPARENT TESTA GLABRA2 defines trichome cell shape by modulating actin cytoskeleton in Arabidopsis thaliana.

The Arabidopsis (Arabidopsis thaliana) TRANSPARENT TESTA GLABRA2 (TTG2) gene encodes a WRKY transcription factor that regulates a range of development events like trichome, seed coat, and atrichoblast formation. Loss-of-function of TTG2 was previously shown to reduce or eliminate trichome specification and branching. Here, we report the identification of an allele of TTG2, ttg2-6.

Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases.

Background: In optical coherence tomography (OCT) scans of patients with inherited retinal diseases (IRDs), the measurement of the thickness of the outer nuclear layer (ONL) has been well established as a surrogate marker for photoreceptor preservation. Current automatic segmentation tools fail in OCT segmentation in IRDs, and manual segmentation is time-consuming.

Methods And Material: Patients with IRD and an available OCT scan were screened for the present study.

Reconstructing disease dynamics for mechanistic insights and clinical benefit.

Diseases change over time, both phenotypically and in their underlying molecular processes. Though understanding disease progression dynamics is critical for diagnostics and treatment, capturing these dynamics is difficult due to their complexity and the high heterogeneity in disease development between individuals. We present TimeAx, an algorithm which builds a comparative framework for capturing disease dynamics using high-dimensional, short time-series data.

AXR1 modulates trichome morphogenesis through mediating ROP2 stability in Arabidopsis.

Cell differentiation and morphogenesis are crucial for the establishment of diverse cell types and organs in multicellular organisms. Trichome cells offer an excellent paradigm for dissecting the regulatory mechanisms of plant cell differentiation and morphogenesis due to their unique growth characteristics. Here, we report the isolation of an Arabidopsis mutant, aberrantly branched trichome 3-1 (abt3-1), with a reduced trichome branching phenotype.

Optical coherence tomography-based misdiagnosis and morphological distinction in pachychoroid neovasculopathy vs. polypoidal choroidal vasculopathy.

Purpose: To evaluate the rate of misdiagnosis of aneurysmatic pachychoroid type 1 choroidal neovascularization/polypoidal choroidal vasculopathy (PAT1/PCV) among cases diagnosed as non-aneurysmatic pachychoroid neovasculopathy (PNV) and to define optical coherence tomography (OCT) features facilitating their distinction.

Methods: The database of the Department of Ophthalmology, Ludwig-Maximilians University Munich, was screened for patients diagnosed with PNV. Multimodal imaging was screened for the presence of choroidal neovascularization (CNV) and aneurysms/polyps.

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species.

In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined.

Identification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methods.

An essential step in the analysis of single-cell RNA sequencing data is to classify cells into specific cell types using marker genes. In this study, we have developed a machine learning pipeline called single-cell predictive marker (SPmarker) to identify novel cell-type marker genes in the Arabidopsis root. Unlike traditional approaches, our method uses interpretable machine learning models to select marker genes.

Long-term ocular damage after recovery from COVID-19: lack of evidence at three months.

Importance: A small number of COVID-19 patients has been reported to suffer from acute keratoconjunctivitis. In very rare cases, acute inflammatory retinal vein occlusion, papillophlebitis or retinopathy have been observed.

Objective: To determine possible long-term effects on the eye, especially on the retina, in patients who had suffered from COVID-19 at least 3 months after recovery.

Plant Cell Identity in the Era of Single-Cell Transcriptomics.

High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells.

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level.

Similar to other complex organisms, plants consist of diverse and specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs. As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression, we report the use of single-nucleus RNA sequencing (sNucRNA-seq) and single-nucleus assay for transposase accessible chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots.

Expression Partitioning of Duplicate Genes at Single Cell Resolution in Roots.

Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralog pairs rapidly return to single copy status whereas, in other pairs, both paralogs are retained and may diverge in expression pattern or function. The effect of a gene - its site of expression and thus the initial locus of its function - occurs at the level of a cell comprising a single cell type at a given state of the cell's development.

Molecular Basis for a Cell Fate Switch in Response to Impaired Ribosome Biogenesis in the Arabidopsis Root Epidermis.

The Arabidopsis () root epidermis consists of a position-dependent pattern of root hair cells and non-hair cells. Underlying this cell type patterning is a network of transcription factors including a central MYB-basic helix-loop-helix-WD40 complex containing WEREWOLF (WER), GLABRA3 (GL3)/ENHANCER OF GLABRA3, and TRANSPARENT TESTA GLABRA1. In this study, we used a genetic enhancer screen to identify , a mutant allele of the ribosome biogenesis factor (RBF) gene (), which caused prospective root hair cells to instead adopt the non-hair cell fate.

Novel Mutants Modify Root-Hair Pattern Formation in Arabidopsis.

The patterning of root-hair and non-hair epidermal cells in the Arabidopsis root is governed by a network of transcriptional regulators. The central MYB-bHLH-WD40 (MBW) transcriptional complex includes the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1). To clarify the role of TTG1, we describe the identification and analysis of two new mutants.

Two Year Visual Acuity and Structural Outcomes in Patients with Diabetic Macular Oedema Treated with Intravitreal Aflibercept - A Retrospective Cohort Study.

Purpose: To assess visual and anatomical outcomes of intravitreal aflibercept for clinically significant diabetic macular oedema (DME).

Methods: For this retrospective single-center cohort study at a tertiary referral center, we performed a data warehouse query to identify 117 treatment-naive patients (139 eyes) undergoing intravitreal treatment with aflibercept for DME between January 2014 and May 2018. Changes in best-corrected visual acuity (BCVA) values (as measured with ETDRS letters), central retinal thickness (CRT) and total macular volume (TVOL) are reported over a two-year period at various time-points.

Gender-related differences in patients treated with intravitreal anti-vascular endothelial growth factor medication for diabetic macular oedema.

Background: Diabetes prevalence is constantly rising, involving the eyes with damage including development of diabetic macular oedema. Since 2012, intravitreal anti-vascular endothelial growth factor medication is available for diabetic macular oedema treatment. Endocrinological studies have shown that fewer women are affected by diabetes.

Nitrate regulation of lateral root and root hair development in plants.

Nitrogen (N) is one of the most important macronutrients for plant growth and development. However, the concentration and distribution of N varies in soil due to a variety of environmental factors. In response, higher plants have evolved a developmentally flexible root system to efficiently take up N under N-limited conditions.

Root Epidermal Cell Patterning Is Modulated by a Critical Residue in the WEREWOLF Transcription Factor.

The Arabidopsis () root epidermis exhibits a position-dependent pattern of root-hair and nonhair cell types. A highly orchestrated network of gene regulatory interactions, including the R2R3-type MYB transcription factor WEREWOLF (WER), is responsible for generating this cell pattern during root development. In this study, we identified a novel mutant from a genetic enhancer screen, designated , that exhibits an abnormal pattern of root-hair and nonhair cells.

QUIRKY regulates root epidermal cell patterning through stabilizing SCRAMBLED to control CAPRICE movement in Arabidopsis.

SCM, a leucine-rich repeat receptor-like kinase, is required for root epidermal cells to appropriately interpret their location and generate the proper cell-type pattern during Arabidopsis root development. Here, via a screen for scm-like mutants we describe a new allele of the QKY gene. We find that QKY is required for the appropriate spatial expression of several epidermal cell fate regulators in a similar manner as SCM in roots, and that QKY and SCM are necessary for the efficient movement of CPC between epidermal cells.

Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells.

Single-cell RNA sequencing (scRNA-seq) has been used extensively to study cell-specific gene expression in animals, but it has not been widely applied to plants. Here, we describe the use of a commercially available droplet-based microfluidics platform for high-throughput scRNA-seq to obtain single-cell transcriptomes from protoplasts of more than 10,000 Arabidopsis () root cells. We find that all major tissues and developmental stages are represented in this single-cell transcriptome population.