A5053257775- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Molecular Biology Techniques and Applications
- Animal Genetics and Reproduction
- Immunotherapy and Immune Responses
- Reproductive Biology and Fertility
- Cancer Immunotherapy and Biomarkers
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Cancer Research and Treatments
- Pluripotent Stem Cells Research
- Veterinary Oncology Research
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Scarabaeidae Beetle Taxonomy and Biogeography
- Machine Learning in Bioinformatics
- Developmental Biology and Gene Regulation
- Chronic Lymphocytic Leukemia Research
- Virus-based gene therapy research
- Cancer Genomics and Diagnostics
- Immune Cell Function and Interaction
Graz University of Technology
2019-2024
Friedrich-Alexander-Universität Erlangen-Nürnberg
2016-2023
University of Rostock
2013-2023
University Medical Center
2016
National Institutes of Health
2009-2015
National Center for Biotechnology Information
2009-2015
Consejo Nacional de Investigaciones Científicas y Técnicas
2007-2012
National Chemical Laboratory
2011
Centro Nacional de Biotecnología
2011
Indiana University Bloomington
2011
The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African laevis with more tractable genetics. Here we present a draft genome sequence assembly X. tropicalis. This encodes than 20,000 protein-coding genes, including orthologs at least 1700 human disease genes. Over 1 million expressed tags validated annotation. More one-third consists transposable elements, unusually prevalent DNA transposons. Like other...
Abstract It has been shown that innate immune responses can adopt adaptive properties such as memory. Whether T cells utilize signaling pathways to diversify their repertoire of effector functions is unknown. Gasdermin E (GSDME) a membrane pore-forming molecule execute pyroptotic cell death and thus serve potential cancer checkpoint. In the present study, we show human express GSDME and, surprisingly, this expression associated with durable viability repurposed for release alarmin...
In most metazoan nuclei, heterochromatin is located at the nuclear periphery in contact with lamina, which provides mechanical stability to nucleus. We show that cultured cells, chromatin decompaction by nucleosome binding protein HMGN5 decreases sturdiness, elasticity and rigidity of Mice overexpressing HMGN5, either globally or only heart, are normal birth but develop hypertrophic heart large cardiomyoctyes, deformed nuclei disrupted lamina die cardiac malfunction. Chromatin seen...
Detailed information about stage-specific changes in gene expression is crucial for understanding the regulatory networks underlying development and various signal transduction pathways contributing to morphogenesis. Here we describe global dynamics during early murine limb development, when cartilage, tendons, muscle, joints, vasculature nerves are specified musculoskeletal system of limbs established. We used whole-genome microarrays identify genes with differential at 5 stages (E9.5...
Abstract MicroRNAs (miRNAs) have been reported to contribute the pathophysiology of multiple sclerosis (MS), an inflammatory disorder central nervous system. Here, we propose a new consensus-based strategy analyse and integrate miRNA gene expression data in MS as well other publically available gain deeper understanding role miRNAs overcome challenges posed by studies with limited patient sample sizes. We processed analysed microarray datasets compared genes blood patients controls. then...
Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss function. Functional information is preserved through conservation the composition transcription factor binding sites (TFBS) in a element. We have developed method that accurately identify pairs functional noncoding orthologs at evolutionarily diverged loci by searching for conserved TFBS arrangements. With an estimated 5% false-positive rate (FPR) approximately 3000 human and zebrafish syntenic loci, we...
The hemibiotrophic plant pathogen Colletotrichum higginsianum infects Brassicaceae and in combination with Arabidopsis thaliana, represents an important model system to investigate various ecologically fungal pathogens their infection strategies. After penetration of cells by appressoria, C. establishes large biotrophic primary hyphae the first infected cell. Shortly thereafter, a switch necrotrophic growth occurs leading invasion neighboring secondary hyphae. In forward genetic screen for...
Abstract Early mouse embryos have an atypical translational machinery that consists of cytoplasmic lattices and is poorly competent for translation. Hence, the impact transcriptomic changes on operational level proteins predicted to be relatively modest. To investigate this, we performed liquid chromatography–tandem mass spectrometry mRNA sequencing at seven developmental stages, from mature oocyte blastocyst, independently validated our data by immunofluorescence qPCR. We detected...
There is as yet no general agreement regarding the most appropriate solution to problem of identifying areas endemism, not even in particular cases. In this study, we compared Endemicity Analysis (EA), Parsimony (PAE), and Biotic Elements (BE) based on their ability identify hypothetical predefined patterns that represent nested, overlapping, disjoint endemism supported by species with different degrees sympatry. We found PAE performs poorly when applied either overlap each other or are...
WNT signaling is critical in most aspects of skeletal development and homeostasis, antagonists are emerging as key regulatory proteins with great promise therapeutic agents for bone disorders. Here we show that Sost its paralog Sostdc1 emerged through ancestral genome duplication their expression patterns have diverged to delineate non-overlapping domains organ systems including musculoskeletal, cardiovascular, nervous, digestive, reproductive respiratory. In the developing limb, display...
Pancreatic cancer is the fourth leading cause for cancer-related death, and early diagnosis one key to improve survival rate of this disease. Molecular biomarkers are an important method diagnostic use in pancreatic cancer. We used data from three mRNA microarray datasets a microRNA dataset (GSE16515, GSE15471, GSE28735, GSE41372) identify potential genes. Differentially expressed genes (DEGs) microRNAs (DEMs) were identified. Functional, pathway enrichment, protein-protein interaction...
In 90% of pancreatic ductal adenocarcinoma cases, genetic alteration the proto-oncogene Kras has occurred, leading to uncontrolled proliferation cancerous cells. Targeting proven be difficult and battle against cancer is ongoing. A promising approach combat was discovery clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system, which can used genetically modify To assess potential a CRISPR/CRISPR-associated protein 9 (Cas9) method eliminate mutations...
COVID-19, the disease caused by SARS-CoV-2 infection, can assume a highly variable course, ranging from asymptomatic which constitutes majority of cases, to severe respiratory failure. This implies diverse host immune response SARS-CoV-2. However, immunological underpinnings underlying these divergent courses remain elusive. We therefore set out longitudinally characterize signatures convalescent COVID-19 patients stratified according their severity. Our unique cohort consists 74 not...
High mobility group N (HMGN) is a family of intrinsically disordered nuclear proteins that bind to nucleosomes, alters the structure chromatin and affects transcription. A major unresolved question extent functional specificity, or redundancy, between various members HMGN protein family. Here, we analyze transcriptional profile cells in which expression has been either deleted doubled. We find both up- downregulation altered cellular transcription profile. Most, but not all changes were...
Transcriptional enhancers integrate the contributions of multiple classes transcription factors (TFs) to orchestrate myriad spatio-temporal gene expression programs that occur during development. A molecular understanding with similar activities requires identification both their unique and shared sequence features. To address this problem, we combined phylogenetic profiling a DNA–based enhancer classifier analyzes TF binding sites (TFBSs) governing co-expressed set. We first assembled small...
Gene expression is controlled by proximal promoters and distal regulatory elements such as enhancers. While the activity of some can be invariant across tissues, enhancers tend to highly tissue-specific. We compiled sets tissue-specific based on gene profiles 79 human tissues cell types. Putative transcription factor binding sites within each set sequences were used train a support vector machine classifier capable distinguishing from control sequences. obtained reliable classifiers for 92%...
Current models of early mouse development assign roles to stochastic processes and epigenetic regulation, which are considered be as influential the genetic differences that exist between strains species Mus musculus. The aim this study was test whether oocytes vary from each other in abundance gene products could influence, prime, or even predetermine developmental trajectories features derivative embryos. Using paradigm inbred strains, we quantified 2010 protein groups (SILAC LC-MS/MS)...
Homeodomain (HD) transcription factor (TF) NKX2-1 critical for the regional specification of medial ganglionic eminence (MGE) as well promoting GABAergic and cholinergic neuron fates via induction TFs such LHX6 LHX8. defines MGE identity in large part through transcriptional repression, while maturation is mediated by activation Here we analyze signaling TF pathways, downstream NKX2-1, required fate maturation.Differential ChIP-seq analysis was used to identify regulatory elements (REs)...
Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears be counterintuitive natural selection: Redundant sequences are expected either diverge and acquire new functions or accumulate mutations become nonfunctional. Nevertheless, we show at least 31% of the enhancer...