A5013942271- Protein purification and stability
- Monoclonal and Polyclonal Antibodies Research
- Analytical Chemistry and Chromatography
- Crystallization and Solubility Studies
- Neuroblastoma Research and Treatments
- Cancer Genomics and Diagnostics
- X-ray Diffraction in Crystallography
- Genomics and Phylogenetic Studies
- Microfluidic and Capillary Electrophoresis Applications
- Bioinformatics and Genomic Networks
- Chromatography in Natural Products
- Viral Infectious Diseases and Gene Expression in Insects
- Neurofibromatosis and Schwannoma Cases
- Endoplasmic Reticulum Stress and Disease
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Acute Lymphoblastic Leukemia research
- Malaria Research and Control
- Protein Degradation and Inhibitors
- Childhood Cancer Survivors' Quality of Life
- Microtubule and mitosis dynamics
- Heat shock proteins research
- 3D Printing in Biomedical Research
Mannheim University of Applied Sciences
2012-2023
Seven Bridges Genomics (United States)
2019-2022
Medical University of Vienna
2022
Creative Commons
2022
St Anna Children's Hospital
2014-2021
St. Anna Children's Cancer Research Institute
2014-2021
Community College of Rhode Island
2016-2017
Simon Fraser University
2009-2014
Software Competence Center Hagenberg (Austria)
2009
University of Applied Sciences Upper Austria
2009
Abstract Background The Amoebozoa constitute one of the primary divisions eukaryotes, encompassing taxa both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis a whole genome assembly Acanthamoeba castellanii ( Ac ) first representative from solitary free-living amoebozoan. Results encodes 15,455 compact intron-rich genes, significant number which are predicted to have arisen through inter-kingdom lateral gene transfer...
Abstract Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment propagation, affecting accuracy of modeling cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 matched patient (PT) samples from 509 models. CNA inferences based on DNA sequencing microarray data displayed substantially higher resolution...
High hyperdiploidy defines the largest genetic entity of childhood acute lymphoblastic leukemia (ALL). Despite its relatively low recurrence risk, this subgroup generates a high proportion relapses. The cause and origin these relapses remains obscure. We therefore explored mutational landscape in hyperdiploid (HD) ALL with whole-exome (n=19) subsequent targeted deep sequencing 60 genes 100 relapsing 51 non-relapsing cases. identified multiple clones at diagnosis that were primarily defined...
Abstract Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established landscapes 536 patient-derived xenograft (PDX) models across 25 types, together mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared human tumors, PDXs typically higher purity fit dynamic driver events molecular properties via multiple...
The remarkable feature of Schwann cells (SCs) to transform into a repair phenotype turned the spotlight on this powerful cell type. SCs provide regenerative environment for axonal re-growth after peripheral nerve injury (PNI) and play vital role in differentiation neuroblastic tumors benign subtype neuroblastoma, tumor originating from neural crest-derived neuroblasts. Hence, understanding their mode-of-action is utmost interest new approaches medicine, but also neuroblastoma therapy....
Abstract Adult Schwann cells (SCs) possess an inherent plastic potential. This plasticity allows SCs to acquire repair-specific functions essential for peripheral nerve regeneration. Here, we investigate whether stromal in benign-behaving neuroblastic tumors adopt a similar cellular state. We profile ganglioneuromas and neuroblastomas, rich poor SC stroma, respectively, nerves after injury, repair SCs. Indeed, share the expression of repair-associated genes. Neuroblastoma cells, derived from...
Plasmodium parasites, the causative agents of malaria, express many variant antigens on cell surfaces. Variant surface (VSAs) are typically organized into large subtelomeric gene families that play critical roles in virulence and immune evasion. Many important aspects VSA function evolution remain obscure, impeding our understanding mechanisms vaccine development. To gain further insights evolution, we comparatively classified examined known across seven species. We identified a set...
The separation of proteins by internally and externally generated pH gradients in chromatofocusing on ion-exchange columns is a well-established analytical method with large number applications. In this work, stoichiometric displacement model was used to describe the retention behavior lysozyme SP Sepharose FF monoclonal antibody Fractogel SO3 (S) linear salt gradient elution. dependence binding charge B elution introduced using protein net model, while equilibrium constant based...
Children with P2RY8-CRLF2-positive acute lymphoblastic leukemia have an increased relapse risk. Their mutational and transcriptional landscape, as well the respective patterns at remain largely elusive. We, therefore, performed integrated analysis of whole-exome RNA sequencing in 41 major clone fusion-positive cases including 19 matched diagnosis/relapse pairs. We detected a variety frequently subclonal highly instable JAK/STAT but also RTK/Ras pathway-activating mutations 76% diagnosis...
Genes underlying important phenotypic differences between Plasmodium species, the causative agents of malaria, are frequently found in only a subset species and cluster at dynamically evolving subtelomeric regions chromosomes. We hypothesized that chromosome-internal genomes harbour additional subset-specific genes underlie human pathogenicity, human-to-human transmissibility, virulence. combined sequence similarity searches with synteny block analyses to identify six published genomes,...
Abstract Background Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the variation this nematode species. Results Here we report on identification genomic between reference strain N2 Hawaiian CB4856, one most genetically distant strains from N2. To identify both small- large-scale variations (GVs), sequenced CB4856 genome using Roche 454 (~400 bps single reads) Illumina GA DNA sequencing methods (101 paired-end...
Neuroblastoma serves as a paradigm for applying tumor genomic data determining patient prognosis and thus treatment allocation. MYCN status, i.e. amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less or even favorable clinical courses neuroblastoma. However, amplification is by far not only genetic change associated with unfavorable courses: so called "segmental chromosomal aberrations", gains losses fragments, can also indicate...
Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for rather striking difference in host specificity huakuii 7653R MAFF303099, several probable determinants also require comparison at level. An improved understanding of mobile genetic elements that can be integrated into main chromosomes form islands would enrich our knowledge how genome dynamics may contribute...
A novel cation-exchange resin, Eshmuno™ S, was compared to Fractogel® SO3- (M) and Toyopearl GigaCap S-650M. The stationary phases have different base matrices, carry specific types of polymeric surface modifications. Three monoclonal antibodies (mAbs) were used as model proteins characterize these chromatographic resins. Results from gradient elutions, stirred batch adsorptions confocal laser scanning microscopic investigations elucidate binding behaviour mAbs onto S the corresponding...
The mobile phase pH is a key parameter of every ion exchange chromatography process. However, mechanistic insights into the influence on equilibrium are rare. This work describes model capturing salt and in chromatography. dependence characteristic protein charge constant introduced to steric mass action based net considering number amino acids interacting with stationary phase. allows description adsorption chromatographed proteins as function pH. parameters were determined for monoclonal...
Abstract Background Evaluating the impact of genomic variations (GV) on protein-coding transcripts is an important step in identifying variants functional significance. Currently available programs for variant annotation depend external databases or annotate multiple affecting same transcript independently, which limits program use to organisms these results potentially incorrect incomplete annotations. Findings We have developed CooVar (Co-occurring Variant Analyzer), a database-independent...
Neuroblastoma is the most common extracranial solid tumor in childhood. The vast majority of metastatic (M) stage patients present with disseminated cells (DTCs) bone marrow (BM) at diagnosis and relapse. Although these represent a major obstacle treatment neuroblastoma patients, insights into their expression profile remained elusive. RNA-Seq study 4/M primary tumors, enriched BM-derived diagnostic relapse DTCs, as well corresponding mononuclear (MNCs) from 53 revealed 322 differentially...
We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access National Cancer Institute-funded PDXNet consortium resources, facilitate collaboration among researchers and make these data easily available for research. The includes sections analysis results, metrics activities, processing protocols training materials data. Currently, contains model information resources from 334 new models across 33 cancer types. Tissue samples of were deposited in NCI's...
Vibrio cholerae, the marine bacterium responsible for diarrheal disease cholera, utilizes a multitude of virulence factors to cause disease. The importance two these factors, toxin co-regulated pilus (TCP) and cholera (CT), has been well documented pandemic O1 epidemic O139 serogroups. In contrast, endemic non-O1 non-O139 serogroups can localized outbreaks cholera-like illness, often in absence TCP CT. One mechanism used by strains is type VI secretion system (T6SS) export toxins across cell...
The recent availability of an expanding collection genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification synteny among multiple genomes. However, development effective easy-to-use methods for identifying such conserved gene clusters genomes-synteny blocks-as well as databases, which host blocks from various groups species (especially eukaryotes) also allow users to run synteny-identification programs, lags...
Correct classification of genes into gene families is important for understanding function and evolution. Although many species have been resolved both computationally experimentally with high accuracy, family in most newly sequenced genomes has not done the same standard. This project designed to develop a strategy effectively accurately classify across genomes. We first examine compare performance computer programs developed automated classification. demonstrate that some programs,...
The ETV6/RUNX1 gene fusion defines the largest genetic subgroup of childhood ALL with overall rapid treatment response. However, up to 15% cases relapse. Because an impaired glucocorticoid pathway is implicated in disease recurrence we studied impact alterations by SNP array analysis 31 relapsed cases. In 58% samples, found deletions various signaling pathway-associated genes, but only NR3C1 and ETV6 prevailed minimal residual poor responding subsequently relapsing (p<0.05). To prove...