A5004957828- Radiomics and Machine Learning in Medical Imaging
- Cancer, Hypoxia, and Metabolism
- Metastasis and carcinoma case studies
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Gastric Cancer Management and Outcomes
- Advanced Proteomics Techniques and Applications
- Alkaline Phosphatase Research Studies
- Free Radicals and Antioxidants
- Chemical Reactions and Isotopes
- Cancer Cells and Metastasis
- Viral gastroenteritis research and epidemiology
- Clostridium difficile and Clostridium perfringens research
- Plant Disease Resistance and Genetics
- Bacterial Identification and Susceptibility Testing
- Vitamin C and Antioxidants Research
- Genomics and Phylogenetic Studies
- Carbon dioxide utilization in catalysis
- Cancer Research and Treatments
- Lung Cancer Diagnosis and Treatment
- Lung Cancer Treatments and Mutations
- Colorectal Cancer Treatments and Studies
- Wheat and Barley Genetics and Pathology
- Muscle metabolism and nutrition
- Infrared Thermography in Medicine
Helmholtz Zentrum München
2017-2023
Technical University of Munich
2014
Insights from the annotated wheat genome Wheat is one of major sources food for much world. However, because bread wheat's a large hybrid mix three separate subgenomes, it has been difficult to produce high-quality reference sequence. Using recent advances in sequencing, International Genome Sequencing Consortium presents an with detailed analysis gene content among subgenomes and structural organization all chromosomes. Examples quantitative trait mapping CRISPR-based modification show...
The domestication of wild emmer wheat led to the selection modern durum wheat, grown mainly for pasta production. We describe 10.45 gigabase (Gb) assembly genome cultivar Svevo. enabled genome-wide genetic diversity analyses revealing changes imposed by thousands years empirical and breeding. Regions exhibiting strong signatures divergence associated with breeding were widespread in several major losses pericentromeric regions. A locus on chromosome 5B carries a gene encoding metal...
The prediction of protein sub-cellular localization is an important step toward elucidating function. For each query sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native in 18 classes for eukaryotes, six bacteria and three archaea. method outputs a score that reflects reliability prediction. has performed on par with or better than any other state-of-the-art method. Here, we report availability LocTree3 as public web server. server includes learning-based...
Tissue sensitivity and response to exercise vary according the time of day alignment circadian clocks, but optimal elicit a desired metabolic outcome is not fully defined. To understand how tissues independently collectively respond timed exercise, we applied systems biology approach. We mapped compared global metabolite responses seven different mouse serum after an acute bout performed at times day. Comparative analyses intra- inter-tissue dynamics, including temporal profiling blood...
Abstract Purpose: Current systems of gastric cancer molecular classification include genomic, molecular, and morphological features. Gastric based on tissue metabolomics remains lacking. This study aimed to define metabolically distinct subtypes identify their clinicopathological characteristics. Experimental Design: Spatial by high mass resolution imaging spectrometry was performed in 362 patients with cancer. K−means clustering used tumor stroma-related metabolites. The identified were...
The response to neoadjuvant chemotherapy (NAC) differs substantially among individual patients with non-small cell lung cancer (NSCLC). Major pathological (MPR) is a histomorphological read-out used assess treatment and prognosis in NSCLC after NAC. Although spatial metabolomics promising tool for evaluating metabolic phenotypes, it has not yet been utilized therapy responses NSCLC. We evaluated the potential application of tissues NAC, using classifier that utilizes mass spectrometry...
Imaging mass spectrometry enables in situ label-free detection of thousands metabolites from intact tissue samples. However, automated steps for multi-omics analyses and interpretation histological images have not yet been implemented data analysis workflows. The characterization molecular properties within cellular features is done via time-consuming, non-objective, irreproducible definitions regions interest, which are often accompanied by a loss spatial resolution due to spectra...
Cachexia is the direct cause of at least 20% cancer-associated deaths. Muscle wasting in skeletal muscle results weakness, immobility, and death secondary to impaired respiratory function. proteins are massively degraded cachexia; nevertheless, molecular mechanisms related this process poorly understood. Previous studies have reported conflicting regarding amino acid abundances cachectic tissues. There a clear need identify processes metabolism context cachexia, especially how different...
Abstract Molecular subtyping of lung squamous cell carcinoma (LUSC) has been performed at the genomic, transcriptomic, and proteomic level. However, LUSC stratification based on tissue metabolomics is still lacking. Combining high-mass-resolution imaging mass spectrometry with consensus clustering, four tumor- stroma-specific subtypes distinct metabolite patterns were identified in 330 patients. The first tumor subtype T1 negatively correlated DNA damage immunological features including CD3,...
High mass resolution matrix-assisted laser desorption/ionization (MALDI) spectrometry imaging (MSI) is a suitable method for biomarker detection several tumor entities. Renal cell carcinoma (RCC) the seventh most common cancer type and accounts more than 80% of all renal tumors. Prognostic biomarkers RCC are still missing. Therefore, we analyzed large, multicenter cohort including three subtypes (clear (ccRCC), papillary (pRCC) chromophobe (chRCC)) by MALDI prognostic detection....
Abstract The response to neoadjuvant therapy can vary widely between individual patients. Histopathological tumor regression grading (TRG) is a strong factor for treatment and survival prognosis of esophageal adenocarcinoma (EAC) patients following surgery. However, TRG systems are usually based on the estimation residual but do not consider stromal or metabolic changes after treatment. Spatial metabolomics analysis powerful tool molecular tissue phenotyping has been used so far in context...
Summary Pseudogenes have a reputation of being ‘evolutionary relics’ or ‘junk DNA ’. While they are well characterized in mammals, studies more complex plant genomes so far been hampered by the absence reference genome sequences. Barley is one economically most important cereals and has size 5.1 Gb. With first high‐quality assembly available for Triticeae crop, we conducted whole‐genome assessment pseudogenes on barley genome. We identified, classified 89 440 gene fragments scattered along...
Shigella spp. are the causative agents of bacterial dysentery and shigellosis, mainly in children living developing countries. The study entire life cycle vivo evaluation vaccine candidates' protective efficacy have been hampered by lack a suitable animal model infection. None studies evaluated so far (rabbit, guinea pig, mouse) allowed recapitulation full shigellosis symptoms upon oral challenge. Historical reports suggested that scurvy both metabolic diseases associated with ascorbate...
Patients with the renal phosphate-wasting disease X-linked hypophosphatemia (XLH) and Hyp mice, murine homolog of XLH, are characterized by loss-of-function mutations in phosphate-regulating endopeptidase (PHEX), leading to excessive secretion bone-derived phosphotropic hormone FGF23. The mineralization defect patients XLH mice is caused a combination local accumulation mineralization-inhibiting molecules bone. However, mechanism which PHEX deficiency regulates bone cell metabolism remains...
Abstract Matrix-assisted laser desorption ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) imaging mass spectrometry (MS) is a powerful technology used to analyze metabolites in various tissues. However, it faces significant challenges studying adipose Poor matrix distribution and crystallization caused by excess liquid lipids on the surface of tissue sections hamper m/z species detection, an adverse effect that particularly presents lipid-rich white (WAT). In this study,...
Asymptomatic anthracosis is the accumulation of black carbon particles in adult human lungs. It a common occurrence, but pathophysiologic significance debatable. Using situ high mass resolution matrix-assisted laser desorption/ionization (MALDI) fourier-transform ion cyclotron resonance (FT-ICR) spectrometry imaging analysis, we discovered noxious carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAH), tobacco-specific nitrosamines, or amines, series 330 patients...
Carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAHs), tobacco-specific nitrosamines, amines, and organohalogens, are known to affect both tumor characteristics patient outcomes in lung squamous cell carcinoma (LUSC); however, the roles of these compounds adenocarcinoma (LUAD) remain unclear. We analyzed 11 carbon-bound LUAD LUSC samples using situ high mass-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass...
Correct tumor subtyping of primary renal tumors is essential for treatment decision in daily routine. Most the can be classified based on morphology alone. Nevertheless, some diagnoses are difficult, and further investigations needed correct subtyping. Besides histochemical investigations, high-mass-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) detect new diagnostic biomarkers hence improve diagnostic.Formalin-fixed paraffin embedded tissue...
Abstract Shigella spp. are the causative agents of bacillary dysentery or shigellosis, mainly in children living developing countries. The study entire life cycle vivo and evaluation vaccine candidates’ protection efficacy have been hampered by lack a suitable animal model infection (1). None ones evaluated so far (mouse, rabbit, guinea pig) allows to recapitulate shigellosis symptoms upon oral challenge. Historical reports suggest that scurvy both metabolic diseases associated with...
<div>Abstract<p>Asymptomatic anthracosis is the accumulation of black carbon particles in adult human lungs. It a common occurrence, but pathophysiologic significance debatable. Using <i>in situ</i> high mass resolution matrix-assisted laser desorption/ionization (MALDI) fourier-transform ion cyclotron resonance (FT-ICR) spectrometry imaging analysis, we discovered noxious carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAH),...
Supplementary Data from Spatial Metabolomics Identifies Distinct Tumor-Specific Subtypes in Gastric Cancer Patients