A5059708829- Metabolomics and Mass Spectrometry Studies
- Fatty Acid Research and Health
- Cancer, Lipids, and Metabolism
- Microbial Metabolic Engineering and Bioproduction
- 14-3-3 protein interactions
- ATP Synthase and ATPases Research
- Fungal and yeast genetics research
- Fermentation and Sensory Analysis
- Biofuel production and bioconversion
- Protein Degradation and Inhibitors
- Horticultural and Viticultural Research
- Analytical Chemistry and Chromatography
- Enzyme Catalysis and Immobilization
- Liver Disease Diagnosis and Treatment
- Fungal Biology and Applications
- Advanced Proteomics Techniques and Applications
- Gene Regulatory Network Analysis
- Cancer, Hypoxia, and Metabolism
- Mass Spectrometry Techniques and Applications
- Diet, Metabolism, and Disease
- Enzyme Production and Characterization
- Microbial Metabolism and Applications
- Diet and metabolism studies
- Lipid metabolism and biosynthesis
- Neural and Behavioral Psychology Studies
VTT Technical Research Centre of Finland
2015-2025
Tieto (Finland)
2009-2021
University of Iowa
2020
University of Salerno
2018-2019
Pontificia Universidad Católica de Chile
2019
University of Manitoba
2018-2019
Uppsala University
2015-2017
Austral University of Chile
2016
BG Klinikum Hamburg
2011
University of California, Davis
2011
Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well proteomic research. Such approaches are used systems biology, functional genomics, biomarker discovery, among others. An ongoing challenge these molecular approaches, however, the development better data processing methods. Here we introduce a new generation popular open-source toolbox, MZmine 2. A key concept 2 software...
Abstract Activation of lipid metabolism is an early event in carcinogenesis and a central hallmark many cancers. However, the precise molecular composition lipids tumors remains generally poorly characterized. The aim present study was to analyze global profiles breast cancer, integrate results protein expression, validate findings by functional experiments. Comprehensive lipidomics conducted 267 human tissues using ultraperformance liquid chromatography/ mass spectrometry. products de novo...
Identification of early mechanisms that may lead from obesity towards complications such as metabolic syndrome is great interest. Here we performed lipidomic analyses adipose tissue in twin pairs discordant for but still metabolically compensated. In parallel studied more evolved states by investigating a separated set individuals considered to be morbidly obese. Despite lower dietary polyunsaturated fatty acid intake, the obese had increased proportions palmitoleic and arachidonic acids...
Data processing and identification of unknown compounds in comprehensive two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC/TOFMS) analysis is a major challenge, particularly when large sample sets are analyzed. Herein, we present method for efficient treatment data produced by GC×GC/TOFMS implemented as freely available open source software package, Guineu. To handle to efficiently utilize all the features vendor (baseline correction, spectral...
Metabolomics experiments are inevitably subject to a component of unwanted variation, due factors such as batch effects, long runs samples, and confounding biological variation. Although the removal this variation is vital step in analysis metabolomics data, it considered gray area which there recognized need develop better understanding procedures statistical methods required achieve statistically relevant optimal outcomes. In paper, we discuss causes experiments, review commonly used...
Interspecific hybridization has proven to be a potentially valuable technique for generating de novo lager yeast strains that possess diverse and improved traits compared their parent strains. To further enhance the value of strain development, it would desirable combine phenotypic from more than two strains, as well remove unwanted hybrids. One such trait, limited industrial use hybrids, is inherent tendency produce phenolic off-flavours; an undesirable trait inherited Saccharomyces...
Abstract Understanding how genetics influences obesity, brain activity and eating behaviour will add important insight for developing strategies weight‐loss treatment, as obesity may stem from different causes individual feeding depend on genetic differences. To this end, we examined an risk allele the FTO gene affects in response to food images of caloric content via functional magnetic resonance imaging (f MRI ). Thirty participants homozygous rs9939609 single nucleotide polymorphism were...
Finding proteins with specific functions by mining modern databases can potentially lead to substantial advancements in wide range of fields, from medicine and biotechnology material science. Currently available algorithms enable based on their sequence or structure. However, activities many proteins, such as enzymes drug targets, are dictated active site residues surroundings rather than the overall structure a protein. Here we present ActSeek -- computer vision-inspired fast program that...
Anthraquinones in the emodin family are produced by bacteria, fungi, and plants. They display various biological activities exploited, e.g., for crop protection, may also be utilized as sustainable, bio-based colorants textile, paints, electronics, cosmetic industries. Anthraquinone pigments from Cortinarius mushrooms have been used artisan dyeing because they stable, colorfast, compatible with methods. However, their chemical synthesis is complex uneconomical, harvesting wild forests...
Mitochondrial pyruvate dehydrogenase (PDH) is important in the production of lipids oleaginous yeast, but other yeast may bypass mitochondria (PDH bypass), converting cytosol to acetaldehyde, then acetate and acetyl CoA which further converted lipids. Using a metabolic model based on Yarrowia lipolytica, we found that introduction this an should result enhanced yield triacylglycerol (TAG) substrate. Trichosporon oleaginosus (formerly Cryptococcus curvatus) can produce TAGs from both glucose...
The filamentous fungus Trichoderma reesei (teleomorph Hypocrea jecorina) is a widely used industrial host organism for protein production. In cultivations, it can produce over 100 g/l of extracellular protein, mostly constituting cellulases and hemicellulases. order to improve production T. the transcriptional regulation secretory pathway factors have been extensively studied. However, metabolism under conditions has not received much attention. To understand physiology we carried out...
Article6 October 2022Open Access Transparent process Predictive evolution of metabolic phenotypes using model-designed environments Paula Jouhten orcid.org/0000-0003-1075-7448 European Molecular Biology Laboratory, Heidelberg, Germany VTT Technical Research Centre Finland Ltd, Espoo, Department Bioproducts and Biosystems, Aalto University, Contribution: Conceptualization, Software, Formal analysis, Investigation, Visualization, Methodology, Writing - original draft, review & editing Search...
Trichoderma reesei is one of the main sources biomass-hydrolyzing enzymes for biotechnology industry. There a need improving its enzyme production efficiency. The use metabolic modeling simulation and prediction this organism’s metabolism potentially valuable tool capabilities. An accurate model needed to perform analysis. A whole-genome T. has been reconstructed together with models 55 related species using reconstruction algorithm CoReCo. previously published CoReCo method improved obtain...
Yeast cryotolerance brings some advantages for wine fermentations, including the improved aromatic complexity of white wines. Naturally cold-tolerant strains are generally less adept at fermentation but fermentative fitness can potentially be through hybridization. Here we studied potential using hybrids involving Saccharomyces eubayanus and a S. cerevisiae strain low-temperature winemaking. Through screening performance in response to variable concentrations sugar, nitrogen temperature,...
Yeasts in the lager brewing group are closely related and consequently do not exhibit significant genetic variability. Here, an artificial Saccharomyces cerevisiae × eubayanus tetraploid interspecies hybrid was created by rare mating, its ability to sporulate produce viable gametes exploited generate phenotypic diversity. Four spore clones obtained from a single ascus were isolated, their brewing-relevant phenotypes assessed. These F1 found differ with respect fermentation performance under...
Eukaryotic metabolism is organized into subcellular compartments enclosed by lipid-membranes. Since most metabolites do not move freely across the membranes, compartmentalization influences metabolic pathway connectivities. Thus, compartmentalizing pathways also in genome-scale models (GEMs) essential for accurate predictions of eukaryotic cells’ phenotypes. Compartmentalization has manually been introduced model Eukaryote GEMs like yeast Saccharomyces cerevisiae . Non-model organisms’ can...
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective to predict other, related species. our methodology, combine several state of art approaches, namely, multiple kernel (MKL), pairwise kernels kernelized structured output prediction supervised graph inference framework. For MKL, recently proposed centered alignment...
Abstract Motivation In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component (PCA) stoichiometric flux analysis. PCA is able to capture main modes variability in a set experiments does not make many prior assumptions about data, but inherently take into account mode structure metabolism. Stoichiometric methods, such as Flux Balance Analysis (FBA) Elementary Mode Analysis, on other hand, metabolic modes, however, they primarily designed...