Analysis of the proteins secreted by Trichoderma harzianum P49P11 under carbon-limited conditions

The wild type strain Trichoderma harzianum was able to synthesize enzymes that can catalyse the hydrolysis of p-nitrophenyl-β-D-glucopyranoside (PNPGase) in glucose-limited chemostat cultures. Fructose/glucose and sucrose conditions provided low levels of PNPGase activity. To investigate whether under these conditions other enzymes were...

Dynamics of the transcriptome and proteome in regions of the brain differ considerably

Human brain research is advancing, facilitated by improved high-throughput techniques and systematically preservation of brain tissue in brain banks. Due to the complex organization and regulation of the brain, most studies only focus on a single aspect of healthy and diseased samples. This research integrates analyses of the transcriptome and...

Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae

Introduction: The switch from quiescence (G0) into G1 and cell cycle progression critically depends on specific nutrients and metabolic capabilities. Conversely, metabolic networks are regulated by enzyme–metabolite interaction and transcriptional regulation that lead to flux modifications to support cell growth. How cells process and...

Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae

Efficient production of fuels and chemicals by metabolically engineered micro-organisms requires availability of precursor molecules for product pathways. In eukaryotic cell factories, heterologous product pathways are usually expressed in the cytosol, which may limit availability of precursors that are generated in other cellular...

Proteomic analysis of methanonatronarchaeum thermophilum AMET1, a representative of a putative new class of euryarchaeota, “methanonatronarchaeia”

The recently discovered Methanonatronarchaeia are extremely halophilic and moderately thermophilic methyl-reducing methanogens representing a novel class-level lineage in the phylum Euryarchaeota related to the class Halobacteria. Here we present a detailed analysis of 1D-nano liquid chromatography–electrospray ionization tandem mass...

Interactive Visual Exploration of 3D Mass Spectrometry Imaging Data Using Hierarchical Stochastic Neighbor Embedding Reveals Spatiomolecular Structures at Full Data Resolution

Technological advances in mass spectrometry imaging (MSI) have contributed to growing interest in 3D MSI. However, the large size of 3D MSI data sets has made their efficient analysis and visualization and the identification of informative molecular patterns computationally challenging. Hierarchical stochastic neighbor embedding (HSNE), a...

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust...

Peptide Fingerprinting Using Single-Molecule Fluorescence

Proteins belong to the most important molecules in living organisms. They function as messengers, transporters and catalysts, and provide cells and tissues with structure. The expression profile of proteins is rich in information, which can be used, for example, in diagnosing diseases. Therefore proteomics, the large scale study of proteins, can...

Molecular responses of Saccharomyces cerevisiae to near-zero growth rates

Single-molecule protein sequencing through fingerprinting: Computational assessment

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we...

A 256 pixel magnetoresistive biosensor microarray in 0.18μm CMOS

Magnetic nanotechnologies have shown significant potential in several areas of nanomedicine such as imaging, therapeutics, and early disease detection. Giant magnetoresistive spin-valve (GMR SV) sensors coupled with magnetic nanotags (MNTs) possess great promise as ultra-sensitive biosensors for diagnostics. We report an integrated sensor...

Computational Biology in Clinical Proteomics and Chromatin Genomics

The work in this thesis is concerned with two very distinct biological fields. The first part pertains to the development of techniques to aid in the search for clinical biomarkers for use in the early detection of cancer. The second part aims to elucidate in what way a genome is organised in a cell nucleus and the functional consequences of...

Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: Novel responses and implications for strain improvement

A transcriptomics and proteomics approach was employed to study the expression changes associated with p-hydroxybenzoate production by the engineered Pseudomonas putida strain S12pa1B1. To establish p-hydroxybenzoate production, phenylalanine-tyrosine ammonia lyase (pal/tal) was introduced to connect the tyrosine biosynthetic and p-coumarate...

Gold nanoparticles: A novel application of spectral imaging in proteomics - preliminary results

The intense research in proteomics is demanding for fast, reliable and easy-to-use methods in order to study the proteome. In this proceeding we report the development of such a novel research tool based on spectral imaging and Resonance Light Scattering gold particles. This method will allow the study of DNA-protein interactions. We suggest a...