Research Interests: Gene expression, Multidisciplinary, Antibiotic Resistance, Quorum Sensing, Genome Analysis, and 17 moreQuinolones, Phenotype, PLoS one, Pseudomonas aeruginosa, Anti-Bacterial Agents, Reproducibility of Results, Microbial Sensitivity Tests, Genetic variation, Proteome analysis, Efflux Pumps, Pseudomonas Aeruginosa, Proteome, Expression analysis, Environmental, Nucleotides, Gene expression profiling, and Down-Regulation
Members of the cholecystokinin (CCK)/gastrin family of pep- tides, including the arthropod sulfakinins, and their cognate receptors, play an important role in the regulation of feeding behavior and energy homeostasis. Despite many efforts... more
Members of the cholecystokinin (CCK)/gastrin family of pep- tides, including the arthropod sulfakinins, and their cognate receptors, play an important role in the regulation of feeding behavior and energy homeostasis. Despite many efforts after the discovery of CCK/gastrin immunoreactivity in nematodes 23 yr ago, the identity of these nematode CCK/gastrin-related peptides has remained a mystery ever since. The Caenorhab- ditis
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-Omics data have become indispensable to systems biology, which aims to describe the full complexity of functional cells, tissues, organs and organisms. Generating vast amounts of data via such methods, researchers have invested in ways... more
-Omics data have become indispensable to systems biology, which aims to describe the full complexity of functional cells, tissues, organs and organisms. Generating vast amounts of data via such methods, researchers have invested in ways of handling and interpreting these. From the large volumes of -omics data that have been gathered over the years, it is clear that the information derived from one -ome is usually far from complete. Now, individual techniques and methods for integration are maturing to the point that researchers can focus on network-based integration rather than simply interpreting single -ome studies. This review evaluates the application of integrated -omics approaches with a focus on Caenorhabditiselegans studies, intending to direct researchers in this field to useful databases and inspiring examples.
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In quantitative shotgun proteomic analyses by liquid chromatography and mass spectrometry, a rigid study design is necessary in order to obtain statistically relevant results. Hypothesis testing, sample size calculation and power... more
In quantitative shotgun proteomic analyses by liquid chromatography and mass spectrometry, a rigid study design is necessary in order to obtain statistically relevant results. Hypothesis testing, sample size calculation and power estimation are fundamental concepts that require consideration upon designing an experiment. For this reason, the reproducibility and variability of the proteomic platform needs to be assessed. In this study, we evaluate the technical (sample preparation), labeling (isobaric labels), and total (biological + technical + labeling + experimental) variability and reproducibility of a workflow that employs a shotgun LC-MS/MS approach in combination with TMT peptide labeling for the quantification of peripheral blood mononuclear cell (PBMC) proteome. We illustrate that the variability induced by TMT labeling is small when compared to the technical variation. The latter is also responsible for a substantial part of the total variation. Prior knowledge about the ex...
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The paradigm saying that release of the brain neuropeptide big prothoracicotropic hormone (PTTH) initiates metamorphosis by activating the Torso-receptor/ERK pathway in larval prothoracic glands (PGs) is widely accepted nowadays. Upon... more
The paradigm saying that release of the brain neuropeptide big prothoracicotropic hormone (PTTH) initiates metamorphosis by activating the Torso-receptor/ERK pathway in larval prothoracic glands (PGs) is widely accepted nowadays. Upon ligand-receptor interaction Ca(2+) enters the PG cells and acts as a secondary messenger. Ecdysteroidogenesis results, later followed by apoptosis. Yet, some data do not fit in this model. In some species decapitated animals can still molt, even repeatedly, and metamorphose. PTTH does not universally occur in all insect species. PGs may also have other functions; PGs as counterpart of the vertebrate thymus? There are also small PTTHs. Finally, PTTH remains abundantly present in adults and plays a role in control of ecdysteroidogenesis (=sex steroid production) in gonads. This is currently documented only in males. This urges a rethinking of the PTTH-PG paradigm. The key question is: Why does PTTH-induced Ca(2+) entry only result in ecdysteroidogenesis ...
Research Interests: Physiology, Calcium, Apoptosis, Female, Animals, and 5 moreMale, Peptides, Homeostasis, Grasshoppers, and ECDYSTEROIDS
Because of their wide range of functions, endogenous peptides have great potential either as drugs themselves or as drug targets. To provide an overview of the current use of peptides as drugs (targets) and describe how improvements in... more
Because of their wide range of functions, endogenous peptides have great potential either as drugs themselves or as drug targets. To provide an overview of the current use of peptides as drugs (targets) and describe how improvements in peptide biochemistry and the application of peptidomics studies can lead to the discovery of new diagnostic and therapeutic targets. We discuss the different peptidomics technologies and their application in the study of human and animal disease models, animal venoms, antimicrobial peptides, G-protein-coupled receptor ligands and biomarkers. At present, peptide drugs represent a small but growing number of pharmaceutical molecules. The peptidomics methodology, which was introduced 7 years ago to study naturally occurring peptides, will lead to a plethora of new peptide drug leads.
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Neuropeptides are small messenger molecules that can be found in all metazoans, where they govern a diverse array of physiological processes. Because neuropeptides seem to be conserved among pest species, selected peptides can be... more
Neuropeptides are small messenger molecules that can be found in all metazoans, where they govern a diverse array of physiological processes. Because neuropeptides seem to be conserved among pest species, selected peptides can be considered as attractive targets for drug discovery. Much can be learned from the model system Caenorhabditis elegans because of the availability of a sequenced genome and state-of-the-art postgenomic technologies that enable characterization of endogenous peptides derived from neuropeptide-like protein (NLP) precursors. Here, we provide an overview of the NLP peptide family in C. elegans and discuss their resemblance with arthropod neuropeptides and their relevance for anthelmintic discovery.
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For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, have been far less studied.... more
For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, have been far less studied. The migratory locust Locusta migratoria, a heterometabolous insect, is one of the most infamous agricultural pests. They undergo a well-known and profound phase transition from the relatively harmless solitary form to a ferocious gregarious form. The underlying regulatory mechanisms of this phase transition are not fully understood, but it is undoubtedly that neuropeptides are involved. However, neuropeptide research in locusts is hampered by the absence of genomic information. Recently, EST (Expressed Sequence Tag) databases from Locusta migratoria were constructed. Using bioinformatical tools, we searched these EST databases specifically for neuropeptide precursors. Based on known locust neuropeptide sequences, we confirmed the sequence of several ...
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Three novel members of the periviscerokinin family could be identified directly from extracts of single abdominal perisympathetic organs of blaberoid cockroaches by means of electrospray ionization-quadrupole time of flight (ESI-QTOF) MS.... more
Three novel members of the periviscerokinin family could be identified directly from extracts of single abdominal perisympathetic organs of blaberoid cockroaches by means of electrospray ionization-quadrupole time of flight (ESI-QTOF) MS. Sequences of these periviscerokinins were confirmed by Edman degradation. Their primary structures are GSSGLIPFGRT-NH2 (Lem-PVK-1), GSSGLISMPRV-NH2 (Lem-PVK-2), and GSSGMIPFPRV-NH2 (Lem-PVK-3). Hitherto only known from the American cockroach, this neuropeptide family contains a highly conserved N-terminus whereas, at the C-terminus, only the penultimate amino-acid residue (Arg) has been found in all members of this peptide family. The identified periviscerokinins are the only abundant myoactive peptides in abdominal perisympathetic organs of blaberoid cockroches and they appear to be absent in the retrocerebral complex. Screening of extracts of single abdominal perisympathetic organs (70-90 microm in diameter), from five different species of the su...
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Despite decades of research, no early-onset biomarkers are currently available for Alzheimer's disease, a cureless neurodegenerative disease afflicting millions worldwide. In this study, transgenic Caenorhabditis elegans were used to... more
Despite decades of research, no early-onset biomarkers are currently available for Alzheimer's disease, a cureless neurodegenerative disease afflicting millions worldwide. In this study, transgenic Caenorhabditis elegans were used to investigate changes in the metabolome after induced expression of amyloid-β. GC- and LC-MS-based platforms determined a total of 157 differential features. Some of these were identified using in-house (GC-MS) or public libraries (LC-MS), revealing changes in allantoin, cystathionine and tyrosine levels. Since C. elegans is far better suited to metabolomics studies than most other model systems, the accordance of these findings with vertebrate literature is promising and argues for further use of C. elegans as a model of human pathology in the study of AD.
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For more than 20 years, reverse pharmacology has been the preeminent strategy to discover the activating ligands of orphan G protein-coupled receptors (GPCRs). The onset of a reverse pharmacology assay is the cloning and subsequent... more
For more than 20 years, reverse pharmacology has been the preeminent strategy to discover the activating ligands of orphan G protein-coupled receptors (GPCRs). The onset of a reverse pharmacology assay is the cloning and subsequent transfection of a GPCR of interest in a cellular expression system. The heterologous expressed receptor is then challenged with a compound library of candidate ligands to identify the receptor-activating ligand(s). Receptor activation can be assessed by measuring changes in concentration of second messenger reporter molecules, like calcium or cAMP. The fluorescence-based calcium mobilization assay described here is a frequently used medium-throughput reverse pharmacology assay. The orphan GPCR is transiently expressed in human embryonic kidney 293T (HEK293T) cells and a promiscuous Gα16 construct is co-transfected. Following ligand binding, activation of the Gα16 subunit induces the release of calcium from the endoplasmic reticulum. Prior to ligand screening, the receptor-expressing cells are loaded with a fluorescent calcium indicator, Fluo-4 acetoxymethyl. The fluorescent signal of Fluo-4 is negligible in cells under resting conditions, but can be amplified more than a 100-fold upon the interaction with calcium ions that are released after receptor activation. The described technique does not require the time-consuming establishment of stably transfected cell lines in which the transfected genetic material is integrated into the host cell genome. Instead, a transient transfection, generating temporary expression of the target gene, is sufficient to perform the screening assay. The setup allows medium-throughput screening of hundreds of compounds. Co-transfection of the promiscuous Gα16, which couples to most GPCRs, allows the intracellular signaling pathway to be redirected towards the release of calcium, regardless of the native signaling pathway in endogenous settings. The HEK293T cells are easy to handle and have proven their efficacy throughout the years in receptor deorphanization assays. However, optimization of the assay for specific receptors may remain necessary.
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Research Interests: Caenorhabditis elegans, Biological Chemistry, Gene expression, Biological Sciences, Animals, and 12 moreIron, Heme, CHEMICAL SCIENCES, Myoglobin, Protein Secondary Structure Prediction, Oxygen, Nitrite reductases, Amino Acid Sequence, Recombinant Proteins, Protein Binding, Hydrogen-Ion Concentration, and Oxidation-Reduction
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Members of the short neuropeptide F (sNPF) family of peptides and their cognate receptors play key roles in a variety of physiological processes in arthropods. In silico screening of GigasDatabase, a specific expressed sequence tag... more
Members of the short neuropeptide F (sNPF) family of peptides and their cognate receptors play key roles in a variety of physiological processes in arthropods. In silico screening of GigasDatabase, a specific expressed sequence tag database from the Pacific oyster Crassostrea gigas, resulted in the identification of a receptor (Cg-sNPFR-like) phylogenetically closely related to sNPF receptors (sNPFRs) of insects. A reverse endocrinology approach was undertaken to identify the peptide ligand(s) of this orphan receptor. Though structurally distinct from insect sNPFs, three RFamide peptides derived from the same precursor, i.e. GSLFRFamide, SSLFRFamide and GALFRFamide, specifically activate the receptor in a dose-dependent manner, with respective EC50 values (half-maximal effective concentrations) of 1.1, 2.1 and 4.1 μmol l(-1). We found that both Cg-sNPFR-like receptor and LFRFamide encoding transcripts are expressed in the oyster central nervous system and in other tissues as well, a...