Biomedical subjects

J Bouwman

Publications and source records attributed to J Bouwman.

9 recordsLinked to original sources

PubMed2006

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation.

Cells adapt to changes in their environment by the concerted action of many different regulatory mechanisms. Examples of such mechanisms are feedback inhibition by intermediates of metabolism, covalent modification of enzymes and changes in the abundance of mRNAs and proteins. These mechanisms act in parallel at different levels in the cellular hierarchy while regulating a single process. Existing hierarchical regulation analysis determines the relative importance of these mechanisms when the cell regulates a transition from one steady-state to another. Here, the analysis is extended to the regulation of time-dependent phenomena, for which two methods are introduced and illustrated with a kinetic model incorporating transcription and translation of metabolic enzymes.

Adaptation, Physiological↗

PubMed2006

Reduced expression of neuropeptide genes in a genome-wide screen of a secretion-deficient mouse.

Activity-dependent changes in synapses rely on functional changes in resident proteins and on gene expression. We addressed the relationship between synapse activity and the expression of synaptic genes by comparing RNA levels in the neocortex of normal mice versus secretion-deficient and therefore synaptically silent munc18-1 (mammalian homologue of Caenorhabditis elegans uncoordinated locomotion-18) null mutants, using microarray expression analysis, real-time quantitative PCR and northern blotting. We hypothesized that genes under the control of synaptic activity would be differentially expressed between mutants and controls. We found that few synaptic genes were differentially expressed. However, most neuropeptide genes with detectable expression on the microarray were differentially expressed, being expressed 3-20-fold higher in control cortex. Several other secreted proteins were also differentially expressed, but genes encoding their receptors and many other synaptic components were not. Differential expression was confirmed by real-time quantitative PCR analysis. In situ hybridization indicated that the difference in neuropeptide expression was uniform and not due to the loss of specific cells in the mutant. In primary sensory neurons, which do not depend on synaptic activity for their input, the differential expression of neuropeptides was not observed. These data argue against a general relationship between the activity of synapses and the expression of their resident proteins, but suggest a link between secretion and the expression of genes encoding the secreted products.

Animals↗

PubMed2005

High-resolution infrared spectroscopy of the charge-transfer complex [Ar-N2]+: a combined experimental/theoretical study.

A combined experimental and theoretical study of the charge-transfer complex [Ar-N(2)](+) is presented. Nearly 50 transitions split by spin-rotation interaction have been observed by means of infrared diode laser absorption spectroscopy in a supersonic planar plasma expansion. The band origin is at 2272.2563(18) cm(-1) and rotational constants in the ground and vibrationally (NN-stretch) excited state amount to 0.128701(8) cm(-1) and 0.128203(8) cm(-1), respectively. The interpretation of the data in terms of a charge switch upon complexation is supported by new ab initio calculations. The best estimate for a linear equilibrium structure yields R(e)(NN)=1.102 A and R(e)(Ar-N)=2.190 A. Predictions for molecular parameters not directly available from the experimental results are presented as well. Furthermore, the electronic structure and Ar-N bonding mechanism of [Ar-N(2)](+) have been analyzed in detail. The Ar-N bond is a textbook example of a classical 2-center-3-electron bond.

Journal Article↗

PubMed2005

The molluscan RING-finger protein L-TRIM is essential for neuronal outgrowth.

The tripartite motif proteins TRIM-2 and TRIM-3 have been put forward as putative organizers of neuronal outgrowth and structural plasticity. Here, we identified a molluscan orthologue of TRIM-2/3, named L-TRIM, which is up-regulated during in vitro neurite outgrowth of central neurons. In adult animals, L-Trim mRNA is ubiquitously expressed at low levels in the central nervous system and in peripheral tissues. Central nervous system expression of L-Trim mRNA is increased during postnatal brain development and during in vitro and in vivo neuronal regeneration. In vitro double-stranded RNA knock-down of L-Trim mRNA resulted in a >70% inhibition of neurite outgrowth. Together, our data establish a crucial role for L-TRIM in developmental neurite outgrowth and functional neuronal regeneration and indicate that TRIM-2/3 family members may have evolutionary conserved functions in neuronal differentiation.

Amino Acid Sequence↗

PubMed2004

Quantification of synapse formation and maintenance in vivo in the absence of synaptic release.

Outgrowing axons in the developing nervous system secrete neurotransmitters and neuromodulatory substances, which is considered to stimulate synaptogenesis. However, some synapses develop independent of presynaptic secretion. To investigate the role of secretion in synapse formation and maintenance in vivo, we quantified synapses and their morphology in the neocortical marginal zone of munc18-1 deficient mice which lack both evoked and spontaneous secretion [Science 287 (2000) 864]. Histochemical analyses at embryonic day 18 (E18) showed that the overall organization of the neocortex and the number of cells were similar in mutants and controls. Western blot analysis revealed equal concentrations of pre- and post-synaptic marker proteins in mutants and controls and immunocytochemical analyses indicated that these markers were targeted to the neuropil of the synaptic layer in the mutant neocortex. Electron microscopy revealed that at E16 immature synapses had formed both in mutants and controls. These synapses had a similar synapse diameter, active zone length and contained similar amounts of synaptic vesicles, which were immuno-positive for two synaptic vesicle markers. However, these synapses were three times less abundant in the mutant. Two days later, E18, synapses in the controls had more total and docked vesicles, but not in the mutant. Furthermore, synapses were now five times less abundant in the mutant. In both mutant and controls, synapse-like structures were observed with irregular shaped vesicles on both sides of the synaptic cleft. These 'multivesicular structures' were immuno-positive for synaptic vesicle markers and were four times more abundant in the mutant. We conclude that in the absence of presynaptic secretion immature synapses with a normal morphology form, but fewer in number. These secretion-deficient synapses might fail to mature and instead give rise to multivesicular structures. These two observations suggest that secretion of neurotransmitters and neuromodulatory substances is required for synapse maintenance, not for synaptogenesis. Multivesicular structures may develop out of unstable synapses.

Animals↗

PubMed2002

Identification of iron sulphide grains in protoplanetary disks.

Sulphur is depleted in cold dense molecular clouds with embedded young stellar objects, indicating that most of it probably resides in solid grains. Iron sulphide grains are the main sulphur species in cometary dust particles, but there has been no direct evidence for FeS in astronomical sources, which poses a considerable problem, because sulphur is a cosmically abundant element. Here we report laboratory infrared spectra of FeS grains from primitive meteorites, as well as from pyrrhotite ([Fe, Ni](1-x)S) grains in interplanetary dust, which show a broad FeS feature centred at approximately 23.5 micrometres. A similar broad feature is seen in the infrared spectra of young stellar objects, implying that FeS grains are an important but previously unrecognized component of circumstellar dust. The feature had previously been attributed to FeO. The observed astronomical line strengths are generally consistent with the depletion of sulphur from the gas phase, and with the average Galactic sulphur/silicon abundance ratio. We conclude that the missing sulphur has been found.

Journal Article↗

PubMed2001

Synapse formation between central neurons requires postsynaptic expression of the MEN1 tumor suppressor gene.

Synapse formation is a crucial step in the development of neuronal circuits and requires precise coordination of presynaptic and postsynaptic activities. However, molecular mechanisms that control the formation of functionally mature synaptic contacts, in particular between central neurons, remain poorly understood. To identify genes that are involved in the formation of central synapses, we made use of molluscan neurons that in culture form synaptic contacts between their somata (soma-soma synapses) in the absence of neurite outgrowth. Using single-cell mRNA differential display, we have identified a molluscan homolog of the multiple endocrine neoplasia type 1 (MEN1) tumor suppressor gene encoding the transcription factor menin as a gene that is upregulated during synapse formation. In vitro antisense knock-down of MEN1 mRNA blocks the formation of mature synapses between different types of identified central neurons. Moreover, immunocytochemistry and cell-specific knock-down of MEN1 mRNA show that postsynaptic but not presynaptic expression is required for synapses to form. Together, our data demonstrate that menin is a synaptogenic factor that is critically involved in a general postsynaptic mechanism of synapse formation between central neurons.

Animals↗

PubMed1996

Characterization of new vacuolar segregation mutants, isolated by screening for loss of proteinase B self-activation.

Part of the vacuole in the mother cell of Saccharomyces cerevisiae is segregated early in the cell cycle to establish a new vacuole in the bud. Investigation of the molecular mechanism of vacuolar segregation has previously been limited by the lack of an efficient screen for mutants defective in this process. We developed a new screening procedure based on a cascade for activation of vacuolar proteases. Carboxypeptidase Y (CPY) is activated by proteinase A (PrA). However, upon PrA depletion, CPY continues to be activated, supposedly by self-sustaining proteinase B (PrB) activity that is transferred from one generation to the next generation through vacuolar segregation. In this study fourteen mutants were isolated that failed to sustain CPY activation upon PrA depletion. While these mutants had altered vacuolar protease-activity levels, two mutants showed specific vacuolar segregation defects. They formed large-budded cells that contained no vacuole or extremely small vacuoles in the bud. These mutants represented two complementation groups, named VAC6 and VAC7. The data indicate that constitutive vacuolar segregation mutants are viable, but that they are unable to transfer proteolytic activities from mother vacuole to the bud. Surprisingly, despite the apparent lack of quantitative vacuolar inheritance, all daughter cells of vac6 and vac7 had obtained a vacuole before cell division.

Aspartic Acid Endopeptidases↗

PubMed1980

Formation of N-nitrosamine and N-nitrosamino acids from food products and nitrite under simulated gastric conditions.

Average-sized portions of a variety of food products were reacted with nitrite under realistically simulated gastric conditions. The aqueous incubation medium contained sodium nitrite (10 mg/l) and potassium thiocyanate to mimic the incoming flux of saliva, as well as pepsin, sodium chloride and hydrochloric acid, reflecting the composition of gastric juice. After incubation for 2 hr at 37 degrees C, volatile N-nitrosamines and N-nitrosamino acids were determined in the reaction mixtures. Nitrosodimethylamine (NDMA) was present in the incubation mixtures of smoked mackerel (8.5 micrograms per portion), canned herring (0.66 micrograms per portion) and beer (0.70 micrograms per 'portion'). Smaller amounts per portion, sometimes of other nitrosamines as well, were observed with canned salmon and anchovy, mustard, yoghurt and coffee brew. Negative results were obtained for canned tuna, soya sauce, ketchup, white bread, 'nasi goreng', tea brew and cocoa milk. Nitrosamino acids were detected in the reaction mixtures of smoked mackerel (58 micrograms per portion), soya sauce (24 micrograms per portion) and canned salmon (6.9 micrograms per portion) and in smaller amounts in those of canned herring, anchovy and cocoa milk. In order to reduce the number of analyses to be performed, most products have been studied only after incubation, so that the nitrosamines and nitrosamino acids found may already have been present -- wholly or partly -- in the original products, before incubation. Such is the case for part of the NDMA in the reaction mixture of smoked mackerel and for all the NDMA in beer. The toxicological implications of these findings remain to be established.

Amino Acids↗