3D numerical investigation of natural circulation between the reactor pressure vessel and the cooling pond of a VVER-440 type reactor in incidental conditions during maintenance

During the annual maintenance of the VVER-440 type reactors, the reactor pressure vessel, the cooling pond and the transfer pond form a connected flow domain. The reactor is cooled by the natural circulation, which develops in one or two main loops. The cooling pond has its own cooling loops. CFD calculations have been performed with the code CFX-4.3 to investigate whether it is possible to cool the reactor core in case the main loops are lost and other emergency systems are not available. The results point out that the cooling system of the cooling pond is not capable of cooling the reactor core with the present connection. Therefore, modifications of the cooling system are investigated which would make it suitable for removing the remanent heat from the core.

Experimental and numerical thermal-hydraulics investigation of a molten salt reactor concept core

In the paper measurement results of experimental modelling of a molten salt fast reactor concept will be presented and compared with three-dimensional computational fluid dynamics (CFD) simulation results. Purpose of this article is twofold, on one hand to introduce a geometry modification in order to avoid the disadvantages of the original geometry and discuss new measurement results. On the other hand to present an analysis in order to suggest a method of proper numerical modelling of the problem based on the comparison of calculation results and measurement data for the new, modified geometry. The investigated concept has a homogeneous cylindrical core without any internal structures. Previous measurements on the scaled and segmented plexiglas model of the concept core and simulation results have shown that this core geometry could be optimized for better thermal-hydraulics characteristics. In case of the original geometry strong undesired flow separation could develop, that could negatively affect the characteristics of the core from neutronics point of view as well. An internal flow distributor plate was designed and installed with the purpose of optimizing the flow field in the core by enhancing its uniformity. Particle image velocimetry (PIV) measurement results of the modified experimental model will be presented and compared to numerical simulation results with the purpose of CFD model validation.

Uncertainty analysis and flow measurements in an experimental mock-up of a molten salt reactor concept

In the paper measurement results from the experimental modelling of a molten salt reactor concept will be presented along with detailed uncertainty analysis of the experimental system. Non-intrusive flow measurements are carried out on the scaled and segmented mock-up of a homogeneous, single region molten salt fast reactor concept. Uncertainty assessment of the particle image velocimetry (PIV) measurement system applied with the scaled and segmented model is presented in detail. The analysis covers the error sources of the measurement system (laser, recording camera, etc.) and the specific conditions (de-warping of measurement planes) originating in the geometry of the investigated domain. Effect of sample size in the ensemble averaged PIV measurements is discussed as well. An additional two-loop-operation mode is also presented and the analysis of the measurement results confirm that without enhancement nominal and other operation conditions will lead to strong unfavourable separation in the core flow. It implies that use of internal flow distribution structures will be necessary for the optimisation of the core coolant flow. Preliminary CFD calculations are presented to help the design of a perforated plate located above the inlet region. The purpose of the perforated plate is to reduce recirculation near the cylindrical wall and enhance the uniformity of the core flow distribution.

Experimental investigation of the MSFR molten salt reactor concept

In the paper experimental modelling and investigation of the MSFR concept will be presented. MSFR is a homogeneous, single region liquid fuelled fast reactor concept. In case of molten salt reactors the core neutron flux and fission distribution is determined by the flow field through distribution and transport of fissile material and delayed neutron precursors. Since the MSFR core is a single region homogeneous volume without internal structures, it is a difficult task to ensure stable flow field, which is strongly coupled to the volumetric heat generation. These considerations suggest that experimental modelling would greatly help to understand the flow phenomena in such geometry. A scaled and segmented experimental mock-up of MSFR was designed and built in order to carry out particle image velocimetry measurements. Basic flow behaviour inside the core region can be investigated and the measurement data can also provide resource for the validation of computational fluid dynamics models. Measurement results of steady state conditions will be presented and discussed.

CFD investigation of flow in the MATIS-H test facility

In this paper steps of calculations for a bare rod bundle and so-called swirl type spacer grid are showed and the effects of choice of model details are examined. The modeled pin bundle and spacer grid geometry are related to rectangular western type PWR fuel assemblies. First a CFD model has been developed for a subchannel of the MATIS-H test facility in order to carry out a mesh independence study. Based on the results a model for the half cross-section of the test bundle has been developed and calculations are carried out with different turbulence models. Translational periodicity is applied in axial direction in order to calculate a fully developed flow, which will be used as inlet boundary condition for spacer grid calculations. Results are compared with LDA (Laser Doppler Anemometry) measurements published in the frame of the OECD NEA MATIS-H benchmark. As a last step a model for rod bundle incorporating swirl type spacer grid is developed and calculations are carried out with different turbulence models using the results of the bare rod bundle simulations as inlet boundary conditions.

CFD analysis of temperature deviations in Gd assembly heads

A CFD model for the head part of the VVER-440 fuel assemblies with Gd burnable poison has been developed. Using this model calculations are performed for some recent Gd assemblies of the Paks NPP with the code ANSYS CFX. The temperature distributions in the assembly heads are determined and the in-core thermocouple signals are evaluated. The computed signals are compared to the in-core measured data of Paks NPP. The study shows that the deviations between the in-core thermocouple signals and the cross-sectional average temperatures at the measurement level depend on the burn-ups of the fuel assemblies. These deviations are significant in the cases of low burn-ups and negligible in the cases of higher burn-ups. This behavior is caused by the depletion of Gd from the three fuel rods near the assembly center.

Analysis of coolant flow in central tube of VVER-440 fuel assemblies

A CFD model has been developed to investigate the coolant flow in the central tube of VVER-440 fuel assemblies. The model has been validated with measured data of Kurchatov Institute. With this model a peripheral and an inner fuel assembly of the core have been investigated and the mass flux and heatup ratios of the central tube flow have been determined. Based on this study, the outlet mass flux of the tube is 1.2 times higher than the inlet mass flux of the rod bundle and heat-up in the tube is 0.35 times lower than the heat-up in the rod bundle. The ratios are not sensitive to the operational conditions within the scope of these investigations. The results of these simulations can be used as boundary conditions for the central tube in the assembly head calculations.

Investigation of coolant mixing in head parts of VVER-440 fuel assemblies with burnable poison

Detailed CFD model for the head parts of the VVER-440 fuel assemblies with burnable poison has been developed. The coolant mixing was analyzed in some typical assemblies with this model and the signals of the in-core thermocouples above the selected assemblies were calculated. The investigations pointed out that the mixing is intensive in these assembly heads but the coolant is not perfectly mixed before reaching the thermocouples. Significant differences between the outlet average coolant temperatures and the thermocouple signals were revealed in the case of the fresh fuels. These deviations can cause about 6 % underestimations in the online monitored assembly powers unless a proper correction is introduced. The coolant mixing was also studied by means of numerical tracers and weight factors of selected rod bundle regions for the in-core thermocouple were determined. Using these weight factors and the outlet enthalpies of the assemblies' subchannels, the thermocouple signals can be corrected.

Numerical simulation on a HPLWR fuel assembly flow with one revolution of wrapped wire spacers

Three dimensional computational-fluid-dynamics simulations are performed for the fluid flow within a 40 rod fuel bundle in a square arrangement with a central moderator channel. To ensure spacing between the rods, the design of the bundle uses thin wires wrapped counter-clockwise around each rod. This geometry is presently investigated in the framework of the European High-Performance Light-Water Reactor (HPLWR), which operates at supercritical pressure of 25 MPa. A section with one revolution located in the evaporator region of the HPLWR core is investigated using hydraulic (to ensure fully developed flow inlet boundary conditions and reference for heated cases) and thermal-hydraulic boundary conditions. The geometry of wrapped wires gives rise to additional mixing and a circulating or ‘sweeping’ flow near the outer and inner regions of the fuel element next to the wall of the so called fuel assembly and moderator box. Some interesting flow features associated with the complex three-dimensional flow with significant transverse velocity components are visualized as the first evaluated result of this diversified investigation.

What mouse mutants teach us about extracellular matrix function

For many years the extracellular matrix was viewed as a benign scaffold for arranging cells within connective tissues, but it is now being redefined as a dynamic, mobile, and flexible key player in defining cellular behavior. Gene targeting, transgene expression, and spontaneous mutations of extracellular matrix proteins in mice have greatly accelerated our mechanistic view of the structural and instructive functions of the extracellular matrix in developmental and regenerative processes. This review summarizes the phenotypes of genetic mouse models carrying mutations in extracellular matrix proteins, with specific emphasis on recent advances. The application of reverse genetics has demonstrated the multifunctionality of matrix proteins in a biological context and, in addition, has brought a novel perspective to the understanding of human pathologies.

The role of collagen II and cartilage fibril-associated molecules in skeletal development

OBJECTIVE

The extracellular matrix (ECM) of hyaline cartilage contains an elaborated collagen fibrillar network, which is essential for the mechanical stability and the proper function of the tissue. Cartilage collagen fibrils consist of collagen II, the quantitatively minor collagens IX and XI, and several non-collagenous fibril-associated proteins. To understand the role some of these molecules in skeletal development, we have generated transgenic mouse strains harboring ablated genes for collagens II and IX, and matrilin-1.

DESIGN

Mice lacking collagen II, collagen IX and matrilin-1 have been established earlier in our laboratory using standard techniques. To determine the consequences of the null mutations we used skeletal staining, histochemical and immunohistochemical assays, in situ hybridization and ultrastructural analysis.

RESULTS

Transgenic mice deficient in collagen II (Col2a1-/-) die at birth and display a severely malformed skeleton characterized by abnormal endochondral ossification and impaired intervertebral disc development. Mice lacking collagen IX (Col9a1-/-) are viable and develop an osteoarthritis-like phenotype in knee joints between 9-12 months of age. To test the possibility that the reduction in collagen II content has an influence on the onset of degenerative changes of articular cartilage, we have generated mice, which are heterozygous for the collagen II null mutation and homozygous for the collagen IX null mutation. Col2a1+/- Col9a1-/- mice show no accelerated development of osteoarthritis compared with the collagen IX knockout animals. Finally, mice lacking matrilin-1, a non-collagenous glycoprotein that binds to both collagen fibrils and aggrecan, develop normally without detectable abnormalities in their skeleton.

CONCLUSIONS

Our transgenic mouse strains carrying null mutations in genes encoding cartilage ECM proteins demonstrate that these proteins have different roles during skeletal development. Collagen II is important for cartilage formation, collagen IX for cartilage maintenance and matrilin-1 is redundant.

Distribution of the collagen-binding integrin alpha10beta1 during mouse development

We have previously identified and characterised the collagen type II-binding integrin subunit alpha10, which is a member of the beta1 family and is expressed by chondrocytes. In the present study, we examined the expression of the alpha10 integrin in various mouse tissues. Immunohistochemical analysis of alpha10 on cryosections from 3-day-old mice demonstrated that alpha10beta1 was present in the hyaline cartilage of joints, vertebral column, trachea and bronchi. In addition, alpha10 was found in the ossification groove of Ranvier, in the aortic and atrioventricular valves of the heart and in the fibrous tissue lining skeletal muscle and ligaments. Overall, the distribution was distinct from that of the collagen-binding integrins alpha1beta1 and alpha2beta1. We also found that alpha10beta1was the dominating collagen-binding integrin during cartilage development. Expression of alpha10 appeared at embryonic day 11.5 (E11.5) at the same time as chondrogenesis started as judged by collagen type II expression. At E13.5, alpha10 was present throughout the anlage as well as in the perichondrium and in mesenchyme just outside the perichondrium, where it localised with collagen type I. Four weeks after birth, alpha10 was prominent both at the articular surface and in the growth plate. In conclusion, we found that integrin alpha10beta1 was a major collagen-binding integrin during cartilage development and in mature hyaline cartilage. In addition, we found that alpha10beta1 was present in some fibrous tissues.

A novel gene, tendin, is strongly expressed in tendons and ligaments and shows high homology with chondromodulin-I

Chondromodulin-I (CHM1) was identified recently as an angiogenesis inhibitor in cartilage. It is highly expressed in the avascular zones of cartilage but is absent in the late hypertrophic region, which is invaded by blood vessels during enchondral ossification. Blast searches with the C-terminal part of CHM1 in available databases led to the identification of human and mouse cDNAs encoding a new protein, Tendin, that shares high homology with CHM1. Based on computer predictions, Tendin is a type II transmembrane protein containing a putative proteinase cleavage and two glycosylation sites. Northern assays with mouse RNAs demonstrated strong expression of a 1.5-kb tendin transcript in the diaphragm, skeletal muscle, and the eye and low levels of expression in all other tissues investigated. In 17.5-day-old mouse embryos, in situ hybridization revealed high levels of tendin transcript in tendons and ligaments. Additional signals were detected in brain and spinal cord, liver, lung, bowels, thymus, and eye. Cartilage, where CHM1 is found, revealed low levels of tendin m-RNA. In adult mice, tendin is expressed in neurons of all brain regions and the spinal cord. The tendin gene is localized in the human Xq22 region, to which several human diseases have been mapped.

Functional consequences of integrin gene mutations in mice

Integrins are cell-surface receptors responsible for cell attachment to extracellular matrices and to other cells. The application of mouse genetics has significantly increased our understanding of integrin function in vivo. In this review, we summarize the phenotypes of mice carrying mutant integrin genes and compare them with phenotypes of mice lacking the integrin ligands.

Characterization of the mouse matrilin-4 gene: a 5' antiparallel overlap with the gene encoding the transcription factor RBP-l

We have isolated and characterized the gene encoding mouse matrilin-4 (Matn4), an extracellular matrix protein present in a broad spectrum of tissues. The gene spanned 16 kb, consisted of 12 exons, and localized to chromosome 2. As in all known matrilin genes, the last intron, separating the exons coding for the coiled-coil domain, did not follow the GT-AG rule and belonged to the subgroup of introns having AT-AC at the ends. Matn4 contained two exons in the 5' UTR that could be alternatively spliced. We localized a major and a minor transcription start site to two different untranslated exons: exon 0a and exon 0b. Matn4 divergently overlapped 5' with the gene encoding RBP-L (for recombining binding protein suppressor of hairless-like; Rbpsuhl), a transcription factor with homology to RBP-JK. Exon 1 of Rbpsuhl was located in the second intron of Matn4, whereas exon 0a, the first exon of Matn4, was located in the second intron of Rbpsuhl. The second exons of the respective genes overlapped in an antisense orientation. We mapped the major transcription start of Rbpsuhl to a position approximately 150 nt upstream of the splice acceptor site of the first intron, leading to the synthesis of a truncated variant of RBP-L probably missing the amino-terminal 121 amino acid residues. We analyzed the expression of the different Matn4 and Rbpsuhl transcripts by quantitative RT-PCR; this showed the highest expression for both genes in lung and brain. In situ hybridization of brain sections showed a partially overlapping expression pattern for the two genes.

Sequence and expression analyses of the UL37 and UL38 genes of Aujeszky's disease virus

Previously, we sequenced the HSV-1 Ul39-Ul40 homologue genes of Aujeszky's disease virus (ADV), also designated as pseudorabies virus (Kaliman et al., 1994a, b). Now we report the nucleotide sequence of the adjacent DNA that encodes Ul38, the 5'-region (750 bp) of Ul37, and the promoter regions between these divergently arranged two genes. The ADV Ul38 gene encodes a protein of 368 amino acids. Amino acid sequence comparison of ADV Ul38 with that of other herpesviruses revealed significant structural homology. In a transcription study using RNase protection assay and Northern blot hybridization, we found that the Ul38 gene had one initiation site, but the Ul37 gene was initiated at two transcription sites with two potential initiator AUGs, one of which was dominant. Comparison of ADV Ul37, Ul38 and ribonucleotide reductase gene expression showed that these genes belong to the same temporal class with early kinetics. Data of structural and transcriptional studies suggest that regulation of the expression of these two ADV genes could differ from that of the HSV-1 virus.

Discoidin domain receptor 1 tyrosine kinase has an essential role in mammary gland development

Various types of collagen have been identified as potential ligands for the two mammalian discoidin domain receptor tyrosine kinases, DDR1 and DDR2. Here, we used a recombinant fusion protein between the extracellular domain of DDR1 and alkaline phosphatase to detect specific receptor binding sites during mouse development. Major sites of DDR1-binding activity, indicative of ligand expression, were found in skeletal bones, the skin, and the urogenital tract. Ligand expression in the uterus during implantation and in the mammary gland during pregnancy colocalized with the expression of the DDR1 receptor. The generation of DDR1-null mice by gene targeting yielded homozygous mutant animals that were viable but smaller in size than control littermates. The majority of mutant females were unable to bear offspring due to a lack of proper blastocyst implantation into the uterine wall. When implantation did occur, the mutant females were unable to lactate. Histological analysis showed that the alveolar epithelium failed to secrete milk proteins into the lumen of the mammary gland. The lactational defect appears to be caused by hyperproliferation and abnormal branching of mammary ducts. These results suggest that DDR1 is a key mediator of the stromal-epithelial interaction during ductal morphogenesis in the mammary gland.

Stage-and tissue-specific expression of a Col2a1-Cre fusion gene in transgenic mice

To achieve chondrocyte-specific deletion of floxed genes we generated a transgenic mouse line expressing the Cre recombinase under the control of the mouse type II collagen gene (Col2a1) regulatory regions. Northern and in situ hybridization analyses demonstrated the expression of the transgene (Col2a1-Cre) in cartilaginous tissues. To test the excision efficiency of Cre, the Col2a1-Cre strain was crossed with the ROSA26 reporter strain. LacZ staining of double transgenic mice revealed Cre activity in both chondrogenic and non-chondrogenic tissues. During early embryonic development (E9.5-11.5), LacZ expression was detected in tissues where the endogenous Col2a1 transcript is expressed such as the otic capsule, notochord, developing brain, sclerotome and mesenchymal condensations of future cartilage. At later stages, Cre activity was observed in all cartilaginous tissues with virtually 100% of chondrocytes being LacZ positive. These data suggest that the Col2a1-Cre mouse strain described here can be useful to achieve Cre-mediated recombination in Col2a1 expressing cells, especially in chondrocytes.

High-throughput functional annotation of novel gene products using document clustering

Gene products differentially expressed in healthy vs. diseased tissues may be considered drug targets since the change in their expression level can be related to the cause and progression of the disease studied. A significant portion of the proteins produced by these genes will be unknown and consequently their function must be characterised. The experimental elucidation of biochemical function must be supported by computational tools which can help predicting the possible function of a given protein from its amino acid sequence. We have designed a high-throughput system which automatically analyses amino acid sequences deduced from differentially represented cDNA clones. The system attempts to assign a biological function to protein sequences by carrying out searches in sequence databanks and by locating functionally relevant motifs in the query sequences. The results delivered by the various prediction methods consist of the annotations of matching sequences and/or motifs, which are free-format texts written by humans and therefore may describe the same concept with synonymous words. It is desirable to present the results in such a way that the annotations describing the same biological function are grouped together. To this end we devised an algorithm that enables the hierarchical clustering of free-format documents based on their contents. The system is capable of detecting and flagging conflicting annotations, and will speed up the interpretation of the function prediction results.

Mammalian skeletogenesis and extracellular matrix: what can we learn from knockout mice?

Formation of the vertebrate skeleton and the proper functions of bony and cartilaginous elements are determined by extracellular, cell surface and intracellular molecules. Genetic and biochemical analyses of human heritable skeletal disorders as well as the generation of knockout mice provide useful tools to identify the key players of mammalian skeletogenesis. This review summarises our recent work with transgenic animals carrying ablated genes for cartilage extracellular matrix proteins. Some of these mice exhibit a lethal phenotype associated with severe skeletal defects (type II collagen-null, perlecan-null), whereas others show mild (type IX collagen-null) or no skeletal abnormalities (matrilin-1-null, fibromodulin-null, tenascin-C-null). The appropriate human genetic disorders are discussed and contrasted with the knockout mice phenotypes.

Structure and mapping of the mouse matrilin-3 gene (Matn3), a member of a gene family containing a U12-type AT-AC intron

The gene for murine matrilin-3, an extracellular matrix protein present in cartilage, was isolated and further characterized. The gene spans 23.4 kb and comprises 8 exons; with one exception, this reflects the modular structure of the protein. The major and a minor transcription start site were determined by RNase protection assays to positions approximately 72 nt and 87 nt upstream of the ATG codon, respectively. The promoter contains a TATA-like box 32 bp upstream of the main transcription start as well as several potential binding sites for eukaryotic transcription factors. As in all known matrilin genes, the last intron, separating the exons coding for the coiled-coil domain, does not follow the GT-AG rule and belongs to the subgroup of introns having AT-AC at the ends that are spliced by the U12-type spliceosome. The mouse matrilin-3 gene does not contain hidden exon sequences coding for the second vWFA-like domain present in all other matrilins. The intron that could possibly contain such sequences instead shows 75% repetitive sequences, indicating an evolutionary process that has led to the loss of sequences coding for vWFA2. Single-strand conformation polymorphism analysis was used to map the Matn3 gene to the proximal end of Chr 12, linked to the genes Synd1, Apob, Dntb, and Kif3c.

Normal skeletal development of mice lacking matrilin 1: redundant function of matrilins in cartilage?

Matrilin 1, or cartilage matrix protein, is a member of a novel family of extracellular matrix proteins. To date, four members of the family have been identified, but their biological role is unknown. Matrilin 1 and matrilin 3 are expressed in cartilage, while matrilin 2 and matrilin 4 are present in many tissues. Here we describe the generation and analysis of mice carrying a null mutation in the Crtm gene encoding matrilin 1. Anatomical and histological studies demonstrated normal development of homozygous mutant mice. Northern blot and biochemical analyses show no compensatory up-regulation of matrilin 2 or 3 in the cartilage of knockout mice. Although matrilin 1 interacts with the collagen II and aggrecan networks of cartilage, suggesting that it may play a role in cartilage tissue organization, studies of collagen extractability indicated that collagen fibril maturation and covalent cross-linking were unaffected by the absence of matrilin 1. Ultrastructural analysis did not reveal any abnormalities of matrix organization. These data suggest that matrilin 1 is not critically required for cartilage structure and function and that matrilin 1 and matrilin 3 may have functionally redundant roles.

Fibromodulin-null mice have abnormal collagen fibrils, tissue organization, and altered lumican deposition in tendon

Fibromodulin is a member of a family of connective tissue glycoproteins/proteoglycans containing leucine-rich repeat motifs. Several members of this gene family bind to fibrillar collagens and are believed to function in the assembly of the collagen network in connective tissues. Here we show that mice lacking a functional fibromodulin gene exhibit an altered morphological phenotype in tail tendon with fewer and abnormal collagen fiber bundles. In fibromodulin-null animals virtually all collagen fiber bundles are disorganized and have an abnormal morphology. Also 10-20% of the bundles in heterozygous mice are similar to the abnormal bundles in fibromodulin-null tail tendon. Ultrastructural analysis of Achilles tendon from fibromodulin-null mice show collagen fibrils with irregular and rough outlines in cross-section. Morphometric analysis show that fibromodulin-null mice have on the average thinner fibrils than wild type animals as a result of a larger preponderance of very thin fibrils in an overall similar range of fibril diameters. Protein and RNA analyses show an approximately 4-fold increase in the content of lumican in fibromodulin-null as compared with wild type tail tendon, despite a decrease in lumican mRNA. These results demonstrate a role for fibromodulin in collagen fibrillogenesis and suggest that the orchestrated action of several leucine-rich repeat glycoproteins/proteoglycans influence the architecture of collagen matrices.

The vasodilator-stimulated phosphoprotein (VASP) is involved in cGMP- and cAMP-mediated inhibition of agonist-induced platelet aggregation, but is dispensable for smooth muscle function

The vasodilator-stimulated phosphoprotein (VASP) is associated with actin filaments and focal adhesions, which form the interface between the cytoskeleton and the extracellular matrix. VASP is phosphorylated by both the cAMP- and cGMP-dependent protein kinases in a variety of cells, including platelets and smooth muscle cells. Since both the cAMP and cGMP signalling cascades relax smooth muscle and inhibit platelet activation, it was speculated that VASP mediates these effects by modulating actin filament dynamics and integrin activation. To study the physiological relevance of VASP in these processes, we inactivated the VASP gene in mice. Adult VASP-deficient mice had normal agonist-induced contraction, and normal cAMP- and cGMP-dependent relaxation of intestinal and vascular smooth muscle. In contrast, cAMP- and cGMP-mediated inhibition of platelet aggregation was significantly reduced in the absence of VASP. Other cAMP- and cGMP-dependent effects in platelets, such as inhibition of agonist-induced increases in cytosolic calcium concentrations and granule secretion, were not dependent on the presence of VASP. Our data show that two different cyclic, nucleotide-dependent mechanisms are operating during platelet activation: a VASP-independent mechanism for inhibition of calcium mobilization and granule release and a VASP-dependent mechanism for inhibition of platelet aggregation which may involve regulation of integrin function.

Collagen II is essential for the removal of the notochord and the formation of intervertebral discs

Collagen II is a fibril-forming collagen that is mainly expressed in cartilage. Collagen II-deficient mice produce structurally abnormal cartilage that lacks growth plates in long bones, and as a result these mice develop a skeleton without endochondral bone formation. Here, we report that Col2a1-null mice are unable to dismantle the notochord. This defect is associated with the inability to develop intervertebral discs (IVDs). During normal embryogenesis, the nucleus pulposus of future IVDs forms from regional expansion of the notochord, which is simultaneously dismantled in the region of the developing vertebral bodies. However, in Col2a1-null mice, the notochord is not removed in the vertebral bodies and persists as a rod-like structure until birth. It has been suggested that this regional notochordal degeneration results from changes in cell death and proliferation. Our experiments with wild-type mice showed that differential proliferation and apoptosis play no role in notochordal reorganization. An alternative hypothesis is that the cartilage matrix exerts mechanical forces that induce notochord removal. Several of our findings support this hypothesis. Immunohistological analyses, in situ hybridization, and biochemical analyses demonstrate that collagens I and III are ectopically expressed in Col2a1-null cartilage. Assembly of the abnormal collagens into a mature insoluble matrix is retarded and collagen fibrils are sparse, disorganized, and irregular. We propose that this disorganized abnormal cartilage collagen matrix is structurally weakened and is unable to constrain proteoglycan-induced osmotic swelling pressure. The accumulation of fluid leads to tissue enlargement and a reduction in the internal swelling pressure. These changes may be responsible for the abnormal notochord removal in Col2a1-null mice. Our studies also show that chondrocytes do not need a collagen II environment to express cartilage-specific matrix components and to hypertrophy. Furthermore, biochemical analysis of collagen XI in mutant cartilage showed that alpha1(XI) and alpha2 (XI) chains form unstable collagen XI molecules, demonstrating that the alpha3(XI) chain, which is an alternative, posttranslationally modified form of the Col2a1 gene, is essential for assembly and stability of triple helical collagen XI.

Endochondral ossification is dependent on the mechanical properties of cartilage tissue and on intracellular signals in chondrocytes

Skeletal elements are formed either by replacing a performed cartilagenous matrix template in a process called endochondral ossification or directly from mesenchyme by a process known as membranous ossification. Longitudinal growth of bones is achieved by growth plates where calcified cartilage is converted into bone. To investigate the role of extracellular matrix as well as intracellular signaling pathways in the formation and growth of bone, the genes coding for type II collagen and cyclic guanosine 3',5'-monophosphate (cGMP)-dependent protein kinase (cGK) II, were disrupted. It is demonstrated that loss of Col2a1 or cGKII led to abnormal endochondral ossification and skeletal development. In cGKII -/- mice, bones derived by membranous ossification developed normally while bones derived by endochondral ossification were shortened. This growth defect was not associated with a general metabolic disturbance. In Col2a1 knockout mice, endochondral ossification was completely absent, whereas membraneous ossification was not affected. Despite the defects in bone formation, invasion of blood vessels into bone cavities and formation of bone marrow occurred in Col2a1-null mice. Taken together, the phenotypes of these two knockout mice show that chondrocytes need a well-functioning extracellular matrix scaffold and a normal cGMP-signaling system for endochondral ossification to form a normal skeleton.

Defective smooth muscle regulation in cGMP kinase I-deficient mice

Regulation of smooth muscle contractility is essential for many important biological processes such as tissue perfusion, cardiovascular haemostasis and gastrointestinal motility. While an increase in calcium initiates smooth muscle contraction, relaxation can be induced by cGMP or cAMP. cGMP-dependent protein kinase I (cGKI) has been suggested as a major mediator of the relaxant effects of both nucleotides. To study the biological role of cGKI and its postulated cross-activation by cAMP, we inactivated the gene coding for cGKI in mice. Loss of cGKI abolishes nitric oxide (NO)/cGMP-dependent relaxation of smooth muscle, resulting in severe vascular and intestinal dysfunctions. However, cGKI-deficient smooth muscle responded normally to cAMP, indicating that cAMP and cGMP signal via independent pathways, with cGKI being the specific mediator of the NO/cGMP effects in murine smooth muscle.

Protein modeling by multiple sequence threading and distance geometry

The application of homology modeling is often limited by the lack of known structures with sufficiently high sequence similarity to the target protein. The recent development of threading methods now enable the identification of likely folding patterns in a number of cases where the structural relatedness between target and template(s) is not detectable at the sequence level. We devised a hybrid method in which fold recognition was performed using the Multiple Sequence Threading (MST) method. The structural equivalences deduced from the threading output were used to guide the distance geometry program DRAGON in the construction of low-resolution C alpha/C beta models. The initial structures were converted to full-atom representation and refined using the general-purpose molecular modeling package QUANTA. The performance of the approach is illustrated on the CASP2 target T0004 (polyribonucleotide nucleotidyl-transferase S1 motif (PNS1) from Escherichia coli, PDB code: 1SRO) for which no obvious homologues with known structure were available. The correct fold of PNS1 was successfully identified, and the model was found to be more similar to the experimental PNS1 structure than the scaffold (C alpha RMSD of 6.2 A compared with 6.4 A). Our results indicate that a sensitive fold recognition algorithm coupled with a distance geometry program capable of rapidly generating initial structures can successfully complement high-resolution homology modeling methods in cases where sequential similarity is low.

Mouse models for extracellular matrix diseases

Mutations of a number of genes encoding for extracellular matrix (ECM) proteins in mice have provided new insights regarding their role during development and disease. Many mouse strains have helped to verify the link between mutation and disease in humans, and others have produced unexpected phenotypes and identified new functions for ECM proteins. Finally, some null mutations in ECM genes provide no phenotypic alterations in mice, confronting the scientific community with a new challenge to search for their functions. This review lists all mouse strains with spontaneous and experimentally induced mutations in ECM genes. The phenotypes of these mice are discussed in comparison with the human diseases.

Sequence, structure and chromosomal localization of Crtm gene encoding mouse cartilage matrix protein and its exclusion as a candidate for murine achondroplasia

The mouse cartilage matrix protein gene (Crtm) was isolated from a cosmid library using a mouse Crtm cDNA fragment as probe. Crtm spans 12.2 kb from the start of translation to the polyadenylation signal sequence and comprises eight exons. Sequencing of the 1.9 kb 5' flanking region revealed a TATA-like box 72 bp upstream from the initiator Met codon as well as several cis-acting motifs known to bind eukaryotic transcription factors. Analysis of the exon-intron junctions demonstrated that the last intron does not follow the gt/ag rule but belongs to the minor class of pre-mRNA introns that contain "at" and "ac" at their 5'and 3' ends, respectively. Single-strand conformation polymorphism analysis was used to map Crtm to the distal part of chromosome 4 between the microsatellite markers D4Mit16 and D4Mit339. Achodroplasia (cn), a recessive skeletal disorder in mice, has already been mapped to this region. Immunostaining for CMP and sequence of Crtm in cn/cn mice failed to reveal any disease-specific mutations, suggesting that mutations in Crtm do not cause achondroplasia.

Regulation of cell-type specific expression of lacZ by the 5'-flanking region of mouse GAD67 gene in the central nervous system of transgenic mice

The transcriptional regulation of the murine gene encoding the 67-kDa form of glutamic acid decarboxylase (GAD67) was studied by beta-galactosidase histochemistry in transgenic mice carrying fusion genes between progressively longer portions of the 5'-upstream regulatory region of GAD67 and E. coli lacZ. No expression was detected in brains of mice carrying 1.3 kb of upstream sequences including a housekeeping and two conventional promoters, and two negative regulatory elements with homology to known silencers. In mice carrying the same portion of the promoter region plus the first intron, lacZ expression in the adult central nervous system was found in few, exclusively neuronal sites. The number of correctly stained GABAergic centres increased dramatically with increasing the length of the 5'-upstream region included in the construct which suggests that multiple putative spatial enhancers are located in this region. Their action is influenced by epigenetic mechanisms that may be due to site-of-integration and transgene copy-number effects. Additional cis-acting elements are needed to obtain fully correct expression in all GABAergic neurons of the adult central nervous system.

Absence of the alpha1(IX) chain leads to a functional knock-out of the entire collagen IX protein in mice

Cartilage fibrils contain collagen II as well as smaller amounts of collagens IX and XI. The three collagens are thought to co-assemble into cartilage-specific arrays. The precise role of collagen IX in cartilage has been addressed previously by generating mice harboring an inactivated Col9a1 gene encoding the alpha1(IX) chain, i.e. one of the three constituent chains of collagen IX (Fässler, R., Schnegelsberg, P. N. J., Dausman, J., Shinya, T., Muragaki, Y., McCarthy, M. T., Olsen, B. R., and Jaenisch, R. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 5070-5074). The animals did not produce alpha1(IX) mRNA or polypeptides and were born with no conspicuous skeletal abnormality but post-natally developed early onset osteoarthritis. Here we show that the deficiency in alpha1(IX) chains leads to a functional knock-out of all polypeptides of collagen IX, whereas the Col9a2 and Col9a3 genes were normally transcribed. Therefore, synthesis of alpha1(IX) polypeptides is essential for the assembly of heterotrimeric collagen IX molecules. Surprisingly, cartilage fibrils of all shapes and banding patterns found in normal newborn, adolescent, or adult mice were formed in transgenic animals, although they lacked collagen IX. Therefore, collagen IX is not essential, and may be functionally redundant, in fibrillogenesis in cartilage in vivo. The protein is required, however, for long term tissue stability, presumably by mediating interactions between fibrillar and extrafibrillar macromolecules.

Distance geometry based comparative modelling

A distance geometry based protein modelling algorithm is presented which relies on the projection of simple model chain coordinates into Euclidean spaces with gradually decreasing dimensionality. Fast embedding was achieved by performing separate distance matrix projections on subsets of the model points. Structural equivalences between the unknown target and related proteins with known structures were deduced either from a mixed sequence/structure multiple alignment or from the output of various fold recognition (threading) approaches. These equivalences were mapped onto the model as structure-specific conserved C alpha atom distances and secondary structure assignments. Additional nonspecific distance restraints derived from general stereochemical properties of folded protein chains were used to guide the modelling process. The method quickly constructed a large number of low-resolution models which could then serve as starting conformations for full-atom refinement. Structure predictions for some targets in the 'Asilomar Challenge' (CASP2) are presented to illustrate potential applications of the approach.

Intestinal secretory defects and dwarfism in mice lacking cGMP-dependent protein kinase II

Cyclic guanosine 3',5'-monophosphate (cGMP)-dependent protein kinases (cGKs) mediate cellular signaling induced by nitric oxide and cGMP. Mice deficient in the type II cGK were resistant to Escherichia coli STa, an enterotoxin that stimulates cGMP accumulation and intestinal fluid secretion. The cGKII-deficient mice also developed dwarfism that was caused by a severe defect in endochondral ossification at the growth plates. These results indicate that cGKII plays a central role in diverse physiological processes.

Cloning, sequencing and expression analysis of mouse cartilage matrix protein cDNA

A cDNA encoding the mouse cartilage matrix protein (CMP) was cloned following the reverse-transcription polymerase chain reaction and rapid amplification of cDNA ends procedures using mRNA isolated from trachea. The open reading frame encodes a product of 500 amino acids. Large parts of the protein have been completely conserved when compared to chicken and human sequences, including all 12 cysteine residues of the mature CMP. In situ hybridization reveals an even distribution of the CMP mRNA in the developing skeleton, which is followed by a zonal distribution paralleling hypertrophy and calcification. From early cartilage differentiation and onwards, CMP transcript is absent in the forming articular surfaces and intervertebral discs. Extraskeletal expression of CMP mRNA was detected in the adult eye.

Homology modelling by distance geometry

BACKGROUND

Unknown protein structures can be predicted from known structures (the scaffolds) with sequences sufficiently homologous to that of the target, based on the observation that similar sequences usually adopt the same fold. When structural equivalences between residues in the scaffold and target proteins are expressed in terms of conserved interatomic distances, the resulting 'distance geometry' representation provides an elegant mechanism for simultaneous restraint satisfaction and bias-free conformation space exploration.

RESULTS

We present a homology modelling algorithm based on distance geometry that relies on the gradual projection of simple model chain coordinates into Euclidean spaces with decreasing dimensionality. The similarity between the unknown target structure and the scaffold proteins with known structures was described by mapping secondary structure assignments and specific distance restraints between C alpha atoms onto the model through a multiple alignment. This information was complemented by additional restraints derived from stereochemical considerations and other general aspects of protein structure such as hydrophobic core formation or the absence of tangled mainchains.

CONCLUSIONS

The method was capable of quickly locating the correct fold even from an alignment with modest average conservation indicating that it could serve as a fast tool for obtaining correct low-resolution starting conformations for detailed refinement.

Global fold determination from a small number of distance restraints

We have designed a distance geometry-based method for obtaining the tertiary fold of a protein from a limited number of structure-specific distance restraints and the secondary structure assignment. Interresidue distances were predicted from patterns of conserved hydrophobic amino acids deduced from multiple alignments. A simple model chain representing the protein was then folded by projecting its distance matrix into Euclidean spaces with gradually decreasing dimensionality until a final three-dimensional embedding was achieved. Tangled conformations produced by the projection steps were eliminated using a novel filtering algorithm. Information on various aspects of protein structure such as accessibility and chirality was incorporated into the conformation refinement, increasing the robustness of the algorithm. The method successfully identified the correct folds of three small proteins from a small number of restraints, indicating that it could serve as a useful computational tool in protein structure determination from NMR data.

Secondary structure formation in model polypeptide chains

Model polypeptide chains were folded into 3-D compact conformations using distance geometry techniques. Interresidue distances were predicted from the hydrophobicity of the monomers and were refined by repeated projections into lower-dimensional spaces. Main-chain hydrogen bond networks were constructed and propagated through the structure by adjusting local conformations to comply with ideal distance constraints around hydrogen bonds. The resulting folds were compact globules with distinct hydrophobic cores and contained secondary structure elements like real protein molecules. Apart from similarity in appearance, several properties of the model chains were also very close to those of native folded polypeptides. The method in its present form can serve as a starting point for the development of a novel structure prediction algorithm.

Calpeptin, a calpain inhibitor, promotes neurite elongation in differentiating PC12 cells

Calpain activity of nerve growth factor (NGF)-induced rat pheochromocytoma (PC12) cells shows a transient diminution in the early phase of differentiation. Calpain activity can be further decreased by a cell-permeable calpain inhibitor, calpeptin, which enhances the effect of NGF by stimulating neurite elongation. The number of neurites sprouted by one cell is not increased by calpeptin. A possible role of calpain inhibition during PC12 cells' early differentiation is discussed.

The zonal expression of chicken cartilage matrix protein gene in the developing skeleton of transgenic mice

Cartilage matrix protein (CMP) is a major noncollagenous glycoprotein of hyaline cartilage with a molecular mass of about 148 kDa. It has been proposed to be involved in matrix organization by its interactions with proteoglycan and type II collagen. The 54-kDa monomers form homotrimers stabilized by disulfide bonds. The gene for chicken cartilage matrix protein was isolated, and its regulation has been studied recently in transient expression experiments. To learn more about the spatial and temporal expression of the gene during ontogenic development, we created transgenic mice via microinjection of a 21.8-kb genomic fragment, encoding the chicken cartilage matrix protein. None of the founder animals exhibited any abnormal phenotype. The developmental stage-specific expression of the transgene was examined by immunostaining with a chicken CMP specific antiserum at different stages of embryonic development in cartilage from different sources: lower and upper limb, vertebrae, ribs and nasal septum. The level of transgene expression showed marked differences in various zones of cartilage. Briefly, high levels were found in the zones of proliferating chondrocytes, while little if any transgene product was detected in the very early and hypertrophic stage of chondrogenesis. The expression pattern of the transgene correlated with the endogenous mouse CMP and did not cause any morphological changes detectable by microscopic analysis of cartilage. These data indicate that the injected CMP gene with its flanking sequences contained all the information necessary for cell type-specific expression in transgenic mice.

Connection topology of proteins

One-dimensional amino acid sequences and three-dimensional folded polypeptide chains were modelled as non-directed graphs in which nodes corresponded to amino acids and arcs represented connections between them. In the case of folded chains, non-backbone connections were assigned to amino acid pairs if their distance was lower than a threshold. Two topological indices, the connectedness number and the effective chain length were devised to compare folding topologies. Loops created by non-backbone connections in the structure graphs were studied by simple graphical representations, revealing the hierarchy in native protein structures.

MAP2: a sensitive cross-linker and adjustable spacer in dendritic architecture

Microtubule-associated protein 2 (MAP2), a long, filamentous molecule thought to cross-link dendritic cytoskeleton, is rich in PEST sequences, putative signals for rapid proteolytic degradation. It is suggested that MAP2 is indeed highly susceptible to protease, e.g. calpain, attack, which is needed for a plastic change, but actual breakdown depends on the regulation of protease(s). Phosphorylation is expected to make the molecule longer and rigid, similarly to what was observed with the related tau protein. Such a structural transition may provide a mechanism for the putative role of MAP2 in dendritic branching.