Identification of a BIBAC clone that co-segregates with the petunia restorer of fertility (Rf) gene.

Molecular markers closely linked to the Restorer of fertility (Rf) locus in petunia were sought by conducting a bulk segregant analysis. The co-segregation of markers and Rf was tested on a large BC1 population produced from two different parental lines carrying Rf. The recombination frequency between OP704 and ECCA/MACT, the two most distal markers utilized in the fine-scale mapping. was significantly different in populations derived from parents that carry different nuclear backgrounds. The fine mapping identified an amplified fragment length polymorphism (AFLP) marker that co-segregates with Rf. A petunia BIBAC library (four genome equivalents), with an average insert size of 70 kb, was constructed and screened with the linked marker. A contiguous map was constructed from three different BIBAC clones that hybridized to the marker. As a result, we have identified a 37.5-kb BIBAC clone that co-segregates with Rf.

Contribution of D-Dimer determination in the exclusion of deep venous thrombosis in spinal cord injury patients.

UNLABELLED: Deep vein thrombosis (DVT) is a common complication of paraplegia despite prophylactic anticoagulant therapy. The diagnosis relies primarily on ultrasonography or phlebography; these investigations are difficult, expensive and can be time-consuming in paraplegic patients. STUDY DESIGN: To evaluate the usefulness of coagulation activation markers in excluding a diagnosis of DVT, D-Dimers, thrombin-antithrombin complexes, prothrombin fragments (F1+2) and activated factor VIIa. OBJECTIVES: To improve the diagnosis of deep venous thrombosis in paraplegic patients. SETTING: This collaborative work was done at Raymond Poincaré Hospital, Garches, France. METHODS: To evaluate the usefulness of coagulation activation markers in excluding a diagnosis of DVT, D-Dimers (D-Di), thrombin-antithrombin (TAT) complexes, prothrombin fragments (F1+2) and activated factor VIIa (FVIIa), were determined in a prospective study of 67 consecutive patients with paraplegia or tetraplegia. Doppler ultrasonography and/or phlebography of the lower limbs and D-Di, TAT, F1+2 level determination were systematically done in each patient at admission to our rehabilitation unit. RESULTS: Despite prophylactic low molecular weight heparin therapy, six of the 67 patients developed DVT diagnosed by radiologic explorations. D-Di levels measured by a reference ELISA (Asserachrom D-Di, Diagnostica Stago) or a new rapid automated turbidimetric test (STA-Liatest D-Di) were greater than 500 ng/ml in all DVT patients and in 40 non-DVT patients, of whom most had urinary tract infections, osteomas, or pressure sores. D-Di values were normal in only 21/67 patients (31%). The negative predictive value of D-Di in our study was 100% since all DVT patients had D-Di values greater than 500 ng/ml. TAT and F1+2 levels were not correlated with D-Di levels but also had a negative predictive value of 100%. Comparison of D-Di levels obtained using the two tests showed that results of the reference ELISA were closely correlated to those of the new rapid automated turbidimetric. TAT, F1+2, and factor VIIa are not useful for measuring hypercoagulability in paraplegic or tetraplegic patients since no rapid tests for determining these parameters are available. CONCLUSION: D-Di levels determined using an ELISA or a new rapid automated turbidimetric test have a good negative predictive value for DVT in paraplegic or tetraplegic patients and may reduce the need for Doppler ultrasonography and/or phlebography by 31%.

Mitochondrial gene organization and expression in petunia male fertile and sterile plants.

In cytoplasmic male-sterile Petunia lines, NADH dehydrogenase subunit 3 (nad3) and ribosomal protein S12 (rps12) are cotranscribed with the chimeric gene pcf and located in the region of the mitochondrial genome associated with cytoplasmic male sterility (CMS) in Petunia. In fertile Petunia line 3704, the genes for nad3 and rps12 are cotranscribed with an unidentified open reading frame (orf143). In the homologous region of fertile line 3699, there is an ORF that lacks a genomic DNA-encoded stop codon; instead an RNA editing event creates a stop codon, resulting in an ORF of 161 codons. While expressed sequences homologous to this open reading frame can be detected in sterile lines, a contiguous orf143/orf161 gene does not exist in the CMS-encoding mitochondrial genome. Transcription at the CMS-associated pcf locus and the fertile orf143/nad3/rps12 locus is complex, with multiple 5' and 3' termini. The presence of the nuclear fertility restorer gene affects the abundance of a transcript class with 5' termini--121 nucleotides before the pcf start codon, and greatly reduces the abundance of a pcf gene product with apparent molecular mass of 25 kDa which is present in both vegetative and reproductive tissues of CMS plants. In addition to the 25 kDa protein product, small amounts of precursor and processed pcf products with higher molecular mass have been detected; their possible role in the CMS phenotype is unknown. Current hypotheses for the mechanism of action of CMS-associated and fertility restorer genes are discussed.

Analysis of major repetitive DNA sequences in the dog (Canis familiaris) genome.

A systematic screening and analysis of repeated DNA sequences from a dog genomic library composed of small DNA inserts enabled us to characterize abundant canine repetitive DNA families. Four main families were identified: i) a group of highly repeated tRNA-derived short interspersed repetitive DNA elements (tRNA-SINEs); ii) another type of SINE-like element that was mainly found inserted into long interspersed repetitive elements (LINEs); iii) LINEs of the L1 type; and iv) satellite or satellite-like DNA. Surprisingly, no SINEs derived from 7SL RNA were found in the dog genome. These data should help in the analysis of canine DNA sequences and in the design of canine genome mapping reagents.

A physical map of 30,000 human genes.

A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.

Tissue factor-dependent vascular endothelial growth factor production by human fibroblasts in response to activated factor VII.

The transmembrane protein tissue factor (TF) is the cell surface receptor for coagulation factor VII (FVII) and activated factor VII (FVIIa). Recently, TF has been identified as a regulator of angiogenesis, tumor growth, and metastasis. This study was designed to link the binding of FVII(a) to its receptor, TF, with the subsequent triggering of angiogenesis through vascular endothelial growth factor (VEGF) production by human lung fibroblasts. We report that incubation of fibroblasts, which express constitutive surface TF, with FVII(a) induces VEGF synthesis. FVII(a)-induced VEGF secretion, assessed by a specific enzyme-linked immunosorbent assay, was time- and concentration-dependent. VEGF secretion was maximal after 24 hours of incubation of the cells with 100 nmol/L FVII(a) and represented a threefold induction of the basal VEGF level. Reverse transcriptase-polymerase chain reaction analysis of VEGF detected three mRNA species of 180, 312, and 384 bp corresponding, respectively, to VEGF121, VEGF165, and VEGF189. A 2.5- to 3.5-fold increase was observed for the 180- and 312-bp transcripts at 12 and 24 hours, respectively. FVII(a)-dependent VEGF production was inhibited by a pool of antibodies against TF, pointing to the involvement of this receptor. On specific active-site inhibition with dansyl-glutamyl-glycinyl-arginyl chloromethyl ketone, FVIIa lost 70% of its capacity to elicit VEGF production. Consistent with this, the native form (zymogen) of FVII only had a 1.8-fold stimulating effect. Protein tyrosine kinase and protein kinase C are involved in signal transduction leading to VEGF production, as shown by the inhibitory effects of genistein and GF 109203X. The results of this study indicate that TF is essential for VIIa-induced VEGF production by human fibroblasts and that its role is mainly linked to the proteolytic activity of the TF-VIIa complex.

A gene map of the human genome.

The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.

A grammar describing 'biological binding operators' to model gene regulation.

The study of the mechanisms involved in the regulation of protein synthesis has become sufficiently advanced that it is appropriate to think about a knowledge formalism. The objective of the syntactic grammar which we present in this article is a representation of these phenomena which take place in the context of the cell. The proposed model considers two types of objects: transcriptional units on DNA and regulatory or structural proteins which are synthesised, and which are, in the case of regulatory proteins, themselves destined to activate or repress other transcriptional units in a later phase. A transcriptional unit is described by the list of its active sites (operator, promoter, binding sites for transcription factors). A regulatory protein is described by the list of its active sites (binding domain, activation domain, binding domain for ligand). The DNA sites and the protein domains are the terminal symbols of the proposed grammar. The interaction of these proteins with the DNA, and in certain cases preliminary interactions between proteins, leads to one of two antagonistic actions: expression or repression of the transcriptional unit. These protein-protein and protein-DNA interactions are grouped into syntactic categories (induction, inhibition, initiation complex, repressor complex, activation complex) which are called biological binding operators. The expression/repression action are described by grammar rules which provide the chain of execution by biological binding operators for the four activable/repressible regulatory systems modulated by positive/negative co-factors. The object of this modelization is the observation of a cell in a given state for a given process which involves a cascade of genes. This grammar is implemented by a simulation program which allows the user to vary the initial state of the cell and also to change parameters related to time and quantity. This syntactic and generative grammar is independent of the specificity of each transcriptional unit. The simulation uses examples which may combine several regulatory systems: the lac operon, regulation of metallothionein, galactose catabolism in yeast, the tryptophan operon, and phage lysogenic/lytic cascades.

The Genexpress Index: a resource for gene discovery and the genic map of the human genome.

Detailed analysis of a set of 18,698 sequences derived from both ends of 10,979 human skeletal muscle and brain cDNA clones defined 6676 functional families, characterized by their sequence signatures over 5750 distinct human gene transcripts. About half of these genes have been assigned to specific chromosomes utilizing 2733 eSTS markers, the polymerase chain reaction, and DNA from human-rodent somatic cell hybrids. Sequence and clone clustering and a functional classification together with comprehensive data base searches and annotations made it possible to develop extensive sequence and map cross-indexes, define electronic expression profiles, identify a new set of overlapping genes, and provide numerous new candidate genes for human pathologies.

[Association of dysfibrinogenemia and thrombosis. Apropos of a family (Fibrinogen Melun) and review of the literature]. / Association dysfibrinogénémie et thrombose. A propos d'une famille (Fibrinogène Melun) et revue de la littérature.

We report a family with history of deep and superficial venous thrombosis. A large number of siblings had numerous episodes of deep venous thrombosis and less frequently arterial thrombosis. The most frequent site was lower limb. Dysfibrinogenaemia seems to play an essential role in predisposition to thromboembolism in this family, other known aetiologies having been excluded. Genetic studies of fibrinogen gene show a point mutation in the gamma chain (364 Asp-Val), the site close to gamma 363 one of the sites involved in fibrin monomers polymerisation, although fibrinogen polymerisation is normal. Review of the 250 families with dysfibrinogenaemia published up to now shows that the prevalence of dysfibrinogenaemia in patients with a history of thromboembolism is about 0.7%, and that thrombosis is observed in about 10% of cases of dysfibrinogenaemia. Abortion risk seems to be increased in women with dysfibrinogenaemia. In contrast thromboembolism risk does not seem to be higher during pregnancy, but may be increased after delivery. The main mechanisms which have been proposed to explain thromboembolism observed in dysfibrinogenaemia are: resistance of the clot to thrombolysis; defective thrombin binding; enhanced platelet aggregation; increased blood viscosity, alteration of clot architecture. This family study together with the previously reported cases supports the hypothesis that there is a link between thrombosis and dysfibrinogenaemia in a small number of patients.

[Hemorrhagic complications of anti-vitamin K treatments]. / Complications hémorragiques des traitements antivitamine K.

Among iatrogenic complications of oral anticoagulation, hemorrhagic complications are the most frequent and potentially lethal. The major hemorrhagic risk is the intensity of anticoagulation. A decrease of this risk is obtained with tapering of INR. Age, sex, anticoagulant therapy, and other personal risk factors as duration of anticoagulation, are factors not admitted by all the authors. Our experience at Hôtel-Dieu University Hospital and the literature data provide evidence that patient follow-up in a specialized center should decrease the incidence of hemorrhagic complications.