WorldWideScience

Sample records for fibronectin eda exon

  1. The group A streptococcal collagen-like protein 1, Scl1, mediates biofilm formation by targeting the EDA-containing variant of cellular fibronectin expressed in wounded tissue

    Science.gov (United States)

    Oliver-Kozup, Heaven; Martin, Karen H.; Schwegler-Berry, Diane; Green, Brett J.; Betts, Courtney; Shinde, Arti V.; Van De Water, Livingston; Lukomski, Slawomir

    2012-01-01

    Summary Wounds are known to serve as portals of entry for group A Streptococcus (GAS). Subsequent tissue colonization is mediated by interactions between GAS surface proteins and host extracellular matrix components. We recently reported that the streptococcal collagen-like protein-1, Scl1, selectively binds the cellular form of fibronectin (cFn) and also contributes to GAS biofilm formation on abiotic surfaces. One structural feature of cFn, which is predominantly expressed in response to tissue injury, is the presence of a spliced variant containing extra domain A (EDA/EIIIA). We now report that GAS biofilm formation is mediated by the Scl1 interaction with EDA-containing cFn. Recombinant Scl1 proteins that bound cFn also bound recombinant EDA within the C-C′ loop region recognized by the α9β1 integrin. The extracellular 2-D matrix derived from human dermal fibroblasts supports GAS adherence and biofilm formation. Altogether, this work identifies and characterizes a novel molecular mechanism by which GAS utilizes Scl1 to specifically target an extracellular matrix component that is predominantly expressed at the site of injury in order to secure host tissue colonization. PMID:23217101

  2. A novel missense mutation (402C-->T) in exon 1 in the EDA gene in a family with X-linked hypohidrotic ectodermal dysplasia

    DEFF Research Database (Denmark)

    Hertz, Jens Michael; Nørgaard Hansen, K; Juncker, I

    1998-01-01

    Hypohidrotic ectodermal dysplasia (EDA), or Christ-Siemens-Touraine syndrome, is clinically characterized by hypohidrosis, hypoodontia and hypotrichosis. The X-linked form of the disease has been mapped to Xq12-q13.1, and a gene from this region has recently been cloned. This gene encodes...... families with hypohidrotic ectodermal dysplasia for mutation in exon 1 of the EDA-gene by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). In one large kindred we identified a novel missense mutation (402C-->T), which changes a histidine to tyrosine at position 54...

  3. [Knocking-out extra domain A alternative splice fragment of fibronectin using a clustered regularly interspaced short palindromic repeats/associated proteins 9 system].

    Science.gov (United States)

    Yang, Yue; Wang, Haicheng; Xu, Shuyu; Peng, Jing; Jiang, Jiuhui; Li, Cuiying

    2015-08-01

    To investigate the effect of the fibronectin extra domain A on the aggressiveness of salivary adenoid cystic carcinoma (SACC) cells, via the clustered regularly interspaced short palindromic repeats (CRISPR)/ associated proteins (Cas) system. One sgRNA was designed to target the upstream of the genome sequences of extra domain A(EDA) exon and the downstream. Then the sgRNA was linked into plasmid PX-330 and transfected into SACC-83 cells. PCR and DNA sequence were used to testify the knockout cells, and the monoclones of EDA absent SACC cells were selected (A+C-2, A+C-6, B+C-10). CCK-8 cell proliferation and invasion was then tested in control group and the experimental group. The sgRNA was successfully linked into PX-330 plasmid. Part of adenoid cystic carcinoma cells' SACC-83 genomic EDA exon was knocked out, and the knockdown efficiency was above 70%, but the total amount of fibronectin did not change significantly. Three monoclones of EDA absent SACC- 83 cells were successfully selected with diminished migration and proliferation. The CRISPR/Cas9 system was a simplified system with relatively high knockout efficiency and EDA knockout could inhibiting SACC cell's mobility and invasiveness.

  4. Control of fibroblast fibronectin expression and alternative splicing via the PI3K/Akt/mTOR pathway

    International Nuclear Information System (INIS)

    White, Eric S.; Sagana, Rommel L.; Booth, Adam J.; Yan, Mei; Cornett, Ashley M.; Bloomheart, Christopher A.; Tsui, Jessica L.; Wilke, Carol A.; Moore, Bethany B.; Ritzenthaler, Jeffrey D.; Roman, Jesse; Muro, Andres F.

    2010-01-01

    Fibronectin (FN), a ubiquitous glycoprotein that plays critical roles in physiologic and pathologic conditions, undergoes alternative splicing which distinguishes plasma FN (pFN) from cellular FN (cFN). Although both pFN and cFN can be incorporated into the extracellular matrix, a distinguishing feature of cFN is the inclusion of an alternatively spliced exon termed EDA (for extra type III domain A). The molecular steps involved in EDA splicing are well-characterized, but pathways influencing EDA splicing are less clear. We have previously found an obligate role for inhibition of the tumor suppressor phosphatase and tensin homologue on chromosome 10 (PTEN), the primary regulator of the PI3K/Akt pathway, in fibroblast activation. Here we show TGF-β, a potent inducer of both EDA splicing and fibroblast activation, inhibits PTEN expression and activity in mesenchymal cells, corresponding with enhanced PI3K/Akt signaling. In pten -/- fibroblasts, which resemble activated fibroblasts, inhibition of Akt attenuated FN production and decreased EDA alternative splicing. Moreover, inhibition of mammalian target of rapamycin (mTOR) in pten -/- cells also blocked FN production and EDA splicing. This effect was due to inhibition of Akt-mediated phosphorylation of the primary EDA splicing regulatory protein SF2/ASF. Importantly, FN silencing in pten -/- cells resulted in attenuated proliferation and migration. Thus, our results demonstrate that the PI3K/Akt/mTOR axis is instrumental in FN transcription and alternative splicing, which regulates cell behavior.

  5. Transforming growth factor-β1 regulates fibronectin isoform expression and splicing factor SRp40 expression during ATDC5 chondrogenic maturation

    International Nuclear Information System (INIS)

    Han Fei; Gilbert, James R.; Harrison, Gerald; Adams, Christopher S.; Freeman, Theresa; Tao Zhuliang; Zaka, Raihana; Liang Hongyan; Williams, Charlene; Tuan, Rocky S.; Norton, Pamela A.; Hickok, Noreen J.

    2007-01-01

    Fibronectin (FN) isoform expression is altered during chondrocyte commitment and maturation, with cartilage favoring expression of FN isoforms that includes the type II repeat extra domain B (EDB) but excludes extra domain A (EDA). We and others have hypothesized that the regulated splicing of FN mRNAs is necessary for the progression of chondrogenesis. To test this, we treated the pre-chondrogenic cell line ATDC5 with transforming growth factor-β1, which has been shown to modulate expression of the EDA and EDB exons, as well as the late markers of chondrocyte maturation; it also slightly accelerates the early acquisition of a sulfated proteoglycan matrix without affecting cell proliferation. When chondrocytes are treated with TGF-β1, the EDA exon is preferentially excluded at all times whereas the EDB exon is relatively depleted at early times. This regulated alternative splicing of FN correlates with the regulation of alternative splicing of SRp40, a splicing factor facilitating inclusion of the EDA exon. To determine if overexpression of the SRp40 isoforms altered FN and FN EDA organization, cDNAs encoding these isoforms were overexpressed in ATDC5 cells. Overexpression of the long-form of SRp40 yielded an FN organization similar to TGF-β1 treatment; whereas overexpression of the short form of SRp40 (which facilitates EDA inclusion) increased formation of long-thick FN fibrils. Therefore, we conclude that the effects of TGF-β1 on FN splicing during chondrogenesis may be largely dependent on its effect on SRp40 isoform expression

  6. Control of fibroblast fibronectin expression and alternative splicing via the PI3K/Akt/mTOR pathway

    Energy Technology Data Exchange (ETDEWEB)

    White, Eric S., E-mail: docew@umich.edu [Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI (United States); Sagana, Rommel L.; Booth, Adam J.; Yan, Mei; Cornett, Ashley M.; Bloomheart, Christopher A.; Tsui, Jessica L.; Wilke, Carol A.; Moore, Bethany B. [Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI (United States); Ritzenthaler, Jeffrey D.; Roman, Jesse [Department of Medicine, University of Louisville School of Medicine, Louisville, KY (United States); Muro, Andres F. [International Centre for Genetic Engineering and Biotechnology, Trieste (Italy)

    2010-10-01

    Fibronectin (FN), a ubiquitous glycoprotein that plays critical roles in physiologic and pathologic conditions, undergoes alternative splicing which distinguishes plasma FN (pFN) from cellular FN (cFN). Although both pFN and cFN can be incorporated into the extracellular matrix, a distinguishing feature of cFN is the inclusion of an alternatively spliced exon termed EDA (for extra type III domain A). The molecular steps involved in EDA splicing are well-characterized, but pathways influencing EDA splicing are less clear. We have previously found an obligate role for inhibition of the tumor suppressor phosphatase and tensin homologue on chromosome 10 (PTEN), the primary regulator of the PI3K/Akt pathway, in fibroblast activation. Here we show TGF-{beta}, a potent inducer of both EDA splicing and fibroblast activation, inhibits PTEN expression and activity in mesenchymal cells, corresponding with enhanced PI3K/Akt signaling. In pten{sup -/-} fibroblasts, which resemble activated fibroblasts, inhibition of Akt attenuated FN production and decreased EDA alternative splicing. Moreover, inhibition of mammalian target of rapamycin (mTOR) in pten{sup -/-} cells also blocked FN production and EDA splicing. This effect was due to inhibition of Akt-mediated phosphorylation of the primary EDA splicing regulatory protein SF2/ASF. Importantly, FN silencing in pten{sup -/-} cells resulted in attenuated proliferation and migration. Thus, our results demonstrate that the PI3K/Akt/mTOR axis is instrumental in FN transcription and alternative splicing, which regulates cell behavior.

  7. Tissue-specific and SRSF1-dependent splicing of fibronectin, a matrix protein that controls host cell invasion

    Science.gov (United States)

    Lopez-Mejia, Isabel Cristina; De Toledo, Marion; Della Seta, Flavio; Fafet, Patrick; Rebouissou, Cosette; Deleuze, Virginie; Blanchard, Jean Marie; Jorgensen, Christian; Tazi, Jamal; Vignais, Marie-Luce

    2013-01-01

    Cell invasion targets specific tissues in physiological placental implantation and pathological metastasis, which raises questions about how this process is controlled. We compare dermis and endometrium capacities to support trophoblast invasion, using matching sets of human primary fibroblasts in a coculture assay with human placental explants. Substituting endometrium, the natural trophoblast target, with dermis dramatically reduces trophoblast interstitial invasion. Our data reveal that endometrium expresses a higher rate of the fibronectin (FN) extra type III domain A+ (EDA+) splicing isoform, which displays stronger matrix incorporation capacity. We demonstrate that the high FN content of the endometrium matrix, and not specifically the EDA domain, supports trophoblast invasion by showing that forced incorporation of plasma FN (EDA–) promotes efficient trophoblast invasion. We further show that the serine/arginine-rich protein serine/arginine-rich splicing factor 1 (SRSF1) is more highly expressed in endometrium and, using RNA interference, that it is involved in the higher EDA exon inclusion rate in endometrium. Our data therefore show a mechanism by which tissues can be distinguished, for their capacity to support invasion, by their different rates of EDA inclusion, linked to their SRSF1 protein levels. In the broader context of cancer pathology, the results suggest that SRSF1 might play a central role not only in the tumor cells, but also in the surrounding stroma. PMID:23966470

  8. ITER EDA and technology

    International Nuclear Information System (INIS)

    Baker, C.C.

    2001-01-01

    The year 1998 was the culmination of the six-year Engineering Design Activities (EDA) of the International Thermonuclear Experimental Reactor (ITER) Project. The EDA results in design and validating technology R and D, plus the associated effort in voluntary physics research, is a significant achievement and major milestone in the history of magnetic fusion energy development. Consequently, the ITER EDA was a major theme at this Conference, contributing almost 40 papers

  9. ITER EDA newsletter. V. 10, special issue

    International Nuclear Information System (INIS)

    2001-07-01

    This ITER EDA Newsletter includes summaries of the reports of ITER EDA JCT Physics unit about ITER physics R and D during the Engineering Design Activities (EDA), ITER EDA JCT Naka JWC ITER technology R and D during the EDA, and Safety, Environment and Health group of ITER EDA JCT, Garching JWS on EDA activities related to safety

  10. ITER EDA technical activities

    International Nuclear Information System (INIS)

    Aymar, R.

    1998-01-01

    Six years of technical work under the ITER EDA Agreement have resulted in a design which constitutes a complete description of the ITER device and of its auxiliary systems and facilities. The ITER Council commented that the Final Design Report provides the first comprehensive design of a fusion reactor based on well established physics and technology

  11. Plasma fibronectin and thyroid function.

    OpenAIRE

    Graninger, W; Pirich, K; Derfler, K; Waldhäusl, W

    1985-01-01

    Plasma fibronectin concentrations up to 85 mg/100 ml were found in hyperthyroid patients. There was a significant correlation between free thyroxine index and plasma fibronectin values. Hypothyroid patients had low to normal fibronectin concentrations. Parallel decreases of thyroid hormones and plasma fibronectin concentrations were noted during treatment with thiamazole. A direct effect of thyroid hormones on fibronectin synthesis seems probable.

  12. Medical sequencing of de novo ectodermal dysplasia in identical twins and evaluation of the potential eligibility for recombinant EDA therapy

    Directory of Open Access Journals (Sweden)

    Adriana Modesto

    2017-09-01

    Full Text Available The purpose of this study was to test two 8-year-old identical twins with ectodermal dysplasia (ED and their unaffected parents for the presence of mutations in the EDA gene with the hypothesis that they might be carrying a de novo mutation in EDA and potentially eligible for recombinant EDA therapy. DNA was extracted using saliva samples obtained from the identical twin girls and both parents. PCR products of Ectodyplasin A (EDA, Ectodysplasin Receptor (EDAR, Ectodysplasin Receptor Associated Death Domain (EDARADD, and Connexin-30 (GJB6 were sequenced by the Sanger method and the results analyzed using a reference sequence. Exons and exon-intron boundaries of EDA, EDAR, EDARADD, and GJB6 were sequenced in both parents and the affected identical twin pair. No mutations were detected in EDA or GJB6. Genetic variants located in the intron of EDAR were found but determined to be non-contributory to the twins’ ED. A microsatellite polymorphism was detected in all four subjects in exon 4 of the EDARADD gene but determined not to be causal to the ED. There was a silent mutation detected in exon 6 of the EDARADD gene of both the daughters and their unaffected mother but also unlikely to be the cause of ED. These results suggest that ED of the subjects is caused by a de novo mutation in a gene not studied here. It is likely these subjects and their future offspring would not benefit from the development of recombinant EDA replacement therapy.

  13. ITER EDA status

    International Nuclear Information System (INIS)

    Aymar, R.

    2001-01-01

    '', each representing a potential real procurement contract for an ITER component. The results, after analysis and evaluation by the JCT, have provided the basis for a JCT ''evaluated cost estimates'' report for all packages (Business Confidential) which was presented during a one week meeting at Garching (29 Jan - 2 Feb 2001) to an Ad Hoc Group of Parties' costing experts. The summary was included in the synoptic paper of the PDD for the Council's information. A meeting of the ITER Test Blanket Working Group (TBWG) was held in October 2000. The group has continued its activities during the period of extension of the EDA with a revised charter on the co-ordination of the development work performed by the Parties and by the JCT leading to a co-ordinated test programme on ITER for a DEMO-relevant tritium breeding blanket. This follows earlier work carried out during the EDA, which formed part of the 1998 Final Design Report. For a concise summary of the meeting see the separate article on the Test Blanket Working Group's Recent Activities in the ITER EDA Newsletter, Vol. 10, No. 2, Feb. 2001

  14. EDA activities related to safety

    International Nuclear Information System (INIS)

    Gordon, C.; Raeder, J.

    2001-01-01

    This article reviews the accomplishments in ITER safety analysis during the course of the Engineering Design Activities (EDA). The key aspects of ITER safety analysis are: effluents and emissions from normal operation, including planned maintenance activities; occupational safety for workers at the facility; radioactive materials and wastes generated during operation and from decommissioning ; potential incidents and accidents and the resulting transients. As a result of the work during the EDA it is concluded that ITER is safe

  15. A Splice Defect in the EDA Gene in Dogs with an X-Linked Hypohidrotic Ectodermal Dysplasia (XLHED) Phenotype.

    Science.gov (United States)

    Waluk, Dominik P; Zur, Gila; Kaufmann, Ronnie; Welle, Monika M; Jagannathan, Vidhya; Drögemüller, Cord; Müller, Eliane J; Leeb, Tosso; Galichet, Arnaud

    2016-09-08

    X-linked hypohidrotic ectodermal dysplasia (XLHED) caused by variants in the EDA gene represents the most common ectodermal dysplasia in humans. We investigated three male mixed-breed dogs with an ectodermal dysplasia phenotype characterized by marked hypotrichosis and multifocal complete alopecia, almost complete absence of sweat and sebaceous glands, and altered dentition with missing and abnormally shaped teeth. Analysis of SNP chip genotypes and whole genome sequence data from the three affected dogs revealed that the affected dogs shared the same haplotype on a large segment of the X-chromosome, including the EDA gene. Unexpectedly, the whole genome sequence data did not reveal any nonsynonymous EDA variant in the affected dogs. We therefore performed an RNA-seq experiment on skin biopsies to search for changes in the transcriptome. This analysis revealed that the EDA transcript in the affected dogs lacked 103 nucleotides encoded by exon 2. We speculate that this exon skipping is caused by a genetic variant located in one of the large introns flanking this exon, which was missed by whole genome sequencing with the illumina short read technology. The altered EDA transcript splicing most likely causes the observed ectodermal dysplasia in the affected dogs. These dogs thus offer an excellent opportunity to gain insights into the complex splicing processes required for expression of the EDA gene, and other genes with large introns. Copyright © 2016 Waluk et al.

  16. A Splice Defect in the EDA Gene in Dogs with an X-Linked Hypohidrotic Ectodermal Dysplasia (XLHED Phenotype

    Directory of Open Access Journals (Sweden)

    Dominik P. Waluk

    2016-09-01

    Full Text Available X-linked hypohidrotic ectodermal dysplasia (XLHED caused by variants in the EDA gene represents the most common ectodermal dysplasia in humans. We investigated three male mixed-breed dogs with an ectodermal dysplasia phenotype characterized by marked hypotrichosis and multifocal complete alopecia, almost complete absence of sweat and sebaceous glands, and altered dentition with missing and abnormally shaped teeth. Analysis of SNP chip genotypes and whole genome sequence data from the three affected dogs revealed that the affected dogs shared the same haplotype on a large segment of the X-chromosome, including the EDA gene. Unexpectedly, the whole genome sequence data did not reveal any nonsynonymous EDA variant in the affected dogs. We therefore performed an RNA-seq experiment on skin biopsies to search for changes in the transcriptome. This analysis revealed that the EDA transcript in the affected dogs lacked 103 nucleotides encoded by exon 2. We speculate that this exon skipping is caused by a genetic variant located in one of the large introns flanking this exon, which was missed by whole genome sequencing with the illumina short read technology. The altered EDA transcript splicing most likely causes the observed ectodermal dysplasia in the affected dogs. These dogs thus offer an excellent opportunity to gain insights into the complex splicing processes required for expression of the EDA gene, and other genes with large introns.

  17. Relevant documents initiating the EDA

    International Nuclear Information System (INIS)

    1993-01-01

    In December 1990, the four ITER Parties successfully concluded the Conceptual Design Activities for ITER. In January, 1991, each of the Parties had decided to enter negotiations on co-operation in the ITER EDA, which are to be conducted under the auspices of the IAEA; and each Party was prepared to receive a letter of invitation from the Director General of the IAEA to participate in those negotiations. Four negotiating meetings were held in 1991, the first being in Vienna, the second in Tokyo, the third in Reston near Washington, and the fourth in Moscow. After completion of the negotiations, each of the Parties proceeded domestically to reach its decision to sign the ITER EDA Agreement and its Protocol 1. All formalities were concluded during the first half of 1992, and the EDA documents were signed in Washington on July 21, 1992. Following the signing, each of the Parties provided the Director General with the names of its two ITER Council members. With the formation of the Council, the EDA had begun. This volume contains the papers developed before the start of the EDA. It begins with the Director General's invitation to participate in the negotiations and ends with the Parties' designations of the ITER Council members. While the evolving text of the Agreement and its Protocol 1 is referred to in some of these papers as an attachment, it is only the final, signed text that is reproduced in this volume

  18. ITER EDA newsletter. V. 2, no. 11

    International Nuclear Information System (INIS)

    1993-11-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains an ITER EDA Status Report, and a report on the Fourth International Fusion Neutronics Workshop at the University of California, Los Angeles Campus, October 20-21, 1993

  19. ITER EDA Newsletter. V.3, no.3

    International Nuclear Information System (INIS)

    1994-03-01

    This ITER EDA Newsletter issue contains reports on (i) the completion of the ITER EDA Protocol 1, (ii) the signing of ITER EDA Protocol 2, (iii) a technical meeting on pumping and fuelling and (iv) a technical meeting on the ITER Tritium Plant

  20. Status of the ITER EDA

    International Nuclear Information System (INIS)

    Aymar, R.

    2000-01-01

    This article summarizes progress made in the ITER Engineering Design Activities in the period between the ITER Meeting in Tokyo (January 2000) and June 2000. Topics: Termination of EDA, Joint Central Team and Support, Task Assignments, ITER Physics, Urgent and High Priority Physics Research Areas

  1. RT-PCR Analysis of ED-A,ED-B, and IIICS Fibronectin Domains: A New Screening Marker For Bladder Cancer

    Directory of Open Access Journals (Sweden)

    M Ahmadi Javid

    2004-12-01

    Full Text Available Background: Fibronectin seems to play a very important role in the progression and invasion of bladder cancer. EDA, EDB, and IIICS domains of fibronectin are not expressed in the adult persons but they’re expressed in different cancers. The aim of this study is to investigate the mRNA of fibronectin in transitional carcinoma cells (TCC of bladder to study these domains. Methods: A total of 20 patients with known bladder cancer were studied. Two of them excluded since their excised tissues were not enough for both the pathological examination and RNA study. Another 20 (control group were normal volunteers who needed bladder operations. The excised tissue was immediately transferred to RNAlater (Ambion,TX. RNA was extracted via RNAWIZ (Ambion, TX. cDNA was made via RevertAid First Strand cDNA Synthesis Kit (Fermentas. PCR of the cDNAs was performed using primers for EDA, EDB, and IIICS (Eurogentec,Belgium. Results: For the first time, we present the expression of the oncofetal fibronectin mRNA in the transitional cell carcinoma of bladder. The high grade muscle invasive (G3T2 tumor, expressed ED-A, ED-B, and IIICS. Expression of ED-A, ED-B, and IIICS was confirmed in the two patients with G3T1 TCC. The four patients with G2Ta and G3Ta expressed both ED-A and ED-B. The four patients with G1T1 tumor expressed ED-A only, similar to the nine patients with G1Ta tumor. None of the normal volunteers expressed the oncofetal extra domains. The sensitivity of ED-A positive fibronectin RNA for detecting TCC of any kind is 100%, and of ED-B was only 35%. The specificity of ED-B positive fibronectin RNA for the high grade TCC is 100%. Conclusion: ED-A, ED-B, and IIICS could be used as useful markers for the diagnosis and following up of bladder carcinoma. Keywords: Transitional Cell Carcinoma, bladder cancer, fibronectin, RT-PCR, oncofetal.

  2. ITER EDA Newsletter. V. 10, no. 7

    International Nuclear Information System (INIS)

    2001-07-01

    This ITER EDA Newsletter presents an overview of meetings held at IAEA Headquarters in Vienna during the week 16-20 July 2001 related to the successful completion of the ITER Engineering Design Activities (EDA). Among them were the final meeting of the ITER Council, the closing ceremony to commemorate the EDA completion, the final meeting of the ITER Management Advisory Committee, a briefing of issues related to ITER developments, and discussions on the possible joint implementation of ITER

  3. Methylation state of the EDA gene promoter in Chinese X-linked hypohidrotic ectodermal dysplasia carriers.

    Directory of Open Access Journals (Sweden)

    Wei Yin

    Full Text Available Hypodontia, hypohidrosis, sparse hair and characteristic faces are the main characters of X-linked hypohidrotic ectodermal dysplasia (XLHED which is caused by genetic ectodysplasin A (EDA deficiency. Heterozygous female carriers tend to have mild to moderate XLHED phenotype, even though 30% of them present no obvious symptom.A large Chinese XLHED family was reported and the entire coding region and exon-intron boundaries of EDA gene were sequenced. To elucidate the mechanism for carriers' tempered phenotype, we analyzed the methylation level on four sites of the promoter of EDA by the pyrosequencing system.A known frameshift mutation (c.573-574 insT was found in this pedigree. Combined with the pedigrees we reported before, 120 samples comprised of 23 carrier females from 11 families and 97 healthy females were analyzed for the methylation state of EDA promoter. Within 95% confidence interval (CI, 18 (78.26% carriers were hypermethylated at these 4 sites.Chinese XLHED carriers often have a hypermethylated EDA promoter.

  4. Oncofetal fibronectins in oral carcinomas

    DEFF Research Database (Denmark)

    Mandel, U; Gaggero, B; Reibel, J

    1994-01-01

    Different isoforms of fibronectin are derived from a single gene by alternative processing of the primary RNA transcript or by posttranslational modifications. We have previously demonstrated that an oncofetal fibronectin (FN) isoform derived by O-glycosylation is highly associated with malignanc...

  5. ITER EDA Newsletter. V. 2, no. 1

    International Nuclear Information System (INIS)

    1993-01-01

    This ITER EDA (Engineering Design Activities) Newsletter issue is dedicated to the description of the ITER EDA Home Teams (European Community, Japan, Russian Federation, USA), in particular their composition, tasks, responsibilities, national support and activities, aimed to design the ITER tokamak

  6. ITER EDA Newsletter. Vol. 1, No. 1

    International Nuclear Information System (INIS)

    1992-11-01

    After the ITER Engineering Design Activities (EDA) Agreement and Protocol 1 had been signed by the four ITER parties on July 21, 1992 and had entered into force, the ITER Council suggested at its first meeting (Vienna, September 10-11, 1992) that the publication of the ITER Newsletter be continued during the EDA with assistance of the International Atomic Energy Agency. This suggestion was supported by the Agency and subsequently the ITER office in Vienna assumed its responsibilities for planning and executing activities related to the publication of the Newsletter. The ITER EDA Newsletter is planned to be a monthly publication aimed at disseminating broad information and understanding, including the description of the personal and institutional involvements in the ITER project in addition to technical facts about it. The responsibility for the Newsletter rests with the ITER council. In this first issue the signing of the ITER EDA Activities and Protocol 1 is reported. The EDA organizational structure is described. This issue also reports on the first ITER EDA council meeting, the opening of the ITER EDA NAKA Co-Centre, the first meeting of the ITER Technical Advisory Committee, activities of special working groups, an ITER Technical Meeting, as well as ''News in Brief'' and ''Coming Events''

  7. ITER EDA newsletter. V. 5, no. 8

    International Nuclear Information System (INIS)

    1996-08-01

    This issue of the Newsletter on the Engineering Design Activities (EDA) for the ITER Tokamak project contains a report on the divertor remote handling development (and of a summer party at the ITER Joint Work Site in Garching, Germany)

  8. ITER EDA newsletter. V. 9, no. 2

    International Nuclear Information System (INIS)

    2000-02-01

    This ITER EDA Newsletter reports on the seventh ITER technical meeting on safety and environment and contains the executive summary of the eleventh ITER scrape-off layer and divertor physics expert group meeting. Individual abstracts have been prepared

  9. Harnessing VLSI System Design with EDA Tools

    CERN Document Server

    Kamat, Rajanish K; Gaikwad, Pawan K; Guhilot, Hansraj

    2012-01-01

    This book explores various dimensions of EDA technologies for achieving different goals in VLSI system design. Although the scope of EDA is very broad and comprises diversified hardware and software tools to accomplish different phases of VLSI system design, such as design, layout, simulation, testability, prototyping and implementation, this book focuses only on demystifying the code, a.k.a. firmware development and its implementation with FPGAs. Since there are a variety of languages for system design, this book covers various issues related to VHDL, Verilog and System C synergized with EDA tools, using a variety of case studies such as testability, verification and power consumption. * Covers aspects of VHDL, Verilog and Handel C in one text; * Enables designers to judge the appropriateness of each EDA tool for relevant applications; * Omits discussion of design platforms and focuses on design case studies; * Uses design case studies from diversified application domains such as network on chip, hospital on...

  10. ITER EDA newsletter. V. 7, no. 7

    International Nuclear Information System (INIS)

    1998-07-01

    This newsletter contains the articles: 'Extraordinary ITER council meeting', 'ITER EDA final safety meeting' and 'Summary report of the 3rd combined workshop of the ITER confinement and transport and ITER confinement database and modeling expert groups'

  11. ITER EDA newsletter. V. 9, no. 8

    International Nuclear Information System (INIS)

    2000-08-01

    This ITER EDA Newsletter reports on the ITER meeting on 29-30 June 2000 in Moscow, summarizes the status report on the ITER EDA by R. Aymar, the ITER Director, and gives overviews of the expert group workshop on transport and internal barrier physics, confinement database and modelling and edge and pedestal physics, and the IEA workshop on transport barriers at edge and core. Individual abstracts have been prepared

  12. ITER EDA newsletter. V. 5, no. 7

    International Nuclear Information System (INIS)

    1996-07-01

    This issue of the Newsletter on the Engineering Design Activities (EDA) for the ITER Tokamak project contains a report on the Tenth ITER Council Meeting, held July 24-25, 1996, in St. Petersburg, Russia; a description of the Status of the ITER EDA by the ITER Director, Dr. R. Aymar; and a report on the so-called Task Number One by the ITER Special Working Group (Basis for the Start of Explorations, presenting possible scenarios toward siting, licensing and host support)

  13. Fibronectin enhances transfection of Staphylococcus aureus.

    OpenAIRE

    Thompson, N E; Bergdoll, M S; Pattee, P A

    1985-01-01

    The factor in normal sera primarily responsible for the enhancement of transfection (and transformation) of Staphylococcus aureus was identified as fibronectin. Serum samples which were depleted of fibronectin by affinity chromatography showed a marked decrease in enhancing activity. Fibronectin isolated from sera of several animal species demonstrated enhancing activity.

  14. ITER EDA newsletter. V. 7, no. 9

    International Nuclear Information System (INIS)

    1998-09-01

    Newsletter containing the two articles 'Parties working on continuation of ITER EDA' and 'ITER exhibit at the Austria Centre, Vienna'. The first article describes efforts of the 4 ITER partners, the European Atomic Energy Community and the governments of Japan, the Russian Federation and the USA, to agree to continuation of the ITER EDA. While the former 3 partners signed an Extension to the EDA, the Americans were refused funding by the US Congress und will therefore be phased out within one year. Copies of the documents signed are provided. The second article reports on exhibition featuring a model of ITER and various other means of information on nuclear fusion which took place at the IAEA Headquarters from the 21st to 25th of September 1998. There is also an article in memoriam of Alexander V. Kashirski, who died on the 29th of September 1998

  15. ITER EDA Newsletter. V. 3, no. 10

    International Nuclear Information System (INIS)

    1994-10-01

    This ITER EDA (Engineering Design Activities) Newsletter issue reports on (i) the ITER-relevant statements made at the occasion of the 15th IAEA fusion conference in Seville, Spain, September 26 - October 1, 1994; (ii) a comprehensive technical presentation of the ITER EDA developments at the same conference; (iii) the first Workshop of the ITER Expert Group on Confinement and Transport, held at the San Diego Joint Work Site on 22-25 August 1994; and (iv) the visit to the San Diego Work Site of the representatives of a local philanthropic group, the ARCS Foundation (Achievement Rewards for College Scientists)

  16. ITER EDA Newsletter. V.4, no.2

    International Nuclear Information System (INIS)

    1995-02-01

    This ITER EDA (Engineering Design Activities) Newsletter issue reports on (i) the exploits of the Special Working Group (SWG-2) designated in Protocol 1 to address task allocations and drafting of Protocol 2; and (ii) a report on the Tritium Plant Group Technical Meeting held at the Naka Joint Work Site on February 1-6, 1995

  17. ITER EDA newsletter. V. 5, no. 9

    International Nuclear Information System (INIS)

    1996-09-01

    This issue of the Newsletter on the Engineering Design Activities (EDA) for the ITER project contains an overview of one of the seven large ITER Research and Development Projects identified by the ITER Director, namely the Vacuum Vessel Sector, as well as an account of computer animation created for ITER

  18. ITER EDA newsletter. V. 7, no. 12

    International Nuclear Information System (INIS)

    1998-12-01

    This edition of the ITER EDA Newsletter is dedicated to celebrate the achievements of the ITER activities at the San Diego Joint Work Site. Articles by E. Velikhov, A. Davies and R. Aymar mark the final days of American participation in the ITER program

  19. ITER EDA Newsletter. V. 3, no. 8

    International Nuclear Information System (INIS)

    1994-08-01

    This ITER EDA (Engineering Design Activities) Newsletter issue reports on the sixth ITER council meeting; introduces the newly appointed ITER director and reports on his address to the ITER council. The vacuum tank for the ITER model coil testing, installed at JAERI, Naka, Japan is also briefly described

  20. ITER EDA newsletter. V. 4, no. 9

    International Nuclear Information System (INIS)

    1995-09-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains reports on the first meeting of the ITER Test Blanket Working Group held 19-21 July 1995 at the ITER Garching Joint Work Site, and on the second workshop of the ITER Expert Group on Confinement and Transport

  1. ITER EDA newsletter. V. 2, no. 12

    International Nuclear Information System (INIS)

    1993-12-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains a report of the Second ITER Technical Committee Meeting on Safety, Environment, and Regulatory Approval, San Diego, USA, November 3-12, 1993, and a summary report on an ITER Magnet Technical Meeting, Naka, Japan, October 5-8, 1993

  2. ITER EDA newsletter. V. 8, no. 11

    International Nuclear Information System (INIS)

    1999-11-01

    This ITER EDA Newsletter contains summary reports on the eleventh meeting of the ITER diagnostic expert group in Cadarache, France, on the ITER JCT presentation at the international conference on fusion reactor materials in Colorado Springs, USA and on the seventh workshop on plasma edge theory in fusion devices in Tajimi, Japan. Individual abstracts are prepared for the three contributions

  3. ITER EDA newsletter. V. 6, no. 2

    International Nuclear Information System (INIS)

    1997-02-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter reports on the ITER divertor development project and its objectives; contains a report on the 16th Energy IAEA Fusion Conference (ITER and other Tokamak Issues) held in Montreal, Canada; 287 papers were selected by the Programme Committee for presentation and 178 posters were presented. 3 figs

  4. ITER EDA newsletter. V. 9, no. 9

    International Nuclear Information System (INIS)

    2000-09-01

    This ITER EDA Newsletter contains the following 5 contributions: CSMC and CSIC charging tests successfully completed; The ITER divertor cassette project meeting; Blanket R and D and design task meeting; IAEA technical committee meeting on fusion safety; ITER L-6 large project ''blanket remote handling and maintenance''

  5. ITER EDA newsletter. V. 10, no. 6

    International Nuclear Information System (INIS)

    2001-06-01

    This ITER EDA Newsletter issue includes information about the ITER Management Advisory Committee Meeting held in Vienna on 16 July 2001 and also a summary of the ninth ITER Technical Meeting on safety and environment held at the ITER Garching Joint Work site, 8 to 10 May, 2001

  6. ITER EDA Newsletter. V. 4, no. 5

    International Nuclear Information System (INIS)

    1995-05-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains comments on the ITER project by the Permanent Representative of the Russian Federation to the International Organizations in Vienna; a report on the ITER Magnet Technical Meeting held at the Joint Work Site at Naka, Japan, April 19-21, 1995; and a contribution entitled ''ITER spouses cross the cultures''

  7. ITER EDA newsletter. V. 8, no. 9

    International Nuclear Information System (INIS)

    1999-09-01

    This edition of the ITER EDA Newsletter contains a contribution by the ITER Director, R. Aymar, on the subject of developments in ITER Physics R and D report on the completion of the ITER central solenoid model coils installation by H. Tsuji, Head fo the Superconducting Magnet Laboratory at JAERI in Naka, Japan. Individual abstracts are prepared for each of the two articles

  8. ITER EDA Newsletter. V. 4, no. 6

    International Nuclear Information System (INIS)

    1995-06-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains a report on the TAC-JCT (Technical Advisory Committee, Joint Technical Team) Informal Technical Reviews and the State Duma Hearings on Fusion (i.e., Parliamentary Hearing on Fusion held in the Russian Federation)

  9. ITER EDA newsletter. V. 10, no. 3

    International Nuclear Information System (INIS)

    2001-03-01

    This issue contains a report on the meeting of the ITER Council (M. Drew), a report on the ITER EDA status (Dr. R. Aymar), a report on the ITER Council tour of the Clarington Site (Dr. D. Dautovich) . Abstracts of the indivdual reports have been included in the database

  10. ITER EDA newsletter. V. 2, no. 9

    International Nuclear Information System (INIS)

    1993-09-01

    This ITER EDA (Engineering Design Activities) Newsletter issue contains a report on the third meeting of the ITER Technical Advisory Committee, a summary report for the ITER Magnetic Technical Meeting, a brief account of the International Workshop on Nuclear Data for Fusion Reactor Technology, and a description of approved arrangements for visiting home team personnel

  11. ITER EDA newsletter. V. 8, no. 12

    International Nuclear Information System (INIS)

    1999-12-01

    This ITER EDA Newsletter reports about the ITER Management Advisory Committee Meeting in Naka, the ITER Technical Advisory Committee Meeting in Naka and the meeting of the ITER SWG-P2 in Vienna. A separate abstract is prepared for each meeting

  12. The Earth Data Analytic Services (EDAS) Framework

    Science.gov (United States)

    Maxwell, T. P.; Duffy, D.

    2017-12-01

    Faced with unprecedented growth in earth data volume and demand, NASA has developed the Earth Data Analytic Services (EDAS) framework, a high performance big data analytics framework built on Apache Spark. This framework enables scientists to execute data processing workflows combining common analysis operations close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using vetted earth data analysis tools (ESMF, CDAT, NCO, etc.). EDAS utilizes a dynamic caching architecture, a custom distributed array framework, and a streaming parallel in-memory workflow for efficiently processing huge datasets within limited memory spaces with interactive response times. EDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be accessed using direct web service calls, a Python script, a Unix-like shell client, or a JavaScript-based web application. New analytic operations can be developed in Python, Java, or Scala (with support for other languages planned). Client packages in Python, Java/Scala, or JavaScript contain everything needed to build and submit EDAS requests. The EDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service enables decision makers to compare multiple reanalysis datasets and investigate trends, variability, and anomalies in earth system dynamics around the globe.

  13. Increased plasma fibronectin concentrations in obesity

    DEFF Research Database (Denmark)

    Andersen, T; Dejgaard, A; Astrup, A

    1987-01-01

    In 23 morbidly obese patients we investigated the influence of a large weight loss (30.6 kg, range 17.5-90.8) on the plasma fibronectin concentrations. Further, changes in plasma fibronectin were related to serum insulin levels and to liver biochemistry. Between the measurements patients had been...... with the degree of hepatic fatty change, declined (p less than 0.01), but the individual change was unrelated with the change in plasma fibronectin. In conclusion, the elevated plasma fibronectin levels in morbidly obese subjects seem to normalize during weight loss. We suggest the normalization to be mediated...

  14. Plasma fibronectin concentrations in morbidly obese patients

    DEFF Research Database (Denmark)

    Dejgaard, A; Andersen, T; Christoffersen, Pernille Yde

    1984-01-01

    Plasma fibronectin concentrations and liver morphology were investigated in 45 morbidly obese subjects (median overweight 88%) and in 42 normal weight controls, matched for sex and age. A significantly (P less than 0.01) raised plasma fibronectin concentration (median 464 mg/l, range 276-862 mg...... in their liver biopsies (r = 0.33, P less than 0.05). Significantly (P less than 0.05) elevated plasma fibronectin concentrations even in obese subjects without hepatic fatty change indicate that liver fat accumulation is no prerequisite of the obesity-related elevation of plasma fibronectin. Raised plasma...

  15. Determination of activated plasma fibronectin using radioactive labelled collagen I

    DEFF Research Database (Denmark)

    Fenger, M

    1984-01-01

    %. The active or activable fibronectin was compared to the immunoreactive fibronectin in plasma from patients with various bacterial diseases. Similar concentrations were detected by the two assays suggesting that all the circulating fibronectin was functionally active. The assay was also applied to determine...... of activating fibronectin. It is concluded that the assay is very convenient to detect biological active fibronectin and to elucidate the structure-function relationship of heparin and heparansulphate in activating fibronectin....

  16. ITER EDA newsletter. V. 1, no. 2

    International Nuclear Information System (INIS)

    1992-12-01

    This second issue of the ITER Newsletter during the EDA (Engineering Design Activities) reports on (i) the second ITER Council Meeting held in the Russian Research Centre (RRC) ''Kurchatov Institute'', Moscow, Russia, December 15-16, 1992, (ii) the opening ceremony of the ITER Council Office at the RRC, (iii) the first meeting of the ITER Management Advisory Committee (MAC), (iv) the start-up of the ITER EDA at Garching, Germany, (v) descriptions of the ITER Co-Centres at Naka, Japan, and (vi) San Diego, USA, (vii) contact persons activities, (viii) the adoption by the ITER Council of the recommendations by the Special Working Group 1 (SWG-1), (ix) news in brief, and (x) coming events

  17. ITER EDA newsletter. V. 5, no.1

    International Nuclear Information System (INIS)

    1996-01-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains reports on the RF-Based ITER JCT (Joint Central Team) Support Design Team (by N. Kornev), the third international workshop on plasma disruptions (by Dr. A. Hassanein and Dr. V. Litunovski) held at Obninsk, Russia, September 28-29, 1995, and the IAEA Advisory Group Meeting on Completion of Fendl-1 and the start of Fendl-2 (by Dr. A.B. Pashchenko); the Fendl library is a comprehensive collection of high-quality nuclear data, selected from the various existing national data libraries, covering the necessary nuclear input data for all physics and engineering aspects of the material development, design, operation, and safety of the ITER project in its current EDA phase

  18. ITER EDA newsletter. V. 5, no. 10

    International Nuclear Information System (INIS)

    1996-10-01

    This issue of the newsletter on the Engineering Design Activities (EDA) for the ITER Tokamak project contains a report on the Fifth ITER Technical Meeting on Safety, Environment, and Regulatory Approval, held September 29 - October 7, 1996 at the ITER San Diego Joint Work Site; and a report on the Fifth ITER Diagnostics Expert Group Workshop and Technical Meeting on Diagnostics held in Montreal, Canada, 12-13 October 1996

  19. ITER EDA newsletter. V. 2, no. 10

    International Nuclear Information System (INIS)

    1993-10-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains progress reports on the Fourth ITER Council Meeting in San Diego, 29 September - 1 October 1993, on the Third Meeting of the ITER Management Advisory Committee (MAC) in Naka, Japan, 16-17 September 1993, and on the flag raising ceremony at the US hosted joint work site in San Diego, California, 1 October 1993

  20. ITER EDA Newsletter. V.4, no.1

    International Nuclear Information System (INIS)

    1995-01-01

    This ITER EDA (Engineering Design Activities) Newsletter issue reports on (i) the seventh ITER Council Meeting held at the Naka Joint Work Site on 14-15 December 1994, (ii) the ''Confinement Modelling and Database Expert Group Workshop'' held in Seville, Spain, 3-4 October 1994, and (iii) the first meeting of the International Organizing Committee for the Seventh International Fusion Reactor Materials Conference

  1. ITER EDA Newsletter. V. 3, no. 11

    International Nuclear Information System (INIS)

    1994-11-01

    This ITER EDA (Engineering Design Activities) Newsletter issue reports on (i) the third Technical Meeting on Safety and Environment held at the San Diego Joint Work Site, October 10-14, 1994; (ii) the ITER Expert Group Meeting on Disruptions, Plasma Control and MHD, held in Seville, Spain, September 29-30, 1994; in addition to a brief contribution on aspects of family life for foreigners at the Naka Joint Work Site

  2. ITER EDA Newsletter. V. 6, no. 5

    International Nuclear Information System (INIS)

    1997-05-01

    This issue of the newsletter on Engineering Design Activities (EDA) for the ITER Tokamak project contains a report on Second International Industries' Liaison meeting which was held in Tokyo on 2-4 April 1997 (by Y. Kaneki, JAIF, Japan); an overview report on the Blanket project (by A. Cardella, I.Ioki (ITER Central Team), W. Daenner (EU Home Team)); and a progress report on microwave reflectometry (by J. Sanchez, Madrid, Spain)

  3. ITER EDA newsletter. V. 8, no. 10

    International Nuclear Information System (INIS)

    1999-10-01

    This ITER EDA Newsletter contains summary reports on the seventh meeting of the ITER physics expert group on energetic particles, heating and steady state operations in Frascati, Italy, on the fifth international symposium on fusion nuclear technology in Rome, Italy and on the IAEA technical committee meeting on electron cyclotron resonance heating physics and technology for fusion devices in Oh-arai, Japan. Individual abstracts are prepared for the three contributions

  4. ITER EDA Newsletter. V. 2, no. 3

    International Nuclear Information System (INIS)

    1993-03-01

    This ITER EDA (Engineering Design Activities) Newsletter issue includes a description of the ITER Joint Central Team's management, the ITER Management System and supporting software progress, activities of the Special Working Group 2, a brief summary of a technical meeting on the experimental approach to the physics of the high density divertor, a summary on the status of the International Fusion Evaluated Nuclear Data Library (FENDL), and an obituary on Dr. Henry Seligman (IAEA)

  5. ITER EDA Newsletter. V.2, no.5

    International Nuclear Information System (INIS)

    1993-05-01

    This ITER EDA (Engineering Design Activities), Newsletter issue includes reports on the third ITER council meeting in Tokyo on the involvement of other countries, on an outline of the report by the Management Advisory Committee (MAC), on such involvement, and on the improvement by the MAC and the ITER Council to proceed with Task Agreements on the Research and Development programme of the Superconductor Coils and Structures Division

  6. ITER EDA newsletter. V. 9, no. 11

    International Nuclear Information System (INIS)

    2000-11-01

    This issue of the ITER EDA Newsletter contains discussions of three meetings, i.e., (1) the Third ITER International Industry Liaison Meeting held in Toronto, Canada (November 7-9, 2000), (2) an informal meeting on ITER developments held in Sorrento, Italy (October 9, 2000), and (3) the Thirteenth Meeting of the ITER Physics Expert Group on Diagnostics held in Naka, Japan (September 21-22, 2000)

  7. ITER EDA Newsletter. V. 3, no. 12

    International Nuclear Information System (INIS)

    1994-12-01

    This ITER EDA (Engineering Design Activities) Newsletter issue reports on (i) the seventh Meeting of the Technical Advisory Committee (TAC-7) held at the Joint Work Site in Naka, Japan, 5-7 December 1994; (ii) the seventh Meeting of the ITER Management Advisory Committee (MAC-7) held at the Naka Joint Work Site, November 30 - December 1, 1994; (iii) the Magnet Technical Meeting, held at the Naka Joint Work Site on November 8-11, 1994

  8. ITER EDA newsletter. V. 7, no. 11

    International Nuclear Information System (INIS)

    1998-11-01

    This ITER EDA Newsletter contains a report on the delivery of the outer module of the CS model coil to Naka by K. Okuno et al, a special lecture by H. Yoshikawa, the president of the Science Council of Japan on the future outlook of nuclear fusion and a report on an ITER display during the 17th IAEA Fusion Energy Conference, held in Yokohama, Japan, from October 19 to 24, 1998

  9. Fibronectin: a chromatin-associated protein?

    Science.gov (United States)

    Zardi, L; Siri, A; Carnemolla, B; Santi, L; Gardner, W D; Hoch, S O

    1979-11-01

    We have previously reported that chromatin preparations from human cultured fibroblasts contain a single homologous serum protein. In this paper we present evidence, based on immunological identity and physicochemical properties, that this serum protein is fibronectin. Furthermore, using a radioimmunoassay system, we have estimated that fibronectin represents about 0.7% of the total protein in both chromatin preparations and whole fibroblasts. Using a nitrocellulose filter assay system, we also show that fibronectin is a DNA-binding protein having an equilibrium constant of 4.6 x 10(-6) M. Equilibrium competition experiments have demonstrated that fibronectin has the ability to differentiate among nucleotides, indicating that fibronectin-DNA interaction is at least partially specific, and that a minimum polymer length of 12-18 nucleotides is required for effective binding to occur. Fibronectin has been isolated readily from plasma using DNA-affinity chromatography. We do not have direct evidence that fibronectin is an actual nonhistone chromosomal protein, but fibronectin is a DNA-binding protein (at least under in vitro assay conditions) and appears to be a normal constituent of chromatin as chromatin is currently isolated from cell nuclei.

  10. Plasma fibronectin concentrations in morbidly obese patients

    DEFF Research Database (Denmark)

    Dejgaard, A; Andersen, T; Christoffersen, Pernille Yde

    1984-01-01

    Plasma fibronectin concentrations and liver morphology were investigated in 45 morbidly obese subjects (median overweight 88%) and in 42 normal weight controls, matched for sex and age. A significantly (P less than 0.01) raised plasma fibronectin concentration (median 464 mg/l, range 276-862 mg....../l) was found in the obese subjects when compared with concentrations in the controls (median 348 mg/l, range 164-536 mg/l). Plasma fibronectin concentrations of the obese patients correlated significantly to their degree of overweight (r = 0.33, P less than 0.05) as well as to the degree of fatty change found...... in their liver biopsies (r = 0.33, P less than 0.05). Significantly (P less than 0.05) elevated plasma fibronectin concentrations even in obese subjects without hepatic fatty change indicate that liver fat accumulation is no prerequisite of the obesity-related elevation of plasma fibronectin. Raised plasma...

  11. ITER EDA newsletter. V. 10, no. 5

    International Nuclear Information System (INIS)

    2001-05-01

    This issue of the ITER EDA Newsletter includes a review of the International Symposium 'ITER days in Moscow' and Canada's bid to host ITER at the Clarington site. In connection with the successful completion of the Engineering Design of the International Thermonuclear Reactor (ITER) and the 50th anniversary of fusion research in the USSR, the Ministry of the Russian Federation for Atomic Energy (Minatom) with the participation of the Russian Academy of Sciences, organized the International Symposium 'ITER days in Moscow' on 7-8 June 2001

  12. ITER EDA Newsletter. V. 3, no. 9

    International Nuclear Information System (INIS)

    1994-09-01

    This ITER EDA (Engineering Design Activities) Newsletter issue contains a description of the ITER Physics Research and Development (F.Perkins), a report on the first meeting of the ITER Divertor Physics and Divertor Modelling and Database Expert Groups (D. Post, G. Janeschitz, R. Stambaugh, M. Shimada), a report on the first meeting of the ITER Physics Expert Group on Diagnostics (A.E. Costley and K.M. Young), and a contribution entitled ''to meet or not to meet? If yes, for how long?'' (L. Golubchikov)

  13. ITER EDA Newsletter. V. 4, no. 7

    International Nuclear Information System (INIS)

    1995-07-01

    This ITER EDA (Engineering Design Activities) Newsletter issue contains reports on (i) the 8th meeting of the ITER Technical Advisory Committee (TAC-8) held on June 29 - July 7, 1995 at the ITER San Diego Work Site, (ii) the 8th meeting of the ITER Management Advisory Committee (MAC-8) held at the ITER San Diego Work Site on July 9-10, 1995, (iii) the 33rd meeting of the International Fusion Research Council (FRC), held July 11, 1995 at the IAEA Headquarters in Vienna, Austria, and (iv) the ITER participation in the fifth topical meeting on Tritium Technology in Fission, Fusion and Isotopic Applications

  14. ITER EDA newsletter. V. 3, no. 2

    International Nuclear Information System (INIS)

    1994-02-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains reports on the Fifth ITER Council Meeting held in Garching, Germany, 27-28 January 1994, a visit (28 January 1994) of an international group of Harvard Fellows to the San Diego Joint Work Site, the Inauguration Ceremony of the EC-hosted ITER joint work site in Garching (28 January 1994), on an ITER Technical Meeting on Assembly and Maintenance held in Garching, Germany, January 19-26, 1994, and a report on a Technical Committee Meeting on radiation effects on in-vessel components held in Garching, Germany, November 15-19, 1993, as well as an ITER Status Report

  15. ITER EDA Newsletter. V. 4, no. 8

    International Nuclear Information System (INIS)

    1995-08-01

    This ITER EDA (Engineering Design Activities) Newsletter issue contains reports on the 8th meeting of the ITER council and on the first Special Review Group (SRG) meeting held 21-23 June, 1995, at the San Diego Joint Work Site, USA. The SWG was established in July 1994 to review the technical, social, and the safety and environmental requirements for siting ITER which will be prepared by the Director and the JCT, and to report the results of the review to the council. Furthermore, a description of the design office at the Garching Joint Work Site is given

  16. ITER EDA newsletter. V. 5, no. 12

    International Nuclear Information System (INIS)

    1996-12-01

    This issue of the newsletter on the Engineering Design Activities (EDA) for the ITER Tokamak project contains a report on the Eleventh ITER Council Meeting held on December 17-18, 1996 in Tokyo, Japan; a report on the Eleventh Meeting of the ITER Technical Advisory Committee (TAC-11) Meeting held 3-7 December, 1996, at the ITER Naka Joint Work Site, Japan; and a report on the Fifth Workshop of the Confinement Modelling and Database Expert Group held in Montreal, Canada, October 13-16, 1996

  17. Field Trial of the Enhanced Data Authentication System (EDAS)

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Maikael A.; Baldwin, George T.; Hymel, Ross W

    2016-05-01

    The goal of the field trial of EDAS was to demonstrate the utility of secure branching of operator instrumentation for nuclear safeguards, identify any unforeseen implementation and application issues with EDAS, and confirm whether the approach is compatible with operator concerns and constraints.

  18. ITER EDA newsletter. V. 10, no. 4

    International Nuclear Information System (INIS)

    2001-04-01

    This ITER EDA Newsletter presents an overview of the Fourteenth Meeting of the ITER Physics Expert Group on Diagnostics which was held at the Institute for Plasma Physics, Juelich, Germany, 21-23 March 2001. The summary of the Meeting covers the discussions of the Expert Group as well as developments reported on similar meetings concerning ongoing work in diagnostic design and ITER relevant diagnostic development work which took place nearly at the same time. In addition, the outline of the material treated at the International Workshop on the Confinement Database and Modelling Expert Group in collaboration with the Edge and Pedestal Physics Expert Group which was held on 2-6 April 2001 at the Plasma Physics Research Centre of Lausanne (CRPP) Switzerland is presented

  19. ITER EDA newsletter. V. 4, no. 11

    International Nuclear Information System (INIS)

    1995-11-01

    This issue of the ITER EDA (Engineering Design Activities) Newsletter contains a report on the Ninth Meeting of the ITER Management Advisory Committee held in St. Petersburg, Russia, on November 3, 1995; a report on the Seventh International Conference on Fusion Reactor Materials held at Obninsk, Russia, 25-29 September, 1995; on the presentation of the ITER Project during a symposium on fusion energy held at Champaign, Illinois, USA, October 1-5, 1995; and on two meetings on ITER diagnostics, i.e., an international workshop on diagnostics for ITER held in Varenna, Italy, 28 August - 1 September, 1995; followed by the Third Diagnostics Expert Group Workshop held September 4-5 in the same location

  20. Dermatopontin interacts with fibronectin, promotes fibronectin fibril formation, and enhances cell adhesion.

    Science.gov (United States)

    Kato, Aiko; Okamoto, Osamu; Ishikawa, Kazushi; Sumiyoshi, Hideaki; Matsuo, Noritaka; Yoshioka, Hidekatsu; Nomizu, Motoyoshi; Shimada, Tatsuo; Fujiwara, Sakuhei

    2011-04-29

    We report that dermatopontin (DP), an abundant dermal extracellular matrix protein, is found in the fibrin clot and in the wound fluid, which comprise the provisional matrix at the initial stage of wound healing. DP was also found in the serum but at a lower concentration than that in wound fluid. DP co-localized with both fibrin and fibronectin on fibrin fibers and interacted with both proteins. Both normal fibroblast and HT1080 cell adhesion to the fibrin-fibronectin matrix were dose-dependently enhanced by DP, and the adhesion was mediated by α5β1 integrin. The cytoskeleton was more organized in the cells that adhered to the fibrin-fibronectin-DP complex. When incubated with DP, fibronectin formed an insoluble complex of fibronectin fibrils as visualized by electron microscopy. The interacting sites of fibronectin with DP were the first, thirteenth, and fourteenth type III repeats (III(1), III(13), and III(14)), with III(13) and III(14) assumed to be the major sites. The interaction between III(2-3) and III(12-14) was inhibited by DP, whereas the interaction between I(1-5) and III(12-14) was specifically and strongly enhanced by DP. Because the interaction between III(2-3) and III(12-14) is involved in forming a globular conformation of fibronectin, and that between I(1-5) and III(12-14) is required for forming fibronectin fibrils, DP promotes fibronectin fibril formation probably by changing the fibronectin conformation. These results suggest that DP has an accelerating role in fibroblast cell adhesion to the provisional matrix in the initial stage of wound healing.

  1. Plasma fibronectin in patients undergoing major surgery

    International Nuclear Information System (INIS)

    Sallam, M.H.M.

    2003-01-01

    Plasma fibronectin in patients undergoing major surgery had been determined before and after operation. The study was done on 15 patients and 15 normal healthy individuals. The study revealed that patients subjected to major operation, their fibronectin level was normal before operation followed by reduction one day post-operation. After one week, fibronectin level raised again nearly to the pre-operations levels. The probable mechanisms of fibronectin in healing processes were discussed. Fibronectin (FN) is a family of structurally and immunologically related high molecular weight glycoproteins that are present in many cell surfaces, in extracellular fluids, in connective tissues and in most membranes. Interaction with certain discrete extracellular substances, such as a glucosaminoglycans (e.g. heparin), fibrin and collagen and with cell surface structure seem to account for many of its biological activities, among which are regulation of adhesion, spreading and locomotion (Mosesson and amrani, 1980). The concentration of Fn in human plasma decreases after extensive destruction such as that occurs in major surgery, burns or other trauma. This decrease has been generally though to be due to increased consumption of soluble plasma Fn in opsonization of particulate and soluble debris from circulation by the reticuloendothelial (RE) system. Fn rapidly appears in injury areas, in experimentally induced blisters, wounded and epithelium tissues (Petersen et al., 1985). Fn accumulates at times of increased vascular permeability and it is produced by cell of blood vessels in response to injury

  2. ITER EDA newsletter. V. 10, no. 1

    International Nuclear Information System (INIS)

    2001-01-01

    This article provides a summary of results of the ITER Physics Committee Meeting, which was held on 14 October 2000 at the ITER Garching Joint Work Site, Germany. The ITER Physics Committee is the body responsible for overseeing, through the seven specialized Expert Groups, the R and D activities contributed voluntarily by the ITER Parties. The Parties' Physics Designated Persons, the Chairs and Co-Chairs of ITER Physics Expert Groups and the JCT members involved attended the Meeting. As usual, the meeting was chaired by the ITER Director, Dr. R. Aymar, who reported on the status of the ITER EDA. Dr. Aymar described the steps being taken in preparing the ITER-FEAT Final Design Report (FDR), and further stated that the Report would be available in time to be of benefit to the Negotiations on the ITER Joint Implementation, expected to start around May 2001. All Parties recognize that the ITER Physics Expert Group structure has been useful in focusing the tokamak physics activity on the ITER-relevant issues and provides an efficient worldwide collaboration on confirming innovative solutions. The concept of an international workshop to be organized as a pre-meeting of each Expert Group meeting, in order to involve U.S. scientists in the discussion of generic tokamak physics issues, was introduced in 2000, with some success, and its goal should be pursued

  3. Peroxynitrite-mediated oxidation of plasma fibronectin.

    Science.gov (United States)

    Degendorfer, Georg; Chuang, Christine Y; Kawasaki, Hiroaki; Hammer, Astrid; Malle, Ernst; Yamakura, Fumiyuki; Davies, Michael J

    2016-08-01

    Fibronectin is a large dimeric glycoprotein present in both human plasma and in basement membranes. The latter are specialized extracellular matrices underlying endothelial cells in the artery wall. Peroxynitrous acid (ONOOH) a potent oxidizing and nitrating agent, is formed in vivo from superoxide and nitric oxide radicals by stimulated macrophages and other cells. Considerable evidence supports ONOOH involvement in human atherosclerotic lesion development and rupture, possibly via extracellular matrix damage. Here we demonstrate that Tyr and Trp residues on human plasma fibronectin are highly sensitive to ONOOH with this resulting in the formation of 3-nitrotyrosine, 6-nitrotryptophan and dityrosine as well as protein aggregation and fragmentation. This occurs with equimolar or greater levels of oxidant, and in a dose-dependent manner. Modification of Tyr was quantitatively more significant than Trp (9.1% versus 1.5% conversion with 500μM ONOOH) after accounting for parent amino acid abundance, but only accounts for a small percentage of the total oxidant added. LC-MS studies identified 28 nitration sites (24 Tyr, 4 Trp) with many of these present within domains critical to protein function, including the cell-binding and anastellin domains. Human coronary artery endothelial cells showed decreased adherence and cell-spreading on ONOOH-modified fibronectin compared to control, consistent with cellular dysfunction induced by the modified matrix. Studies on human atherosclerotic lesions have provided evidence for co-localization of 3-nitrotyrosine and fibronectin. ONOOH-mediated fibronectin modification and compromised cell-matrix interactions, may contribute to endothelial cell dysfunction, a weakening of the fibrous cap of atherosclerotic lesions, and an increased propensity to rupture. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Peroxynitrite-mediated oxidation of plasma fibronectin

    DEFF Research Database (Denmark)

    Degendorfer, Georg; Chuang, Christine Y; Kawasaki, Hiroaki

    2016-01-01

    Fibronectin is a large dimeric glycoprotein present in both human plasma and in basement membranes. The latter are specialized extracellular matrices underlying endothelial cells in the artery wall. Peroxynitrous acid (ONOOH) a potent oxidizing and nitrating agent, is formed in vivo from superoxide...... and nitric oxide radicals by stimulated macrophages and other cells. Considerable evidence supports ONOOH involvement in human atherosclerotic lesion development and rupture, possibly via extracellular matrix damage. Here we demonstrate that Tyr and Trp residues on human plasma fibronectin are highly...... sensitive to ONOOH with this resulting in the formation of 3-nitrotyrosine, 6-nitrotryptophan and dityrosine as well as protein aggregation and fragmentation. This occurs with equimolar or greater levels of oxidant, and in a dose-dependent manner. Modification of Tyr was quantitatively more significant than...

  5. Needs for European decommissioning academy (EDA)

    International Nuclear Information System (INIS)

    Slugen, Vladimir

    2014-01-01

    According to analyses presented at EC meeting focused on decommissioning organized at 11.9.2012 in Brussels, it was stated that at least 500 new international experts for decommissioning will be needed in Europe up to 2025, which means about 35 per year. Having in mind the actual EHRO-N report from 2013 focused on operation of nuclear facilities and an assumption that the ratio between nuclear experts, nuclearized and nuclear aware people is comparable also for decommissioning, as well as the fact that the special study branch for decommissioning in the European countries almost does not exist, this European Decommissioning Academy (EDA) could be helpful in the over-bridging this gap. The main goal is - from about 74% of nuclearized experts (graduated at different technical Universities and increased their nuclear knowledge and skills mostly via on-job training and often in the area of NPP operation) to create nuclear experts for decommissioning via our post-gradual coursed organized in two semester study at our Academy, which will include the lessons, practical exercises in our laboratories, on-site training at NPP V-1 in Jaslovske Bohunice, Slovakia as well as 3 days technical tour to JAVYS (Slovakia), UJV Rez (Czech Rep.) and PURAM (Hungary), respectively. Beside the exams in selected topics (courses), the final thesis written under supervision of recognized experts will be the precondition for graduation and certification of the participants. For the first run of the EDA scheduled on 2014 we would like to focus on VVER decommissioning issues because this reactor type is the most distributed design in the world and many of these units are actually in decommissioning process or will be decommissioned in the near future in Europe. The growing decommissioning market creates a potential for new activities, with highly skilled jobs in an innovative field, involving high-level technologies. A clear global positioning of the EU will stimulate the export of know-how to

  6. EDAS-manual. SATAN - system to analyze tremendous amounts of nuclear data. Vol. 2

    International Nuclear Information System (INIS)

    Goeringer, H.; Gralla, S.; Malzacher, P.; Richter, M.; Schall, D.; Winkelmann, K.

    1988-09-01

    The system to analyze tremendous amounts of nuclear data (SATAN) shows different steps of a special experiment data evaluation called 'Linearisation'. The report contains the EDAS-manual with EDAS-command, TSO-command, macro and procedure. Syntax and usage of EDAS macros are explained. (DG)

  7. 76 FR 19976 - Proposed Information Collection; Comment Request; Survey of EDA Grant Process Improvement

    Science.gov (United States)

    2011-04-11

    ...; Comment Request; Survey of EDA Grant Process Improvement AGENCY: Economic Development Administration.... In 2010, EDA made improvements in its grant application process. The proposed short survey of five to... improvements to the grant application process and to make any necessary adjustments. EDA would like to conduct...

  8. [Infants of diabetic mothers (IDM). II -- Fibronectin and perinatal morbidity].

    Science.gov (United States)

    Martín Carballo, G; Codoceo Alquila, R; Fernández Cano, G; Hawkins Carranza, F; Grande Aragón, C; Velasco Hernando, A; Gracia Bouthelier, R

    1997-09-01

    The objective of this study was to determine fibronectin levels in umbilical cord blood of infants of diabetic mothers (IDM) and evaluate a possible correlation with perinatal pathology. A prospective study of 58 IDM (33 males and 25 females) and 58 control newborns (NB) (33 males and 25 females) was carried out. There were no differences in fibronectin levels between the two groups nor between the sexes. Perinatal morbidity was higher in the IDM group, but there was no correlation between fibronectin levels and the presence of perinatal pathology. Fibronectin levels are not useful in the perinatal evaluation of infants of diabetic mothers.

  9. Sorption of fibronectin to human root surfaces in vitro

    International Nuclear Information System (INIS)

    Mendieta, C.; Caravana, C.; Fine, D.H.

    1990-01-01

    The purpose of this study was to determine the conditions that favor the sorption and retention of human plasma fibronectin to cementum. Rectangular root segments prepared from teeth extracted for orthodontic reasons were mounted on a capillary pipette and immersed in solutions of 125 I fibronectin for assay of cementum sorption under various conditions. Kinetic studies showed sorption to be rapid, with 77% of the maximum fibronectin sorption occurring within 1 minute. Fibronectin sorption was reduced when added in conjunction with serum and was inhibited by monovalent ions (such as sodium), but enhanced in the presence of divalent cations (such as calcium). Exposure of cementum to serum partially blocked subsequent sorption of fibronectin, while cementum bound fibronectin was eluted by subsequent exposure to serum. Treatment of cementum with citric acid pH 1.1 (4 minutes) followed by 5% sodium hypochlorite (5 minutes) caused a significant increase in fibronectin sorption with maximum retention upon subsequent exposure to serum (P less than 0.05). Fibronectin sorption to cementum was: rapid, electrostatic in nature, competitive, reversible, Ca+(+)-facilitated, and maximized by prior treatment of the root with citric acid and sodium hypochlorite. It is concluded that sorption of fibronectin to cementum can be achieved for clinical gain; however, conditions of application can significantly influence both accumulation and subsequent release of root sorbed material

  10. Discriminating stress from cognitive load using a wearable EDA device.

    Science.gov (United States)

    Setz, Cornelia; Arnrich, Bert; Schumm, Johannes; La Marca, Roberto; Tröster, Gerhard; Ehlert, Ulrike

    2010-03-01

    The inferred cost of work-related stress call for prevention strategies that aim at detecting early warning signs at the workplace. This paper goes one step towards the goal of developing a personal health system for detecting stress. We analyze the discriminative power of electrodermal activity (EDA) in distinguishing stress from cognitive load in an office environment. A collective of 33 subjects underwent a laboratory intervention that included mild cognitive load and two stress factors, which are relevant at the workplace: mental stress induced by solving arithmetic problems under time pressure and psychosocial stress induced by social-evaluative threat. During the experiments, a wearable device was used to monitor the EDA as a measure of the individual stress reaction. Analysis of the data showed that the distributions of the EDA peak height and the instantaneous peak rate carry information about the stress level of a person. Six classifiers were investigated regarding their ability to discriminate cognitive load from stress. A maximum accuracy of 82.8% was achieved for discriminating stress from cognitive load. This would allow keeping track of stressful phases during a working day by using a wearable EDA device.

  11. ITER EDA newsletter. V. 2, Nos. 7/8

    International Nuclear Information System (INIS)

    1993-01-01

    This ITER EDA (Engineering Design Activities) Newsletter issue includes a description of the ITER Design Integration Division, and reports on the 5th IAEA Technical Committee Meeting on Developments in Fusion Safety held in Toronto, Canada, 7 - 11 June 1993, and on the International Atomic Energy Agency's Atomic and Plasma-Material Interaction Data Activities in support of the ITER Engineering Design Activities

  12. EDA program IM and ageing: Results of the Dutch contribution

    NARCIS (Netherlands)

    Scholtes, G.

    2014-01-01

    In the scope of the co-operation within the EDA on Insensitive Munitions and ageing, TNO has carried out an investigation on the effects of ageing on the vulnerability characteristics of energetic materials. For this study pristine and accelerated aged RDX-based polymer bonded explosives (PBX) have

  13. Fibronectin in tissue regeneration : timely disassembly of the scaffold is necessary to complete the build

    NARCIS (Netherlands)

    Stoffels, Josephine M. J.; Zhao, Chao; Baron, Wia

    2013-01-01

    Tissue injury initiates extracellular matrix molecule expression, including fibronectin production by local cells and fibronectin leakage from plasma. To benefit tissue regeneration, fibronectin promotes opsonization of tissue debris, migration, proliferation, and contraction of cells involved in

  14. PLC-γ1 Regulates Fibronectin Assembly and Cell Aggregation

    Science.gov (United States)

    Crooke, Cornelia E.; Pozzi, Ambra; Carpenter, Graham F.

    2009-01-01

    Phospholipase C-γ1 (PLC-γ1) mediates cell adhesion and migration through an undefined mechanism. Here, we examine the role of PLC-γ1 in cell-matrix adhesion in a hanging drop assay of cell aggregation. Plcg1 Null (−/−) mouse embryonic fibroblasts formed aggregates that were larger and significantly more resistant to dissociation than cells in which PLC-γ1 is re-expressed (Null + cells). Aggregate formation could be disrupted by inhibition of fibronectin interaction with integrins, indicating that fibronectin assembly may mediate aggregate formation. Fibronectin assembly was mediated by integrin α5β1 in both cell lines, while assays measuring fibronectin assembly revealed increased assembly in the Null cells. Null and Null + cells exhibited equivalent fibronectin mRNA levels and equivalent levels of fibronectin protein in pulse-labeling experiments. However, levels of secreted fibronectin in the conditioned medium were increased in Null cells. The data implicates a negative regulatory role for PLC-γ1 in cell aggregation by controlling the secretion of fibronectin into the media and its assembly into fibrils. PMID:19379731

  15. Determination of activated plasma fibronectin using radioactive labelled collagen I

    DEFF Research Database (Denmark)

    Fenger, M

    1984-01-01

    The plasma concentration of biological active fibronectin was assayed by a protein binding assay using 125I-collagen I as ligand and heparin as activator. The standard curve is linear for a fibronectin range of 1.1-11 pmol (0.5-5.0 micrograms) and the coefficient of variation was less than 10...

  16. Tenascin and fibronectin expression in healing human myocardial scars

    NARCIS (Netherlands)

    Willems, I. E.; Arends, J. W.; Daemen, M. J.

    1996-01-01

    Fibronectin and tenascin are matrix proteins known to be present in early experimental wound healing. As only limited data are available regarding early matrix changes in human myocardial infarction, the presence of tenascin and fibronectin was studied in human myocardial infarctions of different

  17. Determination of activated plasma fibronectin using radioactive labelled collagen I

    DEFF Research Database (Denmark)

    Fenger, M

    1984-01-01

    the structure-function relationship of heparin and heparansulphate in activation of fibronectin. Low-sulphated heparansulphate from umbilical cords and heparin-activated fibronectin but the effect was uncorrelated to anticoagulation activity. Only a small fraction of the heparin was actually capable...

  18. Treponema pallidum receptor binding proteins interact with fibronectin

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, K.M.; Baseman, J.B.; Alderete, J.F.

    1983-06-01

    Analysis of plasma proteins avidly bound to T. pallidum surfaces revealed the ability of T. pallidum to acquire numerous host macromolecules. No acquisition was evident by the avirulent spirochete, T. phagedenis biotype Reiter. Western blotting technology using hyperimmune antifibronectin serum as a probe revealed the ability of virulent treponemes to avidly bind fibronectin from a complex medium such as plasma. The specificity of the tiplike adherence of motile T. pallidum to fibronectin-coated glass surfaces and to fibronectin on HEp-2 cells was reinforced by the observation that pretreatment of coverslips or cell monolayers with monospecific antiserum against fibronectin substantially reduced T. pallidum attachment. The stoichiometric binding of T. pallidum to fibronectin-coated coverslips and the inability of unlabeled or /sup 35/S-radiolabeled treponemes to interact with glass surfaces treated with other plasma proteins further established the specific nature of the interaction between virulent T. pallidum and fibronectin. The avid association between three outer envelope proteins of T. pallidum and fibronectin was also demonstrated. These treponemal surface proteins have been previously identified as putative receptor-binding proteins responsible for T. pallidum parasitism of host cells. The data suggest that surface fibronectin mediates tip-oriented attachment of T. pallidum to host cells via a receptor-ligand mechanism of recognition.

  19. Whole Genome Sequencing Reveals Novel Non-Synonymous Mutation in Ectodysplasin A (EDA) Associated with Non-Syndromic X-Linked Dominant Congenital Tooth Agenesis

    Science.gov (United States)

    Sarkar, Tanmoy; Bansal, Rajesh; Das, Parimal

    2014-01-01

    Congenital tooth agenesis in human is characterized by failure of tooth development during tooth organogenesis. 300 genes in mouse and 30 genes in human so far have been known to regulate tooth development. However, candidature of only 5 genes viz. PAX9, MSX1, AXIN2, WNT10A and EDA have been experimentally established for congenitally missing teeth like hypodontia and oligodontia. In this study an Indian family with multiple congenital tooth agenesis was identified. Pattern of inheritance was apparently autosomal dominant type with a rare possibility to be X-linked. Whole genome sequencing of two affected individuals was carried out which revealed 119 novel non-synonymous single nucleotide variations (SNVs) distributed among 117 genes. Out of these only one variation (c.956G>T) located at exon 9 of X-linked EDA gene was considered as pathogenic and validated among all the affected and unaffected family members and unrelated controls. This variation leads to p.Ser319Ile change in the TNF homology domain of EDA (transcript variant 1) protein. In silico analysis predicts that this Ser319 is well conserved across different vertebrate species and a part of putative receptor binding site. Structure based homology modeling predicts that this amino acid residue along with four other amino acid residues nearby, those when mutated known to cause selective tooth agenesis, form a cluster that may have functional significance. Taken together these results suggest that c.956G>T (p.Ser319Ile) mutation plausibly reduces the receptor binding activity of EDA leading to distinct tooth agenesis in this family. PMID:25203534

  20. Can EDA Combat the Rise of Electronic Counterfeiting?

    Science.gov (United States)

    2012-06-01

    Can EDA Combat the Rise of Electronic Counterfeiting? Farinaz Koushanfar Rice University, Houston, TX Saverio Fazzari Booz Allen Hamilton, Inc...conceptually new security mech- anisms such as physical unclonable functions ( PUFs ). On the other hand, they also directly invalidate numer- ous hardware...the man- ufacturing date and the original buyer. 4.3 Physical Unclonable Functions ( PUFs ) Physical unclonable functions ( PUFs ) are one potential

  1. Propolis Modulates Fibronectin Expression in the Matrix of Thermal Injury

    Directory of Open Access Journals (Sweden)

    Pawel Olczyk

    2014-01-01

    Full Text Available The aim of the study was to assess the propolis effect on fibronectin metabolism in the course of burn wounds healing process. A model of burn wound healing of pig skin was applied. The amount of the released glycoprotein was assessed by a surface plasmon resonance. The profile of extracted fibronectin components was also assessed by an electrophoresis in polyacrylamide gel, with a subsequent immunodetection by Western Blotting. Propolis burn treatment decreased the release of fibronectin components from healing wounds in relation to damages treated with silver sulfadiazine. The main reason of decreased extraction of fibronectin components from wounds treated with propolis was a substantial decrease of degradation product release of the mentioned glycoprotein, which was observed particularly from the 3rd to 5th day of the repair. Wounds treatment with propolis demonstrated, especially in relation to damages treated with silver sulfadiazine, the decreased release of synthesized fibronectin molecules. The obtained results suggest that propolis modifies fibronectin metabolism in the course of wound healing process. The influence of propolis is reflected in prevention of fibronectin biosynthesis as well as its degradation in the wound area. The above-mentioned metabolic changes may decrease the risk of complications in the repair wounds process.

  2. Periodicity of DNA in exons

    Directory of Open Access Journals (Sweden)

    Kinghorn Brian

    2004-08-01

    Full Text Available Abstract Background The periodic pattern of DNA in exons is a known phenomenon. It was suggested that one of the initial causes of periodicity could be the universal (RNYnpattern (R = A or G, Y = C or U, N = any base of ancient RNA. Two major questions were addressed in this paper. Firstly, the cause of DNA periodicity, which was investigated by comparisons between real and simulated coding sequences. Secondly, quantification of DNA periodicity was made using an evolutionary algorithm, which was not previously used for such purposes. Results We have shown that simulated coding sequences, which were composed using codon usage frequencies only, demonstrate DNA periodicity very similar to the observed in real exons. It was also found that DNA periodicity disappears in the simulated sequences, when the frequencies of codons become equal. Frequencies of the nucleotides (and the dinucleotide AG at each location along phase 0 exons were calculated for C. elegans, D. melanogaster and H. sapiens. Two models were used to fit these data, with the key objective of describing periodicity. Both of the models showed that the best-fit curves closely matched the actual data points. The first dynamic period determination model consistently generated a value, which was very close to the period equal to 3 nucleotides. The second fixed period model, as expected, kept the period exactly equal to 3 and did not detract from its goodness of fit. Conclusions Conclusion can be drawn that DNA periodicity in exons is determined by codon usage frequencies. It is essential to differentiate between DNA periodicity itself, and the length of the period equal to 3. Periodicity itself is a result of certain combinations of codons with different frequencies typical for a species. The length of period equal to 3, instead, is caused by the triplet nature of genetic code. The models and evolutionary algorithm used for characterising DNA periodicity are proven to be an effective tool

  3. Plasma fibronectin concentrations in patients with liver diseases

    DEFF Research Database (Denmark)

    Gluud, C; Dejgaard, A; Clemmensen, I

    1983-01-01

    (n = 7); type non A, non B (n = 1] had significantly (P less than 0.01) raised plasma fibronectin concentrations (median 506 mg/l (range 339-804] compared to controls (median 399 mg/l (range 304-462]. Morbidly obese patients with fatty liver (n = 11) had significantly (P less than 0.001) raised...... age- and sex-matched healthy controls in patients with chronic persistent or chronic active hepatitis (n = 7), primary biliary cirrhosis (n = 8), alcoholic fatty liver (n = 9), alcoholic hepatitis (n = 10), and alcoholic cirrhosis (n = 16). Patients with acute viral hepatitis (type A (n = 2); type B......Plasma, obtained just prior to diagnostic liver biopsy in 71 patients with various liver diseases, was examined by electroimmunoassay using immunoglobulin against human fibronectin and purified plasma fibronectin as standard. The plasma fibronectin concentration was not significantly different from...

  4. Fibronectin distribution during the development of fetal rat skin

    DEFF Research Database (Denmark)

    Gibson, W T; Couchman, J R; Weaver, A C

    1983-01-01

    Fibronectin distribution during fetal rat skin development has been studied immunocytochemically at the light and electron microscope level from 16 days of gestation to birth. The dermal-epidermal junction, the dermis, and connective tissue around developing muscle were shown by light microscopy...... to be heavily stained throughout this period. The development of hair follicles from about 18 days onward was not associated with any consistent change in fibronectin distribution. The heavy staining of the upper dermis was associated with a high density of mesenchymal cells, and immunoelectron microscopy...... revealed fibronectin on the surface of many of these cells and in association with the surrounding fine collagen fibrils. At the dermal-epidermal junction, both follicular and interfollicular, fibronectin was localized mainly in the plasma membrane and lamina lucida regions of the basement membrane...

  5. Fetal fibronectin as a predictor of labor in Mexican women

    Directory of Open Access Journals (Sweden)

    Mario I. Ortiz

    2012-05-01

    Full Text Available Background: The presence of fetal fibronectin in vaginal secretions has been regarded as a predictor of labor in pregnant term and preterm. Objective: For this reason the purpose of this study was to evaluate the predictive validity of fibronectin in pregnant women who attended the General Hospital SSH Pachuca, Hidalgo, Mexico. Methodology: We included pregnant patients admitted to hospital for pregnancy control. Fetal fibronectin was determined in all participants and then followed until the onset of labor. Results: A total of 148 patients participated. One group with 53 patients less than 37 weeks gestation, and another group of 95 patients with 37 or more weeks gestation. In general, the test showed an average sensitivity of 72.5% and specificity 82.9% average for both groups. Conclusion: Based on these results, we recommend using fibronectin test in pregnant women after 32 weeks of gestation, both in emergency departments and outpatient clinics.

  6. In Vitro Analysis of Fibronectin-Modified Titanium Surfaces

    Science.gov (United States)

    Chang, Yu-Chi; Lee, Wei-Fang; Feng, Sheng-Wei; Huang, Haw-Ming; Lin, Che-Tong; Teng, Nai-Chia; Chang, Wei Jen

    2016-01-01

    Background Glow discharge plasma (GDP) procedure is an effective method for grafting various proteins, including albumin, type I collagen, and fibronectin, onto a titanium surface. However, the behavior and impact of titanium (Ti) surface modification is yet to be unraveled. Purpose The purpose of this study is to evaluate and analyze the biological properties of fibronectin-grafted Ti surfaces treated by GDP. Materials and Methods Grade II Ti discs were initially cleaned and autoclaved to obtain original specimens. Subsequently, the specimens were GDP treated and grafted with fibronectin to form Ar-GDP (Argon GDP treatment only) and GDP-fib (fibronectin coating following GDP treatment) groups. Blood coagulation test and MG-63 cell culture were performed to evaluate the biological effects on the specimen. Results There was no significant difference between Ar-GDP and GDP-fib groups in blood compatibility analysis. While in the MTT test, cellular proliferation was benefited from the presence of fibronectin coating. The numbers of cells on Ar-GDP and GDP-fib specimens were greater than those in the original specimens after 24 h of culturing. Conclusions GDP treatment combined with fibronectin grafting favored MG-63 cell adhesion, migration, and proliferation on titanium surfaces, which could be attributed to the improved surface properties. PMID:26731536

  7. Parametric analysis and operational performance of EDA-ITER

    International Nuclear Information System (INIS)

    Murakami, Yoshiki; Tsunematsu, Toshihide; Fujieda, Hirobumi.

    1994-06-01

    Confinement capability of EDA-ITER is investigated by using a 0-D model based on CDA physics design guidelines. Confinement enhancement factor (H-factor) is evaluated and required fusion power (P FUS ) for the ignition is calculated. It is found that ignition is possible in H-mode plasma (H=2) when helium accumulation (He) is 10% and P FUS ≥ 1 GW. For Rebut-Lallia scaling law, L-mode (H=1) ignition is possible when P FUS ≥ 3 GW. The required fusion power is, however, more than 4 GW even in H-mode plasmas when the helium accumulation is 20%. Therefore, it is an important future work to study how much helium accumulates in a burning plasma. Capability of steady-state mode operation is also investigated. Required current-drive power for H-mode plasma is about 140 MW when He=10% and the fusion gain Q is more than 5. If the enhanced confinement (H∼3) in high safety factor region (q∼5) can be adoptable, steady-state operation with Q>10 is possible and the required current-drive power is about 60 MW. In spite of the larger fusion power, the divertor heat load of EDA-ITER calculated by scaling models is comparable or smaller than that of CDA-ITER due to the longer connection length. Thermal instability of EDA-ITER is also investigated. The growth time is about 15 s for ITER89 power scaling law. Fusion power excursion is investigated in very preliminary way. It is found that the power rises from 1.5 GW to 3 GW in about 100 s if there is no control. Although this instability could be stabilized by beta limit or helium accumulation effect, it is an important future work since it may cause severe problem. (author)

  8. The emergence of alternative 3' and 5' splice site exons from constitutive exons.

    Directory of Open Access Journals (Sweden)

    Eli Koren

    2007-05-01

    Full Text Available Alternative 3' and 5' splice site (ss events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases. However, only few of the characteristics that distinguish these events from alternative cassette exons are known currently. In this study, we compared the characteristics of constitutive exons, alternative cassette exons, and alternative 3'ss and 5'ss exons. The results revealed that alternative 3'ss and 5'ss exons are an intermediate state between constitutive and alternative cassette exons, where the constitutive side resembles constitutive exons, and the alternative side resembles alternative cassette exons. The results also show that alternative 3'ss and 5'ss exons exhibit low levels of symmetry (frame-preserving, similar to constitutive exons, whereas the sequence between the two alternative splice sites shows high symmetry levels, similar to alternative cassette exons. In addition, flanking intronic conservation analysis revealed that exons whose alternative splice sites are at least nine nucleotides apart show a high conservation level, indicating intronic participation in the regulation of their splicing, whereas exons whose alternative splice sites are fewer than nine nucleotides apart show a low conservation level. Further examination of these exons, spanning seven vertebrate species, suggests an evolutionary model in which the alternative state is a derivative of an ancestral constitutive exon, where a mutation inside the exon or along the flanking intron resulted in the creation of a new splice site that competes with the original one, leading to alternative splice site selection. This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution.

  9. POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons

    Directory of Open Access Journals (Sweden)

    Chonka Ashley

    2008-09-01

    Full Text Available Abstract Background The existence of exons and introns has been known for thirty years. Despite this knowledge, there is a lack of formal research into the categorization of exons. Exon taxonomies used by researchers tend to be selected ad hoc or based on an information poor de-facto standard. Exons have been shown to have specific properties and functions based on among other things their location and order. These factors should play a role in the naming to increase specificity about which exon type(s are in question. Results POEM (Protein Oriented Exon Monikers is a new taxonomy focused on protein proximal exons. It integrates three dimensions of information (Global Position, Regional Position and Region, thus its exon categories are based on known statistical exon features. POEM is applied to two congruent untranslated exon datasets resulting in the following statistical properties. Using the POEM taxonomy previous wide ranging estimates of initial 5' untranslated region exons are resolved. According to our datasets, 29–36% of genes have wholly untranslated first exons. Untranslated exon containing sequences are shown to have consistently up to 6 times more 5' untranslated exons than 3' untranslated exons. Finally, three exon patterns are determined which account for 70% of untranslated exon genes. Conclusion We describe a thorough three-dimensional exon taxonomy called POEM, which is biologically and statistically relevant. No previous taxonomy provides such fine grained information and yet still includes all valid information dimensions. The use of POEM will improve the accuracy of genefinder comparisons and analysis by means of a common taxonomy. It will also facilitate unambiguous communication due to its fine granularity

  10. Generation and characterization of function-blocking anti-ectodysplasin A (EDA) monoclonal antibodies that induce ectodermal dysplasia.

    Science.gov (United States)

    Kowalczyk-Quintas, Christine; Willen, Laure; Dang, Anh Thu; Sarrasin, Heidi; Tardivel, Aubry; Hermes, Katharina; Schneider, Holm; Gaide, Olivier; Donzé, Olivier; Kirby, Neil; Headon, Denis J; Schneider, Pascal

    2014-02-14

    Development of ectodermal appendages, such as hair, teeth, sweat glands, sebaceous glands, and mammary glands, requires the action of the TNF family ligand ectodysplasin A (EDA). Mutations of the X-linked EDA gene cause reduction or absence of many ectodermal appendages and have been identified as a cause of ectodermal dysplasia in humans, mice, dogs, and cattle. We have generated blocking antibodies, raised in Eda-deficient mice, against the conserved, receptor-binding domain of EDA. These antibodies recognize epitopes overlapping the receptor-binding site and prevent EDA from binding and activating EDAR at close to stoichiometric ratios in in vitro binding and activity assays. The antibodies block EDA1 and EDA2 of both mammalian and avian origin and, in vivo, suppress the ability of recombinant Fc-EDA1 to rescue ectodermal dysplasia in Eda-deficient Tabby mice. Moreover, administration of EDA blocking antibodies to pregnant wild type mice induced in developing wild type fetuses a marked and permanent ectodermal dysplasia. These function-blocking anti-EDA antibodies with wide cross-species reactivity will enable study of the developmental and postdevelopmental roles of EDA in a variety of organisms and open the route to therapeutic intervention in conditions in which EDA may be implicated.

  11. Plasma fibronectin supports hemostasis and regulates thrombosis

    Science.gov (United States)

    Wang, Yiming; Reheman, Adili; Spring, Christopher M.; Kalantari, Jalil; Marshall, Alexandra H.; Wolberg, Alisa S.; Gross, Peter L.; Weitz, Jeffrey I.; Rand, Margaret L.; Mosher, Deane F.; Freedman, John; Ni, Heyu

    2014-01-01

    Plasma fibronectin (pFn) has long been suspected to be involved in hemostasis; however, direct evidence has been lacking. Here, we demonstrated that pFn is vital to control bleeding in fibrinogen-deficient mice and in WT mice given anticoagulants. At the site of vessel injury, pFn was rapidly deposited and initiated hemostasis, even before platelet accumulation, which is considered the first wave of hemostasis. This pFn deposition was independent of fibrinogen, von Willebrand factor, β3 integrin, and platelets. Confocal and scanning electron microscopy revealed pFn integration into fibrin, which increased fibrin fiber diameter and enhanced the mechanical strength of clots, as determined by thromboelastography. Interestingly, pFn promoted platelet aggregation when linked with fibrin but inhibited this process when fibrin was absent. Therefore, pFn may gradually switch from supporting hemostasis to inhibiting thrombosis and vessel occlusion following the fibrin gradient that decreases farther from the injured endothelium. Our data indicate that pFn is a supportive factor in hemostasis, which is vital under both genetic and therapeutic conditions of coagulation deficiency. By interacting with fibrin and platelet β3 integrin, pFn plays a self-limiting regulatory role in thrombosis, suggesting pFn transfusion may be a potential therapy for bleeding disorders, particularly in association with anticoagulant therapy. PMID:25180602

  12. Identification of protein features encoded by alternative exons using Exon Ontology.

    Science.gov (United States)

    Tranchevent, Léon-Charles; Aubé, Fabien; Dulaurier, Louis; Benoit-Pilven, Clara; Rey, Amandine; Poret, Arnaud; Chautard, Emilie; Mortada, Hussein; Desmet, François-Olivier; Chakrama, Fatima Zahra; Moreno-Garcia, Maira Alejandra; Goillot, Evelyne; Janczarski, Stéphane; Mortreux, Franck; Bourgeois, Cyril F; Auboeuf, Didier

    2017-06-01

    Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named "Exon Ontology," based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information. © 2017 Tranchevent et al.; Published by Cold Spring Harbor Laboratory Press.

  13. 75 FR 16739 - EDA Participation in the Energy Efficient Building Systems Regional Innovation Cluster Initiative

    Science.gov (United States)

    2010-04-02

    ... investment boards, institutions of higher education including community colleges, and other public and... Federal and non-Federal investments in business development and support, public infrastructure, workforce... as part of the Initiative. EDA seeks an EDA Co-applicant to help facilitate a high degree of...

  14. A novel missense mutation in collagenous domain of EDA gene in a ...

    Indian Academy of Sciences (India)

    was not present in the healthy males and other females in this family, or in additional 200 healthy control individuals. The mutation caused a substitution of a proline with a leucine in. EDA protein (p.P220L), which is located at the third position of the 13th Gly-X-Y repeat, and may affect the stability and multimerzation of EDA.

  15. Brain fibronectin expression in prenatally irradiated mice

    International Nuclear Information System (INIS)

    Meznarich, H.K.; McCoy, L.S.; Bale, T.L.; Stiegler, G.L.; Sikov, M.R.

    1993-01-01

    Activation of gene transcription by radiation has been recently demonstrated in vivo. However, little is known on the specificity of these alterations on gene transcription. Prenatal irradiation is a known teratogen that affects the developing mammalian central nervous system (CNS). Altered neuronal migration has been suggested as a mechanism for abnormal development of prenatally irradiated brains. Fibronectin (FN), an extracellular glycoprotein, is essential for neural crest cell migration and neural cell growth. In addition, elevated levels of FN have been found in the extracellular matrix of irradiated lung. To test whether brain FN is affected by radiation, either FN level in insoluble matrix fraction or expression of FN mRNA was examined pre- and postnatally after irradiation. Mice (CD1), at 13 d of gestation (DG), served either as controls or were irradiated with 14 DG, 17 DG, or 5,6, or 14 d postnatal. Brain and liver were collected from offspring and analyzed for either total FN protein levels or relative mRNAs for FN and tubulin. Results of prenatal irradiation on reduction of postnatal brain weight relative to whole are comparable to that reported by others. Insoluble matrix fraction (IMF) per gram of brain, liver, lung, and heart weight was not significantly different either between control and irradiated groups or between postnatal stages, suggesting that radiation did not affect the IMF. However, total amounts of FN in brain IMF at 17 DG were significantly different (p < .02) between normal (1.66 ± 0.80 μg) and irradiated brains (0.58 ± 0.22 μg). FN mRNA was detectable at 13, 14, and 17 DG, but was not detectable at 6 and 14 d postnatal, indicating that FN mRNA is developmentally regulated. 41 refs., 4 figs., 3 tabs

  16. Raised Vaginal Fluid Fibronectin Level Indicates Premature Rupture of Membrane

    Directory of Open Access Journals (Sweden)

    Amrita Bhowmik

    2012-07-01

    Full Text Available Background: Premature rupture of membrane (PROM is one of the common complications of pregnancy that has major impact on fetal and neonatal outcome. It is the commonest clinical event where a normal pregnancy becomes suddenly a high-risk one for mother and fetus or neonate. Objective: The study was undertaken to investigate whether raised fibronectin level in vaginal fluid may indicate premature rupture of membrane. Materials and Methods: This cross sectional study was conducted in the department of Obstetrics and Gynecology in Sir Salimullah Medical College & Mitford Hospital, Dhaka during the period of January 2006 to December 2007. A total of 114 pregnant women with gestational age 28th week up to 40th week were included. Sixty were PROM (Group I and 54 were non-PROM (Group II subjects. Fibronectin in vaginal fluid was measured by an immunochemical reaction by nephelometer. Statistical analysis was done by SPSS version 10.0. Results: The PROM patients had significantly higher concentration of fibronectin (225.77 ± 115.18 ng/mL compared to that in non-PROM subjects (8.04 ± 16.17 ng/mL (p < 0.001. Conclusion: It can be concluded that in cases of unequivocal rupture or intactness of the membranes, the result of the fibronectin test corresponds well with the clinical situation. So fibronectin is a sensitive test for detection of amniotic fluid in the vagina.

  17. ExonMiner: Web service for analysis of GeneChip Exon array data

    Directory of Open Access Journals (Sweden)

    Imoto Seiya

    2008-11-01

    Full Text Available Abstract Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1 data normalization, (2 statistical analysis based on two-way ANOVA, (3 finding transcripts with significantly different splice patterns, (4 efficient visualization based on heatmaps and barplots, and (5 meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.

  18. Glomerulopathy associated with predominant fibronectin deposits: Exclusion of the genes for fibronectin, villin and desmin as causative genes

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrandt, F.; Strahm, B.; Prochoroff, A.; Cybulla, M.; Brandis, M. [Freiburg Univ. (Germany)] [and others

    1996-05-03

    Glomerulopathy with predominant fibronectin deposits (GFD) is a newly recognized autosomal dominant renal disease that leads to albuminuria, microscopic hematuria, hypertension, renal tubular acidosis type IV, and end-stage renal disease in the second to fourth decade of life. Light microscopy documents extensive deposits in the subendothelial space, which on electron microscopy consist of non-oriented 12 x 125 nm fibers. Deposits are strongly immunoreactive for antibodies to fibronectin. We examined the hypothesis that a genetic defect in the gene for fibronectin is responsible for the disease. In a 197 member pedigree, 13 relatives developed end-stage renal failure from the disease. In 99 individuals haplotype analysis was performed using 6 microsatellite markers spanning a >56 cM interval in chromosome region 2q34, where fibronectin, villin, and desmin map in close proximity. Haplotype analysis resulted in exclusion of the whole range of 78 cM covered by the markers examined. This result excludes fibronectin, villin, and desmin from being the causative genes for GFD in this large kindred. 13 refs., 2 figs.

  19. Control of fibronectin synthesis by rat granulosa cells in culture

    International Nuclear Information System (INIS)

    Skinner, M.K.; Dorrington, J.H.

    1984-01-01

    The secreted and cellular [ 35 S]methionine-radiolabeled proteins of cultured rat granulosa cells were separated by electrophoresis on sodium dodecylsulfate (SDS) polyacrylamide gradient slab gels. From 24 to 72 h of culture FSH increased the intensity of labeling of most of the secreted proteins. A 220,000-dalton protein, however, increased in intensity only in control cultures and became the major secreted protein after 72 h, comprising 20% of the total radiolabeled proteins. This protein was identified as fibronectin by immunoprecipitation. There was no increase in the secreted or cellular fibronectin in FSH- or testosterone- and insulin-treated cultures. These studies indicate that a component of extracellular matrix is a major secretory product of unstimulated immature granulosa cells. As hormones induce the differentiated functions of granulosa cells in culture, the secretion of fibronectin is inhibited

  20. Predicting preterm birth: Cervical length and fetal fibronectin.

    Science.gov (United States)

    Son, Moeun; Miller, Emily S

    2017-12-01

    Spontaneous preterm birth remains the leading cause of neonatal morbidity and mortality worldwide, and accounts for a significant global health burden. Several obstetric strategies to screen for spontaneous preterm delivery, such as cervical length and fetal fibronectin measurement, have emerged. However, the effectiveness of these strategies relies on their ability to accurately predict those pregnancies at increased risk for spontaneous preterm birth (SPTB). Transvaginal cervical shortening is predictive of preterm birth and when coupled with appropriate preterm birth prevention strategies, has been associated with reductions in SPTB in asymptomatic women with a singleton gestation. The use of qualitative fetal fibronectin may be useful in conjunction with cervical length assessment in women with acute preterm labor symptoms, but data supporting its clinical utility remain limited. As both cervical length and qualitative fetal fibronectin have limited capacity to predict preterm birth, further studies are needed to investigate other potential screening modalities. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. ITER-EDA physics design requirements and plasma performance assessments

    International Nuclear Information System (INIS)

    Uckan, N.A.; Galambos, J.; Wesley, J.; Boucher, D.; Perkins, F.; Post, D.; Putvinski, S.

    1996-01-01

    Physics design guidelines, plasma performance estimates, and sensitivity of performance to changes in physics assumptions are presented for the ITER-EDA Interim Design. The overall ITER device parameters have been derived from the performance goals using physics guidelines based on the physics R ampersand D results. The ITER-EDA design has a single-null divertor configuration (divertor at the bottom) with a nominal plasma current of 21 MA, magnetic field of 5.68 T, major and minor radius of 8.14 m and 2.8 m, and a plasma elongation (at the 95% flux surface) of ∼1.6 that produces a nominal fusion power of ∼1.5 GW for an ignited burn pulse length of ≥1000 s. The assessments have shown that ignition at 1.5 GW of fusion power can be sustained in ITER for 1000 s given present extrapolations of H-mode confinement (τ E = 0.85 x τ ITER93H ), helium exhaust (τ* He /τ E = 10), representative plasma impurities (n Be /n e = 2%), and beta limit [β N = β(%)/(I/aB) ≤ 2.5]. The provision of 100 MW of auxiliary power, necessary to access to H-mode during the approach to ignition, provides for the possibility of driven burn operations at Q = 15. This enables ITER to fulfill its mission of fusion power (∼ 1--1.5 GW) and fluence (∼1 MWa/m 2 ) goals if confinement, impurity levels, or operational (density, beta) limits prove to be less favorable than present projections. The power threshold for H-L transition, confinement uncertainties, and operational limits (Greenwald density limit and beta limit) are potential performance limiting issues. Improvement of the helium exhaust (τ* He /τ E ≤ 5) and potential operation in reverse-shear mode significantly improve ITER performance

  2. Endothelium-derived fibronectin regulates neonatal vascular morphogenesis in an autocrine fashion.

    Science.gov (United States)

    Turner, Christopher J; Badu-Nkansah, Kwabena; Hynes, Richard O

    2017-11-01

    Fibronectin containing alternatively spliced EIIIA and EIIIB domains is largely absent from mature quiescent vessels in adults, but is highly expressed around blood vessels during developmental and pathological angiogenesis. The precise functions of fibronectin and its splice variants during developmental angiogenesis however remain unclear due to the presence of cardiac, somitic, mesodermal and neural defects in existing global fibronectin KO mouse models. Using a rare family of surviving EIIIA EIIIB double KO mice, as well as inducible endothelial-specific fibronectin-deficient mutant mice, we show that vascular development in the neonatal retina is regulated in an autocrine manner by endothelium-derived fibronectin, and requires both EIIIA and EIIIB domains and the RGD-binding α5 and αv integrins for its function. Exogenous sources of fibronectin do not fully substitute for the autocrine function of endothelial fibronectin, demonstrating that fibronectins from different sources contribute differentially to specific aspects of angiogenesis.

  3. Fibronectin as predictor of cirrhosis in men who abuse alcohol

    DEFF Research Database (Denmark)

    Junge, Jette; Bentsen, K D; Christoffersen, P

    1988-01-01

    In a study of 142 male alcohol abusers without evidence of cirrhosis the presence of intralobular fibronectin in the liver was investigated in relation to the subsequent development of the disease. All 142 initial biopsy samples showed preserved architecture. During a follow up period of 10...... increased amounts later developed the disease (p less than 0.005). Semiquantitative assessment of the amount of parenchymal fibronectin at an early stage of alcoholic liver disease is of definite predictive value for the development of cirrhosis....

  4. Fibronectin distribution in epithelial and associated tissues of the rat

    DEFF Research Database (Denmark)

    Couchman, J R; Gibson, W T; Thom, D

    1979-01-01

    parts of tissues, such as the sebaceous glands or the matrix, medulla, cortex, and cuticles of the hair and the inner and outer root sheaths, or even in tissues in which there is some cell movement, such as the epidermis. It is, however, characteristic of sites at which cell division is occurring...... surrounding and investing nerve and muscle fibre bundles, and the dermal connective tissue where fibronectin was often associated closely with collagen fibres. At the basement membrane of the dermal/epidermal junction, fibronectin occurred at the plasma membrane of the basal cells and in the lamina lucida...

  5. Hypohidrotic ectodermal dysplasia and immunodeficiency with coincident NEMO and EDA Mutations

    Directory of Open Access Journals (Sweden)

    Michael D. Keller

    2011-11-01

    Full Text Available Ectodermal dysplasias (ED are uncommon genetic disorders resulting in abnormalities in ectodermally-derived structures. Though many ED-associated genes have been described, the NF-κB Essential Modulator (NEMO encoded by the IKBKG gene is unique in that mutations also result in severe humoral and cellular immunologic defects. We describe three unrelated kindreds with defects in both EDA and IKBKG resulting from an X-chromosome crossover. This demonstrates the importance of thorough immunologic consideration of patients with ED even when an EDA etiology is confirmed, and raises the possibility of a specific phenotype arising from coincident mutations in EDA and IKBKB.

  6. Heterologously expressed Staphylococcus aureus fibronectin-binding proteins are sufficient for invasion of host cells

    NARCIS (Netherlands)

    Sinha, B; Francois, P; Que, Y A; Hussain, M; Heilmann, C; Moreillon, P; Lew, D; Krause, K H; Peters, Georg; Herrmann, M

    2000-01-01

    Staphylococcus aureus invasion of mammalian cells, including epithelial, endothelial, and fibroblastic cells, critically depends on fibronectin bridging between S. aureus fibronectin-binding proteins (FnBPs) and the host fibronectin receptor integrin alpha(5)beta(1) (B. Sinha et al., Cell.

  7. Fibronectin as predictor of cirrhosis in men who abuse alcohol

    DEFF Research Database (Denmark)

    Junge, Jette; Bentsen, K D; Christoffersen, P

    1988-01-01

    In a study of 142 male alcohol abusers without evidence of cirrhosis the presence of intralobular fibronectin in the liver was investigated in relation to the subsequent development of the disease. All 142 initial biopsy samples showed preserved architecture. During a follow up period of 10...

  8. Molecular characterization of fibronectin-binding protein of ...

    African Journals Online (AJOL)

    The ability of lactobacilli to adhere to vaginal epithelial surfaces and intestinal tracts is believed to be important to allow colonization and host interaction for persistence. Bacterial adhesins molecules are proteins of which the human host fibronectin serves as a substrate for the attachment of bacteria and play a significant ...

  9. Labor tirib haigused päevavalgele / Eda Laas ; interv. Eevi Kuht

    Index Scriptorium Estoniae

    Laas, Eda

    2005-01-01

    Piiral tegutseva veterinaar- ja toidulabori juhataja Eda Laas peab kõige ohtlikumaks uuritavaks loomahaiguseks ka inimesele levivat surmaga lõppevat marutaudi, mille vastu võitlemiseks on riik eriprogrammi kokku pannud

  10. Fibronectin in cultured rat keratinocytes: distribution, synthesis, and relationship to cytoskeletal proteins

    DEFF Research Database (Denmark)

    Gibson, W T; Couchman, J R; Badley, R A

    1983-01-01

    immunofluorescence staining of cultures grown in the absence of a feeder layer using an antiserum which had been cross-adsorbed with foetal calf serum proteins to remove antibodies which recognised serum fibronectin. The distribution of fibronectin in areas of cell-cell and cell-substratum contact...... of overlap and colinearity of actin and fibronectin filaments. The ability of keratinocytes to produce fibronectin suggests that these cells can contribute to the formation of the basement membrane in skin. The localisation of fibronectin and its close association with actin also suggests that it is involved...

  11. EDA-gram: designing electrodermal activity fingerprints for visualization and feature extraction.

    Science.gov (United States)

    Chaspari, Theodora; Tsiartas, Andreas; Stein Duker, Leah I; Cermak, Sharon A; Narayanan, Shrikanth S

    2016-08-01

    Wearable technology permeates every aspect of our daily life increasing the need of reliable and interpretable models for processing the large amount of biomedical data. We propose the EDA-Gram, a multidimensional fingerprint of the electrodermal activity (EDA) signal, inspired by the widely-used notion of spectrogram. The EDA-Gram is based on the sparse decomposition of EDA from a knowledge-driven set of dictionary atoms. The time axis reflects the analysis frames, the spectral dimension depicts the width of selected dictionary atoms, while intensity values are computed from the atom coefficients. In this way, EDA-Gram incorporates the amplitude and shape of Skin Conductance Responses (SCR), which comprise an essential part of the signal. EDA-Gram is further used as a foundation for signal-specific feature design. Our results indicate that the proposed representation can accentuate fine-grain signal fluctuations, which might not always be apparent through simple visual inspection. Statistical analysis and classification/regression experiments further suggest that the derived features can differentiate between multiple arousal levels and stress-eliciting environments for two datasets.

  12. An Integrated Method Based on PSO and EDA for the Max-Cut Problem.

    Science.gov (United States)

    Lin, Geng; Guan, Jian

    2016-01-01

    The max-cut problem is NP-hard combinatorial optimization problem with many real world applications. In this paper, we propose an integrated method based on particle swarm optimization and estimation of distribution algorithm (PSO-EDA) for solving the max-cut problem. The integrated algorithm overcomes the shortcomings of particle swarm optimization and estimation of distribution algorithm. To enhance the performance of the PSO-EDA, a fast local search procedure is applied. In addition, a path relinking procedure is developed to intensify the search. To evaluate the performance of PSO-EDA, extensive experiments were carried out on two sets of benchmark instances with 800 to 20,000 vertices from the literature. Computational results and comparisons show that PSO-EDA significantly outperforms the existing PSO-based and EDA-based algorithms for the max-cut problem. Compared with other best performing algorithms, PSO-EDA is able to find very competitive results in terms of solution quality.

  13. Delignification of miscanthus using ethylenediamine (EDA) with or without ammonia and subsequent enzymatic hydrolysis to sugars.

    Science.gov (United States)

    Padmanabhan, Sasisanker; Schwyter, Philippe; Liu, Zhongguo; Poon, Geoffrey; Bell, Alexis T; Prausnitz, John M

    2016-06-01

    Pretreatment of miscanthus is essential for efficient enzymatic production of cellulosic ethanol. This study reports a possible pretreatment method for miscanthus using aqueous ethylenediamine (EDA) for 30 min at 180 °C with or without ammonia. The mass ratio of miscanthus to EDA was varied from 1:3, 1:1, and 1:0.5, keeping the mass ratio of miscanthus to liquid (EDA + Water) constant at 1:8. The ammonia-to-miscanthus ratio was 1:0.25. After pretreatment with a ratio of 1:3 miscanthus to EDA, about 75 % of the lignin was removed from the raw miscanthus with 90 % retention of cellulose and 50 % of hemicellulose in the recovered solid. Enzymatic hydrolysis of the recovered solid miscanthus gave 63 % glucose and 62 % xylose conversion after 72 h. EDA provides an effective pretreatment for miscanthus, achieving good delignification and enhanced sugar yield by enzyme hydrolysis. Results using aqueous EDA with or without ammonia are much better than those using hot water and compare favorably with those using aqueous ammonia. The delignification efficiency of EDA pretreatment is high compared to that for hot-water pretreatment and is nearly as efficient as that obtained for aqueous-ammonia pretreatment.

  14. Fibronectin distribution in epithelial and associated tissues of the rat

    DEFF Research Database (Denmark)

    Couchman, J R; Gibson, W T; Thom, D

    1979-01-01

    Specific antiserum was used to investigate the distribution of the extracellular glycoprotein, fibronectin, in rat skin and tongue tissue by light and electron microscopy with immunofluorescence and immunoperoxidase techniques. We conclude that fibronectin is absent from stable, differentiated...... parts of tissues, such as the sebaceous glands or the matrix, medulla, cortex, and cuticles of the hair and the inner and outer root sheaths, or even in tissues in which there is some cell movement, such as the epidermis. It is, however, characteristic of sites at which cell division is occurring...... in contact with an extracellular scaffolding, such as basement membrane or loose connective tissue. Conspicuous examples were in the glassy membrane and connective tissue sheath associated with the follicular epithelium, the basement membrane underlying vascular endothelial cells, the connective tissues...

  15. Studies of Fibronectin-Binding Proteins of Streptococcus equi

    OpenAIRE

    Lannergård, Jonas; Flock, Margareta; Johansson, Staffan; Flock, Jan-Ingmar; Guss, Bengt

    2005-01-01

    Streptococcus equi subsp. equi is the causative agent of strangles, a disease of the upper respiratory tract in horses. The initiation of S. equi subsp. equi infection is likely to involve cell surface-anchored molecules mediating bacterial adhesion to the epithelium of the host. The present study describes the cloning and characterization of FNEB, a fibronectin-binding protein with cell wall-anchoring motifs. FNEB can thus be predicted as cell surface located, contrary to the two previously ...

  16. Preparation of Bioactive Titanium Surfaces via Fluoride and Fibronectin Retention

    OpenAIRE

    Elias, Carlos Nelson; Gravina, Patricia Abdo; Silva Filho, Costa e; Nascente, Pedro Augusto de Paula

    2012-01-01

    Statement of Problem. The chemical or topographic modification of the dental implant surface can affect bone healing, promote accelerated osteogenesis, and increase bone-implant contact and bonding strength. Objective. In this work, the effects of dental implant surface treatment and fibronectin adsorption on the adhesion of osteoblasts were analyzed. Materials and Methods. Two titanium dental implants (Porous-acid etching and PorousNano-acid etching followed by fluoride ion modification) wer...

  17. Preparation of Bioactive Titanium Surfaces via Fluoride and Fibronectin Retention

    Directory of Open Access Journals (Sweden)

    Carlos Nelson Elias

    2012-01-01

    Full Text Available Statement of Problem. The chemical or topographic modification of the dental implant surface can affect bone healing, promote accelerated osteogenesis, and increase bone-implant contact and bonding strength. Objective. In this work, the effects of dental implant surface treatment and fibronectin adsorption on the adhesion of osteoblasts were analyzed. Materials and Methods. Two titanium dental implants (Porous-acid etching and PorousNano-acid etching followed by fluoride ion modification were characterized by high-resolution scanning electron microscopy, atomic force microscopy, and X-ray diffraction before and after the incorporation of human plasma fibronectin (FN. The objective was to investigate the biofunctionalization of these surfaces and examine their effects on the interaction with osteoblastic cells. Results. The evaluation techniques used showed that the Porous and PorousNano implants have similar microstructural characteristics. Spectrophotometry demonstrated similar levels of fibronectin adsorption on both surfaces (80%. The association indexes of osteoblastic cells in FN-treated samples were significantly higher than those in samples without FN. The radioactivity values associated with the same samples, expressed as counts per minute (cpm, suggested that FN incorporation is an important determinant of the in vitro cytocompatibility of the surfaces. Conclusion. The preparation of bioactive titanium surfaces via fluoride and FN retention proved to be a useful treatment to optimize and to accelerate the osseointegration process for dental implants.

  18. Structural analysis of the ITER EDA magnet system

    International Nuclear Information System (INIS)

    Titus, P.H.

    1995-01-01

    The most recent design of the ITER magnet system is easier to assemble and is expected to be more conventionally manufactured. A stainless steel case with pancake wound plates replaces the earlier poloidally wrapped plate Toroidal Field (TF) coil design. The number of TF coils has been reduced from 24 to 20 to ease access. The price for these improvements has been an increase in radial build of the TF coil, and a reallocation of space within the reactor. The TF and central solenoid (CS) are still bucked, making their interface an important area to simulate in structural models. Out-of-plane (OOP) forces are no longer supported by keys between TF legs. The TF case is strong enough to support most of the load when, it in turn, is supported by additional external structures. The most significant of these structures are the upper and lower crowns. A fluted torque shell on the outside of the CS provides a bearing surface for the TF and this along with the CS, and the TF inner legs, takes the global twist applied to the central column of the machine. A US Home team contribution has been a large scale global finite element model which addresses details of construction, and results of this model are presented. Cyclic case bending, torque shell shear, CS shear, the effects of assembly gaps, are presented. The case supports a large portion of the OOP loading, and the possibility of removal or simplifications in the OOP structures is discussed. CS Shear stresses from local conductor behavior are combined with the shears from the global behavior and the total shear is compared with the insulation shear allowable used in the ITER EDA. A smaller structural model has been used to simulate multiple pulse frictional effects, and results of this model are shown

  19. Fibronectin changes in eosinophilic meningitis with blood-CSF barrier disruption.

    Science.gov (United States)

    Shyu, Ling-Yuh; Hu, Ming-E; Chou, Chun-Hui; Chen, Ke-Min; Chiu, Ping-Sung; Lai, Shih-Chan

    2015-01-01

    Fibronectin, which is present at relatively low levels in healthy central nervous systems (CNS), shows increased levels in meningitis. In this study, fibronectin processing was correlated with the increased permeability of the blood-cerebrospinal fluid (CSF) barrier as well as with the formation of eosinophil infiltrates in angiostrongyliasis meningitis. The immunohistochemistry results show matrix metalloproteinase-9 (MMP-9) is localized in the choroid plexus epithelium. Coimmunoprecipitation demonstrated fibronectin strongly binds MMP-9. Furthermore, treatment with the MMP-9 inhibitor GM6001 significantly inhibited fibronectin processing, reduced the blood-CSF barrier permeability, and decreased the eosinophil counts. The decreased fibronectin processing in CSF implies decreased cellular invasion of the subarachnoid space across the blood-CSF barrier. Therefore, increased fibronectin processing may be associated with barrier disruption and participate in the extravasation and migration of eosinophils into the CNS during experimental parasitic infection. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Diverse splicing patterns of exonized Alu elements in human tissues.

    Directory of Open Access Journals (Sweden)

    Lan Lin

    2008-10-01

    Full Text Available Exonization of Alu elements is a major mechanism for birth of new exons in primate genomes. Prior analyses of expressed sequence tags show that almost all Alu-derived exons are alternatively spliced, and the vast majority of these exons have low transcript inclusion levels. In this work, we provide genomic and experimental evidence for diverse splicing patterns of exonized Alu elements in human tissues. Using Exon array data of 330 Alu-derived exons in 11 human tissues and detailed RT-PCR analyses of 38 exons, we show that some Alu-derived exons are constitutively spliced in a broad range of human tissues, and some display strong tissue-specific switch in their transcript inclusion levels. Most of such exons are derived from ancient Alu elements in the genome. In SEPN1, mutations of which are linked to a form of congenital muscular dystrophy, the muscle-specific inclusion of an Alu-derived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity after the divergence of humans and chimpanzees. Our results imply that some Alu exonization events may have acquired adaptive benefits during the evolution of primate transcriptomes.

  1. Self-assembly of fibronectin mimetic peptide-amphiphile nanofibers

    Science.gov (United States)

    Rexeisen, Emilie Lynn

    Many therapeutic strategies incorporate peptides into their designs to mimic the natural protein ligands found in vivo. A few examples are the short peptide sequences RGD and PHSRN that mimic the primary and synergy-binding domains of the extracellular matrix protein, fibronectin, which is recognized by the cell surface receptor, alpha5beta 1 integrin. Even though scaffold modification with biomimetic peptides remains one of the most promising approaches for tissue engineering, the use of these peptides in therapeutic tissue-engineered products and drug delivery systems available on the commercial market is limited because the peptides are not easily able to mimic the natural protein. The design of a peptide that can effectively target the alpha5beta1 integrin would greatly increase biomimetic scaffold therapeutic potential. A novel peptide containing both the RGD primary binding domain and PHSRN synergy-binding domain for fibronectin joined with the appropriate linker should bind alpha 5beta1 integrin more efficiently and lead to greater cell adhesion over RGD alone. Several fibronectin mimetic peptides were designed and coupled to dialkyl hydrocarbon tails to make peptide-amphiphiles. The peptides contained different linkers connecting the two binding domains and different spacers separating the hydrophobic tails from the hydrophilic headgroups. The peptide-amphiphiles were deposited on mica substrates using the Langmuir-Blodgett technique. Langmuir isotherms indicated that the peptide-amphiphiles that contained higher numbers of serine residues formed a more tightly packed monolayer, but the increased number of serines also made transferring the amphiphiles to the mica substrate more difficult. Atomic force microscopy (AFM) images of the bilayers showed that the headgroups might be bent, forming small divots in the surface. These divots may help expose the PHSRN synergy-binding domain. Parallel studies undertaken by fellow group members showed that human

  2. A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA.

    Science.gov (United States)

    O'Brown, Natasha M; Summers, Brian R; Jones, Felicity C; Brady, Shannon D; Kingsley, David M

    2015-01-28

    Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

  3. Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

    Science.gov (United States)

    Dong, Xianjun; Navratilova, Pavla; Fredman, David; Drivenes, Øyvind; Becker, Thomas S; Lenhard, Boris

    2010-03-01

    Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived the disappearance of their host genes after whole-genome duplication (WGD) in teleosts, we discover a set of 38 candidate cis-regulatory coding exons (RCEs) with predicted target genes. These elements demonstrate evolutionary separation of overlapping protein-coding and regulatory information after WGD in teleosts. We present evidence that the corresponding mammalian exons are still under both coding and non-coding selection pressure, are more conserved than other protein coding exons in the host gene and several control sets, and share key characteristics with highly conserved non-coding elements in the same regions. Their dual function is corroborated by existing experimental data. Additionally, we show examples of human exon remnants stemming from the vertebrate 2R WGD. Our findings suggest that long-range cis-regulatory inputs for developmental genes are not limited to non-coding regions, but can also overlap the coding sequence of unrelated genes. Thus, exonic regulatory elements in GRBs might be functionally equivalent to those in non-coding regions, calling for a re-evaluation of the sequence space in which to look for long-range regulatory elements and experimentally test their activity.

  4. Exon - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ontents Exons in variants Data file File name: astra_exon.zip File URL: ftp://ftp.biosciencedbc.jp/archive/a... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Exon - ASTRA | LSDB Archive ...

  5. The fibronectin-binding integrins alpha5beta1 and alphavbeta3 differentially modulate RhoA-GTP loading, organization of cell matrix adhesions, and fibronectin fibrillogenesis

    DEFF Research Database (Denmark)

    Danen, Erik H J; Sonneveld, Petra; Brakebusch, Cord

    2002-01-01

    We have studied the formation of different types of cell matrix adhesions in cells that bind to fibronectin via either alpha5beta1 or alphavbeta3. In both cases, cell adhesion to fibronectin leads to a rapid decrease in RhoA activity. However, alpha5beta1 but not alphavbeta3 supports high levels...... subunits, we find that the extracellular domain of beta1 controls RhoA activity. By expressing both beta1 and beta3 at high levels, we show that beta1-mediated control of the levels of beta3 is important for the distribution of focal contacts. Our findings demonstrate that the pattern of fibronectin...... receptors expressed on a cell dictates the ability of fibronectin to stimulate RhoA-mediated organization of cell matrix adhesions....

  6. Maternal and fetal plasma concentrations of endothelin, lipidhydroperoxides, glutathione peroxidase and fibronectin in relation to abnormal umbilical artery velocimetry.

    NARCIS (Netherlands)

    Karsdorp, V.H.M.; Bast, A.; van Kamp, G.J.; Bouman, A.A.; Dekker, G.A.; van Vugt, J.M.G.; van Geijn, H.

    1998-01-01

    Objective: To study plasma concentrations of endothelin (ET), lipidhydroperoxides (LOOH), glutathione peroxidase (GSHpx) and fibronectin in relation to abnormal umbilical artery velocimetry. Study design: Plasma concentrations of ET, LOOH, GSHpx and fibronectin were measured in fetal and maternal

  7. SPR imaging biosensor for the quantitation of fibronectin concentration in blood samples.

    Science.gov (United States)

    Sankiewicz, Anna; Romanowicz, Lech; Pyc, Marlena; Hermanowicz, Adam; Gorodkiewicz, Ewa

    2018-02-20

    The purpose of this study was presentation of a new biosensor capable of determination of fibronectin. This biosensor was based on the specific interaction of anti-fibronectin antibody produced in rabbit with fibronectin. The surface plasmon resonance imaging (SPRI) technique was used as a detecting method. Optimization and characterization properties of the biosensor were studied. The determination of fibronectin concentration in natural samples was done. The results were compared with a reference method (Enzyme-Linked Immunosorbent Assay-ELISA). The analytically useful dynamic response range of biosensor is between 5 and 400ngmL -1 . The detection limit is 1.5ngmL -1 and limit quantification is 5ngmL -1 . The proposed SPRI biosensor showed good selectivity for potential interferences. It was applied to determine fibronectin concentrations in plasma of healthy donors and of patients after thermal injury. Good correlations between results obtained using the SPRI biosensor and ELISA test (correlation coefficients for healthy donors 0.996, for patients 0.984) were obtained. The average fibronectin concentration of healthy donors was 140.5±24.6μgmL -1 and the average fibronectin concentration of patients was 601.5±72.1μgmL -1 , which was in agreement with results obtained by other investigators. The obtained results indicate that the developed biosensor may be a candidate for monitoring fibronectin concentration in blood samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Quantification of fibronectin as a method to assess ex vivo extracellular matrix remodeling

    DEFF Research Database (Denmark)

    Bager, Cecilie Liv; Gudmann, N.; Willumsen, N.

    2016-01-01

    -terminus of fibronectin was developed (FBN-C). The assay was evaluated in relation to specificity, technical performance and as a marker for quantification of fibronectin in cartilage and cancer ex vivo models. The ELISA was specific and technically stable. Cleavage of tumor tissue with MMP-2 released significantly...

  9. Fibronectin-degrading activity of Trypanosoma cruzi cysteine proteinase plays a role in host cell invasion.

    Science.gov (United States)

    Maeda, Fernando Yukio; Cortez, Cristian; Izidoro, Mario Augusto; Juliano, Luiz; Yoshida, Nobuko

    2014-12-01

    Trypanosoma cruzi, the agent of Chagas disease, binds to diverse extracellular matrix proteins. Such an ability prevails in the parasite forms that circulate in the bloodstream and contributes to host cell invasion. Whether this also applies to the insect-stage metacyclic trypomastigotes, the developmental forms that initiate infection in the mammalian host, is not clear. Using T. cruzi CL strain metacyclic forms, we investigated whether fibronectin bound to the parasites and affected target cell invasion. Fibronectin present in cell culture medium bound to metacyclic forms and was digested by cruzipain, the major T. cruzi cysteine proteinase. G strain, with negligible cruzipain activity, displayed a minimal fibronectin-degrading effect. Binding to fibronectin was mediated by gp82, the metacyclic stage-specific surface molecule implicated in parasite internalization. When exogenous fibronectin was present at concentrations higher than cruzipain can properly digest, or fibronectin expression was stimulated by treatment of epithelial HeLa cells with transforming growth factor beta, the parasite invasion was reduced. Treatment of HeLa cells with purified recombinant cruzipain increased parasite internalization, whereas the treatment of parasites with cysteine proteinase inhibitor had the opposite effect. Metacyclic trypomastigote entry into HeLa cells was not affected by anti-β1 integrin antibody but was inhibited by anti-fibronectin antibody. Overall, our results have indicated that the cysteine proteinase of T. cruzi metacyclic forms, through its fibronectin-degrading activity, is implicated in host cell invasion. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  10. A novel missense mutation in collagenous domain of EDA gene in a ...

    Indian Academy of Sciences (India)

    P220L mutation of EDA responsible for XLHED affects the highly evolution conserved Proline residue 220. The multiple alignments of 19 repeats of Gly-x-y are all highly conserved in 14 species (rabbit, chick, pig, sheep, dog, cow, dolphin, rat, mouse, baboon, macaque, gorilla, chimpanzee and human). Journal of Genetics.

  11. A novel missense mutation in collagenous domain of EDA gene in a ...

    Indian Academy of Sciences (India)

    mutation of EDA responsible for XLHED affects the highly evolution conserved Proline residue 220. The multiple alignments of 19 repeats of Gly-x-y are all highly conserved in 14 species (rabbit, chick, pig, sheep, dog, cow, dolphin, rat, mouse, baboon, macaque, gorilla, chimpanzee and human). Journal of Genetics.

  12. SDR: A Better Trigger for Adaptive Variance Scaling in Normal EDAs

    NARCIS (Netherlands)

    P.A.N. Bosman (Peter); J. Grahl; F. Rothlauf; D. Thierens (Dirk)

    2007-01-01

    htmlabstractRecently, advances have been made in continuous, normal-distribution-based Estimation-of-Distribution Algorithms (EDAs) by scaling the variance up from the maximum-likelihood estimate. When done properly, such scaling has been shown to prevent premature convergence on slope-like regions

  13. 76 FR 5501 - Request for Comments: Review and Improvement of EDA's Regulations

    Science.gov (United States)

    2011-02-01

    .... As part of the Administration's commitment to open government and in response to Executive Order... rulemaking that reflects current economic development practice to advance an innovative economy. DATES... preparing American regions for growth and success in the worldwide economy. EDA partners with stakeholders...

  14. Guidance of mesenchymal stem cells on fibronectin structured hydrogel films.

    Directory of Open Access Journals (Sweden)

    Annika Kasten

    Full Text Available Designing of implant surfaces using a suitable ligand for cell adhesion to stimulate specific biological responses of stem cells will boost the application of regenerative implants. For example, materials that facilitate rapid and guided migration of stem cells would promote tissue regeneration. When seeded on fibronectin (FN that was homogeneously immmobilized to NCO-sP(EO-stat-PO, which otherwise prevents protein binding and cell adhesion, human mesenchymal stem cells (MSC revealed a faster migration, increased spreading and a more rapid organization of different cellular components for cell adhesion on fibronectin than on a glass surface. To further explore, how a structural organization of FN controls the behavior of MSC, adhesive lines of FN with varying width between 10 µm and 80 µm and spacings between 5 µm and 20 µm that did not allow cell adhesion were generated. In dependance on both line width and gaps, cells formed adjacent cell contacts, were individually organized in lines, or bridged the lines. With decreasing sizes of FN lines, speed and directionality of cell migration increased, which correlated with organization of the actin cytoskeleton, size and shape of the nuclei as well as of focal adhesions. Together, defined FN lines and gaps enabled a fine tuning of the structural organization of cellular components and migration. Microstructured adhesive substrates can mimic the extracellular matrix in vivo and stimulate cellular mechanisms which play a role in tissue regeneration.

  15. Fibronectin matrix assembly requires distinct contributions from Rho kinases I and -II

    DEFF Research Database (Denmark)

    Yoneda, Atsuko; Ushakov, Dmitriy; Multhaupt, Hinke A B

    2006-01-01

    ) by small interfering RNA treatment blocked fibronectin matrix assembly, although the phenotypes were distinct and despite persistence of the alternate kinase. Remnant fibronectin on ROCK-deficient fibroblasts was mostly punctate and more deoxycholate soluble compared with controls. Fibronectin matrix...... assembly defects in ROCK-deficient cells did not result from decreased synthesis/secretion, altered fibronectin mRNA splicing, metalloproteinase activity, or alpha5beta1 integrin dysfunction. Rescue could be effected by ROCK protein restoration or phosphomimetic myosin light chain expression. However......, the effect of ROCK I deficiency on fibronectin matrix assembly was secondary to altered cell surface morphology, rich in filopodia, resulting from high GTP-Cdc42 levels. Total internal reflection microscopy revealed that a submembranous pool of myosin light chain in control cells was missing in ROCK II...

  16. Fibronectin in cultured rat keratinocytes: distribution, synthesis, and relationship to cytoskeletal proteins

    DEFF Research Database (Denmark)

    Gibson, W T; Couchman, J R; Badley, R A

    1983-01-01

    The aim of this study was to investigate whether epidermal cells can synthesise fibronectin and whether the distribution of this glycoprotein is related to the adhesion and cytoskeletal organisation of these cells. The production of fibronectin by newborn rat epidermal cells was shown by indirect......, characteristically in the form of short radial stitches, was examined in more detail using immunoelectron microscopy with colloidal gold as marker. This showed the close proximity of fibronectin to the cell membrane, with the ventral surface and fine cellular processes showing the heaviest labelling, and also...... revealed evidence of a relationship between external fibronectin and internal structure in epidermal cells. Immunofluorescence showed that tonofilaments (keratin) and microtubules were present as fibrillar arrays but were not related to fibronectin distribution. Vimentin and desmin were absent. Actin...

  17. Zebrafish eda and edar mutants reveal conserved and ancestral roles of ectodysplasin signaling in vertebrates.

    Directory of Open Access Journals (Sweden)

    Matthew P Harris

    2008-10-01

    Full Text Available The genetic basis of the development and variation of adult form of vertebrates is not well understood. To address this problem, we performed a mutant screen to identify genes essential for the formation of adult skeletal structures of the zebrafish. Here, we describe the phenotypic and molecular characterization of a set of mutants showing loss of adult structures of the dermal skeleton, such as the rays of the fins and the scales, as well as the pharyngeal teeth. The mutations represent adult-viable, loss of function alleles in the ectodysplasin (eda and ectodysplasin receptor (edar genes. These genes are frequently mutated in the human hereditary disease hypohidrotic ectodermal dysplasia (HED; OMIM 224900, 305100 that affects the development of integumentary appendages such as hair and teeth. We find mutations in zebrafish edar that affect similar residues as mutated in human cases of HED and show similar phenotypic consequences. eda and edar are not required for early zebrafish development, but are rather specific for the development of adult skeletal and dental structures. We find that the defects of the fins and scales are due to the role of Eda signaling in organizing epidermal cells into discrete signaling centers of the scale epidermal placode and fin fold. Our genetic analysis demonstrates dose-sensitive and organ-specific response to alteration in levels of Eda signaling. In addition, we show substantial buffering of the effect of loss of edar function in different genetic backgrounds, suggesting canalization of this developmental system. We uncover a previously unknown role of Eda signaling in teleosts and show conservation of the developmental mechanisms involved in the formation and variation of both integumentary appendages and limbs. Lastly, our findings point to the utility of adult genetic screens in the zebrafish in identifying essential developmental processes involved in human disease and in morphological evolution.

  18. The "alternative" choice of constitutive exons throughout evolution.

    Directory of Open Access Journals (Sweden)

    Galit Lev-Maor

    2007-11-01

    Full Text Available Alternative cassette exons are known to originate from two processes-exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons during evolution. We compiled a dataset of orthologous exons from human and mouse that are constitutively spliced in one species but alternatively spliced in the other. Examination of these exons suggests that the common ancestors were constitutively spliced. We show that relaxation of the 5' splice site during evolution is one of the molecular mechanisms by which exons shift from constitutive to alternative splicing. This shift is associated with the fixation of exonic splicing regulatory sequences (ESRs that are essential for exon definition and control the inclusion level only after the transition to alternative splicing. The effect of each ESR on splicing and the combinatorial effects between two ESRs are conserved from fish to human. Our results uncover an evolutionary pathway that increases transcriptome diversity by shifting exons from constitutive to alternative splicing.

  19. Optimized Exon-Exon Junction Library and its Application on Rodents' Brain Transcriptome Analysis

    Directory of Open Access Journals (Sweden)

    Tong-Hai Dou

    2017-05-01

    Full Text Available ABSTRACT Background: Alternative splicing (AS, which plays an important role in gene expression and functional regulation, has been analyzed on genome-scale by various bioinformatic approaches based on RNA-seq data. Compared with the huge number of studies on mouse, the AS researches approaching the rat, whose genome is intermedia between mouse and human, were still limited. To enrich the knowledge on AS events in rodents' brain, we perfomed a comprehensive analysis on four transcriptome libraries (mouse cerebrum, mouse cerebellum, rat cerebrum, and rat cerebellum, recruiting high-throughput sequencing technology. An optimized exon-exon junction library approach was introduced to adapt the longer RNA-seq reads and to improve mapping efficiency. Results: In total, 7,106 mouse genes and 2,734 rat genes were differentially expressed between cerebrum and cerebellum, while 7,125 mouse genes and 1,795 rat genes exhibited varieties on transcript variant level. Only half of the differentially expressed exon-exon junctions could be reflected at gene expression level. Functional cluster analysis showed that 32 pathways in mouse and 9 pathways in rat were significantly enriched, and 6 of them were in both. Interestingly, some differentially expressed transcript variants did not show difference on gene expression level, such as PLCβ1 and Kcnma1. Conclusion: Our work provided a case study of a novel exon-exon junction strategy to analyze the expression of genes and isoforms, helping us understand which transcript contributes to the overall expression and further functional change.

  20. Fibronectin tetrapeptide is target for syphilis spirochete cytadherence

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, D.D.; Baseman, J.B.; Alderete, J.F.

    1985-11-01

    The syphilis bacterium, Treponema pallidum, parasitizes host cells through recognition of fibronectin (Fn) on cell surfaces. The active site of the Fn molecule has been identified as a four-amino acid sequence, arg-gly-asp-ser (RGDS), located on each monomer of the cell-binding domain. The synthetic heptapeptide gly-arg-gly-asp-ser-pro-cys (GRGDSPC), with the active site sequence RGDS, specifically competed with SVI-labeled cell-binding domain acquisition by T. pallidum. Additionally, the same heptapeptide with the RGDS sequence diminished treponemal attachment to HEp-2 and HT1080 cell monolayers. Related heptapeptides altered in one key amino acid within the RGDS sequence failed to inhibit Fn cell-binding domain acquisition or parasitism of host cells by T. pallidum. The data support the view that T. pallidum cytadherence of host cells is through recognition of the RGDS sequence also important for eukaryotic cell-Fn binding.

  1. A fibronectin receptor on Candida albicans mediates adherence of the fungus to extracellular matrix

    International Nuclear Information System (INIS)

    Klotz, S.A.; Smith, R.L.

    1991-01-01

    Binding of fibronectin, an extracellular matrix (ECM) protein, to Candida albicans was measured, and adherence of the fungus to immobilized ECM proteins, fibronectin, laminin, types I and IV collagen, and subendothelial ECM was studied. 125I-labeled fibronectin was inhibited from binding to the fungus by unlabeled human plasma fibronectin and by Arg-Gly-Asp (RGD), Gly-Arg-Gly-Glu-Ser-Pro (GRGESP), and Gly-Arg-Gly-Asp-Thr-Pro (GRGDTP), but binding was not inhibited by Gly-Arg-Gly-Asp-Ser-Pro. Soluble fibronectin, RGD, GRGESP, and GRGDTP also inhibited fungal adherence to the individual immobilized ECM proteins in a complex pattern, but only soluble fibronectin (10(-7) M) inhibited fungal adherence to subendothelial ECM. Thus, C. albicans possesses at least one type of cell surface receptor for binding soluble fibronectin that can be inhibited with peptides. This receptor apparently is used to bind the fungus to immobilized ECM proteins and to subendothelial ECM and may play a role in the initiation of disseminated disease by bloodborne fungi by providing for adherence of the microorganisms to ECM proteins

  2. Defects in MAP1S-mediated autophagy turnover of fibronectin cause renal fibrosis.

    Science.gov (United States)

    Xu, Guibin; Yue, Fei; Huang, Hai; He, Yongzhong; Li, Xun; Zhao, Haibo; Su, Zhengming; Jiang, Xianhan; Li, Wenjiao; Zou, Jing; Chen, Qi; Liu, Leyuan

    2016-05-01

    Excessive deposition of extracellular matrix proteins in renal tissues causes renal fibrosis and renal function failure. Mammalian cells primarily use the autophagy-lysosome system to degrade misfolded/aggregated proteins and dysfunctional organelles. MAP1S is an autophagy activator and promotes the biogenesis and degradation of autophagosomes. Previously, we reported that MAP1S suppresses hepatocellular carcinogenesis in a mouse model and predicts a better prognosis in patients suffering from clear cell renal cell carcinomas. Furthermore, we have characterized that MAP1S enhances the turnover of fibronectin, and mice overexpressing LC3 but with MAP1S deleted accumulate fibronectin and develop liver fibrosis because of the synergistic impact of LC3-induced over-synthesis of fibronectin and MAP1S depletion-caused impairment of fibronectin degradation. Here we show that a suppression of MAP1S in renal cells caused an impairment of autophagy clearance of fibronectin and an activation of pyroptosis. Depletion of MAP1S in mice leads to an accumulation of fibrosis-related proteins and the development of renal fibrosis in aged mice. The levels of MAP1S were dramatically reduced and levels of fibronectin were greatly elevated in renal fibrotic tissues from patients diagnosed as renal atrophy and renal failure. Therefore, MAP1S deficiency may cause the accumulation of fibronectin and the development of renal fibrosis.

  3. Fibronectin-Containing Extracellular Vesicles Protect Melanocytes against Ultraviolet Radiation-Induced Cytotoxicity.

    Science.gov (United States)

    Bin, Bum-Ho; Kim, Dae-Kyum; Kim, Nan-Hyung; Choi, Eun-Jeong; Bhin, Jinhyuk; Kim, Sung Tae; Gho, Yong Song; Lee, Ai-Young; Lee, Tae Ryong; Cho, Eun-Gyung

    2016-05-01

    Skin melanocytes are activated by exposure to UV radiation to secrete melanin-containing melanosomes to protect the skin from UV-induced damage. Despite the continuous renewal of the epidermis, the turnover rate of melanocytes is very slow, and they survive for long periods. However, the mechanisms underlying the survival of melanocytes exposed to UV radiation are not known. Here, we investigated the role of melanocyte-derived extracellular vesicles in melanocyte survival. Network analysis of the melanocyte extracellular vesicle proteome identified the extracellular matrix component fibronectin at a central node, and the release of fibronectin-containing extracellular vesicles was increased after exposure of melanocytes to UVB radiation. Using an anti-fibronectin neutralizing antibody and specific inhibitors of extracellular vesicle secretion, we demonstrated that extracellular vesicles enriched in fibronectin were involved in melanocyte survival after UVB radiation. Furthermore, we observed that in the hyperpigmented lesions of patients with melasma, the extracellular space around melanocytes contained more fibronectin compared with normal skin, suggesting that fibronectin is involved in maintaining melanocytes in pathological conditions. Collectively, our findings suggest that melanocytes secrete fibronectin-containing extracellular vesicles to increase their survival after UVB radiation. These data provide important insight into how constantly stimulated melanocytes can be maintained in pathological conditions such as melasma. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Universal Alternative Splicing of Noncoding Exons

    DEFF Research Database (Denmark)

    Deveson, Ira W; Brunck, Marion E; Blackburn, James

    2018-01-01

    The human transcriptome is so large, diverse, and dynamic that, even after a decade of investigation by RNA sequencing (RNA-seq), we have yet to resolve its true dimensions. RNA-seq suffers from an expression-dependent bias that impedes characterization of low-abundance transcripts. We performed......, indicative of regulation by a deeply conserved splicing code. We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution....

  5. Kommunikatsioonijuht saab aidata arsti ja patsienti / Eda Amur, Anneli Bogens, Svea Talving, Krista Valdvee ; intervjueerinud Küllike Heide

    Index Scriptorium Estoniae

    2013-01-01

    Meditsiinivaldkonna kommunikatsiooniga seotud küsimuste ja probleemide üle arutlevad nelja haigla kommunikatsioonijuhid: Eda Amur Pärnu haiglast, Anneli Bogens Ida-Viru keskhaiglast, Svea Talving Ida-Tallinna keskhaiglast ning Krista Valdvee Viljandi haiglast

  6. Involvement of and interaction between WNT10A and EDA mutations in tooth agenesis cases in the Chinese population.

    Science.gov (United States)

    He, Huiying; Han, Dong; Feng, Hailan; Qu, Hong; Song, Shujuan; Bai, Baojing; Zhang, Zhenting

    2013-01-01

    Dental agenesis is the most common, often heritable, developmental anomaly in humans. Although WNT10A gene mutations are known to cause rare syndromes associated with tooth agenesis, including onycho-odontodermal dysplasia (OODD), Schöpf-Schulz-Passarge syndrome (SSPS), hypohidrotic ectodermal dysplasia (HED), and more than half of the cases of isolated oligodontia recently, the genotype-phenotype correlations and the mode of inheritance of WNT10A mutations remain unclear. The phenotypic expression with WNT10A mutations shows a high degree of variability, suggesting that other genes might function with WNT10A in regulating ectodermal organ development. Moreover, the involvement of mutations in other genes, such as EDA, which is also associated with HED and isolated tooth agenesis, is not clear. Therefore, we hypothesized that EDA mutations interact with WNT10A mutations to play a role in tooth agenesis. Additionally, EDA, EDAR, and EDARADD encode signaling molecules in the Eda/Edar/NF-κB signaling pathways, we also checked EDAR and EDARADD in this study. WNT10A, EDA, EDAR and EDARADD were sequenced in 88 patients with isolated oligodontia and 26 patients with syndromic tooth agenesis. The structure of two mutated WNT10A and two mutated EDA proteins was analyzed. Digenic mutations of both WNT10A and EDA were identified in 2 of 88 (2.27%) isolated oligodontia cases and 4 of 26 (15.38%) syndromic tooth agenesis cases. No mutation in EDAR or EDARADD gene was found. WNT10A and EDA digenic mutations could result in oligodontia and syndromic tooth agenesis in the Chinese population. Moreover, our results will greatly expand the genotypic spectrum of tooth agenesis.

  7. Involvement of and interaction between WNT10A and EDA mutations in tooth agenesis cases in the Chinese population.

    Directory of Open Access Journals (Sweden)

    Huiying He

    Full Text Available BACKGROUND: Dental agenesis is the most common, often heritable, developmental anomaly in humans. Although WNT10A gene mutations are known to cause rare syndromes associated with tooth agenesis, including onycho-odontodermal dysplasia (OODD, Schöpf-Schulz-Passarge syndrome (SSPS, hypohidrotic ectodermal dysplasia (HED, and more than half of the cases of isolated oligodontia recently, the genotype-phenotype correlations and the mode of inheritance of WNT10A mutations remain unclear. The phenotypic expression with WNT10A mutations shows a high degree of variability, suggesting that other genes might function with WNT10A in regulating ectodermal organ development. Moreover, the involvement of mutations in other genes, such as EDA, which is also associated with HED and isolated tooth agenesis, is not clear. Therefore, we hypothesized that EDA mutations interact with WNT10A mutations to play a role in tooth agenesis. Additionally, EDA, EDAR, and EDARADD encode signaling molecules in the Eda/Edar/NF-κB signaling pathways, we also checked EDAR and EDARADD in this study. METHODS: WNT10A, EDA, EDAR and EDARADD were sequenced in 88 patients with isolated oligodontia and 26 patients with syndromic tooth agenesis. The structure of two mutated WNT10A and two mutated EDA proteins was analyzed. RESULTS: Digenic mutations of both WNT10A and EDA were identified in 2 of 88 (2.27% isolated oligodontia cases and 4 of 26 (15.38% syndromic tooth agenesis cases. No mutation in EDAR or EDARADD gene was found. CONCLUSIONS: WNT10A and EDA digenic mutations could result in oligodontia and syndromic tooth agenesis in the Chinese population. Moreover, our results will greatly expand the genotypic spectrum of tooth agenesis.

  8. A technical evaluation of the EDA radon gas continuous monitoring system

    International Nuclear Information System (INIS)

    Bigu, J.

    1979-04-01

    Extensive laboratory and underground tests were conducted with a radon gas continuous monitoring system built by EDA Instruments Inc. The system consists of several remote radon gas sensors linked via signal cables to a central control unit that fully controls the operation of the radon monitors. The system enables four operations to be performed: sampling, background, flush and bypass. The sequence and duration of these functions is programmable. Up to 20 functions in any desired pattern each lasting from 1 min to 23 hr 59 min can be programmed. Several programs were used during the experiments in order to obtain radon and thoron gas levels. The performance of the EDA system was quite satisfactory. It is suggested that ruggedization as well as some other modifications be introdouced into the system to: a) better withstand the harsh underground environment; and b) improve its performance

  9. Modulating Calcium Signals to Boost AON Exon Skipping for DMD

    Science.gov (United States)

    2017-10-01

    mutations amenable exon 44 skipping to correct reading frame. It has been suggested that boys with these mutations have a milder disease course due to an...reprogrammed lines demonstrate increased levels of endogenous exon 44 skipping to restore reading frame (Fig 3). Further, preliminary findings indicate...45. We anticipate writing 1 or 2 manuscripts from our findings in the next reporting period: 1) developing and using our well developed exon 45 and

  10. EDAS: An Evaluation Prototype for Autonomic Event-Driven Adaptive Security in the Internet of Things

    Directory of Open Access Journals (Sweden)

    Waqas Aman

    2015-07-01

    Full Text Available In Internet of Things (IoT, the main driving technologies are considered to be tiny sensory objects. These objects cannot host traditional preventive and detective technologies to provide protection against the increasing threat sophistication. Furthermore, these solutions are limited to analyzing particular contextual information, for instance network information or files, and do not provide holistic context for risk analysis and response. Analyzing a part of a situation may lead to false alarms and later to unnecessary and incorrect configurations. To overcome these concerns, we proposed an event-driven adaptive security (EDAS model for IoT. EDAS aims to observe security events (changes generated by various things in the monitored IoT environment, investigates any intentional or unintentional risks associated with the events and adapts to it autonomously. It correlates different events in time and space to reduce any false alarms and provides a mechanism to predict attacks before they are realized. Risks are responded to autonomically by utilizing a runtime adaptation ontology. The mitigation action is chosen after assessing essential information, such as the risk faced, user preferences, device capabilities and service requirements. Thus, it selects an optimal mitigation action in a particular adverse situation. The objective of this paper is to investigate EDAS feasibility and its aptitude as a real-world prototype in a remote patient monitoring context. It details how EDAS can be a practical choice for IoT-eHealth in terms of the security, design and implementation features it offers as compared to traditional security controls. We have explained the prototype’s major components and have highlighted the key technical challenges.

  11. ITER EDA newsletter. V. 3, no. 1. (International Thermonuclear Experimental Reactor Engineering Design Activities)

    International Nuclear Information System (INIS)

    1994-01-01

    This issues of the ITER EDA (Engineering Design Activities) Newsletter contains reports on the Fourth ITER Management Advisory Committee Meeting (MAC) held at San Diego, USA, 13-14 January, 1994, a Technical Committee Meeting on Plasma Equilibrium and Control held at Naka, Japan, 9-12 November 1993, and a Technical Committee Meeting on Radio-Frequency Heating and Current Drive held in Garching, Germany, 21-26 October 1993

  12. Characteristics of transposable element exonization within human and mouse.

    Directory of Open Access Journals (Sweden)

    Noa Sela

    Full Text Available Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.

  13. Probe selection and expression index computation of Affymetrix Exon Arrays.

    Directory of Open Access Journals (Sweden)

    Yi Xing

    2006-12-01

    Full Text Available There is great current interest in developing microarray platforms for measuring mRNA abundance at both gene level and exon level. The Affymetrix Exon Array is a new high-density gene expression microarray platform, with over six million probes targeting all annotated and predicted exons in a genome. An important question for the analysis of exon array data is how to compute overall gene expression indexes. Because of the complexity of the design of exon array probes, this problem is different in nature from summarizing gene-level expression from traditional 3' expression arrays.In this manuscript, we use exon array data from 11 human tissues to study methods for computing gene-level expression. We showed that for most genes there is a subset of exon array probes having highly correlated intensities across multiple samples. We suggest that these probes could be used as reliable indicators of overall gene expression levels. We developed a probe selection algorithm to select such a subset of highly correlated probes for each gene, and computed gene expression indexes using the selected probes.Our results demonstrate that probe selection improves gene expression estimates from exon arrays. The selected probes can be used in future analyses of other exon array datasets to compute gene expression indexes.

  14. Disruption of the palatal rugae pattern in Tabby (eda) mutant mice.

    Science.gov (United States)

    Charles, Cyril; Pantalacci, Sophie; Peterkova, Renata; Peterka, Miroslav; Laudet, Vincent; Viriot, Laurent

    2007-12-01

    The eda mouse gene is linked with anomalies of ectodermal derivatives, such as hair, glands, and teeth. The palatal rugae (oral mucosa foldings on the hard palate) are also ectodermal derivatives. Therefore, we searched for and compared palatal rugae anomalies of Tabby mice bearing a mutation in the eda gene with their wild-type counterparts. We compared the number and shape of palatal rugae in 179 mutant and 102 wild-type mice from four different stocks of Tabby mice. Palatal rugae anomalies were documented at a low frequency in wild-type mice of different backgrounds, which may reflect a lack of robustness of palatal rugae development. However, the proportion of anomalies observed in the C57BL/6J background makes us recommend avoiding its use in further palate studies. We showed statistically that the phenotypic variability seen in wild-type animals is further increased in Tabby mutants. The anomalies mainly included various forms of reduction, with rugae IV-VI being more frequently affected. Those rugae were shortened, dotted or absent (mainly ruga V). By analogy to the role played by eda in other ectodermal derivatives, we propose that it might play a role in defining the pattern of the palatal rugae.

  15. Anastellin, an FN3 Fragment with Fibronectin Polymerization Activity, Resembles Amyloid Fibril Precursors

    Energy Technology Data Exchange (ETDEWEB)

    Briknarova, Klara (The Burnham Institute); Akermann, Maria (The Burnham Institute); Hoyt, David W.(BATTELLE (PACIFIC NW LAB)); Ruoslahti, Erkki (The Burnham Institute); Ely, Kathryn R.(The Burnham Institute)

    2003-08-01

    Anastellin is a carboxy-terminal fragment of the 1st FN3 domain from human fibronectin. It is capable of polymerizing fibronectin in vitro, and it displays anti-tumor, antimetastatic and anti-angiogenic properties in vivo. We have determined the structure of anastellin using nuclear magnetic resonance spectroscopy and identified residues critical for its activity. Anastellin exhibits dynamic fluctuations and conformational exchange in solution. Its overall topology is very similar to the corresponding region of full-length FN3 domains. However, its hydrophobic core becomes solvent accessible and some of its -strands lose their protection against hydrogen bonding to -strands from other molecules. These features seem to be relevant for the fibronectin polymerization activity of anastellin and resemble the characteristics of amyloid fibril precursors. We suggest that this analogy is not random and may reflect similarities between fibronectin and amyloid fibril formation.

  16. Ail Binding to Fibronectin Facilitates Yersinia pestis Binding to Host Cells and Yop Delivery▿

    OpenAIRE

    Tsang, Tiffany M.; Felek, Suleyman; Krukonis, Eric S.

    2010-01-01

    Yersinia pestis, the causative agent of plague, evades host immune responses and rapidly causes disease. The Y. pestis adhesin Ail mediates host cell binding and is critical for Yop delivery. To identify the Ail receptor(s), Ail was purified following overexpression in Escherichia coli. Ail bound specifically to fibronectin, an extracellular matrix protein with the potential to act as a bridge between Ail and host cells. Ail expressed by E. coli also mediated binding to purified fibronectin, ...

  17. Interaction between fibronectin and β1 integrin is essential for tooth development.

    Directory of Open Access Journals (Sweden)

    Kan Saito

    Full Text Available The dental epithelium and extracellular matrix interact to ensure that cell growth and differentiation lead to the formation of teeth of appropriate size and quality. To determine the role of fibronectin in differentiation of the dental epithelium and tooth formation, we analyzed its expression in developing incisors. Fibronectin mRNA was expressed during the presecretory stage in developing dental epithelium, decreased in the secretory and early maturation stages, and then reappeared during the late maturation stage. The binding of dental epithelial cells derived from postnatal day-1 molars to a fibronectin-coated dish was inhibited by the RGD but not RAD peptide, and by a β1 integrin-neutralizing antibody, suggesting that fibronectin-β1 integrin interactions contribute to dental epithelial-cell binding. Because fibronectin and β1 integrin are highly expressed in the dental mesenchyme, it is difficult to determine precisely how their interactions influence dental epithelial differentiation in vivo. Therefore, we analyzed β1 integrin conditional knockout mice (Intβ1lox-/lox-/K14-Cre and found that they exhibited partial enamel hypoplasia, and delayed eruption of molars and differentiation of ameloblasts, but not of odontoblasts. Furthermore, a cyst-like structure was observed during late ameloblast maturation. Dental epithelial cells from knockout mice did not bind to fibronectin, and induction of ameloblastin expression in these cells by neurotrophic factor-4 was inhibited by treatment with RGD peptide or a fibronectin siRNA, suggesting that the epithelial interaction between fibronectin and β1 integrin is important for ameloblast differentiation and enamel formation.

  18. Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery.

    Science.gov (United States)

    Tsang, Tiffany M; Felek, Suleyman; Krukonis, Eric S

    2010-08-01

    Yersinia pestis, the causative agent of plague, evades host immune responses and rapidly causes disease. The Y. pestis adhesin Ail mediates host cell binding and is critical for Yop delivery. To identify the Ail receptor(s), Ail was purified following overexpression in Escherichia coli. Ail bound specifically to fibronectin, an extracellular matrix protein with the potential to act as a bridge between Ail and host cells. Ail expressed by E. coli also mediated binding to purified fibronectin, and Ail-mediated E. coli adhesion to host cells was dependent on fibronectin. Ail expressed by Y. pestis bound purified fibronectin, as did the Y. pestis adhesin plasminogen activator (Pla). However, a KIM5 Delta ail mutant had decreased binding to host cells, while a KIM5 Delta pla mutant had no significant defect in adhesion. Furthermore, treatment with antifibronectin antibodies decreased Ail-mediated adhesion by KIM5 and the KIM5 Delta pla mutant, indicating that the Ail-fibronectin interaction was important for cell binding. Finally, antifibronectin antibodies inhibited the KIM5-mediated cytotoxicity of host cells in an Ail-dependent fashion. These data indicate that Ail is a key adhesin that mediates binding to host cells through interaction with fibronectin on the surface of host cells, and this interaction is important for Yop delivery by Y. pestis.

  19. Ail Binding to Fibronectin Facilitates Yersinia pestis Binding to Host Cells and Yop Delivery▿

    Science.gov (United States)

    Tsang, Tiffany M.; Felek, Suleyman; Krukonis, Eric S.

    2010-01-01

    Yersinia pestis, the causative agent of plague, evades host immune responses and rapidly causes disease. The Y. pestis adhesin Ail mediates host cell binding and is critical for Yop delivery. To identify the Ail receptor(s), Ail was purified following overexpression in Escherichia coli. Ail bound specifically to fibronectin, an extracellular matrix protein with the potential to act as a bridge between Ail and host cells. Ail expressed by E. coli also mediated binding to purified fibronectin, and Ail-mediated E. coli adhesion to host cells was dependent on fibronectin. Ail expressed by Y. pestis bound purified fibronectin, as did the Y. pestis adhesin plasminogen activator (Pla). However, a KIM5 Δail mutant had decreased binding to host cells, while a KIM5 Δpla mutant had no significant defect in adhesion. Furthermore, treatment with antifibronectin antibodies decreased Ail-mediated adhesion by KIM5 and the KIM5 Δpla mutant, indicating that the Ail-fibronectin interaction was important for cell binding. Finally, antifibronectin antibodies inhibited the KIM5-mediated cytotoxicity of host cells in an Ail-dependent fashion. These data indicate that Ail is a key adhesin that mediates binding to host cells through interaction with fibronectin on the surface of host cells, and this interaction is important for Yop delivery by Y. pestis. PMID:20498264

  20. Functionalization of silicone rubber for the covalent immobilization of fibronectin.

    Science.gov (United States)

    Völcker, N; Klee, D; Höcker, H; Langefeld, S

    2001-02-01

    Surface modification techniques were employed in order to provide functionalized silicone rubber with enhanced cytocompatibility. Acrylic acid (AAc), methacrylic acid (MAAc) and glycidylmethacrylate (GMA) were graft-co-polymerized onto the surface of silicone induced by an argon plasma and thermal initiation. The polymerizations were carried out in solution, in the case of acrylic acid a vapor phase graft-co-polymerization subsequent to argon plasma activation was carried out as well. Human fibronectin (hFn), which acts as a cell adhesion mediator for fibroblasts, was immobilized by making use of the generated carboxylic or epoxy groups, respectively. Surface analysis was accomplished by means of X-ray photoelectron spectroscopy (XPS), infrared spectroscopy in attenuated total reflection mode (IR-ATR), scanning electron microscopy (SEM), atomic force microscopy (AFM) and dynamic contact angle measurements using the Wilhelmy-plate method. The amount of immobilized active hFn was semiquantified by enzyme-linked immunosorbent assay (ELISA) using a structure-specific antibody against the cell-binding domain of hFn. In vitro testing showed a remarkable difference between surfaces exposing adsorbed-only and surfaces with covalently immobilized hFn. Copyright 2001 Kluwer Academic Publishers

  1. [Urinary laminin and fibronectin level in children with nephritic syndrome].

    Science.gov (United States)

    Korzeniecka-Kozerska, Agata; Zoch-Zwierz, Walentyna Maria; Wasilewska, Anna; Taranta-Janusz, Katarzyna; Tenderenda, Edyta; Zelazowska-Rutkowska, Beata

    2009-04-01

    Laminin (LN) and fibronectin (FN) are important extra cellular matrix (ECM) proteins. Disturbance between production and degradation of ECM proteins contributes to renal scarring. The aim of the study was evaluation the levels of urinary LN and FN in children with proteinuria in nephrotic syndrome (NS). Examinations were conducted on 71 children, 3-15 years old: (A)--44 children with NS (proteinuria above 50 mg/kg b.v./24 hours); (B)--27 children without proteinuria (remission NS). Control group (K)--30 healthy children. Concentration of LN and FN were determined by EIA. In urine of children with NS (A) urinary concentration of LN significantly increased, in comparison to control (K) (p0.05). In children with remission of NS (B) urinary concentration of LN was unchanged (p>0.05), but concentration of FN significantly decreased (p<0.05). In renal biopsies majority children of A group presented minimal changes, but majority children of B group presented hyalinization of renal tubules. Nephrotic proteinuria disturbs production of LN and increases its urinary excretion, but did not influence on urinary excretion of FN.

  2. Interdomain association in fibronectin: insight into cryptic sites and fibrillogenesis

    Science.gov (United States)

    Vakonakis, Ioannis; Staunton, David; Rooney, Luke M; Campbell, Iain D

    2007-01-01

    The process by which fibronectin (FN), a soluble multidomain protein found in tissue fluids, forms insoluble fibrillar networks in the extracellular matrix is poorly understood. Cryptic sites found in FN type III domains have been hypothesized to function as nucleation points, thereby initiating fibrillogenesis. Exposure of these sites could occur upon tension-mediated mechanical rearrangement of type III domains. Here, we present the solution structures of the second type III domain of human FN (2FNIII), and that of an interaction complex between the first two type III domains (1−2FNIII). The two domains are connected through a long linker, flexible in solution. A weak but specific interdomain interaction maintains 1−2FNIII in a closed conformation that associates weakly with the FN N-terminal 30 kDa fragment (FN30 kDa). Disruption of the interdomain interaction by amino-acid substitutions dramatically enhances association with FN30 kDa. Truncation analysis of 1−2FNIII reveals that the interdomain linker is necessary for robust 1−2FNIII–FN30 kDa interaction. We speculate on the importance of this interaction for FN function and present a possible mechanism by which tension could initiate fibrillogenesis. PMID:17464288

  3. Fibronectin-Grafted Titanium Dental Implants: An In Vivo Study

    Directory of Open Access Journals (Sweden)

    Yu-Chi Chang

    2016-01-01

    Full Text Available Modification of the physiochemical properties of titanium surfaces using glow discharge plasma (GDP and fibronectin coating has been shown to enhance the surface hydrophilicity, surface roughness, cell adhesion, migration, and proliferation. This in vivo study aimed to evaluate the bone integration efficacy of a biologically modified implant surface. Two different surface-modified implants (Ar-GDP and GDP-fib were placed in the mandibular premolar area of six beagle dogs for 2–8 weeks. Three techniques [histologic evaluation, resonance frequency analysis (RFA, and microcomputed tomography (micro-CT evaluation] were used to detect the implant stability and bone-implant contact. The implant stability quotient values of GDP-fib implants were significantly greater than the Ar-GDP implants at 2 and 4 weeks (P<0.01. The bone volume/total volume ratio of GDP-fib implants was greater than the Ar-GDP implants in micro-CT evaluation. A high positive correlation was observed between RFA and micro-CT measurements. At 2 weeks, osteoblasts were seen to line the implant surface, and multinuclear osteoclasts could be seen on the surface of old parent bone. After 8 weeks, a majority of the space in the wound chamber appeared to be replaced by bone. Enhancement of the stability of biologically modified implants was proved by the results of RFA, micro-CT, and histological analysis. This enhanced stability may help fasten treatment and be clinically beneficial.

  4. Attachment of mycobacteria to fibronectin-coated surfaces.

    Science.gov (United States)

    Ratliff, T L; McGarr, J A; Abou-Zeid, C; Rook, G A; Stanford, J L; Aslanzadeh, J; Brown, E J

    1988-05-01

    This report investigates the extent of the expression of fibronectin (FN) binding properties among the mycobacteria and provides preliminary characteristics of the bacterial molecule(s) mediating attachment. Eight BCG substrains, three Mycobacterium tuberculosis strains and four other mycobacterial species all expressed FN-binding capacity. Treatment of organisms with detergent prior to the binding assay destroyed the FN-binding capacity of BCG but not that of Staphylococcus aureus. Trypsin pretreatment eliminated the FN-binding capacity of both BCG and S. aureus. [35S]Methionine-labelled material in supernatants from BCG and M. tuberculosis cultures attached to FN-coated surfaces. These culture supernatants inhibited the attachment of BCG but not S. aureus to FN-coated surfaces. This inhibitory activity of the supernatants was removed by affinity chromatography on FN-Sepharose but was not affected by similar passage over a control column (human serum albumin attached to Sepharose). These results demonstrate that the ability to bind FN is present in all mycobacterial species tested and suggest that attachment is mediated by trypsin-sensitive cell-surface component(s).

  5. Fibronectin Pattern in Benign Hyperplasia and Cancer of the Prostate

    Directory of Open Access Journals (Sweden)

    Miroslava M. Janković

    2008-01-01

    Full Text Available Fibronectin (FN is a multifunctional glycoprotein involved in cell-matrix interactions. It exhibits a complex pattern of forms differing in respect to aminoacid and oligosaccharide composition. In this study we examined glycobiochemical and functional properties of the FN in benign prostatic hyperplasia (BPH and prostatic cancer (PCa, attempting to resolve disease-related differences. Two BPH sera pools and three PCa sera pools were used as the FN source. The affinity-purified molecule was characterized by SDS-PAGE, immuno- and lectin blot, lectin-affinity chromatography and adhesion assay. BPH FN existed as intact molecule, giving the main immunoreactive band at 220 kDa. In contrast, PCa FN comprised three main immunoreactive fragments of 140, 110 and 90 kDa. As for glycosylation the ratio of altogether lectin-reactive PCa FN was different from that of BPH FN manifested as a decrease of Con A- and an increase of LCA-reactive moieties. Fibroblasts adhered to both FN preparations in a concentration dependent manner, but with a significantly lower efficiency to PCa FN. The results obtained showing distinct structural characteristics of PCa FN compared to BPH FN could be important for modulation of its ligand and recognition properties expressed as gain or loss of functions or as specific markers of its origin.

  6. Competitive adsorption of fibronectin and albumin on hydroxyapatite nanocrystals

    International Nuclear Information System (INIS)

    Tagaya, Motohiro; Ikoma, Toshiyuki; Yoshioka, Tomohiko; Tanaka, Junzo; Hanagata, Nobutaka

    2011-01-01

    Competitive adsorption of two-component solutions containing fibronectin (Fn) and albumin (Ab) on hydroxyapatite (HAp) nanocrystals was analyzed in situ using the quartz crystal microbalance with dissipation (QCM-D) technique. Adsorption of the one-component protein (Fn or Ab) and the two-component proteins adjusted to different molar ratios of Fn to Ab at a fixed Fn concentration was investigated. The frequency shift (Δf; Hz) and the dissipation energy shift (ΔD) were measured with the QCM-D technique, and the viscoelastic changes of adlayers were evaluated by the saturated ΔD/Δf value and the Voigt-based viscoelastic model. For the adsorption of the one-component protein, the Fn adlayer showed a larger mass and higher viscoelasticity than the Ab adlayer, indicating the higher affinity of Fn on HAp. For the adsorption of the two-component proteins, the viscoelastic properties of the adlayers became elastic with increase in Ab concentration, whereas the adsorption mass was similar to that of Fn in the one-component solution regardless of the Ab concentration. The specific binding mass of the Ab antibody to the adlayers increased with increase in Ab concentration, whereas that of the Fn antibody decreased. Therefore, Fn preferentially adsorbs on HAp and Ab subsequently interacts with the adlayers, indicating that the interfacial viscoelasticity of the adlayers was dominated by the interaction between Fn and Ab.

  7. Competitive adsorption of fibronectin and albumin on hydroxyapatite nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Tagaya, Motohiro; Ikoma, Toshiyuki; Yoshioka, Tomohiko; Tanaka, Junzo [Department of Metallurgy and Ceramics Science, Tokyo Institute of Technology, Tokyo 152-8550 (Japan); Hanagata, Nobutaka, E-mail: tagaya.m.aa@m.titech.ac.jp [Biomaterials Center, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047 (Japan)

    2011-06-15

    Competitive adsorption of two-component solutions containing fibronectin (Fn) and albumin (Ab) on hydroxyapatite (HAp) nanocrystals was analyzed in situ using the quartz crystal microbalance with dissipation (QCM-D) technique. Adsorption of the one-component protein (Fn or Ab) and the two-component proteins adjusted to different molar ratios of Fn to Ab at a fixed Fn concentration was investigated. The frequency shift ({Delta}f; Hz) and the dissipation energy shift ({Delta}D) were measured with the QCM-D technique, and the viscoelastic changes of adlayers were evaluated by the saturated {Delta}D/{Delta}f value and the Voigt-based viscoelastic model. For the adsorption of the one-component protein, the Fn adlayer showed a larger mass and higher viscoelasticity than the Ab adlayer, indicating the higher affinity of Fn on HAp. For the adsorption of the two-component proteins, the viscoelastic properties of the adlayers became elastic with increase in Ab concentration, whereas the adsorption mass was similar to that of Fn in the one-component solution regardless of the Ab concentration. The specific binding mass of the Ab antibody to the adlayers increased with increase in Ab concentration, whereas that of the Fn antibody decreased. Therefore, Fn preferentially adsorbs on HAp and Ab subsequently interacts with the adlayers, indicating that the interfacial viscoelasticity of the adlayers was dominated by the interaction between Fn and Ab.

  8. Competitive adsorption of fibronectin and albumin on hydroxyapatite nanocrystals

    Science.gov (United States)

    Tagaya, Motohiro; Ikoma, Toshiyuki; Hanagata, Nobutaka; Yoshioka, Tomohiko; Tanaka, Junzo

    2011-06-01

    Competitive adsorption of two-component solutions containing fibronectin (Fn) and albumin (Ab) on hydroxyapatite (HAp) nanocrystals was analyzed in situ using the quartz crystal microbalance with dissipation (QCM-D) technique. Adsorption of the one-component protein (Fn or Ab) and the two-component proteins adjusted to different molar ratios of Fn to Ab at a fixed Fn concentration was investigated. The frequency shift (Δf Hz) and the dissipation energy shift (ΔD) were measured with the QCM-D technique, and the viscoelastic changes of adlayers were evaluated by the saturated ΔD/Δf value and the Voigt-based viscoelastic model. For the adsorption of the one-component protein, the Fn adlayer showed a larger mass and higher viscoelasticity than the Ab adlayer, indicating the higher affinity of Fn on HAp. For the adsorption of the two-component proteins, the viscoelastic properties of the adlayers became elastic with increase in Ab concentration, whereas the adsorption mass was similar to that of Fn in the one-component solution regardless of the Ab concentration. The specific binding mass of the Ab antibody to the adlayers increased with increase in Ab concentration, whereas that of the Fn antibody decreased. Therefore, Fn preferentially adsorbs on HAp and Ab subsequently interacts with the adlayers, indicating that the interfacial viscoelasticity of the adlayers was dominated by the interaction between Fn and Ab.

  9. Competitive adsorption of fibronectin and albumin on hydroxyapatite nanocrystals

    Directory of Open Access Journals (Sweden)

    Motohiro Tagaya, Toshiyuki Ikoma, Nobutaka Hanagata, Tomohiko Yoshioka and Junzo Tanaka

    2011-01-01

    Full Text Available Competitive adsorption of two-component solutions containing fibronectin (Fn and albumin (Ab on hydroxyapatite (HAp nanocrystals was analyzed in situ using the quartz crystal microbalance with dissipation (QCM-D technique. Adsorption of the one-component protein (Fn or Ab and the two-component proteins adjusted to different molar ratios of Fn to Ab at a fixed Fn concentration was investigated. The frequency shift (Δf; Hz and the dissipation energy shift (ΔD were measured with the QCM-D technique, and the viscoelastic changes of adlayers were evaluated by the saturated ΔD/Δf value and the Voigt-based viscoelastic model. For the adsorption of the one-component protein, the Fn adlayer showed a larger mass and higher viscoelasticity than the Ab adlayer, indicating the higher affinity of Fn on HAp. For the adsorption of the two-component proteins, the viscoelastic properties of the adlayers became elastic with increase in Ab concentration, whereas the adsorption mass was similar to that of Fn in the one-component solution regardless of the Ab concentration. The specific binding mass of the Ab antibody to the adlayers increased with increase in Ab concentration, whereas that of the Fn antibody decreased. Therefore, Fn preferentially adsorbs on HAp and Ab subsequently interacts with the adlayers, indicating that the interfacial viscoelasticity of the adlayers was dominated by the interaction between Fn and Ab.

  10. Kinetics of conformational changes of fibronectin adsorbed onto model surfaces.

    Science.gov (United States)

    Baujard-Lamotte, L; Noinville, S; Goubard, F; Marque, P; Pauthe, E

    2008-05-01

    Fibronectin (FN), a large glycoprotein found in body fluids and in the extracellular matrix, plays a key role in numerous cellular behaviours. We investigate FN adsorption onto hydrophilic bare silica and hydrophobic polystyrene (PS) surfaces using Fourier transform infrared spectroscopy-attenuated total reflection (FTIR-ATR) in aqueous medium. Adsorption kinetics using different bulk concentrations of FN were followed for 2h and the surface density of adsorbed FN and its time-dependent conformational changes were determined. When adsorption occurs onto the hydrophilic surface, FN molecules keep their native conformation independent of the adsorption conditions, but the amount of adsorbed FN increases with time and the bulk concentration. Although the protein surface density is the same on the hydrophobic PS surface, this has a strong impact on the average conformation of the adsorbed FN layer. Indeed, interfacial hydration changes induced by adsorption onto the hydrophobic surface lead to a decrease in unhydrated beta-sheet content and cause an increase in hydrated beta-strand and hydrated random domain content of adsorbed FN. This conformational change is mainly dependent on the bulk concentration. Indeed, at low bulk concentrations, the secondary structures of adsorbed FN molecules undergo strong unfolding, allowing an extended and hydrated conformation of the protein. At high bulk concentrations, the molecular packing reduces the unfolding of the stereoregular structures of the FN molecules, preventing stronger spreading of the protein.

  11. Naturally occuring nucleosome positioning signals in human exons and introns

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren; Chauvin, Yves

    1996-01-01

    We describe the structural implications of a periodic pattern found in human exons and introns by hidden Markov models. We show that exons (besides the reading frame) have a specific sequential structure in the form of a pattern with triplet consensus non-T(A/T)G, and a minimal periodicity...

  12. SFS, a Novel Fibronectin-Binding Protein from Streptococcus equi, Inhibits the Binding between Fibronectin and Collagen

    Science.gov (United States)

    Lindmark, Hans; Guss, Bengt

    1999-01-01

    The obligate parasitic bacterium Streptococcus equi subsp. equi is the causative agent of strangles, a serious disease of the upper respiratory tract in horses. In this study we have, using shotgun phage display, cloned from S. equi subsp. equi and characterized a gene, called sfs, encoding a protein termed SFS, representing a new type of fibronectin (Fn)-binding protein. The sfs gene was found to be present in all 50 isolates of S. equi subsp. equi tested and in 41 of 48 S. equi subsp. zooepidemicus isolates tested. The sfs gene is down-regulated during growth in vitro compared to fnz, a previously characterized gene encoding an Fn-binding protein from S. equi subsp. zooepidemicus. Sequence comparisons revealed no similarities to previously characterized Fn-binding proteins, but high scores were obtained against collagen. Besides similarity due to the high content of glycine, serine, and proline residues present in both proteins, there was a nine-residue motif present both in collagen and in the Fn-binding domain of SFS. By searching the Oklahoma S. pyogenes database, we found that this motif is also present in a potential cell surface protein from S. pyogenes. Protein SFS was found to inhibit the binding between Fn and collagen in a concentration-dependent way. PMID:10225899

  13. Definition of the native and denatured type II collagen binding site for fibronectin using a recombinant collagen system.

    Science.gov (United States)

    An, Bo; Abbonante, Vittorio; Yigit, Sezin; Balduini, Alessandra; Kaplan, David L; Brodsky, Barbara

    2014-02-21

    Interaction of collagen with fibronectin is important for extracellular matrix assembly and regulation of cellular processes. A fibronectin-binding region in collagen was identified using unfolded fragments, but it is not clear if the native protein binds fibronectin with the same primary sequence. A recombinant bacterial collagen is utilized to characterize the sequence requirement for fibronectin binding. Chimeric collagens were generated by inserting the putative fibronectin-binding region from human collagen into the bacterial collagen sequence. Insertion of a sufficient length of human sequence conferred fibronectin affinity. The minimum sequence requirement was identified as a 6-triplet sequence near the unique collagenase cleavage site and was the same in both triple-helix and denatured states. Denaturation of the chimeric collagen increased its affinity for fibronectin, as seen for mammalian collagens. The fibronectin binding recombinant collagen did not contain hydroxyproline, indicating hydroxyproline is not essential for binding. However, its absence may account, in part, for the higher affinity of the native chimeric protein and the lower affinity of the denatured protein compared with type II collagen. Megakaryocytes cultured on chimeric collagen with fibronectin affinity showed improved adhesion and differentiation, suggesting a strategy for generating bioactive materials in biomedical applications.

  14. Cooperative effects of fibronectin matrix assembly and initial cell-substrate adhesion strength in cellular self-assembly.

    Science.gov (United States)

    Brennan, James R; Hocking, Denise C

    2016-03-01

    The cell-dependent polymerization of intercellular fibronectin fibrils can stimulate cells to self-assemble into multicellular structures. The local physical cues that support fibronectin-mediated cellular self-assembly are largely unknown. Here, fibronectin matrix analogs were used as synthetic adhesive substrates to model cell-matrix fibronectin fibrils having different integrin-binding specificity, affinity, and/or density. We utilized this model to quantitatively assess the relationship between adhesive forces derived from cell-substrate interactions and the ability of fibronectin fibril assembly to induce cellular self-assembly. Results indicate that the strength of initial, rather than mature, cell-substrate attachments correlates with the ability of substrates to support fibronectin-mediated cellular self-assembly. The cellular response to soluble fibronectin was bimodal and independent of the integrin-binding specificity of the substrate; increasing soluble fibronectin levels above a critical threshold increased aggregate cohesion on permissive substrates. Once aggregates formed, continuous fibronectin polymerization was necessary to maintain cohesion. During self-assembly, soluble fibronectin decreased cell-substrate adhesion strength and induced aggregate cohesion via a Rho-dependent mechanism, suggesting that the balance of contractile forces derived from fibronectin fibrils within cell-cell versus cell-substrate adhesions controls self-assembly and aggregate cohesion. Thus, initial cell-substrate attachment strength may provide a quantitative basis with which to build predictive models of fibronectin-mediated microtissue fabrication on a variety of substrates. Cellular self-assembly is a process by which cells and extracellular matrix (ECM) proteins spontaneously organize into three-dimensional (3D) tissues in the absence of external forces. Cellular self-assembly can be initiated in vitro, and represents a potential tool for tissue engineers to

  15. The Eating Disorder Assessment for DSM-5 (EDA-5): Development and Validation of a Structured Interview for Feeding and Eating Disorders

    Science.gov (United States)

    Sysko, Robyn; Glasofer, Deborah R.; Hildebrandt, Tom; Klimek, Patrycja; Mitchell, James E.; Berg, Kelly C.; Peterson, Carol B.; Wonderlich, Stephen A.; Walsh, B. Timothy

    2016-01-01

    Objective Existing measures for DSM-IV eating disorder diagnoses have notable limitations, and there are important differences between DSM-IV and DSM-5 feeding and eating disorders. This study developed and validated a new semi-structured interview, the Eating Disorders Assessment for DSM-5 (EDA-5). Method Two studies evaluated the utility of the EDA-5. Study 1 compared the diagnostic validity of the EDA-5 to the Eating Disorder Examination (EDE) and evaluated the test-retest reliability of the new measure. Study 2 compared the diagnostic validity of an EDA-5 electronic application (“app”) to clinician interview and self-report assessments. Results In Study 1, the kappa for EDE and EDA-5 eating disorder diagnoses was 0.74 across all diagnoses (n= 64), with a range of κ=0.65 for Other Specified Feeding or Eating Disorder (OSFED)/Unspecified Feeding or Eating Disorder (USFED) to κ=0.90 for Binge Eating Disorder (BED). The EDA-5 test-retest kappa coefficient was 0.87 across diagnoses. For Study 2, clinical interview versus “app” conditions revealed a kappa of 0.83 for all eating disorder diagnoses (n=71). Across individual diagnostic categories, kappas ranged from 0.56 for OSFED/USFED to 0.94 for BN. Discussion High rates of agreement were found between diagnoses by EDA-5 and the EDE, and EDA-5 and clinical interviews. As this study supports the validity of the EDA-5 to generate DSM-5 eating disorders and the reliability of these diagnoses, the EDA-5 may be an option for the assessment of Anorexia Nervosa, Bulimia Nervosa, and BED. Additional research is needed to evaluate the utility of the EDA-5 in assessing DSM-5 feeding disorders. PMID:25639562

  16. The eating disorder assessment for DSM-5 (EDA-5): Development and validation of a structured interview for feeding and eating disorders.

    Science.gov (United States)

    Sysko, Robyn; Glasofer, Deborah R; Hildebrandt, Tom; Klimek, Patrycja; Mitchell, James E; Berg, Kelly C; Peterson, Carol B; Wonderlich, Stephen A; Walsh, B Timothy

    2015-07-01

    Existing measures for DSM-IV eating disorder diagnoses have notable limitations, and there are important differences between DSM-IV and DSM-5 feeding and eating disorders. This study developed and validated a new semistructured interview, the Eating Disorders Assessment for DSM-5 (EDA-5). Two studies evaluated the utility of the EDA-5. Study 1 compared the diagnostic validity of the EDA-5 with the Eating Disorder Examination (EDE) and evaluated the test-retest reliability of the new measure. Study 2 compared the diagnostic validity of an EDA-5 electronic application ("App") with clinician interview and self-reported assessments. In Study 1, the kappa for EDE and EDA-5 eating disorder diagnoses was 0.74 across all diagnoses (n = 64), with a range of κ = 0.65 for other specified feeding or eating disorder/unspecified feeding or eating disorder to κ = 0.90 for binge eating disorder. The EDA-5 test-retest kappa coefficient was 0.87 across diagnoses. For Study 2, clinical interview versus App conditions revealed a kappa of 0.83 for all eating disorder diagnoses (n = 71). Across individual diagnostic categories, kappas ranged from 0.56 for other specified feeding or eating disorder/unspecified feeding or eating disorder to 0.94 for BN. High rates of agreement were found between diagnoses by EDA-5 and the EDE, and EDA-5 and clinical interviews. Because this study supports the validity of the EDA-5 to generate DSM-5 eating disorders and the reliability of these diagnoses, the EDA-5 may be an option for the assessment of anorexia nervosa, bulimia nervosa, and binge eating disorder. Additional research is needed to evaluate the utility of the EDA-5 in assessing DSM-5 feeding disorders. © 2015 Wiley Periodicals, Inc.

  17. Synthesis and Layout of an Asynchronous Network-on-Chip using Standard EDA Tools

    DEFF Research Database (Denmark)

    Müller, Christoph; Kasapaki, Evangelia; Sørensen, Rasmus Bo

    2014-01-01

    Asynchronous circuit design is well understood but design tools supporting asynchronous design are largely lacking, and designers are limited to using conventional EDA-tools. These tools have a built-in synchronous mind-set and this complicates their use for asynchronous implementation. One example...... is the key role that clock signals play in specifying time-constraints for the synthesis. In this paper explain how we handled the synthesis and layout of an asynchronous network-on-chip for a multi-core platform. Focus is on the design process while the actual NOC-design and its performance are presented...

  18. Exonization of a LINE1 fragment implicated in X-linked hypohidrotic ectodermal dysplasia in cattle

    DEFF Research Database (Denmark)

    Karlskov-Mortensen, Peter; Cirera Salicio, Susanna; Nielsen, Ole Lerberg

    2011-01-01

    A case of X-linked hypohidrotic ectodermal dysplasia (XHED) was identified in a family of Danish Red Holstein cattle. The ectodysplasin-signalling protein (EDA) is known to be central in the normal development of ectodermal structures, and mutations in the ectodysplasin A (EDA) gene have been rep...

  19. Skipping Multiple Exons to Treat DMD-Promises and Challenges.

    Science.gov (United States)

    Aslesh, Tejal; Maruyama, Rika; Yokota, Toshifumi

    2018-01-02

    Duchenne muscular dystrophy (DMD) is a lethal disorder caused by mutations in the DMD gene. Antisense-mediated exon-skipping is a promising therapeutic strategy that makes use of synthetic nucleic acids to skip frame-disrupting exon(s) and allows for short but functional protein expression by restoring the reading frame. In 2016, the U.S. Food and Drug Administration (FDA) approved eteplirsen, which skips DMD exon 51 and is applicable to approximately 13% of DMD patients. Multiple exon skipping, which is theoretically applicable to 80-90% of DMD patients in total, have been demonstrated in animal models, including dystrophic mice and dogs, using cocktail antisense oligonucleotides (AOs). Although promising, current drug approval systems pose challenges for the use of a cocktail AO. For example, both exons 6 and 8 need to be skipped to restore the reading frame in dystrophic dogs. Therefore, the cocktail of AOs targeting these exons has a combined therapeutic effect and each AO does not have a therapeutic effect by itself. The current drug approval system is not designed to evaluate such circumstances, which are completely different from cocktail drug approaches in other fields. Significant changes are needed in the drug approval process to promote the cocktail AO approach.

  20. Tumor angiogenesis in the absence of fibronectin or its cognate integrin receptors.

    Directory of Open Access Journals (Sweden)

    Patrick A Murphy

    Full Text Available Binding of α5β1 and αvβ3/β5 integrin receptors on the endothelium to their fibronectin substrate in the extracellular matrix has been targeted as a possible means of blocking tumor angiogenesis and tumor growth. However, clinical trials of blocking antibodies and peptides have been disappointing despite promising preclinical results, leading to questions about the mechanism of the inhibitors and the reasons for their failure. Here, using tissue-specific and inducible genetics to delete the α5 and αv receptors in the endothelium or their fibronectin substrate, either in the endothelium or globally, we show that both are dispensable for tumor growth, in transplanted tumors as well as spontaneous and angiogenesis-dependent RIP-Tag-driven pancreatic adenocarcinomas. In the nearly complete absence of fibronectin, no differences in vascular density or the deposition of basement membrane laminins, ColIV, Nid1, Nid2, or the TGFβ binding matrix proteins, fibrillin-1 and -2, could be observed. Our results reveal that fibronectin and the endothelial fibronectin receptor subunits, α5 and αv, are dispensable for tumor angiogenesis, suggesting that the inhibition of angiogenesis induced by antibodies or small molecules may occur through a dominant negative effect, rather than a simple functional block.

  1. Increased biosynthesis and processing of fibronectin in fibroblasts from diabetic mice

    International Nuclear Information System (INIS)

    Phan-Thanh, L.; Robert, L.; Derouette, J.C.; Labat-Robert, J.

    1987-01-01

    Diabetic connective tissues exhibit a deranged regulation of extracellular matrix biosynthesis. Fibronectin is shown to be increased in human dermal connective tissue by immunofluorescence, mainly at the dermoepidermal and capillary basement membranes. The rate of fibronectin biosynthesis, excretion, and incorporation in a pericellular polymeric form was investigated using genetically diabetic KK mouse skin and fibroblasts as compared to swiss and C57BL mouse skin and fibroblasts. The rate of incorporation of [ 35 S]methionine into proteins recovered in the culture medium or in deoxycholate and NaDodSO 4 or urea extracts was investigated. The rate of incorporation in the medium and deoxycholate extracts was comparable. However, the relative rate of incorporation of the tracer in the NaDodSO 4 -extractable, pericellular polymeric form was increased in the diabetic KK fibroblasts both for total proteins and for fibronectin. In pulse-chase experiments, the deoxycholate-soluble and NaDodSO 4 -soluble fractions exhibited a precursor-product relationship. The rate of passage of fibronectin from the deoxycholate-soluble (cellular compartment) form to the NaDodSO 4 -soluble (pericellular polymeric) form was strongly accelerated in the diabetic fibroblast cultures. These results confirm the increased rate of synthesis of fibronectin in diabetic fibroblasts as well as its processing from the cellular compartment to the polymeric pericellular form

  2. Chemically grafted fibronectin for use in QCM-D cell studies.

    Science.gov (United States)

    Kandel, Judith; Lee, Hyun-Su; Sobolewski, Peter; Tomczyk, Nancy; Composto, Russell J; Eckmann, David M

    2014-08-15

    Traditionally, fibronectin has been used as a physisorbed surface coating (physFN) in cell culture experiments due to its critical role in cell adhesion. However, because the resulting layer is thick, unstable, and of unpredictable uniformity, this method of fibronectin deposition is unsuitable for some types of research, including quartz crystal microbalance (QCM) experiments involving cells. Here, we present a new method for chemical immobilization of fibronectin onto silicon oxide surfaces, including QCM crystals pre-coated with silicon oxide. We characterize these chemically coated fibronectin surfaces (chemFN) as well as physFN ones using spectroscopic ellipsometry (SE), Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM), and contact angle measurements. A cell culture model demonstrates that cells on chemFN and physFN surfaces exhibit similar viability, structure, adhesion and metabolism. Finally, we perform QCM experiments using cells on both surfaces which demonstrate the superior suitability of chemFN coatings for QCM research, and provide real-time QCM-D data from cells subjected to an actin depolymerizing agent. Overall, our method of chemical immobilization of fibronectin yields great potential for furthering cellular experiments in which thin, stable and uniform coatings are desirable. As QCM research with cells has been rather limited in success thus far, we anticipate that this new technique will particularly benefit this experimental system by availing it to the much broader field of cell mechanics. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Hsp90 Binds Directly to Fibronectin (FN) and Inhibition Reduces the Extracellular Fibronectin Matrix in Breast Cancer Cells

    Science.gov (United States)

    Kenyon, Amy; Dhanani, Karim C. H.; Prinsloo, Earl; Edkins, Adrienne L.

    2014-01-01

    Heat shock protein 90 (Hsp90) has been identified in the extracellular space and has been shown to chaperone a finite number of extracellular proteins involved in cell migration and invasion. We used chemical cross-linking and immunoprecipitation followed by tandem mass spectrometry (MS/MS) to isolate a complex containing Hsp90 and the matrix protein fibronectin (FN) from breast cancer cells. Further analysis showed direct binding of Hsp90 to FN using an in vitro co-immunoprecipitation assay, a solid phase binding assay and surface plasmon resonance (SPR) spectroscopy. Confocal microscopy showed regions of co-localisation of Hsp90 and FN in breast cancer cell lines. Exogenous Hsp90β was shown to increase the formation of extracellular FN matrix in the Hs578T cell line, whilst knockdown or inhibition of Hsp90 led to a reduction in the levels of both soluble and insoluble FN and could be partially rescued by addition of exogenous Hsp90β. Treatment of cells with novobiocin led to internalization of FN into vesicles that were positive for the presence of the lysosomal marker, LAMP-1. Taken together, the direct interaction between FN and Hsp90, as well as the decreased levels of both soluble and insoluble FN upon Hsp90 inhibition or knockdown, suggested that FN may be a new client protein for Hsp90 and that Hsp90 was involved in FN matrix assembly and/or stability. The identification of FN as a putative client protein of Hsp90 suggests a role for Hsp90 in FN matrix stability, which is important for a number of fundamental cellular processes including embryogenesis, wound healing, cell migration and metastasis. PMID:24466266

  4. A novel splicing silencer generated by DMD exon 45 deletion junction could explain upstream exon 44 skipping that modifies dystrophinopathy.

    Science.gov (United States)

    Dwianingsih, Ery Kus; Malueka, Rusdy Ghazali; Nishida, Atsushi; Itoh, Kyoko; Lee, Tomoko; Yagi, Mariko; Iijima, Kazumoto; Takeshima, Yasuhiro; Matsuo, Masafumi

    2014-08-01

    Duchenne muscular dystrophy (DMD), a progressive muscle-wasting disease, is mostly caused by exon deletion mutations in the DMD gene. The reading frame rule explains that out-of-frame deletions lead to muscle dystrophin deficiency in DMD. In outliers to this rule, deletion junction sequences have never previously been explored as splicing modulators. In a Japanese case, we identified a single exon 45 deletion in the patient's DMD gene, indicating out-of-frame mutation. However, immunohistochemical examination disclosed weak dystrophin signals in his muscle. Reverse transcription-PCR amplification of DMD exons 42 to 47 revealed a major normally spliced product with exon 45 deletion and an additional in-frame product with deletion of both exons 44 and 45, indicating upstream exon 44 skipping. We considered the latter to underlie the observed dystrophin expression. Remarkably, the junction sequence cloned by PCR walking abolished the splicing enhancer activity of the upstream intron in a chimeric doublesex gene pre-mRNA in vitro splicing. Furthermore, antisense oligonucleotides directed against the junction site counteracted this effect. These indicated that the junction sequence was a splicing silencer that induced upstream exon 44 skipping. It was strongly suggested that creation of splicing regulator is a modifier of dystrophinopathy.

  5. Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies.

    Science.gov (United States)

    Toh, Zhi Yon Charles; Thandar Aung-Htut, May; Pinniger, Gavin; Adams, Abbie M; Krishnaswarmy, Sudarsan; Wong, Brenda L; Fletcher, Sue; Wilton, Steve D

    2016-01-01

    Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels) manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes.

  6. Human facial skin detection in thermal video to effectively measure electrodermal activity (EDA)

    Science.gov (United States)

    Kaur, Balvinder; Hutchinson, J. Andrew; Leonard, Kevin R.; Nelson, Jill K.

    2011-06-01

    In the past, autonomic nervous system response has often been determined through measuring Electrodermal Activity (EDA), sometimes referred to as Skin Conductance (SC). Recent work has shown that high resolution thermal cameras can passively and remotely obtain an analog to EDA by assessing the activation of facial eccrine skin pores. This paper investigates a method to distinguish facial skin from non-skin portions on the face to generate a skin-only Dynamic Mask (DM), validates the DM results, and demonstrates DM performance by removing false pore counts. Moreover, this paper shows results from these techniques using data from 20+ subjects across two different experiments. In the first experiment, subjects were presented with primary screening questions for which some had jeopardy. In the second experiment, subjects experienced standard emotion-eliciting stimuli. The results from using this technique will be shown in relation to data and human perception (ground truth). This paper introduces an automatic end-to-end skin detection approach based on texture feature vectors. In doing so, the paper contributes not only a new capability of tracking facial skin in thermal imagery, but also enhances our capability to provide non-contact, remote, passive, and real-time methods for determining autonomic nervous system responses for medical and security applications.

  7. A Cascade of Wnt, Eda, and Shh Signaling Is Essential for Touch Dome Merkel Cell Development.

    Directory of Open Access Journals (Sweden)

    Ying Xiao

    2016-07-01

    Full Text Available The Sonic hedgehog (Shh signaling pathway regulates developmental, homeostatic, and repair processes throughout the body. In the skin, touch domes develop in tandem with primary hair follicles and contain sensory Merkel cells. The developmental signaling requirements for touch dome specification are largely unknown. We found dermal Wnt signaling and subsequent epidermal Eda/Edar signaling promoted Merkel cell morphogenesis by inducing Shh expression in early follicles. Lineage-specific gene deletions revealed intraepithelial Shh signaling was necessary for Merkel cell specification. Additionally, a Shh signaling agonist was sufficient to rescue Merkel cell differentiation in Edar-deficient skin. Moreover, Merkel cells formed in Fgf20 mutant skin where primary hair formation was defective but Shh production was preserved. Although developmentally associated with hair follicles, fate mapping demonstrated Merkel cells primarily originated outside the hair follicle lineage. These findings suggest that touch dome development requires Wnt-dependent mesenchymal signals to establish reciprocal signaling within the developing ectoderm, including Eda signaling to primary hair placodes and ultimately Shh signaling from primary follicles to extrafollicular Merkel cell progenitors. Shh signaling often demonstrates pleiotropic effects within a structure over time. In postnatal skin, Shh is known to regulate the self-renewal, but not the differentiation, of touch dome stem cells. Our findings relate the varied effects of Shh in the touch dome to the ligand source, with locally produced Shh acting as a morphogen essential for lineage specification during development and neural Shh regulating postnatal touch dome stem cell maintenance.

  8. Platelet-rich plasma and chronic wounds: remaining fibronectin may influence matrix remodeling and regeneration success.

    Science.gov (United States)

    Moroz, Andrei; Deffune, Elenice

    2013-11-01

    Platelet-rich plasma has been largely used as a therapeutic option for the treatment of chronic wounds of different etiologies. The enhanced regeneration observed after the use of platelet-rich plasma has been systematically attributed to the growth factors that are present inside platelets' granules. We hypothesize that the remaining plasma and platelet-bound fibronectin may act as a further bioactive protein in platelet-rich plasma preparations. Recent reports were analyzed and presented as direct evidences of this hypotheses. Fibronectin may directly influence the extracellular matrix remodeling during wound repair. This effect is probably through matrix metalloproteinase expression, thus exerting an extra effect on chronic wound regeneration. Physicians should be well aware of the possible fibronectin-induced effects in their future endeavors with PRP in chronic wound treatment. Copyright © 2013 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

  9. Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob L; Penny, David

    2007-01-01

    Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in Cae...

  10. Human glucose phosphate isomerase: Exon mapping and gene structure

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Weiming; Lee, Pauline; Beutler, E. [Scripps Research Inst., La Jolla, CA (United States)

    1995-10-10

    The structure of the gene for human glucose phosphate isomerase (GPI) has been determined. Three GPI clones were isolated from a human genomic library by using a full-length GPI cDNA probe and were characterized. Oligonucleotides based on the known cDNA sequence were used as primers in amplification and sequence analyses. This led to the identification of the exon-intron junctions. By this approach, 18 exons and 17 introns have been identified. The exons range in size from 44 to 431 nucleotides. The intronic sequences surrounding the exons provide useful information for the identification of mutations that give rise to human GPI deficiency associated with chronic hemolytic anemia. 13 refs., 4 figs., 1 tab.

  11. Exon silencing by UAGG motifs in response to neuronal excitation.

    Directory of Open Access Journals (Sweden)

    Ping An

    2007-02-01

    Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

  12. Lectins as probes for assessing the accessibility of N-linked glycans in relation to the conformational changes of fibronectin.

    Science.gov (United States)

    Agniel, Rémy; Vendrely, Charlotte; Poulouin, Laurent; Bascetin, Rümeyza; Benachour, Hamanou; Gallet, Olivier; Leroy-Dudal, Johanne

    2015-12-01

    Fibronectin, a ≈ 450-kDa protein with 4-9% (w/w) glycosylation, is a key component of extracellular matrices and has a high conformational lability regarding its functions. However, the accessibility and the role of glycosylated moieties associated with the conformational changes of fibronectin are poorly understood. Using lectins as probes, we developed an approach comprising dynamic light scattering, turbidimetry measurements, and isothermal titration calorimetry to assess the accessibility of glycosylated moieties of fibronectin undergoing thermal-induced conformational changes. Among a set of 14 lectins, fibronectin mainly reacted with mannose-binding lectins, specifically concanavalin A. When temperature was raised from 25 to 50 °C, fibronectin underwent progressive unfolding, but the conformation of concanavalin A was unaffected. Dynamic light scattering, turbidimetry measurements, and isothermal titration calorimetry showed increased concanavalin A binding to fibronectin during progressive thermal-induced unfolding of the protein core. Such data suggest that mannosylated residues are progressively exposed as fibronectin unfolds. Because oligosaccharide moieties can be differently exposed to cells, and the cell's responses could be modified physiologically or pathologically, modulation of fibronectin sugar chains could be relevant to its biological functions. Thus, lectins might be useful tools to probe the glycosylation accessibility accompanying changes in protein core folding, for which a better understanding would be of value for biological and biomedical research. Copyright © 2015 John Wiley & Sons, Ltd.

  13. A synthetic peptide from the COOH-terminal heparin-binding domain of fibronectin promotes focal adhesion formation

    DEFF Research Database (Denmark)

    Woods, A; McCarthy, J B; Furcht, L T

    1993-01-01

    Cell adhesion to extracellular matrix molecules such as fibronectin involves complex transmembrane signaling processes. Attachment and spreading of primary fibroblasts can be promoted by interactions of cell surface integrins with RGD-containing fragments of fibronectin, but the further process o...

  14. DMPD: The interrelated role of fibronectin and interleukin-1 in biomaterial-modulatedmacrophage function. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16978691 The interrelated role of fibronectin and interleukin-1 in biomaterial-modulatedm...(.svg) (.html) (.csml) Show The interrelated role of fibronectin and interleukin-1 in biomaterial-modulatedm...and interleukin-1 in biomaterial-modulatedmacrophage function. Authors Schmidt DR, Kao WJ. Publication Bioma

  15. A synthetic peptide from the COOH-terminal heparin-binding domain of fibronectin promotes focal adhesion formation

    DEFF Research Database (Denmark)

    Woods, A; McCarthy, J B; Furcht, L T

    1993-01-01

    of focal adhesion and stress fiber formation requires additional interactions. Heparin-binding fragments of fibronectin can provide this signal. The COOH-terminal heparin-binding domain of fibronectin contains five separate heparin-binding amino acid sequences. We show here that all five sequences...

  16. Escherichia coli EDA is a novel fusion expression partner to improve solubility of aggregation-prone heterologous proteins.

    Science.gov (United States)

    Kang, Yoon-Sik; Song, Jong-Am; Han, Kyung-Yeon; Lee, Jeewon

    2015-01-20

    Since the use of solubility enhancer proteins is one of the effective methods to produce active recombinant proteins within Escherichia coli, the development of a novel fusion expression partner that can be applied to various aggregation-prone proteins is of crucial importance. In our previous work, two-dimensional electrophoresis (2-DE) was employed to systematically analyze the E. coli BL21 (DE3) proteome profile in response to heat treatment, and KDPG aldolase (EDA) was identified as a heat-responsive and aggregation-resistant protein. When used as fusion expression partner, EDA significantly increased the solubility of seven aggregation-prone heterologous proteins in the E. coli cytoplasm. The efficacy of EDA as a fusion expression partner was evaluated through the analysis of bioactivity or secondary structure of several target proteins: EDA-fusion expression resulted in the synthesis of bioactive human ferritin light chain and bacterial arginine deiminase and the formation of correct secondary structure of human granulocyte colony stimulation factor. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. The anticipated mean shift and cluster registration in mixture-based EDAs for multi-objective optimization

    NARCIS (Netherlands)

    P.A.N. Bosman (Peter); J. Branke

    2010-01-01

    htmlabstractIt is known that in real-valued Single-Objective (SO) optimization with Gaussian Estimation-of-Distribution Algorithms (EDAs), it is important to take into account how distribution parameters change in subsequent generations to prevent inefficient convergence as a result of overfitting,

  18. 75 FR 23676 - Solicitation of Applications for the i6 Challenge Under EDA's Economic Adjustment Assistance Program

    Science.gov (United States)

    2010-05-04

    ..., 2010. Winning Applicants should expect to receive grant awards by fall of 2010. EDA will hold an online... strategic opportunities while minimizing short- and long-term threats; A sound strategy to support... commercialization potential, patenting, licensing, venture formation, financing, and marketing; Adequate financial...

  19. Dynamics of fibronectin adsorption on TiO2 surfaces.

    Science.gov (United States)

    Sousa, S R; Brás, M Manuela; Moradas-Ferreira, P; Barbosa, M A

    2007-06-19

    In the present work we analyze the dynamics of fibronectin (FN) adsorption on two different stable titanium oxides, with varied surface roughness, and chemically similar to those used in clinical practice. The two types of titanium oxide surfaces used were TiO2 sputtered on Si (TiO2 sp) and TiO2 formed on commercially pure titanium after immersion in H2O2 (TiO2 cp). Surface characterization was previously carried out using different techniques (Sousa, S. R.; Moradas-Ferreira, P.; Melo, L. V.; Saramago, B.; Barbosa, M. A. Langmuir 2004, 20 (22), 9745-9754). Imaging and roughness analysis before and after FN adsorption used atomic force microscopy (AFM) in tapping mode, in air, and in magnetic alternating current mode, in liquid (water). FN adsorption as a function of time was followed by X-ray photoelectron spectroscopy (XPS), by radiolabeling of FN with 125I (125I-FN), and by ellipsometry. Exchangeability studies were performed using FN and HSA. AFM roughness analysis revealed that, before FN adsorption, both TiO2 surfaces exhibited a lower root-mean-square (Rq) and maximum peak with the depth of the maximum valley (Rmax) roughness in air than in water, due to TiO2 hydration. After protein adsorption, the same behavior was observed for the TiO2 sp substrate, while Rq and Rmax roughness values in air and in water were similar in the case of the TiO2 cp substrate, for the higher FN concentration used. Surface roughness was always significantly higher on the TiO2 cp surfaces. AFM led to direct visualization of adsorbed FN on both surfaces tested, indicating that after 10 min of FN incubation the TiO2 sp surface was partially covered by FN. The adsorbed protein seems to form globular aggregates or ellipsoids, and FN aggregates coalesce, forming clusters as the time of adsorption and the concentration increase. Radiolabeling of FN revealed that a rapid adsorption occurs on both surfaces and the amount adsorbed increased with time, reaching a maximum after 60 min of

  20. Exon expression and alternatively spliced genes in Tourette Syndrome.

    Science.gov (United States)

    Tian, Yingfang; Liao, Isaac H; Zhan, Xinhua; Gunther, Joan R; Ander, Bradley P; Liu, Dazhi; Lit, Lisa; Jickling, Glen C; Corbett, Blythe A; Bos-Veneman, Netty G P; Hoekstra, Pieter J; Sharp, Frank R

    2011-01-01

    Tourette Syndrome (TS) is diagnosed based upon clinical criteria including motor and vocal tics. We hypothesized that differences in exon expression and splicing might be useful for pathophysiology and diagnosis. To demonstrate exon expression and alternatively spliced gene differences in blood of individuals with TS compared to healthy controls (HC), RNA was isolated from the blood of 26 un-medicated TS subjects and 23 HC. Each sample was run on Affymetrix Human Exon 1.0 ST (HuExon) arrays and on 3' biased U133 Plus 2.0 (HuU133) arrays. To investigate the differentially expressed exons and transcripts, analyses of covariance (ANCOVA) were performed, controlling for age, gender, and batch. Differential alternative splicing patterns between TS and HC were identified using analyses of variance (ANOVA) models in Partek. Three hundred and seventy-six exon probe sets were differentially expressed between TS and HC (raw P |1.2|) that separated TS and HC subjects using hierarchical clustering and Principal Components Analysis. The probe sets predicted TS compared to HC with a >90% sensitivity and specificity using a 10-fold cross-validation. Ninety genes (transcripts) had differential expression of a single exon (raw P < 0.005) and were predicted to be alternatively spliced (raw P < 0.05) in TS compared to HC. These preliminary findings might provide insight into the pathophysiology of TS and potentially provide prognostic and diagnostic biomarkers. However, the findings are tempered by the small sample size and multiple comparisons and require confirmation using PCR or deep RNA sequencing and a much larger patient population. Copyright © 2010 Wiley-Liss, Inc.

  1. Exonization of the LTR transposable elements in human genome

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2007-08-01

    Full Text Available Abstract Background Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary mechanism by which retrotransposons contribute to structural gene evolution is through insertion into an intron or a gene flanking region, and subsequent incorporation into an exon. Results We found that Long Terminal Repeat (LTR retrotransposons are associated with 1,057 human genes (5.8%. In 256 cases LTR retrotransposons were observed in protein-coding regions, while 50 distinct protein coding exons in 45 genes were comprised exclusively of LTR RetroTransposon Sequence (LRTS. We go on to reconstruct the evolutionary history of an alternatively spliced exon of the Interleukin 22 receptor, alpha 2 gene (IL22RA2 derived from a sequence of retrotransposon of the Mammalian apparent LTR retrotransposons (MaLR family. Sequencing and analysis of the homologous regions of genomes of several primates indicate that the LTR retrotransposon was inserted into the IL22RA2 gene at least prior to the divergence of Apes and Old World monkeys from a common ancestor (~25 MYA. We hypothesize that the recruitment of the part of LTR as a novel exon in great ape species occurred prior to the divergence of orangutans and humans from a common ancestor (~14 MYA as a result of a single mutation in the proto-splice site. Conclusion Our analysis of LRTS exonization events has shown that the patterns of LRTS distribution in human exons support the hypothesis that LRTS played a significant role in human gene evolution by providing cis-regulatory sequences; direct incorporation of LTR sequences into protein coding regions was observed less frequently. Combination of computational and experimental approaches used for tracing the history of the LTR exonization process of IL22RA2 gene presents a promising strategy that could facilitate further studies of transposon initiated gene evolution.

  2. Immunohistochemical detection of fibronectin in human thymus-comparison between groups of different ages

    International Nuclear Information System (INIS)

    Ali, S.; Minhas, L.A.; Arshad, M.; Hameed, W.

    2009-01-01

    To compare distribution of fibronectin content in various parts of human thymus between groups of different ages using immunohistochemistry. Comparative study. Forty specimens from tissue sections of human thymus were separated into two groups with 20 specimens in each group: Group A consisted of specimens from the patients of 1-25 years and Group B of specimens from patients beyond 40 years. These specimens were fixed in 10% formalin solution and processed for paraffin embedding. Five micron thick sections were made. Immunohistochemical staining was utilized to localize fibronectin in various regions of human thymus (capsule, connective tissue between lobules, cortex, medulla and areas around blood vessels). Statistically highly significant difference was found between two groups with a marked increase in the distribution of fibronectin content of the thymic capsule, the connective tissue between the lobules, areas around the blood vessels, and the medulla and cortex of the thymus in Group B compared to Group A. The fibronectin content in human thymus in its various regions shows a marked increase in aged people as compared to younger ones. (author)

  3. The effect of fibronectin on structural and biological properties of single walled carbon nanotube

    Energy Technology Data Exchange (ETDEWEB)

    Mottaghitalab, Fatemeh [Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Farokhi, Mehdi [National cell bank of Iran, Pasteur Institute, Tehran (Iran, Islamic Republic of); Atyabi, Fatemeh [Department of Pharmaceutical Nanoechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Omidvar, Ramin [Department of Biomedical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran (Iran, Islamic Republic of); Shokrgozar, Mohammad Ali, E-mail: mashokrgozar@pasteur.ac.ir [National cell bank of Iran, Pasteur Institute, Tehran (Iran, Islamic Republic of); Sadeghizadeh, Majid, E-mail: sadeghma@modares.ac.ir [Department Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of)

    2015-06-01

    Highlights: • Increasing the cytocompatibility of single walled carbon nanotube by loading fibronectin. • Enhancing the hydrophilicity and nanosurface roughness of single walled carbon nanotube after loading fibronectin. • Fibronectin makes the surface properties of single walled carbon nanotube more suitable for cell proliferation and growth. - Abstract: Despite the attractive properties of carbon nanotubes (CNTs), cytoxicity and hydrophobicity are two main considerable features which limit their application in biomedical fields. It was well established that treating CNTs with extracellular matrix components could reduce these unfavourable characteristics. In an attempt to address these issues, fibronectin (FN) with different concentrations was loaded on single walled carbon nanotubes (SWCNTs) substrate. Scanning electron microscope, atomic force microscopy (AFM), contact angles and X-ray photoelectron spectroscopy (XPS) were preformed in order to characterize FN loaded SWCNTs substrates. According to XPS and AFM results, FN could interact with SWCNTs and for this, the hydrophilicity of SWCNTs was improved. Additionally, SWCNT modified with FN showed less cytotoxicity compared with neat SWCNT. Finally, FN was shown to act as an interesting extracellular component for enhancing the biological properties of SWCNT.

  4. Fibrinogen and fibronectin binding cooperate for valve infection and invasion in Staphylococcus aureus experimental endocarditis

    NARCIS (Netherlands)

    Que, Yok-Ai; Haefliger, Jacques-Antoine; Piroth, Lionel; François, Patrice; Widmer, Eleonora; Entenza, José M; Sinha, Bhanu; Herrmann, Mathias; Francioli, Patrick; Vaudaux, Pierre; Moreillon, Philippe

    2005-01-01

    The expression of Staphylococcus aureus adhesins in Lactococcus lactis identified clumping factor A (ClfA) and fibronectin-binding protein A (FnBPA) as critical for valve colonization in rats with experimental endocarditis. This study further analyzed their role in disease evolution. Infected

  5. Plasma concentration of fibronectin is decreased in patients with hypertrophic cardiomyopathy.

    Science.gov (United States)

    Fucikova, Alena; Lenco, Juraj; Tambor, Vojtech; Rehulkova, Helena; Pudil, Radek; Stulik, Jiri

    2016-12-01

    To confirm the initial iTRAQ-based proteomic findings related to the plasma fibronectin level and hypertrophic cardiomyopathy using an antibody-based assay. The iTRAQ technique was used for the discovery proteomic analysis of the pooled plasma samples. The ELISA was used for verification of fibronectin plasma concentration in individual samples. Additional five related plasma proteins were assessed: matrix metalloproteinase 2, matrix metalloproteinase 9, tissue inhibitor of metalloproteinase 1, tissue inhibitor of metalloproteinase 2 and brain natriuretic peptide. The plasma fibronectin level in patients with hypertrophic cardiomyopathy was significantly lower in comparison to the healthy subjects [215.5±47.3μg/ml, n=17 vs. 376.7±134.8μg/ml, n=17; p<0.0001]. In this study we present and confirm our initial proteomic findings and we suggest fibronectin as a potential indicator of an extracellular matrix remodeling related to the hypertrophic cardiomyopathy. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. The effect of fibronectin on structural and biological properties of single walled carbon nanotube

    International Nuclear Information System (INIS)

    Mottaghitalab, Fatemeh; Farokhi, Mehdi; Atyabi, Fatemeh; Omidvar, Ramin; Shokrgozar, Mohammad Ali; Sadeghizadeh, Majid

    2015-01-01

    Highlights: • Increasing the cytocompatibility of single walled carbon nanotube by loading fibronectin. • Enhancing the hydrophilicity and nanosurface roughness of single walled carbon nanotube after loading fibronectin. • Fibronectin makes the surface properties of single walled carbon nanotube more suitable for cell proliferation and growth. - Abstract: Despite the attractive properties of carbon nanotubes (CNTs), cytoxicity and hydrophobicity are two main considerable features which limit their application in biomedical fields. It was well established that treating CNTs with extracellular matrix components could reduce these unfavourable characteristics. In an attempt to address these issues, fibronectin (FN) with different concentrations was loaded on single walled carbon nanotubes (SWCNTs) substrate. Scanning electron microscope, atomic force microscopy (AFM), contact angles and X-ray photoelectron spectroscopy (XPS) were preformed in order to characterize FN loaded SWCNTs substrates. According to XPS and AFM results, FN could interact with SWCNTs and for this, the hydrophilicity of SWCNTs was improved. Additionally, SWCNT modified with FN showed less cytotoxicity compared with neat SWCNT. Finally, FN was shown to act as an interesting extracellular component for enhancing the biological properties of SWCNT

  7. How the new optoelectronic design automation industry is taking advantage of preexisting EDA standards

    Science.gov (United States)

    Nesmith, Kevin A.; Carver, Susan

    2014-05-01

    With the advancements in design processes down to the sub 7nm levels, the Electronic Design Automation industry appears to be coming to an end of advancements, as the size of the silicon atom becomes the limiting factor. Or is it? The commercial viability of mass-producing silicon photonics is bringing about the Optoelectronic Design Automation (OEDA) industry. With the science of photonics in its infancy, adding these circuits to ever-increasing complex electronic designs, will allow for new generations of advancements. Learning from the past 50 years of the EDA industry's mistakes and missed opportunities, the photonics industry is starting with electronic standards and extending them to become photonically aware. Adapting the use of pre-existing standards into this relatively new industry will allow for easier integration into the present infrastructure and faster time to market.

  8. First Exon Length Controls Active Chromatin Signatures and Transcription

    Directory of Open Access Journals (Sweden)

    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  9. Intron Retention and TE Exonization Events in ZRANB2

    Directory of Open Access Journals (Sweden)

    Sang-Je Park

    2012-01-01

    Full Text Available The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2, contains arginine/serine-rich (RS domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3 between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3. Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species. Human, rhesus monkey, crab-eating monkey, African-green monkey, and marmoset harbor the exon derived from LINE element (Plat_L3. RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys and were expressed via intron retention (IR. Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution.

  10. Adhesion of Trypanosoma cruzi trypomastigotes to fibronectin or laminin modifies tubulin and paraflagellar rod protein phosphorylation.

    Directory of Open Access Journals (Sweden)

    Eliciane C Mattos

    Full Text Available BACKGROUND: The unicellular parasite Trypanosoma cruzi is the causative agent of Chagaś disease in humans. Adherence of the infective stage to elements of the extracellular matrix (ECM, as laminin and fibronectin, is an essential step in host cell invasion. Although members of the gp85/TS, as Tc85, were identified as laminin and fibronectin ligands, the signaling events triggered on the parasite upon binding to these molecules are largely unexplored. METHODOLOGY/PRINCIPAL FINDINGS: Viable infective parasites were incubated with laminin, fibronectin or bovine serum albumin for different periods of time and the proteins were separated by bidimensional gels. The phosphoproteins were envisaged by specific staining and the spots showing phosphorylation levels significantly different from the control were excised and identified by MS/MS. The results of interest were confirmed by immunoblotting or immunoprecipitation and the localization of proteins in the parasite was determined by immunofluorescence. Using a host cell-free system, our data indicate that the phosphorylation contents of T. cruzi proteins encompassing different cellular functions are modified upon incubation of the parasite with fibronectin or laminin. CONCLUSIONS/SIGNIFICANCE: Herein it is shown, for the first time, that paraflagellar rod proteins and α-tubulin, major structural elements of the parasite cytoskeleton, are predominantly dephosphorylated during the process, probably involving the ERK1/2 pathway. It is well established that T. cruzi binds to ECM elements during the cell infection process. The fact that laminin and fibronectin induce predominantly dephosphorylation of the main cytoskeletal proteins of the parasite suggests a possible correlation between cytoskeletal modifications and the ability of the parasite to internalize into host cells.

  11. Protein F, a fibronectin-binding protein, is an adhesin of the group A streptococcus Streptococcus pyogenes.

    Science.gov (United States)

    Hanski, E; Caparon, M

    1992-07-01

    Binding to fibronectin has been suggested to play an important role in adherence of the group A streptococcus Streptococcus pyrogenes to host epithelial cells; however, the identity of the streptococcal fibronectin receptor has been elusive. Here we demonstrate that the fibronectin-binding property of S. pyogenes is mediated by protein F, a bacterial surface protein that binds fibronectin at high affinity. The gene encoding protein F (prtF) produced a functional fibronectin-binding protein in Escherichia coli. Insertional mutagenesis of the cloned gene generated a mutation that resulted in the loss of fibronectin-binding activity. When this mutation was introduced into the S. pyrogenes chromosome by homologous recombination with the wild-type allele, the resulting strains no longer produced protein F and lost their ability to bind fibronectin. The mutation could be complemented by prtF introduced on a plasmid. Mutants lacking protein F had a much lower capacity to adhere to respiratory epithelial cells. These results demonstrate that protein F is an important adhesin of S. pyogenes.

  12. Escherichia coli F-18 and E. coli K-12 eda mutants do not colonize the streptomycin-treated mouse large intestine.

    OpenAIRE

    Sweeney, N J; Laux, D C; Cohen, P S

    1996-01-01

    The Escherichia coli human fecal isolates F-18 and K-12 are excellent colonizers of the streptomycin-treated mouse intestine. E. coli F-18 and E. coli K-12 eda mutants (unable to utilize glucuronate, galacturonate, and gluconate) were constructed by insertional mutagenesis. Neither the E. coli F-18 eda nor the E. coli K-12 eda mutant was able to colonize the streptomycin-treated mouse intestine, whether they were fed to mice together with their respective parental strains or alone. Complement...

  13. Reversible optic neuropathy with OPA1 exon 5b mutation

    DEFF Research Database (Denmark)

    Cornille, K.; Milea, D.; Amati-Bonneau, P.

    2008-01-01

    A new c.740G>A (R247H) mutation in OPA1 alternate spliced exon 5b was found in a patient presenting with bilateral optic neuropathy followed by partial, spontaneous visual recovery. R247H fibroblasts from the patient and his unaffected father presented unusual highly tubular mitochondrial network......, significant increased susceptibility to apoptosis, oxidative phosphorylation uncoupling, and altered OPA1 protein profile, supporting the pathogenicity of this mutation. These results suggest that the clinical spectrum of the OPA1-associated optic neuropathies may be larger than previously described......, and that spontaneous recovery may occur in cases harboring an exon 5b mutation Udgivelsesdato: 2008/5...

  14. Antisense-induced exon skipping for duplications in Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    van Ommen Gert-Jan B

    2007-07-01

    Full Text Available Abstract Background Antisense-mediated exon skipping is currently one of the most promising therapeutic approaches for Duchenne muscular dystrophy (DMD. Using antisense oligonucleotides (AONs targeting specific exons the DMD reading frame is restored and partially functional dystrophins are produced. Following proof of concept in cultured muscle cells from patients with various deletions and point mutations, we now focus on single and multiple exon duplications. These mutations are in principle ideal targets for this approach since the specific skipping of duplicated exons would generate original, full-length transcripts. Methods Cultured muscle cells from DMD patients carrying duplications were transfected with AONs targeting the duplicated exons, and the dystrophin RNA and protein were analyzed. Results For two brothers with an exon 44 duplication, skipping was, even at suboptimal transfection conditions, so efficient that both exons 44 were skipped, thus generating, once more, an out-of-frame transcript. In such cases, one may resort to multi-exon skipping to restore the reading frame, as is shown here by inducing skipping of exon 43 and both exons 44. By contrast, in cells from a patient with an exon 45 duplication we were able to induce single exon 45 skipping, which allowed restoration of wild type dystrophin. The correction of a larger duplication (involving exons 52 to 62, by combinations of AONs targeting the outer exons, appeared problematic due to inefficient skipping and mistargeting of original instead of duplicated exons. Conclusion The correction of DMD duplications by exon skipping depends on the specific exons targeted. Its options vary from the ideal one, restoring for the first time the true, wild type dystrophin, to requiring more 'classical' skipping strategies, while the correction of multi-exon deletions may need the design of tailored approaches.

  15. [Eda Kalmre. The human sausage factory : a study of post-war rumour in Tartu] / Véronique Vincent-Campion

    Index Scriptorium Estoniae

    Vincent-Campion, Véronique

    2015-01-01

    Arvustus: Kalmre, Eda. The human sausage factory : a study of post-war rumour in Tartu. Amsterdam ; New York : Rodopi, 2013. (On the boundary of two worlds : identity, freedom, and moral imagination in the Baltics, 1570-7121 ; 34)

  16. Fibroblast invasive migration into fibronectin/fibrin gels requires a previously uncharacterized dermatan sulfate-CD44 proteoglycan

    DEFF Research Database (Denmark)

    Clark, Richard A F; Lin, Fubao; Greiling, Doris

    2004-01-01

    After tissue injury, fibroblast migration from the peri-wound collagenous stroma into the fibrin-laden wound is critical for granulation tissue formation and subsequent healing. Recently we found that fibroblast transmigration from a collagen matrix into a fibrin matrix required the presence...... of fibronectin. Several integrins-alpha 4 beta 1, alpha 5 beta 1, and alpha v beta 3-with known fibronectin binding affinity were necessary for this invasive migration. Here we examined another family of cell surface receptors: the proteoglycans. We found that dermatan sulfate was required for fibroblast...... including heparan sulfate and chondroitin sulfate, and as such can bind fibronectin. We found that CD44H, the non-spliced isoform of CD44, was necessary for fibroblast invasion into fibronectin/fibrin gels. Resting fibroblasts expressed mostly nonglycanated CD44H core protein, which became glycanated...

  17. Syndecan-4 binding to the high affinity heparin-binding domain of fibronectin drives focal adhesion formation in fibroblasts

    DEFF Research Database (Denmark)

    Woods, A; Longley, R L; Tumova, S

    2000-01-01

    Cell adhesion to extracellular matrix involves signaling mechanisms which control attachment, spreading and the formation of focal adhesions and stress fibers. Fibronectin can provide sufficient signals for all three processes, even when protein synthesis is prevented by cycloheximide. Primary...

  18. Investigation of ANGPTL3 expression, exon sequence and promotor ...

    African Journals Online (AJOL)

    like proteins, has been demonstrated to affect lipid metabolism by inhibiting the activity of lipoprotein lipase (LPL). Objective: To compare the ANGPTL3 mRNA and protein expression, exon mutation and promoter district CpG island methylation ...

  19. Polymorphism of exon 3 of the HLA-G gene

    DEFF Research Database (Denmark)

    Hviid, T V; Meldgaard, Michael; Sørensen, S

    1997-01-01

    rate of embryos. HLA-G seems to play an important role in the feto-maternal relationship. The polymorphism of the HLA-G locus is not fully clarified. One study has shown extensive nucleotide sequence variation in the exon 3 (alpha-2 domain) in healthy African Americans. A few studies in other...... populations have only revealed a limited polymorphism. We investigated the polymorphism of the exon 3 of HLA-G by means of Polymerase Chain Reaction (PCR)-Single Strand Conformation Polymorphism (SSCP)- and DNA sequencing analysis in a Danish population. We detected four single-base substitutions in exon 3...... compared to the sequence of HLA-6.0 (G*01011); one of these has not been reported before. We also found a deletion of the first base of codon 130 or the third of codon 129 in a heterozygous individual. This study, together with previous results, suggests that the polymorphism of exon 3 of the HLA-G gene...

  20. Designing exons for human olfactory receptor gene subfamilies ...

    Indian Academy of Sciences (India)

    Prakash

    The loci of olfactory receptors (ORs) in the human genome occur in clusters ranging ... [Hassan Sk S, Choudhury P P, Pal A, Brahmachary R L and Goswami A 2010 Designing exons for human olfactory receptor gene subfamilies using a mathematical .... Acknowledgements. This work was supported by the Department of.

  1. Cloud-based adaptive exon prediction for DNA analysis.

    Science.gov (United States)

    Putluri, Srinivasareddy; Zia Ur Rahman, Md; Fathima, Shaik Yasmeen

    2018-02-01

    Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing. True identification of exon regions in a DNA sequence is a key task in bioinformatics, which helps in disease identification and design drugs. Three base periodicity property of exons forms the basis of all exon identification techniques. Adaptive signal processing techniques found to be promising in comparison with several other methods. Several adaptive exon predictors (AEPs) are developed using variable normalised least mean square and its maximum normalised variants to reduce computational complexity. Finally, performance evaluation of various AEPs is done based on measures such as sensitivity, specificity and precision using various standard genomic datasets taken from National Center for Biotechnology Information genomic sequence database.

  2. Origin of introns by 'intronization' of exonic sequences

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Penny, David

    2008-01-01

    The mechanisms of spliceosomal intron creation have proved elusive. Here we describe a new mechanism: the recruitment of internal exonic sequences ('intronization') in Caenorhabditis species. The numbers of intronization events and introns gained by other mechanisms are similar, suggesting that i...

  3. Molecular characterization of exon 28 of von Willebrand's factor ...

    African Journals Online (AJOL)

    Background: Polymorphisms in von Willebrand factor (VWF) gene are an important contributor to the expression of VWF gene and differences in ethnic distribution of these single nucleotide polymorphisms (SNPs) exists. Aims: Our objective was to molecularly characterize the exon 28 of the VWF gene in the three major ...

  4. Antisense mediated exon skipping therapy for duchenne muscular dystrophy (DMD)

    DEFF Research Database (Denmark)

    Brolin, Camilla; Shiraishi, Takehiko

    2011-01-01

    Duchenne Muscular Dystrophy (DMD) is a lethal disease caused by mutations in the dystrophin gene (DMD) that result in the absence of essential muscle protein dystrophin. Among many different approaches for DMD treatment, exon skipping, mediated by antisense oligonucleotides, is one of the most...

  5. Polymorphism of exon 3 of the HLA-G gene

    DEFF Research Database (Denmark)

    Hviid, T V; Meldgaard, Michael; Sørensen, S

    1997-01-01

    populations have only revealed a limited polymorphism. We investigated the polymorphism of the exon 3 of HLA-G by means of Polymerase Chain Reaction (PCR)-Single Strand Conformation Polymorphism (SSCP)- and DNA sequencing analysis in a Danish population. We detected four single-base substitutions in exon 3...... compared to the sequence of HLA-6.0 (G*01011); one of these has not been reported before. We also found a deletion of the first base of codon 130 or the third of codon 129 in a heterozygous individual. This study, together with previous results, suggests that the polymorphism of exon 3 of the HLA-G gene...... rate of embryos. HLA-G seems to play an important role in the feto-maternal relationship. The polymorphism of the HLA-G locus is not fully clarified. One study has shown extensive nucleotide sequence variation in the exon 3 (alpha-2 domain) in healthy African Americans. A few studies in other...

  6. Exon duplications in the ATP7A gene

    DEFF Research Database (Denmark)

    Mogensen, Mie; Skjørringe, Tina; Kodama, Hiroko

    2011-01-01

    BACKGROUND: Menkes disease (MD) is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene. Thirty-three Menkes patients in whom no mutation had been detected with standard diagnostic tools were screened for exon duplications in the ATP7A gene. ME...

  7. Another face of the Treacher Collins syndrome (TCOF1) gene: identification of additional exons.

    Science.gov (United States)

    So, Rolando B; Gonzales, Bianca; Henning, Dale; Dixon, Jill; Dixon, Michael J; Valdez, Benigno C

    2004-03-17

    Treacher Collins syndrome (TCS) is characterized by an abnormality in craniofacial development during early embryogenesis. TCS is caused by mutations in the gene TCOF1, which encodes the nucleolar phosphoprotein treacle. Genetic and proteomic characterizations of TCS/treacle are based on the previously reported 26 exons of TCOF1. Here, we report the identification of 231-nucleotide (nt) exon 6A (between exons 6 and 7) and 108-nt exon 16A (between exons 16 and 17). Isoforms with exon 6A are up to 3.7-fold more abundant than alternatively spliced variants without exon 6A, but only minor isoforms contain exon 16A. Exon 6A encodes a peptide sequence containing basic and acidic domains similar to 10 other exons of TCOF1. Unlike the other exons, exon 6A encodes a nuclear localization signal (NLS) which does not, however, alter the nucleolar localization of full-length treacle. The discovery of exons 6A and 16A is relevant to mutational analysis of the TCOF1 gene in TCS patients, and to functional analysis of its gene product.

  8. Silibinin inhibits fibronectin induced motility, invasiveness and survival in human prostate carcinoma PC3 cells via targeting integrin signaling

    Energy Technology Data Exchange (ETDEWEB)

    Deep, Gagan [Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO (United States); University of Colorado Cancer Center, University of Colorado Denver, Aurora, CO (United States); Kumar, Rahul; Jain, Anil K. [Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO (United States); Agarwal, Chapla [Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO (United States); University of Colorado Cancer Center, University of Colorado Denver, Aurora, CO (United States); Agarwal, Rajesh, E-mail: Rajesh.agarwal@ucdenver.edu [Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO (United States); University of Colorado Cancer Center, University of Colorado Denver, Aurora, CO (United States)

    2014-10-15

    Highlights: • Silibinin inhibits fibronectin-induce motile morphology in PC3 cells. • Silibinin inhibits fibronectin-induced migration and invasion in PC3 cells. • Silibinin targets fibronectin-induced integrins and downstream signaling molecule. - Abstract: Prostate cancer (PCA) is the 2nd leading cause of cancer-related deaths among men in the United States. Preventing or inhibiting metastasis-related events through non-toxic agents could be a useful approach for lowering high mortality among PCA patients. We have earlier reported that natural flavonoid silibinin possesses strong anti-metastatic efficacy against PCA however, mechanism/s of its action still remains largely unknown. One of the major events during metastasis is the replacement of cell–cell interaction with integrins-based cell–matrix interaction that controls motility, invasiveness and survival of cancer cells. Accordingly, here we examined silibinin effect on advanced human PCA PC3 cells’ interaction with extracellular matrix component fibronectin. Silibinin (50–200 μM) treatment significantly decreased the fibronectin (5 μg/ml)-induced motile morphology via targeting actin cytoskeleton organization in PC3 cells. Silibinin also decreased the fibronectin-induced cell proliferation and motility but significantly increased cell death in PC3 cells. Silibinin also inhibited the PC3 cells invasiveness in Transwell invasion assays with fibronectin or cancer associated fibroblasts (CAFs) serving as chemoattractant. Importantly, PC3-luc cells cultured on fibronectin showed rapid dissemination and localized in lungs following tail vein injection in athymic male nude mice; however, in silibinin-treated PC3-luc cells, dissemination and lung localization was largely compromised. Molecular analyses revealed that silibinin treatment modulated the fibronectin-induced expression of integrins (α5, αV, β1 and β3), actin-remodeling (FAK, Src, GTPases, ARP2 and cortactin), apoptosis (cPARP and

  9. Systematic analysis of alternative first exons in plant genomes

    Directory of Open Access Journals (Sweden)

    Zeng Changqing

    2007-10-01

    Full Text Available Abstract Background Alternative splicing (AS contributes significantly to protein diversity, by selectively using different combinations of exons of the same gene under certain circumstances. One particular type of AS is the use of alternative first exons (AFEs, which can have consequences far beyond the fine-tuning of protein functions. For example, AFEs may change the N-termini of proteins and thereby direct them to different cellular compartments. When alternative first exons are distant, they are usually associated with alternative promoters, thereby conferring an extra level of gene expression regulation. However, only few studies have examined the patterns of AFEs, and these analyses were mainly focused on mammalian genomes. Recent studies have shown that AFEs exist in the rice genome, and are regulated in a tissue-specific manner. Our current understanding of AFEs in plants is still limited, including important issues such as their regulation, contribution to protein diversity, and evolutionary conservation. Results We systematically identified 1,378 and 645 AFE-containing clusters in rice and Arabidopsis, respectively. From our data sets, we identified two types of AFEs according to their genomic organisation. In genes with type I AFEs, the first exons are mutually exclusive, while most of the downstream exons are shared among alternative transcripts. Conversely, in genes with type II AFEs, the first exon of one gene structure is an internal exon of an alternative gene structure. The functionality analysis indicated about half and ~19% of the AFEs in Arabidopsis and rice could alter N-terminal protein sequences, and ~5% of the functional alteration in type II AFEs involved protein domain addition/deletion in both genomes. Expression analysis indicated that 20~66% of rice AFE clusters were tissue- and/or development- specifically transcribed, which is consistent with previous observations; however, a much smaller percentage of Arabidopsis

  10. Betal-integrins in the primary cilium of MDCK cells potentiate fibronectin-induced Ca2+ signalling

    DEFF Research Database (Denmark)

    Prætorius, Helle; Prætorius, Jeppe; Nielsen, Søren

    2004-01-01

    of fibronectin, a β1-integrin ligand, to mature MDCK cells with an IC50 of 0.02 mg/l. In immature, nonciliated cells or in deciliated mature cells, the IC50 was 0.40 mg/l. Blocking the fibronectin-binding sites of β1-integrin with RGD peptide prevented the Ca2+ signal. Cross-linking of β1-integrins by Sambucus...

  11. A Splice Defect in the EDA Gene in Dogs with an X-Linked Hypohidrotic Ectodermal Dysplasia (XLHED) Phenotype

    OpenAIRE

    Waluk, Dominik P.; Zur, Gila; Kaufmann, Ronnie; Welle, Monika M.; Jagannathan, Vidhya; Dr?gem?ller, Cord; M?ller, Eliane J.; Leeb, Tosso; Galichet, Arnaud

    2016-01-01

    X-linked hypohidrotic ectodermal dysplasia (XLHED) caused by variants in the EDA gene represents the most common ectodermal dysplasia in humans. We investigated three male mixed-breed dogs with an ectodermal dysplasia phenotype characterized by marked hypotrichosis and multifocal complete alopecia, almost complete absence of sweat and sebaceous glands, and altered dentition with missing and abnormally shaped teeth. Analysis of SNP chip genotypes and whole genome sequence data from the three a...

  12. Serum and plasma fibronectin binds to complement reacted immune complexes primarily via Clq

    DEFF Research Database (Denmark)

    Baatrup, G; Svehag, S E

    1986-01-01

    The binding of fibronectin to human Clq, C3b, and complement-reacted immune complexes (IC) was investigated by enzyme-linked immunosorbent assays. Microplates were coated with BSA followed by incubation with rabbit-anti-BSA IgG or F(ab')2 fragments of rabbit anti-BSA. Incubation of the solid phase...... with serum at 37 degrees C caused attachment of Clq and C3b. Addition of EDTA to the serum inhibited the binding of C3b, but not Clq, whereas substitution of the anti-BSA IgG on the solid phase with the F(ab')2 fragments abrogated the Clq, but not the C3b binding. Fibronectin binding was observed after...

  13. Pedro de Castañeda: su pintura para el refectorio del Colegio Mayor de San Ildefonso (1553

    Directory of Open Access Journals (Sweden)

    González Ramos, Roberto

    2003-09-01

    Full Text Available El pintor Pedro de Castañeda es un artista poco conocido, activo en la zona de Alcalá de Henares en las décadas centrales del siglo XVI. Se sabe que junto a su hijo Juan fue colaborador del entallador y traductor de Vitruvio Miguel de Urrea. Pedro de Castañeda pintó un cirial que había tallado Urrea para la iglesia parroquial de Camarma de Esteruelas, trabajo por el que ambos cobraron cierta cantidad en 1540, y en 1550 colaboró con ese entallador y con Claudio de Arciniega, ayudado por Juan, en la obra de los retablos colaterales de la iglesia de Daganzo de Arriba (perdidos, realizando su pintura. Parece que se trata del mismo artista el Pedro Castañeda que se documenta trabajando en la zona de Segovia, concretamente en dos retablos para la iglesia de Cascajares del Fresno. Falleció en 1557…

  14. Oxidative damage to fibronectin. 2. The effect of H2O2 and the hydroxyl radical

    International Nuclear Information System (INIS)

    Vissers, M.C.; Winterbourn, C.C.

    1991-01-01

    The effect of H2O2 and the hydroxyl radical (.OH) on fibronectin was investigated. .OH was generated in three ways: (1) by radiolysis with 60Co under N2O, or by the Fenton system using either (2) equimolar Fe(2+)-EDTA and H2O2 or (3) H2O2 and catalytic amounts of Fe(2+)-EDTA recycled with ascorbate. Each system had a different effect. H2O2 alone caused no changes, even at an 800-fold molar excess. Radiolytic .OH caused a rapid loss of tryptophan fluorescence, an increase in bityrosine fluorescence, and extensive crosslinking. The Fenton system using Fe-EDTA, H2O2, and ascorbate caused a loss in tryptophan fluorescence, a smaller increase in bityrosine than was seen with radiolytic .OH, and a threefold increase in carbonyl groups. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis fragmentation of fibronectin was seen. In contrast, when .OH was generated with equimolar Fe-EDTA and H2O2, the only change was a small increase in bityrosine fluorescence at the highest dose of oxidant. None of the systems used affected cysteine. All the changes except the loss of tryptophan by radiolytic .OH were completely inhibited with mannitol. The differences seen with radiolytic .OH and the Fe-EDTA, H2O2, ascorbate system were not solely due to O2 in the latter system since similar results were obtained under N2. The differences between radiolytic .OH and the Fenton systems could be partly due to the components of the latter systems reacting with .OH and thus competing with fibronectin. The authors results demonstrate that the extent and type of fibronectin damage by .OH is dependent on the mode of radical generation

  15. Incorporation of fibronectin to enhance cytocompatibility in multilayer elastin-like protein scaffolds for tissue engineering

    OpenAIRE

    Ravi, Swathi; Caves, Jeffrey M.; Martinez, Adam W.; Haller, Carolyn A.; Chaikof, Elliot L.

    2012-01-01

    Recombinant, elastin-like protein (ELP) polymers are of significant interest for the engineering of compliant, resilient soft tissues due to a wide range of tunable mechanical properties, biostability, and biocompatibility. Here, we enhance endothelial cell (EC) and mesenchymal stem cell compatibility with ELP constructs by addition of fibronectin (Fn) to the surface or bulk of ELP hydrogels. We find that cell adhesion, proliferation, and migration can be modulated by Fn addition. Adsorption ...

  16. Inhibition of hyaluronan synthesis reduces versican and fibronectin levels in trabecular meshwork cells.

    Directory of Open Access Journals (Sweden)

    Kate E Keller

    Full Text Available Hyaluronan (HA is a major component of the extracellular matrix (ECM and is synthesized by three HA synthases (HAS. Similarities between the HAS2 knockout mouse and the hdf mutant mouse, which has a mutation in the versican gene, suggest that HA and versican expression may be linked. In this study, the relationship between HA synthesis and levels of versican, fibronectin and several other ECM components in trabecular meshwork cells from the anterior segment of the eye was investigated. HA synthesis was inhibited using 4-methylumbelliferone (4MU, or reduced by RNAi silencing of each individual HAS gene. Quantitative RT-PCR and immunoblotting demonstrated a reduction in mRNA and protein levels of versican and fibronectin. Hyaluronidase treatment also reduced versican and fibronectin levels. These effects could not be reversed by addition of excess glucose or glucosamine or exogenous HA to the culture medium. CD44, tenascin C and fibrillin-1 mRNA levels were reduced by 4MU treatment, but SPARC and CSPG6 mRNA levels were unaffected. Immunostaining of trabecular meshwork tissue after exposure to 4MU showed an altered localization pattern of HA-binding protein, versican and fibronectin. Reduction of versican by RNAi silencing did not affect HA concentration as assessed by ELISA. Together, these data imply that HA concentration affects synthesis of certain ECM components. Since precise regulation of the trabecular meshwork ECM composition and organization is required to maintain the aqueous humor outflow resistance and intraocular pressure homeostasis in the eye, coordinated coupling of HA levels and several of its ECM binding partners should facilitate this process.

  17. Immunofluorescent histological studies of the role of fibronectin in the expression of the associative preferences of embryonic tissues.

    Science.gov (United States)

    Armstrong, P B; Armstrong, M T

    1981-08-01

    The identity of the chemical factors controlling the spreading behaviour of sheets of cells was examined in organ culture. When aggregates of two dissimilar tissues are apposed in organ culture, one tissue spreads reproducibly over the surface of the second. The present study employed indirect immunofluorescent localization techniques to evaluate the hypothesis that the spreading behaviour of chick embryonic heart tissue in culture is dominated by the presence or absence of the cell-surface and extracellular matrix protein fibronectin in the surface layers of the aggregates. Specifically, the hypothesis proposes that aggregates that display surface fibronectin earlier after culturing and/or in higher quantities segregate internally to aggregates that are slower to develop a surface layer of fibronectin or in which this layer contains reduced amounts of fibronectin. The hypothesis has been supported for 3 categories of behaviour of chick embryo heart tissue: (1) myocyte aggregates spread over myocyte aggregates containing a 20% admixture of heart fibroblasts, which in turn spread over heart fibroblast aggregates; (2) 5-day embryonic ventricle-tissue fragments maintained in culture for 0.5 days spread over ventricle fragments cultured for 2.5 days; and (3) 2-day embryonic ventricle spreads over 5-day ventricle. In all these situations, the aggregate type that segregates to an internal position displays more fibronectin at its surface than aggregate types that spread to occupy an external position. Evidence is presented that the fibronectin in heart tissue aggregates is elaborated by heart fibroblasts.

  18. Tuning Mesenchymal Stem Cell Response onto Titanium-Niobium-Hafnium Alloy by Recombinant Fibronectin Fragments.

    Science.gov (United States)

    Herranz-Diez, C; Mas-Moruno, C; Neubauer, S; Kessler, H; Gil, F J; Pegueroles, M; Manero, J M; Guillem-Marti, J

    2016-02-03

    Since metallic biomaterials used for bone replacement possess low bioactivity, the use of cell adhesive moieties is a common strategy to improve cellular response onto these surfaces. In recent years, the use of recombinant proteins has emerged as an alternative to native proteins and short peptides owing to the fact that they retain the biological potency of native proteins, while improving their stability. In the present study, we investigated the biological effect of two different recombinant fragments of fibronectin, spanning the 8-10th and 12-14th type III repeats, covalently attached to a new TiNbHf alloy using APTES silanization. The fragments were studied separately and mixed at different concentrations and compared to a linear RGD, a cyclic RGD and the full-length fibronectin protein. Cell culture studies using rat mesenchymal stem cells demonstrated that low to medium concentrations (30% and 50%) of type III 8-10th fragment mixed with type III 12-14th fragment stimulated cell spreading and proliferation compared to RGD peptides and the fragments separately. On the other hand, type III 12-14th fragment alone or mixed at low volume percentages ≤50% with type III 8-10th fragment increased alkaline phosphatase levels compared to the other molecules. These results are significant for the understanding of the role of fibronectin recombinant fragments in cell responses and thus to design bioactive coatings for biomedical applications.

  19. Structure of a fibronectin type III-like module from Clostridium thermocellum

    International Nuclear Information System (INIS)

    Alahuhta, Markus; Xu, Qi; Brunecky, Roman; Adney, William S.; Ding, Shi-You; Himmel, Michael E.; Lunin, Vladimir V.

    2010-01-01

    The 1.6 Å resolution structure of a fibronectin type III-like module from Clostridium thermocellum with two molecules in the asymmetric unit is reported. The 1.6 Å resolution structure of a fibronectin type III-like module from Clostridium thermocellum with two molecules in the asymmetric unit is reported. The crystals used for data collection belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 35.43, b = 45.73, c = 107.72 Å, and the structure was refined to an R factor of 0.166. Structural comparisons found over 800 similar structures in the Protein Data Bank. The broad range of different proteins or protein domains with high structural similarity makes it especially demanding to classify these proteins. Previous studies of fibronectin type III-like modules have indicated that they might function as ligand-binding modules, as a compact form of peptide linkers or spacers between other domains, as cellulose-disrupting modules or as proteins that help large enzyme complexes remain soluble

  20. Expression of extracellular matrix proteins: tenascin-C, fibronectin and galectin-3 in prostatic adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Monika Ulamec

    2015-12-01

    Full Text Available Introduction: The interchanged stromal-epithelial relations and altered expression profiles of various extracellular matrix (ECM proteins creates a suitable microenvironment for cancer development and growth. We support the opinion that remodeling of the extracellular matrix (ECM plays an important role in the cancer progression. The aim of this study was to examine the expression of ECM proteins tenascin-C, fibronectin and galectin-3 in prostatic adenocarcinoma. Methods: Glands and surrounding stroma were analyzed in randomly selected specimens from 52 patients with prostate cancer and 28 patients with benign prostatic hyperplasia (BHP. To evaluate the intensity of tenascin-C, fibronectin and galectin-3 expression the percentage of positively immunostained stromal cells was examined.Results: Compared to BPH, stroma of prostatic adenocarcinoma showed statistically significant increase in tenascin-C expression (p<0.001, predominantly around neoplastic glands, while fibronectin (p=0.001 and galectin-3 (p<0.001 expression in the same area was decreased.Conclusions: Our study confirms changes in the expression of ECM proteins of prostate cancer which may have important role in the cancer development.

  1. Zinc induces structural reorganization of gelatin binding domain from human fibronectin and affects collagen binding.

    Science.gov (United States)

    Graille, Marc; Pagano, Maurice; Rose, Thierry; Ravaux, Michèle Reboud; van Tilbeurgh, Herman

    2010-06-09

    Fibronectin is a modular extracellular matrix protein involved in cell adhesion, cell motility, wound healing, and maintenance of cell morphology. It is composed of multiple repeats of three distinct modules: F(I), F(II), and F(III). Various combinations of these modules create fragments able to interact with different constituents of the extracellular matrix. Here, we present the 2.5-A resolution crystal structure of its 45-kDa gelatin-binding domain (GBD; 6F(I)-1F(II)-2F(II)-7F(I)-8F(I)-9F(I)), which also corresponds to the C-terminal half of the migration stimulating factor, a Fn splice variant expressed in human breast cancers. GBD forms a very compact zinc-mediated homodimer, in stark contrast with previous structures of fibronectin fragments. Most remarkably, 8F(I) no longer adopts the canonical F(I) fold but is composed of two long strands that associate with 7F(I) and 9F(I) into a large beta-sheet superdomain. Binding studies in solution confirmed that Zn induces conformational rearrangements and causes loss of binding of Fn-GBD to high-affinity collagen peptides. These data suggest the Zn may play a regulatory role for the cellular functions of fibronectin.

  2. Tenascin C promiscuously binds growth factors via its fifth fibronectin type III-like domain.

    Directory of Open Access Journals (Sweden)

    Laura De Laporte

    Full Text Available Tenascin C (TNC is an extracellular matrix protein that is upregulated during development as well as tissue remodeling. TNC is comprised of multiple independent folding domains, including 15 fibronectin type III-like (TNCIII domains. The fifth TNCIII domain (TNCIII5 has previously been shown to bind heparin. Our group has shown that the heparin-binding fibronectin type III domains of fibronectin (FNIII, specifically FNIII12-14, possess affinity towards a large number of growth factors. Here, we show that TNCIII5 binds growth factors promiscuously and with high affinity. We produced recombinant fragments of TNC representing the first five TNCIII repeats (TNCIII1-5, as well as subdomains, including TNCIII5, to study interactions with various growth factors. Multiple growth factors of the platelet-derived growth factor (PDGF family, the fibroblast growth factor (FGF family, the transforming growth factor beta (TGF-β superfamily, the insulin-like growth factor binding proteins (IGF-BPs, and neurotrophins were found to bind with high affinity to this region of TNC, specifically to TNCIII5. Surface plasmon resonance was performed to analyze the kinetics of binding of TNCIII1-5 with TGF-β1, PDGF-BB, NT-3, and FGF-2. The promiscuous yet high affinity of TNC for a wide array of growth factors, mediated mainly by TNCIII5, may play a role in multiple physiological and pathological processes involving TNC.

  3. Power amplifiers for the S-, C-, X- and Ku-bands an EDA perspective

    CERN Document Server

    Božanić, Mladen

    2016-01-01

    This book provides a detailed review of power amplifiers, including classes and topologies rarely covered in books, and supplies sufficient information to allow the reader to design an entire amplifier system, and not just the power amplification stage. A central aim is to furnish readers with ideas on how to simplify the design process for a preferred power amplifier stage by introducing software-based routines in a programming language of their choice. The book is in two parts, the first focusing on power amplifier theory and the second on EDA concepts. Readers will gain enough knowledge of RF and microwave transmission theory, principles of active and passive device design and manufacturing, and power amplifier design concepts to allow them to quickly create their own programs, which will help to accelerate the transceiver design process. All circuit designers facing the challenge of designing an RF or microwave power amplifier for frequencies from 2 to 18 GHz will find this book to be a valuable asset.

  4. CONVERSATORIO CON EL PROFESOR ROMÁN CASTAÑEDA SEPÚLVEDA

    Directory of Open Access Journals (Sweden)

    VICTOR IGNACIO LÓPEZ RÍOS

    2015-01-01

    Full Text Available El profesor Castañeda es una de las figuras más relevantes en Física, tanto a nivel regional como nacional. Es un honor para la facultad de Ciencias de la Universidad Nacional de Colombia, sede Medellín tenerlo entre la planta de sus docentes. Es un profesor que se ha distinguido como investigador de primera línea en óptica donde ha integrado un grupo de colaboradores en esta área, siendo reconocido como uno de los grupos de investigación más consolidados a nivel nacional, lo cual se refleja en el gran número de publicaciones tanto nacionales como internacionales. También se destaca su espíritu colaborador en labores de índole administrativa tanto en la Facultad de Ciencias como en la Sede, donde ha desempeñado cargos como Director de la DIME. Además, es notable su personalidad polifacética ya que ha incursionado en la escritura de relatos cortos. Como escritor, ha logrado publicar un libro de cuentos.

  5. Exonic deletions of FXN and early-onset Friedreich ataxia.

    Science.gov (United States)

    Anheim, Mathieu; Mariani, Louise-Laure; Calvas, Patrick; Cheuret, Emmanuel; Zagnoli, Fabien; Odent, Sylvie; Seguela, Claire; Marelli, Cecilia; Fritsch, Marlène; Delaunoy, Jean-Pierre; Brice, Alexis; Dürr, Alexandra; Koenig, Michel

    2012-07-01

    Friedreich ataxia (FA) is the most frequent type of autosomal recessive cerebellar ataxia, occurring at a mean age of 16 years. Nearly 98% of patients with FA present with homozygous GAA expansions in the FXN gene. The remaining patients are compound heterozygous for an expansion and a point mutation. Patients who are compound heterozygous for an exonic deletion and an expansion are exquisitely rare. To describe 6 patients affected with FA due to an exonic deletion mutation (FAexdel) and to compare these 6 patients with FAexdel with 46 patients consecutively diagnosed with typical FA due to homozygous GAA expansion and whose small expansions were within the same range as that of the expansions of the patients with FAexdel. Description of a series. Academic research. Six patients with FAexdel and 46 patients with typical FA. FXN gene analysis, including assessments of GAA expansion and exon sequencing and determination of exonic copy numbers using multiplex ligation-dependent probe amplification. We identified 6 patients with FA who presented with the combination of 1 GAA expansion and 1 FXN exonic deletion. The mean (SD) age at onset of the disease was earlier for patients with FAexdel (7 [4] years [range, 3-12 years]) than for patients with typical FA (15 [5] years [range, 6-30 years]) (P = .001), and the median time to confinement to wheelchair was shorter for patients with FAexdel (20 years) than for patients with typical FA (28 years) (P = .002). There was no difference between the mean (SD) size of the expansion for the patients with FAexdel (780 [256] GAA triplet repeat sequences [range, 340-1070 GAA triplet repeat sequences]) and the mean (SD) size of the short expansion for the patients with typical FA (634 [163] GAA triplet repeat sequences [range, 367-1000 GAA triplet repeat sequences]) (P = .10). The mean disease duration before becoming wheelchair bound was shorter for patients with FAexdel (9 years) than for patients with typical FA (13 years), and the

  6. Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

    Directory of Open Access Journals (Sweden)

    Maayan Amit

    2012-05-01

    Full Text Available During evolution segments of homeothermic genomes underwent a GC content increase. Our analyses reveal that two exon-intron architectures have evolved from an ancestral state of low GC content exons flanked by short introns with a lower GC content. One group underwent a GC content elevation that abolished the differential exon-intron GC content, with introns remaining short. The other group retained the overall low GC content as well as the differential exon-intron GC content, and is associated with longer introns. We show that differential exon-intron GC content regulates exon inclusion level in this group, in which disease-associated mutations often lead to exon skipping. This group's exons also display higher nucleosome occupancy compared to flanking introns and exons of the other group, thus “marking” them for spliceosomal recognition. Collectively, our results reveal that differential exon-intron GC content is a previously unidentified determinant of exon selection and argue that the two GC content architectures reflect the two mechanisms by which splicing signals are recognized: exon definition and intron definition.

  7. THE EXON 5, 6, 7, 8 OF P53 MUTATIONS IN ORAL SQUAMOUS CELLS CARCINOMA

    Directory of Open Access Journals (Sweden)

    Retno P Rahayu

    2012-04-01

    Full Text Available Genetic instability may underlie the etiology of multistep carcinogenesis. The altered p53 gene observed in tumors may represent the expression of such instability and may allow the accumulation of other gene alterations caused by multiple mechanism. p53 gene is the guardian of the genome, that is why we pay more attention to this gene. In this study, we evaluated the significance of p53 mutation in 55 patient with oral squamous carcinoma. Thirty among them underwent well-differentiated carcinoma, while the remaining 25 patients underwent poorly differentiated carcinoma. The mutations were detected by PCR-SSCP (Single strand Conformational Polymorphism analysis in the region between exon 5 and exon 8. The results indicated that the p53 mutation in exon 5 (40%, exon 6 (28%, exon 7 (24% and exon 8 (8% were associated with poorly differentiated carcinoma, whereas mutation in exon 5 (10%, exon 6 (30%, exon 7 (40% and exon 8 (20% were associated with well-differentiated carcinoma. These observations suggest that p53 mutation in exon 5, 6, and 7 have strong correlation with poorly differentiated in oral squamous carcinoma while well-differentiated level was related with mutation in exon 6,7 and 8.

  8. Hypothesis testing approaches to the exon prediction problem.

    Science.gov (United States)

    Vilardell, Mireia; Sánchez-Pla, Alex

    2006-12-15

    Many gene identification methods assign scores to gene elements prior to their assembly into predicted genes. The scoring system is often based on log-likelihood ratios. These methods usually perform well but it is difficult to interpret how significant a score is. We have developed several tests of significance for the scores: (1) a sum-of-scores test (SST), (2) an intersection-union test (IUT), based on a multiple hypothesis testing interpretation of an exon's score and (3) a meta-analytical approach (MA), which combines several P-values, corresponding to the exon's parts, to yield a global P-value. We performed simulation studies, which show that the MA has better sensitivity and specificity than other methods and is easier to interpret by non-expert users. This is an improvement over other methods and is especially relevant for users who would like to predict incomplete gene sequences.

  9. Impact of sub-inhibitory antibiotics on fibronectin-mediated host cell adhesion and invasion by Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Rasigade Jean

    2011-12-01

    Full Text Available Abstract Background Staphylococcus aureus is a well-armed pathogen prevalent in severe infections such as endocarditis and osteomyelitis. Fibronectin-binding proteins A and B, encoded by fnbA/B, are major pathogenesis determinants in these infections through their involvement in S. aureus adhesion to and invasion of host cells. Sub-minimum inhibitory concentrations (sub-MICs of antibiotics, frequently occurring in vivo because of impaired drug diffusion at the infection site, can alter S. aureus phenotype. We therefore investigated their impact on S. aureus fibronectin-mediated adhesiveness and invasiveness. Methods After in vitro challenge of S. aureus 8325-4 and clinical isolates with sub-MICs of major anti-staphylococcal agents, we explored fnbA/B transcription levels, bacterial adhesiveness to immobilised human fibronectin and human osteoblasts in culture, and bacterial invasion of human osteoblasts. Results Oxacillin, moxifloxacin and linezolid led to the development of a hyper-adhesive phenotype in the fibronectin adhesion assay that was consistent with an increase in fnbA/B transcription. Conversely, rifampin treatment decreased fibronectin binding in all strains tested without affecting fnbA/B transcription. Gentamicin and vancomycin had no impact on fibronectin binding or fnbA/B transcription levels. Only oxacillin-treated S. aureus displayed a significantly increased adhesion to cultured osteoblasts, but its invasiveness did not differ from that of untreated controls. Conclusion Our findings demonstrate that several antibiotics at sub-MICs modulate fibronectin binding in S. aureus in a drug-specific fashion. However, hyper- and hypo- adhesive phenotypes observed in controlled in vitro conditions were not fully confirmed in whole cell infection assays. The relevance of adhesion modulation during in vivo infections is thus still uncertain and requires further investigations.

  10. Layer-by-layer construction of the heparin/fibronectin coatings on titanium surface:stability and functionality

    Science.gov (United States)

    Li, Guicai; Yang, Ping; Huang, Nan

    Layer-by-layer assembly as a versatile bottom-up nanofabrication technique has been widely used in the development of biomimetic materials with superior mechanical and biological properties. In this study, layer-by-layer assembled heparin/fibronectin biofunctional films were fabricated on titanium (Ti) surface to enhance the blood anticoagulation and accelerate the endothelialization simultaneously. The wettability and chemical changes of the assembled films were investigated by static water contact angle measurement and fourier transform infrared spectroscopy (FTIR). The morphology of modified Ti surfaces were observed using scanning electron microscopy (SEM). The real time assembly process was in-situ monitored by quartz crystal microbalance with dissipation (QCM-D). The stability of the films was evaluated by measuring the changes in wettability and the quantity of heparin and fibronectin on the surfaces. The anticoagulation properties of the films were quantitatively rated using Activated partial thromboplastin time (APTT) analysis. New peaks of hydroxyl and amino group were observed on the assembled Ti srufaces by FTIR. The contact angles varied among the films with different bilayer numbers, indicating the successful graft of the heparin and fibronectin layer-by-layer. QCM-D results showed that the frequency shift increased with the bilayer numbers, and the heparin and fibronectin could form multilayers. The assembly films were stable after incubation in PBS for 24 h based on the results of the contact angle measurement and the quantity of heparin and fibronectin analysis. APTT results suggested that the assembled films kept excellent antithrombotic properties. All these results revealed that the assembled heparin/fibronectin films with stabiltiy and anticoagulation property could be firmly formed on titanium surfaces. Our study further demonstrates that layer-by-layer assembly of heparin and fibronectin will provide a potential and effective tool for

  11. A simple physical model predicts small exon length variations.

    Directory of Open Access Journals (Sweden)

    2006-04-01

    Full Text Available One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among these, three-nucleotide variations at so-called NAGNAG tandem acceptor sites have recently attracted considerable attention, and it has been suggested that these variations are regulated and serve to fine-tune protein forms by the addition or removal of a single amino acid. In this paper we first show that in-frame exon length variations are generally overrepresented and that this overrepresentation can be quantitatively explained by the effect of nonsense-mediated decay. Our analysis allows us to estimate that about 50% of frame-shifted coding transcripts are targeted by nonsense-mediated decay. Second, we show that a simple physical model that assumes that the splicing machinery stochastically binds to nearby splice sites in proportion to the affinities of the sites correctly predicts the relative abundances of different small length variations at both boundaries. Finally, using the same simple physical model, we show that for NAGNAG sites, the difference in affinities of the neighboring sites for the splicing machinery accurately predicts whether splicing will occur only at the first site, splicing will occur only at the second site, or three-nucleotide splice variants are likely to occur. Our analysis thus suggests that small exon length variations are the result of stochastic binding of the spliceosome at neighboring splice sites. Small exon length variations occur when there are nearby alternative splice sites that have similar affinity for the splicing machinery.

  12. The Exon-Florio National Security Test for Foreign Investment

    Science.gov (United States)

    2010-02-04

    Asia, Latin America, the Carribean , and North America. 24 Peninsular and Oriental Steam Company is a leading ports operator and transport company...CRS Report for Congress Prepared for Members and Committees of Congress The Exon-Florio National Security Test for Foreign Investment...c11173008 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour

  13. Variants affecting exon skipping contribute to complex traits.

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    Younghee Lee

    Full Text Available DNA variants that affect alternative splicing and the relative quantities of different gene transcripts have been shown to be risk alleles for some Mendelian diseases. However, for complex traits characterized by a low odds ratio for any single contributing variant, very few studies have investigated the contribution of splicing variants. The overarching goal of this study is to discover and characterize the role that variants affecting alternative splicing may play in the genetic etiology of complex traits, which include a significant number of the common human diseases. Specifically, we hypothesize that single nucleotide polymorphisms (SNPs in splicing regulatory elements can be characterized in silico to identify variants affecting splicing, and that these variants may contribute to the etiology of complex diseases as well as the inter-individual variability in the ratios of alternative transcripts. We leverage high-throughput expression profiling to 1 experimentally validate our in silico predictions of skipped exons and 2 characterize the molecular role of intronic genetic variations in alternative splicing events in the context of complex human traits and diseases. We propose that intronic SNPs play a role as genetic regulators within splicing regulatory elements and show that their associated exon skipping events can affect protein domains and structure. We find that SNPs we would predict to affect exon skipping are enriched among the set of SNPs reported to be associated with complex human traits.

  14. Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

    Directory of Open Access Journals (Sweden)

    Mironov Andrey A

    2009-06-01

    Full Text Available Abstract Background Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of recently gained, rodent-specific alternative exons. Results We projected the data about alternative splicing of mouse genes to the rat, human, and dog genomes, and identified exons conserved in the rat genome, but missing in more distant genomes. We estimated the frequency of rodent-specific exons while controlling for possible residual conservation of spurious exons. The frequency of rodent-specific exons is higher among predominantly skipped exons and exons disrupting the reading frame. Separation of all genes by the rate of sequence evolution and by gene families has demonstrated that rodent-specific cassette exons are more frequent in rapidly evolving genes and in rodent-specific paralogs. Conclusion Thus we demonstrated that recently gained exons tend to occur in fast-evolving genes, and their inclusion rate tends to be lower than that of older exons. This agrees with the theory that gain of alternative exons is one of the major mechanisms of gene evolution.

  15. Efficient use of a translation start codon in BDNF exon I.

    Science.gov (United States)

    Koppel, Indrek; Tuvikene, Jürgen; Lekk, Ingrid; Timmusk, Tõnis

    2015-09-01

    The brain-derived neurotrophic factor (BDNF) gene contains a number of 5' exons alternatively spliced with a common 3' exon. BDNF protein is synthesized from alternative transcripts as a prepro-precursor encoded by the common 3' exon IX, which has a translation start site 21 bp downstream of the splicing site. BDNF mRNAs containing exon I are an exception to this arrangement as the last three nucleotides of this exon constitute an in-frame AUG. Here, we show that this AUG is efficiently used for translation initiation in PC12 cells and cultured cortical neurons. Use of exon I-specific AUG produces higher levels of BDNF protein than use of the common translation start site, resulting from a higher translation rate. No differences in protein degradation, constitutive or regulated secretion were detected between BDNF isoforms with alternative 5' termini. As the BDNF promoter preceding exon I is known to be highly regulated by neuronal activity, our results suggest that the function of this translation start site may be efficient stimulus-dependent synthesis of BDNF protein. The brain-derived neurotrophic factor (BDNF) gene contains multiple untranslated 5' exons alternatively spliced to one common protein-coding 3' exon. However, exon I contains an in-frame ATG in a favorable translation context. Here, we show that use of this ATG is associated with more efficient protein synthesis than the commonly used ATG in exon IX. © 2015 International Society for Neurochemistry.

  16. Dynamic 3D cell rearrangements guided by a fibronectin matrix underlie somitogenesis.

    Directory of Open Access Journals (Sweden)

    Gabriel G Martins

    Full Text Available Somites are transient segments formed in a rostro-caudal progression during vertebrate development. In chick embryos, segmentation of a new pair of somites occurs every 90 minutes and involves a mesenchyme-to-epithelium transition of cells from the presomitic mesoderm. Little is known about the cellular rearrangements involved, and, although it is known that the fibronectin extracellular matrix is required, its actual role remains elusive. Using 3D and 4D imaging of somite formation we discovered that somitogenesis consists of a complex choreography of individual cell movements. Epithelialization starts medially with the formation of a transient epithelium of cuboidal cells, followed by cell elongation and reorganization into a pseudostratified epithelium of spindle-shaped epitheloid cells. Mesenchymal cells are then recruited to this medial epithelium through accretion, a phenomenon that spreads to all sides, except the lateral side of the forming somite, which epithelializes by cell elongation and intercalation. Surprisingly, an important contribution to the somite epithelium also comes from the continuous egression of mesenchymal cells from the core into the epithelium via its apical side. Inhibition of fibronectin matrix assembly first slows down the rate, and then halts somite formation, without affecting pseudopodial activity or cell body movements. Rather, cell elongation, centripetal alignment, N-cadherin polarization and egression are impaired, showing that the fibronectin matrix plays a role in polarizing and guiding the exploratory behavior of somitic cells. To our knowledge, this is the first 4D in vivo recording of a full mesenchyme-to-epithelium transition. This approach brought new insights into this event and highlighted the importance of the extracellular matrix as a guiding cue during morphogenesis.

  17. Contribution of fibronectin-binding protein to pathogenesis of Streptococcus equi ssp. zooepidemicus.

    Science.gov (United States)

    Yi, Li; Wang, Yang; Ma, Zhe; Zhang, Hui; Li, Yue; Zheng, Jun-xi; Yang, Yong-chun; Lu, Cheng-ping; Fan, Hong-jie

    2013-04-01

    Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is responsible for a wide variety of infections in many species. Fibronectin-binding protein is a bacterial cell surface protein, which specifically binds fibronectin (FN). Considering the specific role of FN-binding protein in host-pathogen interactions, we investigated the function of a novel FN-binding domain in the FN-binding protein (FNZ) of S. zooepidemicus. Five recombinant FNZ gene fragments [N1 (amino acids, 38-197), N2 (amino acids, 38-603), N3 (amino acids, 41-315), N4 (amino acids, 192-370), and N5 (amino acids, 38-225)] were expressed in Escherichia coli, and their FN-binding activities were tested. The results showed that amino acids 192-225 in the NH2 -terminal region of FNZ could be responsible for binding fibronectin. The FNZ knockout mutant was constructed in S. zooepidemicus, which results in the reduced capacity to adhere to HEp-2 cell, defective virulence in vivo, decreased biofilm formation, and decreased colonization capacity in blood, liver, lung, and spleen tissues of mice as compared to the wild type. These results suggest that FNZ participates in biofilm formation, FN binding, cell adhesion, and pathogenesis of S. zooepidemicus. Furthermore, this work offers a novel FN-binding domain within FNZ, which will help in further characterization of S. zooepidemicus FN-binding properties. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  18. Role of fibronectin in primary mesenchyme cell migration in the sea urchin

    OpenAIRE

    1985-01-01

    We studied the effect of fibronectin (FN) on the behavior of primary mesenchyme cells isolated from sea urchin mesenchyme blastulae in vitro using a time-lapse technique. The migration of isolated primary mesenchyme cells reconstituted in seawater and horse serum is dependent on the presence or absence of exogenous FN in the culture media. The cells in FN, 4 and 40 micrograms/ml, show a high percentage of migration and migrate long distances, whereas a higher concentration of FN at 400 microg...

  19. Changes of fibronectin and laminin in radiation pulmonary injury of rats

    International Nuclear Information System (INIS)

    Bai Yunhong; Wang Dewen; Xu Zaihai; Yang Yi

    1995-01-01

    The changes of fibronectin (FN) and laminin (LN) in the rat lungs irradiated locally with 30 Gy were observed by light microscopy, electron microscopy and immunohistochemistry. The results indicated that distribution of FN and LN in the irradiated lungs was random, the content of FN apparently increased in early phase and gradually decreased in late phase, and the content of LN increased all the way in various degrees. The results suggest that FN is mainly related to the generation and development of early pathological changes in radiation pulmonary injury, whereas LN is related to its entire process

  20. PROCESS FOR THE PRODUCTION OF DISSOLVING PULP FROM TREMA ORIENTALIS (NALITA) BY PREHYDROLYSIS KRAFT AND SODA-ETHYLENEDIAMINE (EDA) PROCESS

    OpenAIRE

    M. A. Quaiyyum; A. Noori; Labooni Ahsan; M. Sarwar Jahan

    2008-01-01

    This paper presents a preliminary study for the production of dissolving pulp from Trema orientalis (Nalita). Water prehydrolysis kraft and soda-ethylenediamine (EDA) pulping for the production of dissolving pulp from T. orientalis was investigated. Prehydrolysis at 150 and 170 oC did not produce pulp with high α-cellulose content when using the kraft process. But addition of 0.25 % H2SO4 in prehydrolysis liquor increased the purity of the pulp with the sacrifice of pulp yield and viscosity. ...

  1. The Fibronectin-Binding Protein EfbA Contributes to Pathogenesis and Protects against Infective Endocarditis Caused by Enterococcus faecalis

    Science.gov (United States)

    Singh, Kavindra V.; La Rosa, Sabina Leanti; Somarajan, Sudha R.; Roh, Jung Hyeob

    2015-01-01

    EfbA is a PavA-like fibronectin adhesin of Enterococcus faecalis previously shown to be important in experimental urinary tract infection. Here, we expressed and purified the E. faecalis OG1RF EfbA and confirmed that this protein binds with high affinity to immobilized fibronectin, collagen I, and collagen V. We constructed an efbA deletion mutant and demonstrated that its virulence was significantly attenuated (P endocarditis model. Furthermore, efbA deletion resulted in diminished ability to bind fibronectin (P endocarditis (P = 0.008 versus control). Taken together, our results demonstrate that EfbA is an important factor involved in E. faecalis endocarditis and that rEfbA immunization is effective in preventing such infection, likely by interfering with bacterial adherence. PMID:26351286

  2. Cell shape and spreading of stromal (mesenchymal) stem cells cultured on fibronectin coated gold and hydroxyapatite surfaces

    DEFF Research Database (Denmark)

    Dolatshahi-Pirouz, Alireza; Jensen, T H L; Kolind, K

    2011-01-01

    . In subsequent cell studies with hMSC's we studied the cell spreading, cytoskeletal organization and cell morphology on the respective surfaces. When the cells were adsorbed on the uncoated substrates, a diffuse cell actin cytoskeleton was revealed, and the cells had a highly elongated shape. On the fibronectin...... coated surfaces the cells adapted to a more polygonal shape with a well-defined actin cytoskeleton, while a larger cell area and roundness values were observed for cells cultured on the coated surfaces. Among the coated surfaces a slightly larger cell area and roundness values was observed on HA......In order to identify the cellular mechanisms leading to the biocompatibility of hydroxyapatite implants, we studied the interaction of human bone marrow derived stromal (mesenchymal) stem cells (hMSCs) with fibronectin-coated gold (Au) and hydroxyapatite (HA) surfaces. The adsorption of fibronectin...

  3. Mutations in Exons 9 and 13 of KIT Gene Are Rare Events in Gastrointestinal Stromal Tumors

    Science.gov (United States)

    Lasota, Jerzy; Wozniak, Agnieszka; Sarlomo-Rikala, Maarit; Rys, Janusz; Kordek, Radzislaw; Nassar, Aziza; Sobin, Leslie H.; Miettinen, Markku

    2000-01-01

    Gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors of the gastrointestinal tract, typically express the KIT protein. Activating mutations in the juxtamembrane domain (exon 11) of the c-kit gene have been shown in a subset of GISTs. These mutations lead into ligand-independent activation of the tyrosine kinase of c-kit, and have a transforming effect in vitro. Several groups have studied the clinical implication of the c-kit mutation status of exon 11 in GISTs and a possible relationship between c-kit mutations and malignant behavior has been established. Recently, a 1530ins6 mutation in exon 9 and missense mutations, 1945A>G in exon 13 of the c-kit gene were reported. The frequency and clinical importance of these findings are unknown. In this study we evaluated 200 GISTs for the presence of mutations in exons 9 and 13 of c-kit. Six cases revealed 1530ins6 mutation in exon 9 and two cases 1945A>G mutation in exon 13. All tumors with mutations in exon 9 and 13 lacked mutations in exon 11 of c-kit. None of the analyzed tumors had more than one type of c-kit mutation. All but one of the eight tumors with mutations in exon 9 or 13 of the c-kit gene were histologically and clinically malignant. All four of six cases with exon 9 mutation of which location of primary tumor was known, were small intestinal, suggesting that this type of mutation could preferentially occur in small intestinal tumors. Exon 9 and 13 mutations seem to be rare, and they cover only a small portion (8%) of the balance of GISTs that do not have mutations in exon 11 of c-kit. This finding indicates that other genetic alterations may activate c-kit in GISTs, or that KIT is not activated by mutations in all cases. PMID:11021812

  4. Regulation of ionizing radiation-induced adhesion of breast cancer cells to fibronectin by alpha5beta1 integrin.

    Science.gov (United States)

    Lee, Shin Hee; Cheng, Huiwen; Yuan, Ye; Wu, Shiyong

    2014-06-01

    Ionizing radiation (IR) is commonly used for cancer therapy, however, its potential influence on cancer metastatic potential remains controversial. In this study, we elucidated the role of integrins in regulation of IR-altered adhesion between breast cancer cells and extracellular matrix (ECM) proteins, which is a key step in the initial phase of metastasis. Our data suggest that the extent of effect that ionizing radiation had on cell adhesion depended on the genetic background of the breast cancer cells. Ionizing radiation was a better adhesion inducer for p53-mutated cells, such as MDA-MB-231 cells, than for p53 wild-type cells, such as MCF-7 cells. While IR-induced adhesions between MDA-MB-231 cells to fibronectin, laminin, collagen I and collagen IV, only blocking of the adhesion between α5β1 integrin and fibronectin using anti-α5β1 integrin antibody could completely inhibit the radiation-induced adhesion of the cells. A soluble Arg-Gly-Asp peptide, the binding motif for fibronectin binding integrins, could also reduce the adhesion of the cells to fibronectin with or without ionizing radiation exposure. The inhibition of the cell-fibronectin interaction also affected, but did not always correlate with, transwell migration of the cancer cells. In addition, our data showed that the total expression of α5 integrin and surface expression of α5β1 integrin were increased in the cells treated with ionizing radiation. The increased surface expression of α5β1 integrin, along with the adhesion between the cells and fibronectin, could be inhibited by both ataxia telangiectasia mutated (ATM) and Rad3-related (ATR) kinase inhibitors. These results suggested that ATM/ATR-mediated surface expression of α5β1 integrin might play a central role in regulation of ionizing radiation-altered adhesion.

  5. Novel EDA or EDAR Mutations Identified in Patients with X-Linked Hypohidrotic Ectodermal Dysplasia or Non-Syndromic Tooth Agenesis

    Directory of Open Access Journals (Sweden)

    Binghui Zeng

    2017-10-01

    Full Text Available Abstract: Both X-linked hypohidrotic ectodermal dysplasia (XLHED and non-syndromic tooth agenesis (NSTA result in symptoms of congenital tooth loss. This study investigated genetic causes in two families with XLHED and four families with NSTA. We screened for mutations of WNT10A, EDA, EDAR, EDARADD, PAX9, MSX1, AXIN2, LRP6, and WNT10B through Sanger sequencing. Whole exome sequencing was performed for the proband of NSTA Family 4. Novel mutation c.1051G>T (p.Val351Phe and the known mutation c.467G>A (p.Arg156His of Ectodysplasin A (EDA were identified in families with XLHED. Novel EDA receptor (EDAR mutation c.73C>T (p.Arg25*, known EDA mutation c.491A>C (p.Glu164Ala, and known Wnt family member 10A (WNT10A mutations c.511C>T (p.Arg171Cys and c.742C>T (p.Arg248* were identified in families with NSTA. The novel EDA and EDAR mutations were predicted as being pathogenic through bioinformatics analyses and structural modeling. Two variants of WNT10A, c.374G>A (p.Arg125Lys and c.125A>G (p.Asn42Ser, were found in patients with NSTA. The two WNT10A variants were predicted to affect the splicing of message RNA, but minigene experiments showed normal splicing of mutated minigenes. This study uncovered the genetic foundations with respect to six families with XLHED or NSTA. We identified six mutations, of which two were novel mutations of EDA and EDAR. This is the first report of a nonsense EDAR mutation leading to NSTA.

  6. Time course of fibronectin in the peri-implant tissue and neointima formation after functional implantation of polyester-based vascular prostheses with different porosity in pigs

    Energy Technology Data Exchange (ETDEWEB)

    Patrzyk, Maciej; Hoene, Andreas [Department of Surgery, Ernst Moritz Arndt University Greifswald, Friedrich-Loeffler-Str. 23, D-17489 Greifswald (Germany); Jarchow, Raymond [Computation Centre, Ernst Moritz Arndt University Greifswald, Felix-Hausdorff-Str. 12, D-17489 Greifswald (Germany); Wilhelm, Lutz [Department of Surgery, Hospital Demmin, Loitzer Str. 1, D-17109 Demmin (Germany); Walschus, Uwe; Schlosser, Michael [Research Group of Predictive Diagnostics of the Department of Medical Biochemistry and Molecular Biology and Institute of Pathophysiology, Ernst Moritz Arndt University Greifswald, Greifswalder Str. 11c, D-17495 Karlsburg (Germany); Zippel, Roland, E-mail: schlosse@uni-greifswald.d [Department of Surgery, Elbland Hospital Center, Weinbergstr. 8, D-01589 Riesa (Germany)

    2010-10-01

    Intima hyperplasia, resulting from extracellular matrix (ECM) secretion, can lead to vascular prosthesis occlusion and is a major problem in vascular surgery. Fibronectin might contribute to ongoing ECM secretion. However, the exact role of fibronectin and its influence on neointima formation remains unclear. This study was aimed at investigating the time course of the fibronectin area fraction and neointima formation following the functional implantation of three different polyester vascular prostheses into pigs. The infrarenal aorta from 15 animals (n = 5/group) was replaced by prosthesis segments with low, medium and high primary porosity. After 7, 14, 21, 28 and 116 days, the prostheses were morphometrically examined. Overall, the fibronectin area fraction was inversely correlated with the neointima thickness, demonstrating high fibronectin levels in the early phase (days 7 and 14) and low levels in the later phase with almost complete neointima formation (days 21-116). Throughout the study, fibronectin levels were highest at the proximal anastomosis region. The low porosity prosthesis had the highest fibronectin area fraction and a delayed neointima formation in the middle phase (days 21 and 28) but the highest neointima lining on day 116. The results indicate a relationship between fibronectin and neointima formation with the prosthesis porosity, demonstrating the importance of the textile design for tissue reactions following implantation.

  7. Quantification of fibronectin adsorption to silicone-rubber cell culture substrates.

    Science.gov (United States)

    Cunningham, James J; Nikolovski, Janeta; Linderman, Jennifer J; Mooney, David J

    2002-04-01

    As the role of mechanical force in cellular signaling gained recognition, investigators designed a number of devices to deliver controlled regimens of mechanical force to cultured cells. One type of device uses thin silicone-rubber membranes to support monolayer cell adhesion and to transmit mechanical force in the form of biaxial strain. We have observed that cell attachment and spreading are impaired on these membranes compared to polystyrene, even when both are passively coated with identical amounts of extracellular matrix. The purpose of these studies was to quantify the efficiency and stability of passive matrix adsorption onto commercially available elastic culture substrates. A theoretically saturating density (1 microg/cm2) of fibronectin was added to each well, and the initial efficiency of adsorption to the walls and elastic membranes was found to be 31 +/- 2% of the protein added. Strikingly, when the protein adsorbed specifically to the membranes was quantified after seven days, only 10-26 ng/cm2 fibronectin were present, revealing that most of the adsorption is to the sides of the wells. These results indicate that the adsorption of matrix proteins to silicone-rubber substrates is relatively inefficient and that investigators who use these systems must be aware of this fact and design their experiments accordingly.

  8. A biosynthetic nerve guide conduit based on silk/SWNT/fibronectin nanocomposite for peripheral nerve regeneration.

    Directory of Open Access Journals (Sweden)

    Fatemeh Mottaghitalab

    Full Text Available As a contribution to the functionality of nerve guide conduits (NGCs in nerve tissue engineering, here we report a conduit processing technique through introduction and evaluation of topographical, physical and chemical cues. Porous structure of NGCs based on freeze-dried silk/single walled carbon nanotubes (SF/SWNTs has shown a uniform chemical and physical structure with suitable electrical conductivity. Moreover, fibronectin (FN containing nanofibers within the structure of SF/SWNT conduits produced through electrospinning process have shown aligned fashion with appropriate porosity and diameter. Moreover, fibronectin remained its bioactivity and influenced the adhesion and growth of U373 cell lines. The conduits were then implanted to 10 mm left sciatic nerve defects in rats. The histological assessment has shown that nerve regeneration has taken places in proximal region of implanted nerve after 5 weeks following surgery. Furthermore, nerve conduction velocities (NCV and more myelinated axons were observed in SF/SWNT and SF/SWNT/FN groups after 5 weeks post implantation, indicating a functional recovery for the injured nerves. With immunohistochemistry, the higher S-100 expression of Schwann cells in SF/SWNT/FN conduits in comparison to other groups was confirmed. In conclusion, an oriented conduit of biocompatible SF/SWNT/FN has been fabricated with acceptable structure that is particularly applicable in nerve grafts.

  9. IL-4 impairs wound healing potential in the skin by repressing fibronectin expression.

    Science.gov (United States)

    Serezani, Ana P M; Bozdogan, Gunseli; Sehra, Sarita; Walsh, Daniel; Krishnamurthy, Purna; Sierra Potchanant, Elizabeth A; Nalepa, Grzegorz; Goenka, Shreevrat; Turner, Matthew J; Spandau, Dan F; Kaplan, Mark H

    2017-01-01

    Atopic dermatitis (AD) is characterized by intense pruritis and is a common childhood inflammatory disease. Many factors are known to affect AD development, including the pleiotropic cytokine IL-4. Yet little is known regarding the direct effects of IL-4 on keratinocyte function. In this report RNA sequencing and functional assays were used to define the effect of the allergic environment on primary keratinocyte function and wound repair in mice. Acute or chronic stimulation by IL-4 modified expression of more than 1000 genes expressed in human keratinocytes that are involved in a broad spectrum of nonoverlapping functions. Among the IL-4-induced changes, repression of fibronectin critically impaired the human keratinocyte wound response. Moreover, in mouse models of spontaneous and induced AD-like lesions, there was delayed re-epithelialization. Importantly, topical treatment with fibronectin restored the epidermal repair response. Keratinocyte gene expression is critically shaped by IL-4, altering cell fate decisions, which are likely important for the clinical manifestations and pathology of allergic skin disease. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  10. Novel 3D modeling methods for virtual fabrication and EDA compatible design of MEMS via parametric libraries

    International Nuclear Information System (INIS)

    Schröpfer, Gerold; Lorenz, Gunar; Rouvillois, Stéphane; Breit, Stephen

    2010-01-01

    This paper provides a brief summary of the state-of-the-art of MEMS-specific modeling techniques and describes the validation of new models for a parametric component library. Two recently developed 3D modeling tools are described in more detail. The first one captures a methodology for designing MEMS devices and simulating them together with integrated electronics within a standard electronic design automation (EDA) environment. The MEMS designer can construct the MEMS model directly in a 3D view. The resulting 3D model differs from a typical feature-based 3D CAD modeling tool in that there is an underlying behavioral model and parametric layout associated with each MEMS component. The model of the complete MEMS device that is shared with the standard EDA environment can be fully parameterized with respect to manufacturing- and design-dependent variables. Another recent innovation is a process modeling tool that allows accurate and highly realistic visualization of the step-by-step creation of 3D micro-fabricated devices. The novelty of the tool lies in its use of voxels (3D pixels) rather than conventional 3D CAD techniques to represent the 3D geometry. Case studies for experimental devices are presented showing how the examination of these virtual prototypes can reveal design errors before mask tape out, support process development before actual fabrication and also enable failure analysis after manufacturing.

  11. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure.

    Science.gov (United States)

    Gelfman, Sahar; Cohen, Noa; Yearim, Ahuvi; Ast, Gil

    2013-05-01

    DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon-intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking introns, and the other with similar GC content in exons and introns. The first group has higher nucleosome occupancy on exons than introns, whereas the second group exhibits weak nucleosome marking of exons, suggesting another type of epigenetic marker distinguishes exons from introns when GC content is similar. We find different and specific patterns of DNA methylation in each of the GC architectures; yet in both groups, DNA methylation clearly marks the exons. Exons of the leveled GC architecture exhibit a significantly stronger DNA methylation signal in relation to their flanking introns compared to exons of the differential GC architecture. This is accentuated by a reduction of the DNA methylation level in the intronic sequences in proximity to the splice sites and shows that different epigenetic modifications mark the location of exons already at the DNA level. Also, lower levels of methylated CpGs on alternative exons can successfully distinguish alternative exons from constitutive ones. Three positions at the splice sites show high CpG abundance and accompany elevated nucleosome occupancy in a leveled GC architecture. Overall, these results suggest that DNA methylation affects exon recognition and is influenced by the GC architecture of the exon and flanking introns.

  12. Clinical phenotypes as predictors of the outcome of skipping around DMD exon 45.

    Science.gov (United States)

    Findlay, Andrew R; Wein, Nicolas; Kaminoh, Yuuki; Taylor, Laura E; Dunn, Diane M; Mendell, Jerry R; King, Wendy M; Pestronk, Alan; Florence, Julaine M; Mathews, Katherine D; Finkel, Richard S; Swoboda, Kathryn J; Howard, Michael T; Day, John W; McDonald, Craig; Nicolas, Aurélie; Le Rumeur, Elisabeth; Weiss, Robert B; Flanigan, Kevin M

    2015-04-01

    Exon-skipping therapies aim to convert Duchenne muscular dystrophy (DMD) into less severe Becker muscular dystrophy (BMD) by altering pre-mRNA splicing to restore an open reading frame, allowing translation of an internally deleted and partially functional dystrophin protein. The most common single exon deletion-exon 45 (Δ45)-may theoretically be treated by skipping of either flanking exon (44 or 46). We sought to predict the impact of these by assessing the clinical severity in dystrophinopathy patients. Phenotypic data including clinical diagnosis, age at wheelchair use, age at loss of ambulation, and presence of cardiomyopathy were analyzed from 41 dystrophinopathy patients containing equivalent in-frame deletions. As expected, deletions of either exons 45 to 47 (Δ45-47) or exons 45 to 48 (Δ45-48) result in BMD in 97% (36 of 37) of subjects. Unexpectedly, deletion of exons 45 to 46 (Δ45-46) is associated with the more severe DMD phenotype in 4 of 4 subjects despite an in-frame transcript. Notably, no patients with a deletion of exons 44 to 45 (Δ44-45) were found within the United Dystrophinopathy Project database, and this mutation has only been reported twice before, which suggests an ascertainment bias attributable to a very mild phenotype. The observation that Δ45-46 patients have typical DMD suggests that the conformation of the resultant protein may result in protein instability or altered binding of critical partners. We conclude that in DMD patients with Δ45, skipping of exon 44 and multiexon skipping of exons 46 and 47 (or exons 46-48) are better potential therapies than skipping of exon 46 alone. © 2015 American Neurological Association.

  13. Genomic V exons from whole genome shotgun data in reptiles.

    Science.gov (United States)

    Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

    2014-08-01

    Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

  14. Exon Shuffling and Origin of Scorpion Venom Biodiversity

    Directory of Open Access Journals (Sweden)

    Xueli Wang

    2016-12-01

    Full Text Available Scorpion venom is a complex combinatorial library of peptides and proteins with multiple biological functions. A combination of transcriptomic and proteomic techniques has revealed its enormous molecular diversity, as identified by the presence of a large number of ion channel-targeted neurotoxins with different folds, membrane-active antimicrobial peptides, proteases, and protease inhibitors. Although the biodiversity of scorpion venom has long been known, how it arises remains unsolved. In this work, we analyzed the exon-intron structures of an array of scorpion venom protein-encoding genes and unexpectedly found that nearly all of these genes possess a phase-1 intron (one intron located between the first and second nucleotides of a codon near the cleavage site of a signal sequence despite their mature peptides remarkably differ. This observation matches a theory of exon shuffling in the origin of new genes and suggests that recruitment of different folds into scorpion venom might be achieved via shuffling between body protein-coding genes and ancestral venom gland-specific genes that presumably contributed tissue-specific regulatory elements and secretory signal sequences.

  15. Ail Protein Binds Ninth Type III Fibronectin Repeat (9FNIII) within Central 120-kDa Region of Fibronectin to Facilitate Cell Binding by Yersinia pestis*

    Science.gov (United States)

    Tsang, Tiffany M.; Annis, Douglas S.; Kronshage, Malte; Fenno, Jesse T.; Usselman, Lisa D.; Mosher, Deane F.; Krukonis, Eric S.

    2012-01-01

    The Yersinia pestis adhesin molecule Ail interacts with the extracellular matrix protein fibronectin (Fn) on host cells to facilitate efficient delivery of cytotoxic Yop proteins, a process essential for plague virulence. A number of bacterial pathogens are known to bind to the N-terminal region of Fn, comprising type I Fn (FNI) repeats. Using proteolytically generated Fn fragments and purified recombinant Fn fragments, we demonstrated that Ail binds the centrally located 120-kDa fragment containing type III Fn (FNIII) repeats. A panel of monoclonal antibodies (mAbs) that recognize specific epitopes within the 120-kDa fragment demonstrated that mAb binding to 9FNIII blocks Ail-mediated bacterial binding to Fn. Epitopes of three mAbs that blocked Ail binding to Fn were mapped to a similar face of 9FNIII. Antibodies directed against 9FNIII also inhibited Ail-dependent cell binding activity, thus demonstrating the biological relevance of this Ail binding region on Fn. Bacteria expressing Ail on their surface could also bind a minimal fragment of Fn containing repeats 9–10FNIII, and this binding was blocked by a mAb specific for 9FNIII. These data demonstrate that Ail binds to 9FNIII of Fn and presents Fn to host cells to facilitate cell binding and delivery of Yops (cytotoxins of Y. pestis), a novel interaction, distinct from other bacterial Fn-binding proteins. PMID:22447929

  16. Ail protein binds ninth type III fibronectin repeat (9FNIII) within central 120-kDa region of fibronectin to facilitate cell binding by Yersinia pestis.

    Science.gov (United States)

    Tsang, Tiffany M; Annis, Douglas S; Kronshage, Malte; Fenno, Jesse T; Usselman, Lisa D; Mosher, Deane F; Krukonis, Eric S

    2012-05-11

    The Yersinia pestis adhesin molecule Ail interacts with the extracellular matrix protein fibronectin (Fn) on host cells to facilitate efficient delivery of cytotoxic Yop proteins, a process essential for plague virulence. A number of bacterial pathogens are known to bind to the N-terminal region of Fn, comprising type I Fn (FNI) repeats. Using proteolytically generated Fn fragments and purified recombinant Fn fragments, we demonstrated that Ail binds the centrally located 120-kDa fragment containing type III Fn (FNIII) repeats. A panel of monoclonal antibodies (mAbs) that recognize specific epitopes within the 120-kDa fragment demonstrated that mAb binding to (9)FNIII blocks Ail-mediated bacterial binding to Fn. Epitopes of three mAbs that blocked Ail binding to Fn were mapped to a similar face of (9)FNIII. Antibodies directed against (9)FNIII also inhibited Ail-dependent cell binding activity, thus demonstrating the biological relevance of this Ail binding region on Fn. Bacteria expressing Ail on their surface could also bind a minimal fragment of Fn containing repeats (9-10)FNIII, and this binding was blocked by a mAb specific for (9)FNIII. These data demonstrate that Ail binds to (9)FNIII of Fn and presents Fn to host cells to facilitate cell binding and delivery of Yops (cytotoxins of Y. pestis), a novel interaction, distinct from other bacterial Fn-binding proteins.

  17. Application of calcium phosphates and fibronectin as complementary treatment for osteoporotic bone fractures.

    Science.gov (United States)

    Plaza, Javier Quintana; Garzón, Lorena Benito; Gimenez, Beatriz Bravo; Moraleda, Belén Fernández-Montes; Collía, Francisco; Rodríguez-Lorenzo, Luis M

    2016-09-01

    The gradual aging of the population results in increased incidence of osteoporotic bone fractures. In a good quality bone, the fixation with the usual methods is adequate, but not in osteoporotic bone, in which consolidation delays and other complications are common, with failure rates for screws up to 25%. To test fibronectin loaded hydroxyapatite as a complementary treatment for osteoporotic fractures. This study was performed in a vivo model; 42 female osteoporotic adult rabbits 4-5kg (White New Zealand) were used. Two groups (hydroxyapatite and fibronectin loaded hydroxyapatite) and a control group were tested. 3 time points 24h, 48h and 5days were studied. Defects were created in both femurs, in one of them, a cannulated screw (4mm) and a biocompatible material were placed; in the other femur a screw was inserted without supplemented material forming the control group. Osteoporosis was induced from models already known throughout administration of steroids. Samples were analyzed histologically and through imaging (micro Ct). Basal levels of BMD are observed below to normal when compared to other studies (0.25/0.3 instead of 0.4). Global and dependent of time analysis of samples, show no significant differences for samples analyzed. However, an important trend was noted for variables that define the trabecular bone microarchitecture. Indices that define trabecular microarchitecture in the comparative analysis found to have statistical differences (p<0.01). Osteosynthesis in an osteoporotic bone is a challenge for the surgeon, due to a reduced bone mineral density and different bone architecture. The main finding was the verification of the hypothesis that the trabecular bone parameters increases with our augmentation material in weak rabbit bone quality. Also, the histological analyses of samples show an increase of non inflammatory cells in protein samples (OHAp-Fn) from the first 24hours. An early response of rabbit osteroporotic bone to a complementary

  18. The pavA gene of Streptococcus pneumoniae encodes a fibronectin-binding protein that is essential for virulence

    NARCIS (Netherlands)

    Holmes, AR; McNab, R; Millsap, KW; Rohde, M; Hammerschmidt, S; Mawdsley, JL; Jenkinson, HF

    Streptococcus pneumoniae colonizes the nasopharynx in up to 40% of healthy subjects, and is a leading cause of middle ear infections (otitis media), meningitis and pneumonia. Pneumococci adhere to glycosidic receptors on epithelial cells and to immobilized fibronectin, but the bacterial adhesins

  19. The hairpin structure of the 6F11F22F2 fragment from human fibronectin enhances gelatin binding

    Science.gov (United States)

    Pickford, Andrew R.; Smith, Steven P.; Staunton, David; Boyd, Jonathan; Campbell, Iain D.

    2001-01-01

    The solution structure of the 6F11F22F2 fragment from the gelatin-binding region of fibronectin has been determined (Protein Data Bank entry codes 1e88 and 1e8b). The structure reveals an extensive hydrophobic interface between the non-contiguous 6F1 and 2F2 modules. The buried surface area between 6F1 and 2F2 (∼870 Å2) is the largest intermodule interface seen in fibronectin to date. The dissection of 6F11F22F2 into the 6F11F2 pair and 2F2 results in near-complete loss of gelatin-binding activity. The hairpin topology of 6F11F22F2 may facilitate intramolecular contact between the matrix assembly regions flanking the gelatin-binding domain. This is the first high-resolution study to reveal a compact, globular arrangement of modules in fibronectin. This arrangement is not consistent with the view that fibronectin is simply a linear ‘string of beads’. PMID:11285216

  20. Osseoconductivity of a Specific Streptavidin-Biotin-Fibronectin Surface Coating of Biotinylated Titanium Implants - A Rabbit Animal Study.

    Science.gov (United States)

    Kämmerer, Peer W; Lehnert, Michael; Al-Nawas, Bilal; Kumar, Vinay V; Hagmann, Sebastien; Alshihri, Abdulmonem; Frerich, Bernhard; Veith, Michael

    2015-10-01

    Biofunctionalized implant surfaces may accelerate bony integration and increase long-term stability. The aim of the study was to evaluate the osseous reaction toward biomimetic titanium implants surfaces coated with quasicovalent immobilized fibronectin in an in vivo animal model. A total of 84 implants (uncoated [control 1, n = 36], streptavidin-biotin coated [test 1, n = 24], streptavidin-biotin-fibronectin coated [test 2, n = 24]) were inserted 1 mm supracortically in the proximal tibia of 12 rabbits. The samples were examined after 3 and 6 weeks. Total bone-implant contact (tBIC; %), bone-implant contact in the cortical (cBIC; %) and in the spongious bone (sBIC; %) as well as the percentage of linear bone fill (PLF; %) were evaluated. After 3 weeks, streptavidin-biotin-fibronectin implants had a significant higher sBIC (p = .043) and PLF (p = .007) compared with the uncoated samples. After 6 weeks, this difference was significant for tBIC (p = .016) and cBIC (p biotin-coated implants showed less bone growth at both time points of all examined parameters when compared with their counterparts (all p biotin-fibronectin system on smooth surface titanium shows a beneficial faster osseous healing in vivo. Besides, an antifouling effect of the streptavidin-biotin coating was proven. © 2015 Wiley Periodicals, Inc.

  1. Clinical value of indicators of cationic proteins, leukocytes myeloperoxidase and fibronectin blood plasma in viral meningitis in children

    Directory of Open Access Journals (Sweden)

    O. G. Kimirilova

    2017-01-01

    Full Text Available Objective: was to establish clinical and diagnostic value of cytochemical indices of peripheral blood leukocytes (cationic protein and myeloperoxidase, fibronectin blood plasma to assess the severity, predict the course and outcome of viral meningitis in children.Subjects and methods. In 450 patients with viral meningitis (enterovirus, arbovirus, parotitic, herpesviral, adenovirus etiology at the age of 14 years, the parameters of the microbicidal system of leukocytes (cation proteins, myeloperoxidase and fibronectin blood plasma were determined. Etiological diagnosis of meningitis was confirmed by release of viral RNA from blood and cerebrospinal fluid by the polymerase chain reaction, enzyme-linked immunosorbent assay (ELISA.The results and conclusion. Found that severe, prolonged duration, lethal outcome of viral meningitis in children are accompanied by sugnificant suppression of cationic proteins, myeloperoxidase, fibronectin blood plasma, maximally expressed in lethal outcomes, compared with the severe form, but with a favorable outcome and control. Settings imbalance cationic proteins, myeloperoxidase, fibronectin blood plasma are objective criteria of the adaptation syndrome that reflects the state of the phagocytosis system in viral meningitis in children and can be considered as additional criteria for predicting the course and outcome of disease.

  2. Interaction of intraocular lenses with fibronectin and human lens epithelial cells: Effect of chemical composition and aging.

    Science.gov (United States)

    Tortolano, Lionel; Serrano, Carole; Jubeli, Emile; Saunier, Johanna; Yagoubi, Najet

    2015-12-01

    The aim of this study is to investigate in vitro interactions between hydrophobic acrylate intraocular lenses (IOLs) and their biological environment. The influence of lens chemical composition and aging on fibronectin (FN) adsorption and on IOLs cytotoxicity on human lens epithelial cells was examined. Cytotoxicity of acrylate monomers used in IOLs manufacture was also investigated. Four different IOLs were included in the study: Acrysof(®), Tecnis(®), EnVista(®), and iSert(®). Implants were artificially aged in a xenon arc chamber to simulate 2 years of light exposure. Fibronectin adsorption on IOL surface was quantified using ELISA and correlated to surface roughness determined with AFM. Direct contact cytotoxicity was determined with the MTT assay and cell morphology was observed with light microscopy. Results showed that fibronectin adsorption did not differ significantly among IOLs, whatever their chemical composition. Moreover, aging conditions did not impact fibronectin adsorption. All IOLs were biocompatible even after applying 2-year aging conditions, with cell viability higher than 70%. Five acrylate monomers appeared to be toxic in the range of concentrations tested, but no monomer release from the IOLs could be detected during accelerated 2-year incubation with saline solution. This study did not reveal an influence of chemical composition and aging on protein adsorption and on biocompatibility. © 2015 Wiley Periodicals, Inc.

  3. EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

    Science.gov (United States)

    Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

    2014-11-01

    The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection. © 2014 John Wiley & Sons Ltd.

  4. Staurosporine allows dystrophin expression by skipping of nonsense-encoding exon.

    Science.gov (United States)

    Nishida, Atsushi; Oda, Ayaka; Takeuchi, Atsuko; Lee, Tomoko; Awano, Hiroyuki; Hashimoto, Naohiro; Takeshima, Yasuhiro; Matsuo, Masafumi

    2016-09-01

    Antisense oligonucleotides that induce exon skipping have been nominated as the most plausible treatment method for dystrophin expression in dystrophin-deficient Duchenne muscular dystrophy. Considering this therapeutic efficiency, small chemical compounds that can enable exon skipping have been highly awaited. In our previous report, a small chemical kinase inhibitor, TG003, was shown to enhance dystrophin expression by enhancing exon skipping. Staurosporine (STS), a small chemical broad kinase inhibitor, was examined for enhanced skipping of a nonsense-encoding dystrophin exon. STS was added to culture medium of HeLa cells transfected with minigenes expressing wild-type or mutated exon 31 with c.4303G>T (p.Glu1435X), and the resulting mRNAs were analyzed by RT-PCR amplification. Dystrophin mRNA and protein were analyzed in muscle cells treated with STS by RT-PCR and western blotting, respectively. STS did not alter splicing of the wild-type minigene. In the mutated minigene, STS increased the exon 31-skipped product. A combination of STS and TG003 did not significantly increase the exon 31-skipped product. STS enhanced skipping of exon 4 of the CDC-like kinase 1 gene, whereas TG003 suppressed it. Two STS analogs with selective kinase inhibitory activity did not enhance the mutated exon 31 skipping. When immortalized muscle cells with c.4303G>T in the dystrophin gene were treated with STS, skipping of the mutated exon 31 and dystrophin expression was enhanced. STS, a broad kinase inhibitor, was shown to enhance skipping of the mutated exon 31 and dystrophin expression, but selective kinase inhibitors did not. Copyright © 2016 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

  5. Different morphotypes of the tabby (EDA) dentition in the mouse mandible result from a defect in the mesio-distal segmentation of dental epithelium

    Czech Academy of Sciences Publication Activity Database

    Peterková, Renata; Kristenová, Pavlína; Lesot, H.; Lisi, S.; Vonesch, J. L.; Gendrault, J. L.; Peterka, Miroslav

    2002-01-01

    Roč. 5, - (2002), s. 215-226 ISSN 1397-5927 R&D Projects: GA AV ČR IAA7039901; GA ČR GA304/02/0448; GA MŠk OC B8.10 Institutional research plan: CEZ:AV0Z5039906 Keywords : development * ectodermal dysplasia * EDA Subject RIV: EA - Cell Biology

  6. Cooperative Binding and Activation of Fibronectin by a Bacterial Surface Protein*

    Science.gov (United States)

    Marjenberg, Zoe R.; Ellis, Ian R.; Hagan, Robert M.; Prabhakaran, Sabitha; Höök, Magnus; Talay, Susanne R.; Potts, Jennifer R.; Staunton, David; Schwarz-Linek, Ulrich

    2011-01-01

    Integrin-dependent cell invasion of some pathogenic bacteria is mediated by surface proteins targeting the extracellular matrix protein fibronectin (FN). Although the structural basis for bacterial FN recognition is well understood, it has been unclear why proteins such as streptococcal SfbI contain several FN-binding sites. We used microcalorimetry to reveal cooperative binding of FN fragments to arrays of binding sites in SfbI. In combination with thermodynamic analyses, functional cell-based assays show that SfbI induces conformational changes in the N-terminal 100-kDa region of FN (FN100kDa), most likely by competition with intramolecular interactions defining an inactive state of FN100kDa. This study provides insights into how long range conformational changes resulting in FN activation may be triggered by bacterial pathogens. PMID:21059652

  7. Integrin α5β1, the Fibronectin Receptor, as a Pertinent Therapeutic Target in Solid Tumors

    Energy Technology Data Exchange (ETDEWEB)

    Schaffner, Florence; Ray, Anne Marie; Dontenwill, Monique, E-mail: monique.dontenwill@unistra.fr [UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Tumoral signaling and therapeutic targets, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch (France)

    2013-01-15

    Integrins are transmembrane heterodimeric proteins sensing the cell microenvironment and modulating numerous signalling pathways. Changes in integrin expression between normal and tumoral cells support involvement of specific integrins in tumor progression and aggressiveness. This review highlights the current knowledge about α5β1 integrin, also called the fibronectin receptor, in solid tumors. We summarize data showing that α5β1 integrin is a pertinent therapeutic target expressed by tumoral neovessels and tumoral cells. Although mainly evaluated in preclinical models, α5β1 integrin merits interest in particular in colon, breast, ovarian, lung and brain tumors where its overexpression is associated with a poor prognosis for patients. Specific α5β1 integrin antagonists will be listed that may represent new potential therapeutic agents to fight defined subpopulations of particularly aggressive tumors.

  8. Effect of fibronectin adsorption on osteoblastic cellular responses to hydroxyapatite and alumina

    International Nuclear Information System (INIS)

    Kawashita, Masakazu; Hasegawa, Maki; Kudo, Tada-aki; Kanetaka, Hiroyasu; Miyazaki, Toshiki; Hashimoto, Masami

    2016-01-01

    Initial cellular responses following implantation are important for inducing osteoconduction. We investigated cell adhesion, spreading, proliferation and differentiation of mouse MC3T3-E1 osteoblastic cells on untreated or fibronectin (Fn)-coated discs of hydroxyapatite (HAp) or alpha-type alumina (α-Al 2 O 3 ). Fn coating significantly enhanced adhesion and spreading of MC3T3-E1 cells on HAp, but did not affect MC3T3-E1 cell proliferation and differentiation on HAp or α-Al 2 O 3 . Fn-coated HAp likely does not stimulate pre-osteoblast cells to initiate the process of osteoconduction; however, Fn adsorption might affect the response of inflammatory cells to the implanted material or, in conjunction with other serum proteins, stimulate pre-osteoblast cell proliferation and differentiation. Further studies on the effect of serum proteins in cell culture and the efficacy of Fn-coated HAp and α-Al 2 O 3 in vivo are warranted. - Highlights: • We studied osteoblast-like MC3T3-E1 cell responses on fibronectin (Fn)-coated discs (HAp/α-Al 2 O 3 ). • Fn adsorption enhanced adhesion and spreading of MC3T3-E1 cells on HAp but not on α-Al 2 O 3 . • Fn adsorption hardly affected proliferation and differentiation of MC3T3-E1 cells on HAp and α-Al 2 O 3 . • Fn adsorption might stimulate osteoconduction on HAp along with other serum proteins.

  9. Laminin and fibronectin treatment leads to generation of dendritic cells with superior endocytic capacity.

    Directory of Open Access Journals (Sweden)

    Samuel García-Nieto

    2010-04-01

    Full Text Available Sampling the microenvironment at sites of microbial exposure by dendritic cells (DC and their subsequent interaction with T cells in the paracortical area of lymph nodes are key events for initiating immune responses. Most of our knowledge of such events in human is based on in vitro studies performed in the absence of extracellular matrix (ECM proteins. ECM in basement membranes and interstitial spaces of different tissues, including lymphoid organs, plays an important role in controlling specific cellular functions such as migration, intracellular signalling and differentiation. The aim of this study was, therefore, to investigate the impact of two abundant ECM components, fibronectin and laminin, on the phenotypical and functional properties of DC and how that might influence DC induced T-cell differentiation.Human monocyte derived DC were treated with laminin and fibronectin for up to 48 hours and their morphology and phenotype was analyzed using scanning electron microscopy, flow cytometry and real time PCR. The endocytic ability of DC was determined using flow cytometry. Furthermore, co-culture of DC and T cells were established and T cell proliferation and cytokine profile was measured using H(3-thymidine incorporation and ELISA respectively. Finally, we assessed formation of DC-T cell conjugates using different cell trackers and flow cytometry. Our data show that in the presence of ECM, DC maintain a 'more immature' phenotype and express higher levels of key endocytic receptors, and as a result become significantly better endocytic cells, but still fully able to mature in response to stimulation as evidenced by their superior ability to induce antigen-specific T cell differentiation.These studies underline the importance of including ECM components in in vitro studies investigating DC biology and DC-T cell interaction. Within the context of antigen specific DC induced T cell proliferation, inclusion of ECM proteins could lead to

  10. Expression of laminin 5, fibronectin, and epithelium-associated integrins in recurrent aphthous ulcers.

    Science.gov (United States)

    Richards, D W; MacPhail, L A; Dekker, N; Greenspan, D; Greenspan, J S; Lozada-Nur, F; Regezi, J A

    1996-07-01

    Recurrent aphthous ulceration (RAU) is characterized by an ulcerated lesion that persists longer than traumatic ulcers of similar size. This delayed healing phase of the lesion was investigated for extracellular matrix components and matrix receptors (integrins). The hypothesis tested was that aphthous ulcers may lack key extracellular matrix components, or their receptors, that are necessary for the migration of marginal keratinocytes from the ulcer edge. We immunocytochemically stained biopsy specimens of RAUs and non-involved mucosal specimens from HIV+ and non-infected individuals to investigate the presence and distribution of molecules reported to be associated with reepithelialization of mucosal and cutaneous wounds. Fibronectin, laminin type 5 (kalinin), and integrin subunits beta 1, beta 4, alpha 6, and alpha v were consistently found at the margins of RAU, as they are in traumatic ulcers. The alpha 5 and beta 6 subunits were not always present. We also found alpha v in the intact stratified squamous epithelium adjacent to ulcers. Immunohistochemical stains showed distruption in the deposition of laminin 5 and an apparent lack of fibronectin at the edges of some ulcers. Although these tissue results do not determine which integrin subunits are paired with each other, they do show some alterations in their expression in RAU. Absence of one or more of these molecules at the migrating front may contribute to delayed epithelial regeneration. It is likely that the absence or inappropriate expression of keratinocyte integrins or their extracellular matrix receptors occurs after the causative factors (currently unknown) of the lesion are gone. The reason for the altered expression of these molecules may be related to the secretory products (including lymphokines and proteinases) of the lymphocytic infiltrate.

  11. Interaction of phosphorylcholine with fibronectin coatings: Surface characterization and biological performances

    Energy Technology Data Exchange (ETDEWEB)

    Montaño-Machado, Vanessa, E-mail: vanessa.montano-machado.1@ulaval.ca [Laboratory for Biomaterials and Bioengineering, Dept. of Min-Met-Materials Eng., & University Hospital Research Center, Laval University, University Campus, PLT-1745G, Québec, Québec, G1 V 0A6 (Canada); ERRMECe, University of Cergy-Pontoise, Site Saint-Martin, 2 Avenue Adolphe Chauvin, 95302 Cergy-Pontoise Cedex (France); Noël, Céline, E-mail: celine.noel@unamur.be [Research Centre in Physics of Matter and Radiation (PMR), Université de Namur, 61 rue de Bruxelles, B-5000 Namur (Belgium); Chevallier, Pascale, E-mail: pascale.chevallier@crchudequebec.ulaval.ca [Laboratory for Biomaterials and Bioengineering, Dept. of Min-Met-Materials Eng., & University Hospital Research Center, Laval University, University Campus, PLT-1745G, Québec, Québec, G1 V 0A6 (Canada); Turgeon, Stéphane, E-mail: stephane.turgeon@crchudequebec.ulaval.ca [Laboratory for Biomaterials and Bioengineering, Dept. of Min-Met-Materials Eng., & University Hospital Research Center, Laval University, University Campus, PLT-1745G, Québec, Québec, G1 V 0A6 (Canada); Houssiau, Laurent, E-mail: laurent.houssiau@unamur.be [Research Centre in Physics of Matter and Radiation (PMR), Université de Namur, 61 rue de Bruxelles, B-5000 Namur (Belgium); Pauthe, Emmanuel, E-mail: emmanuel.pauthe@u-cergy.fr [ERRMECe, University of Cergy-Pontoise, Site Saint-Martin, 2 Avenue Adolphe Chauvin, 95302 Cergy-Pontoise Cedex (France); and others

    2017-02-28

    Highlights: • Fibronectin/phosphorylcholine coatings on plasma deposited fluorocarbon films were created. • The effect of several coating techniques on the surface biological performances was evaluated. • XPS, DWCA, immunostaining and ToF-SIMS (imaging and depth profiling) techniques were applied. • Potential for cardiovascular applications was showed by endothelial cell and blood interactions. - Abstract: Coating medical devices with several bioactive molecules is an interesting approach to achieve specific biological targets upon the interaction of the biomaterial with the living environment. In this work, a fluorocarbon polymer (CF{sub x}) was first deposited by plasma treatment on stainless steel (SS) substrate and thereafter, coatings containing fibronectin (FN) and phosphorylcholine (PRC) were created for cardiovascular applications. These two biomolecules were chosen to promote endothelialization and to avoid thrombus formation, respectively. Adsorption and grafting techniques were applied – and combined – to accomplish 4 different coatings containing both molecules. However, big challenge was found to characterize a small molecule (PRC: 184 g/mol) interacting with a protein (FN: 450 kD). For the first time XPS, dynamic water contact angle, immunostaining and ToF-SIMS (imaging and depth profiling) analyses were combined to accomplish the characterization of such a coating. The most encouraging biological performances were obtained for samples where FN was grafted to the CF{sub x} film followed by the adsorption of PRC: proliferation of endothelial cells and hemocompatibility properties were observed. Promising coatings for cardiovascular applications were developed. The relevance of characterizing the coatings with high sensitive techniques and the further correlation with their biological performances were evidenced.

  12. Silk-based biomaterials functionalized with fibronectin type II promotes cell adhesion.

    Science.gov (United States)

    Pereira, Ana Margarida; Machado, Raul; da Costa, André; Ribeiro, Artur; Collins, Tony; Gomes, Andreia C; Leonor, Isabel B; Kaplan, David L; Reis, Rui L; Casal, Margarida

    2017-01-01

    The objective of this work was to exploit the fibronectin type II (FNII) module from human matrix metalloproteinase-2 as a functional domain for the development of silk-based biopolymer blends that display enhanced cell adhesion properties. The DNA sequence of spider dragline silk protein (6mer) was genetically fused with the FNII coding sequence and expressed in Escherichia coli. The chimeric protein 6mer+FNII was purified by non-chromatographic methods. Films prepared from 6mer+FNII by solvent casting promoted only limited cell adhesion of human skin fibroblasts. However, the performance of the material in terms of cell adhesion was significantly improved when 6mer+FNII was combined with a silk-elastin-like protein in a concentration-dependent behavior. With this work we describe a novel class of biopolymer that promote cell adhesion and potentially useful as biomaterials for tissue engineering and regenerative medicine. This work reports the development of biocompatible silk-based composites with enhanced cell adhesion properties suitable for biomedical applications in regenerative medicine. The biocomposites were produced by combining a genetically engineered silk-elastin-like protein with a genetically engineered spider-silk-based polypeptide carrying the three domains of the fibronectin type II module from human metalloproteinase-2. These composites were processed into free-standing films by solvent casting and characterized for their biological behavior. To our knowledge this is the first report of the exploitation of all three FNII domains as a functional domain for the development of bioinspired materials with improved biological performance. The present study highlights the potential of using genetically engineered protein-based composites as a platform for the development of new bioinspired biomaterials. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  13. Exonic variants associated with development of aspirin exacerbated respiratory diseases.

    Directory of Open Access Journals (Sweden)

    Seung-Woo Shin

    Full Text Available Aspirin-exacerbated respiratory disease (AERD is one phenotype of asthma, often occurring in the form of a severe and sudden attack. Due to the time-consuming nature and difficulty of oral aspirin challenge (OAC for AERD diagnosis, non-invasive biomarkers have been sought. The aim of this study was to identify AERD-associated exonic SNPs and examine the diagnostic potential of a combination of these candidate SNPs to predict AERD. DNA from 165 AERD patients, 397 subjects with aspirin-tolerant asthma (ATA, and 398 normal controls were subjected to an Exome BeadChip assay containing 240K SNPs. 1,023 models (210-1 were generated from combinations of the top 10 SNPs, selected by the p-values in association with AERD. The area under the curve (AUC of the receiver operating characteristic (ROC curves was calculated for each model. SNP Function Portal and PolyPhen-2 were used to validate the functional significance of candidate SNPs. An exonic SNP, exm537513 in HLA-DPB1, showed the lowest p-value (p = 3.40×10-8 in its association with AERD risk. From the top 10 SNPs, a combination model of 7 SNPs (exm537513, exm83523, exm1884673, exm538564, exm2264237, exm396794, and exm791954 showed the best AUC of 0.75 (asymptotic p-value of 7.94×10-21, with 34% sensitivity and 93% specificity to discriminate AERD from ATA. Amino acid changes due to exm83523 in CHIA were predicted to be "probably damaging" to the structure and function of the protein, with a high score of '1'. A combination model of seven SNPs may provide a useful, non-invasive genetic marker combination for predicting AERD.

  14. Exon microarray analysis of human dorsolateral prefrontal cortex in alcoholism.

    Science.gov (United States)

    Manzardo, Ann M; Gunewardena, Sumedha; Wang, Kun; Butler, Merlin G

    2014-06-01

    Alcohol abuse is associated with cellular and biochemical disturbances that impact upon protein and nucleic acid synthesis, brain development, function, and behavioral responses. To further characterize the genetic influences in alcoholism and the effects of alcohol consumption on gene expression, we used a highly sensitive exon microarray to examine mRNA expression in human frontal cortex of alcoholics and control males. Messenger RNA was isolated from the dorsolateral prefrontal cortex (dlPFC; Brodmann area 9) of 7 adult alcoholic (6 males, 1 female, mean age 49 years) and 7 matched controls. Affymetrix Human Exon 1.0 ST array was performed according to standard procedures and the results analyzed at the gene level. Microarray findings were validated using quantitative reverse transcription polymerase chain reaction, and the ontology of disturbed genes characterized using Ingenuity Pathway Analysis (IPA). Decreased mRNA expression was observed for genes involved in cellular adhesion (e.g., CTNNA3, ITGA2), transport (e.g., TF, ABCA8), nervous system development (e.g., LRP2, UGT8, GLDN), and signaling (e.g., RASGRP3, LGR5) with influence over lipid and myelin synthesis (e.g., ASPA, ENPP2, KLK6). IPA identified disturbances in network functions associated with neurological disease and development including cellular assembly and organization impacting on psychological disorders. Our data in alcoholism support a reduction in expression of dlPFC mRNA for genes involved with neuronal growth, differentiation, and signaling that targets white matter of the brain. Copyright © 2014 by the Research Society on Alcoholism.

  15. Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

    Directory of Open Access Journals (Sweden)

    Charles W Sugnet

    2006-01-01

    Full Text Available Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families.

  16. Determination of exon 7 SMN1 deletion in Iranian patients and ...

    Indian Academy of Sciences (India)

    DNA. Further, a segment of the albumin gene, exon 12, was chosen by optimization which had similar amplification effi- ciency during log-linear phase compared to the target SMN1 exon 7 DNA segment. The quantitative real-time PCR assay utilized primers that specifically amplified SMN1 gene. To distinguish SMN1 from.

  17. The role of exon shuffling in shaping protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    França Gustavo S

    2010-12-01

    Full Text Available Abstract Background Physical protein-protein interaction (PPI is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains, self-interacting (able to interact with another copy of themselves and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

  18. Cure and guard. Chronicity in Insane Asylum La Castañeda, Mexico City, 1910-1968

    Directory of Open Access Journals (Sweden)

    Cristina Sacristán

    2017-12-01

    Full Text Available The article questions the binomial that associates the chronicity and incurability of mental illness with the custodialism of the asylum through a case study, Asylum La Castañeda in Mexico, from 1910 to 1968. We contrast the discourses about the cure and chronicity constructed by Mexican psychiatrists and the statistical trends of patients admitted: new admissions, readmissions, discharges, length of stay, and diagnoses in the light of new treatments. We concluded that according to the doctors, the asylum therapeutic function was severely affected by chronicity and overpopulation, but according to statistics, 80% of the patients had only one admission with a 15-month hospitalization and the long-term confinement rates of readmissions did not impact statistically; two-thirds of the patients left the asylum, and since the 1950s in the context of new therapeutics.

  19. Data Management in Scholarly Journals and Possible Roles for Libraries – Some Insights from EDaWaX

    Directory of Open Access Journals (Sweden)

    Sven Vlaeminck

    2013-06-01

    Full Text Available In this paper we summarize the findings of an empirical study conducted by the EDaWaX-Project. 141 economics journals were examined regarding the quality and extent of data availability policies that should support replications of published empirical results in economics. This paper suggests criteria for such policies that aim to facilitate replications. These criteria were also used for analysing the data availability policies we found in our sample and to identify best practices for  data policies of scholarly journals in economics. In addition, we also evaluated the journals’ data archives and checked the percentage of articles associated with research data. To conclude, an appraisal as to how scientific libraries might support the linkage of publications to underlying research data in cooperation with researchers, editors, publishers and data centres is presented.

  20. The Impact of Assimilating Precipitation-affected Radiance on Cloud and Precipitation in Goddard WRF-EDAS Analyses

    Science.gov (United States)

    Lin, Xin; Zhang, Sara Q.; Zupanski, M.; Hou, Arthur Y.; Zhang, J.

    2015-01-01

    High-frequency TMI and AMSR-E radiances, which are sensitive to precipitation over land, are assimilated into the Goddard Weather Research and Forecasting Model- Ensemble Data Assimilation System (WRF-EDAS) for a few heavy rain events over the continental US. Independent observations from surface rainfall, satellite IR brightness temperatures, as well as ground-radar reflectivity profiles are used to evaluate the impact of assimilating rain-sensitive radiances on cloud and precipitation within WRF-EDAS. The evaluations go beyond comparisons of forecast skills and domain-mean statistics, and focus on studying the cloud and precipitation features in the jointed rainradiance and rain-cloud space, with particular attentions on vertical distributions of height-dependent cloud types and collective effect of cloud hydrometers. Such a methodology is very helpful to understand limitations and sources of errors in rainaffected radiance assimilations. It is found that the assimilation of rain-sensitive radiances can reduce the mismatch between model analyses and observations by reasonably enhancing/reducing convective intensity over areas where the observation indicates precipitation, and suppressing convection over areas where the model forecast indicates rain but the observation does not. It is also noted that instead of generating sufficient low-level warmrain clouds as in observations, the model analysis tends to produce many spurious upperlevel clouds containing small amount of ice water content. This discrepancy is associated with insufficient information in ice-water-sensitive radiances to address the vertical distribution of clouds with small amount of ice water content. Such a problem will likely be mitigated when multi-channel multi-frequency radiances/reflectivity are assimilated over land along with sufficiently accurate surface emissivity information to better constrain the vertical distribution of cloud hydrometers.

  1. BB0347, from the lyme disease spirochete Borrelia burgdorferi, is surface exposed and interacts with the CS1 heparin-binding domain of human fibronectin.

    Directory of Open Access Journals (Sweden)

    Robert A Gaultney

    Full Text Available The causative agent of Lyme disease, Borrelia burgdorferi, codes for several known fibronectin-binding proteins. Fibronectin a common the target of diverse bacterial pathogens, and has been shown to be essential in allowing for the development of certain disease states. Another borrelial protein, BB0347, has sequence similarity with these other known fibronectin-binding proteins, and may be important in Lyme disease pathogenesis. Herein, we perform an initial characterization of BB0347 via the use of molecular and biochemical techniques. We found that BB0347 is expressed, produced, and presented on the outer surface of intact B. burgdorferi. We also demonstrate that BB0347 has the potential to be important in Lyme disease progression, and have begun to characterize the nature of the interaction between human fibronectin and this bacterial protein. Further work is needed to define the role of this protein in the borrelial infection process.

  2. Clinical and molecular consequences of exon 78 deletion in DMD gene.

    Science.gov (United States)

    Traverso, Monica; Assereto, Stefania; Baratto, Serena; Iacomino, Michele; Pedemonte, Marina; Diana, Maria Cristina; Ferretti, Marta; Broda, Paolo; Minetti, Carlo; Gazzerro, Elisabetta; Madia, Francesca; Bruno, Claudio; Zara, Federico; Fiorillo, Chiara

    2018-03-19

    We present a 13-year-old patient with persistent increase of serum Creatine Kinase (CK) and myalgia after exertion. Skeletal muscle biopsy showed marked reduction of dystrophin expression leading to genetic analysis of DMD gene by MLPA, which detected a single deletion of exon 78. To the best of our knowledge, DMD exon 78 deletion has never been described in literature and, according to prediction, it should lead to loss of reading frame in the dystrophin gene. To further assess the actual effect of exon 78 deletion, we analysed cDNA from muscle mRNA. This analysis confirmed the absence of 32 bp of exon 78. Exclusion of exon 78 changes the open reading frame of exon 79 and generate a downstream stop codon, producing a dystrophin protein of 3703 amino acids instead of 3685 amino acids. Albeit loss of reading frame usually leads to protein degradation and severe phenotype, in this case, we demonstrated that deletion of DMD exon 78 can be associated with a functional protein able to bind DGC complex and a very mild phenotype. This study adds a novel deletion in DMD gene in human and helps to define the compliance between maintaining/disrupting the reading frame and clinical form of the disease.

  3. The identification of exons from the MED/PSACH region of human chromosome 19

    Energy Technology Data Exchange (ETDEWEB)

    Li, Quan-Yi; Brook, J.D. [Univ. of Nottingham (United Kingdom); Lennon, G.G. [Lawrence Livermore National Lab., Livermore, CA (United States)

    1996-03-01

    We have used exon amplification to identify putative transcribed sequences from an 823-kb contig consisting of 28 cosmids that form a minimum tiling path from the interval 19p12-p13.1. This region contains the genes responsible for multiple epiphyseal dysplasia (MED) and pseudoachondroplasia (PSACH). We have trapped 66 exons (an average of 2.4 exons per cosmid) from pools of 2 or 3 cosmids. The majority of exons (51.5%) show only weak similarity or no similarity (36.3%) to sequences in current databases. Six of 8 exons examined from these groups, however, show cross-species sequence conservation, indicating that many of them probably represent authentic exons. Eight exons show identity or significant similarity to ESTs or known genes, including the human TNF receptor 3{prime}-flanking region gene, human epoxide hydrolase (EPHX), human growth/differentiation factor (GOF-1), human myocyte-specific enhancer factor 2, the rat neurocan gene, and the human cartilage oligomeric matrix protein gene (COMP). Mutations in this latter gene have recently been shown to be responsible for MED and PSACH. 33 refs., 4 figs., 2 tabs.

  4. Identification, characterization and expression of novel Sex Hormone Binding Globulin alternative first exons in the human prostate

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    de Torres Inés

    2009-06-01

    Full Text Available Abstract Background The human Sex Hormone Binding Globulin (SHBG gene, located at 17p13.1, comprises, at least, two different transcription units regulated by two different promoters. The first transcription unit begins with the exon 1 sequence and is responsible for the production of plasma SHBG by the hepatocytes, while the second begins with an alternative exon 1 sequence, which replaces the exon 1 present in liver transcripts. Alternative exon 1 transcription and translation has only been demonstrated in the testis of transgenic mice containing an 11-kb human SHBG transgene and in the human testis. Our goal has been to further characterize the 5' end of the SHBG gene and analyze the presence of the SHBG alternative transcripts in human prostate tissue and derived cell lines. Results Using a combination of in silico and in vitro studies, we have demonstrated that the SHBG gene, along with exon 1 and alternative exon 1 (renamed here exon 1A, contains four additional alternative first exons: the novel exons 1B, 1C, and 1E, and a previously identified exon 1N, which has been further characterized and renamed as exon 1D. We have shown that these four alternative first exons are all spliced to the same 3' splice site of SHBG exon 2, and that exon 1A and the novel exon 1B can be spliced to exon 1. We have also demonstrated the presence of SHBG transcripts beginning with exons 1B, 1C and 1D in prostate tissues and cell lines, as well as in several non-prostatic cell lines. Finally, the alignment of the SHBG mammalian sequences revealed that, while exons 1C, 1D and 1E are very well conserved phylogenetically through non-primate mammal species, exon 1B probably aroused in apes due to a single nucleotide change that generated a new 5' splice site in exon 1B. Conclusion The identification of multiple transcription start sites (TSS upstream of the annotated first exon of human SHBG, and the detection of the alternative transcripts in human prostate

  5. Sequence variations of the MHC class I gene exon 2 and exon 3 between infected and uninfected chickens challenged with Marek's disease virus.

    Science.gov (United States)

    Wang, Ye; Qiu, Mohan; Yang, Jiandong; Zhao, Xiaoling; Wang, Yan; Zhu, Qing; Liu, Yiping

    2014-01-01

    The major histocompatibility complex (MHC) among chickens has been well established as being associated with disease resistance and pathogens infection, but the genetic differences in MHC between chickens susceptible to certain infections and those chickens that remain uninfected have not been sufficiently determined. In this study, we sought the genetic basis that may underlie differences in susceptibility to infection among chickens by challenging four groups of broilers with Marek's disease virus (MDV). Over the course of the experiment, lesions began to appear between 21 and 35 days post challenge (dpc), and commercial broilers were not necessarily better than indigenous chickens in terms of disease resistance. The four groups showed neutral resistance to MDV infection validated by challenge results and evolutionary analysis of exons 2 and 3 of the MHC class I region. Several variable sites in exon 2 and exon 3 were exclusively appeared in infected chickens. Exon 3 was likely more crucial than exon 2 in disease resistance. Our observations offered a support for a potential association between promiscuous pathogens and conspicuous genetic diversity in the MHC class I region. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Tracking the evolution of alternatively spliced exons within the Dscam family

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    Vision Todd J

    2006-02-01

    Full Text Available Abstract Background The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17, potentially generating 38,016 protein isoforms. This degree of transcript diversity has not been found in mammalian homologs of Dscam. We examined the molecular evolution of exons within this gene family to locate the point of divergence for this alternative splicing pattern. Results Using the fruit fly Dscam exons 4, 6, 9 and 17 as seed sequences, we iteratively searched sixteen genomes for homologs, and then performed phylogenetic analyses of the resulting sequences to examine their evolutionary history. We found homologs in the nematode, arthropod and vertebrate genomes, including homologs in several vertebrates where Dscam had not been previously annotated. Among these, only the arthropods contain homologs arranged in tandem arrays indicative of mutually exclusive splicing. We found no homologs to these exons within the Arabidopsis, yeast, tunicate or sea urchin genomes but homologs to several constitutive exons from fly Dscam were present within tunicate and sea urchin. Comparing the rate of turnover within the tandem arrays of the insect taxa (fruit fly, mosquito and honeybee, we found the variants within exons 4 and 17 are well conserved in number and spatial arrangement despite 248–283 million years of divergence. In contrast, the variants within exons 6 and 9 have undergone considerable turnover since these taxa diverged, as indicated by deeply branching taxon-specific lineages. Conclusion Our results suggest that at least one Dscam exon array may be an ancient duplication that predates the divergence of deuterostomes from protostomes but that there is no evidence for the presence of arrays in the common ancestor of vertebrates. The different patterns of conservation and turnover among the Dscam exon arrays

  7. H-1 and N-15 resonance assignment of the second fibronectin type III module of the neural cell adhesion molecule

    DEFF Research Database (Denmark)

    Kiselyov, Vladislav V; Berezin, Vladimir; Bock, Elisabeth

    2008-01-01

    We report here the NMR assignment of the second fibronectin type III module of the neural cell adhesion molecule (NCAM). This module has previously been shown to interact with the fibroblast growth factor receptor (FGFR), and the FGFR-binding site was mapped by NMR to the FG-loop region of the mo......We report here the NMR assignment of the second fibronectin type III module of the neural cell adhesion molecule (NCAM). This module has previously been shown to interact with the fibroblast growth factor receptor (FGFR), and the FGFR-binding site was mapped by NMR to the FG-loop region...... of the module. The FG-loop region also contains a putative nucleotide-binding motif, which was shown by NMR to interact with ATP. Furthermore, ATP was demonstrated to inhibit binding of the second F3 module of NCAM to FGFR....

  8. Shotgun Proteomics Identifies Serum Fibronectin as a Candidate Diagnostic Biomarker for Inclusion in Future Multiplex Tests for Ectopic Pregnancy

    Science.gov (United States)

    Brown, Jeremy K.; Lauer, Katarina B.; Ironmonger, Emily L.; Inglis, Neil F.; Bourne, Tom H.; Critchley, Hilary O. D.; Horne, Andrew W.

    2013-01-01

    Ectopic pregnancy (EP) is difficult to diagnose early and accurately. Women often present at emergency departments in early pregnancy with a ‘pregnancy of unknown location’ (PUL), and diagnosis and exclusion of EP is challenging due to a lack of reliable biomarkers. The objective of this study was to identify novel diagnostic biomarkers for EP. Shotgun proteomics, incorporating combinatorial-ligand library pre-fractionation, was used to interrogate pooled sera (n = 40) from women undergoing surgery for EP, termination of viable intrauterine pregnancy and management of non-viable intrauterine pregnancy. Western blot was used to validate results in individual sera. ELISAs were developed to interrogate sera from women with PUL (n = 120). Sera were collected at time of first symptomatic presentation and categorized according to pregnancy outcome. The main outcome measures were differences between groups and area under the receiver operating curve (ROC). Proteomics identified six biomarker candidates. Western blot detected significant differences in levels of two of these candidates. ELISA of sera from second cohort revealed that these differences were only significant for one of these candidates, fibronectin. ROC analysis of ability of fibronectin to discriminate EP from other pregnancy outcomes suggested that fibronectin has diagnostic potential (ROC 0.6439; 95% CI 0.5090 to 0.7788; P>0.05), becoming significant when ‘ambiguous’ medically managed PUL excluded from analysis (ROC 0.6538; 95% CI 0.5158 to 0.7918; P<0.05). Fibronectin may make a useful adjunct to future multiplex EP diagnostic tests. PMID:23826180

  9. Increased expression of fibronectin and the α5β1 integrin in angiogenic cerebral blood vessels of mice subject to hypobaric hypoxia

    Science.gov (United States)

    Milner, Richard; Hung, Stephanie; Erokwu, Bernadette; Dore-Duffy, Paula; LaManna, Joseph C.; del Zoppo, Gregory J.

    2008-01-01

    The extracellular matrix (ECM) is an important regulator of angiogenesis and vascular remodeling. We showed previously that angiogenic capillaries in the developing CNS express high levels of fibronectin and its receptor α5β1 integrin, and that this expression is developmentally downregulated. As cerebral hypoxia leads to an angiogenic response, we sought to determine whether angiogenic vessels in the adult CNS re-express fibronectin and the α5β1 integrin. Ten-week old mice were subject to hypobaric hypoxia for 0, 4, 7 and 14 days, and fibronectin/integrin expression examined. Fibronectin and the α5 integrin subunit were strongly upregulated on capillaries in the hypoxic CNS, with the effect maximal at the earliest time point examined (4 days). Immunofluorescent studies demonstrated that the α5 integrin was expressed by angiogenic endothelial cells. In light of the defined angiogenic role for fibronectin in other systems, this work suggests that induction of fibronectin-α5β1 integrin expression may be an important molecular switch driving angiogenesis in the hypoxic CNS. PMID:18343155

  10. The effect of Centella asiatica, vitamins, glycolic acid and their mixtures preparations in stimulating collagen and fibronectin synthesis in cultured human skin fibroblast.

    Science.gov (United States)

    Hashim, Puziah

    2014-03-01

    Centella asiatica (Linn.) Urban is well known in promoting wound healing and provides significant benefits in skin care and therapeutic products formulation. Glycolic acid and vitamins also play a role in the enhancement of collagen and fibronectin synthesis. Here, we evaluate the specific effect of Centella asiatica (CA), vitamins, glycolic acid and their mixture preparations to stimulate collagen and fibronectin synthesis in cultured human fibroblast cells. The fibroblast cells are incubated with CA, glycolic acid, vitamins and their mixture preparations for 48 h. The cell lysates were analyzed for protein content and collagen synthesis by direct binding enzyme immunoassay. The fibronectin of the cultured supernatant was measured by sandwich enzyme immunoassay. The results showed that CA, glycolic acid, vitamins A, E and C significantly stimulate collagen and fibronectin synthesis in the fibroblast. Addition of glycolic acid and vitamins to CA further increased the levels of collagen and fibronectin synthesis to 8.55 and 23.75 μg/100 μg, respectively. CA, glycolic acid, vitamins A, E, and C, and their mixtures demonstrated stimulatory effect on both extra-cellular matrix synthesis of collagen and fibronectin in in vitro studies on human foreskin fibroblasts, which is beneficial to skin care and therapeutic products formulation.

  11. Familial MTC with RET exon 8 Gly533Cys mutation: origin and prevalence of second malignancy

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    Katerina Saltiki

    2017-10-01

    Full Text Available Introduction: High prevalence of RET p.Gly533Cys (c.1597G > T has been found in familial MTC in Greece (exon 8 fMTC. We studied their origin and compared clinical characteristics with non-exon 8 fMTC. Methods: 102 fMTC (FMTC and MEN2A patients (31.4% males were followed for 2.9–37 years (median 6 years. Fifty-one carried the RET exon 8 mutation; the remaining were non-exon 8 fMTC (exons 10, 11, 13, 14. Pre-, post-operative calcitonin, disease extent at diagnosis and follow-up and families’ place of origin were recorded. Results: Exon 8 fMTC were older (42.3 ± 13.3 vs 30.8 ± 17.8 years, P < 0.001, including index cases (P = 0.016. In index cases, the stage at diagnosis was more favorable in exon 8 fMTC compared to non-exon 8 fMTC (stage I and II: 65% vs 23.8%, stage III: 25% vs 57.1%, stage IV: 10% vs 19%, P = 0.025. More favorable outcome was noted in exon 8 fMTCs (remission: 72.5% vs 45.8%, stable disease: 27.5% vs 41.7%, progression: 0.0% vs 12.5%, P = 0.001. Exon 8 fMTC patients carried more frequently a second malignancy (25.5% vs 6.3%, P = 0.009; 69% of these were PTCs. Exon 8 fMTC patients were significantly older at diagnosis compared to non-exon 8 moderate-risk RET carriers and presented more favorable clinical outcome (remission: 72.5% vs 50%, stable disease: 27.5% vs 41.7%, progression: 0.0% vs 8.3%, P = 0.021. This difference remained when only index cases were analyzed. ‘Hot spots’ in the origin of exon 8 fMTCs families were recognized. No phenotype or outcome differences were found between the exon 8 families from the various regions. Conclusions: In exon 8 fMTCs’ older age, favorable disease stage at diagnosis and favorable outcome suggest slow disease progression compared to non-exon 8 fMTC. Compared with moderate-risk RET mutation carriers, exon 8 fMTC patients have a more favorable clinical outcome. The higher prevalence of second malignancies, especially PTC, not previously reported, merits further investigation

  12. Structural and functional analysis of an anchorless fibronectin-binding protein FBPS from Gram-positive bacterium Streptococcus suis.

    Science.gov (United States)

    Musyoki, Abednego Moki; Shi, Zhongyu; Xuan, Chunling; Lu, Guangwen; Qi, Jianxun; Gao, Feng; Zheng, Beiwen; Zhang, Qiangmin; Li, Yan; Haywood, Joel; Liu, Cuihua; Yan, Jinghua; Shi, Yi; Gao, George F

    2016-11-29

    The anchorless fibronectin-binding proteins (FnBPs) are a group of important virulence factors for which the structures are not available and the functions are not well defined. In this study we performed comprehensive studies on a prototypic member of this group: the fibronectin-/fibrinogen-binding protein from Streptococcus suis (FBPS). The structures of the N- and C-terminal halves (FBPS-N and FBPS-C), which together cover the full-length protein in sequence, were solved at a resolution of 2.1 and 2.6 Å, respectively, and each was found to be composed of two domains with unique folds. Furthermore, we have elucidated the organization of these domains by small-angle X-ray scattering. We further showed that the fibronectin-binding site is located in FBPS-C and that FBPS promotes the adherence of S suis to host cells by attaching the bacteria via FBPS-N. Finally, we demonstrated that FBPS functions both as an adhesin, promoting S suis attachment to host cells, and as a bacterial factor, activating signaling pathways via β1 integrin receptors to induce chemokine production.

  13. Fibronectin is essential for reparative cardiac progenitor cell response after myocardial infarction.

    Science.gov (United States)

    Konstandin, Mathias H; Toko, Haruhiro; Gastelum, Grady M; Quijada, Pearl; De La Torre, Andrea; Quintana, Mercedes; Collins, Brett; Din, Shabana; Avitabile, Daniele; Völkers, Mirko; Gude, Natalie; Fässler, Reinhard; Sussman, Mark A

    2013-07-05

    Adoptive transfer of cardiac progenitor cells (CPCs) has entered clinical application, despite limited mechanistic understanding of the endogenous response after myocardial infarction (MI). Extracellular matrix undergoes dramatic changes after MI and therefore might be linked to CPC-mediated repair. To demonstrate the significance of fibronectin (Fn), a component of the extracellular matrix, for induction of the endogenous CPC response to MI. This report shows that presence of CPCs correlates with the expression of Fn during cardiac development and after MI. In vivo, genetic conditional ablation of Fn blunts CPC response measured 7 days after MI through reduced proliferation and diminished survival. Attenuated vasculogenesis and cardiogenesis during recovery were evident at the end of a 12-week follow-up period. Impaired CPC-dependent reparative remodeling ultimately leads to continuous decline of cardiac function in Fn knockout animals. In vitro, Fn protects and induces proliferation of CPCs via β₁-integrin-focal adhesion kinase-signal transducer and activator of transcription 3-Pim1 independent of Akt. Fn is essential for endogenous CPC expansion and repair required for stabilization of cardiac function after MI.

  14. Fibronectin is Essential for Reparative Cardiac Progenitor Cell Response Following Myocardial Infarction

    Science.gov (United States)

    Konstandin, Mathias H.; Toko, Haruhiro; Gastelum, Grady M.; Quijada, Pearl; De La Torre, Andrea; Quintana, Mercedes; Collins, Brett; Din, Shabana; Avitabile, Daniele; Völkers, Mirko; Gude, Natalie; Fässler, Reinhard; Sussman, Mark A.

    2013-01-01

    Rationale Adoptive transfer of cardiac progenitor cells (CPCs) has entered clinical application despite limited mechanistic understanding of the endogenous response following myocardial infarction (MI). Extracellular matrix (ECM) undergoes dramatic changes after MI and therefore might be linked to CPC-mediated repair. Objective Demonstrate the significance of Fibronectin (Fn), a component of the ECM, for induction of the endogenous CPC response to MI. Methods and Results This report shows that presence of CPCs correlates with expression of Fn during cardiac development and after MI. In vivo, genetic conditional ablation of Fn blunts CPC response measured 7 days after MI through reduced proliferation and diminished survival. Attenuated vasculogenesis and cardiogenesis during recovery was evident at the end of a 12 week follow-up period. Impaired CPC-dependent reparative remodeling ultimately leads to continuous decline of cardiac function in Fn knockout animals. In vitro, Fn protects and induces proliferation of CPCs via β1-Integrin-FAK-Stat3-Pim1 but Akt-independent mechanism. Conclusion Fn is essential for endogenous CPC expansion and repair needed for stabilization of cardiac function after MI. PMID:23652800

  15. Synergistic Interactions of a Synthetic Lubricin-Mimetic with Fibronectin for Enhanced Wear Protection

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    Roberto C. Andresen Eguiluz

    2017-06-01

    Full Text Available Lubricin (LUB, a major mucinous glycoprotein of mammalian synovial fluids, is believed to provide excellent lubrication to cartilage surfaces. Consequently, when joint disease or replacement leads to increased friction and surface damage in the joint, robust synthetic LUB alternatives that could be used therapeutically to improve lubrication and surface protection are needed. Here, we report the characterization of a lubricating multiblock bottlebrush polymer whose architecture was inspired by LUB, and we investigate the role of fibronectin (FN, a glycoprotein found in the superficial zone of cartilage, in mediating the tribological properties of the polymer upon shear between mica surfaces. Our surface forces apparatus (SFA normal force measurements indicate that the lubricin-mimetic (mimLUB could be kept anchored between mica surfaces, even under high contact pressures, when an intermediate layer of FN was present. Additional SFA friction measurements show that FN would also extend the wearless friction regime of the polymer up to pressures of 3.4 MPa while ensuring stable friction coefficients (μ ≈ 0.28. These results demonstrate synergistic interactions between mimLUB and FN in assisting the lubrication and wear protection of ideal (mica substrates upon shear. Collectively, these findings suggest that our proposed mimLUB might be a promising alternative to LUB, as similar mechanisms could potentially facilitate the interaction between the polymer and cartilage surfaces in articular joints and prosthetic implants in vivo.

  16. Stimulatory effects of advanced glycation endproducts (AGEs) on fibronectin matrix assembly.

    Science.gov (United States)

    Pastino, Alexandra K; Greco, Todd M; Mathias, Rommel A; Cristea, Ileana M; Schwarzbauer, Jean E

    2017-05-01

    Advanced glycation endproducts (AGEs) are a heterogeneous group of compounds that form via non-enzymatic glycation of proteins throughout our lifespan and at a higher rate in certain chronic diseases such as diabetes. AGEs contribute to the progression of fibrosis, in part by stimulating cellular pathways that affect gene expression. Long-lived ECM proteins are targets for non-enzymatic glycation but the question of whether the AGE-modified ECM leads to excess ECM accumulation and fibrosis remains unanswered. In this study, cellular changes due to AGE accretion in the ECM were investigated. Non-enzymatic glycation of proteins in a decellularized fibroblast ECM was achieved by incubating the ECM in a solution of methylglyoxal (MGO). Mass spectrometry of fibronectin (FN) isolated from the glycated matrix identified twenty-eight previously unidentified MGO-derived AGE modification sites including functional sites such as the RGD integrin-binding sequence. Mesangial cells grown on the glycated, decellularized matrix assembled increased amounts of FN matrix. Soluble AGE-modified bovine serum albumin (BSA) also stimulated FN matrix assembly and this effect was reduced by function-blocking antibodies against the receptor for AGE (RAGE). These results indicate that cells respond to AGEs by increasing matrix assembly and that RAGE is involved in this response. This raises the possibility that the accumulation of ECM during the progression of fibrosis may be enhanced by cell interactions with AGEs on a glycated ECM. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Fibronectin peptides that bind PDGF-BB enhance survival of cells and tissue under stress

    Science.gov (United States)

    Lin, Fubao; Zhu, Jia; Tonnesen, Marcia G.; Taira, Breena R.; McClain, Steve A.; Singer, Adam J.; Clark, Richard A.F.

    2013-01-01

    Stressors after injury from a multitude of factors can lead to cell death. We have identified four fibronectin (FN) peptides, two from the first FN type III repeat (FNIII1), one from the 13th FN type III repeat (FNIII13), and one from FN variable region (IIICS), that when tethered to a surface acted as platelet-derived growth factor-BB (PDGF-BB) enhancers to promote cell survival. One of the FNIII1 peptides and its smallest (14mer) bioactive form (P12) were also active in solution. Specifically, P12 bound PDGF-BB (KD = 200nM), enhanced adult human dermal fibroblast (AHDF) survival under serum starvation, oxidative or endoplasmic reticulum (ER) stressors, and limited burn injury progression in a rat hot comb model. Furthermore, P12 inhibited ER stress-induced c-Jun N-terminal kinase (JNK) activation. Although many growth factors have been found to bind FN directly or indirectly, this is the first report to identify peptide sequences of growth factor-binding sites in FN. The finding of these novel peptides further delineated how the extracellular matrix protein FN can support cell survival. Since the peptide P12 is active in either soluble form or tethered to a substrate, it will have multifactorial uses as a bioactive in tissue engineering. PMID:24126844

  18. Biocompatibility and Favorable Response of Mesenchymal Stem Cells on Fibronectin-Gold Nanocomposites

    Science.gov (United States)

    Hung, Huey-Shan; Tang, Cheng-Ming; Lin, Chien-Hsun; Lin, Shinn-Zong; Chu, Mei-Yun; Sun, Wei-Shen; Kao, Wei-Chien; Hsien-Hsu, Hsieh

    2013-01-01

    A simple surface modification method, comprising of a thin coating with gold nanoparticles (AuNPs) and fibronectin (FN), was developed to improve the biocompatibility required for cardiovascular devices. The nanocomposites from FN and AuNPs (FN-Au) were characterized by the atomic force microscopy (AFM), UV-Vis spectrophotometry (UV-Vis), and Fourier transform infrared spectroscopy (FTIR). The biocompatibility of the nanocomposites was evaluated by the response of monocytes and platelets to the material surface in vitro. FN-Au coated surfaces demonstrated low monocyte activation and platelet activation. The behavior of human umbilical cord-derived mesenchymal stem cells (MSCs) on FN-Au was further investigated. MSCs on FN-Au nanocomposites particularly that containing 43.5 ppm of AuNPs (FN-Au 43.5 ppm) showed cell proliferation, low ROS generation, as well as increases in the protein expression levels of matrix metalloproteinase-9 (MMP-9) and endothelial nitric oxide synthase (eNOS), which may account for the enhanced MSC migration on the nanocomposites. These results suggest that the FN-Au nanocomposite thin film coating may serve as a potential and simple solution for the surface modification of blood-contacting devices such as vascular grafts. PMID:23826082

  19. Evaluation of a quantitative fetal fibronectin test for spontaneous preterm birth in symptomatic women.

    Science.gov (United States)

    Abbott, Danielle S; Radford, Samara K; Seed, Paul T; Tribe, Rachel M; Shennan, Andrew H

    2013-02-01

    The purpose of this study was to determine whether quantification of cervicovaginal fluid fetal fibronectin (fFN) improves diagnostic accuracy of spontaneous preterm birth (sPTB) in symptomatic women. A prospective blinded predefined secondary analysis of a larger study of cervicovaginal fluid fFN concentration (nanograms per milliliter) in women symptomatic of preterm labor (n =300 women; 22-35 weeks' gestation) with a Hologic 10Q system (Hologic, Marlborough, MA). Clinicians were blinded to the result until after the delivery, but the qualitative Hologic TLI(IQ) fFN result was made available. The positive predictive value for sPTB (<34 weeks' gestation) increased from 19%, 32%, 61%, and 75% with increasing thresholds (10, 50, 200, and 500 ng/mL, respectively). Compared with <10 ng/mL fFN, the relative risk of delivery was 5.6 (95% confidence interval [CI], 1.05-29.57), 7.9 (95% CI, 1.38-45.0), 22.8 (95% CI, 3.84-135.5), and 51.3 (95% CI, 12.49-211.2; P < .01). Quantitative fFN provides thresholds (10 and 200 ng/mL) in addition to the qualitative method (50 ng/mL) to discriminate the risk of sPTB in symptomatic women. Copyright © 2013 Mosby, Inc. All rights reserved.

  20. The fibronectin synergy site re-enforces cell adhesion and mediates a crosstalk between integrin classes.

    Science.gov (United States)

    Benito-Jardón, Maria; Klapproth, Sarah; Gimeno-LLuch, Irene; Petzold, Tobias; Bharadwaj, Mitasha; Müller, Daniel J; Zuchtriegel, Gabriele; Reichel, Christoph A; Costell, Mercedes

    2017-01-16

    Fibronectin (FN), a major extracellular matrix component, enables integrin-mediated cell adhesion via binding of α5β1, αIIbβ3 and αv-class integrins to an RGD-motif. An additional linkage for α5 and αIIb is the synergy site located in close proximity to the RGD motif. We report that mice with a dysfunctional FN-synergy motif ( Fn1 syn/syn ) suffer from surprisingly mild platelet adhesion and bleeding defects due to delayed thrombus formation after vessel injury. Additional loss of β3 integrins dramatically aggravates the bleedings and severely compromises smooth muscle cell coverage of the vasculature leading to embryonic lethality. Cell-based studies revealed that the synergy site is dispensable for the initial contact of α5β1 with the RGD, but essential to re-enforce the binding of α5β1/αIIbβ3 to FN. Our findings demonstrate a critical role for the FN synergy site when external forces exceed a certain threshold or when αvβ3 integrin levels decrease below a critical level.

  1. Fibronectin promotes differentiation of neural crest progenitors endowed with smooth muscle cell potential

    International Nuclear Information System (INIS)

    Costa-Silva, Bruno; Coelho da Costa, Meline; Melo, Fernanda Rosene; Neves, Cynara Mendes; Alvarez-Silva, Marcio; Calloni, Giordano Wosgrau; Trentin, Andrea Goncalves

    2009-01-01

    The neural crest (NC) is a model system used to investigate multipotency during vertebrate development. Environmental factors control NC cell fate decisions. Despite the well-known influence of extracellular matrix molecules in NC cell migration, the issue of whether they also influence NC cell differentiation has not been addressed at the single cell level. By analyzing mass and clonal cultures of mouse cephalic and quail trunk NC cells, we show for the first time that fibronectin (FN) promotes differentiation into the smooth muscle cell phenotype without affecting differentiation into glia, neurons, and melanocytes. Time course analysis indicated that the FN-induced effect was not related to massive cell death or proliferation of smooth muscle cells. Finally, by comparing clonal cultures of quail trunk NC cells grown on FN and collagen type IV (CLIV), we found that FN strongly increased both NC cell survival and the proportion of unipotent and oligopotent NC progenitors endowed with smooth muscle potential. In contrast, melanocytic progenitors were prominent in clonogenic NC cells grown on CLIV. Taken together, these results show that FN promotes NC cell differentiation along the smooth muscle lineage, and therefore plays an important role in fate decisions of NC progenitor cells

  2. Adipose progenitor cells increase fibronectin matrix strain and unfolding in breast tumors

    Science.gov (United States)

    Chandler, E. M.; Saunders, M. P.; Yoon, C. J.; Gourdon, D.; Fischbach, C.

    2011-02-01

    Increased stiffness represents a hallmark of breast cancer that has been attributed to the altered physicochemical properties of the extracellular matrix (ECM). However, the role of fibronectin (Fn) in modulating the composition and mechanical properties of the tumor-associated ECM remains unclear. We have utilized a combination of biochemical and physical science tools to evaluate whether paracrine signaling between breast cancer cells and adipose progenitor cells regulates Fn matrix assembly and stiffness enhancement in the tumor stroma. In particular, we utilized fluorescence resonance energy transfer imaging to map the molecular conformation and stiffness of Fn that has been assembled by 3T3-L1 preadipocytes in response to conditioned media from MDA-MB231 breast cancer cells. Our results reveal that soluble factors secreted by tumor cells promote Fn expression, unfolding, and stiffening by adipose progenitor cells and that transforming growth factor-β serves as a soluble cue underlying these changes. In vivo experiments using orthotopic co-transplantation of primary human adipose-derived stem cells and MDA-MB231 into SCID mice support the pathological relevance of our results. Insights gained by these studies advance our understanding of the role of Fn in mammary tumorigenesis and may ultimately lead to improved anti-cancer therapies.

  3. Interactions between fibronectin and chondroitin sulfate are modulated by molecular context.

    Science.gov (United States)

    Barkalow, F J; Schwarzbauer, J E

    1994-02-11

    Interactions between fibronectin (FN) and glycosaminoglycans are essential for extracellular matrix morphology and cell adhesion. One of the most abundant glycosaminoglycans is chondroitin sulfate, and here we show that recombinant FNs (deminectins (DN)) containing the carboxyl-terminal cell, heparin, and fibrin domains bind specifically to chondroitin sulfate in affinity chromatography assays. Using a panel of mutant DNs, important determinants for chondroitin sulfate binding have been localized to repeats III13 and III14 within the heparin domain. In particular, mutation of an arginine pair in repeat III13 to neutral residues ablated binding to chondroitin sulfate as we previously reported for heparin (Barkalow, F.J.B., and Schwarzbauer, J.E. (1991) J. Biol. Chem. 266, 7812-7818). These results, in combination with the ability of heparin and chondroitin sulfate to compete for binding to DNs, demonstrate that these two glycosaminoglycans interact with similar or overlapping sites in FN. One important difference between FN interactions with heparin and chondroitin sulfate is that, while FN and DNs bound equally to heparin, FN bound less efficiently than DNs to chondroitin sulfate. Reduced binding to chondroitin sulfate was also observed with a larger recombinant FN lacking internal repeats III1-7 indicating that the amino-terminal region acts to limit binding to the carboxyl-terminal domain. Our results demonstrate that interactions between FN and chondroitin sulfate are modulated by molecular context.

  4. DAMPs Synergize with Cytokines or Fibronectin Fragment on Inducing Chondrolysis but Lose Effect When Acting Alone

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    Lei Ding

    2017-01-01

    Full Text Available Objective and Design. To investigate whether endogenous damage-associated molecular patterns (DAMPs or alarmins originated from mitochondria or nucleus stimulates inflammatory response in articular chondrocytes to cause chondrolysis which leads to cartilage degradation featured in posttraumatic osteoarthritis (PTOA. Materials. Primary cultures of bovine or human chondrocytes isolated from cartilage of weight-bearing joints. Treatment. Chondrocytes were subjected to mitochondrial DAMPs (MTDs or HMGB1, a nuclear DAMP (NuD, with or without the presence of an N-terminal 29 kDa fibronectin fragment (Fn-f or proinflammatory cytokines (IL-1β and TNF-α. Injured cartilage-conditioned culturing medium containing a mixture of DAMPs was employed as a control. After 24 hrs, the protein expression of cartilage degrading metalloproteinases and iNOS in culture medium or cell lysates was examined with Western blotting, respectively. Results. HMGB1 was synergized with IL-1β in upregulating expression of MMP-3, MMP-13, ADAMTS-5, ADAM-8, and iNOS. Moreover, a moderate synergistic effect was detected between HMGB1 and Fn-f or between MTDs and TNF-α on MMP-3 expression. However, when acting alone, MTDs or HMGB1 did not upregulate cartilage degrading enzymes or iNOS. Conclusion. MTDs or HMGB1 could only stimulate inflammatory response in chondrocytes with the presence of cytokines or Fn-f.

  5. Quantitative fetal fibronectin predicts preterm birth in women with bulging fetal membranes.

    Science.gov (United States)

    Fiorini, Francesco; Isted, Alexander; Hezelgrave, Natasha L; Shennan, Andrew H

    2016-08-01

    To assess the predictive value of quantitative fetal fibronectin (fFN) concentration in cervicovaginal fluid for spontaneous preterm birth in women with bulging fetal membranes. This was a prospective observational study from five UK tertiary centres of a cohort of women with singleton pregnancy and bulging fetal membranes presenting between 18 and 32 weeks of gestation (n=62), in the period 2010-2014. fFN concentrations in cervicovaginal fluid were measured both quantitatively and qualitatively at presentation in all women. Predictive statistics and receiver operating characteristic (ROC) curves were calculated for both tests to predict spontaneous preterm birth within 14 days from testing and before 34 weeks of gestation. 62 eligible women with bulging fetal membranes were recruited from screening of 2571 women at high risk of preterm birth. The median gestational age was 24(+0) (LQ-UQ, 21(+2)-25(+3)) at presentation and 34(+4) (25(+2)-39(+0)) at delivery, with a median time from testing to delivery of 58 days (17-110). Concentration of quantitative fFN at presentation correlated negatively with time to delivery (Spearman's rs=-0.615, pmembranes, suggesting that fFN leakage could potentially be an active process. This may aid the clinical management of this high-risk group in the future. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Motogenic Sites in Human Fibronectin Are Masked by Long Range Interactions

    Science.gov (United States)

    Vakonakis, Ioannis; Staunton, David; Ellis, Ian R.; Sarkies, Peter; Flanagan, Aleksandra; Schor, Ana M.; Schor, Seth L.; Campbell, Iain D.

    2009-01-01

    Fibronectin (FN) is a large extracellular matrix glycoprotein important for development and wound healing in vertebrates. Recent work has focused on the ability of FN fragments and embryonic or tumorigenic splicing variants to stimulate fibroblast migration into collagen gels. This activity has been localized to specific sites and is not exhibited by full-length FN. Here we show that an N-terminal FN fragment, spanning the migration stimulation sites and including the first three type III FN domains, also lacks this activity. A screen for interdomain interactions by solution-state NMR spectroscopy revealed specific contacts between the Fn N terminus and two of the type III domains. A single amino acid substitution, R222A, disrupts the strongest interaction, between domains 4–5FnI and 3FnIII, and restores motogenic activity to the FN N-terminal fragment. Anastellin, which promotes fibril formation, destabilizes 3FnIII and disrupts the observed 4–5FnI-3FnIII interaction. We discuss these findings in the context of the control of cellular activity through exposure of masked sites. PMID:19366708

  7. Structural and functional analysis of the fibronectin-binding protein FNE from Streptococcus equi spp. equi.

    Science.gov (United States)

    Tiouajni, Mounira; Durand, Dominique; Blondeau, Karine; Graille, Marc; Urvoas, Agathe; Valerio-Lepiniec, Marielle; Guellouz, Asma; Aumont-Nicaise, Magali; Minard, Philippe; van Tilbeurgh, Herman

    2014-12-01

    Streptococcus equi is a horse pathogen belonging to Lancefield group C. Infection by S. equi ssp. equi causes strangles, a serious and highly contagious disease of the upper respiratory tract. S. equi ssp. equi secretes a fibronectin (Fn)-binding protein, FNE, that does not contain cell wall-anchoring motifs. FNE binds to the gelatin-binding domain (GBD) of Fn, composed of the motifs (6) FI (12) FII (789) FI . FNE lacks the canonical Fn-binding peptide repeats observed in many microbial surface components recognizing adhesive matrix molecules. We found that the interaction between FNE and the human GBD is mediated by the binding of the disordered C-terminal region (residues 208-262) of FNE to the (789) FI GBD subfragment. The crystal structure of FNE showed that it is similar to the minor pilus protein Spy0125 of Streptococcus pyogenes, found at the end of pilus polymers and responsible for adhesion. FNE and Spy0125 both have a superimposable internal thioester bond between highly conserved Cys and Gln residues. Small-angle X-ray scattering of the FNE-(789) FI complex provided a model that aligns the C-terminal peptide of FNE with the E-strands of the FI domains, adopting the β-zipper extension model observed in previous structures of microbial surface components recognizing adhesive matrix molecule adhesion peptides bound to FI domains. © 2014 FEBS.

  8. Characterization of soluble fibronectin binding to Bacille Calmette-Guérin.

    Science.gov (United States)

    Aslanzadeh, J; Brown, E J; Quillin, S P; Ritchey, J K; Ratliff, T L

    1989-10-01

    Fibronectin (FN), a 420 kDa glycoprotein, consists of two similar subunits linked by a disulphide bond near the C-terminal end. FN is present in soluble and matrix forms in various body fluids and tissues and has been shown to bind to variety of organisms. We characterized the conditions required for 125I-FN binding to Bacille Calmette-Guérin (BCG). The binding was dose-dependent, reached saturation within 3 min, and was essentially irreversible for at least 24 h under optimal binding conditions at pH 6.0. In contrast, the binding was reversible (greater than 90% in 24 h) when the pH was increased to 10.0. Scatchard analysis of the dose-response experiments produced a straight line, suggesting the presence of a single class of FN receptor on BCG. 125I-FN binding was trypsin-sensitive, suggesting that the BCG-binding molecule is a protein. The number of FN receptors was determined to be 8000-15,000 per bacterium. 125I-FN binding was pH dependent, with maximal binding at acidic pH. 125I-FN binding was sensitive to the presence of NaCl, with 0.08 M-NaCl inhibiting binding by 85%. These data demonstrate that soluble FN binds to a trypsin-sensitive cell-surface component of BCG in an essentially irreversible manner.

  9. Incorporation of fibronectin to enhance cytocompatibility in multilayer elastin-like protein scaffolds for tissue engineering.

    Science.gov (United States)

    Ravi, Swathi; Caves, Jeffrey M; Martinez, Adam W; Haller, Carolyn A; Chaikof, Elliot L

    2013-07-01

    Recombinant, elastin-like protein (ELP) polymers are of significant interest for the engineering of compliant, resilient soft tissues due to a wide range of tunable mechanical properties, biostability, and biocompatibility. Here, we enhance endothelial cell (EC) and mesenchymal stem cell compatibility with ELP constructs by addition of fibronectin (Fn) to the surface or bulk of ELP hydrogels. We find that cell adhesion, proliferation, and migration can be modulated by Fn addition. Adsorption of Fn to the hydrogel surface is more efficient than bulk blending. Surface immobilization of Fn by genipin crosslinking leads to stability without loss of bioactivity. Gels of varying mechanical modulus do not alter cell adhesion, proliferation, and migration in the range we investigate. However, more compliant gels promote an EC morphology suggesting tubulogenesis or network formation, whereas stiffer gels promote cobblestone morphology. Multilayer structures consisting of thin ELP sheets reinforced with collagen microfiber are fabricated and laminated through the culture of MSCs at layer interfaces. High cell viability in the resulting three-dimensional constructs suggests the applicability of Fn to the design of strong, resilient artificial blood vessels and other soft tissue replacements. Copyright © 2012 Wiley Periodicals, Inc.

  10. Biocompatibility and favorable response of mesenchymal stem cells on fibronectin-gold nanocomposites.

    Directory of Open Access Journals (Sweden)

    Huey-Shan Hung

    Full Text Available A simple surface modification method, comprising of a thin coating with gold nanoparticles (AuNPs and fibronectin (FN, was developed to improve the biocompatibility required for cardiovascular devices. The nanocomposites from FN and AuNPs (FN-Au were characterized by the atomic force microscopy (AFM, UV-Vis spectrophotometry (UV-Vis, and Fourier transform infrared spectroscopy (FTIR. The biocompatibility of the nanocomposites was evaluated by the response of monocytes and platelets to the material surface in vitro. FN-Au coated surfaces demonstrated low monocyte activation and platelet activation. The behavior of human umbilical cord-derived mesenchymal stem cells (MSCs on FN-Au was further investigated. MSCs on FN-Au nanocomposites particularly that containing 43.5 ppm of AuNPs (FN-Au 43.5 ppm showed cell proliferation, low ROS generation, as well as increases in the protein expression levels of matrix metalloproteinase-9 (MMP-9 and endothelial nitric oxide synthase (eNOS, which may account for the enhanced MSC migration on the nanocomposites. These results suggest that the FN-Au nanocomposite thin film coating may serve as a potential and simple solution for the surface modification of blood-contacting devices such as vascular grafts.

  11. EGF is highly expressed in hepatocellular carcinoma (HCC) and promotes motility of HCC cells via fibronectin.

    Science.gov (United States)

    Liu, Zongcai; Chen, Danyang; Ning, Fen; Du, Jun; Wang, Haifang

    2018-05-01

    Better understanding of metastasis process would allow for the development of effective approaches to treat hepatocellular carcinoma (HCC). Recent literature has highlighted the fundamental role of interaction between tumor cells and their microenvironment components in tumor metastasis. Aberrant expression of epidermal growth factor (EGF) induces highly malignant HCC, and activated EGF/EGFR signaling is correlated with an aggressive phenotype and intrahepatic metastasis. Thus, EGF in the tumor microenvironment may influence the behavior of HCC cells. In this study, for the first time, we studied the expression of EGF in HCCs, and the potential role of EGF in the motility of HCC cells and the underlying mechanisms. It was demonstrated that EGF was highly expressed in HCCs and positively associated with higher tumor grade. In addition, EGF promoted the migration and invasion of HCC cells mainly via induction of fibronectin (FN) in vitro. Mechanistically, EGF simultaneously increased the nuclear translocation and PKC mediated phosphorylation of p65 which could bind to the -356 bp to -259 bp fragment of FN promoter, leading to a markedly increased activity of FN promoter in HCC cells. These results highlight the potential role of EGF in promoting HCC metastasis, demonstrate a novel pathway for regulation of FN expression and provide potential targets for HCC prevention and treatment. © 2018 Wiley Periodicals, Inc.

  12. Fibronectin-binding protein TDE1579 affects cytotoxicity of Treponema denticola.

    Science.gov (United States)

    Xu, Xiaoping; Steffensen, Bjorn; Robichaud, Trista K; Mikhailova, Margarita; Lai, Veronica; Montgomery, Ryan; Chu, Lianrui

    2015-12-01

    While FbpA, a family of bacterial fibronectin (FN) binding proteins has been studied in several gram-positive bacteria, the gram-negative Treponema denticola, an anaerobic periodontal pathogen, also has an overlooked fbp gene (tde1579). In this research, we confirm that recombinant Fbp protein (rFbp) of T. denticola binds human FN with a Kdapp of 1.5 × 10(-7) M and blocks the binding of T. denticola to FN in a concentration-dependent manner to a level of 42%. The fbp gene was expressed in T. denticola. To reveal the roles of fbp in T. denticola pathogenesis, an fbp isogenic mutant was constructed. The fbp mutant had 51% reduced binding ability to human gingival fibroblasts (hGF). When hGF were challenged with T. denticola, the fbp mutant caused less cell morphology change, had 50% reduced cytotoxicity to hGF, and had less influence on the growth of hGF cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Adsorption and conformational modification of fibronectin and fibrinogen adsorbed on hydroxyapatite. A QCM-D study.

    Science.gov (United States)

    Fernández-Montes Moraleda, Belén; San Román, Julio; Rodríguez-Lorenzo, Luís M

    2016-10-01

    Hydroxyapatite is a bioactive ceramic frequently used for bone engineering/replacement. One of the parameters that influence the biological response to implanted materials is the conformation of the first adsorbed protein layer. In this work, the adsorption and conformational changes of two fibroid serum proteins; fibronectin and fibrinogen adsorbed onto four different hydroxyapatite powders are studied with a Quartz Crystal Microbalance with Dissipation (QCM-D). Each of the calcined apatites adsorbs less protein than their corresponding synthesized samples. Adsorption on synthesized samples yields always an extended conformation whereas a reorganization of the layer is observed for the calcined samples. Fg acquires a "Side on" conformation in all the samples at the beginning of the experiment except for one of the synthesized samples where an "End-on" conformation is obtained during the whole experiment. The Extended conformation is the active conformation for Fn. This conformation is favored by apatites with large specific surface area (SSA) and on highly concentrated media. Apatite surface features should be considered in the selection or design of materials for bone regeneration, since it is possible to control the conformation mode of attachment of Fn and Fg by an appropriate selection of them. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2585-2594, 2016. © 2016 Wiley Periodicals, Inc.

  14. Hepatitis B Virus Stimulated Fibronectin Facilitates Viral Maintenance and Replication through Two Distinct Mechanisms.

    Directory of Open Access Journals (Sweden)

    Sheng Ren

    Full Text Available Fibronectin (FN is a high molecular weight extracellular matrix protein that functions in cell adhesion, growth, migration, and embryonic development. However, little is known about the role of FN during viral infection. In the present study, we found significantly higher levels of FN in sera, and liver tissues from hepatitis B virus (HBV patients relative to healthy individuals. HBV expression enhanced FN mRNA and protein levels in the hepatic cell lines Huh7 and HepG2. HBV infection of susceptible HepG2-sodium taurocholate co-transporting polypeptide cells also increased FN expression. We also found that transcriptional factor specificity protein 1 was involved in the induction of FN by HBV. Knockdown of FN expression significantly inhibited HBV DNA replication and protein synthesis through activating endogenous IFN-α production. In addition, FN interacted with the transforming growth factor β-activated protein kinase 1 (TAK1 and TAK1-binding protein complex and attenuated interferon signaling by inhibiting TAK1 phosphorylation. Furthermore, the nuclear translocation of NF-κB/p65 was found to be inhibited by FN. We also observed that FN promoted HBV enhancers to support HBV expression. These results suggest novel functions of endogenous FN involved in immune evasion and maintenance of HBV replication.

  15. Two novel Jk(null) alleles derived from 222C>A in Exon 5 and 896G>A in Exon 9 of the JK gene.

    Science.gov (United States)

    Liu, Hsueng-Mei; Lin, Jeong-Shi; Chen, Pei-Shan; Lyou, Jau-Yi; Chen, Ying-Ju; Tzeng, Cheng-Hwai

    2009-02-01

    Polynesian Jk(null) is well known for its mutation as Intron 5 g>a at the 3' splice acceptor site. After sequencing analysis, however, it was noticed that only three of eight samples with the Jknull phenotype carried typical homozygous Polynesian Jk(null) mutation. Five others were noted to be unreported heterozygous Polynesian Jk(null) mutation. An investigation was then conducted to characterize the underlying mechanism leading to this particular Jk(null) genotype. Genomic DNA covering 5'-untranslated region exons and intervening introns of the JK gene was amplified by polymerase chain reaction, and the fragments were directly sequenced. The sequencing results were compared with those published in literature and related biologic Web sites. In all five samples with a heterozygous Polynesian Jk(null) mutation, additional mutations were identified. Two samples carried missense mutations: 222C>A (Asn74Lys) in Exon 5 and 499A>G (Met167Val) in Exon 7. Three others had missense mutation 896G>A (Gly299Glu) in Exon 9. These substituted amino acids were located either near or at transmembrane domains, respectively. In addition, two polymorphic nucleotides at positions -103 (a>g) and -119(c>a) from the 3' end of Intron 1 were also Polynesian mutation-related. In contrast to the typical homozygous Polynesian Jk(null) mutation, two novel heterozygous Jk(null) alleles were noted to be associated with the Jknull phenotype. One carried missense mutation 222C>A in Exon 5, and the other had 896G>A missense mutation in Exon 9. These findings may have implications in designing a molecular screening assay for people with the Jknull phenotype.

  16. Exon Redefinition by a Point Mutation within Exon 5 of the Glucose-6-Phosphatase Gene is the Major Cause of Glycogen Storage Disease Type 1a in Japan

    OpenAIRE

    Kajihara, Susumu; Matsuhashi, Sachiko; Yamamoto, Kyosuke; Kido, Keiko; Tsuji, Kazue; Tanae, Ayako; Fujiyama, Shigetoshi; Itoh, Tadashi; Tanigawa, Keiichiro; Uchida, Masako; Setoguchi, Yoichi; Motomura, Mitsuaki; Mizuta, Toshihiko; Sakai, Takahiro

    1995-01-01

    Glycogen storage disease (GSD) type 1a (von Gierke disease) is an autosomal recessive disorder caused by a deficiency in microsomal glucose-6-phosphatase (G6Pase). We have identified a novel mutation in the G6Pase gene of a individual with GSD type 1a. The cDNA from the patient's liver revealed a 91-nt deletion in exon 5. The genomic DNA from the patient's white blood cells revealed no deletion or mutation at the splicing junction of intron 4 and exon 5. The 3' splicing occurred 91 bp from th...

  17. Characterization of the in vitro expressed autoimmune rippling muscle disease immunogenic domain of human titin encoded by TTN exons 248-249

    Energy Technology Data Exchange (ETDEWEB)

    Zelinka, L. [Biomedical Sciences Program, Kent State University, Kent, OH (United States); McCann, S.; Budde, J.; Sethi, S.; Guidos, M.; Giles, R. [Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, One University Plaza, Youngstown, OH 44555 (United States); Walker, G.R., E-mail: grwalker@ysu.edu [Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, One University Plaza, Youngstown, OH 44555 (United States); Biomedical Sciences Program, Kent State University, Kent, OH (United States)

    2011-08-05

    Highlights: {yields} Affinity purification of the autoimmune rippling muscle disease immunogenic domain of titin. {yields} Partial sequence analysis confirms that the peptides is in the I band region of titin. {yields} This region of the human titin shows high degree of homology to mouse titin N2-A. -- Abstract: Autoimmune rippling muscle disease (ARMD) is an autoimmune neuromuscular disease associated with myasthenia gravis (MG). Past studies in our laboratory recognized a very high molecular weight skeletal muscle protein antigen identified by ARMD patient antisera as the titin isoform. These past studies used antisera from ARMD and MG patients as probes to screen a human skeletal muscle cDNA library and several pBluescript clones revealed supporting expression of immunoreactive peptides. This study characterizes the products of subcloning the titin immunoreactive domain into pGEX-3X and the subsequent fusion protein. Sequence analysis of the fusion gene indicates the cloned titin domain (GenBank ID: (EU428784)) is in frame and is derived from a sequence of N2-A spanning the exons 248-250 an area that encodes the fibronectin III domain. PCR and EcoR1 restriction mapping studies have demonstrated that the inserted cDNA is of a size that is predicted by bioinformatics analysis of the subclone. Expression of the fusion protein result in the isolation of a polypeptide of 52 kDa consistent with the predicted inferred amino acid sequence. Immunoblot experiments of the fusion protein, using rippling muscle/myasthenia gravis antisera, demonstrate that only the titin domain is immunoreactive.

  18. Analysis of KIT expression and KIT exon 11 mutations in canine oral malignant melanomas.

    Science.gov (United States)

    Murakami, A; Mori, T; Sakai, H; Murakami, M; Yanai, T; Hoshino, Y; Maruo, K

    2011-09-01

    KIT, a transmembrane receptor tyrosine kinase, is one of the specific targets for anti-cancer therapy. In humans, its expression and mutations have been identified in malignant melanomas and therapies using molecular-targeted agents have been promising in these tumours. As human malignant melanoma, canine malignant melanoma is a fatal disease with metastases and the poor response has been observed with all standard protocols. In our study, KIT expression and exon 11 mutations in dogs with histologically confirmed malignant oral melanomas were evaluated. Although 20 of 39 cases were positive for KIT protein, there was no significant difference between KIT expression and overall survival. Moreover, polymerase chain reaction amplification and sequencing of KIT exon 11 in 17 samples did not detect any mutations and proved disappointing. For several reasons, however, KIT expression and mutations of various exons including exon 11 should be investigated in more cases. © 2011 Blackwell Publishing Ltd.

  19. Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels.

    Science.gov (United States)

    Boettger, Linda M; Salem, Rany M; Handsaker, Robert E; Peloso, Gina M; Kathiresan, Sekar; Hirschhorn, Joel N; McCarroll, Steven A

    2016-04-01

    One of the first protein polymorphisms identified in humans involves the abundant blood protein haptoglobin. Two exons of the HP gene (encoding haptoglobin) exhibit copy number variation that affects HP protein structure and multimerization. The evolutionary origins and medical relevance of this polymorphism have been uncertain. Here we show that this variation has likely arisen from many recurring deletions, more specifically, reversions of an ancient hominin-specific duplication of these exons. Although this polymorphism has been largely invisible to genome-wide genetic studies thus far, we describe a way to analyze it by imputation from SNP haplotypes and find among 22,288 individuals that these HP exonic deletions associate with reduced LDL and total cholesterol levels. We further show that these deletions, and a SNP that affects HP expression, appear to drive the strong association of cholesterol levels with SNPs near HP. Recurring exonic deletions in HP likely enhance human health by lowering cholesterol levels in the blood.

  20. Recurring exon deletions in the haptoglobin (HP) gene associate with lower blood cholesterol levels

    Science.gov (United States)

    Boettger, Linda M.; Salem, Rany M.; Handsaker, Robert E.; Peloso, Gina; Kathiresan, Sekar; Hirschhorn, Joel; McCarroll, Steven A.

    2016-01-01

    Two exons of the human haptoglobin (HP) gene exhibit copy number variation that affects HP multimerization and underlies one of the first protein polymorphisms identified in humans. The evolutionary origins and medical significance of this polymorphism have been uncertain. Here we show that this variation has likely arisen from the recurring reversion of an ancient hominin-specific duplication of these exons. Though this polymorphism has been largely invisible to genome-wide genetic studies to date, we describe a way to analyze it by imputation from SNP haplotypes and find among 22,288 individuals that these HP exonic deletions associate with reduced LDL and total cholesterol levels. We show that these deletions, and a SNP that affects HP expression, are the likely drivers of the strong but complex association of cholesterol levels to SNPs near HP. Recurring exonic deletions in the haptoglobin gene likely enhance human health by lowering cholesterol levels in the blood. PMID:26901066

  1. Exploratory and spatial data analysis (EDA-SDA) for determining regional background levels and anomalies of potentially toxic elements in soils from Catorce-Matehuala, Mexico

    Science.gov (United States)

    Chiprés, J.A.; Castro-Larragoitia, J.; Monroy, M.G.

    2009-01-01

    The threshold between geochemical background and anomalies can be influenced by the methodology selected for its estimation. Environmental evaluations, particularly those conducted in mineralized areas, must consider this when trying to determinate the natural geochemical status of a study area, quantifying human impacts, or establishing soil restoration values for contaminated sites. Some methods in environmental geochemistry incorporate the premise that anomalies (natural or anthropogenic) and background data are characterized by their own probabilistic distributions. One of these methods uses exploratory data analysis (EDA) on regional geochemical data sets coupled with a geographic information system (GIS) to spatially understand the processes that influence the geochemical landscape in a technique that can be called a spatial data analysis (SDA). This EDA-SDA methodology was used to establish the regional background range from the area of Catorce-Matehuala in north-central Mexico. Probability plots of the data, particularly for those areas affected by human activities, show that the regional geochemical background population is composed of smaller subpopulations associated with factors such as soil type and parent material. This paper demonstrates that the EDA-SDA method offers more certainty in defining thresholds between geochemical background and anomaly than a numeric technique, making it a useful tool for regional geochemical landscape analysis and environmental geochemistry studies.

  2. Propiedades psicométricas de la Escala para la Detección de la Ansiedad Social (EDAS en una muestra de adolescentes chilenos

    Directory of Open Access Journals (Sweden)

    Pablo Vera-Villarroe

    2007-01-01

    Full Text Available En el presente estudio instrumental examinamos la fiabilidad y validez estructural de la versión chilena de la Escala para la Detección de la Ansiedad Social (EDAS, utilizando una muestra de 1040 adolescentes (rango de edad entre 13 y 18 años. El análisis de validez indicó que en cada una de las subescalas (Evitación, Grado de ansiedad e Interferencia tan sólo se apreció una sola dimensión que explicó más de un 40% de la varianza. Los coeficientes de fiabilidad obtenidos (alfa de Guttman- Cronbach y de Spearman-Brown fueron altos en cada una de las subescalas. No se encontraron diferencias significativas debidas al sexo, a la edad y a la interacción entre el sexo y la edad, excepto el efecto debido a la edad en las subescalas Grado de Ansiedad e Interferencia. Los resultados, en general, aportan evidencia empírica a favor de la fiabilidad y la validez de la versión chilena de la EDAS. Se propone evaluar la relación entre EDAS y otros instrumentos similares en la población chilena.

  3. Decoding of exon splicing patterns in the human RUNX1-RUNX1T1 fusion gene.

    Science.gov (United States)

    Grinev, Vasily V; Migas, Alexandr A; Kirsanava, Aksana D; Mishkova, Olga A; Siomava, Natalia; Ramanouskaya, Tatiana V; Vaitsiankova, Alina V; Ilyushonak, Ilia M; Nazarov, Petr V; Vallar, Laurent; Aleinikova, Olga V

    2015-11-01

    The t(8;21) translocation is the most widespread genetic defect found in human acute myeloid leukemia. This translocation results in the RUNX1-RUNX1T1 fusion gene that produces a wide variety of alternative transcripts and influences the course of the disease. The rules of combinatorics and splicing of exons in the RUNX1-RUNX1T1 transcripts are not known. To address this issue, we developed an exon graph model of the fusion gene organization and evaluated its local exon combinatorics by the exon combinatorial index (ECI). Here we show that the local exon combinatorics of the RUNX1-RUNX1T1 gene follows a power-law behavior and (i) the vast majority of exons has a low ECI, (ii) only a small part is represented by "exons-hubs" of splicing with very high ECI values, and (iii) it is scale-free and very sensitive to targeted skipping of "exons-hubs". Stochasticity of the splicing machinery and preferred usage of exons in alternative splicing can explain such behavior of the system. Stochasticity may explain up to 12% of the ECI variance and results in a number of non-coding and unproductive transcripts that can be considered as a noise. Half-life of these transcripts is increased due to the deregulation of some key genes of the nonsense-mediated decay system in leukemia cells. On the other hand, preferred usage of exons may explain up to 75% of the ECI variability. Our analysis revealed a set of splicing-related cis-regulatory motifs that can explain "attractiveness" of exons in alternative splicing but only when they are considered together. Cis-regulatory motifs are guides for splicing trans-factors and we observed a leukemia-specific profile of expression of the splicing genes in t(8;21)-positive blasts. Altogether, our results show that alternative splicing of the RUNX1-RUNX1T1 transcripts follows strict rules and that the power-law component of the fusion gene organization confers a high flexibility to this process. Copyright © 2015 Elsevier Ltd. All rights

  4. Corrosion resistance and biocompatibility of magnesium alloy modified by alkali heating treatment followed by the immobilization of poly (ethylene glycol), fibronectin and heparin.

    Science.gov (United States)

    Pan, Changjiang; Hu, Youdong; Hou, Yu; Liu, Tao; Lin, Yuebin; Ye, Wei; Hou, Yanhua; Gong, Tao

    2017-01-01

    In recent years, magnesium alloys are attracting more and more attention as a kind of biodegradable metallic biomaterials, however, their uncontrollable biodegradation speed in vivo and the limited surface biocompatibility hinder their clinical applications. In the present study, with the aim of improving the corrosion resistance and biocompatibility, the magnesium alloy (AZ31B) surface was modified by alkali heating treatment followed by the self-assembly of 3-aminopropyltrimethoxysilane (APTMS). Subsequently, poly (ethylene glycol) (PEG) and fibronectin or fibronectin/heparin complex were sequentially immobilized on the modified surface. The results of attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS) confirmed that the above molecules were successfully immobilized on the magnesium alloy surface. An excellent hydrophilic surface was obtained after the alkali heating treatment while the hydrophilicity decreased to some degree after the self-assembly of APTMS, the surface hydrophilicity was gradually improved again after the immobilization of PEG, fibronectin or fibronectin/heparin complex. The corrosion resistance of the control magnesium alloy was significantly improved by the alkali heating treatment. The self-assembly of APTMS and the following immobilization of PEG further enhanced the corrosion resistance of the substrates, however, the grafting of fibronectin or fibronectin/heparin complex slightly lowered the corrosion resistance. As compared to the pristine magnesium alloy, the samples modified by the immobilization of PEG and fibronectin/heparin complex presented better blood compatibility according to the results of hemolysis assay and platelet adhesion as well as the activated partial thromboplastin time (APTT). In addition, the modified substrates had better cytocompatibility to endothelial cells due to the improved anticorrosion and the introduction of fibronectin. The substrates

  5. Evolution of the Exon-Intron Structure in Ciliate Genomes.

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    Vladyslav S Bondarenko

    Full Text Available A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively, but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33-35 bp, 47-51 bp, and 78-80 bp. In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short

  6. Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

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    Obed Ramírez-Sánchez

    2016-12-01

    Full Text Available Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa, average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt]. Streptophyta have on average only ∼5.7 exons of medium size (∼230 nt. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400 nt. Among subcellular compartments, membrane proteins are the largest (∼520 aa, whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240 aa. Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.

  7. Campylobacter jejuni en niños con enfermedad diarréica aguda (E.D.A

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    Fabio Carmona V.

    1987-06-01

    Full Text Available En el período comprendido entre el 15 de septiembre de 1985 y septiembre 30 de 1986 fueron estudiados en Cali, Valle, Colombia, 231 niños que consultaron por enfermedad diarreica aguda (EDA; 137 provenían del Hospital Infantil, Club Noel y el resto del Centro de Salud de Siloé y del Hospital Universitario del Valle (HUV. El estudio de heces mostró Campylobacter jejuni (CJ en 31 (13.4%. Los 137 pacientes del Club Noel fueron estudiados también buscando Salmonella, Shigella, E. coli enterotoxigénico, encontrándose que el CJ fue el único gérmen en 13 pacientes (9.5% de los 19 aislamientos logrados en esta Institución. Todos los pacientes cursaron con los signos y síntomas típicos de la enfermedad; fiebre, diarrea, vómito, deposición mucosa o sanguinolenta. En cuanto al sexo hubo una relación niño:niña de 2:1 y el grupo de edad más comprometido fue hasta los 2 años, con promedio máximo hacia los 12 meses.

  8. Pharmacological activation of the EDA/EDAR signaling pathway restores salivary gland function following radiation-induced damage.

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    Grace Hill

    Full Text Available Radiotherapy of head and neck cancers often results in collateral damage to adjacent salivary glands associated with clinically significant hyposalivation and xerostomia. Due to the reduced capacity of salivary glands to regenerate, hyposalivation is treated by substitution with artificial saliva, rather than through functional restoration of the glands. During embryogenesis, the ectodysplasin/ectodysplasin receptor (EDA/EDAR signaling pathway is a critical element in the development and growth of salivary glands. We have assessed the effects of pharmacological activation of this pathway in a mouse model of radiation-induced salivary gland dysfunction. We report that post-irradiation administration of an EDAR-agonist monoclonal antibody (mAbEDAR1 normalizes function of radiation damaged adult salivary glands as determined by stimulated salivary flow rates. In addition, salivary gland structure and homeostasis is restored to pre-irradiation levels. These results suggest that transient activation of pathways involved in salivary gland development could facilitate regeneration and restoration of function following damage.

  9. Endogenous Multiple Exon Skipping and Back-Splicing at the DMD Mutation Hotspot.

    Science.gov (United States)

    Suzuki, Hitoshi; Aoki, Yoshitsugu; Kameyama, Toshiki; Saito, Takashi; Masuda, Satoru; Tanihata, Jun; Nagata, Tetsuya; Mayeda, Akila; Takeda, Shin'ichi; Tsukahara, Toshifumi

    2016-10-13

    Duchenne muscular dystrophy (DMD) is a severe muscular disorder. It was reported that multiple exon skipping (MES), targeting exon 45-55 of the DMD gene, might improve patients' symptoms because patients who have a genomic deletion of all these exons showed very mild symptoms. Thus, exon 45-55 skipping treatments for DMD have been proposed as a potential clinical cure. Herein, we detected the expression of endogenous exons 44-56 connected mRNA transcript of the DMD using total RNAs derived from human normal skeletal muscle by reverse transcription polymerase chain reaction (RT-PCR), and identified a total of eight types of MES products around the hotspot. Surprisingly, the 5' splice sites of recently reported post-transcriptional introns (remaining introns after co-transcriptional splicing) act as splicing donor sites for MESs. We also tested exon combinations to generate DMD circular RNAs (circRNAs) and determined the preferential splice sites of back-splicing, which are involved not only in circRNA generation, but also in MESs. Our results fit the current circRNA-generation model, suggesting that upstream post-transcriptional introns trigger MES and generate circRNA because its existence is critical for the intra-intronic interaction or for extremely distal splicing.

  10. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor

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    Hou, Zhiqiang; Su, Lijing; Pei, Jimin; Grishin, Nick V.; Zhang, Hong (UTSMC)

    2017-08-01

    In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.

  11. Molecular characterization of exon 3 of caprine myostatin gene in Marwari goat

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    Jai Prakash Khichar

    2016-06-01

    Full Text Available Aim: To estimate genetic variability in exon 3 of caprine myostatin gene in Marwari goats. Materials and Methods: A total of 120 blood samples from unrelated Marwari goats were randomly collected from different villages of Bikaner (Rajasthan, India. Genomic DNA was extracted from whole blood using blood DNA isolation kit (Himedia Ltd. as per manufacturer’s protocol. The quality of extracted genomic DNA was checked on 0.8% agarose gel. Specifically designed a primer set for caprine myostatin (MSTN gene (Genebank accession no. DQ167575 was used to amplify the exon 3 region of MSTN gene in Marwari goat. The genetic variability in exon 3 of MSTN gene in Marwari goat was assessed on 8% polyacrylamide gel electrophoresis to detect single strand conformation polymorphism (SSCP pattern. Results: The exon 3 of MSTN gene in Marwari goat showed two types of conformation patterns on 8% polyacrylamide gel. One of the patterns showed only two bands and was considered as genotype AA, whereas another pattern having an extra band was designated as genotype AB. The frequencies of AA and AB genotype for exon 3 region of MSTN gene were calculated as 0.90 and 0.10, respectively. Conclusion: Low level of polymorphism was observed at exon 3 region of MSTN gene in Marwari goat through SSCP analysis. This information could be utilized in future breeding plan to exploit the unique characteristics of Marwari goat of Rajasthan.

  12. Inactivating Mutation screening of Exon 6 and Exon 10E of FSHR gene in women with Polycystic Ovarian Syndrome in Vellore population

    Science.gov (United States)

    Sekar, Nishu; Sapre, Madhura; Kale, Vaikhari; Prabhu, Yogamaya D.; Renu, Kaviyarasi; Ramgir, Shalaka S.; Abilash, V. G.

    2017-11-01

    Polycystic Ovarian syndrome (PCOS) is a major cause of infertility in females of reproducing age and is typified by oligo-anovulation, hyperandrogenism, hirsutism and polycystic ovaries. FSHR gene located on chromosome 2 p21 is responsible for the normal follicular development and any deletion or mutation in the gene affects the interaction of FSH with its receptor. Thus, it becomes the candidate gene for PCOS study. Inactivating mutation in FSHR gene limits the receptor’s function by creating a complete block, changing the receptor-ligand complex or the basic hormone signal transduction.To screen the inactivating mutations in Exon 6 and Exon 10E of FSHR gene in women diagnosed with PCOS.PCR-RFLP analysis indicated that there were no inactivating mutations found in Exon 6 and Exon 10E. Variations in hormone levels were seen amongst the PCOS patients. There were no inactivating mutations found in FSHR gene of the women diagnosed with PCOS according to the Rotterdam criteria in Vellore population.

  13. Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?

    Science.gov (United States)

    Zhao, Shanrong; Xi, Li; Zhang, Baohong

    2015-01-01

    In recent years, RNA-seq is emerging as a powerful technology in estimation of gene and/or transcript expression, and RPKM (Reads Per Kilobase per Million reads) is widely used to represent the relative abundance of mRNAs for a gene. In general, the methods for gene quantification can be largely divided into two categories: transcript-based approach and 'union exon'-based approach. Transcript-based approach is intrinsically more difficult because different isoforms of the gene typically have a high proportion of genomic overlap. On the other hand, 'union exon'-based approach method is much simpler and thus widely used in RNA-seq gene quantification. Biologically, a gene is expressed in one or more transcript isoforms. Therefore, transcript-based approach is logistically more meaningful than 'union exon'-based approach. Despite the fact that gene quantification is a fundamental task in most RNA-seq studies, however, it remains unclear whether 'union exon'-based approach for RNA-seq gene quantification is a good practice or not. In this paper, we carried out a side-by-side comparison of 'union exon'-based approach and transcript-based method in RNA-seq gene quantification. It was found that the gene expression levels are significantly underestimated by 'union exon'-based approach, and the average of RPKM from 'union exons'-based method is less than 50% of the mean expression obtained from transcript-based approach. The difference between the two approaches is primarily affected by the number of transcripts in a gene. We performed differential analysis at both gene and transcript levels, respectively, and found more insights, such as isoform switches, are gained from isoform differential analysis. The accuracy of isoform quantification would improve if the read coverage pattern and exon-exon spanning reads are taken into account and incorporated into EM (Expectation Maximization) algorithm. Our investigation discourages the use of 'union exons'-based approach in gene

  14. Canine and human gastrointestinal stromal tumors display similar mutations in c-KIT exon 11

    International Nuclear Information System (INIS)

    Gregory-Bryson, Emmalena; Bartlett, Elizabeth; Kiupel, Matti; Hayes, Schantel; Yuzbasiyan-Gurkan, Vilma

    2010-01-01

    Gastrointestinal stromal tumors (GISTs) are common mesenchymal neoplasms in the gastrointestinal tract of humans and dogs. Little is known about the pathogenesis of these tumors. This study evaluated the role of c-KIT in canine GISTs; specifically, we investigated activating mutations in exons 8, 9, 11, 13, and 17 of c-KIT and exons 12, 14, and 18 of platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), all of which have been implicated in human GISTs. Seventeen canine GISTs all confirmed to be positive for KIT immunostaining were studied. Exons 8, 9, 11, 13 and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA, were amplified from DNA isolated from formalin-fixed paraffin-embedded samples. Of these seventeen cases, six amplicons of exon 11 of c-KIT showed aberrant bands on gel electrophoresis. Sequencing of these amplicons revealed heterozygous in-frame deletions in six cases. The mutations include two different but overlapping six base pair deletions. Exons 8, 9, 13, and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA had no abnormalities detected by electrophoresis and sequencing did not reveal any mutations, other than synonymous single nucleotide polymorphisms (SNPs) found in exon 11 of c-KIT and exons 12 and 14 of PDGFRA. The deletion mutations detected in canine GISTs are similar to those previously found in the juxtamembrane domain of c-KIT in canine cutaneous mast cell tumors in our laboratory as well as to those reported in human GISTs. Interestingly, none of the other c-KIT or PDGFRA exons showed any abnormalities in our cases. This finding underlines the critical importance of c-KIT in the pathophysiology of canine GISTs. The expression of KIT and the identification of these activating mutations in c-KIT implicate KIT in the pathogenesis of these tumors. Our results indicate that mutations in c-KIT may be of prognostic significance and that targeting KIT may be a rational approach to treatment of these malignant tumors. This study further

  15. Alterations in Fibronectin Type III Domain Containing 1 Protein Gene Are Associated with Hypertension.

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    Alan Y Deng

    Full Text Available Multiple quantitative trait loci (QTLs for blood pressure (BP have been detected in rat models of human polygenic hypertension. Great challenges confronting us include molecular identifications of individual QTLs. We first defined the chromosome region harboring C1QTL1 to a segment of 1.9 megabases that carries 9 genes. Among them, we identified the gene encoding the fibronectin type III domain containing 1 protein (Fndc1/activator of G protein signaling 8 (Ags8 to be the strongest candidate for C1QTL1, since numerous non-synonymous mutations are found. Moreover, the 5' Fndc1/Ags8 putative promoter contains numerous mutations that can account for its differential expression in kidneys and the heart, prominent organs in modulating BP, although the Fndc1/Ags8 protein was not detectable in these organs under our experimental conditions. This work has provided the premier evidence that Fndc1/Ags8 is a novel and strongest candidate gene for C1QTL1 without completely excluding other 8 genes in the C1QTL1-residing interval. If proven true by future in vivo function studies such as single-gene Fndc1/Ags8 congenics, transgenesis or targeted-gene modifications, it might represent a part of the BP genetic architecture that operates in the upstream position distant from the end-phase physiology of BP control, since it activates a Gbetagamma component in a signaling pathway. Its functional role could validate the concept that a QTL in itself can influence BP 'indirectly' by regulating other genes downstream in a pathway. The elucidation of the mechanisms initiated by Fndc/Ags8 variations will reveal novel insights into the BP modulation via a regulatory hierarchy.

  16. Fibulin-1 suppression of fibronectin-regulated cell adhesion and motility.

    Science.gov (United States)

    Twal, W O; Czirok, A; Hegedus, B; Knaak, C; Chintalapudi, M R; Okagawa, H; Sugi, Y; Argraves, W S

    2001-12-01

    Fibulin-1 is an extracellular matrix protein often associated with fibronectin (FN) in vivo. In this study, the ability of fibulin-1 to modulate adhesion, spreading and motility-promoting activities of FN was investigated. Fibulin-1 was found to have pronounced inhibitory effects on the cell attachment and spreading promoted by FN. Fibulin-1 was also found to inhibit the motility of a variety of cell types on FN substrata. For example, the FN-dependent haptotactic motility of breast carcinoma (MDA MB231) cells, epidermal carcinoma (A431), melanoma (A375 SM), rat pulmonary aortic smooth muscle cells (PAC1) and Chinese hamster ovary (CHO) cells was inhibited by the presence of fibulin-1 bound to FN-coated Boyden chamber membranes. Cells transfected to overproduce fibulin-1 displayed reduced velocity, distance of movement and persistence time on FN substrata. Similarly, the incorporation of fibulin-1 into FN-containing type I collagen gels inhibited the invasion of endocardial cushion mesenchymal cells migrating from cultured embryonic heart explants. By contrast, incorporation of fibulin-1 into collagen gels lacking FN had no effect on the migration of endocardial cushion cells. These results suggest that the motility-suppressive effects of fibulin-1 might be FN specific. Furthermore, such effects are cell-type specific, in that the migration of gingival fibroblasts and endothelial cells on FN substrata is not responsive to fibulin-1. Additional studies found that the mechanism for the motility-suppressive effects of fibulin-1 does not involve perturbations of interactions between alpha5beta1 or alpha4 integrins, or heparan sulfate proteoglycans with FN. However, fibulin-1 was found to inhibit extracellular signal regulated kinase (ERK) activation and to suppress phosphorylation of myosin heavy chain. This ability to influence signal transduction cascades that modulate the actin-myosin motor complex might be the basis for the effects of fibulin-1 on adhesion and

  17. Geometry-driven cell organization determines tissue growths in scaffold pores: consequences for fibronectin organization.

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    Pascal Joly

    Full Text Available To heal tissue defects, cells have to bridge gaps and generate new extracellular matrix (ECM. Macroporous scaffolds are frequently used to support the process of defect filling and thus foster tissue regeneration. Such biomaterials contain micro-voids (pores that the cells fill with their own ECM over time. There is only limited knowledge on how pore geometry influences cell organization and matrix production, even though it is highly relevant for scaffold design. This study hypothesized that 1 a simple geometric description predicts cellular organization during pore filling at the cell level and that 2 pore closure results in a reorganization of ECM. Scaffolds with a broad distribution of pore sizes (macroporous starPEG-heparin cryogel were used as a model system and seeded with primary fibroblasts. The strategies of cells to fill pores could be explained by a simple geometrical model considering cells as tensioned chords. The model matched qualitatively as well as quantitatively by means of cell number vs. open cross-sectional area for all pore sizes. The correlation between ECM location and cell position was higher when the pores were not filled with tissue (Pearson's coefficient ρ = 0.45±0.01 and reduced once the pores were closed (ρ = 0.26±0.04 indicating a reorganization of the cell/ECM network. Scaffold pore size directed the time required for pore closure and furthermore impacted the organization of the fibronectin matrix. Understanding how cells fill micro-voids will help to design biomaterial scaffolds that support the endogenous healing process and thus allow a fast filling of tissue defects.

  18. Predicting fibrosis worsening in obese patients with NASH through parenchymal fibronectin, HOMA-IR, and hypertension.

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    Sorrentino, Paolo; Terracciano, Luigi; D'Angelo, Salvatore; Ferbo, Umberto; Bracigliano, Alessandra; Vecchione, Raffaela

    2010-02-01

    Few published studies have examined the results obtained from repeat liver biopsies in obese patients with nonalcoholic fatty liver disease (NAFLD). The progressive form of this disease may be largely limited to a subgroup of NAFLD patients with nonalcoholic steatohepatitis (NASH). The presence of intralobular fibronectin (Fn) and other variables was investigated in relation to subsequent fibrosis progression. In this prospective study, 271 obese patients admitted to the hospital with NAFLD and abnormal liver enzymes were scheduled to undergo a repeat liver biopsy at least 5 years after the initial biopsy. After excluding cirrhotic patients, basal biopsy specimens obtained from patients who underwent a second liver biopsy were stained with antibodies against Fn. The progression of fibrosis in the follow-up sample was correlated with the amount of Fn and other clinicopathological variables. We obtained a second liver biopsy from 149 patients after a median time of 6.4 years. Of these, 132 showed suitable Fn staining for semi-quantitative assessments. In all, 44 out of 83 patients (53%) with basal NASH showed fibrosis progression by at least one stage in the second liver biopsy. The amount of Fn (odds ratio=14.1; PHOMA-IR) scores (>8, odds ratio=1.9; P=0.004) were independent predictive factors of worsening fibrosis. A semi-quantitative assessment of the amount of parenchymal Fn present at an early stage in obese patients with NASH is valuable for predicting the progression of fibrosis. Similarly, lobular Fn deposition may be a sensitive and early indicator of active fibrogenetic processes in the liver. Hypertension and higher HOMA-IR scores are other clinical independent risk factors that predict the progression of fibrosis.

  19. Fibronectin-integrin signaling is required for L-glutamine's protection against gut injury.

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    Stefanie Niederlechner

    Full Text Available Extracellular matrix (ECM stabilization and fibronectin (FN-Integrin signaling can mediate cellular protection. L-glutamine (GLN is known to prevent apoptosis after injury. However, it is currently unknown if ECM stabilization and FN-Integrin osmosensing pathways are related to GLN's cell protective mechanism in the intestine.IEC-6 cells were treated with GLN with or without FN siRNA, integrin inhibitor GRGDSP, control peptide GRGESP or ERK1/2 inhibitors PD98059 and UO126 under basal and stressed conditions. Cell survival measured via MTS assay. Phosphorylated and/or total levels of cleaved caspase-3, cleaved PARP, Bax, Bcl-2, heat shock proteins (HSPs, ERK1/2 and transcription factor HSF-1 assessed via Western blotting. Cell size and F-actin morphology quantified by confocal fluorescence microscopy and intracellular GLN concentration by LC-MS/MS.GLN's prevention of FN degradation after hyperthermia attenuated apoptosis. Additionally, inhibition of FN-Integrin interaction by GRGDSP and ERK1/2 kinase inhibition by PD98059 inhibited GLN's protective effect. GRGDSP attenuated GLN-mediated increases in ERK1/2 phosphorylation and HSF-1 levels. PD98059 and GRGDSP also decreased HSP levels after GLN treatment. Finally, GRGDSP attenuated GLN-mediated increases in cell area size and disrupted F-actin assembly, but had no effect on intracellular GLN concentrations.Taken together, this data suggests that prevention of FN degradation and the FN-Integrin signaling play a key role in GLN-mediated cellular protection. GLN's signaling via the FN-Integrin pathway is associated with HSP induction via ERK1/2 and HSF-1 activation leading to reduced apoptosis after gut injury.

  20. Utilization of fetal fibronectin testing and pregnancy outcomes among women with symptoms of preterm labor

    Science.gov (United States)

    Blackwell, Sean C; Sullivan, Erin M; Petrilla, Allison A; Shen, Xian; Troeger, Kathleen A; Byrne, James D

    2017-01-01

    Objectives To identify pregnant health plan members triaged through the emergency department (ED), including labor and delivery (ELD) units, with symptoms of preterm labor (PTL), and evaluate the use of fetal fibronectin (fFN) testing; and to calculate the rate of hospitalization and timing of delivery in relation to the ED visit. Methods Retrospective cohort study using Medical Outcomes Research for Effectiveness and Economics Registry®, a national multipayer claims database. A cohort of pregnant women evaluated in an ELD with a diagnosis of PTL from June 2012 through November 2015 was identified. The proportion of women with PTL who received fFN testing was calculated. Results A total of 23,062 patients met the criteria for inclusion in the study. The rate of fFN testing prior to delivery was 12.0%. Of the 23,062 patients included in the analysis, 75.9% were discharged home. Of those who were discharged from the emergency room, one in five went on to deliver within 3 days and almost 96% of this group was not screened for the presence of fFN. Of the remaining 24.1% of patients admitted to the hospital, 91.3% delivered during their stay. In a sensitivity analysis, the percentage of women who delivered within 3 days of the ELD encounter was lower for women who received fFN testing only (6.6%) versus those who had a history of transvaginal ultrasound (TVUS) only (21.6%). Furthermore, the rate of delivery within 3 days was lowest among patients who had both fFN testing and TVUS (4.7%). Conclusion The utilization of fFN testing is 12%. The majority of pregnant patients triaged through the ELD with symptomatic PTL do not receive an fFN test. As part of PTL evaluation, fFN testing may identify women at increased risk for preterm delivery and help determine appropriate patient management. PMID:29042802

  1. Radiation induced changes in the expression of fibronectin, Pai-1, MMP in rat glomerular epithelial cell

    International Nuclear Information System (INIS)

    Park, Woo Yoon; Kim, Won Dong; Zheng, Ying; Ha, Tae Sun; Kim, Jae Sung; Cho, Moon June

    2006-01-01

    Renal irradiation can lead to the development of radiation nephropathy, and this is characterized by the accumulation of extracellular matrix and final fibrosis. To determine the possible role of the glomerular epithelial cell, the radiation-induced changes in the expression of its genes associated with the extracellular matrix were analyzed. Rat glomerular epithelial cells (GEpC) were irradiated with a single dose of 0, 2, 5, 10 and 20 Gy with using 6 MV LINAC (Siemens, USA), and the samples were collected 6, 24, 48 and 72 hours post-irradiation, respectively. Northern blotting, western blotting and zymography were used to measure the expression level of fibronectin (Fn), plasminogen activator inhibitor-1 (Pai-1), matrix metalloproteinases-2, 9 (MMP-2, 9), tissue inhibitor of metalloproteinases-2 (TIMP-2), tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator (u-PA). Irradiation with a single dose of 10 Gy resulted in a significant increase in Fn mRNA since 24 hours post-irradiation, and a single dose of 5 and 10 Gy significantly increased the Fn immunoreactive protein measured 48 hours post-irradiation. An increase in Pai-mRNA and protein was also observed and especially, a single dose of 10 Gy significantly increased the mRNA measured 24 and 48 hours post-irradiation. The active MMP-2 measured 24 hours post-irradiation slightly increased in a dose dependent manner, but this increase did not reach statistical significance. The levels of MMP-9, TIMP-2, t-PA and u-PA appeared unaltered after irradiation. Irradiation of the glomerular epithelial cells altered the expression of genes associated with the extracellular matrix, implying that the glomerular epithelial cell may be involved in the development of radiation nephropathy

  2. Radiation induced changes in the expression of fibronectin, Pai-1, MMP in rat glomerular epithelial cell

    Energy Technology Data Exchange (ETDEWEB)

    Park, Woo Yoon; Kim, Won Dong; Zheng, Ying; Ha, Tae Sun [Chungbuk National University, Cheongju (Korea, Republic of); Kim, Jae Sung [Seoul National University, Seoul (Korea, Republic of); Cho, Moon June [Chungnam National University, Daejeon (Korea, Republic of)

    2006-03-15

    Renal irradiation can lead to the development of radiation nephropathy, and this is characterized by the accumulation of extracellular matrix and final fibrosis. To determine the possible role of the glomerular epithelial cell, the radiation-induced changes in the expression of its genes associated with the extracellular matrix were analyzed. Rat glomerular epithelial cells (GEpC) were irradiated with a single dose of 0, 2, 5, 10 and 20 Gy with using 6 MV LINAC (Siemens, USA), and the samples were collected 6, 24, 48 and 72 hours post-irradiation, respectively. Northern blotting, western blotting and zymography were used to measure the expression level of fibronectin (Fn), plasminogen activator inhibitor-1 (Pai-1), matrix metalloproteinases-2, 9 (MMP-2, 9), tissue inhibitor of metalloproteinases-2 (TIMP-2), tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator (u-PA). Irradiation with a single dose of 10 Gy resulted in a significant increase in Fn mRNA since 24 hours post-irradiation, and a single dose of 5 and 10 Gy significantly increased the Fn immunoreactive protein measured 48 hours post-irradiation. An increase in Pai-mRNA and protein was also observed and especially, a single dose of 10 Gy significantly increased the mRNA measured 24 and 48 hours post-irradiation. The active MMP-2 measured 24 hours post-irradiation slightly increased in a dose dependent manner, but this increase did not reach statistical significance. The levels of MMP-9, TIMP-2, t-PA and u-PA appeared unaltered after irradiation. Irradiation of the glomerular epithelial cells altered the expression of genes associated with the extracellular matrix, implying that the glomerular epithelial cell may be involved in the development of radiation nephropathy.

  3. Disruption of integrin-fibronectin complexes by allosteric but not ligand-mimetic inhibitors.

    Science.gov (United States)

    Mould, A Paul; Craig, Susan E; Byron, Sarah K; Humphries, Martin J; Jowitt, Thomas A

    2014-12-15

    Failure of Arg-Gly-Asp (RGD)-based inhibitors to reverse integrin-ligand binding has been reported, but the prevalence of this phenomenon among integrin heterodimers is currently unknown. In the present study we have investigated the interaction of four different RGD-binding integrins (α5β1, αVβ1, αVβ3 and αVβ6) with fibronectin (FN) using surface plasmon resonance. The ability of inhibitors to reverse ligand binding was assessed by their capacity to increase the dissociation rate of pre-formed integrin-FN complexes. For all four receptors we showed that RGD-based inhibitors (such as cilengitide) were completely unable to increase the dissociation rate. Formation of the non-reversible state occurred very rapidly and did not rely on the time-dependent formation of a high-affinity state of the integrin, or the integrin leg regions. In contrast with RGD-based inhibitors, Ca2+ (but not Mg2+) was able to greatly increase the dissociation rate of integrin-FN complexes, with a half-maximal response at ~0.4 mM Ca2+ for αVβ3-FN. The effect of Ca2+ was overcome by co-addition of Mn2+, but not Mg2+. A stimulatory anti-β1 monoclonal antibody (mAb) abrogated the effect of Ca2+ on α5β1-FN complexes; conversely, a function-blocking mAb mimicked the effect of Ca2+. These results imply that Ca2+ acts allosterically, probably through binding to the adjacent metal-ion-dependent adhesion site (ADMIDAS), and that the α1 helix in the β subunit I domain is the key element affected by allosteric modulators. The data suggest an explanation for the limited clinical efficacy of RGD-based integrin antagonists, and we propose that allosteric antagonists could prove to be of greater therapeutic benefit.

  4. Separating the contributions to 15N transverse relaxation in a fibronectin type III domain

    International Nuclear Information System (INIS)

    Meekhof, Alison E.; Freund, Stefan M.V.

    1999-01-01

    In proteins, dynamic mobility is an important feature of structure, stability, and biomolecular recognition. Uniquely sensitive to motion throughout the milli- to picosecond range, rates of transverse relaxation, R2, are commonly obtained for the characterization of chemical exchange, and the construction of motional models that attempt to separate overall and internal mobility. We have performed an in-depth study of transverse relaxation rates of backbone 15N nuclei in TNfn31-90, the third fibronectin type III domain from human tenascin. By combining the results of spin-echo (CPMG) and off-resonance T1ρ experiments, we present R2 rates at effective field strengths of 2 to 40 krad/s, obtaining a full spectrum of 16 independent R2 data points for most residues. Collecting such a large number of replicate measurements provides insight into intrinsic uncertainties. The median standard deviation in R2 for non-exchanging residues is 0.31, indicating that isolated measurements may not be sufficiently accurate for a precise interpretation of motional models. Chemical exchange events on a timescale of 570 μs were observed in a cluster of residues at the C terminus. Rates of exchange for five other residues were faster than the sampled range of frequencies and could not be determined. Averaged 'exchange free' transverse relaxation rates, R20, were used to calculate the diffusion tensor for rotational motion. Despite a highly asymmetric moment of inertia, the narrow angular dispersion of N-H vectors within the β sandwich proves insufficient to define deviations from isotropic rotation. Loop residues provide exclusive evidence for axially symmetric diffusion (Dpar/Dper=1.55)

  5. Fibronectin induces macrophage migration through a SFK-FAK/CSF-1R pathway.

    Science.gov (United States)

    Digiacomo, Graziana; Tusa, Ignazia; Bacci, Marina; Cipolleschi, Maria Grazia; Dello Sbarba, Persio; Rovida, Elisabetta

    2017-07-04

    Integrins, following binding to proteins of the extracellular matrix (ECM) including collagen, laminin and fibronectin (FN), are able to transduce molecular signals inside the cells and to regulate several biological functions such as migration, proliferation and differentiation. Besides activation of adaptor molecules and kinases, integrins transactivate Receptor Tyrosine Kinases (RTK). In particular, adhesion to the ECM may promote RTK activation in the absence of growth factors. The Colony-Stimulating Factor-1 Receptor (CSF-1R) is a RTK that supports the survival, proliferation, and motility of monocytes/macrophages, which are essential components of innate immunity and cancer development. Macrophage interaction with FN is recognized as an important aspect of host defense and wound repair. The aim of the present study was to investigate on a possible cross-talk between FN-elicited signals and CSF-1R in macrophages. FN induced migration in BAC1.2F5 and J774 murine macrophage cell lines and in human primary macrophages. Adhesion to FN determined phosphorylation of the Focal Adhesion Kinase (FAK) and Src Family Kinases (SFK) and activation of the SFK/FAK complex, as witnessed by paxillin phosphorylation. SFK activity was necessary for FAK activation and macrophage migration. Moreover, FN-induced migration was dependent on FAK in either murine macrophage cell lines or human primary macrophages. FN also induced FAK-dependent/ligand-independent CSF-1R phosphorylation, as well as the interaction between CSF-1R and β1. CSF-1R activity was necessary for FN-induced macrophage migration. Indeed, genetic or pharmacological inhibition of CSF-1R prevented FN-induced macrophage migration. Our results identified a new SFK-FAK/CSF-1R signaling pathway that mediates FN-induced migration of macrophages.

  6. Technetium-99m labeling and fibronectin binding ability of Corynebacterium diphtheriae

    International Nuclear Information System (INIS)

    Souza, S.M.S.; Nagao, P.E.; Bernardo-Filho, M.; Pereira, G.A.; Napoleao, F.; Andrade, A.F.B.; Hirata Junior, R.; Mattos-Guaraldi, A.L.

    2004-01-01

    The use of radionuclides has permitted advances in areas of clinical and scientific knowledge. Several molecules and cells have been labelled with Technetium-99m ( 99m Tc). The stannous chloride (SnCl 2 ) has a significant influence on the labeling and stability of 99m Tc radiotracers. The frequent risk of diphtheria epidemics has intensified interest in the virulence factors of Corynebacterium diphtheriae. Although studies have looked at potential adhesins including haemagglutinins and exposed sugar residues, the molecular basis of mechanisms of adherence remains unclear. Adherence of pathogens to mammalian tissues may be mediated by fibronectin (FN) found in body fluids, matrix of connective tissues, and cell surfaces. In the present study we evaluated the binding ability to human plasma FN by 99m Tc labeled-C.diphtheriae. Due to adverse effects of stannous ions, microorganisms were submitted to survival and filamentation induction assays. Data showed a dose dependent susceptibility to SnCl 2 bactericidal effects. Cell filamentation was observed for concentrations of SnCl 2 > 110 μg/ml. Adherence levels of 99m Tc labelled 241strain to coverslips coated with 20 μg/ml FN were higher (P = 0.0037) than coated with bovine serum albumin. FN binding by the sucrose fermenting 241 C. diphtheriae strain (8.9% + 2.6) was significantly lower (P=0.0139) than Staphylococcus aureus Cowan I strain (34.1% ± 1.2). Therefore, bacterial 99m Tc labeling represents an additional tool that may contribute to the comprehension of C. diphtheriae interactions with host receptors such as FN that act as biological organizers by holding bacterial cells in position and guiding their migration. (author)

  7. Wild-type p53 controls the level of fibronectin expression in breast cancer cells.

    Science.gov (United States)

    You, Daeun; Jung, Seung Pil; Jeong, Yisun; Bae, Soo Youn; Kim, Sangmin

    2017-10-01

    Aberrant fibronectin (FN) expression is associated with poor prognosis, cell adhesion, and cell motility in a variety of cancer cells. In this study, we investigated the relationship between p53 and FN expression in breast cancer cells. Basal FN expression was significantly decreased by treatment with the p53 activator III, RITA, in MCF7 breast cancer cells with wild-type p53. In addition, overexpression of wild-type p53 markedly decreased the level of FN expression in p53-mutant breast cancer cells. To examine the mechanism underlying the relationship between p53 and FN expression, we treated MCF7 breast cancer cells with the tumor promoter TPA (12-O-tetradecanoylphorbol-13-acetate). Our results showed that basal FN expression was increased by TPA treatment in a time-dependent manner. In contrast, the level of p53 expression was decreased by TPA treatment. However, the expression of FN and p53 was not altered by TPA in p53-mutant breast cancer cells. Furthermore, the alterations in FN and p53 expression in response to TPA were prevented by a specific MEK inhibitor, UO126. Finally, we demonstrated that TPA triggers degradation of p53 through the proteasomal pathway in MCF7 cells. TPA-induced FN expression was decreased by the proteasome inhibitor MG132. Under the same condition, p53 protein expression, but not mRNA expression, was reversed by MG132. Taken together, our data demonstrate that the level of FN expression is associated with the status and expression of p53 in breast cancer cells.

  8. Fibronectin promotes proplatelet formation in the human megakaryocytic cell line UT-7/TPO.

    Science.gov (United States)

    Kawaguchi, Tatsuya; Hatano, Ryo; Yamaguchi, Kyoji; Nawa, Katsuhiko; Hashimoto, Ryuji; Yokota, Hiroshi

    2012-01-01

    We investigated PPF (proplatelet formation) in the human megakaryocytic cell line UT-7/TPO in vitro and signal transduction pathways responsible for PPF. The megakaryocytic cell lines are useful for studying megakaryocyte biology, although PPF is induced only in the presence of phorbol ester. TPO (thrombopoietin) stimulates megakaryocyte proliferation and differentiation; however, no PPF occurred in the megakaryocytic cell lines, even after the addition of TPO. Therefore, factors other than TPO may play an important role in the process of PPF. As PPF occurs in the bone marrow in vivo, we noted extracellular matrix proteins and found that soluble FN (fibronectin) induced potent PPF in UT-7/TPO without phorbol ester. A Western blot analysis showed that the expression of integrins was not increased by FN treatment. Anti-β1 antibody and the RGD (arginine-glycine-aspartate) peptide inhibited FN-induced PPF. This result indicates that the signal originated from integrin β1, which is essential to inducing PPF in UT-7/TPO. Results of the experiments using several inhibitors suggest that activation of the MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase]-ERK and PI3K (phosphoinositide 3-kinase) pathways are necessary for PPF. The phosphorylation of ERK gradually increased for 2 h after the addition of soluble FN, which suggests that activation of ERK is essential for the initial induction of FN-induced PPF in UT-7/TPO. UT-7/TPO is a useful cell line that enables us to study the signals of PPF without effects of chemical compounds. © The Author(s) Journal compilation © 2012 Portland Press Limited

  9. A Brassica exon array for whole-transcript gene expression profiling.

    Directory of Open Access Journals (Sweden)

    Christopher G Love

    2010-09-01

    Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

  10. Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila.

    Directory of Open Access Journals (Sweden)

    Daniela Brites

    Full Text Available In insects and crustaceans, the Down syndrome cell adhesion molecule (Dscam occurs in many different isoforms. These are produced by mutually exclusive alternative splicing of dozens of tandem duplicated exons coding for parts or whole immunoglobulin (Ig domains of the Dscam protein. This diversity plays a role in the development of the nervous system and also in the immune system. Structural analysis of the protein suggested candidate epitopes where binding to pathogens could occur. These epitopes are coded by regions of the duplicated exons and are therefore diverse within individuals. Here we apply molecular population genetics and molecular evolution analyses using Daphnia magna and several Drosophila species to investigate the potential role of natural selection in the divergence between orthologs of these duplicated exons among species, as well as between paralogous exons within species. We found no evidence for a role of positive selection in the divergence of these paralogous exons. However, the power of this test was low, and the fact that no signs of gene conversion between paralogous exons were found suggests that paralog diversity may nonetheless be maintained by selection. The analysis of orthologous exons in Drosophila and in Daphnia revealed an excess of non-synonymous polymorphisms in the epitopes putatively involved in pathogen binding. This may be a sign of balancing selection. Indeed, in Dr. melanogaster the same derived non-synonymous alleles segregate in several populations around the world. Yet other hallmarks of balancing selection were not found. Hence, we cannot rule out that the excess of non-synonymous polymorphisms is caused by segregating slightly deleterious alleles, thus potentially indicating reduced selective constraints in the putative pathogen binding epitopes of Dscam.

  11. Allelic combinations of promoter and exon 2 in DQB1 in dogs and wolves.

    Science.gov (United States)

    Berggren, Karin T; Seddon, Jennifer M

    2008-07-01

    Polymorphism of PBRs of the major histocompatibility complex (MHC) genes is well recognized, but the polymorphism also extends to proximal promoter regions. Examining DQB1 variability in dogs and wolves, we identified 7 promoter variants and 13 exon 2 alleles among 89 dogs, including a previously unknown DQB1 exon 2 allele, and 8 promoter variants and 9 exon 2 alleles among 85 wolves. As expected from previous studies and from a close chromosomal location, strong linkage disequilibrium was demonstrated in both wolves and dogs by having significantly fewer promoter/exon 2 combinations than expected from simulations of randomized data sets. Interestingly, we noticed weaker haplotypic associations in dogs than in wolves. Dogs had twice as many promoter/exon 2 combinations as wolves and an almost 2-fold difference in the number of exon 2 alleles per promoter variant. This difference was not caused by an admixture of breeds in our group of dogs because the high ratio of observed to expected number of haplotypes persisted within a single dog breed, the German Shepherd. Ewens-Watterson tests indicated that both the promoter and exon 2 are under the balancing selection, and both regions appear to be more recently derived in the dog than in the wolf. Hence, although reasons for the differences are unknown, they may relate to altered selection pressure on patterns of expression. Deviations from normal MHC expression patterns have been associated with autoimmune diseases, which occur frequently in several dog breeds. Further knowledge about these deviations may help us understand the source of such diseases.

  12. Immunocytochemical Localization of Glia-Derived Nexin, Laminin and Fibronectin on the Surface or Extracellular Matrix of C6 Rat Glioma Cells, Astrocytes and Fibroblasts.

    Science.gov (United States)

    Halfter, W.; Reinhard, E.; Liverani, D.; Ortman, R.; Monard, D.

    1989-07-01

    The expression and cellular distribution of glia-derived nexin (GDN), laminin and fibronectin on C6 rat glioma cells, rat brain astrocytes and rat fibroblasts were investigated by immunoblotting and immunocytochemistry. Western blot analysis of C6 cell homogenates confirmed the specificities of the antibodies. Immunocytochemical staining of C6 cells, astrocytes and fibroblasts showed that laminin, fibronectin and GDN were abundant on the surface of glioma cells and astrocytes whereas on fibroblasts fibronectin was abundant though only traces of GDN and laminin could be detected. The light microscopy data were confirmed by ultrastructural studies showing that each antigen was present on the surface of the C6 rat glioma cells as numerous spots with slightly different distribution patterns for each of the antigens. In fibroblast cultures, the antigens were also localized in the extracellular matrix in the vicinity of the cells. Migrating fibroblasts but not migrating glioma cells or astrocytes deposit the matrix-proteins onto the substratum leaving behind a track of GDN, laminin and fibronectin. When the cells were treated with heparin prior to antibody incubation, the GDN immunoreactivity completely disappeared, whereas the distribution and abundance of laminin and fibronectin was not affected. Our data show that GDN binds, possibly by a heparin-like molecule, to the outer surface of cells or to the extracellular matrix and may protect cells and matrix proteins against proteolytic degradation.

  13. Fibronectin-induced VEGF receptor and calcium channel transactivation stimulate GLUT-1 synthesis and trafficking through PPARγ and TC10 in mouse embryonic stem cells.

    Science.gov (United States)

    Suh, Han Na; Han, Ho Jae

    2013-05-01

    Extracellular matrix (ECM) mediates interactions between integrin and growth factor receptor (GFR) or ion channel. Although this crosstalk promotes integration of the downstream signal pathways and then regulates cellular function, the effect of ECM on glucose transporter (GLUT) in stem cells has not been elucidated. Therefore, we examined the effect of fibronectin on GLUT-1 expression, trafficking, and its related signal pathways in mouse embryonic stem cells (mESCs). Fibronectin increased 2-deoxyglucose (DG) uptake and GLUT-1 protein expression that were blocked by transcription or translation inhibitors. Integrin α5β1-bound fibronectin increased 2-DG uptake through cluster formation with vascular endothelial growth factor receptor (VEGFR) 2, and then activated Ras and PI3K/Akt. In another pathway, integrin α5β1 displayed structural and functional interactions with calcium channels, and stimulated 2-DG uptake through calcium influx and PKC activation. Akt and PKC-induced PPARγ phosphorylation enhanced the decreased expression of PPARγ protein, and subsequently increased GLUT-1 protein synthesis and 2-DG uptake. Fibronectin stimulated TC10 activity and cytoskeleton (F-actin) rearrangement, followed by GLUT-1 trafficking. In conclusion, integrin-bound fibronectin stimulates GLUT-1 synthesis through VEGFR2/Ras/PI3K/Akt and calcium channel/Ca(2+)/PKC, which are merged at PPARγ and GLUT-1 trafficking through TC10 and F-actin. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Fibronectin in the ascitic fluid of cirrhotic patients: correlation with biochemical risk factors for the development of spontaneous bacterial peritonitis

    Directory of Open Access Journals (Sweden)

    R.C.A. Mesquita

    1997-07-01

    Full Text Available Cirrhotic patients (23 with alcoholic cirrhosis, 5 with posthepatitic cirrhosis and 2 with cryptogenic cirrhosis with ascites and portal hypertension were studied and divided into two groups corresponding to high or low risk to develop spontaneous bacterial peritonitis (SBP related to the concentration of total protein in the ascitic fluid (A-TP: group I (high risk: A-TP£1.5 g/dl and group II (low risk: A-TP>1.5 g/dl. Fibronectin (FN, C3 and C4 concentrations were measured by radial immunodiffusion while total protein was measured by the biuret method. The mean values (group I vs group II of C3 (12.59 ± 4.72 vs 24.53 ± 15.58 mg/dl, C4 (4.26 ± 3.87 vs 7.26 ± 4.14 mg/dl and FN (50.47 ± 12.49 vs 75.89 ± 24.70 mg/dl in the ascitic fluid were significantly lower (P<0.05 in the group considered to be at high risk for SBP. No significant difference was observed in the plasma/ascites fibronectin ratio (3.91 ± 1.21 vs 3.80 ± 1.26 or gradient (131.46 ± 64.01 vs 196.96 ± 57.38 between groups. Fibronectin in ascites was significantly correlated to C3 (r = 0.76, C4 (r = 0.58, total protein (r = 0.73 and plasma FN (r = 0.58 (P<0.05. The data suggest that the FN concentration in ascites is related to the opsonic capacity of this fluid, and that its concentration in the ascitic fluid may be a biochemical risk factor indicator for the development of spontaneous bacterial peritonitis

  15. Staphylococcus aureus keratinocyte invasion is dependent upon multiple high-affinity fibronectin-binding repeats within FnBPA.

    Directory of Open Access Journals (Sweden)

    Andrew M Edwards

    2011-04-01

    Full Text Available Staphylococcus aureus is a commensal organism and a frequent cause of skin and soft tissue infections, which can progress to serious invasive disease. This bacterium uses its fibronectin binding proteins (FnBPs to invade host cells and it has been hypothesised that this provides a protected niche from host antimicrobial defences, allows access to deeper tissues and provides a reservoir for persistent or recurring infections. FnBPs contain multiple tandem fibronectin-binding repeats (FnBRs which bind fibronectin with varying affinity but it is unclear what selects for this configuration. Since both colonisation and skin infection are dependent upon the interaction of S. aureus with keratinocytes we hypothesised that this might select for FnBP function and thus composition of the FnBR region. Initial experiments revealed that S. aureus attachment to keratinocytes is rapid but does not require FnBRs. By contrast, invasion of keratinocytes was dependent upon the FnBR region and occurred via similar cellular processes to those described for endothelial cells. Despite this, keratinocyte invasion was relatively inefficient and appeared to include a lag phase, most likely due to very weak expression of α(5β(1 integrins. Molecular dissection of the role of the FnBR region revealed that efficient invasion of keratinocytes was dependent on the presence of at least three high-affinity (but not low-affinity FnBRs. Over-expression of a single high-affinity or three low-affinity repeats promoted invasion but not to the same levels as S. aureus expressing an FnBPA variant containing three high-affinity repeats. In summary, invasion of keratinocytes by S. aureus requires multiple high-affinity FnBRs within FnBPA, and given the importance of the interaction between these cell types and S. aureus for both colonisation and infection, may have provided the selective pressure for the multiple binding repeats within FnBPA.

  16. Síntesis Óptima de Mecanismos utilizando un EDA basado en la Distribución Normal

    Directory of Open Access Journals (Sweden)

    Ivvan Valdez

    2013-01-01

    Full Text Available El problema de síntesis de mecanismos consiste en determinar las dimensiones de los eslabones a fin de que éstos puedan completar una tarea, la cual es definida por el posicionamiento en un conjunto de puntos denominados puntos de precisión. En este trabajo se aborda este problema como un ejercicio de optimización, que minimiza la distancia entre la posición de un mecanismo propuesto y los puntos de precisión, tomando como variables de decisión las dimensiones del mecanismo, su sistema coordenado relativo y parámetros que determinan la velocidad del mismo y la posición inicial. La propuesta final es un algoritmo para el diseño automatizado de mecanismos que cumplan en lo mayor posible con la tarea deseada. Se utilizó un Algoritmo de Estimación de Distribución (EDA, por sus siglas en inglés, el cual aproxima el óptimo mediante muestreos subsecuentes de una distribución Normal multivariada, donde cada muestra representa una propuesta de un mecanismo. Después, se simula y se mide la diferencia entre los puntos de precisión y las posiciones del mecanismo propuesto, los mejores mecanismos se utilizan para actualizar la distribución de búsqueda en cada generación (iteración del algoritmo hasta que converge a un punto de bajo costo de la función objetivo. Se utilizó el método propuesto para la síntesis automatizada de un mecanismo plano de 4 barras de cadena cinemática cerrada. Los resultados obtenidos son diseños óptimos aproximados, que superan a otros reportados en la literatura especializada. El método propuesto representa una alternativa eficaz para la síntesis automatizada de mecanismos. Los resultados son altamente competitivos con otros reportados en la literatura. La propuesta presenta además ventajas contra otras similares, en el sentido de que puede utilizarse para aproximar un número arbitrario de puntos de precisión, sin aumentar la dimensionalidad del problema, adicionalmente puede ser utilizado para la s

  17. Deletion of exon 26 of the dystrophin gene is associated with a mild Becker muscular dystrophy phenotype

    DEFF Research Database (Denmark)

    Witting, Nanna; Duno, Morten; Vissing, John

    2011-01-01

    With the possible introduction of exon skipping therapy in Duchenne muscular dystrophy, it has become increasingly important to know the role of each exon of the dystrophin gene to protein expression, and thus the phenotype. In this report, we present two related men with an unusually mild BMD...... calf hypertrophy was noted. Creatine kinase was normal or raised maximally to 500 U/l. The muscle biopsy was myopathic with increased fiber size variation and many internal nuclei, but no dystrophy. No comorbidity was found. In both cases, western blot showed a reduced dystrophin band. Genetic...... evaluation revealed a deletion of exon 26 of the dystrophin gene in both. This is the first description of patients with a exon 26 deletion of the dystrophin gene. Assuming the proband's comorbidity is unrelated, exon 26 deletion results in a very mild phenotype. This might be of interest in planning exon...

  18. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

    Energy Technology Data Exchange (ETDEWEB)

    Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla; Conboy, John G.

    2008-11-07

    In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.

  19. [Genetic diagnosis for a family without exonic deletions and duplications of dystrophin gene].

    Science.gov (United States)

    Li, Tao; Hou, Qiaofang; Wu, Dong; Wang, Hongdan; Liu, Hongyan; Yang, Yangli; Zhang, Chaoyang; Ding, Xuebing; Liao, Shixiu

    2015-02-01

    To conduct genetic diagnosis for a family in which no exonic deletions and duplications of the dystrophin gene were detected. Potential exonic deletions and duplications of the dystrophin gene were initially analyzed with using multiplex ligation-dependent probe amplification (MLPA). Subsequently, all of the 79 exons of the dystrophin gene of the proband and a pregnant woman from the family were analyzed with PCR amplification and DNA sequencing. Following identification of the causative mutation, prenatal diagnosis was provided. MLPA analysis had detected no exonic deletions and duplications of the dystrophin gene. Sequence analysis has identified a C>T mutation on the 22nd nucleotide position of the 70th exon of the dystrophin gene (c.10108 C>T), which has replaced the codon CGA to a stop codon (TGA). The patient's mother and sister were both heterozygous for the same mutation. Upon prenatal diagnosis, the fetus was found to be positive for the Y chromosome sex-determining gene (SRY) and has carried above mutation. The result of short tandem repeat linkage analysis also confirmed that the fetus has inherited the mutant X chromosome. The causative mutation of the dystrophin gene has been discovered in an affected family, which has enabled prenatal diagnosis of the disease.

  20. hnRNP F directs formation of an exon 4 minus variant of tumor-associated NADH oxidase (ENOX2).

    Science.gov (United States)

    Tang, Xiaoyu; Kane, Vanessa D; Morré, Dorothy M; Morré, D James

    2011-11-01

    HUVEC or mouse 3T3 cells infected with SV-40 generate within 3 to 5 days post-infection an ENOX2 species corresponding to the exon-4 minus splice variant of a tumor-associated NADH oxidase (ENOX2 or tNOX) expressed at the cancer cell surface. This study was to seek evidence for splicing factors that might direct formation of the exon 4 minus ENOX2 splice variant. To determine if silencing of ENOX2 exon 4 occurs because of motifs located in exon 4, transfections were performed on MCF-10A (mammary non-cancer), BT-20 (mammary cancer), and HeLa (cervical cancer) cells using a GFP minigene construct containing either a constitutively spliced exon (albumin exon 2) or the alternatively spliced ENOX2 exon 4 between the two GFP halves. Removal of exon 4 from the processed RNA of the GFP minigene construct occurred with HeLa and to a lesser extent with BT-20 but not in non-cancer MCF-10A cells. The Splicing Rainbow Program was used to identify all of the possible hnRNPs binding sites of exon 4 of ENOX2. There are 8 Exonic Splicing Silencers (ESSs) for hnRNP binding in the exon 4 sequences. Each of these sites were mutated by site-directed mutagenesis to test if any were responsible for the splicing skip. Results showed MutG75 ESS mutation changed the GFP expression which is a sign of splicing silence, while other mutations did not. As MutG75 changed the ESS binding site for hnRNP F, this result suggests that hnRNP F directs formation of the exon 4 minus variant of ENOX2.

  1. Modulation of splicing of the preceding intron by antisense oligonucleotide complementary to intra-exon sequence deleted in dystrophin Kobe

    Energy Technology Data Exchange (ETDEWEB)

    Takeshima, Y.; Matuso, M.; Sakamoto, H.; Nishio, H. [Kobe Univ. School of Medicine and Science (Japan)

    1994-09-01

    Molecular analysis of dystrophin Kobe showed that exon 19 of the dystrophin gene bearing a 52 bp deletion was skipped during splicing, although the known consensus sequences at the 5{prime} and 3{prime} splice site of exon 19 were maintained. These data suggest that the deleted sequence of exon 19 may function as a cis-acting factor for exact splicing for the upstream intron. To investigate this potential role, an in vitro splicing system using dystrophin precursors was established. A two-exon precursor containing exon 18, truncated intron 18, and exon 19 was accurately spliced. However, splicing of intron 18 was dramatically inhibited when wild exon 19 was replaced with mutated exon 19. Even though the length of exon 19 was restored to normal by replacing the deleted sequence with other sequence, splicing of intron 18 was not fully reactivated. Characteristically, splicing of intron 18 was inactivated more markedly when the replaced sequence contained less polypurine stretches. These data suggested that modification of the exon sequence would result in a splicing abnormality. Antisense 31 mer 2`-O-methyl ribonucleotide was targeted against 5{prime} end of deleted region of exon 19 to modulate splicing of the mRNA precursor. Splicing of intron 18 was inhibited in a dose- and time-dependent manner. This is the first in vitro evidence to show splicing of dystrophin pre-mRNA can be managed by antisense oligonucleotides. These experiments represent an approach in which antisense oligonucleotides are used to restore the function of a defective dystrophin gene in Duchenne muscular dystrophy by inducing skipping of certain exons during splicing.

  2. Categorization of 77 dystrophin exons into 5 groups by a decision tree using indexes of splicing regulatory factors as decision markers.

    Science.gov (United States)

    Malueka, Rusdy Ghazali; Takaoka, Yutaka; Yagi, Mariko; Awano, Hiroyuki; Lee, Tomoko; Dwianingsih, Ery Kus; Nishida, Atsushi; Takeshima, Yasuhiro; Matsuo, Masafumi

    2012-03-31

    Duchenne muscular dystrophy, a fatal muscle-wasting disease, is characterized by dystrophin deficiency caused by mutations in the dystrophin gene. Skipping of a target dystrophin exon during splicing with antisense oligonucleotides is attracting much attention as the most plausible way to express dystrophin in DMD. Antisense oligonucleotides have been designed against splicing regulatory sequences such as splicing enhancer sequences of target exons. Recently, we reported that a chemical kinase inhibitor specifically enhances the skipping of mutated dystrophin exon 31, indicating the existence of exon-specific splicing regulatory systems. However, the basis for such individual regulatory systems is largely unknown. Here, we categorized the dystrophin exons in terms of their splicing regulatory factors. Using a computer-based machine learning system, we first constructed a decision tree separating 77 authentic from 14 known cryptic exons using 25 indexes of splicing regulatory factors as decision markers. We evaluated the classification accuracy of a novel cryptic exon (exon 11a) identified in this study. However, the tree mislabeled exon 11a as a true exon. Therefore, we re-constructed the decision tree to separate all 15 cryptic exons. The revised decision tree categorized the 77 authentic exons into five groups. Furthermore, all nine disease-associated novel exons were successfully categorized as exons, validating the decision tree. One group, consisting of 30 exons, was characterized by a high density of exonic splicing enhancer sequences. This suggests that AOs targeting splicing enhancer sequences would efficiently induce skipping of exons belonging to this group. The decision tree categorized the 77 authentic exons into five groups. Our classification may help to establish the strategy for exon skipping therapy for Duchenne muscular dystrophy.

  3. Los pacientes del Manicomio La Castañeda y sus diagnósticos. Una propuesta desde la historia cuantitativa (México, 1910-1968

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    Ríos Molina, Andrés

    2016-06-01

    Full Text Available During its 58 years in operation (1910-1968, the Manicomio General La Castañeda housed 61,480 people. In this paper, we present an overview of the general characteristic of the patients based on a 20% sample of the overall population. We divided the text in three sections: in the first part we argue that the history of the institution comprises three distinctive periods characterized by demographic changes that coincide with administrative reforms. In the second, we present the general characteristics of La Castañeda's psychiatric population. Finally, we describe the most salient demographic changes, which stemmed either from socio-political events, technological innovations or clinical transformations. Some of the most salient results of the analysis of the sample show that the inmate population had short periods of hospitalization in the asylum (an average of 18 month, as well as a lower mortality rate (24.2% in comparison to contemporary mental institutions. Families played a fundamental role in the care of their mad relatives, which accounts for the relatively short periods of hospitalization as well as the low death rates. Consequently, for this particular institution, chronic patients weren't such a serious problem as believed.El Manicomio General La Castañeda, fundado en la Ciudad de México, albergó a 61.480 pacientes entre 1910 y 1968. El objetivo de este artículo es presentar un panorama general de la población que ingresó a esta institución y los diagnósticos que recibieron los internos, análisis realizado a partir de una base de datos construida con una muestra de 20% de la población total. El artículo se divide en tres partes: en la primera, proponemos tres etapas para comprender la historia de La Castañeda cuya periodización es definida por cambios demográficos que coinciden con reformas administrativas; en la segunda, exponemos las características generales de la población psiquiátrica de La Castañeda; y

  4. Respiratory tract responses to dust: Relationships between dust burden, lung injury, alveolar macrophage fibronectin release, and the development of pulmonary fibrosis

    Energy Technology Data Exchange (ETDEWEB)

    Driscoll, K.E.; Maurer, J.K.; Lindenschmidt, R.C.; Romberger, D.; Rennard, S.I.; Crosby, L. (Procter Gamble Company, Cincinnati, OH (USA))

    1990-10-01

    A multidisciplinary approach was used to investigate the responses of the respiratory tract to silica (SiO2) or titanium dioxide (TiO2). Rats were intratracheally instilled with 5-100 mg/kg of dust and bronchoalveolar lavage fluid (BALF) lactate dehydrogenase (LDH) and total protein (TP) and ex vivo alveolar macrophage (AM) fibronectin release assessed on Days 7, 14, and 28 after exposure. Lung dust burdens were determined on Days 1, 7, and 28 after instillation. Both dusts elicited dose-related increases in BALF LDH and TP, a response which was more pronounced and progressive with SiO2. All doses of SiO2 elicited persistent increases in AM fibronectin release. TiO2 stimulated persistent increases in AM fibronectin release at greater than or equal to 50 mg/kg, with transient or no effect at less than or equal to 10 mg/kg. Increased SiO2 retention was observed for all doses and TiO2 retention was increased only at doses greater than or equal to 50 mg/kg. In vitro exposure of naive AM to SiO2 or TiO2 did not stimulate AM fibronectin release. Histopathology demonstrated fibrosis at all SiO2 doses; only TiO2 doses greater than or equal to 50 mg/kg resulted in fibrosis. These results reveal an association between increased dust retention, lung injury, activation of AM fibronectin release, and the development of fibrosis. The magnitude and temporal pattern of responses clearly differentiated SiO2 from TiO2. The correlation of BALF markers of lung injury and increased AM fibronectin release with the development of fibrosis supports the use of these parameters as predictive biomarkers of dust-induced interstitial lung disease.

  5. Candidate gene analysis of tooth agenesis identifies novel mutations in six genes and suggests significant role for WNT and EDA signaling and allele combinations.

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    Sirpa Arte

    Full Text Available Failure to develop complete dentition, tooth agenesis, is a common developmental anomaly manifested most often as isolated but also as associated with many developmental syndromes. It typically affects third molars or one or few other permanent teeth but severe agenesis is also relatively prevalent. Here we report mutational analyses of seven candidate genes in a cohort of 127 probands with non-syndromic tooth agenesis. 82 lacked more than five permanent teeth excluding third molars, called as oligodontia. We identified 28 mutations, 17 of which were novel. Together with our previous reports, we have identified two mutations in MSX1, AXIN2 and EDARADD, five in PAX9, four in EDA and EDAR, and nine in WNT10A. They were observed in 58 probands (44%, with a mean number of missing teeth of 11.7 (range 4 to 34. Almost all of these probands had severe agenesis. Only few of the probands but several relatives with heterozygous genotypes of WNT10A or EDAR conformed to the common type of non-syndromic tooth agenesis, incisor-premolar hypodontia. Mutations in MSX1 and PAX9 affected predominantly posterior teeth, whereas both deciduous and permanent incisors were especially sensitive to mutations in EDA and EDAR. Many mutations in EDAR, EDARADD and WNT10A were present in several families. Biallelic or heterozygous genotypes of WNT10A were observed in 32 and hemizygous or heterozygous genotypes of EDA, EDAR or EDARADD in 22 probands. An EDARADD variant were in seven probands present together with variants in EDAR or WNT10A, suggesting combined phenotypic effects of alleles in distinct genes.

  6. Candidate Gene Analysis of Tooth Agenesis Identifies Novel Mutations in Six Genes and Suggests Significant Role for WNT and EDA Signaling and Allele Combinations

    Science.gov (United States)

    Arte, Sirpa; Parmanen, Satu; Pirinen, Sinikka; Alaluusua, Satu; Nieminen, Pekka

    2013-01-01

    Failure to develop complete dentition, tooth agenesis, is a common developmental anomaly manifested most often as isolated but also as associated with many developmental syndromes. It typically affects third molars or one or few other permanent teeth but severe agenesis is also relatively prevalent. Here we report mutational analyses of seven candidate genes in a cohort of 127 probands with non-syndromic tooth agenesis. 82 lacked more than five permanent teeth excluding third molars, called as oligodontia. We identified 28 mutations, 17 of which were novel. Together with our previous reports, we have identified two mutations in MSX1, AXIN2 and EDARADD, five in PAX9, four in EDA and EDAR, and nine in WNT10A. They were observed in 58 probands (44%), with a mean number of missing teeth of 11.7 (range 4 to 34). Almost all of these probands had severe agenesis. Only few of the probands but several relatives with heterozygous genotypes of WNT10A or EDAR conformed to the common type of non-syndromic tooth agenesis, incisor-premolar hypodontia. Mutations in MSX1 and PAX9 affected predominantly posterior teeth, whereas both deciduous and permanent incisors were especially sensitive to mutations in EDA and EDAR. Many mutations in EDAR, EDARADD and WNT10A were present in several families. Biallelic or heterozygous genotypes of WNT10A were observed in 32 and hemizygous or heterozygous genotypes of EDA, EDAR or EDARADD in 22 probands. An EDARADD variant were in seven probands present together with variants in EDAR or WNT10A, suggesting combined phenotypic effects of alleles in distinct genes. PMID:23991204

  7. Molecular evolution of the leptin exon 3 in some species of the family Canidae

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    Switonski Marek

    2003-09-01

    Full Text Available Abstract The structure of the leptin gene seems to be well conserved. The polymorphism of this gene in four species belonging to the Canidae family (the dog (Canis familiaris – 16 different breeds, the Chinese racoon dog (Nyctereutes procyonoides procyonoides, the red fox (Vulpes vulpes and the arctic fox (Alopex lagopus were studied with the use of single strand conformation polymorphism (SSCP, restriction fragment length polymorphism (RFLP and DNA sequencing techniques. For exon 2, all species presented the same SSCP pattern, while in exon 3 some differences were found. DNA sequencing of exon 3 revealed the presence of six nucleotide substitutions, differentiating the studied species. Three of them cause amino acid substitutions as well. For all dog breeds studied, SSCP patterns were identical.

  8. [For the good of the nation's economy: therapeutic work and public assistance at La Castañeda asylum in Mexico City, 1929-32].

    Science.gov (United States)

    Sacristán, Cristina

    2005-01-01

    Founded in 1910, by 1930 Mexico City's La Castañeda insane asylum was grappling with the problem of a massive number of chronic patients, a situation that earned it an image as a warehouse for the sick more than a place of treatment. Psychiatrists endeavored to restore the asylum's legitimacy by publicizing a nineteenth-century treatment which projected the public image that the mentally ill could be as productive as anyone else: work therapy. The government born of the Mexican revolution supported this proposal because the guiding objective behind public assistance for underprivileged groups was to make them part of the country's productive life via the market.

  9. Silk-fibronectin protein alloy fibres support cell adhesion and viability as a high strength, matrix fibre analogue

    Science.gov (United States)

    Jacobsen, Matthew M.; Li, David; Gyune Rim, Nae; Backman, Daniel; Smith, Michael L.; Wong, Joyce Y.

    2017-04-01

    Silk is a natural polymer with broad utility in biomedical applications because it exhibits general biocompatibility and high tensile material properties. While mechanical integrity is important for most biomaterial applications, proper function and integration also requires biomaterial incorporation into complex surrounding tissues for many physiologically relevant processes such as wound healing. In this study, we spin silk fibroin into a protein alloy fibre with whole fibronectin using wet spinning approaches in order to synergize their respective strength and cell interaction capabilities. Results demonstrate that silk fibroin alone is a poor adhesive surface for fibroblasts, endothelial cells, and vascular smooth muscle cells in the absence of serum. However, significantly improved cell attachment is observed to silk-fibronectin alloy fibres without serum present while not compromising the fibres’ mechanical integrity. Additionally, cell viability is improved up to six fold on alloy fibres when serum is present while migration and spreading generally increase as well. These findings demonstrate the utility of composite protein alloys as inexpensive and effective means to create durable, biologically active biomaterials.

  10. Signal mingle: Micropatterns of BMP-2 and fibronectin on soft biopolymeric films regulate myoblast shape and SMAD signaling

    Science.gov (United States)

    Fitzpatrick, Vincent; Fourel, Laure; Destaing, Olivier; Gilde, Flora; Albigès-Rizo, Corinne; Picart, Catherine; Boudou, Thomas

    2017-01-01

    In vivo, bone morphogenetic protein 2 (BMP-2) exists both in solution and bound to the extracellular matrix (ECM). While these two modes of presentation are known to influence cell behavior distinctly, their role in the niche microenvironment and their functional relevance in the genesis of a biological response has sparsely been investigated at a cellular level. Here we used the natural affinity of BMP-2 for fibronectin (FN) to engineer cell-sized micropatterns of BMP-2. This technique allowed the simultaneous control of the spatial presentation of fibronectin-bound BMP-2 and cell spreading. These micropatterns induced a specific actin and adhesion organization around the nucleus, and triggered the phosphorylation and nuclear translocation of SMAD1/5/8 in C2C12 myoblasts and mesenchymal stem cells, an early indicator of their osteoblastic trans-differentiation. We found that cell spreading itself potentiated a BMP-2-dependent phosphorylation of SMAD1/5/8. Finally, we demonstrated that FN/BMP-2-mediated early SMAD signaling depended on LIM kinase 2 and ROCK, rather than myosin II activation. Altogether, our results show that FN/BMP-2 micropatterns are a useful tool to study the mechanisms underlying BMP-2-mediated mechanotransduction. More broadly, our approach could be adapted to other combinations of ECM proteins and growth factors, opening an exciting avenue to recreate tissue-specific niches in vitro.

  11. A conserved gene family encodes transmembrane proteins with fibronectin, immunoglobulin and leucine-rich repeat domains (FIGLER

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    Haga Christopher L

    2007-09-01

    Full Text Available Abstract Background In mouse the cytokine interleukin-7 (IL-7 is required for generation of B lymphocytes, but human IL-7 does not appear to have this function. A bioinformatics approach was therefore used to identify IL-7 receptor related genes in the hope of identifying the elusive human cytokine. Results Our database search identified a family of nine gene candidates, which we have provisionally named fibronectin immunoglobulin leucine-rich repeat (FIGLER. The FIGLER 1–9 genes are predicted to encode type I transmembrane glycoproteins with 6–12 leucine-rich repeats (LRR, a C2 type Ig domain, a fibronectin type III domain, a hydrophobic transmembrane domain, and a cytoplasmic domain containing one to four tyrosine residues. Members of this multichromosomal gene family possess 20–47% overall amino acid identity and are differentially expressed in cell lines and primary hematopoietic lineage cells. Genes for FIGLER homologs were identified in macaque, orangutan, chimpanzee, mouse, rat, dog, chicken, toad, and puffer fish databases. The non-human FIGLER homologs share 38–99% overall amino acid identity with their human counterpart. Conclusion The extracellular domain structure and absence of recognizable cytoplasmic signaling motifs in members of the highly conserved FIGLER gene family suggest a trophic or cell adhesion function for these molecules.

  12. mRNA Display Selection of a High-Affinity, Modification-Specific Phospho-IκBα-Binding Fibronectin

    Science.gov (United States)

    Olson, C. Anders; Liao, Hsiang-I; Sun, Ren; Roberts, Richard W.

    2009-01-01

    The complexity of the human proteome is greatly expanded by post-translational modifications. New tools capable of recognizing these modifications in a sequence-specific fashion provide a route to purify these modified proteins, to alter protein trafficking, and to visualize signal transduction in real time. Here, we have evolved novel, modification-specific ligands that target phosphorylated IκBα. To do this, we employed mRNA display-based in vitro selection using a 30-trillion-member protein library based on the fibronectin type III domain. The selection yielded one fibronectin molecule, 10C17C25, that binds a phospho-IκBα peptide with Kd = 18 nM and is over 1000-fold specific compared to the nonphosphorylated peptide. 10C17C25 specifically recognizes endogenous phosphorylated IκBα from mammalian cell extract and stabilizes phospho-IκBα in vivo. We also incorporated 10C17C25 into a FRET indicator that detects IκB kinase (IKK) activity in vitro, demonstrating the utility of selecting designed adaptors for kinase activity sensors. PMID:18590330

  13. mRNA display selection of a high-affinity, modification-specific phospho-IkappaBalpha-binding fibronectin.

    Science.gov (United States)

    Olson, C Anders; Liao, Hsiang-I; Sun, Ren; Roberts, Richard W

    2008-08-15

    The complexity of the human proteome is greatly expanded by post-translational modifications. New tools capable of recognizing these modifications in a sequence-specific fashion provide a route to purify these modified proteins, to alter protein trafficking, and to visualize signal transduction in real time. Here, we have evolved novel, modification-specific ligands that target phosphorylated IkappaBalpha. To do this, we employed mRNA display-based in vitro selection using a 30-trillion-member protein library based on the fibronectin type III domain. The selection yielded one fibronectin molecule, 10C17C25, that binds a phospho-IkappaBalpha peptide with K d = 18 nM and is over 1000-fold specific compared to the nonphosphorylated peptide. 10C17C25 specifically recognizes endogenous phosphorylated IkappaBalpha from mammalian cell extract and stabilizes phospho-IkappaBalpha in vivo. We also incorporated 10C17C25 into a FRET indicator that detects IkappaB kinase (IKK) activity in vitro, demonstrating the utility of selecting designed adaptors for kinase activity sensors.

  14. Extracellular matrix inspired surface functionalization with heparin, fibronectin and VEGF provides an anticoagulant and endothelialization supporting microenvironment

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xue [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China); Liu, Tao [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China); Jiangsu Provincial Key Laboratory for Interventional Medical Devices, Huaiyin Institute of Technology, Huai’an (China); Chen, Yuan [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China); Zhang, Kun [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China); School of Life Science, Zhengzhou University, Zhengzhou (China); Maitz, Manfred F. [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China); Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials, Hohe Str. 06, 01069 Dresden (Germany); Pan, Changjiang [Jiangsu Provincial Key Laboratory for Interventional Medical Devices, Huaiyin Institute of Technology, Huai’an (China); Chen, Junying, E-mail: chenjy@263.net [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China); Huang, Nan [Key Laboratory of Advanced Technology for Materials of Chinese Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu (China)

    2014-11-30

    Highlights: • Surface modification with fibronectin, heparin and VEGF could selectively anticoagulant and promote endothelialization. • The bioactivity of biomolecules was more efficiently maintained via specific intermolecular interaction. • Poly-l-lysine interlayer was more feasible and the degradation product had no harm to human body. - Abstract: The biocompatibility of currently used coronary artery stent is still far from perfect, which closely related to insufficient endothelialization and thrombus formation. In this study, heparin, fibronectin and VEGF were immobilized on Ti surface to construct a multifunctional microenvironment with favorable properties to inhibit thrombosis formation and promote endothelialization simultaneously. The microenvironment on Ti surface was characterized in detail and demonstrated that the Hep/Fn/VEGF biofunctional coating was constructed successfully on Ti surface. The influence of surface properties such as chemical composition, roughness, hydrophilicity, and binding density of biomolecules on the performances of hemocompatibility and cytocompatibility was evaluated and discussed. Modified surface significantly enhanced the AT III binding density and prolonged the clotting time. In vitro platelet adhesion and activation assays further proved that the modified surface presented favorable anti-coagulant property. In addition, the proliferation of endothelial progenitor cells (EPCs) and endothelial cells (ECs) on the Hep/Fn/VEGF biofunctional coating was significantly promoted. In conclusion, the Hep/Fn/VEGF biofunctional coating was successfully constructed with desirable anticoagulant and endothelialization supporting properties. This work may provide a promising approach for biofunctional surface modification of coronary artery stent to acquire a desired multifunctional microenvironment.

  15. Extracellular matrix inspired surface functionalization with heparin, fibronectin and VEGF provides an anticoagulant and endothelialization supporting microenvironment

    International Nuclear Information System (INIS)

    Wang, Xue; Liu, Tao; Chen, Yuan; Zhang, Kun; Maitz, Manfred F.; Pan, Changjiang; Chen, Junying; Huang, Nan

    2014-01-01

    Highlights: • Surface modification with fibronectin, heparin and VEGF could selectively anticoagulant and promote endothelialization. • The bioactivity of biomolecules was more efficiently maintained via specific intermolecular interaction. • Poly-l-lysine interlayer was more feasible and the degradation product had no harm to human body. - Abstract: The biocompatibility of currently used coronary artery stent is still far from perfect, which closely related to insufficient endothelialization and thrombus formation. In this study, heparin, fibronectin and VEGF were immobilized on Ti surface to construct a multifunctional microenvironment with favorable properties to inhibit thrombosis formation and promote endothelialization simultaneously. The microenvironment on Ti surface was characterized in detail and demonstrated that the Hep/Fn/VEGF biofunctional coating was constructed successfully on Ti surface. The influence of surface properties such as chemical composition, roughness, hydrophilicity, and binding density of biomolecules on the performances of hemocompatibility and cytocompatibility was evaluated and discussed. Modified surface significantly enhanced the AT III binding density and prolonged the clotting time. In vitro platelet adhesion and activation assays further proved that the modified surface presented favorable anti-coagulant property. In addition, the proliferation of endothelial progenitor cells (EPCs) and endothelial cells (ECs) on the Hep/Fn/VEGF biofunctional coating was significantly promoted. In conclusion, the Hep/Fn/VEGF biofunctional coating was successfully constructed with desirable anticoagulant and endothelialization supporting properties. This work may provide a promising approach for biofunctional surface modification of coronary artery stent to acquire a desired multifunctional microenvironment

  16. High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains.

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    Daniel R Woldring

    Full Text Available Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >105 binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3-3.9; median: 2.1; standard deviation: 1.1 supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site.

  17. Development of detection method for novel fusion gene using GeneChip exon array.

    Science.gov (United States)

    Wada, Yusaku; Matsuura, Masaaki; Sugawara, Minoru; Ushijima, Masaru; Miyata, Satoshi; Nagasaki, Koichi; Noda, Tetsuo; Miki, Yoshio

    2014-02-18

    Fusion genes have been recognized to play key roles in oncogenesis. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired. We introduced a new method of detecting the novel fusion gene by using GeneChip Exon Array that enables exon expression analysis on a whole-genome scale and TAIL-PCR. To screen genes with abnormal exon expression profiles, we developed computational program, and confirmed that the program was able to search the fusion partner gene using Exon Array data of T-cell acute lymphocytic leukemia (T-ALL) cell lines. It was reported that the T-ALL cell lines, ALL-SIL, BE13 and LOUCY, harbored the fusion gene NUP214-ABL1, NUP214-ABL1 and SET-NUP214, respectively. The program extracted the candidate genes with abnormal exon expression profiles: 1 gene in ALL-SIL, 1 gene in BE13, and 2 genes in LOUCY. The known fusion partner gene NUP214 was included in the genes in ALL-SIL and LOUCY. Thus, we applied the proposed program to the detection of fusion partner genes in other tumors. To discover novel fusion genes, we examined 24 breast cancer cell lines and 20 pancreatic cancer cell lines by using the program. As a result, 20 and 23 candidate genes were obtained for the breast and pancreatic cancer cell lines respectively, and seven genes were selected as the final candidate gene based on information of the EST data base, comparison with normal cell samples and visual inspection of Exon expression profile. Finding of fusion partners for the final candidate genes was tried by TAIL-PCR, and three novel fusion genes were identified. The usefulness of our detection method was confirmed. Using this method for more samples, it is thought that fusion genes can be identified.

  18. Multi-exon deletions of the FBN1 gene in Marfan syndrome

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    Schrijver Iris

    2001-10-01

    Full Text Available Abstract Background Mutations in the fibrillin -1 gene (FBN1 cause Marfan syndrome (MFS, an autosomal dominant multi-system connective tissue disorder. The 200 different mutations reported in the 235 kb, 65 exon-containing gene include only one family with a genomic multi-exon deletion. Methods We used long-range RT-PCR for mutation detection and long-range genomic PCR and DNA sequencing for identification of deletion breakpoints, allele-specific transcript analyses to determine stability of the mutant RNA, and pulse-chase studies to quantitate fibrillin synthesis and extracellular matrix deposition in cultured fibroblasts. Southern blots of genomic DNA were probed with three overlapping fragments covering the FBN1 coding exons Results Two novel multi-exon FBN1 deletions were discovered. Identical nucleotide pentamers were found at or near the intronic breakpoints. In a Case with classic MFS, an in-frame deletion of exons 42 and 43 removed the C-terminal 24 amino acids of the 5th LTBP (8-cysteine domain and the adjacent 25th calcium-binding EGF-like (6-cysteine domain. The mutant mRNA was stable, but fibrillin synthesis and matrix deposition were significantly reduced. A Case with severe childhood-onset MFS has a de novo deletion of exons 44–46 that removed three EGF-like domains. Fibrillin protein synthesis was normal, but matrix deposition was strikingly reduced. No genomic rearrangements were detected by Southern analysis of 18 unrelated MFS samples negative for FBN1 mutation screening. Conclusions Two novel deletion cases expand knowledge of mutational mechanisms and genotype/phenotype correlations of fibrillinopathies. Deletions or mutations affecting an LTBP domain may result in unstable mutant protein cleavage products that interfere with microfibril assembly.

  19. High resolution melting for mutation scanning of TP53 exons 5–8

    International Nuclear Information System (INIS)

    Krypuy, Michael; Dobrovic, Alexander; Ahmed, Ahmed Ashour; Etemadmoghadam, Dariush; Hyland, Sarah J; Australian Ovarian Cancer Study Group; Fazio, Anna de; Fox, Stephen B; Brenton, James D; Bowtell, David D

    2007-01-01

    p53 is commonly inactivated by mutations in the DNA-binding domain in a wide range of cancers. As mutant p53 often influences response to therapy, effective and rapid methods to scan for mutations in TP53 are likely to be of clinical value. We therefore evaluated the use of high resolution melting (HRM) as a rapid mutation scanning tool for TP53 in tumour samples. We designed PCR amplicons for HRM mutation scanning of TP53 exons 5 to 8 and tested them with DNA from cell lines hemizygous or homozygous for known mutations. We assessed the sensitivity of each PCR amplicon using dilutions of cell line DNA in normal wild-type DNA. We then performed a blinded assessment on ovarian tumour DNA samples that had been previously sequenced for mutations in TP53 to assess the sensitivity and positive predictive value of the HRM technique. We also performed HRM analysis on breast tumour DNA samples with unknown TP53 mutation status. One cell line mutation was not readily observed when exon 5 was amplified. As exon 5 contained multiple melting domains, we divided the exon into two amplicons for further screening. Sequence changes were also introduced into some of the primers to improve the melting characteristics of the amplicon. Aberrant HRM curves indicative of TP53 mutations were observed for each of the samples in the ovarian tumour DNA panel. Comparison of the HRM results with the sequencing results revealed that each mutation was detected by HRM in the correct exon. For the breast tumour panel, we detected seven aberrant melt profiles by HRM and subsequent sequencing confirmed the presence of these and no other mutations in the predicted exons. HRM is an effective technique for simple and rapid scanning of TP53 mutations that can markedly reduce the amount of sequencing required in mutational studies of TP53

  20. Characterization of major histocompatibility complex (MHC DRB exon 2 and DRA exon 3 fragments in a primary terrestrial rabies vector (Procyon lotor.

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    Sarrah Castillo

    Full Text Available The major histocompatibility complex (MHC presents a unique system to explore links between genetic diversity and pathogens, as diversity within MHC is maintained in part by pathogen driven selection. While the majority of wildlife MHC studies have investigated species that are of conservation concern, here we characterize MHC variation in a common and broadly distributed species, the North American raccoon (Procyon lotor. Raccoons host an array of broadly distributed wildlife diseases (e.g., canine distemper, parvovirus and raccoon rabies virus and present important human health risks as they persist in high densities and in close proximity to humans and livestock. To further explore how genetic variation influences the spread and maintenance of disease in raccoons we characterized a fragment of MHC class II DRA exon 3 (250 bp and DRB exon 2 (228 bp. MHC DRA was found to be functionally monomorphic in the 32 individuals screened; whereas DRB exon 2 revealed 66 unique alleles among the 246 individuals screened. Between two and four alleles were observed in each individual suggesting we were amplifying a duplicated DRB locus. Nucleotide differences between DRB alleles ranged from 1 to 36 bp (0.4-15.8% divergence and translated into 1 to 21 (1.3-27.6% divergence amino acid differences. We detected a significant excess of nonsynonymous substitutions at the peptide binding region (P = 0.005, indicating that DRB exon 2 in raccoons has been influenced by positive selection. These data will form the basis of continued analyses into the spatial and temporal relationship of the raccoon rabies virus and the immunogenetic response in its primary host.

  1. Exon redefinition by a point mutation within exon 5 of the glucose-6-phosphatase gene is the major cause of glycogen storage disease type 1a in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Kajihara, Susumu; Yamamoto, Kyosuke; Kido, Keiko [Saga Medical (Japan)] [and others

    1995-09-01

    Glycogen storage disease (GSD) type 1a (von Gierke disease) is an autosomal recessive disorder caused by a deficiency in microsomal glucose-6-phosphatase (G6Pase). We have identified a novel mutation in the G6Pase gene of a individual with GSD type 1a. The cDNA from the patient`s liver revealed a 91-nt deletion in exon 5. The genomic DNA from the patient`s white blood cells revealed no deletion or mutation at the splicing junction of intron 4 and exon 5. The 3{prime} splicing occurred 91 bp from the 5{prime} site of exon 5 (at position 732 in the coding region), causing a substitution of a single nucleotide (G to T) at position 727 in the coding region. Further confirmation of the missplicing was obtained by transient expression of allelic minigene constructs into animal cells. Another eight unrelated families of nine Japanese patients were all found to have this mutation. This mutation is a new type of splicing mutation in the G6Pase gene, and 91% of patients and carriers suffering from GSD1a in Japan are detectable with this splicing mutation. 28 refs., 5 figs., 2 tabs.

  2. Exon redefinition by a point mutation within exon 5 of the glucose-6-phosphatase gene is the major cause of glycogen storage disease type 1a in Japan.

    Science.gov (United States)

    Kajihara, S; Matsuhashi, S; Yamamoto, K; Kido, K; Tsuji, K; Tanae, A; Fujiyama, S; Itoh, T; Tanigawa, K; Uchida, M

    1995-09-01

    Glycogen storage disease (GSD) type 1a (von Gierke disease) is an autosomal recessive disorder caused by a deficiency in microsomal glucose-6-phosphatase (G6Pase). We have identified a novel mutation in the G6Pase gene of a individual with GSD type 1a. The cDNA from the patient's liver revealed a 91-nt deletion in exon 5. The genomic DNA from the patient's white blood cells revealed no deletion or mutation at the splicing junction of intron 4 and exon 5. The 3' splicing occurred 91 bp from the 5' site of exon 5 (at position 732 in the coding region), causing a substitution of a single nucleotide (G to T) at position 727 in the coding region. Further confirmation of the missplicing was obtained by transient expression of allelic minigene constructs into animal cells. Another eight unrelated families of nine Japanese patients were all found to have this mutation. This mutation is a new type of splicing mutation in the G6Pase gene, and 91% of patients and carriers suffering from GSD1a in Japan are detectable with this splicing mutation.

  3. Neonatal Marfan syndrome caused by an exon 25 mutation of the fibrillin-1 gene.

    Science.gov (United States)

    Elçioglu, N H; Akalin, F; Elçioglu, M; Comeglio, P; Child, A H

    2004-01-01

    Neonatal Marfan syndrome caused by an exon 25 mutation of the Fibrillin-1 gene: We describe a male infant with severe arachnodactyly, hypermobility of the fingers, flexion contractures of elbows, wrists, hips, and knees, microretrognathia, crumpled ears, rockerbottom feet, loose redundant skin, and lens dislocations. Cardiac valve insufficiency and aortic dilatation resulted in cardiac failure, decompensated with digitalisation and death occurred at the age of 4 months. This case represents the severe end of the clinical spectrum of Marfan syndrome, namely neonatal Marfan syndrome. Molecular diagnostic analyses confirmed a de novo exon 25 mutation in the FBN1 gene.

  4. Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

    Science.gov (United States)

    Sharma, Alok; Nguyen, Hieu; Cai, Lu; Lou, Hua

    2015-01-01

    In contrast to cell type-specific pre-mRNA alternative splicing, mechanisms controlling activity-dependent alternative splicing is under-studied and not well understood. In a recent study, we conducted a comprehensive analysis of calcium-mediated mechanism that regulates alternative exon skipping in mouse cardiomyocytes. Our results reveal a strong link between histone hyperacetylation and skipping of cassette exons, and provide support to the kinetic coupling model of the epigenetic regulation of alternative splicing at the chromatin level. PMID:26325491

  5. Antisense PMO found in dystrophic dog model was effective in cells from exon 7-deleted DMD patient.

    Science.gov (United States)

    Saito, Takashi; Nakamura, Akinori; Aoki, Yoshitsugu; Yokota, Toshifumi; Okada, Takashi; Osawa, Makiko; Takeda, Shin'ichi

    2010-08-18

    Antisense oligonucleotide-induced exon skipping is a promising approach for treatment of Duchenne muscular dystrophy (DMD). We have systemically administered an antisense phosphorodiamidate morpholino oligomer (PMO) targeting dystrophin exons 6 and 8 to a dog with canine X-linked muscular dystrophy in Japan (CXMD(J)) lacking exon 7 and achieved recovery of dystrophin in skeletal muscle. To date, however, antisense chemical compounds used in DMD animal models have not been directly applied to a DMD patient having the same type of exon deletion. We recently identified a DMD patient with an exon 7 deletion and tried direct translation of the antisense PMO used in dog models to the DMD patient's cells. We converted fibroblasts of CXMD(J) and the DMD patient to myotubes by FACS-aided MyoD transduction. Antisense PMOs targeting identical regions of dog and human dystrophin exons 6 and 8 were designed. These antisense PMOs were mixed and administered as a cocktail to either dog or human cells in vitro. In the CXMD(J) and human DMD cells, we observed a similar efficacy of skipping of exons 6 and 8 and a similar extent of dystrophin protein recovery. The accompanying skipping of exon 9, which did not alter the reading frame, was different between cells of these two species. Antisense PMOs, the effectiveness of which has been demonstrated in a dog model, achieved multi-exon skipping of dystrophin gene on the FACS-aided MyoD-transduced fibroblasts from an exon 7-deleted DMD patient, suggesting the feasibility of systemic multi-exon skipping in humans.

  6. An exon skipping-associated nonsense mutation in the dystrophin gene uncovers a complex interplay between multiple antagonistic splicing elements.

    Science.gov (United States)

    Disset, A; Bourgeois, C F; Benmalek, N; Claustres, M; Stevenin, J; Tuffery-Giraud, Sylvie

    2006-03-15

    A nonsense mutation c.4250T>A (p.Leu1417X) in the dystrophin gene of a patient with an intermediate phenotype of muscular dystrophy induces partial in-frame skipping of exon 31. On the basis of UV cross-linking assays and pull-down analysis, we present evidence that the skipping of this exon is because of the creation of an exonic splicing silencer, which acts as a highly specific binding site (UAGACA) for a known repressor protein, hnRNP A1. Recombinant hnRNP A1 represses exon inclusion both in vitro and in vivo upon transient transfection of C2C12 cells with Duchenne muscular dystrophy (DMD) minigenes carrying the c.4250T>A mutation. Furthermore, we identified a downstream splicing enhancer in the central region of exon 31. This region functions as a Tra2beta-dependent exonic splicing enhancer (ESE) in vitro when inserted into a heterologous splicing reporter, and deletion of the ESE showed that incorporation of exon 31 depends on the Tra2beta-dependent enhancer both in the wild-type and mutant context. We conclude that dystrophin exon 31 contains juxtaposed sequence motifs that collaborate to regulate exon usage. This is the first elucidation of the molecular mechanism leading to exon skipping in the dystrophin gene and allowing the occurrence of a milder phenotype than the expected DMD phenotype. The knowledge of which cis-acting sequence within an exon is important for its definition will be essential for the alternative gene therapy approaches based on modulation of splicing to bypass DMD-causing mutations in the endogenous dystrophin gene.

  7. Antisense PMO found in dystrophic dog model was effective in cells from exon 7-deleted DMD patient.

    Directory of Open Access Journals (Sweden)

    Takashi Saito

    Full Text Available BACKGROUND: Antisense oligonucleotide-induced exon skipping is a promising approach for treatment of Duchenne muscular dystrophy (DMD. We have systemically administered an antisense phosphorodiamidate morpholino oligomer (PMO targeting dystrophin exons 6 and 8 to a dog with canine X-linked muscular dystrophy in Japan (CXMD(J lacking exon 7 and achieved recovery of dystrophin in skeletal muscle. To date, however, antisense chemical compounds used in DMD animal models have not been directly applied to a DMD patient having the same type of exon deletion. We recently identified a DMD patient with an exon 7 deletion and tried direct translation of the antisense PMO used in dog models to the DMD patient's cells. METHODOLOGY/PRINCIPAL FINDINGS: We converted fibroblasts of CXMD(J and the DMD patient to myotubes by FACS-aided MyoD transduction. Antisense PMOs targeting identical regions of dog and human dystrophin exons 6 and 8 were designed. These antisense PMOs were mixed and administered as a cocktail to either dog or human cells in vitro. In the CXMD(J and human DMD cells, we observed a similar efficacy of skipping of exons 6 and 8 and a similar extent of dystrophin protein recovery. The accompanying skipping of exon 9, which did not alter the reading frame, was different between cells of these two species. CONCLUSION/SIGNIFICANCE: Antisense PMOs, the effectiveness of which has been demonstrated in a dog model, achieved multi-exon skipping of dystrophin gene on the FACS-aided MyoD-transduced fibroblasts from an exon 7-deleted DMD patient, suggesting the feasibility of systemic multi-exon skipping in humans.

  8. Disease-causing mutations in exon 11 of the medium-chain acyl-CoA dehydrogenase gene

    DEFF Research Database (Denmark)

    Andresen, B S; Jensen, T G; Bross, P

    1994-01-01

    spot. Here we describe the results from sequence analysis of exon 11 and part of the flanking introns from 36 compound heterozygous patients with MCAD deficiency. We have identified four previously unknown disease-causing mutations (M301T, S311R, R324X, and E359X) and two silent mutations in exon 11...

  9. Polymorphism in the Alternative Donor Site of the Cryptic Exon of LHCGR: Functional Consequences and Associations with Testosterone Level.

    Science.gov (United States)

    Liu, Wei; Han, Bing; Zhu, Wenjiao; Cheng, Tong; Fan, Mengxia; Wu, Jiajun; Yang, Ying; Zhu, Hui; Si, Jiqiang; Lyu, Qifeng; Chai, Weiran; Zhao, Shuangxia; Song, Huaidong; Kuang, Yanping; Qiao, Jie

    2017-04-03

    Selective splicing is a feature of luteinizing hormone receptor (LHCGR). A cryptic exon (LHCGR-exon 6A) was found to be derived from alternative splicing in intron 6 of the LHCGR gene, which including two transcripts LHCGR-exon 6A-long and LHCGR-exon 6A-short. We addressed the functional consequences of SNP rs68073206, located at the +5 position of an alternative 5' splice donor site, and observed its association with male infertility in the subjects with azoospermia, oligoasthenozoospermia and normozoospermia. The translation product of splicing variant LHCGR-exon 6A was expressed in the cytoplasm and exhibited no affinity with [ 125 I]-hCG. No dominant negative effect was observed in cells co-expressed with LHCGR-exon 6A and wild-type LHCGR. The long transcript (LHCGR-exon 6A-long) was significantly elevated in the granulosa cells with G/G genotypes, which could be reproduced in vitro by mini-gene construct transfection. Genotyping analysis showed no association between rs68073206 and male infertility. However, this polymorphism was significantly associated with testosterone levels in normozoospermic subjects (n = 210). In conclusion, SNP rs68073206 in the splicing site of the cryptic exon 6A of the LHCGR gene affect the splicing pattern in the gene, which may play a role in the modulation of the LHCGR sensitivity in the gonads.

  10. Efficient Skipping of Single Exon Duplications in DMD Patient-Derived Cell Lines Using an Antisense Oligonucleotide Approach.

    Science.gov (United States)

    Wein, Nicolas; Vulin, Adeline; Findlay, Andrew R; Gumienny, Felecia; Huang, Nianyuan; Wilton, Steve D; Flanigan, Kevin M

    2017-01-01

    Exon skipping strategies in Duchenne muscular dystrophy (DMD) have largely been directed toward altering splicing of exons flanking out-of-frame deletions, with the goal of restoring an open mRNA reading frame that leads to production of an internally deleted but partially functional dystrophin protein. We sought to apply exon skipping to duplication mutations, assuming that the inherently limited efficiency of antisense oligonucleotide-induced exon skipping would more frequently skip a single copy of a duplicated exon, rather than both and result in significant amounts of wild-type DMD mRNA. We tested this hypothesis in fibroblast cell lines derived from patients with a variety of single or multiple exon duplications that have been modified to allow transdifferentiation into a myogenic lineage. Using a variety of 2'O-methyl antisense oligonucleotides, significant skipping was induced for each duplication leading to a wild-type transcript as a major mRNA product. This study provides another proof of concept for the feasibility of therapeutic skipping in patients carrying exon duplications in order to express wild-type, full-length mRNA, although careful evaluation of the skipping efficiency should be performed as some exons are easier to skip than others. Such a personalized strategy is expected to be highly beneficial for this subset of DMD patients, compared to inducing expression of an internally-deleted dystrophin.

  11. The exon-3 deleted growth hormone receptor polymorphism predisposes to long-term complications of acromegaly

    NARCIS (Netherlands)

    Wassenaar, M. J. E.; Biermasz, N. R.; Pereira, A. M.; van der Klaauw, A. A.; Smit, J. W. A.; Roelfsema, F.; van der Straaten, T.; Cazemier, M.; Hommes, D. W.; Kroon, H. M.; Kloppenburg, M.; Guchelaar, H.-J.; Romijn, J. A.

    2009-01-01

    The aim of the study was to evaluate the impact of the genomic deletion of exon 3 of the GH receptor (d3GHR) on long-term clinical outcome of acromegaly in a well-characterized cohort of patients with long-term remission of acromegaly. We conducted a cross-sectional study. The presence of the d3GHR

  12. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

    Directory of Open Access Journals (Sweden)

    Aramburu Ander

    2010-11-01

    Full Text Available Abstract Background Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored. Results We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP and sensitivity (ST of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results. Conclusions The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.

  13. A novel first exon directs hormone-sensitive transcription of the pig prolactin receptor

    Science.gov (United States)

    Endocrine, paracrine, and autocrine prolactin (PRL) acts through its receptor (PRLR) to confer a wide range of biological functions, including its established role during lactation.We have identified a novel first exon of the porcine PRLR that gives rise to three different mRNA transcripts. Transcri...

  14. Association between A59V polymorphism in exon 3 of leptin gene ...

    African Journals Online (AJOL)

    ONOS

    2010-09-06

    Sep 6, 2010 ... We used the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique to screen for DNA polymorphisms of the leptin gene in 255 cows of Iranian Holstein. Amplified region is located in exon 3 of leptin gene. The genomic bovine leptin sequences, which consist of three ...

  15. Mutations in exon 10 of the RET proto-oncogene in Hirschsprung`s disease

    Energy Technology Data Exchange (ETDEWEB)

    Attie, T.; Eng, C.; Mulligan, L.M. [Hospital des Enfants-Malades, Paris (France)] [and others

    1994-09-01

    Hirschsprung`s disease (HSCR) is a frequent congenital malformation ascribed to the absence of autonomic ganglion cells in the terminal hindgut. Recently, we have identified mutations in the RET proto-oncogene in HSCR families. Mutations of the RET gene have also been reported in multiple endocrine neoplasia type 2A (MEN 2A) and familial medullary thyroid carcinoma (FMTC). While RET mutations in HSCR are scattered on the whole coding sequence, MEN 2A and FMTC mutations are clustered in 5 cystein codons of exons 10 and 11. Here, we report on HSCR families carrying mutations in exon 10 of the RET gene, one of them involving a cystein codon. Germ-line mutations in exon 10 of the RET gene may contribute to either an early development defect (HSCR) or inherited predisposition to cancer (MEN 2A and FMTC), probable depending on the nature and location of the mutation. These data also suggest that HSCR patients with mutations in exon 10 might subsequently prove to be at risk for MEN 2A or FMTC since several MEN 2A/HSCR associations have been reported.

  16. Mucopolysaccharidosis IVA: Four new exonic mutations in patients with N-acetylgalactosamine-6-sulfate sulfatase deficiency

    Energy Technology Data Exchange (ETDEWEB)

    Tomatsu, Shunji; Fukuda, Seiji; Yamagishi, Atsushi [Gifu Univ. (Japan)] [and others

    1996-05-01

    We report four new mutations in Japanese patients with mucopolysaccharidosis IVA (MPSIVA) who were heterozygous for a common double gene deletion. A nonsense mutation of CAG to TAG at codon 148 in exon 4 was identified, resulting in a change of Q to a stop codon and three missense mutations: V (GTC) to A (GCC) at codon 138 in exon 4, P (CCC) to S (TCC) at codon 151 in exon 5, and P (CCC) to L (CTC) at codon 151 in exon 5. Introduction of these mutations into the normal GALNS cDNA and transient expression in cultured fibroblasts resulted in a significant decrease in the enzyme activity. V138A and Q148X mutations result in changes of restriction site, which were analyzed by restriction-enzyme assay. P151S and P151L mutations that did not alter the restriction site were detected by direct sequencing or allele specific oligohybridization. Detection of the double gene deletion was initially done using Southern blots and was confirmed by PCR. Haplotypes were determined using seven polymorphisms to the GALNS locus in families with the double gene deletion. Haplotype analysis showed that the common double gene deletion occurred on a single haplotype, except for some variation in a VNTR-like polymorphism. This finding is consistent with a common founder for all individuals with this mutation. 48 refs., 5 figs., 1 tab.

  17. Genotyping of RHD by multiplex polymerase chain reaction analysis of six RHD-specific exons

    NARCIS (Netherlands)

    Maaskant-van Wijk, P. A.; Faas, B. H.; de Ruijter, J. A.; Overbeeke, M. A.; von dem Borne, A. E.; van Rhenen, D. J.; van der Schoot, C. E.

    1998-01-01

    Qualitative RHD variants are the result of the replacement of RHD exons by their RHCE counterparts or of point mutations in RHD causing amino acid substitutions. For RHD typing, the use of at least two RHD typing polymerase chain reaction (PCR) assays directed at different regions of RHD is advised

  18. Prevalence of the exon 2 deletion of the COMMD1 gene in ...

    Indian Academy of Sciences (India)

    rier appears to be related to the reduced biliary excretion of stored copper resulting from a genetic derangement in cop- per metabolism (Hardy 1984; Hyun and Filippich 2004). A mutation resulting in the deletion of exon 2 in the COMMD1. (formerly known as Murr1) gene was found to be responsible for copper toxicosis in a ...

  19. Therapeutic antisense-induced exon skipping in cultured muscle cells from six different DMD patients

    NARCIS (Netherlands)

    Aartsma-Rus, Annemieke; Janson, Anneke A. M.; Kaman, Wendy E.; Bremmer-Bout, Mattie; den Dunnen, Johan T.; Baas, Frank; van Ommen, Gert-Jan B.; van Deutekom, Judith C. T.

    2003-01-01

    The dystrophin deficiency leading to the severely progressing muscle degeneration in Duchenne muscular dystrophy (DMD) patients is caused by frame-shifting mutations in the DMD gene. We are developing a reading frame correction therapy aimed at the antisense-induced skipping of targeted exons from

  20. Deletion of SNURF/SNRPN U1B and U1B* upstream exons in a ...

    Indian Academy of Sciences (India)

    SNURF/SNRPN U1B and U1B* upstream exons in a child with developmental delay and excessive weight. J. Genet. 95, 621–624]. Introduction ... motor and language development and behavioural abnorma- lities (Buiting 2010). PWS is caused ... Here, we report an examination of a child diagnosed as overweight with mild ...

  1. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation.

    NARCIS (Netherlands)

    Tarpey, P.S.; Smith, R.; Pleasance, E.; Whibley, A.; Edkins, S.; Hardy, C.; O'Meara, S.; Latimer, C.; Dicks, E.; Menzies, A.; Stephens, P.; Blow, M.; Greenman, C.; Xue, Y.; Tyler-Smith, C.; Thompson, D.; Gray, K.; Andrews, J.; Barthorpe, S.; Buck, G.; Cole, J.; Dunmore, R.; Jones, D.; Maddison, M.; Mironenko, T.; Turner, R.; Turrell, K.; Varian, J.; West, S.; Widaa, S.; Wray, P.; Teague, J.; Butler, A.; Jenkinson, A.; Jia, M.; Richardson, D.; Shepherd, R.; Wooster, R.; Tejada, M.I.; Martinez, F.; Carvill, G.; Goliath, R.; Brouwer, A.P.M. de; Bokhoven, H. van; Esch, H. van; Chelly, J.; Raynaud, M.; Ropers, H.H.; Abidi, F.E.; Srivastava, A.K.; Cox, J.; Luo, Y.; Mallya, U.; Moon, J.; Parnau, J.; Mohammed, S.; Tolmie, J.L.; Shoubridge, C.; Corbett, M.; Gardner, A.; Haan, E.; Rujirabanjerd, S.; Shaw, M.A.; Vandeleur, L.; Fullston, T.; Easton, D.F.; Boyle, J.; Partington, M.; Hackett, A.; Field, M.; Skinner, C.; Stevenson, R.E.; Bobrow, M.; Turner, G.; Schwartz, C.E.; Gecz, J.; Raymond, F.L.; Futreal, P.A.; Stratton, M.R.

    2009-01-01

    Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR),

  2. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

    Science.gov (United States)

    Gretchen H. Roffler; Stephen J. Amish; Seth Smith; Ted Cosart; Marty Kardos; Michael K. Schwartz; Gordon Luikart

    2016-01-01

    Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding...

  3. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping

    Czech Academy of Sciences Publication Activity Database

    Divina, Petr; Kvitkovicova, Andrea; Buratti, E.; Vorechovsky, I.

    2009-01-01

    Roč. 17, č. 6 (2009), s. 759-765 ISSN 1018-4813 Institutional research plan: CEZ:AV0Z50520514 Keywords : mutation * cryptic splice site * exon skipping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.564, year: 2009

  4. Duchenne muscular dystrophy in a female with compound heterozygous contiguous exon deletions.

    Science.gov (United States)

    Takeshita, Eri; Minami, Narihiro; Minami, Kumiko; Suzuki, Mikiya; Awashima, Takeya; Ishiyama, Akihiko; Komaki, Hirofumi; Nishino, Ichizo; Sasaki, Masayuki

    2017-06-01

    Females with Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) mutations rarely exhibit clinical symptoms from childhood, although potential mechanisms for symptoms associated with DMD and BMD in females have been reported. We report the case of a female DMD patient with a clinical course indistinguishable from that of a male DMD patient, and who possessed compound heterozygous contiguous exon deletions in the dystrophin gene. She exhibited Gowers' sign, calf muscle hypertrophy, and a high serum creatine kinase level at 2 years. Her muscle pathology showed most of the fibers were negative for dystrophin immunohistochemical staining. She lost ambulation at 11 years. Multiplex ligation-dependent probe amplification analysis of this gene detected one copy of exons 48-53; she was found to be a BMD carrier with an in-frame deletion. Messenger RNA from her muscle demonstrated out-of-frame deletions of exons 48-50 and 51-53 occurring on separate alleles. Genomic DNA from her lymphocytes demonstrated the accurate deletion region on each allele. To our knowledge, this is the first report on a female patient possessing compound heterozygous contiguous exon deletions in the dystrophin gene, leading to DMD. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Dual exon skipping in myostatin and dystrophin for Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    van Ommen Gert Jan B

    2011-04-01

    Full Text Available Abstract Background Myostatin is a potent muscle growth inhibitor that belongs to the Transforming Growth Factor-β (TGF-β family. Mutations leading to non functional myostatin have been associated with hypermuscularity in several organisms. By contrast, Duchenne muscular dystrophy (DMD is characterized by a loss of muscle fibers and impaired regeneration. In this study, we aim to knockdown myostatin by means of exon skipping, a technique which has been successfully applied to reframe the genetic defect of dystrophin gene in DMD patients. Methods We targeted myostatin exon 2 using antisense oligonucleotides (AON in healthy and DMD-derived myotubes cultures. We assessed the exon skipping level, transcriptional expression of myostatin and its target genes, and combined myostatin and several dystrophin AONs. These AONs were also applied in the mdx mice models via intramuscular injections. Results Myostatin AON induced exon 2 skipping in cell cultures and to a lower extent in the mdx mice. It was accompanied by decrease in myostatin mRNA and enhanced MYOG and MYF5 expression. Furthermore, combination of myostatin and dystrophin AONs induced simultaneous skipping of both genes. Conclusions We conclude that two AONs can be used to target two different genes, MSTN and DMD, in a straightforward manner. Targeting multiple ligands of TGF-beta family will be more promising as adjuvant therapies for DMD.

  6. Exon skipping: a first in class strategy for Duchenne muscular dystrophy.

    Science.gov (United States)

    Niks, Erik H; Aartsma-Rus, Annemieke

    2017-02-01

    Exon skipping is a therapeutic approach for Duchenne muscular dystrophy (DMD) that has been in development for close to two decades. This approach uses antisense oligonucleotides (AONs) to modulate pre-mRNA splicing of dystrophin transcripts to restore the disrupted DMD reading frame. The approach has moved from in vitro proof of concept studies to the clinical trial phase and marketing authorization applications with regulators. The first AON (eteplirsen) has recently received accelerated approval by the Food and Drug Administration in the US. Areas covered: In this review the authors explain the antisense-mediated exon skipping approach, outline how it needs be tailored for different DMD mutation types and describe the challenges and opportunities for each mutation type. The authors summarize the clinical development of antisense-mediated exon 51 skipping, and discuss methods to improve efficiency. Finally, the authors provide their opinion on current developments and identify topics for future prioritization. Expert opinion: Exon skipping development has been a learning experience for all those involved. Aside from an approved therapy, its development has yielded side benefits including the development of tools for clinical trials and has increased collaboration between academics, patients, industry and regulators.

  7. Loss of Endocan tumorigenic properties after alternative splicing of exon 2

    Directory of Open Access Journals (Sweden)

    Scherpereel Arnaud

    2008-01-01

    Full Text Available Abstract Background Endocan was originally described as a dermatan sulfate proteoglycan found freely circulating in the blood. Endocan expression confers tumorigenic properties to epithelial cell lines or accelerate the growth of already tumorigenic cells. This molecule is the product of a single gene composed of 3 exons. Previous data showed that endocan mRNA is subject to alternative splicing with possible generation of two protein products. In the present study we identified, and functionally characterized, the alternative spliced product of the endocan gene: the exon 2-deleted endocan, called endocanΔ2. Methods Stable, endocanΔ2-overexpressing cell lines were generated to investigate the biological activities of this new alternatively spliced product of endocan gene. Tumorigenesis was studied by inoculating endocan and endocanΔ2 expressing cell lines subcutaneously in SCID mice. Biochemical properties of endocan and endocanΔ2 were studied after production of recombinant proteins in various cell lines of human and murine origin. Results Our results showed that the exon 2 deletion impairs synthesis of the glycan chain, known to be involved in the pro-tumoral effect of endocan. EndocanΔ2 did not promote tumor formation by 293 cells implanted in the skin of severe combined immunodeficient (SCID mice. Conclusion Our results emphasize the key role of the polypeptide sequence encoded by the exon 2 of endocan gene in tumorigenesis, and suggest that this sequence could be a target for future therapies against cancer.

  8. Exon expression arrays as a tool to identify new cancer genes

    NARCIS (Netherlands)

    M. Schutte (Mieke); F. Elstrodt (Fons); L.B.C. Bralten (Linda); J.H.A. Nagel (Jord); E. Duijm (Elza); A. Hollestelle (Antoinette); M.J. Vuerhard (Maartje); M. Wasielewski (Marijke); J.K. Peeters (Justine); P.J. van der Spek (Peter); P.A.E. Sillevis Smitt (Peter); P.J. French (Pim)

    2008-01-01

    textabstractBackground: Identification of genes that are causally implicated in oncogenesis is a major goal in cancer research. An estimated 10-20% of cancer-related gene mutations result in skipping of one or more exons in the encoded transcripts. Here we report on a strategy to screen in a global

  9. Concurrent mutation in exons 1 and 2 of the K-ras oncogene in colorectal cancer

    Directory of Open Access Journals (Sweden)

    Fiorella Guadagni

    2012-01-01

    Full Text Available The K-ras gene is frequently mutated in colorectal cancer and has been associated with tumor initiation and progression; approximately 90% of the activating mutations are found in codons 12 and 13 of exon 1 and just under 5% in codon 61 located in exon 2. These mutations determine single aminoacidic substitutions in the GTPase pocket leading to a block of the GTP hydrolytic activity of the K-ras p21 protein, and therefore to its constitutive activation. Point mutations in sites of the K-ras gene, other than codons 12, 13 and 61, and other types of genetic alterations, may occur in a minority of cases, such as in the less frequent cases of double mutations in the K-ras gene. However, all mutations in this gene, even those which occur in non-canonical sites or double mutations, are relevant oncogenic alterations in colorectal cancer and may underlie K-ras pathway hyperactivation. In the present study, we report the case of a patient with colorectal cancer presenting a concurrent point mutation in exons 1 and 2 of the K-ras gene, a GGT to TGT substitution (Glycine to Cysteine at codon 12, and a GAC to AAC substitution (Aspartic Acid to Asparagine at codon 57. In addition, we found in the same patient’s sample a silent polymorphism at codon 11 (Ala11Ala of exon 1. (Folia Histochemica et Cytobiologica 2011; Vol. 49, No. 4, pp. 729–733

  10. Longitudinal changes in glucocorticoid receptor exon 1(F) methylation and psychopathology after military deployment

    NARCIS (Netherlands)

    Schür, R. R.; Boks, M. P.; Rutten, B. P. F.; Daskalakis, N. P.; de Nijs, L.; van Zuiden, M.; Kavelaars, A.; Heijnen, C. J.; Joëls, M.; Kahn, R. S.; Geuze, E.; Vermetten, E.; Vinkers, C. H.

    2017-01-01

    Several cross-sectional studies have demonstrated the relevance of DNA methylation of the glucocorticoid receptor exon 1(F) region (GR-1(F)) for trauma-related psychopathology. We conducted a longitudinal study to examine GR-1(F) methylation changes over time in relation to trauma exposure and the

  11. Longitudinal changes in glucocorticoid receptor exon 1F methylation and psychopathology after military deployment

    NARCIS (Netherlands)

    Schür, R R; Boks, M P; Rutten, Bart P. F.; Daskalakis, N.P.; de Nijs, Laurence; van Zuiden, M.; Kavelaars, A; Heijnen, C J; Joëls, M; Kahn, R S; Geuze, E; Vermetten, E; Vinkers, C H

    2017-01-01

    Several cross-sectional studies have demonstrated the relevance of DNA methylation of the glucocorticoid receptor exon 1F region (GR-1F) for trauma-related psychopathology. We conducted a longitudinal study to examine GR-1F methylation changes over time in relation to trauma exposure and the

  12. Genetic variation at Exon2 of TLR4 gene and its association with ...

    African Journals Online (AJOL)

    This study was conducted to analyze the polymorphisms of chicken Toll-like receptors 4(TLR4) gene and aimed to provide a theoretical foundation for a further research on correlation between chicken TLR4 gene and disease resistance. Genetic variations at exon 2 of TLR4 gene in 14 chicken breeds and the red jungle ...

  13. Loss of Endocan tumorigenic properties after alternative splicing of exon 2

    International Nuclear Information System (INIS)

    Depontieu, Florence; Grigoriu, Bogdan-Dragos; Scherpereel, Arnaud; Adam, Estelle; Delehedde, Maryse; Gosset, Philippe; Lassalle, Philippe

    2008-01-01

    Endocan was originally described as a dermatan sulfate proteoglycan found freely circulating in the blood. Endocan expression confers tumorigenic properties to epithelial cell lines or accelerate the growth of already tumorigenic cells. This molecule is the product of a single gene composed of 3 exons. Previous data showed that endocan mRNA is subject to alternative splicing with possible generation of two protein products. In the present study we identified, and functionally characterized, the alternative spliced product of the endocan gene: the exon 2-deleted endocan, called endocanΔ2. Stable, endocanΔ2-overexpressing cell lines were generated to investigate the biological activities of this new alternatively spliced product of endocan gene. Tumorigenesis was studied by inoculating endocan and endocanΔ2 expressing cell lines subcutaneously in SCID mice. Biochemical properties of endocan and endocanΔ2 were studied after production of recombinant proteins in various cell lines of human and murine origin. Our results showed that the exon 2 deletion impairs synthesis of the glycan chain, known to be involved in the pro-tumoral effect of endocan. EndocanΔ2 did not promote tumor formation by 293 cells implanted in the skin of severe combined immunodeficient (SCID) mice. Our results emphasize the key role of the polypeptide sequence encoded by the exon 2 of endocan gene in tumorigenesis, and suggest that this sequence could be a target for future therapies against cancer

  14. Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila

    NARCIS (Netherlands)

    Brites, Daniela; Encinas-Viso, Francisco; Ebert, Dieter; Du Pasquier, Louis; Haag, Christoph R.

    2011-01-01

    In insects and crustaceans, the Down syndrome cell adhesion molecule (Dscam) occurs in many different isoforms. These are produced by mutually exclusive alternative splicing of dozens of tandem duplicated exons coding for parts or whole immunoglobulin (Ig) domains of the Dscam protein. This

  15. Folding Landscape of Mutant Huntingtin Exon1: Diffusible Multimers, Oligomers and Fibrils, and No Detectable Monomer.

    Directory of Open Access Journals (Sweden)

    Bankanidhi Sahoo

    Full Text Available Expansion of the polyglutamine (polyQ track of the Huntingtin (HTT protein above 36 is associated with a sharply enhanced risk of Huntington's disease (HD. Although there is general agreement that HTT toxicity resides primarily in N-terminal fragments such as the HTT exon1 protein, there is no consensus on the nature of the physical states of HTT exon1 that are induced by polyQ expansion, nor on which of these states might be responsible for toxicity. One hypothesis is that polyQ expansion induces an alternative, toxic conformation in the HTT exon1 monomer. Alternative hypotheses posit that the toxic species is one of several possible aggregated states. Defining the nature of the toxic species is particularly challenging because of facile interconversion between physical states as well as challenges to identifying these states, especially in vivo. Here we describe the use of fluorescence correlation spectroscopy (FCS to characterize the detailed time and repeat length dependent self-association of HTT exon1-like fragments both with chemically synthesized peptides in vitro and with cell-produced proteins in extracts and in living cells. We find that, in vitro, mutant HTT exon1 peptides engage in polyQ repeat length dependent dimer and tetramer formation, followed by time dependent formation of diffusible spherical and fibrillar oligomers and finally by larger, sedimentable amyloid fibrils. For expanded polyQ HTT exon1 expressed in PC12 cells, monomers are absent, with tetramers being the smallest molecular form detected, followed in the incubation time course by small, diffusible aggregates at 6-9 hours and larger, sedimentable aggregates that begin to build up at 12 hrs. In these cell cultures, significant nuclear DNA damage appears by 6 hours, followed at later times by caspase 3 induction, mitochondrial dysfunction, and cell death. Our data thus defines limits on the sizes and concentrations of different physical states of HTT exon1 along the

  16. Fibronectin type III (FN3) modules of the neuronal cell adhesion molecule L1 interact directly with the fibroblast growth factor (FGF) receptor

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Li, Shizhong; Hinsby, Anders Mørkeberg

    2008-01-01

    The neuronal cell adhesion molecule (CAM) L1 promotes axonal outgrowth, presumably through an interaction with the fibroblast growth factor receptor (FGFR). The present study demonstrates a direct interaction between L1 fibronectin type III (FN3) modules I-V and FGFR1 immunoglobulin (Ig) modules II...

  17. Fibronectin has a dual role in locomotion and anchorage of primary chick fibroblasts and can promote entry into the division cycle

    DEFF Research Database (Denmark)

    Couchman, J R; Rees, D A; Green, M R

    1982-01-01

    Fibronectin (FN), which is already known to be a natural factor for fibroblast spreading on substrata, has now been shown to be essential for two distinct types of adhesion with different biological functions in chick heart fibroblasts, namely adhesion directed toward locomotion and toward statio...... for stationary anchorage can be dramatically enhanced by addition of cell-derived FN at an appropriate stage, and this promotes entry into the growth cycle. New macromolecular synthesis in addition to FN is necessary for focal adhesion development but not for locomotion....... stationary anchorage for growth. Manipulation of culture conditions and the use of antisera of differing specificities has demonstrated that both exogenous and cell-derived FN are important in each process. The organization of the fibronectin-containing matrix differs between the two states. Immunoelectron...... microscopy with a colloidal gold marker reveals the presence of small membrane-associated plaques of fibronectin in motile cells with associated submembranous specialization. A fibrillar matrix containing fibronectin is dominant in nonmotile, growing fibroblasts. The development of focal adhesions...

  18. Accumulation of fibronectin in the heart after myocardial infarction: a putative stimulator of adhesion and proliferation of adipose-derived stem cells

    NARCIS (Netherlands)

    van Dijk, A.; Niessen, H.W.M.; Ursem, W.; Twisk, J.W.; Visser, F.C.; van Milligen-Kummer, F.J.

    2008-01-01

    Stem cell therapy is a promising treatment after myocardial infarction (MI). A major problem in stem cell therapy, however, is that only a small proportion of stem cells applied to the heart can survive and differentiate into cardiomyocytes. We hypothesized that fibronectin in the heart after MI

  19. Rapid fetal fibronectin testing to predict preterm birth in women with symptoms of premature labour: a systematic review and cost analysis

    NARCIS (Netherlands)

    N.V. Deshpande (Niteen Vijay); A.D.I. van Asselt (Antoinette); F. Tomini; N. Armstrong (Nigel); A. Allen (Alex); C. Noake; K.S. Khan (Kalid); J.L. Severens (Hans); J. Kleijnen (Jos); M. Westwood (Marie)

    2013-01-01

    markdownabstract__Background__: Premature birth is defined as birth of before 37 completed weeks' gestation. Not all pregnant women showing symptoms of preterm labour will go on to deliver before 37weeks' gestation. Hence, addition of fetal fibronectin (fFN) testing to the diagnostic workup of

  20. Rapid fetal fibronectin testing to predict preterm birth in women with symptoms of premature labour : a systematic review and cost analysis

    NARCIS (Netherlands)

    Deshpande, S N; van Asselt, A D I; Tomini, F; Armstrong, N; Allen, A; Noake, C; Khan, K; Severens, J L; Kleijnen, J; Westwood, M E

    2013-01-01

    BACKGROUND: Premature birth is defined as birth of before 37 completed weeks' gestation. Not all pregnant women showing symptoms of preterm labour will go on to deliver before 37 weeks' gestation. Hence, addition of fetal fibronectin (fFN) testing to the diagnostic workup of women with suspected

  1. The behaviour of fibroblasts migrating from chick heart explants: changes in adhesion, locomotion and growth, and in the distribution of actomyosin and fibronectin

    DEFF Research Database (Denmark)

    Couchman, J R; Rees, D A

    1979-01-01

    towards efficient locomotion whilst maintaining a high degree of spreading. Also during the first 48 h there is little production of extracellular fibronectin and the growth rate is low. Later, these fibroblasts develop focal contacts and focal adhesions together with actomyosin bundles, with a parallel...

  2. THE HEPARIN-BINDING DOMAIN AND V REGION OF FIBRONECTIN REGULATE APOPTOSIS BY SUPPRESSION OF P53 AND C-MYC IN HUMAN PRIMARY CELLS

    Science.gov (United States)

    In apoptosis the tumor suppressor p53 and oncogene c-myc, are usually upregulated. However, we report here an alternate pathway of regulation that is triggered by inflammatory-associated matrix fragments of fibronectin (FN) and leads to apoptosis. It is mediated by transcriptio...

  3. Quantitative fetal fibronectin and cervical length to predict preterm birth in asymptomatic women with previous cervical surgery.

    Science.gov (United States)

    Vandermolen, Brooke I; Hezelgrave, Natasha L; Smout, Elizabeth M; Abbott, Danielle S; Seed, Paul T; Shennan, Andrew H

    2016-10-01

    Quantitative fetal fibronectin testing has demonstrated accuracy for prediction of spontaneous preterm birth in asymptomatic women with a history of preterm birth. Predictive accuracy in women with previous cervical surgery (a potentially different risk mechanism) is not known. We sought to compare the predictive accuracy of cervicovaginal fluid quantitative fetal fibronectin and cervical length testing in asymptomatic women with previous cervical surgery to that in women with 1 previous preterm birth. We conducted a prospective blinded secondary analysis of a larger observational study of cervicovaginal fluid quantitative fetal fibronectin concentration in asymptomatic women measured with a Hologic 10Q system (Hologic, Marlborough, MA). Prediction of spontaneous preterm birth (<30, <34, and <37 weeks) with cervicovaginal fluid quantitative fetal fibronectin concentration in primiparous women who had undergone at least 1 invasive cervical procedure (n = 473) was compared with prediction in women who had previous spontaneous preterm birth, preterm prelabor rupture of membranes, or late miscarriage (n = 821). Relationship with cervical length was explored. The rate of spontaneous preterm birth <34 weeks in the cervical surgery group was 3% compared with 9% in previous spontaneous preterm birth group. Receiver operating characteristic curves comparing quantitative fetal fibronectin for prediction at all 3 gestational end points were comparable between the cervical surgery and previous spontaneous preterm birth groups (34 weeks: area under the curve, 0.78 [95% confidence interval 0.64-0.93] vs 0.71 [95% confidence interval 0.64-0.78]; P = .39). Prediction of spontaneous preterm birth using cervical length compared with quantitative fetal fibronectin for prediction of preterm birth <34 weeks of gestation offered similar prediction (area under the curve, 0.88 [95% confidence interval 0.79-0.96] vs 0.77 [95% confidence interval 0.62-0.92], P = .12 in the cervical

  4. Use of epitope libraries to identify exon-specific monoclonal antibodies for characterization of altered dystrophins in muscular dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen thi Man; Morris, G.E. (North East Wales Inst., Clwyd (United Kingdom))

    1993-06-01

    The majority of mutations in Xp21-linked muscular dystrophy (MD) can be identified by PCR or Southern blotting, as deletions or duplications of groups of exons in the dystrophin gene, but it is not always possible to predict how much altered dystrophin, if any, will be produced. Use of exon-specific monoclonal antibodies (mAbs) on muscle biopsies from MD patients can, in principle, provide information on both the amount of altered dystrophin produced and, when dystrophin is present, the nature of the genetic deletion or point mutation. For this purpose, mAbs which recognize regions of dystrophin encoded by known exons and whose binding is unaffected by the absence of adjacent exons are required. To map mAbs to specific exons, random [open quotes]libraries[close quotes] of expressed dystrophin fragments were created by cloning DNAseI digestion fragments of a 4.3-kb dystrophin cDNA into a pTEX expression vector. The libraries were then used to locate the epitopes recognized by 48 mAbs to fragments of 25--60 amino acids within the 1,434-amino-acid dystrophin fragment used to produce the antibodies. This is sufficiently detailed to allow further refinement by using synthetic peptides and, in many cases, to identify the exon in the DMD (Duchenne MD) gene which encodes the epitope. To illustrate their use in dystrophin analysis, a Duchenne patient with a frameshift deletion of exons 42 and 43 makes a truncated dystrophin encoded by exons 1--41, and the authors now show that this can be detected in the sarcolemma by mAbs up to and including those specific for exon 41 epitopes but not by mAbs specific for exon 43 or later epitopes. 38 refs., 2 figs., 4 tabs.

  5. Mutasi titik hingga mutasi frameshift gen INSR exon 22 pada pasien penderita diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Fatchiyah Fatchiyah

    2012-02-01

    Full Text Available Mutations of human insulin and insulin receptor family can lead autosomal dominant syndrome on diabetes, fasting hyperinsulinemia, and insulin receptor family can lead autosomal dominant syndrome on diabetes, fasting hyperinsulinemia, and insulin resistant. The aim of this research was to identify mutation types of hINSR gene exon 22 which mutation hot spot region. To analyze hINSR gene exon 22 of DM patient and control, we isolated DNA from their blood. DNA was then amplified by PCR using a set of primer for exon 22. PCR product was sequenced by Sequencer and nucleotide sequence analyzed by BLAST analysis. According to Gene Bank database, hINSR gene has two variant with Gene ID 3643, at chromosome 19p13.3-p13.2, and has 22 exons with mRNA 4200bp. The result of research showed that the mutation types of hINS gene exon 22 of DM patients are point mutation, single base deletion and substitution. We found mutation of single deletion at Met eletion at Met1295 Cys1295 and Glut1300 Gly1300, also point mutation are at Met1296 Ser1296 and Trp1299 Ala1299 and Met1389 Iso1389. Because these two deletion are so close, the polypeptids sequence of these changed as frameshift mutation, normal IR has six amino acids -Met Arg Met Cys rp lut- and DM patient has differed the five amino acids - Cys Ala Ser Ala Gly. According to the mutation of DM patient, the IR protein function against tyrosine kinase become abnormal, perhaps its were correlated with genetic syndrom genetic syndrome of insulin resistance. e of insulin resistance.

  6. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

    Science.gov (United States)

    Roffler, Gretchen H.; Amish, Stephen J.; Smith, Seth; Cosart, Ted F.; Kardos, Marty; Schwartz, Michael K.; Luikart, Gordon

    2016-01-01

    Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositan and bayescan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.

  7. Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.

    Science.gov (United States)

    Marquez, Yamile; Höpfler, Markus; Ayatollahi, Zahra; Barta, Andrea; Kalyna, Maria

    2015-07-01

    Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also identify such AS events in human and use these two sets to analyse their features, regulation, functional impact, and evolutionary origin. As these events involve introns with features of both introns and protein-coding exons, we name them exitrons (exonic introns). Though exitrons were detected as a subset of retained introns, they are clearly distinguishable, and their splicing results in transcripts with different fates. About half of the 1002 Arabidopsis and 923 human exitrons have sizes of multiples of 3 nucleotides (nt). Splicing of these exitrons results in internally deleted proteins and affects protein domains, disordered regions, and various post-translational modification sites, thus broadly impacting protein function. Exitron splicing is regulated across tissues, in response to stress and in carcinogenesis. Intriguingly, annotated intronless genes can be also alternatively spliced via exitron usage. We demonstrate that at least some exitrons originate from ancestral coding exons. Based on our findings, we propose a "splicing memory" hypothesis whereby upon intron loss imprints of former exon borders defined by vestigial splicing regulatory elements could drive the evolution of exitron splicing. Altogether, our studies show that exitron splicing is a conserved strategy for increasing proteome plasticity in plants and animals, complementing the repertoire of AS events. © 2015 Marquez et al.; Published by Cold Spring Harbor Laboratory Press.

  8. ATX-LPA1 axis contributes to proliferation of chondrocytes by regulating fibronectin assembly leading to proper cartilage formation.

    Science.gov (United States)

    Nishioka, Tatsuji; Arima, Naoaki; Kano, Kuniyuki; Hama, Kotaro; Itai, Eriko; Yukiura, Hiroshi; Kise, Ryoji; Inoue, Asuka; Kim, Seok-Hyung; Solnica-Krezel, Lilianna; Moolenaar, Wouter H; Chun, Jerold; Aoki, Junken

    2016-03-23

    The lipid mediator lysophosphatidic acid (LPA) signals via six distinct G protein-coupled receptors to mediate both unique and overlapping biological effects, including cell migration, proliferation and survival. LPA is produced extracellularly by autotaxin (ATX), a secreted lysophospholipase D, from lysophosphatidylcholine. ATX-LPA receptor signaling is essential for normal development and implicated in various (patho)physiological processes, but underlying mechanisms remain incompletely understood. Through gene targeting approaches in zebrafish and mice, we show here that loss of ATX-LPA1 signaling leads to disorganization of chondrocytes, causing severe defects in cartilage formation. Mechanistically, ATX-LPA1 signaling acts by promoting S-phase entry and cell proliferation of chondrocytes both in vitro and in vivo, at least in part through β1-integrin translocation leading to fibronectin assembly and further extracellular matrix deposition; this in turn promotes chondrocyte-matrix adhesion and cell proliferation. Thus, the ATX-LPA1 axis is a key regulator of cartilage formation.

  9. Phase I clinical trial of fibronectin CH296-stimulated T cell therapy in patients with advanced cancer.

    Directory of Open Access Journals (Sweden)

    Takeshi Ishikawa

    Full Text Available BACKGROUND: Previous studies have demonstrated that less-differentiated T cells are ideal for adoptive T cell transfer therapy (ACT and that fibronectin CH296 (FN-CH296 together with anti-CD3 resulted in cultured cells that contain higher amounts of less-differentiated T cells. In this phase I clinical trial, we build on these prior results by assessing the safety and efficacy of FN-CH296 stimulated T cell therapy in patients with advanced cancer. METHODS: Patients underwent fibronectin CH296-stimulated T cell therapy up to six times every two weeks and the safety and antitumor activity of the ACT were assessed. In order to determine immune function, whole blood cytokine levels and the number of peripheral regulatory T cells were analyzed prior to ACT and during the follow up. RESULTS: Transferred cells contained numerous less-differentiated T cells greatly represented by CD27+CD45RA+ or CD28+CD45RA+ cell, which accounted for approximately 65% and 70% of the total, respectively. No ACT related severe or unexpected toxicities were observed. The response rate among patients was 22.2% and the disease control rate was 66.7%. CONCLUSIONS: The results obtained in this phase I trial, indicate that FN-CH296 stimulated T cell therapy was very well tolerated with a level of efficacy that is quite promising. We also surmise that expanding T cell using CH296 is a method that can be applied to other T- cell-based therapies. TRIAL REGISTRATION: UMIN UMIN000001835.

  10. Berberine Suppresses TPA-Induced Fibronectin Expression through the Inhibition of VEGF Secretion in Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Sangmin Kim

    2013-11-01

    Full Text Available Background/Aims: Berberine (BBR is an isoquinoline alkaloid and is beneficial for the anticancer effect on a variety of human tumor cells. However, BBR's anti-angiogenesis property and its clinical potential as an inhibitor of tumor angiogenesis in breast cancer cells have not been fully elucidated. Here, we investigated the effect of BBR on TPA-induced VEGF and fibronectin (FN as well as VEGF-induced FN in breast cancer cells. Methods: The secretion of VEGF protein was detected by ELISA. Fibronectin mRNA and protein expression was analyzed by Real-Time PCR and western blotting, respectively. The overexpressions of CA-MEK, and CA-Akt were examined by adenovirus system. Results: Our results showed that TPA, a tumor promoter, significantly increased the level of VEGF and FN expression in both MCF7 and T47D breast cancer cells. On the other hand, TPA-induced VEGF and FN expression was suppressed by LY294002, a PI-3K inhibitor. In contrast, the level of FN expression also significantly increased by constitutively active (CA-AKT overexpression. We also found that TPA-induced VEGF and FN expression was decreased by BBR treatment. Finally, our results showed that VEGF augmented the expression of FN whereas VEGF-induced FN expression was decreased by BBR treatment. Conclusion: Taken together, we suggest that BBR may suppress TPA-induced VEGF and FN as well as VEGF-induced FN through the inhibition of the PI-3K/AKT pathway in breast cancer cells. Therefore, we suggest that BBR may be used as a candidate drug for the inhibition of angiogenesis of human breast cancer.

  11. Spreading, proliferation and differentiation of human dental pulp stem cells on chitosan scaffolds immobilized with RGD or fibronectin.

    Science.gov (United States)

    Asghari Sana, Farzin; Çapkın Yurtsever, Merve; Kaynak Bayrak, Gökçe; Tunçay, Ekin Özge; Kiremitçi, Arlin S; Gümüşderelioğlu, Menemşe

    2017-08-01

    Nowadays, human dental pulp stem cells (hDPSCs) became more attractive for therapeutic purposes because of their high proliferation and differentiation potential. Thus, coupling the desired cellular characteristics of hDPSCs with good biomaterial properties of the chitosan scaffolds provide an interesting approach for tissue engineering applications. On the other hand, scaffold surface modification is also needed to promote stem cell adhesion since chitosan lacks adhesion motifs to support direct cell anchorage. In this study, hDPSCs were isolated from third molars of healthy female individuals (aged 16-25) with enzymatic digestion. For cell culture studies, the chitosan scaffolds which have approximately 9 mm diameter and 2 mm thickness with interconnected structure were prepared by freeze-drying. To support cellular attachment the scaffolds were covalently immobilized with either RGD (arginine-glycine-aspartic acid) or fibronectin (Fn) molecules. Cells were seeded on chitosan scaffolds with or without immobilized RGD and fibronectin. Cell attachment, spreading, adhesion behaviors and proliferation capacity were examined by scanning electron microscopy, immunofluorescence staining and PrestoBlue ® assays, respectively. In addition, differentiation potential of hDPSCs on Fn immobilized chitosan scaffolds was determined with real time reverse transcriptase polymerase chain reaction analysis. The results showed that chitosan scaffolds were not able to support stem cell attachment. hDPSCs on chitosan scaffolds formed spheroids more quickly and the size of spheroids were smaller than on chitosan-RGD while Fn-immobilized chitosan scaffolds strongly supported cellular attachment but not odontogenic differentiation. The results suggest that the Fn-immobilized chitosan scaffolds may serve as good three-dimensional substrates for dental pulp stem cell attachment and proliferation. In the case of dental regeneration, they must be supported by appropriate biosignals to

  12. Focal adhesion kinase and paxillin promote migration and adhesion to fibronectin by swine skeletal muscle satellite cells

    Science.gov (United States)

    Wang, Dan; Gao, Chun-qi; Chen, Rong-qiang; Jin, Cheng-long; Li, Hai-chang; Yan, Hui-chao; Wang, Xiu-qi

    2016-01-01

    The focal adhesion kinase (FAK) signaling pathway contributes to the cell migration and adhesion that is critical for wound healing and regeneration of damaged muscle, but its function in skeletal muscle satellite cells (SCs) is less clear. We compared the migration and adhesion of SCs derived from two species of pig (Lantang and Landrace) in vitro, and explored how FAK signaling modulates the two processes. The results showed that Lantang SCs had greater ability to migrate and adhere to fibronection (P < 0.05) than Landrace SCs. Compared to Landrace SCs, Lantang SCs expressed many more focal adhesion (FA) sites, which were indicated by the presence of p-paxillin (Tyr118), and exhibited less F-actin reorganization 24 h after seeding onto fibronectin. Levels of p-FAK (Tyr397) and p-paxillin (Tyr118) were greater (P < 0.05) in Lantang SCs than Landrace SCs after migration for 24 h. Similarly, Lantang SCs showed much higher levels of p-FAK (Tyr397), p-paxillin (Tyr118) and p-Akt (Ser473) than Landrace SCs 2 h after adhesion. Treatment with the FAK inhibitor PF-573228 (5 or 10 μmol/L) inhibited Lantang SC migration and adhesion to fibronectin (P < 0.05), decreased levels of p-paxillin (Tyr118) and p-Akt (Ser473) (P < 0.05), and suppressed the formation of FA sites on migrating SCs. Thus FAK appears to play a key role in the regulation of SC migration and adhesion necessary for muscle regeneration. PMID:27127174

  13. Selective targeting of tumour neovasculature by a radiohalogenated human antibody fragment specific for the ED-B domain of fibronectin

    International Nuclear Information System (INIS)

    Demartis, S.; Tarli, L.; Neri, D.; Borsi, L.; Zardi, L.

    2001-01-01

    Angiogenesis is a characteristic feature of many aggressive tumours and other disorders. Antibodies capable of binding to new blood vessels, but not to mature vessels, could be used as selective targeting agents for immunoscintigraphic and radioimmunotherapeutic applications. Here we show that scFv(L19), a recombinant human antibody fragment with sub-nanomolar affinity for the ED-B domain of fibronectin, a marker of angiogenesis, can be stably labelled with iodine-125 and astatine-211 with full retention of immunoreactivity, using a trimethyl-stannyl benzoate bifunctional derivative. Biodistribution studies in mice bearing two different types of tumour grafted subcutaneously, followed by ex vivo micro-autoradiographic analysis, revealed that scFv(L19) rapidly localises around tumour blood vessels, but not around normal vessels. Four hours after intravenous injection of the stably radioiodinated scFv(L19), tumour to blood ratios were 6:1 in mice bearing the F9 murine teratocarcinoma and 9:1 in mice bearing an FE8 rat sarcoma. As expected, all other organs (including kidney) contained significantly less radioactivity than the tumour. Since the ED-B domain of fibronectin has an identical sequence in mouse and man, scFv(L19) is a pan-species antibody and the results presented here suggest clinical utility of radiolabelled scFv(L19) for the scintigraphic detection of angiogenesis in vivo. Furthermore, it should now be possible to investigate scFv(L19) for the selective delivery of 211 At to the tumour neovasculature, causing the selective death of tumour endothelial cells and tumour collapse. (orig.)

  14. Combination of collagen and fibronectin to design biomimetic interfaces: Do these proteins form layer-by-layer assemblies?

    Science.gov (United States)

    Mauquoy, Sara; Dupont-Gillain, Christine

    2016-11-01

    Layer-by-layer (LbL) assembly is a surface modification method which may bring complexity to biointerfaces designed to control cell-material interactions. This work aims at investigating the LbL assembly of two extracellular matrix proteins, collagen (Col) and fibronectin (Fn), on polystyrene substrates. LbL assembly, which is widely applied to polyelectrolytes, is not easily transferred to proteins. Different buffers and conditions are tested, and LbL assembly is compared to the simultaneous adsorption of Fn and Col. Build-up and properties of the films are monitored using quartz crystal microbalance, ellipsometry, water contact angle measurements, and atomic force microscopy. Results show that denatured Col leads to smoother films, and that the addition of a polyethyleneimine anchoring layer increases film thickness. A more regular construction and thicker films are obtained with Hepes (pH 7.4) compared to other buffers. However, the LbL assembly is not sustainable and stops after the deposition of a few layers. Films obtained by simultaneous adsorption have lower water contact angles, different morphologies, lower water content and are as thick or thicker compared to the ones prepared by the LbL method. The present work shows that collagen and fibronectin are not involved in a true LbL assembly process. The obtained biointerfaces however exhibit different properties compared to those obtained by the one-step adsorption of these proteins. These differences could be exploited to control cell fate. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Alternative splicing of exon 17 and a missense mutation in exon 20 of the insulin receptor gene in two brothers with a novel syndrome of insulin resistance (congenital fiber-type disproportion myopathy)

    DEFF Research Database (Denmark)

    Vorwerk, P; Christoffersen, C T; Müller, J

    1999-01-01

    to be compound heterozygotes for mutations in the IR gene. The maternal allele was alternatively spliced in exon 17 due to a point mutation in the -1 donor splice site of the exon. The abnormal skipping of exon 17 shifts the amino acid reading frame and leads to a truncated IR, missing the entire tyrosine kinase......The insulin receptor (IR) in two brothers with a rare syndrome of congenital muscle fiber type disproportion myopathy (CFTDM) associated with diabetes and severe insulin resistance was studied. By direct sequencing of Epstein-Barr virus-transformed lymphocytes both patients were found...

  16. EDA-EMERGE : An FP7 initial training network to equip the next generation of young scientists with the skills to address the complexity of environmental contamination with emerging pollutants

    NARCIS (Netherlands)

    Brack, Werner; Govender, Selvan; Schulze, Tobias; Krauss, Martin; Hu, Meng; Muz, Melis; Hollender, Juliane; Schirmer, Kristin; Schollee, Jennifer; Hidasi, Anita; Slobodnik, Jaroslav; Rabova, Zuzana; Ait-Aissa, Selim; Sonavane, Manoj; Carere, Mario; Lamoree, Marja; Leonards, Pim; Tufi, Sara; Ouyang, Xiyu; Schriks, Merijn; Thomas, Kevin; De Almeida, Ana Catarina; Froment, Jean; Hammers-Wirtz, Monika; Ahel, Marijan; Koprivica, Sanja; Hollert, Henner; Seiler, Thomas Benjamin; Di Paolo, Carolina; Tindall, Andrew; Spirhanzlova, Petra

    2013-01-01

    The initial training network consortium novel tools in effect-directed analysis to support the identification and monitoring of emerging toxicants on a European scale (EDA-EMERGE) was formed in response to the seventh EU framework program call to train a new generation of young scientists (13 PhD

  17. 2′-O-Methyl RNA/Ethylene-Bridged Nucleic Acid Chimera Antisense Oligonucleotides to Induce Dystrophin Exon 45 Skipping

    Directory of Open Access Journals (Sweden)

    Tomoko Lee

    2017-02-01

    Full Text Available Duchenne muscular dystrophy (DMD is a fatal muscle-wasting disease characterized by dystrophin deficiency from mutations in the dystrophin gene. Antisense oligonucleotide (AO-mediated exon skipping targets restoration of the dystrophin reading frame to allow production of an internally deleted dystrophin protein with functional benefit for DMD patients who have out-of-frame deletions. After accelerated US approval of eteplirsen (Exondys 51, which targets dystrophin exon 51 for skipping, efforts are now focused on targeting other exons. For improved clinical benefits, this strategy requires more studies of the delivery method and modification of nucleic acids. We studied a nucleotide with a 2′-O,4′-C-ethylene-bridged nucleic acid (ENA, which shows high nuclease resistance and high affinity for complementary RNA strands. Here, we describe the process of developing a 2′-O-methyl RNA(2′-OMeRNA/ENA chimera AO to induce dystrophin exon 45 skipping. One 18-mer 2′-OMeRNA/ENA chimera (AO85 had the most potent activity for inducing exon 45 skipping in cultured myotubes. AO85 was administered to mdx mice without significant side effects. AO85 transfection into cultured myotubes from 13 DMD patients induced exon 45 skipping in all samples at different levels and dystrophin expression in 11 patients. These results suggest the possible efficacy of AO-mediated exon skipping changes in individual patients and highlight the 2′-OMeRNA/ENA chimera AO as a potential fundamental treatment for DMD.

  18. Molecular effects of autoimmune-risk promoter polymorphisms on expression, exon choice, and translational efficiency of interferon regulatory factor 5.

    Science.gov (United States)

    Clark, Daniel N; Lambert, Jared P; Till, Rodney E; Argueta, Lissenya B; Greenhalgh, Kathryn E; Henrie, Brandon; Bills, Trieste; Hawkley, Tyson F; Roznik, Marinya G; Sloan, Jason M; Mayhew, Vera; Woodland, Loc; Nelson, Eric P; Tsai, Meng-Hsuan; Poole, Brian D

    2014-05-01

    The rs2004640 single nucleotide polymorphism and the CGGGG copy-number variant (rs77571059) are promoter polymorphisms within interferon regulatory factor 5 (IRF5). They have been implicated as susceptibility factors for several autoimmune diseases. IRF5 uses alternative promoter splicing, where any of 4 first exons begin the mRNA. The CGGGG indel is in exon 1A's promoter; the rs2004640 allele creates a splicing recognition site, enabling usage of exon 1B. This study aimed at characterizing alterations in IRF5 mRNA due to these polymorphisms. Cells with risk polymorphisms exhibited ~2-fold higher levels of IRF5 mRNA and protein, but demonstrated no change in mRNA stability. Quantitative PCR demonstrated decreased usage of exons 1C and 1D in cell lines with the risk polymorphisms. RNA folding analysis revealed a hairpin in exon 1B; mutational analysis showed that the hairpin shape decreased translation 5-fold. Although translation of mRNA that uses exon 1B is low due to a hairpin, increased IRF5 mRNA levels in individuals with the rs2004640 risk allele lead to higher overall protein expression. In addition, several new splice variants of IRF5 were sequenced. IRF5's promoter polymorphisms alter first exon usage and increase transcription levels. High levels of IRF5 may bias the immune system toward autoimmunity.

  19. Delineation of the Marfan phenotype associated with mutations in exons 23-32 of the FBN1 gene

    Energy Technology Data Exchange (ETDEWEB)

    Putnam, E.A.; Cho, M.; Milewicz, D.M. [Univ. of Texas-Houston Medical School, Houston, TX (United States)] [and others

    1996-03-29

    Marfan syndrome is a dominantly inherited connective tissue disorder with a wide range of phenotypic severity. The condition is the result of mutations in FBN1, a large gene composed of 65 exons encoding the fibrillin-1 protein. While mutations causing classic manifestations of Marfan syndrome have been identified throughout the FBN1 gene, the six previously characterized mutations resulting in the severe, perinatal lethal form of Marfan syndrome have clustered in exons 24-32 of the gene. We screened 8 patients with either neonatal Marfan syndrome or severe cardiovascular complications of Marfan syndrome for mutations in this region of the gene. Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. This analysis documented mutations in exons 25-27 of the FBN1 mutations in 6 of these patients. These results, taken together with previously published FBN1 mutations in this region, further define the phenotype associated with mutations in exons 24-32 of the FBN1 gene, information important for the development of possible diagnostic tests and genetic counseling. 49 refs., 4 figs., 2 tabs.

  20. Identification of small molecule and genetic modulators of AON-induced dystrophin exon skipping by high-throughput screening.

    Directory of Open Access Journals (Sweden)

    Debra A O'Leary

    Full Text Available One therapeutic approach to Duchenne Muscular Dystrophy (DMD recently entering clinical trials aims to convert DMD phenotypes to that of a milder disease variant, Becker Muscular Dystrophy (BMD, by employing antisense oligonucleotides (AONs targeting splice sites, to induce exon skipping and restore partial dystrophin function. In order to search for small molecule and genetic modulators of AON-dependent and independent exon skipping, we screened approximately 10,000 known small molecule drugs, >17,000 cDNA clones, and >2,000 kinase- targeted siRNAs against a 5.6 kb luciferase minigene construct, encompassing exon 71 to exon 73 of human dystrophin. As a result, we identified several enhancers of exon skipping, acting on both the reporter construct as well as endogenous dystrophin in mdx cells. Multiple mechanisms of action were identified, including histone deacetylase inhibition, tubulin modulation and pre-mRNA processing. Among others, the nucleolar protein NOL8 and staufen RNA binding protein homolog 2 (Stau2 were found to induce endogenous exon skipping in mdx cells in an AON-dependent fashion. An unexpected but recurrent theme observed in our screening efforts was the apparent link between the inhibition of cell cycle progression and the induction of exon skipping.

  1. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

    Directory of Open Access Journals (Sweden)

    Sugnet Charles

    2006-12-01

    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  2. Characterization of TTN Novex Splicing Variants across Species and the Role of RBM20 in Novex-Specific Exon Splicing

    Directory of Open Access Journals (Sweden)

    Zhilong Chen

    2018-02-01

    Full Text Available Titin (TTN is a major disease-causing gene in cardiac muscle. Titin (TTN contains 363 exons in human encoding various sizes of TTN protein due to alternative splicing regulated mainly by RNA binding motif 20 (RBM20. Three isoforms of TTN protein are produced by mutually exclusive exons 45 (Novex 1, 46 (Novex 2, and 48 (Novex 3. Alternatively splicing in Novex isoforms across species and whether Novex isoforms are associated with heart disease remains completely unknown. Cross-species exon comparison with the mVISTA online tool revealed that exon 45 is more highly conserved across all species than exons 46 and 48. Importantly, a conserved region between exons 47 and 48 across species was revealed for the first time. Reverse transcript polymerase chain reaction (RT-PCR and DNA sequencing confirmed a new exon named as 48′ in Novex 3. In addition, with primer pairs for Novex 1, a new truncated form preserving introns 44 and 45 was discovered. We discovered that Novex 2 is not expressed in the pig, mouse, and rat with Novex 2 primer pairs. Unexpectedly, three truncated forms were identified. One TTN variant with intron 46 retention is mainly expressed in the human and frog heart, another variant with co-expression of exons 45 and 46 exists predominantly in chicken and frog heart, and a third with retention of introns 45 and 46 is mainly expressed in pig, mouse, rat, and chicken. Using Rbm20 knockout rat heart, we revealed that RBM20 is not a splicing regulator of Novex variants. Furthermore, the expression levels of Novex variants in human hearts with cardiomyopathies suggested that Novexes 2 and 3 could be associated with dilated cardiomyopathy (DCM and/or arrhythmogenic right ventricular cardiomyopathy (ARVC. Taken together, our study reveals that splicing diversity of Novex exons across species and Novex variants might play a role in cardiomyopathy.

  3. Novel exon-exon breakpoint in CIC-DUX4 fusion sarcoma identified by anchored multiplex PCR (Archer FusionPlex Sarcoma Panel).

    Science.gov (United States)

    Loke, Benjamin Nathanael; Lee, Victor Kwan Min; Sudhanshi, Jain; Wong, Meng Kang; Kuick, Chik Hong; Puhaindran, Mark; Chang, Kenneth Tou En

    2017-08-01

    We describe the clinical and pathological features and novel genetic findings of a case of CIC-DUX4 sarcoma occurring in the thigh of a 35-year-old man. Fusion gene detection using a next-generation sequencing-based anchored multiplex PCR technique (Archer FusionPlex Sarcoma Panel) was used to identify the novel fusion breakpoints of this CIC-DUX4 sarcoma using formalin-fixed and paraffin-embedded tumour material. This CIC-DUX4 sarcoma has a novel fusion breakpoint between exon 20 of the CIC gene and exon 1 of the DUX4 gene. This case report describes an additional case of CIC-DUX4 sarcoma with a novel fusion breakpoint, and demonstrates the value of this next-generation sequencing-based anchored multiplex PCR technique (Archer FusionPlex Sarcoma Panel) in both diagnosis for patient care and in identification of a novel fusion breakpoint in this tumour type. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  4. Differences in exon expression and alternatively spliced genes in blood of multiple sclerosis compared to healthy control subjects.

    Science.gov (United States)

    Tian, Yingfang; Apperson, Michelle L; Ander, Bradley P; Liu, Dazhi; Stomova, Boryana S; Jickling, Glen C; Enriquez, Richelle; Agius, Mark A; Sharp, Frank R

    2011-01-01

    Using whole genome exon microarrays 120 exons were differentially expressed between medication-free multiple sclerosis (MS) subjects in remission and healthy control subjects (HS) (p|1.2|). These exons differentiated MS from HS using cluster analyses, principal components analyses (PCAs) and cross-validation. In addition, 340 genes (transcripts) were predicted to be alternatively spliced in MS compared to HS. These findings may provide insight into the pathophysiology of MS and potentially provide prognostic and diagnostic biomarkers. However, given that multiple comparisons were performed on a very small sample, these preliminary findings require confirmation using a much larger independent cohort. Copyright © 2010 Elsevier B.V. All rights reserved.

  5. Andrés Felipe Castañeda Morales. Encantos y peligros de la ciudad nocturna. Cali 1910-1930.

    Directory of Open Access Journals (Sweden)

    Héctor Cuevas Arenas

    2016-07-01

    Full Text Available La noche como espacio de prácticas y relaciones sociales, de proyectos y contingencias entre los distintos actores, así como la exploración de valoraciones, experiencias y expectativas que se generaban sobre dicho horario, constituye una temática todavía inédita para la historiografía colombiana.Con este antecedente, el trabajo de Castañeda aporta desde una mirada descriptiva en la cimentación de este objeto de estudio, con un ejercicio interdisciplinar donde confluyen la historia social urbana y la de la vida cotidiana, junto a los aportes de la Comunicación Social, la Antropología y la Sociología urbana, e incluso la Literatura.

  6. Processes of attention to children and adolescents under 20 years in La Castañeda: evolution of the concept of childhood in psychiatry

    Directory of Open Access Journals (Sweden)

    Jorge Escotto-Morett

    2017-07-01

    Full Text Available Today, there is evidence that shows that children and adolescents can experience developmental problems and psychiatric disorders. This was possible because of two main reasons, the evolution of the concept of infancy and the progress made in medical and psychiatric diagnostic classification. This manuscript offers a glance to early psychiatric attention in Mexico, particularly the care processes provided to 36 children and adolescents under twenty, admitted in the mental asylum La Castañeda, during the first half of the XX century. Admission causes, length of stay, diagnosis, treatment and discharge motives, are some of the aspects described in this study. Finally, it also reflects about the challenge it is for a child psychiatric hospital nowadays, with such a history, to become an innovative institution able to claim a place in the medical field in favor of those minors that can barely defend themselves.

  7. The Ru-NO bonding in nitrosyl-[poly(1-pyrazolyl)borate]ruthenium complexes: a theoretical insight based on EDA

    Energy Technology Data Exchange (ETDEWEB)

    Caramori, Giovanni F.; Kunitz, Andre G.; Coimbra, Daniel F.; Garcia, Leone C.; Fonseca, David E.P., E-mail: giovanni.caramori@ufsc.br [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Centro de Ciencias Fisicas e Matematicas. Dept. de Quimica

    2013-09-15

    The lability of NO{sup +} group in [TpRuCl{sub 2}(NO)]{sup q} (Tp = BL(pyrazol-1-yl){sub 3}) complexes was evaluated at the light of energy decomposition analysis (Su-Li EDA). The electronic effects of different pseudoaxial substituents (L = H, pyrazolyl anion, pyrazole, isoxazole and isothiazole) on the nature of Ru-NO bonding were evaluated considering complexes in ground (GS) and in metastable (MS1 and MS2) states. (Ru-NO){sup 6} bond nature in [TpRuCl{sub 2}(NO)]{sup q} (Tp = BL(pyrazol-1-yl){sub 3}) complexes is in essence covalent, but with a still significant electrostatic character. The nature of pseudoaxial substituents has a direct effect on the magnitude of (Ru-NO){sup 6} bonds. (author)

  8. Exonization of active mouse L1s: a driver of transcriptome evolution?

    Directory of Open Access Journals (Sweden)

    Badge Richard

    2007-10-01

    Full Text Available Abstract Background Long interspersed nuclear elements (LINE-1s, L1s have been recently implicated in the regulation of mammalian transcriptomes. Results Here, we show that members of the three active mouse L1 subfamilies (A, GF and TF contain, in addition to those on their sense strands, conserved functional splice sites on their antisense strands, which trigger multiple exonization events. The latter is particularly intriguing in the light of the strong antisense orientation bias of intronic L1s, implying that the toleration of antisense insertions results in an increased potential for exonization. Conclusion In a genome-wide analysis, we have uncovered evidence suggesting that the mobility of the large number of retrotransposition-competent mouse L1s (~2400 potentially active L1s in NCBIm35 has significant potential to shape the mouse transcriptome by continuously generating insertions into transcriptional units.

  9. Vitamin D receptor B1 and exon 1d: functional and evolutionary analysis.

    Science.gov (United States)

    Gardiner, Edith M; Esteban, Luis M; Fong, Colette; Allison, Susan J; Flanagan, Judith L; Kouzmenko, Alexander P; Eisman, John A

    2004-05-01

    The vitamin D receptor (VDR) shares a conserved structural and functional organization with other nuclear receptor (NR) superfamily members. For many NRs, N-terminal variant isoforms that display distinct cell-, stage- and promoter-specific actions have been identified. The novel VDR isoform VDRB1, with a 50 amino acid N-terminal extension, is produced from low abundance transcripts that contain exon 1d of the human VDR locus. There is evidence for the conservation of this exon in other mammalian and avian species. The transactivation differences between VDRB1 and the original VDR, clarified here, provide insights into mechanisms that may contribute to functional differences and potentially distinct physiological roles for these two VDR isoforms.

  10. BRCA1 Exon 11, a CERES (Composite Regulatory Element of Splicing Element Involved in Splice Regulation

    Directory of Open Access Journals (Sweden)

    Claudia Tammaro

    2014-07-01

    Full Text Available Unclassified variants (UV of BRCA1 can affect normal pre-mRNA splicing. Here, we investigate the UV c.693G>A, a “silent” change in BRCA1 exon 11, which we have found induces aberrant splicing in patient carriers and in vitro. Using a minigene assay, we show that the UV c.693G>A has a strong effect on the splicing isoform ratio of BRCA1. Systematic site-directed mutagenesis of the area surrounding the nucleotide position c.693G>A induced variable changes in the level of exon 11 inclusion/exclusion in the mRNA, pointing to the presence of a complex regulatory element with overlapping enhancer and silencer functions. Accordingly, protein binding analysis in the region detected several splicing regulatory factors involved, including SRSF1, SRSF6 and SRSF9, suggesting that this sequence represents a composite regulatory element of splicing (CERES.

  11. fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.

    Science.gov (United States)

    McCall, Matthew N; Jaffee, Harris A; Irizarry, Rafael A

    2012-12-01

    Frozen robust multiarray analysis (fRMA) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. Here, we extend the fRMA algorithm to two new microarray platforms--Affymetrix Human Exon and Gene 1.0 ST--by modifying the fRMA probe-level model and extending the frma package to work with oligo ExonFeatureSet and GeneFeatureSet objects. All packages are implemented in R. Source code and binaries are freely available through the Bioconductor project. Convenient links to all software and data packages can be found at http://mnmccall.com/software mccallm@gmail.com.

  12. Screening of BRCA1 sequence variants within exon 11 by heteroduplex analysis

    Directory of Open Access Journals (Sweden)

    Lucian Negura

    2013-03-01

    Full Text Available Germ-line mutations of either BRCA1 or BRCA2 represents the major hereditary risk to breast and ovariancancer. Screening for mutations in these genes is now standard practice in molecular diagnosis, opening the way tooncogenetic counselling and follow-up. Because mutations in both BRCA1 and BRCA2 are distributed throughout theloci, accepted clinical protocols involve screening their entire coding regions. Systematic Sanger sequencing is time andmoney consuming. Therefore, a lot of pre-screening techniques evolved over time in order to identify anomalousamplicons prior to sequencing. Because BRCA mutations are always heterozygous, heteroduplex analysis proved to be asuitable pre-screening step. We previously implemented mismatch specific endonuclease heteroduplex analysis forBRCA1 exon7. Here we show the utility of the same method for mutations and SNPs found in BRCA1 exon 11

  13. Hexose enhances oligonucleotide delivery and exon skipping in dystrophin-deficient mdx mice.

    Science.gov (United States)

    Han, Gang; Gu, Ben; Cao, Limin; Gao, Xianjun; Wang, Qingsong; Seow, Yiqi; Zhang, Ning; Wood, Matthew J A; Yin, HaiFang

    2016-03-11

    Carbohydrate-based infusion solutions are widely used in the clinic. Here we show that co-administration of phosphorodiamidate morpholino oligomers (PMOs) with glucose enhances exon-skipping activity in Duchenne muscular dystrophy (DMD) mdx mice. We identify a glucose-fructose (GF) formulation that potentiates PMO activity, completely corrects aberrant Dmd transcripts, restores dystrophin levels in skeletal muscles and achieves functional rescue without detectable toxicity. This activity is attributed to enhancement of GF-mediated PMO uptake in the muscle. We demonstrate that PMO cellular uptake is energy dependent, and that ATP from GF metabolism contributes to enhanced cellular uptake of PMO in the muscle. Collectively, we show that GF potentiates PMO activity by replenishing cellular energy stores under energy-deficient conditions in mdx mice. Our findings provide mechanistic insight into hexose-mediated oligonucleotide delivery and have important implications for the development of DMD exon-skipping therapy.

  14. Selective Blockade of Periostin Exon 17 Preserves Cardiac Performance in Acute Myocardial Infarction.

    Science.gov (United States)

    Taniyama, Yoshiaki; Katsuragi, Naruto; Sanada, Fumihiro; Azuma, Junya; Iekushi, Kazuma; Koibuchi, Nobutaka; Okayama, Keita; Ikeda-Iwabu, Yuka; Muratsu, Jun; Otsu, Rei; Rakugi, Hiromi; Morishita, Ryuichi

    2016-02-01

    We previously reported that overexpression of full-length periostin, Pn-1, resulted in ventricular dilation with enhanced interstitial collagen deposition in a rat model. However, other reports have documented that the short-form splice variants Pn-2 (lacking exon 17) and Pn-4 (lacking exons 17 and 21) promoted cardiac repair by angiogenesis and prevented cardiac rupture after acute myocardial infarction. The apparently differing findings from those reports prompted us to use a neutralizing antibody to selectively inhibit Pn-1 by blockade of exon 17 in a rat acute myocardial infarction model. Administration of Pn neutralizing antibody resulted in a significant decrease in the infarcted and fibrotic areas of the myocardium, which prevented ventricular wall thinning and dilatation. The inhibition of fibrosis by Pn neutralizing antibody was associated with a significant decrease in gene expression of fibrotic markers, including collagen I, collagen III, and transforming growth factor-β1. Importantly, the number of α-smooth muscle actin-positive myofibroblasts was significantly reduced in the hearts of animals treated with Pn neutralizing antibody, whereas cardiomyocyte proliferation and angiogenesis were comparable in the IgG and neutralizing antibody groups. Moreover, the level of Pn-1 expression was significantly correlated with the severity of myocardial infarction. In addition, Pn-1, but not Pn-2 or Pn-4, inhibited fibroblast and myocyte attachment, which might account for the cell slippage observed during cardiac remodeling. Collectively, these results indicate that therapeutics that specifically inhibit Pn exon-17, via a neutralizing antibody or drug, without suppressing other periostin variants might offer a new class of medication for the treatment of acute myocardial infarction patients. © 2015 American Heart Association, Inc.

  15. GM2 Activator Deficiency Caused by a Homozygous Exon 2 Deletion in GM2A.

    Science.gov (United States)

    Hall, Patricia L; Laine, Regina; Alexander, John J; Ankala, Arunkanth; Teot, Lisa A; Lidov, Hart G W; Anselm, Irina

    2017-05-25

    GM2 activator (GM2A) deficiency (OMIM 613109) is a rare lysosomal storage disorder, with onset typically in infancy or early childhood. Clinically, it is almost indistinguishable from Tay-Sachs disease (OMIM 272800) or Sandhoff disease (OMIM 268800); however, traditionally available biochemical screening tests will most likely reveal normal results. We report a 2-year-old male with initially normal development until the age of 9 months, when he presented with developmental delay and regression. Workup at that time was unrevealing; at 15 months, he had abnormal brain MRI findings and a cherry red spot on ophthalmological examination. Family history and all laboratory studies were uninformative. The combination of a cherry red spot and developmental regression was strongly suggestive of a lysosomal storage disorder. Sequence analysis of GM2A did not reveal any pathogenic variants; however, exon 2 of GM2A could not be amplified by PCR, raising suspicion for a large, homozygous deletion. Subsequent copy number analysis confirmed a homozygous deletion of exon 2 in GM2A. This is the first reported case of GM2A deficiency being caused by a whole exon deletion. We describe previously unreported electron microscopy findings in this disease, thus expanding the clinical and variant spectrum for GM2 activator deficiency. These findings demonstrate the increased degree of suspicion required for diagnosis of this rare disorder. Brief Summary: This case of GM2 activator deficiency was caused by a homozygous deletion in GM2A, demonstrating the need to include exon level copy number analysis in any workup to fully exclude this disorder.

  16. Rat tenascin-R gene: structure, chromosome location and transcriptional activity of promoter and exon 1.

    Science.gov (United States)

    Leprini, A; Gherzi, R; Vecchi, E; Borsi, L; Zardi, L; Siri, A

    1998-01-01

    Tenascin-R is an extracellular matrix protein expressed exclusively in the central nervous system where it is thought to play a relevant role in regulating neurite outgrowth. We have i) cloned the cDNA of the rat tenascin-R 5' region; ii) defined its genomic organization, obtaining the sequence of two novel untranslated exons; iii) mapped the gene to rat chromosome 13q23 and suggested a previously unreported synteny between rat chromosome 13q23, human chromosome 1q24, and mouse chromosome 4E; and iv) sequenced and characterized the elements responsible for its neural cell-restricted transcription. We found that two discrete regions of the rat gene (the first in the proximal promoter, the second in the first exon) are independently able to activate to a high degree the transcription of a reporter gene in either human or rat neuroblastoma cell lines but not in other cell lines. Based on this observation, we re-evaluated the arrangement of transcriptionally active regions in the human tenascin-R gene we recently cloned and found that the human gene also contains an exon sequence able to initiate and sustain transcription independently of promoter sequences.

  17. MED12 exon 2 mutations in phyllodes tumors of the breast

    International Nuclear Information System (INIS)

    Nagasawa, Satoi; Maeda, Ichiro; Fukuda, Takayo; Wu, Wenwen; Hayami, Ryosuke; Kojima, Yasuyuki; Tsugawa, Ko-ichiro; Ohta, Tomohiko

    2015-01-01

    Exon 2 of MED12, a subunit of the transcriptional mediator complex, has been frequently mutated in uterine leiomyomas and breast fibroadenomas; however, it has been rarely mutated in other tumors. Although the mutations were also found in uterine leiomyosarcomas, the frequency was significantly lower than in uterine leiomyomas. Here, we examined the MED12 mutation in phyllodes tumors, another biphasic tumor with epithelial and stromal components related to breast fibroadenomas. Mutations in MED12 exon 2 were analyzed in nine fibroadenomas and eleven phyllodes tumors via Sanger sequencing. A panel of cancer- and sarcoma-related genes was also analyzed using Ion Torrent next-generation sequencing. Six mutations in fibroadenomas, including those previously reported (6/9, 67%), and five mutations in phyllodes tumors (5/11, 45%) were observed. Three mutations in the phyllodes tumors were missense mutations at Gly44, which is common in uterine leiomyomas and breast fibroadenomas. In addition, two deletion mutations (in-frame c.133-144del12 and loss of splice acceptor c.100-68-137del106) were observed in the phyllodes tumors. No other recurrent mutation was observed with next-generation sequencing. Frequent mutations in MED12 exon 2 in the phyllodes tumors suggest that it may share genetic etiology with uterine leiomyoma, a subgroup of uterine leiomyosarcomas and breast fibroadenoma

  18. Whole exon 5 and intron 5 replaced by RHCE in DVa(Hus).

    Science.gov (United States)

    Shao, Chaopeng; Xiong, Wen; Wang, Wei

    2004-01-01

    The DVa(Hus) was previously investigated through cDNA analysis, which revealed an RHD-CE(5)-D hybrid allele. However, the 5' and 3' breakpoints remain unknown. In this article, gene recombinations between the RHD and RHCE alleles were investigated by a combination approach of a sequence-specific primer PCR (PCR-SSP) and an RHD full-length coding region sequencing method on two Chinese subjects with weak D phenotypes. The hybrid Rhesus box of each individual was also investigated through an established PCR-based method. As a result, two partial D phenotypes, DVa(Hus) and DVI type III, were identified, each carrying one hybrid RHD-CE-D allele. The two samples were also serotyped with Rh phontypes of DccEe and DCcee, respectively. Other sequencing analyses of the DVaHus sample showed that the sequence of intron 4 is identical with RHD, whereas the whole sequence of exon 5 and intron 5 is identical with RHCE except for seven polymorphisms in the intron 5. We may concluded that in the case of this Chinese DVa(Hus), the whole exon 5 and complete intron 5 of a total segment of 1801 nucleotides were replaced by RHCE suggesting that the breakpoints of the replaced region are the 5' end of the exon 5 and the 3' end of the intron 5.

  19. Un gene con intrones en vez de exones / Envejecimiento Prematuro de la Piel

    Directory of Open Access Journals (Sweden)

    Tobías Mojica

    1996-04-01

    Full Text Available Un gene con intrones en vez de exones. La noción de que los genes son discontinuos (compuestos de exones e intrones en forma alterna y en cuya organización los exones representan regiones presentes, por medio del código genético en las proteínas, y los intrones nadie sabe todavía que representan produjo una cierta cantidad de desasosiego entre los genetistas mayores de edad, pero hoy día es ampliamente aceptada, con poco o ningún dolor, y se ha convertido en parte del cánon científico. / Envejecimiento Prematuro de la Piel. La exposición a largo plazo de la piel a la luz ultravioleta proveniente del sol resulta en daño al colágeno de la piel y a la elastina de la matriz extracelular; se cree que este daño es responsable de la apariencia típicamente arrugadita de la piel expuesta al sol por mucho tiempo (como en los vaqueros de los comerciales de la televisión.

  20. Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells.

    Directory of Open Access Journals (Sweden)

    Winston Koh

    Full Text Available Circular RNAs comprise a poorly understood new class of noncoding RNA. In this study, we used a combination of targeted deletion, high-resolution splicing detection, and single-cell sequencing to deeply probe ASXL1 circular splicing. We found that efficient circular splicing required the canonical transcriptional start site and inverted AluSx elements. Sequencing-based interrogation of isoforms after ASXL1 overexpression identified promiscuous linear splicing between all exons, with the two most abundant non-canonical linear products skipping the exons that produced the circular isoforms. Single-cell sequencing revealed a strong preference for either the linear or circular ASXL1 isoforms in each cell, and found the predominant exon skipping product is frequently co-expressed with its reciprocal circular isoform. Finally, absolute quantification of ASXL1 isoforms confirmed our findings and suggests that standard methods overestimate circRNA abundance. Taken together, these data reveal a dynamic new view of circRNA genesis, providing additional framework for studying their roles in cellular biology.