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41.
Michon IN Hauer AD von der Thüsen JH Molenaar TJ van Berkel TJ Biessen EA Kuiper J 《Biochimica et biophysica acta》2002,1591(1-3):87-97
Restenosis after angioplasty occurs in 30-40% of the treated patients. To develop a strategy to deliver drugs to restenotic lesions, we selected phages that bind to proliferating vascular smooth muscle cells (VSMC), from a random constraint 15-mer peptide phage display library. Phages were selected for binding to cultured primary aortic VSMC (in vitro biopanning) and selected for binding to denudated carotid arteries in mice (in vivo biopanning). In vitro biopanning did not result in a consensus sequence, but recurring FLGW and LASR amino acid motifs were identified. In vivo biopanning resulted in two consensus peptides 5G6 (CNIWGVVLSWIGVFPEC) and 5E5 (CESLWGGLMWTIGLSDC). Surprisingly, these two sequences were recovered after both in vitro and in vivo biopanning, but predominantly in vivo. Moreover, a strong recurring motif, IGR, was identified in the in vivo clones. The consensus phages 5G6 and 5E5 bind selectively to VSMC compared to other cell types. Furthermore, they bind preferentially to proliferating VSMC compared to VSMC that were growth arrested, and are effectively internalized by their target cells. The specific binding capacities of 5G6 and 5E5 phages suggest that these peptide sequences can be used for targeting of restenotic lesions, in which proliferating VSMC are the dominant cell type. 相似文献
42.
Victoria?BrankinEmail author Marcus?RP?Mitchell Bob?Webb Morag?G?Hunter 《Reproductive biology and endocrinology : RB&E》2003,1(1):55
Oocyte control of granulosa and theca cell function may be mediated by several growth factors via a local feedback loop(s)
between these cell types. This study examined both the role of oocyte-secreted factors on granulosa and thecal cells, cultured
independently and in co-culture, and the effect of stem cell factor (SCF); a granulosa cell derived peptide that appears to
have multiple roles in follicle development. Granulosa and theca cells were isolated from 2–6 mm healthy follicles of mature
porcine ovaries and cultured under serum-free conditions, supplemented with: 100 ng/ml LR3 IGF-1, 10 ng/ml insulin, 100 ng/ml
testosterone, 0–10 ng/ml SCF, 1 ng/ml FSH (granulosa), 0.01 ng/ml LH (theca) or 1 ng/ml FSH and 0.01 ng/ml LH (co-culture)
and with/without oocyte conditioned medium (OCM) or 5 oocytes. Cells were cultured in 96 well plates for 144 h, after which
viable cell numbers were determined. Medium was replaced every 48 h and spent medium analysed for steroids. 相似文献
43.
A. E. Melchinger R. K. Gumber R. B. Leipert M. Vuylsteke M. Kuiper 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(3-4):503-512
Prediction of the means and genetic variances in segregating generations could help to assess the breeding potential of base
populations. In this study, we investigated whether the testcross (TC) means and variances of F3 progenies from F1 crosses in European maize can be predicted from the TC means of their parents and F1 crosses and four measures of parental genetic divergence: genetic distance (GD) determined by 194 RFLP or 691 AFLPTM
1 markers, mid-parent heterosis (MPH), and absolute difference between the TC means of parents (∣P1−P2∣). The experimental materials comprised six sets of crosses; each set consisted of four elite inbreds from the flint or dent
germplasm and the six possible F1 crosses between them, which were evaluated for mid-parent heterosis. Testcross progenies of these materials and 20 random
F3 plants per F1 cross were produced with a single-cross tester from the opposite heterotic group and evaluated in two environments. The characters
studied were plant height, dry matter content and grain yield. The genetic distance between parent lines ranged between 0.17
and 0.70 for RFLPs and between 0.14 and 0.57 for AFLPs in the six sets. Testcross-means of parents, F1 crosses, and F3 populations averaged across the six crosses in a particular set generally agreed well for all three traits. Bartlett’s test
revealed heterogeneous TC variances among the six crosses in all sets for plant height, in four sets for grain yield and in
five sets for dry matter content. Correlations among the TC means of the parents, F1 crosses, and F3 populations were highly significant and positive for all traits. Estimates of the TC variance among F3 progenies for the 36 crosses showed only low correlations with the four measures of parental genetic divergence for all traits.
The results demonstrated that for our material, the TC means of the parents or the parental F1 cross can be used as predictors for the TC means of F3 populations. However, the prediction of the TC variance remains an unsolved problem.
Received: 4 August 1997 / Accepted: 17 November 1997 相似文献
44.
Alexandros?KanterakisEmail author Jo?l?Kuiper George?Potamias Morris?A.?Swertz 《Source code for biology and medicine》2015,10(1):14
Background
Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols.Results
We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page.Conclusions
PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams.Availability
PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.45.
Benjamin D. Kuiper Bradley J. Keusch Tamaria G. Dewdney Poorvi Chordia Kyla Ross Joseph S. Brunzelle Iulia A. Kovari Rodger MacArthur Hossein Salimnia Ladislau C. Kovari 《Biochemistry and Biophysics Reports》2015
HIV-1 protease (PR) is a 99 amino acid protein responsible for proteolytic processing of the viral polyprotein – an essential step in the HIV-1 life cycle. Drug resistance mutations in PR that are selected during antiretroviral therapy lead to reduced efficacy of protease inhibitors (PI) including darunavir (DRV). To identify the structural mechanisms associated with the DRV resistance mutation L33F, we performed X-ray crystallographic studies with a multi-drug resistant HIV-1 protease isolate that contains the L33F mutation (MDR769 L33F). In contrast to other PR L33F DRV complexes, the structure of MDR769 L33F complexed with DRV reported here displays the protease flaps in an open conformation. The L33F mutation increases noncovalent interactions in the hydrophobic pocket of the PR compared to the wild-type (WT) structure. As a result, L33F appears to act as a molecular anchor, reducing the flexibility of the 30s loop (residues 29–35) and the 80s loop (residues 79–84). Molecular anchoring of the 30s and 80s loops leaves an open S1/S1′ subsite and distorts the conserved hydrogen-bonding network of DRV. These findings are consistent with previous reports despite structural differences with regards to flap conformation. 相似文献
46.
Heather C. Kuiper Brandi L. Langsdorf Cristobal L. Miranda Jacqueline Joss Carole Jubert John E. Mata Jan F. Stevens 《Free radical biology & medicine》2010,48(1):65-72
The breakdown of polyunsaturated fatty acids (PUFAs) under conditions of oxidative stress results in the formation of lipid peroxidation (LPO) products. These LPO products such as 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) can contribute to the development of cardiovascular and neurodegenerative diseases and cancer. Conjugation with glutathione, followed by further metabolism to mercapturic acid (MA) conjugates, can mitigate the effects of these LPO products in disease development by facilitating their excretion from the body. We have developed a quantitative method to simultaneously assess levels of 4-oxo-2-nonen-1-ol (ONO)-MA, HNE-MA, and 1,4-dihydroxy-2-nonene (DHN)-MA in human urine samples utilizing isotope-dilution mass spectrometry. We are also able to detect 4-hydroxy-2-nonenoic acid (HNA)-MA, 4-hydroxy-2-nonenoic acid lactone (HNAL)-MA, and 4-oxo-2-nonenoic acid (ONA)-MA with this method. The detection of ONO-MA and ONA-MA in humans is significant because it demonstrates that HNE/ONE branching occurs in the breakdown of PUFAs and suggests that ONO may contribute to the harmful effects currently associated with HNE. We were able to show significant decreases in HNE-MA, DHN-MA, and total LPO-MA in a group of seven smokers upon smoking cessation. These data demonstrate the value of HNE and ONE metabolites as in vivo markers of oxidative stress. 相似文献
47.
Angiogenesis is not impaired in connective tissue growth factor (CTGF) knock-out mice. 总被引:3,自引:0,他引:3
Esther J Kuiper Peggy Roestenberg Christoph Ehlken Vincent Lambert Henny Bloys van Treslong-de Groot Karen M Lyons Hans-Jürgen T Agostini Jean-Marie Rakic Ingeborg Klaassen Cornelis J F Van Noorden Roel Goldschmeding Reinier O Schlingemann 《The journal of histochemistry and cytochemistry》2007,55(11):1139-1147
Connective tissue growth factor (CTGF) is a member of the CCN family of growth factors. CTGF is important in scarring, wound healing, and fibrosis. It has also been implicated to play a role in angiogenesis, in addition to vascular endothelial growth factor (VEGF). In the eye, angiogenesis and subsequent fibrosis are the main causes of blindness in conditions such as diabetic retinopathy. We have applied three different models of angiogenesis to homozygous CTGF(-/-) and heterozygous CTGF(+/-) mice to establish involvement of CTGF in neovascularization. CTGF(-/-) mice die around birth. Therefore, embryonic CTGF(-/-), CTGF(+/-), and CTGF(+/+) bone explants were used to study in vitro angiogenesis, and neonatal and mature CTGF(+/-) and CTGF(+/+) mice were used in models of oxygen-induced retinopathy and laser-induced choroidal neovascularization. Angiogenesis in vitro was independent of the CTGF genotype in both the presence and the absence of VEGF. Oxygen-induced vascular pathology in the retina, as determined semi-quantitatively, and laser-induced choroidal neovascularization, as determined quantitatively, were also not affected by the CTGF genotype. Our data show that downregulation of CTGF levels does not affect neovascularization, indicating distinct roles of VEGF and CTGF in angiogenesis and fibrosis in eye conditions. 相似文献
48.
49.
Peeters RP van den Beld AW Attalki H Toor Hv de Rijke YB Kuiper GG Lamberts SW Janssen JA Uitterlinden AG Visser TJ 《American journal of physiology. Endocrinology and metabolism》2005,289(1):E75-E81
Type II deiodinase (D2) is important in the regulation of local thyroid hormone bioactivity in certain tissues. D2 in skeletal muscle may also play a role in serum triiodothyronine (T(3)) production. In this study, we identified a polymorphism in the 5'-UTR of the D2 gene (D2-ORFa-Gly3Asp). We investigated the association of D2-ORFa-Gly3Asp, and of the previously identified D2-Thr92Ala polymorphism, with serum iodothyronine levels. D2-ORFa-Gly3Asp was identified by sequencing the 5'-UTR of 15 randomly selected individuals. Genotypes for D2-ORFa-Gly3Asp were determined in 156 healthy blood donors (age 46.3 +/- 12.2 yr) and 349 ambulant elderly men (age 77.7 +/- 3.5 yr) and related to serum iodothyronine and TSH levels. D2-ORFa-Asp(3) had an allele frequency of 33.9% in blood bank donors and was associated with serum thyroxine (T(4); Gly/Gly vs. Gly/Asp vs. Asp/Asp = 7.06 +/- 0.14 vs. 6.74 +/- 0.15 vs. 6.29 +/- 0.27 microg/dl, P = 0.01), free T(4) (1.22 +/- 0.02 vs. 1.16 +/- 0.02 vs. 1.06 +/- 0.04 ng/dl, P = 0.001), reverse T(3) (P = 0.01), and T(3)/T(4) ratio (P = 0.002) in a dose-dependent manner, but not with serum T(3) (P = 0.59). In elderly men, D2-ORFa-Asp(3) had a similar frequency but was not associated with serum iodothyronine levels. This new polymorphism in the 5'-UTR of D2 is associated with iodothyronine levels in blood donors but not in elderly men. We hypothesize that this might be explained by the decline in skeletal muscle size during aging, resulting in a relative decrease in the contribution of D2 to serum T(3) production. 相似文献
50.