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Ramalho AS, Beck S, Meyer M, Penque D, Cutting GR, Amaral MD. Five percent of normal cystic fibrosis transmembrane conductance regulator mRNA ameliorates the severity of pulmonary disease in cystic fibrosis. Am J Respir Cell Mol Biol 2002; 27:619-27. [PMID: 12397022 DOI: 10.1165/rcmb.2001-0004oc] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Estimates of the level of transcripts from the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene required to develop a CF phenotype range from 4-20% of normal. Due to the importance of obtaining reliable data on this issue for therapeutic strategies, we developed a novel polymerase chain reaction-based method to quantify CFTR transcripts and applied it to the analysis of nasal epithelium RNA of five patients with CF and the 3272-26A>G/F508del genotype. We calculated that 8.2 +/- 0.84% of the total CFTR RNA present in these five patients is normal full-length CFTR mRNA. We then demonstrated (in nasal samples from F508del carriers, n = 30) that the abundance of full-length F508del CFTR transcripts is reduced compared with wild-type transcripts, and estimated that the average ratio of F508del/wild-type transcripts is 0.87 +/- 0.06. To determine the amount of full-length transcripts relative to levels found in normal individuals, we corrected for the lower abundance of the F508del transcripts and calculated that the five patients with CF have, on average, 4.7 +/- 0.45% of the normal level of wild-type CFTR mRNA. Because these patients have mild CF compared with F508del homozygotes, this CFTR mRNA level appears to be sufficient to avoid the severe complications of the disease.
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Novik KL, Nimmrich I, Genc B, Maier S, Piepenbrock C, Olek A, Beck S. Epigenomics: genome-wide study of methylation phenomena. Curr Issues Mol Biol 2002; 4:111-28. [PMID: 12432963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
Epigenetics is one of the key areas of future research that can elucidate how genomes work. It combines genetics and the environment to address complex biological systems such as the plasticity of our genome. While all nucleated human cells carry the same genome, they express different genes at different times. Much of this is governed by epigenetic changes resulting in differential methylation of our genome--or different epigenomes. Individual studies over the past decades have already established the involvement of DNA methylation in imprinting, gene regulation, chromatin structure, genome stability and disease, especially cancer. Now, in the wake of the Human Genome Project (HGP), epigenetic phenomena can be studied genome-wide and are giving rise to a new field, epigenomics. Here, we review the current and future potential of this field and introduce the pilot study towards the Human Epigenome Project (HEP).
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Schwenn O, Troost R, Vogel A, Grus F, Beck S, Pfeiffer N. Ocular pulse amplitude in patients with open angle glaucoma, normal tension glaucoma, and ocular hypertension. Br J Ophthalmol 2002; 86:981-4. [PMID: 12185121 PMCID: PMC1771281 DOI: 10.1136/bjo.86.9.981] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND/AIM Intraocular pressure (IOP) is not a fixed constant value but rather has pulsatile components associated with cardiac action. The SmartLens dynamic observing tonometer (odc, Ophthalmic Development Company AG, Zurich, Switzerland) can measure and record simultaneously IOP and ocular pulse amplitude (OPA). It was the aim of this study to evaluate OPA in patients with primary open angle glaucoma (POAG) and high IOP, normal tension glaucoma (NTG), and ocular hypertension (OHT). Furthermore, the authors examined whether there were any correlations with blood pressure. METHODS 80 subjects were divided into four groups (n=20): 20 patients each with POAG, NTG, and OHT and 20 volunteers without any ocular pathology except for cataract served as a control group. RESULTS The OPA of the POAG group was not statistically significant different from the control group and from the OHT group. However, OPA was statistically significant lower (p<0.01) in the NTG group compared with all other groups. The OPA of the OHT group was slightly higher compared to the healthy volunteers (p=0.09) and to the POAG patients (p=0.09). No statistically significant correlations with blood pressure could be detected. A logistic regression model was established which identified OPA as an independent risk factor for NTG. CONCLUSIONS The study demonstrated a decrease in OPA of patients suffering from NTG. Thus, measuring of OPA by the SmartLens dynamic observing tonometer could be helpful in the detection of NTG patients.
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Allcock RJN, Atrazhev AM, Beck S, de Jong PJ, Elliott JF, Forbes S, Halls K, Horton R, Osoegawa K, Rogers J, Sawcer S, Todd JA, Trowsdale J, Wang Y, Williams S. The MHC haplotype project: a resource for HLA-linked association studies. TISSUE ANTIGENS 2002; 59:520-1. [PMID: 12445322 DOI: 10.1034/j.1399-0039.2002.590609.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Collin GB, Marshall JD, Ikeda A, So WV, Russell-Eggitt I, Maffei P, Beck S, Boerkoel CF, Sicolo N, Martin M, Nishina PM, Naggert JK. Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alström syndrome. Nat Genet 2002; 31:74-8. [PMID: 11941369 DOI: 10.1038/ng867] [Citation(s) in RCA: 246] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alström syndrome is a homogeneous autosomal recessive disorder that is characterized by childhood obesity associated with hyperinsulinemia, chronic hyperglycemia and neurosensory deficits. The gene involved in Alström syndrome probably interacts with genetic modifiers, as subsets of affected individuals present with additional features such as dilated cardiomyopathy, hepatic dysfunction, hypothyroidism, male hypogonadism, short stature and mild to moderate developmental delay, and with secondary complications normally associated with type 2 diabetes, such as hyperlipidemia and atherosclerosis. Our detection of an uncharacterized transcript, KIAA0328, led us to identify the gene ALMS1, which contains sequence variations, including four frameshift mutations and two nonsense mutations, that segregate with Alström syndrome in six unrelated families. ALMS1 is ubiquitously expressed at low levels and does not share significant sequence homology with other genes reported so far. The identification of ALMS1 provides an entry point into a new pathway leading toward the understanding of both Alström syndrome and the common diseases that characterize it.
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Rabis A, Ziemer B, Wulff-Molder D, Meisel M, Beck S. Triorganophosphine-dithiomonometaphosphoryl halides. Acta Crystallogr C 2002; 58:O247-50. [PMID: 11932556 DOI: 10.1107/s0108270102004080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2002] [Accepted: 03/01/2002] [Indexed: 11/10/2022] Open
Abstract
The title compounds, ethyldiphenylphosphine-dithiomonometaphosphoryl chloride, EtPh(2)P-->PS(2)Cl, C(14)H(15)ClP(2)S(2), (I), and tris-n-propylphosphine-dithiomonometaphosphoryl chloride and bromide, nPr(3)P-->PS(2)Cl, C(9)H(21)ClP(2)S(2), (II), and nPr(3)P-->PS(2)Br, C(9)H(21)BrP(2)S(2), (III), respectively, are the first phosphine-stabilized dithiomonometaphosphoryl halides to be structurally characterized. In the tris-n-propylphosphine derivatives, the central P-->P donor-acceptor bond becomes longer in the order bromo < chloro < fluoro. Substitution of the tris-n-propylphosphine group in (II) by the more bulky ethyldiphenylphosphine group also leads to a longer P-->P bond. These structural features agree with the observed 31P NMR data. In (II) and (III), the central P-P bond coincides with the crystallographic threefold axis, entailing site-occupational disorder for the S(2)Y group.
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Walker B, Milne S, Beck S, Kaufman J. 17. Genes encoding the transporters associated with antigen processing in the chicken are situated between the classical MHC class I genes and are highly polymorphic. Res Vet Sci 2002. [DOI: 10.1016/s0034-5288(02)90019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Beck S, Trowsdale J. The human major histocompatability complex: lessons from the DNA sequence. Annu Rev Genomics Hum Genet 2002; 1:117-37. [PMID: 11701627 DOI: 10.1146/annurev.genom.1.1.117] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The entire 3.6-MbpDNA sequence of a human major histocompatibility complex derived from a composite of DNA clones from different haplotypes, was completed in 1999, primarily through the work of four main groups. At that time, it was the longest contiguous human DNA sequence to have been determined. The sequence is of extremely high quality and accuracy. In this review, we discuss how the DNA sequence has facilitated our understanding of the biology and genetics of the major histocompatibility complex. We suggest some ways in which the sequence may be exploited in the future to explore the relationship between the extraordinary polymorphism of the region and its association with both autoimmune and infectious diseases.
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Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL, Bailey J, Barlow KF, Bates KN, Beard LM, Beare DM, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Brown AJ, Buck D, Burrill W, Butler AP, Carder C, Carter NP, Chapman JC, Clamp M, Clark G, Clark LN, Clark SY, Clee CM, Clegg S, Cobley VE, Collier RE, Connor R, Corby NR, Coulson A, Coville GJ, Deadman R, Dhami P, Dunn M, Ellington AG, Frankland JA, Fraser A, French L, Garner P, Grafham DV, Griffiths C, Griffiths MN, Gwilliam R, Hall RE, Hammond S, Harley JL, Heath PD, Ho S, Holden JL, Howden PJ, Huckle E, Hunt AR, Hunt SE, Jekosch K, Johnson CM, Johnson D, Kay MP, Kimberley AM, King A, Knights A, Laird GK, Lawlor S, Lehvaslaiho MH, Leversha M, Lloyd C, Lloyd DM, Lovell JD, Marsh VL, Martin SL, McConnachie LJ, McLay K, McMurray AA, Milne S, Mistry D, Moore MJ, Mullikin JC, Nickerson T, Oliver K, Parker A, Patel R, Pearce TA, Peck AI, Phillimore BJ, Prathalingam SR, Plumb RW, Ramsay H, Rice CM, Ross MT, Scott CE, Sehra HK, Shownkeen R, Sims S, Skuce CD, Smith ML, Soderlund C, Steward CA, Sulston JE, Swann M, Sycamore N, Taylor R, Tee L, Thomas DW, Thorpe A, Tracey A, Tromans AC, Vaudin M, Wall M, Wallis JM, Whitehead SL, Whittaker P, Willey DL, Williams L, Williams SA, Wilming L, Wray PW, Hubbard T, Durbin RM, Bentley DR, Beck S, Rogers J. The DNA sequence and comparative analysis of human chromosome 20. Nature 2001; 414:865-71. [PMID: 11780052 DOI: 10.1038/414865a] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.
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Troost R, Vogel A, Beck S, Schwenn O, Grus F, Pfeiffer N. Clinical comparison of two intraocular pressure measurement methods: SmartLens dynamic observing tonography versus Goldmann. Graefes Arch Clin Exp Ophthalmol 2001; 239:889-92. [PMID: 11820692 DOI: 10.1007/s00417-001-0376-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
PURPOSE To compare intraocular pressure measurements obtained with SmartLens, a gonioscopic contact lens, to those from Goldmann applanation tonometry. METHODS Eighty volunteers (20 healthy individuals and 60 glaucoma patients from the university eye hospital's outpatient department) were examined using conventional Goldmann tonometry and the new SmartLens tool. For each device three replicate measurements were performed. A paired t-test and the corresponding mean difference confidence interval approach were used to assess deviations in location of the two tonometric methods; the test procedure of Maloney and Rastogi was used for comparison of precision in paired data. Intraindividual differences were evaluated according to the approach of Altman and Bland. RESULTS There was a mean difference of 5.6 mmHg (95% CI: 4.3 mmHg; 6.8 mmHg; P<0.01) in intraocular pressure between the two methods with a significant overestimation by SmartLens tonometry compared to Goldmann tonometry (P<0.01). The 95%-limits of agreement ranged from -5.4 mmHg to +16.6 mmHg for individual patients. The measurement method variance of SmartLens was higher (Maloney-Rastogi test; P <0.01). The mean coefficients of variation for intraindividual replicates were 10.1% (SmartLens) and 3.8% (Goldmann; P <0.01). CONCLUSIONS Accepting Goldmann tonometry as gold standard for intraocular pressure measurement, the SmartLens method shows considerable variation and therefore is not proven to be an adequate substitute for Goldmann tonometry.
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Amaral MD, Pacheco P, Beck S, Farinha CM, Penque D, Nogueira P, Barreto C, Lopes B, Casals T, Dapena J, Gartner S, Vásquez C, Pérez-Frías J, Olveira C, Cabanas R, Estivill X, Tzetis M, Kanavakis E, Doudounakis S, Dörk T, Tümmler B, Girodon-Boulandet E, Cazeneuve C, Goossens M, Blayau M, Verlingue C, Vieira I, Féréc C, Claustres M, des Georges M, Clavel C, Birembaut P, Hubert D, Bienvenu T, Adoun M, Chomel JC, De Boeck K, Cuppens H, Lavinha J. Cystic fibrosis patients with the 3272-26A>G splicing mutation have milder disease than F508del homozygotes: a large European study. J Med Genet 2001; 38:777-83. [PMID: 11732487 PMCID: PMC1734751 DOI: 10.1136/jmg.38.11.777] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kammer T, Beck S, Erb M, Grodd W. The influence of current direction on phosphene thresholds evoked by transcranial magnetic stimulation. Clin Neurophysiol 2001; 112:2015-21. [PMID: 11682339 DOI: 10.1016/s1388-2457(01)00673-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES To quantify phosphene thresholds evoked by transcranial magnetic stimulation (TMS) in the occipital cortex as a function of induced current direction. METHODS Phosphene thresholds were determined in 6 subjects. We compared two stimulator types (Medtronic-Dantec and Magstim) with monophasic pulses using the standard figure-of-eight coils and systematically varied hemisphere (left and right) and induced current direction (latero-medial and medio-lateral). Each measurement was made 3 times, with a new stimulation site chosen for each repetition. Only those stimulation sites were investigated where phosphenes were restricted to one visual hemifield. Coil positions were stereotactically registered. Functional magnetic resonance imaging (fMRI) of retinotopic areas was performed in 5 subjects to individually characterize the borders of visual areas; TMS stimulation sites were coregistered with respect to visual areas. RESULTS Despite large interindividual variance we found a consistent pattern of phosphene thresholds. They were significantly lower if the direction of the induced current was oriented from lateral to medial in the occipital lobe rather than vice versa. No difference with respect to the hemisphere was found. Threshold values normalized to the square root of the stored energy in the stimulators were lower with the Medtronic-Dantec device than with the Magstim device. fMRI revealed that stimulation sites generating unilateral phosphenes were situated at V2 and V3. Variability of phosphene thresholds was low within a cortical patch of 2x2cm(2). Stimulation over V1 yields phosphenes in both visual fields. CONCLUSIONS The excitability of visual cortical areas depends on the direction of the induced current with a preference for latero-medial currents. Although the coil positions used in this study were centered over visual areas V2 and V3, we cannot rule out the possibility that subcortical structures or V1 could actually be the main generator for phosphenes.
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Beck S, Mockenhaupt FP, Bienzle U, Eggelte TA, Thompson WN, Stark K. Multiplicity of Plasmodium falciparum infection in pregnancy. Am J Trop Med Hyg 2001; 65:631-6. [PMID: 11716126 DOI: 10.4269/ajtmh.2001.65.631] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Little is known about the distribution and disease association of multiple Plasmodium falciparum infections in pregnant women. Genotyping of the merozoite surface protein-1 region was performed in 332 P. falciparum infected pregnant women in Ghana, and clinical and epidemiologic data were obtained. Overall, 68% of the women were infected with more than one strain (mean number of strains per carrier = 2.9). The multiplicity of infection decreased significantly with an increasing number of pregnancies, and infection with multiple P. falciparum strains was significantly associated with anemia. In logistic regression, women infected with four or more strains were 2.3 times more likely to be anemic than women harboring fewer strains. This association, however, was only observed in women with up to three pregnancies. The results suggest that with increasing gravidity and subsequent infections with multiple strains effective immune mechanisms against more and more strains develop. In pregnant women, the multiplicity of infection may be an important factor for the acquisition and maintenance of immunity against malaria.
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Beck S. Changing styles of drinking; alcohol use in the Balkans. EAST EUROPEAN QUARTERLY 2001; 18:395-413. [PMID: 11616899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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Wagner CA, Ott M, Klingel K, Beck S, Melzig J, Friedrich B, Wild KN, Bröer S, Moschen I, Albers A, Waldegger S, Tümmler B, Egan ME, Geibel JP, Kandolf R, Lang F. Effects of the serine/threonine kinase SGK1 on the epithelial Na(+) channel (ENaC) and CFTR: implications for cystic fibrosis. Cell Physiol Biochem 2001; 11:209-18. [PMID: 11509829 DOI: 10.1159/000051935] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cystic fibrosis (CF) is characterized by impaired Cl(-) secretion and increased Na(+) reabsorption in several tissues including respiratory epithelium. Many CFTR mutations have been identified over the past years. However, only a poor correlation between the genotype and lung phenotype was found suggesting additional factors influencing the phenotype and course of the disease. The serine/threonine kinase SGK1 has recently been shown to stimulate the activity of the epithelial Na(+) channel ENaC. A variety of stimuli such as aldosterone, cell shrinkage, insulin or TGF-beta1 stimulate transcription and activate the SGK1 kinase. Here we further examined the effects of SGK1 on ENaC and CFTR which have mutual interactions and we analyzed sgk1 mRNA abundance in lung tissue from CF patients. Coexpression of CFTR and h-SGK1 in Xenopus oocytes increased ENaC currents as previously described. In addition CFTR mediated currents were also stimulated. h-SGK1 accelerated the expression of the amiloride sensitive Na(+)- current in Xenopus oocytes paralleled by increased ENaC-protein abundance in the oocyte membrane, an effect which was reversed by a h-SGK1(K127R) mutation lacking the ATP-binding site. The cation selectivity or Na(+) affinity were not affected. However, coexpression of h-SGK1 with ENaC altered the sensitivity of the Na(+)-channel to the inhibitors amiloride and triamterene. The inhibitory effect of CFTR expression on ENaC current was not affected by coexpression of h-SGK1 in Xenopus oocytes. Lung tissue from CF patients strongly expressed the serine/threonine kinase h-sgk1 which was not the case for non-CF lung tissue. Loss of CFTR function itself in a CF lung epithelial cell line did not increase SGK1 expression. In summary, enhanced expression of h-SGK1 in epithelial cells of CF-lung tissue may be a novel pathophysiological factor contributing to increased Na(+) channel activity and thus to increased Na(+) transport in CF.
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Degré M, Ranneberg-Nilsen T, Beck S, Rollag H, Fiane AE. Human cytomegalovirus productively infects porcine endothelial cells in vitro. Transplantation 2001; 72:1334-7. [PMID: 11602867 DOI: 10.1097/00007890-200110150-00028] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The possibility that human cytomegalovirus (HCMV) may infect porcine endothelial cells (ECs) was investigated. This may be relevant during xenotransplantation of porcine cells or organs into human recipients. METHODS HCMV was inoculated into low-passage porcine ECs. Replication of virus was detected by development of characteristic cytopathogenic effect. Appearance of immediate early, early, and late antigens was studied by immunocytochemical staining. Infectious virus was detected in human fibroblast cells. Presence of HCMV RNA was studied by Northern Blot and reverse transcriptase polymerase chain reaction. RESULTS All parameters indicated that a fresh clinical HCMV isolate productively infects porcine ECs. The same cells do not fully support replication of the laboratory strain Ad 169. CONCLUSION Our results may indicate the possibility of cross-species infectivity of HCMV to porcine cells.
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Vogel A, Beck S, Schwenn O, Grus F, Krummenauer F, Pfeiffer N. [Reproducibility of measurement of ocular pulse amplitude and intraocular pressure using Smartlens]. Ophthalmologe 2001; 98:944-9. [PMID: 11699315 DOI: 10.1007/s003470170041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND SmartLens (ODC Ophthalmic Development Company AG, Zürich) is a contact lens tonometer, which allows continuous registration of intraocular pressure (IOP) and ocular pulse amplitude (OPA) and simultaneous ophthalmoscopy. The purpose of this study was to evaluate the intra- and interobserver variability and reliability of intraocular pressure and ocular pulse amplitude measurements using SmartLens. METHODS To evaluate the intraobserver variability, intraocular pressure (IOP) and ocular pulse amplitude (OPA) were both measured 5 times in 10 healthy eyes by one observer. To evaluate the interobserver variability, intraocular pressure and ocular pulse amplitude were measured by 3 different observers in 10 healthy eyes. Data description is based on coefficients of variation (SD/mean in %), statistical inference on ANOVA-based reliability estimation. RESULTS The coefficient of the intraobserver variation was 9.57% for the IOP and 14.5% for the OPA (SD IOP: +/- 1.64 mmHg, SD OPA: +/- 0.39 mmHg). The coefficient of the interobserver variation with 5 replicate measurements was 10.16% for the IOP and 14% for the OPA (SD IOP: +/- 1.83 mmHg, SD OPA: +/- 0.4 mmHg). The interobserver reliability was 87% for the IOP and 86% for the OPA. One of the three observers obtained significantly higher IOP and OPA values. CONCLUSIONS SmartLens is a reasonably precise and reliable device for IOP as well as OPA measurements but the results were not found to be observer independent.
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Asakawa S, Takayanagi A, Sasaki T, Shimizu A, Shintani A, Kawasaki K, Mungall AJ, Beck S, Minoshima S, Shimizu N. The genomic structure and promoter region of the human parkin gene. Biochem Biophys Res Commun 2001; 286:863-8. [PMID: 11527378 DOI: 10.1006/bbrc.2001.5490] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Parkin has been identified as a causative gene of the autosomal recessive juvenile parkinsonism (AR-JP). In this study, we determined the genomic structure of the Parkin gene and identified a core promoter region based on the DNA sequence of 1.4 Mb. The 5'-flanking region contained no apparent TATA or CAAT box elements but several putative cis-elements for various transcription factors. The GC- and CpG-rich regions were observed not only in the 5'-flanking sequence but also in the 5'-part of the first intron of Parkin. We identified an exact starting point of Parkin transcription. A core promoter region was determined by transfecting a series of deletion constructs with a dual luciferase reporter system into human neuroblastoma cells. Furthermore, we located a neighboring novel gene in a head-to-head direction with Parkin with only a 198-bp interval.
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Trowsdale J, Barten R, Haude A, Stewart CA, Beck S, Wilson MJ. The genomic context of natural killer receptor extended gene families. Immunol Rev 2001; 181:20-38. [PMID: 11513141 DOI: 10.1034/j.1600-065x.2001.1810102.x] [Citation(s) in RCA: 231] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The two sets of inhibitory and activating natural killer (NK) receptor genes belong either to the Ig or to the C-type lectin superfamilies. Both are extensive and diverse, comprising genes of varying degrees of relatedness, indicative of a process of iterative duplication. We have constructed gene maps to help understand how and when NK receptor genes developed and the nature of their polymorphism. A cluster of over 15 C-type lectin genes, the natural killer complex is located on human chromosome 12p13.1, syntenic with a region in mouse that borders multiple Ly49 loci. The equivalent locus in man is occupied by a single pseudogene, LY49L. The immunoglobulin superfamily of loci, the leukocyte receptor complex (LRC), on chromosome 19q13.4, contains many polymorphic killer cell immunoglobulin-like receptor (KIR) genes as well as multiple related sequences. These include immunoglobulin-like transcript (ILT) (or leukocyte immunoglobulin-like receptor genes), leukocyte-associated inhibitory receptor genes (LAIR), NKp46, Fc alphaR and the platelet glycoprotein receptor VI locus, which encodes a collagen-binding molecule. KIRs are expressed mostly on NK cells and some T cells. The other LRC loci are more widely expressed. Further centromeric of the LRC are sets of additional loci with weak sequence similarity to the KIRs, including the extensive CD66(CEA) and Siglec families. The LRC-syntenic region in mice contains no orthologues of KIRs. Some of the KIR genes are highly polymorphic in terms of sequence as well as for presence/absence of genes on different haplotypes. Some anchor loci, such as KIR2DL4, are present on most haplotypes. A few ILT loci, such as ILT5 and ILT8, are polymorphic, but only ILT6 exhibits presence/absence variation. This knowledge of the genomic organisation of the extensive NK superfamilies underpins efforts to understand the functions of the encoded NK receptor molecules. It leads to the conclusion that the functional homology of human KIR and mouse Ly49 genes arose by convergent evolution. NK receptor immunogenetics has interesting parallels with the major histocompatibility complex (MHC) in which some of the polymorphic genes are ligands for NK molecules. There are hints of an ancient genetic relationship between NK receptor genes and MHC-paralogous regions on chromosomes 1, 9 and 19. The picture that emerges from both complexes is of eternal evolutionary restlessness, presumably in response to resistance to disease.
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MESH Headings
- Animals
- Base Sequence
- Chromosome Mapping
- Chromosomes, Human, Pair 19/genetics
- Evolution, Molecular
- Genome, Human
- Humans
- Killer Cells, Natural/immunology
- Leukocytes/immunology
- Ligands
- Mice
- Minisatellite Repeats
- Molecular Sequence Data
- Multigene Family
- Polymorphism, Genetic
- Receptors, Immunologic/genetics
- Receptors, KIR
- Receptors, KIR2DL4
- Sequence Homology, Nucleic Acid
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Younger RM, Amadou C, Bethel G, Ehlers A, Lindahl KF, Forbes S, Horton R, Milne S, Mungall AJ, Trowsdale J, Volz A, Ziegler A, Beck S. Characterization of clustered MHC-linked olfactory receptor genes in human and mouse. Genome Res 2001; 11:519-30. [PMID: 11282967 PMCID: PMC311051 DOI: 10.1101/gr.gr-1603r] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Olfactory receptor (OR) loci frequently cluster and are present on most human chromosomes. They are members of the seven transmembrane receptor (7-TM) superfamily and, as such, are part of one of the largest mammalian multigene families, with an estimated copy number of up to 1000 ORs per haploid genome. As their name implies, ORs are known to be involved in the perception of odors and possibly also in other, nonolfaction-related, functions. Here, we report the characterization of ORs that are part of the MHC-linked OR clusters in human and mouse (partial sequence only). These clusters are of particular interest because of their possible involvement in olfaction-driven mate selection. In total, we describe 50 novel OR loci (36 human, 14 murine), making the human MHC-linked cluster the largest sequenced OR cluster in any organism so far. Comparative and phylogenetic analyses confirm the cluster to be MHC-linked but divergent in both species and allow the identification of at least one ortholog that will be useful for future regulatory and functional studies. Quantitative feature analysis shows clear evidence of duplications of blocks of OR genes and reveals the entire cluster to have a genomic environment that is very different from its neighboring regions. Based on in silico transcript analysis, we also present evidence of extensive long-distance splicing in the 5'-untranslated regions and, for the first time, of alternative splicing within the single coding exon of ORs. Taken together with our previous finding that ORs are also polymorphic, the presented data indicate that the expression, function, and evolution of these interesting genes might be more complex than previously thought.
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221
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Beck S. Home visit 2002. HOME HEALTHCARE NURSE 2001; 19:197-9. [PMID: 11985250 DOI: 10.1097/00004045-200104000-00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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222
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Böhmer C, Wagner CA, Beck S, Moschen I, Melzig J, Werner A, Lin JT, Lang F, Wehner F. The shrinkage-activated Na(+) conductance of rat hepatocytes and its possible correlation to rENaC. Cell Physiol Biochem 2001; 10:187-94. [PMID: 11093028 DOI: 10.1159/000016349] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
At moderate cell shrinkage, activation of Na(+) channels is the most prominent mechanism of regulatory cell volume increase in rat hepatocytes. The amiloride sensitivity of these channels suggests a relation to the family of epithelial Na(+) channels (ENaCs). The present study was performed to determine the pharmacological profile of shrinkage-activated Na(+) channels and to test for ENaC expression in primary cultures of rat hepatocytes; in addition, the influence of the cell volume regulated serine/threonine kinase hSGK on activity and pharmacological profile of rENaC was examined in Xenopus oocytes. Conventional electrophysiology in hepatocytes reveals that the shrinkage-activated Na(+) channel is inhibited by amiloride and EIPA with IC(50) values of 6.0 and 0.12 micromol/l, respectively. Western blots and RT-PCR demonstrate that rat hepatocytes do express all three subunits (alpha, beta, gamma) of ENaC. Coexpression of hSGK with rENaC in Xenopus oocytes reveals that the kinase stimulates ENaC by a factor of 4. Moreover, hSGK decreases the affinity to amiloride (increase of IC(50) from 0.12 to 0.26 micromol/l) and increases the affinity to EIPA (decrease of IC(50) from 250 to 50 micromol/l). In conclusion, rat hepatocytes express ENaC, which is activated by the cell volume-sensitive kinase hSGK. ENaC may contribute to the Na(+) channels activated by osmotic cell shrinkage in hepatocytes, whereby the relatively low amiloride and high EIPA sensitivity of the channel could at least be partially due to modification by SGK, which decreases the amiloride and increases the EIPA sensitivity of ENaC.
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223
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Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. [PMID: 11237011 DOI: 10.1038/35057062] [Citation(s) in RCA: 14529] [Impact Index Per Article: 631.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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224
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Rhodes DA, Stammers M, Malcherek G, Beck S, Trowsdale J. The cluster of BTN genes in the extended major histocompatibility complex. Genomics 2001; 71:351-62. [PMID: 11170752 DOI: 10.1006/geno.2000.6406] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We sequenced the 170-kb cluster of BTN genes in the extended major histocompatibility complex region, 4 Mb telomeric of human leukocyte antigen class I genes, at 6p22.1. The cluster consists of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The main complex is composed of six genes, from two subfamilies, BTN2 and BTN3, arranged in pairs. This alternating pattern must have evolved by duplications of an original block of two genes, one from each subfamily. The sequences from the two subfamilies share approximately 50% amino acid identity. By analysis of repeat elements within each block, these duplications may be dated to approximately 100 million years ago, at about the time of the branching of the Rodentia and Primate lineages. The single BTN1A1 (butyrophilin) gene was positioned approximately 25 kb centromeric to the cluster. Each gene covers approximately 12 kb and consists of seven (BTN2 subfamily) or nine (BTN3 subfamily) coding exons. The predicted leader sequence, immunoglobulin-like IgV (variable)/IgC (constant) ectodomains, and the predicted transmembrane domain are encoded on separate exons and are separated from a B30.2 domain by a variable number of very short exons, 21 and 27 nucleotides in length. BTN transcripts were detected in all tissues examined. Alternative splicing, involving particularly the carboxyl-terminal B30.2 domain, was a notable feature. Most transcripts of BTN2 subfamily genes contained this domain, whereas BTN3 genes did not. Using immunofluorescence, we showed surface expression of BTN-green fluorescent protein fusions in mammalian cell transfectants.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Blotting, Southern
- Butyrophilins
- CHO Cells
- Cell Membrane/metabolism
- Chromosome Mapping
- Chromosomes, Human, Pair 6
- Cricetinae
- DNA, Complementary/metabolism
- Exons
- Expressed Sequence Tags
- Genetic Markers
- Green Fluorescent Proteins
- Haplotypes
- HeLa Cells
- Homozygote
- Humans
- Luminescent Proteins/metabolism
- Major Histocompatibility Complex
- Membrane Glycoproteins/genetics
- Microscopy, Fluorescence
- Models, Genetic
- Molecular Sequence Data
- Multigene Family
- Polymorphism, Genetic
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- RNA, Spliced Leader
- Recombinant Fusion Proteins/metabolism
- Repetitive Sequences, Nucleic Acid
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Transfection
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225
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Kammer T, Beck S, Thielscher A, Laubis-Herrmann U, Topka H. Motor thresholds in humans: a transcranial magnetic stimulation study comparing different pulse waveforms, current directions and stimulator types. Clin Neurophysiol 2001; 112:250-8. [PMID: 11165526 DOI: 10.1016/s1388-2457(00)00513-7] [Citation(s) in RCA: 279] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To evaluate the stimulation effectiveness of different magnetic stimulator devices with respect to pulse waveform and current direction in the motor cortex. METHODS In 8 normal subjects we determined motor thresholds of transcranial magnetic stimulation in a small hand muscle. We used focal figure-of-eight coils of 3 common stimulators (Dantec Magpro, Magstim 200 and Magstim Rapid) and systematically varied current direction (postero-anterior versus antero-posterior, perpendicular to the central sulcus) as well as pulse waveform (monophasic versus biphasic). The coil position was kept constant with a stereotactic positioning device. RESULTS Motor thresholds varied consistently with changing stimulus parameters, despite substantial interindividual variability. By normalizing the values with respect to the square root of the energy of the capacitors in the different stimulators, we found a homogeneous pattern of threshold variations. The normalized Magstim threshold values were consistently higher than the normalized Dantec thresholds by a factor of 1.3. For both stimulator types the monophasic pulse was more effective if the current passed the motor cortex in a postero-anterior direction rather than antero-posterior. In contrast, the biphasic pulse was weaker with the first upstroke in the postero-anterior direction. We calculated mean factors for transforming the intensity values of a particular configuration into that of another configuration by normalizing the different threshold values of each individual subject to his lowest threshold value. CONCLUSIONS Our transformation factors allow us to compare stimulation intensities from studies using different devices and pulse forms. The effectiveness of stimulation as a function of waveform and current direction follows the same pattern as in a peripheral nerve preparation (J Physiol (Lond) 513 (1998) 571).
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