Biomedical subjects

Christian Becker

Publications and source records attributed to Christian Becker.

33 records · Page 2Linked to original sources

PubMed2005

Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification.

Whole-genome DNA amplification by multiple displacement (MD-WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD-WGA. We observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra-assay reproducibility of the genotyping technique used. However, MD-WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3-fold reduction of noncalled SNPs by combining the results from two independent MD-WGA reactions. This indicated that inter-reaction variations rather than specific chromosomal loci reduced the efficiency of MD-WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD-WGA appears to be the current method of choice to amplify genomic DNA for array-based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.

Genome, Human↗

PubMed2005

Application of genomewide SNP arrays for detection of simulated susceptibility loci.

The prospect of SNP-based genomewide association analysis has been extensively discussed, but practical experiences remain limited. We performed an association study using a recently developed array of 11,555 SNPs distributed throughout the human genome. A total of 104 DNA samples were hybridized to these chips with an average call rate of 97% (range 85.3-98.6%). The resulting genomewide scans were applied to distinguish between carriers and noncarriers of 37 test variants, used as surrogates for monogenic disease traits. The test variants were not contained in the chip and had been determined by other methods. Without adjustment for multiple testing, the procedure detected 24% of the test variants, but the positive predictive value was low (2%). Adjustment for multiple testing eliminated most false-positive associations, but the share of true positive associations decreased to 10-12%. We also simulated fine-mapping of susceptibility loci by restricting testing to the immediate neighborhood of test variants (+/-5 Mb). This increased the proportion of correctly identified test variants to 22-27%. Simulation of a bigenic inheritance reduced the sensitivity to 1%. Similarly adverse effect had reduction of allelic penetrance. In summary, we demonstrate the feasibility and considerable specificity of SNP array-based association studies to detect variants underlying monogenic, highly penetrant traits. The outcome is affected by allelic frequencies of chip SNPs, by the ratio between simulated "cases" and "controls," and by the degree of linkage disequilibrium. A major improvement is expected from raising the density of the SNP array.

Alleles↗

PubMed2005

Isolation and expansion of tumor-specific CD4+ T-cells by means of cytokine secretion.

A major objective of immune analysis in the setting of cancer, cancer vaccination, and therapy is to accurately characterize and isolate functional T-cells elicited by a tumor. Secretion of cytokines is an important function of activated effector and memory T-cells. The cytokine secretion assay (CSA) directly assesses T-cells secreting cytokines after a short restimulation in vitro. Cells can be stained for surface markers enabling characterization of subsets. Viable cytokine-secreting T-cells can be isolated for expansion and further functional testing or adoptive transfer. Since the method is not restricted to any antigen or major histocompatibility complex (MHC) haplotype, it enables us to detect CD8+ as well as CD4+ T-cells reacting against a wide vary of tumor-associated antigens, ranging from particular known tumor antigens to whole tumor cells and crude tumor lysates. Thus, the method provides a valuable tool to analyze and isolate functional tumor-responsive T-cells according to one of their effector functions.

Animals↗

PubMed2005

Dendritic cells: sentinels of immunity and tolerance.

The induction of effective antigen-specific T-cell immunity to pathogens without the initiation of autoimmunity has evolved as a sophisticated and highly balanced immunoregulatory mechanism. This mechanism assures the generation of antigen-specific effector cells as well as the induction and maintenance of antigen-specific tolerance to self-structures of the body. As professional antigen-presenting cells of the immune system, dendritic cells (DC) are ideally positioned throughout the entire body and equipped with a unique capability to transport antigens from the periphery to lymphoid tissues. There is growing evidence that DC, besides their well-known immunostimulatory properties, also induce and regulate T-cell tolerance in the periphery. This regulatory function of DC is strictly dependent on their different stages of maturation and activation. Additionally, immunosuppressive agents and cytokines further influence the functions of maturing DC. The regulatory properties of DC include induction of T-cell anergy, apoptosis, and the generation of T-cells with regulatory capacities. This brief review summarizes the current knowledge about the immunoregulatory role of DC as guardians for the induction of T-cell immunity and tolerance.

Animals↗

PubMed2005

Chemical synthesis approaches to the engineering of ion channels.

Chemoselective ligation strategies have previously provided synthetic access to water-soluble proteins with novel properties, and more recently these strategies have been used to prepare ion channels. Examples of ion channels prepared by total chemical synthesis include bacterial mechanosensitive channels, and viral ion channels. Chemical protein synthesis allows for the generation of ion channel proteins with both native, and engineered structural or conductance properties.

Animals↗

PubMed2004

Generation of mature fat pads in vitro and in vivo utilizing 3-D long-term culture of 3T3-L1 preadipocytes.

Tissue-inherent factors such as cell-cell and cell-extracellular matrix interactions are regarded to exert a potentially large impact on adipogenesis as well as on secretory functions of adipose tissue. However, an appropriate 3-D adipogenesis model useful for addressing such interactions is still lacking. In this study, using tissue-engineering techniques, we demonstrate for the first time the development of coherent fat pads consisting of unilocular signet-ring cells in vitro. The constructs were generated by differentiating 3T3-L1 preadipocytes on 3-D polymeric scaffolds for either 9, 21, or 35 days in vitro. Only long-term culture yielded uniform tissues histologically comparable to native fat. Light and scanning electron microscopy provided direct evidence of 3-D tissue coherence and cell-cell contact in a tissue context, which was in strong contrast to conventional 2-D monolayer culture. Further differences between the two culture systems included enhanced secretion of leptin in 3-D tissue culture and differences in laminin expression (mRNA and protein level). Increase of triglyceride content over culture time and mRNA expression of other adipocyte genes, such as PPARgamma and Glut-4, were found to be similar. Implantation of long-term differentiated tissue constructs in nude mice resulted in further development and maintenance of fat pads. The presented model system is suggested to contribute to a better understanding of adipose tissue development and function facilitating studies on tissue-inherent interactions in vitro and in vivo.

3T3-L1 Cells↗

PubMed2004

Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy.

We identified three consanguineous Austrian kindreds with 15 members affected by autosomal recessive childhood-onset severe retinal dystrophy, a genetically heterogeneous group of disorders characterized by degeneration of the photoreceptor cells. A whole-genome scan by microarray analysis of single-nucleotide polymorphisms (ref. 2) identified a founder haplotype and defined a critical interval of 1.53 cM on chromosome 14q23.3-q24.1 that contains the gene associated with this form of retinal dystrophy. RDH12 maps in this region and encodes a retinol dehydrogenase proposed to function in the visual cycle. A homozygous 677A-->G transition (resulting in Y226C) in RDH12 was present in all affected family members studied, as well as in two Austrian individuals with sporadic retinal dystrophy. We identified additional mutations in RDH12 in 3 of 89 non-Austrian individuals with retinal dystrophy: a 5-nucleotide deletion (806delCCCTG) and the transition 565C-->T (resulting in Q189X), each in the homozygous state, and 146C-->T (resulting in T49M) and 184C-->T (resulting in R62X) in compound heterozygosity. When expressed in COS-7 cells, Cys226 and Met49 variants had diminished and aberrant activity, respectively, in interconverting isomers of retinol and retinal. The severe visual impairment of individuals with mutations in RDH12 is in marked contrast to the mild visual deficiency in individuals with fundus albipunctatus caused by mutations in RDH5, encoding another retinal dehydrogenase. Our studies show that RDH12 is associated with retinal dystrophy and encodes an enzyme with a unique, nonredundant role in the photoreceptor cells.

Adult↗

PubMed2004

Haplotypes and SNPs in 13 lipid-relevant genes explain most of the genetic variance in high-density lipoprotein and low-density lipoprotein cholesterol.

Single nucleotide polymorphisms (SNPs) and derived haplotypes within multiple genes may explain genetic variance in complex traits; however, this hypothesis has not been rigorously tested. In an earlier study we analyzed six genes and have now expanded this investigation to include 13. We studied 250 families including 1054 individuals and measured lipid phenotypes. We focused on low-density cholesterol (LDL), high-density cholesterol (HDL) and their ratio (LDL/HDL). A component analysis of the phenotypic variance relying on a standard genetic model' showed that the genetic variance on LDL explained 26%, on HDL explained 38% and on LDL/HDL explained 28% of the total variance, respectively. Genotyping of 93 SNPs in 13 lipid-relevant genes generated 230 haplotypes. The association of haplotypes in all the genes tested explained a major fraction of the genetic phenotypic variance component. For LDL, the association with haplotypes explained 67% and for HDL 58% of the genetic variance relative to the polygenic background. We conclude that these haplotypes explain most of the genetic variance in LDL, HDL and LDL/HDL in these representative German families. An analysis of the contribution to the genetic variance at each locus showed that APOE (50%), CETP (28%), LIPC (9%), APOB (8%) and LDLR (5%) influenced variation in LDL. LIPC (53%), CETP (25%), ABCA1 (10%), LPL (6%) and LDLR (6%) influenced the HDL variance. The LDL/HDL ratio was primarily influenced by APOE (36%), CETP (27%) and LIPC (31%). This expanded analysis substantially increases the explanation of genetic variance on these complex traits.

Cholesterol, HDL↗

PubMed2004

Human CD25+ regulatory T cells: two subsets defined by the integrins alpha 4 beta 7 or alpha 4 beta 1 confer distinct suppressive properties upon CD4+ T helper cells.

Down-regulation of autoreactive T cell responses in vivo includes cell-contact-dependent as well as contact-independent mechanisms. Infectious tolerance is a contact-dependent mechanism used by naturally occurring CD25(+) T regulatory cells (Tregs) to confer suppressive activity upon conventional CD4(+) T cells thereby generating secondary T helper suppressor cells(Th(sup)), which inhibit T cell activation via soluble mediators. Here, we describe two distinct subsets of human Tregs, characterized by expression of either the alpha(4)beta(7) integrin or the alpha(4)beta(1) integrin. Upon activation, both subsets show an enhanced expression of FoxP3, recently described as a key transcription factor of murine Tregs. In addition, both are able to convey suppressive capacity to conventional CD4(+) T cells. However, the properties of Treg subsets are rather distinct: alpha(4)beta(7) (+)Tregs induce IL-10-producing Th(sup) (Tr1-like), whereas alpha(4)beta(1) (+) Tregs induce TGF-beta-producing Th(sup) (Th3-like). Our findings reconcile conflicting results by clearly demonstrating that suppression through naturally occurring CD25(+) Tregs is primary cell-contact-dependent but is subsequently followed by cell-contact-independent T cell inhibition mediated by second-generation Tr1- and Th3-like Th(sup) via the soluble factors IL-10 and TGF-beta.

Humans↗

PubMed2003

Candidate gene analysis of the human metabotropic glutamate receptor type 4 (GRM4) in patients with juvenile myoclonic epilepsy.

Hereditary factors play a major role in the genetically complex etiology of juvenile myoclonic epilepsy (JME). Linkage studies in families of JME probands suggest a susceptibility locus (EJM1) for idiopathic generalized epilepsy (IGE) in the chromosomal region 6p21.3 near the HLA region. The gene encoding the metabotropic glutamate receptor type 4 (GRM4) has been localized within the EJM1-region and represents a high-ranking candidate gene. Therefore, we have sequenced the coding regions and regulatory GRM4 sequences in 20 IGE probands who were derived from families of JME probands providing positive linkage evidence to the HLA-DQ locus. Our mutation analysis detected three synonymous exonic single nucleotide polymorphisms (SNP; exon-7: c.1455T > C, exon-8: c.2002A > G, exon-10: c.2733C > T), one SNP in the 3'-untranslated region (c.2890A > G), and two intronic SNPs (intron-3: IVS3 + 2732A > G, intron-7: IVS7 + 39C > T). None of the identified SNPs was likely to affect receptor function or gene expression. The population-based association study did not show significant differences in the allele and genotype frequencies of the common c.1455T > C SNP between 144 German JME probands and 144 healthy population controls (P > 0.84). Likewise, the family-based transmission disequilibrium test did not indicate a preferential transmission of exon-7 SNP alleles in 31 informative parent-child transmissions (P = 0.86). Our results provide no evidence that genetic variation of the GRM4 gene confers susceptibility to JME-related IGE syndromes.

Adolescent↗

PubMed2003

Volcanic emissions of mercury to the atmosphere: global and regional inventories.

A comprehensive, time-averaged inventory of subaerial emissions of mercury from volcanoes that were active between 1980 and 2000 is derived based on the Hg/SO(2) ratios of the exhalations. Worldwide flux of mercury from volcanic eruptions is estimated to be 57 t/year while the flux from degassing activities is 37.6 t/year. After correcting for 'unmeasured' SO(2) emissions, the total global flux of Hg to the atmosphere is estimated to be 112 t/year. There are regional differences in average emissions during the 20-year period, with the estimated fluxes being 29 t/year in South and Central America, 27 t/year in Southeast Asia; 24 t/year in North America (including Hawaii), 4.1 t/year in Australia, 3.4 t/year in Japan and northern Asia, 3.1 t/year in Europe and western Asia and 2.3 t/year in Africa.

Air Pollutants↗

PubMed2003

Treatment of human pancreatic cancer in mice with angiogenic inhibitors.

Tumor growth is dependent on the balance of positive and negative regulators of angiogenesis. Antiangiogenic compounds inhibit endothelial cell biology in vitro and angiogenesis in vivo. Therefore antiangiogenic therapy presumes to be an effective treatment for pancreatic cancer. We wanted to determine the effect of antiangiogenic therapy on the growth of human pancreatic cancer in a mouse model. The angiogenesis inhibitors TNP-470 and antiangiogenic antithrombin III (aaATIII) were tested in vitro for their ability to inhibit endothelial cell proliferation. These inhibitors, along with the known antiangiogenic molecule endostatin, were then employed to treat two different primary human pancreatic cancers implanted subcutaneously into the dorsa of immunodeficient (SCID) mice. Treated tumors were examined histologically for microvessel density, apoptosis, and proliferation. All three inhibitors suppressed the growth of pancreatic tumors in vivo. Immunohistochemical analysis revealed increased degrees of apoptosis and reduced microvessel density in treated tumors compared to untreated tumors, although tumor cell proliferation was the same in both groups. None of the inhibitors tested significantly inhibited proliferation of human pancreatic cancer cells, although both TNP-470 and aaATIII were able to inhibit the proliferation of endothelial cells. The observed tumor suppression may be due to increased tumor cell apoptosis as a result of capillary dropout. These studies show that after the angiogenic switch in a human tumor, there is residual production of angiogenesis inhibitors.

Angiogenesis Inhibitors↗

PubMed2002

Failure to replicate an allelic association between an exon 8 polymorphism of the human alpha(1A) calcium channel gene and common syndromes of idiopathic generalized epilepsy.

The present replication study tested the validity of a previously reported allelic association between a single nucleotide polymorphism in exon 8 (SNP8) of the gene encoding the alpha(1A)-calcium channel subunit (CACNA1A) and common subtypes of idiopathic generalized epilepsy (IGE). Pyrosequencing was applied to assess the SNP8 genotypes in 354 unrelated German IGE probands, both parents of 118 IGE probands, and 186 healthy control subjects of German descent. Our population-based association analysis did not provide evidence for an allelic association of SNP8 with either IGE or two phenotypically more homogeneous IGE subtypes, consisting of either 139 probands with juvenile myoclonic epilepsy or 207 probands whose IGE started with typical absence seizures (P>0.72). In addition, the transmission disequilibrium test did not indicate a preferential transmission of SNP8 alleles in 97 informative parent-child transmissions (McNemar chi(2)=0.093, df=1, P=0.76). Accordingly, we failed to confirm previous evidence that genetic variation of the CACNA1A gene confers susceptibility to common IGE syndromes.

Alleles↗

PubMed2002

Association of the 867Asp variant of the human anion exchanger 3 gene with common subtypes of idiopathic generalized epilepsy.

Genetic factors play a major role in the etiology of idiopathic generalized epilepsies (IGE). Our recent genome-wide search revealed suggestive evidence for a susceptibility locus for common IGE syndromes in the chromosomal region 2q36. The gene encoding the anion exchanger isoform 3 (AE3; gene symbol: SLC4A3) has been mapped to this candidate region. AE3 is prominently expressed in the brain and performs an electroneutral exchange of chloride and bicarbonate. To study the potential role of AE3 in the epileptogenesis of IGE, we performed a mutation analysis of the AE3 coding region, including the adjacent exon/intron boundaries, and the 5'-untranslated region in 16 IGE probands of families linked to chromosome 2q36 (cumulative two-point lod score: Z=5.32 at D2S371). Three exonic sequence variants were found: exon 17: 2600C/A, Ala867Asp; exon 21: 3391C/T, Leu1131Leu; exon 23: 3771G/A, 3'-UTR. Our subsequent population-based association study of the Ala867Asp substitution polymorphism revealed a significant increase of the 867Asp variant in 366 unrelated German IGE patients compared with 183 German control subjects (chi(2)=5.37, df=1, P=0.021). Consistently, the transmission disequilibrium test (TDT) of 121 parent-child trios showed a significant preferential transmission of the 867Asp allele (McNemar chi(2)=5.81, df=1, P=0.016). Our results support the hypothesis that variation of the AE3 gene confers a common but small susceptibility effect to the etiology of a broad spectrum of IGE syndromes.

Alleles↗

PubMed2002

Tumor vascularity: evaluation in a murine model with contrast-enhanced color Doppler US effect of angiogenesis inhibitors.

PURPOSE: To determine the ability of contrast material-enhanced ultrasonography (US) to depict tumor growth and vascularity in a murine model of prostate carcinoma treated with an angiogenic inhibitor. MATERIALS AND METHODS: Thirty-five genetically engineered mice with spontaneously occurring prostate tumors were monitored on a weekly basis with gray-scale and color Doppler US with a 15-MHz linear transducer. Eighteen mice were treated with an adenoviral vector to deliver a soluble form of the Flk1 receptor (VEGFR-2), a vascular endothelial growth factor receptor designed to block tumor angiogenesis. The remaining 17 animals were injected with saline and used as controls. Tumor volumes were calculated on the basis of serial US measurements. Color Doppler US was performed in every tumor before and after intravenous injection of 0.1 mL per kilogram of body weight of a US contrast agent. US images were evaluated for tumor size, pattern of vascularity, and extent of vascularity (vascularity index). Findings at US were correlated with findings at autopsy in 30 animals. RESULTS: Estimates of tumor volume at US correlated well with tumor measurements at autopsy (r =.89, P <.001). Marked differences in tumor size and slope of increasing tumor volume were evident at US between treated and control mice after treatment (P <.016, analysis of variance). The US contrast agent markedly increased color Doppler US signal intensity with an 800% (from 10% to 12,700%) change in the mean number of color pixels per imaging field, and showed vascularity in areas of tumor not identified on precontrast images in 70% (109 of 156 studies). No correlation was found between the pattern of vascularity or vascularity index before or after contrast material administration and tumor size, treatment status, or histologic assessment of tumor vascularity. CONCLUSION: Contrast-enhanced US improves visualization of tumor vascularity. However, histologic patterns of tumor vascularity do not correlate with Doppler US depiction of blood flow in these vessels.

Angiogenesis Inhibitors↗