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71.
Adorján P Distler J Lipscher E Model F Müller J Pelet C Braun A Florl AR Gütig D Grabs G Howe A Kursar M Lesche R Leu E Lewin A Maier S Müller V Otto T Scholz C Schulz WA Seifert HH Schwope I Ziebarth H Berlin K Piepenbrock C Olek A 《Nucleic acids research》2002,30(5):e21
Aberrant DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation occurs in a tumour type-specific manner. However, large-scale analysis of candidate genes has so far been hampered by the lack of high throughput assays for methylation detection. We have developed the first microarray-based technique which allows genome-wide assessment of selected CpG dinucleotides as well as quantification of methylation at each site. Several hundred CpG sites were screened in 76 samples from four different human tumour types and corresponding healthy controls. Discriminative CpG dinucleotides were identified for different tissue type distinctions and used to predict the tumour class of as yet unknown samples with high accuracy using machine learning techniques. Some CpG dinucleotides correlate with progression to malignancy, whereas others are methylated in a tissue-specific manner independent of malignancy. Our results demonstrate that genome-wide analysis of methylation patterns combined with supervised and unsupervised machine learning techniques constitute a powerful novel tool to classify human cancers. 相似文献
72.
Spinocerebellar ataxia type 3 (SCA3) is a polyglutamine disorder caused by a CAG repeat expansion in the coding region of a gene encoding ataxin-3, a protein of yet unknown function. Based on a comprehensive computational analysis, we propose a structural model and structure-based functions for ataxin-3. Our predictive strategy comprises the compilation of multiple sequence and structure alignments of carefully selected proteins related to ataxin-3. These alignments are consistent with additional information on sequence motifs, secondary structure, and domain architectures. The application of complementary methods revealed the homology of ataxin-3 to ENTH and VHS domain proteins involved in membrane trafficking and regulatory adaptor functions. We modeled the structure of ataxin-3 using the adaptin AP180 as a template and assessed the reliability of the model by comparison with known sequence and structural features. We could further infer potential functions of ataxin-3 in agreement with known experimental data. Our database searches also identified an as yet uncharacterized family of proteins, which we named josephins because of their pronounced homology to the Josephin domain of ataxin-3. 相似文献
73.
dos Santos Fagundes I Rotta LN Schweigert ID Valle SC de Oliveira KR Huth Krüger A Souza KB Souza DO Perr ML 《Neurochemical research》2001,26(3):245-249
We have investigated the glycine, serine and leucine metabolism in slices of various rat brain regions of 14-day-old or adult rats, using [1-14C]glycine, [2-14C]glycine, L-[3-14C]serine and L-[U-14C]leucine. We showed that the [1-14C]glycine oxidation to CO2 in all regions studied occurs almost exclusively through its cleavage system (GCS) in brains of both 14-day-old and adults rats. In 14-day-old rats, the highest oxidation of [1-14C]glycine was in cerebellum and the lowest in medulla oblongata. In these animals, the L-[U-14C]leucine oxidation was lower than the [1-14C]glycine oxidation, except in medulla oblongata where both oxidations were the same. Serine was the amino acid that showed lowest oxidation to CO2 in all structure studied. In adult rats brains, the highest oxidation of [1-14C]glycine was in cerebral cortex and the lowest in medulla oblongata. We have not seen difference in the lipid synthesis from both glycine labeled, neither in 14-day-old rats nor in adult ones, indicating that the lipids formed from glycine were not neutral. Lipid synthesis from serine was significantly high than lipid synthesis and from all other amino acids studied in all studied structures. Protein synthesis from L-[U-14C]leucine was significantly higher than that from glycine in all regions and ages studied. 相似文献
74.
Rico Fischer Andreas Ensslin Gemma Rutten Markus Fischer David Schellenberger Costa Michael Kleyer Andreas Hemp Sebastian Paulick Andreas Huth 《PloS one》2015,10(4)
Tropical forests are carbon-dense and highly productive ecosystems. Consequently, they play an important role in the global carbon cycle. In the present study we used an individual-based forest model (FORMIND) to analyze the carbon balances of a tropical forest. The main processes of this model are tree growth, mortality, regeneration, and competition. Model parameters were calibrated using forest inventory data from a tropical forest at Mt. Kilimanjaro. The simulation results showed that the model successfully reproduces important characteristics of tropical forests (aboveground biomass, stem size distribution and leaf area index). The estimated aboveground biomass (385 t/ha) is comparable to biomass values in the Amazon and other tropical forests in Africa. The simulated forest reveals a gross primary production of 24 tcha-1yr-1. Modeling above- and belowground carbon stocks, we analyzed the carbon balance of the investigated tropical forest. The simulated carbon balance of this old-growth forest is zero on average. This study provides an example of how forest models can be used in combination with forest inventory data to investigate forest structure and local carbon balances. 相似文献
75.
Mineral weathering is the primary source of long-term buffering capacity in soils and is important for forest nutrient sustainability. Regional assessments of weathering rates in Canada and the U.S. have employed an empirical clay-based Soil Texture Approximation (STA) owing to limited data availability, although the STA is rarely calibrated before application to a study area. Soil weathering rates estimated with the STA at 75 sites in Canadian forests (6–367 eq ha?1 year?1) were on average seven times lower than estimates obtained using the PROFILE model and when mineralogy was not available, the Analysis to Mineralogy model and parameter estimation (143–2,119 eq ha?1 year?1). Comparison with a catchment mass balance at a subset of sites in Ontario (n = 19) demonstrated the reliability of PROFILE weathering estimates. A revised (generalized) STA model for total base cation weathering was developed at the 75 study sites to incorporate soil silt content (%) and loss-on-ignition (LOI, %) (BC w = (1.73 + 0.03 · silt ? 0.06 · LOI) · 1,000 · depth). The model performance (R adj 2 = 73%) and relative bias (?1%) suggested that the revised STA may have broad application to forest soils in Canada but may not necessarily be suited to all soil texture classes. 相似文献
76.
77.
Katja Behnke Maaria Loivamäki Ina Zimmer Heinz Rennenberg Jörg-Peter Schnitzler Sandrine Louis 《Photosynthesis research》2010,104(1):5-17
In the present study, we combined transient temperature and light stress (sunfleck) and comparably analyzed photosynthetic
gas exchange in Grey poplar which has been genetically modified in isoprene emission capacity. Overall, we demonstrate that
for poplar leaves the ability to emit isoprene is crucial to maintain photosynthesis when exposed to sunflecks. Net CO2 assimilation and electron transport rates were strongly impaired in sunfleck-treated non-isoprene emitting poplars. Similar
impairment was not detected when the leaves were exposed to high light (lightflecks) only. Within 10 h non-isoprene emitting
poplars recovered from sunfleck-related impairment as indicated by chlorophyll fluorescence and microarray analysis. Unstressed
leaves of non-isoprene emitting poplars had higher ascorbate contents, but also higher contents of malondialdehyde than wild-type.
Microarray analyses revealed lipid and chlorophyll degradation processes in the non-isoprene emitting poplars. Thus, there
is evidence for an adjustment of the antioxidative system in the non-isoprene emitting poplars even under normal growth conditions. 相似文献
78.
Siegbert Rieg Benjamin Meier Eva Fähnrich Anja Huth Dirk Wagner Winfried V Kern Hubert Kalbacher 《BMC microbiology》2010,10(1):61
Background
Members of the genus Nocardia are ubiquitous environmental saprophytes capable to cause human pulmonary, disseminated and cutaneous nocardiosis or bovine mastitis. Innate immunity appears to play an important role in early defense against Nocardia species. To elucidate the contribution of antimicrobial peptides (AMPs) in innate defense against Nocardia, the activity of human α-defensins human neutrophil peptides (HNPs) 1-3, human β-defensin (hBD)-3 and cathelicidin LL-37 as well as bovine β-defensins lingual and tracheal antimicrobial peptides (LAP, TAP) and bovine neutrophil-derived indolicidin against four important Nocardia species was investigated. 相似文献79.
Dietrich CG Martin IV Porn AC Voigt S Gartung C Trautwein C Geier A 《American journal of physiology. Gastrointestinal and liver physiology》2007,293(3):G585-G590
Fasting induces numerous adaptive changes in metabolism by several central signaling pathways, the most important represented by the HNF4alpha/PGC-1alpha-pathway. Because HNF4alpha has been identified as central regulator of basolateral bile acid transporters and a previous study reports increased basolateral bile acid uptake into the liver during fasting, we hypothesized that HNF4alpha is involved in fasting-induced bile acid uptake via upregulation of basolateral bile acid transporters. In rats, mRNA of Ntcp, Oatp1, and Oatp2 were significantly increased after 48 h of fasting. Protein expression as determined by Western blot showed significant increases for all three transporters 72 h after the onset of fasting. Whereas binding activity of HNF1alpha in electrophoretic mobility shift assays remained unchanged, HNF4alpha binding activity to the Ntcp promoter was increased significantly. In line with this result, we found significantly increased mRNA expression of HNF4alpha and PGC-1alpha. Functional studies in HepG2 cells revealed an increased endogenous NTCP mRNA expression upon cotransfection with either HNF4alpha, PGC-1alpha, or a combination of both. We conclude that upregulation of the basolateral bile acid transporters Ntcp, Oatp1, and Oatp2 in fasted rats is mediated via the HNF4alpha/PGC-1alpha pathway. 相似文献
80.
The variant inv(2)(p11.2q13) is a genuinely recurrent rearrangement but displays some breakpoint heterogeneity 总被引:1,自引:0,他引:1
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Fickelscher I Liehr T Watts K Bryant V Barber JC Heidemann S Siebert R Hertz JM Tumer Z Simon Thomas N 《American journal of human genetics》2007,81(4):847-856
Human chromosome 2 contains large blocks of segmental duplications (SDs), both within and between proximal 2p and proximal 2q, and these may contribute to the frequency of the common variant inversion inv(2)(p11.2q13). Despite their being cytogenetically homogeneous, we have identified four different breakpoint combinations by fluorescence in situ hybridization mapping of 40 cases of inv(2)(p11.2q13) of European origin. For the vast majority of inversions (35/40), the breakpoints fell within the same spanning BACs, which hybridized to both 2p11.2 and 2q13 on the normal and inverted homologues. Sequence analysis revealed that these BACs contain a significant proportion of intrachromosomal SDs with sequence homology to the reciprocal breakpoint region. In contrast, BACs spanning the rare breakpoint combinations contain fewer SDs and with sequence homology only to the same chromosome arm. Using haplotype analysis, we identified a number of related family subgroups with identical or very closely related haplotypes. However, the majority of cases were not related, demonstrating for the first time that the inv(2)(p11.2q13) is a truly recurrent rearrangement. Therefore, there are three explanations to account for the frequent observation of the inv(2)(p11.2q13): the majority have arisen independently in different ancestors, while a minority either have been transmitted from a common founder or have different breakpoints at the molecular cytogenetic level. 相似文献