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991.
992.
Summary . We consider a set of independent Bernoulli trials with possibly different success probabilities that depend on covariate values. However, the available data consist only of aggregate numbers of successes among subsets of the trials along with all of the covariate values. We still wish to estimate the parameters of a modeled relationship between the covariates and the success probabilities, e.g., a logistic regression model. In this article, estimation of the parameters is made from a Bayesian perspective by using a Markov chain Monte Carlo algorithm based only on the available data. The proposed methodology is applied to both simulation studies and real data from a dose–response study of a toxic chemical, perchlorate. 相似文献
993.
Bacteriophage T4 UvsY is a recombination mediator protein that promotes assembly of the UvsX-ssDNA presynaptic filament. UvsY helps UvsX to displace T4 gene 32 protein (gp32) from ssDNA, a reaction necessary for proper formation of the presynaptic filament. Here we use DNA stretching to examine UvsY interactions with single DNA molecules in the presence and absence of gp32 and a gp32 C-terminal truncation (*I), and show that in both cases UvsY is able to destabilize gp32-ssDNA interactions. In these experiments UvsY binds more strongly to dsDNA than ssDNA due to its inability to wrap ssDNA at high forces. To support this hypothesis, we show that ssDNA created by exposure of stretched DNA to glyoxal is strongly wrapped by UvsY, but wrapping occurs only at low forces. Our results demonstrate that UvsY interacts strongly with stretched DNA in the absence of other proteins. In the presence of gp32 and *I, UvsY is capable of strongly destabilizing gp32-DNA complexes in order to facilitate ssDNA wrapping, which in turn prepares the ssDNA for presynaptic filament assembly in the presence of UvsX. Thus, UvsY mediates UvsX binding to ssDNA by converting rigid gp32-DNA filaments into a structure that can be strongly bound by UvsX. 相似文献
994.
SIRT3 interacts with the daf-16 homolog FOXO3a in the mitochondria, as well as increases FOXO3a dependent gene expression 总被引:1,自引:0,他引:1 下载免费PDF全文
Jacobs KM Pennington JD Bisht KS Aykin-Burns N Kim HS Mishra M Sun L Nguyen P Ahn BH Leclerc J Deng CX Spitz DR Gius D 《International journal of biological sciences》2008,4(5):291-299
Cellular longevity is a complex process relevant to age-related diseases including but not limited to chronic illness such as diabetes and metabolic syndromes. Two gene families have been shown to play a role in the genetic regulation of longevity; the Sirtuin and FOXO families. It is also established that nuclear Sirtuins interact with and under specific cellular conditions regulate the activity of FOXO gene family proteins. Thus, we hypothesize that a mitochondrial Sirtuin (SIRT3) might also interact with and regulate the activity of the FOXO proteins. To address this we used HCT116 cells overexpressing either wild-type or a catalytically inactive dominant negative SIRT3. For the first time we establish that FOXO3a is also a mitochondrial protein and forms a physical interaction with SIRT3 in mitochondria. Overexpression of a wild-type SIRT3 gene increase FOXO3a DNA-binding activity as well as FOXO3a dependent gene expression. Biochemical analysis of HCT116 cells over expressing the deacetylation mutant, as compared to wild-type SIRT3 gene, demonstrated an overall oxidized intracellular environment, as monitored by increase in intracellular superoxide and oxidized glutathione levels. As such, we propose that SIRT3 and FOXO3a comprise a potential mitochondrial signaling cascade response pathway. 相似文献
995.
Karen Bersine Valance E. F. Brenneis Robyn C. Draheim A. Michelle Wargo Rub Jeannette E. Zamon Rodney K. Litton Susan A. Hinton Mark D. Sytsma Jeffery R. Cordell John W. Chapman 《Biological invasions》2008,10(8):1381-1388
Estuaries play an important role as nurseries and migration corridors for Chinook salmon and other fishes. The invasive New
Zealand mudsnail, Potamopyrgus antipodarum (Gray, 1843), has been noted in the Columbia River Estuary and other estuaries in the western USA, yet no studies have addressed
the estuarine impacts of this invader. Our data show P. antipodarum is currently found in five peripheral bays and many tributaries of the Columbia River Estuary, where it can constitute a
major portion of the benthic invertebrate biomass and where it co-occurs with native amphipod species. We review the history
of the P. antipodarum invasion in the Columbia River Estuary and discuss potential impacts on estuarine food webs. We also report the first occurrence
of P. antipodarum in the diet of juvenile Chinook salmon from the Columbia River Estuary. Although present in Chinook diets at very low frequencies,
our observations of P. antipodarum in Chinook gut contents may represent early stages of food web change due to the establishment of dense estuarine snail populations.
Additional research is needed to determine the effects of P. antipodarum on benthic resources, native benthic invertebrates, and benthic predators. We encourage biologists working in western USA
estuaries to be alert to the possibility of encountering P. antipodarum in benthic habitats and predator diets.
相似文献
Jeannette E. ZamonEmail: |
996.
Cook MB Graubard BI Quraishi SM Yeager M Chanock SJ Crenshaw A Erickson RL Rubertone MV Thomas G McGlynn KA 《Human genetics》2008,123(4):409-418
Much evidence supports the premise that population genetic variation contributes significantly to the risk of testicular germ-cell
tumor (TGCT). However, investigations of the association between genomic markers and TGCT susceptibility are scarce. Single
nucleotide polymorphisms (SNPs) at the locus 8q24 have recently been found to be associated with prostate, colorectal and
breast cancer. The US Servicemen’s testicular tumor environmental and endocrine determinants (STEED) study was used to investigate
the association of 15 specific 8q24 SNPs with TGCT and its two main histologic groups of seminoma and nonseminoma. Conditional
and unconditional logistic regression models, adjusted for the matching variables of year of birth, race/ethnicity and serum
date, were utilized to produce odds ratios (OR) and 95% confidence intervals (95%CI). The analysis included 680 controls and
568 TGCT cases. In the TGCT analysis, no SNP was associated with risk in both heterozygotes and variant homozygotes. When
stratified by histology the seminoma analysis also showed no association with the 8q24 SNPs. Conversely, the analysis of nonseminomas
had three tentative associations (rs6470494, ORgenotype AG = 1.15, 95%CI: 0.86–1.54; ORgenotype GG = 1.68, 95%CI: 1.04–2.73; p for trend = 0.04) (rs13254738, ORgenotype GT = 1.04, 95%CI: 0.77–1.40; ORgenotype TT = 1.62, 95%CI: 1.06–2.49; p for trend = 0.07) (rs10505476, ORgenotype CT = 0.67, 95%CI: 0.50, 0.91; ORgenotype TT = 0.81, 95%CI: 0.47–1.39; p for trend = 0.04). There was no linkage disequilibrium between any of the 8q24 SNPs analyzed in this population. In conclusion,
this study has found little evidence for an association between the reported 8q24 SNPs and TGCTs, although the findings for
nonseminoma may be worth further investigation. 相似文献
997.
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays
Romesh Stanislaus Mark Carey Helena F Deus Kevin Coombes Bryan T Hennessy Gordon B Mills Jonas S Almeida 《BMC bioinformatics》2008,9(1):555
Background
Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest. 相似文献998.
Intracellular vesicle traffic that enables delivery of proteins between the endoplasmic reticulum, Golgi and various endosomal subcompartments is one of the hallmarks of the eukaryotic cell. Its evolutionary history is not well understood but the process itself and the core vesicle traffic machinery are believed to be ancient. We show here that the 4-vinyl reductase (V4R) protein domain present in bacteria and archaea is homologous to the Bet3 subunit of the TRAPP1 vesicle-tethering complex that is conserved in all eukaryotes. This suggests, for the first time, a prokaryotic origin for one of the key eukaryotic trafficking proteins. 相似文献
999.
Increasing sensitivity of Ca2+ spark detection in noisy images by application of a matched-filter object detection algorithm 下载免费PDF全文
Microscopic calcium (Ca2+) events (such as Ca2+ sparks) are an important area for study, as they help clarify the mechanism(s) underlying intracellular signaling. In the heart, Ca2+ sparks occur as a result of Ca2+ release from the sarcoendoplasmic reticulum, via ryanodine receptor channels. Measurement of Ca2+ spark properties can provide valuable information about the control of ryanodine receptor channel gating in situ, but requires high spatiotemporal resolution imaging, which produces noisy datasets that are problematic for spark detection. Automated detection algorithms may overcome visual detection bias, but missed and false-positive events can distort the distribution of measured Ca2+ spark properties. We present a sensitive and reliable method for the automated detection of Ca2+ sparks in datasets obtained using confocal line-scanning or total internal reflection fluorescence microscopy. This matched-filter detection algorithm (MFDA) employs a user-defined object, chosen to mimic Ca2+ spark properties, and the experimental dataset is searched for instances of the object. Detection certainty is provided by nonparametric statistical testing. The supplied codes can also refine the search object on the basis of those detected to further increase detection sensitivity. In comparison to a commonly used, intensity-thresholding algorithm, the MFDA is more sensitive and reliable, particularly at low signal/noise ratios. The MFDA can also be easily adapted to other signal-detection problems in noisy datasets. 相似文献
1000.