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991.
Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the
protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However,
this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new
approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural
template that contains all assignable residues. To overcome the inherent computational complexity of such a global search,
we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments.
In the first stage, a list of strings of resonances (CA-links) is generated via exhaustive searches for short segments of
sequentially connected residues in a protein (local templates), and then ranked by the agreement of the experimental 13Cα chemical shifts and 15N-1H RDCs to the predicted values for each local template. In the second stage, the top CA-links for different local templates
in stage I are combinatorially connected to produce CA-links for all assignable residues. The resulting CA-links are ranked
for resonance assignment according to their measured RDCs and predicted values from a tertiary structure. Since the final
RDC ranking of CA-links includes all assignable residues and the assignment is derived from a “global minimum”, our approach
is far less reliant on the quality of experimental data and structural templates. The present approach is validated with the
assignments of several proteins, including a 42 kDa maltose binding protein (MBP) using RDCs and structural templates of varying
quality. Since backbone resonance assignment is an essential first step for most of biomolecular NMR applications and is often
a bottleneck for large systems, we expect that this new approach will improve the efficiency of the assignment process for
small and medium size proteins and will extend the size limits assignable by current methods for proteins with structural
models. 相似文献
992.
Wenhua Xiang Shaohui Liu Xiangwen Deng Aihua Shen Xiangdong Lei Dalun Tian Meifang Zhao Changhui Peng 《Ecological Research》2011,26(4):697-711
Applying allometric equations in combination with forest inventory data is an effective approach to use when qualifying forest
biomass and carbon storage on a regional scale. The objectives of this study were to (1) develop general allometric tree component
biomass equations and (2) investigate tree biomass allocation patterns for Pinus massoniana, a principal tree species native to southern China, by applying 197 samples across 20 site locations. The additive allometric
equations utilized to compute stem, branch, needle, root, aboveground, and total tree biomass were developed by nonlinear
seemingly unrelated regression. Results show that the relative proportion of stem biomass to tree biomass increased while
the contribution of canopy biomass to tree biomass decreased as trees continued to grow through time. Total root biomass was
a large biomass pool in itself, and its relative proportion to tree biomass exhibited a slight increase with tree growth.
Although equations employing stem diameter at breast height (dbh) alone as a predictor could accurately predict stem, aboveground,
root, and total tree biomass, they were poorly fitted to predict the canopy biomass component. The inclusion of the tree height
(H) variable either slightly improved or did not in any way increase model fitness. Validation results demonstrate that these
equations are suitable to estimate stem, aboveground, and total tree biomass across a broad range of P. massoniana stands on a regional scale. 相似文献
993.
Tian M Win J Savory E Burkhardt A Held M Brandizzi F Day B 《Molecular plant-microbe interactions : MPMI》2011,24(5):543-553
Pseudoperonospora cubensis is a biotrophic oomycete pathogen that causes downy mildew of cucurbits, a devastating foliar disease threatening cucurbit production worldwide. We sequenced P. cubensis genomic DNA using 454 pyrosequencing and obtained random genomic sequences covering approximately 14% of the genome, thus providing the first set of useful genomic sequence information for P. cubensis. Using bioinformatics approaches, we identified 32 putative RXLR effector proteins. Interestingly, we also identified 29 secreted peptides with high similarity to RXLR effectors at the N-terminal translocation domain, yet containing an R-to-Q substitution in the first residue of the translocation motif. Among these, a family of QXLR-containing proteins, designated as PcQNE, was confirmed to have a functional signal peptide and was further characterized as being localized in the plant nucleus. Internalization of secreted PcQNE into plant cells requires the QXLR-EER motif. This family has a large number of near-identical copies within the P. cubensis genome, is under diversifying selection at the C-terminal domain, and is upregulated during infection of plants, all of which are common characteristics of characterized oomycete effectors. Taken together, the data suggest that PcQNE are bona fide effector proteins with a QXLR translocation motif, and QXLR effectors are prevalent in P. cubensis. Furthermore, the massive duplication of PcQNE suggests that they might play pivotal roles in pathogen fitness and pathogenicity. 相似文献
994.
Takahashi H Arstikaitis P Prasad T Bartlett TE Wang YT Murphy TH Craig AM 《Neuron》2011,69(2):287-303
Neurotrophin receptor tyrosine kinases (Trks) have well-defined trophic roles in nervous system development through kinase activation by neurotrophins. Yet Trks have typical cell-adhesion domains and express noncatalytic isoforms, suggesting additional functions. Here we discovered noncatalytic TrkC in an unbiased hippocampal neuron-fibroblast coculture screen for proteins that trigger differentiation of neurotransmitter release sites in axons. All TrkC isoforms, but not TrkA or TrkB, function directly in excitatory glutamatergic synaptic adhesion by neurotrophin-independent high-affinity trans binding to axonal protein tyrosine phosphatase receptor PTPσ. PTPσ triggers and TrkC mediates clustering of postsynaptic molecules in dendrites, indicating bidirectional synaptic organizing functions. Effects of a TrkC-neutralizing antibody that blocks TrkC-PTPσ interaction and TrkC knockdown in culture and in?vivo reveal essential roles of TrkC-PTPσ in glutamatergic synapse formation. Thus, postsynaptic TrkC trans interaction with presynaptic PTPσ generates bidirectional adhesion and recruitment essential for excitatory synapse development and positions these signaling molecules at the center of synaptic pathways. 相似文献
995.
996.
Enhancement of methane production from cassava residues by biological pretreatment using a constructed microbial consortium 总被引:2,自引:0,他引:2
Qinghua Zhang Jiang HeMin Tian Zhonggui Mao Lei Tang Jianhua ZhangHongjian Zhang 《Bioresource technology》2011,102(19):8899-8906
In the study, a stable thermophilic microbial consortium with high cellulose-degradation ability was successfully constructed. That several species of microbes coexisted in this consortium was proved by DGGE (denaturing gradient gel electrophoresis) and sequence analysis. The cooperation and symbiosis of these microbes in this consortium enhanced their cellulose-degradation ability. The pretreatment of cassava residues mixing with distillery wastewater prior to anaerobic digestion was investigated by using this microbial consortium as inoculums in batch bioreactors at 55 °C. The experimental results showed that the maximum methane yield (259.46 mL/g-VS) of cassava residues was obtained through 12 h of pretreatment by this microbial consortium, which was 96.63% higher than the control (131.95 mL/g-VS). In addition, it was also found that the maximum methane yield is obtained when the highest filter paper cellulase (FPase), carboxymethyl cellulase (CMCase) and xylanase activity and soluble COD (sCOD) are produced. 相似文献
997.
Lan T Liu W Xie X Xu S Huang K Peng J Shen X Liu P Wang L Xia P Huang H 《Molecular endocrinology (Baltimore, Md.)》2011,25(12):2094-2105
Diabetic nephropathy is characterized by accumulation of glomerular extracellular matrix proteins, such as fibronectin (FN). Here, we investigated whether sphingosine kinase (SphK)1 pathway is responsible for the elevated FN expression in diabetic nephropathy. The SphK1 pathway and FN expression were examined in streptozotocin-induced diabetic rat kidney and glomerular mesangial cells (GMC) exposed to high glucose (HG). FN up-regulation was concomitant with activation of the SphK1 pathway as reflected in an increase in the expression and activity of SphK1 and sphingosine 1-phosphate (S1P) production in both diabetic kidney and HG-treated GMC. Overexpression of wild-type SphK1 (SphK(WT)) significantly induced FN expression, whereas treatment with a SphK inhibitor, N,N-dimethylsphingosine, or transfection of SphK1 small interference RNA or dominant-negative SphK1 (SphK(G82D)) abolished HG-induced FN expression. Furthermore, addition of exogenous S1P significantly induced FN expression in GMC with an induction of activator protein 1 (AP-1) activity. Inhibition of AP-1 activity by curcumin attenuated the S1P-induced FN expression. Finally, by inhibiting SphK1 activity, both N,N-dimethylsphingosine and SphK(G82D) markedly attenuated the HG-induced AP-1 activity. Taken together, these results demonstrated that the SphK1 pathway plays a critical role in matrix accumulation in GMC under diabetic condition, suggesting that the SphK1 pathway could be a potential therapeutic target for diabetic nephropathy. 相似文献
998.
Epistatic miniarray profiling (E-MAP) is a powerful tool for analyzing gene functions and their biological relevance. However, E-MAP data suffers from large proportion of missing values, which often results in misleading and biased analysis results. It is urgent to develop effective missing value estimation methods for E-MAP. Although several independent algorithms can be applied to achieve this goal, their performance varies significantly on different datasets, indicating different algorithms having their own advantages and disadvantages. In this paper, we propose a novel ensemble approach EMDI based on the high-level diversity to impute missing values that consists of two global and four local base estimators. Experimental results on five E-MAP datasets show that EMDI outperforms all single base algorithms, demonstrating an appropriate combination providing complementarity among different methods. Comparison results between several fusion strategies also demonstrate that the proposed high-level diversity scheme is superior to others. EMDI is freely available at www.csbio.sjtu.edu.cn/bioinf/EMDI/. 相似文献
999.
Shi P Wang H Xi Z Shi C Xiong Y Tian C 《Protein science : a publication of the Protein Society》2011,20(1):224-228
Site‐specific 19F chemical shift and side chain relaxation analysis can be applied on large size proteins. Here, one‐dimensional 19F spectra and T1, T2 relaxation data were acquired on a SH3 domain in aqueous buffer containing 60% glycerol, and a nine‐transmembrane helices membrane protein diacyl‐glycerol kinase (DAGK) in dodecyl phosphochoine (DPC) micelles. The high quality of the data indicates that this method can be applied to site‐specifically analyze side chain internal mobility of membrane proteins or large size proteins. 相似文献
1000.
Yang Y Miller KJ Zhu Y Hong Y Tian Y Murugesan N Gu Z O'Tanyi E Keim WJ Rohrbach KW Johnghar S Behnia K Pelleymounter MA Carlson KE Ewing WR 《Bioorganic & medicinal chemistry letters》2011,21(22):6856-6860
Obesity remains a significant public health issue leading to Type II diabetes and cardiovascular disease. CB1 antagonists have been shown to suppress appetite and reduce body weight in animal models as well as in humans. Evaluation of pre-clinical CB1 antagonists to establish relationships between in vitro affinity and in vivo efficacy parameters are enhanced by ex vivo receptor occupancy data. Synthesis and biological evaluation of a novel and highly selective radiolabeled CB1 antagonist is described. The radioligand was used to conduct ex vivo receptor occupancy studies. 相似文献