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71.
PConPy is an open-source Python module for generating protein contact maps, distance maps and hydrogen bond plots. These maps can be generated in a number of publication-quality vector and raster image formats. Contact maps can be annotated with secondary structure and hydrogen bond assignments. PConPy offers a more flexible choice of contact definition parameters than existing toolkits, most notably a greater choice of inter-residue distance metrics. PConPy can be used as a stand-alone application or imported into existing source code. A web-interface to PConPy is also available for use. AVAILABILITY: The PConPy web-interface and source code can be accessed from its website at http://www.csse.unimelb.edu.au/~hohkhkh1/pconpy/. CONTACT: hohkhkh1@csse.unimelb.edu.au 相似文献
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73.
Beisvåg V Kauffmann A Malone J Foy C Salit M Schimmel H Bongcam-Rudloff E Landegren U Parkinson H Huber W Brazma A Sandvik AK Kuiper M 《BioTechniques》2011,50(1):27-31
While minimum information about a microarray experiment (MIAME) standards have helped to increase the value of the microarray data deposited into public databases like ArrayExpress and Gene Expression Omnibus (GEO), limited means have been available to assess the quality of this data or to identify the procedures used to normalize and transform raw data. The EMERALD FP6 Coordination Action was designed to deliver approaches to assess and enhance the overall quality of microarray data and to disseminate these approaches to the microarray community through an extensive series of workshops, tutorials, and symposia. Tools were developed for assessing data quality and used to demonstrate how the removal of poor-quality data could improve the power of statistical analyses and facilitate analysis of multiple joint microarray data sets. These quality metrics tools have been disseminated through publications and through the software package arrayQualityMetrics. Within the framework provided by the Ontology of Biomedical Investigations, ontology was developed to describe data transformations, and software ontology was developed for gene expression analysis software. In addition, the consortium has advocated for the development and use of external reference standards in microarray hybridizations and created the Molecular Methods (MolMeth) database, which provides a central source for methods and protocols focusing on microarray-based technologies. 相似文献
74.
Shuba Krishnan Jo?o A. Paredes Xiaoshan Zhou Raoul V. Kuiper Kjell Hultenby Sophie Curbo Anna Karlsson 《The Journal of biological chemistry》2014,289(47):32835-32844
Mitochondrial DNA depletion caused by thymidine kinase 2 (TK2) deficiency can be compensated by a nucleoside kinase from Drosophila melanogaster (Dm-dNK) in mice. We show that transgene expression of Dm-dNK in Tk2 knock-out (Tk2−/−) mice extended the life span of Tk2−/− mice from 3 weeks to at least 20 months. The Dm-dNK+/−Tk2−/− mice maintained normal mitochondrial DNA levels throughout the observation time. A significant difference in total body weight due to the reduction of subcutaneous and visceral fat in the Dm-dNK+/−Tk2−/− mice was the only visible difference compared with control mice. This indicates an effect on fat metabolism mediated through residual Tk2 deficiency because Dm-dNK expression was low in both liver and fat tissues. Dm-dNK expression led to increased dNTP pools and an increase in the catabolism of purine and pyrimidine nucleotides but these alterations did not apparently affect the mice during the 20 months of observation. In conclusion, Dm-dNK expression in the cell nucleus expanded the total dNTP pools to levels required for efficient mitochondrial DNA synthesis, thereby compensated the Tk2 deficiency, during a normal life span of the mice. The Dm-dNK+/− mouse serves as a model for nucleoside gene or enzyme substitutions, nucleotide imbalances, and dNTP alterations in different tissues. 相似文献
75.
Susanne C. Feil David B. Ascher Michael J. Kuiper Rodney K. Tweten Michael W. Parker 《Journal of molecular biology》2014
Cholesterol-dependent cytolysins (CDCs) are a large family of bacterial toxins that exhibit a dependence on the presence of membrane cholesterol in forming large pores in cell membranes. Significant changes in the three-dimensional structure of these toxins are necessary to convert the soluble monomeric protein into a membrane pore. We have determined the crystal structure of the archetypical member of the CDC family, streptolysin O (SLO), a virulence factor from Streptococcus pyogenes. The overall fold is similar to previously reported CDC structures, although the C-terminal domain is in a different orientation with respect to the rest of the molecule. Surprisingly, a signature stretch of CDC sequence called the undecapeptide motif, a key region involved in membrane recognition, adopts a very different structure in SLO to that of the well-characterized CDC perfringolysin O (PFO), although the sequences in this region are identical. An analysis reveals that, in PFO, there are complementary interactions between the motif and the rest of domain 4 that are lost in SLO. Molecular dynamics simulations suggest that the loss of a salt bridge in SLO and a cation–pi interaction are determining factors in the extended conformation of the motif, which in turn appears to result in a greater flexibility of the neighboring L1 loop that houses a cholesterol-sensing motif. These differences may explain the differing abilities of SLO and PFO to efficiently penetrate target cell membranes in the first step of toxin insertion into the membrane. 相似文献
76.
Vuylsteke M. Mank R. Brugmans B. Stam P. Kuiper M. 《Molecular breeding : new strategies in plant improvement》2000,6(3):265-276
AFLP® markers generated by CNG methylation sensitive (PstI/MseI) and CNG methylation insensitive (EcoRI/MseI) enzyme combinations and AFLP markers collected from hypomethylated (PstI/MseI) and hypermethylated (m
PstI/MseI) regions were compared for their polymorphism information content, sampling variance and patterns of genetic diversity in a representative sample of 33 inbred lines of maize (Zea mays L.). We demonstrate that the mean polymorphism information content generated by sets of PstI/MseI and m
PstI/MseI markers (0.38) is significantly higher than by sets ofEcoRI/MseI markers (0.33). Also the sampling variance highlighted the distinctive nature of the (m)
PstI/MseI markers: to achieve a mean standard deviation of 5% in the estimation of genetic distance among the 33 inbreds, the PstI/MseI and m
PstI/MseI marker sets (135 and 129 markers, respectively) are clearly smaller than the EcoRI/MseI marker set (173 markers). A further minimizing of the sampling variance of AFLP data in the estimation of genetic similarities was obtained by reducing marker information redundancy by selecting markers evenly distributed over each chromosome: a set of only 106 AFLP markers, sampled conditionally on their genetic map position, was required for a mean standard deviation of 5% in the estimation of genetic distance among the 33 inbreds. 相似文献
77.
J Trapman P Klaassen G G Kuiper J A van der Korput P W Faber H C van Rooij A Geurts van Kessel M M Voorhorst E Mulder A O Brinkmann 《Biochemical and biophysical research communications》1988,153(1):241-248
A cDNA clone has been isolated from a library prepared of mRNA of human breast cancer T47D cells with an oligonucleotide probe homologous to part of the region encoding the DNA-binding domain of steroid receptors. The clone has a size of 1505 bp and sequence analysis revealed an open reading frame of 1356 bp. The deduced amino acid sequence displays two highly conserved regions identified as the putative DNA-binding and hormone binding domains respectively of steroid receptors. Expression of this cDNA clone in COS cells produces a nuclear protein with all the binding characteristics of the human androgen receptor (hAR). The gene encoding the cDNA is assigned to the human X-chromosome. High levels of three hybridizing mRNA species of 11, 8.5 and 4.7 kb respectively are found in the human prostate cancer cell line (LNCaP), which contains elevated levels of hAR. The present data provide evidence that we have isolated a cDNA that encodes a major part of the human androgen receptor. 相似文献
78.
79.
Hydrological regulation drives regime shifts: evidence from paleolimnology and ecosystem modeling of a large shallow Chinese lake 总被引:2,自引:0,他引:2
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Xiangzhen Kong Qishuang He Bin Yang Wei He Fuliu Xu Annette B. G. Janssen Jan J. Kuiper Luuk P. A. van Gerven Ning Qin Yujiao Jiang Wenxiu Liu Chen Yang Zelin Bai Min Zhang Fanxiang Kong Jan H. Janse Wolf M. Mooij 《Global Change Biology》2017,23(2):737-754
Quantitative evidence of sudden shifts in ecological structure and function in large shallow lakes is rare, even though they provide essential benefits to society. Such ‘regime shifts’ can be driven by human activities which degrade ecological stability including water level control (WLC) and nutrient loading. Interactions between WLC and nutrient loading on the long‐term dynamics of shallow lake ecosystems are, however, often overlooked and largely underestimated, which has hampered the effectiveness of lake management. Here, we focus on a large shallow lake (Lake Chaohu) located in one of the most densely populated areas in China, the lower Yangtze River floodplain, which has undergone both WLC and increasing nutrient loading over the last several decades. We applied a novel methodology that combines consistent evidence from both paleolimnological records and ecosystem modeling to overcome the hurdle of data insufficiency and to unravel the drivers and underlying mechanisms in ecosystem dynamics. We identified the occurrence of two regime shifts: one in 1963, characterized by the abrupt disappearance of submerged vegetation, and another around 1980, with strong algal blooms being observed thereafter. Using model scenarios, we further disentangled the roles of WLC and nutrient loading, showing that the 1963 shift was predominantly triggered by WLC, whereas the shift ca. 1980 was attributed to aggravated nutrient loading. Our analysis also shows interactions between these two stressors. Compared to the dynamics driven by nutrient loading alone, WLC reduced the critical P loading and resulted in earlier disappearance of submerged vegetation and emergence of algal blooms by approximately 26 and 10 years, respectively. Overall, our study reveals the significant role of hydrological regulation in driving shallow lake ecosystem dynamics, and it highlights the urgency of using multi‐objective management criteria that includes ecological sustainability perspectives when implementing hydrological regulation for aquatic ecosystems around the globe. 相似文献
80.
Genetic diversity and its relationship to hybrid performance in maize as revealed by RFLP and AFLP markers 总被引:50,自引:0,他引:50
P. Ajmone Marsan P. Castiglioni F. Fusari M. Kuiper M. Motto 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(2):219-227
The challenge to maize breeders is to identify inbred lines that produce highly heterotic hybrids. In the present study we
surveyed genetic divergence among 13 inbred lines of maize using DNA markers and assessed the relationship between genetic
distance and hybrid performance in a diallel set of crosses between them. The parental lines were assayed for DNA polymorphism
using 135 restriction fragment length polymorphisms (RFLPs) and 209 amplified-fragment polymorphisms (AFLPs). Considerable
variation among inbreds was detected with RFLP and AFLP markers. Moreover AFLPs detect polymorphisms more efficiently in comparison
to RFLPs, due to the larger number of loci assayed in a single PCR reaction. Genetic distances (GDs), calculated from RFLP
and AFLP data, were greater among lines belonging to different heterotic groups compared to those calculated from lines of
the same heterotic group. Cluster analysis based on GDs revealed associations among lines which agree with expectations based
on pedigree information. The GD values of the 78 F1 crosses were partioned into general (GGD) and specific (SGD) components. Correlations of GD with F1 performance for grain yield were positive but too small to be of predictive value. The correlations of SGDs, particularly
those based on AFLP data, with specific combining-ability effects for yield may have a practical utility in predicting hybrid
performance.
Received: 15 August 1997 / Accepted: 19 September 1997 相似文献