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排序方式: 共有186条查询结果,搜索用时 46 毫秒
51.
Using simulated data, we compared five methods of phylogenetic tree
estimation: parsimony, compatibility, maximum likelihood, Fitch-
Margoliash, and neighbor joining. For each combination of substitution
rates and sequence length, 100 data sets were generated for each of 50
trees, for a total of 5,000 replications per condition. Accuracy was
measured by two measures of the distance between the true tree and the
estimate of the tree, one measure sensitive to accuracy of branch lengths
and the other not. The distance-matrix methods (Fitch- Margoliash and
neighbor joining) performed best when they were constrained from estimating
negative branch lengths; all comparisons with other methods used this
constraint. Parsimony and compatibility had similar results, with
compatibility generally inferior; Fitch- Margoliash and neighbor joining
had similar results, with neighbor joining generally slightly inferior.
Maximum likelihood was the most successful method overall, although for
short sequences Fitch- Margoliash and neighbor joining were sometimes
better. Bias of the estimates was inferred by measuring whether the
independent estimates of a tree for different data sets were closer to the
true tree than to each other. Parsimony and compatibility had particular
difficulty with inaccuracy and bias when substitution rates varied among
different branches. When rates of evolution varied among different sites,
all methods showed signs of inaccuracy and bias.
相似文献
52.
The current paucity of data on the genetic structure of parasitic helminth populations results partly from the lack of a suitable molecular technique for assigning genotypes to small individuals. This report describes the cloning of the mitochondrial DNA (mtDNA) from a small parasitic nematode, Ostertagia ostertagi, and the potential use of this cloned mtDNA as a hybridization probe to detect genetic variation among individuals. By using cloned, homologous mtDNA, labeled to high specific activity, mtDNA restriction site variation can be assayed among individual O. ostertagi for at least 10 restriction enzymes. 相似文献
53.
J Westling P Cipullo S H Hung H Saft J B Dame B M Dunn 《Protein science : a publication of the Protein Society》1999,8(10):2001-2009
Members of the aspartic proteinase family of enzymes have very similar three-dimensional structures and catalytic mechanisms. Each, however, has unique substrate specificity. These distinctions arise from variations in amino acid residues that line the active site subsites and interact with the side chains of the amino acids of the peptides that bind to the active site. To understand the unique binding preferences of plasmepsin II, an enzyme of the aspartic proteinase class from the malaria parasite, Plasmodium falciparum, chromogenic octapeptides having systematic substitutions at various positions in the sequence were analyzed. This enabled the design of new, improved substrates for this enzyme (Lys-Pro-Ile-Leu-Phe*Nph-Ala/Glu-Leu-Lys, where * indicates the cleavage point). Additionally, the crystal structure of plasmepsin II was analyzed to explain the binding characteristics. Specific amino acids (Met13, Ser77, and Ile287) that were suspected of contributing to active site binding and specificity were chosen for site-directed mutagenesis experiments. The Met13Glu and Ile287Glu single mutants and the Met13Glu/Ile287Glu double mutant gain the ability to cleave substrates containing Lys residues. 相似文献
54.
Dame RT 《Molecular microbiology》2005,56(4):858-870
The bacterial chromosomal DNA is folded into a compact structure called nucleoid. The shape and size of this 'body' is determined by a number of factors. Major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid, which are the topic of this MicroReview. Although many of these proteins were identified more than 25 years ago, the molecular mechanisms involved in the organization and compaction of DNA have only started to become clear in recent years. Many of these new insights can be attributed to the use of recently developed biophysical techniques. 相似文献
55.
Dame RT Luijsterburg MS Krin E Bertin PN Wagner R Wuite GJ 《Journal of bacteriology》2005,187(5):1845-1848
The nucleoid-associated protein H-NS is thought to play an essential role in the organization of bacterial chromatin in Escherichia coli. Homologues, often with very low sequence identity, are found in most gram-negative bacteria. Microscopic analysis reveals that, despite limited sequence identity, their structural organization results in similar DNA binding properties. 相似文献
56.
Dhanashree?A?Paranjpe D?Anitha MK?Chandrashekaran Amitabh?Joshi Vijay?Kumar?SharmaEmail author 《BMC developmental biology》2005,5(1):5
Background
In insects, circadian clocks have been implicated in affecting life history traits such as pre-adult development time and adult lifespan. Studies on the period (per) mutants of Drosophila melanogaster, and laboratory-selected lines of Bactrocera cucurbitae suggested a close link between circadian clocks and development time. There is a possibility of clock genes having pleiotropic effects on clock period and pre-adult development time. In order to avoid such pleiotropic effects we have used wild type flies of same genotype under environments of different periodicities, which phenotypically either speeded up or slowed down the eclosion clock of D. melanogaster. 相似文献57.
Richard Dame David Bushek Dennis Allen Alan Lewitus Don Edwards Eric Koepfler Leah Gregory 《Aquatic Ecology》2002,36(1):51-65
Coastal ecosystems are easily overexploited and changed by physical and biological factors. In this paper, we discuss current ideas and arguments for coastal ecosystem management with an emphasis on systems that have large bivalve filter feeder components. For centuries the species or population approach has been utilized in fisheries management. With the growing knowledge base on specific environmental effects and relationships, it has become increasingly evident that a broad or holistic approach to fisheries management in these systems is usually more appropriate. An ongoing ecosystem scale experiment in which oysters are completely removed from tidal creeks is described and used as a case study. The experimental design takes estimates of the systems carrying capacity into account. Using the population or species approach to monitor the oysters, the only observable change after the experimental manipulation was a slight increase in summer somatic growth and elevated recruitment of oysters in creeks with oyster reefs removed. These data are interpreted as an indication that the creeks with oysters present are below or near carrying capacity. However, when nekton, plankton and water chemistry data are also examined a much more complicated picture emerges. During the summer growing season, nekton biomass in all creeks is often greater than oyster biomass. Also, our calculations show that oysters do not produce enough ammonium to satisfy phytoplankton productivity, but nekton, water column remineralization and sediments can account for most of the deficit. Finally, microflagellates, which are a preferred food for the oysters, dominate the phytoplankton during the summer growing season and diatoms dominate the colder months. The timing of the change in phase of phytoplankton dominance seems to mirror the seasonal arrival and departure times of nekton in the creeks. We argue that dense bivalve reefs and beds are indicative of intense positive feedback loops that make their ecosystems susceptible to dramatic changes in structure. Such changes have not been reported for natural systems, but are found in systems influenced by over-fishing, nutrient loading and pollution. Thus, the management of sustainable fisheries in coastal ecosystems requires an understanding of the ecosystem science and the realization that systems dominated by bivalves exhibit complex responses that are not easily explained by linear dynamics. 相似文献
58.
Peng Liu Arthur H. Robbins Melissa R. Marzahn Scott H. McClung Charles A. Yowell Stanley M. Stevens Jr. John B. Dame Ben M. Dunn 《PloS one》2015,10(10)
The rodent malaria parasite Plasmodium berghei is a practical model organism for experimental studies of human malaria. Plasmepsins are a class of aspartic proteinase isoforms that exert multiple pathological effects in malaria parasites. Plasmepsins residing in the food vacuole (FV) of the parasite hydrolyze hemoglobin in red blood cells. In this study, we cloned PbPM4, the FV plasmepsin gene of P. berghei that encoded an N-terminally truncated pro-segment and the mature enzyme from genomic DNA. We over-expressed this PbPM4 zymogen as inclusion bodies (IB) in Escherichia coli, and purified the protein following in vitro IB refolding. Auto-maturation of the PbPM4 zymogen to mature enzyme was carried out at pH 4.5, 5.0, and 5.5. Interestingly, we found that the PbPM4 zymogen exhibited catalytic activity regardless of the presence of the pro-segment. We determined the optimal catalytic conditions for PbPM4 and studied enzyme kinetics on substrates and inhibitors of aspartic proteinases. Using combinatorial chemistry-based peptide libraries, we studied the active site preferences of PbPM4 at subsites S1, S2, S3, S1’, S2’ and S3’. Based on these results, we designed and synthesized a selective peptidomimetic compound and tested its inhibition of PbPM4, seven FV plasmepsins from human malaria parasites, and human cathepsin D (hcatD). We showed that this compound exhibited a >10-fold selectivity to PbPM4 and human malaria parasite plasmepsin 4 orthologs versus hcatD. Data from this study furthesr our understanding of enzymatic characteristics of the plasmepsin family and provides leads for anti-malarial drug design. 相似文献
59.
MK Parr F Botrè A Na? J Hengevoss P Diel G Wolber 《Biology of sport / Institute of Sport》2015,32(2):169-173
Increasing numbers of dietary supplements with ecdysteroids are marketed as “natural anabolic agents”. Results of recent studies suggested that their anabolic effect is mediated by estrogen receptor (ER) binding. Within this study the anabolic potency of ecdysterone was compared to well characterized anabolic substances. Effects on the fiber sizes of the soleus muscle in rats as well the diameter of C2C12 derived myotubes were used as biological readouts. Ecdysterone exhibited a strong hypertrophic effect on the fiber size of rat soleus muscle that was found even stronger compared to the test compounds metandienone (dianabol), estradienedione (trenbolox), and SARM S 1, all administered in the same dose (5 mg/kg body weight, for 21 days). In C2C12 myotubes ecdysterone (1 µM) induced a significant increase of the diameter comparable to dihydrotestosterone (1 µM) and IGF 1 (1.3 nM). Molecular docking experiments supported the ERβ mediated action of ecdysterone. To clarify its status in sports, ecdysterone should be considered to be included in the class “S1.2 Other Anabolic Agents” of the list of prohibited substances of the World Anti-Doping Agency. 相似文献
60.
Muhammad Nasir Nafees Ahmad Christian MK Sieber Amir Latif Salman Akbar Malik Abdul Hameed 《Journal of biomedical science》2013,20(1):70