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1.
For several species of lepidoptera, most of the approximately 350-bp
mitochondrial control-region sequences were determined. Six of these
species are in one genus, Jalmenus; are closely related; and are believed
to have undergone recent rapid speciation. Recent speciation was supported
by the observation of low interspecific sequence divergence. Thus, no
useful phylogeny could be constructed for the genus. Despite a surprising
conservation of control-region length, there was little conservation of
primary sequences either among the three lepidopteran genera or between
lepidoptera and Drosophila. Analysis of secondary structure indicated only
one possible feature in common--inferred stem loops with higher-than-random
folding energies-- although the positions of the structures in different
species were unrelated to regions of primary sequence similarity. We
suggest that the conserved, short length of control regions is related to
the observed lack of heteroplasmy in lepidopteran mitochondrial genomes. In
addition, determination of flanking sequences for one Jalmenus species
indicated (i) only weak support for the available model of insect 12S rRNA
structure and (ii) that tRNA translocation is a frequent event in the
evolution of insect mitochondrial genomes.
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2.
Combined monte carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers 下载免费PDF全文
We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine (POPC). The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer in a constant volume and temperature ensemble. The procedure is applied to bilayers of 128 molecules of POPC with 4628 water molecules, and 128 molecules of DOPC with 4825 water molecules. Progress toward equilibration is almost three times as fast in central processing unit (CPU) time compared with a purely molecular dynamics (MD) simulation. Equilibration is complete, as judged by the lack of energy drift in 200-ps runs of continuous MD. After the equilibrium state was reached, as determined by agreement between the simulation volume per lipid molecule with experiment, continuous MD was run in an ensemble in which the lateral area was restrained to fluctuate about a mean value and a pressure of 1 atm applied normal to the bilayer surface. Three separate continuous MD runs, 200 ps in duration each, separated by 10,000 CBMC steps, were carried out for each system. Properties of the systems were calculated and averaged over the three separate runs. Results of the simulations are presented and compared with experimental data and with other recent simulations of POPC and DOPC. Analysis of the hydration environment in the headgroups supports a mechanism by which unsaturation contributes to reduced transition temperatures. In this view, the relatively horizontal orientation of the unsaturated bond increases the area per lipid, resulting in increased water penetration between the headgroups. As a result the headgroup-headgroup interactions are attenuated and shielded, and this contributes to the lowered transition temperature. 相似文献
3.
Simon W. Ginzinger Christian X. Weichenberger Manfred J. Sippl 《Journal of biomolecular NMR》2010,47(1):33-40
Understanding the relationship between protein structure and biological function is a central theme in structural biology.
Advances are severely hampered by errors in experimentally determined protein structures. Detection and correction of such
errors is therefore of utmost importance. Electron densities in molecular structures obey certain rules which depend on the
molecular environment. Here we present and discuss a new approach that relates electron densities computed from a structural
model to densities expected from prior observations on identical or closely related molecular environments. Strong deviations
of computed from expected densities reveal unrealistic molecular structures. Most importantly, structure analysis and error
detection are independent of experimental data and hence may be applied to any structural model. The comparison to state-of-the-art
methods reveals that our approach is able to identify errors that formerly remained undetected. The new technique, called
RefDens, is accessible as a public web service at . 相似文献
4.
Rapposch S Eliskases-Lechner F Ginzinger W 《Applied and environmental microbiology》1999,65(12):5597-5599
The growth of facultatively heterofermentative lactobacilli (FHL) on cell suspensions of the homofermentative Lactobacillus helveticus was investigated. Osmotic lysis of L. helveticus led to a significant increase of ribose. It decreased steadily in parallel with the growth of FHL, strongly suggesting that the bacteria used ribose as a growth substrate. 相似文献
5.
6.
The construction of a consistent protein chemical shift database is an important step toward making more extensive use of
this data in structural studies. Unfortunately, progress in this direction has been hampered by the quality of the available
data, particularly with respect to chemical shift referencing, which is often either inaccurate or inconsistently annotated.
Preprocessing of the data is therefore required to detect and correct referencing errors. In an earlier study we developed
CheckShift, a program for performing this task automatically. Now we spent substantial effort in improving the running time
of the CheckShift algorithm, which resulted in an running time decrease of 90%, thereby achieving equivalent quality to the
former version of CheckShift. The reason for the running time decrease is twofold. Firstly we improved the search for the
optimal re-referencing offset considerably. Secondly, as CheckShift is based on a secondary structure prediction from the
amino acid sequence (formally PsiPred was used), we evaluated a wide range of available secondary structure prediction programs
focusing on the special needs of the CheckShift algorithm. The results of this evaluation prove empirically that we can use
faster secondary structure prediction programs than PsiPred without sacrificing CheckShift’s accuracy. Very recently Wang
and Markley (2009) gave a small list of extreme outliers of the former version of the CheckShift web-server. Those were due to the empirical
reduction of the search space implemented in the old version. The new version of CheckShift now gives very similar results
to RefDB and LACS for all outliers mentioned in Table 1 of Wang and Markley (2009). 相似文献
7.
Loksum Wong Cameron J Weadick Claire Kuo Belinda SW Chang Vincent Tropepe 《BMC developmental biology》2010,10(1):100
Background
The Dmbx1 gene is important for the development of the midbrain and hindbrain, and mouse gene targeting experiments reveal that this gene is required for mediating postnatal and adult feeding behaviours. A single Dmbx1 gene exists in terrestrial vertebrate genomes, while teleost genomes have at least two paralogs. We compared the loss of function of the zebrafish dmbx1a and dmbx1b genes in order to gain insight into the molecular mechanism by which dmbx1 regulates neurogenesis, and to begin to understand why these duplicate genes have been retained in the zebrafish genome. 相似文献8.
Unusual molecular evolution of an Adh pseudogene in Drosophila 总被引:2,自引:0,他引:2
Sullivan DT; Starmer WT; Curtiss SW; Menotti-Raymond M; Yum J 《Molecular biology and evolution》1994,11(3):443-458
9.
Growth of Facultatively Heterofermentative Lactobacilli on Starter Cell Suspensions 总被引:1,自引:1,他引:0 下载免费PDF全文
The growth of facultatively heterofermentative lactobacilli (FHL) on cell suspensions of the homofermentative Lactobacillus helveticus was investigated. Osmotic lysis of L. helveticus led to a significant increase of ribose. It decreased steadily in parallel with the growth of FHL, strongly suggesting that the bacteria used ribose as a growth substrate. 相似文献