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911.
Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction
of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However,
it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper
presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability
upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and
order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing
rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm,
iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed
analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability
change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type
and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting
protein stability change, especially when one requires more understandable knowledge. 相似文献
912.
Botulinum neurotoxins type A (BoNT/A) are highly potent toxins, but are also useful in the treatment of illnesses. We studied
the properties of BoNT/A at various temperatures and pH values in order to understand its toxicity and structure variations.
The pH values of the environment of BoNT/A are obtained by changing the protonation states of certain titratable residue groups.
Our results show that certain parts of the protein are active at acidic pH environments or at high temperatures. The protein
is more stable in neutral environments at normal human body temperature, whereas, at high temperature, the protein is more
stable in acidic environments. Also, the three domains of the protein tend to have relative motion rather than within individual
domains. 相似文献
913.
Mutsumi Nakamura Takafumi Nagamine Chisato Harada Kiyoshi Tajima Hiroki Matsui Yoshimi Benno 《Current microbiology》2003,47(1):0071-0074
The objective of this study was to ligate the xylanase gene A (xynA) isolated from Ruminococcus albus 7 into the promoter and signal-peptide region of the lichenase [β-(1,3-1,4)-glucanase] gene of Streptococcus bovis JB1. This fusion gene was inserted into the pSBE11 vector, and the resulting recombinant, plasmid pXA, was used to transform
S. bovis 12-U-1 cells. The transformant, S. bovis 12UXA, secreted the xylanase, which was stable against freeze-thaw treatment and long-time incubation at 37°C. The introduction
of pXA and production of xylanase did not affect cell growth, and the xylanase produced degraded xylan from oat-spelt and
birchwood.
Received: 24 June 2002 / Accepted: 7 October 2002 相似文献
914.
Bacillus sphaericus LP1-G, belonging to flagellar serotype H3, has been found to have moderate toxicity against two resistant Culex quinquefasciatus colonies (RLCq1 and RLCq2) and the susceptible contrast (SLCq). With an aim of screening mosquitocidal acting factor, a partial genome library was prepared from a partial HindIII digest of the total DNA from Bacillus sphaericus LP1-G. Two thousand twenty Escherichia coli clones were screened for toxicity against susceptible SLCq, and a toxic clone, designated E-UL68, was chosen for further study. The recombinant E-UL68 performed toxicity against both susceptible and two resistant colonies, having the same level of toxicity as that of wide-type strain LP1-G. Sequence analysis revealed that the inserted fragment was composed of 3876 nucleotides and contained a complete gene, whose sequence was identical to that of the mtx gene from B. sphaericus SSII-1. Because the binary toxin produced during sporulation of strain LP1-G has no activity against the target mosquitoes, this indicates that the Mtx toxin or other active factors might perhaps be responsible for the toxicity of LP1-G against different colonies of mosquito larvae.Received: 7 October 2002 / Accepted: 4 November 2002 相似文献
915.
We investigated the mycorrhizal status of perennial xeric plant species occurring in the "matorral xerófilo" (arid tropical scrub) and the ecotone of the "selva baja caducifolia" (tropical deciduous forest) communities in the semiarid valley of Tehuacán-Cuicatlán, south-central Mexico. The perennial species examined are dominant/codominant elements within the "matorral xerófilo" and the "selva baja caducifolia", both endangered communities in the Biosphere Reserve Tehuacán-Cuicatlán Valley. Of the 50 sampled species, 45 were mycorrhizal. To our knowledge, we report arbuscular mycorrhizae (AM) for the first time in 37 species, of which 21 are endemic to Mexico and nine are endemic to the Valley. We also report AM for the first time in three genera, Buddleja, Hechtia and Zornia, and in one plant family, Buddlejaceae. Beaucarnea gracilis, a threatened species, and Mimosa purpusii, a potentially rare species, are both mycorrhizal. This is the first study of the mycorrhizal status of plant species within the Valley. 相似文献
916.
Luis Giménez 《Helgoland Marine Research》2003,56(4):265-273
Chasmagnathus granulata is a South American crab occurring in estuarine salt marshes of the Brazilian, Uruguayan and Argentine coasts. Life history
is characterized by an export strategy of its larval stages. I reviewed information on experimental manipulation of salinity
during embryonic and larval development (pre- and posthatching salinities), and on habitat characteristics of C. granulata in order to determine potential effects of larval response to salinity in the field and to suggest consequences for the population
structure. Local populations are spread over coastal areas with different physical characteristics. Benthic phases occupy
estuaries characterized by different patterns of salinity variation, and release larvae to coastal waters characterized by
strong salinity gradients. The zoea 1 of C. granulata showed a strong acclimatory response to low salinity. This response operated only during the first weeks of development (during
zoeae 1 and 2) since subsequent larval survival at low posthatching salinities was consistently low. Larvae developing at
low salinity frequently followed a developmental pathway with five instead of four zoeal stages. The ability to acclimate
and the variability in larval development (i.e. the existence of alternative developmental pathways) could be interpreted
as a strategy to buffer environmental variability at spatial scales of local or population networks. Early survivorship and
production of larvae may be relatively high across a rather wide range of variability in salinity (5–32‰). Plastic responses
to low salinity would therefore contribute to maintain a certain degree of population connectivity and persistence regardless
of habitat heterogeneity.
Electronic Publication 相似文献
917.
Olivier Demeure Christine Renard Martine Yerle Thomas Faraut Juliette Riquet Annie Robic Thomas Schiex Anette Rink Denis Milan 《Mammalian genome》2003,14(1):71-80
On porcine Chromosome 7, the region surrounding the MHC region contains QTL influencing many traits including growth, back
fat thickness, and carcass composition. Towards the identification of the responsible gene(s), this article describes an increase
of density of the radiated hybrid map of SSC 7 in the q11-q14 region and the comparative analysis of gene order on the porcine
RH map and human genome assembly. Adding 24 new genes in this region, we were able to build a framework map that fills in
gaps on the previous maps. The new software Carthagene was used to build a robust framework in this region. Comparative analysis
of human and porcine maps revealed a global conservation of gene order and of distances between genes. A rearranged fragment
of around 3.7 Mb was, however, found in the pig approximately 20 Mb upstream from the expected location on the basis of the
human map. This rearrangement, found by RH mapping on the IMpRH 7.000 rads panel, has been confirmed by two-color FISH and
by mapping on the high resolution IMNpRH2 12.000 rads panel. The rearranged fragment contains two microsatellites found at
the most likely QTL location in the INRA QTL experiment. It also contains the BMP5 gene, which, together with CLPS, could
be considered as a possible candidate. 相似文献
918.
The walking rhythm is known to show phase shift or "reset" in response to external impulsive perturbations. We tried to elucidate functional roles of the phase reset possibly used for the neural control of locomotion. To this end, a system with a double pendulum as a simplified model of the locomotor control and a model of bipedal locomotion were employed and analyzed in detail. In these models, a movement corresponding to the normal steady-state walking was realized as a stable limit cycle solution of the system. Unexpected external perturbations applied to the system can push the state point of the system away from its limit cycle, either outside or inside the basin of attraction of the limit cycle. Our mathematical analyses of the models suggested functional roles of the phase reset during walking as follows. Function 1: an appropriate amount of the phase reset for a given perturbation can contribute to relocating the system's state point outside the basin of attraction of the limit cycle back to the inside. Function 2: it can also be useful to reduce the convergence time (the time necessary for the state point to return to the limit cycle). In experimental studies during walking of animals and humans, the reset of walking rhythm induced by perturbations was investigated using the phase transition curve (PTC) or the phase resetting curve (PRC) representing phase-dependent responses of the walking. We showed, for the simple double-pendulum model, the existence of the optimal phase control and the corresponding PTC that could optimally realize the aforementioned functions in response to impulsive force perturbations. Moreover, possible forms of PRC that can avoid falling against the force perturbations were predicted by the biped model, and they were compared with the experimentally observed PRC during human walking. Finally, physiological implications of the results were discussed. 相似文献
919.
Evidence is provided for a close link between glutamate (Glu) synthesis and the production of reducing power by the oxidative pentose phosphate pathway (OPPP) in barley ( Hordeum vulgare L. var. Alfeo) root plastids. A rapid procedure for isolating organelles gave yields of plastids of over 30%, 60% of which were intact. The formation of Glu by intact plastids fed with glutamine and 2-oxoglutarate, both substrates of glutamate synthase (GOGAT), depends on glucose-6-phosphate (Glc-6-P) supply. The whole process exhibited an apparent K(m Glc-6-P) of 0.45 mM and is abolished by azaserine, a specific inhibitor of GOGAT; ATP caused a decrease in the rate of Glu formation. Glucose and other sugar phosphates were not as effective in supporting Glu synthesis with respect to Glc-6-P; only ribose-5-phosphate, an intermediate of OPPP, supported rates equivalent to Glc-6-P. Glucose-6-phosphate dehydrogenase (Glc6PDH) rapidly purified from root plastids showed an apparent K(m Glc-6-P) of 0.96 mM and an apparent K(m NADP)(+) of 9 micro M. The enzyme demonstrated high tolerance to NADPH, exhibiting a K(i) (NADPH) of 58.6 micro M and selectively reacted with antibodies against potato plastidic, but not chloroplastic, Glc6PDH isoform. The data support the hypothesis that plastidic OPPP is the main site of reducing power supply for GOGAT within the plastids, and suggest that the plastidic OPPP would be able to sustain Glu synthesis under high NADPH:NADP(+) ratios even if the plastidic Glc6PDH may not be functioning at its highest rates. 相似文献
920.
The paper focuses on the effect of a nine-year utilisation of the peat-bark substrate and crop rotation of six main forest
tree species on changes in the substrate enzymatic activity during successive rotation cycles.
The study was conducted in the forest nursery in the years 1989–1997. Seedlings of Scots pine Pinus sylvestris, Norway spruce Picea abies, European larch Larix decidua, pendiculate oak Quercus robur, common beech Fagus silvatica, and silver birch Betula overrucosa were grown on peat-bark substrate. The activity of soil enzymes: betaglucosidase, invertase, urease, asparginase, acid phosphatase
and dehydrogenases was assessed. The succession of three 3-year crop rotation cycles with species following each other according
to the rotation plan was subject to observations.
The obtained results have confirmed recent suppositions that the tree species and their rotation modify soil enzymatic activity.
The enzymatic activity of the peat-bark substrate changed after each three-year crop rotation cycle and decreased with time.
After the second crop rotation cycle the activity of betaglucosidase, urease, asparginase was found to be lower, and the activity
of invertase and dehydrogenases — higher. After three crop rotation cycles the positive effect of appropriate species rotation
on the enzymatic activity of the substrate was noted. 相似文献