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71.
Rykunov D Steinberger E Madrid-Aliste CJ Fiser A 《Journal of structural and functional genomics》2009,10(1):95-99
Improvements in comparative protein structure modeling for the remote target-template sequence similarity cases are possible
through the optimal combination of multiple template structures and by improving the quality of target-template alignment.
Recently developed MMM and M4T methods were designed to address these problems. Here we describe new developments in both
the alignment generation and the template selection parts of the modeling algorithms. We set up a new scoring function in
MMM to deliver more accurate target-template alignments. This was achieved by developing and incorporating into the composite
scoring function a novel statistical pairwise potential that combines local and non-local terms. The non-local term of the
statistical potential utilizes a shuffled reference state definition that helped to eliminate most of the false positive signal
from the background distribution of pairwise contacts. The accuracy of the scoring function was further increased by using
BLOSUM mutation table scores. 相似文献
72.
Parthasarathy Sampathkumar Frances Lu Xun Zhao Zhenzhen Li Jeremiah Gilmore Kevin Bain Marc E. Rutter Tarun Gheyi Kenneth D. Schwinn Jeffrey B. Bonanno Ursula Pieper J. Eduardo Fajardo Andras Fiser Steven C. Almo Subramanyam Swaminathan Mark R. Chance David Baker Shane Atwell Devon A. Thompson J. Spencer Emtage Stephen R. Wasserman Andrej Sali J. Michael Sauder Stephen K. Burley 《Proteins》2010,78(14):3056-3062
73.
Abstract: We present the first record of the cardiid genus Monodacna from the Pliocene of Anatolia, Turkey. Monodacna imrei sp. nov. was found in the Pliocene Killik Formation from the western margin of the Baklan Basin, in very marginal brackish to freshwater lacustrine deposits. The new record extends the stratigraphic range of the modern Ponto‐Caspian genus back into the Pliocene and adds to earlier evidence that modern Ponto‐Caspian taxa originated in the Pliocene of south‐western Turkey. 相似文献
74.
A. SOTO J. J. ROBLEDO‐ARNUNCIO S. C. GONZÁLEZ‐MARTÍNEZ P. E. SMOUSE R. ALÍA 《Molecular ecology》2010,19(7):1396-1409
Quaternary climatic fluctuations have left contrasting historical footprints on the neutral genetic diversity patterns of existing populations of different tree species. We should expect the demography, and consequently the neutral genetic structure, of taxa less tolerant to particular climatic extremes to be more sensitive to long‐term climate fluctuations. We explore this hypothesis here by sampling all six pine species found in the Iberian Peninsula (2464 individuals, 105 populations), using a common set of chloroplast microsatellite markers, and by looking at the association between neutral genetic diversity and species‐specific climatic requirements. We found large variation in neutral genetic diversity and structure among Iberian pines, with cold‐enduring mountain species (Pinus uncinata, P. sylvestris and P. nigra) showing substantially greater diversity than thermophilous taxa (P. pinea and P. halepensis). Within species, we observed a significant positive correlation between population genetic diversity and summer precipitation for some of the mountain pines. The observed pattern is consistent with the hypotheses that: (i) more thermophilous species have been subjected to stronger demographic fluctuations in the past, as a consequence of their maladaptation to recurrent glacial cold stages; and (ii) altitudinal migrations have allowed the maintenance of large effective population sizes and genetic variation in cold‐tolerant species, especially in more humid regions. In the light of these results and hypotheses, we discuss some potential genetic consequences of impending climate change. 相似文献
75.
QIANQIAN ZHANG XINPENG FAN JOHN C. CLAMP KHALED A. S. AL‐RASHEID WEIBO SONG 《The Journal of eukaryotic microbiology》2010,57(6):483-493
ABSTRACT. The marine scuticociliate Paratetrahymena parawassi n. sp. is described on the basis of morphology, especially infraciliature, and the sequence of its small subunit (SSU) rRNA gene to become the second known member of its genus. Paratetrahymena and other ciliates in the order Loxocephalida possess a mixture of morphological and morphogenetic features characteristic of the subclasses Hymenostomatia and Scuticociliatia. Accordingly, we used SSU rRNA sequences to analyze the phylogeny of Paratetrahymena and three other loxocephalid genera. Paratetrahymena and Cardiostomatella vermiformis formed a moderately well‐supported clade that diverged at a deep level from all other scuticociliates, supporting separation of loxocephalids from other scuticociliates as a suprafamilial taxon. Sathrophilus holtae was a sister taxon to Paratetrahymena and Cardiostomatella in a poorly supported, unresolved relationship; nevertheless, association of all three genera into a single clade was supported by an approximately unbiased (AU) test. Any association of these genera singly or as a group with the Hymenostomatia was rejected decisively by AU tests and by a complete absence in the loxocephalids of the unique nucleotide identities that distinguish hymenostomes. Therefore, the morphological and morphogenetic similarities of loxocephalids to hymenostomes may be plesiomorphies, and the conflicting mix of scuticociliate and hymenostome characteristics seen in loxocephalids may result from differing rates of character evolution. Dexiotrichides pangi and Urocentrum, which is currently classified as a peniculid, formed a small clade that associated with hymenostomes and peritrichs. Monophyly of the Loxocephalida with Dexiotrichides and/or Urocentrum included was not rejected by AU; however, inclusion of Urocentrum in the Peniculia was rejected by AU tests. A hypothesis is offered to explain the lack of resolution of loxocephalid ciliates and Urocentrum in phylogenetic trees, namely that their phylogenetic positions are influenced by a combination of heterogeneous data and long‐branch attraction caused by poor representation of taxa in analyses. The well‐known genus Cyclidium, a member of the order Pleuronematida, was revealed to be polyphyletic as a byproduct of our analyses of loxocephalids. In particular, Cyclidium porcatum appears to fall outside the clade containing typical members of the subclass Scuticociliatia and thus invites investigation as a possible member of the order Loxocephalida. 相似文献
76.
77.
78.
Jason AL Jeffery Peter A Ryan Scott A Lyons Brian H Kay 《Australian Journal of Entomology》2002,41(4):339-344
Abstract Coquillettidia linealis is a severe pest on some of the Moreton Bay islands in Queensland, Australia, but little is known of its breeding habitats and biology. Because of its high abundance and its association with Ross River (RR) and Barmah Forest (BF) viruses by field isolation, its vector competence was evaluated in the laboratory by feeding dilutions of both viruses in blood. For RR, Cq. linealis was of comparable efficiency to Ochlerotatus vigilax (Skuse), recognised as being a major vector. Results were as follows for Cq. linealis and Oc. vigilax , respectively: dose to infect 50%, 102.2 and <101.7 CCID50 /mosquito; 88% and 90% disseminated infection at 4 days postinfection; transmission at 4 days with rates of 68−92% and 25−60%. For BF dose to infect 50%, 102.7 and 102.0 ; disseminated infection rates on first transmission day (day 6), 40% and 70%; transmission rates of 8−16% and 0−10%. As a capillary-tube method was used rather than suckling mice to demonstrate transmission, transmission rates may be underestimates. This, the first study of the vector competence of Cq. linealis in Australia, demonstrates that this species deserves control on the southern Moreton Bay islands. 相似文献
79.
80.
P. S. Fiser R. W. Fairfull C. Hansen P. L. Panich J. N. B. Shrestha L. Underhill 《Molecular reproduction and development》1993,34(2):190-195
The effect of thawing velocities ranging from 10°C/min to 1.800°C/min on the motility and acrosomal integrity of boar spermatozoa frozen at 1°C/min (suboptimal), 5°C/min, and 30°C/min (optimal) rate was studied with the sperm suspended for freezing in diluent containing 2, 4, or 6% of glycerol (v/v). The influence of thawing on sperm survival depends on the rate at which the sperm had been frozen. In semen frozen at a suboptimal rate of 1°C/min, the percentage of motile sperm (FMP) initially fell to 3.5–4.0% when the thawing rose to 200°C/ min, but, with further increases in thawing rate, increased and reached peak values (10.3–11.0% FMP) after thawing at 1,800°C/min. The percentage of sperm with normal apical ridge (NAR) also increased moderately with thawing rate, but the degree of improvement decreased as the glycerol level was increased. In semen frozen at 1°C/min, acrosomal integrity (NAR) was best maintained in 2% glycerol, reaching 22.9% NAR after thawing at 1,800°C/min. In semen frozen at the optimal rate of 30°C/min, the increases in thawing rates above 200°C/min substantially improved motility. Motility was generally higher in semen protected by 4 or 6% glycerol, with the peak values of 44 or 46% FMP, respectively, after thawing at 1,200°C/min. The proportion of sperm with NAR also increased with thawing rate, but as in the case of suboptimally frozen sperm it was influenced negatively by the glycerol concentration. The peak value 53% NAR was recorded in semen protected by 2% glycerol, frozen at 30°C/min, and thawed at 1,200°C/min. In view of the inverse relationship between FMP and NAR, selection of optimal conditions from among the interacting variables, freezing rate, glycerol concentration, and thawing rate requires compromising between maximal FMP and maximal NAR. Accordingly, we have adopted as optimal a protocol with a thawing rate of 1,200°C/min, a freezing rate of 30°C/min and concentrations of 3% glycerol. © 1993 Wiley-Liss, Inc. 相似文献