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121.
122.
GPS?Raghava Stephen?MJ?Searle Patrick?C?Audley Jonathan?D?Barber Geoffrey?J?BartonEmail author 《BMC bioinformatics》2003,4(1):47
Background
The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. 相似文献123.
Dairy cows often have to choose which of two sides to enter in the milking parlour. Some cows are very consistent in this choice, and it is common to assume that when these cows are more disturbed are being milked in their non-preferred side. Such disturbance might involve significantly poor welfare. In order to assess this assumption, we decided to study the behaviour and milk yield of dairy cows and their relationships with side preference in the milking parlour. The study was carried out at Cambridge University Farm, in a two-sided tandem milking parlour. The data collection followed the daily management routine. We recorded the side chosen by each cow (left or right) during 40 milking sessions. Data from 70 cows, which were present in at least 25 milking sessions (mode=36), were included in the statistical analysis. Cows' reactivity (CR) during premilking udder preparation, time spent fitting the milking cluster (FT), milk yield (MY) and duration of milking (DM) were measured. There was evident individual variation in the consistency of side choice. Individual differences (ANOVA, P<0.001) were also found in CR, FT, MY and DM; although these variables were not significantly affected by the side or the interaction animalxside (ANOVA, P>0.05). The comparison between left and right side means (paired t-test) of these variables did not show significant differences (P>0.05). We concluded that there is no evidence that the cows were discomforted or stressed when milked in the non-preferred side of the milking parlour. 相似文献
124.
A phylogenetic survey using the polymerase chain reaction (PCR) has
identified four major P element subfamilies in the saltans and willistoni
species groups of Drosophila. One subfamily, containing about half of the
sequences studied, consists of elements that are very similar to the
canonical (and active) P element from D. melanogaster. Within this
subfamily, nucleotide sequence differentiation among different copies from
the same species and among elements from different species is relatively
low. This observation suggests that the canonical elements are relatively
recent additions to the genome or, less likely, are evolving slowly
relative to the other subfamilies. Elements belonging to the three
noncanonical lineages are distinct from the canonical elements and from one
another. Furthermore, there is considerably more sequence variation, on the
average, within the noncanonical subfamilies compared to the canonical
elements. Horizontal transfer and the coexistence of multiple,
independently evolving element subfamilies in the same genome may explain
the distribution of P elements in the saltans and willistoni species
groups. Such explanations are not mutually exclusive, and each may be
involved to varying degrees in the maintenance of P elements in natural
populations of Drosophila.
相似文献
125.
Gortat A San-Roman MJ Vannier C Schmidt AA 《The Journal of biological chemistry》2012,287(6):4232-4247
Bin/Amphiphysin/Rvs (BAR) domain-containing proteins are essential players in the dynamics of intracellular compartments. The BAR domain is an evolutionarily conserved dimeric module characterized by a crescent-shaped structure whose intrinsic curvature, flexibility, and ability to assemble into highly ordered oligomers contribute to inducing the curvature of target membranes. Endophilins, diverging into A and B subgroups, are BAR and SH3 domain-containing proteins. They exert activities in membrane dynamic processes such as endocytosis, autophagy, mitochondrial dynamics, and permeabilization during apoptosis. Here, we report on the involvement of the third α-helix of the endophilin A BAR sequence in dimerization and identify leucine 215 as a key residue within a network of hydrophobic interactions stabilizing the entire BAR dimer interface. With the combination of N-terminal truncation retaining the high dimerization capacity of the third α-helices of endophilin A and leucine 215 substitution by aspartate (L215D), we demonstrate the essential role of BAR sequence-mediated dimerization on SH3 domain partnership. In comparison with wild type, full-length endophilin A2 heterodimers with one protomer bearing the L215D substitution exhibit very significant changes in membrane binding and shaping activities as well as a dramatic decrease of SH3 domain partnership. This suggests that subtle changes in the conformation and/or rigidity of the BAR domain impact both the control of membrane curvature and downstream binding to effectors. Finally, we show that expression, in mammalian cells, of endophilin A2 bearing the L215D substitution impairs the endocytic recycling of transferrin receptors. 相似文献
126.
Vicente Ramírez Sjoerd Van der Ent Javier García-Andrade Alberto Coego Corné MJ Pieterse Pablo Vera 《BMC plant biology》2010,10(1):199
Background
Upon appropriate stimulation, plants increase their level of resistance against future pathogen attack. This phenomenon, known as induced resistance, presents an adaptive advantage due to its reduced fitness costs and its systemic and broad-spectrum nature. In Arabidopsis, different types of induced resistance have been defined based on the signaling pathways involved, particularly those dependent on salicylic acid (SA) and/or jasmonic acid (JA). 相似文献127.
128.
Molecular evolution of the period gene in Drosophila athabasca 总被引:1,自引:0,他引:1
We measured nucleotide variability within and between the three semispecies
of the Drosophila athabasca complex, at the period (per) gene by using a
polymerase chain reaction-based four-cutter restriction- enzyme analysis.
The levels of polymorphism varied considerably between the three
semispecies. Our results for per, combined with previous data for X-linked
allozymes, suggest that the X chromosome in the western- northern
semispecies is less variable than expected under an equilibrium-neutral
model. Both the pattern of divergence between the semispecies and a
cladistic clustering of per haplotypes support the previously hypothesized
grouping of eastern A and eastern B as the two most recently diverged
semispecies. A 21-bp in-frame segment in the region of per which shares
sequence similarity with the neuronal development gene single minded is
deleted in all eastern A and eastern B flies examined but is present in all
of the western-northern flies and all other published per sequences.
Despite these hints that there may be significant differences at the per
gene between the semispecies, especially the western-northern group versus
the two eastern groups, there is no compelling evidence that per is
involved in the mating song differences between the semispecies.
相似文献
129.
130.
Cyclins are indispensable elements of the cell cycle and derangement of their function can lead to cancer formation. Recent studies have also revealed more mechanisms through which cyclins can express their oncogenic potential. This review focuses on the aberrant expression of G1/S cyclins and especially cyclin D and cyclin E; the pathways through which they lead to tumour formation and their involvement in different types of cancer. These elements indicate the mechanisms that could act as targets for cancer therapy. 相似文献