bluuebunny/crossref_metadata_2025 huggingface dataset:
Reversible switches between male–male and male–female mating behaviour by male damselflies
Authors: Van Gossum H , De Bruyn L , Stoks R
Published: June 2005

For many animal groups, both sexes have been reported to attempt to mate with members of their own sex. Such behaviour challenges theories of sexual selection, which predict optimization of reproductive success. We tested male mate choice between opposite- and same-sex members in the damselfly
Ischnura elegans
. Binary choice experiments were conducted following exposure periods in insectaries with only males or with both sexes present. We show that switches in choice between the opposite sex and the same sex can be induced and reversed again by changing the social context. We argue that the observed reversibility in male–male- and male–female-directed mating behaviour is maladaptive and a consequence of strong selection on a male's ability to alter choice between different female colour morphs.
Derivative formulae and errors for non-uniformly spaced points
Authors: Bowen M.K , Smith Ronald
Published: May 2005

Lagrange interpolation estimates a function at a reference positionΧfrom known values of the function at distinct non-uniformly spaced pointsx1, …,xn. Here, the correspondingn-point finite-difference formulae are derived to estimate derivatives up to ordern−1 atΧ. A recurrence relation is derived that permits the errors to be determined as a Taylor series to any accuracy. The error coefficient multiplying then+jth derivative is a polynomial of orderj+1 in the elementary symmetric functions for the displacementsx1−Χ,…,xn−Χ. Appendices state finite-difference formulae to estimate the derivatives and the first four error terms forn=1,…,5.
Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic
Authors: Cook Charles E , Yue Qiaoyun , Akam Michael
Published: June 2005

For over a century the relationships between the four major groups of the phylum Arthropoda (Chelicerata, Crustacea, Hexapoda and Myriapoda) have been debated. Recent molecular evidence has confirmed a close relationship between the Crustacea and the Hexapoda, and has included the suggestion of a paraphyletic Hexapoda. To test this hypothesis we have sequenced the complete or near-complete mitochondrial genomes of three crustaceans (
Parhyale hawaiensis
,
Squilla mantis
and
Triops longicaudatus
), two collembolans (
Onychiurus orientalis
and
Podura aquatica
) and the insect
Thermobia domestica
. We observed rearrangement of transfer RNA genes only in
O. orientalis
,
P. aquatica
and
P. hawaiensis
. Of these, only the rearrangement in
O. orientalis
, an apparent autapomorphy for the collembolan family Onychiuridae, was phylogenetically informative.

We aligned the nuclear and amino acid sequences from the mitochondrial protein-encoding genes of these taxa with their homologues from other arthropod taxa for phylogenetic analysis. Our dataset contains many more Crustacea than previous molecular phylogenetic analyses of the arthropods. Neighbour-joining, maximum-likelihood and Bayesian posterior probabilities all suggest that crustaceans and hexapods are mutually paraphyletic. A crustacean clade of Malacostraca and Branchiopoda emerges as sister to the Insecta
sensu stricto
and the Collembola group with the maxillopod crustaceans. Some, but not all, analyses strongly support this mutual paraphyly but statistical tests do not reject the null hypotheses of a monophyletic Hexapoda or a monophyletic Crustacea. The dual monophyly of the Hexapoda and Crustacea has rarely been questioned in recent years but the idea of both groups' paraphyly dates back to the nineteenth century. We suggest that the mutual paraphyly of both groups should seriously be considered.
Absolute instability of the von Kármán, Bödewadt and Ekman flows between a rotating disc and a stationary lid
Authors: Jasmine Hosne Ara , Gajjar Jitesh S.B
Published: June 2005

The stability of a family of boundary-layer flows, which includes the von Kármán, Bödewadt and Ekman flows for a rotating incompressible fluid between a rotating disc and a stationary lid, is investigated. Numerical computations with the use of a spectral method are carried out to analyse absolute and convective instability. It is shown that the stability of the system is enhanced with a decrease in distance between the disc and the lid.
Receptivity of boundary layers to distributed wall vibrations
Authors: Kerimbekov Ruslan M , Ruban Anatoly I
Published: June 2005

Linear three-dimensional receptivity of boundary layers to distributed wall vibrations in the large Reynolds number limit (
Re
→∞) is studied in this paper. The fluid motion is analysed by means of the multiscale asymptotic technique combined with the method of matched asymptotic expansions. The body surface is assumed to be perturbed by small-amplitude oscillations being tuned in resonance with the neutral Tollmien–Schlichting wave at a certain point on the wall. The characteristic length of the resonance region is found to be O(
Re
−3/16
), which follows from the condition that the boundary-layer non-parallelism and the wave amplitude growth have the same order of magnitude. The amplitude equation is derived as a solvability condition for the inhomogeneous boundary-value problem. Investigating detuning effects, we consider perturbations in the form of a wave packet with a narrow O(
Re
−3/16
) discrete or continuous spectrum concentrated near the resonant wavenumber and frequency. The boundary-layer laminarization based on neutralizing the oncoming Tollmien–Schlichting waves (or wave packets) is also discussed.
Dichotomous splicing signals in exon flanks
Authors: Zhang Xiang H-F. , Leslie Christina S. , Chasin Lawrence A.
Published: June 2005

Intronic elements flanking the splice-site consensus sequences are thought to play a role in pre-mRNA splicing. However, the generality of this role, the catalog of effective sequences, and the mechanisms involved are still lacking. Using molecular genetic tests, we first showed that the ∼50-nt intronic flanking sequences of exons beyond the splice-site consensus are generally important for splicing. We then went on to characterize exon flank sequences on a genomic scale. The G+C content of flanks displayed a bimodal distribution reflecting an exaggeration of this base composition in flanks relative to the gene as a whole. We divided all exons into two classes according to their flank G+C content and used computational and statistical methods to define pentamers of high relative abundance and phylogenetic conservation in exon flanks. Upstream pentamers were often common to the two classes, whereas downstream pentamers were totally different. Upstream and downstream pentamers were often identical around low G+C exons, and in contrast, were often complementary around high G+C exons. In agreement with this complementarity, predicted base pairing was more frequent between the flanks of high G+C exons. Pseudo exons did not exhibit this behavior, but rather tended to form base pairs between flanks and exon bodies. We conclude that most exons require signals in their immediate flanks for efficient splicing. G+C content is a sequence feature correlated with many genetic and genomic attributes. We speculate that there may be different mechanisms for splice site recognition depending on G+C content.
Discovering functional transcription-factor combinations in the human cell cycle
Authors: Zhu Zhou , Shendure Jay , Church George M.
Published: June 2005

With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G2-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.
Analysis of 5′ junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5′-end attachment requiring microhomology-mediated end-joining
Authors: Zingler Nora , Willhoeft Ute , Brose Hans-Peter , Schoder Volker , Jahns Thomas , Hanschmann Kay-Martin O. , Morrish Tammy A. , Löwer Johannes , Schumann Gerald G.
Published: June 2005

Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3′-end of an L1 copy to the genomic target, but the subsequent integration steps leading to the attachment of the 5′-end to the chromosomal DNA are still cause for speculation. By applying bioinformatics to analyze the 5′ junctions of recent L1 insertions in the human genome, we provide evidence that L1 uses at least two distinct mechanisms to link the 5′-end of the nascent L1 copy to its genomic target. While 5′-truncated L1 elements show a statistically significant preference for short patches of overlapping nucleotides between their target site and the point of truncation, full-length insertions display no distinct bias for such microhomologies at their 5′-ends. In a second genome-wide approach, we analyzed Alu elements to examine whether these nonautonomous retrotransposons, which are thought to be mobilized through L1 proteins, show similar characteristics. We found that Alu elements appear to be predominantly integrated via a pathway not involving overlapping nucleotides. The results indicate that a cellular nonhomologous DNA end-joining pathway may resolve intermediates from incomplete L1 retrotransposition events and thus lead to 5′ truncations.
Ablation of cerebellar nuclei prevents H-reflex down-conditioning in rats
Authors: Chen Xiang Yang , Wolpaw Jonathan R.
Published: June 2005

While studies of cerebellar involvement in learning and memory have
described plasticity within the cerebellum, its role in acquisition of
plasticity elsewhere in the CNS is largely unexplored. This study set out to
determine whether the cerebellum is needed for acquisition of the spinal cord
plasticity that underlies operantly conditioned decrease in the H-reflex, the
electrical analog of the spinal stretch reflex. Rats in which the cerebellar
output nuclei dentate and interpositus (DIN) had been ablated were exposed for
50 d to the H-reflex down-conditioning protocol. DIN ablation, which in itself
had no significant long-term effect on H-reflex size, entirely prevented
acquisition of a smaller H-reflex. Since previous studies show that
corticospinal tract (CST) transection also prevents down-conditioning while
transection of the rubrospinal tract and other major descending tracts does
not, this result implies that DIN output that affects cortex is essential for
generation of the CST activity that induces the spinal cord plasticity, which
is, in turn, directly responsible for the smaller H-reflex. The result extends
the role of the cerebellum in learning and memory to include participation in
induction of plasticity elsewhere in the CNS, specifically in the spinal cord.
The cerebellum might simply support processes in sensorimotor cortex or
elsewhere that change the spinal cord, or the cerebellum itself might undergo
plasticity similar to that occurring with vestibulo-ocular reflex (VOR) or
eyeblink conditioning.
Electrolytic lesions of the dorsal hippocampus disrupt renewal of conditional fear after extinction
Authors: Ji Jinzhao , Maren Stephen
Published: June 2005

There is a growing body of evidence that the hippocampus is critical for
context-dependent memory retrieval. In the present study, we used Pavlovian
fear conditioning in rats to examine the role of the dorsal hippocampus (DH)
in the context-specific expression of fear memory after extinction (i.e.,
renewal). Pre-training electrolytic lesions of the DH blunted the expression
of conditional freezing to an auditory conditional stimulus (CS), but did not
affect the acquisition of extinction to that CS. In contrast, DH lesions
impaired the context-specific expression of extinction, eliminating the
renewal of fear normally observed to a CS presented outside of the extinction
context. Post-extinction DH lesions also eliminated the context dependence of
fear extinction. These results are consistent with those using pharmacological
inactivation of the DH and suggest that the DH is required for using
contextual stimuli to regulate the expression of fear to a Pavlovian CS after
extinction.
A role for Synapsin in associative learning: The Drosophila
larva as a study case
Authors: Michels Birgit , Diegelmann Sören , Tanimoto Hiromu , Schwenkert Isabell , Buchner Erich , Gerber Bertram
Published: June 2005

Synapsins are evolutionarily conserved, highly abundant vesicular
phosphoproteins in presynaptic terminals. They are thought to regulate the
recruitment of synaptic vesicles from the reserve pool to the
readily-releasable pool, in particular when vesicle release is to be
maintained at high spiking rates. As regulation of transmitter release is a
prerequisite for synaptic plasticity, we use the fruit fly Drosophila
to ask whether Synapsin has a role in behavioral plasticity as well; in fruit
flies, Synapsin is encoded by a single gene (syn). We tackled this
question for associative olfactory learning in larval Drosophila by
using the deletion mutant syn97CS, which had been
backcrossed to the Canton-S wild-type strain (CS) for 13 generations. We
provide a molecular account of the genomic status of
syn97CS by PCR and show the absence of gene product on
Western blots and nerve-muscle preparations. We found that olfactory
associative learning in syn97CS larvae is reduced to
∼50% of wild-type CS levels; however, responsiveness to the
to-be-associated stimuli and motor performance in untrained animals are
normal. In addition, we introduce two novel behavioral control procedures to
test stimulus responsiveness and motor performance after “sham
training.” Wild-type CS and syn97CS perform
indistinguishably also in these tests. Thus, larval Drosophila can be
used as a case study for a role of Synapsin in associative learning.
Modulation of memory consolidation by the basolateral amygdala or nucleus accumbens shell requires concurrent dopamine receptor activation in both brain regions
Authors: LaLumiere Ryan T. , Nawar Erene M. , McGaugh James L.
Published: June 2005

Previous findings indicate that the basolateral amygdala (BLA) and the nucleus accumbens (NAc) interact in influencing memory consolidation. The current study investigated whether this interaction requires concurrent dopamine (DA) receptor activation in both brain regions. Unilateral, right-side cannulae were implanted into the BLA and the ipsilateral NAc shell or core in male Sprague-Dawley rats (∼300 g). One week later, the rats were trained on an inhibitory avoidance (IA) task and, 48 h later, they were tested for retention. Drugs were infused into the BLA and NAc shell or core immediately after training. Post-training intra-BLA infusions of DA enhanced retention, as assessed by latencies to enter the shock compartment on the retention test. Infusions of the general DA receptor antagonistcis-Flupenthixol (Flu) into the NAc shell (but not the core) blocked the memory enhancement induced by the BLA infusions of DA. In the reverse experiment, post-training intra-NAc shell infusions of DA enhanced retention and Flu infusions into the BLA blocked the enhancement. These findings indicate that BLA modulation of memory consolidation requires concurrent DA receptor activation in the NAc shell but not the core. Similarly, NAc shell modulation of memory consolidation requires concurrent DA receptor activation in the BLA. Together with previous findings, these results suggest that the dopaminergic innervation of the BLA and NAc shell is critically involved in the modulation of memory consolidation.
Crystallization and crystal manipulation of the Pterocarpus angolensis seed lectin
Authors: Loris Remy , Garcia-Pino Abel , Buts Lieven , Bouckaert Julie , Beeckmans Sonia , De Greve Henri , Wyns Lode
Published: June 2005

The Man/Glc-specific legume lectin from the seeds of the African bloodwood tree (Pterocarpus angolensis) was crystallized in the presence of the disaccharide ligand Man(α1-3)ManMe. Small crystals initially appeared from a preliminary screen, but proved difficult to reproduce. The initial crystals were used to prepare microseeds, leading to a reproducible crystallization protocol. All attempts to obtain crystals directly of the ligand-free protein or of other carbohydrate complexes failed. However, the Man(α1-3)ManMe co-crystals withstand soaking with ten other carbohydrates known to bind to the lectin. Soaking for 15 min in 100 mM carbohydrate typically resulted in complete replacement of Man(α1-3)ManMe by the desired carbohydrate despite the involvement of lattice contacts at the binding site. Transferring the crystals for two weeks in carbohydrate-free artificial mother liquor resulted in the complete removal of the sugar from one of the two monomers in the asymmetric unit. Additional treatment of these crystals with 100 mM EDTA for two weeks resulted in removal of the structural calcium and manganese ions, which is accompanied by significant structural rearrangements of the loops that constitute the carbohydrate-binding site.
Optimizing protein crystal growth through dynamic seeding
Authors: Zhu De-Yu , Zhu Yong-Qun , Xiang Ye , Wang Da-Cheng
Published: June 2005

A dynamic seeding method that is different from the conventional method of seeding drops that have been equilibrated is described. The method basically consists of two steps. Firstly, microseeding was used in association with adjustment of the seeding-drop components, including buffer, additive and concentrations of the precipitants and protein, in order to screen suitable seeding conditions under which microseeds are seeded into a new non-equilibrated drop as the dynamic macroseed drop for the following step. Secondly, after being equilibrated for various times against the reservoir solution, the macroseed drops were used to prepare a dilution series with which the qualified crystals could be harvested using macroseeding. Compared with a conventional seeding technique, this method is distinct with a dynamic situation of macroseed drops before macroseeding and a non-equilibrium serial seeding where all the seeds are seeded into new non-equilibrated drops and the micro/macroseeding are efficiently combined into a whole system. The method simplifies control of the number of microseeds because an excess of microseeds has little effect on the final result. The method also simplifies the manipulation of macroseeds by optimizing the equilibration time and the dilution multiple of the macroseed drops before macroseeding. This dynamic seeding technique has been used in the crystallization of novel protein CutCm, which has a fast crystal-growth rate, and proved that the method is useful for optimizing protein crystallization.
Extracting trends from two decades of microgravity macromolecular crystallization history
Authors: Judge Russell A. , Snell Edward H. , van der Woerd Mark J.
Published: June 2005

Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.
The role of protein and surfactant interactions in membrane-protein crystallization
Authors: Berger Bryan W. , Gendron Colleen M. , Robinson Clifford R. , Kaler Eric W. , Lenhoff Abraham M.
Published: June 2005

The interactions leading to crystallization of the integral membrane protein bacteriorhodopsin solubilized in n-octyl-β-D-glucoside were investigated. Osmotic second virial coefficients were measured by self-interaction chromatography in the presence of sodium malonate, sodium formate and ammonium sulfate. Attractive protein–detergent complex (PDC) interactions were observed as the surfactant cloud-point temperature was approached for each salt, suggesting that surfactant interactions may play an important role in promoting PDC crystallization. Dynamic light scattering and tensiometry measurements show that the interaction trends are strongly influenced by micelle structure and surfactant phase behavior, both of which are sensitive to salt and surfactant concentration. Overall, detailed investigations using a combination of experimental techniques can provide insight into the complex nature of PDC interactions, which is essential to developing rational approaches to membrane-protein crystallization.
Crystallization and preliminary X-ray analysis of strictosidine synthase and its complex with the substrate tryptamine
Authors: Koepke Juergen , Ma Xueyan , Fritzsch Günter , Michel Hartmut , Stöckigt Joachim
Published: June 2005

Strictosidine synthase (STR1) is a central enzyme that participates in the biosynthesis of almost all plant monoterpenoid indole alkaloids. After heterologous expression in Escherichia coli, crystals of STR1 and its substrate complex with tryptamine were obtained by the hanging-drop technique at 302–304 K with potassium sodium tartrate tetrahydrate as precipitant. All crystals belong to space group R3. The native STR1 crystals diffract to 2.95 Å and have unit-cell parameters a = b = 150.3, c = 122.4 Å. The tryptamine complex crystals diffract to 2.38 Å, with unit-cell parameters a = b = 147.3, c = 122.3 Å.
Quantitative imaging by confocal scanning fluorescence microscopy of protein crystallization via liquid–liquid phase separation
Authors: Vivarès Denis , Kaler Eric W. , Lenhoff Abraham M.
Published: June 2005

Metastable states such as liquid–liquid phase separation, aggregation and gelation can affect protein crystallization but their positive or negative effects are only partially understood. In this work, mixtures of PEG (MW 10 kDa) and a large model protein, glucose isomerase (MW 173 kDa), have been studied to characterize the effect of a metastable liquid–liquid phase separation on protein crystallization. Fluorescence labeling allowed confocal fluorescence microscopy observations and quantification of the partitioning of the protein and PEG between the liquid phases and showed two steps in the crystallization process. Two crystallization mechanisms within the liquid domain were revealed, yielding two different polymorphs. With one polymorph, few crystals nucleated and grew droplet-by-droplet in the dispersed concentrated liquid phase, while for the other homogeneous crystal nucleation and growth occurred independently and simultaneously in numerous droplets of the concentrated phase. The results demonstrate the substantial possible complexity of crystallization behavior, as well as its sensitivity to the location of the conditions on the phase diagram and to the physicochemical properties of the system.
Crystallization of an anti-factor IX antibody and its complex
Authors: Shi Xiaoli , Li Yongdong , Bian Chuanbing , Zhao Gengxiang , Huang Mingdong
Published: June 2005

Initiation, propagation and regulatory processes of blood coagulation occur at the cell surface. During blood coagulation, many coagulation factors are anchored onto cell-surface membranes through their N-terminal carboxyglutamic acid-rich (Gla) domains found on such vitamin K-dependent blood coagulation factors as factors VII, IX, X, prothrombin, factors C and S. 10C12 is a conformation-specific calcium-dependent anti-factor IX antibody, which is directed at the calcium-stabilized Gla domain and interferes with factor IX–membrane interaction. In a variety of animal models, 10C12 has been demonstrated to be effective anticoagulant in attenuating thrombosis without severe bleeding. The crystallization of the Fab fragment of 10C12 and its complex with the Gla domain of human factor IX was not trivial. Here, the crystallization conditions and unusual aspects of this crystallization process are reported.
High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?
Authors: Leulliot Nicolas , Trésaugues Lionel , Bremang Michael , Sorel Isabelle , Ulryck Nathalie , Graille Marc , Aboulfath Ilham , Poupon Anne , Liger Dominique , Quevillon-Cheruel Sophie , Janin Joël , van Tilbeurgh Herman
Published: June 2005

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.
The mechanism of high-pressure-induced ordering in a macromolecular crystal
Authors: Lin Tianwei , Schildkamp Wilfried , Brister Keith , Doerschuk Peter C. , Somayazulu Maddury , Mao Ho-kwang , Johnson John E.
Published: June 2005

A previous study showed that the diffraction from cubic crystals of an icosahedral virus, cowpea mosaic virus (CPMV), was dramatically improved under elevated hydrostatic pressure. This use of pressure may have a significant impact on structural biology if it is found to be generally applicable. There were two types of cubic crystals assigned in either an I23 or P23 space group. They show the same rhombic dodecahedral morphology at atmospheric pressure. The crystals assigned to the I23 space group diffracted X-rays to higher resolution than those with P23 space group. The assignment of P23 space group was owing to the presence of reflections with indices of h + k + l = (2n + 1) (odd reflections), which are forbidden in space group I23. Analysis of the odd reflections from the P23 crystals at atmospheric pressure showed that they can originate from a rotational disorder in the I23 crystals. The odd reflections were eliminated with the application of 3.5 kbar of pressure, which transformed the crystals from the apparently primitive cell to the body-centered I23 space group with dramatic improvement in diffraction. A mechanistic model is proposed to describe the induction of order by rectifying the imperfection, which is consistent with the experimental data.
Investigation of the protein pre-crystallization solution using analytical ultracentrifugation
Authors: Yoshizaki Izumi , Sakai Miyo , Matsuura Yoshiki
Published: June 2005

Analytical ultracentrifugation was used to study the crystal growth units in hen egg-white lysozyme pre-crystallization solution. Solutions containing various concentrations of lysozyme and NaCl in 50 mM sodium acetate buffer were used for experiments. The crystallization solution was ultracentrifuged using a mode where the sedimentation and diffusion are in equilibrium. The protein concentration gradient in the centrifugation cell was measured by light absorption and the molecular weight was calculated from the concentration gradient data. The results were analyzed assuming that the molecules have no interaction with each other. In all solutions except for 0.4 M NaCl, 30 mg ml−1 lysozyme solution, it was shown that the molecular weight falls in the range 12 000–16 500 Da. In 0.4 M NaCl, 30 mg ml−1 lysozyme solution no analysis was made because crystals appeared at the bottom of the cell after centrifugation. Since the calculated molecular weight of lysozyme monomer is 14 400 Da, it was concluded that the lysozyme molecule predominantly exists as a monomer in undersaturated and supersaturated solutions.
Investigating crystal-growth mechanisms with and without LB template: protein transfer from LB to crystal
Authors: Pechkova Eugenia , Fiordoro Stefano , Fontani David , Nicolini Claudio
Published: June 2005

Protein nanocrystallography has recently been introduced as a unique nanotechnology-based approach to forming stable protein crystals and to characterize them down to atomic resolution. In particular, a protein nanostuctured template appears to be capable of stimulating nucleation and crystal growth of so far unsolved proteins. In the present communication, aimed at investigating the lysozyme crystal-growth mechanisms with and without nanotemplate, the lysozymes appear to transfer directly from the nanostructured film into the drop to trigger the formation of the crystal, therefore highlighting the physical interpretation of the mechanism for nanotemplate-induced protein crystallization.
Different crystal packing in Fab–protein L semi-disordered peptide complex
Authors: Ménez Renée , Housden Nicholas G. , Harrison Stephen , Jolivet-Reynaud Colette , Gore Michael G. , Stura Enrico Adriano
Published: June 2005

Proteins and peptides with variable degrees of disorder are a challenge for protein crystallization. These may be completely disordered or just contain regions with a high degree of mobility that may be represented by a multitude of discretely defined conformations. These difficulties are not insurmountable, but it may be unreasonable to expect a clean result from a structural point of view. The complex between a murine monoclonal antibody (19D9D6) and a synthetic peptide that encompasses the first 45 residues of the core protein of Hepatitis C virus that is poorly structured in solution has been crystallized. In order to make the crystallization possible, use was made of a single immunoglobulin-binding domain of protein L from Peptostreptococcus magnus (PpL), a bacterial protein that can bind the variable region (Fv) of a large population of antibodies through its light chain with no interference with antibody–antigen recognition. Crystals were obtained in different space groups where the size of the cavity that accommodates the peptide is different, although many of the crystal contacts and the overall lattice are preserved. The peptide can be considered to be semi-disordered and the larger cavity accommodates a better ordered peptide than the smaller one. The lattice is of interest for the design of a scaffold system for the crystallization of peptide-tagged proteins since a cavity that accommodates a disordered entity might be able to host ordered proteins of the same size and shape as the cavity. Here, the differences between the lattices formed by this trimolecular complex are described and it is discussed how such a system may be adapted to the crystallization of peptide-tagged proteins.
Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl
Authors: Kamo Masayuki , Inouye Kuniyo , Nagata Koji , Tanokura Masaru
Published: June 2005

The activity of thermolysin (EC 3.4.24.27) is greatly enhanced by high concentrations of neutral salts. For instance, 4 M NaCl enhances the activity 13–15-fold [Holmquist & Vallée (1976), Biochemistry, 15, 101–107; Inouye (1992), J. Biochem. (Tokyo), 112, 335–340]. To clarify the structural basis of the activation of thermolysin by high concentrations of NaCl, we have developed a new method to introduce 4 M NaCl into the P6122 crystal of thermolysin originally grown without NaCl. The crystal obtained by this method diffracted X-rays to 2.43 Å. No unit-cell parameter change was observed except the length of the c axis, which was elongated by 9.6% by the introduction of 4 M NaCl.
A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization
Authors: Walter Thomas S. , Diprose Jonathan M. , Mayo Chris J. , Siebold Christian , Pickford Mike G. , Carter Lester , Sutton Geoff C. , Berrow Nick S. , Brown James , Berry Ian M. , Stewart-Jones Guillaume B. E. , Grimes Jonathan M. , Stammers David K. , Esnouf Robert M. , Jones E. Yvonne , Owens Ray J. , Stuart David I. , Harlos Karl
Published: June 2005

Crystallization trials at the Division of Structural Biology in Oxford are now almost exclusively carried out using a high-throughput workflow implemented in the Oxford Protein Production Facility. Initial crystallization screening is based on nanolitre-scale sitting-drop vapour-diffusion experiments (typically 100 nl of protein plus 100 nl of reservoir solution per droplet) which use standard crystallization screening kits and 96-well crystallization plates. For 294 K crystallization trials the barcoded crystallization plates are entered into an automated storage system with a fully integrated imaging system. These plates are imaged in accordance with a pre-programmed schedule and the resulting digital data for each droplet are harvested into a laboratory information-management system (LIMS), scored by crystal recognition software and displayed for user analysis via a web-based interface. Currently, storage for trials at 277 K is not automated and for imaging the crystallization plates are fed by hand into an imaging system from which the data enter the LIMS. The workflow includes two procedures for nanolitre-scale optimization of crystallization conditions: (i) a protocol for variation of pH, reservoir dilution and protein:reservoir ratio and (ii) an additive screen. Experience based on 592 crystallization projects is reported.
Development of a fully automated macromolecular crystallization/observation robotic system, HTS-80
Authors: Miyatake Hideyuki , Kim Seong-Hoon , Motegi Itsuro , Matsuzaki Hirofumi , Kitahara Hideyoshi , Higuchi Akira , Miki Kunio
Published: June 2005

A robotic system has been developed to be used for macromolecular crystallization and observation in typical university laboratories with a research focus on protein crystallography. The system consists of three major parts: a dispenser unit, a storage unit and an observation unit. This system is designed to automatically perform all of the processes involved in crystallization and observation without requiring any manual operations. The dispenser and observation units can carry out both sitting-drop vapor-diffusion procedures and microbatch procedures. With this system, the procedures are controlled by a personal computer running GUI-based software. After the dispensing of protein solution into the crystallization plates, they are automatically transferred to the storage units, followed by automatic observation according to a required schedule with arbitrary intervals. At each stage of crystallization, droplets in the crystallization plates are examined by original image-processing software in order to evaluate the appearance of the crystals.
van der Waals phase transition in protein solutions
Authors: Wills Peter R. , Winzor Donald J.
Published: June 2005

The van der Waals equation of state for imperfect gases is applied to solutions of macromolecules, especially to explain the fluid–fluid phase transition in protein solutions, a phenomenon of much interest in relation to protein crystallization. The van der Waals b parameter corresponds to the total excluded volume per pair of molecules and can be calculated from independently known molecular properties. It is comprised of terms resulting from hard-sphere and net charge–charge interactions. The experimentally determined second virial coefficient B
2 can then be used to obtain the equilibrium constant for dimerization K
2, a phenomenologically accessible measure of the van der Waals a parameter. Sedimentation equilibrium is recommended as the technique for measuring B
2 most accurately. More general results are used to make a minor quantitative correction to the van der Waals prediction concerning the criterion for the fluid–fluid phase transition. Calculations of the effect of inert co-solutes on the phase transition may prove useful in choosing crystallization conditions.
Surface morphology and kinetic properties in rapid growth of EAFP protein crystals investigated by atomic force microscopy
Authors: Wang Sheng , Li Genpei , Xiang Ye , Huang Ren-Huai , Zhang Ying , Wang Da-Cheng
Published: June 2005

The whole process of EAFP protein monoclinic crystal growth with an extremely fast rate has been observed by atomic force microscopy. The results showed that the patterns of the growth images in rapidly growing crystals are complicated. The two-dimensional multi-layered stacks of growth steps are characteristic of higher supersaturation and the growth of steps proceeds in a manner of strong anisotropic spiral dislocations dominantly under lower supersaturation conditions. The complex dislocation sources, including multiple dislocation and multi-interacting single dislocation sources, the constant step-split and the propagation of trooped steps were observed on the {100} surfaces of growing EAFP crystals. The step height of each layer generated either by two-dimensional nucleation at higher supersaturation or by screw dislocation at lower supersaturation is about 2–3 nm, which corresponds to the length of the crystallographic unit cell. Although the rate of advancement for each growth step is similar to that of other protein crystal growth, the unique way of the propagation distinct with the trooped steps, by which a bundle of steps are strapped together, would be responsible for the rapid growth of EAFP crystals. All features show a possible mechanism by which the fast growth of EAFP crystals could be attained. The structural basis of the growth mechanism is also discussed.
Crystallization of soluble urokinase receptor (suPAR) in complex with urokinase amino-terminal fragment (1–143)
Authors: Huang Mingdong , Mazar Andrew P. , Parry Graham , Higazi Abd Al-Roof , Kuo Alice , Cines Douglas B.
Published: June 2005

Urokinase-type plasminogen activator (urokinase, uPA) and its receptor, uPAR, have been implicated in cell adhesion, migration, tissue remodelling and tumour-cell invasion. uPAR has three domains and is anchored to membranes by a glycosyl-phosphatidylinositol (GPI) anchor. Recombinant uPAR without its GPI anchor, soluble uPAR (suPAR), tends to oligomerize, making it difficult to crystallize. The amino-terminal fragment (ATF) of uPA is the major receptor-binding determinant in suPAR and binds to suPAR with nanomolar affinity, indistinguishable from membrane-bound uPAR. It is shown that uPA is capable of dissociating the oligomerization of suPAR and the crystallization of the suPAR–ATF complex is reported here. The resulting crystals diffract to 3.1 Å using a synchrotron X-ray source.
Closed‐form solution of monocular vision‐based relative pose determination for RVD spacecrafts
Authors: Zhang Shijie , Cao Xibin
Published: June 2005

Purpose

To give a closed‐form solution of the relative pose determination problem based on monocular vision during final approach phase of spacecraft Rendzvous and Docking.

Design/methodology/approach

Based on the assumption of scaled orthographic projection, the model of perspective projection is simplified by representing the relative attitude using unit quaternion. Then a closed‐form solution is derived. Subsequently, this study correct the approximate solution to compensate the error caused by the assumption of scaled orthographic projection.

Findings

Extensive simulation studies were conducted for the validation of the proposed algorithm using Matlab™. When there are no relative attitudes between RVD spacecrafts, target distance for camera=2‐20 m. The simulation results show that the largest relative error of corrected relative position parameters is about 0.12 percent. When distance between RVD spacecrafts exceeds 5 m, the largest error of corrected relative attitude parameters are less than 0.3°. When the distance between spacecrafts are constant, the relative attitude parameters are changed, respectively, the simulition results show the largest relative error of relative position is 1 percent, and largest error of estimated relative attitude is 1.2°, when a relative attitude angle reaches 20°.

Originality/value

The proposed algorithm avoids the multiple results problem in determining the relative position and attitude parameters and the closed‐form solution is simple and effective, is more suitable for on‐board implementation.
Control of longitudinal movement of a plane using combined model reference adaptive control
Authors: Duarte‐Mermoud Manuel A. , Rioseco Jaime S. , González Rodrigo I.
Published: June 2005

Purpose

To apply and simulate under different conditions, the combined model reference adaptive control (CMRAC) technique to control the pitch angle in a subsonic plane. Comparisons with the classical PID controller and the adaptive direct MRAC are also performed.

Design/methodology/approach

The methodology used in this work is the CMRAC. This is a relatively new adaptive control technique which combines the information coming from the identification procedure as well as that from the direct control scheme, and use it in the adaptive laws. The identification parameters and the controller parameters are simultaneously adjusted using the identification error, the control error and the so‐called close‐loop identification error. This combination has shown to improve the transient behavior of the adaptive systems.

Findings

This control scheme has been tested by simulation on a model of a CESSNA 182 plane, to control the pitch angle (longitudinal movement). The results have been compared with other control approaches such as the classical PID and the adaptive direct MRAC. Although the PID control satisfies all the control specifications as much as the CMRAC, it is not able to adapt when changes in the operating conditions occur, as in the case of the CMRAC. The direct MRAC does no perform well in this study.

Research limitations/implications

The implementation at practical level remains to be studied and analyzed, to verify the theoretical and simulation results presented here.

Practical implications

The main advantage of the proposed method is that it behaves well even under different operating conditions, which is one of the most important characteristics for an implementation at practical level.

Originality/value

It is the first time in the control literature that the CMRAC is applied to control the pitch angle of a plane in a longitudinal movement. The results are quite promising remaining the practical implementation to verify the performance of the proposed scheme under real conditions.
Hybrid design methods of cascade profile based on variational principles
Authors: Zheng Yao , Gao‐Lian Liu , Xiao‐Jiang Wu
Published: June 2005

Purpose

Provides two hybrid methods for the aerodynamic design of cascade profiles, of which the design constraints are the combination of aerodynamic and geometric conditions.

Design/methodology/approach

In the first method, the design constrain is composed of the velocity (or pressure) distribution on part of the blade surface and the geometry of the rest part. In the second method, the aerodynamic load distribution, i.e. the pressure difference between the suction and pressure surfaces, and the blade thickness distribution are employed as the design constrain. These constraints, together with all the other boundary conditions, are involved in the stationary conditions of a variational principle. The solution domain, i.e. the blade‐to‐blade passage, is transformed into a square in the image plane, while the blade contour is projected to a straight line; thus, the difficulty caused by the unknown geometry of profile is avoided. Finite element method is employed to produce the calculation code.

Findings

Applications show the accuracy and the flexibility of the two methods, which can satisfy the different needs from blade design. Finally, the possibility of combining the hybrid methods with the through‐flow method is discussed, which would develop the present methods to three‐dimensional design of cascades.

Research limitations/implications

The design methods are limited to frictionless flow.

Practical implications

A design software of cascade profiles based on this method has been developed, and will be provided to the engineering users for cascade design.

Originality/value

The hybrid methods developed in this paper can satisfy the demands from different aspects of engineering designs: aerodynamics, strength, manufacture, etc.
Library participation in campus web portals: an initial survey
Authors: Stoffel Bruce , Cunningham Jim
Published: June 2005

Purpose

To determine the extent and nature of library involvement in campus portal development.

Design/methodology/approach

Campus technology staff from US colleges and universities participating in the JA‐SIG uPortal open‐source software project were surveyed.

Findings

All respondents indicated having an active campus portal. A majority of respondents had at least one library feature on their campus portal. Some library features included automated display of information specific to the portal user such as library account information. Collaboration between campus and library staff was a common theme among institutions successfully deploying library features.

Research limitations/implications

Findings are based on a small sample of campuses currently deploying portals. Recommended follow‐up studies include surveys of institutions using proprietary portal software and surveys of library staff and end‐users.

Originality/value

While considerable research has been done on library portals, this paper is unique in its exploration of library participation in broader campus portal initiatives. Portal features discussed and illustrated in this paper might serve as models for libraries interested in developing a presence on their campus portal.
Visibility as a factor in library selection of ready reference web resources
Authors: Sowards Steven W.
Published: June 2005

Purpose

To determine the most popular entries on library ready reference web sites and the role of visibility in the selection of resources.

Design/methodology/approach

Ready reference web sites of 100 American libraries were examined, for a census of the most frequently selected online resources. The dates of news, library and online media coverage were considered for specific tools, to explain their prominence.

Findings

Early publicity for web tools was found to be an important element in their relative popularity as choices for library web sites.

Research limitations/implications

The date on which a given web resource became well known among librarians can only be estimated from media reports, not proved. Additional study could establish the frequency with which libraries modify their ready reference web sites and investigate why other resources of comparable quality have not become as popular.

Originality/value

The paper shows that early visibility plays a role in librarians' selection of web resources that is rarely mentioned in discussions of selection criteria.