bluuebunny/crossref_metadata_2025 huggingface dataset:
Spindle-independent condensation-mediated segregation of yeast ribosomal DNA in late anaphase
Authors: Machín Félix , Torres-Rosell Jordi , Jarmuz Adam , Aragón Luis
Published: January 2005

Mitotic cell division involves the equal segregation of all chromosomes during anaphase. The presence of ribosomal DNA (rDNA) repeats on the right arm of chromosome XII makes it the longest in the budding yeast genome. Previously, we identified a stage during yeast anaphase when rDNA is stretched across the mother and daughter cells. Here, we show that resolution of sister rDNAs is achieved by unzipping of the locus from its centromere-proximal to centromere-distal regions. We then demonstrate that during this stretched stage sister rDNA arrays are neither compacted nor segregated despite being largely resolved from each other. Surprisingly, we find that rDNA segregation after this period no longer requires spindles but instead involves Cdc14-dependent rDNA axial compaction. These results demonstrate that chromosome resolution is not simply a consequence of compacting chromosome arms and that overall rDNA compaction is necessary to mediate the segregation of the long arm of chromosome XII.
Effects of Arp2 and Arp3 nucleotide-binding pocket mutations on Arp2/3 complex function
Authors: Martin Adam C. , Xu Xiao-Ping , Rouiller Isabelle , Kaksonen Marko , Sun Yidi , Belmont Lisa , Volkmann Niels , Hanein Dorit , Welch Matthew , Drubin David G.
Published: January 2005

Contributions of actin-related proteins (Arp) 2 and 3 nucleotide state to Arp2/3 complex function were tested using nucleotide-binding pocket (NBP) mutants in Saccharomyces cerevisiae. ATP binding by Arp2 and Arp3 was required for full Arp2/3 complex nucleation activity in vitro. Analysis of actin dynamics and endocytosis in mutants demonstrated that nucleotide-bound Arp3 is particularly important for Arp2/3 complex function in vivo. Severity of endocytic defects did not correlate with effects on in vitro nucleation activity, suggesting that a critical Arp2/3 complex function during endocytosis may be structural rather than catalytic. A separate class of Arp2 and Arp3 NBP mutants suppressed phenotypes of mutants defective for actin nucleation. An Arp2 suppressor mutant increased Arp2/3 nucleation activity. Electron microscopy of Arp2/3 complex containing this Arp2 suppressor identified a structural change that also occurs upon Arp2/3 activation by nucleation promoting factors. These data demonstrate the importance of Arp2 and Arp3 nucleotide binding for nucleating activity, and Arp3 nucleotide binding for maintenance of cortical actin cytoskeleton cytoarchitecture.
Actin-myosin–based contraction is responsible for apoptotic nuclear disintegration
Authors: Croft Daniel R. , Coleman Mathew L. , Li Shuixing , Robertson David , Sullivan Teresa , Stewart Colin L. , Olson Michael F.
Published: January 2005

Membrane blebbing during the apoptotic execution phase results from caspase-mediated cleavage and activation of ROCK I. Here, we show that ROCK activity, myosin light chain (MLC) phosphorylation, MLC ATPase activity, and an intact actin cytoskeleton, but not microtubular cytoskeleton, are required for disruption of nuclear integrity during apoptosis. Inhibition of ROCK or MLC ATPase activity, which protect apoptotic nuclear integrity, does not affect caspase-mediated degradation of nuclear proteins such as lamins A, B1, or C. The conditional activation of ROCK I was sufficient to tear apart nuclei in lamin A/C null fibroblasts, but not in wild-type fibroblasts. Thus, apoptotic nuclear disintegration requires actin-myosin contractile force and lamin proteolysis, making apoptosis analogous to, but distinct from, mitosis where nuclear disintegration results from microtubule-based forces and from lamin phosphorylation and depolymerization.
A multistep, GTP-driven mechanism controlling the dynamic cycling of nucleostemin
Authors: Tsai Robert Y.L. , McKay Ronald D.G.
Published: January 2005

Nucleostemin (NS) was identified as a stem cell– and cancer cell–enriched nucleolar protein that controls the proliferation of these cells. Here, we report the mechanism that regulates its dynamic shuttling between the nucleolus and nucleoplasm. The nucleolar residence of nucleostemin involves a transient and a long-term binding by the basic and GTP-binding domains, and a dissociation mechanism mediated by the COOH-terminal region. This cycle is propelled by the GTP binding state of nucleostemin. We propose that a rapid nucleostemin cycle is designed to translate extra- and intra-cellular signals into the amount of nucleostemin in the nucleolus in a bidirectional and fast manner.
Generation of nonidentical compartments in vesicular transport systems
Authors: Heinrich Reinhart , Rapoport Tom A.
Published: January 2005

How can organelles communicate by bidirectional vesicle transport and yet maintain different protein compositions? We show by mathematical modeling that a minimal system, in which the basic variables are cytosolic coats for vesicle budding and membrane-bound soluble N-ethyl-maleimide–sensitive factor attachment protein receptors (SNAREs) for vesicle fusion, is sufficient to generate stable, nonidentical compartments. A requirement for establishing and maintaining distinct compartments is that each coat preferentially packages certain SNAREs during vesicle budding. Vesicles fuse preferentially with the compartment that contains the highest concentration of cognate SNAREs, thus further increasing these SNAREs. The stable steady state is the result of a balance between this autocatalytic SNARE accumulation in a compartment and the distribution of SNAREs between compartments by vesicle budding. The resulting nonhomogeneous SNARE distribution generates coat-specific vesicle fluxes that determine the size of compartments. With nonidentical compartments established in this way, the localization and cellular transport of cargo proteins can be explained simply by their affinity for coats.
A role for myosin VI in postsynaptic structure and glutamate receptor endocytosis
Authors: Osterweil Emily , Wells David G. , Mooseker Mark S.
Published: January 2005

Myosin VI (Myo6) is an actin-based motor protein implicated in clathrin-mediated endocytosis in nonneuronal cells, though little is known about its function in the nervous system. Here, we find that Myo6 is highly expressed throughout the brain, localized to synapses, and enriched at the postsynaptic density. Myo6-deficient (Snell's waltzer; sv/sv) hippocampus exhibits a decrease in synapse number, abnormally short dendritic spines, and profound astrogliosis. Similarly, cultured sv/sv hippocampal neurons display decreased numbers of synapses and dendritic spines, and dominant-negative disruption of Myo6 in wild-type hippocampal neurons induces synapse loss. Importantly, we find that sv/sv hippocampal neurons display a significant deficit in the stimulation-induced internalization of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid–type glutamate receptors (AMPARs), and that Myo6 exists in a complex with the AMPAR, AP-2, and SAP97 in brain. These results suggest that Myo6 plays a role in the clathrin-mediated endocytosis of AMPARs, and that its loss leads to alterations in synaptic structure and astrogliosis.
Nuclear transport of single molecules
Authors: Kubitscheck Ulrich , Grünwald David , Hoekstra Andreas , Rohleder Daniel , Kues Thorsten , Siebrasse Jan Peter , Peters Reiner
Published: January 2005

The mechanism by which macromolecules are selectively translocated through the nuclear pore complex (NPC) is still essentially unresolved. Single molecule methods can provide unique information on topographic properties and kinetic processes of asynchronous supramolecular assemblies with excellent spatial and time resolution. Here, single-molecule far-field fluorescence microscopy was applied to the NPC of permeabilized cells. The nucleoporin Nup358 could be localized at a distance of 70 nm from POM121-GFP along the NPC axis. Binding sites of NTF2, the transport receptor of RanGDP, were observed in cytoplasmic filaments and central framework, but not nucleoplasmic filaments of the NPC. The dwell times of NTF2 and transportin 1 at their NPC binding sites were 5.8 ± 0.2 and 7.1 ± 0.2 ms, respectively. Notably, the dwell times of these receptors were reduced upon binding to a specific transport substrate, suggesting that translocation is accelerated for loaded receptor molecules. Together with the known transport rates, our data suggest that nucleocytoplasmic transport occurs via multiple parallel pathways within single NPCs.
Going in GTP cycles in the nucleolus
Authors: Misteli Tom
Published: January 2005

Proteins are directed to cellular compartments by specific localization signals. A GTP-driven cycle has now been identified as a mechanism for protein targeting to the nucleolus. The involvement of a GTP switch suggests that nucleolar localization can be regulated and may be responsive to extracellular stimuli via signaling pathways. The uncovered mechanism also implies that localization is determined by increased retention rather than directed targeting.
Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells
Authors: Pan-Hammarström Qiang , Jones Anne-Marie , Lähdesmäki Aleksi , Zhou Wei , Gatti Richard A. , Hammarström Lennart , Gennery Andrew R. , Ehrenstein Michael R.
Published: January 2005

Class switch recombination (CSR) is a region-specific, transcriptionally regulated, nonhomologous recombinational process that is initiated by activation-induced cytidine deaminase (AID). The initial lesions in the switch (S) regions are subsequently processed and resolved, leading to recombination of the two targeted S regions. The mechanisms by which repair and ligation of the broken DNA ends occurs is still elusive. Recently, a small number of patients lacking DNA ligase IV, a critical component of the nonhomologous end joining (NHEJ) machinery, have been identified. We show that these patients display a considerably increased donor/acceptor homology at Sμ–Sα junctions compared with healthy controls. In contrast, Sμ–Sγ junctions show an increased frequency of insertions but no increase in junctional homology. These altered patterns of junctional resolution may be related to differences in the homology between the Sμ and the downstream isotype S regions, and could reflect different modes of switch junction resolution when NHEJ is impaired. These findings link DNA ligase IV, and thus NHEJ, to CSR.
Prevention of UV radiation–induced immunosuppression by IL-12 is dependent on DNA repair
Authors: Schwarz Agatha , Maeda Akira , Kernebeck Kerstin , van Steeg Harry , Beissert Stefan , Schwarz Thomas
Published: January 2005

The immunostimulatory cytokine IL-12 is able to antagonize immunosuppression induced by solar/ultraviolet (UV) radiation via yet unknown mechanisms. IL-12 was recently found to induce deoxyribonucleic acid (DNA) repair. UV-induced DNA damage is an important molecular trigger for UV-mediated immunosuppression. Thus, we initiated studies into immune restoration by IL-12 to discern whether its effects are linked to DNA repair. IL-12 prevented both UV-induced suppression of the induction of contact hypersensitivity and the depletion of Langerhans cells, the primary APC of the skin, in wild-type but not in DNA repair-deficient mice. IL-12 did not prevent the development of UV-induced regulatory T cells in DNA repair-deficient mice. In contrast, IL-12 was able to break established UV-induced tolerance and inhibited the activity of regulatory T cells independent of DNA repair. These data identify a new mechanism by which IL-12 can restore immune responses and also demonstrate a link between DNA repair and the prevention of UV-induced immunosuppression by IL-12.
Cyclical modulation of sphingosine-1-phosphate receptor 1 surface expression during lymphocyte recirculation and relationship to lymphoid organ transit
Authors: Lo Charles G. , Xu Ying , Proia Richard L. , Cyster Jason G.
Published: January 2005

Sphingosine-1-phosphate receptor 1 (S1P1) was recently shown to be required for lymphocyte egress from lymphoid organs. Here we have examined the relationship between S1P1 abundance on the cell and egress efficiency. Using an integrin neutralization approach to separate the processes of entry and exit, we show that pertussis toxin treatment reduces lymphocyte egress from lymph nodes. Retrovirally mediated S1P1 overexpression is sufficient to reduce B cell accumulation in the splenic white pulp and to promote egress of activated T cells from lymph nodes, whereas S1P1+/−cells have reduced lymph node exit efficiency. Furthermore, lymphocyte S1P1 is down-regulated in the blood, up-regulated in lymphoid organs, and down-regulated again in the lymph. We propose that cyclical ligand-induced modulation of S1P1 on circulating lymphocytes contributes to establishing their lymphoid organ transit time.
Dynamic regulation of PU.1 expression in multipotent hematopoietic progenitors
Authors: Nutt Stephen L. , Metcalf Donald , D'Amico Angela , Polli Matthew , Wu Li
Published: January 2005

PU.1 is an Ets family transcription factor that is essential for fetal liver hematopoiesis. We have generated a PU.1gfp reporter strain that allowed us to examine the expression of PU.1 in all hematopoietic cell lineages and their early progenitors. Within the bone marrow progenitor compartment, PU.1 is highly expressed in the hematopoietic stem cell, the common lymphoid progenitor, and a proportion of common myeloid progenitors (CMPs). Based on Flt3 and PU.1 expression, the CMP could be divided into three subpopulations, Flt3+ PU.1hi, Flt3− PU.1hi, and Flt3− PU.1lo CMPs. Colony-forming assays and in vivo lineage reconstitution demonstrated that the Flt3+ PU.1hi and Flt3− PU.1hi CMPs were efficient precursors for granulocyte/macrophage progenitors (GMPs), whereas the Flt3− PU.1lo CMPs were highly enriched for committed megakaryocyte/erythrocyte progenitors (MEPs). CMPs have been shown to rapidly differentiate into GMPs and MEPs in vitro. Interestingly, short-term culture revealed that the Flt3+ PU.1hi and Flt3− PU.1hi CMPs rapidly became CD16/32high (reminiscent of GMPs) in culture, whereas the Flt3− PU.1lo CMPs were the immediate precursors of the MEP. Thus, down-regulation of PU.1 expression in the CMP is the first molecularly identified event associated with the restriction of differentiation to erythroid and megakaryocyte lineages.
NFATc2 and NFATc3 transcription factors play a crucial role in suppression of CD4+ T lymphocytes by CD4+ CD25+ regulatory T cells
Authors: Bopp Tobias , Palmetshofer Alois , Serfling Edgar , Heib Valeska , Schmitt Steffen , Richter Christoph , Klein Matthias , Schild Hansjörg , Schmitt Edgar , Stassen Michael
Published: January 2005

The phenotype of NFATc2−/− c3−/− (double knockout [DKO]) mice implies a disturbed regulation of T cell responses, evidenced by massive lymphadenopathy, splenomegaly, and autoaggressive phenomena. The population of CD4+ CD25+ T cells from DKO mice lacks regulatory capacity, except a small subpopulation that highly expresses glucocorticoid-induced tumor necrosis factor receptor family–related gene (GITR) and CD25. However, neither wild-type nor DKO CD4+ CD25+ regulatory T cells (T reg cells) are able to suppress proliferation of DKO CD4+ CD25− T helper cells. Therefore, combined NFATc2/c3 deficiency is compatible with the development of CD4+ CD25+ T reg cells but renders conventional CD4+ T cells unresponsive to suppression, underlining the importance of NFAT proteins for sustaining T cell homeostasis.
IL-12– and IL-23–induced T helper cell subsets
Authors: Bettelli Estelle , Kuchroo Vijay K.
Published: January 2005

Traditionally, CD4+ T cells have been separated into two different subsets named T helper (Th)1 and Th2. A new IL-23–driven subset of Th cells called ThIL-17 has now been described. The data suggest that IL-23 plays an important role in the differentiation of autoreactive pathogenic T cells. Whether these IL-23–induced ThIL-17 cells are a unique subset or are related to other Th subsets is discussed.
Broadening the horizons for yellow fever
Authors: Van Epps Heather L.
Published: January 2005

The vaccine against yellow fever is one of the safest and most effective ever developed. With an outstanding record in humans, has this live attenuated vaccine been overlooked as a promising vector for the development of vaccines against pathogens outside its own genus? Recent studies, including a report by Tao et al. on page 201 of this issue, have sparked renewed interest.
Poset fiber theorems
Authors: Björner Anders , Wachs Michelle , Welker Volkmar
Published: January 2005

Suppose thatf:P→Qf:P \to Qis a poset map whose fibersf−1(Q≤q)f^{-1}(Q_{\le q})are sufficiently well connected. Our main result is a formula expressing the homotopy type ofPPin terms ofQQand the fibers. Several fiber theorems from the literature (due to Babson, Baclawski and Quillen) are obtained as consequences or special cases. Homology, Cohen-Macaulay, and equivariant versions are given, and some applications are discussed.
Plane Cremona maps, exceptional curves and roots
Authors: Alberich-Carramiñana Maria
Published: January 2005

We address three different questions concerning exceptional and root divisors (of arithmetic genus zero and of self-intersection

−
1

-1

and

−
2

-2

, respectively) on a smooth complex projective surface

S
S

which admits a birational morphism

π
\pi

to

P

2

\mathbb {P}^{2}

. The first one is to find criteria for the properness of these divisors, that is, to characterize when the class of

C
C

is in the

W
W

-orbit of the class of the total transform of some point blown up by

π
\pi

if

C
C

is exceptional, or in the

W
W

-orbit of a simple root if

C
C

is root, where

W
W

is the Weyl group acting on

Pic
⁡
S

\operatorname {Pic}S

; we give an arithmetical criterion, which adapts an analogous criterion suggested by Hudson for homaloidal divisors, and a geometrical one. Secondly, we prove that the irreducibility of the exceptional or root divisor

C
C

is a necessary and sufficient condition in order that

π

∗

(
C
)

\pi _{\ast } (C)

could be transformed into a line by some plane Cremona map, and in most cases for its contractibility. Finally, we provide irreducibility criteria for proper homaloidal, exceptional and effective root divisors.
On the theory of elliptic functions based on ₂𝐹₁(\frac{1}3,\frac{2}3;\frac{1}2;𝑧)
Authors: Shen Li-Chien
Published: January 2005

Based on properties of the hypergeometric series

2

F

1

(

1
3

,

2
3

;

1
2

;
z
)

{}_{2}F_{1}(\frac {1}{3},\frac {2}{3};\frac {1}{2};z)

, we develop a theory of elliptic functions that shares many striking similarities with the classical Jacobian elliptic functions.
Blow-up examples for second order elliptic PDEs of critical Sobolev growth
Authors: Druet Olivier , Hebey Emmanuel
Published: January 2005

Let

(
M
,
g
)

(M,g)

be a smooth compact Riemannian manifold of dimension

n
≥
3

n \ge 3

, and

Δ
g

=
−
d
i

v
g

∇

\Delta _g = -div_g\nabla

be the Laplace-Beltrami operator. Let also

2
⋆

2^\star

be the critical Sobolev exponent for the embedding of the Sobolev space

H
1
2

(
M
)

H_1^2(M)

into Lebesgue’s spaces, and

h
h

be a smooth function on

M
M

. Elliptic equations of critical Sobolev growth such as

(
E
)

Δ
g

u
+
h
u
=

u

2
⋆

−
1

\begin{equation*} (E)\qquad \qquad \qquad \qquad \qquad \qquad \Delta _gu + hu = u^{2^\star -1} \qquad \qquad \qquad \qquad \qquad \qquad \end{equation*}

have been the target of investigation for decades. A very nice

H
1
2

H_1^2

-theory for the asymptotic behaviour of solutions of such equations has been available since the 1980’s. The

C
0

C^0

-theory was recently developed by Druet-Hebey-Robert. Such a theory provides sharp pointwise estimates for the asymptotic behaviour of solutions of

(
E
)

(E)

. It was used as a key point by Druet to prove compactness results for equations such as

(
E
)

(E)

. An important issue in the field of blow-up analysis, in particular with respect to previous work by Druet and Druet-Hebey-Robert, is to get explicit nontrivial examples of blowing-up sequences of solutions of

(
E
)

(E)

. We present such examples in this article.
Inertia law for spectral stability of solitary waves in coupled nonlinear Schrödinger equations
Authors: Pelinovsky Dmitry E.
Published: January 2005

Spectral stability analysis for solitary waves is developed in the context of the Hamiltonian system of coupled nonlinear Schrödinger equations. The linear eigenvalue problem for a non–self–adjoint operator is studied with two self–adjoint matrix Schrödinger operators. Sharp bounds on the number and type of unstable eigenvalues in the spectral problem are found from the inertia law for quadratic forms, associated with the two self–adjoint operators. Symmetry–breaking stability analysis is also developed with the same method.
Resource partitioning among flower visitors and evolution of nectar concealment in multi–species communities
Authors: Rodríguez-Gironés Miguel A. , Santamaría Luis
Published: January 2005

The plant community within which flower evolution takes place has largely been ignored. We develop two models for the evolution of nectar concealment when flowers are visited by legitimate pollinators and flower parasites. When there is a single plant species, no level of nectar concealment is evolutionarily stable: any population can be invaded by mutants exhibiting a higher level of nectar concealment. However, the presence of a second flower species with exposed nectar and not subject to evolution breaks the runaway process. In the presence of open flowers, depending on the fitness function there may be an evolutionarily stable level of nectar concealment, or more complex evolutionary dynamics, with nectar concealment fluctuating within a bounded range. Concealment of nectar from flower parasites can evolve even if it implies decreasing the accessibility of nectar to legitimate pollinators.
Mechanical heating by active galaxies
Authors: Begelman Mitchell C. , Ruszkowski Mateusz
Published: January 2005

Jets and winds are significant channels for energy loss from accreting black holes. These outflows mechanically heat their surroundings, through shocks as well as gentler forms of heating. We discuss recent efforts to understand the nature and distribution of mechanical heating by central active galactic nuclei (AGN) in clusters of galaxies, using numerical simulations and analytic models. Specifically, we will discuss whether the relatively gentle ‘effervescent heating’ mechanism can compensate for radiative losses in the central regions of clusters, and account for the excess entropy observed at larger radii. J. Binney (2005
Phil. Trans. R. Soc. A
,
363
, 739−749, doi: 10.1098/rsta.2004.1520) discusses the possible role of violent, episodic heating by AGN in clusters.
Advances in protein and small-molecule charge-density refinement methods usingMoPro
Authors: Jelsch Christian , Guillot Benoit , Lagoutte Angelique , Lecomte Claude
Published: January 2005

With an increasing number of biological macromolecule structures solved at ultra-high resolution and with the advances of supramolecular chemistry, it becomes necessary to extend to large systems experimental charge-density study methods that are usually applied to small molecules. The latest developments in the refinement programMoPro(Molecular Properties), dedicated to the charge-density refinement at (sub)atomic resolution of structures ranging from small molecules to biological macromolecules, are presented.MoProuses the Hansen & Coppens [Acta Cryst.(1978), A34, 909–921] multipolar pseudo-atom model for the electron-density refinement. Alternative methods are also proposed, such as modelling bonding and lone-pair electron density by virtual spherical atoms. For proteins at atomic resolution, a charge-density database developed in the laboratory enables the transfer of multipolar parameters. The program allows complex refinement strategies to be written and has numerous restraints, constraints and analysis tools for use in the structure and electron-density analysis. New kappa and multipolar parameter restraints/constraints are also implemented and discussed. Furthermore, constraints on the electron density, such as local symmetry and atom equivalence, are easily defined. Some examples of applications, from small molecules to large unit cells (including the enzyme aldose reductase), are given in order to guide theMoProuser and to show the large field of applicability of this code.
COMPACK: a program for identifying crystal structure similarity using distances
Authors: Chisholm James Alexander , Motherwell Sam
Published: January 2005

A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.
Reduction in diffuso-convective disturbances in nanovolume protein crystallization experiments
Authors: Carter Daniel C. , Rhodes Percy , McRee Duncan E. , Tari Leslie W. , Dougan Douglas R. , Snell Gyorgy , Abola Enrique , Stevens Raymond C.
Published: January 2005

Preliminary studies suggest that protein crystallization experiments using nanoliter-volume protein crystallization droplets may produce equal or better quality protein crystals compared with those grown using microliter volumes, and sometimes produce crystals in nanoliter volumes when microliter volumes are unable to produce diffraction-quality crystals. Computations and numerical modelling studies were performed to compare the influence of solutal convective disturbances around growing crystals and different drop volumes. These studies suggest that both crystal size and drop size contribute to a marked reduction in diffuso-convective disturbances in nanoliter drops and thus to the observed quality enhancements.
Distribution and Burgers vectors of dislocations in semiconductor wafers investigated by rocking-curve imaging
Authors: Lübbert Daniel , Ferrari Claudio , Mikulík Petr , Pernot Petra , Helfen Lukas , Verdi Nicola , Korytár Dušan , Baumbach Tilo
Published: January 2005

The method called `rocking-curve imaging' (RCI) has recently been developed to visualize lattice imperfections in large crystals such as semiconductor wafers with high spatial resolution. The method is based on a combination of X-ray rocking-curve analysis and digital X-ray diffraction topography. In this article, an extension of the method is proposed by which dislocation densities in large-scale samples (semiconductor wafer crystals) can be quantified and their variation across the sample surface determined in an instrumentally simple way. Results from a nearly dislocation-free S-doped InP crystal and a semi-insulating GaAs are presented; both display a clearly non-random distribution of dislocations.
Comparative evaluation of the March and generalized spherical harmonic preferred orientation models using X-ray diffraction data for molybdite and calcite powders
Authors: Sitepu Husin , O'Connor Brian H. , Li Deyu
Published: January 2005

Preferred crystallographic orientation,i.e.texture in crystalline materials powder diffraction data, can cause serious systematic errors in phase composition analysis and also in crystal structure determination. The March model [Dollase (1986).J. Appl. Cryst.19, 267–272] has been used widely in Rietveld refinement for correcting powder diffraction intensities with respect to the effects of preferred orientation. In the present study, a comparative evaluation of the March model and the generalized spherical harmonic [Von Dreele (1997).J. Appl. Cryst.30, 517–525] description for preferred orientation was performed with X-ray powder diffraction data for molybdite (MoO3) and calcite (CaCO3) powders uniaxially pressed at five different pressures. Additional molybdite and calcite powders, to which 50% by weight silica gel had been added, were prepared to extend the range of preferred orientations considered. The patterns were analyzed initially assuming random orientation of the crystallites and subsequently the March model was used to correct the preferred orientation. The refinement results were compared with parallel refinements conducted with the generalized spherical harmonic [Sitepu (2002).J. Appl. Cryst.35,274–277]. The results obtained show that the generalized spherical harmonic description generally provided superior figures-of-merit compared with the March model results.
An overview of reconstructability analysis
Authors: Zwick Martin
Published: January 2005

This paper is an overview of reconstructability analysis (RA), an approach to discrete multivariate modeling developed in the systems community. RA includes set‐theoretic modeling of relations and information‐theoretic modeling of frequency and probability distribution. It thus encompasses both statistical and nonstatistical problems. It overlaps with logic design and machine learning in engineering and with log‐linear modeling in the social sciences. Its generality gives it considerable potential for knowledge representation and data mining.
Construction of main sequence of gene based on “method of factor reconstruction analysis”
Authors: Zhihong Zhang , Pengtao Wang , Huaqing Liu , Guangfu Shu
Published: January 2005

The decipher, analysis and research of gene sequence is the most challenging problem that scientists all over the world are trying their best to solve. This paper introduces the application of factor reconstruction analysis in this field, its process and steps in using this kind of method. The resulting computation and analysis is presented.
Reconstructability analysis detection of optimal gene order in genetic algorithms
Authors: Zwick Martin , Shervais Stephen
Published: January 2005

The building block hypothesis implies that genetic algorithm efficiency will be improved if sets of genes that improve fitness through epistatic interaction are near to one another on the chromosome. We demonstrate this effect with a simple problem, and show that information‐theoretic reconstructability analysis can be used to decide on optimal gene ordering.
The New Zealand common smelt: biology and ecology
Authors: Ward F. J. , Northcote T. G. , Boubée J. A. T.
Published: January 2005

The common smelt is one of the most widespread indigenous freshwater fishes in New Zealand. One other member of the family Retropinnidae, Stokellia anisodon(Stokell), is present but is confined to a small region of the South Island. There are many diadromous as well as river and lake resident populations, the latter, sometimes a result of introductions to serve as forage fish for trout. Diadromous smelt spawn during austral autumn–winter on sand bars of lower riverine reaches. Larval stages inhabit coastal marine waters, and the postlarvae to immature stages re‐enter rivers and some lowland lakes. Diadromous smelt are distinguished from lowland lake resident forms by high vertebral but low gill raker numbers and larger size and from those present in some isolated waters, by high vertebral numbers alone. Lake or reservoir resident smelt usually spawn in austral spring–summer on sandy shallows at stream mouths or along shorelines. Verified smelt ages (otolith analyses) indicate that in some populations most smelt mature and spawn after c. 1 year. Adult smelt feed on a spectrum of primarily invertebrate animals ranging from small zooplankters to insects and occasionally small fishes. Smelt are a major prey for both brown trout and rainbow trout. Adult smelt are a minor food for the Maori people. As postlarvae they are a component of a few ‘whitebait’ fisheries. Most smelt populations are increasingly affected by environmental changes induced by human activities. Although many studies have examined problems affecting smelt, further effort is required, along with more basic research.
Larvae of Crystallodytes pauciradiatus(Perciformes: Creediidae) from Easter Island, South Pacific
Authors: Landaeta M. F. , Herrera G. , Castro L. R.
Published: January 2005

Larvae of Crystallodytes pauciradiatus(Creediidae) are described from 47 individuals (2·9–21·3 mm). They are elongate, slender, lightly pigmented, have prominent preopercular spines and unique small spines on the lower jaw. Early stages are restricted to the nearshore water around Easter Island, South Pacific.
The role of salinity in structuring the fish assemblages in a tropical estuary
Authors: Barletta M. , Barletta‐Bergan A. , Saint‐Paul U. , Hubold G.
Published: January 2005

The present study describes the seasonal changes of the fish species composition in three areas of the main channel of the Caeté River estuary, Brazil. The fish faunas of each habitat differed in density, biomass and species composition. Mean fish density and biomass for the Caeté River estuary channel was 0·25 individuals m−2 and 0·9 g m−2 respectively. Analysis of catch data showed that the number of species, total density and total biomass differed significantly between areas and seasons. For the most important species, the mean density of Cathorops spixii, Aspredinichthys filamentosus, Aspredo sp. 2, Pimelodus blochii, Pseudauchnipterus nodosus and Macrodon ancylodon, differed significantly between seasons while the mean density of Stellifer rastrifer, Stellifer microps, Aspredo aspredo, Aspredo sp. 1 and Cynoscion acoupa did not. The mean biomass of these species, with exception of S. microps and Aspredo sp. 1, also differed significantly between seasons. In the Caeté estuary seasonal salinity fluctuations appeared to be the main factor that structured the fish assemblage in the entire estuarine system. At least 85% of the species captured by the artisanal and subsistence fisheries in the Bragantine region required estuarine conditions to complete their life cycle.
Effects of waterborne complexing agents on silver uptake and depuration in rainbow trout
Authors: Bertram B. O. B. , Playle R. C.
Published: January 2005

Rainbow trout Oncorhynchus mykiss(c. 60 g) were exposed for 1 week to 0·1 μM silver as AgNO3 in ion poor water (Ca c. 150 μM, pH c. 8, water temperature 13° C) with or without waterborne organic matter (27 mg C l−1 as Aldrich humic acid), thiosulphate (5 μM Na2S2O3) or chloride (4 mM KCl). Organic matter decreased Ag accumulation by the gills initially, but did not decrease Ag accumulation by plasma or liver. Thiosulphate decreased the amount of Ag accumulated by the gills for the entire 1 week exposure but had no effect on Ag concentrations in the plasma, liver or bile. Chloride had no effect on Ag uptake in any of the tissues examined. All three complexing agents reduced the decreases in plasma Na and Cl concentrations caused by Ag. To study the effects of waterborne complexing agents on Ag depuration, rainbow trout were exposed to 0·1 μM AgNO3 for 1 week then placed for 8 days in Ag‐free, ion poor water with or without waterborne organic matter (55 mg C l−1) or thiosulphate (5 μM). These complexing agents did not alter depuration of Ag from the gills, plasma, liver or bile. Thus, once Ag has entered a fish, subsequent elimination of internal Ag is not affected by external complexing agents.
In vitro pattern‐related effects of forskolin on melanophore adrenoceptor‐mediated responses of winter flounder
Authors: Burton D.
Published: January 2005

In vitro experiments were performed on melanophores on scales carrying small slips of skin (scale slips) sampled from the white spot, dark band and general background components of patterning in winter flounder Pseudopleuronectes americanus. In vitro, forskolin (10−4 to 10−7 M) was employed to increase melanophore intracellular cytosolic adenosine‐3′‐5′‐monophosphate (cAMP) levels by stimulating adenylate cyclase. Such increase shifted noradrenaline concentration‐response curves to the right, general background melanophores being least sensitive to the forskolin, indicating a relatively higher proportion of α2‐adrenoceptors, and those from white spots the most sensitive. Melanosome dispersion, in balanced salt solution, was also enhanced by such raised levels of cAMP. Without forskolin, melanophores from white spots displayed the shortest pigment dispersion time in balanced salt solution, the slower melanophores from the other pattern components being those most affected by the addition of forskolin. The results demonstrate that differences in melanophore physiological responsiveness associated with flatfish patterns involve differential intracellular levels of cAMP, as well as differences in melanophore size and rates of melanosome movement.
Treatment of factor XI inhibitor using recombinant activated factor VIIa
Authors: Bern M. M. , Sahud M. , Zhukov O. , Qu K. , Mitchell W.
Published: January 2005

Summary.  A 30‐year‐old female with severe factor XI deficiency of 0–2% acquired factor XI inhibitor following many infusions for fresh frozen plasma (FFP) for surgical procedures starting at 4 years of age. Seven months before this inhibitor was diagnosed, surgery was complicated by prolonged bleeding resistant to FFP, requiring epsilon aminocaproic acid (EACA) and surgical packing. The inhibitor was measured at 2.2 Bethesda units, 7 months since the last FFP. The inhibitor was confirmed as specific anti‐XI and anti‐XIa binding by patient's IgG to immobilized factor XI and factor XIa from whole plasma and purified IgG. For repair of a painful anterior cruciate ligament (ACL) defect she was given recombinant factor VIIa (rVIIa) at 90 μg kg−1, starting one‐half hour preoperatively and continued every 2 h for 8 h when haemostasis was complete. Thereafter the rVIIa was given every 3 h for two doses, and then every 4 h for four doses at which time she was discharged on EACA which was continued for 6 days. There was excellent haemostasis during and following the surgery. There was no evidence of consumptive coagulopathy, with no change in the fibrinogen, platelet count, or D‐D dimer; and no increase of platelet factor 4, beta‐thromboglobulin, or prothrombin fragment F 1.2. The thrombin‐antithrombin complex increased over baseline after 24 h. There was no postoperative deep vein thrombosis or pulmonary embolus. In this patient with a factor XI inhibitor, the recombinant factor VIIa was effective and safe, ensuring adequate haemostasis with no thrombotic complications. This product which was designed for patients with inhibitors to factor VIII or factor IX, and factor VII deficiency, has now been given successfully to four patients with factor XI inhibitors.
Pregnancy and oral contraceptives in factor V deficiency: a study of 22 patients (five homozygotes and 17 heterozygotes) and review of the literature
Authors: Girolami A. , Scandellari R. , Lombardi A.M. , Girolami B. , Bortoletto E. , Zanon E.
Published: January 2005

Summary.  Information on the effect of pregnancy or oral contraceptives (OC) in congenital factor V (FV) deficiency is scanty. The personal investigation of five homozygous and 17 female heterozygous showed that patients with severe deficiency bleed considerably at the time of delivery. However, bleeding can be controlled properly by administration of fresh frozen plasma with excellent foetal outcome. The safe level for adequate haemostasis seems around 25% of normal. On the contrary, heterozygote patients show no significant postpartum bleeding and therefore need no substitution therapy. Oral contraceptives were taken and well tolerated by four of our homozygous patients and appear to be beneficial because they cause a decrease in menometrorrhagies thereby improving the anaemia and decreasing transfusional needs. One patient took hormonal replacement therapy with no undue effects. No thrombosis was noted in the propositae during oral contraceptive therapy. The review of the literature has allowed the gathering of information on 20 additional pregnancies. The foetal outcome was satisfactory in every instance. Excessive bleeding was noted in 11 pregnancies. In seven of the remaining pregnancies, no undue bleeding was noted thanks to appropriate substitution therapy. In the remaining two pregnancies no bleeding was noted and no substitution therapy was given. No data are apparently available in the literature about the use of OCs in FV deficiency.
Molecular characterization of two novel mutations causing factor X deficiency in a Chinese pedigree
Authors: Wang W.‐B. , Fu Q.‐H. , Zhou R.‐F. , Wu W.‐M. , Ding Q.‐L. , Hu Y.‐Q. , Wang X.‐F. , Wang H.‐L. , Wang Z.‐Y.
Published: January 2005

Summary.  Factor X (FX) deficiency is a rare bleeding disorder inherited as an autosomal recessive trait. In this study, we investigated the molecular basis of FX deficiency in a Chinese pedigree. The proposita showed a markedly prolonged activated partial thromboplastin time and a mild prolongation of prothrombin time. The levels of FX antigen and FX activity were 58.6% and 2.5%, respectively. Molecular analysis revealed that the proposita was compound heterozygous for two novel mutations: IVS1 + 1G > A and G1185A (Arg347His). The aberrant transcripts from the IVS1 + 1G > A mutant allele were not detected by analyzing the splicing pattern of ectopic transcripts in leukocytes of the patient with nested polymerase chain reaction after reverse transcription. We thus hypothesize that the mRNA molecules originating from the IVS1 + 1G > A mutation were rapidly destroyed in vivo. Site‐directed mutagenesis of FX cDNA was used to introduce FXG1185A mutation, and wild‐type as well as mutant FX proteins were expressed by transient transfection in HEK 293 cells. Normal FX antigen levels both in the conditioned media of cells expressing the mutant and in cell lysates were detected by an enzyme‐linked immunoadsorbent assay. Evaluation of wild‐type and mutant coagulant activity demonstrated that the FX molecules carrying the Arg347His mutation have dramatically decreased activity.
Effects of haemophilic arthropathy on health‐related quality of life and socio‐economic parameters
Authors: Fischer K. , van der Bom J. G. , Mauser‐Bunschoten E. P. , Roosendaal G. , van den Berg H. M.
Published: January 2005

Summary.  Although prophylactic treatment is advised for all children with severe haemophilia, the optimal regimen is still under discussion. Should all joint bleeds be prevented, or can a limited amount of arthropathy be tolerated in adulthood without loss of quality of life? To answer this question, the effect of haemophilic arthropathy on health‐related quality of life (HRQoL) needs to be quantified. In a retrospective study, the effect of arthropathy on HRQoL and socio‐economic parameters was assessed in a single‐centre cohort of 96 patients with severe and moderate haemophilia with a minimum age of 13 years. Arthropathy was measured by the radiological Pettersson score of the elbows, knees and ankles (maximum: 78 points). HRQoL was assessed by the Short Form 36 (SF36), measuring eight domains of health. Labourforce participation and medical consumption were assessed using a separate questionnaire. Patients were studied at a mean age of 28.6 years (range: 13–54), the mean time between evaluation and the last Pettersson score was 0.4 years (SD: 1.1). The overall median Pettersson score was 13 (range: 0–78). There was a trend towards lower quality of life with increasing Pettersson scores and age, especially in the physical domains of the SF36. An age‐adjusted analysis showed that arthropathy had a small but significant effect on HRQoL in the domain of ‘physical function’ of the SF36, but not on its other domains, or on labourforce participation and medical consumption. Thus suggesting that the SF36 can be used to assess the effects of haemophilic arthropathy, especially in the domain of ‘physical function’.
Preservation of a transgenic strain of the sawfly, Athalia rosae (Hymenoptera) by artificial fertilization using cryopreserved sperm
Authors: Hatakeyama M. , Sumitani M.
Published: January 2005

Germline transformation using a piggyBac‐derived vector is feasible in the sawfly, Athalia rosae. A previously generated transgenic line carrying green fluorescence protein (GFP) genes as reporters was successfully maintained and preserved without consecutive rearing. Sperm taken from males that were frozen directly in liquid nitrogen and stored at −80 °C for a year were microinjected into mature unfertilized eggs dissected from female ovaries. A fraction of the sperm‐injected eggs was fertilized and developed into diploid females, and all of them expressed GFP. Haploid male progeny from these females segregated into GFP‐positive and GFP‐negative individuals in a ratio of 1 : 1 indicating heterozygosity of the parental females. The GFP genes were stably inherited staying at the location where they were originally integrated.
Tissue localization and regulation by juvenile hormone of human allergen Bla g 4 from the German cockroach,Blattella germanica(L.)
Authors: Fan Y. , Gore J. C. , Redding K. O. , Vailes L. D. , Chapman M. D. , Schal C.
Published: January 2005

The German cockroach,Blattella germanica(L.), produces several potent protein aeroallergens, including Bla g 4, a ∼20 kDa lipocalin. RT‐PCR, Northern analyses andin situhybridization showed that Bla g 4 is expressed only in the adult male reproductive system. Western blotting and ELISA with rBla g 4 antiserum detected immunoreactivity in the utricles and the conglobate gland, but not in other tissues of the male reproductive system. The Bla g 4 protein content of males increased from adult emergence to day 14, but during copulation Bla g 4 was depleted in the male and transferred to the female within the spermatophore. Topical application of juvenile hormone III stimulated Bla g 4 production by both conglobate gland and utricles.
The mosquito Aedes aegypti (L.) leucokinin receptor is a multiligand receptor for the three Aedes kinins
Authors: Pietrantonio P. V. , Jagge C. , Taneja‐Bageshwar S. , Nachman R. J. , Barhoumi R.
Published: January 2005

A cDNA cloned from Aedes aegypti (L.) (Aedae) female Malpighian tubule (AY596453) encodes a 584 amino acid residue protein (65.2 kDa) predicted as a G protein‐coupled receptor and orthologue of the drosokinin receptor from Drosophila melanogaster and highly similar to the tick Boophilus microplus myokinin receptor (AF228521). Based on the similarity to this Aedes sequence, we also propose a correction for the Anopheles gambiae protein sequence EAA05450. When expressed in CHO‐K1 cells, the Aedes receptor behaved as a multiligand receptor and functionally responded to concentrations ≥ 1 nm of Aedae kinins 1–3, respectively, as determined by a calcium bioluminescence plate assay and single cell intracellular calcium measurements by confocal fluorescence cytometry. Estimates of EC50 values by the plate assay were 16.04 nm for Aedae‐K‐3, 26.6 nm for Aedae‐K‐2 and 48.8 nm for Aedae‐K‐1 and were statistically significantly different. These results suggest that the observed differences in physiological responses to the three Aedes kinins in the Aedes isolated Malpighian tubule reported elsewhere could now be explained by differences in intracellular signalling events triggered by the different peptides on the same receptor and not necessarily due to the existence of various receptors for the three Aedes kinins.