bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of IgG4 assays using whole parasite extract and BmR1 recombinant antigen in determining antibody prevalence in brugian filariasis
Authors: Noordin Rahmah , Wahyuni Sitti , Mangali Andarias , Huat Lim Boon , Yazdanbakhsh Maria , Sartono Erliyani
Published: September 2004

Background

Brugia malayi is endemic in several Asian countries with the highest prevalence in Indonesia. Determination of prevalence of lymphatic filariasis by serology has been performed by various investigators using different kinds of antigen (either soluble worm antigen preparations or recombinant antigens). This investigation compared the data obtained from IgG4 assays using two different kinds of antigen in a study on prevalence of antibodies to B. malayi.

Methods

Serum samples from a transmigrant population and life long residents previously tested with IgG4 assay using soluble worm antigen (SWA-ELISA), were retested with an IgG4 assay that employs BmR1 recombinant antigen (BmR1 dipstick [Brugia Rapid™]). The results obtained with the two antigens were compared, using Pearson chi-square and McNemar test.

Results

There were similarities and differences in the results obtained using the two kinds of antigen (SWA and BmR1). Similarities included the observation that assays using both antigens demonstrated an increasing prevalence of IgG4 antibodies in the transmigrant population with increasing exposure to the infection, and by six years living in the area, antibody prevalence was similar to that of life-long residents. With regards to differences, of significance is the demonstration of similar antibody prevalence in adults and children by BmR1 dipstick whereas by SWA-ELISA the antibody prevalence in adults was higher than in children.

Conclusions

Results and conclusions made from investigations of prevalence of anti-filarial IgG4 antibody in a population would be affected by the assay employed in the study.
Real time electrocardiogram QRS detection using combined adaptive threshold
Authors: Christov Ivaylo I
Published: September 2004

Background

QRS and ventricular beat detection is a basic procedure for electrocardiogram (ECG) processing and analysis. Large variety of methods have been proposed and used, featuring high percentages of correct detection. Nevertheless, the problem remains open especially with respect to higher detection accuracy in noisy ECGs

Methods

A real-time detection method is proposed, based on comparison between absolute values of summed differentiated electrocardiograms of one of more ECG leads and adaptive threshold. The threshold combines three parameters: an adaptive slew-rate value, a second value which rises when high-frequency noise occurs, and a third one intended to avoid missing of low amplitude beats.

Two algorithms were developed: Algorithm 1 detects at the current beat and Algorithm 2 has an RR interval analysis component in addition.

The algorithms are self-adjusting to the thresholds and weighting constants, regardless of resolution and sampling frequency used. They operate with any number L of ECG leads, self-synchronize to QRS or beat slopes and adapt to beat-to-beat intervals.

Results

The algorithms were tested by an independent expert, thus excluding possible author's influence, using all 48 full-length ECG records of the MIT-BIH arrhythmia database. The results were: sensitivity Se = 99.69 % and specificity Sp = 99.65 % for Algorithm 1 and Se = 99.74 % and Sp = 99.65 % for Algorithm 2.

Conclusion

The statistical indices are higher than, or comparable to those, cited in the scientific literature.
Leukaemia incidence among workers in the shoe and boot manufacturing industry: a case-control study
Authors: Forand Steven P
Published: September 2004

Background

Previous reports have indicated an excess of leukaemia in Broome County, New York, particularly in the Town of Union. Surveillance of cancer incidence data indicates that a large proportion of these cases occurred among males ages 65 and older. Shoe and boot manufacturing has been the largest single industry in this area throughout much of the past century. Occupational studies from Europe suggest a link between leukaemia and employment in the shoe and boot manufacturing industry. However, researchers have not found a positive association between leukaemia and employment in the shoe industry among workers in the United States.

Methods

A matched case-control study was conducted to investigate the association between leukaemia incidence among males 65 and older and employment in the shoe and boot manufacturing industry. Thirty-six cases of leukaemia occurring between 1981–1990; among males age 65 and older; residing in the town of Union met the study case criteria. Death certificates were obtained for each of the cases. These were matched to death certificates of 144 controls on date of death and date of birth +/- 1 year. Death certificates were then examined to determine the employer and occupation of each study subject. Conditional logistic regression was used to determine the risk of leukaemia among those working in the industry.

Results

The risk of both leukaemia (OR = 1.47; 95% CI 0.70, 3.09) and acute myeloid leukaemia (OR = 1.19; 95% CI 0.33, 4.28) were elevated among those employed in the shoe and boot manufacturing industry, however neither was statistically significant.

Conclusion

The results, though suggestive of an association between leukaemia and employment in the shoe and boot manufacturing industry, were not statistically conclusive due mainly to limited study power. Several additional limitations may also have prevented the observance of more conclusive findings. Better exposure assessment, information on length of exposure and types of job held, control of confounding factors and information on chemicals used by this company would strengthen any future investigation.
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
Authors: Wang Xiu-Jie , Reyes José L , Chua Nam-Hai , Gaasterland Terry
Published: September 2004

Background

A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some miRNAs and their time- and tissue-specific expression patterns make experimental miRNA identification difficult. We present here a computational method for genome-wide prediction of Arabidopsis thaliana microRNAs and their target mRNAs. This method uses characteristic features of known plant miRNAs as criteria to search for miRNAs conserved between Arabidopsis and Oryza sativa. Extensive sequence complementarity between miRNAs and their target mRNAs is used to predict miRNA-regulated Arabidopsis transcripts.

Results

Our prediction covered 63% of known Arabidopsis miRNAs and identified 83 new miRNAs. Evidence for the expression of 25 predicted miRNAs came from northern blots, their presence in the Arabidopsis Small RNA Project database, and massively parallel signature sequencing (MPSS) data. Putative targets functionally conserved between Arabidopsis and O. sativa were identified for most newly identified miRNAs. Independent microarray data showed that the expression levels of some mRNA targets anti-correlated with the accumulation pattern of their corresponding regulatory miRNAs. The cleavage of three target mRNAs by miRNA binding was validated in 5' RACE experiments.

Conclusions

We identified new plant miRNAs conserved between Arabidopsis and O. sativa and report a wide range of transcripts as potential miRNA targets. Because MPSS data are generated from polyadenylated RNA molecules, our results suggest that at least some miRNA precursors are polyadenylated at certain stages. The broad range of putative miRNA targets indicates that miRNAs participate in the regulation of a variety of biological processes.
Microarray analysis of microRNA expression in the developing mammalian brain
Authors: Miska Eric A , Alvarez-Saavedra Ezequiel , Townsend Matthew , Yoshii Akira , Šestan Nenad , Rakic Pasko , Constantine-Paton Martha , Horvitz H Robert
Published: September 2004

Background

MicroRNAs are a large new class of tiny regulatory RNAs found in nematodes, plants, insects and mammals. MicroRNAs are thought to act as post-transcriptional modulators of gene expression. In invertebrates microRNAs have been implicated as regulators of developmental timing, neuronal differentiation, cell proliferation, programmed cell death and fat metabolism. Little is known about the roles of microRNAs in mammals.

Results

We isolated 18-26 nucleotide RNAs from developing rat and monkey brains. From the sequences of these RNAs and the sequences of the rat and human genomes we determined which of these small RNAs are likely to have derived from stem-loop precursors typical of microRNAs. Next, we developed a microarray technology suitable for detecting microRNAs and printed a microRNA microarray representing 138 mammalian microRNAs corresponding to the sequences of the microRNAs we cloned as well as to other known microRNAs. We used this microarray to determine the profile of microRNAs expressed in the developing mouse brain. We observed a temporal wave of expression of microRNAs, suggesting that microRNAs play important roles in the development of the mammalian brain.

Conclusion

We describe a microarray technology that can be used to analyze the expression of microRNAs and of other small RNAs. MicroRNA microarrays offer a new tool that should facilitate studies of the biological roles of microRNAs. We used this method to determine the microRNA expression profile during mouse brain development and observed a temporal wave of gene expression of sequential classes of microRNAs.
Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae
Authors: Boyer Jeanne , Badis Gwenaël , Fairhead Cécile , Talla Emmanuel , Hantraye Florence , Fabre Emmanuelle , Fischer Gilles , Hennequin Christophe , Koszul Romain , Lafontaine Ingrid , Ozier-Kalogeropoulos Odile , Ricchetti Miria , Richard Guy-Franck , Thierry Agnès , Dujon Bernard
Published: September 2004

We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.
Membrane retrieval in neutrophils during phagocytosis: inhibition by M protein-expressingS. pyogenesbacteria
Authors: Bauer Susanne , Tapper Hans
Published: September 2004

During phagocytosis and phagosome maturation, complex membrane traffic events must be coordinated. We have observed, using fluorescent fluid-phase and membrane markers, that in the human neutrophil, internalization of nonopsonized, Gram-positive bacteria, but not of latex beads, is accompanied by a rapid and localized formation of pinosomal structures. This pinocytic response is calcium-dependent but insensitive to actin cytoskeleton disruption and wortmannin treatment. Contrary to what we observe, endosomal structures usually are considered to participate in phagosome formation by providing necessary membrane to forming phagosomes. Instead, our results show a coupling between neutrophil secretory and membrane-retrieval processes during phagosome maturation, and we suggest that the observed, localized pinocytic response is linked to the secretion of azurophilic granules toward nascent phagosomes. Accordingly, M and M-like protein-expressing Streptococcus pyogenes bacteria, which are able to survive inside neutrophil phagosomes, inhibit both the secretion of azurophilic granules to phagosomes and pinosome formation.
Natural killer cells inhibit hepatitis C virus expression
Authors: Li Yuan , Zhang Ting , Ho Chun , Orange Jordan S , Douglas Steven D , Ho Wen-Zhe
Published: September 2004

Natural killer (NK) cells are critical in host innate defense against certain viruses. The role of NK cells in controlling hepatitis C virus (HCV) remains obscure. We examined whether NK cells are capable of inhibiting HCV expression in human hepatic cells. When NK cells are cultured with the HCV replicon-containing hepatic cells, they have no direct cytolytic effect but release soluble factor(s) suppressing HCV RNA expression. Media conditioned by NK cell lines (NK-92 and YTS) or primary NK cells isolated from healthy donors contain interferon γ (IFN-γ) and potently inhibit HCV RNA expression. Ligation of CD81 on NK cells inhibits IFN-γ production and results in decreased anti-HCV activity. In addition, the antibodies to IFN-γ or IFN-γ receptors abolish the anti-HCV activity of NK cell-conditioned media. The role of IFN-γ in NK cell-mediated, anti-HCV activity is supported by the observation that NK cell-conditioned media enhanced expression of signal transducer and activator of transcription-1, a nuclear factor that is essential in IFN-γ-mediated antiviral pathways. NK cell-conditioned media have the ability to stimulate intracellular IFN-α expression in the hepatic cells, suggesting a mechanism responsible for NK cell-mediated, anti-HCV activity. Thus, NK cells hold the potential to play a vital role in controlling HCV replication in hepatic cells using an IFN-γ-dependent mechanism.
Foxp1regulates cardiac outflow tract, endocardial cushion morphogenesis and myocyte proliferation and maturation
Authors: Wang Bin , Weidenfeld Joel , Lu Min Min , Maika Shanna , Kuziel William A. , Morrisey Edward E. , Tucker Philip W.
Published: September 2004

We have recently described a new subfamily of Fox genes, Foxp1/2/4, which are transcriptional repressors and are thought to regulate important aspects of development in several tissues, including the lung, brain, thymus and heart. Here, we show that Foxp1 is expressed in the myocardium as well as the endocardium of the developing heart. To further explore the role of Foxp1 in cardiac development, we inactivated Foxp1 through gene targeting in embryonic stem cells. Foxp1 mutant embryos have severe defects in cardiac morphogenesis, including outflow tract septation and cushion defects, a thin ventricular myocardial compact zone caused by defects in myocyte maturation and proliferation, and lack of proper ventricular septation. These defects lead to embryonic death at E14.5 and are similar to those observed in other mouse models of congenital heart disease, including Sox4 and Nfatc1 null embryos. Interestingly, expression of Sox4 in the outflow tract and cushions of Foxp1 null embryos is significantly reduced, while remodeling of the cushions is disrupted, as demonstrated by reduced apoptosis and persistent Nfatc1 expression in the cushion mesenchyme. Our results reveal a crucial role for Foxp1in three aspects of cardiac development: (1) outflow tract development and septation, (2) tissue remodeling events required for cardiac cushion development, and (3) myocardial maturation and proliferation.
Highly specific interactions between bHLH transcription factors and chromatin during retina development
Authors: Skowronska-Krawczyk Dorota , Ballivet Marc , Dynlacht Brian D. , Matter Jean-Marc
Published: September 2004

Basic helix-loop-helix (bHLH) transcription factors such as atonal homolog 5 (ATH5) and neurogenin 2 (NGN2) determine crucial events in retinogenesis. Using chromatin immunoprecipitation, we demonstrate that their interactions with target promoters undergo dynamic changes as development proceeds in the chick embryo. Chick ATH5 associates with its own promoter and with the promoter of the β3 nicotinic receptor specifically in retinal ganglion cells and their precursors. NGN2 binds to the ATH5 promoter in retina but not in optic tectum, suggesting that interactions between bHLH factors and chromatin are highly tissue specific. The transcriptional activations of both promoters correlate with dimethylation of lysine 4 on histone H3. Inactivation of the ATH5 promoter in differentiated neurons is accompanied by replication-independent chromatin de-methylation. This report is one of the first demonstrations of correlation between gene expression, binding of transcription factors and chromatin modification in a developing neural tissue.
ketteandblown fuseinteract genetically during the second fusion step of myogenesis inDrosophila
Authors: Schröter Roxane H. , Lier Simone , Holz Anne , Bogdan Sven , Klämbt Christian , Beck Lothar , Renkawitz-Pohl Renate
Published: September 2004

Drosophila myoblast fusion proceeds in two steps. The first one gives rise to small syncytia, the muscle precursor cells, which then recruit further fusion competent myoblasts to reach the final muscle size. We have identified Kette as an essential component for myoblast fusion. In kette mutants, founder cells and fusion-competent myoblasts are determined correctly and overcome the very first fusion. But then, at the precursor cell stage, fusion is interrupted. At the ultrastructural level,fusion is characterised by cell-cell recognition, alignment, formation of prefusion complexes, electron dense plaques and membrane breakdown. In kette mutants, electron dense plaques of aberrant length accumulate and fusion is interrupted owing to a complete failure of membrane breakdown. Furthermore, we show that kette interacts genetically with blown fuse (blow) which is known to be required to proceed from prefusion complexes to the formation of the electron dense plaques. Interestingly, a surplus of Kette can replace Blow function during myogenesis. We propose a model in which Dumbfounded/Sticks and stones-dependent cell adhesion is mediated over Rolling Pebbles, Myoblast city, Crk, Blown fuse and Kette, and thus induces membrane fusion.
Action offat, four-jointed, dachsousanddachsin distal-to-proximal wing signaling
Authors: Cho Eunjoo , Irvine Kenneth D.
Published: September 2004

In the Drosophila wing, distal cells signal to proximal cells to induce the expression of Wingless, but the basis for this distal-to-proximal signaling is unknown. Here, we show that three genes that act together during the establishment of tissue polarity, fat, four-jointed and dachsous, also influence the expression of Wingless in the proximal wing. fat is required cell autonomously by proximal wing cells to repress Wingless expression, and misexpression of Wingless contributes to proximal wing overgrowth in fat mutant discs. Four-jointed and Dachsous can influence Wingless expression and Fat localization non-autonomously, consistent with the suggestion that they influence signaling to Fat-expressing cells. We also identify dachs as a gene that is genetically required downstream of fat, both for its effects on imaginal disc growth and for the expression of Wingless in the proximal wing. Our observations provide important support for the emerging view that Four-jointed, Dachsous and Fat function in an intercellular signaling pathway,identify a normal role for these proteins in signaling interactions that regulate growth and patterning of the proximal wing, and identify Dachs as a candidate downstream effector of a Fat signaling pathway.
Germ cell-autonomous Wunen2 is required for germline development inDrosophilaembryos
Authors: Hanyu-Nakamura Kazuko , Kobayashi Satoru , Nakamura Akira
Published: September 2004

In many animals, primordial germ cells (PGCs) migrate through the embryo towards the future gonad, a process guided by attractive and repulsive cues provided from surrounding somatic cells. In Drosophila, the two related lipid phosphate phosphatases (LPPs), Wunen (Wun) and Wun2, are thought to degrade extracellular substrates and to act redundantly in somatic cells to provide a repulsive environment to steer the migration of PGCs, or pole cells. Wun and Wun2 also affect the viability of pole cells, because overexpression of either one in somatic cells causes pole cell death. However, the means by which they regulate pole cell migration and survival remains elusive. We report that Wun2 has a maternal function required for the survival of pole cells during their migration to the gonad. Maternal wun2 RNA was found to be concentrated in pole cells and pole cell-specific expression of wun2 rescued the pole cell death phenotype of the maternal wun2 mutant, suggesting that wun2 activity in pole cells is required for their survival. Furthermore, we obtained genetic evidence that pole cell survival requires a proper balance of LPP activity in pole cells and somatic cells. We propose that Wun2 in pole cells competes with somatic Wun and Wun2 for a common lipid phosphate substrate, which is required by pole cells to produce their survival signal. In somatic cells, Wun and Wun2 may provide a repulsive environment for pole cell migration by depleting this extracellular substrate.
TGFβ superfamily signals are required for morphogenesis of the kidney mesenchyme progenitor population
Authors: Oxburgh Leif , Chu Gerald C. , Michael Simon K. , Robertson Elizabeth J.
Published: September 2004

The TGFβ superfamily plays diverse and essential roles in kidney development. Gdf11 and Bmp4 are essential for outgrowth and positioning of the ureteric bud, the inducer of metanephric mesenchyme. During nephrogenesis, Bmp7 is required for renewal of the mesenchyme progenitor population. Additionally, in vitro studies demonstrate inhibitory effects of BMPs and TGFβs on collecting duct branching and growth. Here,we explore the predicted models of TGFβ superfamily function by cell-specific inactivation of Smad4, a key mediator of TGFβsignaling. Using a HoxB7cre transgene expressed in ureteric bud and collecting duct, we find that development of the collecting duct is Smad4 independent. By contrast, removal of Smad4 in nephrogenic mesenchyme using the Bmp7cre/+ allele leads to disorganization of the nephrogenic mesenchyme and impairment of mesenchyme induction. Smad4-deficient metanephric mesenchyme does not display defects in inducibility in LiCl or spinal cord induction assays. However, in situ hybridization and lineage analysis of Smad4 null mesenchyme cells at E11.5 show that the nephrogenic mesenchyme does not aggregate tightly around the ureteric bud tips, but remains loosely associated, embedded within a population of cells expressing markers of both nephrogenic mesenchyme and peripheral stroma. We conclude that the failure of recruitment of nephrogenic mesenchyme leaves a primitive population of mesenchyme at the periphery of the kidney. This population is gradually depleted, and by E16.5 the periphery is composed of cells of stromal phenotype. This study uncovers a novel role for TGFβ superfamily signaling in the recruitment and/or organization of the nephrogenic mesenchyme at early time-points of kidney development. Additionally, we present conclusive genetic lineage mapping of the collecting duct and nephrogenic mesenchyme.
HOXA13 regulates the expression of bone morphogenetic proteins 2 and 7 to control distal limb morphogenesis
Authors: Knosp Wendy M. , Scott Virginia , Bächinger Hans Peter , Stadler H. Scott
Published: September 2004

In humans and mice, loss of HOXA13 function causes defects in the growth and patterning of the digits and interdigital tissues. Analysis of Hoxa13 expression reveals a pattern of localization overlapping with sites of reduced Bmp2 and Bmp7 expression in Hoxa13mutant limbs. Biochemical analyses identified a novel series of Bmp2and Bmp7 enhancer regions that directly interact with the HOXA13 DNA-binding domain and activate gene expression in the presence of HOXA13. Immunoprecipitation of HOXA13-Bmp2 and HOXA13-Bmp7 enhancer complexes from the developing autopod confirm that endogenous HOXA13 associates with these regions. Exogenous application of BMP2 or BMP7 partially rescues the Hoxa13 mutant limb phenotype, suggesting that decreased BMP signaling contributes to the malformations present in these tissues. Together, these results provide conclusive evidence that HOXA13 regulates Bmp2 and Bmp7 expression, providing a mechanistic link between HOXA13, its target genes and the specific developmental processes affected by loss of HOXA13 function.
GSK3 is a multifunctional regulator ofDictyosteliumdevelopment
Authors: Schilde Christina , Araki Tsuyoshi , Williams Hazel , Harwood Adrian , Williams Jeffrey G.
Published: September 2004

Glycogen synthase kinase 3 (GSK3) is a central regulator of metazoan development and the Dictyostelium GSK3 homologue, GskA, also controls cellular differentiation. The originally derived gskA-null mutant exhibits a severe pattern formation defect. It forms very large numbers of pre-basal disc cells at the expense of the prespore population. This defect arises early during multicellular development, making it impossible to examine later functions of GskA. We report the analysis of a gskA-null mutant, generated in a different parental strain, that proceeds through development to form mature fruiting bodies. In this strain, Ax2/gskA–,early development is accelerated and slug migration greatly curtailed. In a monolayer assay of stalk cell formation, the Ax2/gskA– strain is hypersensitive to the stalk cell-inducing action of DIF-1 but largely refractory to the repressive effect exerted by extracellular cAMP. During normal development, apically situated prestalk cells express the ecmBgene just as they commit themselves to stalk cell differentiation. In the Ax2/gskA– mutant, ecmB is expressed throughout the prestalk region of the slug, suggesting that GskA forms part of the repressive signalling pathway that prevents premature commitment to stalk cell differentiation. GskA may also play an inductive developmental role, because microarray analysis identifies a large gene family, the 2C family, that require gskA for optimal expression. These observations show that GskA functions throughout Dictyostelium development, to regulate several key aspects of cellular patterning.
Outer dense fibre protein 2 (ODF2) is a self-interacting centrosomal protein with affinity for microtubules
Authors: Donkor Fatima F. , Mönnich Maren , Czirr Eva , Hollemann Thomas , Hoyer-Fender Sigrid
Published: September 2004

Outer dense fibre protein 2 (ODF2) is a major protein of sperm tail outer dense fibres which are prominent sperm tail-specific cytoskeletal structures. Moreover, ODF2 was also identified as a widespread component of the centrosomal scaffold and was found to associate preferentially with the appendages of the mother centriole [Nakagawa, Y., Yamane, Y., Okanoue, T., Tsukita, S. and Tsukita, S. (2001) Mol. Biol. Cell 12, 1687-1697]. Secondary structure predictions indicated ODF2 as an overall coiled-coil protein with a putative fibre forming capacity. To investigate its potential functions in generating the centrosomal scaffold and in microtubule nucleation we asked whether ODF2 is able to form a fibrillar structure by self-association in vivo and if it interacts with microtubules. By cytological investigation of transfected mammalian cells expressing ODF2-GFP fusion proteins and in vitro coprecipitation assays we could demonstrate that ODF2 is a self-interacting protein that forms a fibrillar structure partially linked to the microtubule network. Microtubule cosedimentation and coprecipitation assays indicated ODF2 as a microtubule-associated protein. However, we could not demonstrate a direct interaction of ODF2 with tubulin, suggesting that binding of endogenous ODF2 to the axonemal as well as to centrosomal microtubules may be mediated by, as yet, unknown proteins.
The role of myosin heavy chain phosphorylation in Dictyostelium motility, chemotaxis and F-actin localization
Authors: Heid Paul J. , Wessels Deborah , Daniels Karla J. , Gibson D. Phillip , Zhang Hui , Voss Ed , Soll David R.
Published: September 2004

To assess the role of myosin II heavy chain (MHC) phosphorylation in basic motility and natural chemotaxis, the Dictyostelium mhcA null mutant mhcA-, mhcA- cells rescued with a myosin II gene that mimics the constitutively unphosphorylated state (3XALA) and mhcA- cells rescued with a myosin II gene that mimics the constitutively phosphorylated state (3XASP), were analyzed in buffer and in response to the individual spatial, temporal and concentration components of a cAMP wave using computer-assisted methods. Each mutant strain exhibited unique defects in cell motility and chemotaxis. Although mhcA- cells could crawl with some polarity and showed chemotaxis with highly reduced efficiency in a spatial gradient of cAMP, they were very slow, far less polar and more three-dimensional than control cells. They were also incapable of responding to temporal gradients of cAMP, of chemotaxis in a natural wave of cAMP or streaming late in aggregation. 3XASP cells were faster and chemotactically more efficient than mhcA- cells, but still incapable of responding to temporal gradients of cAMP, chemotaxis in natural waves of cAMP or streaming late in aggregation. 3XALA cells were fast, were able to respond to temporal gradients of cAMP, and responded to natural waves of cAMP. However, they exhibited a 50% reduction in chemotactic efficiency, could not stream late in aggregation and could not enter the streams of control cells in mixed cultures. F-actin staining further revealed that while the presence of unphosphorylated MHC was essential for the increase in F-actin in the cytoplasm in response to the increasing temporal gradient of cAMP in the front of a natural wave, the actual dephosphorylation event was essential for the associated increase in cortical F-actin. The results of these studies indicate that MHC phosphorylation-dephosphorylation, like myosin II regulatory light chain phosphorylation-dephosphorylation, represents a potential downstream target of the regulatory cascades emanating from the different phases of the wave.
v-Src accelerates spontaneous motility via phosphoinositide 3-kinase, phospholipase C and phospholipase D, but abrogates chemotaxis in Rat-1 and MDCK cells
Authors: Platek Anna , Mettlen Marcel , Camby Isabelle , Kiss Robert , Amyere Mustapha , Courtoy Pierre J.
Published: September 2004

In Rat-1 fibroblasts, v-Src causes a profound remodelling of cortical actin cytoskeleton. This transformation includes membrane ruffling, a hallmark of the leading edge in migrating cells, and results from activation of phosphoinositide 3-kinase (PI 3-kinase), phospholipase C (PLC) and phospholipase D (PLD). We therefore reexamined whether motility is constitutively triggered by v-Src and studied whether this response is controlled by the same signalling pathway. The study was performed using Rat-1/tsLA29 and MDCK/tsLA31 cells, each harbouring a different thermosensitive v-Src kinase, active at 34°C but inactivated at 40°C. In both cell lines, overnight v-Src activation induced transformation and accelerated spontaneous motility by approximately twofold, as evidenced by wound-healing assay and by single-cell track, time-lapse recording in Dunn chambers. Inhibitors of PI 3-kinase, PLC and PLD selectively abrogated acceleration of motility by v-Src. Since mechanisms that co-ordinate spontaneous, as distinct from oriented, cell migration are separable, we further analysed in Dunn chambers chemotactic response of Rat-1/tsLA29 cells to PDGF and of MDCK/tsLA31 cells to EGF. In both cases, v-Src decreased the steady-state level of growth factor receptors at the cell surface twofold, and abrogated movement directionality at comparable level of occupancy as in non-transformed cells. The burst of pinocytosis in response to growth factors was also abolished by v-Src. Altogether, these results indicate that v-Src triggers motility in a PI 3-kinase-, PLC- and PLD-dependent manner, but abrogates directionality by suppressing polarised signalling downstream of growth factor receptors.
Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development
Authors: Næsted Henrik , Holm Agnethe , Jenkins Tom , Nielsen H. Bjørn , Harris Cassandra A. , Beale Michael H. , Andersen Mathias , Mant Alexandra , Scheller Henrik , Camara Bilal , Mattsson Ole , Mundy John
Published: September 2004

The stable, recessive Arabidopsis variegated 3 (var3) mutant exhibits a variegated phenotype due to somatic areas lacking or containing developmentally retarded chloroplasts and greatly reduced numbers of palisade cells. The VAR3 gene, isolated by transposon tagging, encodes the 85.9 kDa VAR3 protein containing novel repeats and zinc fingers described as protein interaction domains. VAR3 interacts specifically in yeast and in vitro with NCED4, a putative polyene chain or carotenoid dioxygenase, and both VAR3 and NCED4 accumulate in the chloroplast stroma. Metabolic profiling demonstrates that pigment profiles are qualitatively similar in wild type and var3, although var3 accumulates lower levels of chlorophylls and carotenoids. These results indicate that VAR3 is a part of a protein complex required for normal chloroplast and palisade cell development.
Signaling pathways controlling primordial germ cell migration in zebrafish
Authors: Dumstrei Karin , Mennecke Rebecca , Raz Erez
Published: September 2004

During their migration, zebrafish primordial germ cells (PGCs) rely on directional cues provided by the chemokine SDF-1a, whose receptor is CXCR4b. The molecular mechanisms whereby CXCR4b activation is interpreted intracellularly into directional migration are not known. Here we investigate the role of two important biochemical pathways - G-protein-dependent and phosphoinositide 3-kinase (PI3K)-dependent signaling - in directing PGC migration in zebrafish. We show that G proteins of the Gi family are essential for directional migration but not for PGC motility. Inhibition of PI3K signaling in PGCs slows down their migration and leads to abnormal cell morphology as well as to reduced stability of filopodia. Invariably, during directed PGC migration, the distribution of the products of PI3K activity - phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P3] and/or phosphatidylinositol (3,4)bisphosphate [PtdIns(3,4)P2] - is not polarized, and reducing the level of these 3-phosphoinositides does not affect the ability of PGCs to migrate directionally. We therefore conclude that Gi-dependent signaling is essential for directional migration, whereas the PI3K pathway is important for the actual motility of PGCs.
The RacGEF Tiam1 inhibits migration and invasion of metastatic melanoma via a novel adhesive mechanism
Authors: Uhlenbrock Katharina , Eberth Alexander , Herbrand Ulrike , Daryab Neda , Stege Patricia , Meier Friedegund , Friedl Peter , Collard John G. , Ahmadian Mohammad Reza
Published: September 2004

Rho-like GTPases such as RhoA, Rac1 and Cdc42 are key regulators of actin-dependent cell functions including cell morphology, adhesion and migration. Tiam1 (T lymphoma invasion and metastasis 1), a guanine nucleotide exchange factor that activates Rac, is an important regulator of cell shape and invasiveness in epithelial cells and fibroblasts. Overexpression of Tiam1 in metastatic melanoma cells converted the constitutive mesenchymal phenotype into an epithelial-like phenotype. This included the induction of stringent cell-cell contacts mediated by the Ig-like receptor ALCAM (activated leukocyte cell adhesion molecule) and actin redistribution to cell-cell junctions. This phenotypic switch was dependent on increased Rac but not Rho activity, and on the redistribution and adhesive function of ALCAM, whereas cadherins were not involved. Although cell proliferation was significantly enhanced, the gain of cell-cell junctions strongly counteracted cell motility and invasion as shown for two- and three-dimensional collagen assays as well as invasion into human skin reconstructs. The reverse transition from mesenchymal invasive to a resident epithelial-like phenotype implicates a role for Tiam1/Rac signaling in the control of cell-cell contacts through a novel ALCAM-mediated mechanism.
Light-dependent subcellular translocation of Gqα in Drosophila photoreceptors is facilitated by the photoreceptor-specific myosin III NINAC
Authors: Cronin Michelle A. , Diao Fengqiu , Tsunoda Susan
Published: September 2004

We examine the light-dependent subcellular translocation of the visual Gqα protein between the signaling compartment, the rhabdomere and the cell body in Drosophila photoreceptors. We characterize the translocation of Gqα and provide the first evidence implicating the involvement of the photoreceptor-specific myosin III NINAC in Gqα transport. Translocation of Gqα from the rhabdomere to the cell body is rapid, taking less than 5 minutes. Higher light intensities increased the quantity of Gqα translocated out of the rhabdomeres from 20% to 75%, consistent with a mechanism for light adaptation. We demonstrate that translocation of Gqα requires rhodopsin, but none of the known downstream phototransduction components, suggesting that the signaling pathway triggering translocation occurs upstream of Gqα. Finally, we show that ninaC mutants display a significantly reduced rate of Gqα transport from the cell body to the rhabdomere, suggesting that NINAC might function as a light-dependent plus-end motor involved in the transport of Gqα.
Multiple Experts vs. Multiple Methods: Combining Correlation Assessments
Authors: Winkler Robert L. , Clemen Robert T.
Published: September 2004

Averaging forecasts from several experts has been shown to lead to improved forecasting accuracy and reduced risk of bad forecasts. Similarly, it is accepted knowledge in decision analysis that an expert can benefit from using more than one assessment method to look at a situation from different viewpoints. In this paper, we investigate gains in accuracy in assessing correlations by averaging different assessments from a single expert and/or from multiple experts. Adding experts and adding methods can both improve accuracy, with diminishing returns to extra experts or methods. The gains are generally much greater from adding experts than from adding methods, and restricting the set of experts to those who do particularly well individually leads to the greatest improvements in the averaged assessments. The variability of assessment accuracy decreases considerably as the number of experts or methods increases, implying a large risk reduction. We discuss conditions under which the general pattern of results obtained here might be expected to be similar or different in other situations with multiple experts and/or multiple methods.
Value of Information in Portfolio Decision Analysis
Authors: Keisler Jeffrey
Published: September 2004

It can be time consuming to use decision analysis to allocate resources over a portfolio of projects. It may be possible to attain most of the value added by decision analysis in significantly less time. This paper defines and compares different analytic strategies in terms of the resulting value added for a range of simulated portfolios. A portfolio consists of a set of candidate projects or investments of uncertain value. The value of each project may be estimated with or without the additional information provided by decision-analytic methods. Projects are then completely prioritized and funded in order of the ratio of their expected net present value to their cost, or partially prioritized and funded whenever this ratio exceeds a predefined threshold level. The portfolio funded under the various analytic strategies is compared against a strawman alternative of random funding decisions. The value added through disciplined prioritization often exceeds the additional value added through the more costly step of developing refined estimates of project values. Intermediate approaches, including threshold approaches and the application of triage rules to determine which projects to analyze, are found to be useful but not robust.
A Comparison of VaR and CVaR Constraints on Portfolio Selection with the Mean-Variance Model
Authors: Alexander Gordon J. , Baptista Alexandre M.
Published: September 2004

In this paper, we analyze the portfolio selection implications arising from imposing a value-at-risk (VaR) constraint on the mean-variance model, and compare them with those arising from the imposition of a conditional value-at-risk (CVaR) constraint. We show that for a given confidence level, a CVaR constraint is tighter than a VaR constraint if the CVaR and VaR bounds coincide. Consequently, a CVaR constraint is more effective than a VaR constraint as a tool to control slightly risk-averse agents, but in the absence of a risk-free security, has a perverse effect in that it is more likely to force highly risk-averse agents to select portfolios with larger standard deviations. However, when the CVaR bound is appropriately larger than the VaR bound or when a risk-free security is present, a CVaR constraint “dominates” a VaR constraint as a risk management tool.
Decentralized Pricing and Capacity Decisions in a Multitier System with Modular Assembly
Authors: Bernstein Fernando , DeCroix Gregory A.
Published: September 2004

We model a modular assembly system in which a final assembler outsources some of the assembly task to first-tier suppliers (subassemblers), who produce modules made up of multiple components. The assembler sets module prices it will pay to the subassemblers, the subassemblers set component prices they will pay to suppliers, and then all players choose how much capacity to install, with the minimum capacity choice determining system capacity. Finally, stochastic end-product demand is observed and all players produce (and are paid for) the same number of units—the minimum of demand and system capacity.

We characterize equilibrium price and capacity choices, and then use that characterization to derive results regarding higher-level structural choices by the assembler—such as how to group components into modules and which suppliers to choose as subassemblers. We also compare performance of the system to a traditional assembly system with an assembler and suppliers but without subassemblers.
ANNIVERSARY ARTICLE: Option Pricing: Valuation Models and Applications
Authors: Broadie Mark , Detemple Jerome B.
Published: September 2004

This paper surveys the literature on option pricing from its origins to the present. An extensive review of valuation methods for European- and American-style claims is provided. Applications to complex securities and numerical methods are surveyed. Emphasis is placed on recent trends and developments in methodology and modeling.
Which GARCH Model for Option Valuation?
Authors: Christoffersen Peter , Jacobs Kris
Published: September 2004

Characterizing asset return dynamics using volatility models is an important part of empirical finance. The existing literature on GARCH models favors some rather complex volatility specifications whose relative performance is usually assessed through their likelihood based on a time series of asset returns. This paper compares a range of GARCH models along a different dimension, using option prices and returns under the risk-neutral as well as the physical probability measure. We judge the relative performance of various models by evaluating an objective function based on option prices. In contrast with returns-based inference, we find that our option-based objective function favors a relatively parsimonious model. Specifically, when evaluated out-of-sample, our analysis favors a model that, besides volatility clustering, only allows for a standard leverage effect.
Inventory Management with Asset-Based Financing
Authors: Buzacott John A. , Zhang Rachel Q.
Published: September 2004

Most of the traditional models in production and inventory control ignore the financial states of an organization and can lead to infeasible practices in real systems. This paper is the first attempt to incorporate asset-based financing into production decisions. Instead of setting a known, exogenously determined budgetary constraint as most existing models suggest, we model the available cash in each period as a function of assets and liabilities that may be updated periodically according to the dynamics of the production activities. Furthermore, our models allow different interest rates on cash balance and outstanding loans, which is an enhancement over most traditional models in that inventory financed by a loan may be more expensive than that by out-of-pocket cash. We demonstrate the importance of joint consideration of production and financing decisions in a start-up setting in which the ability to grow the firm is mainly constrained by its limited capital and dependence on bank financing. We then explain the motivation for asset-based financing by examining the decision making at a bank and a set of retailers in a newsvendor setting.
Acute Onset of Pancreatitis with Concomitant Use of Tenofovir and Didanosine
Authors: Kirian Margaret A , Higginson Robert T , Fulco Patricia Pecora
Published: September 2004

OBJECTIVE

To report a case of pancreatitis associated with the combined use of didanosine and tenofovir.

Case Summary

A 51-year-old white man with HIV was initiated on antiretroviral therapy with didanosine 250 mg/day, tenofovir 300 mg/day, lamivudine 300 mg/day, stavudine 60 mg/day, and efavirenz 600 mg/day. Didanosine was prescribed at a reduced dosage due to the known interaction with tenofovir. Despite this dosage adjustment, the patient developed acute pancreatitis 10 weeks after antiretrovirals were initiated. Pancreatitis resolved spontaneously after antiretroviral discontinuation.

DISCUSSION

Our report of didanosine-induced pancreatitis secondary to concurrent use with tenofovir is the third reported case that utilized a reduced didanosine dosage. Five previous pancreatitis reports have been described using full-strength didanosine with tenofovir. The exact mechanism of action for this interaction is unknown. Utilizing the Naranjo probability scale to assess causality, a possible adverse drug reaction was determined.

CONCLUSIONS

Tenofovir and didanosine may be used cautiously in antiretroviral combination therapy. Reduced didanosine dosage (250 mg) should be used to reduce serum didanosine concentrations and subsequent toxicities. Practitioners should be aware that a significant drug interaction with resulting pancreatitis may occur even when a reduced dosage is prescribed.
Confrontation and Hearsay: A Critique of Crawford
Authors: Ho H. L.
Published: September 2004

In the recent case of Crawford v Washington, the United States Supreme Court took a new interpretation of the right of confrontation, as it is expressed in the Confrontation Clause of the Sixth Amendment to the United States' Constitution, and of the relation of that right to the hearsay doctrine. According to the majority, no ‘testimonial’ statement is admissible as evidence of the fact stated unless the maker of the statement is unavailable to testify at the trial and there was a prior opportunity to cross-examine him. This article examines the reasoning in Crawford, the concept of a ‘testimonial’ statement, and the application of the decision in subsequent cases. While the ruling in Crawford purports to be true to the letter and spirit of the Confrontation Clause, there are grounds to be critical of the reasoning of the majority and of the merits of the new approach.