bluuebunny/crossref_metadata_2025 huggingface dataset:
Integral membrane proteins of the chloroplast envelope: Identification and subcellular localization of new transporters
Authors: Ferro Myriam , Salvi Daniel , Rivière-Rolland Hélène , Vermat Thierry , Seigneurin-Berny Daphné , Grunwald Didier , Garin Jérôme , Joyard Jacques , Rolland Norbert
Published: September 2002

A two-membrane system, or envelope, surrounds plastids. Because of the integration of chloroplast metabolism within the plant cell, the envelope is the site of many specific transport activities. However, only a few proteins involved in the processes of transport across the chloroplast envelope have been identified already at the molecular level. To discover new envelope transporters, we developed a subcellular proteomic approach, which is aimed to identify the most hydrophobic envelope proteins. This strategy combined the use of highly purified and characterized membrane fractions, extraction of the hydrophobic proteins with organic solvents, SDS/PAGE separation, and tandem mass spectrometry analysis. To process the large amount of MS/MS data, a
blast
-based program was developed for searching in protein, expressed sequence tag, and genomic plant databases. Among the 54 identified proteins, 27 were new envelope proteins, with most of them bearing multiple α-helical transmembrane regions and being very likely envelope transporters. The present proteomic study also allowed us to identify common features among the known and newly identified putative envelope inner membrane transporters. These features were used to mine the complete
Arabidopsis
genome and allowed us to establish a virtual plastid envelope integral protein database. Altogether, both proteomic and
in silico
approaches identified more than 50 candidates for the as yet previously uncharacterized plastid envelope transporters. The predictable function of some of these proteins opens up areas of investigation that may lead to a better understanding of the chloroplast metabolism. The present subcellular proteomic approach is amenable to the analysis of the hydrophobic core of other intracellular membrane systems.
The anaphase promoting complex/cyclosome is required during development for modified cell cycles
Authors: Kashevsky Helena , Wallace Julie A. , Reed Bruce H. , Lai Cary , Hayashi-Hagihara Aki , Orr-Weaver Terry L.
Published: September 2002

Animals and plants use modified cell cycles to achieve particular developmental strategies. In one common example, most animals and plants have tissues in which the cells become polyploid or polytene by means of an S–G cycle, but the mechanism by which mitosis is inhibited in the endo cycle is not understood. The
Drosophila
morula
(
mr
) gene regulates variant cell cycles, because in addition to disrupting the archetypal cycle (G
1
–S–G
2
–M),
mr
mutations affect the rapid embryonic (S–M) divisions as well as the endo cycle (S–G) that produces polyploid cells. In dividing cells
mr
mutations cause a metaphase arrest, and endo cycling nurse cells inappropriately reenter mitosis in
mr
mutants. We show
mr
encodes the APC2 subunit of the anaphase promoting complex/cyclosome. This finding demonstrates that anaphase promoting complex/cyclosome is required not only in proliferating cells but also to block mitosis in some endo cycles. The
mr
mutants further indicate that transient mitotic functions in endo cycles change chromosome morphology from polytene to polyploid.
Mothers’ conceptions of child competence in contexts of poverty: The Philippines, St Vincent, and the United States
Authors: Durbrow Eric H. , Pen Liane F. , Masten Ann , Sesma Art , Williamson Ian
Published: September 2002

To explore mothers’ conceptions of child competence in three contexts of poverty, 58 mothers in a Filipino village, a Caribbean village, and an inner-city American homeless shelter described competent children in their communities. Interview responses addressed several questions. First, do mothers in these diverse settings share similar criteria in evaluating children? As expected, all three groups of mothers described competent children as well-behaved and obedient, satisfactory students, helpful in the family, and friendly with peers. Second, are adolescents less likely than younger children to be identi” ed spontaneously as examples of competence? In contrast to Filipino mothers, American shelter and Caribbean village mothers were unlikely to identify adolescent boys as competent. Lastly, what were mothers’ explanations for children’s competence? All mothers emphasised parenting as the most important factor in fostering competence, but differed on secondary factors. Results suggest that similarities may reflect shared concerns in adapting to poverty as well as shared salience in developmental tasks across these cultures. Differences in maternal conceptions may reflect demands and opportunities specific to each context.
Raising the Standard of Management Education for Electronic Commerce Professionals
Authors: Joseph Richard
Published: September 2002

The teaching of electronic commerce in universities has become a growth industry in itself. The rapid expansion of electronic commerce programmes raises the question of what actually is being taught. The association of electronic commerce as primarily a technical or information technology (IT) phenomenon has not been sufficient to constrain it to IT and information systems departments. Business schools have been keen entrants into the electronic commerce coursework race and they are developing electronic commerce programmes in an environment where there is no agreed definition of the term. This paper draws on the work of Kenneth Boulding who argued that the dynamics of change in society are largely a product of changing skills and the way these skills are arranged into roles at the organizational level. It is argued that an overly technical interpretation of electronic commerce narrows the skills being acquired as part of formal education. Universities, under pressure from the market and technological change, are changing their roles resulting in a further narrowing of the breadth of issues that is seen as legitimate to be included as electronic commerce. The outcome is that aspiring electronic commerce professionals are not being exposed to a wide enough agenda of ideas and concepts that will assist them to make better business decisions.
Catching the Wave: German Media on September 11
Authors: Haes Joachim W. H.
Published: September 2002

This paper describes reactions in the German publication Der Spiegel to the attacks of September 11. The paper starts by describing the live reporting in the German media and then analyzes the Der Spiegel edition of September 15. The aim is to give an idea of how European journalists handled the situation and how different conclusions developed.
Morris A. Copeland: A Case Study in the History of Institutional Economics
Authors: Rutherford Malcolm
Published: September 2002

Morris A. Copeland's work and career as an institutional economist has been the subject of only one significant paper (Millar 1980) and is not well known today, even among institutionalists. The standard histories of institutional economics have tended to focus on a few leading figures, notably Thorstein Veblen, Wesley C. Mitchell, John R. Commons, and Clarence Ayres, and have largely ignored the many others (some of whom had outstanding careers) associated with the movement. This narrow focus has given a misleading impression both of the institutionalist movement itself and also of the nature of the institutionalist contribution to economics. The examination of Copeland's career, treated as a case study in the history of institutional economics, can help correct this problem. Copeland is a perfect candidate for such a case study due to his central place within the interwar institutionalist movement, his teachers, the contacts he maintained, his work in both academic economics and in public service, and his professional standing within economics more generally.
Design Methodology of a 32‐bit Arithmetic Logic Unit with an Adaptive Leaf‐cell Based Layout Technique
Authors: Cho Kiseon , Song Minkyu
Published: September 2002

In general, an arithmetic logic unit (ALU) of a DSP core is composed of an adder, multiplier and shifter. In order to obtain a high‐performance 32‐bit ALU, in this paper, an adaptive leaf‐cell based layout technique is proposed. Thus novel architectures of 64‐bit adder, 32 × 32‐bit multiplier, and 32‐bit shifter are proposed. The architecture of the proposed 64‐bit adder is based on the conditional select addition with regular adaptive multiplexers. Secondly, novel optimized data compressors with a compound logic are proposed in a 32 × 32‐bit multiplier. Finally, a shift algorithm with a pre‐mask decoder is proposed for the 32‐bit barrel shifter. They have been fabricated with 0.25 μm 1‐poly 5‐metal CMOS process, and we have obtained desired experimental results.
Energy Minimization Under Area and Performance Constraints for Multimedia Applications Realized on Embedded Cores
Authors: Zervas N. D. , Masselos K. , Karayiannis Y. A. , Goutis C. E.
Published: September 2002

A systematic methodology for energy dissipation reduction of multimedia applications realized on architectures based on embedded cores and application specific data memory organization is proposed. Performance and area are explicitly taken into account. The proposed methodology includes two major steps: A high‐level code transformation step that reorganizes the original description of the target application. The second major step includes the determination of the processor, memory and bus organization of the system and is briefly described. Experimental results from several real‐life demonstrators prove the impact of the high level step of the proposed methodology.
p21-activated kinase 4 interacts with integrin αvβ5 and regulates αvβ5-mediated cell migration
Authors: Zhang Hongquan , Li Zhilun , Viklund Eva-Karin , Strömblad Staffan
Published: September 2002

p21-activated kinase 1 (PAK1) can affect cell migration (Price et al., 1998; del Pozo et al., 2000) and modulate myosin light chain kinase and LIM kinase, which are components of the cellular motility machinery (Edwards, D.C., L.C. Sanders, G.M. Bokoch, and G.N. Gill. 1999. Nature Cell Biol. 1:253–259; Sanders, L.C., F. Matsumura, G.M. Bokoch, and P. de Lanerolle. 1999. Science. 283:2083–2085). We here present a novel cell motility pathway by demonstrating that PAK4 directly interacts with an integrin intracellular domain and regulates carcinoma cell motility in an integrin-specific manner. Yeast two-hybrid screening identified PAK4 binding to the cytoplasmic domain of the integrin β5 subunit, an association that was also found in mammalian cells between endogenous PAK4 and integrin αvβ5. Furthermore, we mapped the PAK4 binding to the membrane-proximal region of integrin β5, and identified an integrin-binding domain at aa 505–530 in the COOH terminus of PAK4. Importantly, engagement of integrin αvβ5 by cell attachment to vitronectin led to a redistribution of PAK4 from the cytosol to dynamic lamellipodial structures where PAK4 colocalized with integrin αvβ5. Functionally, PAK4 induced integrin αvβ5–mediated, but not β1-mediated, human breast carcinoma cell migration, while no changes in integrin cell surface expression levels were observed. In conclusion, our results demonstrate that PAK4 interacts with integrin αvβ5 and selectively promotes integrin αvβ5–mediated cell migration.
Discrete Role for Cytosolic Phospholipase A2α in Platelets
Authors: Wong Dennis A. , Kita Yoshihiro , Uozumi Naonori , Shimizu Takao
Published: September 2002

Among several different types of phospholipase A2 (PLA2), cytosolic PLA2 (cPLA2)α and group IIA (IIA) secretory PLA2 (sPLA2) have been studied intensively. To determine the discrete roles of cPLA2α in platelets, we generated two sets of genetically engineered mice (cPLA2α−/−/sPLA2-IIA−/− and cPLA2α−/−/sPLA2-IIA+/+) and compared their platelet function with their respective wild-type C57BL/6J mice (cPLA2α+/+/sPLA2-IIA−/−) and C3H/HeN (cPLA2α+/+/sPLA2-IIA+/+). We found that cPLA2α is needed for the production of the vast majority of thromboxane (TX)A2 with collagen stimulation of platelets. In cPLA2α-deficient mice, however, platelet aggregation in vitro is only fractionally decreased because small amounts of TX produced by redundant phospholipase enzymes sufficiently preserve aggregation. In comparison, adenosine triphosphate activation of platelets appears wholly independent of cPLA2α and sPLA2-IIA for aggregation or the production of TX, indicating that these phospholipases are specifically linked to collagen receptors. However, the lack of high levels of TX limiting vasoconstriction explains the in vivo effects seen: increased bleeding times and protection from thromboembolism. Thus, cPLA2α plays a discrete role in the collagen-stimulated production of TX and its inhibition has a therapeutic potential against thromboembolism, with potentially limited bleeding expected.
The CD16+ (FcγRIII+) Subset of Human Monocytes Preferentially Becomes Migratory Dendritic Cells in a Model Tissue Setting
Authors: Randolph Gwendalyn J. , Sanchez-Schmitz Guzman , Liebman Ronald M. , Schäkel Knut
Published: September 2002

Much remains to be learned about the physiologic events that promote monocytes to become lymph-homing dendritic cells (DCs). In a model of transendothelial trafficking, some monocytes become DCs in response to endogenous signals. These DCs migrate across endothelium in the ablumenal-to-lumenal direction (reverse transmigration), reminiscent of the migration into lymphatic vessels. Here we show that the subpopulation of monocytes that expresses CD16 (Fcγ receptor III) is predisposed to become migratory DCs. The vast majority of cells derived from CD16+ monocytes reverse transmigrated, and their presence was associated with migratory cells expressing high levels of CD86 and human histocompatibility leukocyte antigen (HLA)-DR, and robust capacity to induce allogeneic T cell proliferation. A minority of CD16− monocytes reverse transmigrated, and these cells stimulated T cell proliferation less efficiently. CD16 was not functionally required for reverse transmigration, but promoted cell survival when yeast particles (zymosan) were present as a maturation stimulus in the subendothelial matrix. The cell surface phenotype and migratory characteristics of CD16+ monocytes were inducible in CD16− monocytes by preincubation with TGFβ1. We propose that CD16+ monocytes may contribute significantly to precursors for DCs that transiently survey tissues and migrate to lymph nodes via afferent lymphatic vessels.
CD4+ T Cells from Glutamic Acid Decarboxylase (GAD)65-specific T Cell Receptor Transgenic Mice Are Not Diabetogenic and Can Delay Diabetes Transfer
Authors: Tarbell Kristin V. , Lee Mark , Ranheim Erik , Chao Cheng Chi , Sanna Maija , Kim Seon-Kyeong , Dickie Peter , Teyton Luc , Davis Mark , McDevitt Hugh
Published: September 2002

Glutamic acid decarboxylase (GAD)65 is an early and important antigen in both human diabetes mellitus and the nonobese diabetic (NOD) mouse. However, the exact role of GAD65-specific T cells in diabetes pathogenesis is unclear. T cell responses to GAD65 occur early in diabetes pathogenesis, yet only one GAD65-specific T cell clone of many identified can transfer diabetes. We have generated transgenic mice on the NOD background expressing a T cell receptor (TCR)-specific for peptide epitope 286–300 (p286) of GAD65. These mice have GAD65-specific CD4+ T cells, as shown by staining with an I-Ag7(p286) tetramer reagent. Lymphocytes from these TCR transgenic mice proliferate and make interferon γ, interleukin (IL)-2, tumor necrosis factor (TNF)-α, and IL-10 when stimulated in vitro with GAD65 peptide 286–300, yet these TCR transgenic animals do not spontaneously develop diabetes, and insulitis is virtually undetectable. Furthermore, in vitro activated CD4 T cells from GAD 286 TCR transgenic mice express higher levels of CTL-associated antigen (CTLA)-4 than nontransgenic littermates. CD4+ T cells, or p286-tetramer+CD4+ Tcells, from GAD65 286–300-specific TCR transgenic mice delay diabetes induced in NOD.scid mice by diabetic NOD spleen cells. This data suggests that GAD65 peptide 286–300-specific T cells have disease protective capacity and are not pathogenic.
CD4+CD25+ Immunoregulatory T Cells
Authors: Cohen José L. , Trenado Aurélie , Vasey Douglas , Klatzmann David , Salomon Benoît L.
Published: September 2002

CD4+CD25+ immunoregulatory T cells play a pivotal role in preventing organ-specific autoimmune diseases and in tolerance induction to allogeneic organ transplants. We investigated whether these cells could also control graft-versus-host disease (GVHD), the main complication after allogeneic hematopoietic stem cell transplantation (HSCT). Here, we show that the few CD4+CD25+ T cells naturally present in the transplant regulate GVHD because their removal from the graft dramatically accelerates this disease. Furthermore, the addition of freshly isolated CD4+CD25+ T cells at time of grafting significantly delays or even prevents GVHD. Ex vivo–expanded CD4+CD25+ regulatory T cells obtained after stimulation by allogeneic recipient-type antigen-presenting cells can also modulate GVHD. Thus, CD4+CD25+ regulatory T cells represent a new therapeutic tool for controlling GVHD in allogeneic HSCT. More generally, these results outline the tremendous potential of regulatory T cells as therapeutics.
CD28-dependent Activation of Protein Kinase B/Akt Blocks Fas-mediated Apoptosis by Preventing Death-inducing Signaling Complex Assembly
Authors: Jones Russell G. , Elford Alisha R. , Parsons Michael J. , Wu Linda , Krawczyk Connie M. , Yeh Wen-Chen , Hakem Razqallah , Rottapel Robert , Woodgett James R. , Ohashi Pamela S.
Published: September 2002

The T cell costimulatory molecule CD28 is important for T cell survival, yet both the signaling pathways downstream of CD28 and the apoptotic pathways they antagonize remain poorly understood. Here we demonstrate that CD4+ T cells from CD28-deficient mice show increased susceptibility to Fas-mediated apoptosis via a phosphatidylinositol 3-kinase (PI3K)-dependent pathway. Protein kinase B (PKBα/Akt1) is an important serine/threonine kinase that promotes survival downstream of PI3K signals. To understand how PI3K-mediated signals downstream of CD28 contribute to T cell survival, we examined Fas-mediated apoptosis in T cells expressing an active form of PKBα. Our data demonstrate that T cells expressing active PKB are resistant to Fas-mediated apoptosis in vivo and in vitro. PKB transgenic T cells show reduced activation of caspase-8, BID, and caspase-3 due to impaired recruitment of procaspase-8 to the death-inducing signaling complex (DISC). Similar alterations are seen in T cells from mice which are haploinsufficient for PTEN, a lipid phosphatase that regulates phosphatidylinositol-3,4,5-trisphosphate (PIP3) and influences PKBα activity. These findings provide a novel link between CD28 and an important apoptosis pathway in vivo, and demonstrate that PI3K/PKB signaling prevents apoptosis by inhibiting DISC assembly.
Single Channel Properties of Rat Acid–sensitive Ion Channel-1α, -2a, and -3 Expressed in Xenopus Oocytes
Authors: Zhang Ping , Canessa Cecilia M.
Published: September 2002

The mammalian nervous system expresses proton-gated ion channels known as acid-sensing ion channels (ASICs). Depending on their location and specialization some neurons express more than one type of ASIC where they may form homo- or heteromeric channels. Macroscopic characteristics of the ASIC currents have been described, but little is known at the single channel level. Here, we have examined the properties of unitary currents of homomeric rat ASIC1α, ASIC2a, and ASIC3 expressed in Xenopus oocytes with the patch clamp technique. We describe and characterize properties unique to each of these channels that can be used to distinguish the various types of ASIC channels expressed in mammalian neurons. The amplitudes of the unitary currents in symmetrical Na+ are similar for the three types of channels (23–18 pS) and are not voltage dependent. However, ASIC1α exhibits three subconductance states, ASIC2a exhibits only one, and ASIC3 none. The kinetics of the three types of channels are different: ASIC1α and ASIC2a shift between modes of activity, each mode has different open probability and kinetics. In contrast, the kinetics of ASIC3 are uniform throughout the burst of activity. ASIC1α, ASIC2a, and ASIC3 are activated by external protons with apparent pH50 of 5.9, 5.0, and 5.4, respectively. Desensitization in the continual presence of protons is fast and complete in ASIC1α and ASIC3 (2.0 and 4.5 s−1, respectively) but slow and only partial in ASIC2a (0.045 s−1). The response to external Ca2+ also differs: μM concentrations of extracellular Ca2+ are necessary for proton gating of ASIC3 (EC50 = 0.28 μM), whereas ASIC1α and ASIC2a do not require Ca2+. In addition, Ca2+ inhibits ASIC1α (KD = 9.2 ± 2 mM) by several mechanisms: decrease in the amplitude of unitary currents, shortening of the burst of activity, and decrease in the number of activated channels. Contrary to previous reports, our results indicate that the Ca2+ permeability of ASIC1α is very small.
The Effects of HCl and CaCl2 Injections on Intracellular Calcium and pH in Voltage-clamped Snail (Helix aspersa) Neurons
Authors: Thomas Roger C.
Published: September 2002

To investigate the mechanisms by which low intracellular pH influences calcium signaling, I have injected HCl, and in some experiments CaCl2, into snail neurons while recording intracellular pH (pHi) and calcium concentration ([Ca2+]i) with ion-sensitive microelectrodes. Unlike fluorescent indicators, these do not increase buffering. Slow injections of HCl (changing pHi by 0.1–0.2 pH units min−1) first decreased [Ca2+]i while pHi was still close to normal, but then increased [Ca2+]i when pHi fell below 6.8–7. As pHi recovered after such an injection, [Ca2+]i started to fall but then increased transiently before returning to its preinjection level. Both the acid-induced decrease and the recovery-induced increase in [Ca2+]i were abolished by cyclopiazonic acid, which empties calcium stores. Caffeine with or without ryanodine lowered [Ca2+]i and converted the acid-induced fall in [Ca2+]i to an increase. Injection of ortho-vanadate increased steady-state [Ca2+]i and its response to acidification, which was again blocked by CPA. The normal initial response to 10 mM caffeine, a transient increase in [Ca2+]i, did not occur with pHi below 7.1. When HCl was injected during a series of short CaCl2 injections, the [Ca2+]i transients (recorded as changes in the potential (VCa) of the Ca2+-sensitive microelectrode), were reduced by only 20% for a 1 pH unit acidification, as was the rate of recovery after each injection. Calcium transients induced by brief depolarizations, however, were reduced by 60% by a similar acidification. These results suggest that low pHi has little effect on the plasma membrane calcium pump (PMCA) but important effects on the calcium stores, including blocking their response to caffeine. Acidosis inhibits spontaneous calcium release via the RYR, and leads to increased store content which is unloaded when pHi returns to normal. Spontaneous release is enhanced by the rise in [Ca2+]i caused by inhibiting the PMCA.
Combined Antiviral-Antimediator Treatment for the Common Cold
Authors: Gwaltney Jack M. , Winther Birgit , Patrie James T. , Hendley J. Owen
Published: September 2002

A randomized, controlled, double-masked clinical trial was conducted with a combination antiviral-antimediator treatment for experimental rhinovirus colds. In all, 150 healthy men and women (aged 18–51 years) were randomly assigned to 1 of 3 groups: intranasal interferon (IFN)–α2b (6×106 U every 12 h × 3) plus oral chlorpheniramine (12 mg extended release) and ibuprofen (400 mg) every 12 h for 4.5 days (n=59 subjects); intranasal placebo plus oral chlorpheniramine and ibuprofen (n=61 subjects); or intranasal and oral placebos (n=30 subjects). Treatment was started 24 h after intranasal viral challenge. During the 4.5 days of treatment with IFN-α2b, chlorpheniramine, and ibuprofen, the daily mean total symptom score was reduced by 33%–73%, compared with placebo. Treatment reduced the severity of rhinorrhea, sneezing, nasal obstruction, sore throat, cough, and headache and reduced nasal mucus production, nasal tissue use, and virus concentrations in nasal secretions. IFN-α2b added to the effectiveness of chlorpheniramine and ibuprofen and was well tolerated
An Approach to an Analysis of the Arterial Pulse Wave I. Oscillations in an Attenuating Line
Authors: M G Taylor
Published: September 2002

The Telegraph equations have been used to obtain expressions for the following quantities in an attenuating electric transmission line:

1. the input impedance in terms of the length of an open-circuited line,

2. the modulus of the voltage as a function of the distance along an open-circuited line,

3. the ` apparent phase velocity at a point ' along a line, as a function of the distance from the origin and the nature of the termination,

4. the ` apparent phase velocity over a finite interval ' for the same type of line,

5. the modulus of the reflection coefficient in terms of (4).

Numerical examples have been computed for (1)-(4) and are presented.

The use of the attenuating electric line as a model in approaching an understanding of the dynamics of the arterial circulation is outlined, and the limitations discussed.
Association of PI-3 Kinase with PAK1 Leads to Actin Phosphorylation and Cytoskeletal Reorganization
Authors: Papakonstanti Evangelia A. , Stournaras Christos
Published: September 2002

The family of p21-activated kinases (PAKs) have been implicated in the rearrangement of actin cytoskeleton by acting downstream of the small GTPases Rac and Cdc42. Here we report that even though Cdc42/Rac1 or Akt are not activated, phosphatidylinositol-3 (PI-3) kinase activation induces PAK1 kinase activity. Indeed, we demonstrate that PI-3 kinase associates with the N-terminal regulatory domain of PAK1 (amino acids 67–150) leading to PAK1 activation. The association of the PI-3 kinase with the Cdc42/Rac1 binding-deficient PAK1(H83,86L) confirms that the small GTPases are not involved in the PI-3 kinase-PAK1 interaction. Furthermore, PAK1 was activated in cells expressing the dominant-negative forms of Cdc42 or Rac1. Additionally, we show that PAK1 phosphorylates actin, resulting in the dissolution of stress fibers and redistribution of microfilaments. The phosphorylation of actin was inhibited by the kinase-dead PAK1(K299R) or the PAK1 autoinhibitory domain (PAK1(83–149)), indicating that PAK1 was responsible for actin phosphorylation. We conclude that the association of PI-3 kinase with PAK1 regulates PAK1 kinase activity through a Cdc42/Rac1-independent mechanism leading to actin phosphorylation and cytoskeletal reorganization.
Release of Hepatocyte Growth Factor from Mechanically Stretched Skeletal Muscle Satellite Cells and Role of pH and Nitric Oxide
Authors: Tatsumi Ryuichi , Hattori Akihito , Ikeuchi Yoshihide , Anderson Judy E. , Allen Ronald E.
Published: September 2002

Application of mechanical stretch to cultured adult rat muscle satellite cells results in release of hepatocyte growth factor (HGF) and accelerated entry into the cell cycle. Stretch activation of cultured rat muscle satellite cells was observed only when medium pH was between 7.1 and 7.5, even though activation of satellite cells was accelerated by exogenous HGF over a pH range from 6.9 to 7.8. Furthermore, HGF was only released in stretched cultures when the pH of the medium was between 7.1 and 7.4. Conditioned medium from stretched satellite cell cultures stimulated activation of unstretched satellite cells, and the addition of anti-HGF neutralizing antibodies to stretch-conditioned medium inhibited the stretch activation response. Conditioned medium from satellite cells that were stretched in the presence of nitric-oxide synthase (NOS) inhibitorNω-nitro-l-arginine methyl ester hydrochloride did not accelerate activation of unstretched control satellite cells, and HGF was not released into the medium. Conditioned medium from unstretched cells that were treated with a nitric oxide donor, sodium nitroprusside dihydrate, was able to accelerate the activation of satellite cells in vitro, and HGF was found in the conditioned medium. Immunoblot analysis indicated that both neuronal and endothelial NOS isoforms were present in satellite cell cultures. Furthermore, assays of NOS activity in stretched satellite cell cultures demonstrated that NOS is stimulated when satellite cells are stretched in vitro. These experiments indicate that stretch triggers an intracellular cascade of events, including nitric oxide synthesis, which results in HGF release and satellite cell activation.
Dissection of Transient Oxidative Stress Response inSaccharomyces cerevisiaeby Using DNA Microarrays
Authors: Koerkamp Marian Groot , Rep Martijn , Bussemaker Harmen J. , Hardy Guy P.M.A. , Mul Adri , Piekarska Kasia , Szigyarto Cristina Al-Khalili , de Mattos Joost M. Teixeira , Tabak Henk F.
Published: September 2002

Yeast cells were grown in glucose-limited chemostat cultures and forced to switch to a new carbon source, the fatty acid oleate. Alterations in gene expression were monitored using DNA microarrays combined with bioinformatics tools, among which was included the recently developed algorithm REDUCE. Immediately after the switch to oleate, a transient and very specific stress response was observed, followed by the up-regulation of genes encoding peroxisomal enzymes required for fatty acid metabolism. The stress response included up-regulation of genes coding for enzymes to keep thioredoxin and glutathione reduced, as well as enzymes required for the detoxification of reactive oxygen species. Among the genes coding for various isoenzymes involved in these processes, only a specific subset was expressed. Not the general stress transcription factors Msn2 and Msn4, but rather the specific factor Yap1p seemed to be the main regulator of the stress response. We ascribe the initiation of the oxidative stress response to a combination of poor redox flux and fatty acid-induced uncoupling of the respiratory chain during the metabolic reprogramming phase.
An analysis of gene-finding programs for Neurospora
crassa
Authors: Kraemer Eileen , Wang Jian , Guo Jinhua , Hopkins Samuel , Arnold Jonathan
Published: September 2002

Motivation: Computational gene identification plays an important role in genome projects. The approaches used in gene identification programs are often tuned to one particular organism, and accuracy for one organism or class of organism does not necessarily translate to accurate predictions for other organisms. In this paper we evaluate five computer programs on their ability to locate coding regions and to predict gene structure in Neurospora crassa. One of these programs (FFG) was designed specifically for gene-finding in N.crassa , but the model parameters have not yet been fully ‘tuned’, and the program should thus be viewed as an initial prototype. The other four programs were neither designed nor tuned for N.crassa.

Results: We describe the data sets on which the experiments were performed, the approaches employed by the five algorithms: GenScan, HMMGene, GeneMark, Pombe and FFG, the methodology of our evaluation, and the results of the experiments. Our results show that, while none of the programs consistently performs well, overall the GenScan program has the best performance on sensitivity and Missing Exons (ME) while the HMMGene and FFG programs have good performance in locating the exons roughly. Additional work motivated by this study includes the creation of a tool for the automated evaluation of gene-finding programs, the collection of larger and more reliable data sets for N.crassa , parameterization of the model used in FFG to produce a more accurate gene-finding program for this species, and a more in-depth evaluation of the reasons that existing programs generally fail for N.crassa.

Availability: Data sets, the FFG program source code, and links to the other programs analyzed are available at http://jerry.cs.uga.edu/~wang/genefind.html

Contact: eileen@cs.uga.edu

* To whom correspondence should be addressed.
Model-based clustering and data transformations for gene
expression data
Authors: Yeung K. Y. , Fraley C. , Murua A. , Raftery A. E. , Ruzzo W. L.
Published: September 2002

Motivation: Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particular, model-based clustering assumes that the data is generated by a finite mixture of underlying probability distributions such as multivariate normal distributions. The issues of selecting a ‘good’ clustering method and determining the ‘correct’ number of clusters are reduced to model selection problems in the probability framework. Gaussian mixture models have been shown to be a powerful tool for clustering in many applications.

Results: We benchmarked the performance of model-based clustering on several synthetic and real gene expression data sets for which external evaluation criteria were available. The model-based approach has superior performance on our synthetic data sets, consistently selecting the correct model and the number of clusters. On real expression data, the model-based approach produced clusters of quality comparable to a leading heuristic clustering algorithm, but with the key advantage of suggesting the number of clusters and an appropriate model. We also explored the validity of the Gaussian mixture assumption on different transformations of real data. We also assessed the degree to which these real gene expression data sets fit multivariate Gaussian distributions both before and after subjecting them to commonly used data transformations. Suitably chosen transformations seem to result in reasonable fits.

Availability: Mclust is available at http://www.stat.washington.edu/fraley/mclust. The software for the diagonal model is under development.

Contact: kayee@cs.washington.edu

Supplementary information: http://www.cs.washington.edu/homes/kayee/model

* To whom all correspondence should be addressed.
PIRA PCR designer for restriction analysis of single nucleotide
polymorphisms
Authors: Ke Xiayi , Collins Andrew , Ye Shu
Published: September 2002

Summary: Primer-introduced restriction analysis (PIRA-PCR) is widely used to detect Single Nucleotide Polymorphisms (SNPs). To create artificial Restriction Fragment Length Polymorphism (RFLP), a mismatch is usually introduced near the \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(3{^\prime}\) \end{document}end of the primer that is close to the mutation of interest. We describe in this report a www-based computer program that screens for the suitable mismatches, designs the primers, lists the appropriate restriction enzymes and other related information.

Availability: The computer program, with related descriptions, is available at http://cedar.genetics.soton.ac.uk/public_html/primer2.html.

Contact: xke@soton.ac.uk
InterProScan – an integration platform for the
signature-recognition methods in InterPro
Authors: Zdobnov Evgeni M. , Apweiler Rolf
Published: September 2002

Summary: InterProScan is a tool that scans given protein sequences against the protein signatures of the InterPro member databases, currently – PROSITE, PRINTS, Pfam, ProDom and SMART. The number of signature databases and their associated scanning tools as well as the further refinement procedures make the problem complex. InterProScan is designed to be a scalable and extensible system with a robust internal architecture.

Availability: The Perl-based InterProScan implementation is available from the EBI ftp server (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request. We provide the public web interface (http://www.ebi.ac.uk/interpro/scan.html) as well as email submission server (interproscan@ebi.ac.uk).

Contact: Evgueni.Zdobnov@EBI.ac.uk

* To whom correspondence should be addressed.
BioLayout—an automatic graph layout algorithm for
similarity visualization
Authors: Enright Anton J. , Ouzounis Christos A.
Published: September 2002

Summary: Graph layout is extensively used in the field of mathematics and computer science, however these ideas and methods have not been extended in a general fashion to the construction of graphs for biological data. To this end, we have implemented a version of the Fruchterman Rheingold graph layout algorithm, extensively modified for the purpose of similarity analysis in biology. This algorithm rapidly and effectively generates clear two (2D) or three-dimensional (3D) graphs representing similarity relationships such as protein sequence similarity. The implementation of the algorithm is general and applicable to most types of similarity information for biological data.

Availability: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout

Contact: enright@ebi.ac.uk
Why are complementary DNA strands symmetric?
Authors: Baisnée Pierre-François , Hampson Steve , Baldi Pierre
Published: September 2002

Motivation: Over sufficiently long windows, complementary strands of DNA tend to have the same base composition. A few reports have indicated that this first-order parity rule extends at higher orders to oligonucleotide composition, at least in some organisms or taxa. However, the scientific literature falls short of providing a comprehensive study of reverse-complement symmetry at multiple orders and across the kingdom of life. It also lacks a characterization of this symmetry and a convincing explanation or clarification of its origin.

Results: We develop methods to measure and characterize symmetry at multiple orders, and analyze a wide set of genomes, encompassing single- and double-stranded RNA and DNA viruses, bacteria, archae, mitochondria, and eukaryota. We quantify symmetry at orders 1 to 9 for contiguous sequences and pools of coding and non-coding upstream regions, compare the observed symmetry levels to those predicted by simple statistical models, and factor out the effect of lower-order distributions. We establish the universality and variability range of first-order strand symmetry, as well as of its higher-order extensions, and demonstrate the existence of genuine high-order symmetric constraints. We show that ubiquitous reverse-complement symmetry does not result from a single cause, such as point mutation or recombination, but rather emerges from the combined effects of a wide spectrum of mechanisms operating at multiple orders and length scales.

Contact: baisnee@ics.uci.eduhampson@ics.uci.edupfbaldi@ics.uci.edu

Data: http://promoter.ics.uci.edu/RevCompSym/

* To whom correspondence should be addressed.
Tagging gene and protein names in biomedical text
Authors: Tanabe Lorraine , Wilbur W. John
Published: September 2002

Motivation: The MEDLINE database of biomedical abstracts contains scientific knowledge about thousands of interacting genes and proteins. Automated text processing can aid in the comprehension and synthesis of this valuable information. The fundamental task of identifying gene and protein names is a necessary first step towards making full use of the information encoded in biomedical text. This remains a challenging task due to the irregularities and ambiguities in gene and protein nomenclature. We propose to approach the detection of gene and protein names in scientific abstracts as part-of-speech tagging, the most basic form of linguistic corpus annotation.

Results: We present a method for tagging gene and protein names in biomedical text using a combination of statistical and knowledge-based strategies. This method incorporates automatically generated rules from a transformation-based part-of-speech tagger, and manually generated rules from morphological clues, low frequency trigrams, indicator terms, suffixes and part-of-speech information. Results of an experiment on a test corpus of 56K MEDLINE documents demonstrate that our method to extract gene and protein names can be applied to large sets of MEDLINE abstracts, without the need for special conditions or human experts to predetermine relevant subsets.

Availability: The programs are available on request from the authors.

Contact: tanabe@ncbi.nlm.nih.gov
TFBS: Computational framework for transcription factor binding site analysis
Authors: Lenhard Boris , Wasserman Wyeth W.
Published: September 2002

Motivation: TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system.

Availability and Supplementary Information: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/

Contact: Boris.Lenhard@cgb.ki.se

* To whom correspondence should be addressed.
Molecular cloning and functional characterization of human vesicular glutamate transporter 3
Authors: Takamori Shigeo , Malherbe Pari , Broger Clemens , Jahn Reinhard
Published: September 2002

Glutamate is the major excitatory neurotransmitter in the mammalian CNS. It is loaded into synaptic vesicles by a proton gradient‐dependent uptake system and is released by exocytosis upon stimulation. Recently, two mammalian isoforms of a vesicular glutamate transporter, VGLUT1 and VGLUT2, have been identified, the expression of which enables quantal release of glutamate from glutamatergic neurons. Here, we report a novel isoform of a human vesicular glutamate transporter (hVGLUT3). The predicted amino acid sequence of hVGLUT3 shows 72% identity to both hVGLUT1 and hVGLUT2. hVGLUT3 functions as a vesicular glutamate transporter with similar properties to the other isoforms when it is heterologously expressed in a neuroendocrine cell line. Although mammalian VGLUT1 and VGLUT2 exhibit a complementary expression pattern covering all glutamatergic pathways in the CNS, expression of hVGLUT3 overlaps with them in some brain areas, suggesting molecular diversity that may account for physiological heterogeneity in glutamatergic synapses.
Windows of Opportunity: Window Subseries Empirical Variance Estimators in International Relations
Authors: Heagerty Patrick , Ward Michael D. , Gleditsch Kristian Skrede
Published: September 2002

We show that temporal, spatial, and dyadic dependencies among observations complicate the estimation of covariance structures in panel databases. Ignoring these dependencies results in covariance estimates that are often too small and inferences that may be more confident about empirical patterns than is justified by the data. In this article, we detail the development of a nonparametric approach, window subseries empirical variance estimators (WSEV), that can more fully capture the impact of these dependencies on the covariance structure. We illustrate this approach in a simulation as well as with a statistical model of international conflict similar to many applications in the international relations literature.
The performance of VPI‐coated paper for temporary corrosion prevention of metals
Authors: Subramanian A. , Rathina Kumar R. , Natesan M. , Vasudevan T.
Published: September 2002

The efficacy of octylamine as a vapour phase corrosion inhibitor in different corrosive environments for carbon steel, copper and brass, and its biocidal action, have been examined. The protection of these metals from atmospheric corrosion using VPI (octylamine)‐impregnated paper was monitored by visual observation, weight loss measurements, polarisation scans and impedance measurements. The long‐term protection given by octylamine‐impregnated paper to these metals was examined by Stevenson’s chamber test. It was found that octylamine offered more than 80 per cent protection against atmospheric corrosion for carbon steel, copper and brass.
Preparing leadership to manage change during divestiture, acquisition or joint venture
Authors: Harris Helmer Jill
Published: September 2002

Describes a set of tools and techniques that have been designed to assist leaders in communicating and managing the change that accompanies divestiture, acquisition and joint venture. It primarily focuses on a training program that consists of best practices and learnings from previous activities and literature, focused on: tips on managing your reaction to change; dealing with the impact of change on individuals; communicating the divestiture/acquisition/joint venture; working with survivors of the change; and protecting the business and employees in times of change. Also highlights some additional steps that have been taken to design tools that assist in understanding the impact that divestiture, acquisition and joint venture could have in the organization.
The TeleTOP initiative: new learning, new technology
Authors: Collis Betty
Published: September 2002

In response to the challenge to make learning more flexible while at the same time maintaining the positive qualities of classroom and campus‐based settings, the TeleTOP Initiative at the University of Twente has grown from a faculty initiative to an internationally recognised Web‐based learning support product and change method. TeleTOP as a product and the educational ideas motivating it are now being used in a number of company learning settings, particularly the Shell Learning Centre in The Netherlands. Gives an overview of the growth, results, and current status of the initiative as well as key educational and strategic principles that underlie its success.
Sales forecasting for strategic resource planning
Authors: Wacker John G. , Lummus Rhonda R.
Published: September 2002

The purpose of this article is twofold. First, the article examines how managers can make more effective use of sales forecasts for strategic resource allocation decisions. Second, the article identifies those research issues in forecasting that must be addressed to better understand the managerial side of forecasting. Managers can improve resource planning by understanding the limitations of forecasts. These limitations are exemplified through several strategic forecasting paradoxes that managers must recognize. The paradoxes suggested here are: first, the most important managerial decisions a company can make are based on the least accurate forecasts; second, the most useful forecast information for resource planning is the least accurate; and, third, the organizations that need the most accurate forecast have the largest forecast error. By recognizing these paradoxes managers can devote their attention to improving the use and implementation of the forecast for better resource decisions. At the same time, future research should focus on broadening the understanding of the role of forecasts in strategic decision making.