bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrins engage mitochondrial function for signal transduction by a mechanism dependent on Rho GTPases
Authors: Werner Erica , Werb Zena
Published: July 2002

We show here the transient activation of the small GTPase Rac, followed by a rise in reactive oxygen species (ROS), as necessary early steps in a signal transduction cascade that lead to NFκB activation and collagenase-1 (CL-1)/matrix metalloproteinase-1 production after integrin-mediated cell shape changes. We show evidence indicating that this constitutes a new mechanism for ROS production mediated by small GTPases. Activated RhoA also induced ROS production and up-regulated CL-1 expression. A Rac mutant (L37) that prevents reorganization of the actin cytoskeleton prevented integrin-induced CL-1 expression, whereas mutations that abrogate Rac binding to the neutrophil NADPH membrane oxidase in vitro (H26 and N130) did not. Instead, ROS were produced by integrin-induced changes in mitochondrial function, which were inhibited by Bcl-2 and involved transient membrane potential loss. The cells showing this transient decrease in mitochondrial membrane potential were already committed to CL-1 expression. These results unveil a new molecular mechanism of signal transduction triggered by integrin engagement where a global mitochondrial metabolic response leads to gene expression rather than apoptosis.
A cryptic fragment from fibronectin's III1 module localizes to lipid rafts and stimulates cell growth and contractility
Authors: Hocking Denise C. , Kowalski Katherine
Published: July 2002

The interaction of cells with the extracellular matrix (ECM) form of fibronectin (FN) triggers changes in growth, migration, and cytoskeletal organization that differ from those generated by soluble FN. As cells deposit and remodel their FN matrix, the exposure of new epitopes may serve to initiate responses unique to matrix FN. To determine whether a matricryptic site within the III1 module of FN modulates cell growth or cytoskeletal organization, a recombinant FN with properties of matrix FN was constructed by directly linking the cryptic, heparin-binding COOH-terminal fragment of III1 (III1H) to the integrin-binding III8–10 modules (glutathione-S-transferase [GST]–III1H,8–10). GST–III1H,8–10 specifically stimulated increases in cell growth and contractility; integrin ligation alone was ineffective. A construct lacking the integrin-binding domain (GST–III1H,2–4) retained the ability to stimulate cell contraction, but was unable to stimulate cell growth. Both GST–III1H,2–4 and matrix FN colocalized with caveolin and fractionated with low-density membrane complexes by a mechanism that required heparan sulfate proteoglycans. Disruption of caveolae inhibited the FN- and III1H-mediated increases in cell contraction and growth. These data suggest that a portion of ECM FN partitions into lipid rafts and differentially regulates cytoskeletal organization and growth, in part, through the exposure of a neoepitope within the conformationally labile III1 module.
A role for regulated binding of p150Glued to microtubule plus ends in organelle transport
Authors: Vaughan Patricia S. , Miura Pedro , Henderson Matthew , Byrne Belinda , Vaughan Kevin T.
Published: July 2002

A subset of microtubule-associated proteins, including cytoplasmic linker protein (CLIP)-170, dynactin, EB1, adenomatous polyposis coli, cytoplasmic dynein, CLASPs, and LIS-1, has been shown recently to target to the plus ends of microtubules. The mechanisms and functions of this binding specificity are not understood, although a role in encouraging microtubule elongation has been proposed. To extend previous work on the role of dynactin in organelle transport, we analyzed p150Glued by live-cell imaging. Time-lapse analysis of p150Glued revealed targeting to the plus ends of growing microtubules, requiring the NH2-terminal cytoskeleton-associated protein–glycine rich domain, but not EB1 or CLIP-170. Effectors of protein kinase A modulated microtubule binding and suggested p150Glued phosphorylation as a factor in plus-end binding specificity. Using a phosphosensitive monoclonal antibody, we mapped the site of p150Glued phosphorylation to Ser-19. In vivo and in vitro analysis of phosphorylation site mutants revealed that p150Glued phosphorylation mediates dynamic binding to microtubules. To address the function of dynamic binding, we imaged GFP-p150Glued during the dynein-dependent transport of Golgi membranes. Live-cell analysis revealed a transient interaction between Golgi membranes and GFP-p150Glued–labeled microtubules just prior to transport, implicating microtubules and dynactin in a search–capture mechanism for minus-end–directed organelles.
ATP regulates the differentiation of mammalian skeletal muscle by activation of a P2X5 receptor on satellite cells
Authors: Ryten Mina , Dunn Philip M. , Neary Joseph T. , Burnstock Geoffrey
Published: July 2002

ATP is well known for its role as an intracellular energy source. However, there is increasing awareness of its role as an extracellular messenger molecule (Burnstock, 1997). Although evidence for the presence of receptors for extracellular ATP on skeletal myoblasts was first published in 1983 (Kolb and Wakelam), their physiological function has remained unclear. In this paper we used primary cultures of rat skeletal muscle satellite cells to investigate the role of purinergic signaling in muscle formation. Using immunocytochemistry, RT-PCR, and electrophysiology, we demonstrate that the ionotropic P2X5 receptor is present on satellite cells and that activation of a P2X receptor inhibits proliferation, stimulates expression of markers of muscle cell differentiation, including myogenin, p21, and myosin heavy chain, and increases the rate of myotube formation. Furthermore, we demonstrate that ATP application results in a significant and rapid increase in the phosphorylation of MAPKs, particularly p38, and that inhibition of p38 activity can prevent the effect of ATP on cell number. These results not only demonstrate the existence of a novel regulator of skeletal muscle differentiation, namely ATP, but also a new role for ionotropic P2X receptors in the control of cell fate.
Dominant regulation of interendothelial cell gap formation by calcium-inhibited type 6 adenylyl cyclase
Authors: Cioffi Donna L. , Moore Timothy M. , Schaack Jerry , Creighton Judy R. , Cooper Dermot M.F. , Stevens Troy
Published: July 2002

Acute transitions in cytosolic calcium ([Ca2+]i) through store-operated calcium entry channels catalyze interendothelial cell gap formation that increases permeability. However, the rise in [Ca2+]i only disrupts barrier function in the absence of a rise in cAMP. Discovery that type 6 adenylyl cyclase (AC6; EC 4.6.6.1) is inhibited by calcium entry through store-operated calcium entry pathways provided a plausible explanation for how inflammatory [Ca2+]i mediators may decrease cAMP necessary for endothelial cell gap formation. [Ca2+]i mediators only modestly decrease global cAMP concentrations and thus, to date, the physiological role of AC6 is unresolved. Present studies used an adenoviral construct that expresses the calcium-stimulated AC8 to convert normal calcium inhibition into stimulation of cAMP, within physiologically relevant concentration ranges. Thrombin stimulated a dose-dependent [Ca2+]i rise in both pulmonary artery (PAECs) and microvascular (PMVEC) endothelial cells, and promoted intercellular gap formation in both cell types. In PAECs, gap formation was progressive over 2 h, whereas in PMVECs, gap formation was rapid (within 10 min) and gaps resealed within 2 h. Expression of AC8 resulted in a modest calcium stimulation of cAMP, which virtually abolished thrombin-induced gap formation in PMVECs. Findings provide the first direct evidence that calcium inhibition of AC6 is essential for endothelial gap formation.
Autotaxin has lysophospholipase D activity leading to tumor cell growth and motility by lysophosphatidic acid production
Authors: Umezu-Goto Makiko , Kishi Yasuhiro , Taira Akitsu , Hama Kotaro , Dohmae Naoshi , Takio Koji , Yamori Takao , Mills Gordon B. , Inoue Keizo , Aoki Junken , Arai Hiroyuki
Published: July 2002

Autotaxin (ATX) is a tumor cell motility–stimulating factor, originally isolated from melanoma cell supernatants. ATX had been proposed to mediate its effects through 5′-nucleotide pyrophosphatase and phosphodiesterase activities. However, the ATX substrate mediating the increase in cellular motility remains to be identified. Here, we demonstrated that lysophospholipase D (lysoPLD) purified from fetal bovine serum, which catalyzes the production of the bioactive phospholipid mediator, lysophosphatidic acid (LPA), from lysophosphatidylcholine (LPC), is identical to ATX. The Km value of ATX for LPC was 25-fold lower than that for the synthetic nucleoside substrate, p-nitrophenyl-tri-monophosphate. LPA mediates multiple biological functions including cytoskeletal reorganization, chemotaxis, and cell growth through activation of specific G protein–coupled receptors. Recombinant ATX, particularly in the presence of LPC, dramatically increased chemotaxis and proliferation of multiple different cell lines. Moreover, we demonstrate that several cancer cell lines release significant amounts of LPC, a substrate for ATX, into the culture medium. The demonstration that ATX and lysoPLD are identical suggests that autocrine or paracrine production of LPA contributes to tumor cell motility, survival, and proliferation. It also provides potential novel targets for therapy of pathophysiological states including cancer.
Identification of the Lateral Interaction Surfaces of Human Histocompatibility Leukocyte Antigen (HLA)-DM with HLA-DR1 by Formation of Tethered Complexes That Present Enhanced HLA-DM Catalysis
Authors: Stratikos Efstratios , Mosyak Lidia , Zaller Dennis M. , Wiley Don C.
Published: July 2002

Human histocompatibility leukocyte antigen (HLA)-DM is a major histocompatibility complex (MHC)-like protein that catalyzes exchange of antigenic peptides from MHC class II molecules. To investigate the molecular details of this catalysis we created four covalent complexes between HLA-DM and the MHC class II allele DR1. We introduced a disulfide bond between the naturally occurring cysteine β46 on HLA-DM and an engineered cysteine on the end of a linker attached to either the NH2- or the COOH terminus of an antigenic peptide that is tightly bound on DR1. We find that when DM is attached to the NH2 terminus of the peptide, it can, for all linker lengths tested, catalyze exchange of the peptide with a half-life a few minutes (compared with uncatalyzed t1/2 > 100 h). This rate, which is several orders of magnitude greater than the one we obtain in solution assays using micromolar concentrations of HLA-DM, is dominated by a concentration independent factor, indicating an intramolecular catalytic interaction within the complex. A similar complex formed at the COOH terminus of the peptide shows no sign of DM-specific intramolecular catalysis. Restrictions on the possible interaction sites imposed by the length of the linkers indicate that the face of DR1 that accommodates the NH2 terminus of the antigenic peptide interacts with the lateral face of HLA-DM that contains cysteine β46.
Effect of Na+ Flow on Cd2+ Block of Tetrodotoxin-resistant Na+ Channels
Authors: Kuo Chung-Chin , Lin Ting-Jiun , Hsieh Chi-Pan
Published: July 2002

Tetrodotoxin-resistant (TTX-R) Na+ channels are 1,000-fold less sensitive to TTX than TTX-sensitive (TTX-S) Na+ channels. On the other hand, TTX-R channels are much more susceptible to external Cd2+ block than TTX-S channels. A cysteine (or serine) residue situated just next to the aspartate residue of the presumable selectivity filter “DEKA” ring of the TTX-R channel has been identified as the key ligand determining the binding affinity of both TTX and Cd2+. In this study we demonstrate that the binding affinity of Cd2+ to the TTX-R channels in neurons from dorsal root ganglia has little intrinsic voltage dependence, but is significantly influenced by the direction of Na+ current flow. In the presence of inward Na+ current, the apparent dissociation constant of Cd2+ (∼200 μM) is ∼9 times smaller than that in the presence of outward Na+ current. The Na+ flow–dependent binding affinity change of Cd2+ block is true no matter whether the direction of Na+ current is secured by asymmetrical chemical gradient (e.g., 150 mM Na+ vs. 150 mM Cs+ on different sides of the membrane, 0 mV) or by asymmetrical electrical gradient (e.g., 150 mM Na+ on both sides of the membrane, −20 mV vs. 20 mV). These findings suggest that Cd2+ is a pore blocker of TTX-R channels with its binding site located in a multiion, single-file region near the external pore mouth. Quantitative analysis of the flow dependence with the flux-coupling equation reveals that at least two Na+ ions coexist with the blocking Cd2+ ion in this pore region in the presence of 150 mM ambient Na+. Thus, the selectivity filter of the TTX-R Na+ channels in dorsal root ganglion neurons might be located in or close to a multiion single-file pore segment connected externally to a wide vestibule, a molecular feature probably shared by other voltage-gated cationic channels, such as some Ca2+ and K+ channels.
Current-dependent Block of Rabbit Sino-Atrial Node If Channels by Ivabradine
Authors: Bucchi Annalisa , Baruscotti Mirko , DiFrancesco Dario
Published: July 2002

“Funny” (f-) channels have a key role in generation of spontaneous activity of pacemaker cells and mediate autonomic control of cardiac rate; f-channels and the related neuronal h-channels are composed of hyperpolarization-activated, cyclic nucleotide–gated (HCN) channel subunits. We have investigated the block of f-channels of rabbit cardiac sino-atrial node cells by ivabradine, a novel heart rate-reducing agent. Ivabradine is an open-channel blocker; however, block is exerted preferentially when channels deactivate on depolarization, and is relieved by long hyperpolarizing steps. These features give rise to use-dependent behavior. In this, the action of ivabradine on f-channels is similar to that reported of other rate-reducing agents such as UL-FS49 and ZD7288. However, other features of ivabradine-induced block are peculiar and do not comply with the hypothesis that the voltage-dependence of block is entirely attributable to either the sensitivity of ivabradine-charged molecules to the electrical field in the channel pore, or to differential affinity to different channel states, as has been proposed for UL-FS49 (DiFrancesco, D. 1994. Pflugers Arch. 427:64–70) and ZD7288 (Shin, S.K., B.S. Rotheberg, and G. Yellen. 2001. J. Gen. Physiol. 117:91–101), respectively. Experiments where current flows through channels is modified without changing membrane voltage reveal that the ivabradine block depends on the current driving force, rather than voltage alone, a feature typical of block induced in inwardly rectifying K+ channels by intracellular cations. Bound drug molecules do not detach from the binding site in the absence of inward current through channels, even if channels are open and the drug is therefore not “trapped” by closed gates. Our data suggest that permeation through f-channel pores occurs according to a multiion, single-file mechanism, and that block/unblock by ivabradine is coupled to ionic flow. The use-dependence resulting from specific features of If block by ivabradine amplifies its rate-reducing ability at high spontaneous rates and may be useful to clinical applications.
Simple air turbine for high speed opticaI applications
Authors: W L Bond  , D L Hecht
Published: July 2002

A simply constructed air-turbine air-bearing motor is described which is used to rotate dye-doped plastic through a laser beam at speeds up to 28 000 cm s-1. The turbine has excellent speed stability (5 parts in 105) for use in this and other high speed optical applications in the rotation speed range from 104 to 2 × 105 rev min-l.
Numerical Modelling of Velocity and Temperature Distributions of the Buoyancy Convection Effect in KNbO3Melt
Authors: Liu Zhao-Hua  , Jin Wei-Qing  , Pan Zhi-Lei
Published: July 2002

Numerical modelling of velocity and temperature fields in high-temperature KNbO3melt of a loop-shaped Pt wire heater is carried out by using the commercial computational code ANSYS for the mathematical solution of the governing equations. Based on the experimental boundary conditions and the Boussinesq approximation, the numerical modelling of a steady and two-dimensional model is applied to study the process under consideration of the buoyancy-driven convection condition. The result is compared with the previous experimental and theoretical data obtained in our laboratory, and the former is in agreement with the latter. Thus a theoretical guide for reasonable growth conditions is provided by studying in depth the real fluid flow effects in the crystal growth from the melt.
Small GTP-binding Protein TC10 Differentially Regulates Two Distinct Populations of Filamentous Actin in 3T3L1 Adipocytes
Authors: Kanzaki Makoto , Watson Robert T. , Hou June Chunqiu , Stamnes Mark , Saltiel Alan R. , Pessin Jeffrey E.
Published: July 2002

TC10 is a member of the Rho family of small GTP-binding proteins that has previously been implicated in the regulation of insulin-stimulated GLUT4 translocation in adipocytes. In a manner similar to Cdc42-stimulated actin-based motility, we have observed that constitutively active TC10 (TC10/Q75L) can induce actin comet tails in Xenopus oocyte extracts in vitro and extensive actin polymerization in the perinuclear region when expressed in 3T3L1 adipocytes. In contrast, expression of TC10/Q75L completely disrupted adipocyte cortical actin, which was specific for TC10, because expression of constitutively active Cdc42 was without effect. The effect of TC10/Q75L to disrupt cortical actin was abrogated after deletion of the amino terminal extension (ΔN-TC10/Q75L), whereas this deletion retained the ability to induce perinuclear actin polymerization. In addition, alteration of perinuclear actin by expression of TC10/Q75L, a dominant-interfering TC10/T31N mutant or a mutant N-WASP protein (N-WASP/ΔVCA) reduced the rate of VSV G protein trafficking to the plasma membrane. Furthermore, TC10 directly bound to Golgi COPI coat proteins through a dilysine motif in the carboxyl terminal domain consistent with a role for TC10 regulating actin polymerization on membrane transport vesicles. Together, these data demonstrate that TC10 can differentially regulate two types of filamentous actin in adipocytes dependent on distinct functional domains and its subcellular compartmentalization.
Contribution of Ena/VASP Proteins to Intracellular Motility ofListeriaRequires Phosphorylation and Proline-rich Core but Not F-Actin Binding or Multimerization
Authors: Geese Marcus , Loureiro Joseph J. , Bear James E. , Wehland Jürgen , Gertler Frank B. , Sechi Antonio S.
Published: July 2002

The Listeria model system has been essential for the identification and characterization of key regulators of the actin cytoskeleton such as the Arp2/3 complex and Ena/vasodilator-stimulated phosphoprotein (VASP) proteins. Although the role of Ena/VASP proteins in Listeria motility has been extensively studied, little is known about the contributions of their domains and phosphorylation state to bacterial motility. To address these issues, we have generated a panel of Ena/VASP mutants and, upon expression in Ena/VASP-deficient cells, evaluated their contribution to Ena/VASP function in Listeria motility. The proline-rich region, the putative G-actin binding site, and the Ser/Thr phosphorylation of Ena/VASP proteins are all required for efficientListeria motility. Surprisingly, the interaction of Ena/VASP proteins with F-actin and their potential ability to form multimers are both dispensable for their involvement in this process. Our data suggest that Ena/VASP proteins contribute toListeria motility by regulating both the nucleation and elongation of actin filaments at the bacterial surface.
GLUT4 Retention in Adipocytes Requires Two Intracellular Insulin-regulated Transport Steps
Authors: Zeigerer Anja , Lampson Michael A. , Karylowski Ola , Sabatini David D. , Adesnik Milton , Ren Mindong , McGraw Timothy E.
Published: July 2002

Insulin regulates glucose uptake into fat and muscle by modulating the distribution of the GLUT4 glucose transporter between the surface and interior of cells. The GLUT4 trafficking pathway overlaps with the general endocytic recycling pathway, but the degree and functional significance of the overlap are not known. In this study of intact adipocytes, we demonstrate, by using a compartment-specific fluorescence-quenching assay, that GLUT4 is equally distributed between two intracellular pools: the transferrin receptor-containing endosomes and a specialized compartment that excludes the transferrin receptor. These pools of GLUT4 are in dynamic communication with one another and with the cell surface. Insulin-induced redistribution of GLUT4 to the surface requires mobilization of both pools. These data establish a role for the general endosomal system in the specialized, insulin-regulated trafficking of GLUT4. Trafficking through the general endosomal system is regulated by rab11. Herein, we show that rab11 is required for the transport of GLUT4 from endosomes to the specialized compartment and for the insulin-induced translocation to the cell surface, emphasizing the importance of the general endosomal pathway in the specialized trafficking of GLUT4. Based on these findings we propose a two-step model for GLUT4 trafficking in which the general endosomal recycling compartment plays a specialized role in the insulin-regulated traffic of GLUT4. This compartment-based model provides the framework for understanding insulin-regulated trafficking at a molecular level.
Hybrid alignment: high-performance with universal statistics
Authors: Yu Yi-Kuo , Bundschuh Ralf , Hwa Terence
Published: July 2002

The score statistics of a recently introduced `hybrid alignment' algorithm is studied in detail numerically. An extensive survey across the 2216 models of protein domains contained in the Pfam v5.4 database (Bateman et al., Nucleic Acids Res., 28, 263–266, 2000) verifies the theoretical predictions: For the position-specific scoring functions used in the Pfam models, the score statistics of hybrid alignment obey the Gumbel distribution, with the key Gumbel parameter λ taking on the asymptotic value 1 universally for all models. Thus, the use of hybrid alignment eliminates the time-consuming computer simulations normally needed to assign p-values to alignment scores, freeing the users to experiment with different scoring parameters and functions. The performance of the hybrid algorithm in detecting sequence homology is also studied. For protein sequences from the SCOP database (Murzin et al., J. Mol. Biol., 247, 536–540, 1995) using uniform scoring functions, the performance is found to be comparable to the best of the existing methods. Preliminary results using the PfamA database suggest that the hybrid algorithm achieves similar performance as existing methods for position-specific scoring systems as well. Hybrid alignment is thereby established as a high performance alignment algorithm with well-characterized, universal statistics.

Contact: yyu@fau.edu

* Present address: Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, OH 43210-1106, USA
DMLE+: Bayesian linkage disequilibrium gene mapping
Authors: Reeve Jeff P. , Rannala Bruce
Published: July 2002

Summary: The program DMLE+ allows Bayesian inference of the location of a gene carrying a mutation influencing a discrete trait (such as a disease) and/or other parameters of interest (such as mutation age) based on the observed linkage disequilibrium at multiple genetic markers. DMLE+ uses either individual marker genotypes, or haplotypes, integrates over uncertain population allele frequencies, and can incorporate prior information about gene location from an annotated human genome sequence.

Availability: DMLE+ is available in both Windows GUI and portable UNIX command line versions at http://dmle.org

Contact: queries@dmle.orgbrannala@ualberta.ca

* To whom correspondence should be addressed.
Income Mobility and the Earned Income Tax Credit
Authors: Horowitz John B.
Published: July 2002

Households who work full‐time at minimum wage jobs earn more than the phasein range of the Earned Income Tax Credit (EITC). This means that the EITC mainly acts as a negative income tax. However, most families are eligible to receive the EITC for a relatively short time. Seventy‐four percent of new EITC families will lose their eligibility in two years or less. Sixty‐one percent of families already on the EITC will lose their eligibility in three years or less. EITC families are much more mobile than AFDC families. The main reason that families gain or lose EITC eligibility is changes in earnings.
Explaining U.S. Federal Deficits: 1889–1998
Authors: Goff Brian L. , Tollison Robert D.
Published: July 2002

We review and jointly test various competing theoretical and empirical models of U.S. federal deficits using annual data from 1889 to 1998. We find that tax smoothing matters and that political and interest group/distributional factors are also present in our results.
An efficient genetic screen in mammalian cultured cells
Authors: Schmelzl Birgit , Geli M Isabel
Published: July 2002

Genetic approaches in mammalian cultured cells had limited success because the isolation of mutants and the identification of the mutated genes were often difficult. In the present report, we describe the establishment of a novel genetic screen in Cos‐7 cells that allows rapid identification of polypeptides whose overexpression inhibits a certain cellular process. We demonstrate that this approach can be used successfully to isolate partial cDNAs whose overexpression specifically interfered with the clathrin‐mediated endocytosis of transferrin.
Homeotic transformations of the axial skeleton that accompany a targeted deletion of E2f6
Authors: Storre Jörg , Elsässer Hans‐Peter , Fuchs Miriam , Ullmann Diana , Livingston David M , Gaubatz Stefan
Published: July 2002

E2F transcription factors play an important role in regulating mammalian cell proliferation. E2F6, the most recently identified E2F family member, is a transcriptional repressor. In an effort to ascertain the in vivo biological function of E2F6, we have generated an E2f6 mutant mouse strain. Mice lacking E2F6 are viable and healthy. Surprisingly, E2f6−/− embryonic fibroblasts proliferate normally. However, E2f6−/− animals display overt homeotic transformations of the axial skeleton that are strikingly similar to the skeletal transformations observed in polycomb mutant mice. This observation is compatible with the recent finding that endogenous E2F6 and one or more mammalian polycomb proteins are components of the same multiprotein complex. The accumulated evidence suggests that, during development, E2F6 participates in the recruitment of polycomb proteins to specific target promoters.
A Statistical Model of Bilateral Cooperation
Authors: Przeworski Adam , Vreeland James Raymond
Published: July 2002

In most situations of bilateral cooperation we can observe only whether or not potential partners actually cooperate. Yet we often want to know what factors lead the actors to enter into and continue cooperation. The model we develop—a dynamic version of bivariate probit with partial observability—permits one to estimate the probabilities that either of two parties would want to cooperate and to identify the factors that affect these probabilities. As an illustration, we focus on agreements between national governments and the International Monetary Fund. The model should have a wide applicability.
In vitro
uses of biological cryoprotectants
Authors: Lillford Peter J. , Holt Chris B.
Published: July 2002

Ice can be anything from a highly destructive agent in agriculture to a useful building material. Established industries are based on the known rules of physics and chemistry which allow some control of amounts of ice or ice crystal geometry. However, organisms have much more subtle requirements to maintain their delicate internal structure if they are to survive freezing. As a result they have selected specific molecules for freezing–point depression, osmotic regulation, ice nucleation and crystal growth inhibition. All these active species may have potential commercial use once they are identified, understood and produced at economic scales. We examine the progress made so far in extending biological subtlety into commercial processes, and look for prospects for further innovation.
Trichome morphogenesis: a cell–cycle perspective
Authors: Schnittger A. , Hülskamp M.
Published: July 2002

Arabidopsis leaf hairs (trichomes) are polyploid epidermal cells with a predictable branching pattern. More than 15 genes have been identified that are involved in the regulation of branching. The cloning of theZWICHEL,ANGUSTIFOLIAandSTICHELgenes points to two mechanistic aspects of branch formation: (i) a role of the microtubule cytoskeleton; and (ii) a link to the regulation of cell divisions. The latter aspect is supported by the recent identification of anArabidopsismutant with multicellular trichomes, thesiamesemutant, suggesting thatArabidopsistrichomes are evolutionarily derived from multicellular forms. We speculate that the spatial information for branch formation is derived from mechanisms employed in cell divisions.
MicroRNAs in plants
Authors: Reinhart Brenda J. , Weinstein Earl G. , Rhoades Matthew W. , Bartel Bonnie , Bartel David P.
Published: July 2002

MicroRNAs (miRNAs) are an extensive class of ∼22-nucleotide noncoding RNAs thought to regulate gene expression in metazoans. We find that miRNAs are also present in plants, indicating that this class of noncoding RNA arose early in eukaryotic evolution. In this paper 16Arabidopsis miRNAs are described, many of which have differential expression patterns in development. Eight are absolutely conserved in the rice genome. The plant miRNA loci potentially encode stem–loop precursors similar to those processed by Dicer (a ribonuclease III) in animals. Mutation of an Arabidopsis Dicer homolog, CARPEL FACTORY, prevents the accumulation of miRNAs, showing that similar mechanisms direct miRNA processing in plants and animals. The previously described roles of CARPEL FACTORY in the development of Arabidopsis embryos, leaves, and floral meristems suggest that the miRNAs could play regulatory roles in the development of plants as well as animals.
The transcriptional repressor Brinker antagonizes Wingless signaling
Authors: Saller Elisabeth , Kelley Ann , Bienz Mariann
Published: July 2002

In the embryonic midgut of Drosophila, Wingless (Wg) signaling elicits threshold-specific transcriptional response, that is, low-signaling levels activate target genes, whereas high-signaling levels repress them. Wg-mediated repression of the HOX gene Ultrabithorax (Ubx) is conferred by a response sequence within the Ubx B midgut enhancer, called WRS-R. It further depends on the Teashirt (Tsh) repressor, which acts through the WRS-R without binding to it. Here, we show that Wg-mediated repression of UbxB depends on Brinker, which binds to the WRS-R. Furthermore, Brinker blocks transcriptional activation by ubiquitous Wg signaling. Brinker binds to Tsh in vitro, recruits Tsh to the WRS-R, and we find mutual physical interactions between Brinker, Tsh, and the corepressor dCtBP. This suggests that the three proteins may form a ternary repressor complex at the WRS-R to quench the activity of the nearby-bound dTCF/Armadillo transcription complex. Finally, brinker andtsh produce similar mutant phenotypes in the ventral epidermis, and double mutants mimic overactive Wg signaling in this tissue. This suggests that Brinker may have a widespread function in antagonizing Wg signaling.
Nercc1, a mammalian NIMA-family kinase, binds the Ran GTPase and regulates mitotic progression
Authors: Roig Joan , Mikhailov Alexei , Belham Christopher , Avruch Joseph
Published: July 2002

The protein kinase NIMA is an indispensable pleiotropic regulator of mitotic progression in Aspergillus. Although several mammalian NIMA-like kinases (Neks) are known, none appears to have the broad importance for mitotic regulation attributed to NIMA. Nercc1 is a new NIMA-like kinase that regulates chromosome alignment and segregation in mitosis. Its NIMA-like catalytic domain is followed by a noncatalytic tail containing seven repeats homologous to those of the Ran GEF, RCC1, a Ser/Thr/Pro-rich segment, and a coiled-coil domain. Nercc1 binds to another NIMA-like kinase, Nek6, and also binds specifically to the Ran GTPase through both its catalytic and its RCC1-like domains, preferring RanGDP in vivo. Nercc1 exists as a homooligomer and can autoactivate in vitro by autophosphorylation. Nercc1 is a cytoplasmic protein that is activated during mitosis and is avidly phosphorylated by active p34Cdc2. Microinjection of anti-Nercc1 antibodies in prophase results in spindle abnormalities and/or chromosomal misalignment. In Ptk2 cells the outcome is prometaphase arrest or aberrant chromosome segregation and aneuploidy, whereas in CFPAC-1 cells prolonged arrest in prometaphase is the usual response. Nercc1 and its partner Nek6 represent a new signaling pathway that regulates mitotic progression.
Targeted mutagenesis by homologous recombination inD. melanogaster
Authors: Rong Yikang S. , Titen Simon W. , Xie Heng B. , Golic Mary M. , Bastiani Michael , Bandyopadhyay Pradip , Olivera Baldomero M. , Brodsky Michael , Rubin Gerald M. , Golic Kent G.
Published: July 2002

We used a recently developed method to produce mutant alleles of five endogenousDrosophilagenes, including the homolog of thep53tumor suppressor. Transgenic expression of the FLP site-specific recombinase and the I-SceI endonuclease generates extrachromosomal linear DNA molecules in vivo. These molecules undergo homologous recombination with the corresponding chromosomal locus to generate targeted alterations of the host genome. The results address several questions about the general utility of this technique. We show that genes not near telomeres can be efficiently targeted; that no knowledge of the mutant phenotype is needed for targeting; and that insertional mutations and allelic substitutions can be easily produced.
G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis
Authors: Tachibana Makoto , Sugimoto Kenji , Nozaki Masami , Ueda Jun , Ohta Tsutomu , Ohki Misao , Fukuda Mikiko , Takeda Naoki , Niida Hiroyuki , Kato Hiroyuki , Shinkai Yoichi
Published: July 2002

Covalent modification of histone tails is crucial for transcriptional regulation, mitotic chromosomal condensation, and heterochromatin formation. Histone H3 lysine 9 (H3-K9) methylation catalyzed by the Suv39h family proteins is essential for establishing the architecture of pericentric heterochromatin. We recently identified a mammalian histone methyltransferase (HMTase), G9a, which has strong HMTase activity towards H3-K9 in vitro. To investigate the in vivo functions of G9a, we generated G9a-deficient mice and embryonic stem (ES) cells. We found that H3-K9 methylation was drastically decreased in G9a-deficient embryos, which displayed severe growth retardation and early lethality. G9a-deficient ES cells also exhibited reduced H3-K9 methylation compared to wild-type cells, indicating that G9a is a dominant H3-K9 HMTase in vivo. Importantly, the loss of G9a abolished methylated H3-K9 mostly in euchromatic regions. Finally, G9a exerted a transcriptionally suppressive function that depended on its HMTase activity. Our results indicate that euchromatic H3-K9 methylation regulated by G9a is essential for early embryogenesis and is involved in the transcriptional repression of developmental genes.
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Authors: Daubin Vincent , Gouy Manolo , Perrière Guy
Published: July 2002

It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.
Distinct Physiological Roles of Fructokinase Isozymes Revealed by Gene-Specific Suppression of Frk1 and Frk2Expression in Tomato
Authors: Odanaka Saori , Bennett Alan B. , Kanayama Yoshinori
Published: July 2002

There are two divergent fructokinase isozymes, Frk1 and Frk2 in tomato (Lycopersicon esculentum Mill.) plants. To investigate the physiological functions of each isozyme, the expression of each fructokinase mRNA was independently suppressed in transgenic tomato plants, and the respective phenotypes were evaluated. Suppression of Frk1 expression resulted in delayed flowering at the first inflorescence. Suppression ofFrk2 did not effect flowering time but resulted in growth inhibition of stems and roots, reduction of flower and fruit number, and reduction of seed number per fruit. Localization ofFrk1 and Frk2 mRNA accumulation by in situ hybridization in wild-type tomato fruit tissue indicated thatFrk2 is expressed specifically in early tomato seed development. Fruit hexose and starch content were not effected by the suppression of either Frk gene alone. The results collectively indicate that flowering time is specifically promoted by Frk1 and that Frk2 plays specific roles in contributing to stem and root growth and to seed development. Because Frk1 andFrk2 gene expression was suppressed individually in transgenic plants, other significant metabolic roles of fructokinases may not have been observed if Frk1 and Frk2 play, at least partially, redundant metabolic roles.
Ethylene Emission and Responsiveness to Applied Ethylene Vary among Poa Species That Inherently Differ in Leaf Elongation Rates
Authors: Fiorani Fabio , Bögemann Gerard M. , Visser Eric J.W. , Lambers Hans , Voesenek Laurentius A.C.J.
Published: July 2002

A plant's ability to produce and respond to ethylene is essential for its vegetative growth. We studied whole-shoot ethylene emission and leaf growth responses to applied ethylene in fourPoa spp. that differ inherently in leaf elongation rate and whole-plant relative growth rate. Compared with the fast-growingPoa annua and Poa trivialis, the shoots of the slow-growing species Poa alpina and Poa compressa emitted daily 30% to 50% less ethylene, and their leaf elongation rate was more strongly inhibited when ethylene concentration was increased up to 1 μL L−1. To our surprise, however, low ethylene concentrations (0.02–0.03 μL L−1) promoted leaf growth in the two slow-growing species; at the same concentrations, leaf elongation rate of the two fast-growing species was only slightly inhibited. All responses were observed within 20 min after ethylene applications. Although ethylene generally inhibits growth, our results show that in some species, it may actually stimulate growth. Moreover, in the two slow-growingPoa spp., both growth stimulation and inhibition occurred in a narrow ethylene concentration range, and this effect was associated with a much lower ethylene emission. These findings suggest that the regulation of ethylene production rates and perception of the gas may be more crucial during leaf expansion of these species under non-stressful conditions and that endogenous ethylene concentrations are not large enough to saturate leaf growth responses. In the two fast-growing species, a comparatively higher ethylene endogenous concentration may conversely be present and sufficiently high to saturate leaf elongation responses, invariably leading to growth inhibition.
Leucine-Derived Cyano Glucosides in Barley
Authors: Nielsen Kirsten Annette , Olsen Carl Erik , Pontoppidan Katrine , Møller Birger Lindberg
Published: July 2002

Barley (Hordeum vulgare) seedlings contain five cyano glucosides derived from the amino acid l-leucine (Leu). The chemical structure and the relative abundance of the cyano glucosides were investigated by liquid chromatography-mass spectrometry and nuclear magnetic resonance analyses using spring barley cultivars with high, medium, and low cyanide potential. The barley cultivars showed a 10-fold difference in their cyano glucoside content, but the relative content of the individual cyano glucosides remained constant. Epiheterodendrin, the only cyanogenic glucoside present, comprised 12% to 18% of the total content of cyano glucosides. It is proposed that the aglycones of all five cyano glucosides are formed by the initial action of a cytochrome P450 enzyme of the CYP79 family convertingl-Leu into Z-3-methylbutanal oxime and subsequent action of a less specific CYP71E enzyme converting the oxime into 3-methylbutyro nitrile and mediating subsequent hydroxylations at the α-, as well as β- and γ-, carbon atoms. Presence of cyano glucosides in the barley seedlings was restricted to leaf tissue, with 99% confined to the epidermis cell layers of the leaf blade. Microsomal preparations from epidermal cells were not able to convertl-[14C]Leu into the biosynthetic intermediate, Z-3-methylbutanal-oxime. This was only achieved using microsomal preparations from other cell types in the basal leaf segment, demonstrating translocation of the cyano glucosides to the epidermal cell layers after biosynthesis. A β-glucosidase able to degrade epiheterodendrin was detected exclusively in yet a third compartment, the endosperm of the germinating seed. Therefore, in barley, a putative function of cyano glucosides in plant defense is not linked to cyanide release.
Cloning and Characterization of the Abscisic Acid-Specific Glucosyltransferase Gene from Adzuki Bean Seedlings
Authors: Xu Zheng-Jun , Nakajima Masatoshi , Suzuki Yoshihito , Yamaguchi Isomaro
Published: July 2002

The glycosylated forms of abscisic acid (ABA) have been identified from many plant species and are known to be the forms of ABA-catabolism, although their (physiological) roles have not yet been elucidated. ABA-glucosyltransferase (-GTase) is thought to play a key role in the glycosylation of ABA. We isolated an ABA-inducible GTase gene from UDP-GTase homologs obtained from adzuki bean (Vigna angularis) seedlings. The deduced amino acid sequence (accession no. AB065190) showed 30% to 44% identity with the known UDP-GTase homologs. The recombinant protein with a glutathioneS-transferase-tag was expressed in Escherichia coli and showed enzymatic activity in an ABA-specific manner. The enzymatic activity was detected over a wide pH range from 5.0 to 9.0, the optimum range being between pH 6.0 and 7.3, in a citrate and Tris-HCl buffer. The product from racemic ABA and UDP-d-glucose was identified to be ABA-GE by gas chromatography/mass spectrometry. The recombinant GTase (rAOG) converted 2-trans-(+)-ABA better than (+)-S-ABA and (−)-R-ABA. Although trans-cinnamic acid was slightly converted to its conjugate by the GTase, (−)-PA was not at all. The mRNA level was increased by ABA application or by water stress and wounding. We suggest that the gene encodes an ABA-specific GTase and that its expression is regulated by environmental stress.
SOS4, A Pyridoxal Kinase Gene, Is Required for Root Hair Development in Arabidopsis
Authors: Shi Huazhong , Zhu Jian-Kang
Published: July 2002

Root hair development in plants is controlled by many genetic, hormonal, and environmental factors. A number of genes have been shown to be important for root hair formation. Arabidopsissalt overly sensitive 4 mutants were originally identified by screening for NaCl-hypersensitive growth. TheSOS4 (Salt Overly Sensitive 4) gene was recently isolated by map-based cloning and shown to encode a pyridoxal (PL) kinase involved in the production of PL-5-phosphate, which is an important cofactor for various enzymes and a ligand for certain ion transporters. The root growth of sos4 mutants is slower than that of the wild type. Microscopic observations revealed thatsos4 mutants do not have root hairs in the maturation zone. The sos4 mutations block the initiation of most root hairs, and impair the tip growth of those that are initiated. The root hairless phenotype of sos4 mutants was complemented by the wild-type SOS4 gene. SOS4promoter-β-glucuronidase analysis showed thatSOS4 is expressed in the root hair and other hair-like structures. Consistent with SOS4 function as a PL kinase, in vitro application of pyridoxine and pyridoxamine, but not PL, partially rescued the root hair defect in sos4 mutants. 1-Aminocyclopropane-1-carboxylic acid and 2,4-dichlorophenoxyacetic acid treatments promoted root hair formation in both wild-type andsos4 plants, indicating that geneticallySOS4 functions upstream of ethylene and auxin in root hair development. The possible role of SOS4 in ethylene and auxin biosynthesis is discussed.
Genome Properties of the Diatom Phaeodactylum tricornutum
Authors: Scala Simona , Carels Nicolas , Falciatore Angela , Chiusano Maria Luisa , Bowler Chris
Published: July 2002

Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivity and for the biogeochemical cycling of minerals such as silica. However, very little is known about diatom cell biology or about their genome structure. For diatom researchers to take advantage of genomics and post-genomics technologies, it is necessary to establish a model diatom species.Phaeodactylum tricornutum is an obvious candidate because of its ease of culture and because it can be genetically transformed. Therefore, we have examined its genome composition by the generation of approximately 1,000 expressed sequence tags. Although more than 60% of the sequences could not be unequivocally identified by similarity to sequences in the databases, approximately 20% had high similarity with a range of genes defined functionally at the protein level. It is interesting that many of these sequences are more similar to animal rather than plant counterparts. Base composition at each codon position and GC content of the genome were compared with Arabidopsis, maize (Zea mays), andChlamydomonas reinhardtii. It was found that distribution of GC within the coding sequences is as homogeneous inP. tricornutum as in Arabidopsis, but with a slightly higher GC content. Furthermore, we present evidence that the P. tricornutum genome is likely to be small (less than 20 Mb). Therefore, this combined information supports the development of this species as a model system for molecular-based studies of diatom biology. The nucleotide sequence data reported has been deposited in GenBank Nucleotide Sequence Database (dbEST section) under accession nos. BI306757 through BI307753.