bluuebunny/crossref_metadata_2025 huggingface dataset:
Reversal of Tumor-induced Dendritic Cell Paralysis by CpG Immunostimulatory Oligonucleotide and Anti–Interleukin 10 Receptor Antibody
Authors: Vicari Alain P. , Chiodoni Claudia , Vaure Céline , Aït-Yahia Smina , Dercamp Christophe , Matsos Fabien , Reynard Olivier , Taverne Catherine , Merle Philippe , Colombo Mario P. , O'Garra Anne , Trinchieri Giorgio , Caux Christophe
Published: September 2002

Progressing tumors in man and mouse are often infiltrated by dendritic cells (DCs). Deficient antitumor immunity could be related to a lack of tumor-associated antigen (TAA) presentation by tumor-infiltrating DCs (TIDCs) or to a functional defect of TIDCs. Here we investigated the phenotype and function of TIDCs in transplantable and transgenic mouse tumor models. Although TIDCs could encompass various known DC subsets, most had an immature phenotype. We observed that TIDCs were able to present TAA in the context of major histocompatibility complex class I but that they were refractory to stimulation with the combination of lipopolysaccharide, interferon γ, and anti-CD40 antibody. We could revert TIDC paralysis, however, by in vitro or in vivo stimulation with the combination of a CpG immunostimulatory sequence and an anti-interleukin 10 receptor (IL-10R) antibody. CpG or anti–IL-10R alone were inactive in TIDCs, whereas CpG triggered activation in normal DCs. In particular, CpG plus anti–IL-10R enhanced the TAA-specific immune response and triggered de novo IL-12 production. Subsequently, CpG plus anti–IL-10R treatment showed robust antitumor therapeutic activity exceeding by far that of CpG alone, and elicited antitumor immune memory.
Naturally Occurring Mutations at the Acetylcholine Receptor Binding Site Independently Alter ACh Binding and Channel Gating
Authors: Sine Steven M. , Shen Xing-Ming , Wang Hai-Long , Ohno Kinji , Lee Won-Yong , Tsujino Akira , Brengmann Joan , Bren Nina , Vajsar Jiri , Engel Andrew G.
Published: September 2002

By defining functional defects in a congenital myasthenic syndrome (CMS), we show that two mutant residues, located in a binding site region of the acetylcholine receptor (AChR) epsilon subunit, exert opposite effects on ACh binding and suppress channel gating. Single channel kinetic analysis reveals that the first mutation, εN182Y, increases ACh affinity for receptors in the resting closed state, which promotes sequential occupancy of the binding sites and discloses rate constants for ACh occupancy of the nonmutant αδ site. Studies of the analogous mutation in the δ subunit, δN187Y, disclose rate constants for ACh occupancy of the nonmutant αε site. The second CMS mutation, εD175N, reduces ACh affinity for receptors in the resting closed state; occupancy of the mutant site still promotes gating because a large difference in affinity is maintained between closed and open states. εD175N impairs overall gating, however, through an effect independent of ACh occupancy. When mapped on a structural model of the AChR binding site, εN182Y localizes to the interface with the α subunit, and εD175 to the entrance of the ACh binding cavity. Both εN182Y and εD175 show state specificity in affecting closed relative to desensitized state affinities, suggesting that the protein chain harboring εN182 and εD175 rearranges in the course of receptor desensitization. The overall results show that key residues at the ACh binding site differentially stabilize the agonist bound to closed, open and desensitized states, and provide a set point for gating of the channel.
Light-dependent K+ Channels in the Mollusc Onchidium Simple Photoreceptors Are Opened by cGMP
Authors: Gotow Tsukasa , Nishi Takako
Published: September 2002

Light-dependent K+ channels underlying a hyperpolarizing response of one extraocular (simple) photoreceptor, Ip-2 cell, in the marine mollusc Onchidium ganglion were examined using cell-attached and inside-out patch-clamp techniques. A previous report (Gotow, T., T. Nishi, and H. Kijima. 1994. Brain Res. 662:268–272) showed that a depolarizing response of the other simple photoreceptor, A-P-1 cell, results from closing of the light-dependent K+ channels that are activated by cGMP. In the cell-attached patch recordings of Ip-2 cells, external artificial seawater (ASW) was replaced with a modified ASW containing 150 mM K+ and 200 mM Mg2+ to suppress any synaptic input and to maintain the membrane potential constant. When Ip-2 cells were equilibrated with this modified ASW, the internal K+ concentration was estimated to be 260 mM. Light-dependent single-channels in the cell-attached patch on these cells were opened by light but scarcely by voltage. After confirming the light-dependent channel activity in the cell-attached patches, an application of cGMP to the excised inside-out patches newly activated a channel that disappeared on removal of cGMP. Open and closed time distributions of this cGMP-activated channel could be described by the sum of two exponents with time constants τo1, τo2 and τc1, τc2, respectively, similar to those of the light-dependent channel. In both the channels, τo1 and τo2 in ms ranges were similar to each other, although τc2 over tens of millisecond ranges was different. τo1, τo2, and the mean open time τo were both independent of light intensity, cGMP concentration, and voltage. In both channels, the open probability increased as the membrane was depolarized, without changing any of τo2 or τo. In both, the reversal potentials using 200- and 450-mM K+-filled pipettes were close to the K+ equilibrium potentials, suggesting that both the channels are primarily K+ selective. Both the mean values of the channel conductance were estimated to be the same at 62 and 91 pS in 200- and 450-mM K+ pipettes at nearly 0 mV, respectively. Combining these findings with those in the above former report, it is concluded that cGMP is a second messenger which opens the light-dependent K+ channel of Ip-2 to cause hyperpolarization, and that the channel is the same as that of A-P-1 closed by light.
Slow Inactivation Does Not Block the Aqueous Accessibility to the Outer Pore of Voltage-gated Na Channels
Authors: Struyk Arie F. , Cannon Stephen C.
Published: September 2002

Slow inactivation of voltage-gated Na channels is kinetically and structurally distinct from fast inactivation. Whereas structures that participate in fast inactivation are well described and include the cytoplasmic III-IV linker, the nature and location of the slow inactivation gating mechanism remains poorly understood. Several lines of evidence suggest that the pore regions (P-regions) are important contributors to slow inactivation gating. This has led to the proposal that a collapse of the pore impedes Na current during slow inactivation. We sought to determine whether such a slow inactivation-coupled conformational change could be detected in the outer pore. To accomplish this, we used a rapid perfusion technique to measure reaction rates between cysteine-substituted side chains lining the aqueous pore and the charged sulfhydryl-modifying reagent MTS-ET. A pattern of incrementally slower reaction rates was observed at substituted sites at increasing depth in the pore. We found no state-dependent change in modification rates of P-region residues located in all four domains, and thus no change in aqueous accessibility, between slow- and nonslow-inactivated states. In domains I and IV, it was possible to measure modification rates at residues adjacent to the narrow DEKA selectivity filter (Y401C and G1530C), and yet no change was observed in accessibility in either slow- or nonslow-inactivated states. We interpret these results as evidence that the outer mouth of the Na pore remains open while the channel is slow inactivated.
The Cardiac Output and Blood Volume of the Anaesthetized Cat
Authors: A C Groom  , S Rowlands
Published: September 2002

1. The cardiac output and blood volume have been measured in thirty-two cats by an indicator dilution

2. In six experiments both32P-labelled red cells and131I-labelled human serum albumin were used as indicators. In the rest one or other indicator was used.

3. Cardiac output of the cat anaesthetized with chloralose is 113±30 ml/min/kg (32 animals).

4. Repeated determinations show random variations of cardiac output to be about 5%.

5. The blood volume of the cat anaesthetized with chloralose is 49·0±10 ml/kg (25 animals) and the ` central ' blood volume, as defined, 16·9±1·2 ml/kg.

6. The ratio of the value of the whole body haematocrit to that of the arterial haematocrit is 0·93±0·09. The causes of the large variation are considered.

7. The accuracy of the technique and its advantages are discussed.
The Sensitivity of Blood Cells to Light of Different Wavelengths
Authors: K W Keohane  , W K Metcalf
Published: September 2002

1. Lymphocytes and polymorphonuclear leucocytes are very sensitive to radiation of 265 mμ and 254 mμ. This corresponds to a region of the spectrum in which the nucleic acids and nucleoproteins have a strong absorption. Whilst polymorphs are also sensitive to 404 mμ, lymphocytes are not appreciably affected by visible light.

2. Haemolysis of mammalian red cells occurred following irradiation with monochromatic ultra-violet light of 265 mμ.

3. Irradiation with visible light caused the conversion of haemoglobin to methaemoglobin.

4. The time for haemolysis to commence was dependent on the intensity of the light falling on the cell.

5. The duration of the process of haemolysis was independent of the light intensity.

6. The products of haemolysis did not precipitate further haemolysis nor did they affect the white cells.

7. Red cells in hypertonic saline failed to haemolyze even after 12 hours' irradiation.

8. Irradiation causes disc-sphere transformation followed by haemolysis of both mammalian and non-mammalian cells.
A Biochemical Change in the Blood in Pregnancy and Malignant Disease
Authors: W K Metcalf
Published: September 2002

1. An increased sensitivity of intact red cells to nitrites has been demonstrated in children, pregnant women and patients with carcinomata.

2. The cause of this phenomenon is as yet unexplained.

3. Further work is needed before the reliability of this technique as a test for carcinoma or pregnancy can be assessed.
A critical survey of ionospheric temperatures
Authors: N C Gerson
Published: September 2002

The relative order of importance of the various methods available for the evaluation of temperature from an ionospheric parameter is (a) temperature and collisional frequency, (b) temperature and auroral scale heights, (c) temperature and electron concentration, (d) temperature and the influx function, and (e) temperature and the recombination coefficient. Method (e), still in its infancy, does not yet permit accurate temperature evaluations in the ionosphere. Some indication of a diurnal temperature variation may be obtained from method (d).

The probable temperature-altitude relationship in the atmospheric regions 100-400 km., as determined by several techniques, is tabulated below:

Upper Atmospheric Temperatures (°K.)Altitude (km.)Method of DeterminationCollisional frequenciesAuroral scale heightsElectron concentration100300219-150825531-20013501580-25021752073-30024002455-330--1530-268035032252704-4003450--500--2200-3910

These values are considered to represent mean annual temperatures at middle latitudes.

The electron and gas temperatures are essentially identical. If the free electrons have an excess of energy (as may result during an ionization process) this energy is quickly distributed among the gas and other particles.

Thermal equilibrium and therefore a Maxwellian velocity distribution of the atmospheric particles exists among the gaseous constituents in the range 100-400 km. The kinetic temperature is therefore equivalent to the gas temperature. Fluctuation phenomena and deviations of the particles from a Maxwellian velocity distribution probably do not occur in the terrestrial atmosphere until much higher altitudes.

A totally ionized atmosphere below 400 km. does not agree with the experimental evidence inasmuch as the temperature deduced on such a basis will not support the observed number density.

Tentatively it has been shown that no large diurnal temperature variations are found in the altitude range 100-400 km. Preliminary estimates of a probable rate of heating based upon the dissipation of excess energy absorbed during an ionization process appear to confirm the preceding statement. However, the rate of heating attributable to non-detectable absorption processes, to large electrical currents in the ionosphere or to the bombardment by large numbers of high energy electrons is unknown.

The existence of temperatures much higher than those given in the above Table would be difficult to explain in the terrestrial atmosphere. Indeed, it may be qualitatively concluded that the maximum atmospheric temperatures occur in the ionospheric regions at an altitude near or somewhat above 400 km. Above this temperature maximum, a general decrease probably occurs to meet the atmospheric boundary temperature with interstellar space. A temperature maximum near the ionospheric regions probably arises from the various absorption or heating processes together with a sufficient number density of particles.
The evolution of the solar system
Authors: M M Woolfson
Published: September 2002

A brief description of the solar system is given which highlights those features that a plausible theory should explain. A review of theories up to 1960 sets the scene for the description of more modern work and also points out the major features for which explanations are difficult to find. The major obstacle, on which all the older theories founder, is the explanation of the distribution of angular momentum in the system whereby the planets with 0·14% of the mass possess 98% of the angular momentum. The other problem, which has been more recently emphasized by Hoyle, is the slow rotation of the Sun, which is difficult to explain in terms of it having condensed from material possessing the basic galactic rotation.

The modern theories described are:

Hoyle's nebula theory, which invokes the transfer of angular momentum by magnetic forces;

the accretion theory, which proposes that planetary material was captured by the Sun from an interstellar cloud;

McCrea's floccule theory, which describes the solar system as having formed from initial condensations of planetary mass;

the capture theory, which proposes that the Sun captured planets from a tidal filament drawn out of a light star;

a nebula theory proposed by Urey based on chemical evidence derived primarily from meteorites.
Point Contact Andreev Reflection Measurement of the Spin
Polarization of Ferromagnetic Alloy NiFeSb
Authors: Li Zhuang-Zhi  , Tao Hong-Jie  , Wen Hai-Hu  , Zhang Ming  , Liu Zhu-Hong  , Cui Yu-Ting  , Wu Guang-Heng
Published: September 2002

We have studied the temperature-dependent and barrier-strength-dependent
Andreev reflection tunnelling spectroscopy with point contacts consisting
of the newly synthesized half-metallic alloy NiFeSb and a Nb tip. By fitting the
data to the generalized Blonder-Tinkham-Klapwijk theory, a spin
polarization P = 0.52 has been obtained.
Coherence and Decoherence of a Localized Excitation on a
Surface Adatom
Authors: Gao Shi-Wu  , H. Petek  , J. Aizpurua  , P. Apell
Published: September 2002

A theory of coherent excitation of a localized state on an adatom by
two-photon photoemission spectroscopy (TR-2PPE) is presented within a
microscopic model and the time-dependent formalism. Coherent oscillation
and incoherent population decay of the excitation are obtained, and are
shown to attain well-defined lifetime constants only in the long-delay
limit. In addition, we have found a competing excitation channel via electron
transfer. The theory is applied to Cs/Cu (111), which reproduces a few
qualitative features observed in recent experiments. The effect of
atomic motion on the 2PPE spectra, which manifests dominantly as a
redshift in the spectrum, has been analysed.
Function of Dynein and Dynactin in Herpes Simplex Virus Capsid Transport
Authors: Döhner Katinka , Wolfstein André , Prank Ute , Echeverri Christophe , Dujardin Denis , Vallee Richard , Sodeik Beate
Published: September 2002

After fusion of the viral envelope with the plasma membrane, herpes simplex virus type 1 (HSV1) capsids are transported along microtubules (MTs) from the cell periphery to the nucleus. The motor ATPase cytoplasmic dynein and its multisubunit cofactor dynactin mediate most transport processes directed toward the minus-ends of MTs. Immunofluorescence microscopy experiments demonstrated that HSV1 capsids colocalized with cytoplasmic dynein and dynactin. We blocked the function of dynein by overexpressing the dynactin subunit dynamitin, which leads to the disruption of the dynactin complex. We then infected such cells with HSV1 and measured the efficiency of particle binding, virus entry, capsid transport to the nucleus, and the expression of immediate-early viral genes. High concentrations of dynamitin and dynamitin-GFP reduced the number of viral capsids transported to the nucleus. Moreover, viral protein synthesis was inhibited, whereas virus binding to the plasma membrane, its internalization, and the organization of the MT network were not affected. We concluded that incoming HSV1 capsids are propelled along MTs by dynein and that dynein and dynactin are required for efficient viral capsid transport to the nucleus.
Dual Regulation of Actin Rearrangement through Lysophosphatidic Acid Receptor in Neuroblast Cell Lines: Actin Depolymerization by Ca2+-α-Actinin and Polymerization by Rho
Authors: Fukushima Nobuyuki , Ishii Isao , Habara Yoshiaki , Allen Cara B. , Chun Jerold
Published: September 2002

Lysophosphatidic acid (LPA) is a potent lipid mediator with actions on many cell types. Morphological changes involving actin polymerization are mediated by at least two cognate G protein-coupled receptors, LPA1/EDG-2 or LPA2/EDG-4. Herein, we show that LPA can also induce actin depolymerization preceding actin polymerization within single TR mouse immortalized neuroblasts. Actin depolymerization resulted in immediate loss of membrane ruffling, whereas actin polymerization resulted in process retraction. Each pathway was found to be independent: depolymerization mediated by intracellular calcium mobilization, and α-actinin activity and polymerization mediated by the activation of the small Rho GTPase. α-Actinin–mediated depolymerization seems to be involved in growth cone collapse of primary neurons, indicating a physiological significance of LPA-induced actin depolymerization. Further evidence for dual regulation of actin rearrangement was found by heterologous retroviral transduction of either lpa1orlpa2in B103 cells that neither express LPA receptors nor respond to LPA, to confer both forms of LPA-induced actin rearrangements. These results suggest that diverging intracellular signals from a single type of LPA receptor could regulate actin depolymerization, as well as polymerization, within a single cell. This dual actin rearrangement may play a novel, important role in regulation of the neuronal morphology and motility during brain development.
Cytoplasmic Localization of Wis1 MAPKK by Nuclear Export Signal Is Important for Nuclear Targeting of Spc1/Sty1 MAPK in Fission Yeast
Authors: Nguyen Aaron Ngocky , Ikner Aminah D. , Shiozaki Mitsue , Warren Sasha M. , Shiozaki Kazuhiro
Published: September 2002

Mitogen-activated protein kinase (MAPK) cascade is a ubiquitous signaling module that transmits extracellular stimuli through the cytoplasm to the nucleus; in response to activating stimuli, MAPKs translocate into the nucleus. Mammalian MEK MAPK kinases (MAPKKs) have in their N termini an MAPK-docking site and a nuclear export signal (NES) sequence, which are known to play critical roles in maintaining ERK MAPKs in the cytoplasm of unstimulated cells. Herein, we show that the Wis1 MAPKK of the stress-activated Spc1 MAPK cascade in fission yeast also has a MAPK-docking site and an NES sequence in its N-terminal domain. Unexpectedly, an inactivating mutation to the NES of chromosomal wis1+does not affect the subcellular localization of Spc1 MAPK, whereas this NES mutation disturbs the cytoplasmic localization of Wis1. However, when Wis1 is targeted to the nucleus by fusing to a nuclear localization signal sequence, stress-induced nuclear translocation of Spc1 is abrogated, indicating that cytoplasmic Wis1 is required for nuclear transport of Spc1 upon stress. Moreover, we have observed that a fraction of Wis1 translocates into the nucleus in response to stress. These results suggest that cytoplasmic localization of Wis1 MAPKK by its NES is important for stress signaling to the nucleus.
Molecular Cloning and Functional Expression of the Rat 175-kDa Hyaluronan Receptor for Endocytosis
Authors: Zhou Bin , Weigel Janet A. , Saxena Amit , Weigel Paul H.
Published: September 2002

We recently purified the rat liver hyaluronan receptor for endocytosis (HARE) and found abundant expression of 175- and ∼300-kDa HARE species in sinusoidal endothelial cells of the liver, spleen, and lymph nodes. We report herein the first cloning and functional expression of the rat 175-kDa HARE. Peptide sequences were obtained from the purified 175-kDa HARE, and degenerate oligonucleotide primers were designed for reverse transcription-polymerase chain reaction and cDNA cloning. Results of 5′-rapid amplification of cDNA ends, Northern analysis, N-terminal sequence, and antibody reactivity analyses indicated the absence of mRNA directly encoding the 175-kDa HARE. This protein is most likely derived from a larger precursor. Accordingly, we constructed an artificial 4.7-kb cDNA encoding the 1431 amino acid 175-kDa HARE. The predicted type I membrane protein has a mass of 156,393 Da and a pI of 7.86. The 175-kDa HARE cDNA, fused to the N-terminal leader sequence of the Ig κ-chain, was transfected transiently into COS-7 cells and stably into SK-Hep-1 cells, respectively, to assess hyaluronan or hyaluronic acid (HA)-binding activity and endocytosis. In both cases, HARE expression and HA-binding activity were detected. Furthermore, stable SK-175HARE cells demonstrated specific endocytosis of125I-HA and receptor recycling. Fluorescence-activated cell sorting analysis confirmed that recombinant HARE was expressed on the cell surface and that fluorescent HA uptake was inhibited by a specific blocking monoclonal antibody against HARE. Additionally, HARE was substantially colocalized with clathrin, but not with internalized HA that was delivered to lysosomes. The results confirm that recombinant 175-kDa HARE is an authentic endocytic receptor for HA and that this receptor can function independently of the ∼300-kDa HARE. HARE is the first functionally identified member of a protein family that shares a similar organization of Fasciclin, epidermal growth factor-like, Xlink, and transmembrane domains.
The Microtubule-destabilizing Kinesin XKCM1 Regulates Microtubule Dynamic Instability in Cells
Authors: Kline-Smith Susan L. , Walczak Claire E.
Published: September 2002

The dynamic activities of cellular microtubules (MTs) are tightly regulated by a balance between MT-stabilizing and -destabilizing proteins. Studies in Xenopus egg extracts have shown that the major MT destabilizer during interphase and mitosis is the kinesin-related protein XKCM1, which depolymerizes MT ends in an ATP-dependent manner. Herein, we examine the effects of both overexpression and inhibition of XKCM1 on the regulation of MT dynamics in vertebrate somatic cells. We found that XKCM1 is a MT-destabilizing enzyme in PtK2 cells and that XKCM1 modulates cellular MT dynamics. Our results indicate that perturbation of XKCM1 levels alters the catastrophe frequency and the rescue frequency of cellular MTs. In addition, we found that overexpression of XKCM1 or inhibition of KCM1 during mitosis leads to the formation of aberrant spindles and a mitotic delay. The predominant spindle defects from excess XKCM1 included monoastral and monopolar spindles, as well as small prometaphase-like spindles with improper chromosomal attachments. Inhibition of KCM1 during mitosis led to prometaphase spindles with excessively long MTs and spindles with partially separated poles and a radial MT array. These results show that KCM1 plays a critical role in regulating both interphase and mitotic MT dynamics in mammalian cells.
Scd5p and Clathrin Function Are Important for Cortical Actin Organization, Endocytosis, and Localization of Sla2p in Yeast
Authors: Henry Kenneth R. , D'Hondt Kathleen , Chang JiSuk , Newpher Thomas , Huang Kristen , Hudson R. Tod , Riezman Howard , Lemmon Sandra K.
Published: September 2002

SCD5 was identified as a multicopy suppressor of clathrin HC-deficient yeast. SCD5 is essential, but anscd5-Δ338 mutant, expressing Scd5p with a C-terminal truncation of 338 amino acids, is temperature sensitive for growth. Further studies here demonstrate that scd5-Δ338affects receptor-mediated and fluid-phase endocytosis and normal actin organization. The scd5-Δ338 mutant contains larger and depolarized cortical actin patches and a prevalence of G-actin bars.scd5-Δ338 also displays synthetic negative genetic interactions with mutations in several other proteins important for cortical actin organization and endocytosis. Moreover, Scd5p colocalizes with cortical actin. Analysis has revealed that clathrin-deficient yeast also have a major defect in cortical actin organization and accumulate G-actin. Overexpression ofSCD5 partially suppresses the actin defect of clathrin mutants, whereas combining scd5-Δ338 with a clathrin mutation exacerbates the actin and endocytic phenotypes. Both Scd5p and yeast clathrin physically associate with Sla2p, a homologue of the mammalian huntingtin interacting protein HIP1 and the related HIP1R. Furthermore, Sla2p localization at the cell cortex is dependent on Scd5p and clathrin function. Therefore, Scd5p and clathrin are important for actin organization and endocytosis, and Sla2p may provide a critical link between clathrin and the actin cytoskeleton in yeast, similar to HIP1(R) in animal cells.
c-erbB2–induced Disruption of Matrix Adhesion and Morphogenesis Reveals a Novel Role for Protein Kinase B as a Negative Regulator of α2β1Integrin Function
Authors: Lindberg Lachmi E. , Hedjazifar Shahram , Baeckström Dan
Published: September 2002

Overexpression of the growth factor receptor subunit c-erbB2, leading to its ligand-independent homodimerization and activation, has been implicated in the pathogenesis of mammary carcinoma. Here, we have examined the effects of c-erbB2 on the adhesive properties of a mammary epithelial cell line, HB2/tnz34, in which c-erbB2 homodimerization can be induced by means of a transfected hybrid “trk-neu” construct. trk-neu consists of the extracellular domain of the trkA nerve growth factor (NGF) receptor fused to the transmembrane and cytoplasmic domains of c-erbB2, allowing NGF-induced c-erbB2 homodimer signaling. Both spreading and adhesion on collagen surfaces were impaired on c-erbB2 activation in HB2/tnz34 cells. Antibody-mediated stimulation of α2β1integrin function restored adhesion, suggesting a direct role for c-erbB2 in integrin inactivation. Using pharmacological inhibitors and transient transfections, we identified signaling pathways required for suppression of integrin function by c-erbB2. Among these was the MEK-ERK pathway, previously implicated in integrin inactivation. However, we could also show that downstream of phosphoinositide-3-kinase (PI3K), protein kinase B (PKB) acted as a previously unknown, potent inhibitor of integrin function and mediator of the disruptive effects of c-erbB2 on adhesion and morphogenesis. The integrin-linked kinase, previously identified as a PKB coactivator, was also found to be required for integrin inactivation by c-erbB2. In addition, the PI3K-dependent mTOR/S6 kinase pathway was shown to mediate c-erbB2–induced inhibition of adhesion (but not spreading) independently of PKB. Overexpression of MEK1 or PKB suppressed adhesion without requirement for c-erbB2 activation, suggesting that these two pathways partake in integrin inhibition by targeting common downstream effectors. These results demonstrate a major novel role for PI3K and PKB in regulation of integrin function.
Yarrowia lipolyticaCells Mutant for thePEX24Gene Encoding a Peroxisomal Membrane Peroxin Mislocalize Peroxisomal Proteins and Accumulate Membrane Structures Containing Both Peroxisomal Matrix and Membrane Proteins
Authors: Tam Yuen Yi C. , Rachubinski Richard A.
Published: September 2002

Peroxins are proteins required for peroxisome assembly and are encoded by the PEX genes. Functional complementation of the oleic acid–nonutilizing strain mut1-1 of the yeastYarrowia lipolytica has identified the novel gene,PEX24. PEX24 encodes Pex24p, a protein of 550 amino acids (61,100 Da). Pex24p is an integral membrane protein of peroxisomes that exhibits high sequence homology to two hypothetical proteins encoded by the open reading frames YHR150W andYDR479C of the Saccharomyces cerevisiaegenome. Pex24p is detectable in wild-type cells grown in glucose-containing medium, and its levels are significantly increased by incubation of cells in oleic acid–containing medium, the metabolism of which requires intact peroxisomes. pex24 mutants are compromised in the targeting of both matrix and membrane proteins to peroxisomes. Although pex24 mutants fail to assemble functional peroxisomes, they do harbor membrane structures that contain subsets of peroxisomal proteins.
Clastosome: A Subtype of Nuclear Body Enriched in 19S and 20S Proteasomes, Ubiquitin, and Protein Substrates of Proteasome
Authors: Lafarga Miguel , Berciano Maria Teresa , Pena Emma , Mayo Isabel , Castaño Jose G. , Bohmann Dirk , Rodrigues João Pedro , Tavanez João Paulo , Carmo-Fonseca Maria
Published: September 2002

Nuclear bodies represent a heterogeneous class of nuclear structures. Herein, we describe that a subset of nuclear bodies is highly enriched in components of the ubiquitin–proteasome pathway of proteolysis. We coined the term clastosome (from the Greekklastos, broken and soma, body) to refer to this type of nuclear body. Clastosomes contain a high concentration of 1) ubiquitin conjugates, 2) the proteolytically active 20S core and the 19S regulatory complexes of the 26S proteasome, and 3) protein substrates of the proteasome. Although detected in a variety of cell types, clastosomes are scarce under normal conditions; however, they become more abundant when proteasomal activity is stimulated. In contrast, clastosomes disappear when cells are treated with proteasome inhibitors. Protein substrates of the proteasome that are found concentrated in clastosomes include the short-lived transcription factors c-Fos and c-Jun, adenovirus E1A proteins, and the PML protein. We propose that clastosomes are sites where proteolysis of a variety of protein substrates is taking place.
DIANA-EST: a statistical analysis
Authors: Hatzigeorgiou Artemis G. , Fiziev Petko , Reczko Martin
Published: September 2002

Motivation: Expressed Sequence Tags (ESTs) are next to cDNA sequences as the most direct way to locate in silico the genes of the genome and determine their structure. Currently ESTs make up more than 60% of all the database entries. The goal of this work is the development of a new program called DNA Intelligent Analysis for ESTs (DIANA-EST) based on a combination of Artificial Neural Networks (ANN) and statistics for the characterization of the coding regions within ESTs and the reconstruction of the encoded protein.

Results: 89.7% of the nucleotides from an independent test set with 127 ESTs were predicted correctly as to whether they are coding or non coding.

Availability: The program is available upon request from the author.

Contact: Present address: Department of Genetics, University of Pennsylvania, School of Medicine, 475 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6145, USA. artemis@pcbi.upenn.edu.
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT
Authors: Kretschmann Ernst , Fleischmann Wolfgang , Apweiler Rolf
Published: September 2002

Motivation: The gap between the amount of newly submitted protein data and reliable functional annotation in public databases is growing. Traditional manual annotation by literature curation and sequence analysis tools without the use of automated annotation systems is not able to keep up with the ever increasing quantity of data that is submitted. Automated supplements to manually curated databases such as TrEMBL or GenPept cover raw data but provide only limited annotation. To improve this situation automatic tools are needed that support manual annotation, automatically increase the amount of reliable information and help to detect inconsistencies in manually generated annotations.

Results: A standard data mining algorithm was successfully applied to gain knowledge about the Keyword annotation in SWISS-PROT. 11 306 rules were generated, which are provided in a database and can be applied to yet unannotated protein sequences and viewed using a web browser. They rely on the taxonomy of the organism, in which the protein was found and on signature matches of its sequence. The statistical evaluation of the generated rules by cross-validation suggests that by applying them on arbitrary proteins 33% of their keyword annotation can be generated with an error rate of 1.5%. The coverage rate of the keyword annotation can be increased to 60% by tolerating a higher error rate of 5%.

Availability: The results of the automatic data mining process can be browsed on http://golgi.ebi.ac.uk:8080/Spearmint/ Source code is available upon request.

Contact: kretsch@ebi.ac.uk
Sequence and structural aspects of functional diversification

in class I α-mannosidase evolution
Authors: Jordan I. King , Bishop G. Reid , Gonzalez Daniel S.
Published: September 2002

Motivation: Class I α-mannosidases comprise a homologous and functionally diverse family of glycoside hydrolases. Phylogenetic analysis based on an amino acid sequence alignment of the catalytic domain of class I α-mannosidases reveals four well-supported phylogenetic groups within this family. These groups include a number of paralogous members generated by gene duplications that occurred as far back as the initial divergence of the crown-group of eukaryotes. Three of the four phylogenetic groups consist of enzymes that have group-specific biochemical specificity and/or sites of activity. An attempt has been made to uncover the role that natural selection played in the sequence and structural divergence between the phylogenetically and functionally distinct Endoplasmic Reticulum (ER) and Golgi apparatus groups.

Results: Comparison of site-specific amino acid variability profiles for the ER and Golgi groups revealed statistically significant evidence for functional diversification at the sequence level and indicated a number of residues that are most likely to have played a role in the functional divergence between the two groups. The majority of these sites appear to contain residues that have been fixed within one organelle-specific group by positive selection. Somewhat surprisingly these selected residues map to the periphery of the α-mannosidase catalytic domain tertiary structure. Changes in these peripherally located residues would not seem to have a gross effect on protein function. Thus diversifying selection between the two groups may have acted in a gradual manner consistent with the Darwinian model of natural selection.

Contact: bishogr@millsaps.edu

* To whom correspondence should be addressed.
Principal component analysis for clustering gene expression
data
Authors: Yeung K. Y. , Ruzzo W. L.
Published: September 2002

Motivation: There is a great need to develop analytical methodology to analyze and to exploit the information contained in gene expression data. Because of the large number of genes and the complexity of biological networks, clustering is a useful exploratory technique for analysis of gene expression data. Other classical techniques, such as principal component analysis (PCA), have also been applied to analyze gene expression data. Using different data analysis techniques and different clustering algorithms to analyze the same data set can lead to very different conclusions. Our goal is to study the effectiveness of principal components (PCs) in capturing cluster structure. Specifically, using both real and synthetic gene expression data sets, we compared the quality of clusters obtained from the original data to the quality of clusters obtained after projecting onto subsets of the principal component axes.

Results: Our empirical study showed that clustering with the PCs instead of the original variables does not necessarily improve, and often degrades, cluster quality. In particular, the first few PCs (which contain most of the variation in the data) do not necessarily capture most of the cluster structure. We also showed that clustering with PCs has different impact on different algorithms and different similarity metrics. Overall, we would not recommend PCA before clustering except in special circumstances.

Contact: kayee@cs.washington.edu

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

* To whom correspondence should be addressed.
Detecting the impact of sequencing errors on SAGE data
Authors: Colinge Jacques , Feger Georg
Published: September 2002

Summary: SAGE data are obtained by sequencing short DNA tags. Due to the mistakes in DNA sequencing, SAGE data contain errors. We propose a new approach to identify tags whose abundance is biased by sequencing errors. This approach is based on a concept of neighbourhood: abundant tags can contaminate tags whose sequence is very close. The application of our approach reveals that moderately abundant tags can be generated by sequencing errors uniquely. It also allows for detecting correct rare tags.

Availability: Software is available only to non-profit entities and for non-commercial purposes upon request.

Contact: Georg.Feger@serono.com

* To whom all correspondence should be addressed.

2 Present address: GeneProt Inc., Pré-de-la-Fontaine 2, CH-1217 Meyrin, Switzerland.
CHROMA: consensus-based colouring of multiple alignments for
publication
Authors: Goodstadt Leo , Ponting Chris P.
Published: September 2002

CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

* To whom correspondence should be addressed.
BioWAP, mobile Internet service for bioinformatics
Authors: Riikonen Pentti , Boberg Jorma , Salakoski Tapio , Vihinen Mauno
Published: September 2002

Summary: We have developed a new Internet service, which provides mobile access to bioinformatics databases and software tools. The BioWAP service facilitates access to basic bioinformatics databases and analysis tools from everywhere without a PC or a laptop computer. Both open source bioinformatics program suites and Internet services, which are not designed for mobile Internet access, were utilized in the BioWAP service.

Availability: The BioWAP service starting page can be browsed with any WAP terminal from http://bioinf.uta.fi/wml/welcome.wml.

Contact: Mauno.Vihinen@uta.fi

* To whom correspondence should be addressed.
Analysis of expression profile using fuzzy adaptive
resonance theory
Authors: Tomida Shuta , Hanai Taizo , Honda Hiroyuki , Kobayashi Takeshi
Published: September 2002

Motivation: It is well understood that the successful clustering of expression profiles give beneficial ideas to understand the functions of uncharacterized genes. In order to realize such a successful clustering, we investigate a clustering method based on adaptive resonance theory (ART) in this report.

Results: We apply Fuzzy ART as a clustering method for analyzing the time series expression data during sporulation of Saccharomyces cerevisiae. The clustering result by Fuzzy ART was compared with those by other clustering methods such as hierarchical clustering, k-means algorithm and self-organizing maps (SOMs). In terms of the mathematical validations, Fuzzy ART achieved the most reasonable clustering. We also verified the robustness of Fuzzy ART using noised data. Furthermore, we defined the correctness ratio of clustering, which is based on genes whose temporal expressions are characterized biologically. Using this definition, it was proved that the clustering ability of Fuzzy ART was superior to other clustering methods such as hierarchical clustering, k-means algorithm and SOMs. Finally, we validate the clustering results by Fuzzy ART in terms of biological functions and evidence.

Availability: The software is available at http//www.nubio.nagoya-u.ac.jp/proc/index.html

Contact: taizo@brs.kyushu-u.ac.jp

* To whom correspondence should be addressed. Present address: Laboratory for Applied Biological Regulation Technology, School of Bioresource and Bioenvironmental Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
A branch-and-bound algorithm for the inference of ancestral amino-acid
sequences when the replacement rate varies among sites: Application to the
evolution of five gene families
Authors: Pupko Tal , Pe'er Itsik , Hasegawa Masami , Graur Dan , Friedman Nir
Published: September 2002

Motivation: We developed an algorithm to reconstruct ancestral sequences, taking into account the rate variation among sites of the protein sequences. Our algorithm maximizes the joint probability of the ancestral sequences, assuming that the rate is gamma distributed among sites. Our algorithm provably finds the global maximum. The use of ‘joint’ reconstruction is motivated by studies that use the sequences at all the internal nodes in a phylogenetic tree, such as, for instance, the inference of patterns of amino-acid replacement, or tracing the biochemical changes that occurred during the evolution of a given protein family.

Results: We give an algorithm that guarantees finding the global maximum. The efficient search method makes our method applicable to datasets with large number sequences. We analyze ancestral sequences of five gene families, exploring the effect of the amount of among-site-rate-variation, and the degree of sequence divergence on the resulting ancestral states.

Availability and supplementary information: http://evolu3.ism.ac.jp/~tal/

Contact: tal@ism.ac.jp

* To whom correspondence should be addressed.
ShiftDetector: detection of shift mutations
Authors: Seroussi Eyal , Ron Micha , Kedra Darek
Published: September 2002

Motivation: Sequencing of a bi-allelic PCR product, which contains an allele with a deletion/insertion mutation results in a superimposed tracefile following the site of this shift mutation. A trace file of this type hampers the use of current computer programs for base calling. ShiftDetector analyses a sequencing trace file in order to discover if it is a superimposed sequence of two molecules that differ in a shift mutation of 1 to 25 bases. The program calculates a probability score for the existence of such a shift and reconstructs the sequence of the original molecule.

Availability: ShiftDetector is available from http://cowry.agri.huji.ac.il

Contact: seroussi@agri.huji.ac.il

* To whom correspondence should be addressed.
Domain Fishing: a first step in protein comparative modelling
Authors: Contreras-Moreira B. , Bates P.A.
Published: September 2002

Summary: To optimize the search for structural templates in protein comparative modelling, the query sequence is split into domains. The initial list of templates for each domain, extracted from PFAM plus PDB and SCOP, is then ranked according to sequence identity (%ID), coverage and resolution. If %ID is less than 30, secondary structure matching is used to filter out false templates.

Availability: http://www.bmm.icnet.uk/~3djigsaw/dom_fish

Contact: b.contreras-moreira@cancer.org.ukpaul.bates@cancer.org.uk

* To whom correspondence should be addressed.
DiffTool: building, visualizing and querying protein clusters
Authors: Chetouani Farid , Glaser Philippe , Kunst Frank
Published: September 2002

Summary: DiffTool is a resource to build and visualize protein clusters computed from a sequence database. The package provides a clustering tool to construct protein families according to sequence similarities and a web interface to query the corresponding clusters. A subtractive genome analysis tool selects protein families specific for a genome or a group of genomes. For each protein cluster, DiffTool includes access to sequences, coloured multiple alignments and phylogenetic trees.

Availability: A cluster database built from yeast and complete prokaryotic genomes is queryable at http://bioweb.pasteur.fr/seqanal/difftool. All the Perl sources are freely available to non-profit organizations upon request.

Contact: fchetou@infobiogen.fr

* To whom correspondence should be addressed.
The NCTU BioInfo Archive of biological data sets for
bioinformatics research and experimentation
Authors: Hu Yuh-Jyh
Published: September 2002

Most of the current bioinformatics literature lacks an explicit and clear description of the data used in experiments when introducing or evaluating computational tools. Without the exact data set that was fed into computational tools in experiments, any mistaken preparation of the data for later experiments may lead to discrepancy in conclusion. The NCTU BioInfo Archive is a new web-based bioinformatic data archive. It serves as a test bed for evaluating computational tools, as a bridge to link other research communities with bioinformatics, and also as an environment full of motivations and possibilities to encourage more exploratory research in bioinformatics.

Availability: http://bioinfo.cis.nctu.edu.tw

Contact: yhu@cis.nctu.edu.tw
The EBI SRS server—new features
Authors: Zdobnov Evgeny M. , Lopez Rodrigo , Apweiler Rolf , Etzold Thure
Published: September 2002

Motivation: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ‘Nice views’, SRSQuickSearch bookmarklets.

Availability: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.

Contact: EBISRS@ebi.ac.uk