bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear threshold behavior during the loss of Arctic sea ice
Authors: Eisenman I. , Wettlaufer J. S.
Published: December 2008

In light of the rapid recent retreat of Arctic sea ice, a number of studies have discussed the possibility of a critical threshold (or “tipping point”) beyond which the ice–albedo feedback causes the ice cover to melt away in an irreversible process. The focus has typically been centered on the annual minimum (September) ice cover, which is often seen as particularly susceptible to destabilization by the ice–albedo feedback. Here, we examine the central physical processes associated with the transition from ice-covered to ice-free Arctic Ocean conditions. We show that although the ice–albedo feedback promotes the existence of multiple ice-cover states, the stabilizing thermodynamic effects of sea ice mitigate this when the Arctic Ocean is ice covered during a sufficiently large fraction of the year. These results suggest that critical threshold behavior is unlikely during the approach from current perennial sea-ice conditions to seasonally ice-free conditions. In a further warmed climate, however, we find that a critical threshold associated with the sudden loss of the remaining wintertime-only sea ice cover may be likely.
Accurate SHAPE-directed RNA structure determination
Authors: Deigan Katherine E. , Li Tian W. , Mathews David H. , Weeks Kevin M.
Published: December 2008

Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized
Escherichia coli
16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis.
Disruption of the
SRC-1
gene in mice suppresses breast cancer metastasis without affecting primary tumor formation
Authors: Wang Shu , Yuan Yuhui , Liao Lan , Kuang Shao-Qing , Tien Jean Ching-Yi , O'Malley Bert W. , Xu Jianming
Published: December 2008

Steroid receptor coactivator-1 (SRC-1) is a coactivator for nuclear hormone receptors such as estrogen and progesterone receptors and certain other transcription factors such as Ets-2 and PEA3. SRC-1 expression in breast cancer is associated with HER2 and c-Myc expression and with reduced disease-free survival. In this study,
SRC-1
−/−
mice were backcrossed with FVB mice and then cross-bred with MMTV-polyoma middle T antigen (PyMT) mice to investigate the role of SRC-1 in breast cancer. Although mammary tumor initiation and growth were similar in
SRC-1
−/−
/
PyMT
and
wild-type
(
WT
)/
PyMT
mice, genetic ablation of
SRC-1
antagonized PyMT-induced restriction of mammary ductal differentiation and elongation.
SRC-1
−/−
/
PyMT
mammary tumors were also more differentiated than
WT
/
PyMT
mammary tumors. The intravasation of mammary tumor cells and the frequency and extent of lung metastasis were drastically reduced in
SRC-1
−/−
/
PyMT
mice compared with
WT
/
PyMT
mice. Metastatic analysis of transplanted
WT
/
PyMT
and
SRC-1
−/−
/
PyMT
tumors in
SRC-1
−/−
and
WT
recipient mice revealed that SRC-1 played an intrinsic role in tumor cell metastasis. Furthermore, SRC-1 was up-regulated during mammary tumor progression. Disruption of
SRC-1
inhibited Ets-2-mediated HER2 expression and PyMT-stimulated Akt activation in the mammary tumors. Disruption of
SRC-1
also suppressed colony-stimulating factor-1 (CSF-1) expression and reduced macrophage recruitment to the tumor site. These results suggest that SRC-1 specifically promotes metastasis without affecting primary tumor growth. SRC-1 may promote metastasis through mediating Ets-2-mediated HER2 expression and activating CSF-1 expression for macrophage recruitment. Therefore, functional interventions for coactivators like SRC-1 may provide unique approaches to control breast cancer progression and metastasis.
A conserved protonation-dependent switch controls drug binding in the Abl kinase
Authors: Shan Yibing , Seeliger Markus A. , Eastwood Michael P. , Frank Filipp , Xu Huafeng , Jensen Morten Ø , Dror Ron O. , Kuriyan John , Shaw David E.
Published: December 2008

In many protein kinases, a characteristic conformational change (the “DFG flip”) connects catalytically active and inactive conformations. Many kinase inhibitors—including the cancer drug imatinib—selectively target a specific DFG conformation, but the function and mechanism of the flip remain unclear. Using long molecular dynamics simulations of the Abl kinase, we visualized the DFG flip in atomic-level detail and formulated an energetic model predicting that protonation of the DFG aspartate controls the flip. Consistent with our model's predictions, we demonstrated experimentally that the kinetics of imatinib binding to Abl kinase have a pH dependence that disappears when the DFG aspartate is mutated. Our model suggests a possible explanation for the high degree of conservation of the DFG motif: that the flip, modulated by electrostatic changes inherent to the catalytic cycle, allows the kinase to access flexible conformations facilitating nucleotide binding and release.
Essential functions of the Williams-Beuren syndrome-associated TFII-I genes in embryonic development
Authors: Enkhmandakh Badam , Makeyev Aleksandr V. , Erdenechimeg Lkhamsuren , Ruddle Frank H. , Chimge Nyam-Osor , Tussie-Luna Maria Isabel , Roy Ananda L. , Bayarsaihan Dashzeveg
Published: December 2008

GTF2I
and
GTF2IRD1
encoding the multifunctional transcription factors TFII-I and BEN are clustered at the 7q11.23 region hemizygously deleted in Williams-Beuren syndrome (WBS), a complex multisystemic neurodevelopmental disorder. Although the biochemical properties of TFII-I family transcription factors have been studied in depth, little is known about the specialized contributions of these factors in pathways required for proper embryonic development. Here, we show that homozygous loss of either
Gtf2ird1
or
Gtf2i
function results in multiple phenotypic manifestations, including embryonic lethality; brain hemorrhage; and vasculogenic, craniofacial, and neural tube defects in mice. Further analyses suggest that embryonic lethality may be attributable to defects in yolk sac vasculogenesis and angiogenesis. Microarray data indicate that the
Gtf2ird1
homozygous phenotype is mainly caused by an impairment of the genes involved in the TGFβRII/Alk1/Smad5 signal transduction pathway. The effect of
Gtf2i
inactivation on this pathway is less prominent, but downregulation of the endothelial growth factor receptor-2 gene, resulting in the deterioration of vascular signaling, most likely exacerbates the severity of the
Gtf2i
mutant phenotype. A subset of
Gtf2ird1
and
Gtf2i
heterozygotes displayed microcephaly, retarded growth, and skeletal and craniofacial defects, therefore showing that haploinsufficiency of TFII-I proteins causes various developmental anomalies that are often associated with WBS.
A role for the host coatomer and KDEL receptor in early vaccinia biogenesis
Authors: Zhang Leiliang , Lee Stella Y. , Beznoussenko Galina V. , Peters Peter J. , Yang Jia-Shu , Gilbert Hui-ya , Brass Abraham L. , Elledge Stephen J. , Isaacs Stuart N. , Moss Bernard , Mironov Alexander , Hsu Victor W.
Published: December 2008

Members of the poxvirus family have been investigated for their applications as vaccines and expression vectors and, more recently, because of concern for their potential as biological weapons. Vaccinia virus, the prototypic member, evolves through multiple forms during its replication. Here, we show a surprising way by which vaccinia hijacks coatomer for early viral biogenesis. Whereas coatomer forms COPI vesicles in the host early secretory system, vaccinia formation bypasses this role of coatomer, but instead, depends on coatomer interacting with the host KDEL receptor. To gain insight into the viral roles of these two host proteins, we have detected them on the earliest recognized viral forms. These findings not only suggest insights into early vaccinia biogenesis but also reveal an alternate mechanism by which coatomer acts.
Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis
Authors: Chen Chin-Yu , Chang Chia-Chi , Yen Chi-Fu , Chiu Michael T.-K. , Chang Wei-Hau
Published: December 2008

A simple genetic tag-based labeling method that permits specific attachment of a fluorescence probe near the C terminus of virtually any subunit of a protein complex is implemented. Its immediate application to yeast RNA polymerase II (pol II) enables us to test various hypotheses of RNA exit channel by using fluorescence resonance energy transfer (FRET) analysis. The donor dye is labeled on a site near subunit Rpb3 or Rpb4, and the acceptor dye is attached to the 5′ end of RNA transcript in the pol II elongation complex. Both in-gel and single-molecule FRET analysis show that the growing RNA is leading toward Rpb4, not Rpb3, supporting the notion that RNA exits through the proposed channel 1. Distance constraints derived from our FRET results, in conjunction with triangulation, reveal the exit track of RNA transcript on core pol II by identifying amino acids in the vicinity of the 5′ end of RNA and show that the extending RNA forms contacts with the Rpb7 subunit. The significance of RNA exit route in promoter escape and that in cotranscriptional mRNA processing is discussed.
Dorsal Root Ganglion Neurons React to Semaphorin 3A Application through a Biphasic Response that Requires Multiple Myosin II Isoforms
Authors: Brown Jacquelyn A. , Wysolmerski Robert B. , Bridgman Paul C.
Published: December 2008

Growth cone responses to guidance cues provide the basis for neuronal pathfinding. Although many cues have been identified, less is known about how signals are translated into the cytoskeletal rearrangements that steer directional changes during pathfinding. Here we show that the response of dorsal root ganglion (DRG) neurons to Semaphorin 3A gradients can be divided into two steps: growth cone collapse and retraction. Collapse is inhibited by overexpression of myosin IIA or growth on high substrate-bound laminin-1. Inhibition of collapse also prevents retractions; however collapse can occur without retraction. Inhibition of myosin II activity with blebbistatin or by using neurons from myosin IIB knockouts inhibits retraction. Collapse is associated with movement of myosin IIA from the growth cone to the neurite. Myosin IIB redistributes from a broad distribution to the rear of the growth cone and neck of the connecting neurite. High substrate-bound laminin-1 prevents or reverses these changes. This suggests a model for the Sema 3A response that involves loss of growth cone myosin IIA to facilitate actin meshwork instability and collapse, followed by myosin IIB concentration at the rear of the cone and neck region where it associates with actin bundles to drive retraction.
Molecular Architecture of the Centriole Proteome: The Conserved WD40 Domain Protein POC1 Is Required for Centriole Duplication and Length Control
Authors: Keller Lani C. , Geimer Stefan , Romijn Edwin , Yates John , Zamora Ivan , Marshall Wallace F.
Published: December 2008

Centrioles are intriguing cylindrical organelles composed of triplet microtubules. Proteomic data suggest that a large number of proteins besides tubulin are necessary for the formation and maintenance of a centriole's complex structure. Expansion of the preexisting centriole proteome from the green alga Chlamydomonas reinhardtii revealed additional human disease genes, emphasizing the significance of centrioles in normal human tissue homeostasis. We found that two classes of ciliary disease genes were highly represented among the basal body proteome: cystic kidney disease (especially nephronophthisis) syndromes, including Meckel/Joubert-like and oral-facial-digital syndrome, caused by mutations in CEP290, MKS1, OFD1, and AHI1/Jouberin proteins and cone-rod dystrophy syndrome genes, including UNC-119/HRG4, NPHP4, and RPGR1. We further characterized proteome of the centriole (POC) 1, a highly abundant WD40 domain-containing centriole protein. We found that POC1 is recruited to nascent procentrioles and localizes in a highly asymmetrical pattern in mature centrioles corresponding to sites of basal-body fiber attachment. Knockdown of POC1 in human cells caused a reduction in centriole duplication, whereas overexpression caused the appearance of elongated centriole-like structures. Together, these data suggest that POC1 is involved in early steps of centriole duplication as well as in the later steps of centriole length control.
A Shared Mechanism of Adhesion Modulation for Tenascin-C and Fibulin-1
Authors: Williams Selwyn A. , Schwarzbauer Jean E.
Published: December 2008

Adhesion modulatory proteins are important effectors of cell–matrix interactions during tissue remodeling and regeneration. They comprise a diverse group of matricellular proteins that confer antiadhesive properties to the extracellular matrix (ECM). We compared the inhibitory effects of two adhesion modulatory proteins, fibulin-1 and tenascin-C, both of which bind to the C-terminal heparin-binding (HepII) domain of fibronectin (FN) but are structurally distinct. Here, we report that, like tenascin-C, fibulin-1 inhibits fibroblast spreading and cell-mediated contraction of a fibrin–FN matrix. These proteins act by modulation of focal adhesion kinase and extracellular signal-regulated kinase signaling. The inhibitory effects were bypassed by lysophosphatidic acid, an activator of RhoA GTPase. Fibroblast response to fibulin-1, similar to tenascin-C, was dependent on expression of the heparan sulfate proteoglycan syndecan-4, which also binds to the HepII domain. Therefore, blockade of HepII-mediated signaling by competitive binding of fibulin-1 or tenascin-C represents a shared mechanism of adhesion modulation among disparate modulatory proteins.
Deficient SUMO Attachment to Flp Recombinase Leads to Homologous Recombination-dependent Hyperamplification of the Yeast 2 μm Circle Plasmid
Authors: Xiong Ling , Chen Xiaole L. , Silver Hannah R. , Ahmed Noreen T. , Johnson Erica S.
Published: December 2008

Many Saccharomyces cerevisiae mutants defective in the SUMO pathway accumulate elevated levels of the native 2 μm circle plasmid (2 μm). Here we show that accumulation of 2 μm in the SUMO pathway mutants siz1Δ siz2Δ, slx5Δ, and slx8Δ is associated with formation of an aberrant high-molecular-weight (HMW) form of 2 μm. Characterization of this species from siz1Δ siz2Δ showed that it contains tandem copies of the 2 μm sequence as well as single-stranded DNA. Accumulation of this species requires both the 2 μm–encoded Flp recombinase and the cellular homologous recombination repair (HRR) pathway. Importantly, reduced SUMO attachment to Flp is sufficient to induce formation of this species. Our data suggest a model in which Flp that cannot be sumoylated causes DNA damage, whose repair via HRR produces an intermediate that generates tandem copies of the 2 μm sequence. This intermediate may be a rolling circle formed via break-induced replication (BIR), because mutants defective in BIR contain reduced levels of the HMW form. This work also illustrates the importance of using cir° strains when studying mutants that affect the yeast SUMO pathway, to avoid confusing direct functions of the SUMO pathway with secondary effects of 2 μm amplification.
A Histone Deacetylase 4/Myogenin Positive Feedback Loop Coordinates Denervation-dependent Gene Induction and Suppression
Authors: Tang Huibin , Macpherson Peter , Marvin Michael , Meadows Eric , Klein William H. , Yang Xiang-Jiao , Goldman Daniel
Published: December 2008

Muscle activity contributes to formation of the neuromuscular junction and affects muscle metabolism and contractile properties through regulated gene expression. However, the mechanisms coordinating these diverse activity-regulated processes remain poorly characterized. Recently, it was reported that histone deacetylase 4 (HDAC4) can mediate denervation-induced myogenin and nicotinic acetylcholine receptor gene expression. Here, we report that HDAC4 is not only necessary for denervation-dependent induction of genes involved in synaptogenesis (nicotinic acetylcholine receptor and muscle-specific receptor tyrosine kinase) but also for denervation-dependent suppression of genes involved in glycolysis (muscle-specific enolase and phosphofructokinase). In addition, HDAC4 differentially regulates genes involved in muscle fiber type specification by inducing myosin heavy chain IIA and suppressing myosin heavy chain IIB. Consistent with these regulated gene profiles, HDAC4 is enriched in fast oxidative fibers of innervated tibialis anterior muscle and HDAC4 knockdown enhances glycolysis in cultured myotubes. HDAC4 mediates gene induction indirectly by suppressing the expression of Dach2 and MITR that function as myogenin gene corepressors. In contrast, HDAC4 is directly recruited to myocyte enhancer factor 2 sites within target promoters to mediate gene suppression. Finally, we discovered an HDAC4/myogenin positive feedback loop that coordinates gene induction and repression underlying muscle phenotypic changes after muscle denervation.
The Anaphase-promoting Complex Promotes Actomyosin-Ring Disassembly during Cytokinesis in Yeast
Authors: Tully Gregory H. , Nishihama Ryuichi , Pringle John R. , Morgan David O.
Published: December 2008

The anaphase-promoting complex (APC) is a ubiquitin ligase that controls progression through mitosis by targeting specific proteins for degradation. It is unclear whether the APC also contributes to the control of cytokinesis, the process that divides the cell after mitosis. We addressed this question in the yeast Saccharomyces cerevisiae by studying the effects of APC mutations on the actomyosin ring, a structure containing actin, myosin, and several other proteins that forms at the division site and is important for cytokinesis. In wild-type cells, actomyosin-ring constituents are removed progressively from the ring during contraction and disassembled completely thereafter. In cells lacking the APC activator Cdh1, the actomyosin ring contracts at a normal rate, but ring constituents are not disassembled normally during or after contraction. After cytokinesis in mutant cells, aggregates of ring proteins remain at the division site and at additional foci in other parts of the cell. A key target of APCCdh1is the ring component Iqg1, the destruction of which contributes to actomyosin-ring disassembly. Deletion of CDH1 also exacerbates actomyosin-ring disassembly defects in cells with mutations in the myosin light-chain Mlc2, suggesting that Mlc2 and the APC employ independent mechanisms to promote ring disassembly during cytokinesis.
Autophagy Provides Nutrients but Can Lead to Chop-dependent Induction of Bim to Sensitize Growth Factor–deprived Cells to Apoptosis
Authors: Altman Brian J. , Wofford Jessica A. , Zhao Yuxing , Coloff Jonathan L. , Ferguson Emily C. , Wieman Heather L. , Day Amanda E. , Ilkayeva Olga , Rathmell Jeffrey C.
Published: December 2008

Tissue homeostasis is controlled by the availability of growth factors, which sustain exogenous nutrient uptake and prevent apoptosis. Although autophagy can provide an alternate intracellular nutrient source to support essential basal metabolism of apoptosis-resistant growth factor–withdrawn cells, antiapoptotic Bcl-2 family proteins can suppress autophagy in some settings. Thus, the role of autophagy and interactions between autophagy and apoptosis in growth factor–withdrawn cells expressing Bcl-2 or Bcl-xL were unclear. Here we show autophagy was rapidly induced in hematopoietic cells upon growth factor withdrawal regardless of Bcl-2 or Bcl-xL expression and led to increased mitochondrial lipid oxidation. Deficiency in autophagy-essential gene expression, however, did not lead to metabolic catastrophe and rapid death of growth factor–deprived cells. Rather, inhibition of autophagy enhanced survival of cells with moderate Bcl-2 expression for greater than 1 wk, indicating that autophagy promoted cell death in this time frame. Cell death was not autophagic, but apoptotic, and relied on Chop-dependent induction of the proapoptotic Bcl-2 family protein Bim. Therefore, although ultimately important, autophagy-derived nutrients appear initially nonessential after growth factor withdrawal. Instead, autophagy promotes tissue homeostasis by sensitizing cells to apoptosis to ensure only the most apoptosis-resistant cells survive long-term using autophagy-derived nutrients when growth factor deprived.
GM130-dependent Control of Cdc42 Activity at the Golgi Regulates Centrosome Organization
Authors: Kodani Andrew , Kristensen Irene , Huang Lan , Sütterlin Christine
Published: December 2008

The physical proximity of the Golgi apparatus and the centrosome is a unique feature of mammalian cells whose functional significance is only poorly understood. Here, we demonstrate that the previously described regulation of centrosome organization and function by the Golgi protein, GM130, involves a Golgi-associated complex consisting of GM130, the Rho GTPase, Cdc42, and its guanine nucleotide exchange factor, Tuba. We identified Tuba as a novel GM130-interacting protein and showed that this association controls Tuba-mediated activation of Cdc42 at the Golgi apparatus. Blocking either Tuba or Cdc42 activity reproduced the GM130 depletion phenotype of aberrant, nonfunctional centrosomes. Expression of constitutively active Cdc42 bypassed the requirement for GM130 in centrosome regulation, indicating that Cdc42 functions downstream of GM130. Our studies demonstrate that Cdc42 has a novel role in controlling centrosome organization in unstimulated cells in addition to its known function as a regulator of centrosome reorientation in stimulated cells. This first description of a regulatory pathway between the Golgi apparatus and the interphase centrosome that complements the known role of Golgi proteins in controlling spindle formation during mitosis and may provide an explanation for the pericentriolar position of the mammalian Golgi apparatus during interphase.
Supervillin Reorganizes the Actin Cytoskeleton and Increases Invadopodial Efficiency
Authors: Crowley Jessica L. , Smith Tara C. , Fang Zhiyou , Takizawa Norio , Luna Elizabeth J.
Published: December 2008

Tumor cells use actin-rich protrusions called invadopodia to degrade extracellular matrix (ECM) and invade tissues; related structures, termed podosomes, are sites of dynamic ECM interaction. We show here that supervillin (SV), a peripheral membrane protein that binds F-actin and myosin II, reorganizes the actin cytoskeleton and potentiates invadopodial function. Overexpressed SV induces redistribution of lamellipodial cortactin and lamellipodin/RAPH1/PREL1 away from the cell periphery to internal sites and concomitantly increases the numbers of F-actin punctae. Most punctae are highly dynamic and colocalize with the podosome/invadopodial proteins, cortactin, Tks5, and cdc42. Cortactin binds SV sequences in vitro and contributes to the formation of enhanced green fluorescent protein (EGFP)-SV induced punctae. SV localizes to the cores of Src-generated podosomes in COS-7 cells and with invadopodia in MDA-MB-231 cells. EGFP-SV overexpression increases average numbers of ECM holes per cell; RNA interference-mediated knockdown of SV decreases these numbers. Although SV knockdown alone has no effect, simultaneous down-regulation of SV and the closely related protein gelsolin reduces invasion through ECM. Together, our results show that SV is a component of podosomes and invadopodia and that SV plays a role in invadopodial function, perhaps as a mediator of cortactin localization, activation state, and/or dynamics of metalloproteinases at the ventral cell surface.
A Link between FXYD3 (Mat-8)-mediated Na,K-ATPase Regulation and Differentiation of Caco-2 Intestinal Epithelial Cells
Authors: Bibert Stéphanie , Aebischer David , Desgranges Florian , Roy Sophie , Schaer Danièle , Kharoubi-Hess Solange , Horisberger Jean-Daniel , Geering Käthi
Published: December 2008

FXYD3 (Mat-8) proteins are regulators of Na,K-ATPase. In normal tissue, FXYD3 is mainly expressed in stomach and colon, but it is also overexpressed in cancer cells, suggesting a role in tumorogenesis. We show that FXYD3 silencing has no effect on cell proliferation but promotes cell apoptosis and prevents cell differentiation of human colon adenocarcinoma cells (Caco-2), which is reflected by a reduction in alkaline phosphatase and villin expression, a change in several other differentiation markers, and a decrease in transepithelial resistance. Inhibition of cell differentiation in FXYD3-deficient cells is accompanied by an increase in the apparent Na+and K+affinities of Na,K-ATPase, reflecting the absence of Na,K-pump regulation by FXYD3. In addition, we observe a decrease in the maximal Na,K-ATPase activity due to a decrease in its turnover number, which correlates with a change in Na,K-ATPase isozyme expression that is characteristic of cancer cells. Overall, our results suggest an important role of FXYD3 in cell differentiation of Caco-2 cells. One possibility is that FXYD3 silencing prevents proper regulation of Na,K-ATPase, which leads to perturbation of cellular Na+and K+homeostasis and changes in the expression of Na,K-ATPase isozymes, whose functional properties are incompatible with Caco-2 cell differentiation.
Discrete Determinants in ArfGAP2/3 Conferring Golgi Localization and Regulation by the COPI Coat
Authors: Kliouchnikov Lena , Bigay Joëlle , Mesmin Bruno , Parnis Anna , Rawet Moran , Goldfeder Noga , Antonny Bruno , Cassel Dan
Published: December 2008

From yeast to mammals, two types of GTPase-activating proteins, ArfGAP1 and ArfGAP2/3, control guanosine triphosphate (GTP) hydrolysis on the small G protein ADP-ribosylation factor (Arf) 1 at the Golgi apparatus. Although functionally interchangeable, they display little similarity outside the catalytic GTPase-activating protein (GAP) domain, suggesting differential regulation. ArfGAP1 is controlled by membrane curvature through its amphipathic lipid packing sensor motifs, whereas Golgi targeting of ArfGAP2 depends on coatomer, the building block of the COPI coat. Using a reporter fusion approach and in vitro assays, we identified several functional elements in ArfGAP2/3. We show that the Golgi localization of ArfGAP3 depends on both a central basic stretch and a carboxy-amphipathic motif. The basic stretch interacts directly with coatomer, which we found essential for the catalytic activity of ArfGAP3 on Arf1-GTP, whereas the carboxy-amphipathic motif interacts directly with lipid membranes but has minor role in the regulation of ArfGAP3 activity. Our findings indicate that the two types of ArfGAP proteins that reside at the Golgi use a different combination of protein–protein and protein–lipid interactions to promote GTP hydrolysis in Arf1-GTP.
Systematic Analysis inCaenorhabditis elegansReveals that the Spindle Checkpoint Is Composed of Two Largely Independent Branches
Authors: Essex Anthony , Dammermann Alexander , Lewellyn Lindsay , Oegema Karen , Desai Arshad
Published: December 2008

Kinetochores use the spindle checkpoint to delay anaphase onset until all chromosomes have formed bipolar attachments to spindle microtubules. Here, we use controlled monopolar spindle formation to systematically define the requirements for spindle checkpoint signaling in the Caenorhabditis elegans embryo. The results, when interpreted in light of kinetochore assembly epistasis analysis, indicate that checkpoint activation is coordinately directed by the NDC-80 complex, the Rod/Zwilch/Zw10 complex, and BUB-1—three components independently targeted to the outer kinetochore by the scaffold protein KNL-1. These components orchestrate the integration of a core Mad1MDF-1/Mad2MDF-2-based signal, with a largely independent Mad3SAN-1/BUB-3 pathway. Evidence for independence comes from the fact that subtly elevating Mad2MDF-2levels bypasses the requirement for BUB-3 and Mad3SAN-1in kinetochore-dependent checkpoint activation. Mad3SAN-1does not accumulate at unattached kinetochores and BUB-3 kinetochore localization is independent of Mad2MDF-2. We discuss the rationale for a bipartite checkpoint mechanism in which a core Mad1MDF-1/Mad2MDF-2signal generated at kinetochores is integrated with a separate cytoplasmic Mad3SAN-1/BUB-3–based pathway.
In situ measurements of capelin (Mallotus villosus) target strength in the North Pacific Ocean
Authors: Guttormsen Michael A. , Wilson Christopher D.
Published: December 2008

Guttormsen, M. A. and Wilson, C. D. 2009. In situ measurements of capelin (Mallotus villosus) target strength in the North Pacific Ocean. – ICES Journal of Marine Science, 66: 258–263. In situ measurements of capelin (Mallotus villosus) target strength (TS) were collected during summer 2001–2003 near Kodiak Island in the Gulf of Alaska, using a calibrated EK500 echosounder with 38 and 120 kHz split-beam transducers. Targets were detected over dispersed, night-time aggregations using standard acoustic methods, then filtered using a quality-control algorithm to reject invalid targets. The 38 kHz-based, fitted model estimate was TS = 20 log10L− 70.3 (r2 = 0.30), where L is total length of fish. Compared with other studies, the TS-fitted model at 38 kHz was similar to that calculated from swimbladder morphology measurements from St Lawrence estuary capelin (TS = 20 log10L− 69.3), but resulted in greater estimates than models based on in situ measurements of capelin TS in the Barents Sea (TS = 19.1 log10L−74.0) and northern Atlantic Ocean (TS = 20 log10L − 73.1). The large intraspecific variability exhibited in the fitted TS – L models for this species suggests the use of TS measurements from the geographic region where the data were collected.
CYP86A33-Targeted Gene Silencing in Potato Tuber Alters Suberin Composition, Distorts Suberin Lamellae, and Impairs the Periderm's Water Barrier Function
Authors: Serra Olga , Soler Marçal , Hohn Carolin , Sauveplane Vincent , Pinot Franck , Franke Rochus , Schreiber Lukas , Prat Salomé , Molinas Marisa , Figueras Mercè
Published: December 2008

Suberin is a cell wall lipid polyester found in the cork cells of the periderm offering protection against dehydration and pathogens. Its biosynthesis and assembly, as well as its contribution to the sealing properties of the periderm, are still poorly understood. Here, we report on the isolation of the coding sequence CYP86A33 and the molecular and physiological function of this gene in potato (Solanum tuberosum) tuber periderm. CYP86A33 was down-regulated in potato plants by RNA interference-mediated silencing. Periderm from CYP86A33-silenced plants revealed a 60% decrease in its aliphatic suberin load and greatly reduced levels of C18:1 ω-hydroxyacid (approximately 70%) and α,ω-diacid (approximately 90%) monomers in comparison with wild type. Moreover, the glycerol esterified to suberin was reduced by 60% in the silenced plants. The typical regular ultrastructure of suberin, consisting of dark and light lamellae, disappeared and the thickness of the suberin layer was clearly reduced. In addition, the water permeability of the periderm isolated from CYP86A33-silenced lines was 3.5 times higher than that of the wild type. Thus, our data provide convincing evidence for the involvement of ω-functional fatty acids in establishing suberin structure and function.
A Rice Kinase-Protein Interaction Map
Authors: Ding Xiaodong , Richter Todd , Chen Mei , Fujii Hiroaki , Seo Young Su , Xie Mingtang , Zheng Xianwu , Kanrar Siddhartha , Stevenson Rebecca A. , Dardick Christopher , Li Ying , Jiang Hao , Zhang Yan , Yu Fahong , Bartley Laura E. , Chern Mawsheng , Bart Rebecca , Chen Xiuhua , Zhu Lihuang , Farmerie William G. , Gribskov Michael , Zhu Jian-Kang , Fromm Michael E. , Ronald Pamela C. , Song Wen-Yuan
Published: December 2008

Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.
A Small Family of Chloroplast Atypical Thioredoxins
Authors: Dangoor Inbal , Peled-Zehavi Hadas , Levitan Alexander , Pasand Ohad , Danon Avihai
Published: December 2008

The reduction and the formation of regulatory disulfide bonds serve as a key signaling element in chloroplasts. Members of the thioredoxin (Trx) superfamily of oxidoreductases play a major role in these processes. We have characterized a small family of plant-specific Trxs in Arabidopsis (Arabidopsis thaliana) that are rich in cysteine and histidine residues and are typified by a variable noncanonical redox active site. We found that the redox midpoint potential of three selected family members is significantly less reducing than that of the classic Trxs. Assays of subcellular localization demonstrated that all proteins are localized to the chloroplast. Selected members showed high activity, contingent on a dithiol electron donor, toward the chloroplast 2-cysteine peroxiredoxin A and poor activity toward the chloroplast NADP-malate dehydrogenase. The expression profile of the family members suggests that they have distinct roles. The intermediate redox midpoint potential value of the atypical Trxs might imply adaptability to function in modulating the redox state of chloroplast proteins with regulatory disulfides.
Reactive Oxygen Species Production by Potato Tuber Mitochondria Is Modulated by Mitochondrially Bound Hexokinase Activity
Authors: Camacho-Pereira Juliana , Meyer Laudiene Evangelista , Machado Lilia Bender , Oliveira Marcus Fernandes , Galina Antonio
Published: December 2008

Potato tuber (Solanum tuberosum) mitochondria (PTM) have a mitochondrially bound hexokinase (HK) activity that exhibits a pronounced sensitivity to ADP inhibition. Here we investigated the role of mitochondrial HK activity in PTM reactive oxygen species generation. Mitochondrial HK has a 10-fold higher affinity for glucose (Glc) than for fructose (K  MGlc = 140 μ  m versus K  MFrc = 1,375 μ  m). Activation of PTM respiration by succinate led to an increase in hydrogen peroxide (H2O2) release that was abrogated by mitochondrial HK activation. Mitochondrial HK activity caused a decrease in the mitochondrial membrane potential and an increase in oxygen consumption by PTM. Inhibition of Glc phosphorylation by mannoheptulose or GlcNAc induced a rapid increase in H2O2 release. The blockage of H2O2 release sustained by Glc was reverted by oligomycin and atractyloside, indicating that ADP recycles through the adenine nucleotide translocator and F0F1ATP synthase is operative during the mitochondrial HK reaction. Inhibition of mitochondrial HK activity by 60% to 70% caused an increase of 50% in the maximal rate of H2O2 release. Inhibition in H2O2 release by mitochondrial HK activity was comparable to, or even more potent, than that observed for StUCP (S. tuberosum uncoupling protein) activity. The inhibition of H2O2 release in PTM was two orders of magnitude more selective for the ADP produced from the mitochondrial HK reaction than for that derived from soluble yeast (Saccharomyces cerevisiae) HK. Modulation of H2O2 release and oxygen consumption by Glc and mitochondrial HK inhibitors in potato tuber slices shows that hexoses and mitochondrial HK may act as a potent preventive antioxidant mechanism in potato tubers.
A subsurface evacuation model for submarine slope failure
Authors: Bull Suzanne , Cartwright Joe , Huuse Mads
Published: December 2008

Analysis of three‐dimensional (3D) seismic reflection data from the Norwegian continental margin provides an insight into an unusual, buried submarine slope failure, which occurred adjacent to the later Holocene‐age Storegga Slide. The identified failure, informally named the ‘South Vøring Slide’ (SVS), occurs in fine‐grained hemipelagic and contourite sediments on a slope of 0.5°, and is characterised by a deformed seismic facies unit consisting of closely spaced pyramidal blocks and ridges bound by small normal faults striking perpendicular to the slope. The SVS contrasts with other previously described submarine slope failures in that it cannot be explained by a retrogressive model. The defining characteristic is the high relative volume loss. The area affected by sliding has thinned by some 40%, seen in combination with very modest extension in the translation direction, with line length balancing yielding an extension value of only 4.5%. The volume loss is explained by the mobilisation of an approximately 40 m thick interval at the lower part of the unit and its removal from beneath a thin overburden, which subsequently underwent extensional fragmentation. Evidence for the mobilisation of a thick fine‐grained interval in the development of a submarine slope failure from a continental margin setting may have implications for the origins of other large‐scale slope failures on the Norwegian margin and other glacially influenced margins worldwide.
Loss of CD7, independent of galectin‐3 expression, implies a worse prognosis in adult T‐cell leukaemia/lymphoma
Authors: Liu Ting‐Yun , Chen Chien‐Yuan , Tien Hwei‐Fang , Lin Chung‐Wu
Published: December 2008

Aims:  Loss of CD7 is characteristic of adult T‐cell lymphoma/leukaemia (ATLL). Galectin‐3 (Gal‐3) is strongly induced in cultured human T lymphotropic virus‐1‐infected T lymphocytes, and may cause apoptosis through interaction with CD7. The aim was to investigate the clinical relevance of the Gal‐3–CD7 pathway in ATLL.

Methods and results:  Immunohistochemistry for Gal‐3 and CD7 was performed on 22 cases of ATLL in the leukaemic phase. We found that the lymphoma cells were not necessarily Gal‐3+, but Gal‐3+ stromal cells could always be found. Independent of the status of Gal‐3, there was an association of loss of CD7 with a worse prognosis.

Conclusions:  These data suggest that, by down‐regulating CD7, ATLL cells could have escaped Gal‐3‐induced apoptosis to run a more aggressive clinical course.
Reappraisal of synchronous and multifocal mucinous lesions of the female genital tract: a close association with gastric metaplasia
Authors: Mikami Yoshiki , Kiyokawa Takako , Sasajima Yuko , Teramoto Norihiro , Wakasa Tomoko , Wakasa Kenichi , Hata Sakae
Published: December 2008

Aims:  To describe the gastric phenotype of synchronous mucinous metaplasia and neoplasms of the female genital tract (SMMN–FGT).

Methods and results:  Six patients (mean age 57 years, range 39–83 years) were diagnosed with SMMN–FGT. All six patients had mucinous metaplasia of endometrium, which showed features of lobular endocervical glandular hyperplasia (LEGH)/pyloric gland metaplasia (PGM) in five and was associated with mucinous adenocarcinoma in three. Five patients had mucinous metaplasia of the fallopian tubes, of which three showed borderline features. Two patients had mucinous borderline tumour of the ovary. Five patients had cervical lesions including LEGH/PGM associated with either adenocarcinoma in situ or minimal deviation adenocarcinoma of the cervix. All mucinous lesions were positive for HIK1083 and/or MUC6. One patient with minimal deviation adenocarcinoma involving the vagina died of her disease, whereas five patients, including three with microinvasion and three with positive peritoneal cytology or mucinous ascites, were alive without recurrence after a mean follow‐up of 46 months (range 13–102 months).

Conclusions:  There is a close association between SMMN–FGT and LEGH/PGM. Microinvasion and positive peritoneal cytology may not have an influence on outcome.
Balance between early life tolerance and sensitization in allergy: dependence on the timing and intensity of prenatal and postnatal allergen exposure of the mother
Authors: Fusaro Ana Elisa , De Brito Cyro Alves , Taniguchi Eliana Futata , Muniz Bruno Pacola , Victor Jefferson Russo , Orii Noemia Mie , Duarte Alberto José da Silva , Sato Maria Notomi
Published: December 2008

Allergens can be maternally transferred to the fetus or neonate, though it is uncertain how this initial allergen exposure may impact the development of allergy responses. To evaluate the roles of timing and level of maternal allergen exposure in the early life sensitization of progeny, female BALB/c mice were given ovalbumin (OVA) orally during pregnancy, lactation or weekly at each stage to investigate the immunoglobulin E (IgE) antibody production and cellular responsiveness of their offspring. Exposure to OVA during pregnancy was also evaluated in OVA‐specific T‐cell receptor (TCR) transgenic (DO11.10) mice. The effect of prenatal antigen exposure on offspring sensitization was dependent on antigen intake, with low‐dose OVA inducing tolerance followed by neonatal immunization that was sustained even when pups were immunized when 3 weeks old. These offspring received high levels of transforming growth factor‐β via breastfeeding. High‐dose exposure during the first week of pregnancy or perinatal period induced transient inhibition of IgE production following neonatal immunization; although for later immunization IgE production was enhanced in these offspring. Postnatal maternal antigen exposure provided OVA transference via breastfeeding, which consequently induced increased offspring susceptibility to IgE antibody production according to week post‐birth. The effect of low‐dose maternal exposure during pregnancy was further evaluated using OVA transgenic TCR dams as a model. These progeny presented pronounced entry of CD4+ T cells into the S phase of the cell cycle with a skewed T helper type 2 response early in life, revealing the occurrence of allergen priming in utero. The balance between tolerance and sensitization depended on the amount and timing of maternal allergen intake during pregnancy.
Changes in chemokines and chemokine receptor expression on tonsillar B cells upon Epstein–Barr virus infection
Authors: Ehlin‐Henriksson Barbro , Liang Wu , Cagigi Alberto , Mowafi Frida , Klein George , Nilsson Anna
Published: December 2008

Chemokines and chemokine receptors are likely to play important roles in the pathogenesis of Epstein–Barr virus (EBV) ‐associated disease. The primary EBV infection occurs in the oropharynx where the virus infects mainly tonsillar B cells. We have previously shown that CXCR4 expression on tonsillar B cells is modulated by EBV. Here, CXCR5 and CCR7 expression, which is important for migration into lymphoid tissue, was followed for 14 days after EBV infection of tonsillar B cells. Early after infection (2 days) there were only minor changes in CXCR5 and CCR7 expression. However, at day 7 the expression of CXCR5, as well as of CCR7, was decreased and by day 14 these molecules were no longer present at the cell surface. Furthermore, EBV infection affects the chemotactic response to CXCL13 and CCL21 (the ligands for CXCR5 and CCR7, respectively) with a reduction of ligand‐induced migration at day 2. Using gene expression profiling, we identified an additional set of chemokines and chemokine receptors that were changed upon EBV infection in comparison with non‐infected tonsillar B cells. In particular, messenger RNA expression for CCR9 and the complement receptor C5AR1 was increased. Both receptors mediate homing to mucosal tissue. The alterations of the expression of these molecules may lead to retention of EBV‐infected tonsillar B cells in the interfollicular region of the tonsil.
A synergistic interferon‐γ production is induced by mouse hepatitis virus in interleukin‐12 (IL‐12)/IL‐18‐activated natural killer cells and modulated by carcinoembryonic antigen‐related cell adhesion molecules (CEACAM) 1a receptor
Authors: Jacques Alexandre , Bleau Christian , Turbide Claire , Beauchemin Nicole , Lamontagne Lucie
Published: December 2008

The production of interferon‐γ (IFN‐γ) by infiltrating natural killer (NK) cells in liver is involved in the control of mouse hepatitis virus (MHV) infection. The objectives of this study were to identify the mechanisms used by MHV type 3 to modulate the production of IFN‐γ by NK cells during the acute hepatitis in susceptible C57BL/6 mice. Ex vivo and in vitro experiments revealed that NK cells, expressing carcinoembryonic antigen‐related cell adhesion molecules (CEACAM) 1a (the MHV receptor), can produce a higher level of IFN‐γ in the presence of both L2‐MHV3 and interleukin‐12 (IL‐12)/IL‐18. The synergistic production of IFN‐γ by NK cells depends on viral replication rather than viral fixation only, because it is inhibited or not induced in cells infected with ultraviolet‐inactivated viruses and in cells from Ceacam1a−/− mice infected with virulent viruses. The synergistic IFN‐γ production involves the p38 mitogen‐activated protein kinase (MAPK) rather than the extracellular signal‐regulated kinase‐1/2 MAPK signalling pathway. However, the signal triggered through the engagement of CEACAM1a decreases the production of IFN‐γ, when these molecules are cross‐linked using specific monoclonal antibodies. These results suggest that control of acute hepatitis by IFN‐γ‐producing NK cells may depend on both production of IL‐12 and IL‐18 in the liver environment and viral infection of NK cells.
Identification of three distinct subsets of migrating dendritic cells from oral mucosa within the regional lymph nodes
Authors: Chalermsarp Narumon , Azuma Miyuki
Published: December 2008

To investigate the phenotypic and migrational properties of oral mucosal dendritic cells (OMDCs), fluorescein isothiocyanate (FITC) was painted onto mouse buccal mucosa and the expression patterns of functional molecules in FITC‐bearing migrating DCs within the regional lymph nodes (RLNs) were analysed. We found three distinct subpopulations of migrating OMDCs within the RLNs: CD11chi CD207− (F1), CD11cint/lo CD207− (F2) and CD11cint/lo CD207+ (F3). The F1 DCs reached the RLNs earlier (after 24 hr) but diminished immediately. Additionally, F1 DCs expressed high levels of CD11b. The F2 DCs migrated continuously to the RLNs and maintained the highest ratio of all three fractions. The F3 DCs migrated slowly to the RLNs and demonstrated a late peak at 96 hr. In addition, F3 DCs showed the highest CD205 expression levels of all three subsets. All fractions of migrating OMDCs expressed CD80, CD86 and major histocompatibility complex class II at high levels, suggesting that all OMDCs are in a mature stage and have the potential for antigen presentation. All migrating OMDCs lacked CD8α expression. Taken together, our results indicate that the lack of CD207 is one factor that identifies submucosal DCs. Both F1 and F2 DCs lack CD207; F1 DCs are resident and F2 DCs are newly recruited following FITC application. The F3 DCs, which express CD207, are mucosal Langerhans cells that migrate later. The identification of OMDC subsets should facilitate further studies investigating the functional roles of each fraction.