bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction between HMGA1a and the origin recognition complex creates site-specific replication origins
Authors: Thomae Andreas W. , Pich Dagmar , Brocher Jan , Spindler Mark-Peter , Berens Christian , Hock Robert , Hammerschmidt Wolfgang , Schepers Aloys
Published: January 2008

In all eukaryotic cells, origins of DNA replication are characterized by the binding of the origin recognition complex (ORC). How ORC is positioned to sites where replication initiates is unknown, because metazoan ORC binds DNA without apparent sequence specificity. Thus, additional factors might be involved in ORC positioning. Our experiments indicate that a family member of the high-mobility group proteins, HMGA1a, can specifically target ORC to DNA. Coimmunoprecipitations and imaging studies demonstrate that HMGA1a interacts with different ORC subunits
in vitro
and
in vivo
. This interaction occurs mainly in AT-rich heterochromatic regions to which HMGA1a localizes. Fusion proteins of HMGA1a and the DNA-binding domain of the viral factor EBNA1 or the prokaryotic tetracycline repressor, TetR, can recruit ORC to cognate operator sites forming functional origins of DNA replication. When HMGA1a is targeted to plasmid DNA, the prereplicative complex is assembled during G
1
and the amount of ORC correlates with the local concentration of HMGA1a. Nascent-strand abundance assays demonstrate that DNA replication initiates at or near HMGA1a-rich sites. Our experiments indicate that chromatin proteins can target ORC to DNA, suggesting they might specify origins of DNA replication in metazoan cells.
High-resolution cryo-EM structure of the F-actin–fimbrin/plastin ABD2 complex
Authors: Galkin Vitold E. , Orlova Albina , Cherepanova Olga , Lebart Marie-Christine , Egelman Edward H.
Published: January 2008

Many actin binding proteins have a modular architecture, and calponin-homology (CH) domains are one such structurally conserved module found in numerous proteins that interact with F-actin. The manner in which CH-domains bind F-actin has been controversial. Using cryo-EM and a single-particle approach to helical reconstruction, we have generated 12-Å-resolution maps of F-actin alone and F-actin decorated with a fragment of human fimbrin (L-plastin) containing tandem CH-domains. The high resolution allows an unambiguous fit of the crystal structure of fimbrin into the map. The interaction between fimbrin ABD2 (actin binding domain 2) and F-actin is different from any interaction previously observed or proposed for tandem CH-domain proteins, showing that the structural conservation of the CH-domains does not lead to a conserved mode of interaction with F-actin. Both the stapling of adjacent actin protomers and the additional closure of the nucleotide binding cleft in F-actin when the fimbrin fragment binds may explain how fimbrin can stabilize actin filaments. A mechanism is proposed where ABD1 of fimbrin becomes activated for binding a second actin filament after ABD2 is bound to a first filament, and this can explain how mutations of residues buried in the interface between ABD2 and ABD1 can rescue temperature-sensitive defects in actin.
Self-assembly of the plant cell wall requires an extensin scaffold
Authors: Cannon Maura C. , Terneus Kimberly , Hall Qi , Tan Li , Wang Yumei , Wegenhart Benjamin L. , Chen Liwei , Lamport Derek T. A. , Chen Yuning , Kieliszewski Marcia J.
Published: February 2008

Cytokinesis partitions the cell by a cleavage furrow in animals but by a new cross wall in plants. How this new wall assembles at the molecular level and connects with the mother cell wall remains unclear. A lethal
Arabidopsis
embryogenesis mutant designated
root
-,
shoot
-,
hypocotyl-defective
(
rsh
) provides some clues:
RSH
encodes extensin AtEXT3, a structural glycoprotein located in the nascent cross wall or “cell plate” and also in mature cell walls. Here we report that electron micrographs of
rsh
mutant cells lacking RSH extensin correspond to a wall phenotype typified by incomplete cross wall assembly. Biochemical characterization of the purified RSH glycoprotein isolated from wild-type
Arabidopsis
cell cultures confirmed its identity as AtEXT3: a (hydroxy)proline-rich glyco protein comprising 11 identical amphiphilic peptide repeats with a 28-residue periodicity: SOOOOKKH
YVY
KSOOOOVKHYSOOOVYH (O = Hyp), each repeat containing a hydrophobic isodityrosine cross-link motif (YVY, underlined). Atomic force microscopy of RSH glycoprotein imaged its propensity for self-assembly into a dendritic scaffold. Extensin peroxidase catalyzed
in vitro
formation of insoluble RSH gels with concomitant tyrosine cross-linking, hence this likelihood
in muro
. We conclude that self-assembling amphiphiles of lysine-rich RSH extensin form positively charged scaffolds in the cell plate. These react with negatively charged pectin to create an extensin pectate coacervate that may template further orderly deposition of the new cross wall at cytokinesis.
An Activity to Teach Students about Schematic Processing
Authors: Isbell Linda M. , Tyler James M. , Burns Kathleen C.
Published: February 2008

We designed a classroom activity to foster students' understanding of what schemas are and how they function. We used a video of the instructor as an infant to illustrate how schemas influence gender stereotyping. Before the video, we told students that the baby was either a boy or a girl. After the video, students rated whether the baby would grow up to possess stereotypically male or female traits. Students in the video condition displayed a greater increase in schema knowledge than a control group that did not watch the video. Students also evaluated the activity favorably. We suggest other possible variations of this activity.
3D numerical simulations of energy transport in the stochastic boundary of TEXTOR-DED with a finite difference method
Authors: Zagórski R. , Jakubowski M.W. , Kalentev A. , Schmitz O. , Schneider R. , Stepniewski W.
Published: January 2008

The effect of magnetic field line ergodization that eliminates magnetic surfaces (either by a resonant magnetic perturbation like in TEXTOR-DED or by intrinsic plasma effects like in W7-X) imposes the need for plasma transport models being able to describe this properly. To handle the ergodicity the concept of local magnetic coordinates allowing a correct discretization of the transport equations with minimized numerical errors is used. For the simulation of plasma transport in perturbed volume, a numerical method based on the finite difference concept has been developed, using a custom-tailored unstructured grid in local magnetic coordinates. This grid is generated by field line tracing to guarantee complete separation of the large parallel transport along B and that perpendicular to B and the ergodicity of the magnetic field does not limit applicability of the method in contrast to the methods based on finite volume ansatz. Perpendicular and parallel fluxes can be effectively separated in our approach and treated independently in the numerical method which has been implemented in the FINDIF code.

The finite difference code FINDIF is used to investigate the energy transport in the complex 3D TEXTOR-DED tokamak geometry, where the plasma structures and transport are closely related to the structure of the magnetic field lines. Numerical grids have been prepared in order to simulate 12/4 and 6/2 modes of the DED operation, respectively. In particular, the question, what is the role of long and short magnetic field lines in the heat transfer from the core plasma to divertor surface, is addressed. Simulation results are compared with experimentally determined temperature profiles and heat fluxes at the target.
Inactivation of Host Akt/Protein Kinase B Signaling by Bacterial Pore-forming Toxins
Authors: Wiles Travis J. , Dhakal Bijaya K. , Eto Danelle S. , Mulvey Matthew A.
Published: January 2008

Uropathogenic Escherichia coli (UPEC) are the major cause of urinary tract infections (UTIs), and they have the capacity to induce the death and exfoliation of target uroepithelial cells. This process can be facilitated by the pore-forming toxin α-hemolysin (HlyA), which is expressed and secreted by many UPEC isolates. Here, we demonstrate that HlyA can potently inhibit activation of Akt (protein kinase B), a key regulator of host cell survival, inflammatory responses, proliferation, and metabolism. HlyA ablates Akt activation via an extracellular calcium-dependent, potassium-independent process requiring HlyA insertion into the host plasma membrane and subsequent pore formation. Inhibitor studies indicate that Akt inactivation by HlyA involves aberrant stimulation of host protein phosphatases. We found that two other bacterial pore-forming toxins (aerolysin from Aeromonas species and α-toxin from Staphylococcus aureus) can also markedly attenuate Akt activation in a dose-dependent manner. These data suggest a novel mechanism by which sublytic concentrations of HlyA and other pore-forming toxins can modulate host cell survival and inflammatory pathways during the course of a bacterial infection.
Characterization and Antifungal Properties of Wheat Nonspecific Lipid Transfer Proteins
Authors: Sun Jin-Yue , Gaudet Denis A. , Lu Zhen-Xiang , Frick Michele , Puchalski Byron , Laroche André
Published: February 2008

This study simultaneously considered the phylogeny, fatty acid binding ability, and fungal toxicity of a large number of monocot nonspecific lipid transfer proteins (ns-LTP). Nine novel full-length wheat ns-LTP1 clones, all possessing coding sequences of 348 bp, isolated from abiotic- and biotic-stressed cDNA libraries from aerial tissues, exhibited highly conserved coding regions with 78 to 99 and 71 to 100% identity at the nucleotide and amino acid levels, respectively. Phylogenetic analyses revealed two major ns-LTP families in wheat. Eight wheat ns-LTP genes from different clades were cloned into the expression vector pPICZα and transformed into Pichia pastoris. Sodium dodecyl sulfate polyacrylamide gel electrophoresis, Western blotting, and in vitro lipid binding activity assay confirmed that the eight ns-LTP were all successfully expressed and capable of in vitro binding fatty acid molecules. A comparative in vitro study on the toxicity of eight wheat ns-LTP to mycelium growth or spore germination of eight wheat pathogens and three nonwheat pathogens revealed differential toxicities among different ns-LTP. Values indicating 50% inhibition of fungal growth or spore germination of three selected ns-LTP against six fungi ranged from 1 to 7 μM. In vitro lipid-binding activity of ns-LTP was not correlated with their antifungal activity. Using the fluorescent probe SYTOX Green as an indicator of fungal membrane integrity, the in vitro toxicity of wheat ns-LTP was associated with alteration in permeability of fungal membranes.
The Pseudomonas syringae Type III Effector HopAM1 Enhances Virulence on Water-Stressed Plants
Authors: Goel Ajay K. , Lundberg Derek , Torres Miguel A. , Matthews Ryan , Akimoto-Tomiyama Chiharu , Farmer Lisa , Dangl Jeffery L. , Grant Sarah R.
Published: February 2008

Pseudomonas syringae strains deliver diverse type III effector proteins into host cells, where they can act as virulence factors. Although the functions of the majority of type III effectors are unknown, several have been shown to interfere with plant basal defense mechanisms. Type III effectors also could contribute to bacterial virulence by enhancing nutrient uptake and pathogen adaptation to the environment of the host plant. We demonstrate that the type III effector HopAM1 (formerly known as AvrPpiB) enhances the virulence of a weak pathogen in plants that are grown under drought stress. This is the first report of a type III effector that aids pathogen adaptation to water availability in the host plant. Expression of HopAM1 makes transgenic Ws-0 Arabidopsis hypersensitive to abscisic acid (ABA) for stomatal closure and germination arrest. Conditional expression of HopAM1 in Arabidopsis also suppresses basal defenses. ABA responses overlap with defense responses and ABA has been shown to suppress defense against P. syringae pathogens. We propose that HopAM1 aids P. syringae virulence by manipulation of ABA responses that suppress defense responses. In addition, host ABA responses enhanced by type III delivery of HopAM1 protect developing bacterial colonies inside leaves from osmotic stress.
Occurrence of a New Subclade of Leptosphaeria biglobosa in Western Australia
Authors: Vincenot L. , Balesdent M. H. , Li H. , Barbetti M. J. , Sivasithamparam K. , Gout L. , Rouxel T.
Published: February 2008

Stem canker of crucifers is caused by an ascomycete species complex comprising of two main species, Leptosphaeria maculans and L. biglobosa. These are composed of at least seven distinct subclades based on biochemical data or on sequences of internal transcribed spacer (ITS), the mating type MAT1-2 or fragments of actin or β-tubulin genes. In the course of a wide-scale characterization of the race structure of L. maculans from Western Australia, a few isolates from two locations failed to amplify specific sequences of L. maculans, i.e., the mating-type or minisatellite alleles. Based on both pathogenicity tests and ITS size, these isolates were classified as belonging to the L. biglobosa species. Parsimony and distance analyses performed on ITS, actin and β-tubulin sequences revealed that these isolates formed a new L. biglobosa subclade, more related to the Canadian L. biglobosa ‘canadensis’ subclade than to the L. biglobosa ‘australensis’ isolates previously described in Australia (Victoria). They are termed here as L. biglobosa ‘occiaustralensis’. These isolates were mainly recovered from resistant oilseed rape cultivars that included the Brassica rapa sp. sylvestris-derived resistance source, but not from the susceptible cv. Westar. The pathogenicity of L. biglobosa ‘occiaustralensis’ to cotyledons of most oilseed rape genotypes was higher than that of L. biglobosa ‘canadensis’ or L. biglobosa ‘australensis’ isolates.
The Transcription Factor MtSERF1 of the ERF Subfamily Identified by Transcriptional Profiling Is Required for Somatic Embryogenesis Induced by Auxin Plus Cytokinin in Medicago truncatula
Authors: Mantiri Feky R. , Kurdyukov Sergey , Lohar Dasharath P. , Sharopova Natalya , Saeed Nasir A. , Wang Xin-Ding , VandenBosch Kathryn A. , Rose Ray J.
Published: January 2008

Transcriptional profiling of embryogenic callus produced from Medicago truncatula mesophyll protoplasts indicated up-regulation of ethylene biosynthesis and ethylene response genes. Using inhibitors of ethylene biosynthesis and perception, it was shown that ethylene was necessary for somatic embryogenesis (SE) in this model legume. We chose several genes involved in ethylene biosynthesis and response for subsequent molecular analyses. One of these genes is a gene encoding a transcription factor that belongs to the AP2/ERF superfamily and ERF subfamily of transcription factors. We demonstrate that this gene, designated M. truncatula SOMATIC EMBRYO RELATED FACTOR1 (MtSERF1), is induced by ethylene and is expressed in embryogenic calli. MtSERF1 is strongly expressed in the globular somatic embryo and there is high expression in a small group of cells in the developing shoot meristem of the heart-stage embryo. RNA interference knockdown of this gene causes strong inhibition of SE. We also provide evidence that MtSERF1 is expressed in zygotic embryos. MtSERF1 appears to be essential for SE and may enable a connection between stress and development.
The case for sequencing the genome of the electric eel Electrophorus electricus
Authors: Albert J. S. , Zakon H. H. , Stoddard P. K. , Unguez G. A. , Holmberg‐Albert S. K. S. , Sussman M. R.
Published: January 2008

A substantial international community of biologists have proposed the electric eel Electrophorus electricus (Teleostei: Gymnotiformes) as an important candidate for genome sequencing. In this study, the authors outline the unique advantages that a genome sequencing project of this species would offer society for developing new ways of producing and storing electricity. Over tens of millions of years, electric fish have evolved an exceptional capacity to generate a weak (millivolt) electric field in the water near their body from specialized muscle‐derived electric organs, and simultaneously, to sense changes in this field that occur when it interacts with foreign objects. This electric sense is used both to navigate and orient in murky tropical waters and to communicate with other members of the same species. Some species, such as the electric eel, have also evolved a strong voltage organ as a means of stunning prey. This organism, and a handful of others scattered worldwide, convert chemical energy from food directly into workable electric energy and could provide important clues on how this process could be manipulated for human benefit. Electric fishes have been used as models for the study of basic biological and behavioural mechanisms for more than 40 years by a large and growing research community. These fishes represent a rich source of experimental material in the areas of excitable membranes, neurochemistry, cellular differentiation, spinal cord regeneration, animal behaviour and the evolution of novel sensory and motor organs. Studies on electric fishes also have tremendous potential as a model for the study of developmental or disease processes, such as muscular dystrophy and spinal cord regeneration. Access to the genome sequence of E. electricus will provide society with a whole new set of molecular tools for understanding the biophysical control of electromotive molecules, excitable membranes and the cellular production of weak and strong electric fields. Understanding the regulation of ion channel genes will be central for efforts to induce the differentiation of electrogenic cells in other tissues and organisms and to control the intrinsic electric behaviours of these cells. Dense genomic sequence information of E. electricus will also help elucidate the genetic basis for the origin and adaptive diversification of a novel vertebrate tissue. The value of existing resources within the community of electric fish research will be greatly enhanced across a broad range of physiological and environmental sciences by having a draft genome sequence of the electric eel.
Identification and verification of QTL associated with growth traits in two genetic backgrounds of Barramundi (Lates calcarifer)
Authors: Wang C. M. , Lo L. C. , Feng F. , Zhu Z. Y. , Yue G. H.
Published: January 2008

Quantitative trait loci (QTL) affecting growth traits have previously been mapped in linkage groups (LG) 2, 3 and 23 of Barramundi (Lates carcalifer), but these QTL have not been verified in different genetic backgrounds and environments. Here, we report the identification and verification of QTL for growth traits on LG2, 3, 10 and 23 in F1 families constructed using brooders from the Singapore Marine Aquaculture Center (MAC) and from wild stocks collected in Thailand (THAI). The previously detected QTL for body weight and length linked to marker Lca371 on LG2 were confirmed in both the MAC and THAI families, whereas other QTL previously mapped to LG3 and 23 were only detected in one of the two families. QTL for body weight and length were identified in the MAC family, but not in the THAI family, in a region where the insulin‐like growth factor 2 (IGF2) and tyrosine hydroxylase 1 (TH1) genes are located on LG10. Significant epistatic interactions were identified between markers Lca287 on LG2 and IGF2 on LG10 for growth trait QTL in the MAC family, but not in the THAI family. Effects of the IGF2, TH1 and parvalbumin 1 candidate genes were family‐specific. Our results indicate that some but not all QTL are family‐specific in Barramundi.
The effect of a c.‐8G>T polymorphism on the expression of cytochrome b5A and boar taint in pigs
Authors: Peacock J. , Lou Y. , Lundström K. , Squires E. J.
Published: January 2008

The level of cytochrome b5A (CYB5A) in pig testis is correlated with boar taint from androstenone and an AF016388:c.‐8G>T polymorphism in CYB5A has been linked with low androstenone levels in the fat of pigs. In this study, we developed a polymerase chain reaction‐based assay to genotype 1242 boars from eight lines for the c.‐8G>T SNP. The c.‐8T allele was found in all eight lines at a frequency ranging from 1.8% to 20.3% with an overall frequency of 8.6%. Significant deviations from Hardy–Weinberg equilibrium were found in the Hampshire, Landrace and Yorkshire breeds. The homozygous mutant c.‐8TT occurred infrequently and was not found in some lines, but was consistently associated with low androstenone levels in fat. Both CYB5A mRNA and CYB5A protein levels were decreased in the c.‐8TT genotype in a subset of Yorkshire boars, suggesting that low levels of CYB5A protein in the c.‐8TT mutant were not due to inefficient translation of CYB5A mRNA. There were significant but modest marker effects on fat androstenone levels in Landrace, Yorkshire and a Large White/Duroc cross and fat skatole in Duroc and Sire Line breeds. There was no effect of CYB5A genotype on bulbourethral gland length, suggesting that this SNP will not affect reproductive traits. We conclude that the c.‐8G>T SNP in the CYB5A gene has a significant but modest effect on boar taint in male pigs and could be useful in some breeds as part of a panel of SNP markers in a marker‐assisted selection programme to produce low boar taint pigs.
Linkage mapping of the locus responsible for forelimb‐girdle muscular anomaly of Japanese black cattle on bovine chromosome 26
Authors: Masoudi A. A. , Uchida K. , Yokouchi K. , Ohwada K. , Abbasi A. R. , Tsuji T. , Watanabe T. , Hirano T. , Sugimoto Y. , Kunieda T.
Published: January 2008

Forelimb‐girdle muscular anomaly is an autosomal recessive disorder of Japanese black cattle characterized by tremor, astasia and abnormal shape of the shoulders. Pathological examination of affected animals reveals hypoplasia of forelimb‐girdle muscles with reduced diameter of muscle fibres. To identify the gene responsible for this disorder, we performed linkage mapping of the disorder locus using an inbred pedigree including a great‐grand sire, a grand sire, a sire and 26 affected calves obtained from a herd of Japanese black cattle. Two hundred and fifty‐eight microsatellite markers distributed across the genome were genotyped across the pedigree. Four markers on the middle region of bovine chromosome 26 showed significant linkage with the disorder locus. Haplotype analysis using additional markers in this region refined the critical region of the disorder locus to a 3.5‐Mb interval on BTA26 betweenBM4505andMOK2602. Comparative mapping data revealed several potential candidate genes for the disorder, includingNRAP,PDZD8andHSPA12A, which are associated with muscular function.
‘Real‐life’ reduction in cholesterol with statins, 1993 to 2002
Authors: Murphy Michael J. , Wei Li , Watson Alexander D. , MacDonald Thomas M.
Published: January 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Statins reduce cholesterol concentrations and cardiovascular events in randomized clinical trials.

• Much less is known about their impact in the setting of normal care.

WHAT THIS STUDY ADDS

• This is the first study to assess the effectiveness of lipid‐lowering treatment in the general population.

• We have also estimated the resultant impact on major vascular events.

• We have examined the actual and potential impact of lipid‐lowering treatment.

AIMS

To evaluate the impact of lipid‐lowering treatment on cholesterol concentrations in the setting of normal care.

METHODS

This was a retrospective review of all cholesterol measurements made in Tayside, Scotland, between 1993 and 2002, linked to dispensed prescribing data for lipid‐lowering drugs. It was conducted in the setting of normal care and included all patients who underwent cholesterol measurement. The main outcome measure was cholesterol concentration.

RESULTS

A total of 401 489 cholesterol measurements were made on 128 240 patients over the study period. Measurements were categorized as treated and untreated according to whether patients were exposed to lipid‐lowering treatment at the time the total cholesterol concentration was measured. Those categorized as untreated fell by 0.86 mmol l−1 (13.9%) and those categorized as treated by 1.45 mmol l−1 (23.5%). The difference between baseline and follow‐up cholesterol concentrations in intention‐to‐treat patients was 1.53 mmol l−1 (24%) in 2002. In the same year, mean cholesterol concentration was 4.71 mmol l−1 (a fall of 1.65 mmol l−1 or 25.9%) in patients judged to be taking their lipid‐lowering medication, compared with 5.20 mmol l−1 (a fall of 1.16 mmol l−1 or 18.2%) in those judged not to be taking treatment. Cholesterol fell by 0.38 mmol l−1 (6.3%) in a cohort of never treated patients (n = 33 679) between 1993 and 2002.

CONCLUSIONS

The impact of lipid‐lowering drugs on population cholesterol concentrations in the setting of normal care was significant and comparable with the cholesterol reductions seen in the setting of major statin trials, despite a significant proportion of the population receiving low dose treatment. In those subjects judged to be taking their medication, the benefits achieved were substantial. The impact of nondrug factors is indicated by the fall in population cholesterol seen in the absence of lipid‐lowering treatment.
CD49d expression is an independent predictor of overall survival in patients with chronic lymphocytic leukaemia: a prognostic parameter with therapeutic potential
Authors: Shanafelt Tait D. , Geyer Susan M. , Bone Nancy D. , Tschumper Renee C. , Witzig Tom E. , Nowakowski Greg S. , Zent Clive S. , Call Tim G. , LaPlant Betsy , Dewald Gordon W. , Jelinek Diane F. , Kay Neil E.
Published: February 2008

In vitro studies have demonstrated that surface expression of CD49d on chronic lymphocytic leukaemia (CLL) B cells facilitates leukaemic cell–stromal interactions by binding to fibronectin. This interaction reduces both spontaneous and drug‐induced apoptosis. The present study measured CD49d expression by flow cytometry in a cohort of untreated CLL patients previously accrued to a prospective observational study and evaluated the relationship with overall survival (OS). Among the 158 CLL patients tested, the percentage of leukaemic B cells expressing CD49d ranged from 0 to 100%. When all risk factors were treated as continuous variables, CD49d expression showed moderate correlation with expression of ZAP‐70 (r = 0·54; P < 0·0001) and CD38 (r = 0·58; P < 0·0001) but not %IGHV mutation. As a continuous variable, CD49d expression strongly correlated with OS (P < 0·0001). Recursive partitioning analysis suggested the 45% threshold of CD49d expression best predicted OS. Multivariate analysis, controlling for disease stage, ZAP‐70, IGHV status and fluorescent in situ hybridization defects identified CD49d as an independent predictor of OS and was a better predictor of clinical outcome than ZAP‐70, IGHV, or cytogenetics. This observational cohort study suggests that CLL B‐cell expression of CD49d is an easily measurable and independent predictor of OS and CD49d expression in CLL. Importantly, anti‐CD49d antibodies are already approved for treatment of other human diseases. Clinical testing of anti‐CD49d therapy in CLL appears warranted.
The Y606C RET mutation causes a receptor gain of function
Authors: Ercolino T. , Lombardi A. , Becherini L. , Piscitelli E. , Cantini G. , Gaglianò M. S. , Serio M. , Luconi M. , Mannelli M.
Published: January 2008

Context  Medullary thyroid carcinoma (MTC) is the most common feature of multiple endocrine neoplasia type 2A (MEN2A) and occurs in almost all patients affected by germline RET mutations.

Objective  We identified and characterized an activating germline RET point mutation (G>A substitution leading to the heterozygous missense mutation Y606C in exon 10), in a 58‐year‐old female affected by MTC.

Design  The RET/Y606C and RET/C620Y, obtained by site‐directed mutagenesis, as well as the RET/wild‐type (wt) were cloned in an expression vector and transiently transfected in NIH3T3 fibroblasts. In vitro cell model was used to evaluate the effect of Y606C mutation on the RET downstream signalling pathways through Western blot analysis.

Results  We found that the cysteine insertion, due to the Y606C mutation, results in increased receptor dimerization, which is accompanied by an increased tyrosine phosphorylation of the Y905 residue in the RET/Y606C, demonstrating that the Y606C mutation is associated with constitutive receptor activation. As RET activation results in an intracellular signalling cascade involving extracellular signal‐regulated kinases (ERKs), we investigated ERK activity in our transfected cells. Results demonstrated a significant increase in ERK2 phosphorylation in the RET/Y606C vs. the RET/wt and RET/C620Y transfected cells, suggesting an up‐regulation of RET signalling.

Conclusions  All these findings demonstrate that the Y606C mutation is associated with RET constitutive activation and thus has to be considered of pathogenetic relevance in the development of MTC.
Visfatin, low‐grade inflammation and body mass index (BMI)
Authors: Samara Anastasia , Pfister Michèle , Marie Berangère , Visvikis‐Siest Sophie
Published: January 2008

Objective  Visfatin is an adipokine with revealing roles in inflammatory mechanisms but its implication in inflammation related to excessive adiposity/obesity is not studied yet. Our aim was to investigate the relations of visfatin with inflammation markers and body mass index (BMI) in the peripheral blood mononuclear cells (PBMCs), a type of cells closely related to inflammatory mechanisms.

Design  Cross‐sectional study, quantification of visfatin, TNF‐α, IL‐6 mRNA in PBMCs.

Patients  Eighty‐three supposed healthy individuals from the STANISLAS cohort, belonging in three BMI categories: BMI < 25 kg/m2 (lean), 25 kg/m2 ≤ BMI < 30 kg/m2 (overweight) or BMI ≥ 30 kg/m2 (obese).

Measurements  We measured visfatin gene expression (by real‐time quantitative PCR), in relation to gene expression of the pro‐inflammatory cytokines TNF‐α, IL‐6 in PBMCs and to anthropometric parameters (weight, BMI, waist : hip ratio), blood pressure, lipid profile, glucose and inflammatory markers (C‐reactive protein, lymphocyte count).

Results  Visfatin expression in PBMCs was significantly associated with BMI in a negative way (r = –0·21, P = 0·05). Global anova analysis test for lean and over‐weight/obese individuals showed a negative significant association between visfatin expression in PBMCs and BMI both for men and women (P = 0·05 and P = 0·01, respectively) and these associations remained significant after separating subjects in three groups (lean, overweight, obese) for men and women (P = 0·02 and P = 0·05, respectively). Correlation analysis between levels of expression of visfatin and TNF‐α showed a significant positive linear association (r2 = 0·27, P < 0·0001).

Conclusion  These findings reveal a probable new role of visfatin in inflammation reflected in PBMCs, in the context of obesity.
Magnetic resonance imaging methods to reveal the real‐time distribution of nickel in porous media
Authors: Moradi A. B. , Oswald S. E. , Massner J. A. , Pruessmann K. P. , Robinson B. H. , Schulin R.
Published: January 2008

Direct and non‐destructive measurement of the sorption, diffusion and mobility of ions and molecules in porous media has applications in industry and environmental science. We used magnetic resonance imaging (MRI) to visualize the dynamic distribution of paramagnetic nickel (Ni+2) ions in porous media. Various MRI sequences were tested to image Ni2+ at small concentrations. Noisy gradient echo images had poor contrast between samples containing various Ni2+ concentrations. Turbo spin echo and spoiled gradient echo images showed a linear relation between Ni2+ concentrations and signal intensity over a wide range of concentrations. Spoiled gradient echo images resolved Ni2+ concentrations (down to 30 mg litre−1) better than turbo spin echo images. However, for smaller concentrations, uncertainty in intensity values increased. A T1 measurement, obtained using an inversion recovery sequence, showed a linear correlation between T1 and Ni2+ concentration down to 1.5 mg litre−1. In a glass bead medium with an ion exchange resin as an Ni sink, the real‐time development of the Ni2+ depletion zone around the resin, as Ni was sorbed into the resin, was imaged by T1 mapping. A spatial resolution of 0.58 mm and a temporal resolution of less than a minute were achieved. The two‐dimensional Ni2+ gradient that was determined from MRI agreed well with geochemical modelling results. The results of this study showed that MRI, in particular T1 mapping, can quantify microscale behaviour of paramagnetic species in porous media. However, ferromagnetic components that naturally occur in most soils can easily disturb the MRI signal.
Modelling soil temperatures in northern peatlands
Authors: Kettridge N. , Baird A.
Published: January 2008

Methane emissions from northern peatlands are strongly dependent on soil temperatures. Therefore, to predict methane emissions from northern peatlands under future climatic conditions, it is important to simulate the effect of these changing climatic conditions on peat temperatures. This article reports on the development and testing of two one‐dimensional (1D) models used to simulate soil temperatures at shallow depths in a northern peatland. First, the HIP‐Dlet (Heat in Peat – Dirichlet) model applies measured temperatures to the surface boundary of a conduction‐based temperature model. Secondly, the HIP‐Nmann (Heat in Peat – von Neumann) model simulates the surface boundary from standard meteorological measurements. The HIP‐Dlet model provides a reasonable to good approximation of measured temperatures showing that heat transport processes within the soil are adequately simulated. The model does not simulate an advective liquid heat flux. However, only substantial rainfall events (> 70 mm over 3 days) during the study period had any significant effect on model error. Errors in the HIP‐Nmann model were of a similar magnitude to the HIP‐Dlet model. Errors in the HIP‐Dlet model resulted predominantly from errors in the measured soil temperatures. Errors in the HIP‐Nmann were due to errors in the measured soil temperatures and the inaccurate simulation of the surface boundary condition. The development of future peatland temperature models should, therefore, focus on the simulation of the surface boundary condition, particularly the parameterisation of the surface resistance that is shown here to produce significant errors in the modelled soil temperatures.
Spatial scale affects bioclimate model projections of climate change impacts on mountain plants
Authors: TRIVEDI MANDAR R. , BERRY PAMELA M. , MORECROFT MICHAEL D. , DAWSON TERENCE P.
Published: January 2008

Plant species have responded to recent increases in global temperatures by shifting their geographical ranges poleward and to higher altitudes. Bioclimate models project future range contractions of montane species as suitable climate space shifts uphill. The species–climate relationships underlying such models are calibrated using data at either ‘macro’ scales (coarse resolution, e.g. 50 km × 50 km, and large spatial extent) or ‘local’ scales (fine resolution, e.g. 50 m × 50 m, and small spatial extent), but the two approaches have not been compared. This study projected macro (European) and local models for vascular plants at a mountain range in Scotland, UK, under low (+1.7 °C) and high (+3.3 °C) climate change scenarios for the 2080s. Depending on scenario, the local models projected that seven or eight out of 10 focal montane species would lose all suitable climate space at the site. However, the European models projected such a loss for only one species. The cause of this divergence was investigated by cross‐scale comparisons of estimated temperatures at montane species' warm range edges. The results indicate that European models overestimated species' thermal tolerances because the input coarse resolution climate data were biased against the cold, high‐altitude habitats of montane plants. Although tests at other mountain ranges are required, these results indicate that recent large‐scale modelling studies may have overestimated montane species' ability to cope with increasing temperatures, thereby underestimating the potential impacts of climate change. Furthermore, the results suggest that montane species persistence in microclimatic refugia might not be as widespread as previously speculated.
Scaling environmental change through the community‐level: a trait‐based response‐and‐effect framework for plants
Authors: SUDING KATHARINE N. , LAVOREL SANDRA , CHAPIN F. S. , CORNELISSEN JOHANNES H. C. , DÍAZ SANDRA , GARNIER ERIC , GOLDBERG DEBORAH , HOOPER DAVID U. , JACKSON STEPHEN T. , NAVAS MARIE‐LAURE
Published: January 2008

Predicting ecosystem responses to global change is a major challenge in ecology. A critical step in that challenge is to understand how changing environmental conditions influence processes across levels of ecological organization. While direct scaling from individual to ecosystem dynamics can lead to robust and mechanistic predictions, new approaches are needed to appropriately translate questions through the community level. Species invasion, loss, and turnover all necessitate this scaling through community processes, but predicting how such changes may influence ecosystem function is notoriously difficult. We suggest that community‐level dynamics can be incorporated into scaling predictions using a trait‐based response–effect framework that differentiates the community response to environmental change (predicted by response traits) and the effect of that change on ecosystem processes (predicted by effect traits). We develop a response‐and‐effect functional framework, concentrating on how the relationships among species' response, effect, and abundance can lead to general predictions concerning the magnitude and direction of the influence of environmental change on function. We then detail several key research directions needed to better scale the effects of environmental change through the community level. These include (1) effect and response trait characterization, (2) linkages between response‐and‐effect traits, (3) the importance of species interactions on trait expression, and (4) incorporation of feedbacks across multiple temporal scales. Increasing rates of extinction and invasion that are modifying communities worldwide make such a research agenda imperative.
Warming prevents the elevated CO2‐induced reduction in available soil nitrogen in a temperate, perennial grassland
Authors: HOVENDEN MARK J. , NEWTON P. C. D. , CARRAN R. A. , THEOBALD P. , WILLS K. E. , VANDER SCHOOR J. K. , WILLIAMS A. L. , OSANAI Y.
Published: January 2008

Rising atmospheric carbon dioxide concentration ([CO2]) has the potential to stimulate ecosystem productivity and sink strength, reducing the effects of carbon (C) emissions on climate. In terrestrial ecosystems, increasing [CO2] can reduce soil nitrogen (N) availability to plants, preventing the stimulation of ecosystem C assimilation; a process known as progressive N limitation. Using ion exchange membranes to assess the availability of dissolved organic N, ammonium and nitrate, we found that CO2 enrichment in an Australian, temperate, perennial grassland did not increase plant productivity, but did reduce soil N availability, mostly by reducing nitrate availability. Importantly, the addition of 2 °C warming prevented this effect while warming without CO2 enrichment did not significantly affect N availability. These findings indicate that warming could play an important role in the impact of [CO2] on ecosystem N cycling, potentially overturning CO2‐induced effects in some ecosystems.
CD22: an inhibitory enigma
Authors: Walker Jennifer A. , Smith Kenneth G. C.
Published: January 2008

CD22 is an inhibitory coreceptor of the B‐cell receptor (BCR), and plays a critical role in establishing signalling thresholds for B‐cell activation. Like other coreceptors, the ability of CD22 to modulate B‐cell signalling is critically dependent upon its proximity to the BCR, and this in turn is governed by the binding of its extracellular domain to α2,6‐linked sialic acid ligands. Manipulation of CD22 ligand binding in various experimental settings has profound effects on B‐cell signalling, but as yet there is no complete model for how ligand binding in vivo controls normal CD22 function. Several elegant studies have recently shed light on this issue, although the results appear to suggest two mutually exclusive models for the role of ligand binding; in either promoting or inhibiting, CD22 function. We shall therefore discuss these results in detail, and suggest possible approaches by which these conflicting experimental findings might be reconciled. We shall also consider a second important issue in CD22 biology, which relates to the role that defects in this receptor might play in mediating autoimmune disease. We review the current evidence for this, and discuss the importance of genetic background in modifying CD22 function and predisposition to autoimmunity.
The effect of e‐commerce on the integration of IT structure and brand architecture
Authors: Treiblmaier Horst , Strebinger Andreas
Published: January 2008

Abstract.  A company's information technology (IT) structure and its brand architecture are intended to minimize transaction costs both within the organization and between the organization and its customers. Business‐to‐Consumer (B2C) e‐commerce fundamentally alters the structure of those transaction costs relevant to the IT structure and the brand architecture. We conducted a survey among 102 chief information officers and chief marketing officers in 67 of the 100 most important B2C enterprises in Austria. The results show that companies typically implement a certain set of changes in the IT structure and the brand architecture if B2C e‐commerce is highly important to them and that these changes result in a stronger integration within and between the IT structure and the brand architecture. B2C e‐commerce projects thus require closely aligned conceptual, organizational and financial measures in both areas.
Hydrogen peroxide induces expression and activation of AMP‐activated protein kinase in a dental pulp cell line
Authors: Fukuyama Y. , Ohta K. , Okoshi R. , Kizaki H. , Nakagawa K.
Published: January 2008

Aim  To investigate the effects of hydrogen peroxide on cell viability and expression and activation of AMP‐activated protein kinase (AMPK) in rat dental pulp cell line RPC‐C2A.

Methodology  RPC‐C2A cells derived from rat dental pulp were maintained in MEM supplemented with 10% FBS at 37 °C, in a humidified atmosphere at 5% CO2. Cells were cultured in the presence or absence of H2O2 for up to 60 min at concentrations of from 0.1 to 3.0 mmol L−1. Cell viability was analysed by WST‐1 reduction assay. Expression of AMPK subunit isoforms was analysed by Western blotting using antibodies to the catalytic α1 and regulatory β1 and γ1 subunit isoforms. The effect of silencing AMPKα1 on cell viability was determined using siRNA.

Results  Exposure to H2O2 decreased cell viability in a time‐ and dose‐dependent manner. The catalytic AMPKα1 subunit and its activated form, phospho‐AMPKα, increased with exposure to H2O2 in a time‐ and dose‐dependent manner, whereas the regulatory β1 and γ1 subunits showed no change. Downregulation of AMPKα1 resulted in a reduction in cell viability in H2O2‐treated cells at a concentration of 0.1 mmol L−1 for 30 min incubation, indicating an increased sensitivity to H2O2.

Conclusions  Reactive oxygen induced energy fuel gauge enzyme AMPKα expression and its activation by phosphorylation in RPC‐C2A cells, suggesting that AMPK is essential for protection against H2O2‐induced nonapoptotic cell death. Therefore, AMPK may be a therapeutic modulation target for treatment of the dentine–pulp complex injured by reactive oxygen.
Gingival and bone necrosis caused by accidental sodium hypochlorite injection instead of anaesthetic solution
Authors: Pontes F. , Pontes H. , Adachi P. , Rodini C. , Almeida D. , Pinto D.
Published: January 2008

Aim  To report clinical complications (pain, necrotic gingival tissue and bone sequestration) resulting from accidental injection of sodium hypochlorite.

Summary  Root canal treatment is a routine clinical procedure with few reported complications. Sodium hypochlorite (NaOCl) is commonly used as an irrigant during the procedure because of its tissue‐dissolving, antibacterial and lubricating properties. This paper presents a case in which accidental injection of sodium hypochlorite into the lingual gingiva of a female patient caused gingival and bone necrosis. Surgical intervention was required.

Key learning points 

Sodium hypochlorite is dangerous if injected into the tissues.

The presentation of sodium hypochlorite in glass, anaesthetic type cartridges is potentially dangerous, and should be condemned.

All healthcare workers should check carefully the contents of any syringe before injecting into patients.
Micropush‐out bond strengths of gutta‐percha versus thermoplastic synthetic polymer‐based systems – an ex vivo study
Authors: Üreyen Kaya B. , Keçeci A. D. , Orhan H. , Belli S.
Published: January 2008

Aim  To compare the interfacial strength and failure mode of root fillings consisting of different technique–material combinations.

Methodology  Human mandibular premolars (n = 144) instrumented to apical size 40 and .06 taper were divided into 12 experimental groups. The root canals were filled with either gutta‐percha (groups 1–6) or Resilon (groups 7–12) core materials combined with AH Plus (groups 1, 4, 7, 10), Ketac‐Endo (groups 2, 5, 8, 11) or Epiphany (groups 3, 6, 9, 12) using cold lateral compaction (groups 1–3, groups 7–9) or System B with Obtura II (groups 4–6, groups 10–12).

Three serial 1.00 ± 0.05‐mm‐thick root slices were prepared and push‐out tests on the filling material were performed. Interactions amongst the compaction techniques, core materials and sealers were analysed using a three‐way analysis of variance (anova) (P < 0.05). One‐way anova and Duncan’s Multiple Range tests were used to compare the bond strengths of the 12 groups. Fracture modes of all root slices were evaluated stereomicroscopically at ×40 magnification.

Results  All the parameters except compaction techniques had significant interactions (P < 0.05). A significant difference was found amongst the groups (P < 0.05). Gutta‐percha/Ketac‐Endo/cold lateral compaction and gutta‐percha/AH Plus/cold lateral compaction groups had the highest micropush‐out bond strength values (P < 0.05). The number of overall cohesive failures was significantly more than that of adhesive failures (P < 0.05).

Conclusions  The push‐out bond strengths of Resilon/Epiphany combinations were lower than those of gutta‐percha/conventional root canal sealer combinations. Core materials and sealers may affect the push‐out bond strengths of root canal filling materials.