bluuebunny/crossref_metadata_2025 huggingface dataset:
The E-protein Tcf4 interacts with Math1 to regulate differentiation of a specific subset of neuronal progenitors
Authors: Flora Adriano , Garcia Jesus J. , Thaller Christina , Zoghbi Huda Y.
Published: September 2007

Proneural factors represent <10 transcriptional regulators required for specifying all of the different neurons of the mammalian nervous system. The mechanisms by which such a small number of factors creates this diversity are still unknown. We propose that proteins interacting with proneural factors confer such specificity. To test this hypothesis we isolated proteins that interact with Math1, a proneural transcription factor essential for the establishment of a neural progenitor population (rhombic lip) that gives rise to multiple hindbrain structures and identified the E-protein Tcf4. Interestingly, haploinsufficiency of
TCF4
causes the Pitt–Hopkins mental retardation syndrome, underscoring the important role for this protein in neural development. To investigate the functional relevance of the Math1/Tcf4 interaction
in vivo
, we studied
Tcf4
−/−
mice and found that they have disrupted pontine nucleus development. Surprisingly, this selective deficit occurs without affecting other rhombic lip-derived nuclei, despite expression of
Math1
and
Tcf4
throughout the rhombic lip. Importantly, deletion of any of the other E-protein-encoding genes does not have detectable effects on Math1-dependent neurons, suggesting a specialized role for
Tcf4
in distinct neural progenitors. Our findings provide the first
in vivo
evidence for an exclusive function of dimers formed between a proneural basic helix–loop–helix factor and a specific E-protein, offering insight about the mechanisms underlying transcriptional programs that regulate development of the mammalian nervous system.
A tropical nullstellensatz
Authors: Shustin Eugenii , Izhakian Zur
Published: September 2007

We suggest a version of Nullstellensatz over the tropical semiring, the real numbers equipped with operations of maximum and summation.
Erratum to “Left cells and constructible representations”
Authors: Geck Meinolf
Published: September 2007

Thomas Pietraho pointed out a problem in the proof of one of the main results in “Left cells and constructible representations”, Represent. Theory 9 (2005), 385–416. The purpose of this note is to correct this problem.
Myosin VI Is Required for Targeted Membrane Transport during Cytokinesis
Authors: Arden Susan D. , Puri Claudia , Au Josephine Sui-Yan , Kendrick-Jones John , Buss Folma
Published: September 2007

Myosin VI plays important roles in endocytic and exocytic membrane-trafficking pathways in cells. Because recent work has highlighted the importance of targeted membrane transport during cytokinesis, we investigated whether myosin VI plays a role in this process during cell division. In dividing cells, myosin VI undergoes dramatic changes in localization: in prophase, myosin VI is recruited to the spindle poles; and in cytokinesis, myosin VI is targeted to the walls of the ingressing cleavage furrow, with a dramatic concentration in the midbody region. Furthermore, myosin VI is present on vesicles moving into and out of the cytoplasmic bridge connecting the two daughter cells. Inhibition of myosin VI activity by small interfering RNA (siRNA)-mediated knockdown or by overexpression of dominant-negative myosin VI tail leads to a delay in metaphase progression and a defect in cytokinesis. GAIP-interacting protein COOH terminus (GIPC), a myosin VI binding partner, is associated with the function(s) of myosin VI in dividing cells. Loss of GIPC in siRNA knockdown cells results in a more than fourfold increase in the number of multinucleated cells. Our results suggest that myosin VI has novel functions in mitosis and that it plays an essential role in targeted membrane transport during cytokinesis.
1 Martial Arts
Authors: Barchiesi Alessandro
Published: September 2007

This chapter examines strategies which emphasize the active contribution of the poetic text towards the construction of meaning for new Augustan monuments, using the example of the Forum Augusti in Book V. It argues that the role of Mars in his capacity of The Avenger is decisive for the issue of narrative authority and focalization in the episode. It contends that the problem of constructing and debating a meaning for the new Augustan monuments was a serious one for contemporary observers, that the Fasti was not a marginal witness to the collective debate. Ovid innovates the tradition of poetic ecphrasis by intensifying the political responsibility of the verbal monument and the potential of verbal art for bringing out implications and innuendos enshrined in the communal vision of the public artefact.
Agrobacterium VirD2-Binding Protein Is Involved in Tumorigenesis and Redundantly Encoded in Conjugative Transfer Gene Clusters
Authors: Guo Minliang , Hou Qingming , Hew Choy L. , Pan Shen Q.
Published: September 2007

Agrobacterium tumefaciens can transfer oncogenic T-DNA into plant cells; T-DNA transfer is mechanistically similar to a conjugation process. VirD2 is the pilot protein that guides the transfer, because it is covalently associated with single-stranded T-DNA to form the transfer substrate T-complex. We used the VirD2 protein as an affinity ligand to isolate VirD2-binding proteins (VBPs). By pull-down assays and peptide-mass-fingerprint matching, we identified an A. tumefaciens protein designated VBP1 that could bind VirD2 directly. Genome-wide sequence analysis showed that A. tumefaciens has two additional genes encoding proteins highly similar to VBP1, designated vbp2 and vbp3. Like VBP1, both VBP2 and VBP3 also could bind VirD2; all three VBPs contain a putative nucleotidyltransferase motif. Mutational analysis of vbp demonstrated that the three vbp genes could functionally complement each other. Consequently, only inactivation of all three vbp genes highly attenuated the bacterial ability to cause tumors on plants. Although vbp1 is harbored on the megaplasmid pAtC58, vbp2 and vbp3 reside on the linear chromosome. The vbp genes are clustered with conjugative transfer genes, suggesting linkage between the conjugation and virulence factor. The three VBPs appear to contain C-terminal positively charged residues, often present in the transfer substrate proteins of type IV secretion systems. Inactivation of the three vbp genes did not affect the T-strand production. Our data indicate that VBP is a newly identified virulence factor that may affect the transfer process subsequent to T-DNA production.
Antagonistic Control of Powdery Mildew Host Cell Entry by Barley Calcium-Dependent Protein Kinases (CDPKs)
Authors: Freymark Gerald , Diehl Tobias , Miklis Marco , Romeis Tina , Panstruga Ralph
Published: September 2007

Calcium-dependent protein kinases (CDPKs) are known to play pivotal roles in intracellular signaling during abiotic and biotic stress responses. To unravel potential functions of CDPKs in the course of barley (Hordeum vulgare)–powdery mildew (Blumeria graminis) interactions, we systematically analyzed the HvCDPK gene family. We found that, according to the existence of respective expressed sequence tags, at least nine paralogs are expressed in the barley leaf epidermis, the sole target tissue of powdery mildew fungi. We exemplarily selected two HvCDPKs with known full-length coding sequence for functional analysis. Transient expression of a putative constitutive active variant of one of these (HvCDPK4) in Nicotiana benthamiana triggered kinase-dependent mesophyll cell death in tobacco leaves. In a barley mlo mutant genotype, a constitutive active variant of the second paralog, HvCDPK3, partially compromised the highly effective resistance to B. graminis f. sp. hordei. A similar break of mlo resistance was seen upon expression of the junction domain of HvCDPK4, supposed to act as a dominant inhibitor of CDPK activity. Expression of a constitutive active HvCDPK3 or HvCDPK4 form also compromised penetration resistance to the inappropriate wheat powdery mildew fungus. Collectively, our data provide evidence for antagonistic roles of individual CDPK paralogs in the control of host cell entry during the early phase of powdery mildew pathogenesis.
Novel Reiterated Fnr-Type Proteins Control the Production of the Symbiotic Terminal Oxidase cbb3 in Rhizobium etli CFN42
Authors: Granados-Baeza Manuel J. , Gómez-Hernández Nicolás , Mora Yolanda , Delgado María J. , Romero David , Girard Lourdes
Published: September 2007

Symbiotic nitrogen-fixing bacteria express a terminal oxidase with a high oxygen affinity, the cbb3-type oxidase encoded by the fixNOQP operon. Previously, we have shown that, in Rhizobium etli CFN42, the repeated fixNOQP operons (fixNOQPd and fixNOQPf) have a differential role in nitrogen fixation. Only the fixNOQPd operon is required for the establishment of an effective symbiosis; microaerobic induction of this operon is under the control of at least three transcriptional regulators, FixKf, FnrNd, and FnrNchr, belonging to the Crp/Fnr family. In this work, we describe two novel Crp/Fnr-type transcriptional regulators (StoRd and StoRf, symbiotic terminal oxidase regulators) that play differential roles in the control of key genes for nitrogen fixation. Mutations either in stoRd or stoRf enhance the microaerobic expression of both fixNOQP reiterations, increasing also the synthesis of the cbb3-type oxidase in nodules. Despite their structural similarity, a differential role of these genes was also revealed, since a mutation in stoRd but not in stoRf enhanced both the expression of fixKf and the nitrogen-fixing capacity of R. etli CFN42.
Silencing of the N Family of Resistance Genes in Nicotiana edwardsonii Compromises the Hypersensitive Response to Tombusviruses
Authors: Balaji Boovaraghan , Cawly John , Angel Carlos , Zhang Zhanyuan , Palanichelvam Karuppaiah , Cole Anthony , Schoelz James
Published: September 2007

The nontarget effects associated with silencing of the N gene in Nicotiana edwardsonii, an amphidiploid species derived from N. glutinosa and N. clevelandii, have been characterized in this study. The N protein confers resistance to Tobacco mosaic virus (TMV), and is representative of a family of nucleotide-binding site leucine-rich repeat proteins present in N. glutinosa. Previous studies have shown that silencing of the N gene or of other plant genes associated with N-mediated defenses abolishes host resistance to TMV, and this effect can be measured through enhancements in movement or replication of TMV in the N-silenced plants. However, the nontarget effects of gene silencing have not been investigated thoroughly. Notably, are the functions of other resistance (R) genes also affected in experiments designed to silence the N gene? To investigate whether heterologous sequences could silence the N gene, we selected an R gene homolog from N. glutinosa that differed from the N gene by approximately 17%, created a hairpin transgene, and developed transgenic N. edwardsonii plants. Expression of this hairpin in the transgenic N. edwardsonii plants compromised the hypersensitive response to TMV, demonstrating that a single hairpin transgene could silence a block of R genes related by sequence similarity. We then investigated whether the response of N-silenced plants to other viruses would be altered, and found that the hypersensitive response triggered against the tombusviruses Tomato bushy stunt virus and Cymbidium ringspot virus also was compromised. This study indicates that a Tombusvirus R gene shares some homology with the N gene, which could facilitate the cloning of this gene.
Localized Melanization of Appressoria Is Required for Pathogenicity of Venturia inaequalis
Authors: Steiner Ulrike , Oerke Erich-Christian
Published: September 2007

During formation of appressoria produced from conidia and ascospores of Venturia inaequalis, a dark brown ring structure was detected at the base of appressoria. This melanized appressorial ring structure (MARS) was attached to the leaf surface like a sealing ring and formed the fungus–plant interface; it is believed to be required for pathogen penetration of the cuticle. Neither germ tubes nor infection structures beneath the cuticle were found to be visibly melanized. MARS were formed not only on apple leaves but also on leaves of nonhost plants and artificial surfaces differing in hydrophobicity; the formation of appressoria and MARS was confined to hard surfaces. The melanin nature of the ring was confirmed by using melanin biosynthesis inhibitors. Applications prior to inoculation largely inhibited the melanization and reduced infection rate by 45 to 80%; curative applications were not effective. Transmission electron microscopy verified a localized melanization of the cell wall around the penetration pore, and melanin was incorporated into all layers of the fungal cell wall. Appressoria without MARS were not able to infect the plant, suggesting that this structure can be considered to be a pathogenicity factor in V. inaequalis.
Comparative Analysis of Flexible Two-Parameter Models of Plant Disease Epidemics
Authors: Hau B. , Kosman E.
Published: September 2007

Eleven previously published models of plant disease epidemics, given as differential equations with a rate and a shape parameter, are compared using general model characteristics as well as their usefulness in fitting observed data. Six out of the eleven models can be solved analytically resulting in epidemic growth functions, while the others can be solved only numerically. When all 11 differential equations were fitted to two data sets, all models showed a similar goodness of fit, although the shape parameter in some models could not be estimated very precisely. With respect to useful characteristics (exponential population growth at the beginning, ability to generate monomolecular disease progression, and flexibility of the inflection point), the models of Fleming, Kosman-Levy, Birch, Richards and Waggoner, and Rich are recommended. Formulas were established to calculate the point of inflection as well as the weighted absolute and relative rate, respectively, depending on the shape and rate parameter. These formulas allow transformation of the parameter values of one model into those of another model in many cases. If the two models are required to have the same temporal position of the disease progress curve, then the initial disease level at the start of the epidemic or the time when the inflection point is reached have to be transformed.
Differential Activity of Carboxylic Acid Amide Fungicides Against Various Developmental Stages of Phytophthora infestans
Authors: Cohen Yigal , Gisi Ulrich
Published: September 2007

Three carboxylic acid amide (CAA) fungicides, mandipropamid (MPD), dimethomorph (DMM) and iprovalicarb (IPRO) were examined for their effects on various asexual developmental stages of Phytophthora infestans in vitro and in planta. Germination of cystospores and direct germination of sporangia were inhibited with nanomole concentrations of MPD (0.005 μg/ml) and micromole concentrations of DMM (0.05 μg/ml) or IPRO (0.5 μg/ml). A temporary exposure of 1 h to CAAs was not detrimental to germination and infectivity of sporangia or cystospores. CAAs applied to cystospores at 1 h after the onset of germination did not prevent the emergence of germ tubes, but inhibited their further growth and deformed their shape. None of the fungicides affected discharge of zoospores from sporangia or the encystment (cell wall formation/assembly) of the zoospores. Mycelium growth in solid or liquid media was inhibited with micromole concentrations. CAAs mixed with sporangia and drop inoculated onto detached leaves strongly suppressed infection. Curative application at 1 day postinoculation (dpi) required higher concentrations of CAAs than preventive application to inhibit infection and lost its effectiveness at 2 dpi. When sprayed on established late blight lesions 4 days after inoculation, CAAs reduced sporangial production in a dose-dependent manner. Trans-laminar protection of potato or tomato leaves, although achieved with higher doses, was more effective with MPD than with DMM or IPRO. Shade house studies demonstrated superior control of late blight epidemics by MPD compared with the other molecules. The data suggest that germ tube formation by cystospores or sporangia is the most sensitive stage in the life cycle of P. infestans to CAAs. Of the three CAAs, MPD had the highest intrinsic activity against spore germination. This property, together with its better trans-laminar activity, makes MPD more effective than DMM or IPRO in controlling epidemics caused by P. infestans.
Mycoparasitism of Helminthosporium solani by Acremonium strictum
Authors: Rivera-Varas Viviana V. , Freeman Thomas A. , Gudmestad Neil C. , Secor Gary A.
Published: September 2007

Isolates of Helminthosporium solani, the causal agent of silver scurf of potato, collected from multiple locations consistently show white sectoring and rings, differential coloration, and reduced sporulation in culture. It has been accepted that this growth pattern is normal for H. solani cultures. Scanning electron microscopy confirmed the presence of a contaminating fungus in close association with cultures of H. solani. Repeated hyphal tip isolation techniques were used to separate H. solani from the fungal contaminant. Resultant pure cultures of H. solani were uniformly black in color, without white sectors or rings. The contaminating fungus was identified as Acremonium strictum. The purpose of this study was to elucidate the relationship between A. strictum and H. solani, and evaluate the impact of the fungicolous A. strictum on the growth and biology of H. solani. In vitro studies demonstrated that A. strictum significantly reduced sporulation of H. solani isolates from 65 to 35%, spore germination from 53 to 43%, and mycelial growth from 40 to 32% compared with noncontaminated cultures of H. solani. These data indicate that A. strictum is antagonistic to H. solani, and can be considered a mycoparasite. A. strictum reduced H. solani conidia production on minitubers, thereby reducing inoculum for infection. However, treatment with A. strictum does not reduce silver scurf of previously infected tubers. Further studies are warranted to determine the full potential of A. strictum as a biological control agent of H. solanii-incited silver scurf of stored potato tubers and the most effective manner of use.
Genetic Diversity ofXylella fastidiosaStrains from Costa Rica, São Paulo, Brazil, and United States
Authors: Montero-Astúa Mauricio , Hartung John S. , Aguilar Estela , Chacón Carlos , Li Wenbin , Albertazzi Federico J. , Rivera Carmen
Published: September 2007

The diversity of 42 Xylella fastidiosa strains from Costa Rica, São Paulo, Brazil, and the United States were analyzed using the sequence of the 16S rRNA gene by variable number of tandem repeat (VNTR) fragment analysis and by restriction fragment length polymorphisms (RFLP) of a specific polymerase chain reaction (PCR)-amplification product using enzyme CfoI. Limited variability in the sequence of the 16S rRNA gene was observed and, although the separation was not absolute, most strains from Costa Rica clustered with strains from the United States and not with strains from São Paulo. The PCR-RFLP produced different patterns of DNA bands. The same pattern was shared by strains from Costa Rica, the United States, and two coffee strains from São Paulo, but a different pattern was observed in six coffee and orange strains from Brazil. In all, 32 amplification products were scored in the VNTR fragment analysis. The total variation observed among the X. fastidiosa strains had significant (P < 0.001) contributions from both geography and host origin as inferred by Nei's values of genetic diversity and WINAMOVA statistics. The strains from Costa Rica were isolated from diseased grapevines, coffee, and sweet orange and these strains grouped together and could be distinguished from strains from grapevine from the United States or from either coffee or sweet orange from São Paulo. The strains tested from Costa Rica are most likely of local origin, although the possibility that they have been introduced along with horticultural crops cannot be excluded. In either case, they are examples of independent selection of strains of X. fastidiosa affecting coffee and sweet orange. Greater genetic similarity was observed between strains from Costa Rica and the United States than with those from São Paulo.
Cyclic Lipopeptide Surfactant Production by Pseudomonas fluorescens SS101 Is Not Required for Suppression of Complex Pythium spp. Populations
Authors: Mazzola M. , Zhao X. , Cohen M. F. , Raaijmakers J. M.
Published: September 2007

Previously, the zoosporicidal activity and control of Pythium root rot of flower bulbs by Pseudomonas fluorescens SS101 was attributed, in part, to the production of the cyclic lipopeptide surfactant massetolide A. The capacity of strain SS101 and its surfactant-deficient massA mutant 10.24 to suppress populations and root infection by complex Pythium spp. communities resident in orchard soils was assessed on apple and wheat seedlings and on apple rootstocks. Both strains initially became established in soil and persisted in the rhizosphere at similar population densities; however, massA mutant 10.24 typically was detected at higher populations in the wheat rhizosphere and soil at the end of each experiment. Both strains effectively suppressed resident Pythium populations to an equivalent level in the presence or absence of plant roots, and ultimately suppressed Pythium root infection to the same degree on all host plants. When split-root plant assays were employed, neither strain suppressed Pythium spp. infection of the component of the root system physically separated from the bacterium, suggesting that induced systemic resistance did not play a role in Pythium control. Strain SS101 only marginally suppressed in vitro growth of Pythium spp. and growth was not inhibited in the presence of mutant 10.24. When incorporated into the growth medium, the cyclic lipopeptide massetolide A significantly slowed the rate of hyphal expansion for all Pythium spp. examined. Differences in sensitivity were observed among species, with Pythium heterothallicum, P. rostratum, and P. ultimum var. ultimum exhibiting significantly greater tolerance. Pythium spp. populations indigenous to the two soils employed were composed primarily of P. irregulare, P. sylvaticum, and P. ultimum var. ultimum. These Pythium spp. either do not or rarely produce zoospores, which could account for the observation that both SS101 and mutant 10.24 were equally effective in disease control. Collectively, the results showed that (i) Pseudomonas fluorescens SS101 is very effective in controlling diverse Pythium populations on different crops grown in different soils and (ii) production of the cyclic lipopeptide massetolide A does not play a significant role in disease suppression. Other, as yet undefined mechanisms appear to play a significant role in the interaction between P. fluorescens SS101 and soilborne Pythium spp. communities.
Are we underestimating the diversity and incidence of insect bacterial symbionts? A case study in ladybird beetles
Authors: Weinert Lucy A , Tinsley Matthew C , Temperley Matilda , Jiggins Francis M
Published: September 2007

Vertically transmitted bacterial symbionts are common in arthropods. However, estimates of their incidence and diversity are based on studies that test for a single bacterial genus and often only include small samples of each host species. Focussing on ladybird beetles, we collected large samples from 21 species and tested them for four different bacterial symbionts. Over half the species were infected, and there were often multiple symbionts in the same population. In most cases, more females than males were infected, suggesting that the symbionts may be sex ratio distorters. Many of these infections would have been missed in previous studies as they only infect a small proportion of the population. Furthermore, 11 out of the 17 symbionts discovered by us were either in the genusRickettsiaorSpiroplasma, which are rarely sampled. Our results suggest that the true incidence and diversity of bacterial symbionts in insects may be far greater than previously thought.
Susceptible–infected–recovered epidemics in dynamic contact networks
Authors: Volz Erik , Meyers Lauren Ancel
Published: September 2007

Contact patterns in populations fundamentally influence the spread of infectious diseases. Current mathematical methods for epidemiological forecasting on networks largely assume that contacts between individuals are fixed, at least for the duration of an outbreak. In reality, contact patterns may be quite fluid, with individuals frequently making and breaking social or sexual relationships. Here, we develop a mathematical approach to predicting disease transmission on dynamic networks in which each individual has a characteristic behaviour (typical contact number), but the identities of their contacts change in time. We show that dynamic contact patterns shape epidemiological dynamics in ways that cannot be adequately captured in static network models or mass-action models. Our new model interpolates smoothly between static network models and mass-action models using a mixing parameter, thereby providing a bridge between disparate classes of epidemiological models. Using epidemiological and sexual contact data from an Atlanta high school, we demonstrate the application of this method for forecasting and controlling sexually transmitted disease outbreaks.
Drosophila PIWI associates with chromatin and interacts directly with HP1a
Authors: Brower-Toland Brent , Findley Seth D. , Jiang Ling , Liu Li , Yin Hang , Dus Monica , Zhou Pei , Elgin Sarah C.R. , Lin Haifan
Published: September 2007

The interface between cellular systems involving small noncoding RNAs and epigenetic change remains largely unexplored in metazoans. RNA-induced silencing systems have the potential to target particular regions of the genome for epigenetic change by locating specific sequences and recruiting chromatin modifiers. Noting that several genes encoding RNA silencing components have been implicated in epigenetic regulation in Drosophila, we sought a direct link between the RNA silencing system and heterochromatin components. Here we show that PIWI, an ARGONAUTE/PIWI protein family member that binds to Piwi-interacting RNAs (piRNAs), strongly and specifically interacts with heterochromatin protein 1a (HP1a), a central player in heterochromatic gene silencing. The HP1a dimer binds a PxVxL-type motif in the N-terminal domain of PIWI. This motif is required in fruit flies for normal silencing of transgenes embedded in heterochromatin. We also demonstrate that PIWI, like HP1a, is itself a chromatin-associated protein whose distribution in polytene chromosomes overlaps with HP1a and appears to be RNA dependent. These findings implicate a direct interaction between the PIWI-mediated small RNA mechanism and heterochromatin-forming pathways in determining the epigenetic state of the fly genome.
The origins of oncomice: a history of the first transgenic mice genetically engineered to develop cancer
Authors: Hanahan Douglas , Wagner Erwin F. , Palmiter Richard D.
Published: September 2007

This perspective describes the concurrent development in the 1980s of the first transgenic mice genetically engineered to express dominant oncogenes, involving independent researchers who were largely unaware of each other’s strategies and progress. We relate the experimental designs, the pitfalls and challenges encountered, and the eventual success in developing distinctive mouse models of cancer, wherein tumors arose heritably in various organs. These early oncomice have produced a wealth of new knowledge, become topics of intellectual property, and spawned a vibrant field of cancer research that is revealing mechanisms of tumorigenesis and suggesting new therapeutic strategies for treating the human disease.
Structure and oxygen mobility in mayenite (Ca12Al14O33): a high-temperature neutron powder diffraction study
Authors: Boysen H. , Lerch M. , Stys A. , Senyshyn A.
Published: September 2007

The structure of mayenite, Ca12Al14O33, was investigated by neutron powder diffraction up to 1323 K. It has been described previously as a calcium–aluminate framework, in which 32 of the 33 oxygen anions are tightly bound, containing large cages, 1/6 of them being filled randomly by the remaining `free' oxygen. At ambient temperature excess oxygen was found, corresponding to the composition Ca12Al14O33.5 which was attributed to the presence of hydroxide, peroxide and superoxide radicals in the cages. Above 973 K these are lost under vacuum conditions and the composition becomes stoichiometric. From the refined structural parameters it is concluded that the structure is more adequately described as a relatively stable aluminate framework consisting of eightfold rings of AlO4 tetrahedra with disordered Ca and `free' O distributed within. At high temperatures the density of the `free' oxygen is extremely spread out, with the expansion being related to the high ionic conductivity of this material. Since no continuous density distribution between adjacent cages was found and the `free' O forms bonds with part of the Ca, the diffusion proceeds via a jump-like process involving exchange of the `free' oxygen with framework oxygen. The results confirm the recent theoretical predictions of Sushko et al. [(2006), Phys. Rev. B, 73, 014101-1-10].
Experimental charge density of L-alanyl-L-prolyl-L-alanine hydrate: classical multipole and invariom approach, analysis of intra- and intermolecular topological properties
Authors: Kalinowski Roman , Dittrich Birger , Hübschle Christian B. , Paulmann Carsten , Luger Peter
Published: September 2007

A high-resolution dataset of the tripeptide L-alanyl-L-prolyl-L-alanine hydrate was measured at 100 K using synchrotron radiation and CCD area detection. Electron densities were obtained from a full multipole refinement of the X-ray experimental data, from an invariom transfer and from a theoretical calculation. Topological and atomic properties were derived via an AIM analysis [Atoms in Molecules; see Bader (1990). Atoms in Molecules: A Quantum Theory, No. 22 in International Series of Monographs on Chemistry, 1st ed. Oxford: Clarendon Press] of these densities and compared with each other, as well as with results from the literature of other oligopeptides and amino acids. By application of the invariom formalism to a dataset of limited resolution, its performance was compared with a conventional spherical refinement, highlighting the possibility of aspherically modelling routine structure-determination experiments. The hydrogen-bonding scheme was subject to a detailed analysis according to the criteria of Koch & Popelier [(1995), J. Phys. Chem.
99, 9747–9754] as well as to the characterization of Espinosa et al. [(1998), Chem. Phys. Lett.
285, 170–173; (1999), Acta Cryst. B55, 563–572; (2002), J. Chem. Phys.
117, 5529–5542] using the results from the refined and invariom multipole densities as well as the spherical-density model, which are critically compared.
Asymmetric hydrogen bonds in a centrosymmetric environment. III. Quantum mechanical calculations of the potential-energy surfaces for the very short hydrogen bonds in potassium hydrogen dichloromaleate
Authors: Majerz I. , Olovsson I.
Published: September 2007

In the crystal structure of potassium hydrogen dichloromaleate there are two short hydrogen bonds of 2.44 Å. The `heavy-atom' structure is centrosymmetric (space group P\bar 1) with centers of symmetry in the middle of the O—O bonds, suggesting centered hydrogen bonds. However, earlier unconventional types of refinements of the extensive neutron data taken at 30, 90, 135, 170 and 295 K demonstrated that the H atoms are actually non-centered in the hydrogen bonds, although the environment is centrosymmetric. Traditionally it has been assumed that the hydrogen distribution adopts the same symmetry as the environment. Reviewing these unusual results it was considered of great interest to verify that the non-centered locations of the H atoms are reasonable from an energy point of view. Quantum mechanical calculations have now been carried out for the potential-energy surfaces (PES) for both the centered and non-centered locations of the H atoms. In all cases the non-centered positions are closer to the energy minima in the PES than the centered positions, and this result confirms that the structure is best described with non-centered H atoms. There is virtually perfect agreement between the quantum-mechanically derived reaction coordinates (QMRC) and the bond-order reaction coordinates (BORC) derived using Pauling's bond-order concept together with the principle of conservation of bond order. [Part I: Olovsson et al. (2001). Acta Cryst. B57, 311–316; Part II: Olovsson et al. (2002). Acta Cryst. B58, 627–631.]
Do pollen feeding, pupal-mating and larval gregariousness have a single origin in Heliconius butterflies? Inferences from multilocus DNA sequence data
Authors: BELTRÁN MARGARITA , JIGGINS CHRIS D. , BROWER ANDREW V. Z. , BERMINGHAM ELDREDGE , MALLET JAMES
Published: September 2007

Phylogenetic information is useful in understanding the evolutionary history of adaptive traits. Here, we present a well-resolved phylogenetic hypothesis for Heliconius butterflies and related genera. We use this tree to investigate the evolution of three traits, pollen feeding, pupal-mating behaviour and larval gregariousness. Phylogenetic relationships among 60 Heliconiina species (86% of the subtribe) were inferred from partial DNA sequences of the mitochondrial genes cytochrome oxidase I, cytochrome oxidase II and 16S rRNA, and fragments of the nuclear genes elongation factor-1α, apterous, decapentaplegic and wingless (3834 bp in total). The results corroborate previous hypotheses based on sequence data in showing that Heliconius is paraphyletic, with Laparus doris and Neruda falling within the genus, demonstrating a single origin for pollen feeding but with a loss of the trait in Neruda. However, different genes are not congruent in their placement of Neruda; therefore, monophyly of the pollen feeding species cannot be ruled out. There is also a highly supported monophyletic ‘pupal-mating clade’ suggesting that pupal mating behaviour evolved only once in the Heliconiina. Additionally, we observed at least three independent origins for larval gregariousness from a solitary ancestor, showing that gregarious larval behaviour arose after warning coloration.
Gene trap mutagenesis in mice: New perspectives and tools in cancer research
Authors: Yamamura Ken‐ichi , Araki Kimi
Published: September 2007

The complete human DNA sequence of the human genome was published in 2004 and we entered the postgenomic era. However, many studies showed that gene function is much more complex than we expected, and that mutation of disease genes does not give any clue for molecular mechanisms for disease development. Since the first report on gene knockout mice in 1989, knockout mice have been shown to be a powerful tool for functional genomics and for the dissection of developmental processes in human diseases. In accordance with this successful application of knockout mice, three major mouse knockout programs are now underway worldwide, to mutate all protein‐encoding genes in mouse embryonic stem cells using a combination of gene trapping and gene targeting. We developed the exchangeable gene trap method suitable for large scale mutagenesis in mice. In this method we can produce null mutation and post‐insertional modification, enabling replacement of the marker gene with a gene of interest and conditional knockout. We herein discuss the effect of this gene‐driven type approach for cancer research, especially for finding the genes that are related to cancer, but are paid little attention in hypothesis‐driven cancer research. (Cancer Sci 2008; 99: 1–6)
Cyclin‐dependent kinase inhibitors and basement membrane interact to regulate breast epithelial cell differentiation and acinar morphogenesis
Authors: Coppock H. A. , Gilham D. E. , Howell A. , Clarke R. B.
Published: September 2007

Abstract.  Objective: The cyclin‐dependent kinase inhibitors (CDKIs), p21CIP1 and p27KIP1 regulate growth and differentiation in diverse tissue types. We aimed to determine whether p21CIP1 or p27KIP1 could induce a terminally differentiated phenotype in breast cells, and to examine if CDKI expression is regulated by basement membrane interactions. Materials and Methods: Effects of increased CDKI expression on the phenotype of MCF‐10A breast epithelial cells were examined by retroviral transduction of p21CIP1 or p27KIP1 cDNA. Results: Overexpression of p21CIP1 or p27KIP1 reduced MCF‐10A growth rates in monolayer cultures, altered cellular morphology and stimulated accumulation of neutral lipid droplets, suggesting partial lactational differentiation. However, markers of luminal differentiation (oestrogen and progesterone receptors, α‐lactalbumin, β‐casein and adipophilin) were absent when examined by reverse transcriptase‐polymerase chain reaction and immunohistochemistry. Cell‐basement membrane contacts are known to be essential for full mammary epithelial cell differentiation and therefore parental MCF‐10A cells were cultured on a basement membrane preparation (Matrigel) in which they form acini. Immunocytochemistry showed that Ki67, the cell proliferation marker, was initially expressed at high levels and as growth decreased p27KIP1 expression steadily increased. Surprisingly, p21CIP1 was highest at the early stages of acinus growth and was detected in proliferating cells, as demonstrated by colocalization in dual Ki67/p21CIP1 immunofluorescence. Overexpression of p21CIP1 or p27KIP1 impaired formation of acini, whereas their knockdown, using siRNA, increased acinus formation. Conclusion: We conclude that both p21CIP1 and p27KIP1 induce partial secretory differentiation of mammary cells in monolayer, but during acinus morphogenesis in 3D culture they have a highly regulated temporal expression pattern.
The in vitro behaviour and patterns of colony formation of murine epithelial stem cells
Authors: Tudor D. , Chaudry F. , Harper L. , Mackenzie I. C.
Published: September 2007

Abstract.  Objective: The mechanisms of renewal of skin and mucosal epithelia in vivo are associated with hierarchies of stem and amplifying cells organized in distinct spatial patterns. Stem and amplifying characteristics persist after isolation and growth of human keratinocytes in vitro but the pattern for murine keratinocytes has been less clear. Materials and Methods: Murine keratinocytes were grown in low calcium media and examined for their patterns of colony morphologies. Results: We consistently identified three types of colonies, one of which contains concentric zones of amplifying and differentiated cells surrounding a central zone of cells that have patterns of expression and behavioural characteristic of stem cells. This zonal organization facilitated analysis of stem cell formation and loss. Cells in the central stem cell zone undergo rapid symmetric divisions but expansion of this population is partially limited by their peripheral transition into amplifying cells. A striking feature of central zone cells is their enhanced apoptotic susceptibility and stem cell expansion limited by consistently high background rates of apoptosis. This occasionally reaches catastrophic levels with elimination of the entire central zone. Conclusion: In vitro amplification of stem cells for the generation of engineered tissue has tended to focus on control of asymmetric division but these findings suggest that development of mechanisms protecting stem cells from apoptotic changes are also likely to be of particular value.
Carbon allocation in forest ecosystems
Authors: LITTON CREIGHTON M. , RAICH JAMES W. , RYAN MICHAEL G.
Published: September 2007

Carbon allocation plays a critical role in forest ecosystem carbon cycling. We reviewed existing literature and compiled annual carbon budgets for forest ecosystems to test a series of hypotheses addressing the patterns, plasticity, and limits of three components of allocation: biomass, the amount of material present; flux, the flow of carbon to a component per unit time; and partitioning, the fraction of gross primary productivity (GPP) used by a component. Can annual carbon flux and partitioning be inferred from biomass? Our survey revealed that biomass was poorly related to carbon flux and to partitioning of photosynthetically derived carbon, and should not be used to infer either. Are component fluxes correlated? Carbon fluxes to foliage, wood, and belowground production and respiration all increased linearly with increasing GPP (a rising tide lifts all boats). Autotrophic respiration was strongly linked to production for foliage, wood and roots, and aboveground net primary productivity and total belowground carbon flux (TBCF) were positively correlated across a broad productivity gradient. How does carbon partitioning respond to variability in resources and environment? Within sites, partitioning to aboveground wood production and TBCF responded to changes in stand age and resource availability, but not to competition (tree density). Increasing resource supply and stand age, with one exception, resulted in increased partitioning to aboveground wood production and decreased partitioning to TBCF. Partitioning to foliage production was much less sensitive to changes in resources and environment. Overall, changes in partitioning within a site in response to resource supply and age were small (<15% of GPP), but much greater than those inferred from global relationships. Across all sites, foliage production plus respiration, and total autotrophic respiration appear to use relatively constant fractions of GPP – partitioning to both was conservative across a broad range of GPP – but values did vary across sites. Partitioning to aboveground wood production and to TBCF were the most variable – conditions that favored high GPP increased partitioning to aboveground wood production and decreased partitioning to TBCF. Do priorities exist for the products of photosynthesis? The available data do not support the concept of priorities for the products of photosynthesis, because increasing GPP increased all fluxes. All facets of carbon allocation are important to understanding carbon cycling in forest ecosystems. Terrestrial ecosystem models require information on partitioning, yet we found few studies that measured all components of the carbon budget to allow estimation of partitioning coefficients. Future studies that measure complete annual carbon budgets contribute the most to understanding carbon allocation.
Thermodependent bacterial pathogens and mass mortalities in temperate benthic communities: a new case of emerging disease linked to climate change
Authors: BALLY MARC , GARRABOU JOAQUIM
Published: September 2007

In the temperate north‐western Mediterranean Sea, large‐scale disease outbreaks in benthic invertebrate species have recently occurred during climatic anomalies characterized by elevated seawater temperatures. One of the most affected species was the red gorgonian Paramuricea clavata, a key species of highly diverse communities dwelling in dim‐lit habitats in the Mediterranean. From diseased P. clavata colonies, we isolated culturable bacteria associated to tissue lesions in order to investigate their potential as pathogens. Inoculation of four bacterial isolates onto healthy P. clavata in aquaria caused disease signs similar to those observed during the 2003 mortality event. The infection process was dependent on elevated seawater temperatures, in a range of values consistent with recordings performed in the field during the climatic anomalies. Among the four isolates, we identified a Vibrio coralliilyticus strain that showed virulence to P. clavata. This strain was re‐isolated from diseased colonies during the experimentations. V. coralliilyticus has been previously identified as a thermodependent pathogen of a tropical coral species, emphasizing a causal role of this infectious agent in the P. clavata disease. Taking into consideration predicted global warming over the coming decades, a better understanding of the factors and mechanisms that affect the disease process will be of critical importance in predicting future threats to temperate gorgonians communities in the Mediterranean Sea.
Will northern fish populations be in hot water because of climate change?
Authors: SHARMA SAPNA , JACKSON DONALD A. , MINNS CHARLES K. , SHUTER BRIAN J.
Published: September 2007

Predicted increases in water temperature in response to climate change will have large implications for aquatic ecosystems, such as altering thermal habitat and potential range expansion of fish species. Warmwater fish species, such as smallmouth bass, Micropterus dolomieu, may have access to additional favourable thermal habitat under increased surface‐water temperatures, thereby shifting the northern limit of the distribution of the species further north in Canada and potentially negatively impacting native fish communities. We assembled a database of summer surface‐water temperatures for over 13 000 lakes across Canada. The database consists of lakes with a variety of physical, chemical and biological properties. We used general linear models to develop a nation‐wide maximum lake surface‐water temperature model. The model was extended to predict surface‐water temperatures suitable to smallmouth bass and under climate‐change scenarios. Air temperature, latitude, longitude and sampling time were good predictors of present‐day maximum surface‐water temperature. We predicted lake surface‐water temperatures for July 2100 using three climate‐change scenarios. Water temperatures were predicted to increase by as much as 18 °C by 2100, with the greatest increase in northern Canada. Lakes with maximum surface‐water temperatures suitable for smallmouth bass populations were spatially identified. Under several climate‐change scenarios, we were able to identify lakes that will contain suitable thermal habitat and, therefore, are vulnerable to invasion by smallmouth bass in 2100. This included lakes in the Arctic that were predicted to have suitable thermal habitat by 2100.