bluuebunny/crossref_metadata_2025 huggingface dataset:
2D PP/PS‐stereotomography: Application to a real 2D‐OBC dataset
Authors: Alerini M. , Lambaré G. , Baina R. , Podvin P. , Le Bégat S.
Published: February 2008

It has been shown on an ‘ideal’ synthetic dataset that PP/PS‐stereotomography can estimate an accurate velocity model without any pairing of PP‐ and PS‐events. The P‐wave velocity model is first estimated using PP data and then, fixing this velocity field, the S‐wave velocity is estimated using the PS data. This method needed to be evaluated further and we present here the first application of PP/PS‐stereotomography to a real dataset: the 2D East‐West Mahogany OBC line (Gulf of Mexico). We are here confronted with data which do not fit our working assumptions: coherent noise (due to an approximate separation of PP‐ and PS‐events and some remaining multiples), probably some anisotropy and 3D effects. With a careful selection of the stereotomographic picks, which allows one to decrease the effect of the picked coherent noise by the automatic picker, our application can demonstrate the relevance of our approach in the upper part of the profile, where anisotropy and 3D effects might be low. We can thus estimate, without any pairing of PP‐ and PS‐events, a velocity field which provides not only flat common image gathers, but also PP‐ and PS‐depth migrated images located at the same positions. For the deeper part of the profile, a significant shift in depth appears. In addition to possible anisotropy, 3D effects and a more complex velocity field (‘salt body’), this is due to the quality of the PZ‐ and X‐components profiles: The PZ‐component profile where the PP‐stereotomographic picking is performed, is polluted by conflicting converted or multiple events and the X‐component profile, where the PS‐stereotomographic picking is performed, is highly noisy. This study emphasizes the need to develop accurate selection criteria for the stereotomographic picks.
General morphological and biological features of neoplasms: integration of molecular findings
Authors: Diaz‐Cano S J
Published: February 2008

This review highlights the importance of morphology–molecular correlations for a proper implementation of new markers. It covers both general aspects of tumorigenesis (which are normally omitted in papers analysing molecular pathways) and the general mechanisms for the acquired capabilities of neoplasms. The mechanisms are also supported by appropriate diagrams for each acquired capability that include overlooked features such as mobilization of cellular resources and changes in chromatin, transcription and epigenetics; fully accepted oncogenes and tumour suppressor genes are highlighted, while the pathways are also presented as activating or inactivating with appropriate colour coding. Finally, the concepts and mechanisms presented enable us to understand the basic requirements for the appropriate implementation of molecular tests in clinical practice. In summary, the basic findings are presented to serve as a bridge to clinical applications.

The current definition of neoplasm is descriptive and difficult to apply routinely. Biologically, neoplasms develop through acquisition of capabilities that involve tumour cell aspects and modified microenvironment interactions, resulting in unrestricted growth due to a stepwise accumulation of cooperative genetic alterations that affect key molecular pathways. The correlation of these molecular aspects with morphological changes is essential for better understanding of essential concepts as early neoplasms/precancerous lesions, progression/dedifferentiation, and intratumour heterogeneity. The acquired capabilities include self‐maintained replication (cell cycle dysregulation), extended cell survival (cell cycle arrest, apoptosis dysregulation, and replicative lifespan), genetic instability (chromosomal and microsatellite), changes of chromatin, transcription and epigenetics, mobilization of cellular resources, and modified microenvironment interactions (tumour cells, stromal cells, extracellular, endothelium). The acquired capabilities defining neoplasms are the hallmarks of cancer, but they also comprise useful tools to improve diagnosis and prognosis, as well as potential therapeutic targets. The application of these concepts in oncological pathology leads to consideration of the molecular test requirements (Molecular Test Score System) for reliable implementation; these requirements should cover biological effects, molecular pathway, biological validation, and technical validation. Sensible application of molecular markers in tumour pathology always needs solid morphological support.
Dissection of spontaneous cytotoxicity by human intestinal intraepithelial lymphocytes: MIC on colon cancer triggers NKG2D‐mediated lysis through Fas ligand
Authors: Ebert Ellen C , Groh Veronika
Published: February 2008

Human intestinal intraepithelial lymphocytes (IELs), which are T‐cell receptor αβ+ CD8+ T cells located between epithelial cells (ECs), are likely to participate in the innate immune response against colon cancer. IELs demonstrate spontaneous cytotoxic (SC) activity specifically directed against EC tumours but not against other solid tumour types. The aim of this study was to dissect out the mechanism of SC activity, focusing on the interaction of NKG2D on IELs with its ligands [major histocompatibility complex (MHC) class I chain‐related protein (MIC) and UL16 binding protein (ULBP)] found mainly on EC tumours. A novel series of events occurred. The NKG2D–MIC/ULBP interaction induced Fas ligand (FasL) production and FasL‐mediated SC activity against HT‐29 cells and MIC‐transfectants. Tumour necrosis factor‐α and interferon‐γ, produced independently of this interaction, promoted SC activity. The immune synapse was strengthened by the interaction of CD103 on IELs with E‐cadherin on HT‐29 cells. Neither T‐cell receptor nor MHC class I was involved. While the HT‐29 cells were destroyed by soluble FasL, tumour necrosis factor‐α and interferon‐γ, the IELs were resistant to the effects of these mediators and to FasL expressed by the HT‐29 cells. This unidirectional FasL‐mediated cytotoxicity of IELs against HT‐29 cells, triggered through NKG2D, is unique and is likely to be a property of those CD8+ tumour‐infiltrating lymphocytes that phenotypically resemble IELs.
Rapid expansion of lichen woodlands within the closed‐crown boreal forest zone over the last 50 years caused by stand disturbances in eastern Canada
Authors: Girard F. , Payette S. , Gagnon R.
Published: February 2008

Aim  Our two main goals are first to evaluate the resilience of the boreal forest according to latitude across the closed‐crown forest zone using the post‐disturbance distribution and cover of lichen woodlands and closed‐crown forests as a metric, and second to identify the disturbance factors responsible for the regeneration and degradation of the closed‐crown forest according to latitude since the 1950s.

Location  The study area extends between 70°00′ and 72°00′ W and throughout the closed‐crown forest zone, from its southern limit near 47°30′ N to its northern limit at the contact with the lichen woodland zone at around 52°40′ N.

Methods  Recent (1972–2002) and old (1954–1956) aerial photos were used to map the distribution of lichen woodlands across the closed‐crown forest zone. Forest disturbances such as fire, spruce budworm (Choristoneura fumiferana (Clemens)) outbreak, and logging were recorded on each set of aerial photos. Each lichen woodland and stand disturbance was validated by air‐borne surveys and digitized using GIS software.

Results  Over the last 50 years, the area occupied by lichen woodlands has increased according to latitude; that is, 9% of the area that was occupied by closed‐crown forests has shifted to lichen woodlands. Although logging activities have been concentrated in the same areas during the last 50 years, the area covered by logging has increased significantly. Outbreaks by the spruce budworm occurred predominantly in the southern (47°30′ N to 48°30′ N) and central (48°53′ N to 50°42′ N) parts of the study area, where balsam fir stands are extensive. In the northern part of the study area (51°–52°40′ N), extensive fires affected the distribution and cover of closed‐crown forests and lichen woodlands.

Main conclusions  Over the last 50 years, the area occupied by closed‐crown forests has decreased dramatically, and the ecological conditions that allow closed‐crown forests to establish and develop are currently less prevalent. Fire is by far the main disturbance, reducing the ability of natural closed‐crown forests to self‐regenerate whatever the latitude. Given the current biogeographical shift from dense to open forests, the northern part of the closed‐crown forest zone is in a process of dramatic change towards the dominance of northern woodlands.
High tropical net diversification drives the New World latitudinal gradient in palm (Arecaceae) species richness
Authors: Svenning Jens‐Christian , Borchsenius Finn , Bjorholm Stine , Balslev Henrik
Published: February 2008

Aim Species richness exhibits striking geographical variation, but the processes that drive this variation are unresolved. We investigated the relative importance of two hypothesized evolutionary causes for the variation in palm species richness across the New World: time for diversification and evolutionary (net diversification) rate. Palms have a long history in the region, with the major clades diversifying during the Tertiary (65–2 Ma).

Location Tropical and subtropical America (34° N–34° S; 33–120° W).

Methods Using range maps, palm species richness was estimated in a 1° × 1° grid. Mean lineage net diversification was estimated by the mean phylogenetic root distance (MRD), the average number of nodes separating a species from the base of the palm phylogeny for the species in each grid cell. If evolutionary rate limits richness, then richness should increase with MRD. If time limits richness, then old, relict species (with low root distance) should predominantly occur in long‐inhabited and therefore species‐rich areas. Hence, richness should decrease with MRD. To determine the influence of net diversification across different time frames, MRD was computed for subtribe, genus and species levels within the phylogeny, and supplemented with the purely tip‐level measure, mean number of species per genus (MS/G). Correlations and regressions, in combination with eigenvector‐based spatial filtering, were used to assess the relationship between species richness, the net diversification measures, and potential environmental and geographical drivers.

Results Species richness increased with all net diversification measures. The regression models showed that richness and the net diversification measures increased with decreasing (absolute) latitude and, less strongly, with increasing energy/temperature and water availability. These patterns therefore reflect net diversification at both deep and shallow levels in the phylogeny. Richness also increased with range in elevation, but this was only reflected in the MS/G pattern and therefore reflects recent diversification.

Main conclusions The geographical patterns in palm species richness appear to be predominantly the result of elevated net diversification rates towards the equator and in warm, wet climates, sustained throughout most of the Tertiary. Late‐Tertiary orogeny has caused localized increases in net diversification rates that have also made a mark on the richness pattern.
Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans
Authors: BAÏLLE DOROTHÉE , BARRIÈRE ANTOINE , FÉLIX MARIE‐ANNE
Published: February 2008

The nematode Oscheius tipulae belongs to the same family (Rhabditidae) as the model species Caenorhabditis elegans. Both species reproduce through self‐fertilizing hermaphrodites and facultative males. Recent studies have shown that the self‐fertile C. elegans and C. briggsae displayed a 20‐fold lower genetic diversity than the male–female species C. remanei. Several explanations have been put forward to account for this difference, including their mode of reproduction and dynamic population structure. Here, we present the results of extensive worldwide sampling of O. tipulae, which we previously used as a laboratory organism for developmental genetics. We found that O. tipulae is much more widespread and common in soil throughout the world than Caenorhabditis species. We analysed 63 O. tipulae isolates from several continents using amplified fragment length polymorphism (AFLP). We found that O. tipulae harbours a 5‐fold higher genetic diversity than C. elegans and C. briggsae. As in C. elegans, a high proportion of this diversity was found locally. Yet, we detected significant geographical differentiation, both at the worldwide scale with a latitudinal structure and between three localities in France. In summary, O. tipulae exhibited significantly higher levels of genetic diversity and large‐scale geographical structure than C. elegans, despite their shared mode of reproduction. This species difference in genetic diversity may be explained by a number of other differences, such as population size, distribution, migration and dynamics. Due to its widespread occurrence and relatively high genetic diversity, O. tipulae may be a promising study species for evolutionary studies.
Sequencing goes 454 and takes large‐scale genomics into the wild
Authors: ELLEGREN HANS
Published: February 2008

Sometimes, science takes a big leap forward. This is often due to new technology that allows the study of questions previously difficult or even impossible to address. An example of this is provided in this issue (Veraet al. 2008) by the first large‐scale attempt toward genome sequencing of an ecologically important model, based on the new ‘454‐sequencing technology’. Using this new technology, the protein‐coding sequences of the Glanville fritillary butterfly genome have now been largely characterized.
Quantitative disease resistance assessment by real‐time PCR using the Stagonospora nodorum‐wheat pathosystem as a model
Authors: Oliver R. P. , Rybak K. , Shankar M. , Loughman R. , Harry N. , Solomon P. S.
Published: February 2008

Measuring disease resistance accurately and reproducibly is a key requirement for the introgression of partial resistance genes into breeding lines. Here, a qPCR protocol is used to measure fungal biomass, using the wheat‐Stagonospora nodorum pathosystem as a model. Seven cultivars of differing reported resistance levels were used. Fungal biomass taken at 220°C thermal days after inoculation accurately predicts the final grain weight loss. It is concluded that a test based on qPCR methods is specific, quantitative, rapid and objective. Such tests could provide useful and economic tools in the development of robustly resistant crop cultivars.
Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts
Authors: Simpson Craig G. , Fuller John , Maronova Monika , Kalyna Maria , Davidson Diane , McNicol Jim , Barta Andrea , Brown John W. S.
Published: February 2008

Alternative splicing (AS) increases the proteomic and functional capacity of genomes through the generation of alternative mRNA transcripts from the same gene. AS is now estimated to occur in a third of Arabidopsis and rice genes, and includes genes involved in the control of growth and development, responses to stress and signalling. Regulation of AS reflects the interactions between positive and negative cis sequences in the precursor messenger RNA and a range of trans‐acting factors. The levels and activities of these factors differ in different cells and growth conditions. To identify changes in AS in multiple genes simultaneously, we have established a reproducible RT‐PCR panel that can analyse 96 alternative splicing events and accurately measure the ratio of alternatively spliced products. This procedure detected statistically significant changes in AS in different plant organs, in plants grown under different light and day‐length conditions, and in plants overexpressing splicing factors. The system provides a convenient, medium‐throughput means of monitoring changes in AS in multiple genes. It can readily be applied to much larger or targeted sets of gene transcripts to generate information on the significance and regulation of AS in plant growth and development, specific processes and responses to external stimuli.
Mixed‐linkage (1→3),(1→4)‐β‐d‐glucan is not unique to the Poales and is an abundant component of Equisetum arvense cell walls
Authors: Sørensen Iben , Pettolino Filomena A. , Wilson Sarah M. , Doblin Monika S. , Johansen Bo , Bacic Antony , Willats William G. T.
Published: February 2008

Mixed‐linkage (1→3),(1→4)‐β‐d‐glucan (MLG) is widely considered to be a defining feature of the cell walls of plants in the Poales order. However, we conducted an extensive survey of cell‐wall composition in diverse land plants and discovered that MLG is also abundant in the walls of the horsetail Equisetum arvense. MALDI‐TOF MS and monosaccharide linkage analysis revealed that MLG in E. arvense is an unbranched homopolymer that consists of short blocks of contiguous 1,4‐β‐linked glucose residues joined by 1,3‐β linkages. However, in contrast to Poaceae species, MLG in E. arvense consists mostly of cellotetraose rather than cellotetriose, and lacks long 1,4‐β‐linked glucan blocks. Monosaccharide linkage analyses and immunochemical profiling indicated that, in E. arvense, MLG is a component of cell walls that have a novel architecture that differs significantly from that of the generally recognized type I and II cell walls. Unlike in type II walls, MLG in E. arvense does not appear to be co‐extensive with glucuroarabinoxylans but occurs in walls that are rich in pectin. Immunofluorescence and immunogold localization showed that MLG occurs in both young and old regions of E. arvense stems, and is present in most cell types apart from cells in the vascular tissues. These findings have important implications for our understanding of cell‐wall evolution, and also demonstrate that plant cell walls can be constructed in a way not previously envisaged.
Signaling pathways in osteoblast proinflammatory responses to infection by Porphyromonas gingivalis
Authors: Ohno T. , Okahashi N. , Morisaki I. , Amano A.
Published: February 2008

Introduction:  We recently investigated global gene expression in ST2 mouse stromal cells infected by the periodontal pathogen Porphyromonas gingivalis using microarray technology, and found that the bacterium induces a wide range of proinflammatory gene expression. Here, we reported the signaling pathways involved in those proinflammatory responses.

Methods:  ST2 cells and primary calvarial osteoblasts from C3H/HeN, C57BL/6, and MyD88‐deficient (MyD88–/–) mice were infected with P. gingivalis ATCC33277 and its gingipain‐deficient mutant KDP136. Expression of the chemokines CCL5 and CXCL10, and matrix metalloproteinase‐9 (MMP9) were quantified by real‐time polymerase chain reaction, while phosphorylation of protein kinases and degradation of an inhibitor of nuclear factor‐κB, IκB‐α, were detected by Western blotting, and activation of transcriptional factors was determined by a luciferase reporter assay. The effects of inhibitors of transcriptional factors and protein kinases were also investigated.

Results:  Infection by P. gingivalis elicited gene expression of CCL5, CXCL10, and MMP9 in both ST2 cells and osteoblasts. Western blot and reporter assay results revealed activation of nuclear factor‐κB (NF‐κB) and activator protein‐1 transcription factors. The NF‐κB inhibitor suppressed the expression of CCL5 and MMP9, but not that of CXCL10, whereas P. gingivalis infection induced significant CCL5 expression in MyD88–/– osteoblasts. In addition, activation of protease‐activated receptors by trypsin elicited significant induction of CXCL10.

Conclusion:  Our results suggest that various proinflammatory responses in P. gingivalis‐infected stromal/osteoblast cells are NF‐κB‐dependent, but not always dependent on the Toll‐like receptor/MyD88 pathway, while some responses are related to the activation of protease‐activated receptors. Thus, P. gingivalis does not fully utilize well‐established pathogen recognition molecules such as Toll‐like receptors.
Identification of protein differences between two clinical isolates of Streptococcus mutans by proteomic analysis
Authors: Guo L. H. , Wang H. L. , Liu X. D. , Duan J.
Published: February 2008

Introduction:  Streptococcus mutans is generally considered to be the principal etiological agent for dental caries. Different strains of S. mutans may display different virulence mechanisms, so the isolation of the differential proteins is illuminating.

Methods:  S. mutans strains 9‐1 and 9‐2, which both colonized the same oral cavity, were selected after screening for the possession of suspected virulence traits. The soluble cellular proteins were extracted from steady‐state planktonic cells of strains 9‐1 and 9‐2 and were analyzed using high‐resolution two‐dimensional gel electrophoresis. Then, replicate maps of proteins from the two strains were generated. Proteins expressed only in strain 9‐1 or 9‐2 were excised and digested with trypsin by using an in‐gel protocol. Tryptic digests were analyzed using matrix‐assisted laser desorption/ionization time of flight mass spectrometry, by which peptide mass fingerprints were generated, and these were used to assign putative functions according to their homology with the translated sequences in the S. mutans genomic database.

Results:  There were 12 proteins only expressed in strain 9‐1 and three proteins only expressed in strain 9‐2. They were involved in protein biosynthesis, protein folding, cell wall biosynthesis, fatty acid biosynthesis, nucleotide biosynthesis, repair of DNA damage, carbohydrate metabolism, signal transduction, and translation.

Conclusion:  The identification of proteins differentially expressed between strains 9‐1 and 9‐2 provides new information concerning the mechanisms of cariogenesis.
Transcutaneous immunization with an outer membrane protein of Porphyromonas gingivalis without adjuvant elicits marked antibody responses
Authors: Koizumi Y. , Kurita‐Ochiai T. , Yamamoto M.
Published: February 2008

Background/aims:  We have previously reported that specific immunoglobulin G (IgG) antibodies induced by transcutaneous immunization (TCI) with a 40‐kDa outer membrane protein (40k‐OMP) of Porphyromonas gingivalis, with cholera toxin (CT) as adjuvant, inhibited coaggregation by P. gingivalis. In this study, we further pursue the potential of the 40k‐OMP as a transcutaneous vaccine.

Methods/results:  TCI of rats administered 40k‐OMP elicited significant 40k‐OMP‐specific serum IgG and IgA, as well as salivary IgG antibody titers. Importantly, these antibody responses were induced without adjuvant. Thus, both serum and saliva antibody titers induced by TCI with the 40k‐OMP alone were identical to those of 40k‐OMP plus cholera toxin as adjuvant. The serum antibody responses induced by 40k‐OMP persisted for more than 140 days. On the other hand, salivary IgG anti‐40k‐OMP antibodies were gradually decreased. Analysis of antibody‐forming cells (AFCs) confirmed the antibody titers by detecting high numbers of 40k‐OMP‐specific IgG AFCs in spleen and cervical lymph node.

Conclusion:  Since 40k‐OMP‐specific IgG inhibited the coaggregation of P. gingivalis with Streptococcus gordonii, and the hemagglutinin activity of P. gingivalis, TCI with the 40k‐OMP may be important as an adjuvant‐free immunogen for the prevention of chronic periodontitis.
Microbiological changes associated with four different periodontal therapies for the treatment of chronic periodontitis
Authors: Haffajee A. D. , Patel M. , Socransky S. S.
Published: February 2008

Background/aims:  To examine subgingival microbiological changes in chronic periodontitis subjects receiving scaling and root planing (SRP) alone or with systemically administered azithromycin, metronidazole or a sub‐antimicrobial dose of doxycycline.

Methods:  Ninety‐two periodontitis subjects were randomly assigned to receive SRP alone or combined with azithromycin, metronidazole or sub‐antimicrobial dose doxycycline. Subgingival plaque samples taken at baseline, 2 weeks, and 3, 6, and 12 months were analyzed for 40 bacterial species using checkerboard DNA–DNA hybridization. Percentage of resistant species and percentage of sites harboring species resistant to the test antibiotics were determined at each time‐point.

Results:  All treatments reduced counts of red complex species at 12 months, although no significant differences were detected among treatment groups for most species at all time‐points. Both antibiotics significantly reduced counts of red complex species by 2 weeks. Percentage of resistant isolates increased in plaque samples in all adjunctive treatment groups, peaking at the end of administration, but returned to pretreatment levels by 12 months.

Conclusion:  The significant reduction of red and orange complex species at 2 weeks in the subjects receiving SRP plus azithromycin or metronidazole may have contributed to a better clinical response in these treatment groups. Therapy did not appear to create lasting changes in the percentage of resistant isolates or sites harboring resistant species.
Porphyromonas gingivalis gingipains cause G1 arrest in osteoblastic/stromal cells
Authors: Kato T. , Tsuda T. , Inaba H. , Kawai S. , Okahashi N. , Shibata Y. , Abiko Y. , Amano A.
Published: February 2008

Introduction:  The program for mammalian cell growth and division consists of four successive phases; G1, S, G2, and M. Porphyromonas gingivalis may manipulate the host cell cycle to benefit bacterial virulence expression, which likely causes the cell and tissue tropism observed in chronic periodontal infections. We examined P. gingivalis for its effects on cell‐cycle modulation in mouse ST2 osteoblastic/stromal cells.

Methods:  Synchronized ST2 cells were infected with P. gingivalis ATCC33277 (wild‐type, WT), gingipain‐mutants [KDP136 (ΔrgpAΔrgpBΔkgp), KDP129 (ΔrgpAΔrgpB), and KDP133 (Δkgp)], and a fimbria‐deficient mutant (KDP150) for 24 h, then the cell cycle was evaluated using flow cytometry. Cell‐cycle‐related molecule expression was examined with a microarray, as well as with quantitative real‐time polymerase chain reaction and Western blotting assays.

Results:  Both the WT and KDP150 strains significantly inhibited cellular proliferation and arrested the cell cycle in the G0/G1 phase, while the expression levels of the cell‐cycle regulatory molecules cyclin D and cyclin E were also decreased. In contrast, KDP136 did not show any effects. G1 arrest was also clearly induced by KDP129 and KDP133, with KDP129 being more effective.

Conclusion:  The present findings suggest that P. gingivalis gingipains reduce cyclin expression and cause early G1 arrest, leading to the inhibition of cellular proliferation.
Phytophthora infestans‐triggered response of growth‐ and defense‐related genes in potato cultivars with different levels of resistance under the influence of nitrogen availability
Authors: Ros Barbara , Mohler Volker , Wenzel Gerhard , Thümmler Fritz
Published: February 2008

The effects of high and low N concentrations on the Solanum tuberosum–Phytophthora infestans interaction were studied in the potato cultivars Bettina, New York 121, Indira and Arkula, which exhibited different levels of resistance. Aboveground biomass and Chl and N content were significantly higher in all cultivars grown in higher N environments, while C:N ratios were lower, confirming successful application of N. High availability of N significantly increased susceptibility of three of the four potato cultivars, and amounts of pathogen within the infected leaflets determined in a quantitative real‐time reverse transcriptase–polymerase chain reaction reflected this. Differential gene expression of P. infestans‐induced and ‐repressed genes derived from three subtracted cDNA libraries at 0, 24, 48 and 72 h post‐inoculation was studied in parallel. P. infestans attack led to an induction of defense‐related and at the same time repression of growth‐related potato genes mainly encoding photosynthetic genes. High N supply led to higher transcript abundance of photosynthetic genes such as Chl a/b‐binding protein and ribulose bisphosphate carboxylase. N‐dependent suppression of defense‐related compounds in absence of the pathogen was not observed. Better N nutrition appeared to allow the plants to invest more resources in defense reactions.
Transgenic tobacco plants overexpressing polyamine oxidase are not able to cope with oxidative burst generated by abiotic factors
Authors: Moschou Panagiotis N. , Delis Ioannis D. , Paschalidis Konstantinos A. , Roubelakis‐Angelakis Kalliopi A.
Published: February 2008

The molecular and biochemical mechanism(s) of polyamine (PA) action remain largely unknown. Transgenic tobacco plants overexpressing polyamine oxidase (PAO) from Zea mays exhibited dramatically increased expression levels of Mpao and high 1,3‐diaminopropane (Dap) content. All fractions of spermidine and spermine decreased significantly in the transgenic lines. Although Dap was concomitantly generated with H2O2 by PAO, the latter was below the detection limits. To show the mode(s) of H2O2 scavenging, the antioxidant machinery of the transgenics was examined. Specific isoforms of peroxidase, superoxide dismutase and catalase were induced in the transgenics but not in the wild‐type (WT), along with increase in activities of additional enzymes contributing to redox homeostasis. One would expect that because the antioxidant machinery was activated, the transgenics would be able to cope with increased H2O2 generated by abiotic stimuli. However, despite the enhanced antioxidant machinery, further increase in the intracellular reactive oxygen species (ROS) by exogenous H2O2, or addition of methylviologen or menadione to transgenic leaf discs, resulted in oxidative stress as evidenced by the lower quantum yield of PSII, the higher ion leakage, lipid peroxidation and induction of programmed cell death (PCD). These detrimental effects of oxidative burst were as a result of the inability of transgenic cells to further respond as did the WT in which induction of antioxidant enzymes was evident soon following the treatments. Thus, although the higher levels of H2O2 generated by overexpression of Mpao in the transgenics, with altered PA homeostasis, were successfully controlled by the concomitant activation of the antioxidant machinery, further increase in ROS was detrimental to cellular functions and induced the PCD syndrome.
Variety is the Spice of Life: Female Lizards Choose to Associate with Colour‐Polymorphic Male Dyads
Authors: Healey Mo , Uller Tobias , Olsson Mats
Published: February 2008

We test the idea that male colour polymorphism in a lizard (red vs. yellow headed) may be maintained by a female preference for associating (and presumably mating) with both male morphs rather than only one. In female choice experiments on single males of different colours, females did not preferentially associate with either morph. However, when females were allowed to choose between pairs of males of the same vs. different colours, they preferred to associate with male pairs that were polymorphic. We suggest that this may be the result of selection arising from polyandrous mating benefits and show experimentally that polyandry results in increased hatching success. Most theoretical models of the evolution of mate choice assume that mate choice is costly. We test this assumption by releasing females into polymorphic vs. monomorphic groups in the wild, under the hypothesis that females move more between males in polymorphic groups and therefore suffer higher risks of mortality from predation. In accordance with this prediction, females released into polymorphic male groups were less likely to be recaptured than females released into monomorphic groups, with evidence to suggest that this is because of increased mortality and not increased dispersal. We propose that this cost could be (partly) balanced by polyandrous fitness benefits.
Reconciliation in Wolves (Canis lupus): New Evidence for a Comparative Perspective
Authors: Cordoni Giada , Palagi Elisabetta
Published: February 2008

Social animals gain benefits from cooperative behaviours. However, social systems also imply competition and conflict of interest. To cope with dispersal forces, group‐living animals use several peace‐keeping tactics, which have been deeply investigated in primates. Other taxa, however, have been often neglected in this field research. Wolves (Canis lupus) with their high sociality and cooperative behaviour may be a good model species to investigate the reconciliation process. In this study, we provide the first evidence for the occurrence of reconciliation in a group of zoo‐kept wolves. The conciliatory contacts were uniformly distributed across the different sex‐class combinations. We found a linear dominance hierarchy in the colony under study, although the hierarchical relationships did not seem to affect the reconciliation dynamics. Moreover, both aggressors and victims initiated first post‐conflict affinitive contact with comparable rates and both high‐ and low‐intensity conflicts were reconciled with similar percentages. Finally, we found that coalitionary support may be a good predictor for high level of conciliatory contacts in this species.
Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes
Authors: Yao M. Z. , Chen L. , Liang Y. R.
Published: February 2008

Tea plant [Camellia sinensis (L.) O. Kuntze] is an important beverage crop in the world. In recent years many clonal tea cultivars have been released, and they play major roles in improving the production and quality of tea. It is important to understand the genetic diversity and relatedness of these cultivars to avoid inbreeding and narrow genetic basis in future tea breeding. In the present study, genetic diversity and relationship of 48 tea cultivars from China, Japan and Kenya were evaluated by inter‐simple sequence repeat (ISSR) markers. A total of 382 ISSR bands were scored, of which 381 (99.7%) were polymorphic. The ISSR primers showed high ability to distinguish between tea cultivars according to their high Resolving Power (RP) with an average of 7.4. The mean of Nei’s gene diversity (H) and Shannon’s information index (I) were 0.22 and 0.35, respectively. More abundant diversity was revealed among cultivars in China than those in Japan and Kenya. Within Chinese populations, the level of diversity in east China was higher than that in other regions. The coefficient of genetic differentiation (GST) was 0.202, which indicates a high degree of genetic variation within populations. This result was further confirmed by analysis of molecular variance, which revealed the variance component within the populations (92.07%) was obviously larger than that among populations (7.93%). The level of gene flow (Nm) was estimated to be 2.0. This could be explained by frequent natural cross‐pollination and seed dispersal among tea populations. The pairwise similarity coefficient between the cultivars varied from 0.162 to 0.538. A dendrogram of 48 tea cultivars was constructed where all the tested cultivars were divided into two groups. Our data show that the genetic relationship among tea cultivars can be determined by the ISSR markers. This will provide valuable information to assist parental selection in current and future tea breeding programmes.
Developments in nutritional programming illustrated by WinDiets
Authors: Wise A.
Published: February 2008

Summary  Dietary analysis programs have developed considerably over the last two decades and now include many features that people have grown to expect to find while browsing the internet. The range of functions that can be achieved is growing rapidly and includes the production of stand‐alone educational programs that can be used on the internet. These developments are explained in the context of my programming experience using WinDiets, as an example of how programs can currently be designed.
L'APPROCHE PAR LES CAPACITÉS D'AMARTYA SEN: QUELS ENSEIGNEMENTS POUR L'ÉCONOMIE SOCIALE?
Authors: FERRATON Cyrille
Published: February 2008

RESUME*:  Cet article confronte l'approche par les capacités d'Amartya Sen à la perspective de l'économie sociale. Nous exposons dans une première partie l'approche par les capacités. Nous montrons dans une seconde partie que celle‐ci présente une double utilité pour l'économie sociale: une utilité théorique parce qu'elle fournit une « grille de lecture » possible des finalités de l'économie sociale; et une utilité pratique à un double niveau: d'un côté elle donne une nouvelle perspective aux relations entre économie sociale et action publique et de l'autre fournit des instruments d'évaluation à l'économie sociale.
LOOKING THE PART: RUMINATIVE VIEWING AND THE IMAGINATION OF COMMUNITY IN THE EARLY MODERN LOW COUNTRIES
Authors: ROTHSTEIN BRET
Published: February 2008

This essay concerns the visual assertion of corporate identity in Gerard David's Justice of Cambyses (completed 1498). This painting is significant in three respects. First, unlike contemporaneous Flemish treatments of the subject, David's diptych presents judicial practice as earthly rather than spiritual in nature. Second, it privileges the distinction between individuals and the groups they form. Third, it treats Flanders in general and Bruges in particular as the ideal just society. In so doing, David's painting breaks markedly with tradition, positing not only the fact but also the social character of justice. What is more, it does so by defining that character as specifically Flemish, thus articulating a nascent if complex sense of regional identity.
RISING OCCUPATIONAL AND INDUSTRY MOBILITY IN THE UNITED STATES: 1968–97*
Authors: Kambourov Gueorgui , Manovskii Iourii
Published: February 2008

We document and analyze the high level and the substantial increase in worker mobility in the United States over the 1968–97 period at various levels of occupational and industry aggregation. This is important in light of the recent findings that human capital of workers is largely occupation‐ or industry‐specific. To control for measurement error in occupation and industry coding, we develop a method that utilizes the PSID Retrospective Occupation‐Industry Supplemental Data Files. We emphasize the importance of our findings for understanding a number of issues such as the changes in wage inequality, aggregate productivity, job stability, and life‐cycle earnings profiles.
ANTICIPATED UTILITY AND RATIONAL EXPECTATIONS AS APPROXIMATIONS OF BAYESIAN DECISION MAKING*
Authors: Cogley Timothy , Sargent Thomas J.
Published: February 2008

We study a Markov decision problem with unknown transition probabilities. We compute the exact Bayesian decision rule and compare it with two approximations. The first is an infinite‐history, rational‐expectations approximation that assumes that the decision maker knows the transition probabilities. The second is a version of Kreps' anticipated‐utility model in which decision makers update using Bayes' law but optimize in a way that is myopic with respect to their updating of probabilities. For several consumption‐smoothing examples, the anticipated‐utility approximation outperforms the rational expectations approximation. The rational expectations approximation misrepresents the market price of risk.
UNMASKING THE POLLUTION HAVEN EFFECT*
Authors: Levinson Arik , Taylor M. Scott
Published: February 2008

We use theory and empirics to examine the effect of environmental regulations on trade flows. A simple model demonstrates how unobserved heterogeneity, endogeneity, and aggregation issues bias standard measurements of this relationship. A reduced‐form estimate of the model, using data on U.S. regulations and trade with Canada and Mexico for 130 manufacturing industries from 1977 to 1986, indicates that industries whose abatement costs increased most experienced the largest increases in net imports. For the average industry, the change in net imports we ascribe to regulatory costs amounting to 10% of the total increase in trade volume over the period.
SOCIAL ACCOUNTING AND THE PUBLIC SECTOR*
Authors: Aronsson Thomas
Published: February 2008

This article contributes to the theory of social accounting. As such, it tries to extend earlier literature on the welfare equivalence of the comprehensive net national product in two main directions, both of which refer to the public sector. One is by considering welfare measurement problems associated with public good provision and redistributive policy, respectively, when the public revenues are raised by distortionary taxes. The other is by addressing the consequences of a “federation‐like” decision structure, where independent tax and expenditure decisions are made both by the central government and by lower level governments.
Locomotion of the Eurasian nuthatch on vertical and horizontal substrates
Authors: Fujita M. , Kawakami K. , Moriguchi S. , Higuchi H.
Published: February 2008

Legged locomotion of the Eurasian nuthatch Sitta europaea on horizontal and vertical substrates was examined using field observations and experiments. Although previous studies have reported that nuthatches use ‘walking’ on vertical substrates, we found that they usually used ‘hopping’ on both vertical and horizontal substrates. When climbing up a vertical substrate, the feet were staggered in position and small phase differences were observed between the left and right leg movements in the gait. In upward climbing, the body was inclined towards the substrate during the first stance phase similar to other tree‐trunk climbers, but the tail was not used for helping body rotation unlike most tree‐trunk climbers. The staggered position of the feet may allow the legs to play different roles in pulling towards and pushing away from the substrate. In downward climbing, the feet were staggered in position, but the phase difference was quite small. In field observations, the Eurasian nuthatch preferred to move vertically, rather than in an inclined direction.
Habitat disturbances differentially affect individual growth rates in a long‐lived turtle
Authors: Dodd C. Kenneth , Dreslik Michael J.
Published: February 2008

Disturbances often help structure ecological communities, and their impacts may have consequences on population dynamics and long‐term species persistence. Should disturbances affect resources, a trade‐off may result between reproduction and individual growth, which in turn could affect the timing of sexual maturity in animals dependent on reaching a requisite size for the onset of maturation. We used a 14‐year mark–recapture dataset to determine the effects of catastrophic storms and the removal of nonindigenous vegetation on individual growth rates of a long‐lived turtle Terrapene carolina bauri. Adult male growth rates increased 19% after the disturbances, whereas female growth rates decreased by a similar percentage. Juvenile growth rates briefly increased, but as these animals became subadults, their growth rates slowed after disturbance, a change more pronounced in females than males. After the disturbances, the onset of male sexual maturity decreased by c. 1 years (from 10.8 to 9.5 years), female maturity was delayed by 2.5 years (from 8.5 to 11.0 years), and the subadult life stage was extended from 2 to 3.5 years. With resources and habitats similarly available to adults, we hypothesize that adult females diverted resources from growth to reproduction, whereas males allocated available resources to growth. Subadult growth rates decreased regardless of sex, implying that fewer or lower quality prey were available to smaller sized turtles in the years following disturbance. The results of this study suggest that habitat disturbances affected individual growth rates differently according to sex and life stage, which in turn affected the timing of maturation. In long‐lived vertebrates, such perturbations on life‐history traits such as growth rates likely affect population recovery, and may help to explain why turtle populations recover slowly following catastrophic disturbance, even when adult survivability is high.
Cardiac autonomic balance versus cardiac regulatory capacity
Authors: Berntson Gary G. , Norman Greg J. , Hawkley Louise C. , Cacioppo John T.
Published: February 2008

The concept of autonomic balance views autonomic states along a bipolar continuum from sympathetic (S) to parasympathetic (P) dominance, whereas regulatory capacity models emphasize overall autonomic flexibility as a marker of the capacity for regulation. These two concepts were evaluated for their utility in characterizing patterns of autonomic control. Measures of P (high frequency heart rate variability, HF) and S (preejection period, PEP) cardiac control were obtained. A measure of cardiac autonomic balance (CAB) was derived as the difference in the normalized P index minus the S index, and a measure of cardiac autonomic regulation (CAR) was derived as the normalized P index plus the S index. Results reveal that CAR, but not CAB, was a significant predictor of the prior occurrence of a myocardial infarction, net of demographic and other variables, whereas CAB, but not CAR, was a significant predictor of concurrent diabetes.
The pupil as a measure of emotional arousal and autonomic activation
Authors: Bradley Margaret M. , Miccoli Laura , Escrig Miguel A. , Lang Peter J.
Published: February 2008

Pupil diameter was monitored during picture viewing to assess effects of hedonic valence and emotional arousal on pupillary responses. Autonomic activity (heart rate and skin conductance) was concurrently measured to determine whether pupillary changes are mediated by parasympathetic or sympathetic activation. Following an initial light reflex, pupillary changes were larger when viewing emotionally arousing pictures, regardless of whether these were pleasant or unpleasant. Pupillary changes during picture viewing covaried with skin conductance change, supporting the interpretation that sympathetic nervous system activity modulates these changes in the context of affective picture viewing. Taken together, the data provide strong support for the hypothesis that the pupil's response during affective picture viewing reflects emotional arousal associated with increased sympathetic activity.
Proteomic analysis of stargazer mutant mouse neuronal proteins involved in absence seizure
Authors: Ryu Myung‐Jeom , Lee Cheolju , Kim Joon , Shin Hee‐Sup , Yu Myeong‐Hee
Published: February 2008

The stargazer (stg) mutant mouse, having mutation in stargazin, the calcium channel γ2 subunit, exhibited several neurological disorders including spontaneous absence seizure, cerebellar ataxia, and head tossing. To understand the molecular pathogenic mechanism of the absence seizure resulted from the loss of stargazin function, the thalamic proteomes between control mouse and stg mouse were compared. We identified 12 proteins expressed differentially (> 1.6‐fold) by fluorescence two‐dimensional difference gel electrophoresis and tandem mass spectrometry. Six of them are involved in basic metabolism including energy metabolism, three in stress response, two in axonal growth regulation, and one in the endoplasmic reticulum processing. All except mortalin showed decreased level of expression in stg mouse. Two stress‐related proteins, mouse stress induced phosphoprotein 1 and peroxiredoxin 6 exhibited reduced levels of expression in stg mouse, while the level of another stress protein, mortalin was increased. Analysis of oxidative protein carbonylation in thalamic proteome of stg mouse showed higher level of carbonylated proteins in stg mouse than in control mouse. Interestingly, down‐regulation of stress protein mouse stress induced phosphoprotein 1, metabolic enzyme isovaleryl‐CoA dehydrogenase, and the two in neuronal axon growth, collapsin response mediator protein 2 and fascin homolog 1 coincides with the results of our previous study on γ‐butyrolactone‐induced transient absence seizure. Our results suggest that the pathogenesis mechanism underlying absence seizure may involve the molecular events contributed by these proteins.