bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of support staff on pupil engagement and individual attention
Authors: Blatchford Peter , Bassett Paul , Brown Penelope , Webster Rob
Published: May 2009

Despite an unprecedented increase in classroom‐based support staff, there are confusing messages about their appropriate deployment and a lack of systematic evidence on their impact. This article addresses the deployment and impact on pupil engagement and individual attention of support staff, commonly known as teaching assistants (TAs), in terms of: (1) a comparison between TAs and teachers; (2) differences between pupils with and without special educational needs (SEN); and (3) differences between primary and secondary schools. Systematic observations of pupil behaviour in 49 primary and secondary schools showed that support staff presence resulted in increased individualisation of attention and overall teaching, easier classroom control, and that pupils showed more engagement and a more active role in interaction with adults. This supports teachers’ positive view of support staff, but their presence also meant pupils’ contact with teachers declined and at secondary level there was less individual and active interactions between teachers and pupils.
Inference and sentence comprehension in children with specific or pragmatic language impairments
Authors: Adams Catherine , Clarke Elaine , Haynes Rebecca
Published: May 2009

Background: Children with language impairments have difficulty in reporting verbal inferences, but it is unclear whether the source of this problem lies in limitations of language comprehension, an inability to access world knowledge, or the integration of information in discourse. Children with pragmatic language impairments (CwPLI) are often described as having disproportionate difficulty with verbal inference, although there is little empirical support for this view.

Aims: To examine the performance of children with specific language impairment (CwSLI), CwPLI and a control group with typical language development (CwTLD) on a verbal inferential comprehension task; to explore whether CwPLI's verbal inferential comprehension performance are disproportionate to their sentence comprehension difficulties; and to analyse inferential error types made by the three groups.

Methods & Procedures: Sixty‐four children with language impairments (CwLI), aged between 6 and 11 years, participated in an inference comprehension task (IC) and a task of sentence comprehension (SC). For the purpose of analysis, the LI group was then split into two subgroups: CwPLI and CwSLI, using a checklist of pragmatic features. A group of CwTLD were matched to LI children on SC ability and gender; a separate group of CwTLD (CA) was matched to CwLI by age and gender.

Outcomes & Results: CwLI had lower raw scores on the IC task than CA‐matched CwTLD, but similar scores to SC‐matched CwTLD. CwPLI produced lower raw IC scores than CwSLI, and this was the same when age and SC performance were controlled for. CwSLI performed similarly to their SC‐matched and CA‐matched control subjects on the IC task. CwPLI scored significantly less on the IC task than both their SC‐matched and CA‐matched control subjects. A regression analysis showed that age and SC ability account for 36% of the variance on the IC task, but group (SLI versus PLI) status accounts for just 5%. A detailed analysis of error types and item performance on the IC task showed a trend for CwPLI to perform more poorly on developmentally more complex inference items, but there was no evidence for a unique pattern of inference errors in CwPLI.

Conclusions & Implications: Children with language impairments tend to perform like younger children with matched level of sentence comprehension ability on a verbal inference comprehension task. CwPLI have more difficulty with this task than CwSLI, but the distribution of scores shows considerable overlap exists between clinical groups. Sentence comprehension ability, age and, to a lesser extent, group status contribute to verbal inferencing ability in children with language impairments, but other factors may be important. The implications for assessment and intervention are discussed.
Evaluation of speech and language therapy interventions for pre‐school children with specific language impairment: a comparison of outcomes following specialist intensive, nursery‐based and no intervention
Authors: Gallagher Aoife Lily , Chiat Shula
Published: May 2009

Background: Clinical services in the UK are increasingly delivering ‘consultative’ methods of intervention rather than ‘direct’ intensive input for children with receptive and expressive language difficulties, yet there has been little systematic evaluation of these different intervention models.

Aims: To investigate the effectiveness of different models of therapy provision for children with specific language impairment between the ages of 4;00 and 4;06 years.

Methods & Procedures: Twenty‐four children were selected from a specialist waiting list in the London Borough of Lambeth. They were assessed on a range of verbal and non‐verbal skills, and randomly assigned to three different intervention groups. Group 1 received direct intensive speech and language therapy weekly over an 8‐month period at a child development centre; Group 2 received a nursery‐based model of intervention; and Group 3 received review sessions at their local clinic.

Outcome & Results: Statistical analysis before the intervention phase revealed no significant differences in scores between the three groups on a range of clinical and parental measures of language, non‐verbal skills, play and behaviour. At the end of the intervention period the Intensive group showed significantly greater improvement than the No Intervention group on all clinical and parental measures, and significantly greater improvement than the Nursery‐based group on all clinical and parental measures except for expressive grammar.

Conclusions & Implications: The results of this small‐scale study demonstrate that intensive direct speech and language therapy delivered by speech and language therapists was a more effective model of intervention for this clinical group with severe speech and language impairment.
Speech disruptions in the sentence formulation of school‐age children with specific language impairment
Authors: Finneran Denise A. , Leonard Laurence B. , Miller Carol A.
Published: May 2009

Background: Many school‐age children with specific language impairment produce sentences that appear to conform to the adult grammar. It may be premature to conclude from this, however, that their language formulation ability is age appropriate.

Aims: To determine whether a more subtle measure of language use, speech disruptions during sentence formulation, might serve to distinguish children with specific language impairment from their typically developing peers at an age when grammatical accuracy was high. We analysed the rate of speech disruptions in simple sentence production in school‐age children with specific language impairment and typically developing age‐matched peers. We predicted that: (1) the specific language impairment group would exhibit more speech disruptions than the typically developing group as a result of reduced language proficiency even when grammatical accuracy was high; and (2) the specific language impairment group would demonstrate greater reductions in disruption frequency as compared with the typically developing group when given sentences that model the target syntactic structures.

Methods & Procedures: Twenty‐eight children (17 specific language impairment, 11 typically developing, mean = 8;10 years) with no history of stuttering were presented with a series of picture pairs. The examiner described the first picture using a simple sentence and asked the child to repeat the sentence; the child then described the second picture. There were two priming conditions: Matching Syntax condition (paired pictures requiring different syntactic structures) and Different Syntax condition (paired pictures requiring different syntax structures). All testing was audio‐recorded and speech disruptions (repetitions, revisions, fillers, long silent pauses) were transcribed and tabulated for each target response. The data were analysed by analysis of variance (ANOVA).

Outcomes & Results: The specific language impairment group demonstrated a significantly greater number of speech disruptions when compared with the typically developing group. There was no effect for priming.

Conclusions & Implications: School‐age children with specific language impairment appear to have difficulty with sentence formulation when compared with typically developing peers even when grammatical accuracy is high. We concluded that school‐age children with specific language impairment may demonstrate subtle but persistent language formulation difficulties.
Children's use of language context in lexical ambiguity resolution
Authors: Khanna Maya M. , Boland Julie E.
Published: May 2009

Lexical ambiguity resolution was examined in children aged 7 to 10 years and adults. In Experiment 1, participants heard sentences supporting one (or neither) meaning of a balanced ambiguous word in a cross-modal naming paradigm. Naming latencies for context-congruent versus context-incongruent targets and judgements of the relatedness of targets to the sentence served as indices of appropriate context use. While younger children were faster to respond to related targets regardless of the sentence context, older children and adults showed priming only for context-appropriate targets. In Experiment 2, only a single-word context preceded the homophone, and in contrast to Experiment 1, all groups showed contextual sensitivity. Individual working-memory span and inhibition ability were also measured in Experiment 2, and more mature executive function abilities were associated with greater contextual sensitivity. These findings support a developmental model whereby sentential context use for lexical ambiguity resolution increases with age, cognitive processing capacity, and reading skill.
Effect of resonant magnetic perturbations on particle confinement
Authors: Yu Q. , Günter S.
Published: May 2009

The effect of externally applied resonant magnetic perturbations (RMPs) on plasma particle transport is investigated based on two fluid equations. It is found that, depending on the frequency and direction of plasma rotation, the RMP of a moderate amplitude can either increase or decrease the plasma density gradient around the corresponding rational surface. The local density profile flattens only for a sufficiently large RMP.
R&D progress of the high power negative ion accelerator for the ITER NB system at JAEA
Authors: Kashiwagi M. , Taniguchi M. , Dairaku M. , de Esch H.P.L. , Grisham L.R. , Svensson L. , Tobari H. , Umeda N. , Watanabe K. , Sakamoto K. , Inoue T.
Published: May 2009

At JAEA, as the Japan Domestic Agency (JADA) for ITER, a MAMuG (multi-aperture multi-grid) accelerator has been developed to perform the required R&D for the ITER neutral beam (NB) system. As a result of countermeasures to handle excess heat load to the ion source by backstreaming positive ions, H− ion beam current was increased to 0.32 A (the ion current density of 140 A m−2) at a beam energy of 796 keV. This high power beam acceleration simulated the ITER operation condition maintaining the perveance (H− ion current density/beam energy3/2) of the ITER accelerator. After the high power beam operation, the pulse length was successfully extended from 0.2 to 5 s at 550 keV, which yielded a 131 mA H− ion beam as an initial test of the long pulse operation. A test of a single-aperture single-gap (SINGAP) accelerator was performed at JAEA under an ITER R&D task agreement. The objective of this test was to compare two different accelerator concepts (SINGAP and MAMuG) at the same test facility. As a result, the MAMuG accelerator was defined as the baseline design for ITER, due to advantages in its better voltage holding and less electron acceleration. In three-dimensional beam trajectory analyses, the aperture offset at the bottom of the extractor was found to be effective for compensation of beamlet deflection due to their own space charge. It has been analytically demonstrated that these compensated beamlets can be focused at a focal point by adopting the aperture offset at the final grid of the accelerator.
Non-inductive plasma current start-up by EC and RF power in the TST-2 spherical tokamak
Authors: Ejiri A. , Takase Y. , Oosako T. , Yamaguchi T. , Adachi Y. , Watanabe O. , Nagashima Y. , An B.I. , Kobayashi H. , Kurashina H. , Hayashi H. , Matsuzawa H. , Yamada K. , Tojo H. , Masuda T. , Sasaki M. , Kumazawa R. , Kasahara H. , Shimpo F.
Published: May 2009

Non-inductive plasma current start-up by EC and RF power was carried out on the TST-2 device. Low frequency RF (21 MHz) sustainment was demonstrated, and the obtained high βp spherical tokamak configuration has similar equilibrium values as the EC (2.45 GHz) sustained plasma. Equilibrium analysis revealed detailed information on three discharge phases: (i) in the initial current formation phase, the plasma current increases with the stored energy, and the current is in the same order as that predicted by theory. (ii) In the current jump phase, the current density profile, which is peaked near the outboard boundary, is not deformed but increases slowly and the initial closed flux surface appears when the current reaches a maximum. (iii) In the current sustained phase, equilibrium is characterized by the hollowness of the current density profile, and it determines the fraction of the current inside the last closed flux surface to the total current. Both EC and RF injections show a similar equilibrium. While MHD instabilities often terminate the RF sustained plasma, no such phenomenon was observed in the EC sustained plasma.
Analysis of Dom34 and Its Function in No-Go Decay
Authors: Passos Dario O. , Doma Meenakshi K. , Shoemaker Christopher J. , Muhlrad Denise , Green Rachel , Weissman Jonathan , Hollien Julie , Parker Roy
Published: May 2009

Eukaryotic mRNAs are subject to quality control mechanisms that degrade defective mRNAs. In yeast, mRNAs with stalls in translation elongation are targeted for endonucleolytic cleavage by No-Go decay (NGD). The cleavage triggered by No-Go decay is dependent on Dom34p and Hbs1p, and Dom34 has been proposed to be the endonuclease responsible for mRNA cleavage. We created several Dom34 mutants and examined their effects on NGD in yeast. We identified mutations in several loops of the Dom34 structure that affect NGD. In contrast, mutations inactivating the proposed nuclease domain do not affect NGD in vivo. Moreover, we observed that overexpression of the Rps30a protein, a high copy suppressor of dom34Δ cold sensitivity, can restore some mRNA cleavage in a dom34Δ strain. These results identify important functional regions of Dom34 and suggest that the proposed endonuclease activity of Dom34 is not required for mRNA cleavage in NGD. We also provide evidence that the process of NGD is conserved in insect cells. On the basis of these results and the process of translation termination, we suggest a multistep model for the process of NGD.
Revisiting the Role of Cystic Fibrosis Transmembrane Conductance Regulator and Counterion Permeability in the pH Regulation of Endocytic Organelles
Authors: Barriere Herve , Bagdany Miklos , Bossard Florian , Okiyoneda Tsukasa , Wojewodka Gabriella , Gruenert Dieter , Radzioch Danuta , Lukacs Gergely L.
Published: May 2009

Organellar acidification by the electrogenic vacuolar proton-ATPase is coupled to anion uptake and cation efflux to preserve electroneutrality. The defective organellar pH regulation, caused by impaired counterion conductance of the mutant cystic fibrosis transmembrane conductance regulator (CFTR), remains highly controversial in epithelia and macrophages. Restricting the pH-sensitive probe to CFTR-containing vesicles, the counterion and proton permeability, and the luminal pH of endosomes were measured in various cells, including genetically matched CF and non-CF human respiratory epithelia, as well as cftr+/+and cftr−/−mouse alveolar macrophages. Passive proton and relative counterion permeabilities, determinants of endosomal, lysosomal, and phagosomal pH-regulation, were probed with FITC-conjugated transferrin, dextran, and Pseudomonas aeruginosa, respectively. Although CFTR function could be documented in recycling endosomes and immature phagosomes, neither channel activation nor inhibition influenced the pH in any of these organelles. CFTR heterologous overexpression also failed to alter endocytic organellar pH. We propose that the relatively large CFTR-independent counterion and small passive proton permeability ensure efficient shunting of the proton-ATPase–generated membrane potential. These results have implications in the regulation of organelle acidification in general and demonstrate that perturbations of the endolysosomal organelles pH homeostasis cannot be linked to the etiology of the CF lung disease.
TANDEM: integrating automated allele binning into genetics and genomics workflows
Authors: Matschiner Michael , Salzburger Walter
Published: May 2009

Summary: Computer programs for the statistical analysis of microsatellite data use allele length variation to infer, e.g. population genetic parameters, to detect quantitative trait loci or selective sweeps. However, observed allele lengths are usually inaccurate and may deviate from the expected periodicity of repeats. The common practice of rounding to the nearest whole number frequently results in miscalls and underestimations of allelic richness. Manual sorting of allele lengths into discrete classes, a process called binning, is tedious and error-prone. Here, we present a new program for the automated binning of microsatellite allele lengths to overcome these problems and to facilitate high-throughput allele binning.

Availability:  www.evolution.unibas.ch/salzburger/software.htm

Contact:  michael.matschiner@unibas.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Repeated autologous bone marrow mononuclear cell therapy in patients with large myocardial infarction
Authors: Yao Kang , Huang Rongchong , Sun Aijun , Qian Juying , Liu Xuebo , Ge Lei , Zhang Yiqi , Zhang Shuning , Niu Yuhong , Wang Qibing , Zou Yunzeng , Ge Junbo
Published: May 2009

Aims

We sought to determine whether repeat administration of bone marrow mononuclear cells (BMC) can improve left ventricular function compared with a single infusion in patients with large acute myocardial infarction (AMI).

Methods and results

Thirty‐nine patients with a ST‐elevation AMI of the anterior wall and a significantly decreased left ventricular ejection fraction (LVEF 20–39%) were randomly assigned to three groups following primary percutaneous coronary intervention: Group A (n = 12) received a single intracoronary infusion of BMC (1.9 ± 1.2 × 108) at 3–7 days after AMI; Group B (n = 15) received BMC administration both at 3–7 days (2.0 ± 1.4 × 108) and at 3 months (2.1 ± 1.7 × 108); and the control group (CON, n = 12) received one placebo injection at 3–7 days. We noted no severe complications associated with the BMC transfer. The increase in LVEF evaluated by magnetic resonance imaging (MRI) after 12 months in Group B (11.7 ± 2.6%) was significantly greater than that in Group A (7.2 ± 1.6%, P < 0.001) or in CON (2.9 ± 2.0%, P < 0.001). Magnetic resonance imaging‐derived myocardial infarct size decreased significantly in Group B compared with Group A (11.3 ± 2.7% vs. 6.3 ± 1.6%, P < 0.001).

Conclusion

Data from this preliminary study suggest that repeated BMC administration might be a safe and feasible therapeutic strategy for patients with large AMI.
New basal eutherian mammal from the Early Cretaceous Jehol biota, Liaoning, China
Authors: Hu Yaoming , Meng Jin , Li Chuankui , Wang Yuanqing
Published: May 2009

A new genus and species of eutherian mammal,
Acristatherium yanensis
gen. et sp. nov., is described from the Early Cretaceous Jehol biota, China. The new taxon is based on a partial skull that is preserved in three dimensions from the Lujiatun bed of the Yixian Formation and dated 123.2±1.0 Ma. Its right upper and lower dentitions are nearly complete and it has a dental formula 4.1.5.3/3.1.5.3. The new mammal reveals several craniodental characteristics of Early Cretaceous eutherians previously unknown in fossil records of therians, such as a possible vestige of the septomaxilla. The craniodental features of the new taxon are compared with those of relevant Early Cretaceous eutherians and therians. Phylogenetic analyses based on a data matrix containing 70 taxa and 408 characters place
A. yanensis
as the most basal eutherian in the selected group. The morphological differences between
Acristatherium
and
Eomaia
indicate that eutherians already had a significant degree of generic diversification
ca
125 Ma.
Wolbachiaas populations within individual insects: causes and consequences of density variation in natural populations
Authors: Unckless Robert L. , Boelio Lisa M. , Herren Jeremy K. , Jaenike John
Published: May 2009

The population-level dynamics of maternally transmitted endosymbionts, including reproductive parasites, depends primarily on the fitness effects and transmission fidelity of these infections. Although experimental laboratory studies have shown that within-host endosymbiont density can affect both of these factors, the existence of such effects in natural populations has not yet been documented. Using quantitative PCR, we survey the density of male-killingWolbachiain natural populations ofDrosophila innubilafemales from the Chiricahua Mountains of Arizona. We find that there is substantial (20 000-fold) variation inWolbachiadensity among wild flies and that within-hostWolbachiadensity is positively correlated with both the efficacy of male killing and maternal transmission fidelity. MeanWolbachiadensity increases three- to five-fold from early to late in the season. This pattern suggests thatWolbachiadensity declines with fly age, a conclusion corroborated by a laboratory study ofWolbachiadensity as a function of age. Finally, we suggest three alternative hypotheses to account for the approximately lognormal distribution ofWolbachiadensity among wild flies.
Optimal level of inbreeding in the common lizard
Authors: Richard M. , Losdat S. , Lecomte J. , de Fraipont M. , Clobert J.
Published: May 2009

Mate choice with regard to genetic similarity has been rarely considered as a dynamic process. We examined this possibility in breeding populations of the common lizard (
Lacerta vivipara
) kept for several years in semi-natural conditions. We investigated whether they displayed a pattern of mate choice according to the genetic similarity and whether it was context-dependent. Mate choice depended on genetic similarity with the partner and also on age and condition. There was no systematic avoidance of inbreeding. Females of intermediate ages, more monogamous, did not mate with genetically similar partners, whereas younger and older females, more polyandrous, did but highest clutch proportions were associated with intermediate values of pair-relatedness. These results indicate dynamic mate choice, suggesting that individuals of different phenotypes select their partners in different ways according to their genetic similarity. We consider our results in the light of diverse and apparently contradictory theories concerning genetic compatibility, and particularly, optimal inbreeding and inclusive fitness.
Prenatal environmental effects match offspring begging to parental provisioning
Authors: Hinde Camilla A. , Buchanan Katherine L. , Kilner Rebecca M.
Published: May 2009

The solicitation behaviours performed by dependent young are under selection from the environment created by their parents, as well as wider ecological conditions. Here we show how mechanisms acting before hatching enable canary offspring to adapt their begging behaviour to a variable post-hatching world. Cross-fostering experiments revealed that canary nestling begging intensity is positively correlated with the provisioning level of their own parents (to foster chicks). When we experimentally increased food quality before and during egg laying, mothers showed higher faecal androgen levels and so did their nestlings, even when they were cross-fostered before hatching to be reared by foster mothers that had been exposed to a standard regime of food quality. Higher parental androgen levels were correlated with greater levels of post-hatching parental provisioning and (we have previously shown) increased faecal androgens in chicks were associated with greater begging intensity. We conclude that androgens mediate environmentally induced plasticity in the expression of both parental and offspring traits, which remain correlated as a result of prenatal effects, probably acting within the egg. Offspring can thus adapt their begging intensity to variable family and ecological environments.
Dynamics of seasonal outbreaks of black band disease in an assemblage of
Montipora
species at Pelorus Island (Great Barrier Reef, Australia)
Authors: Sato Yui , Bourne David G. , Willis Bette L.
Published: May 2009

Recurring summer outbreaks of black band disease (BBD) on an inshore reef in the central Great Barrier Reef (GBR) constitute the first recorded BBD epizootic in the region. In a 2.7 year study of 485 colonies of
Montipora
species, BBD affected up to 10 per cent of colonies in the assemblage. Mean maximum abundance of BBD reached 16±6 colonies per 100 m
2
(
n
=3 quadrats, each 100 m
2
) in summer, and decreased to 0–1 colony per 100 m
2
in winter. On average, BBD lesions caused 40 per cent tissue loss and 5 per cent of infections led to whole colony mortality. BBD reappearance on previously infected colonies and continuous tissue loss after the BBD signs had disappeared suggest that the disease impacts are of longer duration than indicated by the presence of characteristic signs. Rates of new infections and linear progression of lesions were both positively correlated with seasonal fluctuations in sea water temperatures and light, suggesting that seasonal increases in these environmental parameters promote virulence of the disease. Overall, the impacts of BBD are greater than previously reported on the GBR and likely to escalate with ocean warming.
SNP detection for massively parallel whole-genome resequencing
Authors: Li Ruiqiang , Li Yingrui , Fang Xiaodong , Yang Huanming , Wang Jian , Kristiansen Karsten , Wang Jun
Published: May 2009

Next-generation massively parallel sequencing technologies provide ultrahigh throughput at two orders of magnitude lower unit cost than capillary Sanger sequencing technology. One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole-genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All of this information was integrated into a single quality score for each base under Bayesian theory to measure the accuracy of consensus calling. We tested this methodology using a large-scale human resequencing data set of 36× coverage and assembled a high-quality nonrepetitive consensus sequence for 92.25% of the diploid autosomes and 88.07% of the haploid X chromosome. Comparison of the consensus sequence with Illumina human 1M BeadChip genotyped alleles from the same DNA sample showed that 98.6% of the 37,933 genotyped alleles on the X chromosome and 98% of 999,981 genotyped alleles on autosomes were covered at 99.97% and 99.84% consistency, respectively. At a low sequencing depth, we used prior probability of dbSNP alleles and were able to improve coverage of the dbSNP sites significantly as compared to that obtained using a nonimputation model. Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth.
Large-scale mRNA sequencing determines global regulation of RNA editing during brain development
Authors: Wahlstedt Helene , Daniel Chammiran , Ensterö Mats , Öhman Marie
Published: May 2009

RNA editing by adenosine deamination has been shown to generate multiple isoforms of several neural receptors, often with profound effects on receptor function. However, little is known about the regulation of editing activity during development. We have developed a large-scale RNA sequencing protocol to determine adenosine-to-inosine (A-to-I) editing frequencies in the coding region of genes in the mammalian brain. Using the 454 Life Sciences (Roche) Amplicon Sequencing technology, we were able to determine even low levels of editing with high accuracy. The efficiency of editing for 28 different sites was analyzed during the development of the mouse brain from embryogenesis to adulthood. We show that, with few exceptions, the editing efficiency is low during embryogenesis, increasing gradually at different rates up to the adult mouse. The variation in editing gave receptors like HTR2C and GABAA (gamma-aminobutyric acid type A) a different set of protein isoforms during development from those in the adult animal. Furthermore, we show that this regulation of editing activity cannot be explained by an altered expression of the ADAR proteins but, rather, by the presence of a regulatory network that controls the editing activity during development.
Oil Bodies and Oleosins in Physcomitrella Possess Characteristics Representative of Early Trends in Evolution
Authors: Huang Chien-Yu , Chung Chun-I , Lin Yao-Cheng , Hsing Yue-Ie Caroline , Huang Anthony H.C.
Published: May 2009

Searches of sequenced genomes of diverse organisms revealed that the moss Physcomitrella patens is the most primitive organism possessing oleosin genes. Microscopy examination of Physcomitrella revealed that oil bodies (OBs) were abundant in the photosynthetic vegetative gametophyte and the reproductive spore. Chromatography illustrated the neutral lipids in OBs isolated from the gametophyte to be largely steryl esters and triacylglycerols, and SDS-PAGE showed the major proteins to be oleosins. Reverse transcription-PCR revealed the expression of all three oleosin genes to be tissue specific. This tissue specificity was greatly altered via alternative splicing, a control mechanism of oleosin gene expression unknown in higher plants. During the production of sex organs at the tips of gametophyte branches, the number of OBs in the top gametophyte tissue decreased concomitant with increases in the number of peroxisomes and level of transcripts encoding the glyoxylate cycle enzymes; thus, the OBs are food reserves for gluconeogenesis. In spores during germination, peroxisomes adjacent to OBs, along with transcripts encoding the glyoxylate cycle enzymes, appeared; thus, the spore OBs are food reserves for gluconeogenesis and equivalent to seed OBs. The one-cell-layer gametophyte could be observed easily with confocal microscopy for the subcellular OBs and other structures. Transient expression of various gene constructs transformed into gametophyte cells revealed that all OBs were linked to the endoplasmic reticulum (ER), that oleosins were synthesized in extended regions of the ER, and that two different oleosins were colocated in all OBs.
Nerve growth factor accelerates wound healing in diabetic mice
Authors: Muangman Pornprom , Muffley Lara A. , Anthony Joanne P. , Spenny Michelle L. , Underwood Robert A. , Olerud John E. , Gibran Nicole S.
Published: May 2009

Patients with diabetic neuropathy have reduced numbers of cutaneous nerves, which may contribute to an increased incidence of nonhealing wounds. Nerve growth factor (NGF) has been reported to augment wound closure. We hypothesized that topical 2.5S NGF, a biologically active subunit of the NGF polymer, would accelerate wound repair, augment nerve regeneration, and increase inflammation in excisional wounds in diabetic mice. A full‐thickness 6‐mm punch biopsy wound was created on the dorsum of C57BL/6 J‐m + Leprdb mice (db/db) and heterozygous (db/–) littermates and treated daily with normal saline or 2.5S NGF (1 µg/day or 10 µg/day) on post‐injury days 0–6. Time to closure, wound epithelialization, and degree of inflammation were compared using a Student's t‐test. Color subtractive‐computer‐assisted image analysis was used to quantify immunolocalized nerves in wounds. Non‐overlapping (20×) digital images of the wound were analyzed for nerve profile counts, area density (number of protein gene product 9.5 positive profiles per unit dermal area) and area fraction (protein gene product 9.5 positive area per unit dermal area). Healing times in db/db mice decreased from 30 days in normal saline‐treated mice to 26 days in mice treated with 1 µg/day NGF (p < 0.05) and 24 days in mice treated with 10 µg/day NGF (p < 0.02). A similar trend in db/– mice was not significant. NGF treatment augmented epithelialization in the db/db mice (p < 0.05). Histological evaluation of inflammation in healed wounds showed no statistical difference between treatment groups. Total nerve number, area density, and area fraction were increased in NGF‐treated wounds at 14, 21, and 35 days (p < 0.05). The 2.5 NGF subunit may improve wound closure kinetics by promoting epithelialization and nerve regeneration. Further studies to determine the role of nerves in wound repair are warranted.
Down‐regulation of connective tissue growth factor and type I collagen mRNA expression by connective tissue growth factor antisense oligonucleotide during experimental liver fibrosis
Authors: Uchio Kozue , Graham Mark , Dean Nicholas M. , Rosenbaum Jean , Desmoulière Alexis
Published: May 2009

Transforming growth factor (TGF)‐β1 is a major mediator of liver fibrosis. Connective tissue growth factor (CTGF) mediates TGF‐β1 pro‐fibrogenic effects in vitro, but its in vivo role is unknown. Both TGF‐β1 and CTGF are overexpressed in hepatic stellate cells during liver fibrosis. We have used antisense oligonucleotides to examine the role of CTGF in carbon tetrachloride‐induced liver fibrosis in mice. Mice received carbon tetrachloride together with CTGF or TGF‐β1 antisense oligonucleotides for 2 weeks (preventive model), or carbon tetrachloride for 2 weeks followed by carbon tetrachloride and oligonucleotides for 2 more weeks (curative model). In both models, CTGF and TGF‐β1 oligonucleotides decreased by more than 50 percent the mRNA expression of their targets. Type I collagen mRNA was also decreased by about 40 percent in the preventive experiment. Tissue inhibitor of matrix metalloproteinase‐1 mRNA expression and fibrotic deposition evaluated by Sirius red staining were not modified in any group. In summary, our results suggest that hepatic stellate cells can be targeted in vivo with oligonucleotides, and that reducing CTGF levels can lead to a decrease in fibrogenesis as shown by the reduction in type I collagen expression. The lack of effect on fibrosis may be due to the persistence of high tissue inhibitor of matrix metalloproteinase‐1 expression.
Combined administration of basic fibroblast growth factor protein and the hepatocyte growth factor gene enhances the regeneration of dermis in acute incisional wounds
Authors: Ono Ichiro , Yamashita Toshiharu , Hida Tokimasa , Jin Hai‐Ying , Ito Yoshinori , Hamada Hirobumi , Akasaka Yoshikiyo , Ishii Toshiharu , Jimbow Kowichi
Published: May 2009

Hepatocyte growth factor (HGF) is a ligand for the c‐Met receptor tyrosine kinase. This study was aimed to characterize the role of the HGF gene combined with basic fibroblast growth factor (bFGF) protein in wound healing by administering both of them locally to acute incisional skin wounds created on the backs of rats. The bFGF protein and the HGF gene were administered intradermally after incisional surgery. Apoptotic cells in wound lesions were identified by the terminal deoxynucleotide transferase‐mediated nick‐end labeling method, as well as by immunological detection of active caspase‐3. While there was almost complete suppression of apoptosis with well‐organized wound healing in animals treated with the HGF gene, the combination of bFGF protein and the HGF gene paradoxically resulted in less scarring along with the promotion of apoptosis. Histopathological examination revealed that scar formation was least apparent in rats treated with both bFGF and the HGF gene compared with controls or those treated with the bFGF or the HGF gene alone. It is thought that the combined administration of bFGF and the HGF gene immediately after skin incision may make the healing process occur closer to tissue regeneration through the induction of apoptosis, which occurred 1 week after surgery. HGF supplementation through gene therapy combined with bFGF protein may be an effective strategy for treating wounds, as it increases the apparent regeneration of the dermis to allow for “scarless wound healing.”
Liposome‐mediated transfer of vascular endothelial growth factor cDNA augments survival of random‐pattern skin flaps in the rat
Authors: Liu Paul Y. , Tong Wenjing , Liu Kan , Han Sang Hoon , Wang Xiao Tian , Badiavas Evangelos , Rieger‐Christ Kimberly , Summerhayes Ian
Published: May 2009

Tissue engineering is an application for gene therapy that is in its infancy. We show that simple liposomal‐mediated gene transfer could result in a potentially useful biological effect in the field of wound healing. cDNA encoding the 165 amino acid form of vascular endothelial growth factor complexed to commercially available liposomes was injected into rat skin 1 week before raising a random pattern 3 × 10 cm flap. The flap survival was enhanced by 14 percent, and was accomplished without accessing the arterial inflow of the territory. These results were statistically significant (p < 0.002) and reproducible. No adverse effects were seen. Histological analysis of the angiogenesis localized much of the new vessel formation to the area around the hair follicles. Polymerase chain reaction amplification of extracted flap tissue confirmed the presence of the transgene.
P‐II‐03  Effect of Platelet Derived Wound Healing Factor (PDWHF) on the Angiogenesis in the Cases of Artificial Dermis Grafts
Authors: Kazutaka Soejima , Chen Xin , Masayuki Yamato , Teruo Okano , Motohiro Nozaki
Published: May 2009

Aim: The effect of platelet derived wound healing factor (PDWHF) with or without cultured cells on angiogenesis in the cases of artificial dermis grafts was investigated.

Methods: Wistar strain rats were used for this study. The PDWHF was prepared from platelets. The endothelial cells and fibroblasts were prepared from thoracic aorta and back skin respectively. Then 2 experimental models were designed. 1) Full‐thickness wounds were created on back of the animals. Artificial dermis (TERUDERMIS®, TERUMO Co, Japan) were grafted to the wounds. 2) Femoral artery and vein were isolated as a vascular pedicle and wrapped with a folded sheet of the AD (1 × 2 cm). Prior to AD grafts, the AD were treated with the PDWHF and/or cultured cells.

Results: The combination use of the PDWHF and cultured cells showed best angiogenesis in both experimental models.

Conclusions: The result of the present study revealed that treatment with PDWHF combined with cultured cells accelerate the wound angiogenesis.
Activation of an estrogen/estrogen receptor signaling by BIG3 through its inhibitory effect on nuclear transport of PHB2/REA in breast cancer
Authors: Kim Jung‐Won , Akiyama Miki , Park Jae‐Hyun , Lin Meng‐Lay , Shimo Arata , Ueki Tomomi , Daigo Yataro , Tsunoda Tatsuhiko , Nishidate Toshihiko , Nakamura Yusuke , Katagiri Toyomasa
Published: May 2009

Breast cancer is known to be a hormone‐dependent disease, and estrogens through an interaction with estrogen receptor (ER) enhance the proliferative and metastatic activity of breast tumor cells. Here we show a critical role of transactivation of BIG3, brefeldin A‐inhibited guanine nucleotide‐exchange protein 3, in activation of the estrogen/ER signaling in breast cancer cells. Knocking‐down of BIG3 expression with small‐interfering RNA (siRNA) drastically suppressed the growth of breast cancer cells. Subsequent coimmunoprecipitation and immunoblotting assays revealed an interaction of BIG3 with prohibitin 2/repressor of estrogen receptor activity (PHB2/REA). When BIG3 was absent, stimulation of estradiol caused the translocation of PHB2/REA to the nucleus, enhanced the interaction of PHB2/REA and ERα, and resulted in suppression of the ERα transcriptional activity. On the other hand, when BIG3 was present, BIG3 trapped PHB2/REA in the cytoplasm and inhibited its nuclear translocation, and caused enhancement of ERα transcriptional activity. Our results imply that BIG3 overexpression is one of the important mechanisms causing the activation of the estrogen/ERα signaling pathway in the hormone‐related growth of breast cancer cells. (Cancer Sci 2009)
PDCD4 inhibits the malignant phenotype of ovarian cancer cells
Authors: Wei Zeng‐Tao , Zhang Xia , Wang Xiao‐Yan , Gao Fei , Zhou Cheng‐Jun , Zhu Fa‐Liang , Wang Qun , Gao Qi , Ma Chun‐Hong , Sun Wen‐Sheng , Fu Qing‐Zhao , Chen You‐Hai H. , Zhang Li‐Ning
Published: May 2009

Programmed cell death 4 (PDCD4) is a newly identified tumor suppressor that can inhibit activator protein (AP)‐1 activation and protein translation. Our previous studies indicate that lost or reduced PDCD4 expression is associated with the progression of ovarian carcinoma. However, direct evidence that PDCD4 inhibits malignant phenotype of human cancer cells is limited. In the present study, we found that PDCD4 expression in ovarian cancer cell lines (SKOV3, 3AO, and CAOV3) inhibited significantly their proliferation and cell cycle progression, and induced apoptosis. More importantly, up‐regulation of PDCD4 expression decreased the colony‐forming capacity of ovarian cancer cells in vitro and tumorigenic capacity in mice. These results demonstrate that PDCD4 can suppress the malignant phenotype of ovarian cancer cells, and may represent a novel therapeutic target for the treatment of ovarian cancer. (Cancer Sci 2009)
Cancer stem cell‐like SP cells have a high adhesion ability to the peritoneum in gastric carcinoma
Authors: Nishii Takafumi , Yashiro Masakazu , Shinto Osamu , Sawada Tetsuji , Ohira Masaichi , Hirakawa Kosei
Published: May 2009

Cancer stem cells (CSCs) are considered to be responsible for cancer metastasis, but the evidence to conclusively prove this hypothesis remains uncertain. The side population (SP), as evaluated by a flow cytometric analysis using Hoechst 33342, has been known as CSC‐rich population. The aim of this study was to clarify the characterization of the SP cells in peritoneal metastasis of gastric carcinoma. Gastric cancer cell lines OCUM‐2M, OCUM‐2D, and OCUM‐2MD3 (a daughter cell line with high potential for peritoneal metastasis) were used. We isolated SP cells from OCUM‐2M and OCUM‐2D using flow cytometry. Serial sorting was performed three times to enrich SP cells, and they were designated as OCUM‐2M/SP and OCUM‐2D/SP cells. Flow cytometric analysis showed 0.46%, 0.29%, 5.24%, 6.49%, and 11.3% of the SP cells to be found in OCUM‐2M, OCUM‐2D, OCUM‐2MD3, OCUM‐2M/SP, and OCUM‐2D/SP cells, respectively. The intraperitoneal inoculation of SP cells and OCUM‐2MD3 cells produced peritoneal metastasis, but parent cells did not. The adhesion ability of SP and OCUM‐2MD3 cells was significantly high in comparison to that of parent cells. The expression level of adhesion molecules α2‐, α5‐, β3‐, and β5‐integrin, and CD44, was high in SP cells compared to parent cells. The expression of stemness markers, Oct3/4 and Sox2, increased in the SP‐cell‐injected tumors. These findings suggested that CSC‐like SP cells expressing α2‐, α5‐, β3‐, and β5‐integrin, and CD44, may play an important role for peritoneal metastasis in gastric carcinoma. Oct3/4 and Sox2 may be associated with CSC in gastric cancer. (Cancer Sci 2009)
Dynamics in the tomato root transcriptome on infection with the potato cyst nematode Globodera rostochiensis
Authors: SWIECICKA MAGDALENA , FILIPECKI MARCIN , LONT DIEUWERTJE , VAN VLIET JOKE , QIN LING , GOVERSE ASKA , BAKKER JAAP , HELDER JOHANNES
Published: May 2009

Plant parasitic nematodes infect roots and trigger the formation of specialized feeding sites by substantial reprogramming of the developmental process of root cells. In this article, we describe the dynamic changes in the tomato root transcriptome during early interactions with the potato cyst nematode Globodera rostochiensis. Using amplified fragment length polymorphism‐based mRNA fingerprinting (cDNA‐AFLP), we monitored 17 600 transcript‐derived fragments (TDFs) in infected and uninfected tomato roots, 1–14 days after inoculation with nematode larvae. Six hundred and twenty‐four TDFs (3.5%) showed significant differential expression on nematode infection. We employed GenEST, a computer program which links gene expression profiles generated by cDNA‐AFLP and databases of cDNA sequences, to identify 135 tomato sequences. These sequences were grouped into eight functional categories based on the presence of genes involved in hormone regulation, plant pathogen defence response, cell cycle and cytoskeleton regulation, cell wall modification, cellular signalling, transcriptional regulation, primary metabolism and allocation. The presence of unclassified genes was also taken into consideration. This article describes the responsiveness of numerous tomato genes hitherto uncharacterized during infection with endoparasitic cyst nematodes. The analysis of transcriptome profiles allowed the sequential order of expression to be dissected for many groups of genes and the genes to be connected with the biological processes involved in compatible interactions between the plant and nematode.
Definition of progression risk based on combinations of cellular and molecular markers in patients with Binet stage A chronic lymphocytic leukaemia
Authors: Morabito Fortunato , Cutrona Giovanna , Gentile Massimo , Matis Serena , Todoerti Katia , Colombo Monica , Sonaglio Claudia , Fabris Sonia , Reverberi Daniele , Megna Mauro , Spriano Mauro , Lucia Eugenio , Rossi Edoardo , Callea Vincenzo , Mazzone Carla , Festini Gianluca , Zupo Simonetta , Molica Stefano , Neri Antonino , Ferrarini Manlio
Published: May 2009

IGHV mutational status and ZAP‐70 or CD38 expression correlate with clinical course in B‐cell chronic lymphocytic leukaemia (CLL). The three markers may be discordant in the single case and there is no consensus on their combined use in clinical practise. This multicenter study investigated this issue. Two‐hundred and sixty‐two Binet stage A patients were studied for the three markers. Sixty patients were profiled with HG‐U133A gene expression chips. Disease progression was determined by time from diagnosis to treatment (TTT). The probability of being treatment‐free at 3 years was significantly shorter in patients with unmutated IGHV genes (IGHVunmut 66% vs. 93%, chi square of log‐rank = 30, P < 0·0001), ZAP‐70 positive (ZAP‐70pos 73% vs. 96%, chi square of log‐rank = 8·2, P = 0·004) or CD38‐positive cells (CD38pos 68% vs. 91%, chi square of log‐rank = 21, P < 0·0001). Cox multivariate regression analysis showed that the three markers had an independent predictive value for TTT of similar power. A prognostic system based on presence of none (low‐risk), one (intermediate‐risk) or two or three (high‐risk) markers was generated. Based on such criteria, 56%, 23% and 21% of cases were clustered in low (HR = 1), intermediate [HR = 2·8, 95% confidence interval (CI) 2·4–5·8] and high‐risk group (HR = 8·0, 95% CI 3·9–16·2). Specific transcriptional patterns were significantly associated with risk groups.