bluuebunny/crossref_metadata_2025 huggingface dataset:
Yam (Dioscorea) Husbandry: Cultivating Yams in the Field or Greenhouse
Authors: Mignouna Hodeba D. , Abang Mathew M. , Asiedu Robert , Geeta R.
Published: November 2009

INTRODUCTION

This protocol describes how to cultivate yams (Dioscorea) in the field or greenhouse. It refers especially to the tropical food species but it will also work for temperate species. The tropical food species of Dioscorea grow in warm, sunny climates with temperatures between 25ºC and 30ºC. Short days of 10-11 h result in tuber formation, while days longer than 12 h favor vine growth. Yams require deep, loose, textured loamy soil that is rich in organic matter. They are best planted at the beginning of the rainy season. Mulch around the planted sets protects them from excessive heat and desiccation, especially in areas with hot temperatures and dry weather. It also adds organic matter to the soil, prevents soil erosion, preserves water in the soil, and increases microbial activity in the soil. Yams do not tolerate waterlogged conditions. It is important to stake the plants to allow full exposure of their leaves to light for photosynthetic activity and to reduce disease.
Post-Flask Management of Yam (Dioscorea) Plantlets
Authors: Mignouna Hodeba D. , Abang Mathew M. , Asiedu Robert , Geeta R.
Published: November 2009

INTRODUCTION

This protocol describes how to harden or acclimatize tissue culture-derived yam (Dioscorea) plantlets before transplanting them in the soil. Briefly, the plantlets are first put in pots with a vermiculite and peat moss mixture, and the pots are placed in a humidity chamber, where they are sprayed and watered daily. After 2 wk, the plants are transplanted to pots or plastic bags with ordinary or sterile soil and watered daily. After another 2 wk, they are transplanted into the field.
Producing Yam (Dioscorea) Seeds through Controlled Crosses
Authors: Mignouna Hodeba D. , Abang Mathew M. , Asiedu Robert , Geeta R.
Published: November 2009

INTRODUCTION

This protocol describes how to produce yam (Dioscorea) seeds through controlled pollination of flowers on female plants. Pollination by flower thrips takes place naturally in normal yam-growing environments in the presence of flowering male and female genotypes, although it is not efficient. This protocol leads to the production of hybrid seeds of known parentage for genetic studies and use in breeding programs.
Nuclear Run-On Assay: Figure 1.
Authors: Smale Stephen T.
Published: November 2009

INTRODUCTION

The nuclear run-on assay was developed as a method for establishing that the transcription initiation rate contributes to the regulated expression of mammalian genes. The difference between monitoring gene expression by the nuclear run-on assay versus most other assays is that the nuclear run-on assay provides a measure of the frequency of transcription initiation and is largely independent of the effects of RNA stability. It can also be used to determine whether polymerase pausing or attenuation contributes to gene regulation. Briefly, the nuclear run-on assay begins with samples of cells that contain different steady-state amounts of the mRNA or protein of interest. The cells are chilled, and the plasmid membranes are permeabilized or lysed. These steps result in polymerase pausing. The nuclei are then incubated for a short time at 37°C in the presence of nucleoside triphosphates (NTPs) and radiolabeled uridine 5′-triphosphate (UTP). New transcripts are not initiated during this incubation, but the radiolabeled nucleotide becomes incorporated into transcripts that were being synthesized when the cells were first chilled and lysed. The number of nascent transcripts on the gene at the time of chilling is thought to be proportional to the frequency of transcription initiation. To determine the relative number of nascent transcripts in each sample, the radiolabeled RNA is purified and hybridized to a membrane containing immobilized DNA from the gene of interest. The amount of radioactivity that hybridizes to the membrane is approximately proportional to the number of nascent transcripts.
Assessing Human Variation Data for Signatures of Natural Selection
Authors: Bamshad Mike , Stephens J. Claiborne
Published: November 2009

INTRODUCTION

In this article, we highlight some of the different types of natural selection, their effects on patterns of DNA variation, and some of the statistical tests that are commonly used to detect such effects. We also explain some of the relative strengths and weaknesses of different strategies that can be used to detect signatures of natural selection at individual loci. These strategies are illustrated by their application to empirical data from gene variants that are often associated with differences in disease susceptibility. We briefly outline some of the methods proposed to scan the genome for evidence of selection. Finally, we discuss some of the problems associated with identifying signatures of selection and with making inferences about the nature of the selective process.
Laboratory Methods for High-Throughput Genotyping
Authors: Edenberg Howard J. , Liu Yunlong
Published: November 2009

INTRODUCTION

The genetics of complex diseases has been given a tremendous boost in recent years by the introduction of high-throughput laboratory methods that make it possible to approach larger questions in larger populations and to cover the genome more comprehensively. The ability to determine genotypes of many individuals accurately and efficiently has allowed genetic studies that cover more of the variation within individual genes, instead of focusing only on one or a few coding variants, and to do so in study samples of reasonable power. Chip-based genotyping assays, combined with knowledge of the patterns of coinheritance of markers (linkage disequilibrium [LD]), have stimulated genome-wide association studies (GWAS) of complex diseases. Recent successes of GWAS in identifying specific genes that affect risk for common diseases are dramatic illustrations of how improved technology can lead to scientific breakthroughs. A key issue in high-throughput genotyping is to choose the appropriate technology for your goals and for the stage of your experiment, being cognizant of your sample numbers and resources. This article introduces some of the commonly used methods of high-throughput single-nucleotide polymorphism (SNP) genotyping for different stages of genetic studies and briefly reviews some of the high-throughput sequencing methods just coming into use. It also mentions some recent developments in “next-generation” sequencing that will enable other kinds of studies. This article is not intended to be comprehensive, and because technology in this area is rapidly changing, our comments should be taken as a starting point for further investigation.
Laying the foundations for a new classification of Agaonidae (Hymenoptera: Chalcidoidea), a multilocus phylogenetic approach
Authors: Cruaud Astrid , Jabbour‐Zahab Roula , Genson Gwenaëlle , Cruaud Corinne , Couloux Arnaud , Kjellberg Finn , Van Noort Simon , Rasplus Jean‐Yves
Published: November 2009

A phylogeny of the Agaonidae (Chalcidoidea) in their restricted sense, pollinators ofFicusspecies (Moraceae), is estimated using 4182 nucleotides from six genes, obtained from 101 species representing 19 of the 20 recognized genera, and four outgroups. Data analysed by parsimony and Bayesian inference methods demonstrate that Agaonidae are monophyletic and that the previous classification is not supported. Agaonidae are partitioned into four groups: (i)Tetrapus, (ii)Ceratosolen + Kradibia, (iii) someBlastophaga + Wiebesiaspecies, and (iv) all genera associated with monoecious figs and a fewBlastophagaandWiebesia. The latter group is subdivided into subgroups: (i)Pleistodontes, (ii)Blastophaga psenesand neocaledonianDolichoris, (iii) someBlastophagaandWiebesiaspecies, and (iv)Platyscapa, all afrotropical genera and all genera associated with sectionConosycea. Eleven genera were recovered as monophyletic, six were para‐ or polyphyletic, and two cannot be tested with our data set. Based on our phylogeny we propose a new classification for the Agaonidae. Two new subfamilies are proposed: Tetrapusiinae for the genusTetrapus, and Kradibiinae forCeratosolen + Kradibia.Liporrhopalumis synonymized withKradibiaand the subgenusValisiaofBlastophagais elevated to generic rank. These changes resulted in 36 new combinations. Finally, we discuss the hypothesis of co‐speciation between the pollinators and their host species by comparing the two phylogenies.

 © The Willi Hennig Society 2009.
Insensitive blueberries: a total‐evidence analysis of Disterigma s.l. (Ericaceae) exploring transformation costs
Authors: Pedraza‐Peñalosa Paola
Published: November 2009

Disterigma sensu lato (s.l.) is a polyphyletic genus of neotropical blueberries that comprises 37 species found in Central and South America, mostly in Andean cloud forests and páramos. The present phylogenetic analysis, based on molecular and morphological data for 84% of the species of Disterigma s.l., addressed the monophyly of the genus and identified the putative morphological synapomorphies of the main clades. The sensitivity of the phylogenetic hypotheses to the choice of analytical parameters was addressed in detail, by varying all possible parameters and applying different treatments for indel coding. A total of 29 transformation cost matrices were investigated and all these analyses were performed in POY 4, using direct optimization. A diagnosable Disterigma sensu stricto (s.s.) clade was recovered in all analyses, despite changes in the transformation costs. Additionally, none of the analyses refuted the segregation of D. trimerum, D. ulei, D. pentandrum, D. rimbachii, and D. bracteatum from Disterigma s.s. Although measurements of congruence are used to choose among alternative analytical parameter sets, the behaviour of the RILD index (rescaled incongruence length difference) in this study suggested that it may not be a good measure of congruence and that further studies are necessary to better understand its performance.

 © The Willi Hennig Society 2009.
Evaluating paediatric brain injury services in NSW
Authors: Badge H. , Hancock J. , Waugh M.‐C.
Published: November 2009

Background  Rehabilitation professionals strive to provide high‐quality evidence‐based services for children. Developing systems to measure and monitor the benefits of our services, and health outcomes for children is complex and challenging. The Community Outcome Project aims to introduce systematic outcome measurement across the network of paediatric community‐based brain injury services within the New South Wales Brain Injury Rehabilitation Program (BIRP) to support clinical practice and service evaluation.

Methods  A literature review informed the development of the evaluative framework and identified available paediatric outcome measures which may be appropriate. Extensive consultation with clinicians supported project planning and identified clinical priorities that the outcome measures needed to capture. Outcome measures were shortlisted by matching them to identified clinical priorities, and then trialled in clinical practice. Qualitative feedback regarding clinical utility and feasibility was obtained from clinical staff. The process has utilized change management strategies to ensure the success of the project and keep staff engaged.

Results  The process identified the three main clinical priorities for outcome measurement – family functioning, school performance and participation. Three outcome measures were chosen for the pilot project that is currently underway. They are Family Burden of Injury Interview, Academic Competence and Evaluation Scales and Child and Adolescent Scale of Participation. Plans for analyses of outcome data within the paediatric BIRP services are discussed.

Conclusions  Extensive preparation is required to optimize staff engagement in a project that systematically introduces outcome measures that are useful to clinicians, clients and service providers. Managing the change required is a key focus of the project. Benefits and costs to clinicians and services will be discussed.
Surfactant protein D inhibits mite‐induced alveolar macrophage and dendritic cell activations through TLR signalling and DC‐SIGN expression
Authors: Liu C‐F , Rivere M. , Huang H‐J , Puzo G. , Wang J‐Y
Published: November 2009

Background
Surfactant protein D (SP‐D), a secreted pattern recognition molecule associated with pulmonary innate immunity, has been shown to mediate the clearance of pathogens in multiple ways. However, how SP‐D interacts with alveolar macrophages (AMs) and dendritic cells (DCs) during allergen exposure remains unclear.

Objective
This study was performed to characterize the immunomodulatory effects of SP‐D on mite allergen (Dermatophagoides pteronyssinus, Der p)‐induced inflammatory signalling in AMs and DCs.

Methods
Murine AM, alveolar macrophage cell line derived from BALB/c mice (MH‐S cells), and human monocyte‐derived dendritic cells (MDDC) were used as model systems. The production of nitric oxide (NO) and TNF‐α, expression of surface Toll‐like receptors (TLRs), and expression of the C‐type lectin receptor known as dendritic cell (DC)‐specific ICAM‐grabbing non‐integrin (DC‐SIGN) were measured as a function of pretreatment with SP‐D and subsequent exposure to Der p. Der p‐dependent cellular activations that were modified by SP‐D in these model systems were then identified.

Results
Pretreatment of MH‐S cells with SP‐D reduced Der p‐dependent production of NO, TNF‐α, and the downstream activations of IL‐1 receptor‐associated kinase, mitogen activated protein kinase (MAPK) kinase, and nuclear factor‐κB. SP‐D interacted with CD14 such that CD14 binding to Der p was inhibited and Der p‐induced signalling via TLRs was blocked. DC‐SIGN expression was suppressed by Der p in MH‐S and MDDC; this down‐regulation of DC‐SIGN expression was prevented by pretreatment with SP‐D.

Conclusions
These results indicated that the inhibition of Der p‐induced activation of MH‐S and MDDC by SP‐D is mediated through suppression of the CD14/TLR signalling pathway and maintenance of DC‐SIGN expression, which may protect allergen‐induced airway inflammation.

Cite this as: C‐F Liu, M. Rivere, H‐J Huang, G. Puzo and J‐Y Wang, Clinical & Experimental Allergy, 2010 (40) 111–122.
Tree transpiration varies spatially in response to atmospheric but not edaphic conditions
Authors: Traver Elizabeth , Ewers Brent E. , Mackay David S. , Loranty Michael M.
Published: November 2009

1. Measuring transpiration simultaneously in time and space can establish a better understanding of how to mechanistically scale spatiotemporal values.

2. This study tested the following predictions to falsify a tree hydraulic hypothesis of spatial variation in transpiration: (i) stands with larger trees will a have longer range and greater sill and nugget at a given vapour pressure deficit (D); (ii) the range, sill and nugget will decline faster with increasingDwith larger trees; and (iii) soil moisture, texture and/or N levels will be correlated with transpiration.

3. We used cyclic sampling to efficiently collect spatial sap flux data from 144 trees in two forested stands in northern Wisconsin: an Aspen‐dominated stand with small trees and a Maple–Pine‐dominated stand with larger trees.

4. In the Maple stand, the range of spatial autocorrelation in half‐hourly transpiration dropped from 80 to 20 m with increasedD, whereas in the Aspen stand the range dropped from 55 to 35 m with a similar increase inD.

5. Differences in the range of spatial autocorrelation at a givenDwere driven by sapwood area, which is a function of tree size.

6. These results show that species and tree size as well as individual tree hydraulics drive spatial variability in transpiration with little additional variation explained by the measured edaphic conditions.

7. Scaling from individual tree transpiration to the landscape in time and space should incorporate atmospheric drivers in time and investigate other potential drivers of tree size in space such as light competition.
Male moths provide pollination benefits in the Silene latifolia–Hadena bicruris nursery pollination system
Authors: Labouche Anne‐Marie , Bernasconi Giorgina
Published: November 2009

1. Evolutionary conflicts of interest underlie mutualisms, including plant/pollinator interactions. This is particularly evident in ‘nursery pollination’, in which the pollinators lay eggs inside the flowers and the offspring of the pollinator consume the developing seeds. Low benefit (pollination service) to cost (seed predation) ratios could destabilize such associations towards parasitism.

2. Although in most of the well‐known cases pollen transfer is associated with oviposition, in some systems the males of the seed predator may contribute to pollination, affecting the strength and outcome of the interaction between the plant and their ovipositing pollinators. In addition, in dioecious species male and female plants differ in the direct costs of seed predation and benefits of attracting pollinators, which may lead to sex‐specific strategies.

3. We investigated whether pollinator and plant sex affect pollination in the interaction between dioecious plant Silene latifolia and its nursery pollinator, Hadena bicruris (Noctuidae).

4. Data on visitation behaviour and pollination efficiency in experimental plant patches demonstrate that (i) male moths are equally efficient pollinators as female moths, leading to fruit initiation in around 80% of visits and to fertilization of around 45% of the ovules in one visit; (ii) female and male moths do not preferentially visit flowers of one sex; and (iii) feeding behaviour is sufficient to ensure pollen transfer. However, female moths visited significantly more flowers than male moths.

5. Altogether this suggests that both moth sexes provide a pollination benefit to the plant with no differences in pollination efficiency but that female moths, before seed predation costs are accounted for, seem to provide greater benefits owing to their increased activity. That male moths contribute to seed production likely decreases the plant’s dependency on ovipositing moths for pollination.
Staff attributions about challenging behaviours of people with intellectual disabilities and transactional stress process: a qualitative study
Authors: Cudré‐Mauroux A.
Published: November 2009

Background  Staff explanations about challenging behaviours of people with intellectual disabilities are purported to play a significant role in the way they respond to them. Despite attempts made in research to understand the mechanisms of causality, a lack of association between attributions, emotions and behaviours is reported. This study investigates these relationships within a broader framework including attributions in the transactional stress model of Lazarus and Folkman.

Method  A qualitative design has been selected; semi‐structured interview format was used in order to investigate implication of attributions in stress regarding Weiner's model of helping behaviour. A case study method has been adopted to allow consideration of ecological data, a case study representing a special encounter with a challenging behaviour. Categorical analysis was conducted.

Results  The results suggest three main issues. First, it appears that Weiner's model is too restrictive in order to explain the complexity of contextualised encounters. Second, a need to differentiate types of attributions within a temporal perspective is highlighted. Finally, consideration of the coping role of attributions is suggested.

Conclusions  A need to extent the research concerning attribution is suggested. The insertion of research into ecological contexts and the introduction of coping concept regarding staff attributions of challenging behaviours would allow a broader view of the role of attributions.
Home literacy environment of pre‐school children with intellectual disabilities
Authors: Van Der Schuit M. , Peeters M. , Segers E. , Van Balkom H. , Verhoeven L.
Published: November 2009

Background  For pre‐school children, the home literacy environment (HLE) plays an important role in the development of language and literacy skills. As there is little known about the HLE of children with intellectual disabilities (ID), the aim of the present study was to investigate the HLE of children with ID in comparison with children without disabilities.

Method  Parent questionnaires concerning aspects of the HLE were used to investigate differences between 48 children with ID, 107 children without disabilities of the same chronological age and 36 children without disabilities of the same mental age (MA). Furthermore, for the children with ID, correlations were computed between aspects of the HLE and children's non‐verbal intelligence, speech intelligibility, language and early literacy skills.

Results and conclusions  From the results of the multivariate analyses of variance it could be concluded that the HLE of children with ID differed from that of children in the chronological age group on almost all aspects. When compared with children in the MA group, differences in the HLE remained. However, differences mainly concerned child‐initiated activities and not parent‐initiated activities. Correlation analyses showed that children's activities with literacy materials were positively related with MA, productive syntax and vocabulary age, and book orientation skills. Also, children's involvement during storybook reading was related with their MA, receptive language age, productive syntax and vocabulary age, book orientation and rapid naming of pictures. The amount of literacy materials parents provided was related to a higher productive syntax age and level of book orientation of the children. Parent play activities were also positively related to children's speech intelligibility. The cognitive disabilities of the children were the main cause of the differences found in the HLE between children with ID and children without disabilities. Parents also adapt their level to the developmental level of their child, which may not always be the most stimulating for the children.
Melatonin decreases daytime challenging behaviour in persons with intellectual disability and chronic insomnia
Authors: Braam W. , Didden R. , Maas A. P. H. M. , Korzilius H. , Smits M. G. , Curfs L. M. G.
Published: November 2009

Background Persons with intellectual disability (ID) and sleep problems exhibit more daytime challenging behaviours than persons with ID without sleep problems. Several anecdotal reports suggest that melatonin is not only effective in the treatment of insomnia, but also decreases daytime challenging behaviour. However, the effect of melatonin treatment on daytime challenging behaviour in persons with ID has not been investigated in a randomised controlled trial.

Method We investigated the effects of melatonin on challenging behaviour using data from two randomised controlled trials on the efficacy of melatonin on sleep problems in 49 persons (25 men, 24 women; mean age 18.2 years, SD = 17.1) with ID and chronic insomnia. Participants received either melatonin 5 mg (<6 years 2.5 mg) or placebo during 4 weeks. Daytime challenging behaviour was measured by the Storend Gedragsschaal voor Zwakzinnigen – Maladaptive Behaviour Scale for the Mentally Retarded (SGZ;Kraijer & Kema, 1994) at baseline week and the end of the fourth treatment week. Salivary dim light melatonin onset (DLMO) was measured at baseline and the last day of the fourth treatment week. Sleep logs were used to gather information on sleep parameters.

Results Melatonin treatment significantly reduced SGZ scores, sleep latency, and number and duration of night wakes, and treatment increased total sleep time and advanced DLMO. However, after 4 weeks of treatment, change in SGZ scores did not significantly correlate with change in sleep parameters, nor with change in DLMO. Relatively strong correlations were found between change in SGZ scores, change in DLMO and number of night wakes.

Conclusions Melatonin treatment in persons with ID and chronic insomnia decreases daytime challenging behaviour, probably by improving sleep maintenance or by improving circadian melatonin rhythmicity.
Simvastatin enhances bone formation around titanium implants in rat tibiae
Authors: AYUKAWA Y. , OGINO Y. , MORIYAMA Y. , ATSUTA I. , JINNO Y. , KIHARA M. , TSUKIYAMA Y. , KOYANO K.
Published: November 2009

Summary  Statins are cholesterol‐lowering drugs that have been reported to promote bone formation. The purpose of this study was to investigate the effect of simvastatin on the enhancement of bone formation around titanium implants. Thirty‐week‐old female rats received pure titanium implants in both tibiae. The animals were intra‐peritoneally administered 0, 0·125, 1, 5 or 10 mg kg−1 of simvastatin daily. After 30 days, the animals were sacrificed, and specimens were prepared. The bone contact ratio of the implant, bone density in the medullary canal and percentage of cortical bone were obtained. Markers for bone turnover were also measured using sera collected at the time of euthanasia. In the medullary canal, a scanty amount of bone was observed in the 0, 0·125 and 1 mg kg−1 groups. In contrast, in both the 5 and 10 mg kg−1 groups, thicker bone trabeculae were abundant. Histometric observations showed that the bone contact ratio and the bone density of both groups were significantly greater than those of the other groups (anova, P < 0·01). However, no significant difference in the percentage of cortical bone was found between groups. Serum chemistry showed that statin increased bone formation markers and decreased bone resorption markers. In conclusion, although the dose equivalent to that used in human patients with hypercholesterolemia was not effective, a simvastatin dose of 5 mg kg−1 or higher increased medullary bone formation around the titanium. In contrast, no effect of simvastatin on pre‐existing cortical bone was indicated.
Effects of periodontal afferent inputs on corticomotor excitability in humans
Authors: ZHANG Y. , BOUDREAU S. , WANG M. , WANG K. , SESSLE B. , ARENDT‐NIELSEN L. , SVENSSON P.
Published: November 2009

Summary  The aim of the present study was to determine in humans whether local anaesthesia (LA) or nociceptive stimulation of the periodontal ligaments affects the excitability of the face primary motor cortex (MI) related to the tongue and jaw muscles, as measured by transcranial magnetic stimulation (TMS). Twelve healthy volunteers (11 men, 1 woman, 25·3 ± 4·2 years) participated in two 3‐h sessions separated by 7 days. The LA carbocain or the nociceptive irritant capsaicin was randomly injected into the periodontal ligament of the lower right central incisor. In both sessions, TMS–motor evoked potential (MEP) stimulus–response curves and corticomotor maps were acquired for the tongue and masseter muscles before (baseline) and at 5, 30 and 60 min post‐application of carbocain or capsaicin. Transcranial magnetic stimulation–MEP stimulus–response curves were also acquired at these time points for the first dorsal interosseous (FDI) as an internal control. Burning pain intensity and mechanical sensitivity ratings to a von Frey filament applied to the application site were recorded on an electronic visual analogue scale (VAS). All subjects reported a decreased mechanical sensitivity (anova: P = 0·004) in the LA session and a burning pain sensation (VAS peak pain: 6·4 ± 1·0) in the capsaicin session. No significant changes in cortical excitability of the MI, as reflected by TMS–MEP stimulus–response curves or corticomotor maps for the tongue, masseter or FDI were found between baseline and post‐injection for the LA (anovas: P > 0·22) or capsaicin (anovas: P > 0·16) sessions. These findings suggest that a transient loss or perturbation in periodontal afferent input to the brain from a single incisor is insufficient to cause changes in corticomotor excitability of the face MI, as measured by TMS in humans.
Psychometric properties of the modified Symptom Severity Index (SSI)
Authors: NIXDORF D. R. , JOHN M. T. , WALL M. M. , FRICTON J. R. , SCHIFFMAN E. L.
Published: November 2009

Summary  The psychometric properties of the modified Symptom Severity Index were investigated to assess the relationships among dimensions of pain in temporomandibular disorders (TMD). The 15‐item instrument is composed of ordinal scales assessing five pain dimensions (intensity, frequency, duration, unpleasantness and difficulty to endure) as experienced in three locations (temple, temporomandibular joint (TMJ), masseter). In 108 closed‐lock subjects, Cronbach’s alpha was used to measure internal consistency resulting in 31 of the 105 pair‐wise comparisons ≥0·71. Multilevel exploratory factor analysis was used to assess dimensionality between items. Two factors emerged, termed temple pain and jaw pain. The jaw pain factor comprised the TMJ and masseter locations, indicating that subjects did not differentiate between these two locations. With further analysis, the jaw pain factor could be separated into temporal aspects of pain (frequency, duration) and affective dimensions (intensity, unpleasantness, endurability). Temple pain could not be further reduced; this may have been influenced by concurrent orofacial pains such as headache. Internal consistency was high, with alphas ≥0·92 for scales associated with all factors. Excellent test‐retest reliability was found for repeat testing at 2–48 h in 55 subjects (Intra‐class correlation coefficients = 0·97, 95%CI 0·96–0·99). In conclusion, the modified Symptom Severity Index has excellent psychometric properties for use as an instrument to measure pain in subjects with TMD. The most important characteristic of this pain is location, while the temporal dimensions are important for jaw pain. Further research is needed to confirm these findings and assess relationships between dimensions of pain as experienced in other chronic pain disorders.
Genomic variability associated with the presence of occult hepatitis B virus in HIV co‐infected individuals
Authors: Martin C. M. , Welge J. A. , Shire N. J. , Rouster S. D. , Shata M. T. , Sherman K. E. , Blackard J. T.
Published: November 2009

Summary.  Occult hepatitis B virus (O‐HBV) infection is characterized by the presence of HBV DNA without detectable hepatitis B surface antigen (HBV DNA+/HBsAg−) in the serum. Although O‐HBV is more prevalent during HBV/HIV co‐infection, analysis of HBV mutations in co‐infected patients is limited. In this preliminary study, HBV PreSurface (PreS) and surface (S) regions were amplified from 33 HIV‐positive patient serum samples – 27 chronic HBV (C‐HBV) and six O‐HBV infections. HBV genotype was determined by phylogenetic analysis, while quasispecies diversity was quantified for the PreS, S and overlapping polymerase regions. C‐HBV infections harboured genotypes A, D and G, compared to A, E, G and one mixed A/G infection for O‐HBV. Interestingly, nonsynonymous–synonymous mutation values indicated positive immune selection in three regions for O‐HBV vs one for C‐HBV. Sequence analysis further identified new O‐HBV mutations, in addition to several previously reported mutations within the HBsAg antigenic determinant. Several of these O‐HBV mutations likely contribute to the lack of detectable HBsAg in O‐HBV infection by interfering with detection in serologic assays, altering antigen secretion and/or decreasing replicative fitness.
Management of chronic hepatitis C patients who have relapsed or not responded to pegylated interferon alfa plus ribavirin
Authors: Dieterich D. T. , Rizzetto M. , Manns M. P.
Published: November 2009

Summary.  Development of therapeutic strategies for patients with chronic hepatitis C who experience virological breakthrough, relapse or nonresponse lag behind those for treatment‐naïve patients. The probability of a previously treated patient responding to re‐treatment depends on the nature of the previous regimen, the magnitude of the response to previous treatment and the patient’s characteristics. Relapsers have higher sustained virological response rates than nonresponders when re‐treated with pegylated interferon plus ribavirin. Re‐treatment of nonresponders to pegylated interferon plus ribavirin with the standard 48‐week regimen resulted in an approximate 6% sustained response rate in the EPIC‐3 program. In the REPEAT trial, the sustained response rate was significantly higher in nonresponders to pegylated interferon alfa‐2b (12 kD) plus ribavirin randomized to 72 weeks of peginterferon alfa‐2a (40 kD) plus ribavirin, compared with a 48‐week regimen (16%vs 8%, P = 0.0006). Based on available data, extended treatment is the best option for these individuals. Undetectable viral RNA at week 12 is an important criterion for re‐treatment in the REPEAT and EPIC studies. Maintenance therapy with pegylated interferon is generally ineffective in nonresponders and cannot be recommended. Directly acting antivirals may increase response rates and the burden of adverse events when combined with the standard of care, but will not be available for some years. In conclusion, after careful evaluation of an individual’s benefit–risk ratio, a 72‐week regimen is the preferred strategy for optimizing sustained response rates in patients who have not responded to the standard of care, provided that viral RNA is undetectable at week 12 of re‐treatment.
Turtle groups or turtle soup: dispersal patterns of hawksbill turtles in the Caribbean
Authors: BLUMENTHAL J. M. , ABREU‐GROBOIS F. A. , AUSTIN T. J. , BRODERICK A. C. , BRUFORD M. W. , COYNE M. S. , EBANKS‐PETRIE G. , FORMIA A. , MEYLAN P. A. , MEYLAN A. B. , GODLEY B. J.
Published: November 2009

Despite intense interest in conservation of marine turtles, spatial ecology during the oceanic juvenile phase remains relatively unknown. Here, we used mixed stock analysis and examination of oceanic drift to elucidate movements of hawksbill turtles (Eretmochelys imbricata) and address management implications within the Caribbean. Among samples collected from 92 neritic juvenile hawksbills in the Cayman Islands we detected 11 mtDNA control region haplotypes. To estimate contributions to the aggregation, we performed ‘many‐to‐many’ mixed stock analysis, incorporating published hawksbill genetic and population data. The Cayman Islands aggregation represents a diverse mixed stock: potentially contributing source rookeries spanned the Caribbean basin, delineating a scale of recruitment of 200–2500 km. As hawksbills undergo an extended phase of oceanic dispersal, ocean currents may drive patterns of genetic diversity observed on foraging aggregations. Therefore, using high‐resolution Aviso ocean current data, we modelled movement of particles representing passively drifting oceanic juvenile hawksbills. Putative distribution patterns varied markedly by origin: particles from many rookeries were broadly distributed across the region, while others would appear to become entrained in local gyres. Overall, we detected a significant correlation between genetic profiles of foraging aggregations and patterns of particle distribution produced by a hatchling drift model (Mantel test,r = 0.77,P < 0.001; linear regression,r = 0.83,P < 0.001). Our results indicate that although there is a high degree of mixing across the Caribbean (a ‘turtle soup’), current patterns play a substantial role in determining genetic structure of foraging aggregations (forming turtle groups). Thus, for marine turtles and other widely distributed marine species, integration of genetic and oceanographic data may enhance understanding of population connectivity and management requirements.
Genetic analysis across different spatial scales reveals multiple dispersal mechanisms for the invasive hydrozoan Cordylophora in the Great Lakes
Authors: DARLING JOHN A. , FOLINO‐ROREM NADINE C.
Published: November 2009

Discerning patterns of post‐establishment spread by invasive species is critically important for the design of effective management strategies and the development of appropriate theoretical models predicting spatial expansion of introduced populations. The globally invasive colonial hydrozoan Cordylophora produces propagules both sexually and vegetatively and is associated with multiple potential dispersal mechanisms, making it a promising system to investigate complex patterns of population structure generated throughout the course of rapid range expansion. Here, we explore genetic patterns associated with the spread of this taxon within the North American Great Lakes basin. We collected intensively from eight harbours in the Chicago area in order to conduct detailed investigation of local population expansion. In addition, we collected from Lakes Michigan, Erie, and Ontario, as well as Lake Cayuga in the Finger Lakes of upstate New York in order to assess genetic structure on a regional scale. Based on data from eight highly polymorphic microsatellite loci we examined the spatial extent of clonal genotypes, assessed levels of neutral genetic diversity, and explored patterns of migration and dispersal at multiple spatial scales through assessment of population level genetic differentiation (pairwise FST and factorial correspondence analysis), Bayesian inference of population structure, and assignment tests on individual genotypes. Results of these analyses indicate that Cordylophora populations in this region spread predominantly through sexually produced propagules, and that while limited natural larval dispersal can drive expansion locally, regional expansion likely relies on anthropogenic dispersal vectors.
The cobinamide amidohydrolase (cobyric acid‐forming) CbiZ enzyme: a critical activity of the cobamide remodelling system of Rhodobacter sphaeroides
Authors: Gray Michael J. , Escalante‐Semerena Jorge C.
Published: November 2009

The chemical structures of cobamides [cobalamin (Cbl)‐like compounds] are the same, except for the lower ligand, which in adenosylcobalamin (AdoCbl) is 5,6‐dimethylbenzimidazole, and in adenosylpseudocobalamin (AdopseudoCbl) is adenine. Why the lower ligand of cobamides varies and what the mechanism of lower ligand replacement is are long‐standing questions in the field of B12 biosynthesis. Work reported here uncovers the strategy used by the photosynthetic α‐proteobacterium Rhodobacter sphaeroides to procure the cobamide it needs to grow on acetate as a carbon and energy source. On the basis of genetic and biochemical evidence we conclude that, in R. sphaeroides, the activity of the cobyric acid‐producing amidohydrolase CbiZ enzyme is essential for the conversion of AdopseudoCbl into AdoCbl, the cobamide needed for the catabolism of acetate. The CbiZ enzyme uses AdopseudoCbl as a substrate, but not AdoCbl. Implications of these findings for cobamide remodelling in R. sphaeroides and in other CbiZ‐containing microorganisms are discussed.
Different roles for anti‐sigma factors in siderophore signalling pathways of Pseudomonas aeruginosa
Authors: Mettrick Karla A. , Lamont Iain L.
Published: November 2009

Group IV (extracytoplasmic function) sigma factors direct the expression of a large number of regulons in bacteria. The activities of many Group IV sigma factors are inhibited by members of a family of anti‐sigma factor proteins, with appropriate environmental signals causing the sigma factor to be released for interaction with core RNA polymerase and consequent transcription of target genes. One subgroup of Group IV sigmas directs expression of genes for uptake of siderophores (iron‐chelating compounds) by Gram‐negative bacteria. The activities of these sigma factors are controlled by anti‐sigma factors that span the cytoplasmic membrane. Binding of siderophore by a receptor protein in the outer membrane results in signal transduction from the periplasmic portion to the cytoplasmic portion of the appropriate anti‐sigma factor, with consequent activity of the cognate sigma factor and upregulation of the gene encoding the receptor protein. We have investigated receptor/anti‐sigma/sigma factor signalling pathways for uptake of the siderophores ferrichrome and desferrioxamine by Pseudomonas aeruginosa. In these pathways the ‘anti‐sigma’ proteins are normally required for sigma factor activity and the cytoplasmic parts of the ‘anti‐sigmas’ have ‘pro‐sigma’ activity. We suggest that the family of anti‐sigma factor proteins may be better considered as ‘sigma regulators’.
Expression of the yeast aquaporin Aqy2 affects cell surface properties under the control of osmoregulatory and morphogenic signalling pathways
Authors: Furukawa Kentaro , Sidoux‐Walter Frédéric , Hohmann Stefan
Published: November 2009

Aquaporins mediate rapid and selective water transport across biological membranes. The yeast Saccharomyces cerevisiae possesses two aquaporins, Aqy1 and Aqy2. Here, we show that Aqy2 is involved in controlling cell surface properties and that its expression is controlled by osmoregulatory and morphogenic signalling pathways. Deletion of AQY2 results in diminished fluffy colony morphology while overexpression of AQY2 causes strong agar invasion and adherence to plastic surfaces. Hyper‐osmotic stress inhibits morphological developments including the above characteristics as well as AQY2 expression through the osmoregulatory Hog1 mitogen‐activated protein kinase. Moreover, two pathways known to control morphological developments are involved in regulation of AQY2 expression: the protein kinase A pathway derepresses AQY2 expression through the Sfl1 repressor, and the filamentous growth Kss1 mitogen‐activated protein kinase pathway represses AQY2 expression in a Kss1 activity‐independent manner. The AQY2 expression pattern resembles in many ways that of MUC1/FLO11, which encodes a cell surface glycoprotein required for morphological developments. Our observations suggest a potential link between aquaporins and cell surface properties, and relate to the proposed role of mammalian aquaporins in tumour cell migration and invasion.
The antifungal protein PAF interferes with PKC/MPK and cAMP/PKA signalling of Aspergillus nidulans
Authors: Binder Ulrike , Oberparleiter Christoph , Meyer Vera , Marx Florentine
Published: November 2009

The Penicillium chrysogenum antifungal protein PAF inhibits polar growth and induces apoptosis in Aspergillus nidulans. We report here that two signalling cascades are implicated in its antifungal activity. PAF activates the cAMP/protein kinase A (Pka) signalling cascade. A pkaA deletion mutant exhibited reduced sensitivity towards PAF. This was substantiated by the use of pharmacological modulators: PAF aggravated the effect of the activator 8‐Br‐cAMP and partially relieved the repressive activity of caffeine. Furthermore, the Pkc/mitogen‐activated protein kinase (Mpk) signalling cascade mediated basal resistance to PAF, which was independent of the small GTPase RhoA. Non‐functional mutations of both genes resulted in hypersensitivity towards PAF. PAF did not increase MpkA phosphorylation or induce enzymes involved in the remodelling of the cell wall, which normally occurs in response to activators of the cell wall integrity pathway. Notably, PAF exposure resulted in actin gene repression and a deregulation of the chitin deposition at hyphal tips of A. nidulans, which offers an explanation for the morphological effects evoked by PAF and which could be attributed to the interconnection of the two signalling pathways. Thus, PAF represents an excellent tool to study signalling pathways in this model organism and to define potential fungal targets to develop new antifungals.
LrhA positively controls the expression of the locus of enterocyte effacement genes in enterohemorrhagic Escherichia coli by differential regulation of their master regulators PchA and PchB
Authors: Honda Naoko , Iyoda Sunao , Yamamoto Shouji , Terajima Jun , Watanabe Haruo
Published: November 2009

Genes essential for eliciting pathogenicity of enterohemorrhagic Escherichia coli are located within the locus of enterocyte effacement (LEE). Expression of LEE genes is positively regulated by paralogues PchA, PchB and PchC, which are encoded by separate loci of the chromosome. To elucidate the underlying regulatory mechanism, we screened transposon mutants exhibiting reduced expression of pchA, transcription level of which is highest among the pch genes. Here, we report that the LysR‐homologue A (LrhA) positively regulated the transcription of pchA and pchB. A deletion in lrhA reduced the transcription levels of pchA and pchB to different degrees, and also reduced the expression of LEE‐coded type 3‐secreted protein, EspB. Expression of LrhA from a plasmid restored and markedly increased the transcription levels of pchA and pchB respectively, and highly induced EspB expression. Deletion analysis of the regulatory region showed that both promoter‐proximal (−195 to +88) and promoter‐distal (−418 to −392 for pchA and −391 to −375 for pchB) sequences were required for the LrhA‐mediated upregulation of pchA and pchB genes. Purified His6‐LrhA protein differentially bound to the regulatory regions of pchA/B, suggesting that direct regulation of pchA and pchB genes by LrhA in turn controls the expression of LEE genes.
Dissecting the role of the Tir:Nck and Tir:IRTKS/IRSp53 signalling pathways in vivo
Authors: Crepin Valérie F. , Girard Francis , Schüller Stephanie , Phillips Alan D. , Mousnier Aurelie , Frankel Gad
Published: November 2009

Attaching and effacing (A/E) lesions and actin polymerization, the hallmark of enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC) and Citrobacter rodentium (CR) infections, are dependent on the effector Tir. Phosphorylation of TirEPEC/CR Y474/1 leads to recruitment of Nck and neural Wiskott–Aldrich syndrome protein (N‐WASP) and strong actin polymerization in cultured cells. TirEPEC/CR also contains an Asn‐Pro‐Tyr (NPY454/1) motif, which triggers weak actin polymerization. In EHEC the NPY458 actin polymerization pathway is amplified by TccP/EspFU, which is recruited to Tir via IRSp53 and/or insulin receptor tyrosine kinase substrate (IRTKS). Here we used C. rodentium to investigate the different Tir signalling pathways in vivo. Following infection with wild‐type C. rodentium IRTKS, but not IRSp53, was recruited to the bacterial attachment sites. Similar results were seen after infection of human ileal explants with EHEC. Mutating Y471 or Y451 in TirCR abolished recruitment of Nck and IRTKS respectively, but did not affect recruitment of N‐WASP or A/E lesion formation. This suggests that despite their crucial role in actin polymerization in cultured cells the Tir:Nck and Tir:IRTKS pathways are not essential for N‐WASP recruitment or A/E lesion formation in vivo. Importantly, wild‐type C. rodentium out‐competed the tir tyrosine mutants during mixed infections. These results uncouple the Tir:Nck and Tir:IRTKS pathways from A/E lesion formation in vivo but assign them an important in vivo role.
DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade
Authors: Lemke Justin J. , Durfee Tim , Gourse Richard L.
Published: November 2009

The components of the Escherichia coli flagella apparatus are synthesized in a three‐level transcriptional cascade activated by the master regulator FlhDC. The cascade co‐ordinates the synthesis rates of a large number of gene products with each other and with nutritional conditions. Recent genome‐wide studies have reported that flagellar transcription is altered in cells lacking the transcription regulators DksA or ppGpp, but some or all reported effects could be indirect, and some are contradictory. We report here that the activities of promoters at all three levels of the cascade are much higher in strains lacking dksA, resulting in overproduction of flagellin and hyperflagellated cells. In vitro, DksA/ppGpp inhibits the flhDC promoter and the σ70‐dependent fliA promoter transcribing the gene for σ28. However, DksA and ppGpp do not affect the σ28‐dependent fliA promoter or the σ28‐dependent fliC promoter in vitro, suggesting that the dramatic effects on expression of those genes in vivo are mediated indirectly through direct effects of DksA/ppGpp on FlhDC and σ28 expression. We conclude that DksA/ppGpp inhibits expression of the flagellar cascade during stationary phase and following starvation, thereby co‐ordinating flagella and ribosome assembly and preventing expenditure of scarce energy resources on synthesis of two of the cell's largest macromolecular complexes.