bluuebunny/crossref_metadata_2025 huggingface dataset:
Purification of Bovine Lens and Bacterially Expressed Human Vimentin
Authors: Kuczmarski Edward R. , Goldman Robert D.
Published: February 2007

INTRODUCTION

Intermediate filaments (IF) are major cytoskeletal systems of vertebrate and many nonvertebrate cells whose expression is cell-type specific and developmentally regulated. This protocol describes a method for purifying one type of IF, vimentin, from bovine lens tissue. Purification of human vimentin expressed in Escherichia coli is also described. These methods are useful in the preparation of other IF protein subunits for microinjection studies as well.
Quantitative GUS Activity Assay in Intact Plant Tissue
Authors: Blázquez Miguel
Published: February 2007

INTRODUCTION

The activity of β-glucuronidase (GUS) can be accurately determined in intact plant tissue using 4-methylumbelliferyl β-D-glucuronide (4-MUG) as a substrate. Upon hydrolysis by GUS, the fluorochrome 4-methyl umbelliferone (4-MU) is produced. This method is based on the permeability of both 4-MUG and 4-MU through plant tissue. It consists of incubation of the tissue with the reagent and quantification of the fluorescence emitted by 4-MU in the solution. GUS activity in each sample can be normalized per unit tissue weight, per unit protein (if it is determined in the tissue after the incubation with 4-MUG), or per sample. The latter is particularly useful if GUS is expressed only in a subset of cells within the tissue assayed. The advantage of this method is that since many samples can be assayed with relatively little effort, it is particularly appropriate for large-scale screens. The following protocol has been adapted for the use of 96-well microtiter plates (200-μl wells).
The polarization of hair cells from the inner ear of the lesser spotted dogfish Scyliorhinus canicula
Authors: Lovell J. M. , Findlay M. M. , Harper G. M. , Moate R. M.
Published: February 2007

The polarization of hair cells from the end organs of the inner ear from the lesser spotted dogfish Scyliorhinus canicula from the order Carcharhiniforms (ground sharks) was studied using a scanning electron microscope (SEM), revealing arrays of hair cells with diverse orientations on each of the sensory epithelia. The greatest numbers of hair cells were found on the utricular epithelium and orientated on the horizontal plane, whilst the smallest number were found on the anterior macula neglecta and orientated on the vertical plane. Examination of the posterior macula neglecta revealed a dense profusion of c. 500 000 individual elongate structures, each resembling long microvilli, a finding not previously described in elasmobranch auditory physiology.
Distribution, reproduction and feeding of the Greenland shark Somniosus (Somniosus) microcephalus, with notes on two other sleeper sharks, Somniosus (Somniosus) pacificus and Somniosus (Somniosus) antarcticus
Authors: Yano K. , Stevens J. D. , Compagno L. J. V.
Published: February 2007

The size and depth distribution, stomach contents and reproductive status of Somniosus (Somniosus) microcephalus, Somniosus (Somniosus) pacificus and Somniosus (Somniosus) antarcticus were examined from specimens collected from the North and South Atlantic, North and South Pacific, and the Southern Ocean. Specimens ranged in size from 42 to 480 cm total length, LT, and were taken from depths of 35–1280 m. Stomach contents included coelenterates, gastropods, cephalopods, echinoderms, crustaceans, elasmobranchs, teleosts, penguins, marine mammals and human waste. Female S. (S.) microcephalus mature at c. 450 cm and S. (S.) antarcticus at c. 435 cm LT; a female S. (S.) pacificus of 430 cm was mature. Male S. (S.) microcephalus mature at c. 300 cm, but male S. (S.) antarcticus may not mature until c. 400 cm LT. The size at birth in these three species of Somniosus is c. 40 cm LT.
Tidal migration and patterns in feeding of the four‐eyed fish Anableps anableps L. in a north Brazilian mangrove
Authors: Brenner M. , Krumme U.
Published: February 2007

The tidal migration, temporal and spatial patterns in feeding of the surface‐swimming four‐eyed fish Anableps anableps (Anablepidae) were studied in a macrotidal mangrove area in north Brazil to exemplify the ecology of a tropical intertidal fish. Visual censuses in the main channel showed that abundances were high at low water (LW) and low at high water (HW). Anableps anableps entered the intertidal creeks with the first flood rise. They fed in the inundated mangrove at HW and returned gradually after the ebb current maximum to concentrate again in the subtidal parts of the main channel at LW. This pattern occurred at neap, mid and spring tides throughout the year. The tidal migration was triggered by water level, not by time. In the study area the diet of A. anableps caught with block nets was dominated by intertidal red algae (Catanella sp.). Other important food items were Insecta and Grapsidae. The combination of high inundation and daylight (spring tide‐day) provided the best foraging conditions, probably emphasizing the importance of the above‐water eye. Darkness and low inundation was linked to poorest foraging conditions (neap tide‐night). The quantity of food consumed by A. anableps was clearly influenced by the factors tide, time of day and creek location, but not by size and sex. The qualitative composition of the diet was not influenced by any of the factors, except for mud, which was only ingested at neap tides. The temporal and spatial variability in food consumption suggests that food web modelling in macrotidal areas may lead to misinterpretations of the overall systems dynamics if the spring and neap tide alternation and the diurnal cycle are not considered.
Comparative energy allocation in two sympatric, closely related gobies: the black goby Gobius niger and the grass goby Zosterisessor ophiocephalus
Authors: Fiorin R. , Malavasi S. , Franco A. , Franzoi P.
Published: February 2007

Seasonal energy allocation of lipid reserves into different body tissues was analysed comparatively in two sympatric, closely related gobies: the grass goby Zosterisessor ophiocephalus and the black goby Gobius niger. Lipid reserves were measured in liver, muscle and ovary and compared between the two species within a given sex and seasonal period (reproductive v. non‐reproductive). Furthermore, temporal patterns of lipid reserves were investigated in the two species in relation to gonado‐somatic and liver‐somatic indices, as well as the relationship between size and lipid content. Results showed that the grass goby allocated more lipid reserves in reproduction while the black goby accumulated more reserves in liver and muscle, at a given size, although the temporal patterns of lipid accumulation and depletion were basically similar. Results are discussed in the light of life‐history theories, taking into account both adaptation and evolutionary constraints.
Host preference and specialization in Gnathia sp., a common parasitic isopod of coral reef fishes
Authors: Nagel L. , Grutter A. S.
Published: February 2007

A gnathiid species (Crustacea: Isopoda; one of the most common ectoparasites of coral reef fishes) from the Great Barrier Reef, Australia, was allowed to choose among fishes from three different families to feed on (using two species of fishes per family). Gnathiids showed a strong preference for labrids, rarely feeding on pomacentrids or apogonids. In a separate experiment, gnathiid host preference did not vary among three labrid fish species. Gnathiids that fed on labrids had higher survival than those that fed on apogonids. Male gnathiids that fed on labrids also moulted to the adult stage more quickly. This suggests that host specialization and local adaptation might be occurring between these ectoparasites and their host fishes at the host fish family level.
Continuous treatment of bestatin induces anti‐angiogenic property in endothelial cells
Authors: Mishima Yuji , Terui Yasuhito , Sugimura Natsuhiko , Matsumoto‐Mishima Yuko , Rokudai Akiko , Kuniyoshi Ryoko , Hatake Kiyohiko
Published: February 2007

CD13/aminopeptidase‐N (CD13/APN) is an important regulator of angiogenesis where its expression on activated blood vessels is induced by angiogenic signals. A previous study demonstrated that angiogenesis is suppressed under the presence of high concentrations of aminopeptidase antagonists. However, the mechanisms underlying the inhibition of morphogenesis by aminopeptidase antagonists have not been elucidated. In this study, we have for the first time examined the effects of continuous treatment of therapeutic dose of aminopeptidase antagonists on vascular endothelial capillary‐like tube formation. In the antagonists tested, only bestatin significantly interfered in the capillary tube formation of primary endothelial cells (EC) after treatment for 72 h. Aminopeptidase analysis revealed that inhibitory activity of bestatin was not specific for CD13/APN, and the other inhibitors lacking anti‐angiogenic properties also inhibit cell‐surface aminopeptidase activity as well or more potently than bestatin, suggesting that the angiogenesis‐inhibitory effect of bestatin was not due to inhibition of CD13/APN activity at this concentration. To elucidate the influence of continuous treatment of bestatin on endothelial cells, we performed microarray analysis and revealed that 72‐h treatment of a pharmacokinetic dose of bestatin modulated the several angiogenesis‐related genes including vascular endothelial growth factor (VEGF). Northern blot analysis indicated that modulation of the VEGF gene became obvious after 48 h of treatment. Furthermore, knockdown of the VEGF gene by siRNA remarkably suppressed capillary tube formation and required a higher concentration of exogenous VEGF to reverse the capillary formation ability. These data suggested that bestatin decreases a reactivity of EC to angiogenesis stimuli, and it can be achieved by the regulation of angiogenesis‐related gene expression. (Cancer Sci 2007; 98: 364–372)
Promoter methylation status of the Cyclin D2 gene is associated with poor prognosis in human epithelial ovarian cancer
Authors: Sakuma Michiko , Akahira Jun‐ichi , Ito Kiyoshi , Niikura Hitoshi , Moriya Takuya , Okamura Kunihiro , Sasano Hironobu , Yaegashi Nobuo
Published: February 2007

Gene silencing associated with aberrant DNA methylation of promoter CpG islands is one mechanism through which several genes may be inactivated in human cancers. Cyclin D2, a member of the D‐type cyclins, implicated in cell cycle regulation, differentiation and malignant transformation, is inactivated due to aberrant DNA methylation in several human cancers. In the present study, we examined the promoter methylation status and expression of Cyclin D2 in human epithelial ovarian cancer, and then determined the relationship between methylation status and various clinicopathological variables. Twelve ovarian cancer cell lines and 71 surgical specimens were examined by methylation‐specific polymerase chain reaction and quantitative reverse transcription–polymerase chain reaction to evaluate the methylation status and expression of the Cyclin D2 gene. The relationship between methylation status and various clinicopathological variables was evaluated using statistical analysis. Aberrant methylation of Cyclin D2 was present in five of 12 ovarian cancer cell lines and 16 of 71 primary ovarian cancer tissues. In five cell lines with methylation, expression of the Cyclin D2 gene tended to be lower than in cell lines without methylation. In ovarian cancer tissues, methylation bands were detected in 16 of 71 cases. The methylation status of Cyclin D2 was associated with advanced stage and a residual tumor size (>2 cm) (P = 0.027 and P = 0.031, respectively). Based on univariate analysis, patients with aberrant methylation of the Cyclin D2 promoter had a significantly worse chance of disease‐free survival than those without methylation (P = 0.021). Our results suggest that aberrant promoter methylation of the Cyclin D2 gene is significantly associated with patient prognosis in epithelial ovarian cancer. (Cancer Sci 2007; 98: 380 –386)
3‐D seismic exploration data and the study of shallow marine geology
Authors: Buckley Francis
Published: February 2007

In 2005, Geology Today carried an article (v.22, n.5) describing how 3D exploration seismic data are being used to map sub‐surface structure and stratigraphy, in fine detail, over hundreds and even thousands of square kilometres of the sea bed. The article in question was concerned primarily with the various ways in which 3D seismic data are applied to the study of stratigraphy and basin analysis. However, the potential uses of 3D exploration data for investigating other kinds of geological phenomena are many and varied, and significant advances may be made in our understanding of the geological past using such data. The present article describes how 3D seismic data can be used to investigate aspects of the upper Tertiary and Quaternary geology of marine areas, drawing on examples from the Central North Sea and West Shetland Slope. These originally came to light in the course of conducting geo‐hazard surveys on behalf of the hydrocarbons industry.
Factors influencing nurses’ attitudes towards the use of computerized health information systems in Kuwaiti hospitals
Authors: Alquraini Habib , Alhashem Abdul Majeed , Shah Makhdoom A. , Chowdhury Rafiqul I.
Published: February 2007

Title. Factors influencing nurses’ attitudes towards the use of computerized health information systems in Kuwaiti hospitals

Aim.  This paper reports a survey of nurses’ attitudes towards computerized health information systems, the characteristics that influence these attitudes and the level of nurses’ skills in computer use.

Background.  The use of such systems in developed countries and in some developing countries has already become a reality. However, nurses as a group of care providers have been found to resist computerization, seeing computerized health information systems as dehumanizing, confusing and uncaring. Nurses with more computer experience tend to have more positive views; education and training positively influence attitudes; and younger and less experienced nurses may have more positive attitudes.

Methods.  A structured questionnaire was used to measure the attitudes of nurses working in Kuwait towards computerization. A random sample of 574 nurses working in Ministry of Health hospitals were sent a questionnaire, and 530 replies were received (response rate 92·3%). The data were collected from November 2002 to January 2003.

Findings.  Respondents generally had positive attitudes toward computerized health information systems. Analysis of variance revealed statistically significant differences in attitudes in relation to nationality, level of education, previous experience in computer use, and computer skills (P < 0·05). Multiple regression analysis showed that gender, nationality, education levels, and duration of computer use were statistically significant predictors of attitudes toward computerized health information systems (P < 0·05).

Conclusion.  With adequate computerized health information system training, the implementation of computerized health information systems could be effective for nurses in providing quality health care, as found in other studies.
Making nursing work: breaking through the role confusion of advanced practice nursing
Authors: Gardner Glenn , Chang Anne , Duffield Christine
Published: February 2007

Title. Making nursing work: breaking through the role confusion of advanced practice nursing

Aim.  This paper reports a study to develop a research‐informed model of the service parameters and an analysis framework for advanced practice nursing roles.

Background.  Changing patterns of health care are forcing service planners to examine new service delivery models. Apparent is the call for nursing service that incorporates expanded levels of autonomy, skill and decision‐making. A number of nursing roles conform to this description under the generic title of advanced practice nurse. However, there is confusion in the health service community internationally about nomenclature, role and scope for advanced practice nursing roles. An emerging priority in response to recent developments in the nurse practitioner role is to establish service parameters for advanced practice nursing and to differentiate operationally between advanced practice and practitioner nursing roles.

Methods.  We conducted an interpretive, qualitative examination of the practice of a random sample of nine advanced practice nurses working in three acute care hospitals in south east Queensland, Australia in 2006. Data collection involved individual in‐depth interviews, which were deductively analysed and tested against published advanced practice nursing models.

Results.  The data most comprehensively supported the Strong Model of Advanced Practice as representing the practice experiences of the research participants. This model supports definition of the service parameters and the design of an operational framework for implementation and evaluation of advanced practice nursing roles.

Conclusion.  The findings differentiate advanced practice nurse and nurse practitioner roles, and offer an operational framework to identify, establish and evaluate advanced and extended nursing positions. Subject to further validation, this outcome can provide operational information for implementing innovative nursing roles appropriate to consumer needs and specific health service models.
Enhancing the quality of nursing care in methadone substitute clinics using action research: a process evaluation
Authors: Loth Christien , Schippers Gerard M. , Hart Harm't , Van De Wijngaart Goof
Published: February 2007

Title. Enhancing the quality of nursing care in methadone substitute clinics using action research: a process evaluation

Aim.  This paper is a report of a study to answer the research question: can participative action research help to halt the deterioration in methadone substitution treatment and develop new care strategies which are better geared toward the patients’ needs?

Background.  In the Netherlands, methadone substitute treatment has been the main medical treatment for heroin addiction since the early 1980s. Although effective at first, this methadone provision has deteriorated during the last 15 years. Over time, nursing staff have had to restrict their activities to simply dispensing methadone and have not been able to develop any other interventions, such as outreach care.

Method.  A participative action research process was used in two outpatient methadone substitute treatment clinics. Using the four stages of the cooperative inquiry design of Heron and the knowledge development model of Johns, a diagnosis of all the bottlenecks was made and innovative care strategies were implemented. Reflection meetings were held to offer nursing staff maximum benefit in improving the quality of nursing care.

Findings.  Action research partially succeeded in enhancing care strategies. Of the two clinics involved in the study, one improved both its care organization and patient‐centred outcome. The other managed to improve the organization of the care.

Conclusion.  Participative strategies can be, but are not always, a helpful method for enhancing professional care in addictions nursing. By setting out attainable goals in daily practice, some nurses were able to become active change agents. The development of knowledge is inextricably connected with the growth of new care strategies. Chronic opiate users can benefit from the expansion of professional nursing knowledge.
Psychological determinants of primary care requests for urgent outpatient appointments in elective referrals
Authors: Glozier Nick , Prince Martin
Published: February 2007

Rationale  Wide variations in referral practice from primary to secondary care have been observed. Clinical, demographic and referrer characteristics explain little of this variation. Patient psychological characteristics have been suggested as a potential explanation of this, biasing referral. The objective of this study is to investigate, in a relatively homogeneous population, the effects of patient’s psychological distress and illness beliefs upon GP’s requests for urgent outpatient assessment.

Methods  An inception cohort of 188 primary care referrals to a UK NHS Trust orthopaedic department for potential lower limb arthroplasty was assessed for disease‐related pain and impairment, disability, psychological distress and illness beliefs. Associations between these and primary care requests for urgent outpatient appointments were estimated.

Results  Twenty‐two referrals (12%) requested an urgent outpatient appointment. Illness beliefs of greater personal control (OR 2.18, 95% CI 1.18, 4.05) but not psychological distress (OR 0.39, 95% CI 0.11, 1.36) were independently associated with urgent requests. Greater pain and impairment, co‐morbidity and disability were univariately associated with this request. In both fully adjusted and parsimonious models, only patient beliefs of greater control and disability were independent determinants of this request for urgency.

Conclusions  Among patients referred for assessment for lower limb arthroplasty primary care practitioner’s requests for urgent assessment are influenced by the patient’s belief of how well they can control the symptoms, over and above clinical measures, suggesting patients coping better gain faster access. Global disability appears to be the main clinical determinant, which suggests GPs are making urgent referrals appropriately. There is no evidence of any bias on age, gender or socioeconomic status. This request for urgency leads to these patients waiting 2 months less for an outpatient appointment.
Audit of nasal fracture management in accident and emergency in a district general hospital
Authors: Agrawal Namit , Brayley Nigel
Published: February 2007

Rationale  Nasal fractures are a common occurrence in accident and emergency and dealt with by inexperienced senior house officers. This can lead to inappropriate X‐rays being performed, no proper documentation of septal haematomas and often no follow‐up with a specialist team leading to in some cases complex cosmetic surgery whereas simple manipulation may have sufficed.

Method  We report an ambispective audit carried out on nasal fracture management in a busy district general hospital over a 6‐month period.

Results  46 patients were seen 24 in the first 3 months and 22 the next three. 10 had nasal X‐ray performed initially on audit. Nine had no documentation of septal haematoma and seven had no follow‐up arranged. After appropriate education and the setting up of a department protocol based on best practice, the next cycle was repeated. Two nasal X‐rays were performed looking for foreign bodies, all patients had appropriate documentation of septal haematoma and appropriate follow‐up.

Conclusion  Appropriate education and implementation of departmental guidelines can result in more effective and efficient use of resources when dealing with nasal fractures in accident and emergency.
Geometric approach to segmentation and protein localization in cell culture assays
Authors: RAMAN S. , MAXWELL C. A. , BARCELLOS‐HOFF M. H. , PARVIN B.
Published: February 2007

Cell‐based fluorescence imaging assays are heterogeneous and require the collection of a large number of images for detailed quantitative analysis. Complexities arise as a result of variation in spatial nonuniformity, shape, overlapping compartments and scale (size). A new technique and methodology has been developed and tested for delineating subcellular morphology and partitioning overlapping compartments at multiple scales. This system is packaged as an integrated software platform for quantifying images that are obtained through fluorescence microscopy. Proposed methods are model based, leveraging geometric shape properties of subcellular compartments and corresponding protein localization. From the morphological perspective, convexity constraint is imposed to delineate and partition nuclear compartments. From the protein localization perspective, radial symmetry is imposed to localize punctate protein events at submicron resolution. Convexity constraint is imposed against boundary information, which are extracted through a combination of zero‐crossing and gradient operator. If the convexity constraint fails for the boundary then positive curvature maxima are localized along the contour and the entire blob is partitioned into disjointed convex objects representing individual nuclear compartment, by enforcing geometric constraints. Nuclear compartments provide the context for protein localization, which may be diffuse or punctate. Punctate signal are localized through iterative voting and radial symmetries for improved reliability and robustness. The technique has been tested against 196 images that were generated to study centrosome abnormalities. Corresponding computed representations are compared against manual counts for validation.
Fluctuation X‐ray microscopy: a novel approach for the structural study of disordered materials
Authors: FAN L. , PATERSON D. , McNULTY I. , TREACY M. M. J. , GIBSON J. M.
Published: February 2007

Measuring medium‐range order is a challenging and important problem in the structural study of disordered materials. We have developed a new technique, fluctuation x‐ray microscopy, that offers quantitative insight into medium‐range correlations in disordered materials at nanometre and larger length scales.In this technique, which requires a spatially coherent x‐ray beam, a series of speckle patterns are measured at a large number of locations in a sample using various illumination sizes. Examination of the speckle variance as a function of the illumination spot size allows the structural correlation length to be measured. To demonstrate this technique we have studied polystyrene latex spheres, which serve as a model for a dense random‐packed glass, and for the first time have measured the correlation length in a disordered system by fluctuation X‐ray microscopy. We discuss data analysis and procedures to correct for shot noise and detector noise. This approach could be used to explore medium‐range order and subtle spatial structural changes in a wide range of disordered materials, from soft matter to nanowire arrays, semiconductor quantum dot arrays and magnetic materials.
Size‐selective colloidal‐gold localization in transmission X‐ray microscopy
Authors: STOLLBERG H. , GUTTMANN P. , TAKMAN P. A. C. , HERTZ H. M.
Published: February 2007

Colloidal gold is a useful marker for functional‐imaging experiments in transmission X‐ray microscopy. Due to the low contrast of gold particles with small diameters it is necessary to develop a powerful algorithm to localize the single gold particles. The presented image‐analysis algorithm for identifying colloidal gold particles is based on the combination of a threshold with respect to the local absorption and shape discrimination, realized by fitting a Gaussian profile to the identified regions of interest. The shape discrimination provides the possibility of size‐selective identification and localization of single colloidal gold particles down to a diameter of 50 nm. The image‐analysis algorithm, therefore, has potential for localization studies of several proteins simultaneously and for localization of fiducial markers in X‐ray tomography.
Characterization of uniform ultrathin layer for z‐response measurements in three‐dimensional section fluorescence microscopy
Authors: VICIDOMINI G. , SCHNEIDER M. , BIANCHINI P. , KROL S. , SZELLAS T. , DIASPRO A.
Published: February 2007

Layer‐by‐layer technique is used to adsorb a uniform ultrathin layer of fluorescently labelled polyelectrolytes on a glass cover slip. Due to their thickness, uniformity and fluorescence properties, these ultrathin layers may serve as a simple and applicable standard to directly measure the z‐response of different scanning optical microscopes. In this work we use ultrathin layers to measure the z‐response of confocal, two‐photon excitation and 4Pi laser scanning microscopes. Moreover, due to their uniformity over a wide region, i.e. cover slip surface, it is possible to quantify the z‐response of the system over a full field of view area. This property, coupled with a bright fluorescence signal, enables the use of polyelectrolyte layers for representation on sectioned  imaging property charts: a very powerful method to characterize image formation properties and capabilities (z‐response, off‐axis aberration, spherical aberration, etc.) of a three‐dimensional scanning system. The sectioned imaging property charts method needs a through‐focus dataset taken from such ultrathin layers. Using a comparatively low illumination no significant bleaching occurs during the excitation process, so it is possible to achieve long‐term monitoring of the z‐response of the system. All the above mentioned properties make such ultrathin layers a suitable candidate for calibration and a powerful tool for real‐time evaluation of the optical sectioning capabilities of different three‐dimensional scanning systems especially when coupled to sectioned imaging property charts.
A simple technique of image analysis for specific nuclear immunolocalization of proteins
Authors: CARMONA R. , MACÍAS D. , GUADIX J. A. , PORTILLO V. , PÉREZ‐POMARES J. M. , MUÑOZ‐CHÁPULI R.
Published: February 2007

Colocalization of fluorescent signals in confocal microscopy is usually evaluated by inspecting merged images from different colour channels or by using commercially available software packages. We describe in this paper a simple method for assessment of nuclear localization of proteins in tissue sections through confocal immunolocalization, propidium iodide counterstaining and image analysis. Through a macro command developed for the public domain, Java‐based software imagej, red, green, blue (RGB) images are automatically split in the red and green channels and a new image composed of the nonblack pixels coincident in both channels is created and inverted for better visualization. This method renders images devoid of both, extranuclear staining and background, thus emphasizing the nuclear signal. The resulting images can easily be used for comparison or quantification of the results. Given the simplicity of the technique and the worldwide diffusion of the software utilized, we think that this method could be useful in order to define standards of colocalization in confocal microscopy.
Comments on the paper ‘A novel 3D wavelet‐based filter for visualizing features in noisy biological data’, by Moss et al.
Authors: HENDRIKS C. L. LUENGO , KNOWLES D. W.
Published: February 2007

Moss et al. (2005) describe, in a recent paper, a filter that they use to detect lines. We noticed that the wavelet on which this filter is based is a difference of uniform filters. This filter is an approximation to the second‐derivative operator, which is commonly implemented as the Laplace of Gaussian (or Marr–Hildreth) operator. We have compared Moss' filter with (1) the Laplace of Gaussian operator, (2) an approximation of the Laplace of Gaussian using uniform filters and (3) a few common noise reduction filters. The Laplace‐like operators detect lines by suppressing image features both larger and smaller than the filter size. The noise reduction filters only suppress image features smaller than the filter size. By estimating the signal‐to‐noise ratio and mean square difference of the filtered results, we found that the filter proposed by Moss et al. does not outperform the Laplace of Gaussian operator. We also found that for images with extreme noise content, line detection filters perform better than the noise reduction filters when trying to enhance line structures. In less extreme cases of noise, the standard noise reduction filters perform significantly better than both the Laplace of Gaussian and Moss' filter.
Characterization of transepithelial transport of salicylate by the Malpighian tubules of Drosophila melanogaster and the effects of changes in fluid secretion rate
Authors: RUIZ‐SANCHEZ ESAU , O’DONNELL MICHAEL J.
Published: February 2007

Abstract A radioisotope tracer technique is used to study mechanisms and regulation of transepithelial transport of the plant allelochemical salicylate by the Malpighian tubules of Drosophila melanogaster. Transepithelial transport of salicylate is nearly abolished in Na+‐free saline, and inhibited by ouabain, low K+ or K+‐free bathing saline. In addition, the carboxylates probenecid, unlabelled salicylate, fluorescein, and p‐aminohippuric acid (PAH) significantly inhibit transepithelial transport of salicylate. The sulphonates taurocholate and phenol red also inhibit transepithelial transport of salicylate, whereas amaranth has no effect. Stimulation of fluid secretion by cAMP, cGMP or leucokinin I increases transepithelial transport of salicylate, particularly when the concentration of salicylate in the bathing saline is high. The correlation between the fluid secretion rate and transepithelial transport of salicylate shows that 64% of the changes in salicylate transport can be explained on the basis of changes in fluid secretion rate. The results show that naturally‐occurring plant secondary metabolite salicylate is transported into the lumen of the Mapighian tubules of D. melanogaster by a mechanism similar to that previously described for the prototypical organic anions PAH and fluorescein. In addition, the transepithelial transport of salicylate increases in response to increases in fluid secretion rate.
Quantitative trait loci of tolerance to waterlogging in a European oak (Quercus robur L.): physiological relevance and temporal effect patterns
Authors: PARELLE JULIEN , ZAPATER MARION , SCOTTI‐SAINTAGNE CAROLINE , KREMER ANTOINE , JOLIVET YVES , DREYER ERWIN , BRENDEL OLIVER
Published: February 2007

Quercus robur L. is a mid‐European broadleaved tree species that grows readily on temporary waterlogged soils. An experiment aiming to identify potential markers of tolerance to waterlogging in this species and to assess the degree of genetic control over the corresponding traits was conducted. Quantitative trait loci (QTL) were assessed in an F1 progeny for responses to waterlogging, and the relevance of the observed traits as markers of tolerance was investigated using a precise description of the time course of their expression. Five significant QTL involved in the response to waterlogging were identified. In particular, QTL were detected for the development of hypertrophied lenticels and for the degree of leaf epinasty, but not for the formation of adventitious roots. A multi‐environment QTL model allowed a detailed description of the time course (7 weeks) of the allelic substitution effect of some of these QTL. Correlation clustering identified significant clusters of QTL, at inter‐trait as well as at intra‐trait level. These clusters suggest the occurrence of a genetically controlled response cascade to waterlogging.
A new measurement technique reveals temporal variation in δ18O of leaf‐respired CO2
Authors: BARBOUR MARGARET M. , FARQUHAR GRAHAM D. , HANSON DAVID T. , BICKFORD CHRISTOPHER P. , POWERS HEATH , MCDOWELL NATE G.
Published: February 2007

The oxygen isotope composition of CO2 respired by Ricinus communis leaves (δ18OR) was measured under non‐steady‐state conditions with a temporal resolution of 3 min using a tunable diode laser (TDL) absorption spectrometer coupled to a portable gas exchange system. The SD of δ18O measurement by the TDL was ± 0.2‰ and close to that of traditional mass spectrometers. Further, δ18OR values at isotopic steady state were comparable to those obtained using traditional flask sampling and mass spectrometric techniques for R. communis grown and measured in similar environmental conditions. As well as higher temporal resolution, the online TDL method described here has a number of advantages over mass spectrometric techniques.

At isotopic steady state among plants grown at high light, the ‘one‐way flux’ model was required to accurately predict δ18OR. A comparison of measurements and the model suggests that plants grown under low‐light conditions have either a lower proportion of chloroplast CO2 that isotopically equilibrates with chloroplast water, or more enriched δ18O of CO2 in the chloroplast that has not equilibrated with local water. The high temporal resolution of isotopic measurements allowed the first measurements of δ18OR when stomatal conductance was rapidly changing. Under non‐steady‐state conditions, δ18OR varied between 50 and 220‰ for leaves of plants grown under different light and water environments, and varied by as much as 100‰ within 10 min for a single leaf. Stomatal conductance ranged from 0.001 to 1.586 mol m−2 s−1, and had an important influence on δ18OR under non‐steady‐state conditions not only via effects on leaf water H218O enrichment, but also via effects on the rate of the one‐way fluxes of CO2 into and out of the leaf.
Arabidopsis ESK1 encodes a novel regulator of freezing tolerance
Authors: Xin Zhanguo , Mandaokar Ajin , Chen Junping , Last Robert L. , Browse John
Published: February 2007

The eskimo1 (esk1) mutation of Arabidopsis resulted in a 5.5°C improvement in freezing tolerance in the absence of cold acclimation. Here we show that the increase in freezing tolerance is not associated with any increase in the ability to survive drought or salt stresses, which are similar to freezing in their induction of cellular dehydration. Genome‐wide comparisons of gene expression between esk1‐1 and wild type indicate that mutations at esk1 result in altered expression of transcription factors and signaling components and of a set of stress‐responsive genes. Interestingly, the list of 312 genes regulated by ESK1 shows greater overlap with sets of genes regulated by salt, osmotic and abscisic acid treatments than with genes regulated by cold acclimation or by the transcription factors CBF3 and ICE1, which have been shown to control genetic pathways for freezing tolerance. Map‐based cloning identified the esk1 locus as At3g55990. The wild‐type ESK1 gene encodes a 57‐kDa protein and is a member of a large gene family of DUF231 domain proteins whose members encode a total of 45 proteins of unknown function. Our results indicate that ESK1 is a novel negative regulator of cold acclimation. Mutations in the ESK1 gene provide strong freezing tolerance through genetic regulation that is apparently very different from previously described genetic mechanisms of cold acclimation.
Hormone growth responses of roots of shoot height mutants of pea
Authors: Silva Thomas , Davies Peter J.
Published: February 2007

Growth of the roots vertical roots of 12 genotypes of peas (Pisum sativum), which differed in stem height because of differing gibberellin (GA) or brassinosteroid content or signal transduction, was recorded during continuous exogenous applications of differing concentrations of indoleacetic acid (IAA) and GA3, over a period of 12 h with a sensitivity of 2 μm. IAA was inhibitory to all genotypes tested at concentrations of 0.5 nM and above. The response was rapid, reaching a maximum within 20 min. There was no response to 0.1 nM IAA, and no concentration tested promoted growth. At 0.5 nM the growth rate dropped to the same extent as with higher concentrations but then recovered slowly over about 12 h. Roots of nana (na) plants, which have reduced levels of IAA, partially recovered slowly from the inhibition of even 1 μM IAA, to about 20% of the non‐IAA growth rate after 10 h. When IAA (even 1 μM) was removed the growth rate of all lines slowly recovered over about 9 h after a lag of 1 h. IAA application to horizontal roots prevented bending in response to gravity. Roots of 3‐day‐old pea plants of all genotypes were unresponsive to exogenous GA but 5‐day‐old nana plants showed a gradual increase in elongation rate in response to GA, after a lag of a few hours, possibly because of a depletion of GAs provided from the cotyledons of the young plants. Roots in liquid culture did not branch and gradually became thinner. The growth of cultured roots was about 25% of that of intact plants of the same genotype. GA produced no effect on cultured roots, except in nana where it enhanced elongation. IAA was always inhibitory to growth in culture but stimulated branching. Some shoot‐provided factor is necessary for the normal growth and development of the roots.
Tinea capitis: ringworm of the scalp
Authors: Seebacher C. , Abeck D. , Brasch J. , Cornely O. , Daeschlein G. , Effendy I. , Ginter‐Hanselmayer G. , Haake N. , Hamm G. , Hipler Ch. , Hof H. , Korting H. C. , Kramer A. , Mayser P. , Ruhnke M. , Schlacke K.‐H. , Tietz H.‐J.
Published: February 2007

The guideline tinea capitis, as passed by three German medical societies, is presented in the present study.
Shortening the seed‐to‐seed cycle in artichoke breeding by embryo culture
Authors: Cravero V. , Cointry E.
Published: February 2007

Globe artichoke breeders have two important problems: lengthy seed to seed cycle and seed‐borne diseases caused by fungal pathogens. Both problems can be solved by embryo rescue. The objective of this work was to determine the best moment to isolate and culture the embryos and to determine the optimal in vitro culture conditions for their development. For that purpose embryos were collected from five cultivars in different postpollination stages and transferred into two different culture media. Growth regulators present in the medium resulted in poor root induction, but did induce a better shoot per explant development. Data have shown that 20 days is the optimal time for embryo rescue and that a medium without growth regulators would be more suitable for embryo development.
Molecular and genetic analyses of S RNase allele in Japanese pear ‘Osa‐Nijisseiki’ (Pyrus pyrifolia Nakai)
Authors: Wu H.‐Q. , Zhang S.‐L. , Qu H.‐Y.
Published: February 2007

Japanese pears exhibit S‐RNase‐mediated gametophytic self‐incompatibility, and ‘Osa‐Nijisseiki’ (S2S; SM = stylar‐part mutant) is a self‐compatible mutant from ‘Nijisseiki’ (S2S4), in which the S4‐allele exhibits style‐specific inactivation, but behaves as the functional S4‐allele in pollen. It was unclear how S4 RNase mutated to S RNase, despite many investigations having been carried out. In the present study, the S‐RNase genes in ‘Osa‐Nijisseiki’ and its self‐compatible progenies were systematically investigated at genomic, transcriptional and translational level in comparison with its wild type, ‘Nijisseiki’. The results provided evidence that the S4 RNase gene is present in the genome and expressed in the ‘Osa‐Nijisseiki’ style, especially in the stigma, but is not transmitted to its progenies.
Rapid survey for presence of a blast resistance gene Pi‐ta in rice cultivars using the dominant DNA markers derived from portions of the Pi‐ta gene
Authors: Wang Z. , Jia Y. , Rutger J. N. , Xia Y.
Published: February 2007

The Pi‐ta gene in rice confers resistance to strains of the blast pathogen Magnaporthe grisea (Herbert) Borr. (anamorph Pyricularia oryza Cav.) containing the corresponding avirulence gene AVR‐Pita in a gene‐for‐gene fashion. The Pi‐ta gene is a typical nucleotide‐binding site type resistance gene. Nucleotide sequences distinguishing the resistant Pi‐ta and susceptible pi‐ta alleles were previously identified and used for developing DNA markers for a resistant Pi‐ta haplotype and three susceptible pi‐ta haplotypes. In the present study, the existence of the Pi‐ta gene in 141 rice germplasm accessions was rapidly determined using these markers, and the results were confirmed by inoculating rice germplasm with an M. grisea strain containing AVR‐Pita. The Pi‐ta gene was found in accessions from several major rice producing countries, including China, Colombia, Japan, Vietnam, the Philippines, Iran and the United States. The usefulness of DNA markers for rapid determination of the genotype of rice germplasm was thus demonstrated. The Pi‐ta gene also was found in rice cultivar known to contain the Pi‐ta2 gene, although the allelic relationship of these genes remains to be determined. The presence of the Pi‐ta gene in landrace cultivars in several different geographical locations, the Philippines and Vietnam, other indica rice cultivars in China and Colombia suggest that the Pi‐ta gene may have spontaneously originated in indica rice cultivars. These results are useful for incorporating the Pi‐ta gene into advanced breeding lines by marker‐assisted selection for rice breeding programmes worldwide.
Transfer of new dwarfing genes from the weed species Avena fatua into cultivated oat A. byzantina
Authors: Morikawa T. , Sumiya M. , Kuriyama S.
Published: February 2007

New sources of dwarfing genes were identified from accessions of Avena fatua in Japan and Korea. The dwarfing genes were transferred from backcrossed and self‐pollinated relatives to the cultivated oat ‘Kanota’. In the cultivated form, the dominant dwarfing gene Dw8 showed a relatively lower transmission rate than recessive, semi‐dominant and nondwarfing genes and was characterized by a distinct link with wild gene cluster. This was also supported by the high transmission rate of wild specific SSR alleles. Four dwarf inbred lines (L153, L169a, L169b and L812) were identified as involving a single recessive dwarfing gene(s). The recessive dwarfing genes that showed normal and stable transmission rates in BC1F3 were first reported in hexaploid oats. The L169 segregated two different recessive dwarf lines in BC1, which were selected as semi‐ (L169a) and extreme‐ (L169b) dwarf lines. The L169a was a good genotype with a high grain yield. L288 is a semi‐dwarf line conditioned by a semi‐dominant dwarfing gene, with a unilateral panicle, large florets and good grain quality due to strong resistance to lodging. L342 had a short peduncle, making the panicle compact, and its phenotype was similar to the dwarfness controlled by Dw7, but the dwarfing genes were different.
Visitor assemblages at flowers in a tropical rainforest canopy
Authors: KITCHING R. L. , BOULTER S. L. , HOWLETT B. G. , GOODALL K.
Published: February 2007

Abstract  Canopy crane‐based studies have been carried out to quantify the sets of arthropods that visit the flowers of a suite of common species of trees, palms and vines within the Cape Tribulation study area. Those Orders that increase significantly in abundance between the budding and flowering stages of inflorescences are identified, and multivariate and univariate comparisons have been made first, among coflowering plant species and second, at different seasons for the same plant species. The analysis has been repeated for both the profile of higher arthropod taxa in the samples and for the relative abundances of families of Coleoptera: one of the Orders most frequently suggested as critical in the pollination biology of Australian rainforests. In all cases significant differences are identified among species confirming that the visitor profile is a plant species‐specific phenomenon. Profiles within plant species at different times also differed. At the ordinal level significant differences in visitor profiles associated with coflowering plants, were observed, variously, in Thysanoptera, Diptera, Lepidoptera, Coleoptera and Hymenoptera. Within the Coleoptera significant differences occurred in relative abundances of Scarabaeidae, Phalacridae, Latridiidae and Curculionidae. Seasonal differences in visitation to Syzygium gustavioides, Normanbya normanbyi and Calamus radicalis, reflected differences in Diptera, Lepidoptera, Homoptera, Thysanoptera, Hymenoptera and Araneida. Within the Coleoptera, the Elateridae and Curculionidae varied significantly between occasions. The various forms of flower/arthropod interaction that may be represented in these results are discussed, as are the implications for pollination.