bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of spectral FRET imaging microscopy for monitoring nuclear protein interactions
Authors: CHEN YE , MAULDIN JOSHUA P. , DAY RICHARD N. , PERIASAMY AMMASI 
Published: October 2007

SummaryThe spectral processed Förster resonance energy transfer (psFRET) imaging method provides an effective and fast method for measuring protein–protein interactions in living specimens. The commercially available linear unmixing algorithms efficiently remove the contribution of donor spectral bleedthrough to the FRET signal. However, the acceptor contribution to spectral bleedthrough in the FRET image cannot be similarly removed, since the acceptor spectrum is identical to the FRET spectrum. Here, we describe the development of a computer algorithm that measures and removes the contaminating ASBT signal in the sFRET image. The new method is characterized in living cells that expressed FRET standards in which the donor and acceptor fluorescent proteins are tethered by amino acid linkers of specific lengths. The method is then used to detect the homo‐dimerization of a transcription factor in the nucleus of living cells, and then to measure the interactions of that protein with a second transcription factor.
Resolving the geometry of biomolecules imaged by cryo electron tomography
Authors: BONGINI L. , FANELLI D. , SVENSSON S. , GEDDA M. , PIAZZA F. , SKOGLUND U. 
Published: October 2007

SummaryIn this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immonoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.
Image enhancement for increased dot‐counting efficiency in FISH
Authors: SHAH SHISHIR 
Published: October 2007

Summary Background: The most commonly used molecular cytogenetic technique is fluorescence in situ hybridization (FISH). It has been widely applied in many areas of diagnosis and research, including pre‐natal and post‐natal screening of chromosomal aberrations, pre‐implantation genetic diagnosis, cancer cytogenetics, gene mapping, molecular pathology and developmental molecular biology. The analysis of FISH images consists of detecting fluorescent dots, after which the number of dots per cell can be counted or their relative positions can be measured. A major impediment in the analysis of FISH specimens is signal (dot) quality, which is influenced by the hybridization efficiency and/or the sensitivity of the camera that records the images. Method: In this paper, we present an approach to improve the efficiency of detecting fluorescent signals in FISH images by recovering the radiance map of the camera. This allows us to generate a high‐dynamic‐range image wherein an extended range of the sample radiance captured by the camera can be visualized at distinct intensity values. The resulting higher‐order numeric complexity of the transformed image is adjusted (or simplified) by examining the intensity distribution in each of the three colour channels (red, green and blue), and remapping the intensity values to generate a high‐contrast image with a lower‐order (compressed) dynamic range. The remapping is based on a criterion that optimizes the detection of the hybridized signals, allowing attenuation of saturated intensity values while amplifying low‐intensity signals. Results: A simple dot‐counting algorithm is used to automatically process 2000 FISH images. The images are taken for lymphocytes from cultured blood specimens for cytogenetic testing. Images are manually analyzed by an expert to obtain ground truth for dot counts. A quantitative analysis is performed by comparing results of automated dot detection on images before and after enhancement with the developed algorithms. In addition, common errors in dot counting due to split dots, dust, poor segmentation and overlapping signals are analyzed and the robustness of the developed approach against these errors evaluated. It is observed that dot‐detection efficiency is increased by an average of 9% across all colour channels while reducing errors in missed and false dot counts. Conclusions: Our proposed method and results demonstrate that dot‐counting specificity and sensitivity can be improved by pre‐processing and enhancing the image using the radiance curve of the camera and generating a high‐contrast, remapped high‐dynamic‐range image prior to using any algorithm for dot counting.
Morphology of polystyrene films deposited by RF plasma
Authors: HAÏDOPOULOS M. , MIRABELLA F. , HORGNIES M. , VOLCKE C. , THIRY P.A. , ROUXHET P. , PIREAUX J.‐J. 
Published: October 2007

SummaryA new plasma reactor, set up with a large planar inductively coupled source, is used for the first time to deposit a polymer coating (pPS) from a styrene monomer. This work is devoted to the relationship between external plasma parameters and substrate topography, and pPS coating morphology, which is investigated by scanning electron microscopy and atomic force microscopy. Stainless steel, gold and glass surfaces are used as substrates. It is clearly demonstrated that the film morphology can be controlled by adjustment of RF input power, pressure. The analysis performed further reveals that the pPS film's characteristics strongly depend on the substrate topography and its electrical potential during the discharge. Finally, the plasma duration also strongly influences the morphology of the films. The morphologies obtained include smooth films without any specific feature, worm‐like structures, particles (nanometer‐ and micrometer‐sized) associated along preferential directions and randomly distributed particles (micrometer‐sized). The intrinsic topography of the substrate influences the film structure in the case of thin films (thickness lower than about 100 nm).Polymerization is suggested to take place at the surface in contact with the discharge rather than in the gas phase. Nucleation and growth start preferentially on substrate defects such as polishing scratches.
Three‐dimensional point spread function model for line‐scanning confocal microscope with high‐aperture objective
Authors: DUSCH E. , DORVAL T. , VINCENT N. , WACHSMUTH M. , GENOVESIO A. 
Published: October 2007

SummaryPoint Spread Function (PSF) modelling is an important task in image formation analysis. In confocal microscopy, the exact PSF is rarely known, thus one has to rely on its approximation. An initial estimation is usually performed experimentally by measuring fluorescent beads or analytically by studying properties of the optical system. Yet, fluorescent line‐scanning confocal microscopes are not widespread; therefore, very few adapted models are available in the literature. In this paper, we propose an analytical PSF model for line‐scanning confocal microscopes. Validation is performed by measuring the error between our model and an experimental PSF measured with fluorescent beads, assumed to represent the real PSF. Comparison with existing models is also presented.
Confocal microscopy study of the distribution, content and activity of mitochondria during Paracentrotus lividus development
Authors: MORICI GIOVANNI , AGNELLO MARIA , SPAGNOLO FILIPPO , ROCCHERI MARIA CARMELA , LIEGRO CARLO MARIA DI , RINALDI ANNA MARIA 
Published: October 2007

SummaryIn the present paper we applied confocal microscopy and fluorescence technologies for studying the distribution and the oxidative activity of sea urchin (Paracentrotus lividus) mitochondria during development, by in vivo incubating eggs and embryos with cell‐permeant MitoTracker probes. We calculated, by a mathematical model, the intensity values, the variations of intensity, and the variation index of incorporated fluorochromes. Data demonstrate that mitochondrial mass does not change during development, whereas mitochondrial respiration increases. In addition, starting from 16 blastomeres stage, some regions of the embryo contain organelles more active in oxygen consumption.
Do escaped transgenes persist in nature? The case of an herbicide resistance transgene in a weedy Brassica rapa population
Authors: WARWICK S. I. , LÉGÈRE A. , SIMARD M.‐J. , JAMES T. 
Published: October 2007

AbstractThe existence of transgenic hybrids resulting from transgene escape from genetically modified (GM) crops to wild or weedy relatives is well documented but the fate of the transgene over time in recipient wild species populations is still relatively unknown. This is the first report of the persistence and apparent introgression, i.e. stable incorporation of genes from one differentiated gene pool into another, of an herbicide resistance transgene from Brassica napus into the gene pool of its weedy relative, Brassica rapa, monitored under natural commercial field conditions. Hybridization between glyphosate‐resistant [herbicide resistance (HR)]B. napus and B. rapa was first observed at two Québec sites, Ste Agathe and St Henri, in 2001. B. rapa populations at these two locations were monitored in 2002, 2003 and 2005 for the presence of hybrids and transgene persistence. Hybrid numbers decreased over the 3‐year period, from 85 out of ~200 plants surveyed in 2002 to only five out of 200 plants in 2005 (St Henri site). Most hybrids had the HR trait, reduced male fertility, intermediate genome structure, and presence of both species‐specific amplified fragment length polymorphism markers. Both F1 and backcross hybrid generations were detected. One introgressed individual, i.e. with the HR trait and diploid ploidy level of B. rapa, was observed in 2005. The latter had reduced pollen viability but produced ~480 seeds. Forty‐eight of the 50 progeny grown from this plant were diploid with high pollen viability and 22 had the transgene (1:1 segregation). These observations confirm the persistence of the HR trait over time. Persistence occurred over a 6‐year period, in the absence of herbicide selection pressure (with the exception of possible exposure to glyphosate in 2002), and in spite of the fitness cost associated with hybridization.
Old mice, young islands and competing biogeographical hypotheses
Authors: VAN ZANT JEFFREY L. , WOOTEN MICHAEL C. 
Published: October 2007

AbstractNaturally occurring variation within a small rodent species native to the southeastern USA, Peromyscus polionotus, has interested biologists for nearly a century. This species has contributed significantly to our understanding of geographical variation and has often been presented as an example of adaptive evolution. Much of the interest in this organism has been predicated on assumptions that the species is relatively young (< 300 000 bp) and that coastal populations have a very recent history (< 10 000 bp). To test these assumptions and the prevailing biogeographical hypothesis (Recurrent Invasion), we examined nucleotide sequence data from the cytochrome b and D‐loop mitochondrial regions (2449 bp) for 79 samples of P. polionotus collected across the Gulf Coast region of Florida and Alabama. Samples representing Peromyscus maniculatus bairdii, P. m. sonoriensis, P. m. pallescens, and P. keeni were used as outgroups. The degree of cytochrome b divergence (≈ 4.4%) between P. maniculatus and P. polionotus was higher than expected. Analyses consistently indicated that three distinct groups are represented within P. polionotus from the Gulf Coast region. Among these, coastal populations (beach mice) form a monophyletic group and apparently represent a substantially older group (≈ 200 000 year. separation) than previously recognized. Our results were counter to the core assumptions of the existing biogeographical model but were consistent with an alternative hypothesis (Shore‐line Tracking) which provides a more parsimonious explanation for the observed patterns. This research provides new insight into the evolutionary history of P. polionotus and highlights the importance of considering biogeographical history when evaluating extant patterns of natural variation.
Density‐related changes in selection pattern for major histocompatibility complex genes in fluctuating populations of voles
Authors: BRYJA J. , CHARBONNEL N. , BERTHIER K. , GALAN M. , COSSON J. ‐F. 
Published: October 2007

AbstractHost–pathogen interactions are of particular interest in studies of the interplay between population dynamics and natural selection. The major histocompatibility complex (MHC) genes of demographically fluctuating species are highly suitable markers for such studies, because they are involved in initiating the immune response against pathogens and display a high level of adaptive genetic variation. We investigated whether two MHC class II genes (DQA1,DRB) were subjected to contemporary selection during increases in the density of fossorial water vole (Arvicola terrestris) populations, by comparing the neutral genetic structure of seven populations with that estimated from MHC genes. Tests for heterozygosity excess indicated thatDQA1was subject to intense balancing selection. No such selection operated on neutral markers. This pattern of selection became more marked with increasing abundance. In the low‐abundance phase, when populations were geographically isolated, both overall differentiation and isolation‐by‐distance were more marked for MHC genes than for neutral markers. Model‐based simulations identifiedDQA1as an outlier (i.e. under selection) in a single population, suggesting the action of local selection in fragmented populations. The differences between MHC and neutral markers gradually disappeared with increasing effective migration between sites. In the high‐abundance year,DQA1displayed significantly lower levels of overall differentiation than the neutral markers. This gene therefore displayed stronger homogenization than observed under drift and migration alone. The observed signs of selection were much weaker forDRB. Spatial and temporal fluctuations in parasite pressure and locus‐specific selection are probably the most plausible mechanisms underlying the observed changes in selection pattern during the demographic cycle.
Identification of differentially expressed small non‐coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics
Authors: Del Val Coral , Rivas Elena , Torres‐Quesada Omar , Toro Nicolás , Jiménez‐Zurdo José I. 
Published: October 2007

SummaryBacterial small non‐coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA‐encoding genes in the nitrogen‐fixing endosymbiont Sinorhizobium meliloti, performed by a genome‐wide computational analysis of its intergenic regions. Comparative sequence data from eight related α‐proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non‐coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free‐living and symbiotic conditions. Experimental mapping of the 5′‐ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of α‐proteobacteria with their eukaryotic hosts.
Over‐expression of the Arabidopsis AtMYB41 gene alters cell expansion and leaf surface permeability
Authors: Cominelli Eleonora , Sala Tea , Calvi Daniele , Gusmaroli Giuliana , Tonelli Chiara 
Published: October 2007

SummaryThe Arabidopsis AtMYB41 gene encodes an R2R3‐MYB transcription factor whose expression is not detectable under normal growth conditions in any organ or at any developmental stage analysed. It is expressed at high levels in response to drought, ABA and salt treatments, suggesting a possible role in stress responses. Transgenic lines over‐expressing this transcription factor showed a pleiotropic phenotype similar to that exhibited by some mutants that affect cuticle biosynthesis. This includes a dwarf appearance, dependent on smaller cells with abnormal morphology, enhanced sensitivity to desiccation, and enhanced permeability of leaf surfaces, suggesting discontinuity in the cuticle. The expression of genes involved in lipid metabolism and transport, in cell‐wall modifications and cell expansion, genes coding for membrane‐associated proteins and genes specifically involved in cuticle metabolism was differentially modulated between wild‐type and transgenic plants, suggesting a direct or indirect role of AtMYB41 in the regulation of their transcription. Taken together, our results suggest that AtMYB41 is part of a complex network of transcription factors controlling cell expansion and cuticle deposition in response to abiotic stress.
The GRV2/RME‐8 protein of Arabidopsis functions in the late endocytic pathway and is required for vacuolar membrane flow
Authors: Silady Rebecca A. , Ehrhardt David W. , Jackson Karen , Faulkner Christine , Oparka Karl , Somerville Chris R. 
Published: October 2007

SummaryThe gravitropism defective 2 (grv2) mutants of Arabidopsis thaliana were previously characterized as exhibiting shoot agravitropism resulting from mutations in a homolog of the Caenorhabditis elegans RECEPTOR‐MEDIATED ENDOCYTOSIS‐8 (RME‐8) gene, which is required in C. elegans for endocytosis. A fluorescent protein fusion to the GRV2 protein localized to endosomes in transgenic plants, and vacuolar morphology was altered in grv2 mutants. A defect in vacuolar membrane dynamics provides a mechanistic explanation for the gravitropic defect, and may also account for the presence of an enlarged vacuole in early embryos, together with a nutrient requirement during seedling establishment. The GRV2‐positive endosomes were sensitive to Wortmannin but not brefeldin A (BFA), consistent with GRV2 operating late in the endocytic pathway, prior to delivery of vesicles to the central vacuole. The specific enlargement of GRV2:YFP structures by Wortmannin, together with biochemical data showing that GRV2 co‐fractionates with pre‐vacuolar markers such as PEP12/SYP21, leads us to conclude that in plants GRV2/RME‐8 functions in vesicle trafficking from the multivesicular body/pre‐vacuolar compartment to the lytic vacuole.
Bleomycin‐induced flagellate dermatitis
Authors: Vuerstaek Jeroen D. D. , Frank Jorge , Poblete‐Gutiérrez Pamela 
Published: October 2007

AbstractA 62‐year‐old man with testis carcinoma was treated with bleomycin, cisplatin, and etoposide (BEP). During the second cycle of this chemotherapeutic regimen, he developed nonpruritic, linear erythematous lesions in a flagellate‐like fashion on the trunk and extremities. After a short‐term oral prednison therapy and ceasing bleomycin administration, these lesions completely resolved. Herein, the characteristic cutaneous side effects of bleomycin are discussed.
Sporadic nonsyndromal anterior cervical hypertrichosis: case report and review of the literature
Authors: Heitink Martijn V. , Quaedvlieg Patricia J. F. , Van Neer Francoise J. M. A. , Frank Jorge 
Published: October 2007

AbstractA 13‐year‐old girl presented with cosmetically disturbing excessive hair growth in the anterior cervical region that had been present since birth. An X‐ray of the cervical and lumbosacral spine did not show any ossal changes. Based on the clinical findings, the diagnosis of anterior cervical hypertrichosis was made. We successfully treated the patient with an intense pulsed light source. Here, we briefly discuss and review the clinical presentation and causes of localized and generalized hypertrichosis as well as possible treatment modalities.
Nail pigmentation due to hydroxycarbamide
Authors: Ceulen Roeland P. M. , Frank Jorge , Poblete‐Gutiérrez Pamela 
Published: October 2007

AbstractA 47‐year‐old male developed both longitudinal melanonychia and periungual hyperpigmentation 6 months after initiation of hydroxycarbamide (synonym: hydroxyurea) therapy for chronic myeloproliferative disease. Based on the clinical symptoms observed in this patient, the broad differential diagnostic spectrum of hyperpigmentation of the nails is briefly reviewed here. In individuals who undergo hydroxycarbamide treatment, melanonychia might sometimes be seen as side effect and always has to be differentiated from subungual malignant melanoma.
Juvenile amyopathic dermatomyositis with concomitant heart disease
Authors: Nellen Ruud G. L. , Rijzewijk Joris J. , Frank Jorge , Poblete‐Gutiérrez Pamela 
Published: October 2007

AbstractWithin the group of inflammatory myopathies, dermatomyositis is the most frequent disease occurring in childhood. Although most children usually present with muscle disease and dermatological symptoms, a small number of these patients does not manifest myopathy at the time of disease onset. They are therefore diagnosed with juvenile amyopathic dermatomyositis. Sometimes, other organs systems can also be affected, such as the lung, gastrointestinal tract, and heart. As to the latter, the occurrence of cardiac symptoms such as arrhythmia or conduction defects are rare. Here, we report for the first time a patient with childhood amyopathic dermatomyositis and concomitant congenital heart anomalies, including coarctation of the aorta.
Erythema nodosum as an early sign of Crohn's disease
Authors: Van Der Velden Jaap J. A. J. , Van Marion Ariënne M. W. , Kremer Bernd , Straetmans Jos M. J. A. A. , Henquet Charles J. M. , Frank Jorge 
Published: October 2007

AbstractErythema nodosum is the most common form of septal panniculitis and the most frequent skin manifestation associated with inflammatory bowel disease. Since the development of erythema nodosum is closely related with a variety of disorders and conditions, it can serve as an important early sign of systemic disease. We report on a 25‐year‐old woman with Crohn's disease following a long history of recurrent erythema nodosum.
Lupus erythematosus associated with erythema multiforme: Rowell's syndrome
Authors: Shadid Nadia H. , Thissen Carleine A. C. B. , Van Marion Ariënne M. W. , Poblete‐Gutiérrez Pamela , Frank Jorge 
Published: October 2007

AbstractAbout 45 years ago, the association of lupus erythematosus with erythema multiforme and specific immunological laboratory changes was described for the first time. Since then, several patients with similar constellations of clinical symptoms and laboratory parameters have been reported. Today, this disease is known as Rowell's syndrome. However, the fact that not all patients described previously fit all clinical and immunological characteristics that had been originally reported raised the question if Rowell's syndrome really is an own entity or if the simultaneous occurrence of these clinical and immunological signs is rather incidental. Here, we describe a patient fulfilling most of the criteria of Rowell's syndrome and discuss what is currently known about this rare condition.