bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic quantification of morphological traits via three‐dimensional measurement of Arabidopsis
Authors: Kaminuma Eli , Heida Naohiko , Tsumoto Yuko , Yamamoto Naoki , Goto Nobuharu , Okamoto Naoki , Konagaya Akihiko , Matsui Minami , Toyoda Tetsuro 
Published: April 2004

SummaryMany mutants have been isolated from the model plant Arabidopsis thaliana, and recent important genetic resources, such as T‐DNA knockout lines, facilitate the speed of identifying new mutants. However, present phenotypic analysis of mutant screens depends mainly on qualitative descriptions after visual observation of morphological traits. We propose a novel method of phenotypic analysis based on precise three‐dimensional (3D) measurement by a laser range finder (LRF) and automatic data processing. We measured the 3D surfaces of young plants of two Arabidopsis ecotypes and successfully defined two new traits, the direction of the blade surface and epinasty of the blade, quantitatively. The proposed method enables us to obtain quantitative and precise descriptions of plant morphologies compared to conventional 2D measurement. The method will open a way to find new traits from mutant pools or natural ecotypes based on 3D data.
The tobacco bZIP transcription factor BZI‐1 binds theGH3promoterin vivoand modulates auxin‐induced transcription
Authors: Heinekamp Thorsten , Strathmann Anne , Kuhlmann Markus , Froissard Marine , Müller Axel , Perrot‐Rechenmann Catherine , Dröge‐Laser Wolfgang 
Published: April 2004

SummaryIn order to establish the biological function of the tobaccobasic leucinezipper (bZIP) transcription factor BZI‐1 in hormone signalling, we have analysed transgenic plants which were altered with respect to the protein level or the activation potential of BZI‐1. Overexpression of a dominant‐negative derivative of BZI‐1, lacking the N‐terminal activation domain, resulted in plants displaying reduced internode size, enhanced lateral shoot formation and small, curly leaves. The response to auxin monitored with reference to root organogenesis, epinastic leaf curvature and transcription of the auxin‐inducedGH3gene was reduced.In vitro, BZI‐1 specifically binds toACGTelements (ACEs) present in theGH3promoter.In vivo, binding to theGH3promoter was confirmed by chromatin immunoprecipitation (ChIP). Overexpression of BZI‐1 in transgenic plants did not lead to a significant activation of theGH3target gene. In contrast, plants expressing a VP16 (Herpes simplex virion protein 16)‐BZI‐1 fusion protein showed enhanced auxin‐inducedGH3transcription. However, VP16‐BZI‐1 is insufficient to triggerGH3expression independently of the auxin stimulus. Whereas auxin responsiveness has been shown to be mediated by ARF (auxin response factor) transcription factors, we discuss a function of BZI‐1 assisting in fine‐tuning of auxin‐induced transcription.
Molecular cloning of the potato Gro1‐4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach
Authors: Paal Jürgen , Henselewski Heike , Muth Jost , Meksem Khalid , Menéndez Cristina M. , Salamini Francesco , Ballvora Agim , Gebhardt Christiane 
Published: April 2004

SummaryThe endoparasitic root cyst nematode Globodera rostochiensis causes considerable damage in potato cultivation. In the past, major genes for nematode resistance have been introgressed from related potato species into cultivars. Elucidating the molecular basis of resistance will contribute to the understanding of nematode–plant interactions and assist in breeding nematode‐resistant cultivars. The Gro1 resistance locus to G. rostochiensis on potato chromosome VII co‐localized with a resistance‐gene‐like (RGL) DNA marker. This marker was used to isolate from genomic libraries 15 members of a closely related candidate gene family. Analysis of inheritance, linkage mapping, and sequencing reduced the number of candidate genes to three. Complementation analysis by stable potato transformation showed that the gene Gro1‐4 conferred resistance to G. rostochiensis pathotype Ro1. Gro1‐4 encodes a protein of 1136 amino acids that contains Toll‐interleukin 1 receptor (TIR), nucleotide‐binding (NB), leucine‐rich repeat (LRR) homology domains and a C‐terminal domain with unknown function. The deduced Gro1‐4 protein differed by 29 amino acid changes from susceptible members of the Gro1 gene family. Sequence characterization of 13 members of the Gro1 gene family revealed putative regulatory elements and a variable microsatellite in the promoter region, insertion of a retrotransposon‐like element in the first intron, and a stop codon in the NB coding region of some genes. Sequence analysis of RT‐PCR products showed that Gro1‐4 is expressed, among other members of the family including putative pseudogenes, in non‐infected roots of nematode‐resistant plants. RT‐PCR also demonstrated that members of the Gro1 gene family are expressed in most potato tissues.
The tandem complex of BEL and KNOX partners is required for transcriptional repression of ga20ox1
Authors: Chen Hao , Banerjee Anjan K. , Hannapel David J. 
Published: April 2004

SummaryTwo interacting three amino acid loop extension (TALE) proteins of potato, StBEL5 (Solanum tuberosom BEL 5) and POTH1 (potato homeobox 1), mediate developmental processes by regulating phytohormone levels. Overexpression of either partner alone increased tuber yields by lowering gibberellin (GA) levels and increasing cytokinins. Gel shift assays demonstrated that StBEL5 and POTH1 bind to the regulatory region of ga20 oxidase1 (ga20ox1) from potato, a gene encoding a key enzyme in the GA biosynthetic pathway. In tandem, StBEL5 and POTH1 had a greater binding affinity for the ga20ox1 promoter than either protein alone. The StBEL5–POTH1 heterodimer bound specifically to a composite 10‐bp sequence, containing two TGAC cores. Using a transcription assay, StBEL5 and POTH1 suppressed the activity of the ga20ox1 promoter by more than 50%. Dominant negative constructs containing the protein‐binding domains of StBEL5 or POTH1 blocked the repression activity of StBEL5 or POTH1, respectively. The mutated ga20ox1 promoter that could be bound by the StBEL5 or POTH1 proteins individually but not by the StBEL5–POTH1 heterodimer also abolished the repression activity of StBEL5, POTH1, and the StBEL5–POTH1 heterodimer. These results indicate that the tandem interaction of StBEL5 and POTH1 is essential for regulation of the expression of their target gene.
Real‐time RT‐PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root‐ and shoot‐specific genes
Authors: Czechowski Tomasz , Bari Rajendra P. , Stitt Mark , Scheible Wolf‐Rüdiger , Udvardi Michael K. 
Published: April 2004

SummaryTo overcome the detection limits inherent to DNA array‐based methods of transcriptome analysis, we developed a real‐time reverse transcription (RT)‐PCR‐based resource for quantitative measurement of transcripts for 1465 Arabidopsis transcription factors (TFs). Using closely spaced gene‐specific primer pairs and SYBR® Green to monitor amplification of double‐stranded DNA (dsDNA), transcript levels of 83% of all target genes could be measured in roots or shoots of young Arabidopsis wild‐type plants. Only 4% of reactions produced non‐specific PCR products. The amplification efficiency of each PCR was determined from the log slope of SYBR® Green fluorescence versus cycle number in the exponential phase, and was used to correct the readout for each primer pair and run. Measurements of transcript abundance were quantitative over six orders of magnitude, with a detection limit equivalent to one transcript molecule in 1000 cells. Transcript levels for different TF genes ranged between 0.001 and 100 copies per cell. Only 13% of TF transcripts were undetectable in these organs. For comparison, 22K Arabidopsis Affymetrix chips detected less than 55% of TF transcripts in the same samples, the range of transcript levels was compressed by a factor more than 100, and the data were less accurate especially in the lower part of the response range. Real‐time RT‐PCR revealed 35 root‐specific and 52 shoot‐specific TF genes, most of which have not been identified as organ‐specific previously. Finally, many of the TF transcripts detected by RT‐PCR are not represented in Arabidopsis EST (expressed sequence tag) or Massively Parallel Signature Sequencing (MPSS) databases. These genes can now be annotated as expressed.
The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways
Authors: Cluis Corinne P. , Mouchel Céline F. , Hardtke Christian S. 
Published: April 2004

SummaryThe role of the Arabidopsis transcription factor LONG HYPOCOTYL 5 (HY5) in promoting photomorphogenic development has been extensively characterized. Although the current model for HY5 action largely explains its role in this process, it does not adequately address the root phenotype observed in hy5 mutants. In our search for common mechanisms underlying all hy5 traits, we found that they are partly the result of an altered balance of signaling through the plant hormones auxin and cytokinin. hy5 mutants are resistant to cytokinin application, and double mutant analyses indicate that a decrease in auxin signaling moderates hy5 phenotypes. Microarray analyses and semiquantitative RT‐PCR indicate that two negative regulators of auxin signaling, AUXIN RESISTANT 2 (AXR2)/INDOLE ACETIC ACID 7 (IAA7) and SOLITARY ROOT (SLR)/IAA14, are underexpressed in hy5 mutants. The promoters of these genes contain a putative HY5 binding site, and in line with this observation, HY5 can bind to the promoter of AXR2 in vitro. Increased AXR2 expression in a hy5 background partially rescues the elongated hypocotyl phenotype. In summary, it appears that auxin signaling is elevated in hy5 mutants because HY5 promotes the expression of negative regulators of auxin signaling, thereby linking hormone and light signaling pathways.
Tracing cell fate in brain formation during embryogenesis of the ascidian Halocynthia roretzi
Authors: Taniguchi Kazuto , Nishida Hiroki 
Published: April 2004

Ascidian eggs develop into tadpole larvae. They have a simple central nervous system (CNS) at the dorsal midline. The CNS is formed through neural tube formation at the neurula stage, as in vertebrates. The total number of cells in the CNS is approximately 300. In Halocynthia roretzi, the anterior part of the CNS, which consists of the brain (sensory vesicle) and the visceral ganglion, is exclusively derived from 10 blastomeres at the 110‐cell stage. The anterior CNS is relatively complex and shows remarkable left–right asymmetry, with the lumen of the sensory vesicle, the otolith, and the ocellus on the right side, and the presumed hydrostatic pressure organ on the left side. We labeled these 10 precursor blastomeres – six in the animal hemisphere (a‐line) and four in the vegetal hemisphere (A‐line) – with lineage tracer, and examined the fates in swimming larvae. The clonal organization of the anterior CNS is essentially invariant among individuals, although slight variation in the clonal boundary was observed. There was no extensive mixing between descendants of each precursor. We observed no evidence of cell migration except for two neuronal cells derived from a8.25 blastomeres. The eventual fates of the bilateral blastomeres produced extensive left–right asymmetry. The results suggest that the anterior neural tube rotates in a clockwise direction when viewed from the posterior pole. Staged observation indicated that this rotation takes place during the last 5 h of embryogenesis. We describe detailed positions of descendants of each precursor blastomere. In particular, specific cells of sensory structures were identified by their morphology and staining with specific antibodies and probes. The otolith and ocellus pigment cells were derived from left and right a8.25 blastomeres. Lens cells of the ocellus have a right A8.8 origin, and most of the photoreceptor cells originated from the right A8.7. The presumed pressure organ was formed by descendants of left and right a8.19 and left a8.17 blastomeres. The description of cell lineages of the CNS would facilitate future research to analyze the mechanisms of development of the simple CNS of ascidian tadpole larvae.
Functional role of a high mol mass protein complex in the sea urchin yolk granule
Authors: Perera Aruni , Davis Philip , Robinson John J. 
Published: April 2004

We have investigated the biochemical and functional characteristics of the major protein constituents of the yolk granule organelle present in sea urchin eggs and embryos. Compositional analysis, using sodium dodecyl sulfate polyacrylamide gel electrophoresis, revealed distinctly different polypeptide patterns under reducing and non‐reducing conditions. In the presence of reducing agent, a 240 kDa species dissociated into polypeptides of apparent mol mass 160, 120 and 90 k. The relatedness of these polypeptides to the 240 kDa species was demonstrated in protein gel blot and peptide mapping analyses. The profile of yolk granule polypeptides was dynamic during embryonic development with the disappearance of the 160 kDa species and the coincidental appearance of lower mol mass polypeptides. However, the 240 kDa complex was detected even after the disappearance of the 160 kDa polypeptide. The 240 kDa complex was released from yolk granules in the absence of calcium and the purified species was shown to bind liposomes in a calcium‐dependent manner. In addition, the 240 kDa complex possessed a calcium‐dependent, liposome aggregating activity. The 240 kDa species could also induce the aggregation of yolk granules, previously denuded of the complex following treatment with either ethylenediaminetetraacetic acid or trypsin. Collectively, these results demonstrate the dynamic characteristics of the yolk granule 240 kDa protein complex and offer insights into a possible functional role.
Differentiation of slow and fast fibers in tentacles of Sepia officinalis (Mollusca)
Authors: Grimaldi Annalisa , Tettamanti Gianluca , Brivio Maurizio F. , Valvassori Roberto , De Eguileor Magda 
Published: April 2004

The tentacles of Sepia officinalis are cylindrical muscular structures that can be quickly everted and elongated to capture prey. The combination of both velocity and extensive elongation of the tentacles is due to the presence of both cross‐striated and helical muscles. The complex organization and differentiation of different fibers has been studied in cuttlefish extracted from egg gel coats at different developmental stages, and in completely developed animals. Tentacle muscles start to differentiate centrifugally from the area close to the axial nervous system, where two types of myocytes can be recognized. These populations of myocytes, which may be distinguished morphologically and which express different myosin isoforms, give rise to fast and slow muscles.The presence in molluscs of slow and fast muscles arising from different populations of myocytes, as in vertebrate muscle development, could be considered as an example of evolutionary conservation.
Northern New Zealand Rhegmatogenous Retinal Detachment Study: epidemiology and risk factors
Authors: Polkinghorne Philip J , Craig Jennifer P 
Published: April 2004

Abstract Background: The incidence of retinal detachment in New Zealand is not currently documented in the literature. This study sought to determine the annual incidence of rhegmatogenous retinal detachment (RRD) and associated risk factors in northern New Zealand. Methods: Epidemiological and clinical data were collected for all patients presenting with a RRD in a 12‐month interval in a confined geographical area of New Zealand. Results: One hundred and forty‐one patients presented between May 1997 and April 1998 with a RRD. Five patients presented with bilateral RRD. The mean age at presentation was 53.9 years and the annual incidence for RRD was 11.8 cases per 100 000 people. RRD was more common in males than in females (1.3:1). Ocular trauma, high myopia and cataract extraction were found to be significant risk factors in the development of RRD. Conclusions: The annual incidence of RRD in northern New Zealand is comparable to values reported for other parts of the world and, consistent with previous studies, the incidence of RRD was found to increase with age, and in association with trauma, high myopia and cataract surgery.
Sympathetic ophthalmia following ciliary body laser cyclophotocoagulation for rubeotic glaucoma
Authors: Kumar Nikhil , Chang Andrew , Beaumont Paul 
Published: April 2004

AbstractA 60‐year‐old Asian man presented with left rubeotic glaucoma secondary to a central retinal vein occlusion. He was successfully treated with laser diode cyclophotocoagulation of the ciliary body. Nine months later he developed right progressive visual loss, headache, corneal oedema, anterior chamber cells, flare, mutton fat keratic precipitates, a swollen disc, and a minimal inferior visual field defect. A diagnosis of sympathetic ophthalmia was made, which was confirmed by characteristic findings seen on fluorescein and indocyanine green angiography.
Deposits in artificial corneas: risk factors and prevention
Authors: Hicks Celia R , Chirila Traian V , Werner Liliana , Crawford Geoffrey J , Apple David J , Constable Ian J 
Published: April 2004

Abstract Purpose: To identify risk factors for calcium deposition and pigmented staining within AlphaCor artificial corneas. Methods: Retrospective analysis of data from 72 AlphaCor implantations was conducted. Histological analysis of explants was performed. Results: Eight cases of either intraoptic calcium or pigment deposition occurred in AlphaCor patients between 2.5 and 21 months after implantation. Four cases had diffuse white deposits, confirmed to be calcium and associated with prior coadministration of topical steroids and beta‐blockers. The other four cases had brown deposits, associated with cigarette smoking and topical levobunolol. Conclusion: These findings led to changes in patient management protocols, surgeon training and patient information so as to minimize the risk of further occurrences. No further cases of white deposition have occurred after warning surgeons of the risk associated with certain topical therapy combinations. The risk of brown staining may be difficult to remove completely as it appears that environmental exposure to chemicals may cause deposition in addition to personal smoking habits and topical medications.
Clinical Case Notes
Authors: Landers John , Tang K C , Hing Stephen 
Published: April 2004

AbstractThe visual field can be affected by disorders involving any part of the visual pathway, from the retina to the striate cortex. The pattern of visual field damage can indicate the location of the disorder. The case is presented here of an 8‐year‐old girl with congenital glaucoma. Initial perimetry appeared consistent with glaucomatous field loss; however, this evolved into a homonymous quadrantanopia, indicating the presence of a cerebral lesion as the cause. Computed tomography and magnetic resonance imaging scans detected a large middle cranial fossa arachnoid cyst. Postoperatively there was resolution of the visual field defects secondary to the arachnoid cyst. The pattern of field loss was pivotal in this patient's management. Attention must be paid when caring for the patient with a chronic disease to ensure that concurrent conditions are diagnosed.
Clinical Case Notes
Authors: Garrott Helen M , Walland Mark J 
Published: April 2004

AbstractRaised intraocular pressure and glaucoma have rarely been associated with use of periorbital corticosteroids for dermatological conditions such as blepharitis and eczema. Three cases are described in which periorbital topical corticosteroids appear to have resulted in raised intraocular pressure or glaucoma. Topical corticosteroids used for dermatological conditions around the face and eyes are often regarded as being fairly innocuous with regard to ocular side‐effects. This case series demonstrates that secondary open‐angle glaucoma can be a sight‐threatening consequence, and periorbital steroids should therefore be used cautiously and sparingly, particularly in those with a family history of glaucoma. Intraocular pressure may not always return to normal upon cessation of the drug.
Systemic autonomic function in subjects with primary angle‐closure glaucoma: a comparative study of symptomatic and asymptomatic disease presentation
Authors: Yong Vernon KY , Umapathi Thirugnanam , Aung Tin , Tan Nigel CK , Lee Jong‐Jian , Liew Geok‐Cheng , Yip Chee‐Chew , Foster Paul J , Chew Paul TK 
Published: April 2004

Abstract Background: Autonomic dysfunction is thought to be a contributory factor in primary angle‐closure glaucoma (PACG) by precipitating pupil block in anatomically predisposed eyes. This study aimed to compare systemic autonomic function between subjects who had suffered a previous episode of acute angle closure (symptomatic PACG), those who had asymptomatic PACG, and age and sex‐matched controls. Methods: Tests for systemic parasympathetic function included the heart‐rate response to standing (30:15 ratio), heart‐rate variation during deep breathing, and the ratio of the heart rate at phases IV and II of the Valsalva manoeuvre (Valsalva ratio). For assessment of the sympathetic nervous system, blood pressure was recorded supine and then after 2 and 5 min of standing. A modified sweat test, the sympathetic skin response, was recorded on the palm and sole. Results: A total of 30 subjects were examined: eight previous symptomatic PACG, eight asymptomatic PACG and 14 control subjects. The mean ages were similar, and all except one subject were Chinese. None of the subjects had evidence of systemic dysautonomia. There was no significant difference found between the groups for the 30:15 ratio, heart‐rate variation during deep respiration and the Valsalva ratio. No significant orthostatic hypotension was detected in subjects with PACG. Abnormal sympathetic skin response was not more common in PACG subjects compared to control subjects. Conclusions: This study identified no systemic autonomic dysfunction in people with PACG.