bluuebunny/crossref_metadata_2025 huggingface dataset:
Parathyroid Hormone as a Predictor of Hypocalcemia after Thyroidectomy
Authors: Vescan Allan , Witterick Ian , Freeman Jeremy
Published: December 2005

Objectives: The aims of this study are to ascertain whether parathyroid hormone (PTH) assay before total/completion thyroidectomy followed by levels immediately thereafter in the recovery room and the morning after surgery are a reliable predictor of hypocalcemia at our institution. In addition, to determine the feasibility of early discharge home from hospital after total thyroidectomy on the basis of postoperative PTH levels.

Study Design: Prospective clinical study.

Methods: Two hundred one patients undergoing total thyroidectomy at our institution were enrolled in the study. Preoperative levels of PTH, serum calcium, ionized calcium, and albumin were drawn. In the postoperative phase, the same biochemical markers were taken in the recovery room within 1 hour of the procedure and at a standard time the morning after the procedure. Discharge planning took place as per existing standards.

Results: Two hundred and one patients were reviewed. PTH levels below 1.1 pmol/L within 1 hour of completion or total thyroidectomy were predictive of risk for developing hypocalcemia, requiring calcium replacement therapy. PTH levels above 1.6 pmol/L were predictive of patients who would remain normocalcemic. Patients who fell in between these two values require further monitoring with conventional calcium levels.

Conclusions: At our institution, PTH assays drawn postoperatively are predictive of patients who are at risk for developing hypocalcemia. Early identification of at‐risk patients will facilitate prompt calcium replacement therapy and potential safe early discharge from hospital.
Positron Emission Tomography Scan to Determine the Need for Neck Dissection after Chemoradiation for Head and Neck Cancer: Timing is Everything
Authors: Canning Christopher A. , Gubbels Samuel , Chinn Crispin , Wax Mark , Holland John M.
Published: December 2005

We present a case of a negative positron emission tomography (PET) scan in a patient with pathologic viable cancer at neck dissection.

Study Design: Case Report.

Methods: A 69‐year‐old man presented with clinical stage T2N2c squamous cell cancer of the left tonsil and was treated with definitive chemoradiation. Left‐sided adenopathy decreased but remained palpable after therapy.

Results: PET scan performed 23 days after completion of treatment showed no suspicious uptake in the left neck. Neck dissection performed at 2 months post‐therapy revealed viable tumor in left cervical nodes.

Conclusions: Persistent adenopathy after chemoradiation for head and neck cancer remains a clinical dilemma. A negative PET scan is accurate but only if the scan is performed 3 to 4 months after therapy.
DNA Repair Gene Polymorphisms and Risk of Second Primary Neoplasms and Mortality in Oral Cancer Patients
Authors: Gal Thomas J. , Huang Wen‐Yi , Chen Chu , Hayes Richard B. , Schwartz Stephen M.
Published: December 2005

Objectives/Hypothesis:We tested the hypothesis that polymorphisms in genes involved in DNA repair pathways are associated with the development of second primary neoplasms of the upper aerodigestive tract (UADT), as well as mortality, in patients previously diagnosed with oral squamous cell cancer (OSCC).

Methods:DNA specimens from 279 OSCC patients who had participated in two previous population‐based case‐control studies were assayed for the following polymorphisms: X‐ray repair cross‐complementing (XRCC) 1 Arg399Gln,XRCC3Thr241Met, xeroderma pigmentosum complementing group D (XPD) Lys751Gln, and O6‐methylguanine‐ DNA methyltransferase (MGMT) Leu84Phe and Val143Ile. Baseline demographic information was obtained from personal interviews and tumor characteristics and treatment were obtained from cancer registry files. Cox proportional hazards models were used to calculate hazards ratio (HR) estimates for each polymorphism in relation to the risk of developing second primary neoplasms at any site, UADT, and head and neck. HRs were also determined for associations with all‐cause mortality and oral cancer specific mortality.

Results:A significant increased risk of second neoplasms (all sites combined, as well as for UADT sites and for head and neck squamous cell cancers) was observed amongXRCC3241Met allele homozygotes (HR 2.65–3.44,P< .02). No significant association with the development of second neoplasms was observed for theXRCC1399Gln,XPD751Gln, orMGMT84Phe or 143Ile alleles. Although no associations with oral cancer‐specific mortality were observed, we found a significant inverse association between all‐cause mortality and possessing at least one copy of theXRCC1399Gln allele (HR 0.68, 95% confidence interval [CI] 0.47–0.97,P= .03), as well as a suggestion of a direct association between all‐cause mortality and having one copy of theXRCC3241Met allele (HR 1.39, 95% CI 0.95–2.03,P= .09).

Conclusions:Polymorphisms in the DNA repair enzyme gene XRCC3 241Met was associated with an increased risk of second neoplasms, and polymorphisms of the XRCC1 399Gln gene were associated with a decreased risk of all‐cause mortality in patients with primary OSCC. These findings require confirmation in other populations before the clinical implications can be considered.
Aerodynamics of the Human Larynx During Vocal Fold Vibration
Authors: Plant Randall L.
Published: December 2005

Objectives: The goal of this study was to comprehensively analyze the influence of aerodynamics on laryngeal function. Three specific aspects were considered: 1) a multidimensional comparison of the interaction of subglottic pressure, sound intensity, and fundamental frequency; 2) examination of instantaneous changes in subglottic pressure during each glottic cycle; and 3) determination of the threshold subglottic pressure for vocal fold vibration and its dependence on other aerodynamic factors.

Study Design: Prospective study with six healthy individuals without history of voice disorders.

Methods: The subjects vocalized the vowel sound /i/ with a variety of different intensities, pitch, and sound intensity. Subglottic air pressure, fundamental frequency, sound intensity, and the electroglottography signal were simultaneously measured.

Results: Linear relationships were seen in all subjects between subglottic air pressure and sound intensity, although there were large variations in the slopes of these relationships. Rapid variations in subglottic pressure during each glottic cycle were detected, corresponding to the opening of the vocal folds with each individual vibration. Threshold pressures for vocal fold vibration were dependent primarily on sound intensity and fundamental frequency and tended to be higher at vibration onset than at offset.

Conclusion: The larynx responded in a predictable pattern to general aerodynamic forces, but there was tremendous variability in its specific behavior. Fundamental frequency and sound intensity tended to increase with subglottic air pressure, but that relationship was not seen consistently in all subjects. The relationship between subglottic air pressure and sound intensity was usually linear, unlike the exponential relationship seen in previous studies. Subglottic pressure was noted to undergo rapid change with each glottic cycle in some, but not all, subjects and was most strongly affected by average subglottic pressure. Phonation threshold air pressure was influenced by the sound intensity and, to a smaller extent, by the fundamental frequency of the voiced sound.
Upregulation of Oncostatin M in Allergic Rhinitis
Authors: Kang Hee Joon , Kang Jae Seong , Lee Sang Hag , Hwang Soon Jae , Chae Sung Won , Woo Jeong‐Soo , Lee Heung‐Man
Published: December 2005

Objectives: Oncostatin M is a multifunctional cytokine belonging to the interleukin‐6 family of cytokines. It has been implicated as an important modulator of lower airway remodeling in the setting of asthma. However, there have been few studies regarding a similar role for the upper airway epithelium in the setting of allergic rhinitis. This study was undertaken to investigate the expression of oncostatin M mRNA and protein in normal and allergic rhinitis nasal mucosa and to localize the expression of the oncostatin M protein in allergic rhinitis.

Materials and Methods: Inferior turbinate mucosa samples from 20 patients with perennial allergic rhinitis and 20 matched normal control subjects were obtained. Oncostatin M mRNA was extracted from the inferior turbinate mucosae, then reverse transcriptase‐polymerase chain reaction was performed and analyzed semiquantitatively. Differences in expression levels of oncostatin M protein between samples from allergic rhinitis patients and normal control subjects were analyzed through Western blot, and oncostatin M protein was localized immunohistochemically.

Results: The expression levels of oncostatin M mRNA and protein were significantly upregulated in patients with allergic rhinitis mucosa. Oncostatin M protein was predominantly localized in the surface epithelium, infiltrating inflammatory cells, vascular endothelium, and submucosal glands and was more strongly expressed in the nasal mucosa of patients with allergic rhinitis than in normal control subjects.

Conclusions: Oncostatin M is expressed in the human nasal mucosa and is upregulated in the setting of allergic nasal inflammation. These results suggest a possible contribution of oncostatin M in the remodeling of the nasal mucosa in allergic rhinitis.
Sentinel Lymph Node Biopsy: A Rational Approach for Staging T2N0 Oral Cancer
Authors: Rigual Nestor , Douglas Wade , Lamonica Dominick , Wiseman Sam , Cheney Richard , Hicks Wesley , Loree Thom
Published: December 2005

Objectives/Hypothesis: For oral cancer patients, the presence of neck nodal metastases is the most important disease prognosticator. However, a significant proportion of clinically N0 patients harbor occult microscopic nodal metastasis. Our objective was to determine the feasibility and accuracy of sentinel node biopsy (SNB) in the staging of T2N0 oral carcinoma patients.

Study Design: Prospective analysis.

Methods: Twenty patients with previously untreated N0 oral cavity squamous cell carcinoma were studied. Each patient had an SNB performed using preoperative technetium sulfur colloid lymphoscintigraphy, intraoperative gamma probe guidance, and intraoperative peritumoral injection of 1% isosulfan blue. All patients underwent neck dissection.

The sentinel lymph nodes (SLNs) were sectioned in 2‐ to 3‐mm intervals, formalin fixed, and sectioned at three levels. The non‐SLNs were sectioned in a routine manner for histologic examination.

Results: SLNs were identified in all patients (100%) and accurately predicted the pathologic nodal status in 18 of 20 patients (90%). Tumor was found exclusively in the SLNs in six patients (30%). Two patients had positive SLNs at multiple neck levels. Two patients had a negative SLN and a positive non‐SLN (false‐negative findings). Occult nodal metastases were present in 60% of the cohort.

Conclusions: SNB is a technically feasible and accurate procedure for staging the neck in oral carcinoma patients. However, SNB accuracy is lower for floor of the mouth lesions. The rate of occult nodal metastases identified in this cohort is higher than previously reported in the literature. These results suggest that SNB warrants further multi‐institutional studies.
On worm-like chain models within the three-dimensional continuum mechanics framework
Authors: Ogden Ray W , Saccomandi Giuseppe , Sgura Ivonne
Published: December 2005

In this paper, we review critically some basic models derived from the statistics of long-chain molecules and then discuss the status of such models within the three-dimensional nonlinear theory of elasticity. We draw attention to some deficiencies of certain worm-like chain (WLC) models when viewed within the three-dimensional continuum mechanics framework. Modifications of the WLC models motivated by such considerations and avoiding these deficiencies are then discussed and shown to correspond well with data generated by the exact WLC model.
Beyond barcodes: complex DNA taxonomy of a South Pacific Island radiation
Authors: Monaghan Michael T , Balke Michael , Pons Joan , Vogler Alfried P
Published: December 2005

DNA barcodes can provide rapid species identification and aid species inventories in taxonomically unstudied groups. However, the approach may fail in recently diverged groups with complex gene histories, such as those typically found on oceanic islands. We produced a DNA-based inventory of taxonomically little known diving beetles (genusCopelatus) in the Fiji archipelago, where they are a dominant component of the aquatic invertebrate fauna. Sampling from 25 localities on five islands and analysis of sequences from one nuclear (328 bp histone 3) and three mitochondrial (492 bprrnL, 786 bpcox1, 333 bpcob) gene regions revealed high haplotype diversity, mainly originated since the Pleistocene, and subdivided into three major phylogenetic lineages and 22 statistical parsimony networks. A traditional taxonomic study delineated 25 morphologically defined species that were largely incongruent with the DNA-based groups. Haplotype diversity and their spatial arrangement demonstrated a continuum of relatedness in FijianCopelatus, with evidence for introgression at various hierarchical levels. The study illustrates the difficulties for formal classification in evolutionarily complex lineages, and the potentially misleading conclusions obtained from either DNA barcodes or morphological traits alone. However, the sequence profile of FijianCopelatusprovides an evolutionary framework for the group and a DNA-based reference system for the integration of ecological and other biodiversity data, independent of the Linnaean naming system.
Hierarchical porous materials for tissue engineering
Authors: Jones Julian R , Lee Peter D , Hench Larry L
Published: December 2005

Biological organisms have evolved to produce hierarchical three-dimensional structures with dimensions ranging from nanometres to metres. Replicating these complex living hierarchical structures for the purpose of repair or replacement of degenerating tissues is one of the great challenges of chemistry, physics, biology and materials science. This paper describes how the use of hierarchical porous materials in tissue engineering applications has the potential to shift treatments from tissue replacement to tissue regeneration. The criteria that a porous material must fulfil to be considered ideal for bone tissue engineering applications are listed. Bioactive glass foam scaffolds have the potential to fulfil all the criteria, as they have a hierarchical porous structure similar to that of trabecular bone, they can bond to bone and soft tissue and they release silicon and calcium ions that have been found to up-regulate seven families of genes in osteogenic cells. Their hierarchical structure can be tailored for the required rate of tissue bonding, resorption and delivery of dissolution products. This paper describes how the structure and properties of the scaffolds are being optimized with respect to cell response and that tissue culture techniques must be optimized to enable growth of new bone
in vitro
.
Pore design and engineering for filters and membranes
Authors: Holdich Richard , Kosvintsev Serguei , Cumming Iain , Zhdanov Sergey
Published: December 2005

In filtration, the concept of pore size is not easy to define. In microfiltration, there are numerous advantages in employing a surface filtering membrane, rather than one relying on depth filtration mechanisms from a tortuous pore flow channel. Modern manufacturing techniques provide means to produce surface filtering membranes. For filtration, it is shown that a suitable pore design is an array of long thin slots. An analysis of fluid flow through the slots suggests that a short slot is adequate, but experimental data with suspended material indicates that slot length is important. Using long slots and careful control of the flow through the membrane it is possible to filter deforming particles such as oil drops from water.
Magnetic coupling of waves and oscillations in the lower solar atmosphere: can the tail wag the dog?
Authors: Erdélyi Robert
Published: December 2005

Can the ubiquitously magnetic solar atmosphere have any effect on solar global oscillations? Traditionally, solar atmospheric magnetic fields are considered to be somewhat less important for the existence and characteristic features of solar global oscillations (
p
,
f
and the not-yet-observed
g
-modes). In this paper, I demonstrate the importance of the presence of magnetism and plasma dynamics for global resonant oscillations in the solar atmosphere. In particular, in the lower part of the solar atmosphere there are both coherent and random components of magnetic fields and velocity fields, each of which contribute on its own to the line widths and frequency variations of solar global acoustic waves.

Changes in the coherent large-scale atmospheric magnetic fields cause frequency shifts of global oscillations over a solar cycle. The random character of the continuously emerging, more localized, magnetic carpet (i.e. small-scale, possibly even sub-resolution, loops) gives rise to additional frequency shifts. On the other hand, random and organized surface and sub-surface flows, like surface granulation, meridional flows or differential rotation, also affect the coupling mechanism of global oscillations to the lower magnetic atmosphere. The competition between magnetic fields and flows is inevitable. Finally, I shall discuss how solar global oscillations can resonantly interact with the overlaying inhomogeneous lower solar atmosphere embedded in a magnetic carpet. Line width broadening and distorsion of global acoustic modes will be discussed. The latter is suggested to be tested and measured by using ring-analysis techniques.
The nature of moss and lower atmospheric seismology
Authors: De Pontieu B , Erdélyi R
Published: December 2005

The discovery of so-called solar ‘moss’, i.e. dynamic and bright upper transition region emission at chromospheric heights above active region plage, provides a novel diagnostic to probe the structure, dynamics, energetics and coupling of the magnetized solar chromosphere and transition region. We briefly review observations of the morphology and connectivity in the low solar atmosphere, with a particular focus on the propagation of oscillations and waves in the moss. We also present recent work that combines moss observations and numerical modelling, and which sheds light on the (quasi-periodic) formation of dynamic jets (spicules), and the propagation of normally evanescent oscillations into the corona. We also briefly explore how coronal oscillations could be exploited to determine the connectivity between photosphere and corona, i.e. perform seismology of the lower solar atmosphere.
Numerical modelling of MHD waves in the solar chromosphere
Authors: Carlsson Mats , Bogdan Thomas J
Published: December 2005

Acoustic waves are generated by the convective motions in the solar convection zone. When propagating upwards into the chromosphere they reach the height where the sound speed equals the Alfvén speed and they undergo mode conversion, refraction and reflection. We use numerical simulations to study these processes in realistic configurations where the wavelength of the waves is similar to the length scales of the magnetic field. Even though this regime is outside the validity of previous analytic studies or studies using ray-tracing theory, we show that some of their basic results remain valid: the critical quantity for mode conversion is the angle between the magnetic field and the k-vector: the attack angle. At angles smaller than 30° much of the acoustic, fast mode from the photosphere is transmitted as an acoustic, slow mode propagating along the field lines. At larger angles, most of the energy is refracted/reflected and returns as a fast mode creating an interference pattern between the upward and downward propagating waves. In three-dimensions, this interference between waves at small angles creates patterns with large horizontal phase speeds, especially close to magnetic field concentrations. When damping from shock dissipation and radiation is taken into account, the waves in the low–mid chromosphere have mostly the character of upward propagating acoustic waves and it is only close to the reflecting layer we get similar amplitudes for the upward propagating and refracted/reflected waves. The oscillatory power is suppressed in magnetic field concentrations and enhanced in ring-formed patterns around them. The complex interference patterns caused by mode-conversion, refraction and reflection, even with simple incident waves and in simple magnetic field geometries, make direct inversion of observables exceedingly difficult. In a dynamic chromosphere it is doubtful if the determination of mean quantities is even meaningful.
Damping of magnetohydrodynamic waves by resonant absorption in the solar atmosphere
Authors: Goossens M , Andries J , Arregui I
Published: December 2005

In the last decade we have been overwhelmed by an avalanche of discoveries of magnetohydrodynamic (MHD) waves by the Solar and Heliospheric Observatory and Transition Region and Coronal Explorer observatories. Both standing and propagating versions of fast magnetoacoustic and slow magnetoacoustic MHD waves have been detected. Information on the damping times and damping distances of these waves is less detailed and less accurate than that on periods and amplitudes. Nevertheless, observations show the damping times and damping lengths are often short. Also, different types of MHD waves in different types of magnetic structures likely require different damping mechanisms. The phenomenon of fast damping is well documented for the standing fast magnetosonic kink waves in coronal loops. This paper concentrates on standing fast magnetosonic waves. It reports on results on periods and damping times due to resonant absorption in one-dimensional and two-dimensional models of coronal loops. Special attention is given to multiple modes.
Quasi-mode damping in two-dimensional fully non-uniform coronal loops
Authors: Arregui I , Van Doorsselaere T , Andries J , Goossens M , Kimpe D
Published: December 2005

Resonantly damped fast kink quasi-modes are computed in fully resistive magnetohydrodynamics for fully non-uniform two-dimensional equilibrium models. The equilibrium model is a straight cylindrically symmetric flux tube with a plasma density that is non-uniform both across and along the loop. The variation of density across the loop can cover the whole loop. Our results indicate that the period and damping of coronal loop oscillations mainly depend on the density contrast and the inhomogeneity length-scale and are independent of the details of longitudinal stratification. This study extends previous studies on coronal loop oscillations, and allows for a better comparison between observations and theory.
Solar atmospheric magnetic effects on global acoustic and atmospheric gravity eigenoscillations
Authors: Pintér Balázs
Published: December 2005

Solar global observations suggest that the frequency and the line width of helioseismic acoustic eigenmodes vary with the solar cycle. One reason for the measured changes could be the variation of the global atmospheric magnetic fields. We model global solar oscillations in a plane-parallel, three-layer model within the framework of linear dissipative magnetohydrodynamics, and study the effects of a homogenous, horizontal atmospheric magnetic field on global oscillations. We find magnetoacoustic
f
- and
p
-modes and also atmospheric gravity modes (
g
-modes) among the eigenoscillations of the system. We conclude that changes in the atmospheric magnetic field can, significantly, shift the frequencies and vary the line width of global oscillation modes.
Excitation and damping of disturbances in cylindrical coronal loops
Authors: Terradas Jaume , Oliver Ramón , Ballester José Luis
Published: December 2005

The excitation and damping of transversal coronal loop oscillations is studied using one-and two-dimensional models of line-tied cylindrical loops. By solving the time-dependent magnetohydrodynamic equations it is shown how an initial disturbance generated in the solar corona induces kink mode oscillations. We investigate the effect of the disturbance on a loop with a non-uniform boundary layer. In particular, a strong damping of transversal oscillations due to resonant absorption is found, such as predicted by previous works based on normal mode analysis.
Introduction
Authors: Erdélyi Robert
Published: December 2005

The Sun's magnetic field is responsible for many spectacularly dynamic and intricate phenomena, such as the 11 year solar activity cycle, the hot and tenuous outer atmosphere called the solar corona, and the continuously expanding stream of solar particles known as the solar wind.

Recently, there has been an enormous increase in our understanding of the role of solar magnetism in producing the observed complex atmosphere of the Sun. One such advance has occurred in the detection, by several different high-resolution space instruments on-board the Solar and Heliospheric Observatory and Transition Region and Coronal Explorer satellites, of magnetic waves and oscillations in the solar corona.

The new subjects of solar atmospheric and coronal seismology are undergoing rapid development. The aim of this Scientific Discussion Meeting was to address the progress made through observational, theoretical and numerical studies of wave phenomena in the magnetic solar plasma. Major theoretical and observational advances were reported by a wide range of international scientists and pioneers in this field, followed by lively discussions and poster sessions on the many intriguing questions raised by the new results. Theoretical and observational aspects of magnetohydrodynamic waves and oscillations in general, and how these wave phenomena differ in various regions of the Sun, including sunspots, the transient lower atmosphere and the corona (in magnetic loops, plumes and prominences), were addressed through invited review papers and selected poster presentations. The results of these deliberations are collected together in this volume.
Evolution of alternative splicing after gene duplication
Authors: Su Zhixi , Wang Jianmin , Yu Jun , Huang Xiaoqiu , Gu Xun
Published: December 2005

Alternative splicing and gene duplication are two major sources of proteomic function diversity. Here, we study the evolutionary trend of alternative splicing after gene duplication by analyzing the alternative splicing differences between duplicate genes. We observed that duplicate genes have fewer alternative splice (AS) forms than single-copy genes, and that a negative correlation exists between the mean number of AS forms and the gene family size. Interestingly, we found that the loss of alternative splicing in duplicate genes may occur shortly after the gene duplication. These results support the subfunctionization model of alternative splicing in the early stage after gene duplication. Further analysis of the alternative splicing distribution in human duplicate pairs showed the asymmetric evolution of alternative splicing after gene duplications; i.e., the AS forms between duplicates may differ dramatically. We therefore conclude that alternative splicing and gene duplication may not evolve independently. In the early stage after gene duplication, young duplicates may take over a certain amount of protein function diversity that previously was carried out by the alternative splicing mechanism. In the late stage, the gain and loss of alternative splicing seem to be independent between duplicates.
L1 integration in a transgenic mouse model
Authors: Babushok Daria V. , Ostertag Eric M. , Courtney Christine E. , Choi Janice M. , Kazazian Haig H.
Published: December 2005

To study integration of the human LINE-1 retrotransposon (L1) in vivo, we developed a transgenic mouse model of L1 retrotransposition that displays de novo somatic L1 insertions at a high frequency, occasionally several insertions per mouse. We mapped 3′ integration sites of 51 insertions by Thermal Asymmetric Interlaced PCR (TAIL–PCR). Analysis of integration locations revealed a broad genomic distribution with a modest preference for intergenic regions. We characterized the complete structures of 33 de novo retrotransposition events. Our results highlight the large number of highly truncated L1s, as over 52% (27/51) of total integrants were <1/3 the length of a full-length element. New integrants carry all structural characteristics typical of genomic L1s, including a number with inversions, deletions, and 5′-end microhomologies to the target DNA sequence. Notably, at least 13% (7/51) of all insertions contain a short stretch of extra nucleotides at their 5′ end, which we postulate result from template-jumping by the L1-encoded reverse transcriptase. We propose a unified model of L1 integration that explains all of the characteristic features of L1 retrotransposition, such as 5′ truncations, inversions, extra nucleotide additions, and 5′ boundary and inversion point microhomologies.
Lectin Receptor Kinases Participate in Protein-Protein Interactions to Mediate Plasma Membrane-Cell Wall Adhesions in Arabidopsis
Authors: Gouget Anne , Senchou Virginie , Govers Francine , Sanson Arnaud , Barre Annick , Rougé Pierre , Pont-Lezica Rafael , Canut Hervé
Published: December 2005

Interactions between plant cell walls and plasma membranes are essential for cells to function properly, but the molecules that mediate the structural continuity between wall and membrane are unknown. Some of these interactions, which are visualized upon tissue plasmolysis in Arabidopsis (Arabidopsis thaliana), are disrupted by the RGD (arginine-glycine-aspartic acid) tripeptide sequence, a characteristic cell adhesion motif in mammals. In planta induced-O (IPI-O) is an RGD-containing protein from the plant pathogen Phytophthora infestans that can disrupt cell wall-plasma membrane adhesions through its RGD motif. To identify peptide sequences that specifically bind the RGD motif of the IPI-O protein and potentially play a role in receptor recognition, we screened a heptamer peptide library displayed in a filamentous phage and selected two peptides acting as inhibitors of the plasma membrane RGD-binding activity of Arabidopsis. Moreover, the two peptides also disrupted cell wall-plasma membrane adhesions. Sequence comparison of the RGD-binding peptides with the Arabidopsis proteome revealed 12 proteins containing amino acid sequences in their extracellular domains common with the two RGD-binding peptides. Eight belong to the receptor-like kinase family, four of which have a lectin-like extracellular domain. The lectin domain of one of these, At5g60300, recognized the RGD motif both in peptides and proteins. These results imply that lectin receptor kinases are involved in protein-protein interactions with RGD-containing proteins as potential ligands, and play a structural and signaling role at the plant cell surfaces.
Organ-Specific Expression of Glutathione S-Transferases and the Efficacy of Herbicide Safeners in Arabidopsis
Authors: DeRidder Ben P. , Goldsbrough Peter B.
Published: December 2005

The functions of plant glutathione S-transferases (GSTs) under normal growth conditions are poorly understood, but their activity as detoxification enzymes has been harnessed in agriculture for selective weed control. Herbicide safeners protect monocot crops from herbicide injury but have little effect on weedy monocot or dicot species. Protection by safeners is associated with expression of herbicide-metabolizing enzymes including GSTs, but the basis for selective action of safeners between monocots and dicots is not known. To address this question we have studied the response of Arabidopsis (Arabidopsis thaliana) to various safeners. Benoxacor, fenclorim, and fluxofenim did not protect Arabidopsis from herbicide injury but did induce RNA expression of the glutathione-conjugate transporters encoded by AtMRP1, AtMRP2, AtMRP3, and AtMRP4. These safeners also induced the organ-specific expression of AtGSTU19 and AtGSTF2, two previously characterized Arabidopsis GSTs from different classes of this enzyme family. RNA hybridization, immunoblot, and reporter gene analyses indicated expression of AtGSTU19 induced by safeners predominated in roots. To test the hypothesis that increased expression of AtGSTU19 would be sufficient to provide tolerance to chloroacetamide herbicides, a chimeric gene was produced containing the open reading frame for this GST driven by a constitutive promoter. Plants containing this transgene had a modest increase in AtGSTU19 protein, predominantly in roots, but this had no effect on tolerance to chloroacetamide herbicides. The localized induction of GSTs by safeners in roots of Arabidopsis may explain why these compounds are unable to provide herbicide tolerance to dicot plant species.
Identification of a Glyphosate-Resistant Mutant of Rice 5-Enolpyruvylshikimate 3-Phosphate Synthase Using a Directed Evolution Strategy
Authors: Zhou Min , Xu Honglin , Wei Xiaoli , Ye Zhiqiang , Wei Liping , Gong Weimin , Wang Yongqin , Zhu Zhen
Published: December 2005

5-Enolpyruvylshikimate 3-phosphate synthase (EPSPS) is a key enzyme in the shikimate pathway and is targeted by the wide-spectrum herbicide glyphosate. Here, we describe the use of a selection system based on directed evolution to select glyphosate-resistant mutants of EPSPS. Using this system, the rice (Oryza sativa) EPSPS gene, mutagenized by Error-Prone polymerase chain reaction, was introduced into an EPSPS-deficient Escherichia coli strain, AB2829, and transformants were selected on minimal medium by functional complementation. Three mutants with high glyphosate resistance were identified in three independent glyphosate selection experiments. Each mutant contained a C317→T transition within the EPSPS coding sequence, causing a change of proline-106 to leucine (P106L) in the protein sequence. Glyphosate resistance assays indicated a 3-fold increase in glyphosate resistance of E. coli expressing the P106L mutant. Affinity of the P106L mutant for glyphosate and phosphoenolpyruvate was decreased about 70-fold and 4.6-fold, respectively, compared to wild-type EPSPS. Analysis based on a kinetic model demonstrates that the P106L mutant has a high glyphosate resistance while retaining relatively high catalytic efficiency at low phosphoenolpyruvate concentrations. A mathematical model derived from the Michaelis-Menten equation was used to characterize the effect of expression level and selection conditions on kinetic (Ki and Km) variation of the mutants. This prediction suggests that the expression level is an important aspect of the selection system. Furthermore, glyphosate resistance of the P106L mutant was confirmed in transgenic tobacco (Nicotiana tabacum), demonstrating the potential for using the P106L mutant in transgenic crops.
A Circadian Rhythm-Regulated Tomato Gene Is Induced by Arachidonic Acid and Phythophthora infestans Infection
Authors: Weyman Philip D. , Pan Zhiqiang , Feng Qin , Gilchrist David G. , Bostock Richard M.
Published: December 2005

A cDNA clone of unknown function, DEA1, was isolated from arachidonic acid-treated tomato (Solanum lycopersicum) leaves by differential display PCR. The gene, DEA1, is expressed in response to the programmed cell death-inducing arachidonic acid within 8 h following treatment of a tomato leaflet, 16 h prior to the development of visible cell death. DEA1 transcript levels were also affected by the late blight pathogen ,Phytophthora infestans. To gain further insight into the transcriptional regulation of DEA1, the promoter region was cloned by inverse PCR and was found to contain putative stress-, signaling-, and circadian-response elements. DEA1 is highly expressed in roots, stems, and leaves, but not in flowers. Leaf expression of DEA1 is regulated by circadian rhythms during long days with the peak occurring at midday and the low point midway through the dark period. During short days, the rhythm is lost and DEA1 expression becomes constitutive. The predicted DEA1 protein has a conserved domain shared by the eight-cysteine motif superfamily of protease inhibitors, α-amylase inhibitors, seed storage proteins, and lipid transfer proteins. A DEA1-green fluorescent protein fusion protein localized to the plasma membrane in protoplasts and plasmolysis experiments, suggesting that the native protein is associated with the plasmalemma in intact cells.
Increased Accumulation of Cuticular Wax and Expression of Lipid Transfer Protein in Response to Periodic Drying Events in Leaves of Tree Tobacco
Authors: Cameron Kimberly D. , Teece Mark A. , Smart Lawrence B.
Published: December 2005

Cuticular wax deposition and composition affects drought tolerance and yield in plants. We examined the relationship between wax and dehydration stress by characterizing the leaf cuticular wax of tree tobacco (Nicotiana glauca L. Graham) grown under periodic dehydration stress. Total leaf cuticular wax load increased after each of three periods of dehydration stress using a CH2Cl2 extraction process. Overall, total wax load increased 1.5- to 2.5-fold, but composition of the wax was not altered. Homologous series of wax components were classified into organic groups; n-hentriacontane was the largest component (>75%) with alcohols and fatty acids representing <10% of the entire wax load. An increase in density, but no change in the three-dimensional shape, of leaf wax crystals was evident under low-kV scanning electron microscopy after each drying event. Leaves excised from plants subjected to multiple drying events were more resistant to water loss compared to leaves excised from well-watered plants, indicating that there is a negative relationship between total wax load and epidermal conductance. Lipid transfer proteins (LTPs) are thought to be involved in the transfer of lipids through the extracellular matrix for the formation of cuticular wax. Using northern analysis, a 6-fold increase of tree tobacco LTP gene transcripts was observed after three drying events, providing further evidence that LTP is involved in cuticle deposition. The simplicity of wax composition and the dramatic wax bloom displayed by tree tobacco make this an excellent species in which to study the relationship between leaf wax deposition and drought tolerance.
The Regulator of G-Protein Signaling Proteins Involved in Sugar and Abscisic Acid Signaling in Arabidopsis Seed Germination
Authors: Chen Yun , Ji Fangfang , Xie Hong , Liang Jiansheng , Zhang Jianhua
Published: December 2005

The regulator of G-protein signaling (RGS) proteins, recently identified in Arabidopsis (Arabidopsis thaliana; named as AtRGS1), has a predicted seven-transmembrane structure as well as an RGS box with GTPase-accelerating activity and thus desensitizes the G-protein-mediated signaling. The roles of AtRGS1 proteins in Arabidopsis seed germination and their possible interactions with sugars and abscisic acid (ABA) were investigated in this study. Using seeds that carry a null mutation in the genes encoding RGS protein (AtRGS1) and the α-subunit (AtGPA1) of the G protein in Arabidopsis (named rgs1-2 and gpa1-3, respectively), our genetic evidence proved the involvement of the AtRGS1 protein in the modulation of seed germination. In contrast to wild-type Columbia-0 and gpa1-3, stratification was found not to be required and the after-ripening process had no effect on the rgs1-2 seed germination. In addition, rgs1-2 seed germination was insensitive to glucose (Glc) and sucrose. The insensitivities of rgs1-2 to Glc and sucrose were not due to a possible osmotic stress because the germination of rgs1-2 mutant seeds showed the same response as those of gpa1-3 mutants and wild type when treated with the same concentrations of mannitol and sorbitol. The gpa1-3 seed germination was hypersensitive while rgs1-2 was less sensitive to exogenous ABA. The different responses to ABA largely diminished and the inhibitory effects on seed germination by exogenous ABA and Glc were markedly alleviated when endogenous ABA biosynthesis was inhibited. Hypersensitive responses of seed germination to both Glc and ABA were also observed in the overexpressor of AtRGS1. Analysis of the active endogenous ABA levels and the expression of NCED3 and ABA2 genes showed that Glc significantly stimulated the ABA biosynthesis and increased the expression of NCED3 and ABA2 genes in germinating Columbia seeds, but not in rgs1-2 mutant seeds. These data suggest that AtRGS1 proteins are involved in the regulation of seed germination. The hyposensitivity of rgs1-2 mutant seed germination to Glc might be the result of the impairment of ABA biosynthesis during seed germination.
The Protein Phosphatase AtPP2CA Negatively Regulates Abscisic Acid Signal Transduction in Arabidopsis, and Effects of abh1 on AtPP2CA mRNA
Authors: Kuhn Josef M. , Boisson-Dernier Aurélien , Dizon Marie B. , Maktabi Mohammad H. , Schroeder Julian I.
Published: December 2005

To identify new loci in abscisic acid (ABA) signaling, we screened a library of 35S∷cDNA Arabidopsis (Arabidopsis thaliana)-expressing lines for ABA-insensitive mutants in seed germination assays. One of the identified mutants germinated on 2.5 μ  m ABA, a concentration that completely inhibits wild-type seed germination. Backcrosses and F2 analyses indicated that the mutant exhibits a dominant phenotype and that the ABA insensitivity was linked to a single T-DNA insertion containing a 35S∷cDNA fusion. The inserted cDNA corresponds to a full-length cDNA of the AtPP2CA gene, encoding a protein phosphatase type 2C (PP2C). Northern-blot analyses demonstrated that the AtPP2CA transcript is indeed overexpressed in the mutant (named PP2CAox). Two independent homozygous T-DNA insertion lines, pp2ca-1 and pp2ca-2, were recovered from the Arabidopsis Biological Resource Center and shown to lack full-length AtPP2CA expression. A detailed characterization of PP2CAox and the T-DNA disruption mutants demonstrated that, whereas ectopic expression of a 35S∷AtPP2CA fusion caused ABA insensitivity in seed germination and ABA-induced stomatal closure responses, disruption mutants displayed the opposite phenotype, namely, strong ABA hypersensitivity. Thus our data demonstrate that the PP2CA protein phosphatase is a strong negative regulator of ABA signal transduction. Furthermore, it has been previously shown that the AtPP2CA transcript is down-regulated in the ABA-hypersensitive nuclear mRNA cap-binding protein mutant abh1. We show here that down-regulation of AtPP2CA in abh1 is not due to impaired RNA splicing of AtPP2CA pre-mRNA. Moreover, expression of a 35S∷AtPP2CA cDNA fusion in abh1 partially suppresses abh1 hypersensitivity, and the data further suggest that additional mechanisms contribute to ABA hypersensitivity of abh1.
Grapes on Steroids. Brassinosteroids Are Involved in Grape Berry Ripening
Authors: Symons Gregory M. , Davies Christopher , Shavrukov Yuri , Dry Ian B. , Reid James B. , Thomas Mark R.
Published: December 2005

Fruit ripening is a unique plant developmental process with direct implications for our food supply, nutrition, and health. In contrast to climacteric fruit, where ethylene is pivotal, the hormonal control of ripening in nonclimacteric fruit, such as grape (Vitis vinifera), is poorly understood. Brassinosteroids (BRs) are steroidal hormones, essential for normal plant growth and development but not previously implicated in the ripening of nonclimacteric fruit. Here we show that increases in endogenous BR levels, but not indole-3-acetic acid (IAA) or GA levels, are associated with ripening in grapes. Putative grape homologs of genes encoding BR biosynthesis enzymes (BRASSINOSTEROID-6-OXIDASE and DWARF1) and the BR receptor (BRASSINOSTEROID INSENSITIVE 1) were isolated, and the function of the grape BRASSINOSTEROID-6-OXIDASE gene was confirmed by transgenic complementation of the tomato (Lycopersicon esculentum) extreme dwarf (dx/dx) mutant. Expression analysis of these genes during berry development revealed transcript accumulation patterns that were consistent with a dramatic increase in endogenous BR levels observed at the onset of fruit ripening. Furthermore, we show that application of BRs to grape berries significantly promoted ripening, while brassinazole, an inhibitor of BR biosynthesis, significantly delayed fruit ripening. These results provide evidence that changes in endogenous BR levels influence this key developmental process. This may provide a significant insight into the mechanism controlling ripening in grapes, which has direct implications for the logistics of grape production and down-stream processing.
Role of Petal-Specific Orcinol O-Methyltransferases in the Evolution of Rose Scent
Authors: Scalliet Gabriel , Lionnet Claire , Le Bechec Mickaël , Dutron Laurence , Magnard Jean-Louis , Baudino Sylvie , Bergougnoux Véronique , Jullien Frédéric , Chambrier Pierre , Vergne Philippe , Dumas Christian , Cock J. Mark , Hugueney Philippe
Published: December 2005

Orcinol O-methyltransferase (OOMT) 1 and 2 catalyze the last two steps of the biosynthetic pathway leading to the phenolic methyl ether 3,5-dimethoxytoluene (DMT), the major scent compound of many rose (Rosa x hybrida) varieties. Modern roses are descended from both European and Chinese species, the latter being producers of phenolic methyl ethers but not the former. Here we investigated why phenolic methyl ether production occurs in some but not all rose varieties. In DMT-producing varieties, OOMTs were shown to be localized specifically in the petal, predominanty in the adaxial epidermal cells. In these cells, OOMTs become increasingly associated with membranes during petal development, suggesting that the scent biosynthesis pathway catalyzed by these enzymes may be directly linked to the cells' secretory machinery. OOMT gene sequences were detected in two non-DMT-producing rose species of European origin, but no mRNA transcripts were detected, and these varieties lacked both OOMT protein and enzyme activity. These data indicate that up-regulation of OOMT gene expression may have been a critical step in the evolution of scent production in roses.
Cell Type-Specific Role of the Retinoblastoma/E2F Pathway during Arabidopsis Leaf Development
Authors: Desvoyes Bénédicte , Ramirez-Parra Elena , Xie Qi , Chua Nam-Hai , Gutierrez Crisanto
Published: December 2005

Organogenesis in plants is almost entirely a postembryonic process. This unique feature implies a strict coupling of cell proliferation and differentiation, including cell division, arrest, cell cycle reactivation, endoreplication, and differentiation. The plant retinoblastoma-related (RBR) protein modulates the activity of E2F transcription factors to restrict cell proliferation. Arabidopsis contains a single RBR gene, and its loss of function precludes gamete formation and early development. To determine the relevance of the RBR/E2F pathway during organogenesis, outside its involvement in cell division, we have used an inducible system to inactivate RBR function and release E2F activity. Here, we have focused on leaves where cell proliferation and differentiation are temporally and developmentally regulated. Our results reveal that RBR restricts cell division early during leaf development when cell proliferation predominates, while it regulates endocycle occurrence at later stages. Moreover, shortly after leaving the cell cycle, most of leaf epidermal pavement cells retain the ability to reenter the cell cycle and proliferate, but maintain epidermal cell fate. On the contrary, mesophyll cells in the inner layers do not respond in this way to RBR loss of activity. We conclude that there exists a distinct response of different cells to RBR inactivation in terms of maintaining the balance between cell division and endoreplication during Arabidopsis (Arabidopsis thaliana) leaf development.