bluuebunny/crossref_metadata_2025 huggingface dataset:
Adsorption kinetics and patterning of a Si(111)-7×7 surface by dissociation of methanol
Authors: Tanaka Ken-ichi , Xie Zhao-Xiong
Published: January 2005

CH 3 OH undergoes dissociation on a Si(111)-7×7 surface via a two dimensionally free precursor. The sticking probability attained by the STM (scanning tunneling microscopy) was entirely coverage independent, where the observed image represented the final state of the adsorption. CH3OH dissociates equally on the faulted and unfaulted halves at room temperature. However, the dissociation at the center adatom-rest atom site is four times preferential to that at the corner adatom-rest atom site in each half unit cell. Such site selectivity, center/corner, changes with the occupation of adatoms in corresponding half unit cell, that is, center/corner=4 for the half unit cell with one reacted adatom, but 2.6 and 1.8 for the half unit cells with two and three reacted adatoms, respectively. Such site selectivity is well rationalized by the dissociation depending on the local conformation of the site instead of the local density of states (LDOS). The site selectivity of center/corner is well reproduced by considering the occurrence probability of the whole dissociation pattern. As the STM image represents the final state of the adsorption, if the final step of adsorption involves dissociation of molecule or precursor, the STM image reflects the dissociation probability depending on the local structure. On the other hand, if no dissociation of molecule or precursor is involved at the final step, the adsorption probability might depend on the LDOS. The adsorption of H2S, H2O, and NH3 is also discussed from this general viewpoint of adsorption. The concept of a two dimensionally free precursor will be important to understand the kinetics of heterogeneous catalysis.
The birth of a bubble: A molecular simulation study
Authors: Neimark Alexander V. , Vishnyakov Aleksey
Published: January 2005

We study the nucleation of a bubble in a metastable Lennard-Jones (LJ) fluid, confined to a spherical pore with wetting walls, by a combination of grand canonical, canonical ensemble, and gauge cell Monte Carlo simulation methods complemented by the Voronoi–Delaunay tessellation analysis of statistical geometry of intermolecular cavities. We construct the isotherm of confined fluid in the form of a continuous van der Waals’ loop, in which the unstable backward trajectory between the spinodals corresponds to bubble states. We show that as the degree of metastability increases and the fluid becomes progressively stretched, the decrease of fluid density is associated with the evolution of a population of interstitial intermolecular cavities. At the spinodal, the fluid becomes mechanically unstable: Interstitial cavities partly coalesce into a larger cavity located due to the system symmetry around the pore center. This cavity represents a bubble embryo, which grows at the expense of interstitial cavities. The nucleation barrier is calculated by direct thermodynamic integration along the isotherm. We compare our simulation results to the predictions of the classical nucleation theory and experiments on capillary condensation–evaporation of nitrogen in pores of hybrid organic–inorganic mesoporous molecular sieve HMM-3.
An ab initio study of the structure, torsional potential energy function, and electric properties of disilane, ethane, and their deuterated isotopomers
Authors: Puzzarini Cristina , Taylor Peter R.
Published: January 2005

Highly accurate ab initio computations of the molecular structure and properties, torsional potential energy function, and harmonic force field of disilane and ethane have been carried out. Equilibrium parameters as well as vibrational corrections have been evaluated. In addition, for these systems a vibrational averaging procedure has been employed for calculating the dipole moment of molecules which have no permanent dipole moment, i.e., SiH3SiD3 and CH3CD3. The molecular and spectroscopic properties calculated for ethane and its isotopomers provide a calibration against known experimental data, allowing us to estimate the reliability of our computed results for disilane for which there is much less experimental data. The goal of the present study is to predict the molecular parameters, with estimated uncertainties, that determine the microwave spectrum of SiH3SiD3.
From the double-stranded helix to the chiral nematic phase of B-DNA: A molecular model
Authors: Tombolato Fabio , Ferrarini Alberta
Published: January 2005

B-DNA solutions of suitable concentration form left-handed chiral nematic phases (cholesterics). Such phases have also been observed in solutions of other stiff or semiflexible chiral polymers; magnitude and handedness of the cholesteric pitch are uniquely related to the molecular features. In this work we present a theoretical method and a numerical procedure which, starting from the structure of polyelectrolytes, lead to the prediction of the cholesteric pitch. Molecular expressions for the free energy of the system are obtained on the basis of steric and electrostatic interactions between polymers; the former are described in terms of excluded volume, while a mean field approximation is used for the latter. Calculations have been performed for 130 base pair fragments of B-DNA. The theoretical predictions provide an explanation for the experimental behavior, by showing the counteracting role played by shape and charge chirality of the molecule.
The effect of preamorphization energy on ultrashallow junction formation following ultrahigh-temperature annealing of ion-implanted silicon
Authors: Gable K. A. , Robertson L. S. , Jain Amitabh , Jones K. S.
Published: January 2005

High-power arc lamp design has enabled ultrahigh-temperature (UHT) annealing as an alternative to conventional rapid thermal processing (RTP) for ultrashallow junction formation. The time duration of the UHT annealing technique is significantly reduced from those obtained through conventional RTP. This difference in time may offer the ability to maintain a highly activated ultrashallow junction without being subjected to transient enhanced diffusion (TED), which is typically observed during postimplant thermal processing. In this study, two 200-mm (100) n-type Czochralski-grown Si wafers were preamorphized with either a 48- or a 5-keV Ge+ implant to 5×1014cm2, and subsequently implanted with 3-keV BF2+ molecular ions to 6×1014cm2. The wafers were sectioned and annealed under various conditions in order to investigate the effects of the UHT annealing technique on the resulting junction characteristics. The main point of the paper is to show that the UHT annealing technique is capable of producing a highly activated p-type source∕drain extension without being subjected to TED only when the preamorphization implant is sufficiently deep.
Interface structures and periodic film distortions induced by substrate-surface steps in Gd-doped ceria thin-film growth
Authors: Huang D. X. , Chen C. L. , Jacobson A. J.
Published: January 2005

Gadolinium-doped ceria (Ce0.8Gd0.2O2−δ) thin films were grown on single-crystal (001) LaAlO3 (LAO) substrates by a pulsed laser ablation. The transmission electron microscope observation reveals a unique type of periodic film distortion along the film∕substrate interface. Each distorted film area is associated with a few substrate-surface steps and the spacing between these distorted areas is about 50μm. The distortion starts at the substrate-surface steps and extends into the film along one of the {111} planes at the step-forward direction. The {111} planar defects induced by the nearby steps can interact with each other to form a planar defect network. The structure of the (001) LAO surface, the structure of the film∕substrate interface, and the mechanism of the formation of these {111} planar defects have been analyzed using a high-resolution electron microscopy. Structural models for these planar defects and their interaction are suggested.
Dopant penetration studies through Hf silicate
Authors: Quevedo-Lopez M. A. , Visokay M. R. , Chambers J. J. , Bevan M. J. , LiFatou A. , Colombo L. , Kim M. J. , Gnade B. E. , Wallace R. M.
Published: January 2005

We present a study of the penetration of B, P, and As through Hf silicate (HfSixOy) and the effect of N incorporation in Hf silicate (HfSixOyNz) on dopant penetration from doped polycrystalline silicon capping layers. The extent of penetration through Hf silicate was found to be dependent upon the thermal annealing budget for each dopant investigated as follows: B(T⩾950°C∕60s), P(T⩾1000°C∕20s), and As (T⩾1050°C∕60s). We propose that the enhanced diffusion observed for these dopants in HfSixOy, compared with that of SiO2 films, is related to grain boundary formation resulting from HfSixOy film crystallization. We also find that, as in the case of SiO2, N incorporation inhibits dopant (B, P, and As) diffusion through the Hf silicate and thus penetration into the underlying Si substrate. Only B penetration is clearly observed through HfSiON films for anneals at 1050 °C for durations of 10 s or longer. The calculated B diffusivity through the HfSixOyNz layer is D0=5.2×10−15cm2∕s.
Two-dimensional simulation of a direct-current microhollow cathode discharge
Authors: Kothnur Prashanth S. , Raja Laxminarayan L.
Published: January 2005

Microhollow cathode discharges (MHCD’s) are miniature direct-current discharges that operate at elevated pressures (several tens to hundreds of Torr) with electrode dimensions in the 10–100-μm range. MHCD’s have been proposed for a number of applications based on their unique characteristics such as presence of intense excimer radiation and significant gas heating within the submillimeter discharge volume. A two-dimensional, self-consistent fluid model of a helium MHCD in the high-pressure (several hundreds of Torr), high-current (∼1mA) operating regime is presented in this study. Results indicate that the MHCD operates in an abnormal glow discharge mode with charged and excited metastable species with densities of ∼1020m−3, electron temperatures of approximately tens of eV, and gas temperatures of hundreds of Kelvin above room temperature. Significant discharge activity exists outside of the hollow region. The discharge volume and intensity increases with increasing current and becomes more confined with increasing pressures. Most predictions presented in this paper are in qualitative and quantitative agreement with experimental data for MHCD’s under similar conditions.
Growth and properties of ZnO nanoblade and nanoflower prepared by ultrasonic pyrolysis
Authors: Suh Hyo-Won , Kim Gil-Young , Jung Yeon-Sik , Choi Won-Kook , Byun Dongjin
Published: January 2005

ZnO nanoblades and nanoflowers are synthesized using zinc acetate dihydrate Zn(CH3COO)2∙2H2O dissolved in distilled water by ultrasonic pyrolysis at 380–500°C. Thermogravimetry-differential scanning calorimetry, x-ray diffraction, field-emission scanning electron microscopy, high-resolution transmission electron microscopy, Raman spectroscopy, and low-temperature photoluminescence (PL) were used to characterize the thermal properties, crystalline and optical features of the ZnO nanostructures. The results showed that at 400°C the formation of nanoblades resulted from the simultaneous precipitation and nucleation in zinc acetate precursor. At an elevated temperature of 450°C, decomposition was almost advanced and thus the size of nanopetal became smaller and aggregates became larger by as much as 60nm. The formation of aggregates is explained in terms of random nucleation model. Through PL measurement, nanoblade showed a strong near band-edge emission with negligible deep-level emission and free exciton band-gap energy Eg(0)=3.372eV and Debye temperature β=477±65K by the fitting curve of free exciton peak as a function of temperature to Varshni equation, Eg(T)=Eg(0)−αT2∕(β+T), which are very close to bulk ZnO.
Cellular transformation by the MSP58 oncogene is inhibited by its physical interaction with the PTEN tumor suppressor
Authors: Okumura Koichi , Zhao Mujun , DePinho Ronald A. , Furnari Frank B. , Cavenee Webster K.
Published: January 2005

The PTEN (phosphatase and tensin homologue) tumor suppressor protein contains a single catalytic domain with both lipid and protein phosphatase activities. The remaining C-terminal half of the PTEN protein plays a role in its stability and is mutated in many clinical cancer samples. Here, we report that the PTEN C-terminal domain physically interacts with the forkhead-associated domain of the oncogenic MSP58 protein and that this interaction requires PTEN Thr-366. We further show that while MSP58 transforms
Pten
–/– mouse embryo fibroblasts (MEFs), concurrent introduction of wild-type PTEN causes a dramatic reduction in the number of MSP58-induced transformed foci. This PTEN-mediated inhibition of cellular transformation requires physical interaction as evidenced by the failure of PTEN(T366A) point mutation (residing within the MSP58 interaction domain) to suppress MSP-58-driven transformation. These observations, together with the capacity of catalytically inactive PTEN mutant (G129R) to suppress MSP58 oncogenicity, support the view that the C-terminal region of PTEN directly provides a previously uncharacterized biological function in its ability to regulate cellular transformation.
Low-dose dental computed tomography: significant dose reduction without loss of image quality
Authors: Rustemeyer P. , Streubühr U. , Suttmoeller J.
Published: January 2005

Purpose: To measure and reduce the patient dose during computed tomography (CT) for dental applications.

Material and Methods: Lithium fluoride thermoluminescent dosimeters were implanted in a tissue-equivalent humanoid phantom (Alderson-Rando-Phantom) to determine doses to the thyroid gland, the active bone marrow, the salivary glands, and the eye lens. Dental CT was performed with spiral CT and a dental software package. The usual dental CT technique was compared with a new dose-reduced protocol, which delivered best image quality at lowest possible radiation dose, as tested in a preceding study. Image quality was analysed using a human anatomic head preparation. In addition, the radiation dose was compared with panoramic radiography and digital volume tomography (DVT). Eight radiologists evaluated all images in a blinded fashion. A Wilcoxon rank pair test was used for statistical evaluation.

Results: Radiation dose could be reduced by a factor of 9 (max.) with the new dose-reduced protocol (e.g. bone marrow dose from 23.6 mSv to 2.9 mSv; eye lens from 0.5 mSv to 0.3 mSv; thyroid gland from 2.5 mSv to 0.5 mSv; parotid glands from 2.3 mSv to 0.4 mSv). Dose reduction did not reduce image quality or diagnostic information.

Conclusion: A considerable dose reduction without loss of diagnostic information is achievable in dental CT. As radiation exposure of the presented low-dose protocol is expected to be in the same range as DVT, low-dose dental CT might be superior to DVT, because CT can be used to evaluate soft tissues as well.
Accuracy of cytology for diagnosis of lipomatous tumors: comparison with magnetic resonance and computed tomography findings in 175 cases
Authors: Einarsdóttir H. , Skoog L. , Söderlund V. , Bauer H. C. F.
Published: January 2005

Purpose: To assess the value of fine-needle aspiration cytology in the diagnostic work-up of lipomatous tumors of the extremities and trunk, and to identify specific radiological features that could aid in the preoperative evaluation.

Material and Methods: 175 patients with subfascial lipomatous tumors who had undergone preoperative magnetic resonance imaging or computed tomography and fine-needle aspiration cytology were studied. The percentage of fat within the lesion was visually graded from the images as: none, 1-75%, 75-95%, or 95-100%. The histological and cytological diagnoses were compared and in discordant cases the radiological images were re-reviewed.

Results: There was cytological and histological concordance in 96% of lipomas and in 85% of atypical lipomatous tumors (ALT) and liposarcomas. Most discordant cases exhibited 1-75% fat. Radiological review suggested that cytological sampling problems due to tumor heterogeneity were the main cause of diagnostic difficulties. The majority of tumors with less than 75% fat were liposarcomas, and in no liposarcoma was the fat content higher than 75%. Both ALT and lipoma were found in the 95-100% group.

Conclusion: Cytology can be highly accurate in the diagnosis of lipomatous tumors, including ALT; however, critical comparison with the radiological findings increases diagnostic security. In tumors with fat content visually assessed as less than 75% of the tumor volume, liposarcoma is the most likely diagnosis and a cytological diagnosis of ALT or lipoma should be questioned. In lesions with 75-95% fat, liposarcoma is unlikely, but FNAC is still indicated for safety. In lesions with 95-100% fat, FNAC is only indicated if the differentiation between lipoma and ALT influences the treatment strategy.
Asymptomatic true gallbladder duplication: a case report and review of the literature
Authors: Roldan-Valadez E. , Osorio-Peralta S. , Vivas-Bonilla I. , Vazquez-LaMadrid J. , Alva-Lopez L. F. , Hernandez-Ortiz J.
Published: January 2005

Gallbladder duplication is a rare event, with an incidence at autopsy of about 1/4000, with very few documented symptomatic cases reported. Preoperative diagnosis and differentiation of this malformation are important to prevent inadvertent damage to the biliary system, a complicated postoperative course, and repeat surgery. We present a case of true gallbladder duplication found incidentally during abdominal ultrasonography (US). The diagnosis was made with US and the Y-type duplication was demonstrated with magnetic resonance cholangiopancreatography (MRCP).
Addison's disease associated with widespread abdomino-pelvic visceral calcification due to secondary amyloidosis: a case report
Authors: Korkmaz C. , Kebapçi M.
Published: January 2005

We report the case of a 42-year-old woman who presented with Addison's disease with widespread abdomino-pelvic visceral calcifications due to secondary amyloidosis. AA amyloidosis and calcification were supported by histological evidence of liver tissue. To our knowledge, no other case with such extensive visceral calcification involving the adrenals, liver, ovaries, and renal secondary to amyloidosis has been published.
Multiple Protein Interactions Involving Proposed Extracellular Loop Domains of the Tight Junction Protein Occludin
Authors: Nusrat Asma , Brown G. Thomas , Tom Jeffrey , Drake Alex , Bui Tam T.T. , Quan Cliff , Mrsny Randall J.
Published: January 2005

Occludin is a tetraspan integral membrane protein in epithelial and endothelial tight junction (TJ) structures that is projected to have two extracellular loops. We have used peptides emulating central regions of human occludin's first and second loops, termed O-A:101–121 and O-B:210–228, respectively, to examine potential molecular interactions between these two regions of occludin and other TJ proteins. A superficial biophysical assessment of A:101–121 and O-B:210–228 showed them to have dissimilar solution conformation characteristics. Although O-A:101–121 failed to strongly interact with protein components of the human epithelial intestinal cell line T84, O-B:210–228 selectively associated with occludin, claudin-one and the junctional adhesion molecule (JAM)-A. Further, the presence of O-B:210–228, but not O-A:101–121, impeded the recovery of functional TJ structures. A scrambled peptide sequences of O-B:210–228 failed to influence TJ assembly. These studies demonstrate distinct properties for these two extracellular segments of the occludin protein and provide an improved understanding of how specific domains of occludin may interact with proteins present at TJ structures.
Transcriptional Regulation by a DNA-associated Form of Cyclin D1
Authors: Bienvenu Frédéric , Barré Benjamin , Giraud Sandrine , Avril Sylvie , Coqueret Olivier
Published: January 2005

Besides its function as a cell cycle regulator, cyclin D1 interacts with transcription factors to regulate gene activation. In this study, we show that cyclin D1 is recruited to the p21waf1 promoter by a STAT3-NcoA complex. The association of cyclin D1 with DNA prevented the recruitment of the CBP histone acetylase and RNA polymerase II, leading to an inhibition of the p21waf1 gene. Confirming the transcriptional function of the protein, the expression of the p21waf1 gene was enhanced in cyclin D1–/– fibroblasts or upon siRNA-mediated down-regulation of the cyclin. Moreover, the STAT3-mediated activation of p21waf1 was also inhibited in breast cancer cells containing elevated levels of cyclin D1. Altogether, these results suggest that the transcriptional activities of cyclin D1 might play an important role in the regulation of cell-cycle regulatory genes and that these functions are probably involved in cell transformation.
The LIM/Homeodomain Protein Islet1 Recruits Janus Tyrosine Kinases and Signal Transducer and Activator of Transcription 3 and Stimulates Their Activities
Authors: Hao Aijun , Novotny-Diermayr Veronica , Bian Wei , Lin Baohong , Lim Cheh Peng , Jing Naihe , Cao Xinmin
Published: January 2005

Islet1 (Isl1) belongs to the LIM homeodomain transcription factor family. Its roles in differentiation of motor neurons and organogenesis of pancreas and heart have been revealed. However, less is known about its regulatory mechanism and the target genes. In this study, we identified interactions between Isl1 and Janus tyrosine kinase (JAK), as well as signal transducer and activator of transcription (Stat)3, but not Stat1 and Stat5, in mammalian cells. We found that Isl1 not only forms a complex with Jak1 and Stat3 but also triggers the tyrosine phosphorylation of Jak1 and its kinase activity, thereby elevating the tyrosine phosphorylation, DNA binding activity, and target gene expression of Stat3. In vivo, the tyrosine-phosphorylated Stat3 was colocalized with Isl1 in the nucleus of the mouse motor neurons in spinal cord after nerve injury. Correspondingly, electroporation of Isl1 and Stat3 into the neural tube of chick embryos resulted in the activation of a reporter gene expression controlled by a Stat3 regulatory sequence, and cotransfection of Isl1 and Stat3 promoted the proliferation of the mouse motor neuron cells. Our data suggest a novel role of Isl1 as an adaptor for Jak1 and Stat3 and reveal a possible functional link between LIM homeodomain transcription factors and the Jak-Stat pathway.
p53 C-Terminal Phosphorylation by CHK1 and CHK2 Participates in the Regulation of DNA-Damage-induced C-Terminal Acetylation
Authors: Ou Yi-Hung , Chung Pei-Han , Sun Te-Ping , Shieh Sheau-Yann
Published: January 2005

The tumor suppressor protein p53 mediates stress-induced growth arrest or apoptosis and plays a major role in safeguarding genome integrity. In response to DNA damage, p53 can be modified at multiple sites by phosphorylation and acetylation. We report on the characterization of p53 C-terminal phosphorylation by CHK1 and CHK2, two serine/threonine (Ser/Thr) protein kinases, previously implicated in the phosphorylation of the p53 N terminus. Using tryptic phosphopeptide mapping, we have identified six additional CHK1 and CHK2 sites residing in the final 100 amino acids of p53. Phosphorylation of at least three of these sites, Ser366, Ser378, and Thr387, was induced by DNA damage, and the induction at Ser366 and Thr387 was abrogated by small interfering RNA targeting chk1 and chk2. Furthermore, mutation of these phosphorylation sites has a different impact on p53 C-terminal acetylation and on the activation of p53-targeted promoters. Our results demonstrate a possible interplay between p53 C-terminal phosphorylation and acetylation, and they provide an additional mechanism for the control of the activity of p53 by CHK1 and CHK2.
Regulation of Membrane Trafficking by a Novel Cdc42-related Protein inCaenorhabditis elegansEpithelial Cells
Authors: Jenna S. , Caruso M.-E. , Emadali A. , Nguyên D. T. , Dominguez M. , Li S. , Roy R. , Reboul J. , Vidal M. , Tzimas G. N. , Bossé R. , Chevet E.
Published: January 2005

Rho GTPases are mainly known for their implication in cytoskeleton remodeling. They have also been recently shown to regulate various aspects of membrane trafficking. Here, we report the identification and the characterization of a novel Caenorhabditis elegans Cdc42-related protein, CRP-1, that shows atypical enzymatic characteristics in vitro. Expression in mouse fibroblasts revealed that, in contrast with CDC-42, CRP-1 was unable to reorganize the actin cytoskeleton and mainly localized to trans-Golgi network and recycling endosomes. This subcellular localization, as well as its expression profile restricted to a subset of epithelial-like cells in C. elegans, suggested a potential function for this protein in polarized membrane trafficking. Consistent with this hypothesis, alteration of CRP-1 expression affected the apical trafficking of CHE-14 in vulval and rectal epithelial cells and sphingolipids (C6-NBD-ceramide) uptake and/or trafficking in intestinal cells. However, it did not affect basolateral trafficking of myotactin in the pharynx and the targeting of IFB-2 and AJM-1, two cytosolic apical markers of intestine epithelial cells. Hence, our data demonstrate a function for CRP-1 in the regulation of membrane trafficking in a subset of cells with epithelial characteristics.
A Minus-End–directed Kinesin with Plus-End Tracking Protein Activity Is Involved in Spindle Morphogenesis
Authors: Ambrose J. Christian , Li Wuxing , Marcus Adam , Ma Hong , Cyr Richard
Published: January 2005

Diverse kinesin motor proteins are involved in spindle function; however, the mechanisms by which they are targeted to specific sites within spindles are not well understood. Here, we show that a fusion between yellow fluorescent protein (YFP) and a minus-end–directed Kinesin-14 (C-terminal family) from Arabidopsis, ATK5, localizes to mitotic spindle midzones and regions rich in growing plus-ends within phragmoplasts. Notably, in Arabidopsis interphase cells, YFP::ATK5 localizes to microtubules with a preferential enrichment at growing plus-ends; indicating ATK5 is a plus-end tracking protein (+TIP). This +TIP activity is conferred by regions outside of the C-terminal motor domain, which reveals the presence of independent plus-end tracking and minus-end motor activities within ATK5. Furthermore, mitotic spindles of atk5 null mutant plants are abnormally broadened. Based on these data, we propose a model in which ATK5 uses plus-end tracking to reach spindle midzones, where it then organizes microtubules via minus-end–directed motor activity.
Atg11 Links Cargo to the Vesicle-forming Machinery in the Cytoplasm to Vacuole Targeting Pathway
Authors: Yorimitsu Tomohiro , Klionsky Daniel J.
Published: January 2005

Proteins are selectively packaged into vesicles at specific sites and then delivered correctly to the various organelles where they function, which is critical to the proper physiology of each organelle. The precursor form of the vacuolar hydrolase aminopeptidase I is a selective cargo molecule of the cytoplasm to vacuole targeting (Cvt) pathway and autophagy. Precursor Ape1 along with its receptor Atg19 forms the Cvt complex, which is transported to the pre-autophagosomal structure (PAS), the putative site of Cvt vesicle formation, in a process dependent on Atg11. Here, we show that this interaction occurs through the Atg11 C terminus; subsequent recruitment of the Cvt complex to the PAS depends on central regions within Atg11. Atg11 was shown to physically link several proteins, although the timing of these interactions and their importance are unknown. Our mapping shows that the Atg11 coiled-coil domains are involved in self-assembly and the interaction with other proteins, including two previously unidentified partners, Atg17 and Atg20. Atg11 mutants defective in the transport of the Cvt complex to the PAS affect the localization of other Atg components, supporting the idea that the cargo facilitates the organization of the PAS in selective autophagy. These findings suggest that Atg11 plays an integral role in connecting cargo molecules with components of the vesicle-forming machinery.
Mx-rMx, a Family of Interacting Transposons in the GrowinghATSuperfamily of Maize
Authors: Xu Zhennan , Dooner Hugo K.
Published: January 2005

More than half a century after the discovery of transposable elements, the number of genetically defined autonomous elements that have been isolated and characterized molecularly in any one species remains surprisingly small. Because of its rich genetic history, maize (Zea mays) is, by far, the plant with the largest number of such elements. Yet, even in maize, a maximum of only two autonomous elements have been characterized in any transposon superfamily. This article describes the isolation and molecular and genetic characterization of Mx (for mobile element induced by x-rays), a third autonomous member of the hAT transposon superfamily in maize. Mx is 3731 bp long, ends in 13-bp terminal inverted repeats (TIRs), and causes an 8-bp duplication of the target site. Mx and rMx (for responder to Mx), its 571-bp nonautonomous partner, define a classical family of interacting transposable elements. Surprisingly, the TIRs of Mx and rMx are only 73% identical, and the subterminal sequences are even less so, suggesting that Mx and rMx may represent diverging transposable elements still capable of mobilization by the same transposase. Sequences that are closer to the ends of either Mx or rMx are present in the maize genome. Mx is predicted to encode a 674–amino acid protein that is homologous to the Ac transposase. Although Mx and Ac are closely related, they do not interact. Other data suggest that maize may possess at least five families of hAT transposons that do not interact with each other. The possible origin of noninteracting transposon families within the same superfamily is discussed.
Functional Genomic Analysis of theAUXIN RESPONSE FACTORGene Family Members inArabidopsis thaliana: Unique and Overlapping Functions ofARF7andARF19
Authors: Okushima Yoko , Overvoorde Paul J. , Arima Kazunari , Alonso Jose M. , Chan April , Chang Charlie , Ecker Joseph R. , Hughes Beth , Lui Amy , Nguyen Diana , Onodera Courtney , Quach Hong , Smith Alison , Yu Guixia , Theologis Athanasios
Published: January 2005

The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression. The biological function(s) of most ARFs is poorly understood. Here, we report the identification and characterization of T-DNA insertion lines for 18 of the 23 ARF gene family members in Arabidopsis thaliana. Most of the lines fail to show an obvious growth phenotype except of the previously identified arf2/hss, arf3/ett, arf5/mp, and arf7/nph4 mutants, suggesting that there are functional redundancies among the ARF proteins. Subsequently, we generated double mutants. arf7 arf19 has a strong auxin-related phenotype not observed in the arf7 and arf19 single mutants, including severely impaired lateral root formation and abnormal gravitropism in both hypocotyl and root. Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants. For example, the expression of several genes, such as those encoding members of LATERAL ORGAN BOUNDARIES domain proteins and AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE, are disrupted in the double mutant. The data suggest that the ARF7 and ARF19 proteins play essential roles in auxin-mediated plant development by regulating both unique and partially overlapping sets of target genes. These observations provide molecular insight into the unique and overlapping functions of ARF gene family members in Arabidopsis.
The Role ofKNOXGenes in the Evolution of Morphological Novelty in Streptocarpus
Authors: Harrison Jill , Möller Michael , Langdale Jane , Cronk Quentin , Hudson Andrew
Published: January 2005

The genus Streptocarpus comprises species with diverse body plans. Caulescent species produce leaves from a conventional shoot apical meristem (SAM), whereas acaulescent species lack a conventional SAM and produce only a single leaf (the unifoliate form) or clusters of leaves from the base of more mature leaves (the rosulate form). These distinct morphologies reflect fundamental differences in the role of the SAM and the process of leaf specification. A subfamily of KNOTTED-like homeobox (KNOX) genes are known to be important in regulating meristem function and leaf development in model species with conventional morphologies. To test the involvement of KNOX genes in Streptocarpus evolution, two parologous KNOX genes (SSTM1 and SSTM2) were isolated from species with different growth forms. Their phylogenetic analysis suggested a gene duplication before the subgeneric split of Streptocarpus and resolved species relationships, supporting multiple evolutionary origins of the rosulate and unifoliate morphologies. In S. saxorum, a caulescent species with a conventional SAM, KNOX proteins were expressed in the SAM and transiently downregulated in incipient leaf primordia. The ability of acaulescent species to initiate leaves from existing leaves was found to correlate with SSTM1 expression and KNOX protein accumulation in leaves and to reflect genetic differences at two loci. Neither locus corresponded to SSTM1, suggesting that cis-acting differences in SSTM1 regulation were not responsible for evolution of the rosulate and unifoliate forms. However, the involvement of KNOX proteins in leaf formation in rosulate species suggests that they have played an indirect role in the development of morphological diversity in Streptocarpus.
Shifts in southern endpoints of distribution in rocky intertidal species along the south‐eastern Pacific coast
Authors: Rivadeneira Marcelo M. , Fernández Miriam
Published: January 2005

Aim  Despite the pervasive and well‐documented effects of global warming on species’ ranges in terrestrial taxa and systems, the effect of sea surface warming has been poorly studied in marine systems. Here we analyse changes in the southern endpoints of distribution of rocky intertidal species (gastropods and chitons) along the Chilean coast, and trends in sea surface temperature (SST), using data collected during the last half‐century.

Location  South‐eastern Pacific coast, between 18°20′ S and 42°35′ S.

Methods  Past southern endpoints of distribution were obtained for 10 intertidal species from museum collections and literature reviews. Current endpoints are based on field sampling conducted between 1998 and 2000. Changes in the position of southern endpoints were analysed individually for each species, as well as for the entire assemblage of species included in the analysis. SST records encompassing 51–57 years were obtained from five coastal stations located between 18° and 36° S.

Results and main conclusions  Most species (eight of 10) did not show expansion of their southern endpoint. The proportion of species expanding, contracting or maintaining their southern limit did not differ from chance expectation. On average, species showed small (1° latitude), non‐significant contractions, with low rates of decadal change (0.18° latitude per 10 years). This pattern can be explained by changes in SST, which showed a weak warming trend (and at some sites even cooling) along the Chilean coast during the last 57 years. Our results show that different regional warming trends occur, and suggest that generalizations about poleward shifts in species ranges cannot be made. However, our results support the hypothesis that temperature is a major determinant of species range dynamics.
Cladistic analysis of distributions and endemism (CADE): using raw distributions of birds to unravel the biogeography of the South American aridlands
Authors: Porzecanski Ana Luz , Cracraft Joel
Published: January 2005

Aim To use published distributional and taxonomic information on Neotropical birds in a cladistic analysis of distributions and endemism (CADE) to generate a testable hypothesis of area‐relationships for the arid areas of endemism, particularly those of Central South America (the ‘arid diagonal’), and to clarify the different methodologies commonly associated with parsimony analysis of endemicity (PAE).

Location South America.

Methods Cladistic analysis of distributions and endemism.

Results We obtain a tree where the relationships of most areas are resolved, and we find support for an exclusive clade of Central South American areas, with the Caatinga as sister to both the Chaco and Cerrado.

Main conclusions There is a substantial amount of historical signal in avian distributions, when large numbers of taxa and multiple taxonomic levels are considered. Ecological noise and historical information are more easily distinguished in CADE analyses than they would be in PAE analyses. Based on our results we predict that among aridland birds, the Cerrado and Chaco species will be more closely related to each other than to Caatinga species.
Insular black files (Diptera: Simuliidae) of North America: tests of colonization hypotheses
Authors: Adler Peter H. , Giberson Donna J. , Purcell Lisa A.
Published: January 2005

Aim  To understand factors that facilitate insular colonization by black flies, we tested six hypotheses related to life‐history traits, phylogeny, symbiotes, island area, and distance from source areas.

Location  Four northern islands, all within 150 km of the North American mainland, were included in the study: Isle Royale, Magdalen Islands, Prince Edward Island, and Queen Charlotte Islands.

Methods  Immature black flies and their symbiotes were surveyed in streams on the Magdalen Islands, and the results combined with data from similar surveys on Isle Royale, Prince Edward Island, and the Queen Charlotte Islands. Black flies were analysed chromosomally to ensure that all sibling species were revealed. Tests of independence were used to examine the frequency of life‐history traits and generic representation of black flies on islands vs. source areas.

Results  A total of 13–20 species was found on each of the islands, but no species was unique to any of the islands. The simuliid faunas of the islands reflected the composition of their source areas in aspects of voltinism (univoltine vs. multivoltine), blood feeding (ornithophily vs. mammalophily), and phylogeny (genus Simulium vs. other genera). Five symbiotic species were found on the most distant island group, the Magdalen Islands, supporting the hypothesis that obligate symbiotes are effectively transported to near‐mainland islands. An inverse relationship existed between the number of species per island and distance from the source. The Queen Charlotte Islands did not conform to the species–area relationship.

Main conclusions  The lack of precinctive insular species and an absence of life‐history and phylogenetic characteristics related to the presence of black flies on these islands argue for gene flow and dispersal capabilities of black flies over open waters, possibly aided by winds. However, the high frequency of precinctive species on islands 500 km or more from the nearest mainland indicates that at some distance beyond 100 km, open water provides a significant barrier to colonization and gene exchange. An inverse relationship between number of species and distance from the source suggests that as long as suitable habitat is present, distance plays an important role in colonization. Failure of the Queen Charlotte Islands to conform to an area–richness trend suggests that not all resident species have been found.
Grass water stress estimated from phytoliths in West Africa
Authors: Bremond Laurent , Alexandre Anne , Peyron Odile , Guiot Joël
Published: January 2005

Aim  This study calibrates the relationship between phytolith indices, modern vegetation structure, and a climate parameter (AET/PET, i.e. the ratio of annual actual evapotranspiration to annual potential evapotranspiration), in order to present new proxies for long‐term Quaternary climate and vegetation changes, and model/data comparisons.

Location  Sixty‐two modern soil surface samples from West Africa (Mauritania and Senegal), collected along a latitudinal transect across four bioclimatic zones, were analysed.

Methods  Two phytolith indices are defined as normalized data: (1) humidity‐aridity index [Iph (%) = saddle vs. cross + dumbbell + saddle], and (2) water stress index [fan‐shaped index (Fs) (%) = fan‐shaped vs. sum of characteristic phytoliths]. Vegetation structures are delimited according to Iph and Fs boundaries. Bootstrapped regression methods are used for evaluating the strength of the relationship between the two phytolith indices and AET/PET. Additional modern phytolith assemblages, from Mexico, Cameroon and Tanzania are extracted in order to test the calibration established from the West African samples. Accuracy of the AET/PET phytolith proxy is compared with equivalent pollen proxy from the same area.

Results  Characterization of the grass cover is accurately made through Iph. A boundary of 20 ± 1.4% discriminates tall grass savannas from short grass savannas. Water stress and transpiration experienced by the grass cover can be estimated through Fs. AET/PET is accurately estimated from phytoliths by a transfer function: AET/PET = −0.605 Fs − 0.387 Iph + 0.272 (Iph – 20)2 (r = 0.80 ± 0.04) in the application domain (AET/PET ranging from 0.1 ± 0.04 to 0.45 ± 0.04). Phytolith and pollen estimate with similar precision (rpollen = 0.84 ± 0.04) the AET/PET in the studied area.

Conclusions  This study demonstrates that we can rely on the phytolith indices Iph and Fs to distinguish the different grasslands in tropical areas. Moreover, a new phytolith proxy of AET/PET, linked to water availability, is presented. We suggest from these results that combining phytolith and pollen proxies of AET/PET would help to constrain this climate parameter better, especially when phytolith assemblages are dominated by Panicoideae and Chloridoideae C4‐grass phytoliths, are devoid of Pooideae C3‐grass phytoliths, and occur with a few tropical ligneous woody dicotyledon phytoliths. As AET/PET is a bioclimatic indicator commonly used in vegetation models, such a combination would help to make model/data comparisons more efficient.
Species richness and structure of ant communities in a dynamic archipelago: effects of island area and age
Authors: Badano Ernesto I. , Regidor Héctor A. , Núñez Hector A. , Acosta Rebeca , Gianoli Ernesto
Published: January 2005

Aim  To assess how ant species richness and structure of ant communities are influenced by island age (disturbance history) in a dynamic archipelago.

Location  Cabra Corral dam, Salta Province, north‐west Argentina (25°08′ S, 65°20′ W).

Methods  Ant species richness on remaining fragments (islands) of a flooded forest was determined, as well as island area, isolation and age. Simple linear regressions were performed to assess relationships between ant species richness and those insular variables. Furthermore, a stepwise multiple linear regression analysis was conducted in order to determine the relative influence of each insular variable on ant species richness. Islands were categorized in two age classes (old and young) and co‐occurrence analyses were applied within each class to evaluate changes in community structure because of interspecific competition.

Results  Simple regression analyses indicated a moderate, positive effect of island area on ant species richness. Weak, marginally non‐significant relationships were found between ant species richness and both island isolation and island age, showing the tendency for there to be a decrease in ant species richness with island isolation and that ant species richness might be higher in old islands. The multiple regression analysis indicated that island isolation and age had no significant effects on the number of ant species, island area being the only independent variable retained in the analysis. On the contrary, whereas a random pattern of species co‐occurrence was found on young islands, ant communities in old islands showed a significantly negative pattern of species co‐occurrence, suggesting that the effect of competition on community structure was stronger on older islands than on younger islands.

Main conclusions  Island area was the most important variable explaining ant species richness on the islands of Cabra Corral dam. However, both island isolation and island age (or disturbance history) might also contribute to shape the observed community patterns. The present study also shows that island age significantly affects the strength with which interspecific interactions structure ant communities on islands.
Effects of life‐history traits and species distribution on genetic structure at maternally inherited markers in European trees and shrubs
Authors: Aguinagalde Itziar , Hampe Arndt , Mohanty Aparajita , Martín Juan Pedro , Duminil Jérôme , Petit Rémy J.
Published: January 2005

Aim To examine relationships between life‐history traits, ecological and chorological characteristics of woody plant species and patterns of genetic differentiation among populations as assessed by chloroplast DNA (cpDNA) markers, and to compare them with patterns previously described from nuclear markers.

Location Europe.

Methods Data on cpDNA variation were compiled for 29 temperate European broad‐leaved tree and shrub species. Six qualitative and three quantitative characters of the species were tested for their relationship with two parameters of genetic population differentiation (GSTandNST). Both direct species comparisons and phylogenetically independent contrast analyses were performed.

Results When the phylogeny was not taken into account, five characters were significantly related to levels of population differentiation. The relationship disappeared in all but two cases (distribution type and seed mass) when analyses controlled for phylogenetic relationships among species.

Main conclusions The correlation between distribution type (boreal‐temperate or temperate) and cpDNA differentiation of temperate European woody plant species suggests that their Quaternary history, in particular the location and isolation of their glacial refugia, is an important determinant of their present‐day level of genetic structure. By contrast, the relationship between life‐history traits and genetic differentiation at maternally inherited markers is weaker, especially when phylogenetic effects are controlled for.