bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of interface dislocations effect on polarization distribution of ferroelectric thin films
Authors: Zheng Yue , Wang Biao , Woo C. H.
Published: February 2006

Effects of interfacial dislocations on the properties of ferroelectric thin films are investigated, using the dynamic Ginzburg–Landau equation. Our results confirm the existence of a dead layer near the film/substrate interface. Due to the combined effects of the dislocations and the near-surface eigenstrain relaxation, the ferroelectric properties of about one-third of the film volume suffers.
First-principles study of the (001) surface of cubic BaZrO3 and BaTiO3
Authors: Wang Yuan Xu , Arai Masao , Sasaki Taizo , Wang Chun Lei
Published: February 2006

First-principles density functional calculations are employed to study the (001) surface of BaZrO3 with both BaO and ZrO2 termination. Surface structure and band structure have been obtained. For the ZrO2-terminated surface, the large displacement of the O atoms in the first layer results in the small surface rumpling. In addition, the largest relaxation appears on the second layer atoms but not on the very first layer ones. The analysis of the structure relaxation parameters reveals that the rumpling of the (001) surface for BaZrO3 with the BaO termination is stronger than that of BaTiO3. The origin of the different surface relaxation behavior between the two materials is discussed. The surface state appears in the band structure of the ZrO2-terminated surface of BaZrO3.
Self-synchronized voltage pulse application for dynamic force microscope nano-oxidation
Authors: Kuramochi Hiromi , Ando Kazunori , Tokizaki Takashi , Yokoyama Hiroshi
Published: February 2006

A self-synchronized voltage pulse application method was demonstrated as an effective control of the nano-oxidation using a dynamic force microscope. By creating a cyclic water meniscus using the large oscillation amplitude, self-synchronized voltage pulses can be realized during application of a continuous voltage to the sample. The modification of the probe-sample distance was equal to the change in the applied voltage pulse duration on the order of submicroseconds. This method realized the ultrastable control of the water meniscus formation.
Role of Brownian motion hydrodynamics on nanofluid thermal conductivity
Authors: Evans William , Fish Jacob , Keblinski Pawel
Published: February 2006

We use a kinetic theory based analysis of heat flow in fluid suspensions of solid nanoparticles (nanofluids) to demonstrate that the hydrodynamics effects associated with Brownian motion have only a minor effect on the thermal conductivity of the nanofluid. This analysis is supported by the results of molecular dynamics simulations of heat flow in a model nanofluid with well-dispersed particles. Our findings are consistent with the predictions of the effective medium theory as well as with recent experimental results on well-dispersed metal nanoparticle suspensions.
Cusp instability and phase field in forced velocity solidification of binary alloys
Authors: Kirkaldy J. S.
Published: February 2006

Current phase field processing of our cuspoidal wavelength data by Greenwood et al. [M. Greenwood, M. Haataja, and N. Provatas, Phys. Rev. Lett. 93, 246101 (2004)] exhibits a qualitative positive comparison with the calibrated optimal codes for wavelengths in the intermediate and high velocity zones, but a shortfall for the near-marginal zone, and does not attempt to deal with wave amplitudes. The successful steady state theories as herein expanded to the near-marginal zone and to wave amplitudes offer a further predictive challenge to the asymptotic and potentially more comprehensive time-dependent phase field paradigm.
Field-induced current modulation in epitaxial film of deep-ultraviolet transparent oxide semiconductor Ga2O3
Authors: Matsuzaki Kosuke , Yanagi Hiroshi , Kamiya Toshio , Hiramatsu Hidenori , Nomura Kenji , Hirano Masahiro , Hosono Hideo
Published: February 2006

Epitaxial films of a deep-ultraviolet transparent oxide semiconductor, Ga2O3, were fabricated on α-Al2O3 (0001) substrates by pulsed laser deposition. Four-axes x-ray diffraction measurements revealed that the tin-doped Ga2O3 films have a crystal structure different from any known polymorphs of Ga2O3. Its crystal lattice was determined to be an orthorhombic. Top gate field-effect transistor structures were fabricated using the Ga2O3 epitaxial films for n-channels. The channel conductance was modulated by an order of magnitude by gate voltage at room temperature with an estimated field-effect mobility of 5×10−2cm2(Vs)−1.
Room-temperature ferromagnetism in highly-resistive Ni-doped TiO2
Authors: Cho J. H. , Hwang T. J. , Joh Y. G. , Kim E. C. , Kim Dong Ho , Lee K. J. , Park H. W. , Ri H.-C. , Kim J. P. , Cho C. R.
Published: February 2006

We investigated the magnetic and transport properties of Ni-doped TiO2 films grown by a sol-gel method with Ni concentrations from 1% to 8%. All the samples exhibited ferromagnetism at room temperature identified by optical magnetic circular dichroism along with magnetometer measurement. The microstructural and compositional analysis revealed Ni-rich regions with rather uniform background, indicating that at least two different sources contribute to the observed ferromagnetism. The Hall effect study showed that the carriers are electrons with density lower than 1018cm−3 at room temperature, and no anomalous Hall effect has been observed due to the high resistivity of our samples. The observation of ferromagnetism in highly-resistive Ni-doped TiO2 films questions the carrier-mediated exchange interaction as an origin of ferromagnetism in this material.
Co-planar spin-polarized light-emitting diodes
Authors: Kaestner B. , Wunderlich J. , Sinova J. , Jungwirth T.
Published: February 2006

Studies of spin manipulation in semiconductors have benefited from the possibility of growing these materials of high quality on top of optically active III–V systems. The induced electroluminescence in these layered semiconductor heterostructures has been used for a reliable spin detection. In semiconductors with strong spin-orbit (SO) interaction, the sensitivity of vertical devices may be insufficient, however, because of the separation of the spin aligner part and the spin detection region by one or more heterointerfaces and because of the short spin coherence length. Here we demonstrate that highly sensitive spin detection can be achieved using a lateral arrangement of the spin polarized and optically active regions. Using our co-planar spin-polarized light-emitting diodes we detect electrical field induced spin generation in a semiconductor heterojunction two-dimensional hole gas. The polarization results from spin asymmetric recombination of injected electrons with strongly SO coupled two-dimensional holes. The possibility of detecting spin polarization of a two-dimensional electron gas (2DEG) induced by the local strayfield of a magnetized Co microstructure deposited on top of the 2DEG close to the co-planar diode junction is also demonstrated.
Sensing protein molecules using nanofabricated pores
Authors: Han Anpan , Schürmann Gregor , Mondin Giampietro , Bitterli Roland Andreas , Hegelbach Nicole G. , de Rooij Nico F. , Staufer Urs
Published: February 2006

We report the detection of protein molecules with nanofabricated pores using the resistive pulse sensing method. A 20-nm-thick silicon nitride membrane with a nanofabricated pore measuring about 55nm in diameter separated an electrolyte cell into two compartments. Current spike trains were observed when bovine serum albumin (BSA) was added to the negatively biased compartment. The magnitude of the spikes corresponded to particles 7–9nm in diameter (the size of a BSA molecule) passing through the pore. This suggests that the current spikes were current blockages caused by single BSA molecules. The presented nano-Coulter counting method could be applied to detect single protein molecules in free solution, and to study the translocation of proteins through a pore.
Laser intensity measurement by Thomson scattering
Authors: Gao Ju
Published: February 2006

We have examined the proposed idea [Ju Gao, Phys. Rev. Lett. 93, 243001 (2004)] of using Thomson scattering to characterize the intensity profile of ultraintense laser fields(⩾1018W∕cm2) by calculating the nonlinear Thomson scattering from single and multiple electrons in a Gaussian mode laser field. The results show a close correlation between the spectral features and local laser intensity. The effect may lead to a new scheme of characterizing laser intensity profiles.
Fabrication of freely suspended nanostructures by nanoimprint lithography
Authors: Huang C. C. , Ekinci K. L.
Published: February 2006

We describe an innovative approach to fabricate freely suspended nanometer-scale structures. In this approach based on nanoimprint lithography, the imprint polymer serves as both the pattern mask and the sacrificial layer. The fabrication involves imprinting the pattern to be suspended upon an existing structure, metallizing the pattern, and removing the excess material. To demonstrate the basics, we have fabricated families of suspended beams. This approach potentially possesses all the desirable aspects of nanoimprint lithography and is suitable for use in simple layer-by-layer fabrication.
Alternating current loss in radially arranged superconducting strips
Authors: Mawatari Yasunori , Kajikawa Kazuhiro
Published: February 2006

Analytic expressions for alternating current (ac) loss in radially arranged superconducting strips are presented. We adopt the weight-function approach to obtain the field distributions in the critical state model, and we have developed an analytic method to calculate hysteretic ac loss in superconducting strips for small-current amplitude. We present the dependence of the ac loss in radial strips upon the configuration of the strips and upon the number of strips. The results show that behavior of the ac loss of radial strips carrying bidirectional currents differs significantly from that carrying unidirectional currents.
Improved ferroelectric property of LaNiO3∕Pb(Zr0.2Ti0.8)O3∕LaNiO3 capacitors prepared by chemical solution deposition on platinized silicon
Authors: Han H. , Zhong J. , Kotru S. , Padmini P. , Song X. Y. , Pandey R. K.
Published: February 2006

We report a technique to prepare top and bottom oxide electrodes of LaNiO3 (LNO) for lead zirconate titanate (PZT) films using a chemical solution deposition. LNO/PZT/LNO sandwich structures were prepared on platinized silicon by spin coating combined with rapid thermal annealing. Pt dots were sputtered on top of LaNiO3 film to serve as protective masks during etching of the uncovered LaNiO3 layer using dilute hydrochloric acid. For comparison, Pt/PZT/Pt capacitors were also prepared using the same processing conditions. Electrical measurements were carried out on both Pt/LNO/PZT/LNO/Pt and Pt/PZT/Pt structures. The remnant polarizations and coercive fields for these two capacitors are 17.4 and 21.4μC∕cm2, 71 and 81.5kV∕cm respectively at 5V. The leakage current density for the Pt/LNO/PZT/LNO/Pt structure is about 1.38×10−6A∕cm2 at 5V, which is lower than that of PZT deposited on Pt electrode. After 109 bipolar switching cycles, no significant change in remnant polarization was observed in the Pt/LNO/PZT/LNO/Pt capacitor, in comparison to the Pt/PZT/Pt capacitor which lost more than 50% of its original remnant polarization.
Quantification of the meniscus effect in adhesion force measurements
Authors: Grobelny J. , Pradeep N. , Kim D.-I. , Ying Z. C.
Published: February 2006

Adhesion forces between a gold sphere and flat gold substrate are studied using atomic force microscopy in different environments. The pull-off force measured in a vacuum is found to be a small fraction of that in ambient air or nitrogen atmosphere. Calculations of capillary condensation forces, including the effects of elastic deformation of the contacting bodies and of adsorption layers, reveal that the meniscus force is the dominant source of the observed difference in pull-off forces. The experimental data show that nitrogen purge does not eliminate the meniscus contribution to the pull-off force.
Segmentation of single-walled carbon nanotubes by camera flash
Authors: Lien Der-Hsien , Kuo Hsin-Fu , Hsu Wen-Kuang
Published: February 2006

Previous workers discovered the ignition of fluffy single-walled carbon nanotubes (SWNTs) by camera flash. In this work, it is found that the flash does not ignite the thin SWNT film hung between electrodes, instead, nanotubes are segmented. SWNT segmentation is verified by scanning electron microscopy and in-situ resistance measurements, and an associated mechanism is discussed.
1060
nm
vertical-external-cavity surface-emitting lasers with an optical-to-optical efficiency of 44% at room temperature
Authors: Kim K. S. , Yoo J. R. , Cho S. H. , Lee S. M. , Lim S. J. , Kim J. Y. , Lee J. H. , Kim T. , Park Y. J.
Published: February 2006

We report a high power fundamental transverse mode operation of an optically pumped 1060nm vertical-external-cavity surface-emitting laser. A diamond heat spreader was capillary bonded to the semiconductor surface. A 10W continuous wave operation with optical-to-optical conversion efficiency of 44% was achieved at room temperature. The thermal rollover was not found up to a heat sink temperature of 60°C. High efficiency and good thermal stability were mainly due to the optimization of epitaxial quality and the high conductivity of the diamond heat spreader. We have found that the increase of the round trip loss caused by the heat spreader was about 1%.
Estimation of the cooling times for a metallic tip under laser illumination
Authors: Vurpillot F. , Gault B. , Vella A. , Bouet M. , Deconihout B.
Published: February 2006

The temperature evolution at the apex of a sharply pointed needle submitted to ultrafast pulsed-laser irradiation was determined using a pump-probe method. The laser pulse acts as a pump pulse whereas the probe pulse is a fast high-voltage pulse. Then cooling times are consistent with a heating zone of a few microns with a laser beam polarized along the tip axis and a spot size of 0.8mm.
The high fruit soluble sugar content in wild Lycopersicon species and their hybrids with cultivars depends on sucrose import during ripening rather than on sucrose metabolism
Authors: Balibrea María E. , Martínez-Andújar Cristina , Cuartero Jesús , Bolarín María C. , Pérez-Alfocea Francisco
Published: March 2006

Soluble sugar content has been studied in relation to sucrose metabolism in the hexose-accumulating cultivated tomato Lycopersicon esculentum Mill, the wild relative species Lycopersicon cheesmanii Riley, in the sucrose-accumulating wild relative species Lycopersicon chmielewskii Rick, Kesicky, Fobes & Holle. and in two hexose-accumulating interspecific F1 hybrids (L. esculentum × L. cheesmanii; L. esculentum × L. chmielewskii), cultivated under two irrigation regimes (control: EC = 2.1 and saline: EC = 8.4 dS m–1). Under control conditions the total soluble sugar content (as hexose equivalents) in the ripe fruits of L. cheesmanii was 3-fold higher than in L. esculentum, while L. chmielewskii and both F1 hybrids contained twice as much as the cultivar. With the exception of L. esculentum × L. cheesmanii, salinity increased the sugar content by 1.3 (wild species) and 1.7 times (cultivar and L. esculentum × L. chmielewskii) with respect to control fruits. Wild germplasm or salinity provided two different mechanisms for the increases in fruit sugar content. The hexoses accumulated in ripe fruits were strongly influenced by those accumulated at the start of ripening, but the hydrolysed starch before start of ripening only partially explained the final hexose levels and especially the increase under salinity. The early cell wall acid invertase and the late neutral invertase activities appeared to be related to the amount of hexoses accumulated in ripe fruits. However, no metabolic parameter was positively related to the amount of sugar accumulated (including sucrose). The major differences between genotypes appeared in ripe fruits, in which up to 50% of the total amount of sugars accumulated in the wild species (mainly in L. cheesmanii) and hybrids cannot be explained by the sugars accumulated and the starch hydrolysed before the start of ripening stage. As a consequence, the higher fruit quality of the wild species compared with L. esculentum may depend more on the continuation of sucrose import during ripening than on osmotic or metabolic particularities such as the hexose / sucrose-accumulator character or specific enzyme activities.
The rmc locus does not affect plant interactions or defence-related gene expression when tomato (Solanum lycopersicum) is infected with the root fungal parasite, Rhizoctonia
Authors: Gao Ling-Ling , Smith F. Andrew , Smith Sally E.
Published: March 2006

A tomato mutant with reduced mycorrhizal colonisation, rmc, confers resistance to almost all arbuscular mycorrhizal (AM) fungal species tested, although there is variation in colonisation of different root cell layers by different fungi and one species of AM fungus can colonise this mutant relatively normally. These variations indicate a high degree of specificity in relation to AM colonisation. We explored the possibility of specificity or otherwise in interactions between rmc and three non-AM root-infecting fungi, Rhizoctonia solani anastomosis groups (AG) 4 and AG8, and binucleate Rhizoctonia (BNR). There were no differences between the wild type tomato 76R and rmc in the speed or extent to which these fungi infected roots or caused disease. Infection by R. solani induced high levels of defence-related gene expression in both tomato genotypes relative to non-infected plants. In contrast, with BNR the expression of these genes was not induced or induced to a much lower extent than with R. solani. The expression of defence-related genes with these two non-AM fungi was very similar in the two plant genotypes. It was different from effects observed during colonisation by AM fungi, which enhanced expression of defence-related genes in rmc compared with the wild type tomato. The specificity and molecular mechanisms of rmc in control of AM colonisation are discussed.
Effects of water availability, nitrogen supply and atmospheric CO2 concentrations on plant nitrogen natural abundance values
Authors: Stock William D. , Evans John R.
Published: March 2006

The relative effects of soil N, water supply and elevated atmospheric CO2 on foliar δ15N values were examined. Phalaris arundinacea L. (Holdfast) and Physalis peruviana L. (Cape Gooseberry) were grown for 80 d with three water availability treatments, two atmospheric CO2 concentrations and four N supply rates. Elevated CO2 increased total plant biomass and N for each treatment and decreased allocation to roots, leaf N concentrations and stomatal conductance. Leaves had less negative leaf δ13C values under low water supply associated with decreased stomatal conductance and increased leaf N concentration, which decreased the ratio of intercellular to ambient CO2 concentration. The δ15N value of the supplied nitrate (4.15‰) was similar to the value for Phalaris leaves (4.11‰), but Cape Gooseberry leaves were enriched (6.52‰). The effects of elevated CO2 on leaf δ15N values were small, with Phalaris showing no significant change, while Cape Gooseberry showed a significant (P < 0.05) decline of 0.42 ‰. Variation in δ15N values was unrelated to stomatal conductance, transpiration, differential use of N forms or denitrification. Plants with low foliar N concentrations tended to be depleted in 15N. We suggest that changes in N allocation alter foliar δ15N values under different CO2 and water treatments.
Polypeptide metabolites secreted by the fungal pathogen Eutypa lata participate in Vitis vinifera cell structure damage observed in Eutypa dieback
Authors: Octave Stéphane , Roblin Gabriel , Vachaud Magali , Fleurat-Lessard Pierrette
Published: March 2006

Eutypa dieback is a devastating disease of Vitis vinifera L. caused by the fungal pathogen Eutypa lata. This wood-inhabiting fungus degrades tissues in the trunk and cordons of infected vines and induces symptoms in the foliage. These symptoms have been attributed to the production of toxic metabolites by the pathogen, in particular eutypine. Recently, we have isolated polypeptide compounds secreted by the fungus in artificial culture. The aims of this study were to examine the effects induced in leaves by applying polypeptides and eutypine to detached canes and to compare this to the changes in leaf structure induced by E. lata in the vineyard. In leaves taken from vines infected with E. lata, the changes in mesophyll cells indicate that the fungus has an effect on tissue remote from the infected area. The size of mesophyll cells decreased by more than half, starch content was reduced and tannins were abundant. Plastids, mitochondria and cell walls were highly modified. In leaves taken from healthy canes treated with polypeptides of E. lata, the structure of mesophyll cells was also modified. The cell size did not change, but the tannin content increased and modifications in plastids and mitochondria were similar to those observed in leaves taken from infected vines. The major effect was the complete disorganisation of cell walls. Eutypine had less effect on organelle structure and did not modify the cell wall. In canes treated with polypeptides, vessel-associated cells (VACs) were also damaged. Abundant tannins occurred in the vacuoles of VACs and marked changes were noted in mitochondria, plastids and the protective layer, in particular in the pit at the vessel interface. In these pits, the protective layer, the primary wall and the middle lamella were all highly modified. In contrast, treatment with eutypine induced the development of a large transfer apparatus bordering the unmodified pectocellulose wall. These results illustrate that treatment with polypeptides produced by E. lata may cause changes in mesophyll cells in leaves and VACs in canes, that resemble changes observed in naturally infected vines. Comparatively, the differences with eutypine action were stressed. Both types of toxins may co-operate in vivo to produce the degeneration observed during the disease.
Expression of bacterial starch-binding domains in Arabidopsis increases starch granule size
Authors: Howitt Crispin A. , Rahman Sadequr , Morell Matthew K.
Published: March 2006

Starch is a readily renewable resource that is very widely used for food and industrial purposes; however, greater variation in the functional properties of starch would further extend the use of this biodegradable polymer. Genetic engineering may provide a way to produce designer starches that have the desired properties. Starch-binding domains (SBD) from bacterial enzymes that catabolise starches have the ability to bind two helices of starch and thus have the potential to crosslink starch and / or to be used as anchors for other enzymes that can modify starch properties. In a first step towards novel modification of starch we have investigated the effect of expressing SBDs, singly and in tandem, in planta, and targeting them to the chloroplast in the model plant Arabidopsis thaliana (L.) Heynh. Transgenic plants that contained the SBD from the cyclomaltodextrin glucanotransferase (CGTase) of Thermoanaerobacterium thermosulfurigenes in the chloroplast were produced in both the wild type and the starch excess mutant (sex 1-1) backgrounds. Analysis of starch isolated from the chloroplasts of these lines revealed no significant changes in the amylose : amylopectin ratio, the chain-length distribution of debranched amylopectin or the gelatinisation temperature when compared to the parental line. However, significant changes were observed in the starch granule size with the plants expressing the construct having larger granules. The effect was more pronounced in the sex 1-1 background, and expression of two starch-binding domains linked in tandem had an even greater effect. Despite the starch granules being larger in lines expressing the starch-binding domain, no difference was seen in the starch content of the leaves when compared to parental lines. As the presence of the SBDs in the starch granule only altered granule size, and not other granule properties, they may provide an ideal anchor for targeting starch-modifying enzymes to the site of starch synthesis. This will allow the development of novel modifications of starch during synthesis.
New insights into myosin evolution and classification
Authors: Foth Bernardo J. , Goedecke Marc C. , Soldati Dominique
Published: February 2006

Myosins are eukaryotic actin-dependent molecular motors important for a broad range of functions like muscle contraction, vision, hearing, cell motility, and host cell invasion of apicomplexan parasites. Myosin heavy chains consist of distinct head, neck, and tail domains and have previously been categorized into 18 different classes based on phylogenetic analysis of their conserved heads. Here we describe a comprehensive phylogenetic examination of many previously unclassified myosins, with particular emphasis on sequences from apicomplexan and other chromalveolate protists including the model organism
Toxoplasma
, the malaria parasite
Plasmodium
, and the ciliate
Tetrahymena
. Using different phylogenetic inference methods and taking protein domain architectures, specific amino acid polymorphisms, and organismal distribution into account, we demonstrate a hitherto unrecognized common origin for ciliate and apicomplexan class XIV myosins. Our data also suggest common origins for some apicomplexan myosins and class VI, for classes II and XVIII, for classes XII and XV, and for some microsporidian myosins and class V, thereby reconciling evolutionary history and myosin structure in several cases and corroborating the common coevolution of myosin head, neck, and tail domains. Six novel myosin classes are established to accommodate sequences from chordate metazoans (class XIX), insects (class XX), kinetoplastids (class XXI), and apicomplexans and diatom algae (classes XXII, XXIII, and XXIV). These myosin (sub)classes include sequences with protein domains (FYVE, WW, UBA, ATS1-like, and WD40) previously unknown to be associated with myosin motors. Regarding the apicomplexan “myosome,” we significantly update class XIV classification, propose a systematic naming convention, and discuss possible functions in these parasites.
Mutational unmasking of a tRNA-dependent pathway for preventing genetic code ambiguity
Authors: Williams Amy M. , Martinis Susan A.
Published: February 2006

Aminoacyl-tRNA synthetases establish the genetic code by matching each amino acid with its cognate tRNA. Aminoacylation errors lead to genetic code ambiguity and statistical proteins. Some synthetases have editing activities that clear the wrong amino acid (aa) by hydrolysis of either of two substrates: misactivated aminoacyl-adenylates (“pretransfer” of aa to tRNA) or misacylated aa-tRNA (“posttransfer”). Whereas posttransfer editing can be directly measured, pretransfer editing is difficult to demonstrate, because adenylates are inherently labile and transient, and activity occurs against a background of posttransfer editing. Herein, different mutations in
Escherichia coli
leucyl-tRNA synthetase are combined to unmask the pretransfer pathway. The mutant enzymes completely lack posttransfer editing but prevent misacylations by clearing misactivated adenylates. We hypothesize that these mutations isolate a pretransfer translocation step that moves misactivated adenylates from the activation site for editing. The results highlight how evolution redundantly created two distinct pathways to prevent genetic code ambiguity.
Calcium-dependent regulation of the voltage-gated sodium channel hH1: Intrinsic and extrinsic sensors use a common molecular switch
Authors: Shah Vikas N. , Wingo Tammy L. , Weiss Kevin L. , Williams Christina K. , Balser Jeffrey R. , Chazin Walter J.
Published: February 2006

The function of the human cardiac voltage-gated sodium channel Na
V
1.5 (hH1) is regulated in part by binding of calcium to an EF hand in the C-terminal cytoplasmic domain. hH1 is also regulated via an extrinsic calcium-sensing pathway mediated by calmodulin (CaM) via binding to an IQ motif immediately adjacent to the EF-hand domain. The intrinsic EF-hand domain is shown here to interact with the IQ motif, which controls calcium affinity. Remarkably, mutation of the IQ residues has only a minor effect on CaM affinity but drastically reduces calcium affinity of the EF-hand domain, whereas the Brugada mutation A1924T significantly reduces CaM affinity but has no effect on calcium affinity of the EF-hand domain. Moreover, the differences in the biochemical effects of the mutations directly correlate with contrasting effects on channel electrophysiology. A comprehensive model is proposed in which the hH1 IQ motif serves as a molecular switch, coupling the intrinsic and extrinsic calcium sensors.
Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors
Authors: Akimoto Masayuki , Cheng Hong , Zhu Dongxiao , Brzezinski Joseph A. , Khanna Ritu , Filippova Elena , Oh Edwin C. T. , Jing Yuezhou , Linares Jose-Luis , Brooks Matthew , Zareparsi Sepideh , Mears Alan J. , Hero Alfred , Glaser Tom , Swaroop Anand
Published: February 2006

The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the
Nrl
gene in mice leads to functional cones at the expense of rods. We show that a 2.5-kb
Nrl
promoter segment directs the expression of enhanced GFP specifically to rod photoreceptors and the pineal gland of transgenic mice. GFP is detected shortly after terminal cell division, corresponding to the timing of rod genesis revealed by birthdating studies. In

Nrl
−/−

retinas, the GFP+ photoreceptors express S-opsin, consistent with the transformation of rod precursors into cones. We report the gene profiles of freshly isolated flow-sorted GFP+ photoreceptors from wild-type and

Nrl
−/−

retinas at five distinct developmental stages. Our results provide a framework for establishing gene regulatory networks that lead to mature functional photoreceptors from postmitotic precursors. Differentially expressed rod and cone genes are excellent candidates for retinopathies.
Tbx6-mediated Notch signaling controls somite-specific
Mesp2
expression
Authors: Yasuhiko Yukuto , Haraguchi Seiki , Kitajima Satoshi , Takahashi Yu , Kanno Jun , Saga Yumiko
Published: February 2006

Mesp2 is a transcription factor that plays fundamental roles in somitogenesis, and its expression is strictly restricted to the anterior presomitic mesoderm just before segment border formation. The transcriptional on–off cycle is linked to the segmentation clock. In our current study, we show that a T-box transcription factor, Tbx6, is essential for
Mesp2
expression. Tbx6 directly binds to the
Mesp2
gene upstream region and mediates Notch signaling, and subsequent
Mesp2
transcription, in the anterior presomitic mesoderm. Our data therefore reveal that a mechanism, via Tbx6-dependent Notch signaling, acts on the transcriptional regulation of
Mesp2
. This finding uncovers an additional component of the interacting network of various signaling pathways that are involved in somitogenesis.
Body size, body proportions, and encephalization in a Middle Pleistocene archaic human from northern China
Authors: Rosenberg Karen R. , Zuné Lü , Ruff Christopher B.
Published: February 2006

The unusual discovery of associated cranial and postcranial elements from a single Middle Pleistocene fossil human allows us to calculate body proportions and relative cranial capacity (encephalization quotient) for that individual rather than rely on estimates based on sample means from unassociated specimens. The individual analyzed here (Jinniushan) from northeastern China at 260,000 years ago is the largest female specimen yet known in the human fossil record and has body proportions (body height relative to body breadth and relative limb length) typical of cold-adapted populations elsewhere in the world. Her encephalization quotient of 4.15 is similar to estimates for late Middle Pleistocene humans that are based on mean body size and mean brain size from unassociated specimens.
Picosecond dynamics of a membrane protein revealed by 2D IR
Authors: Mukherjee Prabuddha , Kass Itamar , Arkin Isaiah T. , Zanni Martin T.
Published: February 2006

Fast protein dynamics can be missed with techniques that have relatively slow observation times. Using 2D IR spectroscopy and isotope labeling, we have probed the rapid, picosecond dynamics of a membrane protein in its native environment. By measuring the homogeneous and inhomogeneous IR linewidths of 11 amide I modes (backbone carbonyl stretch), we have captured the structural distributions and dynamics of the CD3ζ protein along its transmembrane segment that are lost with slower time-scale techniques. We find that the homogeneous lifetimes and population relaxation times are the same for almost all of the residues. In contrast, the inhomogeneous linewidths vary significantly with the largest inhomogeneous distribution occurring for residues near the N terminus and the narrowest near the center. This behavior is highly consistent with a recently reported experimental model of the protein and water accessibility as observed by molecular dynamics simulations. The data support the proposed CD3ζ peptide structure, and the simulations point to the structural disorder of water and lipid head-groups as the main source of inhomogeneous broadening. Taken together, this rigorous analysis of the vibrational dynamics of a membrane peptide provides experimental insight into a time regime of motions that has so far been largely unexplored.
Identification of the minimal protein-folding nucleus through loop-entropy perturbations
Authors: Lindberg Magnus O. , Haglund Ellinor , Hubner Isaac A. , Shakhnovich Eugene I. , Oliveberg Mikael
Published: February 2006

To explore the plasticity and structural constraints of the protein-folding nucleus we have constructed through circular permutation four topological variants of the ribosomal protein S6. In effect, these topological variants represent entropy mutants with maintained spatial contacts. The proteins were characterized at two complementary levels of detail: by φ-value analysis estimating the extent of contact formation in the transition-state ensemble and by Hammond analysis measuring the site-specific growth of the folding nucleus. The results show that, although the loop-entropy alterations markedly influence the appearance and structural location of the folding nucleus, it retains a common motif of one helix docking against two strands. This nucleation motif is built around a shared subset of side chains in the center of the hydrophobic core but extends in different directions of the S6 structure following the permutant-specific differences in local loop entropies. The adjustment of the critical folding nucleus to alterations in loop entropies is reflected by a direct correlation between the φ-value change and the accompanying change in local sequence separation.
Sinorhizobium meliloti bluB
is necessary for production of 5,6-dimethylbenzimidazole, the lower ligand of B
12
Authors: Campbell Gordon R. O. , Taga Michiko E. , Mistry Kavita , Lloret Javier , Anderson Peter J. , Roth John R. , Walker Graham C.
Published: March 2006

An insight into a previously unknown step in B
12
biosynthesis was unexpectedly obtained through our analysis of a mutant of the symbiotic nitrogen fixing bacterium
Sinorhizobium meliloti
. This mutant was identified based on its unusually bright fluorescence on plates containing the succinoglycan binding dye calcofluor. The mutant contains a Tn
5
insertion in a gene that has not been characterized previously in
S. meliloti
. The closest known homolog is the
bluB
gene of
Rhodobacter capsulatus
, which is implicated in the biosynthesis of B
12
(cobalamin). The
S. meliloti bluB
mutant is unable to grow in minimal media and fails to establish a symbiosis with alfalfa, and these defects can be rescued by the addition of vitamin B
12
(cyanocobalamin) or the lower ligand of cobalamin, 5,6-dimethylbenzimidazole (DMB). Biochemical analysis demonstrated that the
bluB
mutant does not produce cobalamin unless DMB is supplied. Sequence comparison suggests that BluB is a member of the NADH/flavin mononucleotide (FMN)-dependent nitroreductase family, and we propose that it is involved in the conversion of FMN to DMB.
The colorectal microRNAome
Authors: Cummins Jordan M. , He Yiping , Leary Rebecca J. , Pagliarini Ray , Diaz Luis A. , Sjoblom Tobias , Barad Omer , Bentwich Zvi , Szafranska Anna E. , Labourier Emmanuel , Raymond Christopher K. , Roberts Brian S. , Juhl Hartmut , Kinzler Kenneth W. , Vogelstein Bert , Velculescu Victor E.
Published: February 2006

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the possibility that additional miRNAs are present in the human genome, we have developed an experimental approach called miRNA serial analysis of gene expression (miRAGE) and used it to perform the largest experimental analysis of human miRNAs to date. Sequence analysis of 273,966 small RNA tags from human colorectal cells allowed us to identify 200 known mature miRNAs, 133 novel miRNA candidates, and 112 previously uncharacterized miRNA* forms. To aid in the evaluation of candidate miRNAs, we disrupted the
Dicer
locus in three human colorectal cancer cell lines and examined known and novel miRNAs in these cells. These studies suggest that the human genome contains many more miRNAs than currently identified and provide an approach for the large-scale experimental cloning of novel human miRNAs in human tissues.
Human antibodies for immunotherapy development generated via a human B cell hybridoma technology
Authors: Li Jian , Sai Tao , Berger Marc , Chao Qimin , Davidson Diane , Deshmukh Gaurav , Drozdowski Brian , Ebel Wolfgang , Harley Stephen , Henry Marianne , Jacob Sara , Kline Brad , Lazo Ella , Rotella Frank , Routhier Eric , Rudolph Kathryn , Sage Jeaneen , Simon Paul , Yao Jun , Zhou Yuhong , Kavuru Mani , Bonfield Tracey , Thomassen Mary Jane , Sass Philip M. , Nicolaides Nicholas C. , Grasso Luigi
Published: February 2006

Current strategies for the production of therapeutic mAbs include the use of mammalian cell systems to recombinantly produce Abs derived from mice bearing human Ig transgenes, humanization of rodent Abs, or phage libraries. Generation of hybridomas secreting human mAbs has been previously reported; however, this approach has not been fully exploited for immunotherapy development. We previously reported the use of transient regulation of cellular DNA mismatch repair processes to enhance traits (e.g., affinity and titers) of mAb-producing cell lines, including hybridomas. We reasoned that this process, named morphogenics, could be used to improve suboptimal hybridoma cells generated by means ofex vivoimmunization and immortalization of antigen-specific human B cells for therapeutic Ab development. Here we present a platform process that combines hybridoma and morphogenics technologies for the generation of fully human mAbs specific for disease-associated human antigens. We were able to generate hybridoma lines secreting mAbs with high binding specificity and biological activity. One mAb with strong neutralizing activity against human granulocyte–macrophage colony-stimulating factor was identified that is now considered for preclinical development for autoimmune disease indications. Moreover, these hybridoma cells have proven suitable for genetic optimization using the morphogenics process and have shown potential for large-scale manufacturing.
Global analysis of carbohydrate utilization by
Lactobacillus acidophilus
using cDNA microarrays
Authors: Barrangou Rodolphe , Azcarate-Peril M. Andrea , Duong Tri , Conners Shannon B. , Kelly Robert M. , Klaenhammer Todd R.
Published: February 2006

The transport and catabolic machinery involved in carbohydrate utilization by
Lactobacillus acidophilus
was characterized genetically by using whole-genome cDNA microarrays. Global transcriptional profiles were determined for growth on glucose, fructose, sucrose, lactose, galactose, trehalose, raffinose, and fructooligosaccharides. Hybridizations were carried out by using a round-robin design, and microarray data were analyzed with a two-stage mixed model ANOVA. Differentially expressed genes were visualized by hierarchical clustering, volcano plots, and contour plots. Overall, only 63 genes (3% of the genome) showed a >4-fold induction. Specifically, transporters of the phospho
enol
pyruvate:sugar transferase system were identified for uptake of glucose, fructose, sucrose, and trehalose, whereas ATP-binding cassette transporters were identified for uptake of raffinose and fructooligosaccharides. A member of the LacS subfamily of galactoside-pentose hexuronide translocators was identified for uptake of galactose and lactose. Saccharolytic enzymes likely involved in the metabolism of monosaccharides, disaccharides, and polysaccharides into substrates of glycolysis were also found, including enzymatic machinery of the Leloir pathway. The transcriptome appeared to be regulated by carbon catabolite repression. Although substrate-specific carbohydrate transporters and hydrolases were regulated at the transcriptional level, genes encoding regulatory proteins CcpA, Hpr, HprK/P, and EI were consistently highly expressed. Genes central to glycolysis were among the most highly expressed in the genome. Collectively, microarray data revealed that coordinated and regulated transcription of genes involved in sugar uptake and metabolism is based on the specific carbohydrate provided.
L. acidophilus
's adaptability to environmental conditions likely contributes to its competitive ability for limited carbohydrate sources available in the human gastrointestinal tract.
Retinoic acid is required early during adult neurogenesis in the dentate gyrus
Authors: Jacobs Sharoni , Lie D. Chichung , DeCicco Kathleen L. , Shi Yanhong , DeLuca Luigi M. , Gage Fred H. , Evans Ronald M.
Published: February 2006

Retinoic acid (RA) is commonly used
in vitro
to differentiate stem cell populations including adult neural stem cells into neurons; however, the
in vivo
function of RA during adult neurogenesis remains largely unexplored. We found that depletion of RA in adult mice leads to significantly decreased neuronal differentiation within the granular cell layer of the dentate gyrus. RA contribution to neurogenesis occurs early, for RA deficiency also results in a decrease in newborn cells expressing an immature neuronal marker. Furthermore, although proliferation is unaffected during RA absence, cell survival is significantly reduced. Finally, a screen for retinoid-induced genes identifies metabolic targets including the lipid transporters, CD-36 and ABCA-1, the lipogenic master regulator SREBP1c as well as components of the Wnt signaling pathway. Our results reveal RA as a crucial contributor to early stages of adult neurogenesis and survival
in vivo
.
DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae)
Authors: Smith M. Alex , Woodley Norman E. , Janzen Daniel H. , Hallwachs Winnie , Hebert Paul D. N.
Published: February 2006

Insect parasitoids are a major component of global biodiversity and affect the population dynamics of their hosts. However, identification of insect parasitoids is often difficult, and they are suspected to contain many cryptic species. Here, we ask whether the cytochrome
c
oxidase I DNA barcode could function as a tool for species identification and discovery for the 20 morphospecies of
Belvosia
parasitoid flies (Diptera: Tachinidae) that have been reared from caterpillars (Lepidoptera) in Area de Conservación Guanacaste (ACG), northwestern Costa Rica. Barcoding not only discriminates among all 17 highly host-specific morphospecies of ACG
Belvosia
, but it also raises the species count to 32 by revealing that each of the three generalist species are actually arrays of highly host-specific cryptic species. We also identified likely hybridization among
Belvosia
by using a variable internal transcribed spacer region 1 nuclear rDNA sequence as a genetic covariate in addition to the strategy of overlaying barcode clusters with ecological information. If general, these results will increase estimates of global species richness and imply that tropical conservation and host–parasite interactions may be more complex than expected.
X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation
Authors: Zuo Xiaobing , Cui Guanglei , Merz Kenneth M. , Zhang Ligang , Lewis Frederick D. , Tiede David M.
Published: February 2006

Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space “fingerprints” of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experimental solution x-ray diffraction (SXD). SXD experiments and MD simulations were carried out to test the ability of experiment and simulation to resolve sequence-dependent modifications in helix conformation for B-form DNA. SXD experiments demonstrated that solution-state poly(AT) and poly(A)-poly(T) duplex DNA sequences exist in ensembles close to canonical B-form and B′-form structures, respectively. In contrast, MD simulations analyzed in terms of SXD fingerprints are shown to deviate from experiment, most significantly for poly(A)-poly(T) duplex DNA. Compared with experiment, MD simulation shortcomings were found to include both mismatches in simulated conformer structures and number population within the ensembles. This work demonstrates an experimental approach for quantitatively evaluating MD simulations and other coordinate models to simulate biopolymer structure in solution and suggests opportunities to use solution diffraction data as experimental benchmarks for developing supramolecular force fields optimized for a range ofin situapplications.
Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru
Authors: Biddle Jennifer F. , Lipp Julius S. , Lever Mark A. , Lloyd Karen G. , Sørensen Ketil B. , Anderson Rika , Fredricks Helen F. , Elvert Marcus , Kelly Timothy J. , Schrag Daniel P. , Sogin Mitchell L. , Brenchley Jean E. , Teske Andreas , House Christopher H. , Hinrichs Kai-Uwe
Published: February 2006

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.