bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-consistent solution of Dyson’s equation up to second order for open-shell atomic systems
Authors: Peirs K. , Van Neck D. , Waroquier M.
Published: September 2002

Green’s function techniques are powerful tools for studying interacting many-fermion systems in a structural and diagrammatical way. The central equation in this method is the Dyson equation which determines, through an approximation for the self-energy, the Green’s function of the system. In a previous paper [J. Chem. Phys. 115, 15 (2001)] a self-consistent solution scheme of the Dyson equation up to second order in the interaction, the Dyson(2) scheme, has been presented for closed-shell atoms. In this context, self-consistency means that the electron propagators appearing in a conserving approximation for the self-energy are the same as the solutions of the Dyson equation, i.e., they are fully dressed. In the present paper this scheme is extended to open-shell atoms. The extension is not trivial, due to the loss of spherical symmetry as a result of the partially occupied shells, but can be simplified by applying an appropriate angular averaging procedure. The scheme is validated by studying the second-row atomic systems B, C, N, O, and F. Results for the total binding energy, ionization energy and single-particle levels are discussed in detail and compared with other computational tools and with experiment. In open-valence-shell atoms a new quantity—the electron affinity—appears which was not relevant in closed-shell atoms. The electron affinities are very sensitive to the treatment of electron correlations, and their theoretical estimate is a stringent test for the adequacy of the applied scheme. The theoretical predictions are in good agreement with experiment. Also, the Dyson(2) scheme confirms the nonexistence of a stable negative ion of N. The overall effect of the self-consistent Dyson(2) scheme with regard to the Dyson(1) (i.e., Hartree–Fock) concept, is a systematic shift of all quantities, bringing them closer to the experimental values. The second-order effects turn out to be indispensable for a reasonable reproduction of the electron affinity.
Clusters containing open-shell molecules. III. Quantum five-dimensional/two-surface bound-state calculations on ArnOH van der Waals clusters (X2Π, n=4 to 12)
Authors: Xu Minzhong , Bačić Zlatko , Hutson Jeremy M.
Published: September 2002

This paper presents a theoretical study of the bound states of the open-shell OH radical in its ground electronic state (X2Π) interacting with n Ar atoms, for n from 4 to 12. After freezing the geometry of the Arn cage or subunit at the equilibrium structure (preceding paper), we carry out nonadiabatic five-dimensional quantum dynamics calculations on two coupled potential energy surfaces, using an extension of the method previously applied to closed-shell ArnHF clusters [J. Chem. Phys. 103, 1829 (1995)]. The method is based on a discrete variable representation (DVR) for the translational motion of OH relative to Arn, combined with a finite basis representation of the OH hindered rotation and electronic structure, including spin–orbit effects. The pattern of OH hindered rotor levels in clusters is similar to that in Ar–OH itself, though extended over three to four times the energy range for n=4 to 9. Ar12OH has a nearly spherical shell of Ar atoms around the OH, so the anisotropic splitting is very small. For n=10 and 11, the anisotropy may be viewed as arising from holes in an otherwise spherical shell, and the resulting patterns of hindered rotor levels are inverted versions of those for Ar2OH and Ar–OH.
Additivity of the classical capacity of entanglement-breaking quantum channels
Authors: Shor Peter W.
Published: September 2002

We show that for the tensor product of an entanglement-breaking quantum channel with an arbitrary quantum channel, both the minimum entropy of an output of the channel and the Holevo–Schumacher–Westmoreland capacity are additive. In addition, for the tensor product of two arbitrary quantum channels, we give a bound involving entanglement of formation for the amount of subadditivity (for minimum entropy output) or superadditivity (for classical capacity) that can occur.
Analysis of experimental and simulated vibrational spectra for the antiferroelectric liquid crystal 12OBBB1M6
Authors: Wrzalik R. , Merkel K. , Kocot A. , Cieplak B.
Published: September 2002

Vibrational spectra of the S-2-octyl-4-(4′-[4″-dodecyloxyl-benzoyloxy]) benzoyloxybenzoate have been measured using infrared (IR) and Raman techniques in the solid, in the smectic phase, and in CCl4 and CS2 solution. IR absorbance measurements have been carried out in polarized beam for a homogeneously aligned sample to obtain more details about the orientation of vibrational transition dipole moments. In order to investigate the structure and conformation of the molecule in the crystalline state, molecular dynamics simulations have been performed and dihedral angle distributions have been calculated. The molecular structure and vibrational spectra of the molecule mezogenic core for the most stable conformation have been calculated using the density functional theory with the polarized Gaussian basis set 6-31G*. The predicted force field has been scaled using the scaled quantum-mechanical force field method. The calculated spectrum has been compared with the experimental infrared and the Raman spectra, and as a result detailed vibrational assignments have been reported.
Bending vibrational wave numbers in the ã 3Πu and b̃ 3Πg states of C3
Authors: Tokaryk D. W. , Harvie Duncan J. , Lees Ronald M. , Xu Li-Hong
Published: September 2002

The spectrum of the 050 Σu−3–010 Σg−3 band of the b̃ 3Πg–ã 3Πu electronic transition of C3 is reported. The data, when considered with the previously observed 010 Σu−3–010 Σg−3 band, measure the absolute interval between the 050 Σu−3 and 010 Σu−3 levels of the b̃ 3Πg state. This interval, and the Renner parameters for ã 3Πu and b̃ 3Πg [D. W. Tokaryk and S. Civiš, J. Chem. Phys. 103, 3928 (1995)], allow us to greatly improve estimates of the bending vibrational wave numbers in these electronic states. The values (542.3 cm−1 for ã 3Πu, and 392.4 cm−1 for b̃ 3Πg) predict the origins of all previously reported bands of b̃ 3Πg –ã 3Πu involving bending to within 13 cm−1.
Cahn–Hoffman capillarity vector thermodynamics for curved liquid crystal interfaces with applications to fiber instabilities
Authors: Cheong Ae-Gyeong , Rey Alejandro D.
Published: September 2002

The Cahn–Hoffman capillarity vector thermodynamics for curved anisotropic interfaces is adapted to soft liquid crystalline interfaces. The formalism is used to derive Herring’s capillary pressure equation for anisotropic surfaces, where the role of anchoring energy of liquid crystals is made explicity. It is shown in detail that liquid crystal interfaces have three distinct contributions to capillary pressure: (i) area reduction, (ii) area rotation, and (iii) orientation curvature. General expressions representing these three mechanisms in terms of isotropic and anisotropic surface tensions are derived and used to analyze the Rayleigh capillary instability in thin fibers. It is shown that liquid crystal fibers and filaments are unstable to peristaltic and chiral surface ripple modes. The peristaltic mode leads to droplet formation, while chiral modes produce ripples in the curvature of the fiber. The role of liquid crystal orientation and anchoring energy on mode selection is elucidated and quantified.
Dislocation and morphology control during molecular-beam epitaxy of AlGaN/GaN heterostructures directly on sapphire substrates
Authors: Manfra M. J. , Weimann N. G. , Hsu J. W. P. , Pfeiffer L. N. , West K. W. , Chu S. N. G.
Published: September 2002

We report on the growth and transport characteristics of high-density (∼1013 cm−2) two-dimensional electron gases confined at the AlGaN/GaN interface grown by plasma-assisted molecular-beam epitaxy on sapphire substrates. For structures consisting of a 25 nm Al0.30Ga0.70N barrier deposited on a 2 μm insulating GaN buffer, room-temperature mobilities averaging 1400 cm2/V s at a sheet charge density of 1.0×1013 cm−2 are consistently achieved. Central to our approach is a sequence of two Ga/N ratios during the growth of the insulating GaN buffer layer. The two-step buffer layer allows us to simultaneously optimize the reduction of threading dislocations and surface morphology. Our measured sheet resistivities as low as 350Ω/□ compare favorably with those achieved on sapphire or SiC by any growth method. Representative current–voltage characteristics of high-electron-mobility transistors fabricated from this material are presented.
Deep nitrogen implantation for GaAs microstructuring using pulsed electrochemical etching
Authors: Miao Jianmin , Hartnagel Hans L. , Weiss Bernard L.
Published: September 2002

We present deep ion implantation technology to fabricate the GaAs microstructures for microelectromechanical systems applications. 630 keV and 4 MeV nitrogen ions were used to implant deeply into an n-type GaAs substrate with doses of 2×1014 and 1×1015 cm−2, respectively. The resistivity and I/V characteristics of implanted n-GaAs have been investigated as a function of the annealing temperature. The results demonstrate that the implanted n-GaAs surface layer annealed at 600 °C has the highest resistivity and maximum breakdown voltage. This layer is a semi-insulating layer and has a thickness of 1 and 2.5 μm for implantation with 630 keV and 4 MeV nitrogen ions, respectively. Deep-level transient spectroscopy measurement reveals that the EL2 trap contributes to the formation of semi-insulating GaAs layers. Rutherford backscattering measurements show that there is no significant crystalline damage in the nitrogen implanted GaAs layer. A pulsed electrochemical etching process has been developed to selectively remove n-GaAs, leaving the top patterned semi-insulating GaAs layer as mechanical microstructures. Using this technique, GaAs microstructures, such as cantilevers and cross bridges, have been successfully fabricated.
Electric conductivity of dye modified DNA films with and without light irradiation in various humidities
Authors: Gu Jianhua , Cai Lintao , Tanaka Shinnichi , Otsuka Youichi , Tabata Hitoshi , Kawai Tomoji
Published: September 2002

Dye-DNA complex film was prepared by modifying DNA with acridine orange (AO) and depositing it on gold electrodes having a gap in the order of micrometers. Measurement of the electrical characteristics of the dye-DNA film was performed in a vacuum and in various humidities. A photoinduced conductivity change, which we suggest is caused by band or hopping conduction, was observed at relatively low humidity (20%) and in a vacuum. As the humidity rises to 70% and above, the current jumps from picoampere to milliampere levels. This dramatic resistance change corresponds to a dominant conductor mechanism change from hopping or band conductivity to ion conductivity. These reproducible characteristics of photoinduced and humidity-dependent conductivity suggest that the AO-DNA setup could be used as a photosensitive semiconducting device and as a humidity sensor chip.
Dependence of quantum-dot formation on substrate orientation studied by magnetophotoluminescence
Authors: Maes J. , Hayne M. , Moshchalkov V. V. , Patanè A. , Henini M. , Eaves L. , Main P. C.
Published: September 2002

We have investigated the substrate orientation-dependence of InAs/GaAs quantum dot growth by photoluminescence spectroscopy in very high magnetic fields. An abrupt change from one-dimensional to three-dimensional charge confinement is observed for InAs deposited on (100) GaAs. On the tilted (311)B substrates, the quantum dot morphology is different, resulting in a weaker charge confinement that gradually increases with the amount of deposited InAs. At 1.9 monolayers, the quantum-dot confinement on this substrate orientation is as effective as for the (100) oriented substrates. By studying the confinement of the charges in samples with quantum dots at different stages of development, we are able to give insight into the quantum-dot formation process.
Electroluminescence from low-dimensionally confined crystals of thiophene/p-phenylene co-oligomers
Authors: Yanagi Hisao , Morikawa Takayuki , Hotta Shu
Published: September 2002

Organic electroluminescence from epitaxially oriented needle crystals of a thiophene/p-phenylene co-oligomer was studied. The crystals grown by vapor deposition on a KCl (100) surface were confined in a p-sexiphenyl (p-6P) layer. After deposition of an Al cathode the film was wet transferred onto an indium tin oxide (ITO) coated glass. At a low bias voltage, this cell exhibited homogeneous blue light emission from the p-sexiphenyl layer due to carrier recombination in the ITO/p-6P/Al region. With an increase of the voltage, the electroluminescence band shifted to the longer wavelengths corresponding to the green spectrum of the co-oligomer. This emission was concentrated on the needle crystals and suggested that the injected holes were confined inside this low-dimensional structure and recombined with electrons injected from the p-6P layer.
Phosphorus and arsenic penetration studies through HfSixOy and HfSixOyNz films
Authors: Quevedo-Lopez M. A. , El-Bouanani M. , Kim M. J. , Gnade B. E. , Wallace R. M. , Visokay M. R. , Li-Fatou A. , Bevan M. J. , Colombo L.
Published: September 2002

Phosphorus and arsenic penetration studies from P- and As-doped polycrystalline silicon through HfSixOy and HfSixOyNz (18% N) alternate gate dielectric candidates films into Si(100) are presented using a combination of chemical etching and secondary ion mass spectrometry (SIMS). Penetration is observed through HfSixOy after 1050 and 1000 °C rapid thermal annealing for As and P, respectively. In contrast, As or P dopant penetration is at the SIMS limit of detection for HfSixOyNz films. By modeling the P and As depth profiles in the Si substrate, their respective diffusivities in HfSixOy are higher than the corresponding diffusivities in SiO2. The enhanced dopant diffusivity observed in HfSixOy is proposed to be due to grain boundary formation in the dielectric after crystallization from annealing.
Fabrication of linear colloidal structures for microfluidic applications
Authors: Terray A. , Oakey J. , Marr D. W. M.
Published: September 2002

In this letter, an optical microfabrication and actuation method for the creation of microfluidic structures is described. In this approach, an optical trap is used to position and polymerize colloidal microspheres into linear structures to create particle or cell directing devices within microfluidic channel networks. To demonstrate the utility of these structures, two microscale particulate valves are shown, a passive design that restricts particulate flow in one direction and another design that directs particulate flow to one of two exit channels.
Improved corresponding states scaling of the equations of state of simple fluids
Authors: Ben-Amotz Dor , Gift Alan D. , Levine R. D.
Published: September 2002

The principle of corresponding states is re-examined in the light of recent experimental and theoretical fluid equation of state data compilations. The results are used to critically test and extend the fundamental concept of corresponding states scaling for simple fluids (including rare gases, diatomics and methane). Classical corresponding states scaling based on critical point constants is found to produce weaker universal behavior than a new scaling procedure linked directly to the two intermolecular interaction potential parameters of a Lennard-Jones–6-12 fluid. The improved universal behavior revealed using this Lennard-Jones–corresponding-states scaling may either reflect inaccuracies in previous critical constant estimates, or perhaps point to more fundamental differences between the critical properties of different fluids.
Mössbauer study of FeCoNbBCu hitperm-type alloys
Authors: Blázquez J. S. , Conde A. , Grenèche J. M.
Published: September 2002

FeCoNbBCu alloys have been studied by Mössbauer spectrometry. A high contribution of the interfacial region in the nanocrystalline samples to the hyperfine field distribution is detected. The possible presence of B in the nanocrystalline grains is also discussed. Low values of the hyperfine field with respect to the disordered α-FeCo phase suggest the presence of the ordered α′-FeCo phase. Recrystallization phenomena at the second crystallization stage are confirmed.
Last but Not Least
Authors: Foster Chris , Altschuler Eric L
Published: September 2002

When a simple rectangular grid is drawn toward one's face there is the striking illusion that a spherical bulge is protruding from the grid. This illusion may be helpful in studying the interaction of spatial and motion processing.
A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants
Authors: Bentolila Stéphane , Alfonso Antonio A. , Hanson Maureen R.
Published: September 2002

Known in over 150 species, cytoplasmic male sterility is encoded by aberrant mitochondrial genes that prevent pollen development. The RNA- or protein-level expression of most of the mitochondrial genes encoding cytoplasmic male sterility is altered in the presence of one or more nuclear genes called restorers of fertility that suppress the male-sterile phenotype. Cytoplasmic male sterility/restorer systems have been proven to be an invaluable tool in the production of hybrid seeds. Despite their importance for both the production of major crops such as rice and sunflower and the study of organelle/nuclear interactions in plants, none of the nuclear fertility-restorer genes that reduce the expression of aberrant mitochondrial proteins have previously been cloned. Here we report the isolation of a gene directly involved in the control of the expression of a cytoplasmic male sterility-encoding gene. The
Petunia
restorer of fertility gene product is a mitochondrially targeted protein that is almost entirely composed of 14 repeats of the 35-aa pentatricopeptide repeat motif. In a nonrestoring genotype we identified a homologous gene that exhibits a deletion in the promoter region and is expressed in roots but not in floral buds.
Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: The role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza
Authors: Geiss Gary K. , Salvatore Mirella , Tumpey Terrence M. , Carter Victoria S. , Wang Xiuyan , Basler Christopher F. , Taubenberger Jeffery K. , Bumgarner Roger E. , Palese Peter , Katze Michael G. , García-Sastre Adolfo
Published: September 2002

The NS1 protein of influenza A virus contributes to viral pathogenesis, primarily by enabling the virus to disarm the host cell type IFN defense system. We examined the downstream effects of NS1 protein expression during influenza A virus infection on global cellular mRNA levels by measuring expression of over 13,000 cellular genes in response to infection with wild-type and mutant viruses in human lung epithelial cells. Influenza A/PR/8/34 virus infection resulted in a significant induction of genes involved in the IFN pathway. Deletion of the viral NS1 gene increased the number and magnitude of expression of cellular genes implicated in the IFN, NF-κB, and other antiviral pathways. Interestingly, different IFN-induced genes showed different sensitivities to NS1-mediated inhibition of their expression. A recombinant virus with a C-terminal deletion in its NS1 gene induced an intermediate cellular mRNA expression pattern between wild-type and NS1 knockout viruses. Most significantly, a virus containing the 1918 pandemic NS1 gene was more efficient at blocking the expression of IFN-regulated genes than its parental influenza A/WSN/33 virus. Taken together, our results suggest that the cellular response to influenza A virus infection in human lung cells is significantly influenced by the sequence of the NS1 gene, demonstrating the importance of the NS1 protein in regulating the host cell response triggered by virus infection.
Smaller is better—but not too small: A physical scale for the design of the mammalian pulmonary acinus
Authors: Sapoval Bernard , Filoche M. , Weibel E. R.
Published: September 2002

The transfer of oxygen from air to blood in the lung involves three processes: ventilation through the airways, diffusion of oxygen in the air phase to the alveolar surface, and finally diffusion through tissue into the capillary blood. The latter two steps occur in the acinus, where the alveolar gas-exchange surface is arranged along the last few generations of airway branching. For the acinus to work efficiently, oxygen must reach the last branches of acinar airways, even though some of it is absorbed along the way. This “screening effect” is governed by the relative values of physical factors like diffusivity and permeability as well as size and design of the acinus. Physics predicts that efficient acini should be space-filling surfaces and should not be too large. It is shown that the mammalian acini fulfill these requirements, small mammals being more efficient than large ones both at rest and in exercise.
Selective impairment of reasoning about social exchange in a patient with bilateral limbic system damage
Authors: Stone Valerie E. , Cosmides Leda , Tooby John , Kroll Neal , Knight Robert T.
Published: September 2002

Social exchange is a pervasive feature of human social life. Models in evolutionary biology predict that for social exchange to evolve in a species, individuals must be able to detect cheaters (nonreciprocators). Previous research suggests that humans have a cognitive mechanism specialized for detecting cheaters. Here we provide neurological evidence indicating that social exchange reasoning can be selectively impaired while reasoning about other domains is left intact. The patient, R.M., had extensive bilateral limbic system damage, affecting orbitofrontal cortex, temporal pole, and amygdala. We compared his performance on two types of reasoning problem that were closely matched in form and equally difficult for control subjects: social contract rules (of the form, “If you take the benefit, then you must satisfy the requirement”) and precaution rules (of the form, “If you engage in hazardous activity X, then you must take precaution Y”). R.M. performed significantly worse in social contract reasoning than in precaution reasoning, when compared both with normal controls and with other brain-damaged subjects. This dissociation in reasoning performance provides evidence that reasoning about social exchange is a specialized and separable component of human social intelligence, and is consistent with other research indicating that the brain processes information about the social world differently from other types of information.
Not
I subtraction and
Not
I-specific microarrays to detect copy number and methylation changes in whole genomes
Authors: Li Jingfeng , Protopopov Alexei , Wang Fuli , Senchenko Vera , Petushkov Valentin , Vorontsova Olga , Petrenko Lev , Zabarovska Veronika , Muravenko Olga , Braga Eleonora , Kisselev Lev , Lerman Michael I. , Kashuba Vladimir , Klein George , Ernberg Ingemar , Wahlestedt Claes , Zabarovsky Eugene R.
Published: September 2002

Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of
Not
I clone microarrays and genomic subtraction, because
Not
I recognition sites are closely associated with CpG islands and genes. We show here that the CODE (Cloning Of DEleted sequences) genomic subtraction procedure can be adapted to
Not
I flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A
Not
I-CODE procedure can be used to prepare
Not
I representations (NRs) containing 0.1–0.5% of the total DNA. The NRs contain, on average, 10-fold less repetitive sequences than the whole human genome and can be used as probes for hybridization to
Not
I microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation.
Not
I microarrays offer a powerful tool with which to study carcinogenesis.
Loss of stearoyl–CoA desaturase-1 function protects mice against adiposity
Authors: Ntambi James M. , Miyazaki Makoto , Stoehr Jonathan P. , Lan Hong , Kendziorski Christina M. , Yandell Brian S. , Song Yang , Cohen Paul , Friedman Jeffrey M. , Attie Alan D.
Published: September 2002

Stearoyl–CoA desaturase (SCD) is a central lipogenic enzyme catalyzing the synthesis of monounsaturated fatty acids, mainly oleate (C18:1) and palmitoleate (C16:1), which are components of membrane phospholipids, triglycerides, wax esters, and cholesterol esters. Several SCD isoforms (
SCD1
-
3
) exist in the mouse. Here we show that mice with a targeted disruption of the
SCD1
isoform have reduced body adiposity, increased insulin sensitivity, and are resistant to diet-induced weight gain. The protection from obesity involves increased energy expenditure and increased oxygen consumption. Compared with the wild-type mice the
SCD1
−/− mice have increased levels of plasma ketone bodies but reduced levels of plasma insulin and leptin. In the
SCD1
−/− mice, the expression of several genes of lipid oxidation are up-regulated, whereas lipid synthesis genes are down-regulated. These observations suggest that a consequence of
SCD1
deficiency is an activation of lipid oxidation in addition to reduced triglyceride synthesis and storage.
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation
Authors: Ghosh Avijit , Elber Ron , Scheraga Harold A.
Published: September 2002

An algorithm is applied here to compute folding pathways of staphylococcal protein A, fragment B. Emphasis is on studies of the complete process, starting from an ensemble of fully denatured conformations and ending at the folded state. The stochastic difference equation algorithm is based on optimization of an action that makes it possible to use a large integration step. Motions with typical displacements that change rapidly on the size scale of the step are filtered out, providing numerically stable and approximate solutions. The present approach is unique in maintaining an atomically detailed picture while providing a systematic, controlled approximation to the classical equations of motion. Analysis of 130 trajectories suggests the following folding mechanism for protein A: At an early precollapse phase of the process, a few native hydrogen bonds form near the C terminus of the protein. The hydrogen bonds are formed mostly within the third helix. The next step is chain collapse that occurs in parallel to additional growth of secondary structure seeds. Therefore, the present study does not support a pure hydrophobic collapse, or substantial early formation of secondary structure. At the last step, native tertiary contacts are formed at the same time as the completion of the secondary structure elements. To a large extent, the process is parallel and not sequential. The early formation of the third helix of protein A, fragment B (in the calculation), is consistent with experimental data.
PTP1B antisense oligonucleotide lowers PTP1B protein, normalizes blood glucose, and improves insulin sensitivity in diabetic mice
Authors: Zinker Bradley A. , Rondinone Cristina M. , Trevillyan James M. , Gum Rebecca J. , Clampit Jill E. , Waring Jeffrey F. , Xie Nancy , Wilcox Denise , Jacobson Peer , Frost Leigh , Kroeger Paul E. , Reilly Regina M. , Koterski Sandra , Opgenorth Terry J. , Ulrich Roger G. , Crosby Seth , Butler Madeline , Murray Susan F. , McKay Robert A. , Bhanot Sanjay , Monia Brett P. , Jirousek Michael R.
Published: September 2002

The role of protein-tyrosine phosphatase 1B (PTP1B) in diabetes was investigated using an antisense oligonucleotide in
ob
/
ob
and
db
/
db
mice. PTP1B antisense oligonucleotide treatment normalized plasma glucose levels, postprandial glucose excursion, and HbA
1C
. Hyperinsulinemia was also reduced with improved insulin sensitivity. PTP1B protein and mRNA were reduced in liver and fat with no effect in skeletal muscle. Insulin signaling proteins, insulin receptor substrate 2 and phosphatidylinositol 3 (PI3)-kinase regulatory subunit p50α, were increased and PI3-kinase p85α expression was decreased in liver and fat. These changes in protein expression correlated with increased insulin-stimulated protein kinase B phosphorylation. The expression of liver gluconeogenic enzymes, phosphoenolpyruvate carboxykinase, and fructose-1,6-bisphosphatase was also down-regulated. These findings suggest that PTP1B modulates insulin signaling in liver and fat, and that therapeutic modalities targeting PTP1B inhibition may have clinical benefit in type 2 diabetes.
Coordinated patterns of gene expression for substrate and energy metabolism in skeletal muscle of diabetic mice
Authors: Yechoor Vijay K. , Patti Mary-Elizabeth , Saccone Robert , Kahn C. Ronald
Published: September 2002

Metabolic abnormalities underlying diabetes are primarily the result of the lack of adequate insulin action and the associated changes in protein phosphorylation and gene expression. To define the full set of alterations in gene expression in skeletal muscle caused by diabetes and the loss of insulin action, we have used Affymetrix oligonucleotide microarrays and streptozotocin-diabetic mice. Of the genes studied, 235 were identified as changed in diabetes, with 129 genes up-regulated and 106 down-regulated. Analysis revealed a coordinated regulation at key steps in glucose and lipid metabolism, mitochondrial electron transport, transcriptional regulation, and protein trafficking. mRNAs for all of the enzymes of the fatty acid β-oxidation pathway were increased, whereas those for GLUT4, hexokinase II, the E1 component of the pyruvate dehydrogenase complex, and subunits of all four complexes of the mitochondrial electron transport chain were all coordinately down-regulated. Only about half of the alterations in gene expression in diabetic mice could be corrected toward normal after 3 days of insulin treatment and euglycemia. These data point to as of yet undefined mechanisms for highly coordinated regulation of gene expression by insulin and potential new targets for therapy of diabetes mellitus.
Estimating prokaryotic diversity and its limits
Authors: Curtis Thomas P. , Sloan William T. , Scannell Jack W.
Published: September 2002

The absolute diversity of prokaryotes is widely held to be unknown and unknowable at any scale in any environment. However, it is not necessary to count every species in a community to estimate the number of different taxa therein. It is sufficient to estimate the area under the species abundance curve for that environment. Log-normal species abundance curves are thought to characterize communities, such as bacteria, which exhibit highly dynamic and random growth. Thus, we are able to show that the diversity of prokaryotic communities may be related to the ratio of two measurable variables: the total number of individuals in the community and the abundance of the most abundant members of that community. We assume that either the least abundant species has an abundance of 1 or Preston's canonical hypothesis is valid. Consequently, we can estimate the bacterial diversity on a small scale (oceans 160 per ml; soil 6,400–38,000 per g; sewage works 70 per ml). We are also able to speculate about diversity at a larger scale, thus the entire bacterial diversity of the sea may be unlikely to exceed 2 × 10
6
, while a ton of soil could contain 4 × 10
6
different taxa. These are preliminary estimates that may change as we gain a greater understanding of the nature of prokaryotic species abundance curves. Nevertheless, it is evident that local and global prokaryotic diversity can be understood through species abundance curves and purely experimental approaches to solving this conundrum will be fruitless.
Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions
Authors: Joshi Mahesh S. , Ferguson T. Bruce , Han Tae H. , Hyduke Daniel R. , Liao James C. , Rassaf Tienush , Bryan Nathan , Feelisch Martin , Lancaster Jack R.
Published: September 2002

Although irreversible reaction of NO with the oxyheme of hemoglobin (producing nitrate and methemoglobin) is extremely rapid, it has been proposed that, under normoxic conditions, NO binds preferentially to the minority deoxyheme to subsequently form
S
-nitrosohemoglobin (SNOHb). Thus, the primary reaction would be conservation, rather than consumption, of nitrogen oxide. Data supporting this conclusion were generated by using addition of a small volume of a concentrated aqueous solution of NO to a normoxic hemoglobin solution. Under these conditions, however, extremely rapid reactions can occur before mixing. We have thus compared bolus NO addition to NO generated homogeneously throughout solution by using NO donors, a more physiologically relevant condition. With bolus addition, multiple hemoglobin species are formed (as judged by visible spectroscopy) as well as both nitrite and nitrate. With donor, only nitrate and methemoglobin are formed, stoichiometric with the amount of NO liberated from the donor. Studies with increasing hemoglobin concentrations reveal that the nitrite-forming reaction (which may be NO autoxidation under these conditions) competes with reaction with hemoglobin. SNOHb formation is detectable with either bolus or donor; however, the amounts formed are much smaller than the amount of NO added (less than 1%). We conclude that the reaction of NO with hemoglobin under normoxic conditions results in consumption, rather than conservation, of NO.
The threshold for polyglutamine-expansion protein aggregation and cellular toxicity is dynamic and influenced by aging in
Caenorhabditis
elegans
Authors: Morley James F. , Brignull Heather R. , Weyers Jill J. , Morimoto Richard I.
Published: September 2002

Studies of the mutant gene in Huntington's disease, and for eight related neurodegenerative disorders, have identified polyglutamine (polyQ) expansions as a basis for cellular toxicity. This finding has led to a disease hypothesis that protein aggregation and cellular dysfunction can occur at a threshold of approximately 40 glutamine residues. Here, we test this hypothesis by expression of fluorescently tagged polyQ proteins (Q29, Q33, Q35, Q40, and Q44) in the body wall muscle cells of
Caenorhabditis elegans
and show that young adults exhibit a sharp boundary at 35–40 glutamines associated with the appearance of protein aggregates and loss of motility. Surprisingly, genetically identical animals expressing near-threshold polyQ repeats exhibited a high degree of variation in the appearance of protein aggregates and cellular toxicity that was dependent on repeat length and exacerbated during aging. The role of genetically determined aging pathways in the progression of age-dependent polyQ-mediated aggregation and cellular toxicity was tested by expressing Q82 in the background of
age-1
mutant animals that exhibit an extended lifespan. We observed a dramatic delay of polyQ toxicity and appearance of protein aggregates. These data provide experimental support for the threshold hypothesis of polyQ-mediated toxicity in an experimental organism and emphasize the importance of the threshold as a point at which genetic modifiers and aging influence biochemical environment and protein homeostasis in the cell.
Identification of unstable transcripts in
Arabidopsis
by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes
Authors: Gutiérrez Rodrigo A. , Ewing Rob M. , Cherry J. Michael , Green Pamela J.
Published: September 2002

mRNA degradation provides a powerful means for controlling gene expression during growth, development, and many physiological transitions in plants and other systems. Rates of decay help define the steady state levels to which transcripts accumulate in the cytoplasm and determine the speed with which these levels change in response to the appropriate signals. When fast responses are to be achieved, rapid decay of mRNAs is necessary. Accordingly, genes with unstable transcripts often encode proteins that play important regulatory roles. Although detailed studies have been carried out on individual genes with unstable transcripts, there is limited knowledge regarding their nature and associations from a genomic perspective, or the physiological significance of rapid mRNA turnover in intact organisms. To address these problems, we have applied cDNA microarray analysis to identify and characterize genes with unstable transcripts in
Arabidopsis thaliana
(
AtGUTs
). Our studies showed that at least 1% of the 11,521 clones represented on
Arabidopsis
Functional Genomics Consortium microarrays correspond to transcripts that are rapidly degraded, with estimated half-lives of less than 60 min.
AtGUTs
encode proteins that are predicted to participate in a broad range of cellular processes, with transcriptional functions being over-represented relative to the whole
Arabidopsis
genome annotation. Analysis of public microarray expression data for these genes argues that mRNA instability is of high significance during plant responses to mechanical stimulation and is associated with specific genes controlled by the circadian clock.
An anatomy of normal and malignant gene expression
Authors: Boon Kathy , Osório Elisson C. , Greenhut Susan F. , Schaefer Carl F. , Shoemaker Jennifer , Polyak Kornelia , Morin Patrice J. , Buetow Kenneth H. , Strausberg Robert L. , de Souza Sandro J. , Riggins Gregory J.
Published: September 2002

A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP) uses serial analysis of gene expression (SAGE). Over 5 million transcript tags from more than 100 human cell types have been assembled. To enhance the utility of this data, the CGAP SAGE project created SAGE Genie, a web site for the analysis and presentation of SAGE data (
http://cgap.nci.nih.gov/
SAGE). SAGE Genie provides an automatic link between gene names and SAGE transcript levels, accounting for alternative transcription and many potential errors. These informatics advances provide a rapid and intuitive view of transcript expression in the human body or brain, displayed on the SAGE Anatomic Viewer. We report here an easily accessible view of nearly any gene's expression in a wide variety of malignant and normal tissues.
Patterned variation in murine MHC promoters
Authors: Mitchison N. Avrion , Roes Jürgen
Published: September 2002

To compare variation in regulatory and coding DNA, promoter sequences have been obtained from wild-derived mice and laboratory rats. The sequences are from the proximal promoter of theH2Aa,H2Ab,H2Eb, andH2Kgenes of 24 wild-derived inbred strains and a sample of the corresponding exon 2 sequences and of theRT1.Bagene of six strains of laboratory rat. They reveal a high level of variation in the mouse MHC class II promoters (H2AandH2E), a low level in MHC class I (H2K), and none in the rat. The variation is pronounced in and around the cAMP response element, a major binding site for modulating promoter activity in response to external stimulation. This finding, together with the different levels of variation in MHC classes I and II, is suggestive of natural selection. However, selection operating via the MHC coding sequences must also contribute, as indicated by the minimal variation in both the MHC class II promoter and coding sequences of the rat. Furthermore CIITA (trans-activator of class II) of the mouse has been reported to have minimal variation in its promoter and none in its coding sequence. Taken together these data suggest that the regulatory and coding sequences undergo coselection. Each of the mouse class II promoters has a pattern of variation that appears to be basically dimorphic, with further variation added by recombination/mutation. The dimorphic allelic lineages are in marginally detectable linkage disequilibrium with the exon 2 sequences, particularly in H2Aa, thus lending further support to the coevolution hypothesis.
Tissue-specific silencing of a transgene in rice
Authors: Klöti A. , He X. , Potrykus I. , Hohn T. , Fütterer J.
Published: September 2002

In a transgenic rice line, a β-glucuronidase reporter gene under the control of the rice tungro bacilliform virus promoter became gradually methylated, and gene activity was lost concomitantly. Methylation was observed only in the homozygous offspring and was initially restricted to the promoter region and accompanied by loss of expression in the vascular bundle tissue only. This expression pattern was similar to that of a promoter with a deletion of a vascular bundle expression element. The gene activity could be reestablished by treatment with 5-azacytidine. Methylationper sedid not inhibit the binding to the promoter region of protein factors which also bound to the unmethylated sequence. Instead, promoter methylation enabled the alternative binding of a protein with specificity for sequence and methylation. In further generations of homozygous offspring the methylation spread into the transcribed region and gene activity was completely repressed also in nonvascular cells. The results indicate that different stages are involved in DNA methylation-correlated gene inactivation, and that at least one of them may involve the attraction of a sequence and methylation-specific DNA-binding protein.
Positional cloning of the gene
LIMBIN
responsible for bovine chondrodysplastic dwarfism
Authors: Takeda Haruko , Takami Marika , Oguni Tomoko , Tsuji Takehito , Yoneda Kazuhiro , Sato Hiroaki , Ihara Naoya , Itoh Tomohito , Kata Srinivas R. , Mishina Yuji , Womack James E. , Moritomo Yasuo , Sugimoto Yoshikazu , Kunieda Tetsuo
Published: September 2002

Chondrodysplastic dwarfism in Japanese brown cattle is an autosomal recessive disorder characterized by short limbs. Previously, we mapped the locus responsible for the disease on the distal end of bovine chromosome 6. Here, we narrowed the critical region to ≈2 cM by using linkage analysis, constructed a BAC and YAC contig covering this region, and identified a gene,
LIMBIN
(
LBN
), that possessed disease-specific mutations in the affected calves. One mutation was a single nucleotide substitution leading to an activation of a cryptic splicing donor site and the other was a one-base deletion resulting in a frameshift mutation. Strong expression of the
Lbn
gene was observed in limb buds of developing mouse embryos and in proliferating chondrocytes and bone-forming osteoblasts in long bones. These findings indicate that
LBN
is responsible for bovine chondrodysplastic dwarfism and has a critical role in a skeletal development.
Mechanisms of polarization of the shape of fibroblasts and epitheliocytes: Separation of the roles of microtubules and Rho-dependent actin–myosin contractility
Authors: Omelchenko T. , Vasiliev J. M. , Gelfand I. M. , Feder H. H. , Bonder E. M.
Published: September 2002

Cultured fibroblasts possess a characteristic polarized phenotype manifested by an elongate cell body with an anterior lamella whose cell edge is divided into protrusion-forming and inactive zones. Disruption of the fibroblast microtubule cytoskeleton leads to an increase in Rho-dependent acto-myosin contractile activity and concomitant loss of structural polarity. The functional relationship of myosin-driven contractile activity to loss of fibroblast anterior–posterior polarity is unknown. To dissect the roles of microtubule assembly and of Rho-dependent contractility on structural polarization of cells, polarized fibroblasts and nonpolarized epitheliocytes were treated with the microtubule-depolymerizing drug, nocodazole, and/or the Rho kinase inhibitor, Y-27632. Fibroblasts incubated with Y-27632 increased their degree of polarization by developing a highly elongate cell body with multiple narrow processes extended from the edges of the cell. Treatment of fibroblasts with nocodazole, alone or in combination with Rho kinase inhibitor, produced discoid or polygonal cells having broad, flattened lamellae that did not form long lamellar extensions. Single cultured epitheliocytes of the IAR-2 line do not display anterior–posterior polarization. When treated with Y-27632, the cells acquired a polarized, elongate shape with narrow protrusions and wide lamellas. Nocodazole alone or in combination with Y-27632 did not change the discoid shape of epitheliocytes, however treatment with Y-27632 produced thinning of the lamellar cytoplasm. We conclude that microtubules provide the necessary framework for polarization of fibroblasts and epitheliocytes, whereas Rho-regulated contractility modulates the degree of polarization of fibroblasts and completely inhibits polarization in epitheliocytes.
The structure of a replication initiator unites diverse aspects of nucleic acid metabolism
Authors: Campos-Olivas Ramón , Louis John M. , Clérot Danielle , Gronenborn Bruno , Gronenborn Angela M.
Published: September 2002

Rolling circle replication is a mechanism for copying single-stranded genomes by means of double-stranded intermediates. A multifunctional replication inititiator protein (Rep) is indispensable for the precise initiation and termination of this process. Despite the ubiquitous presence and fundamental importance of rolling circle replication elements, structural information on their respective replication initiators is still missing. Here we present the solution NMR structure of the catalytic domain of Rep, the initiator protein of tomato yellow leaf curl virus. It is composed of a central five-stranded anti-parallel β-sheet, flanked by a small two-stranded β-sheet, a β-hairpin and two α-helices. Surprisingly, the structure reveals that the catalytic Rep domain is related to a large group of proteins that bind RNA or DNA. Identification of Rep as resembling the family of ribonucleoprotein/RNA-recognition motif fold proteins establishes a structure-based evolutionary link between RNA binding proteins, splicing factors, and replication initiators of prokaryotic and eukaryotic single-stranded DNA elements and mammalian DNA tumor viruses.
Lack of acrosome formation in mice lacking a Golgi protein, GOPC
Authors: Yao Ryoji , Ito Chizuru , Natsume Yasuko , Sugitani Yoshinobu , Yamanaka Hitomi , Kuretake Shoji , Yanagida Kaoru , Sato Akira , Toshimori Kiyotaka , Noda Tetsuo
Published: September 2002

The acrosome is a unique organelle that plays an important role at the site of sperm–zona pellucida binding during the fertilization process, and is lost in globozoospermia, an inherited infertility syndrome in humans. Although the acrosome is known to be derived from the Golgi apparatus, molecular mechanisms underlying acrosome formation are largely unknown. Here we show that Golgi-associated PDZ- and coiled-coil motif-containing protein (GOPC), a recently identified Golgi-associated protein, is predominantly localized at the trans-Golgi region in round spermatids, and male mice in which
GOPC
has been disrupted are infertile with globozoospermia. The primary defect was the fragmentation of acrosomes in early round spermatids, and abnormal vesicles that failed to fuse to developing acrosomes were apparent. In later stages, nuclear malformation and an abnormal arrangement of mitochondria, which are also characteristic features of human globozoospermia, were observed. Interestingly, intracytoplasmic sperm injection (ICSI) of such malformed sperm into oocytes resulted in cleavage into blastocysts only when injected oocytes were activated. Thus, GOPC provides important clues to understanding the mechanisms underlying spermatogenesis, and the GOPC-deficient mouse may be a unique and valuable model for human globozoospermia.