bluuebunny/crossref_metadata_2025 huggingface dataset:
Morphology evolution and local electric properties of Au nanoparticles on ZnO thin films
Authors: György E. , Santiso J. , Figueras A. , Giannoudakos A. , Kompitsas M. , Mihailescu I. N.
Published: October 2005

We report the sequential two-step pulsed laser deposition of nanostructures consisting of ZnO thin films covered with Au nanoparticles. Zn and Au targets were alternatively submitted to pulses generated by a frequency tripled Nd:yttrium aluminium garnet (λ=355nm, τ∼10ns, ν=10Hz) laser. The ZnO films were synthesized in 20Pa oxygen pressure, whereas the subsequent Au coverage was applied in vacuum. The dynamics of Au nanoparticles grown on the ZnO thin-films surface was studied by atomic force microscopy as a function of number of laser pulses applied for the ablation of the Au target. The nanoparticle diameters increase with the number of laser pulses while their height decreases. The local electric properties of the uncoated (reference) and coated with Au ZnO thin films was investigated by current sensing mode atomic force microscopy.
Rapid-thermal-processing-based intrinsic gettering for nitrogen-doped Czochralski silicon
Authors: Ma Xiangyang , Fu Liming , Tian Daxi , Yang Deren
Published: October 2005

In order to optimize the intrinsic gettering (IG) process based on the rapid thermal processing (RTP) for nitrogen-doped Czochralski (NCZ) silicon wafer, the effects of RTP and the following nucleation anneal on oxygen precipitation in NCZ silicon and conventional CZ silicon wafers have been comparatively investigated. It was found that, for NCZ silicon, the RTP at enough high temperature (e.g., 1250°C) was necessary for generation of high density of bulk microdefects (BMDs) in the subsequent anneals despite the nitrogen enhancement effect on oxygen precipitation. With enough high concentration of vacancies introduced by the RTP at 1250°C, for the conventional CZ silicon wafer, the vacancy enhancement effect on the nucleation of oxygen precipitates was most significant at 800°C; while for NCZ silicon wafer, the vacancies and nitrogen atoms coacted most remarkably to nucleate the oxygen precipitates during the ramping anneal from 800to1000°C. It was further found that the doped nitrogen is superior to the vacancy to enhance the nucleation of oxygen precipitates at temperatures of 900–1000°C. Moreover, in order to maximize the density of BMDs, the RTP-based IG process for NCZ silicon wafer should be different from that for the conventional CZ silicon wafer.
An electronic criterion for the intrinsic embrittlement of structural intermetallic compounds
Authors: Li W. , Wang Y. , Cai M. , Wang C. W.
Published: October 2005

Development of intermetallics for high-temperature structural applications has long been impeded by their brittleness. To overcome the brittleness, efforts have been devoted to understand the atomic bonding nature of intermetallics. However, there are no simple theoretical or experimental means for investigating the electronic origin of the brittleness. We find a simple experimental method, which employs the Kelvin-probe technique to measure the electron work function. The typical intermetallics in three alloy systems (Ni–Al, Fe–Al, and Ti–Al) were chosen as examples. An electronic criterion was therefore proposed for judging intrinsic brittleness. This criterion could provide some principles for improving the ductility of intermetallics and is also expected to be extendable to other materials (e.g., quasicrystalline alloys and metallic glasses).
Fe
3
O
4
nanowires synthesized by electroprecipitation in templates
Authors: Terrier C. , Abid M. , Arm C. , Serrano-Guisan S. , Gravier L. , Ansermet J.-Ph.
Published: October 2005

We present an electrochemical technique for growing Fe3O4 nanostructures. Hydrazine and iron compounds in an aqueous solution undergo chemical reactions with hydroxides and form magnetite at the surface of the working electrode of an electrochemical cell. Growth of magnetite in nanoscale templates is demonstrated. X-ray diffraction, transmission electron microscopy, electrical transport measurements, and magnetometry confirm the nature of the deposit. Giant magnetoresistance was observed when the nanowires were granular.
Negative electrochemical capacitance for a double-quantum-dot device
Authors: Wei Yadong , Zhao Xuean , Wang Baigeng , Wang Jian
Published: October 2005

We report the theoretical investigation of the electrochemical capacitance of a double-quantum-dot device. Analytic result is obtained using the discrete potential approximation. We find that electrochemical capacitance can be tuned by the interdot coupling t. For large t, the electrochemical capacitance can be negative.
Tungstate polyoxometalates as active components of molecular devices
Authors: Velessiotis D. , Glezos N. , Ioannou-Sougleridis V.
Published: October 2005

Polyoxometalates are a class of well-defined metal oxygen clusters mostly known for their catalytic properties. However, their electronic and optical properties have been used in device applications such as electrochromic displays, dopants for conductive polymers, gas and chemical sensors, capacitors, and electrochemical cells. We fabricate nanodevices based on a composite poly(methyl methacrylate) H3SiW12O40 system and we investigate the effects of electrode material, electrode distance, and molecular concentration on the electronic transport characteristics. It is found that in the case of electrode distances smaller than 50 nm, tunneling effects appear, which are discussed using tunneling theory models. These effects are primarily dependent on the electrode distance and molecular concentration, and less on the electrode material.
Thinning of the cerebral cortex visualized in HIV/AIDS reflects CD4
+
T lymphocyte decline
Authors: Thompson Paul M. , Dutton Rebecca A. , Hayashi Kiralee M. , Toga Arthur W. , Lopez Oscar L. , Aizenstein Howard J. , Becker James T.
Published: October 2005

HIV/AIDS infection is the fourth leading cause of death worldwide, and one in every 100 adults aged 15–49 years is HIV-infected. Forty percent of AIDS patients suffer from neurological symptoms, but the selective profile of damage caused by HIV in the brain is not well understood. Here, we report 3D maps revealing how AIDS affects the human cerebral cortex, identifying the most vulnerable regions and where deficits link with cognitive decline and immune-system suppression. With high-resolution brain MRI scans, we created composite maps of cortical gray-matter thickness in 26 AIDS patients and 14 healthy controls to establish the selective pattern of brain deficits in AIDS. In AIDS, primary sensory, motor, and premotor cortices were 15% thinner. Thinner frontopolar and language cortex correlated with immune system deterioration measured through blood levels of CD4
+
T lymphocytes. Prefrontal and parietal tissue loss correlated with cognitive/motor deficits. T cell depletion and cognitive impairment are, therefore, associated with specific 3D brain-deficit patterns visualized with MRI. These quantitative MRI-based maps reveal that HIV selectively damages the cortex. They provide an approach to gauge the impact of AIDS on the living brain and show that the brain is still vulnerable to infection even when patients are receiving antiretroviral therapy.
Tumor promotion by caspase-resistant retinoblastoma protein
Authors: Borges Helena L. , Bird Jeff , Wasson Katherine , Cardiff Robert D. , Varki Nissi , Eckmann Lars , Wang Jean Y. J.
Published: October 2005

The retinoblastoma (RB) protein regulates cell proliferation and cell death. RB is cleaved by caspase during apoptosis. A mutation of the caspase-cleavage site in the RB C terminus has been made in the mouse
Rb-1
locus; the resulting
Rb-MI
mice are resistant to endotoxin-induced apoptosis in the intestine. The
Rb-MI
mice do not exhibit increased tumor incidence, because the
MI
mutation does not disrupt the
Rb
tumor suppressor function. In this study, we show that
Rb-MI
can promote the formation of colonic adenomas in the
p53-null
genetic background. Consistent with this tumor phenotype,
Rb-MI
reduces colorectal epithelial apoptosis and ulceration caused by dextran sulfate sodium. By contrast,
Rb-MI
does not affect the lymphoma phenotype of
p53-null
mice, in keeping with its inability to protect thymocytes and splenocytes from apoptosis. The Rb-MI protein is expressed and phosphorylated in the tumors, thereby inactivating its growth suppression function. These results suggest that RB tumor suppressor function, i.e., inhibition of proliferation, is inactivated by phosphorylation, whereas RB tumor promoting function, i.e., inhibition of apoptosis, is inactivated by caspase cleavage.
Effects of interface mutations on association modes and electron-transfer rates between proteins
Authors: Kang Seong A. , Crane Brian R.
Published: October 2005

Although bonding networks determine electron-transfer (ET) rates within proteins, the mechanism by which structure and dynamics influence ET across protein interfaces is not well understood. Measurements of photochemically induced ET and subsequent charge recombination between Zn-porphyrin-substituted cytochrome
c
peroxidase and cytochrome
c
in single crystals correlate reactivity with defined structures for different association modes of the redox partners. Structures and ET rates in crystals are consistent with tryptophan oxidation mediating charge recombination reactions. Conservative mutations at the interface can drastically affect how the proteins orient and dispose redox centers. Whereas some configurations are ET inactive, the wild-type complex exhibits the fastest recombination rate. Other association modes generate ET rates that do not correlate with predictions based on cofactor separations or simple bonding pathways. Inhibition of photoinduced ET at <273 K indicates gating by small-amplitude dynamics, even within the crystal. Thus, different associations achieve states of similar reactivity, and within those states conformational fluctuations enable interprotein ET.
Auditory orientation in crickets: Pattern recognition controls reactive steering
Authors: Poulet James F. A. , Hedwig Berthold
Published: October 2005

Many groups of insects are specialists in exploiting sensory cues to locate food resources or conspecifics. To achieve orientation, bees and ants analyze the polarization pattern of the sky, male moths orient along the females' odor plume, and cicadas, grasshoppers, and crickets use acoustic signals to locate singing conspecifics. In comparison with olfactory and visual orientation, where learning is involved, auditory processing underlying orientation in insects appears to be more hardwired and genetically determined. In each of these examples, however, orientation requires a recognition process identifying the crucial sensory pattern to interact with a localization process directing the animal's locomotor activity. Here, we characterize this interaction. Using a sensitive trackball system, we show that, during cricket auditory behavior, the recognition process that is tuned toward the species-specific song pattern controls the amplitude of auditory evoked steering responses. Females perform small reactive steering movements toward any sound patterns. Hearing the male's calling song increases the gain of auditory steering within 2–5 s, and the animals even steer toward nonattractive sound patterns inserted into the speciesspecific pattern. This gain control mechanism in the auditory-to-motor pathway allows crickets to pursue species-specific sound patterns temporarily corrupted by environmental factors and may reflect the organization of recognition and localization networks in insects.
Conformational dependence of a protein kinase phosphate transfer reaction
Authors: Henkelman Graeme , LaBute Montiago X. , Tung Chang-Shung , Fenimore P. W. , McMahon Benjamin H.
Published: October 2005

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. With the protein in TC, the motions involved in reaction are small, with only P
γ
and the catalytic proton moving >0.5 Å. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site.
CK2 phosphorylation of eukaryotic translation initiation factor 5 potentiates cell cycle progression
Authors: Homma Miwako Kato , Wada Ikuo , Suzuki Toshiyuki , Yamaki Junko , Krebs Edwin G. , Homma Yoshimi
Published: October 2005

Casein kinase 2 (CK2) is a ubiquitous eukaryotic Ser/Thr protein kinase that plays an important role in cell cycle progression. Although its function in this process remains unclear, it is known to be required for the G
1
and G
2
/M phase transitions in yeast. Here, we show that CK2 activity changes notably during cell cycle progression and is increased within 3 h of serum stimulation of quiescent cells. During the time period in which it exhibits high enzymatic activity, CK2 associates with and phosphorylates a key molecule for translation initiation, eukaryotic translation initiation factor (eIF) 5. Using MS, we show that Ser-389 and -390 of eIF5 are major sites of phosphorylation by CK2. This is confirmed using eIF5 mutants that lack CK2 sites; the phosphorylation levels of mutant eIF5 proteins are significantly reduced, relative to WT eIF5, both
in vitro
and
in vivo
. Expression of these mutants reveals that they have a dominant-negative effect on phosphorylation of endogenous eIF5, and that they perturb synchronous progression of cells through S to M phase, resulting in a significant reduction in growth rate. Furthermore, the formation of mature eIF5/eIF2/eIF3 complex is reduced in these cells, and, in fact, restricted diffusional motion of WT eIF5 was almost abolished in a GFP-tagged eIF5 mutant lacking CK2 phosphorylation sites, as measured by fluorescence correlation spectroscopy. These results suggest that CK2 may be involved in the regulation of cell cycle progression by associating with and phosphorylating a key molecule for translation initiation.
Essential equilibria
Authors: Govindan Srihari , Wilson Robert
Published: October 2005

The connected uniformly hyperstable sets of a finite game are shown to be precisely the essential components of Nash equilibria.
Plasmodium vivax
: Recent world expansion and genetic identity to
Plasmodium simium
Authors: Lim Chae Seung , Tazi Loubna , Ayala Francisco J.
Published: October 2005

Plasmodium vivax
causes the most geographically widespread human malaria, accounting annually for 70-80 million clinical cases throughout the tropical and subtropical regions of the world's continents. We have analyzed the DNA sequences of the
Csp
(circumsporozoite protein) gene in 24 geographically representative strains of
P. vivax
and 2 of
P. simium
, which parasitizes several species of New World monkeys. The
Csp
sequences are of two types, VK210 and VK247, which differ by three diagnostic amino acid replacements, one in each of the 5′ and 3′ terminal regions [5′ nonrepeat (NR) and 3′ NR] of the gene and in an insertion sequence that precedes the 3′ NR region. The central region of the gene consists of ≈38 repetitive “motifs,” which are alternatively four and five amino acids long, which also are diagnostically different between the VK210 and VK247 types. There are very few synonymous substitutions within and between the two types of strains, which we hypothesize reflects that the worldwide spread of
P. vivax
is very recent. The two
P. simium Csp
sequences belong one to each of the two VK types and are genetically indistinguishable from the corresponding
P. vivax
strains, suggesting that at least two host transfers have occurred between humans and New World monkeys. We exclude as unlikely the possibility that the two types of sequences could have independently arisen in humans and platyrrhines by natural selection. There are reasons favoring each of the two possible directions of host transfer between humans and monkeys.
From nonpeptide toward noncarbon protease inhibitors: Metallacarboranes as specific and potent inhibitors of HIV protease
Authors: Cígler Petr , Kožíšek Milan , Řezáčová Pavlína , Brynda Jíří , Otwinowski Zbyszek , Pokorná Jana , Plešek Jaromír , Grüner Bohumír , Dolečková-Marešová Lucie , Máša Martin , Sedláček Juraj , Bodem Jochen , Kräusslich Hans-Georg , Král Vladimír , Konvalinka Jan
Published: October 2005

HIV protease (PR) represents a prime target for rational drug design, and protease inhibitors (PI) are powerful antiviral drugs. Most of the current PIs are pseudopeptide compounds with limited bioavailability and stability, and their use is compromised by high costs, side effects, and development of resistant strains. In our search for novel PI structures, we have identified a group of inorganic compounds, icosahedral metallacarboranes, as candidates for a novel class of nonpeptidic PIs. Here, we report the potent, specific, and selective competitive inhibition of HIV PR by substituted metallacarboranes. The most active compound, sodium hydrogen butylimino bis-8,8-[5-(3-oxa-pentoxy)-3-cobalt bis(1,2-dicarbollide)]di-ate, exhibited a
K
i
value of 2.2 nM and a submicromolar EC
50
in antiviral tests, showed no toxicity in tissue culture, weakly inhibited human cathepsin D and pepsin, and was inactive against trypsin, papain, and amylase. The structure of the parent cobalt bis(1,2-dicarbollide) in complex with HIV PR was determined at 2.15 Å resolution by protein crystallography and represents the first carborane-protein complex structure determined. It shows the following mode of PR inhibition: two molecules of the parent compound bind to the hydrophobic pockets in the flap-proximal region of the S3 and S3′ subsites of PR. We suggest, therefore, that these compounds block flap closure in addition to filling the corresponding binding pockets as conventional PIs. This type of binding and inhibition, chemical and biological stability, low toxicity, and the possibility to introduce various modifications make boron clusters attractive pharmacophores for potent and specific enzyme inhibition.
D-type cyclins activate division in the root apex to promote seed germination in
Arabidopsis
Authors: Masubelele Nompumelelo H. , Dewitte Walter , Menges Margit , Maughan Spencer , Collins Carl , Huntley Rachael , Nieuwland Jeroen , Scofield Simon , Murray James A. H.
Published: October 2005

Seeds provide survival and dispersal capabilities by protecting the dormant mature plant embryo. Germination and resumption of development under favourable conditions requires the reinitiation of cell growth and division through poorly understood processes. Here we show that four phases of cell division activation during germination in
Arabidopsis
are related to external morphological changes. Cell division initiates in the root apical meristem (RAM) before root protrusion, followed by sequential activation of cell division in the cotyledons, shoot apical meristem (SAM), and secondary meristems. Major changes in transcript levels of >2,000 genes precede root emergence, including expression peaks of six D-type (CYCD) and two A-type cyclins. Two further CYCDs are activated later with the SAM. Early activated CYCDs play key roles in regulating the extent of cell division, because loss-of-function alleles of early CYCDs display reduced division activation and consequential delayed root emergence. Conversely, elevation of early CYCDs increases cell cycle activation in the RAM and promotes embryonic root (radicle) protrusion, whereas a later-acting CYCD does not. These phenotypes, together with their overlapping expression domains, support a cumulative action of a subset of CYCDs in cell cycle reactivation, rather than a complete functional redundancy. This analysis reveals a phenotype associated with loss-of-function of a plant cyclin and demonstrates that D-type cyclins regulate cell cycle reentry during meristem activation to promote successful germination and early seedling growth.
Functions and dysfunctions of the nuclear lamin Ig-fold domain in nuclear assembly, growth, and Emery–Dreifuss muscular dystrophy
Authors: Shumaker Dale K. , Lopez-Soler Reynold I. , Adam Stephen A. , Herrmann Harald , Moir Robert D. , Spann Timothy P. , Goldman Robert D.
Published: October 2005

The non-α-helical C terminus of
Xenopus
lamin B3 (LB3T) inhibits the polymerization of lamin B3
in vitro
and prevents the assembly of nuclei in
Xenopus
egg interphase extracts. To more precisely define the functions of LB3T in nuclear assembly, we have expressed subdomains of LB3T and determined their effects on nuclear assembly in
Xenopus
extracts. The results demonstrate that the Ig-fold motif (LB3T-Ig) is sufficient to inhibit lamin polymerization
in vitro
. Addition of the LB3T-Ig to egg extracts before the introduction of chromatin prevents chromatin decondensation and the assembly of the lamina, membranes, and pore complexes comprising the nuclear envelope. When added to assembled nuclei, LB3T-Ig prevents the further incorporation of lamin B3 into the endogenous lamina and blocks nuclear growth. The introduction of a point mutation in LB3T-Ig (R454W; LB3T-IgRW), known to cause Emery–Dreifuss muscular dystrophy when present in lamin A, does not inhibit lamin polymerization, chromatin decondensation, or nuclear assembly and growth. These results shed light on the specific alterations in lamin functions attributable to a known muscular dystrophy mutation and provide an experimental framework for revealing the effects of other mutations causing a wide range of laminopathies.
Reconfiguring the connectivity of a multiprotein complex: Fusions of yeast TATA-binding protein with Brf1, and the function of transcription factor IIIB
Authors: Kassavetis George A. , Soragni Elisabetta , Driscoll Robert , Geiduschek E. Peter
Published: October 2005

Transcription factor (TF) IIIB, the central transcription initiation factor of RNA polymerase III (pol III), is composed of three subunits, Bdp1, Brf1 and TATA-binding protein (TBP), all essential for normal function
in vivo
and
in vitro
. Brf1 is a modular protein: Its N-proximal half is related to TFIIB and binds similarly to the C-terminal stirrup of TBP; its C-proximal one-third provides most of the affinity for TBP by binding along the entire length of the convex surface and N-terminal lateral face of TBP. A structure-informed triple fusion protein, with TBP core placed between the N- and C-proximal domains of Brf1, has been constructed. The Brf1-TBP triple fusion protein effectively replaces both Brf1 and TBP in TFIIIC-dependent and -independent transcription
in vitro
, and forms extremely stable TFIIIB–DNA complexes that are indistinguishable from wild-type TFIIIB–DNA complexes by chemical nuclease footprinting. Unlike Brf1 and TBP, the triple fusion protein is able to recruit pol III for TATA box-directed transcription of linear and supercoiled DNA in the absence of Bdp1. The Brf1-TBP triple fusion protein also effectively replaces Brf1 function
in vivo
as the intact protein, creating a TBP paralogue in yeast that is privatized for pol III transcription.
Changes in energy metabolism ofMycobacterium tuberculosisin mouse lung and underin vitroconditions affecting aerobic respiration
Authors: Shi Lanbo , Sohaskey Charles D. , Kana Bavesh D. , Dawes Stephanie , North Robert J. , Mizrahi Valerie , Gennaro Maria L.
Published: October 2005

Transcription profiling of genes encoding components of the respiratory chain and the ATP synthesizing apparatus ofMycobacterium tuberculosiswas conductedin vivoin the infected mouse lung, andin vitroin bacterial cultures subjected to gradual oxygen depletion and to nitric oxide treatment. Transcript levels changed dramatically as infection progressed from bacterial exponential multiplication (acute infection) to cessation of bacterial growth (chronic infection) in response to host immunity. The proton-pumping type-I NADH dehydrogenase and theaa3-type cytochromecoxidase were strongly down-regulated. Concurrently, the less energy-efficient cytochromebdoxidase was transiently up-regulated. The nitrate transporter NarK2 was also up-regulated, indicative of increased nitrate respiration. The reduced efficiency of the respiratory chain was accompanied by decreased expression of ATP synthesis genes. Thus, adaptation ofM. tuberculosisto host immunity involves three successive respiratory states leading to decreased energy production. Decreased bacterial counts in mice infected with acydCmutant (defective in the cytochromebdoxidase-associated transporter) at the transition to chronic infection provided initial evidence that thebdoxidase pathway is required forM. tuberculosisadaptation to host immunity.In vitro, NO treatment and hypoxia caused a switch from transcription of type I to type II NADH dehydrogenase. Moreover, cytochromebdoxidase expression increased, but cytochromecoxidase expression decreased slightly (nitric oxide) or not at all (hypoxia). These specific differences in respiratory metabolism duringM. tuberculosisgrowth arrestin vitroandin vivowill guide manipulation ofin vitroconditions to model bacterial adaptation to host immunity.
Evolutionary conservation and diversification of Rh family genes and proteins
Authors: Huang Cheng-Han , Peng Jianbin
Published: October 2005

Rhesus (Rh) proteins were first identified in human erythroid cells and recently in other tissues. Like ammonia transporter (Amt) proteins, their only homologues, Rh proteins have the 12 transmembrane-spanning segments characteristic of transporters. Many think Rh and Amt proteins transport the same substrate,

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, whereas others think that Rh proteins transport CO
2
and Amt proteins NH
3
. In the latter view, Rh and Amt are different biological gas channels. To reconstruct the phylogeny of the Rh family and study its coexistence with and relationship to Amt in depth, we analyzed 111 Rh genes and 260 Amt genes. Although Rh and Amt are found together in organisms as diverse as unicellular eukaryotes and sea squirts, Rh genes apparently arose later, because they are rare in prokaryotes. However, Rh genes are prominent in vertebrates, in which Amt genes disappear. In organisms with both types of genes, Rh had apparently diverged away from Amt rapidly and then evolved slowly over a long period. Functionally divergent amino acid sites are clustered in transmembrane segments and around the gas-conducting lumen recently identified in
Escherichia coli
AmtB, in agreement with Rh proteins having new substrate specificity. Despite gene duplications and mutations, the Rh paralogous groups all have apparently been subject to strong purifying selection indicating functional conservation. Genes encoding the classical Rh proteins in mammalian red cells show higher nucleotide substitution rates at nonsynonymous codon positions than other Rh genes, a finding that suggests a possible role for these proteins in red cell morphogenetic evolution.
ABR1, an APETALA2-Domain Transcription Factor That Functions as a Repressor of ABA Response in Arabidopsis
Authors: Pandey Girdhar K. , Grant John J. , Cheong Yong Hwa , Kim Beom Gi , Li Legong , Luan Sheng
Published: October 2005

The plant hormone abscisic acid (ABA) plays an important role in plant development and stress responses. An important step of ABA action is activation or inactivation of gene expression. Although several transcription factors are identified to function as positive regulators of ABA-induced gene expression, little is known about the negative regulators of ABA-regulated gene expression. Here, we have identified an APETALA2 (AP2) domain transcription factor that serves as a repressor of ABA response during seed germination and ABA- and stress-induced gene expression in Arabidopsis (Arabidopsis thaliana). The expression of the AP2-like ABA repressor 1 (ABR1) gene itself was responsive to ABA and stress conditions including cold, high salt, and drought. Disruption of ABR1 led to hypersensitive response to ABA in seed germination and root growth assays. The mutant plants were also hypersensitive to osmotic stress conditions, such as high salt and high concentrations of mannitol. Further analyses indicated that increased stress sensitivity may result from hypersensitivity to ABA as ABA biosynthesis inhibitor rescued the stress hypersensitivity phenotype. The abr1 mutant plants accumulated significantly higher levels of ABA- and stress-inducible gene transcripts as compared to the wild-type plants, supporting the hypothesis that this AP2 domain protein serves as a repressor of ABA-regulated gene expression.
TheArabidopsisSTV1 Protein, Responsible for Translation Reinitiation, Is Required for Auxin-Mediated Gynoecium Patterning
Authors: Nishimura Taisuke , Wada Takuji , Yamamoto Kotaro T. , Okada Kiyotaka
Published: October 2005

Ribosomal protein L24 (RPL24) is implicated in translation reinitiation of polycistronic genes. A newly isolated Arabidopsis thaliana  short valve1 (stv1) mutant, in which one of the RPL24-encoding genes, RPL24B, is deleted, shows specific defects in the apical-basal patterning of the gynoecium, in addition to phenotypes induced by ribosome deficiency. A similar gynoecium phenotype is caused by mutations in the auxin response factor (ARF) genes ETTIN (ETT) and MONOPTEROS (MP), which have upstream open reading frames (uORFs) in their 5′-transcript leader sequences. Gynoecia of a double mutant of stv1 and a weak ett mutant allele are similar to those of a strong ett allele, and transformation with a uORF-eliminated ETT construct partially suppressed the stv1 gynoecium phenotype, implying that STV1 could influence ETT translation through its uORFs. Analyses of 5′-leader-reporter gene fusions showed that the uORFs of ETT and MP negatively regulate the translation of the downstream major ORFs, indicating that translation reinitiation is an important step for the expression of these proteins. Taken together, we propose that perturbation of translation reinitiation of the ARF transcripts causes the defects in gynoecium patterning observed in the stv1 mutant.
A Large-Scale Screen for Artificial Selection in Maize Identifies Candidate Agronomic Loci for Domestication and Crop Improvement
Authors: Yamasaki Masanori , Tenaillon Maud I. , Vroh Bi Irie , Schroeder Steve G. , Sanchez-Villeda Hector , Doebley John F. , Gaut Brandon S. , McMullen Michael D.
Published: October 2005

Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3′ portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.
Specification and Estimation of Regular Inverse Demand Systems: A Distance Function Approach
Authors: Wong K. K. Gary , McLaren Keith R.
Published: October 2005

To allow realistic policy simulations in a changing environment, inverse demand systems must remain regular over substantial variations in quantities. The distance function is a convenient vehicle for generating such systems. While its use directly yields Hicksian inverse demand functions, those functions will not usually have an explicit representation in terms of the observable variables. However, this problem need not hinder estimation and can be solved by using a numerical inversion estimation approach. This article develops the formal theory for using distance functions in this context and demonstrates the operational feasibility of the method.
Price Discrimination in the Context of Vertical Differentiation: An Application to Canadian Wheat Exports
Authors: Lavoie Nathalie
Published: October 2005

The ability of the Canadian Wheat Board (CWB) to price discriminate in wheat exports is examined. The conceptual model shows that the CWB's ability to exploit cost differences in pricing depends on the extent of differentiation between Canadian and U.S. wheat. This model is implemented using monthly confidential price data for exports to four markets from 1982 to 1994. The empirical results support the conclusions that (1) the CWB has market power emerging from product differentiation, (2) the CWB price discriminates across export markets, and (3) Alchian—Allen effects are important in pricing in markets valuing quality such as Japan and the United Kingdom.
Replacement of Agricultural Price Supports by Area Payments in the European Union and the Effects on Pesticide Use
Authors: Serra Teresa , Zilberman David , Goodwin Barry K. , Hyvonen Keijo
Published: October 2005

This article determines the contribution of recent European Union agricultural policy reforms on the use of pesticides. Our theoretical model extends the multioutput generalization of the Lichtenberg—Zilberman damage control technology model developed by Chambers and Lichtenberg. Our empirical analysis uses farm‐level data for a sample of French farms. Results suggest that price effects on the use of pesticides are always more elastic than area payment effects. This indicates that policy reforms consisting of a reduction in price supports in favor of area payments, may reduce application of crop protection inputs. Such policy changes, which represent a certain degree of decoupling, took place under the 1992 Common Agricultural Policy reforms.
Farm Poverty and Safety Nets
Authors: Gundersen Craig , Offutt Susan
Published: October 2005

Farm families with incomes below the poverty line are far less likely than wealthier farmers to receive farm support payments. Using data from the 1989–2004 Current Population Survey, we find that poor farm families are also not participating in other assistance programs. Controlling for other factors, eligible farm families have substantially lower participation rates in the Food Stamp Program and in Medicaid than eligible nonfarm families. Removing farm safety net program payments would increase the number of farmers eligible for these programs but, in the absence of behavioral changes, would only lead to small increases in the number of recipients.
Optimal Hedging with a Subjective View: An Empirical Bayesian Approach
Authors: Shi Wei , Irwin Scott H.
Published: October 2005

The standard optimal hedging model has been the preferred theoretical model of normative hedging behavior. In empirical applications, the model is often implemented with the parameter certainty equivalent (PCE) procedure. However, the PCE procedure completely ignores parameter estimation risk and subjective views. We develop an “empirical” Bayesian optimal hedging model that not only effectively accommodates parameter estimation risk, but also provides hedgers with a theoretically intuitive yet quantitatively rigorous framework to blend their subjective views and a “marketwide” or “firmwide” consensus in determining optimal hedging positions (ratios).
Genetically Modified Crops: Their Market and Welfare Impacts
Authors: Lence Sergio H. , Hayes Dermot J.
Published: October 2005

A framework is developed for examining price and welfare effects of the introduction of genetically modified (GM) products. In the short run, non‐GM grain generally becomes another identity‐preserved product. However, more profound market effects are observed under some reasonable parameterizations. When calibrated to reflect the U.S. corn market, introducing GM technology increases aggregate welfare over a wide range of scenarios, unless the corresponding production cost savings are small and consumers are seriously concerned about GM products. The possibility that GM technology may reduce aggregate welfare is interesting because the model assumes rational agents and does not include regulatory constraints.
Welfare Impacts of Intellectual Property Protection in the Seed Industry
Authors: Lence Sergio H. , Hayes Dermot J. , McCunn Alan , Smith Stephen , Niebur William S.
Published: October 2005

We examine the welfare impact of different intellectual property protection (IPP) regimes in private sector seed research and development (R&D). We take into account the period after expiration of legal IPP, and require simultaneous equilibrium in markets for R&D, seeds, and final product. Optimal IPP is remarkably insensitive to alternative parameterizations, except for R&D productivity. Results suggest that optimal IPP is greater than IPP in the U.S. seed corn market, but lower than the IPP that could be attained with genetic use restriction technologies. Optimal IPP is much higher than IPP achieved under open‐pollinated crops or where legal IPP is limited.
Estimating Intertemporal Preferences for Natural Resource Allocation
Authors: Howitt Richard E. , Msangi Siwa , Reynaud Arnaud , Knapp Keith C.
Published: October 2005

In this article, we show how the degree of risk aversion, discounting, and preference for intertemporal substitution for a natural resource manager can be structurally estimated within a recursive utility framework. We focus on the management of a reservoir in California, and test the data for consistency with a recursive utility model specification versus standard time‐additive separability. The results show that the data are consistent with a risk‐averse manager with recursive preferences. The data also reject time‐additive separability, with or without risk aversion, such as the standard constant relative risk aversion utility model. The improvement in model fit when recursive preferences are used is notable.
The Farm Diversification Discount
Authors: Katchova Ani L.
Published: October 2005

This article estimates the effect of diversification on farm values, where farms are valued relative to the median specialized farm having the same enterprise. Using data from the Agricultural Resource Management Study, the estimated diversification discount in agriculture is similar to the discount found for corporate firms. The results show that diversified crop/livestock farms had a diversification discount of 5.8% in comparison with specialized crop or livestock farms from 1999 to 2001. Commodity diversified farms had a diversification discount of 9.4% in comparison with commodity specialized farms.
Spatial Complementarity of Forests and Farms: Accounting for Ecosystem Services
Authors: Pattanayak Subhrendu K. , Butry David T.
Published: October 2005

Our article considers the economic contributions of forest ecosystem services, using a case study from Flores, Indonesia, in which forest protection in upstream watersheds stabilize soil and hydrological flows in downstream farms. We focus on the demand for a weak complement to the ecosystem services—farm labor—and account for spatial dependence due to economic interactions, ecosystem processes, and data integration. The estimated models have theoretically expected properties across eight different specifications. We find strong evidence that forest ecosystem services provide economically substantive benefits to local people and that these services would be substantially undervalued if spatial dependence is ignored.
Joint Estimation of Technology Adoption and Land Allocation with Implications for the Design of Conservation Policy
Authors: Moreno Georgina , Sunding David L.
Published: October 2005

One challenge to estimating the parameters of a technology adoption model is that technology is selected jointly with land allocation. The article estimates a nested logit model of technology and crop choices that accounts for unobserved correlation among decisions. Estimation is conducted with a data set of adoptions, in contrast to the more common approach of using cross‐section observations of existing technologies. Estimation results support the choice of a nesting structure as opposed to a more standard multinomial logit model. Adoption of precision irrigation technology is shown to be more sensitive to financial incentives affecting input price and technology cost than suggested by previous studies.
Technology, Labor Wars, and Producer Dynamics: Explaining Consolidation in Beefpacking
Authors: MacDonald James M. , Ollinger Michael E.
Published: October 2005

Beefpacking underwent a dramatic transformation in the 1970s and 1980s, as plants got much larger and industry concentration rose dramatically. We use individual Census Bureau plant records to analyze the sources of the transformation. We find that there were modest but extensive scale economies in packing plants, covering the full range of plant sizes, and that such economies became more important throughout the period of the study. As production shifted to larger plants, we estimate that the industry's aggregate processing costs fell by 35.3% by 2002, compared to what they would have been without consolidation.
Optimal Institutional Mechanisms for Funding Generic Advertising: An Experimental Analysis
Authors: Messer Kent D. , Schmit Todd M. , Kaiser Harry M.
Published: October 2005

Given the uncertain legal status of generic advertising programs for agricultural commodities, alternative voluntary funding institutions are investigated that could provide a high level of benefits to producers. This experimental study simulates key economic and psychological factors that affect voluntary producer contributions to generic advertising. The results suggest that producer referenda play a critical role in increasing contributions and that producer surplus is maximized by a provision point mechanism instituted by producer referendum with thresholds ranging from 68% to 90%, and expected funding from 47% to 77% of the time, depending on the level of advertising effectiveness.
Weak Disposability in Nonparametric Production Analysis with Undesirable Outputs
Authors: Kuosmanen Timo
Published: October 2005

Weak disposability of outputs means that firms can abate harmful emissions by decreasing the activity level. Modeling weak disposability in nonparametric production analysis has caused some confusion. This article identifies a dilemma in these approaches: conventional formulations implicitly and unintentionally assume all firms apply uniform abatement factors. However, it is usually cost‐effective to abate emissions in those firms where the marginal abatement costs are lowest. This article presents a simple formulation of weak disposability that allows for non‐uniform abatement factors and preserves the linear structure of the model.
Serial Nonparticipation in Repeated Discrete Choice Models
Authors: von Haefen Roger H. , Massey D. Matthew , Adamowicz Wiktor L.
Published: October 2005

We consider alternative econometric strategies for addressing serial nonparticipation, that is, repeated choice of the same alternative or same type of alternative across a series of choice occasions, in data typically analyzed within the repeated discrete choice framework. Single and double hurdle variants of the repeated discrete choice model are developed and applied to choice experiment and multisite seasonal recreation demand data. Our results suggest that hurdle models can generate significant improvements in statistical fit and qualitatively different policy implications, particularly in choice experiment applications where the proper treatment of serial nonparticipation is relatively more ambiguous.
Auctions with and without the Right of First Refusal and National Park Service Concession Contracts
Authors: Chouinard Hayley H.
Published: October 2005

The National Park Service has struggled to improve the quality of service provided by concessioners for decades. To address these concerns, the Park Service eliminated the right of first refusal from the largest revenue‐generating concession contract auctions beginning in 2000. This article provides models of concession contract auctions with and without the right of first refusal. The optimal bidding strategies and expected level of service are found. The results confirm the auction without the right of first refusal leads to bids that include a higher level of service.
Role of nitric oxide and prostanoids in attenuation of rapid baroreceptor resetting
Authors: Salgado Maria Cristina O. , Justo Soraia V. S. , Joaquim Luis F. , Fazan Rubens , Salgado Helio C.
Published: October 2005

Because the regulation of vascular function involves complex mutual interactions between nitric oxide (NO) synthase (NOS) and cyclooxygenase (COX) products, we examined the contribution of NO and prostanoids derived from the COX pathway in modulating aortic baroreceptor resetting during an acute (30 min) increase in arterial pressure in anesthetized rats. Increase in pressure was induced either by administration of the nonselective NOS inhibitor NG-nitro-l-arginine methyl ester (l-NAME) or aortic coarctation (COA) with or without treatment with the COX inhibitor indomethacin (INDO) or the selective neuronal NOS inhibitor 1-(2-trifluoromethylphenyl)imidazole (TRIM). The activity of the aortic depressor nerve and arterial pressure were simultaneously recorded, and the degree of resetting was determined by the shift of the pressure-nerve activity curve using the ratio [Δ systolic pressure at 50% of maximum baroreceptor activity/Δ systolic pressure] × 100. The magnitude of pressure rise was similar in the different groups (59 ± 6, 53 ± 5, 53 ± 5, 45 ± 5, 49 ± 3, and 41 ± 3 mmHg for COA, l-NAME, INDO+COA, INDO+l-NAME, TRIM+COA, and TRIM+INDO+COA, respectively, P = 0.27). The degree of resetting that occurred with l-NAME or COA combined with treatment with TRIM was attenuated compared with COA alone (7 ± 4, 5 ± 2, and 31 ± 6%, respectively, P = 0.04). INDO failed to influence baroreceptor resetting to higher pressure but prevented l-NAME- and TRIM-induced effects (20 ± 7, 21 ± 8, and 32 ± 6% for INDO+COA, INDO+l-NAME, and INDO+TRIM+COA, respectively; P = 0.38). Baroreceptor gain was affected only by l-NAME. These findings indicate that NO, probably from neuronal origin, may exert stimulatory influence on the degree of rapid baroreceptor resetting to hypertension that involves COX-derived prostanoids.