bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence of upslope flows at the Pico mountaintop observatory: A case study of orographic flows on a small, volcanic island
Authors: Kleissl J. , Honrath R. E. , Dziobak M. P. , Tanner D. , Val Martín M. , Owen R. C. , Helmig D.
Published: February 2007

Upslope flows caused by mechanical forcing in strong synoptic winds or by buoyant forcing driven by solar heating under weak synoptic winds can influence the air composition at mountaintop observatories. Using meteorological and trace gas measurements at the PICO‐NARE observatory on Pico mountain (Azores Islands, North Atlantic Ocean), the frequency and impact of such orographic flows on a small, volcanic, subtropical island was examined. To determine the origin of mechanically lifted air, upstream kinetic energy was balanced against potential energy gained during uplift (Sheppard's model). Mechanically forced upslope flow is most important during October through April, when the calculated probability of observing marine boundary layer (MBL) air at the observatory near the summit ranges from 35 to 60% per month. In contrast, lower synoptic wind speeds and a more stable lower free troposphere during May–September result in a reduced frequency of MBL impacts (<20%). Buoyant upslope flows (BUF) were quantified through meteorological measurements on the mountain slope in summer 2004. Diurnal cycles of wind direction on the mountain slope consistent with daytime upslope and nighttime downslope flow were found on 24% of the days during late June, July, and August 2004. Buoyant forcing can also occur in the presence of moderate synoptic winds, resulting in enhancement of the mechanically forced upslope flow on the windward side of the mountain. Such conditions were found on 15% of the summer days in 2004. However, on BUF days the specific humidity at the mountaintop was significantly smaller than on the slope, indicating turbulent mixing during ascent or vertical decoupling of air masses. Impacts of BUF or a mixture of buoyant and mechanical upslope flow on O3 or nitrogen oxides mixing ratios at the mountaintop station were rare or extremely small, and no significant diurnal cycle of O3 (expected if daytime BUF of MBL air occurred regularly) was present. Midday increases in isoprene concentrations, a nonmethane hydrocarbon (NMHC) expected to be emitted from vegetation more than 700 m below the PICO‐NARE station, were found on 54% of the days during May–August 2005. No corresponding increase in n‐butane (used for heating and cooking at sea level residences) was detected, suggesting that the air did not originate from as low as sea level. These results indicate that the latitude, size, and topography of Pico island combine to prevent frequent transport of MBL air to the PICO‐NARE station in the summer.
Average excitation energies from time-dependent density functional response theory
Authors: Hu Chunping , Sugino Osamu
Published: February 2007

The authors present an occupation number averaging scheme for time-dependent density functional response theory (TD-DFRT) in frequency domain. The known problem that TD-DFRT within the local (spin) density approximation (LDA/LSDA) inaccurately predicts Rydberg and charge-transfer excitation energies has been reexamined from the methodology of linear response, without explicit correction of the exchange-correlation potential. The working equations of TD-DFRT are adapted to treat arbitrary difference of orbital occupation numbers, using the nonsymmetric matrix form of Casida’s formulation of TD-DFRT [M. E. Casida, in Recent Advances in Density Functional Methods, edited by D. P. Chong (World Scientific, Singapore, 1995), Pt. I, p. 155]. The authors’ scheme is applied to typical closed-shell and open-shell molecular systems by examining the dependence of excitation energies on the fraction of excited electron. Good performance of this modified linear response scheme is shown, and is consistent with the authors’ previous examination by the real-time propagation approach, suggesting that the calculation of average excitation energies might be one of the ways to better decode excitation energies from LDA/LSDA. Different techniques for treating singlet, triplet, and doublet states are discussed.
Spinor extended Lorentz-force-like equations as consequence of a spinorial structure of space-time
Authors: Buitrago J. , Hajjawi S.
Published: February 2007

As previously shown, the special relativistic dynamical equation of the Lorentz force type can be regarded as a consequence of a succession of space-time dependent infinitesimal Lorentz boosts and rotations. This insight indicates that the Lorentz-Force-like equation has a fundamental meaning in physics. We show how this result may be spinorially obtained starting out from the application of an infinitesimal element of SL(2,C) to the individual spinors, which are regarded here as being more fundamental objects than four-vectors. In this way we get a set of new dynamical spinor equations inducing the extended Lorentz-Force-like equation in the Minkowski space-time and geometrically obtain the spinor form of the electromagnetic field tensor. The term extended refers to the dynamics of some additional degrees of freedom that may be associated with the intrinsic spin, namely, with the dynamics of three spacelike mutually orthogonal four-vectors, all of them orthogonal to the linear four-momentum of the object under consideration that finally, in the particle’s proper frame, are identified with the generators of SU(2).
Optical study of H2O ice to 120GPa: Dielectric function, molecular polarizability, and equation of state
Authors: Zha Chang-Sheng , Hemley Russell J. , Gramsch Stephen A. , Mao Ho-kwang , Bassett William A.
Published: February 2007

The refractive index of H2O ice has been measured to 120GPa at room temperature using reflectivity methods. The refractive index increases significantly with pressure on initial compression and exhibits small changes with pressure at previously identified phase transitions. Pressure dependencies of the molecular polarizability show changing slopes in different pressure regions. A general molar refractivity analysis of this change in slope reveals features at 60GPa due to the onset of the ice VII-X transition. Band gap closure in H2O ice is constrained by the dispersion data using a single oscillator dielectric model. Sample thickness measurements obtained from interference patterns yield pressure-volume relations in excellent agreement with those measured by x-ray diffraction.
On the calculation of circular dichroism spectra using quantum wave-packet dynamics with an application to molecular dimers
Authors: Seibt Joachim , Engel Volker
Published: February 2007

Circular dichroism (CD) spectra are calculated from the Fourier transform of a time-correlation function. The latter can efficiently be evaluated by wave-packet propagation methods. This approach is similar to the time-dependent evaluation of absorption or Raman spectra. As an application, correlation functions and CD spectra for a molecular dimer are determined and compared to the case of absorption.
Electronic and structural properties of Ti vacancies on the (001) surface of TiS2: Theoretical scanning tunneling microscopy images
Authors: Amzallag E. , Baraille I. , Martinez H. , Rérat M. , Loudet M. , Gonbeau D.
Published: February 2007

Various defects—either bright or dark triangular defects—are observed on the (001) titanium disulfide surface by ultrahigh vacuum scanning tunneling microscopy. The experimental interpretations of the images available in the literature suggest that a fraction of Ti atoms could be displaced from the octahedral site they occupied to vacant sites of the crystal structure, leading to more or less correlated defects. In this paper, the authors have performed ab initio periodic linear combination of atomic orbitals-generalized gradient approximation (LCAO-GGA) calculations on (5×5) and (4×4) biperiodic supercells to model the electronic and geometrical involvements of Ti vacancy. The relaxed atomic structures of each system and the wave-function character of the defect states are carefully analyzed before the theoretical scanning tunneling microscopy images are generated within the Tersoff-Hamann approximation. The relaxed structure of the Ti vacancy shows an inward movement of the neighboring sulfur atoms at the surface. However, the occupied electronic states of the vacancy at the Fermi level are mainly developed on the atomic orbitals of the first sulfur neighbors at the surface, leading to bright triangular zones on the simulated image.
Diffusion Monte Carlo study of the equation of state of solid ortho-D2
Authors: Operetto Francesco , Pederiva Francesco
Published: February 2007

The authors present results of diffusion Monte Carlo calculations for a system of solid ortho-D2 at different densities, for pressure ranging from 0 up to 350MPa. They compare the equation of state obtained using two of the most used effective intermolecular potentials, i.e., the Silvera-Goldman and the Buck potentials, with experimental data, in order to assess the validity of the model interactions. The Silvera-Goldman potential has been found to provide a satisfactory agreement with experimental results, showing that, as opposed to what recently found for p-H2, three-body forces can be efficiently accounted for by an effective two-body term.
Interfacial charge transfer mechanism in nanostructured TiO2–ZnS coupled network for single electron device applications
Authors: Mohanta D. , Deka M. , Choudhury A.
Published: February 2007

We report on the production of nanoporous TiO2 network sensitized by ZnS nanospheres as an idealized scheme to facilitate interfacial charge transfer effects. The nanoporous TiO2 system was fabricated on the 0.1μm thick Al substrate from titanium isopropoxide [Ti(i−OC3H7)] and 1-butanol (C4H9OH) as requisite precursor. The Zn++ ions are internally adsorbed to provide heterogeneous coupled TiO2–ZnS nanosystem. The I-V response shows transistor characteristics which suggests sharp rise in current with forward biasing voltage before attaining saturation. It is expected that with the increase in signal frequency more number of trap carriers being able to follow signal assist higher carrier transfer rate across the interface in the coupled system and hence saturation current (IS) increases. However, in all the cases saturation occurs around finite biasing voltage, i.e., 3.6V. This ensures that the surface states (which normally lie within the forbidden gap and below the conduction bands for electrons) mainly participate in carrier transfer mechanism within the device. A phenomenon in understanding highly controlled interfacial carrier transport process would find potential in nanoelectronics, e.g., single electron transistor and other single electron devices.
Influence of spin relaxation on magnetoresistance
Authors: Tan S. G. , Jalil M. B. A. , Bala Kumar S.
Published: February 2007

We represent the spin-dependent transport across a pseudospin-valve structure as described by the spin drift-diffusion (SDD) theory by an effective two-current model, in which the spin relaxation effects are globally absorbed into the two effective branch resistances. Our approach has eliminated the need for “spin flip” resistances interconnecting the two spin branches, which have the disadvantage of artificially localizing the effects of spin relaxation to arbitrary spatial points. We confirm the accuracy of our effective two-current model with the full numerical SDD solution. Based on our model, we found that (i) the overall magnetoresistance (MR) is much more sensitive to the spin relaxation effect in the nonmagnetic (NM) layer, compared to that in the ferromagnetic (FM) layers, and that (ii) the effective spin relaxation length λE in the NM layer is intrinsically linked to the conductivity σN,F of the NM and FM layers. We found that λE=λN∕(η)1∕2, where λN is the nominal spin relaxation length in the NM layer and η=(σN∕σF). The analytical link between spin relaxation and conductivity explains the previously described anomalous suppression of MR, when the conductivity ratio η exceeds a certain critical value ηC.
Electrohydrodynamic printing of silver nanoparticles by using a focused nanocolloid jet
Authors: Lee Dae-Young , Shin Yun-Soo , Park Sung-Eun , Yu Tae-U , Hwang Jungho
Published: February 2007

As a direct write technology, the electrohydrodynamic printing of silver nanoparticles by using a focused nanocolloid jet is introduced. In this letter, two categorized types of examples of two-dimensional patterning were printed by using the electrohydrodynamic printing method. A spiral-type inductor was printed to demonstrate the feasibility of the electrohydrodynamic printing as a fabrication process. The printed spiral inductor produced 9.45μH and exhibited approximately five times larger resistivity (9.5μΩcm) than that of bulk silver after the sintering process. Then, complex geometries having square- and round-shape patterns were also printed.
Structural phase transitions of Ge2Sb2Te5 cells with TiN electrodes using a homemade W heater tip
Authors: Kim H. J. , Choi S. K. , Kang S. H. , Oh K. H.
Published: February 2007

The phase transitions of a Ge2Sb2Te5 cell with a volume of 20×20×0.1μm3 were carried out by applying a reset pulse (10V and 50ns) and a subsequent set pulse (5V and 300ns) using a homemade W heater tip fabricated by focused ion beam lithography. The phase transformation from a crystalline state to an amorphous state was confirmed by measuring the I-V curves and observation with a cross-sectional transmission electron microscope both before and after applying the reset pulse. The electron diffraction pattern obtained from the transformed area clearly showed the amorphous state. The resistance value of the transformed amorphous area was two orders higher than that of the original crystalline phase. This difference in the resistance value between the reset and set states was maintained for 20 reset/set pulse cycles. It is expected that this experimental setup can be used to evaluate the fatigue behavior of Ge2Sb2Te5 cells with reset/set pulse cycles.
Eye Vergence is Susceptible to the Hollow-Face Illusion
Authors: Hoffmann Joachim , Sebald Albrecht
Published: February 2007

When an observer looks at a hollow mask of a face, a normal convex face is often perceived [the hollow-face illusion—Gregory 1973, in Illusion in Nature and Art (London: Duckworth) pp 49–96]. We show that in exploring an illusory face, the eyes converge at the illusory and not at the real distances of fixated targets like the tip of the nose. The ‘vergence error’ appears even though the resulting disparities of the two retinal images of the target provide feedback that would allow an immediate correction. It is presumably the success of recognising a familiar object (a face) which overrides the correction of convergence. This suggests that the brain strives for a congruency of eye vergence and distance perception.
Dysfunction of GABA
A
receptor glycolysis-dependent modulation in human partial epilepsy
Authors: Laschet Jacques J. , Kurcewicz Irène , Minier Frédéric , Trottier Suzanne , Khallou-Laschet Jamila , Louvel Jacques , Gigout Sylvain , Turak Baris , Biraben Arnaud , Scarabin Jean-Marie , Devaux Bertrand , Chauvel Patrick , Pumain René
Published: February 2007

A reduction in GABAergic neurotransmission has been put forward as a pathophysiological mechanism for human epilepsy. However, in slices of human epileptogenic neocortex, GABAergic inhibition can be clearly demonstrated. In this article we present data showing an increase in the functional lability of GABAergic inhibition in epileptogenic tissue compared with nonepileptogenic human tissue. We have previously shown that the glycolytic enzyme GAPDH is the kinase involved in the glycolysis-dependent endogenous phosphorylation of the α1-subunit of GABA
A
receptor, a mechanism necessary for maintaining GABA
A
function. In human epileptogenic cortex obtained during curative surgery of patients with partial seizures, we demonstrate an intrinsic deficiency of GABA
A
receptor endogenous phosphorylation resulting in an increased lability of GABAergic currents in neurons isolated from this tissue when compared with neurons from nonepileptogenic human tissue. This feature was not related to a reduction in the number of GABA
A
receptor α1-subunits in the epileptogenic tissue as measured by [
3
H]flunitrazepam photoaffinity labeling. Maintaining the receptor in a phosphorylated state either by favoring the endogenous phosphorylation or by inhibiting a membrane-associated phosphatase is needed to sustain GABA
A
receptor responses in epileptogenic cortex. The increased functional lability induced by the deficiency in phosphorylation can account for transient GABAergic disinhibition favoring seizure initiation and propagation. These findings imply new therapeutic approaches and suggest a functional link to the regional cerebral glucose hypometabolism observed in patients with partial epilepsy, because the dysfunctional GABAergic mechanism depends on the locally produced glycolytic ATP.
Developmental hearing loss eliminates long-term potentiation in the auditory cortex
Authors: Kotak Vibhakar C. , Breithaupt Andrew D. , Sanes Dan H.
Published: February 2007

Severe hearing loss during early development is associated with deficits in speech and language acquisition. Although functional studies have shown a deafness-induced alteration of synaptic strength, it is not known whether long-term synaptic plasticity depends on auditory experience. In this study, sensorineural hearing loss (SNHL) was induced surgically in developing gerbils at postnatal day 10, and excitatory synaptic plasticity was examined subsequently in a brain slice preparation that preserves the thalamorecipient auditory cortex. Extracellular stimuli were applied at layer 6 (L6), whereas evoked excitatory synaptic potentials (EPSPs) were recorded from L5 neurons by using a whole-cell current clamp configuration. In control neurons, the conditioning stimulation of L6 significantly altered EPSP amplitude for at least 1 h. Approximately half of neurons displayed long-term potentiation (LTP), whereas the other half displayed long-term depression (LTD). In contrast, SNHL neurons displayed only LTD after the conditioning stimulation of L6. Finally, the vast majority of neurons recorded from control prehearing animals (postnatal days 9–11) displayed LTD after L6 stimulation. Thus, normal auditory experience may be essential for the maturation of synaptic plasticity mechanisms.
Arabidopsisplasma membrane protein crucial for Ca2+influx and touch sensing in roots
Authors: Nakagawa Yuko , Katagiri Takeshi , Shinozaki Kazuo , Qi Zhi , Tatsumi Hitoshi , Furuichi Takuya , Kishigami Akio , Sokabe Masahiro , Kojima Itaru , Sato Shusei , Kato Tomohiko , Tabata Satoshi , Iida Kazuko , Terashima Asuka , Nakano Masataka , Ikeda Mitsunobu , Yamanaka Takuya , Iida Hidetoshi
Published: February 2007

Plants can sense and respond to mechanical stimuli, like animals. An early mechanism of mechanosensing and response is speculated to be governed by as-yet-unidentified sensory complexes containing a Ca2+-permeable, stretch-activated (SA) channel. However, the components or regulators of such complexes are poorly understood at the molecular level in plants. Here, we report the molecular identification of a plasma membrane protein (designated Mca1) that correlates Ca2+influx with mechanosensing inArabidopsis thaliana.MCA1cDNA was cloned by the functional complementation of lethality of a yeastmid1mutant lacking a putative Ca2+-permeable SA channel component. Mca1 was localized to the yeast plasma membrane as an integral membrane protein and mediated Ca2+influx. Mca1 also increased [Ca2+]cytupon plasma membrane distortion inArabidopsis. The growth ofMCA1-overexpressing plants was impaired in a high-calcium but not a low-calcium medium. The primary roots ofmca1-null plants failed to penetrate a harder agar medium from a softer one. These observations demonstrate that Mca1 plays a crucial role in a Ca2+-permeable SA channel system that leads to mechanosensing inArabidopsis. We anticipate our findings to be a starting point for a deeper understanding of the molecular mechanisms of mechanotransduction in plants.
Fish extinctions alter nutrient recycling in tropical freshwaters
Authors: McIntyre Peter B. , Jones Laura E. , Flecker Alexander S. , Vanni Michael J.
Published: February 2007

There is increasing evidence that species extinctions jeopardize the functioning of ecosystems. Overfishing and other human influences are reducing the diversity and abundance of fish worldwide, but the ecosystem-level consequences of these changes have not been assessed quantitatively. Recycling of nutrients is one important ecosystem process that is directly influenced by fish. Fish species vary widely in the rates at which they excrete nitrogen and phosphorus; thus, altering fish communities could affect nutrient recycling. Here, we use extensive field data on nutrient recycling rates and population sizes of fish species in a Neotropical river and Lake Tanganyika, Africa, to evaluate the effects of simulated extinctions on nutrient recycling. In both of these species-rich ecosystems, recycling was dominated by relatively few species, but contributions of individual species differed between nitrogen and phosphorus. Alternative extinction scenarios produced widely divergent patterns. Loss of the species targeted by fishermen led to faster declines in nutrient recycling than extinctions in order of rarity, body size, or trophic position. However, when surviving species were allowed to increase after extinctions, these compensatory responses had strong moderating effects even after losing many species. Our results underscore the complexity of predicting the consequences of extinctions from species-rich animal communities. Nevertheless, the importance of exploited species in nutrient recycling suggests that overfishing could have particularly detrimental effects on ecosystem functioning.
Biomimetic tissue-engineered anterior cruciate ligament replacement
Authors: Cooper James A. , Sahota Janmeet S. , Gorum W. Jay , Carter Janell , Doty Stephen B. , Laurencin Cato T.
Published: February 2007

There are >200,000 anterior cruciate ligament (ACL) ruptures each year in the United States, and, due to the poor healing properties of the ACL, surgical reconstruction with autograft or allograft tissue is the current treatment of these injuries. To regenerate the ACL, the ideal matrix should be biodegradable, porous, and exhibit sufficient mechanical strength to allow formation of neoligament tissue. Researchers have developed ACL scaffolds with collagen fibers, silk, biodegradable polymers, and composites with limited success. Our group has developed a biomimetic ligament replacement by using 3D braiding technology. In this preliminary
in vivo
rabbit model study for ACL reconstruction, the histological and mechanical evaluation demonstrated excellent healing and regeneration with our cell-seeded, tissue-engineered ligament replacement.
Monitoring the function of membrane transport proteins in detergent-solubilized form
Authors: Quick Matthias , Javitch Jonathan A.
Published: February 2007

Transport proteins constitute ≈10% of most proteomes and play vital roles in the translocation of solutes across membranes of all organisms. Their (dys)function is implicated in many disorders, making them frequent targets for pharmacotherapy. The identification of substrates for members of this large protein family, still replete with many orphans of unknown function, has proven difficult, in part because high-throughput screening is greatly complicated by endogenous transporters present in many expression systems. In addition, direct structural studies require that transporters be extracted from the membrane with detergent, thereby precluding transport measurements because of the lack of a vectorial environment and necessitating reconstitution into proteoliposomes for activity measurements. Here, we describe a direct scintillation proximity-based radioligand-binding assay for determining transport protein function in crude cell extracts and in purified form. This rapid and universally applicable assay with advantages over cell-based platforms will greatly facilitate the identification of substrates for many orphan transporters and allows monitoring the function of transport proteins in a nonmembranous environment.
Selective retention of herpes simplex virus-specific T cells in latently infected human trigeminal ganglia
Authors: Verjans Georges M. G. M. , Hintzen Rogier Q. , van Dun Jessica M. , Poot Angelique , Milikan Johannes C. , Laman Jon D. , Langerak Anton W. , Kinchington Paul R. , Osterhaus Albert D. M. E.
Published: February 2007

Primary infection with herpes simplex virus 1 (HSV-1) and varicella zoster virus (VZV) results in lifelong latent infections of neurons in sensory ganglia such as the trigeminal ganglia (TG). It has been postulated that T cells retained in TG inhibit reactivation of latent virus. The acquisition of TG specimens of individuals within hours after death offered the unique opportunity to characterize the phenotype and specificity of TG-resident T cells in humans. High numbers of activated CD8+T cells expressing a late effector memory phenotype were found to reside in latently infected TG. The T cell infiltrate was oligoclonal, and T cells selectively clustered around HSV-1 but not VZV latently infected neurons. Neuronal damage was not observed despite granzyme B expression by the neuron-interacting CD8+T cells. The TG-resident T cells, mainly CD8+T cells, were directed against HSV-1 and not to VZV, despite neuronal expression of VZV proteins. The results implicate that herpesvirus latency in human TG is associated with a local, persistent T cell response, comprising activated late effector memory CD8+T cells that appear to control HSV-1 latency by noncytolytic pathways. In contrast, T cells do not seem to be directly involved in controlling VZV latency in human TG.
Divergent functions of VTI12 and VTI11 in trafficking to storage and lytic vacuoles in
Arabidopsis
Authors: Sanmartín Maite , Ordóñez Angel , Sohn Eun Ju , Robert Stephanie , Sánchez-Serrano José Juán , Surpin Marci A. , Raikhel Natasha V. , Rojo Enrique
Published: February 2007

The protein storage vacuole (PSV) is a plant-specific organelle that accumulates reserve proteins, one of the main agricultural products obtained from crops. Despite the importance of this process, the cellular machinery required for transport and accumulation of storage proteins remains largely unknown. Interfering with transport to PSVs has been shown to result in secretion of cargo. Therefore, secretion of a suitable marker could be used as an assay to identify mutants in this pathway. CLV3, a negative regulator of shoot stem cell proliferation, is an extracellular ligand that is rendered inactive when targeted to vacuoles. We devised an assay where trafficking mutants secrete engineered vacuolar CLV3 and show reduced meristems, a phenotype easily detected by visual inspection of plants. We tested this scheme in plants expressing VAC2, a fusion of CLV3 to the vacuolar sorting signal from the storage protein barley lectin. In this way, we determined that trafficking of VAC2 requires the SNARE VTI12 but not its close homologue, the conditionally redundant VTI11 protein. Furthermore, a
vti12
mutant is specifically altered in transport of storage proteins, whereas a
vti11
mutant is affected in transport of a lytic vacuole marker. These results demonstrate the specialization of VTI12 and VTI11 in mediating trafficking to storage and lytic vacuoles, respectively. Moreover, they validate the VAC2 secretion assay as a simple method to isolate genes that mediate trafficking to the PSV.
Potential targets of FOXL2, a transcription factor involved in craniofacial and follicular development, identified by transcriptomics
Authors: Batista Frank , Vaiman Daniel , Dausset Jean , Fellous Marc , Veitia Reiner A.
Published: February 2007

FOXL2
is a gene encoding a forkhead transcription factor, whose mutations are responsible for the blepharophimosis-ptosis-epicanthus inversus syndrome that often involves premature ovarian failure. FOXL2 is one of the earliest ovarian markers and it offers, along with its targets, an excellent model to study ovarian development and function in normal and pathological conditions. We have recently shown that the aromatase gene is a target of FOXL2, and only three other targets have been reported so far. To detect potential transcriptional targets of FOXL2, we used DNA chips and quantitative PCR to compare the transcriptomes of granulosa-like cells overexpressing, or not, FOXL2. This analysis showed that mediators of inflammation, apoptotic and transcriptional regulators, genes involved in cholesterol metabolism, and genes encoding enzymes and transcription factors involved in reactive oxygen species detoxification were up-regulated. On the other hand, FOXL2 down-regulated the transcription of several genes involved in proteolysis and signal transduction and in transcription regulation. A bioinformatic analysis was conducted to discriminate between potential target promoters activated and repressed by FOXL2. In addition, the promoters of strongly activated genes were enriched in forkhead recognition sites, suggesting that these genes might be direct FOXL2 targets. Altogether, these results provide insight into the activity of FOXL2 and may help in understanding the mechanisms of pathogenesis of FOXL2 mutations if the targets prove to be the same in the ovary.
Human polymorphism at microRNAs and microRNA target sites
Authors: Saunders Matthew A. , Liang Han , Li Wen-Hsiung
Published: February 2007

MicroRNAs (miRNAs) function as endogenous translational repressors of protein-coding genes in animals by binding to target sites in the 3′ UTRs of mRNAs. Because a single nucleotide change in the sequence of a target site can affect miRNA regulation, naturally occurring SNPs in target sites are candidates for functional variation that may be of interest for biomedical applications and evolutionary studies. However, little is known to date about variation among humans at miRNAs and their target sites. In this study, we analyzed publicly available SNP data in context with miRNAs and their target sites throughout the human genome, and we found a relatively low level of variation in functional regions of miRNAs, but an appreciable level of variation at target sites. Approximately 400 SNPs were found at experimentally verified target sites or predicted target sites that are otherwise evolutionarily conserved across mammals. Moreover, ≈250 SNPs potentially create novel target sites for miRNAs in humans. If some variants have functional effects, they might confer phenotypic differences among humans. Although the majority of these SNPs appear to be evolving under neutrality, interestingly, some of these SNPs are found at relatively high population frequencies even in experimentally verified targets, and a few variants are associated with atypically long-range haplotypes that may have been subject to recent positive selection.
Adrenomedullin gene expression differences in mice do not affect blood pressure but modulate hypertension-induced pathology in males
Authors: Caron Kathleen , Hagaman John , Nishikimi Toshio , Kim Hyung-Suk , Smithies Oliver
Published: February 2007

Adrenomedullin (AM) is a potent vasodilator peptide in plasma at picomolar levels. Polymorphisms in the human
AM
gene have been associated with genetic predisposition to diabetic nephropathy and proteinuria with essential hypertension, and numerous studies have demonstrated that endogenous AM plays a role in protecting the heart and kidneys from fibrosis resulting from cardiovascular disease. Elevated plasma levels of AM are associated with pregnancy and sepsis and with cardiovascular stress and hypertension. However, there are no reports of the effects of genetic differences in the expression of the endogenous
AM
gene and of gender on blood pressure in these circumstances or on the pathological changes accompanying hypertension. To address these questions, we have generated mice having genetically controlled levels of AM mRNA ranging from ≈50% to ≈140% of wild-type levels. These modest changes in
AM
gene expression have no effect on basal blood pressure. Although pregnancy and sepsis increase plasma AM levels, genetically reducing AM production does not affect the transient hypotension that occurs during normal pregnancy or that is induced by treatment with lipopolysaccharide. Nor does the reduction of AM affect chronic hypertension caused by a renin transgene. However, 50% normal expression of AM enhances cardiac hypertrophy and renal damage in male, but not female, mice with a renin transgene. These observations suggest that the effect of gender on the role of AM in counteracting cardiovascular damage in humans merits careful evaluation.
p63 induces key target genes required for epidermal morphogenesis
Authors: Koster Maranke I. , Dai Daisy , Marinari Barbara , Sano Yuji , Costanzo Antonio , Karin Michael , Roop Dennis R.
Published: February 2007

Mice lacking
p63
, a single gene that encodes a group of transcription factors that either contain (TA) or lack (ΔN) a transactivation domain, fail to develop stratified epithelia as well as epithelial appendages and limbs. ΔNp63 isoforms are predominantly expressed during late embryonic and postnatal epidermal development, however, the function of these proteins remains elusive. Using an epidermal-specific inducible knockdown mouse model, we demonstrate that ΔNp63 proteins are essential for maintaining basement membrane integrity and terminal differentiation of keratinocytes. Furthermore, we have identified two ΔNp63α target genes that mediate these processes. We propose that ΔNp63α initially induces expression of the extracellular matrix component Fras1, which is required for maintaining the integrity of the epidermal–dermal interface at the basement membrane. Subsequently, induction of IκB kinase-α by ΔNp63α initiates epidermal terminal differentiation resulting in the formation of the spinous layer. Our data provide insights into the role of ΔNp63α in epidermal morphogenesis and homeostasis, and may contribute to our understanding of the pathogenic mechanisms underlying disorders caused by p63 mutations.
Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas
Authors: Polo Jose M. , Juszczynski Przemyslaw , Monti Stefano , Cerchietti Leandro , Ye Kenny , Greally John M. , Shipp Margaret , Melnick Ari
Published: February 2007

Diffuse large B cell lymphomas (DLBCLs) often express BCL6, a transcriptional repressor required for the formation of normal germinal centers. In a subset of DLBCLs, BCL6 is deregulated by chromosomal translocations or aberrant somatic hypermutation; in other tumors, BCL6 expression may simply reflect germinal center lineage. DLBCLs dependent on BCL6-regulated pathways should exhibit differential regulation of BCL6 target genes. Genomic array ChIP-on-chip was used to identify the cohort of direct BCL6 target genes. This set of genes was enriched in modulators of transcription, chromatin structure, protein ubiquitylation, cell cycle, and DNA damage responses. In primary DLBCLs classified on the basis of gene expression profiles, these BCL6 target genes were clearly differentially regulated in “BCR” tumors, a subset of DLBCLs with increased BCL6 expression and more frequent BCL6 translocations. In a panel of DLBCL cell lines analyzed by expression arrays and classified according to their gene expression profiles, only BCR tumors were highly sensitive to the BCL6 peptide inhibitor, BPI. These studies identify a discrete subset of DLBCLs that are reliant on BCL6 signaling and uniquely sensitive to BCL6 inhibitors. More broadly, these data show how genome-wide identification of direct target genes can identify tumors dependent on oncogenic transcription factors and amenable to targeted therapeutics.
A common variant in combination with a nonsense mutation in a member of the thioredoxin family causes primary ciliary dyskinesia
Authors: Duriez Bénédicte , Duquesnoy Philippe , Escudier Estelle , Bridoux Anne-Marie , Escalier Denise , Rayet Isabelle , Marcos Elisabeth , Vojtek Anne-Marie , Bercher Jean-François , Amselem Serge
Published: February 2007

Thioredoxins belong to a large family of enzymatic proteins that function as general protein disulfide reductases, therefore participating in several cellular processes via redox-mediated reactions. So far, none of the 18 members of this family has been involved in human pathology. Here we identified
TXNDC3
, which encodes a thioredoxin–nucleoside diphosphate kinase, as a gene implicated in primary ciliary dyskinesia (PCD), a genetic condition characterized by chronic respiratory tract infections, left–right asymmetry randomization, and male infertility. We show that the disease, which segregates as a recessive trait, results from the unusual combination of the following two transallelic defects: a nonsense mutation and a common intronic variant found in 1% of control chromosomes. This variant affects the ratio of two physiological
TXNDC3
transcripts: the full-length isoform and a novel isoform,
TXNDC3d7
, carrying an in-frame deletion of exon 7.
In vivo
and
in vitro
expression data unveiled the physiological importance of
TXNDC3d7
(whose expression was reduced in the patient) and the corresponding protein that was shown to bind microtubules. PCD is known to result from defects of the axoneme, an organelle common to respiratory cilia, embryonic nodal cilia, and sperm flagella, containing dynein arms, with, to date, the implication of genes encoding dynein proteins. Our findings, which identify a another class of molecules involved in PCD, disclose the key role of TXNDC3 in ciliary function; they also point to an unusual mechanism underlying a Mendelian disorder, which is an SNP-induced modification of the ratio of two physiological isoforms generated by alternative splicing.
Small RNA-mediated chromatin silencing directed to the 3′ region of the
Arabidopsis
gene encoding the developmental regulator, FLC
Authors: Swiezewski Szymon , Crevillen Pedro , Liu Fuquan , Ecker Joseph R. , Jerzmanowski Andrzej , Dean Caroline
Published: February 2007

Small RNA-mediated chromatin silencing is well characterized for repeated sequences and transposons, but its role in regulating single-copy endogenous genes is unclear. We have identified two small RNAs (30 and 24 nucleotides) corresponding to the reverse strand 3′ to the canonical poly(A) site of
FLOWERING LOCUS C
(
FLC
), an
Arabidopsis
gene encoding a repressor of flowering. Genome searches suggest that these RNAs originate from the
FLC
locus in a genomic region lacking repeats. The 24-nt small RNA, which is most abundant in developing fruits, is absent in mutants defective in RNA polymerase IVa, RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3, components required for RNAi-mediated chromatin silencing. The corresponding genomic region shows histone 3 lysine 9 dimethylation, which was reduced in a
dcl2,3,4
triple mutant. Investigations into the origins of the small RNAs revealed a polymerase IVa-dependent spliced, antisense transcript covering the 3′
FLC
region. Mutation of this genomic region by T-DNA insertion led to
FLC
misexpression and delayed flowering, suggesting that RNAi-mediated chromatin modification is an important component of endogenous pathways that function to suppress
FLC
expression.
Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases
Authors: Moehle Erica A. , Rock Jeremy M. , Lee Ya-Li , Jouvenot Yann , DeKelver Russell C. , Gregory Philip D. , Urnov Fyodor D. , Holmes Michael C.
Published: February 2007

Efficient incorporation of novel DNA sequences into a specific site in the genome of living human cells remains a challenge despite its potential utility to genetic medicine, biotechnology, and basic research. We find that a precisely placed double-strand break induced by engineered zinc finger nucleases (ZFNs) can stimulate integration of long DNA stretches into a predetermined genomic location, resulting in high-efficiency site-specific gene addition. Using an extrachromosomal DNA donor carrying a 12-bp tag, a 900-bp ORF, or a 1.5-kb promoter-transcription unit flanked by locus-specific homology arms, we find targeted integration frequencies of 15%, 6%, and 5%, respectively, within 72 h of treatment, and with no selection for the desired event. Importantly, we find that the integration event occurs in a homology-directed manner and leads to the accurate reconstruction of the donor-specified genotype at the endogenous chromosomal locus, and hence presumably results from synthesis-dependent strand annealing repair of the break using the donor DNA as a template. This site-specific gene addition occurs with no measurable increase in the rate of random integration. Remarkably, we also find that ZFNs can drive the addition of an 8-kb sequence carrying three distinct promoter-transcription units into an endogenous locus at a frequency of 6%, also in the absence of any selection. These data reveal the surprising versatility of the specialized polymerase machinery involved in double-strand break repair, illuminate a powerful approach to mammalian cell engineering, and open the possibility of ZFN-driven gene addition therapy for human genetic disease.
Single-site mutations in the carboxyltransferase domain of plastid acetyl-CoA carboxylase confer resistance to grass-specific herbicides
Authors: Liu Wenjie , Harrison Dion K. , Chalupska Dominika , Gornicki Piotr , O'Donnell Chris C. , Adkins Steve W. , Haselkorn Robert , Williams Richard R.
Published: February 2007

Grass weed populations resistant to aryloxyphenoxypropionate (APP) and cyclohexanedione herbicides that inhibit acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) represent a major problem for sustainable agriculture. We investigated the molecular basis of resistance to ACCase-inhibiting herbicides for nine wild oat (
Avena sterilis
ssp.
ludoviciana
Durieu) populations from the northern grain-growing region of Australia. Five amino acid substitutions in plastid ACCase were correlated with herbicide resistance: Ile-1,781-Leu, Trp-1,999-Cys, Trp-2,027-Cys, Ile-2,041-Asn, and Asp-2,078-Gly (numbered according to the
Alopecurus myosuroides
plastid ACCase). An allele-specific PCR test was designed to determine the prevalence of these five mutations in wild oat populations suspected of harboring ACCase-related resistance with the result that, in most but not all cases, plant resistance was correlated with one (and only one) of the five mutations. We then showed, using a yeast gene-replacement system, that these single-site mutations also confer herbicide resistance to wheat plastid ACCase: Ile-1,781-Leu and Asp-2,078-Gly confer resistance to APPs and cyclohexanediones, Trp-2,027-Cys and Ile-2,041-Asn confer resistance to APPs, and Trp-1,999-Cys confers resistance only to fenoxaprop. These mutations are very likely to confer resistance to any grass weed species under selection imposed by the extensive agricultural use of the herbicides.
Growth of novel protein structural data
Authors: Levitt Michael
Published: February 2007

Contrary to popular assumption, the rate of growth of structural data has slowed, and the Protein Data Bank (PDB) has not been growing exponentially since 1995. Reaching such a dramatic conclusion requires careful measurement of growth of novel structures, which can be achieved by clustering entry sequences, or by using a novel index to down-weight entries with a higher number of sequence neighbors. These measures agree, and growth rates are very similar for entire PDB files, clusters, and weighted chains. The overall sizes of Structural Classification of Proteins (SCOP) categories (number of families, superfamilies, and folds) appear to be directly proportional to the number of deposited PDB files. Using our weighted chain count, which is most correlated to the change in the size of each SCOP category in any time period, shows that the rate of increase of SCOP categories is actually slowing down. This enables the final size of each of these SCOP categories to be predicted without examining or comparing protein structures. In the last 3 years, structures solved by structural genomics (SG) initiatives, especially the United States National Institutes of Health Protein Structure Initiative, have begun to redress the slowing growth of the PDB. Structures solved by SG are 3.8 times less sequence-redundant than typical PDB structures. Since mid-2004, SG programs have contributed half the novel structures measured by weighted chain counts. Our analysis does not rely on visual inspection of coordinate sets: it is done automatically, providing an accurate, up-to-date measure of the growth of novel protein structural data.
Circadian variation of blood pressure and the vascular response to asynchronous stress
Authors: Curtis Anne M. , Cheng Yan , Kapoor Shiv , Reilly Dermot , Price Tom S. , FitzGerald Garret A.
Published: February 2007

The diurnal variation in the incidence of myocardial infarction and stroke may reflect an influence of the molecular clock and/or the time dependence of exposure to environmental stress. The circadian variation in blood pressure and heart rate is disrupted in mice,
Bmal1
−/−
,

Clock
mut

, and

Npas2
mut

, in which core clock genes are deleted or mutated. Although
Bmal1
deletion abolishes the 24-h frequency in cardiovascular rhythms, a shorter ultradian rhythm remains. Sympathoadrenal function is disrupted in these mice, which reflects control of enzymes relevant to both synthesis (phenylethanolamine
N
-methyl transferase) and disposition (monoamine oxidase B and catechol-
O
-methyl transferase) of catecholamines by the clock. Both timing and disruption or mutation of clock genes modulate the magnitude of both the sympathoadrenal and pressor but not the adrenocortical response to stress. Despite diurnal variation of catecholamines and corticosteroids, they are regulated differentially by the molecular clock. Furthermore, the clock may influence the time-dependent incidence of cardiovascular events by controlling the integration of selective asynchronous stress responses with an underlying circadian rhythm in cardiovascular function.
Functional analysis of an individual IFT protein: IFT46 is required for transport of outer dynein arms into flagella
Authors: Hou Yuqing , Qin Hongmin , Follit John A. , Pazour Gregory J. , Rosenbaum Joel L. , Witman George B.
Published: February 2007

Intraflagellar transport (IFT), which is the bidirectional movement of particles within flagella, is required for flagellar assembly. IFT particles are composed of ∼16 proteins, which are organized into complexes A and B. We have cloned Chlamydomonas reinhardtii and mouse IFT46, and show that IFT46 is a highly conserved complex B protein in both organisms. A C. reinhardtii insertional mutant null for IFT46 has short, paralyzed flagella lacking dynein arms and with central pair defects. The mutant has greatly reduced levels of most complex B proteins, indicating that IFT46 is necessary for complex B stability. A partial suppressor mutation restores flagellar length to the ift46 mutant. IFT46 is still absent, but levels of the other IFT particle proteins are largely restored, indicating that complex B is stabilized in the suppressed strain. Axonemal ultrastructure is restored, except that the outer arms are still missing, although outer arm subunits are present in the cytoplasm. Thus, IFT46 is specifically required for transporting outer arms into the flagellum.